Int J Food Microbiol, 2004 Jan 15, 90(2), 171 - 9 Considering the complexity of microbial community dynamics in food safety risk assessment; Powell M et al.; The potential for competitive inhibition to limit the growth of microbial pathogens in food raises questions about the external validity of typical predictive microbiology studies and suggests the need to consider microbial community dynamics in food safety risk assessment . Ecological theory indicates, however, that community dynamics are highly complex and may be very sensitive to initial conditions and random variation . Seemingly incongruous empirical results for Escherichia coli O157:H7 in ground beef are shown to be consistent with a simple theoretical model of interspecific competition . A potential means of incorporating community-level microbial dynamics into the food safety risk assessment process is explored. Biochem Pharmacol, 2004 Jan 15, 67(2), 227 - 34 A new structural class of proteasome inhibitors identified by microbial screening using yeast-based assay; Asai A et al.; A yeast-based growth interference assay was developed utilizing a yeast strain in which expression of Xenopus cyclin A1 was induced to elevate cell division cycle 28 (Cdc28) kinase activity . Since the hyperactivation of Cdc28 kinase in yeast results in a growth-arrest phenotype, compounds which could rescue the cyclin A1-induced growth arrest might be potential new, antitumor drug candidates acting on the cyclin-dependent, kinase-mediated, cell cycle regulation pathway . In the course of our microbial screening program, the new Streptomyces metabolites, belactosins, were identified . As reported previously, belactosin A induced cell cycle arrest at G2/M phase in human cancer cells . However, the molecular mechanism of action was unknown . We herein demonstrate the proteasome inhibition by belactosin A . Belactosin A did not inhibit yeast Cdc28 kinase and human cyclin-dependent kinase in vitro . On the other hand, it inhibited the chymotrypsin-like activity of the rabbit 20S proteasome . From the initial SAR studies, we identified a hydrophobic belactosin A derivative, KF33955, which exhibited a 100-fold greater growth-inhibitory activity against HeLa S3 cells than belactosin A, presumably due to its higher cell permeability . The biochemical analysis using KF33955 suggested that the proteasome inhibitory activity of KF33955 were irreversible and required the beta-lactone moiety to inhibit the proteasome . KF33955 increased the intracellular levels of protein ubiquitination in NIH3T3 cells . In addition, KF33955 treatment resulted in the accumulation of known proteasome substrates in HeLa S3 cells . These results identify belactosin A as a useful lead compound to target proteasome for the treatment of disease whose etiology is dependent on the unregulated ubiquitin-proteasome pathway. Biotechnol Adv, 2004 Feb, 22(4), 287 - 307 Streptokinase--a clinically useful thrombolytic agent; Banerjee A et al.; A failure of hemostasis and consequent formation of blood clots in the circulatory system can produce severe outcomes such as stroke and myocardial infraction . Pathological development of blood clots requires clinical intervention with fibrinolytic agents such as urokinase, tissue plasminogen activator and streptokinase . This review deals with streptokinase as a clinically important and cost-effective plasminogen activator . The aspects discussed include: the mode of action; the structure and structure-function relationships; the structural modifications for improving functionality; recombinant streptokinase; microbial production; and recovery of this protein from crude broths. Int J Cancer, 2004 Feb 10, 108(4), 488 - 92 Chemoprotective effect of caffeic acid phenethyl ester on promotion in a medium-term rat hepatocarcinogenesis assay; Carrasco-Legleu CE et al.; Caffeic acid phenethyl ester (CAPE), a natural honeybee product exhibits a spectrum of biological activities including anti-microbial, anti-inflammatory, antioxidant and anti-tumoral actions . CAPE is also chemopreventive against intestinal, colon and skin cancer . Our aim was to extend the study of its chemoprotective features to the promotion of hepatocarcinogenesis . Male Wistar rats were subjected to a protocol under a modified promotion regimen of the resistant hepatocyte model . The altered hepatic foci (AHF) were quantitatively analyzed by histochemistry and image processing . When given during promotion, CAPE (20 mg/kg) decreased the expression of number and area gamma-glutamyl transpeptidase (GGT) positive AHF by 91% and 97%, respectively . When GGT expression was analyzed by RT-PCR, CAPE drastically decreased and prevented expression of almost all GGT transcripts at this stage of the carcinogenic process . Glutathione S-transferase placental form (GST-P), another protein marker for preneoplastic lesions was measured by Western blot and a decrease of 82% was observed . Additionally, we evaluated the effect of CAPE on the expression of nuclear factor NF-kappaB and found an 85% decrease in nuclear localization of the p65 subunit of NF-kappaB; however, their repressor, IkappaBalpha was not modified . Our results showed that CAPE given during promotion in hepatocarcinogenesis protects against induction of GGT-positive AHF, GST-P protein, GGT mRNA expression and translocation of p65 . This phenomenon was independent of IkappaBalpha degradation . Chembiochem, 2004 Jan 3, 5(1), 87 - 92 Fungal aerobic reductive dechlorination of ethyl 2-chloroacetoacetate by Saccharomyces cerevisiae: mechanism of a novel type of microbial dehalogenation; Jorg G et al.; Saccharomyces cerevisiae reduces the beta-keto ester ethyl 2-chloroacetoacetate to the respective chiral cis- and trans-beta-hydroxy esters . In the course of chiral reduction, competing dehalogenation of the xenobiotic substrate to ethyl acetoacetate occurs, in a reaction mediated by cytosolic glutathione (GSH) . Mechanistically, the dechlorination is a novel type of glutathione-dependent dehalogenation catalysed by an as yet unidentified glutathione-dependent dehalogenase . The first step consists of a nucleophilic replacement of the chloride substituent by glutathione . In the subsequent enzyme-catalysed step, a second glutathione molecule liberates the dehalogenation product by thiolytic attack at the thioether bridge, resulting in a net transfer of two electrons to the substrate and in the formation of glutathione disulfide (GSSG) . Being effective under aerobic conditions and catalysed by a fungus, this reductive dechlorination of an aliphatic substrate is an outstanding example of a novel, glutathione-mediated microbial dehalogenation. Sheng Li Xue Bao, 2003 Dec 25, 55(6), 699 - 704 {Roles of intracellular calcium and monomeric G-proteins in regulating exocytosis of human neutrophils}; Zhu Y et al.; Neutrophils play a major role in host defense against microbial infection . There are some clues indicate that neutrophils may also play a role in the pathophysiology of the airway obstruction in chronic asthma . We studied the roles of intracellular calcium and GTP gamma S in the regulation of neutrophils exocytosis using pipette perfusion and membrane capacitance measurement technique in whole cell patch clamp configuration . The results showed that the membrane capacitance increase induced by calcium revealed a biphasic process . The first phase occurred when the calcium level was between 0.2-14 micromol/L with a plateau amplitude of 1.23 pF and a calcium EC50 of 1.1 micromol/L . This phase might correspond to the release of the tertiary granules . The second phase occurred when the calcium concentration was between 20-70 micromol/L with a plateau increment of 6.36 pF, the calcium EC50 being about 33 micromol/L . This phase might represent the release of the primary and secondary granules . Intracellular calcium also simultaneously increased the exocytotic rate and the eventual extent in neutrophils . On the other hand, GTP gamma S can increase the exocytotic rate in a dose-dependent manner but had no effect on the eventual extent of membrane capacitance increment (>6 pF) if the cell was stimulated for a long period (>20 min) . GTP gamma S (ranging from 20 to 100 micromol/L) induced the neutrophils to release all four types of the granules at very low intracellular calcium level. Blood, 2004 Jun 1, 103(11), 4201 - 6 Epub 2003 Dec 24. A cell-surface molecule selectively expressed on murine natural interferon-producing cells that blocks secretion of interferon-alpha; Blasius A et al.; Natural interferon (IFN)-producing cells (IPCs) recognize certain viruses and DNA containing deoxycytidylate-phosphatedeoxyguanylate (CpG) motifs through the toll-like receptor (TLR) 9, resulting in secretion of IFN-alpha, interleukin 12 (IL-12), and proinflammatory chemokines . Human IPCs are found mainly in inflamed lymph nodes, where they are presumably recruited from the blood to activate both innate and adaptive responses to microbial infections . Demonstrating IPC recruitment and function in murine infection models has been difficult because multiple antibodies are required to distinguish IPCs from other immune cells and very few IPCs can be recovered from lymph nodes . Here we describe a monoclonal antibody (mAb) that exclusively detects murine IPCs in all lymphoid organs under both normal and inflammatory conditions . Using this antibody, we demonstrate that IPCs are normally present in the T-cell zone of lymph nodes and spleen and that inoculation of peripheral tissues with inflammatory stimuli triggers recruitment of IPC into sentinel lymph nodes, whether the stimuli are able to directly stimulate IPCs through TLR or not . Remarkably, we show that incubation of IPCs with the antibody in vitro or administration of the antibody in vivo dramatically reduce secretion of IFN-alpha in response to CpG DNA without causing IPC depletion . Thus, the antibody identifies an IPC-specific surface molecule that, when engaged, inhibits IFN-alpha secretion. Am J Trop Med Hyg, 2003 Nov, 69(5), 455 - 60 Enzootic transmission of Babesia divergens among cottontail rabbits on Nantucket Island, Massachusetts; Goethert HK et al.; Specific ticks seem to locally serve as vector for characteristic microbial assemblages (guilds) comprising spirochetes, piroplasms, ehrlichiae, and arboviruses . Borrelia andersoni and Anaplasma phagocytophilum are intensely transmitted between cottontail rabbits . To test the hypothesis that a piroplasm may also be maintained in rabbits, we sampled these hosts from Nantucket Island, Massachusetts and tested their blood and tissues by a polymerase chain reaction for evidence of infection . Surprisingly, the agent of bovine redwater and of European human babesiosis, Babesia divergens, was detected in 16% of the rabbits sampled during 1998-2002 (> 99% sequence similarity in the 18S ribosomal DNA) . The vector of B . divergens on Nantucket appears to be Ixodes dentatus, a rabbit- and bird-feeding tick that may feed on humans . Although the risk of human infection appears to be minimal, an autochthonously acquired Kentucky case due to this rabbit agent was recently reported . Physicians should entertain the diagnosis of babesiosis due to B . divergens for severe hemolytic febrile syndromes in American patients exposed to sites where rabbits are common. Bull Tokyo Dent Coll, 2003 Aug, 44(3), 149 - 58 Implication of responses to bacterial heat shock proteins, chronic microbial infections, and dental metal allergy in patients with pustulosis palmaris et plantaris; Kosugi M et al.; Pustulosis palmaris et plantaris (PPP) is a chronic relapsing skin disease characterized by sterile intraepidermal pustules and, usually, by scaly erythematous skin on the palm, soles, or both . To determine the primary pathogenic factors involved in the onset of PPP, we analyzed the implications of heat shock proteins (HSPs), which are highly conserved immunogenic proteins, chronic microbial infections including marginal and periapical periodontitis, and delayed type hypersensitivity (DTH) against dental metals examined by patch tests . We found that the titers of IgG against HSPs of Escherichia coli GroEL and Actinobacillus actinomycetemcomitans DnaJ in the sera from PPP patients were higher than those in the control group (GroEL; p < 0.05) . Two patients with PPP had more than 1,000 ng/ml serum IgE level . We found that the average serum IgG antibody level against human cytomegalovirus (HCMV) in the PPP patient group was higher than that of the healthy group (p < 0.05) . DTH against dental metal was found in eight of 22 PPP patients . Six of eight patients reacted against more than two metals . Replacement of dental metal with resin in these patients resulted in the disappearance or remission of PPP . These findings suggest that the immune responses to HSPs produced by oral bacteria, HCMV infection, dental metal allergy, and their combinations are etiological factors for PPP . We concluded that various kinds of examinations, including oral cavity conditions and chronic infections, are essential to determine the major etiologic factors of PPP. JAMA, 2003 Dec 24, 290(24), 3207 - 14 Impact of valve surgery on 6-month mortality in adults with complicated, left-sided native valve endocarditis: a propensity analysis; Vikram HR et al.; CONTEXT: Complicated, left-sided native valve endocarditis causes significant morbidity and mortality in adults . The presumed benefits of valve surgery remain unproven due to lack of randomized controlled trials . OBJECTIVE: To determine whether valve surgery is associated with reduced mortality in adults with complicated, left-sided native valve endocarditis . DESIGN AND SETTING: Retrospective, observational cohort study conducted from January 1990 to January 2000 at 7 Connecticut hospitals . Propensity analyses were used to control for bias in treatment assignment and prognostic imbalances . PATIENTS: Of the 513 adults with complicated, left-sided native valve endocarditis, 230 (45%) underwent valve surgery and 283 (55%) received medical therapy alone . MAIN OUTCOME MEASURE: All-cause mortality at 6 months after baseline . RESULTS: In the 6-month period after baseline, 131 patients (26%) died . In unadjusted analyses, valve surgery was associated with reduced mortality (16% vs 33%; hazard ratio {HR}, 0.43; 95% confidence interval {CI}, 0.29-0.63; P<.001) . After adjustment for baseline variables associated with mortality (including hospital site, comorbidity, congestive heart failure, microbial etiology, immunocompromised state, abnormal mental status, and refractory infection), valve surgery remained associated with reduced mortality (adjusted HR, 0.35; 95% CI, 0.23-0.54; P<.02) . In further analyses of 218 patients matched by propensity scores, valve surgery remained associated with reduced mortality (15% vs 28%; HR, 0.45; 95% CI, 0.23-0.86; P =.01) . After additional adjustment for variables that contribute to heterogeneity and confounding within the propensity-matched group, surgical therapy remained significantly associated with a lower mortality (HR, 0.40; 95% CI, 0.18-0.91; P =.03) . In this propensity-matched group, patients with moderate to severe congestive heart failure showed the greatest reduction in mortality with valve surgery (14% vs 51%; HR, 0.22; 95% CI, 0.09-0.53; P =.001) . CONCLUSIONS: Valve surgery for patients with complicated, left-sided native valve endocarditis was independently associated with reduced 6-month mortality after adjustment for both baseline variables associated with the propensity to undergo valve surgery and baseline variables associated with mortality . The reduced mortality was particularly evident among patients with moderate to severe congestive heart failure. Bioresour Technol, 2004 Apr, 92(2), 173 - 9 Performance of subsurface flow constructed wetland taking pretreated swine effluent under heavy loads; Lee CY et al.; Subsurface flow constructed wetlands (SSFCW) subjected to changing of loading rates are poorly understood, especially when used to treat swine waste under heavy loads . This study employed a SSFCW system to take pretreated swine effluent at three hydraulic retention times (HRT): 8.5-day HRT (Phase I), 4.3-day HRT (Phase II), and 14.7-day HRT (Phase III) . Results showed that the system responded well to the changing hydraulic loads in removing suspended solids (SS) and carbonaceous oxygen demands . The averaged reduction efficiencies for four major constituents in the three phases were: SS 96-99%, chemical oxygen demand (COD) 77-84%, total phosphorus 47-59%, and total nitrogen (TN) 10-24% . While physical mechanisms were dominant in removing pollutants, the contributions of microbial mechanisms increased with the duration of wetland use, achieving 48% of COD removed and 16% of TN removed in the last phase . Water hyacinth made only a minimal contribution to the removal of nutrients . This study suggested that the effluent from SSFCW was appropriate for further treatment in land applications for nutrient assimilation. Proc Nutr Soc, 2003 Aug, 62(3), 727 - 37 Gut failure and abdominal visceral transplantation; Abu-Elmagd K et al.; Despite the reported high survival with total parenteral nutrition (TPN) therapy for patients with intestinal failure, a considerable number of patients do not escape the potential risks of TPN-associated complications, including hepatic failure, vanishing of central venous access and line sepsis . Thus, intestinal, liver-intestinal and multivisceral transplantation have recently emerged to rescue those who can no longer be maintained on TPN . Before this development, and for nearly three decades, small-bowel transplantation was plagued with uncontrolled rejection, graft v . host disease and fatal infection . These barriers stemmed from the large gut lymphoid mass and heavy microbial load contained in the intestinal lumen . The recent improvement in survival after the clinical introduction of tacrolimus with achievement of full enteric nutritional autonomy qualified the procedure by the US Health Care Financing Administration as the standard of care for patients with intestinal and TPN failure . The decision was supported by a decade of clinical experience with cumulative improvement in patient and graft survival . In addition, the introduction of new effective immunoprophylactic agents and novel therapeutic approaches has contributed to a further increase in the therapeutic advantages of the procedure . The present review article outlines the current clinical practice of intestinal transplantation and defines new management strategies with the aim of raising the level of the procedure to be a better alternative therapy for TPN-dependent patients. Nat Immunol, 2004 Jan, 5(1), 88 - 97 Epub 2003 Dec 14. The extracellular matrix protein mindin is a pattern-recognition molecule for microbial pathogens; He YW et al.; Microbial pathogens use a variety of their surface molecules to bind to host extracellular matrix (ECM) components to establish an effective infection . However, ECM components can also serve as an integral part of the innate immunity . Mice lacking expression of mindin (spondin 2), a highly conserved ECM protein, have an impaired ability to clear bacterial infection, and mindin-deficient macrophages show defective responses to a broad spectrum of microbial stimuli . Moreover, mindin binds directly to bacteria and their components and functions as an opsonin for macrophage phagocytosis of bacteria . Thus, mindin is essential in the initiation of the innate immune response and represents a unique pattern-recognition molecule in the ECM for microbial pathogens. Int Arch Occup Environ Health, 2004 Apr, 77(3), 222 - 6 Epub 2003 Dec 19. Indoor air quality and health problems associated with damp floor coverings; Tuomainen A et al.; OBJECTIVES: To study the relationship between a high incidence of bronchial asthma among employees working in an office building and an indoor air problem related to the degradation of polyvinyl chloride (PVC) floor coverings in the building . The indoor air measurements and results of renovations are also described . METHODS: Employees' symptoms were surveyed by a questionnaire, and the incidence of asthma was calculated from the medical records for 1997-2000 . The quality of indoor air was assessed by microbial sampling and by investigation of the building for possible moisture damage . Indoor air was sampled for volatile organic compounds (VOCs) through Tenax adsorbent tubes . In situ volatile emission measurements from the concrete floor were performed via the field and laboratory emission cell (FLEC) method . RESULTS: In an office with approximately 150 employees, eight new cases of asthma were found in 4 years . In addition, the workers complained of respiratory, conjunctival and nasal symptoms . Emissions indicating the degradation of plastic floor coverings (e.g . 2-ethyl-1-hexanol, 1-butanol) were found in the indoor air and floor material samples . The plastic floor coverings, adhesives and the levelling layers were carefully removed from 12 rooms . The VOCs had diffused into the underlying concrete slabs . The concrete was warmed to remove the diffused VOCs from these areas . After the repairs the concentrations of the VOCs indicating the degradation of PVC, decreased, as did the prevalence of the employees' symptoms and several asthma patients' need for medication . CONCLUSIONS: The workers in the office building complained of several respiratory, conjunctival and dermal symptoms . The incidence of adult-onset asthma was approximately nine-times higher than that among Finns employed in similar work . The most probable single cause of the indoor air problem was the degradation of the plastic floor coverings. Plant Cell, 2004 Jan, 16(1), 126 - 43 Epub 2003 Dec 19. The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development; Li L et al.; Jasmonic acid (JA) is a fatty acid-derived signaling molecule that regulates a broad range of plant defense responses against herbivores and some microbial pathogens . Molecular genetic studies in Arabidopsis have established that JA also performs a critical role in anther and pollen development but is not essential for other developmental aspects of the plant's life cycle . Here, we describe the phenotypic and molecular characterization of a sterile mutant of tomato (jasmonic acid-insensitive1 {jai1}) that is defective in JA signaling . Although the mutant exhibited reduced pollen viability, sterility was caused by a defect in the maternal control of seed maturation, which was associated with the loss of accumulation of JA-regulated proteinase inhibitor proteins in reproductive tissues . jai1 plants exhibited several defense-related phenotypes, including the inability to express JA-responsive genes, severely compromised resistance to two-spotted spider mites, and abnormal development of glandular trichomes . We demonstrate that these defects are caused by the loss of function of the tomato homolog of CORONATINE-INSENSITIVE1 (COI1), an F-box protein that is required for JA-signaled processes in Arabidopsis . These findings indicate that the JA/COI1 signaling pathway regulates distinct developmental processes in different plants and suggest a role for JA in the promotion of glandular trichome-based defenses. Environ Microbiol, 2004 Jan, 6(1), 73 - 8 Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients; Lueders T et al.; Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids . SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation . We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients . It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers . Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively . However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results . Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses . This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems. Environ Microbiol, 2004 Jan, 6(1), 60 - 72 Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil; Lueders T et al.; Stable isotope probing (SIP) is a novel technique to characterize structure and in situ function of active microbial populations, which is based on the incorporation of 13C-labelled substrates into nucleic acids . Here, we have traced methylotrophic members of a rice field soil microbial community, which became active upon continuous addition of 13C-methanol (< 22 mM) as studied in microcosms . By combining rRNA- and DNA-based SIP, as well as domain-specific real-time PCR detection of templates in fractions of centrifugation gradients, we were able to detect 13C-labelled bacterial rRNA after 6 days of incubation . Fingerprinting and comparative sequence analysis of 'heavy' bacterial rRNA showed that mostly members of the Methylobacteriaceae and a novel clade within the Methylophilaceae formed part of the indigenous methylotrophic community . Over time, however, the Methylophilaceae were enriched . Unexpectedly, nucleic acids of eukaryotic origin were detected, mostly in intermediately 13C-labelled gradient fractions . These eukaryotes were identified as fungi mostly related to Fusarium and Aspergillus spp., and also Cercozoa, known as predatory soil flagellates . The detection of fungi and protozoa in 13C-enriched nucleic acid fractions suggests a possible involvement in either direct assimilation of label by the fungi, or a food web, i.e . that primary 13C-methanol consuming methylotrophs were decomposed by fungi and grazed by protozoa. Immunopharmacol Immunotoxicol, 2003 Nov, 25(4), 595 - 614 Saliva secretory IgA antibodies against molds and mycotoxins in patients exposed to toxigenic fungi; Vojdani A et al.; Upper respiratory exposure to different environmental antigens results first in the activation of mucosal immunity and production of IgA antibodies in different secretions including saliva . Despite this there is no study, which addresses secretory antibodies against molds and mycotoxins . The purpose of this study was to evaluate mold-specific salivary IgA in individuals exposed to molds and mycotoxins in a water-damaged building environment . Saliva IgA antibody levels against seven different molds and two mycotoxins were studied in 40 patients exposed to molds and in 40 control subjects . Mold-exposed patients showed significantly higher levels of salivary IgA antibodies against one or more mold species . A majority of patients with high IgA antibodies against molds exhibited elevation in salivary IgA against mycotoxins, as well . These IgA antibodies against molds and mycotoxins are specific, since using molds and mycotoxins in immune absorption could reduce antibody levels, significantly . Detection of high counts of molds in water-damaged buildings, strongly suggests the existence of a reservoir of mold spores in the environment . This viable microbial activity with specific mold and mycotoxin IgA in saliva may assist in the diagnosis of mold exposure . Whether mold and mycotoxin specific IgA antibodies detected in saliva are indicative of the role of IgA antibodies in the late phase of type-1 hypersensitivity reaction or in type-2 and type-3 delayed sensitivities is a matter that warrants further investigation. Gesundheitswesen, 2003 Dec, 65(12), 724 - 8 {From the second European drinking water guideline to the new drinking water regulations}; Schoenen D; The new drinking water regulations, effective 1.1.2003, introduced several new and hygienically important changes . The term "drinking water" has changed to "water for human consumption" . The change of the term gives a remarkable extension of the scope of the drinking water regulations . One of the consequences is that the water in buildings in which the water is delivered to the public has now to be controlled as well . The planned measures may help to promote good consequences in case of accidents . The need for treatment makes it necessary to control raw water to a higher degree than before . In case of microbial contamination the water has to be treated by filtration . Disinfection may no longer be the only treatment to ensure a safe drinking water supply . The adherence to the technical rules demanded by the new drinking water regulations may convey much additional security to water supply. Nature, 2003 Dec 18, 426(6968), 878 - 81 A conspicuous nickel protein in microbial mats that oxidize methane anaerobically; Kruger M et al.; Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in the global carbon cycle and in control of greenhouse gas emission . The responsible organisms supposedly reverse the reactions of methanogenesis, but cultures providing biochemical proof of this have not been isolated . Here we searched for AOM-associated cell components in microbial mats from anoxic methane seeps in the Black Sea . These mats catalyse AOM rather than carry out methanogenesis . We extracted a prominent nickel compound displaying the same absorption spectrum as the nickel cofactor F430 of methyl-coenzyme M reductase, the terminal enzyme of methanogenesis; however, the nickel compound exhibited a higher molecular mass than F430 . The apparent variant of F(430) was part of an abundant protein that was purified from the mat and that consists of three different subunits . Determined amino-terminal amino acid sequences matched a gene locus cloned from the mat . Sequence analyses revealed similarities to methyl-coenzyme M reductase from methanogenic archaea . The abundance of the nickel protein (7% of extracted proteins) in the mat suggests an important role in AOM. Science, 2004 Jan 23, 303(5657), 523 - 7 Epub 2003 Dec 18. Editing of CD1d-bound lipid antigens by endosomal lipid transfer proteins; Zhou D et al.; It is now established that CD1 molecules present lipid antigens to T cells, although it is not clear how the exchange of lipids between membrane compartments and the CD1 binding groove is assisted . We report that mice deficient in prosaposin, the precursor to a family of endosomal lipid transfer proteins (LTP), exhibit specific defects in CD1d-mediated antigen presentation and lack Valpha14 NKT cells . In vitro, saposins extracted monomeric lipids from membranes and from CD1, thereby promoting the loading as well as the editing of lipids on CD1 . Transient complexes between CD1, lipid, and LTP suggested a "tug-of-war" model in which lipid exchange between CD1 and LTP is on the basis of their respective affinities for lipids . LTPs constitute a previously unknown link between lipid metabolism and immunity and are likely to exert a profound influence on the repertoire of self, tumor, and microbial lipid antigens. Protein Pept Lett, 2003 Dec, 10(6), 619 - 28 Immobilization of lipases and assay in continuous fixed bed reactor; dos Reis-Costa L et al.; Lipases are versatile enzymes regarding the range of reactions they catalyse and substrates on which they act . They are as well important as catalyst in organic synthesis . Their immobilization on appropriate supports confer them greater stability besides the possibility of operating in continuous reactors . In order to explore these abilities, the reactions involving hydrolysis of p-nitrophenyl acetate (PNPA) and transesterification of PNPA with n-butanol were chosen . Lipases from two different sources were assayed, namely: microbial (Candida rugosa, CRL, Sigma Type VII) and pancreatic (PPL, Sigma, Type II) . Two immobilization methods were also used, namely: 1) . adsorption, using as support the following silica derivatives (150-300 microm e 450micro): phenyl, epoxy, amino and without derivation, and 2) . covalent binding, using glutaraldehyde as binding agent and silica amino as support . This later method led to better results . Hydrolytic activity was 6.1 U/g(support) for CRL and 0.97 U/g(support) for PPL, and of transesterification, 2,8 U/g(support) for CRL and 1,9 U/g(support) for PPL . Stability of the immobilized enzyme as a function of temperature was evaluated for CRL at 40 degrees C and 50 degrees C and for PPL at 32 degrees C and 40 degrees C . The assays were initially carried out batchwise, both for soluble and immobilized enzymes, aiming to the obtention of parameters for the continuous reactor . Lipases immobilized by covalent binding were used in the assays of operational stability in continuous reactors . For PPL in aqueous medium, at 32 degrees C, and CRL in organic medium at 40 degrees C, both operating continuously, no significant loss of activity was detected along the analysis period of 17 days . In the case of CRL in aqueous medium at 40 degrees C there was a loss of activity around 40% after 18 days . For PPL in organic medium at 40 degrees C the loss was 33% after 20 days . Comparing both sources with each other, very different results were obtained . Higher activity was found for CRL, both for hydrolysis and for transesterification reactions, with higher stability in organic medium . PPL showed lower activity as well as higher stability in aqueous medium . The immobilization method by covalent binding showed to be the most appropriate . Immobilized lipases are therefore relatively stable both in aqueous and organic medium. Curr Protein Pept Sci, 2003 Dec, 4(6), 409 - 26 Porphyromonas gingivalis gingipains: the molecular teeth of a microbial vampire; O-Brien-Simpson NM et al.; The gingipains are cell surface Arg- and Lys-specific proteinases of the bacterium Porphyromons gingivalis, which has been associated with periodontitis, a disease that results in the destruction of the teeth-s supporting tissues . The proteinases are encoded by three genes designated rgpA, rgpB and kgp . Arg-specific proteolytic activity is encoded by rgpA/B and the Lys-specific activity by kgp . RgpA and Kgp are polyproteins comprising proteinases with C-terminal adhesin domains that are proteolytically processed . After processing, the domains remain non-covalently associated as complexes on the cell surface . RgpB is also a cell surface proteinase but does not associate with adhesin domains . Using gene knockout P . gingivalis mutants, the proteolytic processing of the gingipain domains has been shown to involve the gingipains themselves as well as C-terminal processing by a carboxypeptidase . A motif in the C-terminal domain of each protein/polyprotein has been identified that is suggested to be involved in attachment to LPS on the cell surface . RgpB lacks a C-terminal adhesin binding motif found in the catalytic domains of RgpA and Kgp . This adhesin binding motif is proposed to be responsible for the non-covalent association of the RgpA and Kgp catalytic domains into the cell surface complexes with the processed adhesin domains . The RgpA-Kgp proteinase-adhesin complexes, through the adhesin domains A1 and A3, have been implicated in colonization of P . gingivalis by binding to other bacteria in subgingival plaque and also binding to crevicular epithelial cells . The RgpA-Kgp complexes also bind to fibrinogen, laminin, collagen type V, fibronectin and hemoglobin . Amino acid sequences likely to be involved in binding to these host proteins have been identified in adhesin domains A1 and A3 . It is proposed that these adhesins target the proteolytic activity to host cell surface matrix proteins and receptors . The continual cycle of binding and degradation of the surface proteins/receptors on epithelial, fibroblast and endothelial cells by the RgpA-Kgp complexes in the gingival tissue leading to cell death would contribute to inflammation, tissue destruction and vascular disruption (bleeding) . P . gingivalis has an obligate growth requirement for iron and protoporphyrin IX, which it preferentially utilizes in the form of hemoglobin . Kgp proteolytic activity is essential for rapid hydrolysis of hemoglobin and it is suggested therefore that a major role of the RgpA-Kgp complexes is in vascular disruption and the binding and rapid degradation of hemoglobin for heme assimilation by P . gingivalis . The RgpA-Kgp complexes also have a major role in the evasion and dysregulation of the host-s immune response . It is proposed that host pro-inflammatory cytokines and cellular receptors close to the infection site may be rapidly and efficiently degraded by the gingipains while the proteinases at lower concentrations distally could result in the promotion of an inflammatory response through activation of proteinase-activated receptors and cytokine release . The culmination of this dysregulation would be tissue destruction and bone resorption . In animal models of disease the RgpA-Kgp complex when used as a vaccine to produce a high titre antibody response protects against challenge with P . gingivalis . Using recombinant domains of RgpA and Kgp as vaccines, it has been demonstrated that the A1 and A3 domains confer protection. Curr Mol Med, 2003 Dec, 3(8), 693 - 706 Naturally arising CD25+CD4+ regulatory T cells in maintaining immunologic self-tolerance and preventing autoimmune disease; Takahashi T et al.; A large body of evidence indicates that T cell-mediated dominant suppression of self-reactive T cells is indispensable for maintaining immunologic unresponsiveness to self-constituents (i.e., self-tolerance) and preventing autoimmune disease . CD25+CD4+ regulatory T cells naturally present in normal animals, in particular, engage in this function, as their reduction or functional abnormality leads to the development of autoimmune disease in otherwise normal animals . They are at least in part produced by the normal thymus as a functionally mature and distinct subpopulation of T cells . Recent studies have demonstrated that CD25+CD4+ regulatory T cells control not only autoimmune reactions but also other immune responses, including tumor immunity, transplantation tolerance and microbial infection . Thus, this unique population of regulatory T cells can be exploited to control pathological as well as physiological immune responses. Nucleic Acids Res, 2004 Jan 1, 32 Database issue, D582 - 5 GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes; Babnigg G et al.; GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at and ftp://bioinformatics.anl.gov/gelbank/) . Currently it includes 131 completed, mostly microbial proteomes available from the National Center for Biotechnology Information . A web interface allows the upload of 2D gel patterns and their annotation for registered users . The images are organized by species, tissue type, separation method, sample type and staining method . The database can be queried based on protein or 2DE-pattern attributes . A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern . The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification . A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization . The website currently presents 233 identifications for 81 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans. Nucleic Acids Res, 2004 Jan 1, 32 Database issue, D281 - 3 The ORFanage: an ORFan database; Siew N et al.; As each newly sequenced genome contains a significant number of protein-coding ORFs that are species-, family- or lineage-specific, many interesting questions arise about the evolution and role of these ORFs and of the genomes they are part of . We refer to these poorly conserved ORFs as singleton or paralogous ORFans if they are unique to one genome, or as orthologous ORFans if they appear only in a family of closely related organisms and have no homolog in other genomes . In order to study and classify ORFans we have constructed the ORFanage, an ORFan database . This database consists of the predicted ORFs in fully sequenced microbial genomes, and enables searching for the three types of ORFans in any subset of the genomes chosen by the user . The ORFanage could help in choosing interesting targets for further genomic and evolutionary studies . The ORFanage is accessible via edu/ORFanage. J Toxicol Environ Health A, 2004 Feb 13, 67(3), 209 - 19 Metalworking fluid--the toxicity of a complex mixture; Gordon T; Various chemicals are used in the manufacture of cooling and lubricating fluids and fall into the classes of straight, soluble, semisynthetic, and synthetic metalworking fluids . The diversity of chemicals and in-use contaminants makes the risk assessment of metalworking fluids quite difficult . Toxicologists have used a number of methods to evaluate the component(s) responsible for the adverse pulmonary effects of metal working fluid aerosols encountered in the workplace . Although investigators have studied the adverse effects of metalworking fluid chemicals alone and in combination, the majority of evidence strongly suggests that the microbial changes that occur in fluid composition, during use and storage in the workplace, are responsible for the pulmonary effects reported for workers exposed to metalworking fluid aerosols . This review discusses the methodologies used to examine the toxicity of the complex nature of modern metalworking fluids and the findings that point toward bacterial endotoxin as a major contributor to their adverse effects. Protein Expr Purif, 2004 Jan, 33(1), 110 - 22 Recombinant cold-adapted trypsin I from Atlantic cod-expression, purification, and identification; Jonsdottir G et al.; Atlantic cod trypsin I is a cold-adapted proteolytic enzyme exhibiting approximately 20 times higher catalytic efficiency (kcat/KM) than its mesophilic bovine counterpart for the simple amide substrate BAPNA . In general, cold-adapted proteolytic enzymes are sensitive to autolytic degradation, thermal inactivation as well as molecular aggregation, even at temperatures as low as 18-25 degrees C which may explain the problems observed with their expression, activation, and purification . Prior to the data presented here, there have been no reports in the literature on the expression of psychrophilic or cold-adapted proteolytic enzymes from fish . Nevertheless, numerous cold-adapted proteolytic microbial enzymes have been successfully expressed in bacteria and yeast . This report describes successful expression, activation, and purification of the recombinant cod trypsin I in the His-Patch ThioFusion Escherichia coli expression system . The E . coli pThioHis expression vector used in the study enabled the formation of a fusion protein between a highly soluble fraction of HP-thioredoxin contained in the vector and the N-terminal end of the precursor form of cod trypsin I . The HP-thioredoxin part of the fusion protein binds to a metal-chelating ProBond column, which facilitated its purification . The cod trypsin I part of the purified fusion protein was released by proteolytic cleavage, resulting in concomitant activation of the recombinant enzyme . The recombinant cod trypsin I was purified to homogeneity on a trypsin-specific benzamidine affinity column . The identity of the recombinant enzyme was demonstrated by electrophoresis and chromatography. Ann N Y Acad Sci, 2003 Nov, 1005, 418 - 22 Dietary microbial toxins and type 1 diabetes; Myers MA et al.; Toxins may promote type 1 diabetes by modifying or damaging the beta cell causing release of autoantigens . Streptomyces is a common soil bacterium that produces many toxic compounds . Some Streptomyces can infect vegetables, raising the possibility of dietary exposure to toxins . We aimed to identify toxins that erode cellular proton gradients in extracts of Streptomyces and infested vegetables and to establish the effect of low doses of these toxins on pancreatic islets in mice . The vacuolar ATPase inhibitors, bafilomycin and concanamycin, and the ionophore, nigericin, were identified in extracts from 4 of 13 Streptomyces isolated from infested potatoes and in potatoes themselves . Injection of bafilomycin A1 into mice impaired glucose tolerance, reduced islet size, and decreased relative beta cell mass . Thus, exposure to small quantities of bafilomycin in the diet may contribute to the cause of type 1 diabetes. Astrobiology, 2003 Fall, 3(3), 531 - 41 Possibilities for the detection of microbial life on extrasolar planets; Knacke RF; We consider possibilities for the remote detection of microbial life on extrasolar planets . The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes . Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms . Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum . These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life . However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses . Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit . Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet . Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets . The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life. Astrobiology, 2003 Fall, 3(3), 471 - 86 Biosignatures of early earths; Pilcher CB; A major goal of NASA's Origins Program is to find habitable planets around other stars and determine which might harbor life . Determining whether or not an extrasolar planet harbors life requires an understanding of what spectral features (i.e., biosignatures) might result from life's presence . Consideration of potential biosignatures has tended to focus on spectral features of gases in Earth's modern atmosphere, particularly ozone, the photolytic product of biogenically produced molecular oxygen . But life existed on Earth for about 1(1/2) billion years before the buildup of atmospheric oxygen . Inferred characteristics of Earth's earliest biosphere and studies of modern microbial ecosystems that share some of those characteristics suggest that organosulfur compounds, particularly methanethiol (CH(3)SH, the sulfur analog of methanol), may have been biogenic products on early Earth . Similar production could take place on extrasolar Earth-like planets whose biota share functional chemical characteristics with Earth life . Since methanethiol and related organosulfur compounds (as well as carbon dioxide) absorb at wavelengths near or overlapping the 9.6-microm band of ozone, there is potential ambiguity in interpreting a feature around this wavelength in an extrasolar planet spectrum. J Appl Microbiol, 2004, 96(1), 10 - 7 Serodiagnosis of infectious diseases with antigen microarrays; Bacarese-Hamilton T et al.; AIMS: To generate protein microarrays by printing microbial antigens on slides to enable the simultaneous determination in human sera of antibodies directed against Toxoplasma gondii, rubella virus, cytomegalovirus and herpes simplex virus (HSV) types 1 and 2 . METHODS AND RESULTS: Antigens were printed on activated glass slides using high-speed robotics . The slides were incubated with serum samples and subsequently with fluorescently labelled secondary antibodies . Human IgG and IgM bound to the printed antigens were detected using confocal scanning microscopy and quantified with internal calibration curves . The microarray assay could detect as little as 0.5 pg of both IgG and IgM bound onto the glass surface . Precision profiles ranged from 1.7 to 18.5% for all the antigens . Microarrays and commercial ELISAs were utilized to detect serum antibodies against the ToRCH antigens in a panel of characterized human sera . Overall >80% concordance was obtained between microarray and ELISA kits in the classification of sera . CONCLUSIONS: These results indicate that the microarray is a suitable assay format for the serodiagnosis of infectious diseases . SIGNIFICANCE AND IMPACT OF STUDY: Antigen microarrays can be optimized for clinical use, their performance is equivalent to ELISA but they offer significant advantages in throughput, convenience and cost. Biotechnol Lett, 2003 Nov, 25(21), 1843 - 6 Microbial synthesis of (R)- and (S)-3,4-dimethoxyamphetamines through stereoselective transamination; Iwasaki A et al.; Two soil isolates, Arthrobactersp . KNK168 and Pseudomonas sp . KNK425, aminated 3,4-dimethoxyphenylacetone in presence of sec-butylamine as an amino donor to yield 3,4-dimethoxyamphetamine (DMA) with different enantioselectivities . The former gave (R)-DMA (>99% e.e.) and the latter the (S)-isomer (>99% e.e.). Ned Tijdschr Geneeskd, 2003 Nov 29, 147(48), 2365 - 70 {Nutrition and health--toxic substances in food}; Rietjens IM et al.; With respect to food, the most important factors causing adverse health effects are: an unbalanced diet, resulting in obesity or vitamin deficiencies, overconsumption of alcohol or fat, the presence of microbial contamination and the presence of natural toxins . Two additional factors, the presence of environmental contaminants and products formed on heating food, may also be of importance . It is generally assumed that, when combined, food-related factors contribute to around 35% of overall cancer incidence . The most important groups of health-threatening compounds to be found in the food chain include natural toxins, such as those produced by plants (phytotoxins), fungi (mycotoxins), marine algae (phycotoxins) and by bacteria, and toxins present in animals for human consumption, especially fish . A second important group of toxic compounds in food consists of environmental contaminants, including heavy metals and persistent organic pollutants, such as dioxins and polychlorinated biphenyls, all of which may unintentionally end up in the food chain . A third group of toxins present in food are those substances produced when food is heated, and include polycyclic aromatic hydrocarbons, heterocyclic amines and acrylamide. Biol Sci Space, 2003 Oct, 17(3), 190 - 1 Organics in chimneys and water samples from deep-sea hydrothermal systems: implications for sub-vent biosphere; Horiuchi T et al.; Searching for life in extreme terrestrial environments can be a model of that for extraterrestrial life . Submarine hydrothermal system is one of promising sites for the frontier of life on the earth . Here seawater and vent chimnies were collected from deep-sea hydrothermal vents at Suiyo Seamount, Izu-bonin arc, Pacific Ocean as a part of Archaean Park Project . Pure seawater sample of 300 degrees C (purity>97%) could be collected . Dissolved and total hydrolyzable amino acids were determined by ion-exchange HPLC, and their enantiomeric ratio was measured by reversed-phase HPLC for the first time . Glycine and serine were two most abundant amino acids, followed by other proteinous amino acids such as alanine, glutamic acid and aspartic acid . Non-proteinous amino acids were detected as minor constituents . Most of the amino acids detected were of the L-form . Thus amino acids of abiotic origin were quite minor, and most of the amino acids detected were formed biologically . These results, together with analytical results of the vent chimney samples, suggest that there is active microbial activities near the hydrothermal systems. Water Res, 2004 Jan, 38(2), 255 - 66 Soluble microbial products formation in anaerobic chemostats in the presence of toxic compounds; Aquino SF et al.; Anaerobic chemostats fed on glucose (approximately 10 g chemical oxygen demand (COD)/L) were used to investigate the effects of toxicity on soluble microbial product (SMP) formation . Addition of the toxic compounds chloroform and chromium increased the net accumulation of SMP, despite reducing the percentage of SMP in the effluent due to the overwhelming production of volatile fatty acids (VFAs) . In the reactor spiked with chloroform the normalized accumulation of SMP (SMP/So) increased from 2% to 8%, whereas in the reactor spiked with Cr (VI) the SMP/So ratio reached as high as 20% after the spike, and in both cases SMP net accumulation was proportional to the concentration of toxicant . After the chloroform and chromium spikes biomass seemed to produce more extra cellular polymeric substances (EPS) suggesting that this might have helped them to cope with the stress . Chromatography results indicate that some of the high MW compounds present in the SMP might have been due to EPS release into the bulk solution, and that other compounds, probably released as a result of cell lysis, were also present . Hydrolysis of EPS did not seem to contribute to SMP accumulation in the presence of toxic compounds, and DNA analysis suggested that cell lysis products was an important contribution to SMP accumulation, in the presence of chromium. J Environ Qual, 2003 Nov-Dec, 32(6), 2067 - 75 Temperature and microbial activity effects on trace element leaching from metalliferous peats; Qureshi S et al.; Due to geochemical processes, peat soils often have elevated concentrations of trace elements, which are gradually released following drainage for agriculture . Our objectives were to use incubation temperatures to vary microbial activity in two metalliferous peats (M7 acidic peat and M3 neutral peat) from the Elba, New York region, and to use periodic leaching to assess the extent of trace element release from these soils . Dried soils were mixed with glass beads to maintain aeration, moistened, and incubated at 4, 16, 28, and 37 degrees C in 10-cm-diameter x 8-cm-tall columns . Five incubation-leaching cycles were performed, each consisting of 7.3 d of incubation (28 d for the final cycle) followed by 16 h of leaching with synthetic acid rain at 2.5 mm h(-1) . Microbial activity was determined initially and after the final leaching by measuring C mineralization following glucose stimulation . Cumulative respiration results were ranked 28 > 16 > 4 > 37 degrees C, with M7 acidic peat respiration values greater than M3 neutral peat at each temperature . Initial leachate pH levels were between 2 and 4, with acidification less pronounced and shorter-lived for the M3 peat . Leachate S, dissolved organic carbon (DOC), NO3-N, and trace elements declined with successive leachings (rebounding slightly in the final M3 leachate), with concentrations typically greater in the M7 leachate . Elemental losses followed the same general ranking (28 > 16 > 4 > 37 degrees C); losses at 28 degrees C were 15 to 22% for As, Cd, Ni, and Zn from the M7 peat; losses from M3 were comparable only for Cu (1%) and Ni (19%) . The correlation of respiration with S, DOC, and trace elements losses indicates that microbial processes mediated the release of trace elements in both peat soils . Neutral M3 peat pH levels limited losses of most analytes. J Environ Qual, 2003 Nov-Dec, 32(6), 2017 - 25 Effect of soil properties on saturated and unsaturated virus transport through columns; Chu Y et al.; Viruses from contaminant sources can be transported through porous media to drinking water wells . The objective of this study was to investigate inactivation and sorption of viruses during saturated and unsaturated transport in different soils . Bacteriophages phiX174 and MS-2, and Br- tracer in a phosphate-buffered saline solution were introduced into saturated and unsaturated soil columns as a step function under constant flow rate and hydraulic conditions . Results showed that significantly greater virus removal occurred in the unsaturated columns than in the saturated columns in the two soils containing high metal oxides content . However, the increase in virus retention under unsaturated conditions was not significant in two other soils having high phosphorus and calcium contents and high pH, and in another soil with high organic matter content . The results imply that the extent of water content effect on inactivation and sorption of viruses can range from significant to minimal depending on the properties of the transport medium . We found that the presence of in situ metal oxides was a significant factor responsible for virus sorption and inactivation . Therefore, soils with high metal oxides content may have the potential to be used as hydrological barriers in preventing microbial contamination in the subsurface environments . We also found that the water content effect on virus removal and inactivation strongly depended on solid properties of the testing medium. J Environ Qual, 2003 Nov-Dec, 32(6), 1992 - 2000 The effect of five forage species on transport and transformation of atrazine and isoxaflutole (balance) in lysimeter leachate; Lin CH et al.; A field lysimeter study with bare ground and five different ground covers was established to evaluate the effect of forage grasses on the fate and transport of two herbicides in leachate . The herbicides were atrazine (ATR; 2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) and isoxaflutole {IXF; 5-cyclopropyl-4-(2-methylsulfonyl-4-trifluormethyl-benzoyl)isoxazole}, which has the commercial name Balance (Aventis Crop Science, Strasbourg, France) . The ground covers included orchardgrass (Dactylis glomerata L.), smooth bromegrass (Bromus inermis Leyss.), tall fescue (Festuca arundinacea Schreb.), timothy (Phleum pratense L.), and switchgrass (Panicum virgatum L.) . The results suggested that the total IXF (parent + metabolites) showed higher mobility than ATR and its metabolites . Differences in the timing of transport reflected the rapid degradation of IXF to the more soluble, stable, and biologically active diketonitrile (DKN) metabolite in the system . Although grass treatments did not promote the hydrolysis of DKN, they significantly reduced its transport in the leachate through enhanced evapotranspiration . Grass treatments significantly enhanced ATR degradation in the leachates and soils, especially through N dealkylation, but they did not reduce total ATR transported in the leachate . Leachate from the orchardgrass lysimeters contained the highest proportion of ATR metabolites (64.2%) . Timothy and smooth bromegrass treatments also displayed a significant increase in ATR metabolites in leachate . Grass-treated lysimeters showed higher microbial biomass carbon than bare ground . For ATR treatments, the proportion of metabolites in the leachate strongly correlated with the elevated soil microbial biomass carbon in forage treatments . In contrast, DKN degradation was poorly correlated with soil microbial biomass carbon, suggesting that DKN degradation is an abiotic process. J Environ Qual, 2003 Nov-Dec, 32(6), 1965 - 77 Spatial variability of nitrous oxide emissions and their soil-related determining factors in an agricultural field; Yanai J et al.; To evaluate spatial variability of nitrous oxide (N2O) emissions and to elucidate their determining factors on a field-scale basis, N2O fluxes and various soil properties were evaluated in a 100- x 100-m onion (Allium cepa L.) field . Nitrous oxide fluxes were determined by a closed chamber method from the one-hundred 10- x 10-m plots . Physical (e.g., bulk density and water content), chemical (e.g., total N and pH), and biological (e.g., microbial biomass C and N) properties were determined from surface soil samples (0-0.1 m) of each plot . Geostatistical analysis was performed to examine spatial variability of both N2O fluxes and soil properties . Multivariate analysis was also conducted to elucidate relationships between soil properties and observed fluxes . Nitrous oxide fluxes were highly variable (average 331 microg N m(-2) h(-1), CV 217%) and were log-normally distributed . Log-transformed N2O fluxes had moderate spatial dependence with a range of >75 m . High N2O fluxes were observed at sites with relatively low elevation . Multivariate analysis indicated that an organic matter factor and a pH factor of the principal component analysis were the main soil-related determining factors of log-transformed N2O fluxes . By combining multivariate analysis with geostatistics, a map of predicted N2O fluxes closely matched the spatial pattern of measured fluxes . The regression equation based on the soil properties explained 56% of the spatially structured variation of the log-transformed N2O fluxes . Site-specific management to regulate organic matter content and water status of a soil could be a promising means of reducing N2O emissions from agricultural fields. J Biol Chem, 2004 Feb 27, 279(9), 7792 - 8 Epub 2003 Dec 13. Vif overcomes the innate antiviral activity of APOBEC3G by promoting its degradation in the ubiquitin-proteasome pathway; Mehle A et al.; Viruses must overcome diverse intracellular defense mechanisms to establish infection . The Vif (virion infectivity factor) protein of human immunodeficiency virus 1 (HIV-1) acts by overcoming the antiviral activity of APOBEC3G (CEM15), a cytidine deaminase that induces G to A hypermutation in newly synthesized viral DNA . In the absence of Vif, APOBEC3G incorporation into virions renders HIV-1 non-infectious . We report here that Vif counteracts the antiviral activity of APOBEC3G by targeting it for destruction by the ubiquitin-proteasome pathway . Vif forms a complex with APOBEC3G and enhances APOBEC3G ubiquitination, resulting in reduced steady-state APOBEC3G levels and a decrease in protein half-life . Furthermore, Vif-dependent degradation of APOBEC3G is blocked by proteasome inhibitors or ubiquitin mutant K48R . A mutation of highly conserved cysteines or the deletion of a conserved SLQ(Y/F)LA motif in Vif results in mutants that fail to induce APOBEC3G degradation and produce non-infectious HIV-1; however, mutations of conserved phosphorylation sites in Vif that impair viral replication do not affect APOBEC3G degradation, suggesting that Vif is important for other functions in addition to inducing proteasomal degradation of APOBEC3G . Vif is monoubiquitinated in the absence of APOBEC3G but is polyubiquitinated and rapidly degraded when APOBEC3G is coexpressed, suggesting that coexpression accelerates the degradation of both proteins . These results suggest that Vif functions by targeting APOBEC3G for degradation via the ubiquitin-proteasome pathway and implicate the proteasome as a site of dynamic interplay between microbial and cellular defenses. J Environ Sci Health A Tox Hazard Subst Environ Eng, 2003, 38(12), 2749 - 58 Bacterial adsorption and transport in saturated soil columns; Banks MK et al.; Microbial activities directly affect the environmental quality of water, soil, and sediments . To improve our understanding of microbial attachment and transport in the subsurface, experimental studies were performed to evaluate bacterial adsorption and transport in two types of soil, Smolan (27% clay) and Haynie (5.5% clay) soils . Results indicate that bacterial breakthrough was slightly faster in columns with lower clay content and that the most rapid rate of bacterial adsorption occurred during the first 60 min of exposure. J Biol Chem, 2004 Mar 19, 279(12), 11777 - 88 Epub 2003 Dec 11. Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases; Pell G et al.; Microbial degradation of the plant cell wall is the primary mechanism by which carbon is utilized in the biosphere . The hydrolysis of xylan, by endo-beta-1,4-xylanases (xylanases), is one of the key reactions in this process . Although amino acid sequence variations are evident in the substrate binding cleft of "family GH10" xylanases (see afmb.cnrs-mrs.fr/CAZY/), their biochemical significance is unclear . The Cellvibrio japonicus GH10 xylanase CjXyn10C is a bi-modular enzyme comprising a GH10 catalytic module and a family 15 carbohydrate-binding module . The three-dimensional structure at 1.85 A, presented here, shows that the sequence joining the two modules is disordered, confirming that linker sequences in modular glycoside hydrolases are highly flexible . CjXyn10C hydrolyzes xylan at a rate similar to other previously described GH10 enzymes but displays very low activity against xylooligosaccharides . The poor activity on short substrates reflects weak binding at the -2 subsite of the enzyme . Comparison of CjXyn10C with other family GH10 enzymes reveals "polymorphisms" in the substrate binding cleft including a glutamate/glycine substitution at the -2 subsite and a tyrosine insertion in the -2/-3 glycone region of the substrate binding cleft, both of which contribute to the unusual properties of the enzyme . The CjXyn10C-substrate complex shows that Tyr-340 stacks against the xylose residue located at the -3 subsite, and the properties of Y340A support the view that this tyrosine plays a pivotal role in substrate binding at this location . The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed. Microbes Infect, 2003 Dec, 5(15), 1389 - 95 Fluctuations in haemocyte density and microbial load may be used as indicators of fungal pathogenicity in larvae of Galleria mellonella; Bergin D et al.; A positive correlation exists between the pathogenicity of bacteria and fungi when evaluated in the insect Galleria mellonella and mice . This work sought to determine whether fluctuations in the number of haemocytes and the proliferation of yeast cells in infected larvae could be used to determine the relative pathogenicity of a range of yeast isolates . Larvae were inoculated with 1 x 10(6) stationary-phase yeast cells and incubated in the dark at 30 degrees C for 48 h . The results indicated that larvae inoculated with the most pathogenic isolates (i.e . those capable of killing >80% of infected larvae) showed a significant reduction in haemocyte density . Larvae inoculated with isolates of low pathogenicity (i.e . capable of killing <20% of infected larvae) demonstrated only a small fluctuation in haemocyte numbers . The most pathogenic yeast isolates proliferated in the larvae, whereas the isolates of low pathogenicity did not . These results demonstrate a relationship between the ability of yeast isolates to kill larvae and changes in haemocyte density and yeast cell density in infected larvae . These end points may extend the applicability of the G . mellonella system for use with a wider range of microbial isolates. Crit Rev Food Sci Nutr, 2003, 43(6), 635 - 44 Lipase mediated upgradation of dietary fats and oils; Gupta R et al.; In the present scenario, fats and oil modification is one of the prime areas in food processing industry that demands novel economic and green technologies . In this respect, tailored vegetable oils with nutritionally important structured triacylglycerols and altered physicochemical properties have a big potential in the future market . In this context, it is well established that lipases especially microbial lipases, which are regiospecific and fatty acid specific, are of immense importance and hence could be exploited for retailoring of vegetable oils . Further, of the bulk available, cheap oils could also be upgraded to synthesize nutritionally important structured triacylglycerols like cocoa butter substitutes, low calorie triacylglycerols, PUFA-enriched and oleic acid enriched oils . It is also possible to change the physical properties of natural oils to convert them into margarines and hard butter with higher melting points or into special low calorie spreads with short or medium chain fatty acids . Today, by and large, fat and oil modifications are carried out chemically following the method of directed inter-esterification . The process is energy intensive and non-specific . Lipase mediated modifications are likely to occupy a prominent place in oil industry for tailoring structured lipids since enzymatic modifications are specific and can be carried out at moderate reaction conditions . However, as a commercial venture, lipases are yet to be fully exploited . Once the technologies are established, the demand of lipases in oil industry is expected to increase tremendously in the near future for specific modifications of fats and oils to meet the changing consumers' dietary requirements. Environ Technol, 2003 Oct, 24(10), 1221 - 34 Composting under controlled conditions; Cronje A et al.; Three cylindrical reactors, each with a working capacity of approximately 200 litres, were used to investigate composting . The process was optimised and conditions were controlled so that composting on a laboratory-scale thermally resembled that occurring in the core of large open heaps . A baseline flow of humidified air aerated the reactors in five-minute bursts . The reactors operated as closed systems with facilities to analyse the composition of the off-gas for ammonia, oxygen and carbon dioxide . Temperature was used to monitor the progress of the process . Heat loss from the reactor surface was compensated for with an external heat source . A basic model of radial conductive heat losses showed that 53 watts per square-metre would be the maximum heat flux needed to keep the temperature difference across the reactor to within a degree when running at 60 degrees C . A heating cable was used, which could supply 150 watts per square-metre, and the radial temperature difference was reduced to within a degree in more than 60% of the recorded temperatures in the case studies presented . The temperature of the composting material was held at 60 degrees C using a high flow rate 'cooling' aeration with temperature feedback . This, however, led to a mean vertical temperature difference of at least 10 degrees C . The aeration strategy resulted in a well-aerated material, which favoured aerobic microbial activity and the temperature increased as a result of the internally generated heat associated with composting . Three-quarters of the ammonia was emitted in the first week. Environ Manage . 2003 Dec 15; {Epub ahead of print} Combining Soil C and N Spatial Variability and Modeling Approaches for Measuring and Monitoring Soil Carbon Sequestration; Cerri CE et al.; The main objective of the study was to investigate soil carbon and nitrogen stocks in five soil types within a 63-ha Amazon degraded pasture area using the Century model and to combine this information with soil C and N spatial variability at Nova Vida ranch in the western Brazilian Amazon . Samples for soil chemical, physical, and biological analyses were collected at eight different georreferenced points in each of five studied soil types . Century was used to simulate soil C and N contents in the 0- to 20-cm layer in each soil type within a 63-ha degraded pasture area . Century accurately simulated the level of total soil C and N for the five soil types, but it was not successful in predicting seasonal variations in microbial biomass C . The influence of soil texture and hydrological process affecting the ability of soils to accumulate soil organic matter were discussed . Scenarios for soil C and N stocks with varying pasture management were examined through a period of 40 years after deforestation . In conclusion, modeling and geostatistical techniques can be used for measuring and monitoring soil C and N stocks . Modeling provides a flexible and powerful way to assess how different scenarios for pasture management and land use change can affect soil C and N dynamics, but it is important to highlight that even the best models (as Century is) need to be used with caution for Kyoto Protocol projects at plot scale and that benchmark sites are needed to augment model predictions. Environ Manage . 2003 Dec 15; {Epub ahead of print} Landscape Modeling of In Situ Soil Respiration in a Forested Watershed of Southeastern Kentucky, USA; Abnee AC et al.; Data on carbon fluxes such as soil respiration are needed to develop strategies for increased carbon sequestration and reduced levels of atmospheric trace gases . Soil respiration is driven by proximal factors (e.g., soil temperature and soil moisture), which affect soil respiration by regulating microbial and root activity, and distal factors (e.g., topography), which affect soil respiration by influencing proximal factors . The objectives of this study were: (1) to relate measured carbon dioxide flux from forest soils to proximal and distal factors; and (2) to develop predictive soil-landscape models of soil respiration across a forested watershed . Carbon dioxide flux from the soil surface was measured monthly for 12 months at sampling points selected using a random stratified approach, with strata established based on slope aspect (NE and SW), slope shape (concave and convex), and slope position (upper, middle, and lower backslope) . We generated empirical models using robust linear regression techniques to examine relationships between soil respiration and both proximal (soil physical and chemical properties) and distal factors (terrain attributes calculated from a 30-m digital elevation model) . In situ soil respiration rates were greater on the NE-facing slopes than the SW-facing slopes . The models that we developed and validated explain up to 66% of variability in measured soil respiration, although seasonal model relationships varied . Soil temperature was the most consistent proximal factor for predicting soil respiration rates, while slope aspect was the most consistent distal factor among the models. Oecologia, 2004 Feb, 138(3), 419 - 25 Epub 2003 Dec 10. Species-specific measurements of ectomycorrhizal turnover under N-fertilization: combining isotopic and genetic approaches; Treseder KK et al.; Ectomycorrhizal fungi play a significant role in the transfer of nutrients between plant and soil pools . Here we combine natural abundance (14)C measurements with restriction fragment length polymorphism (RFLP) to study the effects of nitrogen fertilization on the residence time of carbon within ectomycorrhizal species . We show that the carbon in ectomycorrhizal fungi turns over every 4-5 years, indicating that these fungi are relatively long-lived . Moreover, ectomycorrhizal fungi responded in a species-specific way to fertilization . Cenococcum geophilum contained younger carbon on average in nitrogen-fertilized plots than in control plots, even though turnover rates of the community as a whole did not shift significantly . Our results suggest that the response of ectomycorrhizal fungi to N availability is complex, and alterations in tissue turnover within this microbial pool may vary depending on community structure. Chemosphere, 2004 Feb, 54(8), 1025 - 38 Microbial transformation products of benzoxazolinone and benzoxazinone allelochemicals--a review; Fomsgaard IS et al.; Cyclic hydroxamic acids and lactams are allelochemicals present in the common agricultural crops wheat, rye, and maize . The hydroxamic acids are mainly present in the plants as glucosides . Upon injury or insect attack or when exuded to the soil environment, the hydroxamic acids occur in their unstable agluconic form . In the first step in the transformation of hydroxamic acids, benzoxazolinones are formed spontaneously . It is necessary to elucidate the further microbial transformation of these compounds in the soil environment for a purposeful exploitation of the allelopathic properties of wheat, rye, and maize . In the present paper, the existing knowledge on microbial transformation products of benzoxazolin-2-one (BOA), 6-methoxy-benzoxazolin-2-one (MBOA), and 2-hydroxy-1,4-benzoxazin-3-one (HBOA) was reviewed . Three main groups of transformation products were identified: aminophenoxazinones, malonamic acids, and acetamides . Future research needs concerning the transformation of these chemicals in soil are discussed, when their properties for suppressing weeds and soil-borne diseases are going to be exploited. Mol Gen Mikrobiol Virusol, 2003, (4), 11 - 5 {The pro-dependent folding of microbial proteolytic enzymes}; Demidiuk IV et al.; Modern published data on the folding of microbial proteolytic enzymes mediated through their pro-parts, or on a so-called pro-dependent folding, are surveyed . Various aspects related with the functioning of pro-sequences are under discussion . The possibility to build up, on the basis of one and the same amino-acid sequence, the special protein conformers involving different pro-peptides is in the focus of attention. J Immunol, 2003 Dec 15, 171(12), 6680 - 9 Soluble forms of Toll-like receptor (TLR)2 capable of modulating TLR2 signaling are present in human plasma and breast milk; LeBouder E et al.; Dysregulation of the initial, innate immune response to bacterial infection may lead to septic shock and death . Toll-like receptors (TLRs) play a crucial role in this innate immune response, and yet the regulatory mechanisms controlling microbial-induced TLR triggering are still to be fully understood . We have therefore sought specific regulatory mechanisms that may modulate TLR signaling . In this study, we tested for the possible existence of a functionally active soluble form of TLR2 . We demonstrated the existence of natural soluble forms of TLR2 (sTLR2), which we show to be capable of modulating cell activation . We found that blood monocytes released sTLR2 constitutively and that the kinetics of sTLR2 release increased upon cell activation . Analysis of cells expressing the human TLR2 cDNA or its c-myc-tagged version indicated that sTLR2 resulted from the posttranslational modification of the TLR2 protein in an intracellular compartment . Moreover, an intracellular pool of sTLR2 is maintained . sTLR2 was found naturally expressed in breast milk and plasma . Milk sTLR2 levels mirrored those of the TLR coreceptor soluble CD14 . Depletion of sTLR2 from serum resulted in an increased cellular response to bacterial lipopeptide . Notably, serum sTLR2 was lower in tuberculosis patients . Coimmunoprecipitation experiments and computational molecular docking studies showed an interaction between sTLR2 and soluble CD14 in plasma and milk . These findings suggest the existence of a novel and specific innate immune mechanism regulating microbial-induced TLR triggering, and may lead to new therapeutics for the prevention and/or treatment of severe infectious diseases. Curr Opin Biotechnol, 2003 Dec, 14(6), 597 - 602 Engineering of secondary metabolite pathways; Mijts BN et al.; Nature produces an astonishing wealth of secondary metabolites with important biological functions . To access this diversity of structurally complex chemical compounds for industrial and biomedical applications, cells have been engineered to produce higher levels and/or novel compounds that were previously inaccessible . Recent examples of metabolic and combinatorial engineering illustrate different strategies for the production of secondary metabolites in microbial cells. Appl Microbiol Biotechnol, 2004 Feb, 63(6), 647 - 52 Epub 2003 Dec 06. Functional classification of the microbial feruloyl esterases; Crepin VF et al.; Feruloyl esterases have potential uses over a broad range of applications in the agri-food industries . In recent years, the number of microbial feruloyl esterase activities reported has increased and, in parallel, even more related protein sequences may be discerned in the growing genome databases . Based on substrate utilisation data and supported by primary sequence identity, four sub-classes have been characterised and termed type-A, B, C and D . The proposed sub-classification scheme is discussed in terms of the evolutionary relationships existing between carbohydrate esterases. J Biol Chem, 2004 Feb 27, 279(9), 7856 - 66 Epub 2003 Dec 03. Lysine residues direct the chlorination of tyrosines in YXXK motifs of apolipoprotein A-I when hypochlorous acid oxidizes high density lipoprotein; Bergt C et al.; Oxidized lipoproteins may play an important role in the pathogenesis of atherosclerosis . Elevated levels of 3-chlorotyrosine, a specific end product of the reaction between hypochlorous acid (HOCl) and tyrosine residues of proteins, have been detected in atherosclerotic tissue . Thus, HOCl generated by the phagocyte enzyme myeloperoxidase represents one pathway for protein oxidation in humans . One important target of the myeloperoxidase pathway may be high density lipoprotein (HDL), which mobilizes cholesterol from artery wall cells . To determine whether activated phagocytes preferentially chlorinate specific sites in HDL, we used tandem mass spectrometry (MS/MS) to analyze apolipoprotein A-I that had been oxidized by HOCl . The major site of chlorination was a single tyrosine residue located in one of the protein's YXXK motifs (where X represents a nonreactive amino acid) . To investigate the mechanism of chlorination, we exposed synthetic peptides to HOCl . The peptides encompassed the amino acid sequences YKXXY, YXXKY, or YXXXY . MS/MS analysis demonstrated that chlorination of tyrosine in the peptides that contained lysine was regioselective and occurred in high yield if the substrate was KXXY or YXXK . NMR and MS analyses revealed that the N(epsilon) amino group of lysine was initially chlorinated, which suggests that chloramine formation is the first step in tyrosine chlorination . Molecular modeling of the YXXK motif in apolipoprotein A-I demonstrated that these tyrosine and lysine residues are adjacent on the same face of an amphipathic alpha-helix . Our observations suggest that HOCl selectively targets tyrosine residues that are suitably juxtaposed to primary amino groups in proteins . This mechanism might enable phagocytes to efficiently damage proteins when they destroy microbial proteins during infection or damage host tissue during inflammation. Appl Environ Microbiol, 2003 Dec, 69(12), 7395 - 400 Application of a specific and sensitive radiometric assay for microbial lipase activities in marine water samples from the lagoon of nouméa; Bourguet N et al.; Marine microbiologists commonly assay lipase activities by using a synthetic fluorescent analog, 4-methylumbelliferyl (MUF)-oleate . The technique is convenient, but it is considered to be unspecific because of the structure of this analog . This study reports the design of a new specific and sensitive lipase assay based on the use of a radiolabeled triglyceride, {3H}triolein . Free fatty acids (FFA) resulting from its hydrolysis are isolated as a function of time in a one-step liquid-liquid extraction and then radioassayed . MUF-oleate and {3H}triolein techniques were compared by measuring lipase activities at similar substrate concentrations along a trophic gradient in the Southwest Lagoon of New Caledonia, near Noumea . Hydrolysis rates decreased from the nearshore station to the offshore station and showed similar trends regardless of the technique used . Rates decreased from 5.83 to 0.88 nmol of FFA . liter-1 . h-1 and from 0.76 to 0.23 nmol of 3H-FFA . liter-1 . h-1, respectively . These results appeared to be consistent with bacterial production results, which also decreased similarly (from 0.59 to 0.26 micrograms of C . liter-1 . h-1) . However, the ratio of MUF-oleate activities to {3H}triolein activities, which was constant at the offshore stations (3.8 +/- 0.1), gradually increased at the nearshore stations (from 4.1 to 7.6) . This result shows that the two assays respond in different ways to changes in environmental conditions and validates the need to set up more specific enzymatic assays. Appl Environ Microbiol, 2003 Dec, 69(12), 7310 - 8 Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus); Dunfield KE et al.; The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria . Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities . We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season . The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant . Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot . Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season . Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season . Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season. Appl Environ Microbiol, 2003 Dec, 69(12), 6961 - 8 Physiological and community responses of established grassland bacterial populations to water stress; Griffiths RI et al.; The effects of water stress upon the diversity and culturable activity of bacterial communities in the rhizosphere of an established upland grassland soil have been investigated . Intact monoliths were subjected to different watering regimens over a 2-month period to study community adaptation to moisture limitation and subsequent response to stress alleviation following rewetting . Genetic diversity was analyzed with 16S-based denaturing gradient gel electrophoresis (DGGE) of total soil-extracted DNA (rRNA genes) and RNA (rRNA transcripts) in an attempt to discriminate between total and active communities . Physiological response was monitored by plate counts, total counts, and BIOLOG-GN2 substrate utilization analyses . Controlled soil drying decreased the total number of CFU on all the media tested and also decreased the substrate utilization response . Following rewetting of dried soil, culture-based analyses indicated physiological recovery of the microbial population by the end of the experiment . In contrast, DGGE analyses of community 16S rRNA genes, rRNA transcripts and cultured communities did not reveal any changes relating to the moisture regimens, despite the observed physiological effects . We conclude that the imposed moisture regimen modulated the physiological status of the bacterial community and that bacterial communities in this soil are resistant to water stress . Further, we highlight the need for a reexamination of rRNA transcript-based molecular profiling techniques as a means of describing the active component of soil bacterial communities. Protist, 2003 Oct, 154(3-4), 411 - 8 Cryptic freshwater ciliates in a hypersaline lagoon; Esteban GF et al.; Ubiquitous dispersal of free-living microbial species implies that each and every ecosystem supports a 'seedbank' of microbial species that are imported by random dispersal . However, many of the microbial species present in any particular ecosystem will probably never thrive there because the local environment is unsuitable for their population growth . To test this, we investigated the ciliated protozoa in a hypersaline lagoon in Almeria, Spain, using selective enrichment to reveal typical freshwater species, as the 'signature' of random dispersal . Twenty-four ciliate species, 14 of them not previously recorded from hypersaline waters, were identified in the undiluted waters of the lagoon . But when the salinity was gradually diluted, further species typical of fresh- and brackish waters emerged, indicating that they had persisted in a viable state at the previously high salinity . These additional species increased the recorded ciliate species total for the lagoon to 36 . The species found in the lagoon appeared to be adapted to either high, or variable, or low salinity, implying that they may have originated in a variety of habitats that differed greatly with respect to salinity regime. J Leukoc Biol, 2004 Mar, 75(3), 460 - 6 Epub 2003 Dec 04. The induction of Toll-like receptor tolerance enhances rather than suppresses HIV-1 gene expression in transgenic mice; Bafica A et al.; Microbial-induced proinflammatory pathways are thought to play a key role in the activation of human immunodeficiency virus type 1 (HIV-1) gene expression . The induction of Toll-like receptor (TLR) tolerance leads to a complex reprogramming in the pattern of inflammatory gene expression and down-modulates tumor necrosis factor alpha (TNF-alpha), interleukin (IL)-1, and IL-6 production . Using transgenic (Tg) mice that incorporate the entire HIV-1 genome, including the long-terminal repeat, we have previously demonstrated that a number of different TLR ligands induce HIV-1 gene expression in cultured splenocytes as well as purified antigen-presenting cell populations . Here, we have used this model to determine the effect of TLR-mediated tolerance as an approach to inhibiting microbial-induced viral gene expression in vivo . Unexpectedly, Tg splenocytes and macrophages, rendered tolerant in vitro to TLR2, TLR4, and TLR9 ligands as assessed by proinflammatory cytokine secretion and nuclear factor-kappaB activation, showed enhanced HIV-1 p24 production . A similar enhancement was observed in splenocytes tolerized and then challenged with heterologous TLR ligands . Moreover, TLR2- and TLR4-homotolerized mice demonstrated significantly increased plasma p24 production in vivo despite lower levels of TNF-alpha . Together, these results demonstrate that HIV-1 expression is enhanced in TLR-reprogrammed host cells, possibly reflecting a mechanism used by the virus to escape the effects of microbial-induced tolerance during natural infection in vivo. Crit Rev Oral Biol Med, 2003, 14(6), 399 - 412 Oral microbial heat-shock proteins and their potential contributions to infections; Goulhen F et al.; The oral cavity is a complex ecosystem in which several hundred microbial species normally cohabit harmoniously . However, under certain special conditions, the growth of some micro-organisms with a pathogenic potential is promoted, leading to infections such as dental caries, periodontal disease, and stomatitis . The physiology and pathogenic properties of micro-organisms are influenced by modifications in environmental conditions that lead to the synthesis of specific proteins known as the heat-shock proteins (HSPs) . HSPs are families of highly conserved proteins whose main role is to allow micro-organisms to survive under stress conditions . HSPs act as molecular chaperones in the assembly and folding of proteins, and as proteases when damaged or toxic proteins have to be degraded . Several pathological functions have been associated with these proteins . Many HSPs of oral micro-organisms, particularly periodontopathogens, have been identified, and some of their properties-including location, cytotoxicity, and amino acid sequence homology with other HSPs-have been reported . Since these proteins are immunodominant antigens in many human pathogens, studies have recently focused on the potential contributions of HSPs to oral diseases . The cytotoxicity of some bacterial HSPs may contribute to tissue destruction, whereas the presence of common epitopes in host proteins and microbial HSPs may lead to autoimmune responses . Here, we review the current knowledge regarding HSPs produced by oral micro-organisms and discuss their possible contributions to the pathogenesis of oral infections. Anal Biochem, 2003 Dec 15, 323(2), 188 - 96 Quantification of uridine 5'-diphosphate (UDP)-glucose by high-performance liquid chromatography and its application to a nonradioactive assay for nucleoside diphosphate kinase using UDP-glucose pyrophosphorylase as a coupling enzyme; Dorion S et al.; We describe a method for the detection and quantification of nucleoside diphosphate kinase (NDPK) . NDPK catalyzes the transfer of the gamma-phosphate of cytidine 5'-triphosphate on uridine 5'-diphosphate (UDP) to produce uridine 5'-triphosphate (UTP) . The method uses a nonradioactive coupled enzyme assay in which UTP produced by NDPK is utilized by UDP-glucose pyrophosphorylase . This latter enzyme synthesizes UDP-glucose and inorganic phosphate in the presence of glucose 1-phosphate . UDP-glucose is detected at 260 nm after separation of the reaction mixture by high-performance liquid chromatography (HPLC) on a strong anion-exchange column . The assay is reliable, specific, and linear with respect to time and enzyme amount . Using 15 min incubation time, the method allows detection of NDPK activity below 10 pmol/min . It can be used to analyze kinetic behavior and to quantify NDPK from a wide variety of animal, microbial, and plant sources . It also provides an alternative to radiometric assays and an improvement on pyruvate kinase-linked spectrophotometric assays, which can be hampered by pigments present in crude extracts . Furthermore, we show that the HPLC method developed here can be directly used to assay enzymes for which UDP-glucose is a product. Structure (Camb), 2003 Dec, 11(12), 1527 - 35 Crystal structure of the human myeloid cell activating receptor TREM-1; Radaev S et al.; Triggering receptors expressed on myeloid cells (TREM) are a family of recently discovered receptors that play important roles in innate immune responses, such as to activate inflammatory responses and to contribute to septic shock in response to microbial-mediated infections . To date, two TREM receptors in human and several homologs in mice have been identified . We report the 2.6 A resolution crystal structure of the extracellular domain of human TREM-1 . The overall fold of the receptor resembles that of a V-type immunoglobulin domain with differences primarily located in the N-terminal strand . TREM-1 forms a "head-to-tail" dimer with 4100 A(2) interface area that is partially mediated by a domain swapping between the first strands . This mode of dimer formation is different from the "head-to-head" dimerization that existed in V(H)V(L) domains of antibodies or V domains of T cell receptors . As a result, the dimeric TREM-1 most likely contains two distinct ligand binding sites. Biotechnol Prog, 2003 Nov-Dec, 19(6), 1713 - 20 Purification and concentration of alkaline phosphatase by selective permeabilization of Escherichia coli using reverse micellar solutions; Bansal-Mutalik R et al.; Recovery of alkaline phosphatase (AP) from the periplasm of Escherichia coli using reverse micellar solutions (RMSs) of sodium dioctyl sulfosuccinate (AOT) in aliphatic hydrocarbons has been attempted . A variety of surface-active agents, solvents, and reverse micellar conditions were screened, and an excellent recovery of the enzyme in a concentrated form, with a high purification factor, was obtained in a single-step process . The permeabilization process strongly depended on the water content of the RMS as well as on the amount of water coating the microbial cell surface . The product was almost free from nucleic acids . In addition, because of the low affinity of AOT and the organic solvent for the aqueous phase, contamination by the permeabilizing agents would also be negligible. Biotechnol Prog, 2003 Nov-Dec, 19(6), 1664 - 71 Lipase-catalyzed cellulose acetylation in aqueous and organic media; Yang K et al.; Screening for lipases capable of catalyzing acetylation of cellulosic substrates was conducted in aqueous buffer solution using water-soluble carboxymethyl cellulose (CMC) as substrate . Lipase A12 from Aspergillus niger (A . niger) showed the most promising acetylation activity among 11 tested commercial microbial lipases and was further applied to catalyzing acetylation of solid cellulose in aqueous solution . This reaction was shown to be feasible with an acetylation extent of 0.16 wt % achieved compared with no detectable acetylation in the absence of enzyme . Pretreatments on cellulose substrate by ultrasonic irradiation and surfactant solution only slightly improved the acetylation extent by 44 and 27%, respectively . Alternatively, this lipase-catalyzed acetylation was remarkably improved with solubilized cellulose as substrate in the dimethyl sulfoxide/paraformaldehyde solvent system, with an acetylation extent (7.87 wt %) nearly 50 times higher than that achieved in aqueous solution . This improvement was attributed to (1) the absence of bulk water and the increase in substrate solubility by the transition of reaction media from aqueous solution to organic solvents and (2) the ability of lipase A12 to remain catalytically active in highly polar DMSO . This discovery that the A . niger lipase was capable of surviving its contact with polar solvents was further confirmed by its considerably preserved catalytic activity on CMC acetylation in aqueous media after enzyme pretreatments with organic solvents of various polarities and in mixture media with the aqueous phase partially replaced by organic solvents. Environ Sci Technol, 2003 Nov 15, 37(22), 5150 - 8 Comparative oxidation and net emissions of methane and selected non-methane organic compounds in landfill cover soils; Schuetz C et al.; The surface emissions of methane (CH4) and non-methane organic compounds (NMOCs) were determined at two different areas at a French landfill: a permanently covered and fully vegetated area (40 cm coarse sand + 80 cm of loam) and a temporarily covered area (40 cm of coarse sand) . The 37 NMOCs quantified in the landfill gas samples included alkanes (C1-C10), alkenes (C1-C4), halogenated hydrocarbons (including (H)CFCs), and aromatic hydrocarbons . Both positive and negative CH4 fluxes ranging from -0.01 to 0.008 g m(-2) d(-1) were measured from the permanently covered cell . However, high spatial variation was observed, and a hot spot with a high flux (10 g m(-2) d(-1)) was identified . A higher CH4 emission occurred from the temporarily covered cell (CH4 flux of 49.9 g m(-2) d(-1)) as compared to the permanently covered cell . The NMOC fluxes from the permanently covered zone were all very small with both positive and negative fluxes in the order of 10(-7) to 10(-5) g m(-2) d(-1) . Higher and mainly positive NMOC fluxes in the order of 10(-5) to 10(-4) g m(-2) d(-1) were obtained from the temporarily covered zone . The lower emission from the permanently covered and fully vegetated cell was attributable to the thicker soil layer, which functions as microbial habitat for methanotrophic bacteria . The NMOC oxidation capacity was investigated in soil microcosms incubated with CH4 . Maximal oxidation rates for the halogenated aliphatic compounds varied between 0.06 and 8.56 microg (g of soil)(-1) d(-1) . Fully substituted hydrocarbons (tetrachloromethane, perchloroethylene, CFC-11, CFC-12, and CFC-113) were not degraded in the presence of CH4 and O2 . Benzene and toluene were rapidly degraded, giving very high maximal oxidation rates (28 and 39 microg (g of soil)(-1) d(-1)) . On the basis of the emission measurements and the batch experiments conducted, a general pattern was observed between emissions and biodegradability of various NMOCs . The emissions mainly consisted of compounds that were not degradable or slowly degradable, while an uptake of easily degradable compounds was registered . As an example, perchloroethylene, trichloromethane, CFC-11, and CFC-12 were emitted, while atmospheric consumption of aromatic hydrocarbons and lower chlorinated hydrocarbons such as vinyl chloride, dichloromethane, and chloromethane was observed . This study demonstrates that landfill soil covers show a significant potential for CH4 oxidation and co-oxidation of NMOCs . Under certain conditions, landfills may even function as sinks for CH4 and selected NMOCs, like aromatic hydrocarbons and lower chlorinated compounds. Ying Yong Sheng Tai Xue Bao, 2003 Aug, 14(8), 1385 - 90 {Effects of land use change on carbon storage in terrestrial ecosystem}; Yang J et al.; Terrestrial ecosystem is an important carbon pool, which plays a crucial role in carbon biogeochemical cycle . Human activities such as fossil fuel combustion and land use change have resulted in carbon fluxes from terrestrial ecosystem to the atmosphere, which increased the atmospheric CO2 concentration, and reinforced the greenhouse effect . Land use change affects the structure and function of the terrestrial ecosystem, which causes its change of carbon storage . To a great extent, the change of carbon storage lies in the type of ecosystem and the change of land use patterns . The conversion of forest to agricultural land and pasture causes a large reduction of carbon storage in vegetation and soil, and the decrease of soil carbon concentration is mainly caused by the reduction of detritus, the acceleration of soil organic matter decomposition, and the destroy of physical protection to organic matter due to agricultural practices . The loss of soil organic matter appears at the early stage after deforestation, and the loss rate is influenced by many factors and soil physical, chemical and biological processes . The conversion of agricultural land and pasture to forest and many conservative agricultural practices can sequester atmospheric carbon in vegetation and soil . Vegetation can sequester large amounts of carbon from atmosphere, while carbon accumulation in soil varies greatly because of farming history and soil spatial heterogeneity . Conservative agricultural practices such as no-tillage, reasonable cropping system, and fertilization can influence soil physical and chemical characters, plant growth, quality and quantity of stubble, and soil microbial biomass and its activity, and hence, maintain and increase soil carbon concentration. Lancet, 2003 Nov 29, 362(9398), 1785 - 91 Effect of ultraviolet germicidal lights installed in office ventilation systems on workers' health and wellbeing: double-blind multiple crossover trial; Menzies D et al.; BACKGROUND: Workers in modern office buildings frequently have unexplained work-related symptoms or combinations of symptoms . We assessed whether ultraviolet germicidal irradiation (UVGI) of drip pans and cooling coils within ventilation systems of office buildings would reduce microbial contamination, and thus occupants' work-related symptoms . METHODS: We undertook a double blind, multiple crossover trial of 771 participants . In office buildings in Montreal, Canada, UVGI was alternately off for 12 weeks, then turned on for 4 weeks . We did this three times with UVGI on and three times with it off, for 48 consecutive weeks . Primary outcomes of self-reported work-related symptoms, and secondary outcomes of endotoxin and viable microbial concentrations in air and on surfaces, and other environmental covariates were measured six times . FINDINGS: Operation of UVGI resulted in 99% (95% CI 67-100) reduction of microbial and endotoxin concentrations on irradiated surfaces within the ventilation systems . 771 participants appeared to remain masked, and reported no adverse effects . On the basis of within-person estimates, use of UVGI was associated with significantly fewer work-related symptoms overall (adjusted odds ratio 0.8 {95% CI 0.7-0.99}), as well as respiratory (0.6 {0.4-0.9}) and mucosal (0.7 {0.6-0.9}) symptoms than was non-use . Reduction of work-related mucosal symptoms was greatest among atopic workers (0.6 {0.5-0.8}), and never-smokers (0.7 {0.5-0.9}) . With UVGI on, never-smokers also had large reduction of work-related respiratory (0.4 {0.2-0.9}), and musculoskeletal symptoms (0.5 {0.3-0.9}) . INTERPRETATION: Installation of UGVI in most North American offices could resolve work-related symptoms in about 4 million employees, caused by microbial contamination of heating, ventilation, and air-conditioning systems . The cost of UVGI installation could in the long run prove cost-effective compared with the yearly losses from absence because of building-related illness. Sci Total Environ, 2004 Jan 5, 318(1-3), 187 - 95 Upward mobilization of 137Cs in surface soils of Chamaecyparis obtusa Sieb . et Zucc . (hinoki) plantation in Japan; Fukuyama T et al.; The use of 137Cs has recently been adopted to estimate erosion in hinoki plantations in Japan . However, there have been several reports of the upward mobilization of 137Cs in forest humus layers . In this study, the vertical distribution of 137Cs within the soil profile was measured in a hinoki plantation . In order to confirm the upward migration of 137Cs from mineral soil to fresh surface litter and to identify mechanisms of the transfer, changes in 137Cs specific activity in the contents of litterbags were examined in a hinoki plantation . A controlled laboratory experiment was also conducted to assess the effect of microbial activity on the upward migration of 137Cs . As a result, the higher 137Cs activities in the surface organic layer of a hinoki plantation than in fresh litter and the increasing 137Cs total content of litterbags with time demonstrated the upward mobilization of 137Cs from mineral soil to the surface organic layer . Physical movement of soil particles by raindrop splash was considered an important process in 137Cs upward migration . The results of our laboratory experiment indicate an influence from soil microbial activity on the upward mobilization of 137Cs . Thus, upward migration of 137Cs and constant litter removal by runoff may induce 137Cs loss from steep forested catchments and underestimation of the 137Cs inventory leading to the overestimation of soil redistribution rates. Acta Pharmacol Sin, 2003 Dec, 24(12), 1308 - 13 Molecular diagnostics of atypical pneumonia; Tang YW; The emergence of nucleic acid-based molecular techniques has significantly enhanced laboratory diagnosis and monitoring of atypical pneumonia . These techniques have not only provided rapid and sensitive detection of fastidious microbial organisms but have also played critical roles in identifying and characterizing emerging pathogens that cause atypical pneumonia . Other benefits that molecular techniques can bring to the field include organism differentiation, quantitation, typing, and antibiotic resistance profiles . Gradually becoming standardized and widely available, the future will see some promising molecular methods become a mainstay in clinical laboratories for recognition and diagnosis of atypical pneumonia pathogens. Altern Med Rev, 2003 Nov, 8(4), 395 - 409 Portal to the interior: viral pathogenesis and natural compounds that restore mucosal immunity and modulate inflammation; Williams JE; Most antigens, particularly viruses, enter the body through the mucosal epithelia where they are carried by afferent lymphatics to regional lymph nodes for presentation to the immune system . Although they share immunological similarities, immune processes that protect the mucosa are distinct from innate and acquired immunity . The barrier formed by the intestinal mucosa is the most studied, with its microenvironment having a marked influence on both local and systemic immune responses . A healthy microenvironment and resilient neighboring tissue provide protection against inflammation known to dampen mucosal immunity, promote carcinogenesis, contribute to systemic inflammatory processes, and result in autoimmune diseases . Numerous natural substances improve this microenvironment and thereby enhance immunity against microbial infections . Since mucosal immunity forms the first line of defense against many commonly transmitted pathogens, restoring and maintaining mucosal immunity is critical for disease prevention and intervention . This article discusses the nature of mucosal immunity and its relationship to viral infections and other conditions, and reviews natural compounds that help restore mucosal immunity. Crit Rev Food Sci Nutr, 2003, 43(5), 527 - 86 Effects of combined pressure and temperature on enzymes related to quality of fruits and vegetables: from kinetic information to process engineering aspects; Ludikhuyze L et al.; Throughout the last decade, high pressure technology has been shown to offer great potential to the food processing and preservation industry in delivering safe and high quality products . Implementation of this new technology will be largely