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 microorgani