Huan Jing Ke Xue, 2003 Jul, 24(4), 81 - 4 {Relation between phosphorus and bacterial regrowth in drinking water}; Sang J et al.; In the experiment, a bioassay called Bacterial Regrowth Potential (BRP) was used to investigate the effect of phosphorus on bacterial regrowth in the water sample that was made from some raw water taken from a reservoir located in northern China . It was shown that BRP of water sample increased about 100%-235% when 50 micrograms/L PO4(3-) -P (as NaH2PO4) was added alone . BRP of water sample with various inorganic nutrients (including phosphate) addition had the similar increase compared with BRP of water sample with only 50 micrograms/L PO4(3-) -P addition and BRP of water sample with acetate-C of 1 mg/L addition increased only 30%-40% . These results were clear evidence of phosphorus limitation on bacteria regrowth in the water sample investigated in the experiment . This observation offered novel possibility to restrict microbial regrowth in water distribution system by developing technologies to remove phosphorus efficiently from drinking water. J Biol Chem, 2003 Dec 19, 278(51), 51395 - 407 Epub 2003 Oct 09. Initiation of mucin-type O-glycosylation in dictyostelium is homologous to the corresponding step in animals and is important for spore coat function; Wang F et al.; Like animal cells, many unicellular eukaryotes modify mucin-like domains of secretory proteins with multiple O-linked glycans . Unlike animal mucin-type glycans, those of some microbial eukaryotes are initiated by alpha-linked GlcNAc rather than alpha-GalNAc . Based on sequence similarity to a recently cloned soluble polypeptide hydroxyproline GlcNAc-transferase that modifies Skp1 in the cytoplasm of the social ameba Dictyostelium, we have identified an enzyme, polypeptide alpha-N-acetylglucosaminyltransferase (pp alpha-GlcNAc-T2), that attaches GlcNAc to numerous secretory proteins in this organism . Unlike the Skp1 GlcNAc-transferase, pp alpha-GlcNAc-T2 is predicted to be a type 2 transmembrane protein . A highly purified, soluble, recombinant fragment of pp alpha-GlcNAc-T2 efficiently transfers GlcNAc from UDP-GlcNAc to synthetic peptides corresponding to mucin-like domains in two proteins that traverse the secretory pathway . pp alpha-GlcNAc-T2 is required for addition of GlcNAc to peptides in cell extracts and to the proteins in vivo . Mass spectrometry and Edman degradation analyses show that pp alpha-GlcNAc-T2 attaches GlcNAc in alpha-linkage to the Thr residues of all the synthetic mucin repeats . pp alpha-GlcNAc-T2 is encoded by the previously described modB locus defined by chemical mutagenesis, based on sequence analysis and complementation studies . This finding establishes that the many phenotypes of modB mutants, including a permeability defect in the spore coat, can now be ascribed to defects in mucin-type O-glycosylation . A comparison of the sequences of pp alpha-GlcNAc-T2 and the animal pp alpha-GalNAc-transferases reveals an ancient common ancestry indicating that, despite the different N-acetylhexosamines involved, the enzymes share a common mechanism of action. Mar Pollut Bull, 2003 Oct, 46(10), 1245 - 52 The influence of cyanobacteria on oil polluted intertidal soils at the Saudi Arabian Gulf shores; Barth HJ; In 1991 the second Gulf War lead to the largest oil spill in human history . Over 770 km of coastline from southern Kuwait to Abu Ali Island (Saudi Arabia) were smothered with oil and tar, erasing most of the local plant and animal communities . In the following year cyanobacteria colonized most of the oil polluted shores . In the study area at the Saudi Arabian Gulf coast north of Jubail three different processes were observed that followed the extensive formation of cyanobacterial mats . The first one is desiccation, cracking, and peeling of the cyanobacterial mats, thereby removing the uppermost part of the oiled sediment . The second is the resettlement of burrowing macrofauna like crabs and benthic animals such as gastropods, which outcompete the cyanobacteria again . The third process is further extensive growth of cyanobacteria building thick laminated mats . These layers, completely seal the surface and hence produce an anaerobic milieu which inhibits oil degradation . As long as such cyanobacteria exist, they will prevent microbial oil degradation as well as any resettlement by macrofauna. Biotechnol Adv, 2001 Dec, 19(8), 627 - 62 Production, purification, characterization, and applications of lipases; Sharma R et al.; Lipases (triacylglycerol acylhydrolases, EC 3.1.1.3) catalyze the hydrolysis and the synthesis of esters formed from glycerol and long-chain fatty acids . Lipases occur widely in nature, but only microbial lipases are commercially significant . The many applications of lipases include speciality organic syntheses, hydrolysis of fats and oils, modification of fats, flavor enhancement in food processing, resolution of racemic mixtures, and chemical analyses . This article discusses the production, recovery, and use of microbial lipases . Issues of enzyme kinetics, thermostability, and bioactivity are addressed . Production of recombinant lipases is detailed . Immobilized preparations of lipases are discussed . In view of the increasing understanding of lipases and their many applications in high-value syntheses and as bulk enzymes, these enzymes are having an increasing impact on bioprocessing. Biotechnol Adv, 1991, 9(3), 425 - 42 Insect control with baculoviruses; Fuxa JR; Baculoviruses have been researched extensively for insect control . Three of their features have been particularly attractive: their host specificity and consequential environmental safety, their virulence in host insects, and their capability for causing disease epizootics . There have been four approaches to their use for insect control: as microbial insecticides for short-term insect population suppression, through seasonal colonization or a recurring "booster shot" for control of more than one pest generation, through introduction-establishment where the viral species or strain was not indigenous, and through environmental manipulation to make the ecosystem more favorable for viral epizootics . Actual usage of baculoviruses in pest management has been disappointing, particularly with the microbial insecticide approach, primarily for three reasons: economics, slow speed of kill, and adverse effects of the environment on the viruses . The recombinant-DNA revolution has greatly increased the prospects for baculoviruses in insect pest management. Biotechnol Adv, 1991, 9(2), 217 - 40 Bacterial cell disruption: a key unit operation in the recovery of intracellular products; Harrison ST; The need for microbial cell disruption has hindered the large scale production of commercial biotechnological products of intracellular derivation . The intracellular nature of many recombinant products and the potential use of the bacterial storage product, PHB as a commodity thermoplastic have renewed interest in the improvement of this unit operation . This paper provides a review of processes of a mechanical, physical, chemical or biological nature used for cell disruption on both the laboratory and large scale . Applicability of the techniques to large scale operation is discussed . Modification of existing processes is suggested for the reduction of energy requirements and improved process economics . The requirements for the liberation of granular intracellular products such as inclusion bodies and virus-like yeast particles are distinguished from those for the liberation of soluble products, mainly proteinaceous in nature . The integrated nature of the process with both upstream and downstream processes is addressed . Finally, the recent approach of selective liberation of soluble products of interest is reviewed. Biotechnol Adv, 1990, 8(2), 335 - 46 Beneficial interactions between micro-organisms and roots; Lynch JM; Microbial activity in the rhizosphere can have positive and negative effects on plants . Some of the beneficial processes act by minimizing the negative effects or by modifying the cropping environment to enhance productivity . Processes that are considered here include the provision of nitrogen, phosphorus and iron to the plant, the biocontrol of diseases and deleterious organisms and the stabilization of soil structures . The use of genetic engineering techniques in studying these processes and generating novel strains which may enhance them is discussed, along with the possible consequences of the release of organisms into the environment. Biotechnol Adv, 1990, 8(2), 303 - 19 Microbial cellulose as a specialty chemical; Legge RL; Microbial polysaccharides are extensively used commercially as gelling or suspending agents, as protective colloids or as thickening agents . Until recently, microbial cellulose producing systems such as Acetobacter xylinum, had been used largely as model systems for the study of cellulose biosynthesis . Current advances in molecular biology and biochemical engineering promise to usher microbial cellulose into the specialty chemical market . This review will highlight some of the recent progress made in our understanding of microbial cellulose biochemistry and biosynthesis, describe some of its inherent virtues and identify current unique applications of this versatile biopolymer. Biotechnol Adv, 1989, 7(2), 215 - 39 Advances in bioconversion of anthracycline antibiotics; Grafe U et al.; During the last decade new anthracycline-type structures with potential usefulness in cancer treatment have been supplied both by new microbial strains and by bioconversions of precursor molecules employing cells or enzymes . We highlight recent advances in bioconversion of anthracycline structures with the main focus on late transformations such as are carried out by oxidoreductases. Biotechnol Adv, 1990, 8(1), 261 - 75 The mixed substrate concept, applied for microbial syntheses of metabolites; Babel W; Microbial overproduction of metabolites is a response to suboptimal conditions for growth and multiplication . It is an energy-wasting process in terms of life insofar as a part of energy of the carbon source remains in the metabolite . From an energetic point of view microbial overproduction can be divided into two categories: i) energy-consuming, ii) energy-yielding . The amount of energy required or made available is considered to be responsible for discrepancies between carbon metabolism-determined possible and experimentally obtained yields . Since the expenditure of energy must be provided by oxidation of carbon source more substrate is consumed than required according to the metabolic pathway . In the case of energy-yielding synthesis energy must be discharged . Various possibilities exist . Since metabolic sequences not involved in the synthesis of the proper product are not switched off completely other synthetic processes and even growth can occur . The energy is thus discharged at the expense of substrate . To increase the experimental yield the energy produced or consumed has to be maintained low . This can be achieved by means of substrate mixtures . The synthesis of by-products and growth are difficult to prevent completely . However, growth can be quite desirable since the catalyst is renewed thus making the product synthesis possible. Biotechnol Adv, 1984, 2(2), 149 - 60 Advances in microbial delignification; Eriksson KE; Microbial delignification is a new field of applied research . The progress will therefore run parallel to the development of new basic knowledge on the physiological demands of white-rot fungi to degrade lignin and on new knowledge on enzyme mechanisms involved in lignin degradation.In the last few years both basic and applied research on microbial conversion of lignocellulosic materials have vastly expanded . In certain areas, such as microbial delignification, considerable progress has recently been made . Basidiospores from Sporotrichum pulverulentum and some CEL(-) mutants have been obtained . Crossing of mycelium from single basidiospore cultures of wild-type and CEL(-) mutants will eventually give rise to much better CEL(-) mutants than those which have been used in the past . An understanding of which enzymes are the most important for lignin degradation to take place is also beginning to develop . This review discusses present knowledge and future possibilities in this field. Biotechnol Adv, 1984, 2(1), 1 - 19 Microbial cultures in the utilization of cellulosic materials; Doelle HW; This review elaborates on the most recent microbial development in saccharification of cellulose and cellulase formation . A particular highlight is a new genetic-immunochemical approach investigating the mechanism of adhesion of bacterial cellulase to cellulose during cellulose conversion . New developments and recent reviews in hemicellulose and lignin degradation are also covered. Biotechnol Adv, 1987, 5(1), 47 - 84 Biocatalysis in multi-phase reaction mixtures containing organic liquids; Halling PJ; A wide range of enzymes and whole microbial cells will act as catalysts in reaction mixtures that contain 2 or more phases, one of which is an organic liquid (either a reactant or including water-immiscible organic solvents) . These "biphasic" systems have a variety of structures, knowledge of which aids predictions about biocatalyst activity and stability . There is often a dilute aqueous solution phase (containing the biocatalyst), which may be emulsified with the organic phase, or "trapped" within catalyst particles; sometimes however there may only be traces of water adsorbed to the enzyme or cells . These reaction systems offer several advantages for industrial applications, notably the higher solubilities of many reactants of interest, and the ability of readily available hydrolytic enzymes to catalyse syntheses . The most non-polar organic liquids are least likely to inactivate biocatalysts, though many do remain active with relatively polar solvents . Modification of the biocatalyst may stabilise against inactivation, especially where this is due to direct contact with the phase interface . The mass transfer processes required in these systems remain poorly understood, particularly because the interfacial area is often unknown . Attractive continuous reactors may be operated using a packed bed of catalyst with a trapped aqueous phase. Biotechnol Adv, 1991, 9(4), 643 - 58 Industrial enzymes--developments in production and application; Falch EA; The utilization of gene technology and of new production technologies have made industrial enzymes with improved properties or better cost performance available . This has in turn opened important new areas of enzyme applications . The benefits to the customers are considerable: cost savings in the application process, improved product quality, and in most cases also a significantly reduced impact on the environment . Gene technology offers several benefits to the enzyme industry . This technology enables the use of safe, well-documented host organisms easy to cultivate, the microbial production of enzymes of animal and plant origin, the realization of enhanced efficiency and high product purity, and also the production of enzymes with improved stability and activity . Developments in production technology include advanced control methods, the use of expert systems, and the application of large-scale crystallization . As case stories the development of a lipase and of a cellulase is described . The effect on environment of enzyme application and production is discussed. Biotechnol Adv, 1992, 10(1), 93 - 115 Aeroponics for the culture of organisms, tissues and cells; Weathers PJ et al.; Characteristics of aeroponics are discussed . Contrast is made, where appropriate, with hydroponics and aero-hydroponics as applies to research and commercial applications of nutrient mist technology . Topics include whole plants, plant tissue cultures, cell and microbial cultures, and animal tissue cultures with regard to operational considerations (moisture, temperature, minerals, gaseous atmosphere) and design of apparati. Biotechnol Adv, 1992, 10(1), 1 - 67 Biotransformation of sterols: selective cleavage of the side chain; Ahmad S et al.; This review elaborates on the recent development of microbial sterol biotransformation systems . Particular emphasis is laid on the new enzymatic approach investigating the cleavage of sterol side chain . New developments in the area of immobilized cell system and use of organic media along with recent reviews on side chain cleavage are discussed. Biotechnol Adv, 1997, 15(1), 43 - 58 DNA based biosensors; Zhai J et al.; Compared to advances in enzyme sensors, immunosensors, and microbial biosensors, relatively little work exists on DNA based biosensors . Here we review the DNA based biosensors that rely on nucleic acid hybridization . Major types DNA biosensors--electrochemical, optical, acoustic, and piezoelectric--are introduced and compared . The specificity and response characteristics of DNA biosensors are discussed . Overall, a promising future is foreseen for the DNA based sensor technology. Biotechnol Adv, 1997, 15(3-4), 621 - 32 The microbial degradation of halogenated diaryl ethers; Bunz PV et al.; The structurally related polyhalogenated diaryl ethers such as diphenyl ethers (DEs), dibenzofurans (DFs), and dibenzo-p-dioxins (DDs) are regarded, due to their physicochemical and toxicological properties, as a class of compounds giving reason for serious environmental concern . While the nonhalogenated basic structures are biodegradable under aerobic conditions, there is the need for rather specialized strains to mineralize the halogenated derivatives . Certain halogenated metabolites might cause serious problems such as having inhibitory effects upon the degradation . Anaerobic methanogenic consortia do have the ability to almost completely dehalogenate even polyhalogenated congeners . It has been shown that certain fungi are capable of transforming chlorinated DFs and DDs by the activity of nonspecific enzymes such as lignin-peroxidases. Biotechnol Adv, 2000 Aug, 18(5), 355 - 83 Cellulases and related enzymes in biotechnology; Bhat MK; Basic and applied research on microbial cellulases, hemicellulases and pectinases has not only generated significant scientific knowledge but has also revealed their enormous potential in biotechnology . At present, cellulases and related enzymes are used in food, brewery and wine, animal feed, textile and laundry, pulp and paper industries, as well as in agriculture and for research purposes . Indeed, the demand for these enzymes is growing more rapidly than ever before, and this demand has become the driving force for research on cellulases and related enzymes . The present article is an overview of the biotechnological state-of-the-art for cellulases and related enzymes. J Vet Diagn Invest, 2003 Sep, 15(5), 478 - 80 Cyanide toxicosis in goats after ingestion of California Holly (Heteromeles arbutifolia); Tegzes JH et al.; Cyanogenic glycosides are found in many native and naturalized plants throughout North America . The glycosides themselves are not toxic, but they yield hydrogen cyanide (hydrocyanic or prussic acid) when they are hydrolyzed by beta-glycosidases, either as a result of injury to the plant cells or by microbial action in the rumen . Hydrogen cyanide is readily absorbed from the gastrointestinal tract . Cyanide ion binds with iron in cytochrome oxidase, interfering with cellular respiration . The clinical effects are peracute, often resulting in death less than 1 hour after ingestion . This study describes a case that resulted in significant morbidity and mortality in a herd of goats after exposure to California holly (Heteromeles arbutifolia). J Environ Qual, 2003 Sep-Oct, 32(5), 1641 - 9 In situ reduction of chromium(VI) in heavily contaminated soils through organic carbon amendment; Tokunaga TK et al.; Chromium has become an important soil contaminant at many sites, and facilitating in situ reduction of toxic Cr(VI) to nontoxic Cr(III) is becoming an attractive remediation strategy . Acceleration of Cr(VI) reduction in soils by addition of organic carbon was tested in columns pretreated with solutions containing 1000 and 10 000 mg L(-1) Cr(VI) to evaluate potential in situ remediation of highly contaminated soils . Solutions containing 0,800, or 4000 mg L(-1) organic carbon in the form of tryptic soy broth or lactate were diffused into the Cr(VI)-contaminated soils . Changes in Cr oxidation state were monitored through periodic micro-XANES analyses of soil columns . Effective first-order reduction rate constants ranged from 1.4 x 10(-8) to 1.5 x 10(-7) s(-1), with higher values obtained for lower levels of initial Cr(VI) and higher levels of organic carbon . Comparisons with sterile soils showed that microbially dependent processes were largely responsible for Cr(VI) reduction, except in the soils initially exposed to 10 000 mg L(-1) Cr(VI) solutions that receive little (800 mg L(-1)) or no organic carbon . However, the microbial populations (< or = 2.1 x 10(5) g(-1)) in the viable soils are probably too low for direct enzymatic Cr(VI) reduction to be important . Thus, synergistic effects sustained in whole soil systems may have accounted for most of the observed reduction . These results show that acceleration of in situ Cr(VI) reduction with addition of organic carbon is possible in even heavily contaminated soils and suggest that microbially dependent reduction pathways can be dominant. J Environ Sci Health A Tox Hazard Subst Environ Eng, 2003, 38(11), 2565 - 80 Natural occurrence of arsenic in shallow groundwater, Shanyin, Datong Basin, China; Guo H et al.; In Shanyin, Shanxi province, China, As concentration in shallow groundwater exceeds guide concentrations, set internationally and nationally at 10-50 microg/L, and may reach 1932.0 microg/L, which has resulted in severe clinical symptoms of arsenic toxity . In this article, chemical characteristics of groundwaters containing anomalous As and mechanisms of arsenic release to shallow groundwaters were studied . Groundwaters containing anomalous As in the study area were characterized by higher pH, higher concentration of phosphate, higher concentration of naphthenic acid, and lower concentrations of sulfate and nitrate . Microbial metabolism of sedimentary organic matter, which is present as high as 1.0% organic C, results in the lower concentrations of sulfate and nitrate . The reactions decrease Eh and produce CO2, which promotes the dissolution of carbonates and increases pH . The clay minerals and colloids including organic matters scavenging arsenic would release arsenic to groundwater in higher pH and lower Eh environment . In addition, the competitive absorption between As and anions (such as phosphate and fluoride) contributes to the release of As from kaolinite, montmorillonite, illite, and Fe oxyhydroxides . Naphthenic acid also promotes mobilization and translocation of As in groundwater systems. Adv Exp Med Biol, 2001, 491, 485 - 504 T-independent IgA responses to microbial polysaccharides; Wang D; There is accumulating evidence indicating the presence in vivo of T-independent routes of IgA response in addition to the conventional T-dependent IgA response . Factors influencing these alternative pathways of IgA responses may include the structural characteristics of a stimulating antigen, the nature of responding B cells, and the microenvironment . The structural complexity of polysaccharide antigens has made it difficult to summarize a general scheme for the antibody responses they induce . Instead, one may expect that each individual polysaccharide may be able to create a unique microenvironment by activation of specific cell populations in the repertoires of non-T cell types . A specific pattern of B cell response may thus be elicited by TI stimulation . Recognition of such a unique property of a TI antigens is necessary for us to better understand the T-independent IgA response . Information obtained may have an impact on the development of vaccination strategies directed at the mucosal immunity mediated by IgA antibodies. J Biol Chem, 2003 Dec 26, 278(52), 52179 - 87 Epub 2003 Oct 07. Release of arachidonic acid by stimulation of opsonic receptors in human monocytes: the FcgammaR and the complement receptor 3 pathways; Fernandez N et al.; The role of the opsonic receptors FcgammaR and CR3 on the release of arachidonic acid (AA) by human monocytes was studied using IgG-ovalbumin (OVA) equivalence immune complexes (IC), anti-OVA IgG bound to OVA-coupled latex beads, and C3bi-bound IC . Release of AA was produced by IC and latex-OVA beads bound to IgG, whereas binding of C3bi to IC inhibited the ability of IC to release AA . In contrast, coating of zymosan particles with C3bi enhanced AA release as compared with that produced by non-coated particles . Masking of C3bi on C3bi-bound IC by incubation with anti-C3 IgG resulted in the recovery of their ability to release AA, thereby suggesting that binding of C3b by IC reduces their flogogenic effects, whereas opsonization of microbial walls by complement may enhance their proinflammatory potential . The binding/uptake of opsonized zymosan particles was inhibited by anti-CR3 Ab and C3bi-bound IC, but not by beta-glucan, mannan, and anti-Toll-like receptor 2 Ab . These findings show that cooperative engagement of CR3 on both the lectin-like site involved in beta-glucan binding and the I-domain involved in C3bi binding, as it can be observed in the innate immune response, produces AA release, whereas the unique interaction of C3bi-bound IC with the I-domain of CR3, as it may occur in the adaptive immune response, diverts the IC lattice from a productive interaction with FcgammaR linked to AA release. Appl Environ Microbiol, 2003 Oct, 69(10), 6280 - 7 Comparison of velocity profiles for different flow chamber designs used in studies of microbial adhesion to surfaces; Bakker DP et al.; Flow chambers are commonly used to study microbial adhesion to surfaces under environmentally relevant hydrodynamic conditions . The parallel plate flow chamber (PPFC) is the most common design, and mass transport occurs through slow convective diffusion . In this study, we analyzed four different PPFCs to determine whether the expected hydrodynamic conditions, which control both mass transport and detachment forces, are actually achieved . Furthermore, the different PPFCs were critically evaluated based on the size of the area where the velocity profile was established and constant with a range of flow rates, indicating that valid observations could be made . Velocity profiles in the different chambers were calculated by using a numerical simulation model based on the finite element method and were found to coincide with the profiles measured by particle image velocimetry . Environmentally relevant shear rates between 0 and 10,000 s(-1) could be measured over a sizeable proportion of the substratum surface for only two of the four PPFCs . Two models appeared to be flawed in the design of their inlets and outlets and allowed development of a stable velocity profile only for shear rates up to 0.5 and 500 s(-1) . For these PPFCs the inlet and outlet were curved, and the modeled shear rates deviated from the calculated shear rates by up to 75% . We concluded that PPFCs used for studies of microbial adhesion to surfaces should be designed so that their inlets and outlets are in line with the flow channel . Alternatively, the channel length should be increased to allow a greater length for the establishment of the desired hydrodynamic conditions. Appl Environ Microbiol, 2003 Oct, 69(10), 6018 - 24 Axial dynamics, stability, and interspecies similarity of bacterial community structure in the highly compartmentalized gut of soil-feeding termites (Cubitermes spp.); Schmitt-Wagner D et al.; The highly compartmentalized gut of soil-feeding termites is characterized by pronounced axial dynamics in physicochemical conditions and microbial processes . In a companion paper (D . Schmitt-Wagner, M . W . Friedrich, B . Wagner, and A . Brune, Appl . Environ . Microbiol . 69:6007-6017, 2003), we demonstrated that the variety of physicochemical conditions in the different gut compartments of Cubitermes spp . is reflected in the diversity of the respective intestinal microbial communities . Here, we used molecular fingerprints of 16S rRNA genes of the bacterial community, obtained by terminal restriction fragment length polymorphism (T-RFLP) analysis, to describe the axial dynamics of the bacterial community structure in the different gut sections . Comparison of the T-RFLP profiles with the predicted terminal restriction fragments of the clones in clone libraries of the gut segments in Cubitermes orthognathus confirmed that all hindgut sections harbored distinct bacterial communities . Morisita indices of community similarity, calculated by comparing the different patterns, revealed large differences between the bacterial communities of soil, gut, and nest material and also among the individual gut sections . By contrast, comparison of the homologous gut segments of different Cubitermes species indicated that the three termite species investigated possessed a similar, gut-specific microbiota that remained comparatively stable even during several months of maintenance in the laboratory. Appl Environ Microbiol, 2003 Oct, 69(10), 6000 - 6 Compound-specific isotopic fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot-spring microbial mats; van der Meer MT et al.; Stable carbon isotope fractionations between dissolved inorganic carbon and lipid biomarkers suggest photoautotrophy by Chloroflexus-like organisms in sulfidic and nonsulfidic Yellowstone hot springs . Where co-occurring, cyanobacteria appear to cross-feed Chloroflexus-like organisms supporting photoheterotrophy as well, although the relatively small 13C fractionation associated with cyanobacterial sugar biosynthesis may sometimes obscure this process. Appl Environ Microbiol, 2003 Oct, 69(10), 5875 - 83 Rapid screening for freshwater bacterial groups by using reverse line blot hybridization; Zwart G et al.; The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups . We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters . The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes . The optimized assay was made stringent to discriminate at approximately the single-mismatch level . This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database . Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples . Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes . Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes . Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs. Acta Neurochir Suppl, 2003, 88, 125 - 35 Gene therapy of gliomas; Hamel W et al.; Malignant glioma formation is associated with characteristic genetic alterations, although epigenetic mechanisms may contribute in tumorigenesis . Until recently, our knowledge has mainly been based on chromosomal and molecular studies performed in the last two decades . This has increased tremendously with the advent of new technologies, in particular expression arrays for simultaneous analysis of thousands of genes . Consequently, gene therapy of gliomas may aim at molecular interference with 'gain of function' genes (oncogenes) or replacement of 'loss of function' genes (tumor suppressor genes) . Such approaches require transgene expression in whole tumor cell populations (if not other mechanisms come into play) which cannot be achieved with current vector systems . Hence other strategies have been pursued which may be independent of genes actually involved in tumorigenesis . Microbial genes (e.g . herpes simplex virus thymidine kinase) may be transferred into the tumors allowing for prodrug activation (e.g . ganciclovir) . Furthermore, cytokines or other immunomodulatory genes may be used for vaccination purposes which frequently involves ex vivo transfection of autologous tumor cells with such genes . These approaches proved promising in preclinical studies performed in cell culture and different inbred rodent models . A considerable number of clinical trials have been initiated based on these approaches . Although most therapeutic strategies proved safe, clinical responses fell short of expectations raised by preclinical results . This, to a large extent, has to be attributed to a lag in the development of efficient vector systems . Although much effort has been put into this area of research, neuro-oncologists are still in await of a vector system allowing for selective and efficient tumor cell transduction . This has led to increased interest in distinct but related strategies, e.g . oncolytic viruses or direct intra-tumoral delivery of anti-sense oligonucleotides. Water Sci Technol, 2003, 48(4), 155 - 62 Cellulosic waste degradation by rumen-enhanced anaerobic digestion; Barnes SP et al.; Anaerobic digestion of lignocellulosic material is carried out effectively in many natural microbial ecosystems including the rumen . A rumen-enhanced anaerobic sequencing batch reactor was used to investigate cellulose degradation to give analysis of overall process stoichiometry and rates of hydrolysis . The reactor achieved VFA production rates of 207-236 mg COD/L/h at a loading rate of 10 g/L/d . Overloading of the reactor resulted in elevated production of propionic acid, and on occasion, the presence of succinic acid . With improvements in mixing and solids wasting, the anaerobic sequencing batch reactor system could enable full-scale application of the process for treatment of cellulosic waste material. J Immunol, 2003 Oct 15, 171(8), 3941 - 6 Intratumor CpG-oligodeoxynucleotide injection induces protective antitumor T cell immunity; Lonsdorf AS et al.; Tumor cells are typically poorly immunogenic . The same mechanisms that evolved to avoid the induction of immune responses against self tissues, and, hence, autoimmune disease, also have to be overcome for immune therapy of cancer . Toll-like receptor-activating microbial products such as CpG motif containing DNA are among the primary stimuli that the immune system uses to distinguish between infectious nonself (that is to be attacked) and noninfectious self (that must not be attacked) . We tested in a murine RMA lymphoma/C57BL/6 model whether providing the infectious nonself context in a tumor-by injecting CpG-oligodeoxynucleotides directly into the tumor-would elicit a protective antitumor response . Complete remission of established solid tumors was achieved in immune competent mice, but not in T cell/B cell-deficient RAG-1 knockout mice . Intratumor injection of CpG-oligodeoxynucleotides was shown to induce a tumor-specific CD4(+) and CD8(+) T cell response of the type 1 effector class, and T cells adoptively transferred the protection to RAG-1 knockout mice . The data show that intratumor injection of CpG-oligodeoxynucleotides is a promising strategy for rendering tumors immunogenic. Asian J Surg, 2003 Oct, 26(4), 202 - 4 Long-term storage of small surgical instruments in autoclaved packages; Bhumisirikul W et al.; BACKGROUND: In most operating theatres, unused sterile instruments must be re-sterilized according to preset protocols . Protocols differ among institutions and are not based on strong scientific evidence . OBJECTIVE: To determine and compare the duration of sterility of small instruments packaged in double-layered linen versus plastic-paper envelopes after autoclaving . MATERIALS AND METHODS: Two groups of orthopaedic screws were simultaneously sterilized by autoclaving . In Group 1, each screw was packaged in a double-wrapped linen pack . The screws in Group 2 were individually packaged in an inner wrap of paper and an outer plastic-paper envelope that is commercially available . Unwrapped screws in Group 3 served as controls . During the first 48 weeks, five packages were randomly taken from each group, and from 48 weeks to 96 weeks, 20 packages were taken at random and sent for microbial culture . Five screws from Group 3 were also randomly picked with each sample . RESULTS: Up to 96 weeks, no organisms were cultured from any sample from Groups 1 and 2 . Almost all samples from Group 3 grew several species of bacteria . CONCLUSION: For small metal instruments, autoclaved packages in double-wrapped linen or double-wrapped plastic-paper combinations can be stored safely for at least 96 weeks. J Microbiol Methods, 2003 Nov, 55(2), 371 - 82 Comparison of signature lipid methods to determine microbial community structure in compost; Steger K et al.; The microbial community structure changes substantially during the composting process and simple methods to follow these changes can potentially be used to estimate compost maturity . In this study, two such methods, the microbial identification (MIDI) method and the ester-linked (EL) procedure to determine the composition of long-chain fatty acids, were applied to compost samples of different age . The ability of the two methods to describe the microbial succession was evaluated by comparison with phospholipid fatty acid (PLFA) analysis on the same samples.Samples were taken from a 200-l laboratory compost reactor, treating source-separated organic household waste . During the initial stages of the process, the total concentration of fatty acids in compost samples treated with the EL and MIDI methods was many times higher than with the PLFA method . This was probably due to the presence of fatty acids from the organic material in the original waste . However, this substantial difference between PLFA and the other two methods was not found later in composting . Although the PLFA method gave the most detailed information about the growth and overall succession of the microbial community, the much simpler MIDI and EL methods also successfully described the shift from the initially dominating straight chain fatty acids to iso- and anteiso branched, 10 Me branched and cyclopropane fatty acids in the later stages of the process . Thus, the MIDI and EL extraction methods appear to be suitable for analysis of microbial FAME profiles in compost, particularly in the later stages of the process. Curr Med Chem, 2003 Nov, 10(22), 2351 - 8 From discovery to the coming generation of histone deacetylase inhibitors; Yoshida M et al.; Trichostatin A (TSA) is a Streptomyces metabolite that causes differentiation of murine erythroleukemia cells as well as specific inhibition of the cell cycle of some lower eukaryotes and mammalian cells . The targeted molecule of TSA has been shown by genetic and biochemical analyses to be histone deacetylases (HDACs) . Histone acetylation is a key modification to control transcription, and HDACs are profoundly involved in pathogenesis of cancer through removing acetyl groups from histones and other transcriptional regulators . Trapoxin (TPX) and FK228 (also known as FR901228 and depsipeptide because FK228 = FR901228 = depsipeptide), structurally unrelated microbial metabolites, were also shown to inhibit HDACs . These HDAC inhibitors cause cell cycle arrest, differentiation and/or apoptosis of many tumors, suggesting their usefulness for chemotherapy and differentiation therapy . In addition, HDAC inhibitors play important roles in identifying the specific function of the enzymes . Indeed, we identified tubulin as one of the substrates of HDAC6 by means of differential sensitivity to HDAC inhibitors . Since recent studies have revealed that HDACs are structurally and functionally diverse, it should be important to develop inhibitors specific to individual enzymes as more promising agents for cancer therapy . We have synthesized novel TSA/TPX hybrids, which will serve as a basis for developing enzyme-specific HDAC inhibitors. Curr Pharm Biotechnol, 2003 Oct, 4(5), 339 - 49 Intelligent polyelectrolytes and gels in oral drug delivery; Bromberg L; The present review concerns smart, or intelligent polymers for oral administration that change conformation in aqueous solutions in response to external stimuli such as pH or temperature . We concentrate on charged polymers and gels with polyelectrolyte properties . Because of the ionization at a certain pH or in response to changes in the ionic composition of the solution, a polyelectrolyte has better chances of displaying smart properties than a neutral polymer . When such smart polyelectrolyte is cross-linked by covalent or hydrogen bonding and/or physical aggregation or is entangled, it forms an environmentally sensitive gel capable of swelling and collapse in an aqueous medium . Varying pH, temperature, and microbial flora are found in the gastrointestinal tract, and thus pH- sensitive polymers and gels that can be degraded by specific enzymes and/or inhibit proteolytic enzymes can be tailored for the efficient site-specific therapy . Smart polymers wield a lot of promise in the targeted, site-specific administration where they can provide advantages in loading of sensitive drugs such as proteins and peptides, while releasing the drug at a specific pH or in response to the presence of certain microbial flora. Curr Cancer Drug Targets, 2003 Oct, 3(5), 325 - 30 Natural product origins of Hsp90 inhibitors; Uehara Y; The currently used Hsp90 inhibitors, geldanamycin, herbimycin A and radicicol, were isolated many years ago from Streptomyces and fungi originally for their antiprotozoal activity, herbicidal activity and antifungal activity, respectively . In the mid 1980s, it was found that the benzoquinone ansamycin antibiotics (herbimycin A, geldanamycin, and macbecin) reversed v-Src transformed cells to normal phenotypes, and Bcr-abl was subsequently suggested to be the molecular target for the treatment of chronic myelogenous leukemia through a study using herbimycin A for its selective antioncogenic activity . In 1994, these ansamycins were found to bind to Hsp90 and to cause the degradation of client proteins including Src kinases; further efforts to develop anticancer drugs were made using geldanamycin analogs, and 17AAG was chosen as the best candidate for clinical trials . The number of novel natural products isolated from microbial origins is continuing to increase and is doubling every 10 years . Thus, screening of bioactive substances from natural origins, using assays including defined targets, and developing leads toward drugs via optimized derivatization is a conventional but still promising strategy for drug discovery and development. Syst Appl Microbiol, 2003 Sep, 26(3), 327 - 37 Improved fluorescence in situ hybridization of individual microbial cells using polynucleotide probes: the network hypothesis; Zwirglmaier K et al.; Fluorescence in situ hybridizations using polynucleotide transcript probes (poly-FISH) usually exhibit a ring-shaped halo or corona-like fluorescence signal, whereas hybridizations with oligonucleotide probes (oligo-FISH) result in a uniform and evenly distributed fluorescence throughout the cell . The superiority of poly-FISH in comparison to oligo-FISH regarding the signal intensity and the detection of cells with a low ribosome content suggested a further investigation of the possibilities of polynucleotide probes . Poly-FISH has previously only been described for bacterial cells . In the present study it could also be successfully applied to several yeast species . In addition to that the properties of polynucleotide probes were analyzed by using varying probe lengths and concentrations . This led to the formulation of a hypothesis to explain the characteristic "halo" signal observed with polynucleotide probes . This "network hypothesis" suggests the formation of a network of probes based on the secondary structure of the single stranded RNA probes . Due to the limited permeability of the cell envelope, only part of the probe is linked to its intracellular target site, while the remaining part is located-outside the cell and can form a network by hybridizing with single stranded probes, resulting in the ring-shaped fluorescence signal around the cell . The hypothesis was supported by a number of control experiments including in silico and in vitro analysis of the secondary structure of the probes and hybridizations with probes of defined secondary structures . The network concept provides a new basis for a wider application of poly-FISH. FEBS Lett, 2003 Sep 25, 552(2-3), 99 - 104 The diversity of globin-coupled sensors; Freitas TA et al.; The recently discovered globin-coupled sensors (GCSs) are heme-containing two-domain transducers distinct from the PAS domain superfamily . We have identified an additional 22 GCSs with varying multi-domain C-terminal transmitters through a search of the complete and incomplete microbial genome datasets . The GCS superfamily is composed of two major subfamilies: the aerotactic and gene regulators . We postulate the existence of protoglobin in Archaea as the predecessor to the chimeric GCS. Annu Rev Phytopathol, 2003, 41, 351 - 75 Patterns of pesticide use in California and the implications for strategies for reduction of pesticides; Epstein L et al.; We used the California Pesticide Use Reports to study use of fungicides, bactericides, fumigants, and selected insecticides, primarily for vegetable, fruit, and nut production in California from 1993 to 2000 . There were no obvious trends in decreased use of most compounds used to treat plant disease . However, growers have rapidly adopted recently introduced "conventional" compounds . There is very limited use of microbial biocontrol agents to control plant disease and no indication of an increase . We used case studies to explore the potential of different strategies to reduce pesticide use or risk . There have been reductions in use of organophosphate insecticides, largely by substitution with pyrethroids . Theoretically, replacement of "calendar spray" pesticide programs with "environmentally driven" programs could reduce pesticide use in years with lower disease pressure, but this assumes that the majority of growers currently use a "calendar spray" program and that growers who use less than recommended by an environmentally driven program would not increase their use. Annu Rev Microbiol, 2003, 57, 369 - 94 The uncultured microbial majority; Rappe MS et al.; Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically owing to the sequencing of ribosomal RNA genes cloned from environmental DNA . Currently, only 26 of the approximately 52 identifiable major lineages, or phyla, within the domain Bacteria have cultivated representatives . Evidence from field studies indicates that many of the uncultivated phyla are found in diverse habitats, and some are extraordinarily abundant . In some important environments, including seawater, freshwater, and soil, many biologically and geochemically important organisms are at best only remotely related to any strain that has been characterized by phenotype or by genome sequencing . Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory. Annu Rev Microbiol, 2003, 57, 1 - 27 Gathering no moss; Davies J; I never imagined that I would be asked to write an autobiography in a microbiology tome . For that matter, little did I think that I would consider microbiology the most intriguing subject in the life sciences and the only field I wanted to study . My formal scientific training was in chemistry . This is a recounting of my conversion and the opportunities I have had to work in the microbial sciences with some of the major figures (and characters) during a period of marvelous intensity and productivity . I want to recognize and thank my many distinguished colleagues for the ways in which they have helped me to experience a fruitful and stimulating life as a microbiologist. Nat Prod Res, 2003 Oct, 17(5), 307 - 11 Biopreparation of (-)-(1S,3R,4S,6S)-6-hydroxymenthol and (-)-(1S,3R,4S)-1-hydroxymenthol from 1-menthol by Rhizoctonia solani AG-1-IA and IB; Miyazawa M et al.; Microbial transformation of 1-menthol (1) by six isolates of soil-borne plant pathogenic fungi Rhizoctonia solani AG-1-IA (Rs24, Joichi-2 and RRG97-1) and AG-1-IB (TR22, R147 and 110.4) as a biocatalyst was investigated . Twenty one days precultivation of Rhizoctonia solani AG-1-IA Rs24 and AG-1-IB 110.4 showed excellent yield (98.5-98.6%) of (-)-(1S,3R,4S,6S)-6-hydroxymenthol (2) and (-)-(1S,3R,4S)-1-hydroxymenthol (3) from 1. Mikrobiologiia, 2003 Jul-Aug, 72(4), 547 - 53 {Methanogenic sarcina from an anaerobic microbial community degrading p-toluene sulfonate}; Shcherbakova VA et al.; The methanogenic strain MM isolated from an anaerobic microbial community degrading p-toluene sulfonate showed optimal values of temperature and pH for growth equal to 37 degrees C and 6.3-6.9, respectively . The doubling times of the isolate grown on methanol, acetate, and methylamines under the optimal conditions were 8.8, 19.1, and 10.3-28.1 h, respectively . The growth of strain MM was observed only when the cultivation medium contained casamino acids or p-toluene sulfonate . The G + C content of the DNA of the isolate was 40.3 mol% . This, together with DNA-DNA hybridization data, allowed the new isolate to be identified as a strain of the species Methanosarcina mazei . The new isolate differed from the known representatives of this species in that it was resistant to alkylbenzene sulfonates and able to demethylate p-toluene sulfonate when grown on acetate. Environ Sci Technol, 2003 Sep 15, 37(18), 4157 - 62 Influence of autochthonous dissolved organic carbon and nutrient limitation on alachlor biotransformation in aerobic aquatic systems; Ensz AP et al.; Much work has suggested that the rate of attenuation of water-soluble organic contaminants in aerobic aquatic systems is dependent on the level of secondary nutrients in the water column . For example, the decay rate of alachlor, a common herbicide, was over 10 times higher under hypereutrophic compared with oligotrophic water conditions . It has been presumed that higher water column nutrient levels produce larger microbial communities, resulting in higher rates of alachlor cometabolism . However, most earlier field studies only assessed alachlor fate in systems with full light exposure (FLE) . Therefore, new experiments were performed to assess how variations in light level affect alachlor cometabolism in such systems . Twelve tank mesocosms were maintained using identical nitrogen (N) and phosphorus (P) supply conditions: four units with full light exposure (100% FLE), four with partial shading (19.3% FLE), and four with near complete shading (0.5% FLE) . Alachlor half-lives were found to vary broadly, from 50 to 60 days in higher light units to > 180 days in the 0.5% FLE units . Nutrient analysis indicated that the low light units were severely carbon (C)-limited for microbial decomposition, whereas the other units had excess C relative to N and P . Apparently, reduced light levels cause decreased production of bioavailable C for decomposition, which significantly reduces alachlor cometabolism . The data suggest that water column nutrient levels only correlate with the alachlor decay rate when light levels are high, and that the biodegradable carbon supply must be considered when the fate of water-soluble contaminants in aerobic aquatic systems is assessed. Biochem Biophys Res Commun, 2003 Oct 17, 310(2), 594 - 9 Differential regulation of secretory leukocyte protease inhibitor and elafin by progesterone; King AE et al.; Elafin and secretory leukocyte protease inhibitor (SLPI) are anti-protease and anti-microbial molecules present at mucosal surfaces . Both molecules are expressed in the female reproductive tract where they may be involved in innate immune defence . This study examines the role of progesterone in the regulation of SLPI and elafin . Progesterone treatment increases expression of SLPI mRNA and protein in the T47D breast epithelial cell line and this upregulation is attenuated in the presence of the anti-gestogens, RU486 and ZK98734, confirming the involvement of the nuclear progesterone receptor . A putative progesterone response element has been identified in the SLPI promoter . Progesterone also acts in synergy with the proinflammatory cytokines, IL-1beta and TNFalpha, to increase SLPI . In contrast, progesterone treatment has no direct effect on elafin mRNA expression . In summary, progesterone has a differential effect on SLPI and elafin expression and although both vary within the uterus throughout the menstrual cycle, progesterone is likely to contribute to the direct regulation of SLPI in the female reproductive tract even in the presence of inflammatory agents. Biochem Biophys Res Commun, 2003 Oct 17, 310(2), 542 - 9 Activation of signaling pathways by putative scavenger receptor class A (SR-A) ligands requires CD14 but not SR-A; Kim WS et al.; Macrophage scavenger class A type I and type II receptors (SR-A) are trimeric, integral membrane glycoproteins that bind an unusually broad array of macromolecular ligands . These ligands include modified proteins and lipoproteins, nucleic acids, and a variety of plant and microbial cell wall constituents, such as fucoidan and lipoteichoic acid . Early studies of SR-A functions indicated that the receptors bound, internalized, and degraded their ligands without provoking any macrophage activating signaling events . More recent studies have provided evidence that several SR-A ligands can activate macrophage gene expression via utilization of a receptor-linked, PI3-kinase pathway . To investigate the role of SR-A in engaging signal transduction events, we employed macrophages taken from mice lacking these receptors . Using either fucoidan or lipoteichoic acid, we confirm that both ligands stimulate tyrosine phosphorylation of PI3-kinase and production of modest levels of the cytokine, TNFalpha . However, macrophages taken from SR-A null mice did not differ from wild type macrophages in these responses, indicating that these signaling events arise independently of SR-A activity . Employing mice lacking CD14, a GPI anchored receptor that binds bacterial lipopolysaccharide and signals via activation of Toll-like receptors, we show that the fucoidan and lipoteichoic acid responses are largely abrogated when CD14 is absent . These data do not provide support for direct SR-A involvement in signal transduction events and suggest that the early characterization of these receptors as initiators of a non-phlogistic, pathogen clearance pathway was correct. Plant Cell Rep, 2004 Feb, 22(7), 519 - 22 Epub 2003 Oct 01. Taxonomic discrimination of higher plants by pyrolysis mass spectrometry; Kim SW et al.; Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains . Leaf samples of six species and one variety of higher plants (Rosa multiflora, R . multiflora var . platyphylla, Sedum kamtschaticum, S . takesimense, S . sarmentosum, Hepatica insularis, and H . asiatica) were subjected to PyMS for spectral fingerprinting . Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters . However, canonical variate analysis of PyMS data separated these plants from one another . A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level . These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level. Nature, 2003 Oct 2, 425(6957), 516 - 21 Epub 2003 Sep 07. Molecular identification of a danger signal that alerts the immune system to dying cells; Shi Y et al.; In infections, microbial components provide signals that alert the immune system to danger and promote the generation of immunity . In the absence of such signals, there is often no immune response or tolerance may develop . This has led to the concept that the immune system responds only to antigens perceived to be associated with a dangerous situation such as infection . Danger signals are thought to act by stimulating dendritic cells to mature so that they can present foreign antigens and stimulate T lymphocytes . Dying mammalian cells have also been found to release danger signals of unknown identity . Here we show that uric acid is a principal endogenous danger signal released from injured cells . Uric acid stimulates dendritic cell maturation and, when co-injected with antigen in vivo, significantly enhances the generation of responses from CD8+ T cells . Eliminating uric acid in vivo inhibits the immune response to antigens associated with injured cells, but not to antigens presented by activated dendritic cells . Our findings provide a molecular link between cell injury and immunity and have important implications for vaccines, autoimmunity and inflammation. Biol Pharm Bull, 2003 Oct, 26(10), 1403 - 6 Effect of the spinal drug tramadol on the fatty acid compositions of rabbit spinal cord and brain; Alici HA et al.; Tramadol is an important spinal drug which produces analgesia following intrathecal injection . It is well known that fatty acids (FAs) play an important role in membrane fluidity of the blood-brain barrier (BBB) tissue, which blocks and/or controls the transportation of toxic substances into the brain . The aim of this study was to investigate the effect of a spinal drug (tramadol) on the concentrations and compositions of fatty acid in BBB tissues of New Zealand male rabbits . The total cellular fatty acid profiles of the tissues in three spinal cord sections (cervical, thoracal and lumbar) and in the brain of rabbits with or without drug administration were determined by gas chromatography using Sherlock Microbial Identification System (MIS) software (Microbial ID, Newark, DE, U.S.A.) with a database of FAME profiles for eukary . The relative percentage of the fatty acid methyl ester (FAME), 24 : 1 omega9c nervonic and 17 : 1 omega8c, did not change with tramadol treatments . However, there was an increase in the concentration of the FA 16 : 0, 18 : 1 omega7c DMA, 18 : 1 omega9c, sum in future 4, sum in future 8, sum in future 9, 18 : 0, 20 : 4 omega6c, sum in future 14, 22 : 4 omega6c, in contrast to a decrease in the percentages of the following FAMEs; 20 : 0, 20 : 1 omega9c . In the brain, there was an increase in the concentration of the FA 18 : 1 omega9c, sum in future 8 and 18 : 0, in contrast to a decrease in the percentages of two FAMEs, 16 : 0, 20 : 4 omega6c and 22 : 6 omega3c . The number of fatty acids were 20 in the spinal cord sections and 8 in the brain tissues of control animals compared to 15-18 fatty acids in the spinal cord section and 7 in the brain tissues of drug administered animals . The overall changes in the concentrations and numbers of FAs suggest that the spinal drug tested in this study has a side effect of disrupting of membrane fluidity of the BBB, which may cause neurotoxicity. Proteins, 2003 Nov 1, 53(2), 241 - 51 Analysis of singleton ORFans in fully sequenced microbial genomes; Siew N et al.; Singleton sequence ORFans are orphan ORFs (open reading frames) that have no detectable sequence similarity to any other sequence in the databases . ORFans are of particular interest not only as evolutionary puzzles but also because we can learn little about them using bioinformatics tools . Here, we present a first systematic analysis of singleton ORFans in the first 60 fully sequenced microbial genomes . We show that although ORFans have been underemphasized, the number of ORFans is steadily growing, currently accounting for 23,634 sequences . At the same time, the percentage of ORFans as a fraction of all sequences is slowly diminishing, and is currently about 14% . Short ORFans comprise about 61% of all ORFans . The abundance of short ORFans may be due to a yet unexplained artifact . The data also suggest that the number of longer ORFans may soon diminish as more genomes of closely related organisms become available . To better address the questions about the functions and origins of ORFans, we propose to focus further studies on the longer ORFans, with emphasis on three new types of ORFans: ORFan modules, paralogous ORFans, and orthologous ORFans . We conclude that the large number of ORFans reflects an intrinsic property of the genetic material not yet fully understood . Further computational and experimental studies aimed at understanding Nature's protein diversity should also include ORFans . Prev Vet Med, 2003 Sep 30, 61(1), 59 - 70 Application of phylogeny reconstruction and character-evolution analysis to inferring patterns of directional microbial transmission; Goldberg TL; I used phylogenetic analyses to reconstruct patterns of directional interspecific transmission during a pseudorabies virus outbreak in Illinois, USA, in 1989 . Isolates were recovered from five species: cattle, sheep, goats, pigs, and raccoons (Procyon lotor) . I generated DNA sequences for 16 isolates of pseudorabies virus at the glycoprotein C gene, from which I constructed phylogenetic trees . I then used these trees, in combination with parsimony-based analyses of character evolution, to infer the frequency and direction of interspecific transmission events . Comparing inferred frequencies and directions of transmission to null expectations based on 10,000 random trees indicated a significant excess of transmission events from pigs to pigs and a corresponding lack of transmission events from non-porcine species . These results are concordant with the know biology and natural history of pseudorabies virus, and they demonstrate that retrospective phylogeny reconstruction and analyses of character evolution can be used to investigate the transmission ecology of pathogens. Eur J Immunol, 2003 Oct, 33(10), 2886 - 93 Production of the soluble pattern recognition receptor PTX3 by myeloid, but not plasmacytoid, dendritic cells; Doni A et al.; PTX3 is a prototypic of long pentraxin consisting of an N-terminal portion coupled to a C-terminal pentraxin domain, the latter related to short pentraxins (C-reactive protein and serum amyloid P component) . PTX3 is a soluble pattern recognition receptor, which plays a non-redundant role in resistance against selected pathogens and in female fertility . The present study was designed to analyze the production of PTX3 by human dendritic cells (DC) and to define the role of different innate immunity receptors in its induction . Human monocyte-derived DC produced copious amounts of PTX3in response to microbial ligands engaging different members of the Toll-like receptor (TLR) family (TLR1 through TLR6), whereas engagement of the mannose receptor had no substantial effect . DC werebetter producers of PTX3 than monocytes and macrophages . Freshly isolated peripheral blood myeloid DC produced PTX3 in response to diverse microbial stimuli . In contrast, plasmacytoid DC exposed to influenza virus or to CpG oligodeoxynucleotides engaging TLR9, did not produce PTX3 . PTX3-expressing DC were present in inflammatory lymph nodes from HIV-infected patients . These results suggest that DC of myelomonocytic origin are a major source of PTX3, a molecule which facilitates pathogen recognition and subsequent activation of innate and adaptive immunity. Glycobiology, 2004 Jan, 14(1), 1 - 12 Epub 2003 Sep 26. Default biosynthesis pathway for blood group-related glycolipids in human small intestine as defined by structural identification of linear and branched glycosylceramides in a group O Le(a-b-) nonsecretor; Angstrom J et al.; Glycoconjugates of the GI tract are important for microbial interactions . The expression of histo-blood group glycosyltransferases governs both the expression of blood group determinants and in part the structure and size of the glycoconjugates . Using neutral glycolipids isolated from the small intestine of a rare blood group O Le(a-b-) ABH secretor-negative (nonsecretor) individual we were able to map the "default" pathway of the individual lacking ABO, Lewis, and secretor glycosyltransferases . Structures were deduced with combined analysis of mass spectrometry (MALDI-TOF and ESI-MS/MS), and 1H NMR (500 and 600 MHz) . All structures present at a level >5% were structurally resolved and included two extended structures: Galbeta4(Fucalpha3)GlcNAcbeta3(Galbeta4{Fucalpha3}GlcNAcbeta6)Galbeta4GlcNAcbeta3Galbeta4Glcbeta1Cer and Galbeta3GlcNAcbeta3(Galbeta4{Fucalpha3}GlcNAcbeta6)Galbeta3GlcNAcbeta3Galbeta4Glcbeta1Cer . The first, a novel component, is based on a type 2 chain and bears the Lex glycotopes on both its branches . The second, a major component, is based on a type 1 chain, which bears a 3-linked type 1 precursor (Lec) glycotope and a 6-linked Lex glycotope on its branches . This latter structure is identical to that previously isolated from plasma and characterized by MS and GC-MS but not by NMR . Structural resolution of these structures was supported by reanalysis of the blood group H-active decaosylceramides previously isolated from rat small intestine . Other minor linear monofucosylated penta-, hepta-, and difucosylated octaosylceramides, some bearing blood group determinants, were also identified . The cumulative data were used to define a default biosynthesis pathway where it can be seen that carbohydrate chain extension, in the absence of blood group glycosyltransferases, is controlled and regulated by non-blood group fucosylation and branching with type 2 Galbeta4GlcNAc branches. Indian J Med Sci, 2003 Feb, 57(2), 64 - 5 Concurrent infection with S.typhi and V . cholerae--a case report"; Tankhiwale SS et al.; An eight year old male child presented with symptoms of diarrhoea, vomiting & fever with signs of moderate dehydration . He was treated with tetracyline and fluid replacement therapy . Inspite of treatment and control of diarrhoea and vomiting patient developed gastrointestinal bleeding and tenesmus with continued fever . Deterioration in patient's condition to suspicion of another infection . High level of suspicion and appropriate microbial investigations revealed dual infection with S . typhi and V . cholerae. Science, 2003 Sep 26, 301(5641), 1852 - 3 Public health . Building microbial forensics as a response to bioterrorism; Budowle B et al.; Combating bioterrorism is a challenge to all of us . To be proactive, the U.S . Government has formalized the discipline of "microbial forensics" to deter and attribute perpetrators of such acts . This Policy Forum describes the foundations of the microbial forensics program: the creation of a national bioforensics laboratory, a partnership laboratory network, and a peer-consensus scientific working group and the promulgation of quality assurance guidelines. J Exp Bot, 2003 Nov, 54(392), 2467 - 77 Epub 2003 Sep 25. Two alpha-L-arabinofuranosidase genes in Arabidopsis thaliana are differentially expressed during vegetative growth and flower development; Fulton LM et al.; Glycosyl hydrolases are important mediators of plant cell wall modification during plant development . These enzymes catalyse the hydrolytic release of specific sugars, such as L-arabinose, from the polysaccharide-rich cell wall matrix . The cloning and expression analysis of two genes, AtASD1 and AtASD2, encoding putative alpha-L-arabinofuranosidases in Arabidopsis thaliana are reported here . AtASD1 and AtASD2 identities were assigned on the basis of homology to plant and microbial family 51 glycoside hydrolases . Using RT-PCR, RNA gel blot analysis and reporter gene expression analysis, AtASD1 and AtASD2 were shown to have different developmental expression profiles . High levels of AtASD1 promoter activity are present in multiple tissues during vegetative and reproductive growth . AtASD1 expression is particularly intense in zones of cell proliferation, the vascular system, developing and regressing floral tissues, and floral abscission zones . By comparison, AtASD2 expression is limited to the vasculature of older root tissue and to some floral organs and floral abscission zones. J Anim Physiol Anim Nutr (Berl), 2003 Feb, 87(1-2), 2 - 11 Influence of dietary ss-glucan on growth performance, lymphocyte proliferation, specific immune response and haptoglobin plasma concentrations in pigs; Hiss S et al.; Immunomodulatory feed additives might offer alternatives to anti-microbial growth promoters in swine production . The present study was conducted to assess the effects of beta-1,3/1,6 glucans, i.e . of specific yeast cell wall components, on immune function and growth performance in pigs . After weaning at 4 weeks of age, 75 piglets were allocated to 3 different groups for 4 weeks, the diet was supplemented with 0, 0.015 or 0.03% of beta-glucan, respectively . All animals were vaccinated against porcine reproductive and respiratory syndrome (PRRS) . After 4 weeks, average daily gains (ADG) of beta-glucan treated pigs were not different from the controls . Feed intake was tendentiously (p < 0.1) increased at 0.03%beta-glucan, without alteration of feed efficiency . Serum haptoglobin concentrations at the end of the 4 week treatment were increased in all groups when compared to the initial levels (p < 0.001), without differences between the groups (p > 0.05) . Haptoglobin levels were inversely related to ADG . Lymphocyte proliferation indices were not different in control and treatment groups . Specific vaccination responses, as quantified by the PRRS antibody titres occurred in all animals, but no relation with beta-glucan feeding was observed . Our results indicate marginal benefits of beta-glucan supplements for growth performance and no effect on the immune parameters tested . The observed trend towards increased feed intake needs further elucidation. Environ Microbiol, 2003 Oct, 5(10), 1009 - 15 Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice; Tan Z et al.; Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified nitrogenase gene (nifH) fragments is a rapid technique for profiling of diazotrophic microbial communities without the necessity of cultures for study . Here, we examined the impact of N-fertilization, plant genotype and environmental conditions on diazotrophic microbial populations in association with roots of rice (Oryza species) by T-RFLP community profiling and found marked effects on the composition of the microbial community . We found a rapid change of the diazotrophic population structure within 15 days after application of nitrogen fertilizer and a strong effect of environmental conditions and plant genotype . Control experiments revealed that phylogenetically distantly related nifH genes were proportionately amplified, and that signal strength reflected the relative abundance of nifH genes in the sample within a 10-fold range of template concentrations . These results clearly demonstrated that our T-RFLP method was suitable to reflect compositional differences in the diazotrophic community in a semiquantitative manner and that the diazotrophic rhizosphere communities of rice are not static but presumably rather highly dynamic. Environ Microbiol, 2003 Oct, 5(10), 842 - 9 Novel Proteorhodopsin variants from the Mediterranean and Red Seas; Sabehi G et al.; Proteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently found in the widespread uncultured SAR86 bacterial group in oceanic surface waters . To survey proteorhodopsin diversity, new degenerate sets of proteorhodopsin primers were designed based on a genomic proteorhodopsin gene sequence originating from an Antarctic fosmid library . New proteorhodopsin variants were identified in Red Sea samples that were most similar to the original green-light absorbing proteorhodopsins found in Monterey Bay California . Unlike green-absorbing proteorhodopsins however, these new variants contained a glutamine residue at position 105, the same site recently shown to control spectral tuning in naturally occurring proteorhodopsins . Different proteorhodopsin variants were also found in the Mediterranean Sea . These proteorhodopsins formed new and distinctive proteorhodopsin groups . Phylogenetic analyses show that some of the new variants were very different from previously characterized proteorhodopsins, and formed the deepest branching groups found so far among marine proteorhodopsins . The existence of these varied proteorhodopsin sequences suggests that this class of proteins has undergone substantial evolution . These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa. Biocell, 2003 Aug, 27(2), 163 - 72 Role of mast cells in gastrointestinal mucosal defense; Penissi AB et al.; The purpose of this review, based on studies from our laboratory as well as from others, is to summarize salient features of mast cell immunobiology and to describe their associations with gastrointestinal mucosal defense . Gastrointestinal mast cells are involved in many pathologic effects, such as food hypersensitivity . On the other hand, they also play a protective role in defense against parasitic and microbial infections . Thus, they have both positive and negative effects, but presently the mechanisms that control the balance of these various effects are poorly known . It has been suggested that stabilization of mast cells may be a key mechanism to protect the gastrointestinal tract from injury . Few molecules are known to possess both mast cell stabilizing and gastrointestinal cytoprotective activity . These include zinc compounds, sodium cromoglycate, FPL 52694, ketotifen, aloe vera, certain flavonoids such as quercetin, some sulfated proteoglycans such as chondroitin sulfate and dehydroleucodine . Dehydroleucodine, a sesquiterpene lactone isolated from Artemisia douglasiana Besser, exhibits anti-inflammatory and gastrointestinal cytoprotective action . The lactone stimulates mucus production, and inhibits histamine and serotonin release from intestinal mast cells . The lactone could act as a selective mast cell stabilizer by releasing cytoprotective factors and inhibiting pro-inflammatory mast cell mediators. Best Pract Res Clin Gastroenterol, 2003 Oct, 17(5), 711 - 24 Probiotics: what are they? What are their effects on gut physiology? Fioramonti J, Theodorou V, Bueno L. Probiotics can be defined as microbial cells that have a beneficial effect on the health and well-being of the host . Since the gastrointestinal mucosa is the surface of contact with probiotics, it seems evident that the first effects of probiotics relate to digestive function . A brief review of the literature indicates that probiotics have very few effects on the main physiological functions of the gastrointestinal tract, which are digestion, absorption and propulsion . The main action of probiotics can be summarised as a reinforcement of the intestinal mucosal barrier against deleterious agents . Experimental data indicate that some probiotics reduce pathological alterations in paracellular permeability to large molecules or bacteria, stimulate mucosal immunity, display a trophic action on the mucosa, reduce mucus degradation and interact with mediators of inflammation . Yoghurt may help lactose digestion, and some data needing confirmation indicate a stimulation of water absorption and an acceleration of intestinal transit by some bacteria. J Dairy Sci, 2003 Sep, 86(9), 2940 - 8 Fatty acid composition of mixed-rumen bacteria: effect of concentration and type of forage; Bas P et al.; The effects of concentration and type of forage in the diet on lipid content and fatty acid (FA) composition of rumen bacteria were studied in 14 goats fitted with duodenal cannulas . The goats were fed a complete maintenance diet containing 40, 70, or 100% chopped forage (dry matter basis) in two equal meals . Forage was either corn stover or alfalfa hay . Microbial cell matter (MCM) was isolated by differential centrifugation of duodenal contents . The FA content of the MCM varied from 5 to 11% of DM and decreased with forage level in the diet . Main FA in MCM were C18:0 and C16:0: together they accounted for 70% of total FA in MCM . The mono-unsaturated FA and branched-chain FA (iso-FA and anteiso-FA) each represented about 10% of FA by weight . The proportion of even-chain saturated FA decreased and those of odd- and branched-chain FA increased with increasing forage . With the corn stover-based diet even-chain saturated FA were lower than with the alfalfa hay-based diet, whereas the unsaturated FA, odd-chain FA, and branched-chain FA were higher . The neutral detergent fiber content of the diet seemed to explain most of the variation associated with even-chain saturated FA, and odd- and branched-chain FA . Our results suggest that, for diets not supplemented with fat, mixed rumen bacteria accumulated energy reserves, by increasing synthesis of either even-chain saturated FA, or saturated odd-chain FA and saturated branched-chain FA. Proc Nutr Soc, 2003 May, 62(2), 383 - 92 Consequences of plant phenolic compounds for productivity and health of ruminants; Waghorn GC et al.; Plant phenolic compounds are diverse in structure but are characterised by hydroxylated aromatic rings (e.g . flavan-3-ols) . They are categorised as secondary metabolites, and their function in plants is often poorly understood . Many plant phenolic compounds are polymerised into larger molecules such as the proanthocyanidins (PA; condensed tannins) and lignins . Only the lignins, PA, oestrogenic compounds and hydrolysable tannins will be considered here . Lignins slow the physical and microbial degradation of ingested feed, because of resilient covalent bonding with hemicellulose and cellulose, rather than any direct effects on the rumen per se . The PA are prevalent in browse and are expressed in the foliage of some legumes (e.g . Lotus spp.), but rarely in grasses . They reduce the nutritive value of poor-quality diets, but can also have substantial benefits for ruminant productivity and health when improved temperate forages are fed . Beneficial effects are dependent on the chemical and physical structure, and concentration of the PA in the diet, but they have been shown to improve live-weight gain, milk yield and protein concentration, and ovulation rate . They prevent bloat in cattle, reduce gastrointestinal nematode numbers, flystrike and CH4 production . Some phenolic compounds (e.g . coumestans) cause temporary infertility, whilst those produced by Fusarium fungi found in pasture, silage or stored grains can cause permanent infertility . The HT may be toxic because products of their metabolism can cause liver damage and other metabolic disorders. Proc Nutr Soc, 2003 May, 62(2), 329 - 36 Forage breeding and management to increase the beneficial fatty acid content of ruminant products; Dewhurst RJ et al.; The declining consumption of ruminant products has been partly associated with their high proportion (but not necessarily content) of saturated fatty acids . Recent studies have focused on the less prominent fact that they are also important sources of beneficial fatty acids, including n-3 fatty acids and conjugated linoleic acids . alpha-Linolenic acid (18 : 3n-3) is of particular interest because it also contributes to improved flavour of beef and lamb . Many recent studies showed large effects of special concentrates on levels of fatty acids in milk and meat . However, the 'rumen protection' treatments, needed to ensure a worthwhile level of fatty acid in products, are expensive . Herbage lipids are the cheapest and safest source of these fatty acids and so breeding to increase delivery of fatty acids from plants into ruminant products is an important long-term strategy . Plant lipids usually contain high levels of polyunsaturated fatty acids, particularly 18 : 2n-6 and 18 : 3n-3 which are the precursors of beneficial fatty acids . Whilst some plants are particularly rich in individual fatty acids (e.g . 18 : 3n-3 in linseed), there are also useful levels in grass and clover (Trifolium Spp.) . Levels of fatty acids in forages in relation to species and varieties are considered, as well as management and conservation methods . Relationships between levels of fatty acids and existing traits and genetic markers are identified . The effects of forage treatments on the fatty acid content of ruminant products are reviewed . The higher levels of polyunsaturated fatty acids in milk from cows fed clover silages show that the level of fatty acids in herbage is not the only factor affecting levels of fatty acids in ruminant products . Further effort is needed to characterise susceptibility of unsaturated fatty acids to oxidative loss during field wilting and biohydrogenation losses in the rumen, and the relative importance of plant and microbial processes in these losses . The pathways of lipolysis and lipid oxidation are reviewed and other plant factors which offer potential to breed for reduced losses are considered. Proc Nutr Soc, 2003 May, 62(2), 279 - 90 Plants and plant extracts for improving animal productivity; Greathead H; Plant secondary metabolites are a natural resource that is largely unexploited in 'conventional' animal production systems . They have in the past been generally considered as a source of antinutritional factors, and not as a source of exploitable performance-enhancing compounds . Recent and continuing changes to legislation controlling the use of animal feed additives have stimulated interest in bioactive secondary metabolites as alternative performance enhancers . They are broadly compatible with current thinking on the future of agriculture and food in Europe, and with consumer opinion . Interest has been largely on their manipulative role in the digestive and absorptive processes of the hindgut . The present paper will review the use of plants and their extracts to manipulate the rumen microbial ecosystem to improve the efficiency of rumen metabolism . The bioavailability of secondary metabolites and their actions on peripheral metabolism will be considered with a view to improving animal performance . The challenge of delivering plants and their extracts to animals outdoors in a controlled manner will be discussed . Much of what is known about the beneficial roles of plant secondary metabolites on animal performance is circumstantial and is based on tenuous data . In order to more fully exploit their bioactive properties for the benefit of animal performance, modes of action need to be understood . Uptake will be dependent on proven efficacy and consumer acceptance of assurances relating to safety, welfare and the environment. Nat Rev Mol Cell Biol, 2003 Sep, 4(9), 721 - 32 Trefoil factors: initiators of mucosal healing; Taupin D et al.; Maintaining the integrity of the gastrointestinal tract, despite the continual presence of microbial flora and injurious agents, is essential . Epithelial continuity depends on a family of small, yet abundant, secreted proteins--the trefoil factors (TFFs) . TFFs protect mucous epithelia from a range of insults and contribute to mucosal repair, although the signalling events that mediate these responses are only partially understood. Insect Biochem Mol Biol, 2003 Oct, 33(10), 1011 - 6 Molecular cloning, expression analysis and cellular localization of gomesin, an anti-microbial peptide from hemocytes of the spider Acanthoscurria gomesiana; Lorenzini DM et al.; Gomesin is a cationic anti-microbial peptide of 18 amino acid residues isolated from the hemocytes of unchallenged tarantula spider Acanthoscurria gomesiana . This paper reports the first study of the processing and cellular location of an anti-microbial peptide (AMP) in spiders . Gomesin cDNA sequence analysis indicated that it is processed from a precursor containing a signal peptide (23 amino acid residues) and a negative C-terminal region (43 amino acid residues) . The gomesin gene was constitutively transcribed in hemocytes and the gene product localized in hemocyte granules . The constitutive production of gomesin by a spider is discussed in the context of an ancient mechanism of AMP regulation and storage. J Food Prot, 2003 Sep, 66(9), 1733 - 7 Comparison of indicators of microbial quality of meat during aerobic cold storage; Byun JS et al.; This study was undertaken to evaluate various indicators for the prediction of the microbial quality of pork and beef loins during cold storage at 0 and 4 degrees C under aerobic conditions . Fresh loins of beef and pork were packaged aerobically and stored at 0 +/- 1 degrees C for 22 days and at 4 +/- 1 degrees C for 12 days or until the total plate counts (TPCs) for these loins exceeded 10(8) CFU/ml . During storage, samples were taken periodically for the measurement of TPCs, psychrotrophic bacterial counts, amine contents, volatile basic nitrogen (VBN) values, thiobarbituric acid values, D-glucose contents, L-lactate contents, pH, and electrical conductivity . Correlation coefficients were ca . 0.90 for all indicators except pH and conductivity . However, VBN and D-glucose contents showed the best correlation with bacterial counts at both temperatures for both beef and pork . Therefore, VBN and D-glucose could potentially be used as indicators in predicting the microbial quality of beef and pork during chilled storage under aerobic conditions. J Econ Entomol, 2003 Aug, 96(4), 1066 - 75 Field activity and storage stability of Anagrapha falcifera nucleopolyhedrovirus (AfMNPV) in spray-dried lignin-based formulations; Behle RW et al.; A multiple-embedded nucleopolyhedrovirus isolated from Anagrapha falcifera (Kirby) (AfMNPV) has potential to be developed into a microbial bioinsecticide because the host range includes several economic pests . We tested spray-dried AfMNPV formulations after storage for insecticidal activity based on bioassays with neonate Trichoplusia ni (Hubner) . Eight experimental lignin-based spray-dried formulations, a glycerin-based formulation, and an unformulated sample were made with virus stock from three commercial production lots . Samples of these formulations were stored at 30 degrees C in individually sealed sample containers for destructive sampling after 1, 3, and 6 mo whereas the remaining product was stored in glass jars under refrigeration for up to 30 mo . Spray drying did not significantly reduce the initial LC50s of AfMNPV in experimental formulations compared with unformulated virus that was not spray dried . Refrigerated storage for 6 mo did not significantly lower virus activity of formulated samples compared with the unformulated AfMNPV stored frozen, while samples stored for 30 mo had higher LC50 values determined by both droplet and leaf feeding assays . When stored at 30 degrees C, most formulations (22 of 24) maintained insecticidal activity for 3 mo, but most (21 of 24) lost significant activity after 6 mo of storage . The glycerin-based formulation also lost activity within 6 mo of storage at 30 degrees C when compared with frozen unformulated virus, but did not lose activity when stored refrigerated for up to 30 mo . These formulations were evaluated after 7 mo at 4 degrees C for residual insecticidal activity when applied to field grown cabbage . Insecticidal activity was determined against T . ni neonates for treated leaf samples collected at 3, 7, 27, and 51 h after application of 2.5 x 10(12) obs/ha . Field tests showed no differences in activity among samples of stored formulations and one freshly made formulation . Spray-dried formulations had significantly higher insecticidal activity (67.5% mortality) compared with the unformulated treatment (30% mortality) sampled 3 h after application . At 3, 7, and 27 h after application, the spray-dried formulations had higher residual activity (67%, 59%, and 42% mortality, respectively), compared with the commercial glycerin-based formulation (61%, 38%, and 23% mortality, respectively) . These experiments demonstrated that AfMNPV in lignin-based spray-dried formulations had a shelf-life of up to 3 mo at 30 degrees C and up to 30 mo at 4 degrees C, and with longer residual insecticidal activity in the field compared with unformulated or a glycerin formulation. Adv Space Res, 2003, 31(7), 1693 - 8 The biological component of the life support system for a Martian expedition; Sychev VN et al.; Ground-based experiments at RF SSC-IBMP RAS (State Science Center of Russian Federation--Institute of Biomedical Problems of Russian Academia of Science) were aimed at overall studies of a human-unicellular algae-mineralization LSS (life support system) model . The system was 15 m3 in volume . It contained 45 L of algal suspension with a dry substance density of 10-12 g per liter; water volume, including the algal suspension, was 59 L . More sophisticated model systems with partial substitution of unicellular algae with higher plates (crop area of 15 m2) were tested in three experiments from 1.5 to 2 months in duration . The experiments demonstrated that LSS employing the unicellular algae play not only a macrofunction (regeneration of atmosphere and water) but also carry some other functions (purification of atmosphere, formation of microbial cenosis etc.) providing an adequate human environment . It is also important that functional reliability of the algal regenerative subsystem is secured by a huge number of cells able, in the event of death of a part of population, to recover in the shortest possible time the size of population and, hence, functionality of the LSS autotrophic component . For a long period of time a Martian crew will be detached from Earth's biosphere and for this reason LSS of their vehicle must be highly reliable, robust and redundant . One of the approaches to LSS redundancy is installation of two systems with different but equally efficient regeneration technologies, i.e . physical-chemical and biological . At best, these two systems should operate in parallel sharing the function of regeneration of the human environment . In case of failure or a sharp deterioration in performance of one system the other will, by way of redundancy, increase its throughput to make up for the loss . This LSS design will enable simultaneous handling of a number of critical problems including adequate satisfaction of human environmental needs . c2003 COSPAR . Published by Elsevier Science Ltd . All rights reserved. Microb Ecol, 2003 Nov, 46(4), 429 - 41 Epub 2003 Sep 17. Sediment microbial community composition and methylmercury pollution at four mercury mine-impacted sites; Batten KM et al.; Mercury pollution presents a globally significant threat to human and ecosystem health . An important transformation in the mercury cycle is the conversion of inorganic mercury to methylmercury, a toxic substance that negatively affects neurological function and bioaccumulates in food chains . This transformation is primarily bacterially mediated, and sulfate-reducing bacteria (SRB) have been specifically implicated as key mercury methylators in lake and estuarine sediments . This study used phospholipid fatty acid (PLFA) analysis to investigate sediment microbial community composition at four abandoned mercury mine-impacted sites in the California Coast Range: the Abbott, Reed, Sulphur Bank, and Mt . Diablo mines . Differences in watershed and hydrology among these sites were related to differences in microbial community composition . The Abbott and Sulphur Bank mines had the highest levels of methylmercury . Floc (a type of precipitate that forms when acid mine drainage contacts lake or river water) and sediment samples differed in terms of several important environmental variables and microbial community composition, but did not have statistically different methylmercury concentrations . Quantification of PLFA biomarkers for SRB (10Mel6:0 for Desulfobacter and i17:1 for Desulfovibrio) revealed that Desulfobacter and Desulfovibrio organisms made up higher percentages of overall microbial biomass at the Sulphur Bank and Mt . Diablo mines than at the Abbott and Reed mines . Correlations between these SRB biomarker fatty acids and methylmercury concentrations suggest that Desulfobacter and Desulfovibrio organisms may contribute to methylmercury production in the Abbott, Reed, and Sulphur Bank mines but may not be important contributors to methylmercury in the Mt . Diablo Mine. Microb Ecol, 2003 Oct, 46(3), 312 - 21 Epub 2003 Sep 17. Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado plateau; Garcia-Pichel F et al.; We characterized, at millimeter resolution, bacterial biomass, diversity, and vertical stratification of biological soil crusts in arid lands from the Colorado Plateau . Microscopic counts, extractable DNA, and plate counts of viable aerobic copiotrophs (VAC) revealed that the top centimeter of crusted soils contained atypically large bacterial populations, tenfold larger than those in uncrusted, deeper soils . The plate counts were not always consistent with more direct estimates of microbial biomass . Bacterial populations peaked at the immediate subsurface (1-2 mm) in light-appearing, young crusts, and at the surface (0-1 mm) in well-developed, dark crusts, which corresponds to the location of cyanobacterial populations . Bacterial abundance decreased with depth below these horizons . Spatially resolved DGGE fingerprints of Bacterial 16S rRNA genes demonstrated the presence of highly diverse natural communities, but we could detect neither trends with depth in bacterial richness or diversity, nor a difference in diversity indices between crust types . Fingerprints, however, revealed the presence of marked stratification in the structure of the microbial communities, probably a result of vertical gradients in physicochemical parameters . Sequencing and phylogenetic analyses indicated that most of the naturally occurring bacteria are novel types, with low sequence similarity (83-93%) to those available in public databases . DGGE analyses of the VAC populations indicated communities of lower diversity, with most types having sequences more than 94% similar to those in public databases . Our study indicates that soil crusts represent small-scale mantles of fertility in arid ecosystems, harboring vertically structured, little-known bacterial populations that are not well represented by standard cultivation methods. Microb Ecol . 2003 Sep 17; {Epub ahead of print} The Relationship between Microbial Community Structure and Functional Stability, Tested Experimentally in an Upland Pasture Soil; Griffiths BS et al.; Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure . One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil . Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed . In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined . Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored . The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands . These shifts in microbial community structure were associated with a reduction in functional stability . The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies . RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation . We conclude that the functional stability of decomposition is related to specific components of the microbial community. Curr Opin Infect Dis, 2003 Oct, 16(5), 445 - 51 Helicobacter pylori; Moss SF et al.; PURPOSE OF REVIEW: Helicobacter pylori is an important human pathogen, responsible for most peptic ulcer disease, gastritis and gastric malignancies . H . pylori has several unique features: it is highly adapted for gastric colonization, yet it produces clinical consequences in a small minority, its genome is known, and it is the only bacterium strongly associated with cancer . H . pylori is therefore of great interest to clinicians and researchers of many, often disparate, disciplines . We highlight recent advances in this fast changing field from many different areas . RECENT FINDINGS: The major contentious clinical issues relate to the synergistic gastrotoxic interactions of H . pylori with non-steroidal anti-inflammatory drugs, and a possible association of H . pylori with atherosclerotic events . Accumulating evidence implicates genetic variation in the inflammatory response to H . pylori in the etiology of the increased risk of gastric cancer after H . pylori infection . Studies of pathogenesis have been aided by increasingly sophisticated murine models . The effects in gastric epithelial cells of two of the major virulence factors (genes within the cag pathogenicity island and the vacuolating cytotoxin, VacA) of H . pylori illustrate the complex network of cellular reactions activated by H . pylori . The metabolism of H . pylori is dependent on the availability of hydrogen . SUMMARY: Basic science research into H . pylori continues to elucidate the mechanisms by which H . pylori infection causes disease . These findings have implications for the design of novel therapies and for improving clinical strategies to identify at-risk individuals . Many are also worthy of consideration for other epithelial-microbial interactions. Curr Opin Allergy Clin Immunol, 2003 Oct, 3(5), 347 - 52 The genetics of CD14 in allergic disease; Koppelman GH et al.; PURPOSE OF REVIEW: The 'hygiene hypothesis' implies that infections in early childhood prevent the development of atopy . Atopy is caused by the interaction of the environment with genetic factors . Therefore, both contacts with microbial products such as endotoxin as well as CD14, a gene involved in the immunological response to endotoxin, are discussed in this review . RECENT FINDINGS: CD14 is a multifunctional receptor for endotoxin and other bacterial wall components . Membrane-bound CD14 is expressed on monocytes and macrophages . It forms a complex with Toll-like receptor 4 . Genetic studies have shown an association of variants in the CD14 gene with the prevention of (and severity of) atopy . However, phenotype definitions and the allele that showed association differed between studies . In addition, the presence of endotoxin in house dust appears to be inversely related to atopy in different studies . SUMMARY: It can be hypothesized that different levels of endotoxin exposure could interact with specific CD14 variants in the prevention of atopy . If confirmed in prospective cohort studies, this might represent an important gene by environmental interaction in the development of atopy . This could possibly open ways for the primary prevention of atopy. Curr Opin Allergy Clin Immunol, 2003 Oct, 3(5), 331 - 5 Metropolitan endotoxin exposure, allergy and asthma; Song BJ et al.; PURPOSE OF REVIEW: To review the role of metropolitan endotoxin exposure in asthma and allergy, emphasizing recently published articles (i.e . April 2002-June 2003) . RECENT FINDINGS: In infants and toddlers in metropolitan communities, higher endotoxin levels in house dust are associated with less atopy and increased wheezing in infancy, but this increased risk may normalize by age 4 years . Increased endotoxin levels and exposure in metropolitan households with dogs and sometimes cats is intriguing in light of recent studies suggesting that animal exposure early in life is associated with less allergen sensitization and asthma . Dust endotoxin also appears to serve as a marker for other similar innate immune-stimulatory microbial components called pathogen-associated molecular patterns . Pathogen-associated molecular patterns, such as bacterial DNA, may augment and steer endotoxin-initiated immune responses in an immune-regulatory direction . These findings support the premise that the differences in health outcomes from endotoxin exposure are due to important moderating variables, such as age of exposure, timing of exposure relative to disease development, dose and frequency of exposure, co-exposures, and genetic predispositions in response to endotoxin . SUMMARY: We will discuss (1) endotoxin's ability to exacerbate established atopic disease and asthma; (2) factors influencing endotoxin levels in metropolitan homes; (3) relationships between endotoxin, pet exposure, and atopic disease; (4) endotoxin's paradoxical potential to both abrogate as well as exacerbate asthma; and (5) endotoxin's role as a marker for other similar pathogen-associated molecular patterns. J Biol Chem, 2003 Nov 28, 278(48), 48245 - 50 Epub 2003 Sep 18. Human-specific regulation of alpha 2-6-linked sialic acids; Gagneux P et al.; Many microbial pathogens and toxins recognize animal cells via cell surface sialic acids (Sias) that are alpha 2-3- or alpha 2-8-linked to the underlying glycan chain . Human influenza A/B viruses are unusual in preferring alpha 2-6-linked Sias, undergoing a switch from alpha 2-3 linkage preference during adaptation from animals to humans . This correlates with the expression of alpha 2-6-linked Sias on ciliated human airway epithelial target cells and of alpha 2-3-linked Sias on secreted soluble airway mucins, which are unable to inhibit virus binding . Given several known differences in Sia biology between humans and apes, we asked whether this pattern of airway epithelial Sia linkages is also human-specific . Indeed, we show that since the last common ancestor with apes, humans underwent a concerted bidirectional switch in alpha 2-6-linked Sia expression between airway epithelial cell surfaces and secreted mucins . This can explain why the chimpanzee appears relatively resistant to experimental infection with human Influenza viruses . Other tissues showed additional examples of human-specific increases or decreases in alpha 2-6-linked Sia expression and only one example of a change specific to certain great apes . Furthermore, while human and great ape leukocytes both express alpha 2-6-linked Sias, only human erythrocytes have markedly up-regulated expression . These cell type-specific changes in alpha 2-6-Sia expression during human evolution represent another example of a human-specific change in Sia biology . Because the data set involves multiple great apes, we can also conclude that Sia linkage expression patterns can be conserved during millions of years of evolution within some vertebrate taxa while undergoing sudden major changes in other closely related ones. J Microbiol Methods, 2003 Oct, 55(1), 165 - 72 A high-pressure thermal gradient block for investigating microbial activity in multiple deep-sea samples; Kallmeyer J et al.; Details about the construction and use of a high-pressure thermal gradient block for the simultaneous incubation of multiple samples are presented . Most parts used are moderately priced off-the-shelf components that easily obtainable . In order to keep the pressure independent of thermal expansion of the sample vessels, a back-pressure system with a constant leak rate was installed . Pressure is applied through high-pressure liquid chromatography (HPLC) pumps that run in constant pressure mode with variable flow rate, thereby regulating any pressure fluctuations . The device allows incubations along a wide range of temperatures and pressures and can easily be modified to accommodate different experiments, either biological or chemical . As an application, we present measurements of bacterial sulfate reduction rates in hydrothermal sediments from Guyamas Basin over a wide range of temperatures and pressures . Sulfate reduction rates increase with increasing pressure and show maximum values at pressures higher than in situ. J Microbiol Methods, 2003 Oct, 55(1), 155 - 64 Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale; Webster G et al.; Investigations into the deep marine environment have demonstrated the presence of a significant microbial biomass buried deep within sediments on a global scale . It is now believed that this deep biosphere plays a major role in the global cycling of elements and contains a large reservoir of organic carbon . This paper reports the development of a DNA extraction protocol that addresses the particular problems faced in applying molecular ecological techniques to samples containing very low biomass . Sediment samples were collected from different geographical locations within the Pacific Ocean and include the Ocean Drilling Program (ODP) Leg 190, Nankai Trough Accretionary Prism . Seven DNA extraction protocols were tested and a commercially available DNA extraction kit with modifications was shown to produce higher yields of polymerase chain reaction (PCR)-amplifiable DNA than standard laboratory methods . Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene diversity revealed that template DNA from these extremely low biomass sediment samples was susceptible to PCR bias and random amplification . We propose that it is essential to screen 16S rRNA gene products for bacterial diversity by DGGE or other rapid fingerprinting methods, prior to their use in establishing a representative clone library of deep sub-seafloor bacteria . This represents a cautionary approach to analysis of microbial diversity in such sub-seafloor ecosystems. Chem Phys Lipids, 2003 Oct, 125(2), 103 - 14 Fluorescent organophosphonates as inhibitors of microbial lipases; Oskolkova OV et al.; Short- and long-chain 1-O-alkyl-2-acylaminodeoxyglycero- and alkoxy-alkylphosphonic acid p-nitrophenyl esters were synthesized as inhibitors for analytical and mechanistic studies on lipolytic enzymes . The respective compounds contain perylene or nitrobenzoxadiazole as reporter fluorophores covalently bound to the omega-ends of the respective 2-acylamino- and alkoxy- residues . Their inhibitory effects on the activities of three selected lipases showing different substrate preferences were determined, including the lipases from Rhizopus oryzae, Pseudomonas species, and Pseudomonas cepacia . R . oryzae lipase reacted much better with the single-chain inhibitors than the two-chain deoxyglycerolipids . In contrast, P . cepacia lipase was inactivated by perylene-containing two-chain phosphonate (XXII) to a larger extent as compared to the other inhibitors whereas Pseudomonas species lipase interacted efficiently and without any preferences with all inhibitors used in this study . In summary, the different lipases show a very characteristic reactivity pattern not only with respect to triacylglycerol substrates but also to their structurally related inhibitors . Thus, the novel phosphonates might be useful tools not only for analysis and discrimination of known lipolytic enzymes but also for discovery of yet unknown lipases/esterases in biological samples. Immunity, 2003 Sep, 19(3), 353 - 63 TRAF6 is a critical factor for dendritic cell maturation and development; Kobayashi T et al.; IL-1 receptor (IL-1R)/Toll-like receptor (TLR) family and TNF receptor (TNFR) superfamily members are critical for regulating multiple aspects of dendritic cell (DC) biology . Several signaling pathways associated with each family utilize the adapter molecule, TRAF6, but its role in DCs is unclear . By examining TRAF6-deficient mice and bone marrow (BM) chimeras reconstituted with TRAF6-deficient fetal liver cells, we show that proper DC maturation requires TRAF6 . In response to either microbial components or CD40L, TRAF6-deficient DCs fail to upregulate surface expression of MHCII and B7.2, or produce inflammatory cytokines . Moreover, LPS-treated TRAF6-deficient DCs do not exhibit an enhanced capacity to stimulate naive T cells . Interestingly, a major population of splenic DCs, the CD4(+)CD8alpha(-) subset, is nearly absent in both TRAF6-deficient mice and BM chimeras . Together these results indicate that TRAF6 regulates the critical processes required for maturation, activation, and development of DCs, the primary cellular bridge between innate and adaptive immunity. Expert Opin Ther Targets, 2003 Oct, 7(5), 603 - 12 The Toll-lik