Microorganism

Int Arch Allergy Immunol, 2004 Aug, 134(4), 310 - 23 Epub 2004 Jun 23.
A regulatory role for complement in innate immunity and autoimmunity; Nauta AJ et al.; The complement system comprises a strong defense against various pathogens and is a major component of our innate immune system . While earlier studies have established a crucial role of complement in recognition, opsonization and enhanced phagocytosis of microorganisms by professional phagocytes such as polymorphonuclear leukocytes and macrophages, recent studies delineate an additional role of complement in initiation and maintenance of the acquired immune response . In addition, it seems that opsonization of apoptotic cells by complement may lead to polarization of the response of professional antigen-presenting cells to a more inflammatory or tolerogenic response . The present review summarizes these different contributions of complement to the shaping of the immune balance .

J Nat Prod, 2004 Jun, 67(6), 1032 - 5
Bromophenol derivatives from the red alga Rhodomela confervoides; Zhao J et al.; Eight new bromophenol derivatives, 2,3-dibromo-4,5-dihydroxybenzyl methyl sulfoxide (1), 4-(2,3-dibromo-4,5-dihydroxyphenyl)-3-butene-2-one (2), 2-(3-bromo-5-hydroxy-4-methoxyphenyl)-3-(2,3-dibromo-4,5-dihydroxyphenyl)propionic acid (3), 2-(3-bromo-5-hydroxy-4-methoxyphenyl)-3-(2,3-dibromo-4,5-dihydroxyphenyl)propionic acid methyl ester (4), 2-phenyl-3-(2,3-dibromo-4,5-dihydroxyphenyl)propionic acid (5), 4'-methoxy-2'',3',3''-tribromo-4'',5',5''-trihydroxydiphenylacetic acid (6), and 3-bromo-5-hydroxy-4-methoxyphenylacetic acid (7) and its methyl ester (8), together with a known bromophenol, 3-bromo-5-hydroxy-4-methoxybenzoic acid (9), were isolated from the red alga Rhodomela confervoides . Their structures were elucidated by spectroscopic methods including IR, EIMS, FABMS, ESIMS, HRFABMS, HRESIMS, 1D and 2D NMR, and single-crystal X-ray structure analysis . Compounds 1-4, 8, and 9 were found inactive against several human cancer cell lines and microorganisms.

Pneumologie, 2004 Jun, 58(6), 416 - 27
{HIV and lung}; Lange C et al.; HIV-infection is characterized by a progressive immunodeficiency that predisposes affected persons to opportunistic infections and neoplasias . Pulmonary co-infections play a key role in HIV-infection as the airways are constantly exposed to aerosolized microorganisms during ventilation . In addition to the spectrum of microorganisms that are responsible for the development of community acquired pneumonia in immunocompetent hosts, persons with HIV-infection are vulnerable to infections with organisms that profit from the progressive cellular immune defects . Examples are infections with Pneumocystis jirovecii, non-tuberculous mycobacteria and viral pathogens . In contrast, tuberculosis can occur in all stages of HIV-infection . Following the HIV-pandemic, the incidence of tuberculosis has increased again in many areas of the world . The advent of antiretroviral therapies (ART) in recent years had resulted in a dramatic decrease of HIV-related morbidity and mortality in industrialized countries . As a result of the reconstitution of the immune-system under ARTs the incidence of pulmonary co-infections has also declined substantially in persons living with HIV in countries where these therapies are available.

Environ Technol, 2004 Apr, 25(4), 481 - 9
Evaluation of natural coagulants for direct filtration; Mandloi M et al.; In the present study surjana (Moringa oleifera) seed, maize (Zea mays) and chitosan were used in direct filtration of Bilaoli lake water and evaluated for their efficiency in removing turbidity and microorganisms from water . The experiments with these natural coagulants gave filtered water turbidity less than or almost equal to 1NTU and thereby met the turbidity criteria for drinking water as per WHO guidelines . Bilaoli lake water had low ionic strength and low turbidity which represents one of the most difficult raw waters to treat, but natural coagulants in direct filtration achieved good filtrate quality . The head loss development across the filter bed with chitosan was more than that of alum, while with maize it was comparable to that of alum . With M . oleifera seeds the head loss was much less in comparison to alum . The average most probable number (MPN) reductions obtained with M . oleifera seeds, maize and chitosan were 97.35%, 95.4% and 87.1% respectively, whereas, with alum it was only 7.7%.

FEMS Microbiol Lett, 2004 Jul 1, 236(1), 1 - 6
Mechanisms of G protein-coupled receptor-mediated degranulation; Vines CM et al.; Mast cells and neutrophils play a major role in the innate immune response . Following invasion of the host by microorganisms, these immune cells become activated and release anti-microbial cytotoxic granules in an effort to destroy invading microorganisms in a process termed degranulation . By-products from the degradation of microorganisms can also activate G-protein-coupled receptors (GPCRs), which can further activate immune cells . While degranulation of basophils has been extensively characterized for IgE receptors, the signaling pathways initiated by GPCRs that lead to degranulation and the regulation of these pathways during the degranulation response are areas of active study . This review summarizes the current understanding of the mechanisms involved in the regulation of degranulation through GPCRs.

Am J Trop Med Hyg, 2004 Jun, 70(6), 666 - 9
Balamuthia mandrillaris meningoencephalitis: the first case in southeast Asia; Intalapaporn P et al.; We present a case of 23-year-old man with acute meningoencephalitis, accompanied by inflammation of a nasal ulcer . He had been healthy until six months prior to admission to the hospital when he had a motorcycle accident . A star-shaped wound at his nose was incurred after falling into a swamp . A computed tomogram of the brain showed two nonenhancing hypodense lesions at the left caudate nucleus and the right parietal lobe, ependymitis and leptomeningeal enhancement . A skin biopsy showed chronic noncaseous granulomatous inflammation without demonstrated microorganisms . The patient did not respond to the empirical treatment with cloxacillin, ceftriaxone, and amphotericin B, and eventually died on the thirteenth day of hospitalization . At autopsy, hematoxylin and eosin-stained brain sections showed a chronic necrotizing inflammation with numerous amebic trophozoites and rare cysts . Definitive identification of Balamuthia mandrillaris was made by fluorescent immunohistochemical analysis . There were 10 Naegleria fowleri primary amebic meningoencephalitis, eight Acanthamoeba granulomatous amebic encephalitis, and three Acanthamoeba meningitis in Thailand . To our knowledge, this case is the first reported case of B . mandrillaris in Southeast Asia.

J Immunol, 2004 Jul 1, 173(1), 92 - 9
The third signal in T cell-mediated autoimmune disease?
Darabi K, Karulin AY, Boehm BO, Hofstetter HH, Fabry Z, LaManna JC, Chavez JC, Tary-Lehmann M, Lehmann PV.
The initial event in the pathogenesis of autoimmune disease is thought to be the priming of naive autoreactive T cells by an infection with a cross-reactive microorganism . Although such cross-reactive priming should be a common event, autoimmune disease does not frequently develop . This situation is reflected after the immunization of C57BL/6 mice with the neuroantigen myelin oligodendrocyte glycoprotein (MOG) with CFA, which primes a type 1 T cell response but does not lead to clinical or histological manifestation of experimental allergic encephalomyelitis unless pertussis toxin is injected in addition . We show in this study that, in MOG:CFA-primed mice, the autoimmune CNS pathology develops after intracerebral deposition of TLR9-activating CpG oligonucleotides, but not following non-CpG oligonucleotide injection or after aseptic cryoinjury of the brain . Thus, access of primed MOG-specific Th1 cells to the uninflamed CNS or to CNS undergoing sterile inflammation did not suffice to elicit autoimmune pathology; only if the APC in the target organ were activated in addition by the TLR9-stimulating microbial product did they exert local effector functions . The data suggest that such licensing of APC in the target organ by microbial stimuli represents a checkpoint for functional self-tolerance . Therefore, microorganisms unrelated to the cross-reactive agent that primes the autoreactive T cells could dictate the onset and exacerbation of autoimmune diseases.

Oral Microbiol Immunol, 2004 Aug, 19(4), 217 - 23
Update on human cytomegalovirus in destructive periodontal disease; Slots J; AIM: Human cytomegalovirus (HCMV), a herpesvirus, is discussed in this review as it relates to destructive periodontal disease in humans . RESULTS: HCMV genomic sequences, detected by polymerase chain reaction identification, occur with elevated frequency in severe adult periodontitis, localized and generalized aggressive (juvenile) periodontitis, Papillon-Lefevre syndrome periodontitis, acute necrotizing ulcerative gingivitis, and periodontal abscesses . DISCUSSION: Herpesviruses establish lifelong persistent infections . HCMV infection involves an asymptomatic latent phase interrupted by periods of recrudescence where viral replication and possibly clinical disease become manifest . HCMV reactivation is triggered by a number of immunosuppressive factors, some of which have been shown also to be risk factors/indicators of periodontitis . HCMV periodontal infection may cause release of tissue-destructive cytokines, overgrowth of pathogenic periodontal bacteria, and initiation of cytotoxic or immunopathologic events . CONCLUSIONS: A growing body of data supports the concept that HCMV contributes to severe types of periodontal disease . HCMV infection of the periodontium may alter the immune control of resident microorganisms and be important in a multistage pathogenesis of periodontitis involving viral activation, periodontopathic bacteria, and host immune responses . Understanding the significance of HCMV and other herpesviruses in the development of periodontal disease may have important therapeutic implications . Vaccines against HCMV, which are in various stages of development, need to be evaluated for their ability to decrease the incidence of destructive periodontal disease.

Mikrobiol Z, 2004 Mar-Apr, 66(2), 102 - 8
{Effect of cultivation conditions on the velocity of active sludge microorganisms adaptation to various wastes}; Smyrnova HF et al.; The effect of cultivation conditions--redox potential; medium acidity, chromate concentration, availability and concentration of other heavy metals, immobilization by various carriers--on the velocity of active sludge adaptation to chromate-including sewage has been studied.

Res Microbiol, 2004 Jun, 155(5), 328 - 36
Escherichia coli evolution during stationary phase; Zinser ER et al.; The process of evolution by natural selection has been known for a century and a half, yet the mechanics of selection are still poorly understood . In most cases where natural selection has been studied, the genetic and physiological bases of fitness variation that result in population changes were not identified, leaving only a partial understanding of selection . Starved cultures of the bacterium Escherichia coli present a model system with which to address the genetic and physiological bases of natural selection . This is a model system that also reflects the prevalent state of bacteria in the natural world; due to intense competition for nutrients, microorganisms spend the majority of their lives under starvation conditions . Genetic analyses of a single survivor of starvation identified four adaptive mutations(1) . Investigation of these mutations has revealed insights into the molecular and physiological bases of evolution during prolonged starvation stress.

Sci Total Environ, 2004 Jul 26, 328(1-3), 55 - 68
Permeation liquid membrane as a tool for monitoring bioavailable Pb in natural waters; Slaveykova VI et al.; In order to predict metal bioavailability by microorganisms in natural waters, analytical speciation techniques such as the permeation liquid membrane (PLM) are required . A planar sheet PLM has been characterized by measuring Pb fluxes in the absence and presence of tiron and nitrilotriacetic, iminodiacetic, malonic, citric, polyacrylic and fulvic (Suwannee River fulvic, SRFA) acids . Important parameters such as the diffusion coefficient in the membrane phase and the effective distribution coefficient between the solution and membrane were evaluated in order to determine limiting conditions for the overall transport flux through the membrane . Subsequently, the PLM was tested for its ability to predict bioavailability by the freshwater alga, Chlorella kesslerii by comparing Pb PLM fluxes (JPLM) to Pb biouptake fluxes (Jint) in the absence and presence of the synthetic ligands and SRFA . The capability of the PLM to mimic transport across biological membranes was demonstrated, in particular, from the similarity between the accumulated (PLM, algal) Pb vs . time plots under the different conditions . Under membrane transport limiting conditions, fluxes across both the PLM and biological membranes were proportional to the free metal ion and directly correlated to each other in the zone below saturation of the biological metal uptake sites . The correlation between the different fluxes may be used to predict Pb uptake by C . kesslerii in the presence of the synthetic ligands . However, in the presence of SRFA, the observed Jint was much higher than predicted by results obtained either in the absence or presence of the synthetic ligands .

J Periodontal Res, 2004 Aug, 39(4), 228 - 35
Serum antibodies against the hemoglobin-binding domain (HA2) of Porphyromonas gingivalis; DeCarlo AA et al.; BACKGROUND: The hemoglobin-binding domain (HA2) of the Porphyromonasgingivalis gingipains and hemagglutinins strongly binds hemoglobin and hemin and is thought to play a key role in acquisition of this essential metabolite by the microorganism . METHODS: In this report, we partially characterized human anti-HA2 humoral antibodies and their relationship to periodontal disease in an analysis of titer and function . RESULTS: Overall, serum anti-HA2 antibodies were relatively low and dominated by the immunoglobulin M (IgM) isotype . Pre-therapy titers had a direct association with periodontal health . Levels of P . gingivalis in the plaque were directly related to pre-therapy anti-HA2 IgG levels, and were an important covariant in a significant direct relationship between pre- and post-therapy anti-HA2 titers . Post-therapy anti-HA2 IgG antibody titers were directly related to the capacity of serum IgG fractions to neutralize hemoglobin binding by Lys-gingipain (Kgp) . Further, lower levels of neutralizing activity post-therapy were directly related to severe periodontitis within the patient cohort . CONCLUSIONS: These data suggest that anti-HA2 IgG antibodies correspond directly with periodontal health, possibly through their ability to neutralize P . gingivalis hemoglobin capture . The data also suggest that inadvertent or therapeutic inoculation of P . gingivalis in the plaque may contribute to generation of neutralizing anti-HA2 IgG and improvement of periodontal prognosis . Copyright Blackwell Munksgaard, 2004

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz, 2004 Apr, 47(4), 392 - 404
{Tick-borne human pathogenic microorganisms found in Europe and those considered nonpathogenic . Part I: Ticks and Viruses}; Suss J et al.; The importance of tick-borne encephalitis (TBE) and Lyme borreliosis-the main European tick-borne diseases-is steadily growing . This fact is due to many different factors including climate changes . However, across Europe many other human pathogenic viruses, bacteria, and parasites are found in ticks . This article gives an overview of tick-borne human pathogenic viruses present in Europe as well as those considered nonpathogenic . It also deals with the various species of vector-competent ticks . Among these ticks, viruses from 6 families encompassing 8 genera and 35 species are found,whereby the families Flaviviridae, Bunyaviridae, and Reoviridae with the genera flavivirus, nairovirus, and orbivirus are the most prevalent . Because of their special importance Omsk hemorrhagic fever, louping-ill disease, tick-borne encephalitis, and Crimean-Congo hemorrhagic fever are discussed in detail . Although West Nile virus is mainly transmitted to man by mosquitoes, it is discussed in detail, because West Nile fever has become a good example for a new and rapidly spreading vector-borne disease in the USA and for a recurrent one in Europe . Secondly, besides the mosquito-bird cycle an interesting tick--bird cycle is emerging . The overview clearly demonstrates that in Europe (particularly in Germany) tick-borne viruses, with the exception of TBE, constitute an extremely ignored research subject . This lack of attention is in contrast to their importance and results in a lack of necessary scientific data.

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz, 2004 May, 47(5), 470 - 86
{Tick-borne human pathogenic microorganisms found in Europe and those considered nonpathogenic . Part II: Bacteria, parasites and mixed infections}; Suss J et al.; The importance of tick-borne diseases has significantly increased objectively and subjectively during the last few years . This fact was demonstrated by the description of tick-borne viruses, in particular with respect to tickborne encephalitis published in part I . Here in part II, tick-borne bacteria and parasites will be discussed as well the significance of these agents, their vectors, clinical course, diagnostics, prophylaxis, and therapy . Naturally, Lyme borreliosis, one of the most important tick-borne bacterial illnesses of humans, is the center of our interest . In addition to basic understanding, critical practice-relevant advice regarding all agents is presented . Similarly all tick-borne bacterial diseases such as relapsing fever, tularemia, ehrlichiosis, and rickettsiosis including Q fever will be discussed . Tick-borne zoonotic babesiae are parasites whose veterinary importance has been known for the last 100 years but whose relevance for human medicine only became evident in 1957 . The fact that multiple and mixed infections caused by ticks are possible has been known for years . Taking into account such a high prevalence of the infectious agents in ticks, such multiple infections were to be expected . During the last few years it has become evident that double and multiple infections of humans caused by tick bites occur far more frequently than has been known so far . As a result, in cases of unclear anamnesis,new diagnostic and therapeutic approaches should be taken . In general one can say that considerable additional scientific research is necessary to effectively reduce the incidence of tick-borne diseases.

J Drug Target, 2004 Feb, 12(2), 71 - 8
Oral delivery of pathogens from the intestine to the nervous system; Baird AW et al.; Most therapeutic agents are delivered orally . Consequently, the major classes of therapeutically useful chemicals are partially lipophilic, small molecular weight compounds . They have reasonable permeability coefficient values across cell membranes, including those of intestinal epithelia and vascular endothelia . In contrast, large molecular weight biotechnology compounds have limited usefulness by non-injected routes as a consequence of their low membrane permeability and variable solubility . However, a wide range of infectious agents have developed strategies or have hijacked physiological routings in order to enter the host by the oral route . Efforts to address such issues have refreshed interest in mechanisms by which different types of payloads (including particulates and microorganisms) translocate across gut epithelia and then distribute to target tissues . Special attention is given to the potential role of the enteric nervous system and its plasticity.

Mediators Inflamm, 2004 Feb, 13(1), 25 - 8
Serum levels of tumor necrosis factor-alpha, interleukin-6 and interleukin-8 are not increased in dyspeptic patients with Helicobacter pylori-associated gastritis; Bayraktaroglu T et al.; INTRODUCTION: Helicobacter pylori (H . pylori) is a non-invasive microorganism causing intense gastric mucosal inflammatory and immune reaction . H . pylori-induced gastric mucosal cytokine overproduction has been clearly documented previously . The stomach has a large surface area and continuous spill-over of locally produced cytokines into the blood stream is a possibility . There are few and conflicting data on circulatory proinflammatory cytokine levels in patients with H . pylori infection . MATERIALS AND METHODS: Forty-two dyspeptic patients were enrolled into the study . The presence of H . pylori infection was diagnosed with antral histopathologic examination . After overnight fasting; serum samples were obtained from each patient to determine circulating interleukin (IL)-6, IL-8 and tumor necrosis factor-alpha (TNF-alpha) levels . RESULTS: H . pylori was shown in 30 cases using Giemsa stain in antral histopathologic evaluation . Twelve cases were negative for H . pylori staining . Both the age and sex distribution had an insignificant difference in both H pylori-positive and H . pylori-negative groups . The mean circulatory levels of IL-6, IL-8 and TNF-a in both groups were not different . The situation was same in respect to the serum levels of these cytokines and the degree of inflammation, H . pylori density and activation scores according to Sydney classification . CONCLUSION: We could not show elevated circulatory levels of IL-6, IL-8 and TNF-alpha in H . pylori-infected cases . We believe that H . pylori-related cytokine activation become concentrated on gastric mucosa and this pathogen-induced local inflammatory cascade does not cause changes in circulatory levels of these cytokines . Moreover, there is no correlation between the levels of serum cytokines and Sydney parameters.

J Dairy Sci, 2004 Mar, 87(3), 645 - 51
Disappearance of docosahexaenoic and eicosapentaenoic acids from cultures of mixed ruminal microorganisms; AbuGhazaleh AA et al.; Previous studies showed conflicting results regarding the ability of ruminal microorganisms to hydrogenate docosahexaenoic acid (C22:6, DHA) and eicosapentaenoic acid (C20:5, EPA) . To determine the disappearance of DHA and EPA from mixed ruminal cultures, 2 ruminal in vitro experiments were conducted using graded levels of DHA and EPA . The first experiment examined DHA added at 0, 5, 10, 15, and 20 mg per culture flask . In the second experiment, EPA was added at 0, 5, 10, and 15 mg per culture flask . Docosahexaenoic acid and EPA were incubated in triplicate in 125-mL flasks, and 5 mL of culture contents was taken at 0, 12, and 24 h for fatty acid analysis by gas liquid chromatography . After 24 h of incubation, 4.1, 4.1, 4.0, and 3.3 mg of DHA disappeared from the 5, 10, 15, and 20 mg of DHA cultures, respectively . In the second experiment, 5, 8.3, and 7.1 mg of EPA disappeared after 24 h of incubation for the 5-, 10-, and 15-mg EPA cultures, respectively . Addition of DHA to cultures increased trans-C18:1 fatty acid accumulation by 105, 91, 82, and 74% for the 5, 10-, 15-, and 20-mg cultures, respectively, compared with control . The addition of EPA increased trans-C18:1 fatty acid accumulation by 56, 64, and 55% for the 5-, 10-, and 15-mg EPA cultures, respectively, compared with control . Addition of DHA and EPA to cultures caused a reduction in C18:1 n-9 and C18:2 n-6 biohydrogenation compared with control . Results from these experiments clearly demonstrate the ability of ruminal microorganism to transform DHA and EPA to other fatty acids causing their disappearance from cultures.

Huan Jing Ke Xue, 2004 Mar, 25(2), 145 - 9
{Application of high-efficient cellulose utilization microorganisms in co-composting of vegetable wastes and flower stalk}; Huang DY et al.; An inoculation composing 17 species of cellulose utilization microorganisms was used in co-composting of vegetable wastes and flower stalk, and the efficiency of the inoculation on lignocellulose degradation was studied . The experiments result show that at the beginning of the first stage of composting, inoculating cellulose utilization microorganism in the substrates with 0.5% (V/V) can improve the biomass of the microorganisms into the substrates greatly and make them dominant ones . When the temperature was controlled as 55 degrees C, the biomass of cellulose utilization microorganisms can keep between {symbol: see text} 3.84 x 10(9)-1.80 x 10(10) CFU/g . At the beginning of the second stage, inoculating with 1% (V/V) can improve the temperature during this period effectively . Monitoring of the content of lignocelluloses in the substrate shows that the inoculation of cellulose utilization microorganism can accelerate the degradation of cellulose . The degradation efficiency of cellulose under inoculation condition is 23.64% higher than those without inoculation . This shows that inoculating with cellulose utilization microorganisms in each stage of the composting can greatly decompose the lignocellulose in the substrates, accelerate the co-composting process and improve the quality of composting production.

Huan Jing Ke Xue, 2004 Mar, 25(2), 125 - 8
{Purification capacity of ditch wetland to agricultural non-point pollutants}; Jiang CL et al.; Ditch wetlands have the capacity to remove and purify non-point pollutants from agricultural drainage by sediment retention, plant absorption and microorganism decomposition . Phragmites communis and Zizania latifolia are two main kinds of plants growing naturally in ditch wetlands in the lower reaches of the Yangtze River . They can absorb N and P efficiently, which is the main mechanism of non-point source pollutants purification by wetlands . The harvest of Phragmites communis and Zizania latifolia will take away 463-515 kg/hm2 of N and 127-149 kg/hm2 of P each year, it equal to N and P discharged from 2.3-3.2 hm2 and 1.3-3.0 hm2 of fields respectively in this area . The absorption and decomposition capacity of Zizania latifolia wetland is higher than Phragmites communis wetland . After harvest of plants, wetlands are uncovered to sunlight and oxygen that speeds the transportation and decomposition of nutrients . The amount of organic matters, TN and TP are higher in sediment of harvested area than in that of control . Therefore, seasonal harvest of plants is an efficient measure for wetlands to purify nutrients and alleviate eutrophication of lakes.

Huan Jing Ke Xue, 2004 Mar, 25(2), 104 - 10
{Bio-environmental effects and index of remediation of multi-heavy metals polluted red soils}; Sun B et al.; A pot experiment was conducted to study the bio-environmental effects of lime and organic manure application on red soil and paddy soil derived from red sandstone and polluted by multi-heavy metals . The results indicated that liming decreased the content of soil bioavailable Cu and Pb extracted with 0.05 mol/L HCl, while applying hog manure increased that of Cd . Soil bioavailable heavy metals (HMs) showed an apparent relationship with soil dissolved carbon . Applying lime and organic manure has a positive physiological effect on soil microorganisms and sweet potato . Many indexes, i.e . the number of soil actinomycetes, the content of HMs in the root of sweet potato, showed the remarkable relationship with soil bioavailable Cu, Cd and Pb . However, some indexes of soil and plant only relative to one or two soil bioavailable HMs . For example, soil microbial biomass carbon correspondent with soil bioavailable Cd . Only the content of Cu in the stem and leaf showed a notable relationship with soil effective Cu . Soil effect Cu and Pb rather Cd showed remarkable relation with mean transpiration rate, total biomass and leaf area index of sweet potato . The daily mean value in the seedling stage showed a stronger relationship with soil bioavailable Cu and Pb . Therefore these two physiological indexes can reflect the change of soil metallic contamination.

J Clin Lab Anal, 2004, 18(4), 224 - 30
Rapid, simple, and reliable method for the diagnosis of CAPD peritonitis using the new MMP-9 test kit; Ro Y et al.; The objective of the present study was to evaluate the sensitivity and efficiency of the matrix metalloproteinase-9 (MMP-9) test kit for the diagnosis of bacterial peritonitis in patients undergoing peritoneal dialysis (PD) . Peritoneal effluents were collected from seven continuous ambulatory PD (CAPD) patients with peritonitis, four patients with suspected peritonitis, 30 maintenance PD patients without infection, and seven patients at initiation of PD . The MMP-9 test kit was used to analyze 112 peritoneal effluent samples . These peritoneal effluents were also used to count leukocytes and examine microorganisms . MMP expression was measured by gelatin zymography, and activities were measured by an enzyme-linked immunosorbent assay (ELISA) . The relationship between the reactivity of the test kit and the number of leukocytes in the samples was examined . There was a significant difference in the number of leukocytes in peritoneal effluents between the negative and positive groups detected by the MMP-9 test kit (P < 0.0001) . The results obtained with the MMP-9 test kit were negative for peritoneal effluent samples that did not show increased cell counts . The reactivity of the MMP-9 test kit showed no significant differences among various microorganisms, and remained stable . The MMP-9 test kit appears to be a simple and reliable method for early diagnosis of CAPD peritonitis, and reflects the leukocyte count in peritoneal effluents .

Curr Opin Rheumatol, 2004 Jul, 16(4), 393 - 8
Infectious complications of treatment with biologic agents; Hamilton CD; PURPOSE OF REVIEW: There are three tumor necrosis factor-alpha inhibitors on the US and European markets today, and uncommon but devastating infectious complications accompany their use . This review describes the most important pathogen-specific infections and their relative frequency . Recent literature is summarized that has helped elucidate the pathophysiologic basis for their occurrence . Finally, evolving sets of recommendations for prevention, diagnosis, and treatment of infectious complications of their use are explored . RECENT FINDINGS: Tuberculosis has continued to be the most common pathogen reported in association with infliximab, and less so with etanercept and adalimumab . Determining treated population case rates depends on having an accurate denominator and reflects the local population's latent infection rate . The same is true for histoplasmosis . Other pathogens requiring intact cellular immunity for control of latent infection have also been reported . Specific recommendations for preventive therapy are being made, but prospective clinical trials are needed to assess the risk-benefit of any particular approach . SUMMARY: Microorganisms responsible for the infectious complications associated with anticytokine therapy are generally intracellular pathogens or pathogens that commonly exist in a chronic, latent state and are normally held in check by cell-mediated immunity . Diagnosis requires a high index of suspicion and prompt acquisition of appropriate tissue for microscopic examination and microbiologic culture . Prompt empiric therapy that focuses on the most likely infections is necessary to prevent mortality.

Immunol Rev, 2004 Apr, 198, 185 - 202
The lectin-complement pathway--its role in innate immunity and evolution; Fujita T et al.; Innate immunity was formerly thought to be a non-specific immune response characterized by phagocytosis . However, innate immunity has considerable specificity and is capable of discriminating between pathogens and self . Recognition of pathogens is mediated by a set of pattern recognition receptors, which recognize conserved pathogen-associated molecular patterns (PAMPs) shared by broad classes of microorganisms, thereby successfully defending invertebrates and vertebrates against infection . Lectins, carbohydrate-binding proteins, play an important role in innate immunity by recognizing a wide range of pathogens . Mannose-binding lectin (MBL) and ficolin are lectins composed of a lectin domain attached to collagenous region . However, they use a different lectin domain: a carbohydrate recognition domain (CRD) is responsible for MBL and a fibrinogen-like domain for ficolin . These two collagenous lectins are pattern recognition receptors, and upon recognition of the infectious agent, they trigger the activation of the lectin-complement pathway through attached serine proteases, MBL-associated serine proteases (MASPs) . A similar lectin-based complement system, consisting of the lectin-protease complex and C3, is present in ascidians, our closest invertebrate relatives, and functions in an opsonic manner . We isolated several lectins homologous to MBLs and ficolins and several MASPs in invertebrates and lower vertebrates, and herein we discuss the molecular evolution of these molecules . Based on these findings, it seems likely that the complement system played a pivotal role in innate immunity before the evolution of an acquired immune system in jawed vertebrates.

Immunol Rev, 2004 Apr, 198, 169 - 84
Anti-microbial peptides: from invertebrates to vertebrates; Bulet P et al.; Gene-encoded anti-microbial peptides (AMPs) are widespread in nature, as they are synthesized by microorganisms as well as by multicellular organisms from both the vegetal and the animal kingdoms.These naturally occurring AMPs form a first line of host defense against pathogens and are involved in innate immunity . Depending on their tissue distribution, AMPs ensure either a systemic or a local protection of the organism against environmental pathogens . They are classified into three major groups: (i) peptides with an alpha-helical conformation (insect cecropins, magainins, etc.), (ii) cyclic and open-ended cyclic peptides with pairs of cysteine residues (defensins, protegrin, etc.), and (iii) peptides with an over-representation of some amino acids (proline rich, histidine rich, etc.) . Most AMPs display hydrophobic and cationic properties, have a molecular mass below 25-30 kDa, and adopt an amphipathic structure (alpha-helix, beta-hairpin-like beta-sheet, beta-sheet, or alpha-helix/beta-sheet mixed structures) that is believed to be essential to their anti-microbial action . Interestingly, in recent years, a series of novel AMPs have been discovered as processed forms of large proteins . Despite the extreme diversity in their primary and secondary structures, all natural AMPs have the in vitro particularity to affect a large number of microorganisms (bacteria, fungi, yeast, virus, etc.) with identical or complementary activity spectra . This review focuses on AMPs forming alpha-helices, beta-hairpin-like beta-sheets, beta-sheets, or alpha-helix/beta-sheet mixed structures from invertebrate and vertebrate origins . These molecules show some promise for therapeutic use.

Sci STKE . 2004 Jun 09;2004(237):pe26.
Cold shock response and adaptation at near-freezing temperature in microorganisms; Inouye M et al.; Microorganisms that naturally encounter sharp temperature shifts must develop strategies for responding and adapting to these shifts . Escherichia coli, which are adapted to living at both warm temperatures inside animals and cooler ambient temperatures, respond to low temperatures (10 degrees to 15 degrees C) by adjusting membrane lipid composition and increasing the production of proteins that act as "RNA chaperones" required for transcription and translation and proteins that facilitate ribosomal assembly . In contrast, yeast, which are adapted to cooler temperatures, show a relatively minor cold shock response after temperature shifts from 30 degrees to 10 degrees C but respond with a dramatic increase in the synthesis of trehalose and a heat shock protein when exposed to freezing or near-freezing temperatures . This emphasizes the fact that different groups of microorganisms exhibit distinct types of cold shock responses.

Scand J Infect Dis, 2004, 36(4), 310 - 1
A case of legionellosis during treatment with a TNFalpha antagonist; Wondergem MJ et al.; We report a patient with Legionella pneumophila pneumonia after infliximab therapy for rheumatoid arthritis . Arguments are discussed for an emerging incidence of infections with intracellular microorganisms, granulomatous and non-granulomatous, in patients having received anti-TNFalpha therapy . These discussions consist of clinical and epidemiological data, experimental data in animals, theoretical evidence, and we provide a possible pathogenetic mechanism.

Mikrobiologiia, 2004 Mar-Apr, 73(2), 241 - 7
{Estimation of the total and active microbial biomass in burial mound paleosoils of a different age}; Khomutova TE et al.; Microorganisms that were isolated from steppe soils buried below kurgans from 5800 to 750 years ago were analyzed for the completeness of isolation, total biomass (the sum of glucose-reactivated and resting microbial cells), and active biomass (metabolically active cells) . The metabolic state of microbial communities in buried and modern background soils was estimated from the proportion of active and total biomasses . The paleosoils were found to be characterized by lower total and active biomasses and a lower proportion of active microorganisms as compared to the modern background soils . The age-dependent decrease in the content of active microorganisms in the microbial communities of palesoils was not monotonic . For instance, the 4000-year-old paleosoil was characterized by a high total biomass and a relatively low content of active microorganisms, whereas the 1950-year-old paleosoil was characterized by a relatively low total biomass and a relatively high content of active microorganisms . This could reflect the temporal dynamics of paleoclimatic conditions in the geographic region under study.

Mikrobiologiia, 2004 Mar-Apr, 73(2), 233 - 40
{Mathematic modeling of the dynamics of the interacting population of the rhizosphere microorganisms}; Kravchenko LV et al.; A quantitative model is proposed to describe the population dynamics of associative nitrogen-fixing microorganisms in the plant rhizosphere as dependent on the rate of carbon substrate exudation by plant roots . By changing the values of the basic model parameters, the effect of various factors on the behavior of two competing populations of rhizospheric microorganism can be studied.

Appl Microbiol Biotechnol, 2004 Aug, 65(2), 203 - 10 Epub 2004 Jun 09.
Phylogenetic analysis based on genome-scale metabolic pathway reaction content; Hong SH et al.; Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement . Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content . From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance) . This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways . Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).

Curr Opin Genet Dev, 2004 Apr, 14(2), 133 - 8
Transcriptional regulation in Archaea; Ouhammouch M; During the past few decades, it has become clear that microorganisms can thrive under the most diverse conditions, including extremes of temperature, pressure, salinity and pH . Most of these extremophilic organisms belong to the third domain of life, that of the Archaea . The organisms of this domain are of particular interest because most informational systems that are associated with archaeal genomes and their expression are reminiscent of those seen in Eucarya, whereas, most of their metabolic aspects are similar to those of Bacteria . A better understanding of the regulatory mechanisms of gene expression in Archaea will, therefore, help to integrate the body of knowledge regarding the regulatory mechanisms that underlie gene expression in all three domains of life.

Clin Exp Immunol, 2004 Jul, 137(1), 166 - 72
Increased Fas-mediated apoptosis in polymorphonuclear cells from HIV-infected patients; Salmen S et al.; Neutrophils represent an important line of innate host defence against invading microorganisms and their functional detriment during HIV infection, including accelerated spontaneous cell death, has been shown to contribute to AIDS development . Neutrophils are susceptible to apoptosis via Fas and an interaction between Fas and FasL was suggested originally as a mechanism to explain constitutive neutrophil apoptosis . We have explored some intracellular pathways leading to PMN apoptosis from 28 HIV-infected patients and 24 healthy volunteers . As previously reported, accelerated spontaneous apoptosis was observed in HIV+ patients, but this did not correlate with viral load . Furthermore, an increase in the level of spontaneous apoptosis was detected in neutrophils from HIV-infected patients following inhibition of ERK, suggesting an impairment of this kinase pathway during the early stages of infection which may contribute to PMN dysfunction . An elevated susceptibility to undergo apoptosis was observed following cross-linking of Fas, which correlated both with viral load and co-expression of Fas/FasL surface molecules . Different mechanisms for spontaneous and Fas-induced apoptosis are proposed which together contribute to the neutropenia and secondary infections observed during the progression to AIDS.

Immunol Invest, 2004 May, 33(2), 193 - 212
Normal cell surface expression and selective loss of functions resulting from Phe110 to Ser and Cys126 to Trp substitutions in the formyl peptide receptor; Nanamori M et al.; The N-formyl peptide receptor (FPR) is a G protein-coupled chemoattractant receptor that mediates diverse leukocyte functions when stimulated by bacteria-derived N-formyl peptides such as fMet-Leu-Phe (fMLF) . Impaired neutrophil responsiveness to fMLF parallels increased susceptibility to periodontal microorganisms among patients with localized juvenile periodontitis (LJP) . To determine whether the recently identified FPR mutations in LJP patients are responsible for selective loss of receptor-mediated functions, we prepared and analyzed RBL-2H3 cells expressing FPR bearing Phe110 to Ser (FPR-F110S) or Cys-126 to Trp (FPR-C126W) replacement as well as a FPR double mutant (FPR-FSCW) . All mutant receptors were expressed normally on the cell surface, but were unable to mediate release of beta-hexosaminidase upon fMLF stimulation . FPR-C126W effectively mediated fMLF uptake, an indication of receptor-mediated endocytosis, whereas FPR-F110S and FSCW exhibited markedly reduced ability to uptake fMLF . Both FPR-F110S and FPR-C126W were defective in chemotaxis and displayed reduced Ca2+ mobilization, but mutation at both positions partially restored the ability to respond to fMLF in chemotaxis assay and was nearly normal in Ca2+ mobilization assay . All mutants exhibited diminished accumulation of inositol phosphates . FPR-F110S displayed a delayed and significantly reduced ERK phosphorylation whereas FPR-FSCW nearly lost the ability to phosphorylate ERK . Taken together, these results indicate compromised signaling capabilities due to the FPR mutations, but the loss of function is selective and could be partially rescued by mutations at both positions.

Nat Struct Mol Biol, 2004 Jul, 11(7), 591 - 8 Epub 2004 Jun 13.
Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR; Guo Y et al.; Both the dendritic cell receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR bind human immunodeficiency virus and enhance infection . However, biochemical and structural comparison of these receptors now reveals that they have very different physiological functions . By screening an extensive glycan array, we demonstrated that DC-SIGN and DC-SIGNR have distinct ligand-binding properties . Our structural and mutagenesis data explain how both receptors bind high-mannose oligosaccharides on enveloped viruses and why only DC-SIGN binds blood group antigens, including those present on microorganisms . DC-SIGN mediates endocytosis, trafficking as a recycling receptor and releasing ligand at endosomal pH, whereas DC-SIGNR does not release ligand at low pH or mediate endocytosis . Thus, whereas DC-SIGN has dual ligand-binding properties and functions both in adhesion and in endocytosis of pathogens, DC-SIGNR binds a restricted set of ligands and has only the properties of an adhesion receptor.

Otolaryngol Head Neck Surg, 2004 Jun, 130(6), 681 - 5
The effectiveness of immersion disinfection for flexible fiberoptic laryngoscopes; Bhattacharyya N et al.; OBJECTIVE: We sought to determine whether high-level disinfection renders fiberoptic laryngoscopes free of nonviral infectious microorganisms . METHODS: Six flexible fiberoptic laryngoscopes in heavy use were subjected to surveillance cultures at the beginning, middle, and end of the clinical workday after high-level disinfection to determine if microorganisms could be recovered . Control cultures were obtained by direct contamination of the endoscope with saliva . The rate of microorganism recovery from the endoscopes after high-level disinfection was determined and compared with control specimens . RESULTS: Among a total of 48 cultures submitted from in use but disinfected fiberoptic laryngoscopes, 1 positive culture (positive rate, 2.1%) for mold species was recovered . No positive bacterial cultures occurred . Eleven of 11 (100%) control cultures were positive for bacterial species (P < 0.001) . The confidence interval for the risk of microorganism contamination of a disinfected laryngoscope ranged from 0.11% to 11.6% . CONCLUSION: High-level disinfection provides a reasonably effective method of reducing bacterial and fungal contamination of flexible fiberoptic laryngoscopes . Appropriate surveillance technique should be used in each clinical setting with flexible fiberoptic scopes to ensure adequate disinfection effectiveness.

Int J Food Microbiol, 2004 Jul 15, 94(2), 137 - 59
Predictive modelling of the microbial lag phase: a review; Swinnen IA et al.; This paper summarises recent trends in predictive modelling of microbial lag phenomena . The lag phase is approached from both a qualitative and a quantitative point of view . First, a definition of lag and an analysis of the prevailing measuring techniques for the determination of lag time is presented . Furthermore, based on experimental results presented in literature, factors influencing the lag phase are discussed . Major modelling approaches concerning lag phase estimation are critically assessed . In predictive microbiology, a two-step modelling approach is used . Primary models describe the evolution of microbial numbers with time and can be subdivided into deterministic and stochastic models . Primary deterministic models, e.g., Baranyi and Roberts {Int . J . Food Microbiol . 23 (1994) 277}, Hills and Wright {J . Theor . Biol . 168 (1994) 31} and McKellar {Int . J . Food Microbiol . 36 (1997) 179}, describe the evolution of microorganisms, using one single (deterministic) set of model parameters . In stochastic models, e.g., Buchanan et al . {Food Microbiol . 14 (1997) 313}, Baranyi {J . Theor . Biol . 192 (1998) 403} and McKellar {J . Appl . Microbiol . 90 (2001) 407}, the model parameters are distributed or random variables . Secondary models describe the relation between primary model parameters and influencing factors (e.g., environmental conditions) . This survey mainly focuses on the influence of temperature and culture history on the lag phase during growth of bacteria.

Vaccine, 2004 Jun 23, 22(19), 2374 - 9
Vaccine adjuvant: it makes the difference; Lima KM et al.; The use of protein or DNA in vaccination process rather than living or attenuated microorganism, aims at the increase of the vaccines safety . However, in these cases, the use of adjuvant is frequently required to improve their immunogenicity . In this study, we show the importance of the adjuvant in a vaccine formulation . Vaccines for tuberculosis provide an instructive example, based on the mycobacterial 65 kDa heat shock protein (hsp65) . The same antigen can elicit completely different patterns of immune response depending on how it is administered . Thus, the same antigen might or not protect mice from challenge with Mycobacterium tuberculosis, depending on the formulation . These data suggest that, despite the name, the adjuvant plays a fundamental role on the vaccination process.

Curr Opin Biotechnol, 2004 Jun, 15(3), 199 - 204
The soil metagenome--a rich resource for the discovery of novel natural products; Daniel R; Soil microorganisms have been the most valuable source of natural products, providing industrially important antibiotics and biocatalysts . But, of late, the discovery rate of novel biomolecules using traditional cultivation techniques has been extremely low, as most soil microorganisms cannot be cultured in this way . The development of novel cultivation-dependent and molecular cultivation-independent approaches has paved the way for a new era of product recovery from soil microorganisms . In particular, gene-mining based on the construction and screening of complex libraries derived from the soil metagenome provides opportunities to fully explore and exploit the enormous genetic and metabolic diversity of soil microorganisms . This strategy has already resulted in the isolation of novel biocatalysts and bioactive molecules.

Curr Opin Biotechnol, 2004 Jun, 15(3), 170 - 4
Detection and enumeration of airborne biocontaminants; Stetzenbach LD et al.; The sampling and analysis of airborne microorganisms has received attention in recent years owing to concerns with mold contamination in indoor environments and the threat of bioterrorism . Traditionally, the detection and enumeration of airborne microorganisms has been conducted using light microscopy and/or culture-based methods; however, these analyses are time-consuming, laborious, subjective and lack sensitivity and specificity . The use of molecular methods, such as quantitative polymerase chain reaction amplification, can enhance monitoring strategies by increasing sensitivity and specificity, while decreasing the time required for analysis.

Intervirology, 2004, 47(2), 93 - 101
Establishing the reactivity of monoclonal antibodies against porcine endogenous retrovirus envelope protein; Wang SR et al.; Xenotransplantation of pig organs may be associated with a risk of transmission of microorganisms . Porcine endogenous retroviruses (PERV) are of particular concern since in vitro experiments have demonstrated that human cells are susceptible to such microorganisms . To monitor the transmission of PERV, highly sensitive and specific immunoassays must be developed for clinical surveillance . This report describes the production, preliminary characterization and application of a monoclonal antibody (mAb) against a recombinant PERV envelope (Env) protein . The generated mAb was tested using recombinant PERV Env protein expressed in Escherichia coli, purified PERV virus particles and human 293 cell line infected with PERV . PERV-translated proteins of 15, 70 and 85 kD were recognized specifically using PERV-8E10 mAb and Western blotting . No cross-reactivity was demonstrated with exogenous viral protein (HIV, HTLV and MuLV) . Moreover, PERV-8E10 mAb can be applied to localize PERV proteins using an immunoperoxidase assay . This work reveals that recombinant PERV Env protein and mAb may be effective in detecting antibodies against PERV in xenotransplanted patients, or for butchers who have extensive contact with pigs .

Ann Occup Hyg, 2004 Jun, 48(4), 327 - 38 Epub 2004 Mar 02.
Microbial dustiness and particle release of different biofuels; Madsen AM et al.; Exposure to organic dust originating from biofuels can cause adverse health effects . In the present study we have assessed the dustiness in terms of microbial components and particles of various biofuels by using a rotating drum as a dust generator . Microbial components from straw, wood chips, wood pellets and wood briquettes were quantified by several methods . Excellent correlations (r >/= 0.85, P < 0.0001) were found: between lipopolysaccharide (LPS) (as determined by 3-hydroxy fatty acid analysis) and endotoxin (as determined by a Limulus test), cultivable bacteria, total number of bacteria and muramic acid; between endotoxin and cultivable bacteria, total number of bacteria and muramic acid; between total number of bacteria and muramic acid; between cultivable fungi and total number of fungi . Straw was dustier than the other biofuels in terms of actinomycetes, bacteria, muramic acid, endotoxin, LPS, particle mass and number of particles . One of the wood chips studied and the straws had comparatively high dustiness in terms of fungi, while both wood pellets and wood briquettes had comparatively low dustiness in terms of all microbial components . An initially high particle generation rate of straw and wood chips decreased over time whereas the particle generation rate of wood briquettes and wood pellets increased during a 5 min rotation period . Particles of non-microbial origin may be the determining factor for the health risk in handling briquettes and pellets . Straw dust contained significantly more microorganisms per particle than did wood chip dust, probably because bacteria were most abundant in straw dust . The concentrations of endotoxin and fungi were high in wood and straw dust; dust from one of the straws contained 3610 EU/mg and dust from one of the chips contained 7.3 x 10(6) fungal spores/mg . An exposure to 3 mg of straw or wood chips dust/m(3) (the Swedish and Danish OEL of unspecific inhalable dust) could cause exposures to endotoxin and fungi higher than levels were health symptoms are seen to develop . The very different levels of dustiness in terms of particles and microbial components of different biofuels shows that dustiness is an important health-relevant factor to consider when choosing among biofuels and when designing worksites for handling of biofuels.

Med Sci (Paris), 2004 May, 20(5), 569 - 74
{MUC genes: mucin or not mucin? That is the question}; Porchet N et al.; Mucins are macromolecules lying the cells in contact with external environment and protect the epithelium against constant attacks such as digestive fluids, microorganisms, pollutants, and toxins . Mucins are the main components of mucus and are synthesized and secreted by specialized cells of the epithelium (goblet cells, cells of mucous glands) or non mucin-secreting cells . Human mucin genes show common features: large size of their mRNAs, large nucleotide tandem repeat domains, complex expression both at tissular and cellular level . Since 1987, 21 MUC symbols have been used to designate genes encoding O-glycoproteins containing tandem repeat domains rich in serine, threonine and proline . Some of these genes encode true mucins while others encode non mucin adhesion O-glycoproteins . In this paper, we propose a classification based on sequence similarities and expression areas . Two main families can be distinguished: secreted mucins or gel-forming mucins (MUC2, MUC5AC, MUC5B, MUC6), and membrane-bound mucins (MUC1, MUC3, MUC4, MUC12, MUC17) . Muc-deficient mice will provide important models in the study of functional relationships between these two mucin families.

J Biol Chem, 2004 Aug 6, 279(32), 33192 - 8 Epub 2004 Jun 08.
Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus solfataricus; Napoli A et al.; Induction of DNA damage triggers a complex biological response concerning not only repair systems but also virtually every cell function . DNA topoisomerases regulate the level of DNA supercoiling in all DNA transactions . Reverse gyrase is a peculiar DNA topoisomerase, specific to hyperthermophilic microorganisms, which contains a helicase and a topoisomerase IA domain that has the unique ability to introduce positive supercoiling into DNA molecules . We show here that reverse gyrase of the archaean Sulfolobus solfataricus is mobilized to DNA in vivo after UV irradiation . The enzyme, either purified or in cell extracts, forms stable covalent complexes with UV-damaged DNA in vitro . We also show that the reverse gyrase translocation to DNA in vivo and the stabilization of covalent complexes in vitro are specific effects of UV light irradiation and do not occur with the intercalating agent actinomycin D . Our results suggest that reverse gyrase might participate, directly or indirectly, in the cell response to UV light-induced DNA damage . This is the first direct evidence of the recruitment of a topoisomerase IA enzyme to DNA after the induction of DNA damage . The interaction between helicase and topoisomerase activities has been previously proposed to facilitate aspects of DNA replication or recombination in both Bacteria and Eukarya . Our results suggest a general role of the association of such activities in maintaining genome integrity and a mutual effect of DNA topology and repair.

Annu Rev Nutr, 2004, 24, 327 - 43
Iron, ferritin, and nutrition; Theil EC; Ferritin, a major form of endogenous iron in food legumes such as soybeans, is a novel and natural alternative for iron supplementation strategies where effectiveness is limited by acceptability, cost, or undesirable side effects . A member of the nonheme iron group of dietary iron sources, ferritin is a complex with Fe3+ iron in a mineral (thousands of iron atoms inside a protein cage) protected from complexation . Ferritin illustrates the wide range of chemical and biological properties among nonheme iron sources . The wide range of nonheme iron receptors matched to the structure of the iron complexes that occurs in microorganisms may, by analogy, exist in humans . An understanding of the chemistry and biology of each type of dietary iron source (ferritin, heme, Fe2+ ion, etc.), and of the interactions dependent on food sources, genes, and gender, is required to design diets that will eradicate global iron deficiency in the twenty-first century.

Antonie Van Leeuwenhoek, 2000 Apr, 77(3), 263 - 70
Ammonium and methylammonium uptake in a fertilizer-degrading strain of Ochrobactrum anthropi; Ewen H et al.; The transport of ammonium and methylammonium was studied in a strain of Ochrobactrum anthropi, a microorganism isolated from garden soil and able to degrade methyleneureas which are used as slow-release nitrogen fertilizer . The activity of both transport systems was determined using {14C}methylammonium . Differences between the two transport systems were observed with regard to their pH- and temperature dependence as well as their kinetic parameters and regulation during growth with various nitrogen sources . Ammonium transport was subject to repression by ammonium and to derepression in its absence, while the methylammonium carrier was induced in the presence of methylamine . The ammonium but not the methylammonium transport system was severely inhibited by ammonium, and metabolic poisons inhibited both uptake systems . The analysis of intracellular metabolites using thin-layer chromatography and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry indicated that methylammonium was rapidly metabolized to N-methylglutamate via gamma-N-methylglutamine.

Proteomics, 2004 May, 4(5), 1305 - 13
Web-accessible proteome databases for microbial research; Pleissner KP et al.; The analysis of proteomes of biological organisms represents a major challenge of the post-genome era . Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins . Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations . The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization . A proteome database system for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources . The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification . The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs . H37Rv . By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways . The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly" . The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data . The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria . Currently, the database system includes proteome information for six strains of microorganisms.

J Pediatr Gastroenterol Nutr, 2004 Jul, 39(1), 15 - 27
Nutrition support for pediatric patients with inflammatory bowel disease: a clinical report of the North American Society for Pediatric Gastroenterology, Hepatology And Nutrition; Kleinman RE et al.; Impairment of growth and malnutrition are significant complications of inflammatory bowel disease (IBD) in pediatric patients . Since this topic was last reviewed in these pages (), a number of studies have further explored the epidemiology and pathogenesis of these nutritional complications of IBD in an effort to provide more effective interventions to prevent the long-term consequences of chronic nutrient deficiencies in childhood . In addition, during the past 15 years, the use of selected nutrients and microorganisms (probiotics) as primary or adjunctive therapy for the treatment of IBD has become an emerging area of great interest . The following is a Clinical Report from the Nutrition and Inflammatory Bowel Disease Committees of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition.

Mol Microbiol, 2004 Jun, 52(6), 1543 - 52
Lipoprotein processing is required for virulence of Mycobacterium tuberculosis; Sander P et al.; Lipoproteins are a subgroup of secreted bacterial proteins characterized by a lipidated N-terminus, processing of which is mediated by the consecutive activity of prolipoprotein diacylglyceryl transferase (Lgt) and lipoprotein signal peptidase (LspA) . The study of LspA function has been limited mainly to non-pathogenic microorganisms . To study a potential role for LspA in the pathogenesis of bacterial infections, we have disrupted lspA by allelic replacement in Mycobacterium tuberculosis, one of the world's most devastating pathogens . Despite the presence of an impermeable lipid outer layer, it was found that LspA was dispensable for growth under in vitro culture conditions . In contrast, the mutant was markedly attenuated in virulence models of tuberculosis . Our findings establish lipoprotein metabolism as a major virulence determinant of tuberculosis and define a role for lipoprotein processing in bacterial pathogenesis . In addition, these results hint at a promising new target for therapeutic intervention, as a highly specific inhibitor of bacterial lipoprotein signal peptidases is available.

Rev Environ Health, 2004 Jan-Mar, 19(1), 63 - 82
Phytoremediation: biological cleaning of a polluted environment; Macek T et al.; Phytoremediation is the direct use of living green plants to degrade, contain, or render harmless various environmental contaminants, including recalcitrant organic compounds or heavy metals . The methods involved include phytoextraction, direct phytodegradation, rhizofiltration, phytovolatilization or formation of artificial wetlands, and lagoon systems . More research background and the development of plants tailored for remediation purposes, using genetic engineering and deeper understanding of plant cooperation with microorganisms is needed . This approach is illustrated by our studies of heavy metal uptake improvement or studies of the PCB conversion, which include in-vitro screening of plant species, analysis of the products, evaluation of their toxicity and field plots, and also studies of enzymes and cloning of foreign genes into plants.

J Environ Sci Health B, 2004 May, 39(3), 333 - 51
Bacterial degradation of chlorophenols: pathways, biochemica, and genetic aspects; Solyanikova IP et al.; Chlorophenols belong to the group of toxic and persistent to microbial attack xenobiotics . Nevertheless, due to the adaptation microorganisms acquire the ability to use chlorophenols as the sole source of carbon and energy . The present review describes the diversity of aerobic pathways for the utilization of halogenated phenols by bacteria with the emphasis on the main reactions and intermediates formed, enzymes responsible for these reactions and their genetic basis . Taking into account (i) the fact that enzymes degrading chlorophenols are similar to the ones involved in the conversion of other (chloro)aromatic compounds and (ii) that present numerous publications describing the properties of separated enzymes or encoding their genes are published, this review was planned as the attempt to present both, the most general and specific aspects in chlorophenols degradation with the emphasis on the literature of the last ten years.

EMBO Rep, 2004 May, 5(5), 470 - 6
Multicellular microorganisms: laboratory versus nature; Palkova Z; Our present in-depth knowledge of the physiology and regulatory mechanisms of microorganisms has arisen from our ability to remove them from their natural, complex ecosystems into pure liquid cultures . These cultures are grown under optimized laboratory conditions and allow us to study microorganisms as individuals . However, microorganisms naturally grow in conditions that are far from optimal, which causes them to become organized into multicellular communities that are better protected against the harmful environment . Moreover, this multicellular existence allows individual cells to differentiate and acquire specific properties, such as forming resistant spores, which benefit the whole population . The relocation of natural microorganisms to the laboratory can result in their adaptation to these favourable conditions, which is accompanied by complex changes that include the repression of some protective mechanisms that are essential in nature . Laboratory microorganisms that have been cultured for long periods under optimized conditions might therefore differ markedly from those that exist in natural ecosystems.

Proc Natl Acad Sci U S A, 2004 Jun 15, 101(24), 9091 - 6 Epub 2004 Jun 07.
Genome sequence of Picrophilus torridus and its implications for life around pH 0; Futterer O et al.; The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at up to 65 degrees C, thus they represent the most thermoacidophilic organisms known . Several features that may contribute to the thermoacidophilic survival strategy of P . torridus were deduced from analysis of its 1.55-megabase genome . P . torridus has the smallest genome among nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the highest coding density among thermoacidophiles . An exceptionally high ratio of secondary over ATP-consuming primary transport systems demonstrates that the high proton concentration in the surrounding medium is extensively used for transport processes . Certain genes that may be particularly supportive for the extreme lifestyle of P . torridus appear to have been internalized into the genome of the Picrophilus lineage by horizontal gene transfer from crenarchaea and bacteria . Finally, it is noteworthy that the thermoacidophiles from phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool of genes.

Appl Environ Microbiol, 2004 Jun, 70(6), 3609 - 17
Unusual microbial xylanases from insect guts; Brennan Y et al.; Recombinant DNA technologies enable the direct isolation and expression of novel genes from biotopes containing complex consortia of uncultured microorganisms . In this study, genomic libraries were constructed from microbial DNA isolated from insect intestinal tracts from the orders Isoptera (termites) and Lepidoptera (moths) . Using a targeted functional assay, these environmental DNA libraries were screened for genes that encode proteins with xylanase activity . Several novel xylanase enzymes with unusual primary sequences and novel domains of unknown function were discovered . Phylogenetic analysis demonstrated remarkable distance between the sequences of these enzymes and other known xylanases . Biochemical analysis confirmed that these enzymes are true xylanases, which catalyze the hydrolysis of a variety of substituted beta-1,4-linked xylose oligomeric and polymeric substrates and produce unique hydrolysis products . From detailed polyacrylamide carbohydrate electrophoresis analysis of substrate cleavage patterns, the xylan polymer binding sites of these enzymes are proposed.

Appl Environ Microbiol, 2004 Jun, 70(6), 3528 - 34
Phylogenetic and ecological analysis of novel marine stramenopiles; Massana R et al.; Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research . Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples . Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites . Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries . Phylogenetic analyses indicated the existence of 12 independent clusters . Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters . We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research . Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan . Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.

J Mol Biol, 2004 Jun 25, 340(1), 1 - 7
Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase; Lee BI et al.; l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine . In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A . We have determined the crystal structure of Helicobacter pylori ADC, a tetrameric enzyme, in two forms: the apo structure at 2.0 A resolution and the isoasparagine complex structure at 1.55 A resolution . All subunits of the tetramer are self-processed at the Gly24-Ser25 linkage, producing the smaller beta chain (residues 1-24) and the larger alpha chain (residues 25-117) . Each subunit contains nine beta-strands and three alpha-helices; it is folded into the double-psi beta-barrel structure . In the apo structure, the new amino terminus of the alpha chain, Ser25, is converted into a pyruvoyl group . In the isoasparagine complex structure, the substrate analog is covalently attached to the pyruvoyl group . This structure represents the enzyme-substrate Schiff base intermediate that was proposed to form prior to the decarboxylation step in the catalytic cycle of ADC . Thus our study provides direct structural evidence for the reaction mechanism of ADC.

Mol Immunol, 2004 Jul, 41(5), 479 - 93
Responses to infection and possible recognition strategies in the innate immune system of Caenorhabditis elegans; Nicholas HR et al.; In recent years, researchers investigating innate immunity have begun to use C . elegans as a new model system . The worm has been found to mount protective responses to a variety of fungal and bacterial pathogens . Four signalling pathways involved in such responses have been identified so far: the p38 MAP kinase pathway, the programmed cell death pathway, the TGF-beta pathway and the DAF-2 insulin/IGF-I like signalling pathway . Activation of these pathways can lead to the production of immune effector molecules such as lysozymes, lipases and saposin-like proteins, which can act directly against the invading microorganisms . The signalling pathways used and the effectors produced depend on the nature of the infection, indicating that the worm can detect and discriminate between infecting microorganisms . However, the molecules involved in recognition of pathogens have yet to be identified . The worm genome encodes various proteins which might have this recognition function, such as numerous proteins containing C-type lectin domains . These and other candidates are discussed.

Diagn Microbiol Infect Dis, 2004 Jun, 49(2), 89 - 97
Accurate mapping of mutations of pyrazinamide-resistant Mycobacterium tuberculosis strains with a scanning-frame oligonucleotide microarray; Wade MM et al.; The increasing emergence of drug-resistant Mycobacterium tuberculosis poses significant threat to the treatment of tuberculosis . Conventional susceptibility testing for the front-line tuberculosis drug pyrazinamide (PZA) is difficult, because of the requirement for acid pH for the drug to show activity . Resistance to PZA in M . tuberculosis is caused by mutations in the pncA gene, and detection of pncA mutations can be an indicator of PZA resistance . In this study, we examined the feasibility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect pncA mutations (substitutions, deletions, and insertions) in multiple strains of PZA-resistant M . tuberculosis . The genetic mapping of these mutations is necessary to link the gene sequence to the protein function defined by mutant phenotype . Microarray analysis was performed in a blind manner using 57 isolates of M . tuberculosis for which the sequence of the pncA gene was previously determined . Our results showed that all mutations could be unambiguously detected, suggesting that microarray can be a routine and valuable tool for rapid identification of drug-resistant M . tuberculosis isolates . We expect that mutation mapping with a sliding-frame microarray will accelerate the molecular analysis of drug-resistant M . tuberculosis bacteria and the microorganism populations .

Eur J Haematol, 2004 Jul, 73(1), 62 - 6
Hematologic and molecular spontaneous remission following sepsis in acute monoblastic leukemia with translocation (9;11): a case report and review of the literature; Muller CI et al.; Spontaneous remission in patients with acute myeloid leukemia (AML) is a rarely reported phenomenon of usually short duration . The etiology remains unclear, but an association with preceding blood transfusions or bacterial infections has been reported . Triggered immune responses are suggested to play a potential role in the development of spontaneous remission . Acute monocytic leukemia was diagnosed in a 61-yr-old male patient . Cytogenetic analysis revealed a sole translocation (9;11) (q22;q23) and RT-PCR the MLL/AF9 fusion gene . As a result of the patient's reduced performance status and septic condition, cytostatic therapy was withheld . No microorganisms could be detected . Hematologic and molecular remission occurred after initiating antibiotic therapy without any cytostatic treatment; 29 months after the initial diagnosis, he is in complete remission, and excellent physical condition . Our report includes a review of the literature since 1985, reporting cases of patients with AML and spontaneous remission together with informative cytogenetics . Balanced translocations such as in core binding factor (CBF) leukemias appear somewhat overrepresented . We speculate that AML-specific T cells might be relevant for induction of spontaneous remission and need to be further investigated.

J Infect Dis, 2004 Jun 15, 189(12), 2227 - 34 Epub 2004 May 25.
DNA phasing by TA dinucleotide microsatellite length determines in vitro and in vivo expression of the gp91phox subunit of NADPH oxidase and mediates protection against severe malaria; Uhlemann AC et al.; Reactive oxygen intermediates (ROIs) play a major role in the nonspecific innate immune response to invading microorganisms, such as Plasmodium falciparum . In a search for genetic markers that determine differences in production of ROI, we detected a highly polymorphic region of dinucleotide TA repeats approximately 550 bp upstream of the NADPH oxidase gp91(phox) subunit promoter . We genotyped 183 matched Gabonese children with severe or mild malaria . Repeat lengths TA(11) and TA(16) differed significantly in frequency between mild and severe infection, which suggests protection against severe malaria . Both repeat lengths showed lower levels of NADPH oxidase and promoter activities, which can be explained by a cyclic trend in TA repeat length with a period of approximately 5, which indicates the necessity of correct DNA phasing between 2 possible control regions in the promoter . We provide a molecular model of how DNA phasing generated by TA dinucleotide polymorphisms may influence the expression level and protect against severe malaria.

Plant Physiol, 2004 Jun, 135(2), 1129 - 44 Epub 2004 Jun 04.
Gene expression signatures from three genetically separable resistance gene signaling pathways for downy mildew resistance; Eulgem T et al.; Resistance gene-dependent disease resistance to pathogenic microorganisms is mediated by genetically separable regulatory pathways . Using the GeneChip Arabidopsis genome array, we compared the expression profiles of approximately 8,000 Arabidopsis genes following activation of three RPP genes directed against the pathogenic oomycete Peronospora parasitica . Judicious choice of P . parasitica isolates and loss of resistance plant mutants allowed us to compare the responses controlled by three genetically distinct resistance gene-mediated signaling pathways . We found that all three pathways can converge, leading to up-regulation of common sets of target genes . At least two temporal patterns of gene activation are triggered by two of the pathways examined . Many genes defined by their early and transient increases in expression encode proteins that execute defense biochemistry, while genes exhibiting a sustained or delayed expression increase predominantly encode putative signaling proteins . Previously defined and novel sequence motifs were found to be enriched in the promoters of genes coregulated by the local defense-signaling network . These putative promoter elements may operate downstream from signal convergence points.

Environ Sci Technol, 2004 May 1, 38(9), 2664 - 72
Effect of dissolved organic carbon on the photoproduction of dissolved gaseous mercury in lakes: potential impacts of forestry; O'Driscoll NJ et al.; The production of dissolved gaseous mercury (DGM) in freshwater lakes is induced by solar radiation and is also thought to be linked to processes mediated by dissolved organic carbon (DOC) . Studies investigating these processes using comparisons between lakes are often confounded by differences in DOC content and structure . In this study, we investigated the link between DOC concentrations and DGM production by using tangential ultrafiltration to manipulate DOC concentrations in water samples taken from a given lake . In this way, a range of samples with different DOC concentrations was produced without substantial changes to DOC structure or dissolved ions . This was repeated for four lakes in central Quebec: two with highly logged drainage basins and two with minimally logged drainage basins . On two separate days for each lake, water samples (filtered to remove >99% of microorganisms) with varying DOC concentrations were incubated in clear and dark Teflon bottles on the lake surface . DGM concentrations were measured at 3.5-h intervals over the course of 10.5 h . Levels of DGM concentrations increased with increasing cumulative irradiation for all lakes until approximately 4000 kJ m(-2) (400-750 nm, photosynthetically active radiation (PAR)), when DGM concentrations reached a plateau (between 20 and 200 pg L(-1)) . When we assumed that DGM production was limited by the amount of photoreducible mercury, reversible first-order reaction kinetics fitted the observed data well (r2 ranging between 0.59 and 0.98, p < 0.05 with the exception of N70 100% DOC, 0% DOC, and K2 0% DOC with p = 0.06, 0.10, and 0.11, respectively) . The DGM plateaus were independent of DOC concentrations but differed between lakes . In contrast, photoproduction efficiency (DGMprod) (i.e., the amount of DGM produced per unit radiation (fg L(-1) (kJ/m2)(-1)) below 4000 kJ m(-2) PAR) was linearly proportional to DOC concentration for both logged lakes (r2 = 0.97, p < 0.01) and nonlogged lakes (r2 = 0.52, p = 0.018) studied . Furthermore, logged lakes had a lower DGMprod per unit DOC (p < 0.01) than the nonlogged lakes . In these four lakes, the rate of DGM production per unit PAR was dependent on the concentration of DOC . The DGM plateau was independent of DOC concentration; however, there was a significant difference in DGM plateaus between lakes presumably due to different DOC structures and dissolved ions . This research demonstrates an important mechanism by which logging may exacerbate mercury levels in biota.

Int Microbiol, 2004 Mar, 7(1), 53 - 8
Laboratory diagnosis of brucellosis in a rural endemic area in northeastern Spain; Serra J et al.; Sera obtained from 62 patients from four mountain counties in Catalonia (Northeastern Spain), in whom brucellosis had been diagnosed on the basis of clinical evidence and/or personal history, were analyzed using the rose Bengal test, standard serum agglutination test (SAT), Coombs' test, ELISA, and complement fixation . The diagnosis was further confirmed through blood cultures . Clinical evidence, epidemiology, and the results from serologic tests were used to assign patients to one of two groups: group 1 (n = 38) patients had primary infections, whereas group 2 (n = 24) patients had been previously exposed to the microorganism, i.e . re-infection of group 2 individuals occurred after long periods of time during which no active infection by Brucella had been detected . Receiving-operating charts (ROC) were used to determine the diagnostic value of the different tests and to establish discriminant values . Blood culture was a valuable diagnostic tool in group 1 (0.92 sensitivity) but was inappropriate in group 2 (0.08) . The combination of positive rose Bengal test and agglutination >/=1/160 was valid for diagnosis in group 1 . In group 2, agglutination <1/160 (including negative agglutination) did not rule out brucellosis . The combination of positive rose Bengal test and Coombs' test >/=1/320 was the best diagnostic criterion (0.8 specificity; 1 sensitivity) . ELISA (for IgG, IgM, or both) did not improve diagnostic accuracy.

Appl Microbiol Biotechnol, 2004 Nov, 66(1), 85 - 91 Epub 2004 Nov.
Engineered biosynthesis of 16-membered macrolides that require methoxymalonyl-ACP precursors in Streptomyces fradiae; Rodriguez E et al.; Development of host microorganisms for heterologous expression of polyketide synthases (PKS) that possess the intrinsic capacity to overproduce polyketides with a broad spectrum of precursors supports the current demand for new tools to create novel chemical structures by combinatorial engineering of modular and other classes of PKS . Streptomyces fradiae is an ideal host for development of generic polyketide-overproducing strains because it contains three of the most common precursors--malonyl-CoA, methylmalonyl-CoA and ethylmalonyl-CoA--used by modular PKS, and is a host that is amenable to genetic manipulation . We have expanded the utility of an overproducing S . fradiae strain for engineered biosynthesis of polyketides by engineering a biosynthetic pathway for methoxymalonyl-ACP, a fourth precursor used by many 16-membered macrolide PKS . This was achieved by introducing a set of five genes, fkbG-K from Streptomyces hygroscopicus, putatively encoding the methoxymalonyl-ACP biosynthetic pathway, into the S . fradiae chromosome . Heterologous expression of the midecamycin PKS genes in this strain resulted in 1 g/l production of a midecamycin analog . These results confirm the ability to engineer unusual precursor pathways to support high levels of polyketide production, and validate the use of S . fradiae for overproduction of 16-membered macrolides derived from heterologous PKS that require a broad range of precursors.

J Colloid Interface Sci, 2004 Jul 15, 275(2), 496 - 502
Rapid synthesis of Au, Ag, and bimetallic Au core-Ag shell nanoparticles using Neem (Azadirachta indica) leaf broth; Shankar SS et al.; We report on the use of Neem (Azadirachta indica) leaf broth in the extracellular synthesis of pure metallic silver and gold nanoparticles and bimetallic Au/Ag nanoparticles . On treatment of aqueous solutions of silver nitrate and chloroauric acid with Neem leaf extract, the rapid formation of stable silver and gold nanoparticles at high concentrations is observed to occur . The silver and gold nanoparticles are polydisperse, with a large percentage of gold particles exhibiting an interesting flat, platelike morphology . Competitive reduction of Au3+ and Ag+ ions present simultaneously in solution during exposure to Neem leaf extract leads to the synthesis of bimetallic Au core-Ag shell nanoparticles in solution . Transmission electron microscopy revealed that the silver nanoparticles are adsorbed onto the gold nanoparticles, forming a core-shell structure . The rates of reduction of the metal ions by Neem leaf extract are much faster than those observed by us in our earlier studies using microorganisms such as fungi, highlighting the possibility that nanoparticle biological synthesis methodologies will achieve rates of synthesis comparable to those of chemical methods .

J Chromatogr B Analyt Technol Biomed Life Sci, 2004 Jul 25, 807(1), 139 - 43
ATPS applied to extraction of small molecules - polycetides - and simultaneous clarification of culture media with filamentous microorganisms; Esmanhoto E et al.; Aqueous two-phase systems (ATPS) were applied for extraction of small molecules (polycetides) - retamycin, an anthracyclin, and two red pigments, rubropunctamin and monascorubramin - from the whole culture media of Streptomyces olindensis and Monascus purpureus . ATPS allows, in one step, the separation of the small hydrophobic molecules in the PEG rich phase, from the filamentous microorganisms, which remains in the salt phase . Through experimental designs, the main variables and their levels were defined, as follows: for retamycin extraction, PEG 6000 (10%, w/w), phosphate at 20% (w/w) and pH 6.0 led to the higher partition coefficient, K(r) = 8.2, and yield = 91.3%; for red pigments, the statistical analysis indicate PEG 6000 (20%, w/w) and phosphate at 15% (w/w), for a high partition coefficient, (K(pig) = 113 and 150).

Biotechnol Prog, 2004 May-Jun, 20(3), 692 - 7
Enhanced isoamyl acetate production upon manipulation of the acetyl-CoA node in Escherichia coli; Vadali RV et al.; Coenzyme A (CoA) and its thioester derivative acetyl-Coenzyme A (acetyl-CoA) participate in over 100 different reactions in intermediary metabolism of microorganisms . Earlier results indicated that overexpression of upstream rate-limiting enzyme pantothenate kinase with simultaneous supplementation of precursor pantothenic acid to the culture media increased intracellular CoA levels significantly ( approximately 10-fold) . The acetyl-CoA levels also increased ( approximately 5-fold) but not as much as that of CoA, showing that the carbon flux from the pyruvate node is rate-limiting upon an increase in CoA levels . In this study, pyruvate dehydrogenase was overexpressed under elevated CoA levels to increase carbon flux from pyruvate to acetyl-CoA . This coexpression did not increase intracellular acetyl-CoA levels but increased the accumulation of extracellular acetate . The production of isoamyl acetate, an industrially useful compound derived from acetyl-CoA, was used as a model reporter system to signify the beneficial effects of this metabolic engineering strategy . In addition, a strain was created in which the acetate production pathway was inactivated to relieve competition at the acetyl-CoA node and to efficiently channel the enhanced carbon flux to the ester production pathway . The synergistic effect of cofactor CoA manipulation and pyruvate dehydrogenase overexpression in the acetate pathway deletion mutant led to a 5-fold increase in isoamyl acetate production . Under normal growth conditions the acetate pathway deletion mutant strains accumulate intracellular pyruvate, leading to excretion of pyruvate . However, upon enhancing the carbon flux from pyruvate to acetyl-CoA, the excretion of pyruvate was significantly reduced.

Eur Respir J, 2004 May, 23(5), 685 - 91
Impact of sputum bacteria on airway inflammation and health status in clinical stable COPD; Banerjee D et al.; Chronic obstructive pulmonary disease (COPD) is characterised by sputum production, bacterial colonisation, neutrophilic bronchial airway inflammation and poor health status . The aim of this study was to determine the impact of sputum potentially pathogenic microorganisms (PPMs) on bronchial airway inflammation, health status and plasma fibrinogen levels in subjects with moderate-to-severe COPD during the clinical stable state . Sputum total cell and neutrophil counts, supernatant interleukin-8, leukotriene B4, tumour necrosis factor-alpha and neutrophil elastase levels, neutrophil chemotaxis and plasma fibrinogen levels were estimated . Health status was determined using the St George's Respiratory Questionnaire and the 36-item Short-Form Health Survey questionnaire . Twenty-seven (40%) subjects had PPMs and 40 (60%) non-PPMs in their sputum . Both groups were of similar age, body mass index, smoking history and lung function . The PPMs group showed significantly higher levels of interleukin-8, leukotriene B4, tumour necrosis factor-a, neutrophil elastase and increased neutrophil chemotaxis . They also exhibited worse health status and raised plasma fibrinogen levels compared to the non-PPMs group . In conclusion, subjects with clinically stable moderate-to-severe chronic obstructive pulmonary disease who had potentially pathogenic microorganisms in their sputum demonstrated an exaggerated airway inflammatory response, poorer health status and increased plasma fibrinogen levels than those who had nonpotentially pathogenic microorganisms.

Diagn Cytopathol, 2004 Jun, 30(6), 381 - 5
Airborne fungal spores, pollen grains, and vegetable cells in routine Papanicolaou smears; Martinez-Giron R et al.; The objective was to demonstrate the presence of airborne fungal spores, pollen grains, and vegetable cells in smears and establish their significance . Microscopic examination was of smears stained by the Papanicolaou technique . We found several types of airborne spores (Alternaria, Exserohilum, Aspergillus, Cladosporium, Epicoccum, Curvularia, and Ascosmycete), pollen grains (Lilium, bullrush, Pinus, Acacia, hazelnut, and oak), and several types of vegetable cells . The existence of these structures may be due to intrinsic or to extrinsic contamination of the sample . Anemophilous fungi spores and pollen grains have been shown to possess great allergenic capacity . Pollen grains and vegetable cells may be mistaken for certain microorganisms or malignant cells .

Am J Infect Control, 2004 Jun, 32(4), 235 - 8
Evaluation of a patient education model for increasing hand hygiene compliance in an inpatient rehabilitation unit; McGuckin M et al.; BACKGROUND: Transmission of microorganisms from the hands of health care workers is the main cause of health care-acquired infections . Recent studies on bacterial contamination of hands by medical care specialty found the highest bacterial contamination on the hands of health care workers from rehabilitation units . The objective of this study is to determine the effect of a patient education model on hand hygiene (HH) compliance in a rehabilitation unit . METHODS: A 6-week pre- and post-intervention study with a 3-month follow-up using a patient education model was conducted in a 24-bed inpatient rehabilitation unit located in an acute care hospital . Thirty-five patients were enrolled in the intervention phase of the study after agreeing to ask all health care workers who had direct contact with them, "Did you wash/sanitize your hands?" Compliance with the program was measured through soap/sanitizer usage per resident-day before, during, and after the intervention . RESULTS: Usage increased from 5 HH per resident-day during the preintervention to 9.7 HH per resident-day during the intervention (P <.001), 6.7 HH per resident-day postintervention (6 weeks) (P <.001), and 7.0 HH per resident-day at 3 months (P <.001) . CONCLUSIONS: Patient education increased HH compliance in an inpatient rehabilitation unit by 94% during the 6-week intervention, 34% during the 6 week post intervention, and 40% at 3-month follow-up . This program empowers patients with responsibility for their own care and provides ongoing HH education.

Ann Otol Rhinol Laryngol Suppl, 2004 May, 193, 10 - 4
Diagnosis of chronic rhinosinusitis; Lanza DC; Chronic rhinosinusitis is a multifactorial disease defined as inflammation of the nasal cavity and paranasal sinuses with a history of at least 12 weeks in duration . The major symptoms include facial pressure or pain, nasal obstruction, discharge or purulence, and hyposmia or anosmia . The minor symptoms include fever, halitosis, fatigue, and dental pain . Microorganisms play a significant role in the persistence and origination of the inflammatory process, although the exact role of these organisms in the pathogenesis of chronic rhinosinusitis is unclear . The clinical diagnosis relies heavily on the patient history and physical examination, which may include nasal endoscopy and computed tomography . Diagnostic techniques are here reviewed.

Phytother Res, 2004 May, 18(5), 370 - 2
Effect of Amirkabiria odorastissima mozaffarian on the development and progression of fatty streaks in hypercholesterolemic rabbits; Asgary S et al.; New studies have introduced atherosclerosis as an inflammatory disease . Different factors affect the development of inflammation that can be linked to free radicals, hypertention, diabetes mellitus, genetic changes, hypercholesterolemia and some of the microorganisms . Using anti-inflammatory drugs can be useful in preventing atherosclerosis . Finding drugs from natural sources and without side-effects can be useful . Amirkabiria odoratissima (umbelliferae) is from Iranian fl ora and is used traditionally as an anti-inflammatory drug . This study was designed to assess the effects of this plant on the development and progression of fatty streaks . Male rabbits were fed: (a) rabbit chow; (b) 1% cholesterol diet; (c) cholesterol diet supplemented with the plant; (d) normal diet supplemented with the plant . After 12 weeks, the animals were sacrificed and the aorta, right and left branches of coronary arteries were dissected and histologically processed . Before and after the end of the study, biochemical factors were measured . The amounts of cholesterol, LDL, HDL, triglyceride and fasting blood sugar (FBS) were determined by enzymatic methods, quantitative CRP was determined by turbidimetric methods, malondialdehyde (MDA) and antioxidant capacity were determined by speceterophotometric methods . The results indicate that there is a significant difference between the groups supplemented with herbal medicine and others (p < 0.05) in the mean grade of fatty streak of right and left coronary artery and aorta . At the end of the 12-week period cholesterol, LDL and CRP were significantly reduced in the groups which received herbal medicine (p < 0.05) . The data suggests that Amirkabiria odoratissima Mozaffarian has beneficial effects to prevent development of fatty streak; however, further studies are needed to understand the mechanisms whereby this plant exerts its anti-atherosclerotic effects .

Proc Natl Acad Sci U S A, 2004 Jun 8, 101(23), 8537 - 41 Epub 2004 Jun 01.
Changing concentrations of CO, CH(4), C(5)H(8), CH(3)Br, CH(3)I, and dimethyl sulfide during the Southern Ocean Iron Enrichment Experiments; Wingenter OW et al.; Oceanic iron (Fe) fertilization experiments have advanced the understanding of how Fe regulates biological productivity and air-sea carbon dioxide (CO(2)) exchange . However, little is known about the production and consumption of halocarbons and other gases as a result of Fe addition . Besides metabolizing inorganic carbon, marine microorganisms produce and consume many other trace gases . Several of these gases, which individually impact global climate, stratospheric ozone concentration, or local photochemistry, have not been previously quantified during an Fe-enrichment experiment . We describe results for selected dissolved trace gases including methane (CH(4)), isoprene (C(5)H(8)), methyl bromide (CH(3)Br), dimethyl sulfide, and oxygen (O(2)), which increased subsequent to Fe fertilization, and the associated decreases in concentrations of carbon monoxide (CO), methyl iodide (CH(3)I), and CO(2) observed during the Southern Ocean Iron Enrichment Experiments.

J Bioenerg Biomembr, 2004 Feb, 36(1), 65 - 75
Energy-converting {NiFe} hydrogenases from archaea and extremophiles: ancestors of complex I; Hedderich R; {NiFe} hydrogenases are well-characterized enzymes that have a key function in the H2 metabolism of various microorganisms . In the recent years a subfamily of {NiFe} hydrogenases with unique properties has been identified . The members of this family form multisubunit membrane-bound enzyme complexes composed of at least four hydrophilic and two integral membrane proteins . These six conserved subunits, which built the core of these hydrogenases, have closely related counterparts in energy-conserving NADH:quinone oxidoreductases (complex I) . However, the reaction catalyzed by these hydrogenases differs significantly from the reaction catalyzed by complex I . For some of these hydrogenases the physiological role is to catalyze the reduction of H+ with electrons derived from reduced ferredoxins or poly-ferredoxins . This exergonic reaction is coupled to energy conservation by means of electron-transport phosphorylation . Other members of this hydrogenase family mainly function to provide the cell with reduced ferredoxin with H2 as electron donor in a reaction driven by reverse electron transport . As complex I these hydrogenases function as ion pumps and have therefore been designated as energy-converting {NiFe} hydrogenases.

Proc Natl Acad Sci U S A, 2004 Jun 8, 101(23), 8557 - 62 Epub 2004 May 27.
Ferritin reactions: direct identification of the site for the diferric peroxide reaction intermediate; Liu X et al.; Ferritins managing iron-oxygen biochemistry in animals, plants, and microorganisms belong to the diiron carboxylate protein family and concentrate iron as ferric oxide approximately 10(14) times above the ferric K(s) . Ferritin iron (up to 4,500 atoms), used for iron cofactors and heme, or to trap DNA-damaging oxidants in microorganisms, is concentrated in the protein nanocage cavity (5-8 nm) formed during assembly of polypeptide subunits, 24 in maxiferritins and 12 in miniferritins/DNA protection during starvation proteins . Direct identification of ferritin ferroxidase (F(ox)) sites, complicated by multiple types of iron-ferritin interactions, is now achieved with chimeric proteins where putative F(ox) site residues were introduced singly and cumulatively into an inactive host, an L maxiferritin . A dimagnesium ferritin cocrystal model guided site design and the diferric peroxo F(ox) intermediates (A at 650 nm) monitored activity . Diferric peroxo formation in chimeric and WT proteins had similar K(app) values and Hill coefficients . Catalytic activity required cooperative ferrous substrate binding to two sites A (E, EXXH) and B (E, QXXD) . The weaker B sites in ferritin contrast with stronger B sites (E, EXXH) in diiron carboxylate oxygenases, explaining diferric oxo/hydroxo product release in ferritin vs . diiron cofactor retention in oxygenases . Codons for Q/H and D/E differ by single nucleotides, suggesting simple DNA mutations relate site B diiron substrate sites and diiron cofactor sites in proteins . The smaller k(cat) values in chimeras indicate the absence of second-shell residues important for ferritin substrate-product channeling that, when identified, will outline the entire iron path from ferritin pores through the F(ox) site to the mineral cavity.

J Biol Chem, 2004 Aug 20, 279(34), 36022 - 8 Epub 2004 May 27.
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I; Sansen S et al.; Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms . Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists . The structure of Triticum aestivum xylanase inhibitor-I (TAXI-I), a first member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases, has been determined to 1.7-A resolution . Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytical triad are absent . The structure of the TAXI-I.Aspergillus niger xylanase I complex, at a resolution of 1.8 A, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors.

J Clin Laser Med Surg, 2004 Apr, 22(2), 129 - 39
Comparative study of dentine permeability after apicectomy and surface treatment with 9.6 microm TEA CO2 and Er:YAG laser irradiation; Gouw-Soares S et al.; Failure of apicectomies is generally attributed to dentine surface permeability as well as to the lack of an adequate marginal sealing of the retrofilling material, which allows the percolation of microorganisms and their products from the root canal system to the periodontal region, thus compromising periapical healing . The purpose of this study was to evaluate dentine and the marginal permeability after apicectomy and surface treatment with 9.6 micro m TEA CO(2) or Er:YAG 2.94 micro m laser irradiation . Sixty-five single rooted human endodontically treated teeth were divided into five experimental groups: group I (control), apicectomy with high speed bur; group II, similar procedure to that of group I, followed by dentinal surface treatment with 9.6 micro m CO(2) laser; group III, similar procedure to group I followed by dentinal surface treatment with Er:YAG laser 2.94 micro m; group IV, apicectomy and surface treatment with CO(2) 9.6 micro m laser; and group V, apicectomy and surface treatment with Er:YAG laser 2.94 micro m . The analysis of methylene blue dye infiltration through the dentinal surface and the retrofilling material demonstrated that the samples from the groups that were irradiated with the lasers showed significantly lower infiltration indexes than the ones from the control group . These results were compatible with the structural morphological changes evidenced through SEM analysis . Samples from groups II and IV (9.6 micro m CO(2)) showed clean smooth surfaces, fusion, and recrystallized dentine distributed homogeneously throughout the irradiated area sealing the dentinal tubules . Samples from groups III and V (Er:YAG 2.94 micro m) also presented clean surfaces, without smear layer, but roughly compatible to the ablationed dentine and without evidence of dentinal tubules . Through the conditions of this study, the Er:YAG 2.94 micro m and the 9.6 micro m CO(2) laser used for root canal resection and dentine surface treatment showed a reduction of permeability to methylene blue dye.

New Microbiol, 2004 Apr, 27(2), 133 - 7
Bacterial and viral DNA in periodontal disease: a study using multiplex PCR; Santangelo R et al.; Recent studies have suggested an association between periodontal disease and the presence of Herpesviruses, in particular: Epstein-Barr virus (EBV) and Human Cytomegalovirus (CMV) (Contreras et al., 1999--Contreras et al., 2000--Slots et al., 2000--Ting et al., 2000) . In the work reported in this paper, we use a multiplex Polymerase Chain Reaction (PCR) to compare the presence of Herpesviruses and putative bacterial pathogens in patients with periodontal disease and in healthy individuals . Direct detection of microorganisms with PCR is shown to offer significant advantages in terms of time, effort and cost . The study detected no statistically significant differences between the prevalence of EBV and CMV in patients and controls . The failure to replicate previous findings may be due to differences in the age composition and the geographical and social origins of the study groups . The study detected a significant excess of HSV-1 in periodontal patients . This suggests that the role of Herpesviruses in the pathogenesis of periodontal disease deserves further investigation . The bacterial assay confirmed the results of previous studies showing a strong association between periodontitis and the presence of A . actinomycetemcomitans, P . gingivalis and P . intermedia.

Nat Immunol, 2004 Jun, 5(6), 569 - 73
Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?
Sonnenburg JL, Angenent LT, Gordon JI.
The gut contains our largest collection of resident microorganisms . One obvious question is how microbial communities establish and maintain themselves within a perfused intestine . The answers, which may come in part from observations made by environmental engineers and glycobiologists, have important implications for immunologists who wish to understand how indigenous microbial communities are accommodated . Here we propose that the mucus gel layer overlying the intestinal epithelium is a key contributor to the structural and functional stability of this microbiota and its tolerance by the host.

Methods Mol Biol, 2004, 276, 291 - 304
Capillary isoelectric focusing--mass spectrometry of proteins and protein complexes; Martinovic S et al.; Complex proteome samples require efficient separation and detection methods in order to characterize their protein components . On-line combination of capillary isoelectric focusing (CIEF) with electrospray ionization (ESI) mass spectrometry (MS) is shown as an effective method to analyze complex protein mixtures . Our experience with several microorganisms allowed us to establish successful experimental protocol . Here we use the example of E . coli whole-cell lysate for the CIEF separation and MS detection on the intact protein level . The protocol was further adapted for the analysis of the mixture of noncovalent complexes on the intact complex level.

Mol Immunol, 2004 Jun, 41(4), 411 - 9
Two monoclonal antibodies to precisely the same epitope of type II collagen select non-crossreactive phage clones by phage display: implications for autoimmunity and molecular mimicry; Xu Y et al.; Two monoclonal antibodies (mAb) CB268 and CII-C1 to type II collagen (CII) react with precisely the same conformational epitope constituted by the residues ARGLT on the three chains of the CII triple helix . The antibodies share structural similarity, with most differences in the complementarity determining region 3 of the heavy chain (HCDR3) . The fine reactivity of these mAbs was investigated by screening two nonameric phage-displayed random peptide libraries . For each mAb, there were phage clones (phagotopes) that reacted strongly by ELISA only with the selecting mAb, and inhibited binding to CII only for that mAb, not the alternate mAb . Nonetheless, a synthetic peptide RRLPFGSQM corresponding to an insert from a highly reactive CII-C1-selected phagotope, which was unreactive (and non-inhibitory) with CB268, inhibited the reactivity of CB268 with CII . Most phage-displayed peptides contained a motif in the first part of the molecule that consisted of two basic residues adjacent to at least one hydrophobic residue (e.g . RRL or LRR), but the second portion of the peptides differed for the two mAbs . We predict that conserved CDR sequences interact with the basic-basic-hydrophobic motif, whereas non-conserved amino acids in the binding sites (especially HCDR3) interact with unique peptide sequences and limit cross-reactivity . The observation that two mAbs can react identically with a single epitope on one antigen (CII), but show no cross-reactivity when tested against a second (phagotope) indicates that microorganisms could exhibit mimics capable of initiating autoimmunity without this being evident from conventional assays.

Mol Immunol, 2004 Jun, 41(4), 369 - 76
Genomic and molecular characterization of bovine surfactant protein D (SP-D); Gjerstorff M et al.; Collectins are a group of C-type lectins involved in the innate host defense against pathogens . They selectively recognize non-self glyco-conjugates on the surface of microorganisms and induce lysis, agglutination, and phagocytosis to eliminate invading microorganisms . With the perspective of being able to identify surfactant protein D (SP-D) polymorphisms associated with immune-compromised phenotypes in cattle, we have characterized the gene encoding bovine SP-D and its proximal promoter . Cloning and sequencing of the bSP-D gene, including the complete 5'-untranslated sequence, reveal that the gene comprises nine exons spanning approximately 10.5 kb with an organization resembling the bovine conglutinin gene . The gene localizes to the same locus as the conglutinin gene on Bos taurus chromosome 28 at position q1.8, which also includes the genes encoding CL-43 and CL-46 . Several potential cis-regulatory elements, similar to elements known to regulate the transcription of human SP-D, were identified in the 5'-upstream sequence . RT-PCR analysis revealed that bovine SP-D is heavily expressed in the lung and the trachea, but also in segments of the gastrointestinal tract, the mammary glands and the salivary glands . By genotyping we assigned two potential polymorphisms leading to variations in the amino acid composition of the carbohydrate recognition domain (242 Glu/Val and 268 Ala/Gly).

World J Gastroenterol, 2004 Jun 1, 10(11), 1656 - 8
Maastricht II treatment scheme and efficacy of different proton pump inhibitors in eradicating Helicobacter pylori; Altintas E et al.; AIM: The Maastricht II criteria suggest the use of amoxicillin and clarithromycin in addition to a proton pump inhibitor over 7-10 d as a first line therapy in the eradication of Helicobacter pylori (H pylori) . For each proton pump inhibitor, various rates of eradication have been reported . The present study was to compare the efficacy of different proton pump inhibitors like omeprazole, lansoprazole and pantoprazole in combination with amoxicillin and clarithromycin in the first line eradication of H pylori and to investigate the success of H pylori eradication in our district . METHODS: A total of 139 patients were included having a Helicobacter pylori (+) gastroduodenal disorders diagnosed by means of histology and urease test . Besides amoxicillin (1000 mg twice a day) and clarithromycin (500 mg twice a day), they were randomized to take omeprazole (20 mg twice a day), or lansoprazole (30 mg twice a day), or pantoprozole (40 mg twice a day) for 14 d . Four weeks after the therapy, the eradication was assessed by means of histology and urease test . It was evaluated as eradicated if the H pylori was found negative in both . The complaints (pain in epigastrium, nocturnal pain, pyrosis and bloating) were graded in accordance with the Licert scale . The compliance of the patients was recorded . RESULTS: The eradication was found to be 40.8% in the omeprazole group, 43.5% in the lansoprazole group and 47.4% in the pantoprazole group . Sixty-three out of 139 patients (45%) had eradication . No statistically significant difference was observed between the groups . Significant improvements were seen in terms of the impact on the symptom scores in each group . CONCLUSION: There was no difference between omeprazole, lansoprazole and pantoprazole in H pylori eradication, and the rate of eradication was as low as 45% . Symptoms were improved independent of the eradication in each treatment group . The low eradication rates suggest that the antibiotic resistance or the genetic differences of the microorganism might be in effect . Further studies are required to verify these suggestions.

Ground Water, 2004 May-Jun, 42(3), 329 - 37
Push-pull tests for assessing in situ aerobic cometabolism; Kim Y et al.; Three types of single-well push-pull tests were developed for use in assessing the feasibility of in situ aerobic cometabolism of chlorinated aliphatic hydrocarbons (CAHs) . These included transport tests, biostimulation tests, and activity tests . Transport tests are conducted to evaluate the mobility of solutes used in subsequent tests . These included bromide or chloride (conservative tracers), propane (growth substrate), ethylene, propylene (CAH surrogates), dissolved oxygen (electron acceptor), and nitrate (a minor nutrient) . Tests were conducted at an experimental wellfield of Oregon State University . At this site, extraction phase breakthrough curves for all solutes were similar, indicating apparent conservative transport of the dissolved gases and nitrate prior to biostimulation . Biostimulation tests were conducted to stimulate propane-utilizing activity of indigenous microorganisms and consisted of sequential injections of site ground water containing dissolved propane and oxygen . Biostimulation was detected by the increase in rates of propane and oxygen utilization after each injection . Activity tests were conducted to quantify rates of substrate utilization and to confirm that CAH-transforming activity had likely been stimulated . In particular, the transformation of injected CAH surrogates ethylene and propylene to the cometabolic byproducts ethylene oxide and propylene oxide provided evidence that activity of the monooxygenase enzyme system, responsible for aerobic cometabolic transformations of CAHs, had likely also been stimulated . Estimated zero-order transformation rates decreased in the order propane > ethylene > propylene . The series of push-pull tests developed and field tested in this study should prove useful for conducting rapid, low-cost feasibility assessments for in situ aerobic cometabolism of CAHs.

Microbiol Res, 2004, 159(1), 87 - 95
Changes in whole cell-derived fatty acids induced by naphthalene in bacteria from genus Pseudomonas; Mrozik A et al.; Fatty acid composition during naphthalene utilization was investigated in three strains of bacteria Pseudomonas vesicularis, Pseudomonas stutzeri and Pseudomonas sp . JS150 that expressed different naphthalene degradation abilities . All strains significantly changed their cellular fatty acid profiles as a response to naphthalene exposure . Since naphthalene was present in the medium P . stutzeri increased ratio of saturated/unsaturated fatty acids from 1.1 to 2.1 and Pseudomonas sp . JS150 from 7.5 to 12.0, respectively . In contrast, this ratio decreased from 2.1 to 1.1 in P . vesicularis under the same growth conditions . The changes comprised also alterations in the percentage of selected groups of fatty acids: iso and anteiso, hydroxy and cyclopropane fatty acids . Our results showed that naphthalene induced in tested strains different changes in fatty acids composition . It may suggest that in the presence of naphthalene microorganisms used different adaptive mechanisms to maintain the cells in appropriate physiological state.

Microbiol Res, 2004, 159(1), 1 - 10
Light-mediated "conversation" among microorganisms; Trushin MV; Light emitted from a wide variety of microorganisms was considered previously as a waste product . However, it is becoming apparent that it might be involved in microbial communication . This paper presents information on such a novel mode of communication in different microorganisms.

Arch Biochem Biophys, 2004 Jun 15, 426(2), 132 - 41
Victor Ginsburg's influence on my research of the role of sialic acids in biological recognition; Schauer R; Sialic acids are monosaccharides with relatively strong acidity which belong to the most important molecules of higher animals and also occur in some microorganisms . They are bound to complex carbohydrates and occupy prominent positions, especially in cell membranes . Their structural diversity is high and, correspondingly, the mechanisms for their biosynthesis complex . Sialic acids are involved in a great number of cell functions . Due to their cell surface location these acidic molecules shield macromolecules and cells from enzymatic and immunological attacks and thus contribute to innate immunity . In contrast to this masking role, enabling, for example, blood cells and serum glycoproteins a longer life-time, sialic acids also represent recognition sites for various physiological receptors, such as the selectins and siglecs, as well as for toxins and microorganisms and thus allow their colonization . The recognition function of sialic acids can again be masked by O-acetylation, which modifies the interaction with receptors . Many viruses use sialic acids for the infection of cells . As sialic acids play also a decisive role in tumor biology, they prove to be rather versatile molecules that modulate biological and pathological cellular events in a sensitive way . Thus, they are most prominent representatives of mediators of molecular and cellular recognition.

Best Pract Res Clin Gastroenterol, 2004 Jun, 18(3), 497 - 508
Environmental risk factors (excluding tobacco and microorganisms): critical analysis of old and new hypotheses; Ekbom A et al.; The increase in incidence in both ulcerative colitis and Crohn's disease during the 20th century has led to an abundance of different hypotheses on what sort of exposures are responsible . There has been a special focus on dietary factors, as well as on other exposures introduced on a population-based level, including fast food, cola drinks, toothpaste, antibiotics and oral contraceptives . The aim of this review is to critically assess the results from the different observational studies that have investigated these hypotheses, and also to propose research agendas that should be pursued in the future . The conclusion is that infectious exposures and early bacterial colonization, which are associated with better hygiene early in life and that influence immune function, and possibly oral contraceptives, remain the only exposures of interest for future research into the aetiology of ulcerative colitis and Crohn's disease.

Methods Mol Biol, 2004, 268, 289 - 91
Nontraditional method of evaluating disinfectants: with isolated microorganisms from the food factory; Herrera AG; Cleaning and disinfection in the food industry are critical in the production process, and the efficacy of the disinfectants used is frequently debated . Several factors are involved in the effectiveness of a disinfectant agent . It is important to consider the number and type of microorganism present as well as the physical and chemical characteristics of the water; these factors vary from industry to industry and they determine efficacious disinfection.In the laboratory it is possible to evaluate disinfectants to be used in a particular factory, even though these are different from those reported by international organizations . Some useful practices are: 1 . To use cultures of microorganisms isolated in one's own lab instead of reference cultures . 2 . To use as a diluter the water that is used daily in the factory under question . 3 . To compare different disinfectant products under identical conditions of time and temperature.

Methods Mol Biol, 2004, 268, 127 - 31
Fungal isolation and enumeration in foods; Bueno DJ et al.; Humans have now been growing and storing enough food for a long enough time that some rapidly evolving organisms, such as fungi, are moving into niches created by the exploitation of certain plants as food.Food is expected to be nutritious . The most important of the physicochemical conditions that affects fungal growth is related to the biological state of the food . Living foods, particularly fresh fruits, vegetables, and also grains and nuts before harvest, possess powerful defense mechanisms against microbial invasion . When the specific microorganisms overcome defense mechanisms, the spoilage of a living food starts . Other factors to consider are water activity, hydrogen ion concentration, temperature, gas tension, consistency, nutrient status, specific solute effect, and preservation.The consequences of mold contamination of foods are diverse: unsightly appearance, chemical (removal or change of most of the constituents) and nutritional value changes, modification of organoleptic quality, difficulties in preservation, occupational hazards (mycoses, allergies), and toxicoses (mycotoxicoses).It is possible to recognize a succession of three distinct mycoflora during the storage of cereals, but they can also be mixed: 1 . Field fungi growing and established before harvesting (Alternaria, Fusarium, Helminthosporium, Cladosporium) . 2 . Storage fungi taking over and dominanting in the silo (Aspergillus and Penicillium) . 3 . Advanced decay fungi (Papulospora, Sordaria, Fusarium graminearum, and members of the order Mucorales).

Methods Mol Biol, 2004, 268, 117 - 25
Typing fungal isolates: molecular methods and computerized analysis; Rementeria A et al.; Infections caused by fungi (mycoses) are increasingly reported in many countries owing to greater life expectancy associated with an increase in quality of medical and surgical procedures, as well as the emergence of diseases or infections that affect the immune system such as AIDS . Nosocomial outbreaks of fungal infections are sometimes reported, and typing is then necessary to find the reservoirs, analyze the modes of transmission, study the antifungal susceptibility patterns, and investigate the susceptibility of the host.In addition, the food industry is increasingly demanding typing methods that could help in selection of the best fungal strains, in order to incorporate them in the productive chains and augment the quality and security of food . This is the case for Saccharomyces cerevisiae in the wine industry: the selection and characterization of indigenous or autochthonous strains is an important objective for the production of high-quality certified wines.Several genotyping methods are now widely used for strain delineation of medically or economically important microorganisms belonging to the kingdom Fungi . Most molecular typing methods are comparable to those already described for bacteria, although the peculiarities of their nucleic acids increase the number of available methods . Although typing procedures based on the analysis of nucleic acid sequences have been developed, most genotyping methods currently in use are electrophoretically based, and the procedures include the visual comparison of nucleic acid band profiles or their reading with the help of computerized software.Here we describe some of the most frequently used genotyping methods for fungi, based on polymerase chain reactions (PCR), the isolation of chromosomal or mitochondrial DNA, and their restriction using endonuclease enzymes . The latter methods are exclusive for typing eukaryotic organisms and are based on the expected polymorphism obtained from the separation of large chromosomes using pulsed-field gel electrophoresis (PFGE) and the restriction of mitochondrial or chromosomal DNA . More sophisticated methods, such as those that combine endonuclease restriction with hybridization, are also available, although their use is less extensive and is limited mostly to research laboratories.

J Biol Chem, 2004 Jul 23, 279(30), 31157 - 63 Epub 2004 May 20.
Mammalian antioxidant defenses are not inducible by H2O2; Desaint S et al.; As an approach to understanding how mammals regulate H(2)O(2) toxicity, intracellular concentration to prevent its we analyzed the genome-wide mRNA profile changes of human cells after treatment with a non-toxic H(2)O(2) concentration . We identified a large and essentially late H(2)O(2) response of induced and repressed genes that unexpectedly comprise few or no antioxidants but mostly apoptosis and cell cycle control activities . The requirement of the p53 regulator for regulating about a third of this H(2)O(2) stimulon and the lack of an associated enhancement of total cellular H(2)O(2) scavenging activity further suggest that H(2)O(2) elicits a stress antiproliferative/repair response that does not increase antioxidant defenses . We conclude that mammalian antioxidant defenses are constitutive, a finding that contrasts with the oxidant-inducibility of such defenses in microorganisms . This finding might be important in understanding the role of H(2)O(2) as a key signaling molecule in mammals.

Infect Immun, 2004 Jun, 72(6), 3161 - 70
Comparative analysis of B- and T-cell epitopes of Mycobacterium leprae and Mycobacterium tuberculosis culture filtrate protein 10; Spencer JS et al.; Culture filtrate protein 10 (CFP-10) from Mycobacterium tuberculosis is a well-characterized immunodominant 10-kDa protein antigen known to elicit a very potent early gamma interferon response in T cells from M . tuberculosis-infected mice and humans . The sequence of the Mycobacterium leprae homologue of CFP-10 shows only 40% identity (60% homology) at the protein level with M . tuberculosis CFP-10 and thus has the potential for development as a T- or B-cell reactive antigen for specific diagnosis of leprosy . Antisera raised in mice or rabbits against recombinant M . leprae and M . tuberculosis CFP-10 proteins reacted only with homologous peptides from arrays of overlapping synthetic peptides, indicating that there was no detectable cross-reactivity at the antibody level . Sera from leprosy and tuberculosis patients were also specific for the homologous protein or peptides and showed distinct patterns of recognition for either M . leprae or M . tuberculosis CFP-10 peptides . At the cellular level, only 2 of 45 mouse T-cell hybridomas raised against either M . leprae or M . tuberculosis CFP-10 displayed a cross-reactive response against the N-terminal heterologous CFP-10 peptide, the region that exhibits the highest level of identity in the two proteins; however, the majority of peptide epitopes recognized by mouse T-cell hybridomas specific for each protein did not cross-react with heterologous peptides . Coupled with the human serology data, these results raise the possibility that peptides that could be used to differentiate infections caused by these two related microorganisms could be developed . Immunohistochemical staining of sections of M . leprae-infected nude mouse footpads resulted in strongly positive staining in macrophages and dendritic cells, as well as weaker staining in extracellular areas, suggesting that M . leprae CFP-10, like its homologue in M . tuberculosis, is a secreted protein.

Diabetes Metab Res Rev, 2004 May-Jun, 20 Suppl 1, S68 - 77
A report from the international consensus on diagnosing and treating the infected diabetic foot; Lipsky BA; International consensus group on diagnosing and treating the infected diabetic foot; In persons with diabetes, foot infection, that is, invasion and multiplication of microorganisms in tissues accompanied by tissue destruction or a host inflammatory response, usually begins with skin trauma or ulceration 1 . While most foot infections remain superficial, they can spread to subcutaneous tissues, including muscle, joints, and bone . Many diabetic foot ulcers eventuate in an amputation; infection plays a role in approximately 60% of cases 2-4 . Neuropathy is the main factor leading to skin breaks, while arterial perfusion largely affects infection outcome . Among the factors predisposing diabetic patients to foot infections are ill-defined immunological perturbations 56; foot anatomy may foster proximal spread of infection and ischemic necrosis 78 .

Int J Med Microbiol, 2004 Apr, 293(7-8), 495 - 503
Analysing the action of bacterial toxins in living cells with fluorescence resonance energy transfer (FRET); Majoul I; Bacterial toxins represent small molecules produced by microorganisms . Different toxins act on specific target molecules in mammalian cells . Once discovered, bacterial toxins have been providing tools to study cellular functions and often helped the dissection of complex cellular pathways, e.g . endocytic or secretory trafficking or signal transduction, by virtue of the fact that they either block or activate their specific cellular target molecules . Purified bacterial toxins have also allowed to address many basic biological questions and have provided tools for in vitro and in vivo experimental approaches in many fields of modern biology . The understanding of how bacterial toxins act in living cells often depends on our ability to visualize the trafficking and signaling pathways of these molecules . Fluorescence microscopy and other imaging tools are essential to provide insights into the functional changes induced by these pathogens at the level of individual host cells or single target proteins . Inside a single cell we can measure and quantify the effects of bacterial toxins on specific cellular proteins by microscopic and spectroscopic techniques . Fluorescence resonance energy transfer (FRET) is a high-resolution technique that allows to study protein-protein interactions . FRET can provide distance information in the range of 3- 7 nm between fluorescently labeled bacterial proteins in the live cell and cellular target proteins expressed as chimeras with green fluorescent protein (GFP), or spectrally shifted variants thereof . The purpose of this review is to introduce readers to the main experimental setups for analyses of protein-protein interactions using FRET as well as some applications.

Methods Mol Biol, 2004, 266, 353 - 83
Bacterial taxonomics: finding the wood through the phylogenetic trees; Owen RJ; Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification . There are two basic approaches to classification . Similarities may be derived between microorganisms by numerical taxonomic methods based on a range of present-day observable characteristics (phenetics), drawing in particular on conventional morphological and physiological test characters as well as chemotaxonomic markers such as whole-cell protein profiles, mol% G+C content, and DNA-DNA homologies . By contrast, phylogenetics, the process of reconstructing possible evolutionary relationships, uses nucleotide sequences from conserved genes that act as molecular chronometers . A combination of both phenetics and phylogenetics is referred to as polyphasic taxonomy, and is the recommended strategy in description of new species and genera . Numerical analysis of small-subunit ribosomal RNA genes (rDNA) leading to the construction of branching trees representing the distance of divergence from a common ancestor has provided the mainstay of microbial phylogenetics . The approach has some limitations, particularly in the discrimination of closely related taxa, and there is a growing interest in the use of alternative loci as molecular chronometers, such as gyrA and RNAase P sequences . Comparison of the degree of congruence between phylogenetic trees derived from different genes provides a valuable test of the extent they represent gene trees or species trees . Rapid expansion in genome sequences will provide a rich source of data for future taxonomic analysis that should take into account population structure of taxa and novel methods for analysis of nonclonal bacterial populations.

Methods Mol Biol, 2004, 266, 305 - 22
Discovering new pathogens: culture-resistant bacteria; Lawson AJ; Recent advances in gene-amplification technology and molecular phylogenetics have provided the means of detecting and classifying bacteria directly from their natural habitats without the need for culture . These techniques have revolutionized environmental microbiology, and it is now apparent that the global diversity of microorganisms is much greater than previously thought . In the context of clinical microbiology, this molecular-based approach has facilitated the characterization of culture-resistant bacteria associated with human disease . Examples include Helicobacter heilmannii, a cause of gastritis, Tropheryma whippeli (the agent of Whipple's disease), and the agents of human ehrlichiosis and bacillary angiomatosis . Molecular-based techniques also provide a means of investigating complex bacterial flora within the human ecosystem, such as feces and dental plaque, without the bias of culture-based isolation . This has given a new perspective to the study of polymicrobial infections such as gingivitis, and offers the potential for the detection and identification of novel bacterial pathogens from among complex and numerous endogenous microbial flora.

J Exp Med, 2004 May 17, 199(10), 1295 - 9
Human Mannose-binding Lectin in Immunity: Friend, Foe, or Both?
Casanova JL, Abel L.
Human mannose-binding lectin (MBL) recognizes a wide range of microorganisms and triggers the most ancient pathway of complement activation . However, approximately 5% of individuals lack functional serum MBL and have not been found to be prone to severe infections in prospective studies . These data suggest that human MBL is largely redundant for protective immunity and may even have been subject to counter selection because of a deleterious impact.

Int J Med Microbiol, 2004 Apr, 293 Suppl 37, 152 - 7
Immunological characterization of the complement regulator factor H-binding CRASP and Erp proteins of Borrelia burgdorferi; Kraiczy P et al.; Complement activation plays an important role in the elimination of invading microorganisms . Borrelia (B.) burgdorferi sensu lato the etiological agent of Lyme borreliosis, can resist complement-mediated killing . The mechanism of complement resistance of B . burgdorferi sensu stricto apparently depends on the expression of several outer surface proteins described as CRASPs (complement regulator-acquiring surface proteins) . These borrelial surface proteins are able to bind components of the complement regulatory system, factor H and/or factor H-like protein 1 (FHL-1), two crucial fluid-phase negative regulators of the alternative pathway of complement . It was previously demonstrated that one CRASP is encoded by a member of the erp gene family . The purpose of the study was to use a set of monoclonal antibodies (mAb) and polyclonal antisera to characterize the relatedness of factor H-binding CRASP and Erp proteins among several B . burgdorferi sensu stricto and B . afzelii strains . Based on the observed cross-reactivities between B . burgdorferi sensu stricto strains LW2 and PKa-1, it is concluded that BbCRASP-3 is similar to ErpP, BbCRASP-4 is structurally related to ErpC, and BbCRASP-5 is similar to ErpA . The BaCRASP-2 and BaCRASP-4 proteins of B . afzelii strain EB1 reacted with both anti-ErpA and anti-ErpP antibodies whereas BaCRASP-5 of B . afzelii strain FEM1-D15 exclusively reacted with BbCRASP-3/ErpP specific antibodies . Together, these data indicate that most of the factor H-binding CRASPs are members of the Erp protein family, which represents a polymorphic class of proteins with similar or identical immunological reactivities.

Ying Yong Sheng Tai Xue Bao, 2004 Feb, 15(2), 341 - 4
{Impact of pesticides on biodiversity in agricultural areas}; Wu C et al.; Large amount application of pesticides caused a lot of ecological and environmental problems, among which, the impact of pesticides on biodiversity was most important . In this paper, an overview of the impacts of pesticides on biodiversity in agricultural areas, including the community structure of insects, populations of soil invertebrates and microorganisms, and plant communities was provided, and the reasonable use of pesticides and the measures of protecting biodiversity in agricultural areas were also put forward.

Ying Yong Sheng Tai Xue Bao, 2004 Feb, 15(2), 237 - 40
{Microbial eco-characterization and its restoration in copper reclaimed wasteland in red soil area of China . II . Effects on soil microbial characteristics and community structure}; Long J et al.; Soil microbial features in Lipu copper mining and non-mine soil were studied comparatively . The results indicated that mine soil possessed obviously different microbial features such as lower microbial biomass carbon and soil basal respiration strength, Cmic/Corg decreasing, and higher microbial ecophysiological parameters qCO2, indicating that heavy metal had a depressive impact on soil microbial eco-characteristics . Biolog data showed that mine soil microbial community structure was changed obviously, the speed and quantity of carbon consuming were increased significantly, and the kinds of carbon sources which soil microorganism used were changed, led to consume much more energies for maintaining the normal needs of its life . But the utilization efficiency was lower compared with the control . All the results showed that soil microbial eco-characteristics could be used as a sensitive, effective and liable index of mine soil environment qualities.

Zhonghua Er Ke Za Zhi, 2004 Mar, 42(3), 176 - 9
{Correlation between mannose-binding lectin gene codon 54 polymorphism and susceptibility of Kawasaki disease}; Yang J et al.; OBJECTIVE: Human mannose-binding lectin (MBL) is a C-type serum lectin synthesized by the liver as an acute-phase protein . MBL can bind to glycoproteins terminated with mannose and N-acetylglucosamine present in the cell walls on a variety of microorganisms . Therefore, MBL appears to play an important role in the immune system . Low levels of MBL in human have been associated with a susceptibility to recurrent infections . MBL deficiency and low serum MBL levels are strongly associated with the presence of three point mutations at codon 52, 54 and 57 of exon 1 in the human MBL gene, and in Chinese population, the codon-54 mutation occurs at a frequency of 0.11 - 0.17 . The data suggested that MBL insufficiency might also predispose to the development of autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) . The possibility that Kawasaki disease (KD) is an infectious disease has been discussed and investigated for decades, in light of the implication that infections are involved in the pathogenesis of KD . It has been suggested that MBL insufficiency might predispose to the occurrence of KD . This study was aimed to investigate the genetic association of MBL codon-54 polymorphism in patients with KD, and to investigate possible associations with clinical manifestations of the disease . METHODS: There were 95 patients with KD and 160 healthy subjects in the study . The genotype of MBL gene 54 codon was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) . Clinical characteristics and biochemical examination were also performed . RESULTS: The genotype frequency of heterozygote (GGC/GAC) was significantly higher in KD group than that in healthy subjects (45.2% vs 25.0%, P < 0.01), and the allele frequency of GAC mutation was also higher in KD patients than that in control group (0.258 vs 0.138, P < 0.01) . The variant allele (GAC) was markedly associated with KD (OR = 2.18, 95% CI = 1.38 approximately 3.44, P < 0.05) . But there was no significant difference in the allele frequency of GAC between patients with and without coronary artery lesion (CAL) in KD cases (0.281 vs 0.246, P > 0.05) . In addition, in cases of KD, more patients carrying the variant allele (GAC) had episodes of upper respiratory or gastrointestinal infections prior to the onset of KD than wild homozygotes (P < 0.01) . CONCLUSION: The codon 54 polymorphism of MBL gene was associated with KD . It is possible that MBL gene codon 54 mutation might be related to the pathogenesis of KD.

Rev Invest Clin, 2004 Jan-Feb, 56(1), 27 - 31
{Reactogenicity of the simultaneous administration of influenza and pneumococcal vaccines in adults over 55 years of age}; Ayala-Montiel O et al.; BACKGROUND: Pneumonia is the principal cause of morbidity and mortality in PEMEX medical services . Vaccination against influenza is 72% effective in preventing hospitalizations and 87% effective in preventing deaths related to this virus, and vaccination against pneumococcus is 60% effective in preventing invasive diseases by this microorganism . ACIP recommends use of both vaccines simultaneously in adults over 65 years of age . OBJECTIVES: To describe the frequency, duration and severity of local and systemic reactions related to the simultaneous administration of vaccines against influenza and pneumococcus in adults over 55 years of age, and compare with reactions related to influenza vaccine . MATERIAL AND METHODS: Two hundred-thirty two adults over 55 years of age were randomly assigned to two groups, group A (114 subjects) received influenza vaccine, group B (118 subjects) received influenza and pneumococcus vaccines simultaneously . RESULTS: Comparing the number of subjects with local reactions on the right arm between groups A and B (17 subjects vs . 27 subjects), differences were not statistically significative (p = 0.121) . Systemic reactions were not statistically significative either (p = 0.126) when results were compared between both groups (30 from group A vs . 42 for group B) . CONCLUSIONS: Simultaneous administration of influenza and pneumococcus vaccines has proven to be safety . In the absence of contraindications, there is no reason for not offering both vaccines in the same medical visit.

Med Hypotheses, 2004, 62(6), 861 - 7
Acute coronary syndromes and heart failure may reflect maladaptations of trauma physiology that was shaped during pre-modern evolution; Lee PY et al.; We hypothesize that the pathophysiology of many cardiovascular diseases reflects a maladaptation of the triad of trauma response: adrenergia, inflammation, and coagulation . During biologic evolution, trauma has likely been a prevailing factor in natural selection . Components of the trauma triad act to limit hemorrhage, defend wounds against microorganisms, and initiate reconstruction . Response pathways that enable survival after trauma confer obvious adaptive advantages especially if the individual goes on to reproduce . Modern humans have shaped their own ecologic environment in such a way that the incidence of trauma has waned and previously unseen pathologies have emerged . Manifestations of modern diet, changing lifestyles, and extended lifespan have suddenly created new pathologic challenges to our prehistoric physiologic system . During our evolutionary heritage, endothelial injury and end-organ hypoxia were likely exclusively associated with physical trauma and the responses of the trauma triad were appropriate . Today, endothelial injury is more often precipitated by distinctly modern stressors such as hypertension, smoking, diabetes, and dyslipidemia . The once-adaptive trauma response can maladaptively initiate dangerous, self-propelling cycles of adrenergia, inflammation, and coagulation . Acute coronary syndromes perhaps best exemplify this phenomenon . Congestive heart failure, which often ensues, can similarly be seen as a maladaptation of the trauma triad . Whereas end-organ hypoxia was once commonly associated with trauma, now hypoxia is more often attributable to distinctly modern stressors such as pump failure . The fluid conservation and inflammation that results from the trauma triad was clearly adaptive in our prehistoric past, but in congestive heart failure the response is maladaptive, engendering self-propelling exacerbations of pump failure and vascular disease . Our maladaptive trauma response hypothesis portends new diagnostic and therapeutic paradigms for cardiovascular diseases and has ramifications for many other conditions such as stroke, venous thrombosis, vasculitis, aortic disease, arterial disease, pulmonary embolism, and restenosis.

Res Microbiol, 2004 May, 155(4), 267 - 74
Glucose kinase alone cannot be responsible for carbon source regulation in Streptomyces peucetius var . caesius; Ramos I et al.; Using an antibiotic enrichment procedure, eight mutants of Streptomyces peucetius var . caesius were isolated for their sensitivity to the glucose analogue 2-deoxyglucose (DOG), from a DOG-resistant strain (Dog(R)) . These mutants (Dog(S)) and their parent strain were examined for growth sensitivity to DOG, glucose kinase (Glk) activity, glucose uptake, and sensitivity to repression by glucose and other catabolites derived from it . No correlation was found between Glk levels or glucose uptake and carbon catabolite repression (CCR) in these strains . However, the ratio of glucose uptake to Glk activity, and thus the flux through glycolysis, seemed responsible for this effect . Among several products of glucose catabolism tested, fructose-1,6-bis-phosphate and phosphoenolpyruvate showed significant repression of anthracycline formation . These compounds also reduced anthracycline formation in a Dog(R) mutant insensitive to glucose repression . Our data suggest that Glk alone is not sufficient to elicit CCR in this microorganism, and gives the first physiological evidence supporting the hypothesis that some products of glucose catabolism are involved in CCR in Streptomyces.

Environ Microbiol, 2004 Jun, 6(6), 646 - 50
Hydrogen threshold concentrations in pure cultures of halorespiring bacteria and at a site polluted with chlorinated ethenes; Luijten ML et al.; Halorespiring microorganisms are not only able to oxidize organic electron donors such as formate, acetate, pyruvate and lactate, but also H(2) . Because these microorganisms have a high affinity for H(2), this may be the most important electron donor for halorespiration in the environment . We have studied the role of H(2)-threshold concentrations in pure halorespiring cultures and compared them with mixed cultures and field data . We have found H(2)-threshold values between 0.05 and 0.08 nM for Sulfurospirillum halorespirans, S . multivorans and Dehalobacter restrictus under PCE-reducing and nitrate-reducing conditions . The reduction of PCE and TCE can proceed at H(2) concentrations of below 1 nM at a polluted site . However, for the reduction of lower chlorinated ethenes a higher H(2) concentration is required . This indicates that the measured H(2) concentration in situ can be an indicator of the extent of anaerobic reductive dechlorination.

Cent Eur J Public Health, 2004 Mar, 12 Suppl, S75 - 7
Chemical agents and chemical terrorism; Patocka J et al.; Chemical terrorism is a new threat to the security of mankind, which scale essentially exceeds the impact of use of the most modem firearms . At present time all over the world threats from different radical elements to use radioactive materials, potent poisonous substances and pathogenic microorganisms for terrorist purposes became more frequent . High-toxic chemical substances can fall in terrorist hands through wide range of sources . Potentially misused types of chemical compounds are discussed in this article.

Cent Eur J Public Health, 2004 Mar, 12 Suppl, S31 - 3
Phototoxic activity and the possibilities of its testing; Chobot V et al.; The photodynamically active compounds have been attracting an attention of specialists for relatively long time . The most fruitful period of their research has been probably the last decade . The structures of the photosensitizers are very different . The biological activity is based on a formation of free reactive radicals after an excitation of the molecules of the phototoxins by e.g . UV radiation . Some photosensitizers are used for treatment of various diseases in dermatology and oncology . Since the substances can occur in plants, food or cosmetics, the photodynamic activity of these compounds is necessary to be studied under various conditions . Now e.g . some photochemical reactions, cell cultures, cultures of microorganisms, suspensions of erythrocytes, and different species of animals are used to the research of the photodynamic activity of the substances.

J Clin Monit Comput, 2004 Feb, 18(1), 7 - 12
Computer keyboard and mouse as a reservoir of pathogens in an intensive care unit; Hartmann B et al.; OBJECTIVE: User interfaces of patient data management systems (PDMS) in intensive care units (ICU), like computer keyboard and mouse, may serve as reservoirs for the transmission of microorganisms . Pathogens may be transferred via the hands of personnel to the patient causing nosocomial infections . The purpose of this study was to examine the microbial contamination of computer user interfaces with potentially pathogenic microorganisms, compared with other fomites in a surgical intensive care unit of a tertiary teaching hospital . METHODS: Sterile swab samples were received from patient's bedside computer keyboard and mouse, and three other sites (infusion pumps, ventilator, ward round trolley) in the patient's room in a 14 bed surgical intensive care unit at a university hospital . At the central ward samples from keyboard and mouse of the physician's workstation, and control buttons of the ward's intercom and telephone receiver were obtained . Quantitative and qualitative bacteriological sampling occurred during two periods of three months each on eight nonconsecutive days . RESULTS: In all 14 patients' rooms we collected a total of 1118 samples: 222 samples from keyboards and mice, 214 from infusion pumps and 174 from the ward's trolley . From the central ward 16 samples per formites were obtained (computer keyboard and mouse at the physician's workstation and the ward's intercom and telephone receiver) . Microbacterial analysis from samples in patients' rooms yielded 26 contaminated samples from keyboard and mouse (5.9%) compared with 18 positive results from other fomites within patients' rooms (3.0%; p < 0.02) . At the physician's computer terminal two samples obtained from the mouse (6.3%) showed positive microbial testing whereas the ward's intercom and telephone receiver were not contaminated (p = 0.15) . CONCLUSIONS: The colonization rate for computer keyboard and mouse of a PDMS with potentially pathogenic microorganisms is greater than that of other user interfaces in a surgical ICU . These fomites may be additional reservoirs for the transmision of microorganisms and become vectors for cross-transmission of nosocomial infections in the ICU setting.

J Environ Sci (China), 2004, 16(2), 348 - 52
Sterilization of Escherichia coli cells by the application of pulsed magnetic field; Li M et al.; The inactivation of microorganisms by pulsed magnetic field was studied . It was improved that the application of electromagnetic pulses evidently causes a lethal effect on E . coli cells suspended in phosphate buffer solution Na2HPO4/NaH2PO4 (0.334/0.867 mmol/L) . Experimental results indicated that the survivability (N/N0; where N0 and N are the number of cells survived per milliliter before and after electromagnetic pulses application, respectively) of E . coli decreased with magnetic field intensity B and treatment time t . It was also found that the medium temperatures, the frequencies of pulse f, and the initial bacterial cell concentrations have determinate influences in destruction of E . coli cells by the application of magnetic pulses . The application of an magnetic intensity B = 160 mT at pulses frequency f= 62 kHz and treatment time t = 16 h result in a considerable destruction levels of E . coli cells (N/N0 = 10(-4)) . Possible mechanisms involved in sterilization of the magnetic field treatment were discussed . In order to shorten the treatment time, many groups of parallel inductive coil were used . The practicability test showed that the treatment time was shortened to 4 h with the application of three groups of parallel coil when the survivability of E . coli cells was less than 0.01%; and the power consumption was about 0.2 kWh/m3.

Water Sci Technol, 2004, 49(5-6), 155 - 63
Granulation of Anammox microorganisms in up-flow reactors; Imajo U et al.; Experimental studies were performed to evaluate the feasibility of granulation of Anammox microorganisms for biomass retention in up-flow reactors . Two experimental studies, one using a 6.4-L lab-scale reactor with synthetic medium and the other using a 200-L pilot-scale reactor with half-nitrified reject water from a sludge digester were conducted . To enhance the granulation process, seed granules from a UASB reactor were added to both experimental reactors . Granulation of Anammox microorganisms was observed using both the synthetic medium and the reject water . The core of a large proportion of Anammox granules retained part of the original seed biomass . The Anammox granules had a slightly lower density than the seed granules from the UASB process, but the size and other physical properties were comparable . The successful granulation of the Anammox microorganisms led to a stable nitrogen removal performance . The maximum nitrogen removal rate of the lab-scale reactor was observed to be 2.9 kg/(m3 x d) after 173 days of operation and that of the pilot-scale reactor was 6.4 kg/(m3 x d) after 12 months of operation.

Med Arh, 2003, 57(1 Suppl 2), 77 - 80
{Helicobacter pylori infection, history, diagnosis and therapy}; Mesihovic R; Since 1874, possibility of gastric mucosa infection was discussed as a cause of ulcer forming . In 1893 spirochette in gastric mucosa of animals were described . In 1940 bacteria in gastric mucosa of patients with ulcers and cancers were found . In 1983, a new era in gastroenterology begun with synchronic discoveries of bacterial etiology of chronic gastritis and ulcer disease . Australian scientists Barry Marshall and Robin Warren were the first who publisher results about relations between gastric mucosa spiral microorganisms and chronic gastritis . Previously named Campilobacter--like organisms evolved to Helicobacter pylori . In 1994, International Agency for Research on Cancer (IARC) sorted H . pylori in first class of carcinogenics for etiological role in B-cell lymphoma and gastric cancer.

Med Arh, 2004, 58(1 Suppl 2), 125 - 7
{Electron microscopy study and clinical characteristics of rotavirus disease}; Zvizdic S et al.; In this paper it is been described method of electronic microscopy applied for discovering characteristic morphology of rotaviruses in samples of stools of infected and hospitalized patients . To have electronic microscopy as standard method it is necessary to know morphology or structure of the researched microorganism . In the second part of the paper we have made clinical epidemiological analysis of the rotavirus infection on the examined samples, and made comparison with result of other researches . Out of 78 patients with diarrhea, in 15 or 19.2% have been proofed presents of rotaviruses in the stool samples . All hospitalized patients had diarrhea (100%), vomiting was present in 90.9%, high temperature to 39C in 63.6% and over 39C in 36.4% patients . Stomachache was registered in 36.3% and blood in stool has not been found . Majority of the hospitalized had some respiratory syndromes . Time of hospitalization was between 6 to 13 days with average of 9.5 days . Death of hospitalized was not registered.

Int J Food Microbiol, 2004 May 15, 93(1), 1 - 10
Growth of pulsed electric field exposed Escherichia coli in relation to inactivation and environmental factors; Aronsson K et al.; Pulsed electric fields (PEF) have been proven to inactivate microorganisms during nonthermal conditions and have the potential to replace thermal processing as a method for food preservation . However, there is a need to understand the recovery and growth of survivors and potentially injured microorganisms following PEF processing . The purpose of this investigation was to study the growth of Escherichia coli at 10 degrees C following exposure to electrical field strengths (15, 22.5 and 30 kV/cm) in relation to inactivation and the amount of potentially sublethally injured cells . One medium was used as both a treatment medium and an incubation medium, to study the influence of environmental factors on the inactivation and the growth of the surviving population . The pH (5.0, 6.0 and 7.0) and water activity (1.00, 0.985 and 0.97) of the medium was varied by adding HCl and glycerol, respectively . Growth was followed continuously by measuring the optical density . The time-to-detection (td) and the maximum specific growth rate (micromax) were calculated from these data . Results showed that the PEF process did not cause any obvious sublethal injury to the E . coli cells . The number of survivors was a consequence of the combination of electrical field strength and environmental factors, with pH being the most prominent . Interestingly, the micromax of subsequent growth was influenced by the applied electrical field strength during the process, with an increased micromax at more intense electrical field strengths . In addition, the micromax was also influenced by the pH and water activity . The td, which could theoretically be considered as an increase in shelf life, was found to depend on a complex correlation between electrical field strength, pH and water activity . That could be explained by the fact that the td is a combination of the number of survivors, the recovery of sublethal injured cells and the growth rate of the survivors .

Curr Opin Plant Biol, 2004 Jun, 7(3), 309 - 17
Understanding flux in plant metabolic networks; Schwender J et al.; The revolutionary growth in our ability to identify the 'parts list' of cellular infrastructure in plants in detail, and to alter it with precision, challenges us to develop methods to quantify how these parts function . For components of metabolism, this means mapping fluxes at the level of metabolic networks . Advances in experimental, analytical and software tools for metabolic flux analysis now allow maps of the fluxes through central metabolism to be obtained from the results of stable-isotope-labeling experiments . Such maps have led to notable successes in understanding and engineering metabolic function in microorganisms . Recent studies in plants are giving insight into particular fluxes, such as those of the pentose phosphate pathway, and into general phenomena, such as substrate- or futile-cycles and compartmentation . The importance of experimental design and statistical analysis have been illustrated, and analyses of fluxes in heterotrophic plant tissues have been carried out recently.

Biomacromolecules, 2004 May-Jun, 5(3), 889 - 94
Enzymatic surface-initiated polymerization: a novel approach for the in situ solid-phase synthesis of biocompatible polymer poly(3-hydroxybutyrate); Kim YR et al.; A novel system for surface-initiated enzymatic polymerization of a film of polyhydroxyalkanoate (PHA) on solid surfaces has been developed and characterized . PHAs are aliphatic polyesters produced by a variety of microorganisms as a reserve of carbon and energy, and their properties range from elastomers to thermoplastics, depending on their monomeric composition . The PHA synthase from Ralstonia eutropha H16 was expressed as a poly-histidine fusion in Escherichia coli and immobilized onto several solid substrates through a transition-metal complex, Ni(2+)-nitrilotriacetic acid . The immobilized PHA synthase catalyzed the surface-initiated polymerization of 3-(R)-hydroxybutyryl-CoA, forming a polymer film with a uniform thickness on the surface . In this work, we describe the patterned immobilization of the intact enzyme on silicon and subsequent enzymatic polymerization . The immobilized enzyme had a lower specific activity and did not exhibit a lag phase as compared to the soluble enzyme.

J Eukaryot Microbiol, 2003 Jul-Aug, 50(4), 283 - 92
The molecular evolution and structural organization of self-splicing group I introns at position 516 in nuclear SSU rDNA of myxomycetes; Haugen P et al.; Group I introns are relatively common within nuclear ribosomal DNA of eukaryotic microorganisms, especially in myxomycetes . Introns at position S516 in the small subunit ribosomal RNA gene are particularly common, but have a sporadic occurrence in myxomycetes . Fuligo septica, Badhamia gracilis, and Physarum flavicomum, all members of the family Physaraceae, contain related group IC1 introns at this site . The F . septica intron was studied at the molecular level and found to self-splice as naked RNA and to generate full-length intron RNA circles during incubation . Group I introns at position S516 appear to have a particularly widespread distribution among protists and fungi . Secondary structural analysis of more than 140 S516 group I introns available in the database revealed five different types of organization, including IC1 introns with and without His-Cys homing endonuclease genes, complex twin-ribozyme introns, IE introns, and degenerate group I-like introns . Both intron structural and phylogenetic analyses indicate a multiple origin of the S516 introns during evolution . The myxomycete introns are related to S516 introns in the more distantly related brown algae and Acanthamoeba species . Possible mechanisms of intron transfer both at the RNA- and DNA-levels are discussed in order to explain the observed widespread, but scattered, phylogenetic distribution.

Mol Cell Endocrinol, 2004 Apr 15, 218(1-2), 7 - 20
The role of 17 beta-hydroxysteroid dehydrogenases; Mindnich R et al.; The biological activity of steroid hormones is regulated at the pre-receptor level by several enzymes including 17 beta-hydroxysteroid dehydrogenases (17 beta -HSD) . The latter are present in many microorganisms, invertebrates and vertebrates . Dysfunctions in human 17 beta-hydroxysteroid dehydrogenases result in disorders of biology of reproduction and neuronal diseases, the enzymes are also involved in the pathogenesis of various cancers . 17 beta-hydroxysteroid dehydrogenases reveal a remarkable multifunctionality being able to modulate concentrations not only of steroids but as well of fatty and bile acids . Current knowledge on genetics, biochemistry and medical implications is presented in this review.

J Vet Med B Infect Dis Vet Public Health, 2001 May, 48(4), 313 - 20
Paratuberculosis in red deer (Cervus elaphus): an immunohistochemical study; Paolicchi FA et al.; In the present study, we compared the utility of immunohistochemistry with serological and histological results for the characterization of Mycobacterium avium ssp . paratuberculosis (M . paratuberculosis) in tissues of affected red deer . Bacterial isolation was considered the standard reference . Samples were taken from seven clinically affected animals with typical macroscopic lesions . The enzyme linked immunosorbent assay (ELISA) and the gel diffusion tests (GD) were used for serological determinations . Samples from intestine and mesenteric lymph nodes were processed for bacterial isolation and histology . M . paratuberculosis was isolated from all the animals . Histologically, lymph nodes displayed necrosis and mineralization at the cortical and medullar areas . Ziehl-Neelsen stained bacteria were numerous inside macrophages and Langhans-type giant cells . Giant and epithelioid cells and lymphocytes were prominent at the ileal mucous membrane . The immunostaining of M . paratuberculosis was very clear inside epithelioid and giant cells . Image analysis was carried out to determine the immunostained area . There was total agreement among the methods employed . Immunohistochemistry can be very useful when the microorganism cannot be recovered from tissues or faeces.

Nephrol Dial Transplant, 2004 Jul, 19(7), 1890 - 4 Epub 2004 May 05.
High prevalence of Chlamydia pneumoniae infection in cyclosporin A-induced post-transplant gingival overgrowth tissue and evidence for the possibility of persistent infection despite short-term treatment with azithromycin; Worm HC et al.; BACKGROUND: Cyclosporin A (CsA) induces gingival overgrowth (GO) in up to a quarter of CsA-treated renal transplant recipients . A short-term therapy with azithromycin effectively reduces GO, indicating a possible involvement of microorganisms in the pathogenesis of CsA-induced GO . We aimed to determine if there could be any relationship between infection with Chlamydia pneumoniae and GO pathogenesis . In addition, we determined the long-term persistence rate of C . pneumoniae infection in residual GO tissue when azithromycin treatment failed to eliminate GO . METHODS: Chlamydia pneumoniae IgG and IgM antibody titres were measured by microimmunofluorescence technique in sera of kidney recipients with (n = 11) and without (n = 89) GO . GOs were rated and gingivectomies were performed before treatment with 500 mg of azithromycin for 3 days and at months 6 and 12 post-treatment when C . pneumoniae titres were re-evaluated . Nested polymerase chain reaction was performed to identify C . pneumoniae-specific DNA in GO tissues . Results of C . pneumoniae antibody titres from patients with GO were compared with pair-matched controls without GO . RESULTS: Chlamydia pneumoniae IgM titres were elevated in five of 11 patients with GO and in none without GO, whereas the difference of C . pneumoniae IgG titres between patients with GO and pair-matched controls did not reach significance (P<0.57) . Chlamydia pneumoniae-specific DNA was found in 10 of 11 GO tissue samples pre-treatment . Azithromycin therapy effectively reduced GO and C . pneumoniae IgM titres . In residual GO, C . pneumoniae-specific DNA remained detectable after 1 year in all GO tissue samples despite azithromycin treatment . The C.pneumoniae IgM titres correlated with GO scores . CONCLUSION: Chlamydia pneumoniae infection is highly prevalent in CsA-induced GO . The infection can persist over a long period in residual GO despite short-term azithromycin therapy . The results indicate that CsA immunosuppression enhances C . pneumoniae infection rates in non-cardiovascular tissue.

Appl Environ Microbiol, 2004 May, 70(5), 3091 - 5
Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater; Ortiz-Bernad I et al.; Vanadium can be an important contaminant in groundwaters impacted by mining activities . In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor . Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated . Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h . No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls . Acetate was the most effective of all the electron donors evaluated . When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium . These studies demonstrate that G . metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.

Appl Environ Microbiol, 2004 May, 70(5), 2966 - 73
Metal toxicity affects fungal and bacterial activities in soil differently; Rajapaksha RM et al.; Although the toxic effect of heavy metals on soil microorganism activity is well known, little is known about the effects on different organism groups . The influence of heavy metal addition on total, bacterial, and fungal activities was therefore studied for up to 60 days in a laboratory experiment using forest soil contaminated with different concentrations of Zn or Cu . The effects of the metals differed between the different activity measurements . During the first week after metal addition, the total activity (respiration rate) decreased by 30% at the highest level of contamination and then remained stable during the 60 days of incubation . The bacterial activity (thymidine incorporation rate) decreased during the first days with the level of metal contamination, resulting in a 90% decrease at the highest level of contamination . Bacterial activity then slowly recovered to values similar to those of the control soil . The recovery was faster when soil pH, which had decreased due to metal addition, was restored to control values by liming . Fungal activity (acetate-in-ergosterol incorporation rate) initially increased with the level of metal contamination, being up to 3 and 7 times higher than that in the control samples during the first week at the highest levels of Zn and Cu addition, respectively . The positive effect of metal addition on fungal activity then decreased, but fungal activity was still higher in contaminated than in control soil after 35 days . This is the first direct evidence that fungal and bacterial activities in soil are differently affected by heavy metals . The different responses of bacteria and fungi to heavy metals were reflected in an increase in the relative fungal/bacterial ratio (estimated using phospholipid fatty acid analysis) with increased metal load.

Eur J Biochem, 2004 May, 271(10), 1924 - 37
A (1-->3)-beta-D-glucan recognition protein from the sponge Suberites domuncula . Mediated activation of fibrinogen-like protein and epidermal growth factor gene expression; Perovic-Ottstadt S et al.; Sponges (phylum Porifera) live in a symbiotic relationship with microorganisms, primarily bacteria . Until now, molecular proof for the capacity of sponges to recognize fungi in the surrounding aqueous milieu has not been available . Here we demonstrate, for the demosponge Suberites domuncula (Porifera, Demospongiae, Hadromerida), a cell surface receptor that recognizes (1-->3)-beta-D-glucans, e.g . curdlan or laminarin . This receptor, the (1-->3)-beta-D-glucan-binding protein, was identified and its cDNA analysed . The gene coding for the 45 kDa protein was found to be upregulated in tissue after incubation with carbohydrate . Simultaneously with the increased expression of this gene, two further genes showed an elevated steady state level of expression; one codes for a fibrinogen-like protein and the other for the epidermal growth factor precursor . Expression of the (1-->3)-beta-D-glucan-binding protein and the fibrinogen-like protein occurred in cells on the sponge surface, in the pinacoderm . By Western blotting, the product of the fibrinogen-like protein gene was identified, the recombinant protein isolated, and antibodies raised to this protein . Their application revealed that a 5 kDa factor is produced, which is apparently processed from the 77 kDa epidermal growth factor precursor . Finally, we provided evidence that a tyrosine kinase pathway is initiated in response to exposure to D-glucan; its phosphorylation activity could be blocked by aeroplysinin . In turn, the increased expression of the downstream genes was suppressed . We conclude that sponges possess a molecular mechanism for recognizing fungi via the d-glucan carbohydrates on their surfaces.

J Clin Gastroenterol, 2004 Mar, 38(3), 264 - 71
Epidemiology and pathogenesis of primary biliary cirrhosis; Selmi C et al.; Primary biliary cirrhosis is an autoimmune disease of unknown etiology leading to progressive destruction of small intrahepatic bile ducts and eventually to liver cirrhosis and failure . It is characterized by female predominance (with most cases observed between the ages of 40 and 60) and serum autoantibodies to mitochondrial antigens as highly specific hallmarks . Epidemiologic data indicate a variable incidence and prevalence of the disease . A number of genetic factors have been indicated as playing a role in determining disease susceptibility or progression, although no definitive conclusion has been reached so far . However, as suggested by some epidemiologic observations, a number of environmental factors, including molecular mimicry by either microorganisms or xenobiotics, have also been proposed . A hypothesis gaining support is that environmental factors may trigger disease in genetically predisposed individuals . In this review, the available data regarding the epidemiology and pathogenesis of primary biliary cirrhosis will be described and discussed.

J Clin Virol, 2004 Jun, 30(2), 165 - 74
Evaluation of a multiplex reverse transcriptase PCR ELISA for the detection of nine respiratory tract pathogens; Puppe W et al.; BACKGROUND: A multiplex reverse transcription (RT) polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) was previously developed to detect nine different microorganisms: enterovirus (EV), influenza virus type A (IVA) and type B (IVB), respiratory syncytial virus (RSV), parainfluenzavirus type 1 (PIV1) and type 3 (PIV3), adenovirus (AV), Mycoplasma pneumoniae (Mpn), Chlamydia pneumoniae (Cpn) in a single test . These organisms do not usually colonize the respiratory tract of humans, but, if present, it may be assumed they are involved in respiratory disease . OBJECTIVES AND STUDY DESIGN: The m-RT-PCR-ELISA was tested on (i) culture supernatants of unknown contents, (ii) by determining the analytical sensitivity of 10-fold serial dilutions of culture supernatants and (iii) by determining clinical sensitivity in a retrospective study on 411 clinical specimens . The specimens were re-tested in parallel by m-RT-PCR-ELISA versus the gold standard culture and immunfluorescence, and versus individual RT-PCR . RESULTS: (i) The 9-valent m-RT-PCR-ELISA shows 83% to 100% concordant results on 103 culture supernatants containing different organisms . (ii) The analytical sensitivity was as follows: higher sensitivity of the 9-valent m-RT-PCR-ELISA in comparison to culture in the cases of PIV3, IVA and IVB (factor 10) and AV and EV (factor 100), and lower sensitivity in case of RSV and PIV1 (factor 10) . (iii) The agreement with the gold standard in the kappa statistic was excellent for RSV (kappa = 0.937), IVA (kappa = 0.940), very good for PIV1 (kappa = 0.914), IVB (kappa = 0.907) and satisfactory for PIV3 (kappa = 0.410) . For AV, EV and Mpn the m-RT-PCR-ELISA preliminary could be qualified as very good, based on the data derived on culture supernatants . Information about the validity for Cpn is limited . CONCLUSION: The m-RT-PCR-ELISA is a feasible, sensitive and specific method for detection of a broad spectrum of organisms . It is suitable for individual as well as epidemiological diagnosis.

Acta Med Croatica, 2004, 58(1), 1 - 4
{Biological adequacy--what does it mean?}; Kes P et al.; Appropriate initiation of dialysis is of an outstanding importance in the treatment of patients with end-stage renal disease . It prevents development of irreversible uremic complication and enables selection of the most appropriate dialysis modality for the individual patient . The major causes of morbidity and mortality in dialysis patients are cardiovascular diseases . Hypertension and hyperlipidemia are commonly found in dialysis patients as well as anemia, chronic inflammation and fluid overload, all of which are found to be risk factors for the development of cardiovascular diseases . Arterial hypertension is the main risk factor for left ventricular hypertrophy, and there is clear evidence that control of hypertension has a beneficial effect on left ventricular hypertrophy . It is best achieved by correction of overhydration and maintenance of dry weight . Modern dialysis machines are capable of changing electrolyte concentrations, which reduces intradialytic cardiovascular complications, incidence of cardiac arrhythmias and hypotension . Correction of anemia with erythropoietin results in regression of left ventricular hypertrophy and improvement of the quality of life and defense against microorganisms . Chronic inflammation can be prevented with the use of biocompatible high-flux dialysis membranes and sterile dialysate, which are also important for the prevention of oxidative stress involved in the increase of LDL oxygenation and incorporation into the intimal layer of the vessels . Low molecular weight heparins by their action on lipoprotein lipase serve as an additional factor that suppresses development of atherosclerotic plaque in dialysis patients . Optimal dialysis dose decreases the mortality and morbidity rates . High-flux membranes or prolongation of dialysis session are modalities for dialysis dose improvement . Individualized approach to preparation of dialysis solutions has resulted in better control of fluid overload and intradialytic hyper- or hypotension, reduction in the incidence of arrhythmias, improvement of hemodynamic stability, and delay of renal osteodystrophy . Malnutrition is a relatively common problem in dialysis patients that may be secondary to poor nutritional intake, inadequate amount of dialysis, lack of appetite, acidosis, associated disease, and/or increase in protein catabolism . The most appropriate approach includes individualization of dietary prescription according to the nutritionist's advice, increase of dialysis dose with biocompatible membranes, and use of sterile bicarbonate dialysate with glucose and erythropoietin . The major goal of adequate dialysis is not just improvement in survival of dialysis patients, but also improvement in the quality of their lives.

Med Mycol, 2004 Apr, 42(2), 95 - 106
Protothecosis; Leimann BC et al.; Protothecosis is an infection caused by achlorophyllic algae of the genus Prototheca which rarely affects humans . Some 100 cases have been described in the medical literature, the majority caused by the species P . wickerhamii . The skin is the organ most frequently involved . Diagnosis is performed by isolation of the microorganism in culture or by histopathology . The ideal treatment has not been defined, with amphotericin B and the azoles having been employed . Surgical excision is recommended for small, localized lesions . We describe a case of cutaneous protothecosis on the right fourth finger of a female patient 59 years old with no underlying disease . Administration of itraconazole 400 mg/day for 6 weeks failed to produce an adequate clinical response . Treatment was then changed to fluconazole 200 mg/day, with regression of the lesion.

J Biol Chem, 2004 Jul 9, 279(28), 29752 - 60 Epub 2004 Apr 29.
Solution structure of the tandem Src homology 3 domains of p47phox in an autoinhibited form; Yuzawa S et al.; The phagocyte NADPH oxidase is a multisubunit enzyme responsible for the generation of superoxide anions (O(2).) that kill invading microorganisms . p47(phox) is a cytosolic subunit of the phagocyte NADPH oxidase, which plays a crucial role in the assembly of the activated NADPH oxidase complex . The molecular shapes of the p47(phox) tandem SH3 domains either with or without a polybasic/autoinhibitory region (PBR/AIR) at the C terminus were studied using small angle x-ray scattering . The tandem SH3 domains with PBR/AIR formed a compact globular structure, whereas the tandem SH3 domains lacking the PBR/AIR formed an elongated structure . Alignment anisotropy analysis by NMR based on the residual dipolar couplings revealed that the tandem SH3 domains with PBR/AIR were in good agreement with a globular module corresponding to the split half of the intertwisted dimer in crystalline state . The structure of the globular module was elucidated to represent a solution structure of the tandem SH3 domain in the autoinhibited form, where the PBR/AIR bundled the tandem SH3 domains and the linker forming a closed structure . Once PBR/AIR is released by phosphorylation, rearrangements of the SH3 domains may occur, forming an open structure that binds to the cytoplasmic proline-rich region of membrane-bound p22(phox).

Fish Shellfish Immunol, 2004 Feb, 16(2), 241 - 9
The effect of dietary administration of the fungus Mucor circinelloides on non-specific immune responses of gilthead seabream; Rodriguez A et al.; The immunostimulant potential of the whole fungus Mucor circinelloides administered in the diet to gilthead seabream (Sparus aurata L.) was studied . Three different lyophilised strains were used: the wild-type (R7B) and two mutant strains in the carotene-production pathway which are enriched in lycopene (MU224) or beta-carotene (T31) . Fish were fed diets containing 0 (control) or 10 g of one of the whole M . circinelloides strains per kg feed . After 2, 4 or 6 weeks of treatment the growth rate as well as humoral (lysozyme activity) and cellular (phagocytosis and cytotoxicity) immune responses were determined . The specific growth rate increased slightly with all the M . circinelloides-supplemented diets . Serum lysozyme activity increased slightly (P>0.05) in fish fed the mutant strain-supplemented diets . Of the cellular responses, phagocytosis significantly increased after 6 weeks, in fish fed the wild-type strain-supplemented diets while cytotoxicity increased after 4 weeks in fish fed the beta-carotene-enriched strain-supplemented diet . The immune responses were increased to some degree by diets containing whole M . circinelloides strains . These results are discussed in the light of the on-going search for new microorganisms, wild or mutant-type, for use as immunostimulants in fish farming.

Best Pract Res Clin Gastroenterol, 2004 Apr, 18(2), 241 - 53
Microbial-gut interactions in health and disease . Epithelial cell responses; Mahida YR; Intestinal epithelial cells are unique in that they represent the only host cells that are constantly interacting with a very large bacterial population in the lumen . The single monolayer of epithelial cells consists of subpopulations with distinct functions that include protection against luminal microorganisms . Although the microbial flora remains to be fully characterized, its normal relationship with the host intestinal epithelial cells appears to be predominantly symbiotic or commensal . The molecular complexity of the epithelial-microbial relationship has been shown in studies that have examined the establishment of the resident bacteria in germ-free mice . Recent work has also demonstrated the ability of resident bacteria to enhance epithelial protective responses . The mechanisms by which epithelial cells may avoid pro-inflammatory responses to resident microorganisms, while retaining the capacity to respond to pathogens, are also being characterized.

J Bone Joint Surg Am, 2004 May, 86-A(5), 1065 - 76
Transmission and prevention of occupational infections in orthopaedic surgeons; Wong KC et al.; Microorganisms are transmitted in hospitals mainly by contact, droplet, and airborne routes . Orthopaedic surgeons have a substantial occupational risk of contracting a blood-borne infection because of frequent handling of sharp instruments and objects during operative procedures . Aerosolization means the formation of aerosols and droplets when blood or other body fluids are mechanically disturbed . Smaller particles (<5 microm) will remain suspended in air . Pathogens that can survive in these small airborne particles may cause infection if they are inhaled . Aerosol-generating procedures in patients with tuberculosis or severe acute respiratory syndrome (SARS) may facilitate airborne transmission . The Hospital Infection Control Practices Advisory Committee and the Centers for Disease Control and Prevention have established guidelines for isolation precautions in hospitals.

Environ Sci Technol, 2004 Apr 15, 38(8), 2397 - 405
Metal speciation dynamics and bioavailability: bulk depletion effects; Pinheiro JP et al.; Under conditions of bulk depletion, the speciation and bioavailability of trace metals must be considered at two different time scales: (i) the time scale of the biouptake flux, as determined by diffusion of the bioactive free metal, dissociation of the bioinactive complex species, and the internalization rate; and (ii) the time scale of depletion of the bulk medium . The implications of these two time scales for the speciation dynamics are discussed in terms of experimental conditions . The geometry of the system is taken into accountvia a spherical cellular model . It considers a spherical organism depleting a spherical volume in a nonstirred medium and assumes linear adsorption of the metal atthe biointerface and first-order internalization kinetics . In cases where the rate of biouptake is fully controlled by the internalization step, concentration gradients in the medium are insignificant . Then the biouptake becomes independent of the geometry of the system, and the model has a much simpler solution . Examples of trace metal uptake by microorganisms are analyzed: (i) cobalt uptake by Prochlorococcus in the presence of NTA, under conditions where bulk depletion is the controlling process due to the large number of organisms and high internalization rates, (ii) silver uptake by Chlamydomonas reinhardtii with significant effects of bulk depletion, due to the high internalization rate; (iii) lead uptake by Chlorella vulgaris with pratically negligible bulk depletion due to the low internalization rate of the metal; and (iv) lead uptake by intestinal Caco-2 cells, illustrating the simplification of the bulk depletion model for a system with different geometry where internalization is the rate-controlling step.

Crit Rev Microbiol, 2004, 30(1), 7 - 24
Bacterial separation and concentration from complex sample matrices: a review; Stevens KA et al.; The use of many rapid detection technologies could be expanded if the bacteria were separated, concentrated, and purified from the sample matrix before detection . Specific advantages of bacterial concentration might include facilitating the detection of multiple bacterial strains; removal of matrix-associated assay inhibitors; and provision of adequate sample size reduction to allow for the use of representative food sample sizes and/or small media volumes . Furthermore, bacterial concentration could aid in improving sampling techniques needed to detect low levels of pathogens or sporadic contamination, which may perhaps reduce or even eliminate the need for cultural enrichment prior to detection . Although bacterial concentration methods such as centrifugation, filtration, and immunomagnetic separation have been reported for food systems, none of these is ideal and in many cases a technique optimized for one food system or microorganism is not readily adaptable to others . Indeed, the separation and subsequent concentration of bacterial cells from a food sample during sample preparation continues to be a stumbling block in the advancement of molecular methods for the detection of foodborne pathogens . The purpose of this review is to provide a detailed understanding of the science, possibilities, and limitations of separating and concentrating bacterial cells from the food matrix in an effort to further improve our ability to harness molecular methods for the rapid detection of foodborne pathogens.

Crit Rev Microbiol, 2004, 30(1), 1 - 6
Catastrophe and what to do about it if you are a bacterium: the importance of frameshift mutants; Koch AL; Key problems that bacteria have historically faced are the challenges of the lack of essential nutrients and the presence of antibiotics produced naturally, but there are many other challenges . It appears that for many of these challenges the bacteria have mechanisms encoded in their genomes that are not usually functioning, but may be "turned on" when needed, even if the need only occurs once in hundreds of thousands of generations . Such mechanisms at other times somehow need to be "turned off" because they may cause a slight disadvantage, or even a grave disadvantage to the cell compared with wild-type cells during the time the population is not being challenged . On the other hand, a gene cannot simply be discarded because it might be needed again . How do microorganisms solve the problem of responding to challenges that only occur rarely? I suggest that in most cases, the mutation must occur by the existence of a readily reversible mutation . The mutation in likely the result of a frameshift mutation that caused the response and later another frameshift occurs to return the genome to its original state.

Kidney Blood Press Res, 2004, 27(3), 134 - 42 Epub 2004 Apr 26.
Chlamydia pneumoniae and atherosclerosis: no way-out or long way? What about renal failure patients?
Tsirpanlis G.
Recently, Chlamydia pneumoniae is the microorganism frequently implicated in the infection-based inflammatory atherogenous hypothesis . Although in vitro experimental data and initial sero-epidemiologic, pathology-based studies and antibiotic trials supported this interesting hypothesis, later data are conflicting . Some confounding factors are the causes of uncertainty; lacking of standard methods for C . pneumoniae detection, co-existence of other atherosclerotic risk factors and anti-inflammatory effects of antibiotics used in clinical trials seem to be the principal ones . Standardization of methodology used, antibiotic trials with a different orientation-design and a vaccine preparation that eventually will be tested in clinical trials with a long follow-up, should provide a definite answer regarding the probability C . pneumoniae to be a main, a secondary or an irrelevant factor to atherosclerosis . Studies linking C . pneumoniae to inflammation and accelerated atherosclerosis in renal failure patients are accumulated but limitations are similar to the above mentioned .

Metab Eng, 2004 Apr, 6(2), 133 - 9
Cofactor engineering of intracellular CoA/acetyl-CoA and its effect on metabolic flux redistribution in Escherichia coli; Vadali RV et al.; Coenzyme A (CoA) and its thioester derivatives are important cofactors participating in over 100 different reactions in intermediary metabolism of microorganisms . The time profiles of intracellular CoA and acetyl-CoA levels were studied in an aerobic batch reactor . The CoA level starts at a high value and falls off gradually over the exponential and stationary growth phases, reaching negligible levels at the end of 24h . The acetyl-CoA level, on the other hand, increases initially reaching a maximum and decreases gradually reaching negligible levels after 24h . Overexpressing one of the upstream rate-controlling enzyme the pantothenate kinase with simultaneous supplementation of the precursor pantothenic acid to the culture medium increased the intracellular CoA/acetyl-CoA levels . It was found that supplementation of the precursor pantothenic acid is essential to increase CoA/acetyl-CoA levels . A 10-fold increase in CoA level was observed upon this overexpression in complex medium . Acetyl-CoA levels also increased (5-fold) but not as much as CoA, leaving much of the CoA in free unacetylated form . The increase in intracellular CoA/acetyl-CoA levels led to an increase in carbon flux to the acetate production pathway leading to formation of more acetate in complex medium, whereas no such change in metabolite redistribution was observed in minimal medium.

Environ Sci Technol, 2004 Apr 1, 38(7), 2075 - 81
Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants; Fennell DE et al.; Dehalococcoides ethenogenes strain 195 dechlorinates tetrachloroethene to vinyl chloride and ethene, and its genome has been found to contain up to 17 putative dehalogenase gene homologues, suggesting diverse dehalogenation ability . We amended pure or mixed cultures containing D . ethenogenes strain 195 with 1,2,3,4-tetrachlorodibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin, 2,3-dichlorodibenzo-p-dioxin, 1,2,3,4-tetrachlorodibenzofuran, 2,3,4,5,6-pentachlorobiphenyl, 1,2,3,4-tetrachloronaphthalene, various chlorobenzenes, or a mixture of 2-, 3-, and 4-chlorophenol to determine the dehalogenation ability . D . ethenogenes strain 195 dechlorinated 1,2,3,4-tetrachlorodibenzo-p-dioxin to a mixture of 1,2,4-trichlorodibenzo-p-dioxin and 1,3-dichlorodibenzo-p-dioxin . 2,3,4,5,6- Pentachlorobiphenyl was dechlorinated to 2,3,4,6- and/or 2,3,5,6-tetrachlorobiphenyl and 2,4,6-trichlorobiphenyl . 1,2,3,4-Tetrachloronaphthalene was dechlorinated primarily to an unidentified dichloronaphthalene congener . The predominant end products from hexachlorobenzene dechlorination were 1,2,3,5-tetrachlorobenzene and 1,3,5-trichlorobenzene . We did not detect dechlorination daughter products from monochlorophenols, 2,3-dichlorodibenzo-p-dioxin or 2,3,7,8- tetrachlorodibenzo-p-dioxin . D . ethenogenes strain 195 has the ability to dechlorinate many different types of chlorinated aromatic compounds, in addition to its known chloroethene respiratory electron acceptors . Remediation of sediments contaminated with aromatic halogenated organic pollutants such as polychlorinated biphenyls and polychlorinated dibenzo-p-dioxins could require billions of dollars in the coming years . Harnessing microorganisms such as Dehalococcoides spp . that detoxify these compounds via removal of halogens may lead to cost-effective biotechnological approaches for remediation.

Vet Clin North Am Small Anim Pract, 2004 May, 34(3), 669 - 91
Antifungals and their use in veterinary ophthalmology; Ford MM; Many variables affect the outcome of keratomycosis and systemic fungal infections in animals . These include pathogenicity of the fungal organism(toxins, trophisms, and evasion of host response); previous treatment with topical or systemic corticosteroids, which can have a dramatic negative impact on host defense mechanisms: concurrent systemic illness or immunocompromise: severity/extent of infection; and degree of pain (ie,increased reflex tearing dilutes topical medication) {14} . Experimental work suggests that antibiotics may occasionally exacerbate fungal infections {142},and some researchers advocate that concurrent antibiotic therapy is contraindicated in horses with yeast infections and septate fungal infections unless bacterial infection is also suspected {14} . Nevertheless, given that normal conjunctival flora often include bacteria and fungi and because care of keratomycoses often includes mixed bacterial and fungal infections, the possible dynamics (natural influences and local competition) between ocular surface microorganisms merit further investigation . There are many unanswered questions regarding the accuracy of in vitro susceptibilities and corneal concentration capabilities for antifungal topical medications {14}.Inherent host resistance or other immune interactions between the patient and fungus are perhaps the most important determinants of the outcome but are currently difficult to measure or assess except by subjective clinical observation {14}.

Insect Biochem Mol Biol, 2004 May, 34(5), 415 - 24
Honey bee (Apis mellifera) transferrin-gene structure and the role of ecdysteroids in the developmental regulation of its expression; do Nascimento AM et al.; Social life is prone to invasion by microorganisms, and binding of ferric ions by transferrin is an efficient strategy to restrict their access to iron . In this study, we isolated cDNA and genomic clones encoding an Apis mellifera transferrin (AmTRF) gene . It has an open reading frame (ORF) of 2136 bp spread over nine exons . The deduced protein sequence comprises 686 amino acid residues plus a 26 residues signal sequence, giving a predicted molecular mass of 76 kDa . Comparison of the deduced AmTRF amino acid sequence with known insect transferrins revealed significant similarity extending over the entire sequence . It clusters with monoferric transferrins, with which it shares putative iron-binding residues in the N-terminal lobe . In a functional analysis of AmTRF expression in honey bee development, we monitored its expression profile in the larval and pupal stages . The negative regulation of AmTRF by ecdysteroids deduced from the developmental expression profile was confirmed by experimental treatment of spinning-stage honey bee larvae with 20-hydroxyecdysone, and of fourth instar-larvae with juvenile hormone . A juvenile hormone application to spinning-stage larvae, in contrast, had only a minor effect on AmTRF transcript levels . This is the first study implicating ecdysteroids in the developmental regulation of transferrin expression in an insect species.

Biochem Biophys Res Commun, 2004 May 21, 318(1), 81 - 7
Involvement of colicin in the limited protection of the colicin producing cells against bacteriophage; Lin YH et al.; The restriction/modification system is considered to be the most common machinery of microorganisms for protection against bacteriophage infection . However, we found that mitomycin C induced Escherichia coli containing ColE7-K317 can confer limited protection against bacteriophage M13K07 and lambda infection . Our study showed that degree of protection is correlated with the expression level of the ColE7 operon, indicating that colicin E7 alone or the colicin E7-immunity protein complex is directly involved in this protection mechanism . It was also noted that the degree of protection is greater against the single-strand DNA bacteriophage M13K07 than the double-strand bacteriophage(lambda) . Coincidently, the K(A) value of ColE7-Im either interacting with single-strand DNA (2.94x10(5)M(-1)) or double-strand DNA (1.75x10(5)M(-1)) reveals that the binding affinity of ColE7-Im with ssDNA is 1.68-fold stronger than that of the protein complex interacting with dsDNA . Interaction between colicin and the DNA may play a central role in this limited protection of the colicin-producing cell against bacteriophages . Based on these observations, we suggest that the colicin exporting pathway may interact to some extent with the bacteriophage infection pathway leading to a limited selective advantage for and limited protection of colicin-producing cells against different bacteriophages.

J Hosp Infect, 2004 Apr, 56 Suppl 2, S27 - 39
Reprocessing endoscopes: United States perspective; Rutala WA et al.; Endoscopes are used frequently for the diagnosis and therapy of medical disorders . For example, greater than 10000000 gastrointestinal endoscopic procedures are performed each year in the United States . Failure to employ appropriate cleaning and disinfection/sterilization of endoscopes has been responsible for multiple nosocomial outbreaks and serious, sometimes life-threatening, infections . Flexible endoscopes, by virtue of the site of use, have a high bioburden of microorganisms after use . The bioburden found on flexible gastrointestinal endoscopes following use has ranged from 10(5) to 10(10)CFU/ml, with the highest levels being found in the suction channels . Cleaning dramatically reduces the bioburden on endoscopes . Several investigators have shown a mean log(10) reduction factor of 4 (99.99%) in the microbial contaminants with cleaning alone . Cleaning should be done promptly following each use of an endoscope to prevent drying of secretions, allow removal of organic material, and decrease the number of microbial pathogens . Because the endoscope comes into intimate contact with mucous membranes, high-level disinfection is the reprocessing standard after each patient use . High-level disinfection refers to the use of a disinfectant (e.g., FDA-cleared chemical sterilant or high-level disinfectant) that inactivates all microorganisms (i.e., bacteria, viruses, fungi, mycobacteria) but not high levels of bacterial spores . The disinfection process requires immersion of the endoscope in the high-level disinfectant and ensuring all channels are perfused for the approved contact time (e.g., for ortho-phthaladehyde this is 12 min in the US) . Following disinfection, the endoscope and channels are rinsed with sterile water, filtered water, or tapwater . The channels are then flushed with alcohol and dried using forced air . The endoscope should be stored in a manner that prevents recontamination . A protocol that describes the meticulous manual cleaning process, the appropriate training and evaluation of the reprocessing personnel, and a quality assurance program for endoscopes should be adopted and enforced by each unit performing endoscopic reprocessing.

Cell Biol Int, 2004, 28(4), 243 - 8
Involvement of protein kinases on the process of erythrophagocytis by Entamoeba histolytica; Batista Ede J et al.; Erythrophagocytic capacity of trophozoites of Entamoeba histolytica is considered a factor in the virulence of this pathogenic protozoan . We present evidence showing that such activity resembles the ingestion of microorganisms by highly differentiated phagocytic cells, such as macrophages . Previous treatment of the trophozoites with genistein or tyrphostin, inhibitors of tyrosine protein kinases, with staurosporine, a protein kinase C inhibitor, and wortmannin, a fungal metabolite that inhibits phosphoinositide 3-OH kinase, significantly inhibited their erythrophagocytic capacity.

Artif Life, 2004 Spring, 10(2), 135 - 44
Bifurcation into functional niches in adaptation; White JS et al.; One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification . This issue can be addressed experimentally if replicate populations adapting to identical environments can be investigated in detail . We have studied 501 such replicas using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates . While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures . We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible . This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright.

Oral Microbiol Immunol, 2004 Jun, 19(3), 155 - 9
Identification of a Fusobacterium nucleatum 65 kDa serine protease; Bachrach G et al.; A 65 kDa protease was partially purified from extracellular vesicles of Fusobacterium nucleatum cultures by preparative SDS-PAGE followed by electroelution . The pH optimum of the protease is 7.5-8.0 and its activity could be inhibited by serine protease inhibitors . The protease was found to degrade the extracellular matrix proteins fibrinogen and fibronectin as well as collagen I and collagen IV which were degraded at 37 degrees C but not at 28 degrees C, indicating the presence of a gelatinase activity in these bacteria . The 65 kDa protease was also able to digest the alpha-chains of immunoglobulin A but not immunoglobulin G . The 65 kDa F . nucleatum protease, capable of degrading native proteins, may play an important role in both the nutrition and pathogenicity of these periodontal microorganisms . The degradation of extracellular matrix proteins by bacterial enzymes may contribute to the damage of periodontal tissues, and degradation of IgA may help the evasion of the immune system of the host by the bacteria . Copyright Blackwell Munksgaard, 2004.

Int Tinnitus J, 2003, 9(2), 87 - 91
Interrelations between the middle and inner ear in otitis media; Penha R et al.; This article reviews the importance of the round-window membrane in exposing the labyrinth to or protecting it from the toxic effects of otitis media . Characteristics of the immune system in the human middle ear and middle-ear mechanisms against bacteria are explained . The role of bacteria and bacterial products in inner-ear damage is detailed, and related pathological events are described . The hypothetical role of inflammatory mediators in bacteria-induced inner-ear toxicity is particularly emphasized . Clinical conditions causing these events are detailed, and the most frequently involved microorganisms are mentioned . Finally, round-window membrane macroscopic and microscopic anatomy is discussed, and considerations about the exact role of membrane inflammation--protection versus damage of the inner ear--are expressed.

J Nat Prod, 2004 Apr, 67(4), 553 - 8
Microbial transformations of chalcones: hydroxylation, O-demethylation, and cyclization to flavanones; Sanchez-Gonzalez M et al.; Microorganisms were examined for their potential to catalyze biotransformation reactions that mimic plant biosynthetic processes . Specifically, microorganisms were screened for their abilities to transform selected chalcones to flavonoid and other products . Aspergillus alliaceus UI 315 efficiently transformed 3-(2' ',3' '-dimethoxyphenyl)-1-(2'-hydroxyphenyl)propenone (2'-hydroxy-2,3-dimethoxychalcone) (1) to several products, all of which were characterized by UV, NMR, and mass spectral analyses . A . alliaceus cyclized 1 to three flavanones and to O-demethylated and hydroxylated chalcones, some of which functioned as intermediates in the cyclization process . Inhibition studies using SKF525A, metyrapone, and phenylthiocarbamide with whole cell reactions showed that as many as three cytochrome P450 enzymes may be involved in these reactions . One enzyme catalyzed chalcone cyclization; another, O-demethylation; and a third, hydroxylation of chalcones . Flavonoid products are racemic, unlike the same products that are stereoselectively cyclized in plants . This work shows that microorganisms are capable of cyclizing chalcones to form flavonoid products, thus affording a mimic of plant biosynthetic processes.

Am J Surg Pathol, 2004 Mar, 28(3), 379 - 83
Florid granulomatous reaction in Epstein-Barr virus-positive nonendemic Burkitt lymphomas: report of four cases; Haralambieva E et al.; Epithelioid cell granulomas have been reported in association with a wide range of neoplasms including malignant lymphomas . In lymphoma, this refers mainly to Hodgkin disease and T-cell-derived non-Hodgkin lymphomas where a granulomatous reaction is probably evoked by aberrant cytokine production in the tumor cells or other cells composing the tumor background . Here we report on four cases of sporadic Burkitt lymphoma with unusual florid granulomatous reaction . In all samples, the tumor cells were admixed with numerous epithelioid cells that formed clusters and granulomatous lesions . No microorganisms could be detected at the tissue level, and there were no clinical or laboratory indications of an underlying immunodeficiency . The lymphomas harbored a specific morphology and immunophenotype of Burkitt lymphoma, and the presence of translocation breakpoint in MYC gene was confirmed by interphase fluorescence in situ hybridization . In all four patients, the lymphoma was associated with Epstein-Barr virus infection, detected by EBER in situ hybridization and the latency I phenotype as defined by lack of expression of LMP1 . All four patients were treated with polychemotherapy, achieved a complete remission, and are alive without evidence of disease . We draw attention to this unusual phenomenon as it caused difficulties in interpretation and delayed diagnosis and hypothesize on the possible role of Epstein-Barr virus products.

Mikrobiol Z, 2004 Jan-Feb, 66(1), 78 - 90
{Pathogenicity factors of mollicutes and pathogenesis of some human mycoplasmoses}; Skrypal' IH; The data of pathogenicity factors of mollicutes and mechanisms of the effect of these microorganisms on the organisms they have infected and, first of all, on people occur in countless literary sources . Such data have been accumulated for above 100 year of mycoplasmology existence as science and remain unachievable for most interested specialists . An attempt has been made to generalize in maximum complete volume everything known about pathogenic potential of human and other mollicutes, their pathogenicity factors and mechanisms of their realization on the dramatic changes occurring in the affected organism under the effect of mycoplasmic infection.

Infect Immun, 2004 May, 72(5), 2872 - 8
Mycobacteria inhibit nitric oxide synthase recruitment to phagosomes during macrophage infection; Miller BH et al.; Inducible nitric oxide synthase (iNOS) is a cytoplasmic protein responsible for the generation of nitric oxide (NO . ) in macrophages . In this work, we hypothesized that the intracellular localization of iNOS is significant for effective delivery of NO . to phagosomes containing ingested microorganisms . Using immunofluorescence microscopy and Western blot analysis, iNOS was shown to localize in the vicinity of phagosomes containing latex beads in stimulated macrophages . iNOS also localized to phagosomes containing Escherichia coli . The colocalization of iNOS with ingested latex beads was an actin-dependent process, since treatment with the actin microfilament disrupter cytochalasin D prevented iNOS recruitment to latex bead phagosomes . In contrast to E . coli and inert particle phagosomes, mycobacterial phagosomes did not colocalize with iNOS . This study demonstrates that (i) . iNOS can be recruited to phagosomes; (ii) . this recruitment is dependent on a functional actin cytoskeleton; (iii) . certain microorganisms have the ability to prevent or reduce colocalization with iNOS; and (iv) . spatial exclusion of iNOS may play a role in Mycobacterium tuberculosis pathogenesis.

Curr Opin Biotechnol, 2004 Feb, 15(1), 64 - 9
Use of genome-scale microbial models for metabolic engineering; Patil KR et al.; Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools . Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metabolic network structures . The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data . Genome-scale stoichiometric models of microorganisms represent a first step in this direction.

Trends Plant Sci, 2004 Feb, 9(2), 97 - 104
Nonhost resistance: how much do we know?
Mysore KS, Ryu CM.
Nonhost disease resistance is the most common form of disease resistance exhibited by plants against the majority of potentially pathogenic microorganisms . Recently, several components of nonhost disease resistance have been identified . Nonhost resistance exhibited against bacteria, fungi and oomycetes can be of two types . Type I nonhost resistance does not produce any visible symptoms whereas type II nonhost resistance results in a rapid hypersensitive response with cell death . Strong similarities exist between nonhost and gene-for-gene resistance responses but it is still not clear if the same mechanism is involved in producing these resistance responses.

Mol Microbiol, 2004 May, 52(3), 643 - 50
Stress-directed adaptive mutations and evolution; Wright BE; Comparative biochemistry demonstrates that the metabolites, complex biochemical networks, enzymes and regulatory mechanisms essential to all living cells are conserved in amazing detail throughout evolution . Thus, in order to evolve, an organism must overcome new adverse conditions without creating different but equally dangerous alterations in its ongoing successful metabolic relationship with its environment . Evidence suggests that stable long-term acquisitive evolution results from minor increases in mutation rates of genes related to a particular stress, with minimal disturbance to the balanced and resilient metabolism critical for responding to an unpredictable environment . Microorganisms have evolved specific biochemical feedback mechanisms that direct mutations to genes derepressed by starvation or other stressors in their environment . Transcription of the activated genes creates localized supercoiling and DNA secondary structures with unpaired bases vulnerable to mutation . The resulting mutants provide appropriate variants for selection by the stress involved, thus accelerating evolution with minimal random damage to the genome . This model has successfully predicted mutation frequencies in genes of E . coli and humans . Stressed cells observed in the laboratory over hundreds of generations accumulate mutations that also arise by this mechanism . When this occurs in repair-deficient mutator strains with high rates of random mutation, the specific stress-directed mutations are also enhanced.

Genet Mol Res, 2004 Mar 31, 3(1), 162 - 6
Energetic metabolism of Chromobacterium violaceum; Creczynski-Pasa TB et al.; Chromobacterium violaceum is a free-living microorganism, normally exposed to diverse environmental conditions; it has a versatile energy-generating metabolism . This bacterium is capable of exploiting a wide range of energy resources by using appropriate oxidases and reductases . This allows C . violaceum to live in both aerobic and anaerobic conditions . In aerobic conditions, C . violaceum is able to grow in a minimal medium with simple sugars, such as glucose, fructose, galactose, and ribose; both Embden-Meyerhoff, tricarboxylic acid and glyoxylate cycles are used . The respiratory chain supplies energy, as well as substrates for other metabolic pathways . Under anaerobic conditions, C . violaceum metabolizes glucose, producing acetic and formic acid, but not lactic acid or ethanol . C . violaceum is also able to use amino acids and lipids as an energy supply.

Tuberk Toraks, 2003, 51(1), 52 - 5
{Recurrent Aspiration Pneumonia and Barrett's Esophagus: A Case Report}; Yuksekol I et al.; Gastroesophageal reflux is a condition that causes lung complications by gastric content aspiration in both adults and children . The most common complications are asthma, chronic bronchitis or chronic cough, recurrent pneumonia, pulmonary fibrosis and in children apnea as a result of regurgitation of large amount of gastric content suddenly . The reason of recurrent aspiration pneumonia is the aspiration of gastric content or microorganisms in upper gastrointestinal system . Barrett's esophagus characterized by the conversion of the epithelium of esophagus from squamous to columnar is a histological consequence of gastroesophageal reflux . We are presenting a case of Barrett's esophagus and recurrent pneumonia who had respiratory symptoms and difficulty in swallowing but no symptoms of gastroesophageal reflux . As it has been shown in our case it is difficult to cure the respiratory disease caused by nontreated asymptomatic gastroesophageal reflux.

Int Immunopharmacol, 2004 Apr, 4(4), 475 - 93
Redox and oxidant-mediated regulation of apoptosis signaling pathways: immuno-pharmaco-redox conception of oxidative siege versus cell death commitment; Haddad JJ; The mechanisms controlling apoptosis remain largely obscure . Because apoptosis is an integral part of the developmental program and is frequently the end-result of a temporal course of cellular events, it is referred to as programmed cell death . While there is considerable variation in the signals and requisite cellular metabolic events necessary to induce apoptosis in diverse cell types, the morphological features associated with apoptosis are highly conserved . Free radicals, particularly reactive oxygen species (ROS), have been proposed as common mediators for apoptosis . Many agents that induce apoptosis are either oxidants or stimulators of cellular oxidative metabolism . Conversely, many inhibitors of apoptosis have antioxidant activities or enhance cellular antioxidant defenses . Mammalian cells, therefore, exist in a state of oxidative siege in which survival requires an optimum balance of oxidants and antioxidants . The respiratory tract is subjected to a variety of environmental stresses, including oxidizing agents, particulates and airborne microorganisms that, together, may injure structural and functional lung components and thereby jeopardize the primary lung function of gas exchange . To cope with this challenge, the lung has developed elaborate defense mechanisms that include inflammatory-immune pathways as well as efficient antioxidant defense systems . In the absence of adequate antioxidant defenses, the damage produced is detected by the cell leading to the activation of genes responsible for the regulation of apoptosis, conceivably through stress-responsive transcription factors . Oxidative stress, in addition, may cause a shift in cellular redox state, which thereby modifies the nature of the stimulatory signal and which results in cell death as opposed to proliferation . ROS/redox modifications, therefore, may disrupt signal transduction pathways, can be perceived as abnormal and, under some conditions, may trigger apoptosis .

Xenotransplantation, 2004 May, 11(3), 284 - 94
Infection studies on human cell lines with porcine circovirus type 1 and porcine circovirus type 2; Hattermann K et al.; BACKGROUND: The lack of human donor organs in allotransplantation has led to a proposal for the use of porcine tissues and organs as alternative therapeutic material for humans . Besides immunological problems like graft rejection, one of the major concerns is the transmission of porcine microorganisms as viruses, bacteria and fungi to a human recipient . METHODS: Human cell lines have been infected with porcine circovirus type 1 (PCV1) and porcine circovirus type 2 (PCV2) to investigate whether PCV can infect and replicate in human epithelial cells and lymphocytes . Infection of PCV1 was observed with 293, Hela and Chang liver cells, infection with PCV2 only in Rd cells . In addition, religated viral DNA of PCV1 and PCV2 has been used to transfect adherent human cell lines . RESULTS: PCV1 persisted in most cell lines without causing any visible changes, while PCV2-transfected cells showed a cytopathogenic effect . Presence of PCV DNA was detected in cells and supernatant by PCR, expression of viral proteins by an indirect immune fluorescence assay . A replication assay showed that the replication of PCV DNA was initiated at the origin of replication . When virus-free cells were inoculated with the supernatant of PCV-infected human cells, the infection was not passed . CONCLUSION: Although PCV gene expression and replication took place in human cells, the infection is non-productive . Alteration of protein localization suggests that protein targeting may be disturbed in human cells . Copyright Blackwell Munksgaard, 2004

Anasthesiol Intensivmed Notfallmed Schmerzther, 2004 Apr, 39(4), 204 - 11
{Morphine inhibits complement receptor expression, phagocytosis and oxidative burst by a nitric oxide dependent mechanism}; Menzebach A et al.; OBJECTIVE: Monocytes play a crucial role in the immune response by recognition, ingestion, and intracellular killing of microorganisms . We investigated whether morphine and fentanyl influence CD 11b and CD35 surface receptor expression, phagocytic activity and superoxide anion generation of monocytes in a whole blood flow cytometric assay . METHODS: Whole blood of 13 healthy volunteers was incubated with different morphine and fentanyl concentrations . Expression of surface receptors CD 11b and CD35 was determined by fluorochrome-labelled antibodies . Phagocytic activity was assessed by ingestion of fluorescent bacteria . Conversion of dihydrorhodamin served for oxidative burst measurements . RESULTS: Morphine inhibited monocyte function in a concentration and time dependent manner . Morphine-induced changes were abolished by preincubation with the NO synthase inhibitor N-nitro-l-arginine as well as naloxone . Fentanyl failed to inhibit receptor expression, phagocytosis and reactive oxygen production by monocytes in clinically relevant as well as supraclinical concentrations . CONCLUSION: Our results suggest that these monocyte functions are inhibited by a morphine-stimulated NO release mediated by a mu opiate receptor subtype expressed on the surface of monocytes . In contrast, fentanyl did not share morphine's inhibitory effects on monocyte activity.

J Pediatr Gastroenterol Nutr, 2004 May, 38(5), 463 - 73
Innate immunity of the gut: mucosal defense in health and disease; Yuan Q et al.; The intestine is an important immune organ consisting of a complex cellular network, secreted peptides and proteins and other host defenses . Innate immunity plays a central role in intestinal immune defense against invading pathogens . It also serves as a bridge to the activation of the adaptive immune system . Pattern recognition molecules of microorganisms are an essential component for identifying invading pathogens . Toll-like receptors (TLRs), CARD15/NOD2 and scavenger receptors all serve as the pattern recognition receptors in the innate immune defense system . Secreted bactericidal peptides or defensins produced by the intestinal epithelia represent another crucial element of innate mucosal immune defense . Mutations in pattern recognition receptors and dysfunction of secretory bactericidal peptides may impair host immune defenses leading to an invasion of pathogens resulting in chronic inflammation of the gut . This review updates our current understanding of innate immunity of the gastrointestinal tract.

J Mol Diagn, 2004 May, 6(2), 108 - 14
Early detection and identification of commonly encountered Candida species from simulated blood cultures by using a real-time PCR-based assay; Maaroufi Y et al.; In a recent study, Candida species in clinical blood samples were detected using a real-time PCR-based method (Maaroufi et al, J Clin Microbiol 2003, 41:3293-3298) . For the present study, we evaluated the efficiency of this method as an adjunct to the BACTEC blood culture system to early detection of positivity and negativity of simulated low candidemias . We first established an in vitro correlation between the inoculum of the most frequently encountered Candida species and the time to positivity of these microorganisms . Then, aliquots from blood culture bottles infected with a final average candidal inoculum of 3.18 colony-forming units (CFU)/culture bottle (range, 1 to 6 CFU) were collected at increasing incubation times, and DNA was extracted and submitted to the TaqMan-based PCR assay . To optimize this assay, we evaluated the effect of adding 0.5% bovine serum albumin (BSA) to DNA extracts and found that it decreased the effects of inhibitors . Using specific probes for the tested Candida species, the PCR assay was positive on blood culture aliquots collected from the BACTEC system after a minimum culture turnaround time (TAT) of 3.11 +/- 1.24 hours . Addition of BSA to PCR reaction mixtures improves the TAT (1.84 +/- 0.41 hours) . Hence, the combination of DNA "amplification" in the culture bottles by normal growth with an additional DNA amplification by PCR might be a reliable tool facilitating the early diagnosis of low candidemias.

Cad Saude Publica, 1994 Mar, 10(1), 99 - 110 Epub 2004 Apr 08.
{Chlorine use in water disinfection, trihalomethane formation, and potential risks to public health}; Meyer ST; Before the development of the germ theory relating microorganisms with disease transmission (1880) people believed that diseases were transmitted by odours . Water and sewage disinfection emerged as a method for elimination of odours . There are many disinfecting agents, but chlorine is the main product used to disinfect water . Organic compounds present in water that is chlorinated can result in the formation of trihalomethanes . The latter are basically one atom of carbon, one of hydrogen, and three of a halogen (chlorine, bromine, or iodine) . These are considered carcinogenic compounds and their presence in drinking water should therefore be avoided . Epidemiological research has shown an association between trihalomethane concentration and cancer morbidity and mortality for some types of carcinoma . Nevertheless, there may be more risk than benefit involved in replacing chlorine with other disinfecting agents, since the incidence of water-borne diseases only dropped after water chlorination became a routine procedure.

FEBS Lett, 2004 Apr 23, 564(1-2), 121 - 5
Inhibition of insulin amyloid formation by small stress molecules; Arora A et al.; Amyloidogenic proteins undergo an alternative folding pathway under stressful conditions leading to formation of fibrils having cross beta-sheet structure, which is the hallmark of many neurodegenerative diseases . As a means of surviving against external stress, on the other hand, many microorganisms accumulate small stress molecules to prevent abnormal protein folding and to contribute to protein stability, which hints at the efficacy of the solutes against amyloid formation . The current work demonstrates the effectiveness of small stress molecules such as ectoine, betaine, trehalose, and citrulline on inhibition of insulin amyloid formation in vitro . The inhibitory effects were analyzed by thioflavin T-induced fluorescence, circular dichroism, and atomic force microscopy . This report suggests that naturally occurring small molecules may serve a function that is typically fulfilled by protein chaperones, and it provides a hint for designing inhibitors against amyloid formation associated with neurodegenerative disorders.

Biosens Bioelectron, 2004 Jun 15, 19(11), 1421 - 8
Segmented flow generation by chip reactors for highly parallelized cell cultivation; Grodrian A et al.; Micro system technology offers convenient tools for the production of handling devices for small liquid volumes which can be used in cell cultivation . Here, a modular system for the rapid generation of cell suspension aliquots is presented . The system is used to produce and analyze high numbers of well-separated culture volumes . Selected clones may be retrieved from the system . Therefore, the principle of segmented flow is applied . Portions of aqueous culture medium containing one cell or very small cell ensembles are separated from each other by a nonmiscible liquid like dodecane, tetradecane or mineral oil . In addition, the alkane separates the culture droplets from the innerside of the walls of chip channels and capillaries . This way, compatibility problems between cell wall surfaces and the chemical character of walls are excluded . The separated culture droplets are guided by micro flow transportation in different channel and chamber topologies . The whole system has the character of a serially operating cell processing system . The aliquot generation can be sped up to frequencies of about 30 Hz in each microchannel . That means, that about 10(5) individual cultural volumes can be produced per hour or about 2 million per day . The survival and the growth of microorganisms has been shown for model organisms as well as for organisms from a natural sample (soil).

Biol Cell, 2004 Feb, 96(1), 93 - 101
Calcium signalling during cell interactions with bacterial pathogens; TranVan Nhieu G et al.; The ability of a pathogenic microorganism to cause a disease is conditioned by its ability to colonise a given niche and implicates the expression of specific determinants, i.e . virulence factors, that allow the pathogen to adhere to or to invade epithelial cells . Diseases may be induced by bacteria that replicate extracellularly and alter the epithelial mucosa by producing toxins . Ca2+ signalling has been implicated in various steps of bacterial infection . Bacterial toxins can induce an increase in free cytosolic Ca2+ in host cells, itself required for the toxin-mediated effects . Such toxins, by diffusing in the extracellular media, can act at a distance from the site of infection and have a global effect on the integrity of the epithelium by promoting the expression of pro-inflammatory cytokines . Independent on toxins, bacteria can induce Ca2+ responses that play a role in cytoskeletal rearrangements required for cell binding or internalisation of the microorganism . In some instances, invasion of the epithelium may be followed by bacterial access to deeper tissue, dissemination to other organs, and sometimes persistence in host cells in a parasitic-like mode . Such strategies underline the pathogen abilities to control innate defence cells such as professional phagocytes, and may implicate the diversion of Ca(2+)-dependent cellular processes that normally result in killing of the ingested bacteria . Finally, bacterial pathogens can also induce the cell release of ATP, a Ca2+ agonist, that may expand bacterial cell signalling by a paracrine or autocrine route, leading to enhanced colonisation or enhanced host cell responses to the invading microorganism.

Environ Pollut, 2000 Apr, 108(1), 53 - 9
Characterisation of soil-bound residue fractions of the fungicide dithianon by gel permeation chromatography and polyacrylamide gel electrophoresis; Wanner U et al.; The degradation of the (14)C-labelled fungicide dithianon in an orthic luvisol was investigated under standardized conditions in comparison to stimulated microbial activity by an amendment of maize straw . The compound is characterized by mineralization losses of approximately 33% and the formation of non-extractable bound residues of approximately 63% in 64 days . Despite the major role of microorganisms in mineralizing this compound, the formation of bound residues is not biotically induced . Gel permeation chromatography and polyacrylamide gel electrophoresis, as different size separation techniques of the humic acids fractions, showed differences in the distribution patterns of non-extractable residues depending on the addition of straw material . The results presented support the existence of humic substances in soil as a micellar system rather than as a biopolymer.

Environ Pollut, 2000 Apr, 108(1), 3 - 14
Bound pesticide residues in soils: a review; Gevao B et al.; This article is a review of the current state of knowledge regarding the formation and biological/environmental significance of bound pesticide residues in soils . We begin by defining various terms used in our discussions and identifying the types/classes of pesticides which may be added to soil and interact with it . We then consider various soil properties and aspects of land management which will influence the nature and degree of the soil-pesticide association and discuss the possible physical and chemical binding mechanisms . We then move on to consider the role of microorganisms and other forms of soil biota in bound residue formation and the bioavailability of soil-borne pesticide residues . The review ends with a consideration of the significance of bound pesticide residues.

Environ Pollut, 2000 Jun, 108(3), 405 - 12
Influence of polyacrylamide application to soil on movement of microorganisms in runoff water; Sojka RE et al.; Polyacrylamide (PAM) use in irrigation for erosion control has increased water infiltration and reduced soil erosion . This has improved runoff water quality via lower concentrations of nitrogen, phosphorous, and pesticides, and decreased biological oxygen demand . Since non-toxic high molecular weight anionic PAMs removed clay size sediment particles in flowing water, we hypothesized that PAM would effectively remove or immobilize microorganisms in flowing water . In an agricultural field, we determined the efficacy of PAM-treatment of furrow irrigation water to remove several categories of microorganisms in the inflow and runoff . Treatments were: (1) PAM application and a control; (2) three flow rates; (3) two distances from the inflow point; and (4) three times during each irrigation . After water traveled 1 m at 7.5 and 15.5 l min(-1), PAM-treatment reduced total bacterial and microbial biomass and total fungal biomass relative to the control treatment . After water traveled 40 m at 7.5, 15.5, and 22.5 l min(-1), PAM-treatment reduced algae, the numbers active and total bacteria, active and total fungal length, and total bacterial biomass, total fungal and microbial biomass relative to the control treatment . Although specific organisms were not identified or monitored in this study, the results clearly have implications for controlling the spread of soil-borne plant pathogens and other classes of harmful organisms within and among fields via irrigation water and in re-utilized return flows . Beyond furrow-irrigated agriculture, new methods to manage overland transmission of harmful microorganisms could potentially help control transport of pathogens from animal waste in runoff and groundwater.

Environ Pollut, 2000 Jul, 109(1), 83 - 9
Microbial utilization and transformation of humic acid-like substances extracted from a mixture of municipal refuse and sewage sludge disposed of in a landfill; Filip Z et al.; The purpose of the research was to establish whether humic acid-like substances (HA) related to municipal refuse disposed of in a landfill can resist microbial degradation and if they contribute, in that way, to long-term stabilization of landfill refuse . Using a mixture of 0.1 M Na(4)P(2)O(7) + 0.1 M NaOH, we extracted HA from municipal refuse mixed with sewage sludge and disposed of for up to 12 months, in a 40-m(3) model landfill . In laboratory experiments under aerobic conditions, up to 50% of HA was utilized as a supplementary source of nutrients by an assemblage of soil microorganisms in only 21 days . The microbial utilization was enhanced to over 80%, and up to 98%, respectively, if HA served as the sole source of carbon or nitrogen . Remaining HA which could be re-isolated from microbial cultures were lower in carbon (<12%) and nitrogen (<2.3%) . Spectroscopic analysis (UV, Vis, FTIR) indicated losses, especially in aliphatic structural units, and a relative enhancement in aromatic structures . It was postulated that for their high degree of degradability, HA indigenous to that anthropogenic environment would not play an important role in the long-term stabilization of landfill refuse.

Environ Pollut, 1988, 51(2), 131 - 52
Influence of ozone and simulated acidic rain on microorganisms in the rhizosphere of Sorghum; Shafer SR; Seedlings of a sorghum x sudangrass hybrid in pots of non-sterile soil-sand mix were exposed to ozone (O(3)) at 0, 0.15, or 0.30 microl litre(-1) (7 h day(-1), 3 days week(-1)) and simulated rain (SR) adjusted with H(2)SO(4) + HNO(3) to pH 5.5, 4.0, or 2.5 (2 cm in 1.5 h per event; 2 events week(-1)) over 3 weeks in a greenhouse . Ozone suppressed shoot and root growth, but increased acid content (i.e . pH < 5.5) of SR stimulated shoot growth and had inconsistent effects on root growth . Ozone x SR chemistry interactions significantly affected plant growth . Data for 'total' bacterial populations in the rhizosphere (number of colony-forming units per gram of rhizosphere soil) exhibited a curvilinear relationship with O(3) (maximum at 0.15 microl liter(-1)) . Increased acid content of SR stimulated numbers of 'total' bacteria but suppressed populations of amylolytic bacteria . Ozone and acid content of SR tended to stimulate numbers of fungal propagules in the rhizosphere, but this effect was not significant . Numbers of rhizosphere bacteria capable of phosphatase activity increased linearly with O(3), but only when SR chemistry was characterised by pH 4.0 . Data for other populations of rhizosphere microorganisms did not exhibit significant relationships to O3 x SR chemistry interactions.

Environ Pollut, 1990, 66(1), 21 - 31
The effects of acidic irrigation on soil microorganisms at Kevo, Northern Finland; Kytoviita MM et al.; Effects of simulated acid rain (a mixture of H(2)SO(4) and HNO(3); pH(3)) on soil microbiology were studied in a field experiment in northern Finland . Irrigated control plots received the same amount of spring water (pH 6) as the acid treated plots . Fungal lengths and total bacterial numbers were studied after the treatments had continued for three growing seasons . The numbers of bacteria in five physiological groups (those utilizing starch, protein, pectin, xylan, or cellulose) were measured by MPN (most probable number) techniques . The lengths of total and FDA active fungal hyphae were not significantly different between the acid treated and the control plots . The counts of total bacteria were not significantly different between treatments, but the MPNs of all five physiological groups of bacteria were approximately 60% lower in the acid treated plots than in the controls.

Environ Pollut, 1990, 66(3), 263 - 71
The influence of gut microorganisms on zinc uptake in Helix aspersa; Simkiss K et al.; An artificial diet was prepared that enabled the snail Helix aspersa to be fed food containing varying amounts of metals, antibiotics or bacteria . By this means it is possible to show that the body burden of zinc was significantly correlated with the dietary intake . The snail was, however, able to detect high concentrations of the metal and reduced its intake of such contaminated food . The bacterial population of the alimentary tract modified the amount of zinc absorbed from the diet . It appears, therefore, that biological monitoring programmes, based upon bioaccumulation measurements, should take these influences into account.

Environ Pollut, 1991, 73(1), 1 - 10
Microbial metabolic activities in soils of old-field communities following eleven years of nutrient enrichment; Sutton SD et al.; Effects of 11 years (1978-1988) of nutrient enrichment (fertilizer or sludge) on microbial metabolic activity in soil samples collected from contrasting types of old-field communities were studied during September 1989 . During the 1989 growing season, subplots were manipulated by tilling and/or liming to evaluate mechanisms of ecosystem recovery or were left undisturbed . Metabolic activities of soil microorganisms were determined by measuring dehydrogenase activity within soil samples collected from these subplots . The amounts of 2,3,5-triphenyltetrazolium formazan formed during incubation by the reduction of 2,3,5-triphenyltetrazolium chloride were used to evaluate dehydrogenase activity . Plots that had received long-term applications of sludge or fertilizer had significantly lower rates of microbial activity (P<0.05) than did control plots . Fertilizer and sludge plots treated with lime had significantly higher microbial metabolic activity (P<0.05) than those not receiving lime . Whereas liming stimulated microbial activity to near control levels, tilling had no significant treatment effect.

Environ Pollut, 1992, 76(3), 267 - 78
Responses of microbial populations in the rhizosphere to deposition of simulated acidic rain onto foliage and/or soil; Shafer SR; Air pollutants or some chemicals applied to plant foliage can alter the ecology of the rhizosphere . Experiments were conducted to distinguish among possible foliage-mediated versus soil- or root-mediated effects of acid deposition on microorganism in the rhizosphere . Seedlings of a sorghum x sudangrass hybrid in pots of non-sterile soil-sand mix in a greenhouse were exposed to simulated rain solution adjusted with H(2)SO(4) + HNO(3) to pH 4.9, 4.2, 3.5 or 2.8 . Solutions were applied as simulated rain to foliage and soil, foliage only (soil covered by plastic, and deionized water applied directly to the soil), or soil only (solution applied directly to the soil) . Solutions were applied on 16 days during a 6-week period (1.5 cm deposition in 1 h per application) . Plant shoot and root dry weights and population densities of selected types of bacteria, filamentous actinomycetes and fungi in the rhizosphere were quantified after exposures were completed . Deposition of simulated acidic rain onto foliage alone had no effect on plant biomass or microbial population densities in the rhizosphere (colony-forming units per gram of rhizosphere soil) . However, plant growth was stimulated and all microbial populations in the rhizosphere increased 3- to 8-fold with increased solution acidity (relative to pH 4.9 solution) when solution penetrated the soil . Statistical analyses indicated that the acid dose-population response relationships for soil-only and foliage-and-soil applications were not different . Thus, no foliage-mediated effect of simulated acidic rain on rhizosphere ecology was detected.

Environ Pollut, 1996, 93(1), 1 - 8
Effect of ectomycorrhizae and ammonium on (134)Cs and (85)Sr uptake into Picea abies seedlings; Riesen TK et al.; Microorganisms play an important role in the fixation of radionuclides in forest soils . In particular, fungi have the capacity to absorb and translocate radionuclides . The role of the ectomycorrhizal fungus Hebeloma crustuliniforme in the uptake of radiocaesium ((134)Cs) and radiostrontium ((85)Sr) into seedlings of Norway spruce (Picea abies) was investigated in a pouch test system . Inoculated and non-inoculated seedlings; seedlings inoculated during 8 and 15 weeks; seedlings exposed during 2 and 3 weeks to the radioactive solution; and seedlings grown under low and high ammonium conditions prior to the application of the radionuclides were compared . The final (134)Cs and (85)Sr activity was determined in fine-roots, main-roots, stems and needles . The results showed that ectomycorrhizae reduced the uptake of (134)Cs and (85)Sr . The degree of ectomycorrhization was of crucial importance and seemed to be governed by the period during which ectomycorrhizae were allowed to develop and by the ammonium concentration in the nutrient solution . The radionuclide uptake increased with increasing exposure time . Both radionuclides were predominantly accumulated in fine-roots . However, needles proved to describe best the result of net root uptake and translocation to the shoot . The uptake-and and translocation-rates of (85)Sr were smaller than those of (134)Cs . It is assumed that the translocation is coupled with the intensity of water fluxes through the xylem and that (85)Sr is more readily adsorbed into mycelium or plant tissue relative to (134)Cs . The effect of high ammonium growth conditions was overcome by the effect of ectomycorrhization, except in needles with a very large biomass which behaved as a strong sink and led to a high accumulation of (134)Cs.

Laryngoscope, 2004 Mar, 114(3), 486 - 9
Effectiveness of laser-assisted myringotomy for otitis media in children; Cotter CS et al.; OBJECTIVE: To evaluate the effectiveness of OtoScan CO2 laser-assisted myringotomy (OtoLAM ESC/Sharplan) for acute otitis media and chronic otitis media with effusion (COME) in children . STUDY DESIGN: Retrospective review of 47 children with refractory acute otitis media (RAOM) or COME more than 3 months in duration in a pediatric otolaryngology practice . METHODS: Laser-assisted myringotomy was performed on 47 patients (79 ears) using the OtoLAM device . There were 28 children (ages 0.50-3 years) with RAOM and 19 children (ages 0.58-15 years) with COME . RESULTS: A total of 57.4% of procedures were considered treatment failures . Failures occurred in 53.6% of patients with RAOM on average +/-SD 3.89 +/- 2.16 weeks after the procedure and in 63.2% of patients with COME on average +/-SD 7.25 +/- 5.57 weeks after the procedure . Age, sex, microorganism isolated, myringotomy size, wattage, and laterality did not predict outcome . Ventilation tube insertion was performed in 27 (57.4%) patients . Two patients have persistent tympanic membrane perforations at 2 years . CONCLUSIONS: Laser-assisted myringotomy in children with RAOM and COME was associated with a high incidence of recurrence or persistence of disease and with perforation of the tympanic membrane . Recommendations for use of the OtoLAM should include discussion of high failure rates and the strong likelihood of subsequent ventilation tube insertion . The OtoLAM remains an option for office-based ventilation of the middle ear for families and patients where general anesthesia is a concern.

Crit Care Med, 2004 Mar, 32(3), 839 - 47
Infection in prolonged pediatric critical illness: A prospective four-year study based on knowledge of the carrier state; Sarginson RE et al.; OBJECTIVE: This study was performed to determine the rate, timing, and incidence density of infections occurring in a subgroup of patients requiring a prolonged stay in a regional pediatric intensive care unit . DESIGN: Prospective, observational cohort study over 4 yrs . SETTING: This epidemiologic descriptive study was performed in a university hospital 20-bed pediatric intensive care unit . PATIENTS: Critically ill children requiring > or = 4 days of intensive care . INTERVENTIONS: The microbial carrier state of the children was monitored by surveillance cultures of throat and rectum, obtained on admission and twice weekly afterward . MEASUREMENTS AND MAIN RESULTS: Data are presented on a total of 1,241 children, accounting for 1,443 admissions to the unit, corresponding to 18,203 patient days . The median pediatric index of mortality was 0.063 (interquartile range, 0.025-0.131), and the mortality rate in this subset of children was 9.6% . Five hundred twenty children had infections, an overall infection rate of 41.9% (520 of 1,241); 14.5% (180 of 1,241) of the children developed viral and 33.0% (410 of 1,241) developed bacterial/yeast infections . The incidence of bloodstream infection was 20.1 and lower airway infection 9.1 episodes per 1,000 patient days . We found that 13.3% of the children were infected with a bacterial/yeast microorganism acquired on the pediatric intensive care unit; 4.0% (50 of 1,241) of children developed infections due to resistant microorganisms . There were a total of 803 bacterial/yeast infectious episodes, of which 59.8% (480) were due to microorganisms imported in the patients' admission flora . These primary endogenous infections predominantly occurred within the first week of pediatric intensive care unit stay . The other 38.9% (312) were caused by microorganisms acquired on the pediatric intensive care unit . A total of 38 viral infections (24.5%) were acquired during pediatric intensive care unit stay . CONCLUSIONS: Two thirds of all infections diagnosed in children with prolonged illness on pediatric intensive care unit were due to microorganisms present in the patients' admission flora.

Crit Care Med, 2004 Mar, 32(3), 680 - 5
Accuracy of delayed (24 hours) processing of bronchoalveolar lavage for diagnosing bacterial pneumonia; de Lassence A et al.; OBJECTIVE: Pneumonia in the intensive care unit is associated with a high mortality rate . Diagnostic accuracy is mandatory to improve prognosis . However, in many hospitals, samples from the respiratory tract cannot be immediately processed bacteriologically around the clock . This may complicate therapeutic choice based on invasive diagnostic procedures . We evaluated the effect of storing bronchoalveolar lavage fluid at 4 degrees C for 24 hrs on direct examination and culturing for diagnosing pneumonia . DESIGN: Prospective, paired comparison study . SETTING: Intensive care unit in a university hospital . PATIENTS: A total of 93 bronchoalveolar lavages were performed on 66 intensive care unit patients who were suspected to have bacterial pneumonia . INTERVENTION: Each sample was divided into two; one half was processed immediately (H0), and the other was processed after refrigeration at 4 degrees C for 24 hrs (H24) . MEASUREMENTS AND MAIN RESULTS: All negative H0 culture samples (n = 31) were also negative for pathogens in H24 samples . Sixty two bronchoalveolar lavage cultures yielded one or more microorganisms, giving a total of 113 microorganisms in one or both samples . The results of positive cultures at H0 and H24 for the culturing diagnostic threshold of 10 colony forming units/mL agreed well (Kappa coefficient, 0.84); agreement was even better (Kappa coefficient, 0.85) when possible contaminants were excluded . The bias calculated as the mean difference between paired culture results was 0.195 +/- 1.31 (Delta log) . When considering the accepted threshold of 10 colony forming units/mL, specificity at H24 compared to H0 was excellent (100%), but sensitivity was slightly lower (80%) . CONCLUSION: Delayed processing of bronchoalveolar lavage sampling is an acceptable alternative when immediate culturing cannot be performed because it enables antibiotic administration.

J Clin Periodontol, 2004 May, 31(5), 364 - 9
A preliminary investigation into the ultrastructure of dental calculus and associated bacteria; Tan B et al.; INTRODUCTION: Though dental calculus is generally recognised as comprising mineralised bacteria, areas of non-mineralised bacteria may be present . AIM: To investigate the ultrastructure of non-decalcified young and mature supragingival calculus and subgingival calculus, and the possible presence of internal viable bacteria . Materials and methods: Supragingival calculus was harvested from five patients, 9-10 weeks after scaling and root debridement . Five samples of mature supragingival and subgingival calculus were taken from patients presenting with adult periodontitis . Specimens were fixed and embedded for transmission electron microscopy . RESULTS: The ultrastructure of young and mature supragingival calculus was similar with various large and small crystal types . Non-mineralised channels were observed extending into the calculus, often joining extensive lacunae, both containing intact non-mineralised coccoid and rod-shaped microorganisms . Subgingival calculus possessed more uniform mineralisation without non-mineralised channels and lacunae . CONCLUSION: Supragingival calculus contains non-mineralised areas which contain bacteria and other debris . The viability of the bacteria, and their identification could not be determined in this preliminary investigation . As viable bacteria within these lacunae may provide a source of re-infection, further work needs to be done to identify the bacteria in the lacunae, and to determine their viability.

Microb Ecol, 2004 Apr, 47(3), 236 - 42 Epub 2003 Oct 23.
FISH shows that Desulfotomaculum spp . are the dominating sulfate-reducing bacteria in a pristine aquifer; Detmers J et al.; The hydrochemistry and the microbial diversity of a pristine aquifer system near Garzweiler, Germany, were characterized . Hydrogeochemical and isotopic data indicate a recent activity of sulfate-reducing bacteria in the Tertiary marine sands . The community structure in the aquifer was studied by fluorescence in situ hybridization (FISH) . Up to 7.3 x 10(5) cells/mL were detected by DAPI-staining . Bacteria (identified by the probe EUB338) were dominant, representing 51.9% of the total cell number (DAPI) . Another 25.7% of total cell were affiliated with the domain Archaea as identified by the probe ARCH915 . Within the domain Bacteria, the beta-Proteobacteria were most abundant (21.0% of total cell counts) . Using genus-specific probes for sulfate-reducing bacteria (SRB), 2.5% of the total cells were identified as members of the genus Desulfotomaculum . This reflects the predominant role these microorganisms have been found to play in sulfate-reducing zones of aquifers at other sites . Previously, all SRB cultured from this site were from the spore-forming genera Desulfotomaculum and Desulfosporosinus.

J Food Prot, 2004 Apr, 67(4), 787 - 92
Efficiency of pulsed UV light for microbial decontamination of food powders; Fine F et al.; The aim of this study was to evaluate the efficiency of pulsed light on the destruction of dried microorganisms on fluidized glass beads and to determine treatment parameters (energy level, water activity, final product quality) for process optimization . The applied drying method allowed microorganisms to remain viable on glass beads or dried powdered products with viability yields approaching 100% . The pulsed UV light system enabled an efficient fluidization of food powders, even for granular products (up to 5 mm diameter) and avoided shadowed areas . For Saccharomyces cerevisiae decontamination, the dose effect of UV rays was preponderant with glass beads and quartz plate, and in this case, 58 J/cm2 were required to decrease the microbial population by 7 log . For colored food powders (black pepper and wheat flour), the thermal effect of pulsed light dominated the UV effect.

Med Hypotheses, 2004, 62(5), 773 - 9
Heart disease: the greatest 'risk' factor of them all; Broxmeyer L; By the turn of the last century, flying in the face of over a hundred years of research and clinical observation to the contrary, medicine abandoned the link between infection and atherogenesis; not because it was ever proven wrong, but because it did not fit in with the trends of a medical establishment convinced that chronic disease such as heart disease must be multifactorial, degenerative and non-infectious . Yet it was the very inability of 'established' risk factors such as hypercholesterolemia, hypertension and smoking to completely explain the incidence and trends in cardiovascular disease that resulted in historically repeated calls to search out an infectious cause, a search that began more than a century ago . Today, half of US heart attack victims have acceptable cholesterol levels and 25% or more have none of the "risk factors" associated with heart disease, including smoking, high blood pressure or obesity, most of which are not inconsistent with being caused by infection . Even the case of the traditionalist's latest 2003 JAMA assault to 'debunk' what they call the "50% risk factor myth" falls woefully short under scrutiny . In one group 30% died of heart disease with a cholesterol of at least 240 mg/dl, a condition which also existed in 21% who did not die during the same period . And the overlap was obvious throughout the so-called risk categories . Under such scrutiny, lead author Greenland conceded that if obesity, inactivity and elevated cholesteriol in the elderly are included, just about everyone has a risk factor and he likened the dilemma of people who do or do not wind up with heart disease akin to the susceptibility of people who are exposed to tuberculosis but do not get the disease . In Infections and Atherosclerosis: New Clues from an old Hypothesis? Nieto stressed the need to extend the possible role of infectious agents beyond the three infections which have in recent years been the focus of research: Cytomegalovirus (CMV) Chlamydia pneumoniae and Helicobactor pylori . Mycobacterial disease shares interesting connections to heart disease . Not only is tuberculosis the only microorganism to depend on cholesterol for its pathogenesis but CDC maps for cardiovascular disease bear a striking similarity to those of State and regional TB case rates . Ellis, Hektoen, Osler, McCallum, Swartz, Livingston and Alexander-Jackson all saw clinical and laboratory evidence of a causative relationship between the mycobacteria and heart disease . And Xu showed that proteins of mycobacterial origin actually led to experimental atherosclerosis in laboratory animals Furthermore present day markers suggested as indicators for heart disease susceptibility such as C-Reactive Protein (CRP), interleukin-6 and homocysteine are all similarly elevated in tuberculosis . It therefore behooves us to explore the link between heart disease and typical and atypical tuberculosis.

Sci Total Environ, 2004 May 5, 323(1-3), 63 - 9
Ecotoxicological assessment of doxycycline in aged pig manure using multispecies soil systems; Fernandez C et al.; This paper assesses the ecotoxicity of the antibiotic doxycycline in aged spiked pig manure using a multispecies soil system (MS 3) covering plants, earthworms and soil microorganisms . The study reproduced realistic exposure conditions, as well as higher exposure doses covering the uncertainty factors typically employed for covering interspecies variability . MS 3, consisting of columns of natural sieved soil assembled with earthworms and seeds from three plant species, were employed . Pig manure was spiked with doxycycline (75 or 7500 microg/ml), aged for 15 days under aerobic/anaerobic conditions and added on top of the soil columns (120 ml/column, equivalent to 220 kgN/ha) . Water and doxycycline free manure were used as negative controls . Doxycycline (7500 microg/ml) solution was used as a positive control . No effects on plants or earthworms were observed . Significant effects on soil phosphatase activity, indicating effects on soil microorganisms, were observed at the highest exposure dose, affecting all soil layers in the doxycycline-solution-treated MS 3 (positive control) but only the top layer in the spiked pig manure system . Chemical analysis confirmed the different behavior of doxycycline in both systems (with and without manure) and those effects were observed in soil with measured concentrations over 1 mg/kg soil . The detection of doxycycline in leachates revealed a potential mobility . Leachate concentrations were similar for doxycycline solution and spiked manure treatments.

Immunol Lett, 2004 Mar 29, 92(1-2), 91 - 6
Down-modulation of the antigen receptor by a superantigen for human B cells; Viau M et al.; B cell superantigens (SAgs) have been implicated in human diseases by demonstrating non-clonotypic expansion of B cells bearing certain immunoglobulin variable region genes . One possibility is that, during infection with microorganisms secreting SAgs, these potent molecules might modulate BcR expression . To test this hypothesis, we investigated the potential effects of a SAg, protein L from Peptostreptococcus magnus, on antigen B cell receptor (BcR) surface expression in vitro . Using fluorescence microscopy, we found that this SAg induced down-regulation of BcR expression . This effect was time-, dose-, and temperature-dependent, and shedding of cell surface IgM molecules into the culture supernatant was not detected . These data demonstrate that SAg-mediated down-regulation of the BcR expression occurs primarily as a result of BcR internalization . In addition, two specific inhibitors of protein tyrosine kinases were found to retard the BcR modulation on the cell surface and inhibit SAg-induced receptor internalization, showing that tyrosine phosphorylation is required for subsequent internalization of mIg-ligand complexes . The down-modulation of BcR expression may have pathological consequences in patients infected with microorganisms secreting SAgs.

J Clin Neurosci, 2004 May, 11(4), 389 - 94
Chlamydia pneumoniae infection related atherosclerotic clinical variables on carotid stenosis; Colpan ME et al.; Objective: Research results showed that Chlamydia pneumoniae infection is related to atherosclerosis . C . pneumoniae infection may exacerbate atherogenesis . We investigated the presence of this microorganism for patients who underwent carotid endarterectomy and evaluated clinical values of C . pneumoniae infection on carotid stenosis . Methods: Twenty patients with carotid stenosis were enrolled in this prospective study between 1997 and 1999 . The patients were observed on whether they were positive or negative in four C . pneumoniae measures, namely; IgA titers, IgG titers, presence of electron microscopy, and immunocytochemistry in the endarterectomy specimens . Possible clinical findings for atherosclerosis were also observed of Chlamydial measures such as the percentage of carotid stenosis, cholesterol and triglyceride levels, smoking status, symptomatic or non-transient ischaemic attack or stroke, previous ischaemic event, calcification at surgery, ulceration on angiographies, ulceration at surgery and hypertension were included in this evaluation . Results: Specific C . pneumoniae IgG were detected as positive in 9 (45%) of 20 patient samples . These patients were regarded as having chronic Chlamydia pneumoniae infection . None of the patients were positive for IgA antibody . This result demonstrated no evidence of reinfection . Immunocytochemistry and electron microscopy were positive in 7 (35%) of the 20 patients and correlated with positive serological results . The proportion of previous ischaemic events, calcification at surgery, ulceration on angiography, and ulceration at surgery were found significantly higher ( {Formula: see text} ) for patients who are positive for chlamydial measures than those who are negative . Conclusion: The results of this study demonstrated an association between C . pneumoniae to atherosclerosis . The proportion of patients who are positive for Chlamydia measures (IgG titers, electron microscopy, and immunocytochemistry) is significantly higher for those who were positive for each of these clinical variables (PIE, CALCI, U1, and U2) than who were negative . We emphasise, the higher incidence in clinical variables of PIE, CALCI, U1, and U2 in Chlamydia measures positive group may support the association of C . pneumoniae with atherosclerotic events.

Anal Chem, 2004 Apr 15, 76(8), 2355 - 66
Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring; Dworzanski JP et al.; Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases . The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information . We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins . This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification . To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences . In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software . MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST . To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database . The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database . Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification . It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.

J Agric Food Chem, 2004 Apr 21, 52(8), 2309 - 14
Sphingomonas sp . strain SB5 degrades carbofuran to a new metabolite by hydrolysis at the furanyl ring; Kim IS et al.; Microorganisms capable of degrading carbofuran were isolated from soils and examined for the degradation of this pesticide at ring structure . An isolate that could degrade carbofuran and carbofuran-7-phenol was selected for further studies . The 16S rRNA analysis results showed that the isolate belongs to the genus of Sphingomonas, close to dioxin and dicamba degraders, and is named Sphingomonas sp . SB5 . SB5 did not show any similarity of 16S rRNA to known carbofuran degraders . When time-course degradation of carbofuran by SB5 was examined by solvent extraction combined with liquid chromatographic analysis, almost complete disappearance of carbofuran was observed within 12 h, giving several accumulative metabolites . Bacterial cultures incubated with carbofuran-7-phenol suggested that the accumulated metabolites were derived from carbofuran-7-phenol . The control without SB5 and kanamycin-treated SB5 did not show any metabolite, suggesting a biological involvement in the degradation of carbofuran . GC/MS and LC/MS analyses identified 2-hydroxy-3-(3-methylpropan-2-ol) phenol as one of the accumulated metabolites, suggesting that the strain SB5 could degrade carbofuran-7-phenol by hydrolysis at the furanyl ring . This is the first report to identify 2-hydroxy-3-(3-methylpropan-2-ol) phenol as a new product derived biologically from carbofuran-7-phenol.

Emerg Infect Dis, 2004 Jan, 10(1), 8 - 13
Emerging issues in virus taxonomy; van Regenmortel MH et al.; Viruses occupy a unique position in biology . Although they possess some of the properties of living systems such as having a genome, they are actually nonliving infectious entities and should not be considered microorganisms . A clear distinction should be drawn between the terms virus, virion, and virus species . Species is the most fundamental taxonomic category used in all biological classification . In 1991, the International Committee on Taxonomy of Viruses (ICTV) decided that the category of virus species should be used in virus classification together with the categories of genus and family . More than 50 ICTV study groups were given the task of demarcating the 1,550 viral species that were recognized in the 7th ICTV report, which was published in 2000 . We briefly describe the changes in virus classification that were introduced in that report . We also discuss recent proposals to introduce a nonlatinized binomial nomenclature for virus species.

Mol Plant Microbe Interact, 2004 Apr, 17(4), 343 - 50
Proline accumulation and AtP5CS2 gene activation are induced by plant-pathogen incompatible interactions in Arabidopsis; Fabro G et al.; Accumulation of free L-proline (Pro) is a typical stress response incited by osmotic injuries in plants and microorganisms . Although the protective role of Pro in osmotic stress is not well understood, it is thought to function as compatible osmolyte or as a scavenger of reactive oxygen species (ROS) . Here we show that, in Arabidopsis thaliana, Pro biosynthesis can be activated by incompatible plant-pathogen interactions triggering a hypersensitive response (HR) . Pro accumulates in leaf tissues treated with Pseudomonas syringae pv . tomato avirulent strains (avrRpt2 and avrRpm1) but remains unchanged in leaves infected with isogenic virulent bacteria . Incompatible interactions lead to transcriptional activation of AtP5CS2, but not AtP5CS1, encoding the rate limiting enzyme in Pro biosynthesis pyrroline-5-carboxylate synthase (P5CS) . AtP5CS2:GUS and AtP5CS2:LUC transgenes were induced inside and around the HR lesions produced by avirulent Pseudomonas spp . in transgenic plants . Pro accumulation was faster and stronger when stimulated by avrRpm1 than by avrRpt2, and was compromised in the low-salicylic acid plants NahG and eds5 when signaled through the RPS2-dependent pathway . In addition, Pro content and AtP5CS2 expression were enhanced by ROS in wild-type plants, suggesting that ROS may function as an intermediate signal in AtP5CS2-mediated Pro accumulation.

Mikrobiol Z, 2003 Nov-Dec, 65(6), 43 - 8
{Influence of supplement of agricultural useful strains of microorganisms on microbial coenobia of plant rhizosphere}; Sherstoboieva OV; It was revealed in the fields experiments that the treatment of seeds by microbial preparations (nitrogen fixing, phosphorus mobilizing bacteria and antagonists of phythopatogenic micromycetes) leads to the decrease of quantity of micromycetes and oligotrophoic bacteria in the rhizosphere soil.

Bull Soc Belge Ophtalmol, 2004, (291), 61 - 9
{Endophthalmitis and French law}; Monestier-Carlus D; Endophthalmitis is the nosocomial infection occurring in ophthalmology . In 1988, the French Ministry of Health defined nosocomial infection as an illness caused by microorganisms and contracted in a care establishment . In the same year, decrees and stipulations relating to sanitary safety prescribed new duties for care establishments . Patients who have suffered nosocomial infection can claim compensation either through an administrative tribunal if they were treated in a hospital, or through an ordinary court if they were treated privately . Administrative jurisprudence does not allow for the exoneration of the hospital's responsibility, except where there is proof of an external cause . In ordinary law, where jurisprudence was for many years based on the duty of best efforts, victims were not indemnified . In 1996, the Court of Cassation decided that a clinic is presumed responsible for a nosocomial infection unless it can prove that there was no error on its part . Since 1999, private health establishments have a duty to secure results . The act of 4 March, 2002, states that care establishments, whether public or private, are responsible for damages resulting from nosocomial infections, except where they can prove the existence of an external cause . Where the infection results in permanent partial disability of more than 24%, and is not due to malpractice in the care establishment, the responsibility for damages is taken over by National Solidarity.

J Leukoc Biol, 2004 May, 75(5), 749 - 55 Epub 2004 Jan 14.
Toll-like receptors and the host defense against microbial pathogens: bringing specificity to the innate-immune system; Netea MG et al.; Toll-like receptors (TLRs) have been identified as a major class of pattern-recognition receptors . Recognition of pathogen-associated molecular patterns (PAMPs) by TLRs, alone or in heterodimerization with other TLR or non-TLR receptors, induces signals responsible for the activation of genes important for an effective host defense, especially proinflammatory cytokines . Although a certain degree of redundancy exists between signals induced by the various TLRs, recent studies have identified intracellular pathways specific for individual TLRs . This leads to the release of cytokine profiles specific for particular PAMPs, and thus, TLRs confer a certain degree of specificity to the innate-immune response . In addition to the activation of the innate-immune response, TLR-mediated recognition represents a link between the innate- and acquired-immune systems, by inducing the maturation of dendritic cells and directing the T helper responses . Alternatively, recent data have also suggested TLR-mediated escape mechanisms used by certain pathogenic microorganisms, especially through TLR2 induction of anti-inflammatory cytokines . Finally, the crucial role of TLRs for the host defense against infections has been strengthened recently by the description of patients partially defective in the TLR-activation pathways.

J Leukoc Biol, 2004 Jun, 75(6), 1029 - 35 Epub 2004 Apr 01.
FcgammaRIIa expression with FcgammaRI results in C-reactive protein- and IgG-mediated phagocytosis; Bodman-Smith KB et al.; C-reactive protein (CRP) is a pattern-recognition molecule, which can bind to phosphorylcholine and certain phosphorylated carbohydrates found on the surface of a number of microorganisms . CRP has been shown recently to bind human Fc receptor for immunoglobulin G (IgG; FcgammaR)I and mediate phagocytosis and signaling through the gamma-chain . To date, binding of monomeric CRP to FcgammaRII has been contentious . We demonstrate that erythrocytes opsonized with CRP bind FcgammaRIIa-transfected COS-7 cells . In addition, we demonstrate that FcgammaRI can use FcgammaRIIa R131 and H131 to phagocytose erythrocytes coated with IgG or purified or recombinant CRP in the absence of the gamma-chain . COS-7 cells expressing FcgammaRIIa or FcgammaRI alone did not phagocytose opsonized erythrocytes . Such phagocytosis required the cytoplasmic domain of FcgammaRIIa, as mutation of tyrosine at position 205 and truncation of the cytoplasmic domain from the end of the transmembrane region (position 206), resulting in the loss of the immunoreceptor tyrosine activatory motif, abrogated phagocytosis . FcgammaRIIa R131 was more efficient than FcgammaRIIa H131 at mediating CRP-dependent phagocytosis.

J Environ Qual, 2004 Mar-Apr, 33(2), 612 - 8
Effects of environmental factors on 1,3-dichloropropene hydrolysis in water and soil; Guo M et al.; Hydrolysis is the major pathway for fumigant 1,3-dichloropropene (1,3-D) degradation in water and soil, yet the process is not well understood . Experiments were conducted to investigate the effect of various environmental factors on the rate of 1,3-D hydrolysis . Cis-, trans-1,3-D and their isomeric mixture were spiked into water and Arlington soil (coarse-loamy, mixed, thermic Haplic Durixeralfs) and incubated under different conditions . The rate of 1,3-D hydrolysis in water and soil were evaluated based on its residual amount and Cl- release, respectively . 1,3-D hydrolyzed rapidly in deionized water, with a half-life of 9.8 d at 20 degrees C . The hydrolysis was pH dependent, with low pH inhibiting and high pH favoring the reaction . Other factors such as isomeric differences, photo irradiation, suspended particles, and small amounts of co-solutes had little effect on the reaction . In soil, 1,3-D hydrolyzed following pseudo first-order kinetics . The hydrolysis rate constant increased with soil moisture content and decreased with the initial 1,3-D concentration . At 20 degrees C, > 60% of the 1,3-D applied at < 0.61 g kg(-1) in 10% moisturized soil hydrolyzed within 30 d . The soil particle size and mineralogy had little effect on the reaction rate . Organic matter promoted 1,3-D degradation via direct substitution reactions, and the trans-isomer showed preference over the cis- to react with certain organic molecules . Microbial contributions were initially insignificant, and became important as soil microorganisms adapted to the fumigant . The results suggest that to accelerate 1,3-D degradation, pH, soil moisture, and organic amendment should be considered.

Mikrobiologiia, 2004 Jan-Feb, 73(1), 126 - 32
{A plate method to screen for microorganisms producing xylose isomerase}; Sapunova LI et al.; A plate method was developed to screen for xylose isomerase-producing microorganisms based on the use of 2,3,5-triphenyltetrazolium as an indicator of D-xylulose, the D-xylose isomerization product . The use of this method allows microorganisms to be differentiated by the character of the enzyme synthesis (inducible or constitutive).

Mikrobiologiia, 2004 Jan-Feb, 73(1), 105 - 10
{Distribution of heterotrophic bacteria in Shira lake}; Lobova TI et al.; The study of the horizontal and vertical distribution of heterotrophic bacteria in brackish Lake Shira in summer periods showed that mesophilic bacteria dominated in all areas of the lake, whereas psychrotolerant bacteria dominated in the metalimnion and hypolimnion of its central part . Nonhalophilic bacteria were mostly mesophilic and dominated in coastal waters . Most psychrotolerant bacteria were able to grow in the presence of 5-10% NaCl . Heterotrophic bacteria isolated in different regions of the lake were identified to a generic level . The isolates were classified into autochthonous and allochthonous microorganisms on the bases of their distribution pattern in the lake water, halotolerance, and ability to grow at low temperatures.

Int J Pharm, 2004 Apr 15, 274(1-2), 1 - 33
Chitosan microspheres as a potential carrier for drugs; Sinha VR et al.; Chitosan is a biodegradable natural polymer with great potential for pharmaceutical applications due to its biocompatibility, high charge density, non-toxicity and mucoadhesion . It has been shown that it not only improves the dissolution of poorly soluble drugs but also exerts a significant effect on fat metabolism in the body . Gel formation can be obtained by interactions of chitosans with low molecular counterions such as polyphosphates, sulphates and crosslinking with glutaraldehyde . This gelling property of chitosan allows a wide range of applications such as coating of pharmaceuticals and food products, gel entrapment of biochemicals, plant embryo, whole cells, microorganism and algae . This review is an insight into the exploitation of the various properties of chitosan to microencapsulate drugs . Various techniques used for preparing chitosan microspheres and evaluation of these microspheres have also been reviewed . This review also includes the factors that affect the entrapment efficiency and release kinetics of drugs from chitosan microspheres.

Klin Khir, 2004 Jan, (1), 30 - 3
{The role of endothelin-1 in the pathogenesis of septic shock in the abdominal sepsis}; Krivoruchko IA et al.; Role of endoteline-1 (ET-1) in pathogenesis of septic shock (SS) was studied in 22 patients in the age from 34 to 58 years . There was shown, that ET-1 content in plasma depends on functional level of the adaptation-compensation reaction of organism as an answer on occurrence of SS in patients with abdominal sepsis . This is demonstrated by more high concentration of the index studied in the patients survived and also presence of correlative connection between ET-1 level in plasma of blood, indexes of middle arterial pressure and general peripheral resistance of vessels . There were received preliminary data, witnessing, that circulating cytokines, in particular, interleukin-8, stimulate the heightened production of ET-1 by endothelial cells, what probably in early terms the SS course constitutes the compensatory reaction, directed on elimination of pathogenic microorganisms, securing of reparative processes and maintenance of homeostasis.

Proc Natl Acad Sci U S A, 2004 Mar 30, 101(13), 4596 - 601 Epub 2004 Mar 19.
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota; Rawls JF et al.; Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle . A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology . These contributions are most obvious in the gut, where studies of gnotobiotic mice have disclosed that the microbiota affects a wide range of biological processes, including nutrient processing and absorption, development of the mucosal immune system, angiogenesis, and epithelial renewal . The zebrafish (Danio rerio) provides an opportunity to investigate the molecular mechanisms underlying these interactions through genetic and chemical screens that take advantage of its transparency during larval and juvenile stages . Therefore, we developed methods for producing and rearing germ-free zebrafish through late juvenile stages . DNA microarray comparisons of gene expression in the digestive tracts of 6 days post fertilization germ-free, conventionalized, and conventionally raised zebrafish revealed 212 genes regulated by the microbiota, and 59 responses that are conserved in the mouse intestine, including those involved in stimulation of epithelial proliferation, promotion of nutrient metabolism, and innate immune responses . The microbial ecology of the digestive tracts of conventionally raised and conventionalized zebrafish was characterized by sequencing libraries of bacterial 16S rDNA amplicons . Colonization of germ-free zebrafish with individual members of its microbiota revealed the bacterial species specificity of selected host responses . Together, these studies establish gnotobiotic zebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract.

J Basic Microbiol, 2004, 44(2), 79 - 87
Comparative analysis of laccase-isozymes patterns of several related Polyporaceae species under different culture conditions; Arana-Cuenca A et al.; The study of isozymes has to date been successfully applied in the identification of a number of different microorganisms, particularly fungi . Trametes sp . I-62 (CECT20197) is a white-rot fungus with potential biotechnological applications . It has been identified as Trametes on the basis of the mycelium morphology, but the features observed are not sufficient for its classification at the species level . Given that this strain produces a very characteristic laccase isozyme pattern, in the present work we compared its isozyme profile with the profiles produced by ten other very closely phylogenetically related fungi from the Polyporaceae family . The data indicates that Trametes sp . I-62 could not be included in any of the taxonomically related species which were analysed in the present work . Extracellular laccases were detected in nine of the fungi studied and in four of them namely Trametes subectypus, Trametes pavonia, Trametes ochracea and Trametes gallica, this is the first report of such activity . Given that phylogenetically related fungi growing in the same culture conditions exhibit different laccase patterns, these isozymes could be used as an additional criterion for fungal identification .

Helicobacter, 2004 Apr, 9(2), 138 - 45
Rapid combined characterization of microorganism and host genotypes using a single technology; Hjalmarsson S et al.; BACKGROUND: Genetic information is becoming increasingly important in diagnosis and prognosis of infectious diseases . In this study we investigated the possibility of using a single technology, the Pyrosequencing trade mark technology (Biotage AB, Uppsala, Sweden), to gather several kinds of important genetic information from the human pathogen Helicobacter pylori, as well as from the carrier of the H . pylori infection . MATERIALS AND METHODS: DNA from 87 clinical isolates of H . pylori, 50 isolates from H . pylori-infected transgenic mice and nine gastric biopsies from H . pylori-infected patients was analyzed for targets in the 16S rRNA, 23S rRNA and cytotoxin associated gene A (cagA) genes to determine species identity, clarithromycin susceptibility and virulence level, respectively . In addition, three single nucleotide polymorphisms in the human interleukin-1B (IL-1B) gene, reported to affect the risk of developing gastric cancer, were analyzed in the gastric biopsy samples . RESULTS: All DNA targets were processed and analyzed in parallel, enabling convenient genetic characterization of both pathogen and host . All genotypes were easily and accurately assigned . In the 16S rRNA analysis, 99.83% of the bases were correctly called . CONCLUSIONS: We conclude that genetic analysis using Pyrosequencing trade mark technology was nonlaborious, and gave highly accurate data for different kinds of target . We therefore believe that this technology has the potential to complement or in the future substitute the time-consuming traditional microbial identification and typing methods, as well as enabling rapid typing of relevant host genetic markers.

Evolution Int J Org Evolution, 2004 Feb, 58(2), 245 - 60
Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli; Friesen ML et al.; We investigate adaptive diversification in experimental Escherichia coli populations grown in serial batch cultures on a mixture of glucose and acetate . All 12 experimental lines were started from the same genetically uniform ancestral strain but became highly polymorphic for colony size after 1000 generations . Five populations were clearly dimorphic and thus serve as a model for an adaptive lineage split . We analyzed the ecological basis for this dimorphism by studying bacterial growth curves . All strains exhibit diauxie, that is, sequential growth on the two resources . Thus, they exhibit phenotypic plasticity, using mostly glucose when glucose is abundant, then switching to acetate when glucose concentration is low . However, the coexisting strains differ in their diauxie pattern, with one cluster in the dimorphic populations growing better in the glucose phase, and the other cluster having a much shorter lag when switching to the acetate phase . Using invasion experiments, we show that the dimorphism of these two ecological types is maintained by frequency-dependent selection . Using a mathematical model for the adaptive dynamics of diauxie behavior, we show that evolutionary branching in diauxie behavior is a plausible theoretical scenario . Our results support the hypothesis that, in our experiments, adaptive diversification from a genetically uniform ancestor occurred due to frequency-dependent ecological interactions . Our results have implications for understanding the evolution of cross-feeding polymorphism in microorganisms, as well as adaptive speciation due to frequency-dependent selection on phenotypic plasticity.

J Periodontol, 2004 Feb, 75(2), 221 - 8
IgG antibody levels to Porphyromonas gingivalis and clinical measures in children; Donley CL et al.; BACKGROUND: Periodontopathic clinical markers are poorly understood in the pediatric population . Several studies have proposed Porphyromonas gingivalis (P . gingivalis) and an antibody response to the microorganism as factors in periodontal tissue destruction in children . The objective of this study was to examine the prevalence of P . gingivalis in dental plaque and of serum immunoglobulin G (IgG) antibody levels to P . gingivalis, and their relationship to periodontal clinical measures in children . METHODS: Thirty-one subjects, aged 20 to 163 months, participated in this study . Clinical measures examined included gingivitis, plaque, alveolar bone height, age, gender, ethnicity, medical status, caries, and IgG antibody levels to P . gingivalis . Five ml of blood was collected for serum analysis, and IgG antibody levels to P . gingivalis were determined by using enzyme-linked immunosorbent assay . Plaque samples were examined for the presence of P . gingivalis by DNA-DNA checkerboard . Data were analyzed on a person-level basis for relationships to serum IgG antibody levels to P . gingivalis and on a site-specific level for relationships to the presence of P . gingivalis in plaque . RESULTS: A majority (77%) of the subjects were systemically healthy, non-white (74%), and did not have detectable P . gingivalis in their plaque . Fifty-two percent of the subjects had positive serum IgG antibody levels to P . gingivalis . Based on univariate linear regression, factors related to IgG antibody levels to P . gingivalis (P<0.05) included age, average gingival index (GI), average probing depth, and number of teeth with alveolar bone crest to cemento-enamel junction (ABC-CEJ) distances >2 mm . When all clinical measures were considered together, only age remained statistically significantly related to serum IgG antibody levels to P . gingivalis . CONCLUSIONS: Age is one of the most important factors in the development of the immune response to putative microorganisms such as P . gingivalis in children . The role of IgG as a time-sensitive measure of periodontal health in children needs to be investigated further.

Tsitol Genet, 2003 Nov-Dec, 37(6), 66 - 77
{Effect of UV-B radiation on cytophysiological responses in plants}; Dmytriiev OP et al.; Solar UV-B radiation reaching the Earth's surface is continually increased due to the stratospheric ozone layer depletion . UV-B radiation has been shown to have mutagenic effects damaging DNA, proteins and membranes . During evolution plants developed systems for UV-B perception and effective defense mechanisms . In this review the main UV-B effects, cytophysiological responses of plants and their interactions with microorganisms are analyzed . UV-B-induced signal transduction pathways in plant cells are discussed.

Appl Environ Microbiol, 2004 Apr, 70(4), 2332 - 41
Oxygen-controlled bacterial growth in the sponge Suberites domuncula: toward a molecular understanding of the symbiotic relationships between sponge and bacteria; Muller WE et al.; Sponges (phylum Porifera), known to be the richest producers among the metazoans of bioactive secondary metabolites, are assumed to live in a symbiotic relationship with microorganisms, especially bacteria . Until now, the molecular basis of the mutual symbiosis, the exchange of metabolites for the benefit of the other partner, has not been understood . We show with the demosponge Suberites domuncula as a model that the sponge expresses under optimal aeration conditions the enzyme tyrosinase, which synthesizes diphenols from monophenolic compounds . The cDNA isolated was used as a probe to determine the steady-state level of gene expression . The gene expression level parallels the level of specific activity in sponge tissue, indicating that without aeration the tyrosinase level drops drastically; this effect is reversible . The SB2 bacterium isolated from the sponge surface grew well in M9 minimal salt medium supplemented with the dihydroxylated aromatic compound protocatechuate; this carbon source supported growth more than did glucose . From the SB2 bacterium the protocatechuate gene cluster was cloned and sequenced . This cluster comprises all genes coding for enzymes involved in the conversion of protocatechuate to acetyl coenzyme A . Expression is strongly induced if the bacteria are cultivated on M9-protocatechuate medium; the genes pcaQ (encoding the putative transcriptional activator of the pca operon) and pcaDC were used for quantitative PCR analyses . We conclude that metabolites, in this case diphenols, which might be produced by the sponge S . domuncula are utilized by the sponge surface-associated bacterium for energy generation . This rationale will help to further uncover the symbiotic pathways between sponges and their associated "nonculturable" microorganisms; our approach is flanked by the establishment of an EST (expressed sequence tags) database in our laboratory.

Appl Environ Microbiol, 2004 Apr, 70(4), 2211 - 9
Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes; Cafaro V et al.; Degradation of aromatic hydrocarbons by aerobic bacteria is generally divided into an upper pathway, which produces dihydroxylated aromatic intermediates by the action of monooxygenases, and a lower pathway, which processes these intermediates down to molecules that enter the citric acid cycle . Bacterial multicomponent monooxygenases (BMMs) are a family of enzymes divided into six distinct groups . Most bacterial genomes code for only one BMM, but a few cases (3 out of 31) of genomes coding for more than a single monooxygenase have been found . One such case is the genome of Pseudomonas stutzeri OX1, in which two different monooxygenases have been found, phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) . We have already demonstrated that ToMO is an oligomeric protein whose subunits transfer electrons from NADH to oxygen, which is eventually incorporated into the aromatic substrate . However, no molecular data are available on the structure and on the mechanism of action of PH . To understand the metabolic significance of the association of two similar enzymatic activities in the same microorganism, we expressed and characterized this novel phenol hydroxylase . Our data indicate that the PH P component of PH transfers electrons from NADH to a subcomplex endowed with hydroxylase activity . Moreover, a regulatory function can be suggested for subunit PH M . Data on the specificity and the kinetic constants of ToMO and PH strongly support the hypothesis that coupling between the two enzymatic systems optimizes the use of nonhydroxylated aromatic molecules by the draining effect of PH on the product(s) of oxidation catalyzed by ToMO, thus avoiding phenol accumulation.

Curr Opin Microbiol, 2004 Apr, 7(2), 175 - 84
From aging to virulence: forging connections through the study of copper homeostasis in eukaryotic microorganisms; Rees EM et al.; Recent years have witnessed an explosion in the breadth of investigations on transition metal homeostasis and the subsequent depth of our understanding of metals in biology . Many genes and proteins that serve in the uptake, distribution, sensing and detoxification of one such transition metal, copper, have been identified . Through genetic and biochemical studies, the molecular details of copper uptake are being elucidated, and evidence suggests a largely conserved mechanism for copper acquisition and distribution from yeast to humans . Investigations of the mitochondrial copper pathway reveal the complexity surrounding copper delivery to cytochrome oxidase and highlight additional roles for some of the participants in copper homeostasis, such as a copper chaperone that influences the subcellular distribution of its target for copper incorporation . Furthermore, our understanding of the structure and function of copper transporters, chaperones and cupro-proteins, coupled with the emergence of additional model systems, is providing surprising examples of the integration of copper homeostasis with other physiological and pathophysiological processes and states, such as cancer, aging and virulence.

Curr Opin Microbiol, 2004 Apr, 7(2), 168 - 74
Structural features and mechanisms for sensing high osmolarity in microorganisms; Heermann R et al.; During their lifetime, most organisms experience osmotic stress, mostly due to fluctuating external osmolarities, but also as a result of desiccation or freezing . Under these conditions, the ratio of osmolytes to water and macromolecules in the cells is significantly altered . To survive, cells must continuously sense these alterations and adapt accordingly . Osmolarity is a physico-chemical parameter that causes pleiotropic alterations in cell physiology . Recent research has revealed various mechanisms to sense high external osmolarity, based on monitoring cellular changes that are associated with the altered environment.

J Environ Radioact, 2004, 74(1-3), 221 - 32
Studies with natural and anthropogenic iodine isotopes: iodine distribution and cycling in the global environment; Muramatsu Y et al.; Iodine is an important trace element in geological and biological processes . We summarize here recent results and new data of experiments and observations carried out to improve the understanding of concentration levels and behavior of natural and anthropogenic iodine nuclides in the global environment . The distribution of stable iodine in the Earth's crust was estimated using concentration data in a suite of representative samples and the influence of subduction on the marine iodine cycle was investigated using (129)I systematics on iodine-rich brines from Japan . The importance of microorganisms for the natural iodine cycle is shown in recent studies of iodine sorption on soil and of iodine volatilization from terrestrial and marine environments . Levels of anthropogenic (129)I were measured in samples collected around a spent fuel reprocessing plant in Japan.

Carbohydr Res, 2004 Apr 28, 339(6), 1035 - 40
Two potent competitive inhibitors discriminating alpha-glucosidase family I from family II; Kimura A et al.; The inhibition kinetics for isoacarbose (a pseudotetrasaccharide, IsoAca) and acarviosine-glucose (pseudotrisaccharide, AcvGlc), both of which are derivatives of acarbose, were investigated with various types of alpha-glucosidases obtained from microorganisms, plants, and insects . IsoAca and AcvGlc, competitive inhibitors, allowed classification of alpha-glucosidases into two groups . Enzymes of the first group were strongly inhibited by AcvGlc and weakly by IsoAca, in which the K(i) values of AcvGlc (0.35-3.0 microM) were 21- to 440-fold smaller than those of IsoAca . However, the second group of enzymes showed similar K(i) values, ranging from 1.6 to 8.0 microM for both compounds . This classification for alpha-glucosidases is in total agreement with that based on the similarity of their amino acid sequences (family I and family II) . This indicated that the alpha-glucosidase families I and II could be clearly distinguished based on their inhibition kinetic data for IsoAca and AcvGlc . The two groups of alpha-glucosidases seemed to recognize distinctively the extra reducing-terminal glucose unit in IsoAca.

Dev Comp Immunol, 2004 May 3, 28(5), 443 - 60
Chemokines; Laing KJ et al.; Chemokines are small proteins that control cellular migration . An extensive family of these molecules has been described in mammals containing nearly 50 members . Within this family are four groups, each defined by the different spacing of two N-terminal cysteines, which form disulphide bonds with two other cysteine residues to create the tertiary structure characteristic of chemokines . Recent evidence shows the chemokine family is not unique to mammals, with several members also identified in birds, amphibians and fish, including a primitive vertebrate, the lamprey . Although there is less evidence to define the roles of chemokines in these lower vertebrates, structural similarities allow some predictions to their function, against which further studies are being made . Additionally, some microorganisms (particularly viruses) appear to have copied genes for chemokines, presumably to confuse the immune system of their host . This review aims to bring together the current information concerning identified chemokines throughout vertebrates and microorganisms.

Structure (Camb), 2004 Apr, 12(4), 657 - 67
Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism; Das K et al.; Arginine deiminase (ADI), an enzyme that hydrolyzes arginine to generate energy in many parasitic microorganisms, has potent anticancer activities and can halt growth of solid tumors . We determined the crystal structure of ADI from Mycoplasma arginini in two different forms (1.6 and 2.0 A resolution) using multiple isomorphous replacement . ADI shares common structural features with the arginine-catabolizing enzymes Arg:Gly amidinotransferase and dimethylarginine dimethyl-aminohydrolase; ADI contains an additional domain of five helices . The scissile C-N bonds of the substrates and the catalytic triads (Cys398-His269-Glu213 of ADI) for the three enzymes superimpose on each other . The ADI structure from form I crystals corresponds to a tetrahedral intermediate with four heteroatoms (1S, 2N, 1O) covalently bonded to the reaction-center carbon . The structure from form II crystals represents an amidino-enzyme complex; the reaction-center carbon is covalently bonded to Cys398 sulfur and two nitrogens, and the reacting water molecule is only 2.54 A away.

J Biol Chem, 2004 Jun 18, 279(25), 26058 - 65 Epub 2004 Apr 01.
Two mechanisms for mannose-binding protein modulation of the activity of its associated serine proteases; Chen CB et al.; Serum mannose-binding protein (MBP) neutralizes invading microorganisms by binding to cell surface carbohydrates and activating MBP-associated serine proteases-1, -2, and -3 (MASPs) . MASP-2 subsequently cleaves complement components C2 and C4 to activate the complement cascade . To analyze the mechanisms of activation and substrate recognition by MASP-2, zymogen and activated forms have been produced, and MBP.MASP-2 complexes have been created . These preparations have been used to show that MBP modulates MASP-2 activity in two ways . First, MBP stimulates MASP-2 autoactivation by increasing the rate of autocatalysis when MBP.MASP-2 complexes bind to a glycan-coated surface . Second, MBP occludes accessory C4-binding sites on MASP-2 until activation occurs . Once these sites become exposed, MASP-2 binds to C4 while separate structural changes create a functional catalytic site able to cleave C4 . Only activated MASP-2 binds to C2, suggesting that this substrate interacts only near the catalytic site and not at accessory sites . MASP-1 cleaves C2 almost as efficiently as MASP-2 does, but it does not cleave C4 . Thus MASP-1 probably enhances complement activation triggered by MBP.MASP-2 complexes, but it cannot initiate activation itself.

J Bacteriol, 2004 Apr, 186(8), 2340 - 5
Relationship of critical temperature to macromolecular synthesis and growth yield in Psychrobacter cryopegella; Bakermans C et al.; Most microorganisms isolated from low-temperature environments (below 4 degrees C) are eury-, not steno-, psychrophiles . While psychrophiles maximize or maintain growth yield at low temperatures to compensate for low growth rate, the mechanisms involved remain unknown, as does the strategy used by eurypsychrophiles to survive wide ranges of temperatures that include subzero temperatures . Our studies involve the eurypsychrophilic bacterium Psychrobacter cryopegella, which was isolated from a briny water lens within Siberian permafrost, where the temperature is -12 degrees C . P . cryopegella is capable of reproducing from -10 to 28 degrees C, with its maximum growth rate at 22 degrees C . We examined the temperature dependence of growth rate, growth yield, and macromolecular (DNA, RNA, and protein) synthesis rates for P . cryopegella . Below 22 degrees C, the growth of P . cryopegella was separated into two domains at the critical temperature (T(critical) = 4 degrees C) . RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures . Only the temperature dependence of the DNA synthesis rate changed at T(critical) . When normalized to growth rate, RNA and protein synthesis reached a minimum at T(critical), while DNA synthesis remained constant over the entire temperature range . Growth yield peaked at about T(critical) and declined rapidly as temperature decreased further . Similar to some stenopsychrophiles, P . cryopegella maximized growth yield at low temperatures and did so by streamlining growth processes at T(critical) . Identifying the specific processes which result in T(critical) will be vital to understanding both low-temperature growth and growth over a wide range of temperatures.

Acta Microbiol Pol, 2003, 52 Suppl, 67 - 74
Influence of trans fatty acids on infant and fetus development; Mojska H; Trans isomers are formed from cis unsaturated fatty acids during biohydrogenation by rumen microorganisms and by commercial partial hydrogenation during the processing of vegetable and fish oils . Recent estimates indicate that consumers in Western countries may receive from 0.5-2.1% to 2.5% of total energy intake as trans fatty acids . In recent years special attention has been given to the potential impairment of essential fatty acids metabolism to their long-chain metabolites by trans isomers in humans . These long-chain polyunsaturates metabolities are of great physiological importance during prenatal and postnatal development, as essential membrane components and precursors for synthesis of prostaglandins and other eicosanoids . Humans do not synthesise trans isomers of fatty acids so their presence in human milk is based on the maternal diet . Trans fatty acids content in human milk varied between countries from 0.35% in Africa to 7.2% of total fatty acids in Canada as a result of variation in dietary exposure to trans isomers . Although the negative effect of the human milk trans fatty acids on breast-fed infants is not yet well documented, ingested levels of trans fatty acids by infants may reflect current breastfeeding mothers diet and also the early consumed diet during pregnancy.

Ther Umsch, 2004 Mar, 61(3), 217 - 22
{Prevention of nosocomial infections in the medical office}; Ruef Ch; Nosocomial infections are usually considered to be a problem of hospitals . However, outpatient care is also not without risks to the patient or to the healthcare workers . Cases of iatrogenic infections following invasive acts such as intramuscular injections in medical offices have occurred repeatedly and have resulted in malpractice charges against the physicians involved . This illustrates a need for physicians in private practice to establish a concept for the prevention of nosocomial infections in their office . This concept should include patients as well as healthcare workers and must be adapted to the particular setting of the practice . After implementation of such a concept, it will be possible to provide care to all patients--the routine patient, the routine patient undergoing an invasive procedure, the patient who is colonized with a resistant microorganism, as well as the patient who presents himself with an infectious disease--under conditions that minimize the risk of nosocomial infection to the patient as well as to the healthcare workers . The essential elements of such a concept include written guidelines for disinfection, sterilization and personnel protection . Depending on the type of practice, additional guidelines, i.e . guidelines for reprocessing of endoscopes in a gastroenterology practice, will be needed.

Ther Umsch, 2004 Mar, 61(3), 191 - 6
{Central issues of prevention of nosocomial infections--status in 2004}; Ruef Ch; Despite significant progress in our understanding of their pathogenesis, nosocomial infections remain a major problem in hospitals . They may originate from the endogenous flora of the patient as a result of translocation of microorganisms from a physiologically colonized area to an area, where they act as pathogens . Transmission of microorganisms between patients results in exogenous infections . Healthcare workers may serve as transient carriers and vectors or even as reservoir of these infectious agents . Both, exogenous as well as endogenous nosocomial infections are preventable . Based on knowledge of the mode of transmission, the pathogenesis of and risk factors for infection, it is possible to design appropriate preventive strategies, which must be targeted to the type of infection to be prevented and should also be adapted to the local circumstances in a given hospital . Regardless of the type of infection to be prevented, hand disinfection is a standard measure and remains the most important preventive activity . The approach to the prevention of nosocomial infections has to be interdisciplinary and should involve all areas that are affected by any of the proposed measures . Hospital epidemiology plays a central role in coordinating preventive activities and often sets the priorities for prevention based on the available information . Given the growing complexity and the emergence of new nosocomial threats such as SARS, hospital administrators are well advised to invest sufficiently into their department of hospital hygiene and epidemiology in order to be ready for all the problems that will need to be tackled in the future.

J Gen Appl Microbiol, 2004 Feb, 50(1), 1 - 8
Use of segment-based microarray in the analysis of global gene expression in response to various environmental stresses in the cyanobacterium Anabaena sp . PCC 7120; Sato N et al.; We prepared microarrays that contain genomic sequences of a heterocyst-forming filamentous cyanobacterium Anabaena sp . PCC 7120 . The complete genome of this cyanobacterium codes for about 5,368 protein-coding genes in the main chromosome of 6.4 Mbp . In total, 2,407 DNA segments were selected from the sequencing clones, and amplified by PCR, then spotted on glass slides in duplicate . These microarrays differ from the widely used commercial or custom-made ones for other microorganisms in that each DNA segment was 3-4 kbp long, and contained about 3-4 predicted genes on average . This feature, however, did not decrease the usefulness of the microarrays, since we were able to detect a number of potentially novel genes that are induced in response to nitrogen deprivation, low temperature and drought . In addition, we found some genomic regions in which dozens of contiguous genes are simultaneously regulated . These results suggest that these segment-based microarrays are useful especially for such large genomes as Anabaena, for which the number of genes exceeds either technical or practical limitations.

Enferm Infecc Microbiol Clin, 2004 Apr, 22(4), 227 - 9
{Serological profile of Helicobacter pylori infection in the population of San Luis (Argentina)}; Mattana C et al.; We performed a seroepidemiological study of anti-Helicobacter pylori IgG by a commercial enzyme immunoassay kit (Meridian Diagnostics, USA) in 509 serum samples from 314 randomly selected asymptomatic subjects from among the population, and grouped into children (n 5 124), adolescents (n 5 74) and adults (n 5 116), and in 195 serum samples from subjects presenting clinical gastric symptoms, grouped into children (n 5 38) and adults (n 5 157) . The cut-off value was redefined and set at OD450 5 0.050 . The percentage of seropositive individuals was not significantly different between the two groups of adults studied (75.9% and 80.2%, respectively) (p < 0.05), suggesting a high degree of contact with the microorganism in this region.

Gen Dent, 2003 Mar-Apr, 51(2), 148 - 51
A statistical comparison of denture sanitation using a commercially available denture cleaner with and without microwaving; Goodson LB et al.; Polymethyl-methacrylate dentures, worn by patients for periods ranging from 12 days to 48 years, were cultured and found to be heavily contaminated with a variety of microorganisms both externally and internally . A commercially available denture sanitizer, used as prescribed by the manufacturer, was ineffective at decontaminating the dentures . This study examined the effectiveness of this denture sanitizer when used in combination with a microwaving procedure . Statistical methods were used to compare the decontamination results of the denture sanitizer applied with and without microwaving . The statistical results indicated that the dentures were decontaminated most effectively when the denture sanitizer was used in conjunction with a two-minute microwave procedure.

Gen Dent, 2003 Nov-Dec, 51(6), 570 - 7; quiz 578
An emerging new standard of care: initial and continued treatment for patients with signs and symptoms of active periodontal disease; Graham L; A growing knowledge of periodontal disease has improved dentists' understanding of the disease's etiology, pathophysiology, and natural history . This increased expertise has allowed treatment strategy and outcomes to improve . General dentists are the first to diagnose and treat the disease and it is important for them to understand both the disease and the new methods of treatment . Locally administered time-released antibiotics target specific microorganisms and may inhibit the action of collagenase, an extremely destructive enzyme that is released into periodontal tissues via the host response . This article reviews the disease process and presents a new standard of care that combines traditional debridement with locally administered antibiotics, offering a variety of treatment modalities to general dentists.

Mol Cells, 2004 Feb 29, 17(1), 51 - 6
Differential effect of ginsenoside metabolites on the 5-HT3A receptor-mediated ion current in Xenopus oocytes; Lee BH et al.; Ginsenosides are major active ingredients of Panax ginseng . They have a number of pharmacological and physiological actions and are transformed into compound K (CK) or M4 by intestinal microorganisms . CK is derived from protopanaxadiol (PD) ginsenosides, whereas M4 is derived from protopanaxatriol (PT) ginsenosides . Recent reports show that ginsenosides act as pro-drugs for these metabolites . In previous work we demonstrated that the ginsenoside Rg2 regulates human 5-hydroxytryptamine3A (5-HT3A) receptor channel activity {Choi et al . (2003)} . In the present study, we investigated the effect of CK and M4 on the activity of the human 5-HT3A receptor channel . The 5-HT3A receptor was expressed in Xenopus oocytes, and the current was measured using the two-electrode voltage clamp technique . Treatment with CK or M4 had no effect on oocytes injected with 5-HT3A receptor cRNA . However pretreatment with M4 or CK followed by injection of 5-HT3A receptor cRNA led to reversible inhibition of the 5-HT-induced inward peak current (I(5-HT)) . Half maximal inhibitory concentrations (IC50) of CK and M4 were 36.9 +/- 9.6 and 7.3 +/- 2.2 microM, respectively . Inhibition by M4 was non-competitive and voltage-independent . These results indicate that M4, a metabolite of PT ginsenosides, acts primarily on 5-HT3A receptors and further, that ginsenosides as well as ginsenoside metabolites can influence 5-HT3A receptor channel activity in Xenopus oocytes.

Acta Orthop Belg, 2004 Feb, 70(1), 1 - 10
Animal and human bites: evaluation and management; Stefanopoulos P et al.; Animal bites and to a lesser extent human bites are common trauma cases in accident and emergency units and their incidence is rising . Bite wounds are often deeper than they appear to be and they are potentially contaminated with uncommon microorganisms . They need careful assessment, thorough debridement and preferably delayed primary closure . Tetanus cover and, although controversial, prophylactic antibiotics should be considered after individual assessment of each case, as the golden first steps for their management.

Roum Arch Microbiol Immunol, 2002 Oct-Dec, 61(4), 301 - 14
"Hide-and-seek" as modus vivendi of malaria parasites; Nascutiu AM; In the interaction between a microorganism and its host both partners get challenged . Microorganisms have proved to be clever enough to acquire capabilities of hiding from and escaping the consequences of immune surveillance . Malaria parasites are not exceptions to the rule . We review below some of the escape mechanisms used by plasmodia, evasion mechanisms that depend on the life-cycle stage, route of penetration and microenvironment in which the parasites are established inside the host . The extreme diversity and antigenic variation and/or polymorphism of the parasite, the sequestration phenomenon, the induction of blocking antibodies, are only some of them . The understanding of these parasite strategies is of vital importance in the design of the waited-for malaria vaccine.

Lipids, 2004 Jan, 39(1), 19 - 24
Variations of trans octadecenoic acid in milk fat induced by feeding different starch-based diets to cows; Jurjanz S et al.; The impact of starch sources differing in their velocities of ruminal degradation on the milk fat of dairy cows was studied . The animals received diets containing a slowly degradable (potatoes) or rapidly degradable (wheat) starch concentrate (40% of the dry matter) in a total mixed diet . Milk fat was the only animal performance factor affected: Cows produced significantly less milk fat when fed the wheat diet than the potato diet (-3.3 g/kg, -122 g/d; P < 0.05) . With the wheat diet, milk fat was poorer in short-chain FA and richer in unsaturated long-chain FA, especially in trans octadecenoic acid (4.4 vs . 2.7% of the total FA, P < 0.05) . A very large increase in the isomer trans-10 18:1 (+1.46% of the total FA) was observed . Because no difference in volatile FA concentrations in the rumen was revealed, the increase in trans octadecenoic acids, and particularly the isomer trans-10 18:1, was associated with the larger postprandial drop in ruminal pH with wheat . Similar concentrate levels and FA profiles in both diets indicated that the decrease in milk fat was due to changes in the ruminal environment . Quicker degradation of wheat starch, and hence a greater drop in pH with this diet associated with the absence of any effect on volatile FA, strengthen the hypothesis developed in the literature of enzyme inhibition via increased levels of trans octadecenoic acids, especially the trans-10 isomer . Hence, milk fat can be decreased with rapidly degradable starch sources and not only with high levels of concentrates in the diet or added fat . More detailed work is necessary to elucidate the microorganisms involved and to determine whether metabolic pathways similar to those reported for high-concentrate diets are involved.

Parasite Immunol, 2003 Nov-Dec, 25(11-12), 545 - 52
Interaction of mannan-binding lectin with Trichinella spiralis glycoproteins, a possible innate immune mechanism; Gruden-Movsesijan A et al.; Complex and variable glycoconjugates presented by parasitic nematodes during infection are very important in the host-parasite interplay . Predominantly carbohydrate-rich antigens are involved in the stimulation and modulation of the stage-specific immune response of the host . The non-specific innate immune system, however, acts as the first line of host defence against pathogens, before the appearance of antigen-specific responses . The functional entities of the innate system are lectins that recognize the surface ligands of pathogens: mannan-binding lectin (MBL) is a key recognition element involved in binding oligosaccharide structures exposed on microorganisms . In the present study we investigated whether MBL binds to the parasitic nematode Trichinella spiralis (T . spiralis) . Since the parasite is coated with mannose-containing glycans, these structures could represent potential ligands for MBL and contribute to activation of the innate immune response of the host . Histochemical staining revealed MBL on the surface and internal organs of T . spiralis muscle larvae . MBL bound in a mannose-inhibitable manner to both crude extracts of T . spiralis muscle larvae and larvae excretory/secretory products . Western blot analyses showed that MBL recognized glycoproteins from all stages of T . spiralis . In vitro complement activation assays suggested that MBL is capable of fixing complement components on T . spiralis crude extract coated plates and activating the complement cascade through the 'lectin pathway'.

Biotechnol Bioeng, 2004 Apr 20, 86(2), 163 - 7
Growth behavior of microorganisms using UV-Vis spectroscopy: Escherichia coli; Alupoaei CE et al.; Multiwavelength transmission spectra of microorganisms and cell suspensions consist of combined absorption and scattering phenomena resulting from the interaction of light with microorganisms or cells typically suspended in a nonabsorbing media . The distribution of intensities as a function of wavelength depends on the size, shape, and optical properties of the sample . The optical properties are functions of the chemical composition and the state of aggregation, or association, of the chromophoric groups contained in the microorganisms . This article explores the growth behavior of Escherichia coli from the perspective of multiwavelength UV-Vis spectroscopy . Experimentally, it is demonstrated that the spectral signatures of the microorganism evolve as a function of time . It is also demonstrated that the spectral changes observed during growth are consistent with data reported elsewhere . From the theoretical point of view, it is demonstrated that the spectral signatures can be adequately represented with an interpretation model based on light-scattering theory . The parameters from the interpretation model reflect changes in size and chemical composition known to take place in the microorganisms during growth .

J Nutr, 2004 Apr, 134(4), 868 - 73
The source of long-chain PUFA in formula supplements does not affect the fatty acid composition of plasma lipids in full-term infants; Sala-Vila A et al.; Supplementation of formulas for full-term infants with long-chain (LC) PUFA {arachidonic acid (AA) and docosahexaenoic acid (DHA)} at levels resembling human milk is recommended because they provide biochemical and functional benefits to the neonate . The objective of this work was to determine whether the source of dietary LC-PUFA affects the bioavailability in full-term infants . Treatment groups were as follows: full-term infants were fed from birth to 3 mo breast-milk (n = 11, 0.4 and 0.3 g/100 g total fatty acids as AA and DHA, respectively), formula containing LC-PUFA in the form of egg phospholipids (n = 12), or a formula supplemented with LC-PUFA in the form of triglycerides synthesized by single cells of algal and fungal microorganisms (n = 12) . Both formulas provided 0.4 and 0.1 g/100 g total fatty acids as AA and DHA, respectively . We compared the fatty acid compositions of the main plasma lipid fractions (phospholipids, triglycerides, and cholesteryl esters) at birth and 3 mo . At 3 mo, lower levels of nervonic acid (NA), docosapentaenoic (DPA) acid, and DHA were found in all plasma lipid fractions from infants fed formula compared with those in the human milk-fed infants, irrespective of the source of the formula supplement (P < 0.02) . These data demonstrate that the form of dietary LC-PUFA (triglycerides or phospholipids) does not influence their bioavailability . Similarly, absorption of LC-PUFA depends mainly on the lipid composition of the diet fed . These results suggest that the levels of NA, DPA, and DHA in formulas for full-term infants should be increased.

Bioresour Technol, 2004 Jun, 93(2), 145 - 53
Influences of vermicomposts on field strawberries: 1 . effects on growth and yields; Arancon NQ et al.; Vermicomposts processed commercially from food wastes and paper wastes were applied, to 4.5 m(2) field plots, under high plastic hoop tunnels, at rates of 5 or 10 tha(-1) to evaluate their effects on the growth and yields of strawberries (Fragaria ananasa) var . 'Chandler' . The vermicomposts were incorporated into the top 10 cm of soil and supplemented, based on chemical analyses, with amounts of inorganic NPK fertilizers calculated to equalize the initial fertilizer rates of 85-155-125 kgha(-1) NPK applied to the inorganic fertilizer plots . All treatments were replicated four times, in a completely randomized design, at two field sites on Doles silt loam or Hoytville silty clay loam at Piketon and Fremont, Ohio, respectively . Vermicompost applications increased strawberry growth and yields significantly; including increases of up to 37% in leaf areas, 37% in plant shoot biomass, 40% in numbers of flowers, 36% in numbers of plant runners and 35% in marketable fruit weights . These responses seemed not to be dose-dependent, since strawberries at one site grew fastest and yielded most in response to the 10 tha(-1) vermicompost application rate, whereas they responded positively and similarly to both the 5 and 10 tha(-1) rates of applications at the other site . These responses could not have been mediated by availability of macronutrients, since all plots were supplemented with inorganic fertilizers, to equalize macronutrient inputs for all treatments, but based on other research in our laboratory could have been due to production of plant growth regulators by microorganisms during vermicomposting .

Bioresour Technol, 2004 Jun, 93(2), 139 - 44
Effects of vermicomposts produced from food waste on the growth and yields of greenhouse peppers; Arancon NQ et al.; Vermicomposts, produced commercially from food wastes, were substituted at a range of different concentrations into a soil-less commercial bedding plant container medium, Metro-Mix 360 (MM360), to evaluate their effects on the growth and yields of peppers in the greenhouse . Six-week-old peppers (Capsicum annum L . var . California) were transplanted into 100%, 80%, 60%, 40%, 20% or 10% MM360 substituted with 0%, 10%, 20%, 40%, 60%, 80% and 100% vermicompost . All plants were watered three times weekly with 200 ppm Peter's Nutrient Solution from the time of transplanting up to 107 days . Peppers grown in potting mixtures containing 40% food waste vermicomposts and 60% MM360 yielded 45% more fruit weights and had 17% greater mean number of fruits than those grown in MM360 only . The mean heights, numbers of buds and numbers of flowers of peppers grown in potting mixtures containing 10-80% vermicompost although greater did not differ significantly from those of peppers grown in MM360 . There were no positive correlations between the increases in pepper yields, and the amounts of mineral-N and microbial biomass-N in the potting mixtures, or the concentrations of nitrogen in the shoot tissues of peppers . Factors such as: an improvement of the physical structure of the potting medium, increases in populations of beneficial microorganisms and the potential availability of plant growth-influencing-substances produced by microorganisms in vermicomposts, could have contributed to the increased pepper yields obtained .

Plant Physiol Biochem, 2004 Mar, 42(3), 215 - 23
Isolation of the gene encoding Carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis; Yazawa K et al.; The Arabidopsis thaliana LEC1 gene regulates embryo morphology and seed maturation . For a better understanding of its function, we isolated a carrot (Daucus carota L . cv . US-Harumakigosun) counterpart of this gene, C-LEC1, from a cDNA library of carrot somatic embryos, since carrot is a better model plant for preparing large quantities of somatic embryos at the same developmental stage . The predicted amino acid sequence of C-LEC1 is similar to that of LEC1 and contains regions that are conserved in the heme-activated protein 3 (HAP3) subunit of plants, animals and microorganisms . C-LEC1 expression was detected in embryogenic cells, somatic embryos, and developing seeds . In situ hybridization analysis revealed C-LEC1 expression in the peripheral region of the embryos but not in the endosperm . Expression of C-LEC1 driven by Arabidopsis LEC1 promoter was able to complement the defects of the Arabidopsis lec1-1 mutant . These results suggest that C-LEC1 is a functional homolog of Arabidopsis LEC1, an important regulator of zygotic and somatic embryo development.

Can J Microbiol, 2001 Jan, 47(1), 33 - 40
Glutathione is a target in tellurite toxicity and is protected by tellurite resistance determinants in Escherichia coli; Turner RJ et al.; Tellurite (TeO3(2-)) is highly toxic to most microorganisms . The mechanisms of toxicity or resistance are poorly understood . It has been shown that tellurite rapidly depletes the reduced thiol content within wild-type Escherichia coli . We have shown that the presence of plasmid-borne tellurite-resistance determinants protects against general thiol oxidation by tellurite . In the present study we observe that the tellurite-dependent depletion of cellular thiols in mutants of the glutathione and thioredoxin thiol:redox system was less than in wild-type cells . To identify the type of low-molecular-weight thiol compounds affected by tellurite exposure, the thiol-containing molecules were analyzed by reverse phase HPLC as their monobromobimane derivatives . Results indicated that reduced glutathione is a major initial target of tellurite reactivity within the cell . Other thiol species are also targeted by tellurite, including reduced coenzyme A . The presence of the tellurite resistance determinants kilA and ter protect against the loss of reduced glutathione by as much as 60% over a 2 h exposure . This protection of glutathione oxidation is likely key to the resistance mechanism of these determinants . Additionally, the thiol oxidation response curves were compared between selenite and tellurite . The loss of thiol compounds within the cell recovered from selenite but not to tellurite.

Otolaryngol Pol, 2003, 57(6), 847 - 54
{Evaluation of drug sensitivity of the microorganisms isolated from chronic sinusitis treated by beta lactam antibiotics}; Namyslowski W et al.; The drug sensitiveness to beta-lactam antibiotics of the bacterial flora, taken by sinus puncture from 115 patients with unior bilateral acute exacerbation of chronic maxillary sinusitis was analysed . About 90% of the isolated pathogens, as well as in subgroup treated with amoxicillin with potassium clavulanate and in subgroup treated with cefuroxime axetil showed antibiotic sensitivity . Among isolated pathogens before the treatment, 4 (9.5%) were resistant to the amoxicillin with potassium clavulanate disks in subgroup A and 3 (7.3%) to the cefuroxime axetil in subgroup B . There was only one pathogen isolated in the control evaluation in both group after the treatment.

Izv Akad Nauk Ser Biol, 2004 Jan-Feb, (1), 49 - 58
{The role of the phytogenic field of larch of the pre-fire generation in forming edaphic conditions in burned-out forest areas}; Prokushkin SG et al.; It is shown that larch of the prefire generation is the main edificator at the early stages of restorative successions in burned-out areas . Its environment-forming effect manifests itself most strongly in the phytogenic field of living trees, where edaphic conditions similar to those in primary larch forests are formed within ten years after the fire . This is accompanied by an increase in the numbers of microorganisms utilizing organic and mineral nitrogen, as well as in the rate of nitrogen mineralization in plant microgroups of this zone . Hence, living trees remaining in a burned-out area promote restoration of the initial edaphic conditions.

Saudi Med J, 2004 Mar, 25(3), 331 - 41
Microbial, nutritional and physical quality of commercial and hospital prepared tube feedings in Saudi Arabia; Mokhalalati JK et al.; OBJECTIVE: Blenderized tube feedings (BTF) may present disadvantages over commercially prepared formulas (CPF) . This study compares the microbial safety, nutritional content, and physical properties of BTF versus CPF . METHODS: A total of 18 samples of BTF were collected from 3 hospitals in the Kingdom of Saudi Arabia from August 1999 through to November 1999 . Samples of a CPF were collected for comparison . All samples were analyzed for nutritional content, microbial quality (aerobic plate counts, coliform counts, microorganism growth) and physical characteristics (viscosity, osmolality) . RESULTS: The nutrient content of BTF varied significantly within and between sites . The average intra site variability for all sites ranged from 16-50% . The average variability of the CPF was 4-7% . Between sites, the mean concentration of most nutrients varied by 2-3 fold . The BTF had considerable differences between actual and expected nutrient concentrations, reaching statistical significance in 12 nutrients . The measured concentration of most nutrients in the CPF was within 10% of expected values . The BTF samples had higher viscosity and osmolality than the CPF . All samples of BTF had detectable aerobic plate counts that increased significantly over 4 hours (p<0.0005) . Coliform contamination varied between sites, with 100% contamination at one site . No aerobic plate counts or coliform counts were detected in the CPF samples . CONCLUSION: There is a high degree of variability in nutrient content and physical properties with BTF . Furthermore, BTF are highly contaminated, increasing the risk of nosocomial infections . For these reasons, CPF should replace BTF.

Environ Sci Technol, 2004 Mar 1, 38(5), 1455 - 9
Time-resolved laser fluorescence spectroscopy study on the interaction of curium(III) with Desulfovibrio äspöensis DSM 10631T; Moll H et al.; The influence of microorganisms on migration processes of actinides has to be taken into account for the risk assessment of potential high-level nuclear waste disposal sites . Therefore it is necessary to characterize the actinide-bacteria species formed and to elucidate the reaction mechanisms involved . This work is focused on the sulfate-reducing bacterial (SRB) strain Desulfovibrio aspoensis (D . aspoensis) DSM 10631T which frequently occurs in the deep granitic rock aquifers at the Aspo Hard Rock Laboratory (Aspo HRL), Sweden . We chose Cm(III) due to its high fluorescence spectroscopic sensitivity as a model system for exploring the interactions of trivalent actinides with D . aspoensis in the trace concentration range of 3 x 10(-7) mol/L . A time-resolved laser fluorescence spectroscopy (TRLFS) study has been carried out in the pH range from 3.00 to 7.55 in 0.154 mol/L NaCl . We interpret the pH dependence of the emission spectra with a biosorption forming an inner-sphere surface complex of Cm(III) onto the D . aspoensis cell envelope . This Cm(III)-D . aspoensis-surface complex is characterized by its emission spectrum (peak maximum at 600.1 nm) and its fluorescence lifetime (162 +/- 5 micros) . No evidence was found for incorporation of Cm(III) into the bacterial cells under the chosen experimental conditions.

J Nat Prod, 2004 Mar, 67(3), 510 - 22
Challenges and rewards of research in marine natural products chemistry in Brazil; Berlinck RG et al.; Brazil is blessed with a great biodiversity, which constitutes one of the most important sources of biologically active compounds, even if it has been largely underexplored . As is the case of the Amazon and Atlantic rainforests, the Brazilian marine fauna remains practically unexplored in the search for new biologically active natural products . Considering that marine organisms have been shown to be one of the most promising sources of new bioactive compounds for the treatment of different human diseases, the 8000 km of the Brazilian coastline represents a great potential for finding new pharmacologically active secondary metabolites . This review presents the status of marine natural products chemistry in Brazil, including results reported by different research groups with emphasis on the isolation, structure elucidation, and evaluation of biological activities of natural products isolated from sponges, ascidians, octocorals, and Opistobranch mollusks . A brief overview of the first Brazilian program on the isolation of marine bacteria and fungi, directed toward the production of biologically active compounds, is also discussed . The current multidisciplinary collaborative program under development at the Universidade de Sao Paulo proposes to establish a new paradigm toward the management of the Brazilian marine biodiversity, integrating research on the species diversity, ecology, taxonomy, and biogeography of marine invertebrates and microorganisms . This program also includes a broad screening program of Brazilian marine bioresources, to search for active compounds that may be of interest for the development of new drug leads.

Trends Biotechnol, 2004 Mar, 22(3), 99 - 100
Bioelectric power generation; Tayhas G et al.; In the recent article by Chaudhuri and Lovley, a fuel cell is described in which a microorganism, Rhodoferax ferrireducens, is used to oxidize glucose to carbon dioxide at neutral pH . This reaction occurs via direct bioelectrocatalysis: the microorganism uses the anode itself as the terminal oxidant to which liberated electrons are transferred, and does so with 83% efficiency . These findings are significant because they demonstrate a new approach for harvesting energy from the environment using microorganisms.

Res Microbiol, 2004 Mar, 155(2), 61 - 70
Microaerophilic bacteria transduce energy via oxidative metabolic gearing; Ludwig RA; Heterotrophic microaerophilic bacteria, a diverse and ubiquitous group, are specialized for growth in O2 limited environments . Until recently, microaerophilic bacteria have been grouped with obligate aerobic organisms whose metabolic rates slow in response to physiological O2 limitation . In contrast, microaerophilic bacteria are adapted to maintain essentially constant turnover of primary energy substrates in response to a wide range of physiological O2 . This capacity, oxidative metabolic gearing, allows microaerophilic bacteria to maintain catabolic enzymes, substrates, and cofactors at high steady-state levels . Oxidative metabolic gearing is thus adaptive, as it allows microaerophilic bacteria to respond to changes in physiological O2 relatively rapidly when compared to aerobic, anaerobic, or facultative microorganisms.

Ecotoxicol Environ Saf, 2004 Mar, 57(3), 257 - 69
Review of 15 years of research on ecotoxicology and remediation of land contaminated by agricultural drainage sediment rich in selenium; Wu L; The consequences of elevated Se accumulation at the Kesterson Reservoir National Wildlife Refuge in the Central Valley of California created adverse effects on wildlife and led to extensive research on the behavior of Se in both the wetland and upland ecosystems . Selenium concentrations in water entering the Kesterson Reservoir averaged 300 microg L(-1) . In pond waters 20-30% of the Se was selenate, while only 2% was selenite in the drainage water entering the reservoir . Submerged rooted aquatic plants fed on by water birds were found to contain 18-390 mg Se kg(-1) dry weight . Mosquitofish collected from the San Luis Drain contained 332 mg Se kg(-1), and those collected from the ponds ranged from 339 to 380 mg kg(-1) . Livers of water birds had Se concentrations ranging from 19.9 to 127 mg kg(-1) . The high concentrations of Se accumulation in the food chain of the wetland strongly suggest that Se bioaccumulation was the cause of death and deformity of embryos of the waterfowl nesting at the wetland habitat . In June 1986, the Kesterson Reservoir was closed to drain-water inputs, and the wetland was transformed to an upland grassland . New remedial plans were proposed . These new plans involved soil, water, and vegetation management to dissipate Se by bioaccumulation and volatilization through soil microorganisms and plants . The investigations of the potential transfer of Se from farm land into the crop and vegetables in the Central Valley indicated that plant tissue Se concentrations generally fall in a nonseleniferous category, except that the highest Se concentration of cotton was at a threshold where toxicity in animals could occur at a relatively low frequency . At the Kesterson upland grassland habitat, average total Se concentrations ranged from 500 to 8000 microg kg(-1) and water-extractable Se ranged from 10 to 700 microg kg(-1) in the top 15 cm of soil and varied greatly, by a factor greater than 100, among soil samples . Uptake of Se by the plants was profoundly affected by the soil available Se concentration, soil moisture, pH, soil salinity, soil sulfate concentration, soil reoxidation condition, kind of plant species, and soil-management practices . The rate of soil Se dissipation at the Kesterson grassland system was from 1% (low methylation rate) to 5% (high methylation rate) Se inventory per year and it will take from 46 to 230 years to bring the soil Se down to a normal level, 4 mg Se kg(-1) soil . However, the Kesterson upland grassland habitat had Se bioaccumulation values less than 10% of those of the previous wetland . The potential food-chain contamination at the existing Kesterson grassland is much less problematic . No negative impact on wildlife has been reported for the upland habitat . Plants may contribute to the Se reoxidation process and be able to reduce the movement of Se in the soil . At the Kesterson grassland, the distribution of soil Se is extremely uneven; high levels of soil Se concentrated only in isolated spots . Therefore, leaching of soil Se is not at an area level . It is unlikely that problems of transport of Se from the Kesterson soil to the adjacent uncontaminated environment by leaching can occur.

Ecotoxicol Environ Saf, 2004 Mar, 57(3), 248 - 56
Cassava cyanogens and fish mercury are high but safely consumed in the diet of native Amazonians; Dorea JG; The two most important staple foods (cassava and fish) in the diet of native Amazonians contain neurotoxins (linamarin and monomethyl mercury, MMHg) . These same neurotoxins are public health issues in other parts of the world . Factors such as chemistry, environment, and human ecology determine the endemism of neuropathies caused by consumption of cassava (Manihot esculenta Crantz) and fish . Linamarin is a natural component of cassava tubers that can be destroyed before consumption by proper processing . Furthermore, small amounts of the toxin absorbed by people consuming cassava can be effectively metabolized if the diet contains adequate protein-containing sulfur amino acids . Naturally occurring Hg in the waters of the Amazonian rain forest is methylated to MMHg by microorganisms and bioconcentrated in the aquatic food chain . There is no effective method for MMHg removal from fish . Despite high concentrations of naturally occurring neurotoxins in cassava (linamarin) and fish (MMHg), daily consumption of these foods in large amounts over the course of a lifetime poses no health hazards for Amazonians.

Forensic Sci Int, 2004 Jan 28, 139(2-3), 135 - 40
Preparation of degraded human DNA under controlled conditions; Bender K et al.; DNA typing through analysis of short tandem repeats (STRs) and mitochondrial DNA (mtDNA) by means of the polymerase chain reaction (PCR) and sequencing are the common methods for the forensic identification of persons and reconstruction of kinship, especially when skeletal human remains have to be analyzed . Furthermore, samples typically found at crime scenes may be both quantitatively and qualitatively inadequate since they may contain very scarce and often degraded DNA due to exposure to heat, light, humidity, and microorganisms . In order to improve the performance of STR typing technology in those cases where DNA availability is limited, it would be desirable to have a source of degraded DNA with known properties . For this purpose, we have developed a method to prepare artificially degraded DNA under controlled conditions . By treatment of genomic DNA with sonication and DNAse I we have produced DNA fragments within a defined range of lengths . STR typing of this degraded DNA with a commercially available multiplex kit could only produce partial profiles as indicated by the absence of STR alleles with sizes >200 bp . This artificially degraded DNA can be used for the improvement and standardization of STR typing protocols when only highly degraded DNA is available for analysis.

FEMS Immunol Med Microbiol, 2004 Mar 8, 40(2), 95 - 100
Iron gathering by zoopathogenic fungi; Howard DH; Iron is a metal required by most microorganisms and is prominently used in the transfer of electrons during metabolism . The gathering of iron is, then, an essential process and its fulfillment becomes a crucial pathogenetic event for zoopathogenic fungi . Iron is rather unavailable because it occurs on the earth's surface in its insoluble ferric form in oxides and hydroxides . In the infected host iron is bound to proteins such as transferrin and ferritin . Solubilization of ferric iron is the major problem confronting microorganisms . This process is achieved by two major mechanisms: ferric reduction and siderophore utilization . Ferric reductase is frequently accompanied by a copper oxidase transport system . There is one example of direct ferric iron transport apparently without prior reduction . Ferric reduction may also be accomplished by low molecular mass compounds . Some fungi have evolved a process of iron acquisition involving the synthesis of iron-gathering compounds called siderophores . Even those fungi that do not synthesize siderophores have developed permeases for transport of such compounds formed by other organisms . Fungi can also reductively release iron from siderophores and transport the ferrous iron often by the copper oxidase transport system . There is a great diversity of iron-gathering mechanisms expressed by pathogenic fungi and such diversity may be found even in a single species.

Nat Rev Microbiol, 2004 Feb, 2(2), 151 - 9
What does the future hold for clinical microbiology?
Raoult D, Fournier PE, Drancourt M.
In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation . In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens . The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work.

Nat Rev Microbiol, 2004 Feb, 2(2), 141 - 50
Tapping into microbial diversity; Keller M et al.; Even though significant advances have been made in understanding microbial diversity, most microorganisms are still only characterized by 'molecular fingerprints' and have resisted cultivation . Many different approaches have been developed to overcome the problems associated with cultivation of microorganisms because one obvious benefit would be the opportunity to investigate the previously inaccessible resources that these microorganisms potentially harbour.

Nat Rev Microbiol . 2004 Feb;2(2):91.
Pathogenomics of non-pathogens; Holden M et al.; Analysing the genomes of non-pathogenic microorganisms, in addition to its basic and applied scientific interest, can also shed considerable light on the study of pathogenic microorganisms . Two of the three microorganisms described here are rarely pathogenic, but carry genetic determinants that have previously been identified as being important for the pathogenicity of other microorganisms . This underlines the growing understanding that many so-called 'virulence genes' are probably involved in more general interactions between the microorganism and the host or the environment.

Nat Rev Microbiol, 2003 Oct, 1(1), 17 - 24
The damage-response framework of microbial pathogenesis; Casadevall A et al.; The late twentieth century witnessed the emergence of numerous infectious diseases that are caused by microorganisms that rarely cause disease in normal, healthy immunocompetent hosts . The emergence of these diseases shows that the existing concepts of pathogenicity and virulence do not take into account the fact that both the microorganism and the host contribute to microbial pathogenesis . To address this impediment to studies of host-microorganism interactions, we propose a new theoretical approach to understanding microbial pathogenesis, known as the 'damage-response' framework.

Nat Prod Rep, 2004 Feb, 21(1), 143 - 63 Epub 2004 Jan 09.
Marine-derived fungi: a chemically and biologically diverse group of microorganisms; Bugni TS et al.; A diverse array of secondary metabolites have been isolated and characterized from marine-derived fungi . The structures and biological activities of these metabolites are presented . Additionally, some basic principles of mycology are covered . Overall, 273 structures are presented and the review contains 162 references

Nat Prod Rep, 2004 Feb, 21(1), 1 - 49 Epub 2004 Jan 14.
Marine natural products; Blunt JW et al.; This review covers the literature published in 2002 for marine natural products, with 579 citations (413 for the period January to December 2002) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates and echinoderms . The emphasis is on new compounds (677 for 2002), together with their relevant biological activities, source organisms and country of origin . Syntheses that lead to the revision of structures or stereochemistries have been included (114), including any first total syntheses of a marine natural product.

J Leukoc Biol, 2004 Jul, 76(1), 48 - 57 Epub 2004 Mar 23.
Infection of C57BL/10ScCr and C57BL/10ScNCr mice with Leishmania major reveals a role for Toll-like receptor 4 in the control of parasite replication; Kropf P et al.; The innate immune system is essential for host defense; it senses the presence of potentially pathogenic-invading microorganisms, and the contribution of Toll-like receptors (TLRs) to this response is increasingly recognized . In the present study, we investigated the contribution of TLR4 to the course of cutaneous leishmaniasis in vivo . We used C57BL/10ScNCr (TLR4(0/0)) and C57BL/10ScCr {TLR4/interleukin-12 (IL-12)Rbeta2(0/0)} mice and compared the course of Leishmania major infection, parasite load, cell recruitment, and cytokine profile with those of wild-type C57BL/10ScSn mice . Our results confirm the importance of IL-12 receptor-mediated signaling in resistance to L . major infections . Importantly, we show that the lack of TLR4 results in an increased permissiveness for parasite growth during the innate and adaptive phase of the immune response and in delayed healing of the cutaneous lesions . The use of the tlr4 transgenic mouse strain TCr5 demonstrated unequivocally that TLR4 contributes to the efficient control of Leishmania growth in vivo.

J Microw Power Electromagn Energy, 2001, 36(1), 37 - 45
The effects of microwaves on airborne microorganisms; Hamid M et al.; This paper reports preliminary results of simple experiments carried out to study the effects of microwave irradiation at 2.45 GHz on fungi, yeast and bacteria of the type encountered in food processing plants or in enclosures containing individuals infected with tuberculosis mycobacterium (TB) . The results are sufficiently encouraging to justify further multivariable experiments particularly with air circulation schemes in which the air can be sterilized in a circular cylindrical microwave cavity operating at a higher order mode.

Microb Ecol, 2004 May, 47(4), 427 - 39
The occurrence of lysogenic bacteria and microbial aggregates in the lakes of the McMurdo Dry Valleys, Antarctica; Lisle JT et al.; The McMurdo Dry Valleys of Antarctica form the coldest and driest ecosystem on Earth . Within this region there are a number of perennially ice-covered (3-6 m thick) lakes that support active microbial assemblages and have a paucity of metazoans . These lakes receive limited allochthonous input of carbon and nutrients, and primary productivity is limited to only 6 months per year owing to an absence of sunlight during the austral winters . In an effort to establish the role that bacteria and their associated viruses play in carbon and nutrient cycling in these lakes, indigenous bacteria, free bacteriophage, and lysogen abundances were determined . Total bacterial abundances (TDC) ranged from 3.80 x 10(4) to 2.58 x 10(7) cells mL(-1) and virus-like particle (VLP) abundances ranged from 2.26 x 10(5) to 5.56 x 10(7) VLP mL(-1) . VLP abundances were significantly correlated (P < 0.05) with TDC, bacterial productivity (TdR), chlorophyll a (Chl a), and soluble reactive phosphorus (SRP) . Lysogenic bacteria, determined by induction with mitomycin C, made up between 2.0% and 62.5% of the total population of bacteria when using significant decreases and increases in TDC and VLP abundances, respectively, and 89.5% when using increases in VLP abundances as the sole criterion for a successful induction event . The contribution of viruses released from induced lysogens contributed <0.015% to the total viral production rate . Carbohydrate and protein based organic aggregates were abundant within the water column of the lakes and were heavily colonized by bacteria and VLPs . Alkaline phosphatase activity was detected within the matrix of the aggregates, implying phosphorus deficiency and consortial nutrient exchanges among microorganisms.

Eur J Cardiothorac Surg, 2004 Apr, 25(4), 475 - 9
Primary esophageal repair for Boerhaave's syndrome whatever the free interval between perforation and treatment; Jougon J et al.; OBJECTIVES: Boerhaave's syndrome is the most sinister cause of esophageal perforation responsible with mortality rate ranging from 20 to 30% . Combination of mediastinal contamination with microorganisms, gastric acid and digestives enzymes, long free interval between injury and initiation of treatment causes severe mediastinitis which is fatal in most untreated cases . The aim of this paper is to emphasize primary esophageal repair and resuscitation whatever the free interval from rupture and repair . METHODS: A retrospective review of patients treated for Boerhaave's syndrome in our department from January 1980 to February 2003 was performed . The principle of treatment was surgical treatment and avoidance of esophageal exclusion or esophagectomy whichever was possible . RESULTS: There were 25 patients (17 males and 8 females) . All patients were operated on by primary esophageal repair, except for three who underwent immediate exclusion of the esophagus and one patient who deceased on arrival before being operated . Patients were classified according to free interval between perforation and treatment: group 1 (n=9; 36%) within the 24 h (range from 12 to 24 h) and group 2 (n=16; 64%) more than 24 h (range from 2 to 17 days) . Altogether 6 patients deceased (24%) . In hospital mortality rate for groups 1 and 2 was, respectively, 44% (four patients) and 13% (two patients), not significantly different . Mean hospital stay was 63 days . Two patients developed anastomotic leakage needing esophagectomy and retrosternal coloplasty in one or more steps . One patient developed pleural abscess treated by percutaneous drainage . Three patients presented temporary symptomatic esophageal stenosis, of whom one underwent dilation . CONCLUSIONS: Long free interval before treatment does not preclude primary esophageal repair in Boerhaave's syndrome . Esophageal exclusion may be more often than not avoided in most cases.

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