Bacteriological

Biotechniques, 2003 Nov, 35(5), 976 - 9
Rapid development of gene-tagged microsatellite markers from bacterial artificial chromosome clones using anchored TAA repeat primers; Waldbieser GC et al.; We developed a technique to improve the efficiency of producing TAA repeat microsatellite markers linked to interspecific conserved genes . Template DNA was prepared from cultures derived from single bacterial artificial chromosome (BAC) colonies using a simple alkaline lysis miniprep . The presence of conserved genes in each BAC clone was verified by sequencing with gene-specific primers . The BAC templates were directly sequenced using short tandem repeat-anchored primers (STRAPs), consisting of TAA repeats with one or two unique 3' terminal bases . At least one STRAP provided sufficient 3' flanking sequence from each clone for the design of a BAC-specific primer . The BAC-specific primer was used to sequence back through the tandem repeat and obtain 5' flanking sequence, and a second BAC-specific primer was designed for microsatellite genotype analysis . This technique quickly provided microsatellite markers with an average of 15 tandem repeats for the BAC clones tested . The identification of polymorphic microsatellite loci in these clones permits the identification of alleles linked to candidate genes, placement of conserved genes on genetic linkage maps, and integration of linkage and physical maps.

Infect Dis Obstet Gynecol, 2003, 11(2), 123 - 9
The effect of treating bacterial vaginosis on preterm labor; Tebes CC et al.; OBJECTIVE: Multiple studies suggest that bacterial vaginosis (BV) causes preterm labor; yet its routine treatment remains controversial . In order to help to elucidate this controversy, we performed a thorough review of studies with levels of evidence ranging from I to II-II . METHODS: We searched for all of the studies from the years 1994 to 2001 via Medline's database, including MD Consult and Ovid Mednet . RESULTS: Several trials discovered a decrease in the incidence of preterm labor when BV was treated, but most of those trials were performed on women with a history of preterm labor . However, the majority of trials reviewed advise against treatment of a general low-risk obstetric population, as there was no significant decrease in preterm labor . CONCLUSIONS: Therefore, based on the above studies and the current guidelines of the Centers for Disease Control and Prevention (CDC), treating pregnant women in high-risk populations who are diagnosed with BV provides the clinician with an opportunity to possibly prevent preterm labor in this population . In nulliparous women without a history of preterm birth, treatment is recommended if other risk factors are present (e.g . gonorrhea or chlamydia) . However, in the general low-risk populations, routine screening is not indicated.

Infect Dis Obstet Gynecol, 2003, 11(2), 105 - 8
Bacterial sacroiliitis probably induced by lumbar epidural analgesia; Edelstein S et al.; BACKGROUND: Properly administered, lumbar epidural analgesia provides adequate pain relief during labor and delivery, and is considered to be a safe procedure with limited complications . The prevalence of infection after lumbar epidural analgesia is negligible . INTRODUCTION: Infection of the sacroiliac joint, although very close to the pucture area, has never been reported as a procedure complication . CASE: In this report, we describe a patient who experienced bacterial sacroiliitis a few days after lumbar epidural analgesia for labor . No portal of entry was identified, and we evoked a new potential risk factor that has never been proposed before, namely lumbar epidural analgesia . CONCLUSION: Sacroiliitis must be considered as a rare but serious complication of lumbar epidural analgesia.

Nat Immunol, 2003 Dec, 4(12), 1247 - 53 Epub 2003 Nov 16.
Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility; Smith KD et al.; Toll-like receptor 5 (TLR5) recognizes bacterial flagellin and activates host inflammatory responses . In this study, we examine the nature of the TLR5-flagellin interaction . With deletional, insertional and alanine-scanning mutagenesis, we precisely mapped the TLR5 recognition site on flagellin to a cluster of 13 amino acid residues that participate in intermolecular interactions within flagellar protofilaments and that are required for bacterial motility . The recognition site is buried in the flagellar filament, and monomeric flagellin, but not the filamentous molecule, stimulated TLR5 . Finally, flagellin coprecipitated with TLR5, indicating close physical interaction between the molecules . These studies demonstrate the exquisite ability of the innate immune system to precisely target a conserved site on flagellin that is essential for bacterial motility.

Proc Natl Acad Sci U S A, 2003 Nov 25, 100(24), 13910 - 5 Epub 2003 Nov 17.
Influence of topology on bacterial social interaction; Park S et al.; The environmental topology of complex structures is used by Escherichia coli to create traveling waves of high cell density, a prelude to quorum sensing . When cells are grown to a moderate density within a confining microenvironment, these traveling waves of cell density allow the cells to find and collapse into confining topologies, which are unstable to population fluctuations above a critical threshold . This was first observed in mazes designed to mimic complex environments, then more clearly in a simpler geometry consisting of a large open area surrounding a square (250 x 250 microm) with a narrow opening of 10-30 microm . Our results thus show that under nutrient-deprived conditions bacteria search out each other in a collective manner and that the bacteria can dynamically confine themselves to highly enclosed spaces.

Oral Microbiol Immunol, 2003 Dec, 18(6), 401 - 4
The production of 6-deoxy-L-talan from Actinobacillus actinomycetemcomitans via bacterial coupling in vitro; Suzuki N et al.; A method of producing 6-deoxy-L-talan, the serotype c-specific polysaccharide antigen (SPA) from Actinobacillus actinomycetemcomitans,was established using a whole-cell reaction with two recombinant Escherichia coli strains . The production of serotype c-SPA was investigated using the dot blot assay with anti-A . actinomycetemcomitans NCTC 9710 serum after an 18-h reaction, starting with a solution containing the recombinant E . coli cells, alpha-d-glucose-1-phosphate, and dTTP . Moreover, examination of the time course for 6-deoxy-L-talan production proved that this system ran satisfactorily . This paper is the first report of a convenient method to readily produce the exopolysaccharide from A . actinomycetemcomitans in vitro.

Oral Microbiol Immunol, 2003 Dec, 18(6), 350 - 8
Expression of MHC Class II, CD70, CD80, CD86 and pro-inflammatory cytokines is differentially regulated in oral epithelial cells following bacterial challenge; Han DC et al.; Oral epithelium may play a regulatory role in local immune responses when interacting with bacteria . The present study was undertaken to investigate the effects of selected bacterial pathogens found in periodontal and endodontic infections on oral epithelial cells . Expression of cell surface molecules (major histocompatibility complex (MHC) Class II, CD54, CD70, CD80 and CD86) and secretion of inflammatory cytokines (interleukin (IL)-1beta, IL-6, and tumor necrosis factor (TNF)-alpha) in response to selected bacterial challenge were examined on an immortalized oral epithelial cell line, HOK-18A and a skin epithelial cell line, HaCaT . Actinomyces viscosus, Actinomyces israelii, Fusobacterium nucleatum lipopolysaccharide (LPS) or primary human periradicular exudate from a granuloma were co-cultured with epithelial cells for 4 or 24 h . Subsequently, cell surface expression of MHC Class II, CD54, CD70, CD80 and CD86, along with pro-inflammatory cytokine levels were determined using flow cytometry, ELISA and RT-PCR . Results indicated that the selected oral bacteria have greater effects on oral versus skin epithelial cells . F . nucleatum increased MHC Class II and CD54 (ICAM-1) cell surface expression on HOK-18A and HaCaT cells . A . israelii also had enhancing effects on the expression of CD54 and MHC Class II . A . israelii and LPS induced a 2.8-fold (P < 0.001) and 4.4-fold (P < 0.005) TNF-alpha secretion, respectively, while F . nucleatum and LPS induced a 10-fold (P < 0.0004) and 6-fold (P < 0.01) IL-1beta secretion, respectively by HOK-18A . Interestingly, CD70, CD80, and CD86 were generally decreased upon bacteria and LPS challenge on HOK-18A . The effects of increased MHC Class II and decreased CD70 were also evident with challenge of human periradicular exudate on HOK-18A . The implications of the study are unique in that oral epithelial cells may play both activating and inhibitory roles in the host immune response towards infection by oral bacteria . We introduce a concept of 'dormancy' where the differential expression of key cell surface antigens on oral epithelial cells may keep the recruited immune effector cells in a state of unresponsiveness, thus contributing to the long term quiescent period observed in many periodontal and endodontic lesions.

Nippon Rinsho, 2003 Nov, 61(11), 1892 - 6
{Potentiation of infectivity and pathogenesis of influenza virus by host and bacterial proteases}; Nagatake T; Infectivity and pathogenicity of influenza viruses are based on the interplay between the viral glycoprotein hemagglutinin (HA) and host proteases . HA receives its full biological activities by proteolytic cleavage of a precursor molecule at a definite cleavage site . Proteases selected by the Clara cells in the bronchial epithelia and many kind of bacteria, are virus activate proteases responsible for the cleavage activation and pathogenicity of influenza viruses . Although influenza in normal individuals is usually confined to the upper respiratory tract, the infection often develops into fatal pneumonia in aged patients, where bacterial infections often occur . Synergistic effects of bacterial infections on the pathogenesis of influenza viruses are described in regard to the cleavage activation of HA.

Cell Mol Life Sci, 2003 Oct, 60(10), 2100 - 14
Bacterial oligopeptide-binding proteins; Monnet V; This review focuses on bacterial oligopeptide-binding proteins, which form part of the oligopeptide transport system belonging to the ATP-binding cassette family of transporters . Depending on the bacterial species, these binding proteins (OppA) capture peptides ranging in size from 2 to 18 amino acids from the environment and pass them on to the other components of the oligopeptide transport system for internalisation . Bacteria have developed several strategies to produce these binding proteins, which are periplasmic in Gram- bacteria and membrane-anchored in Gram+, with a higher stoichiometry (probably necessary for efficient transport) than the other components in the transport system . The expression of OppA-encoding genes is clearly modulated by external factors, especially nitrogen compounds, but the mechanisms of regulation are not always clear . The best-understood roles played by OppAs are internalisation of peptides for nutrition and recycling of muropeptides . It has, however, recently become clear that OppAs are also involved in sensing the external medium via specific or non-specific peptides.

Cell Mol Life Sci, 2003 Oct, 60(10), 2034 - 52
The bacterial translocase: a dynamic protein channel complex; de Keyzer J et al.; The major route of protein translocation in bacteria is the so-called general secretion pathway (Sec-pathway) . This route has been extensively studied in Escherichia coli and other bacteria . The movement of preproteins across the cytoplasmic membrane is mediated by a multimeric membrane protein complex called translocase . The core of the translocase consists of a proteinaceous channel formed by an oligomeric assembly of the heterotrimeric membrane protein complex SecYEG and the peripheral adenosine triphosphatase (ATPase) SecA as molecular motor . Many secretory proteins utilize the molecular chaperone SecB for targeting and stabilization of the unfolded state prior to translocation, while most nascent inner membrane proteins are targeted to the translocase by the signal recognition particle and its membrane receptor . Translocation is driven by ATP hydrolysis and the proton motive force . In the last decade, genetic and biochemical studies have provided detailed insights into the mechanism of preprotein translocation . Recent crystallographic studies on SecA, SecB and the SecYEG complex now provide knowledge about the structural features of the translocation process . Here, we will discuss the mechanistic and structural basis of the translocation of proteins across and the integration of membrane proteins into the cytoplasmic membrane.

J Appl Genet, 2003, 44(4), 561 - 84
High divergence rate of sequences located on different DNA strands in closely related bacterial genomes; Mackiewicz P et al.; One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging) . The main cause of the observed bias is the mutational pressure associated with replication . This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate . Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication . Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones . Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences . These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found . The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees . The changing mutational pressure may contribute to arising of genes with new functions as well.

Mol Microbiol, 2003 Nov, 50(3), 763 - 70
Targeting of two signal transduction pathways to different regions of the bacterial cell; Wadhams GH et al.; Components of bacterial chemosensory pathways which sense via transmembrane receptors have been shown to localize to the cell poles . Many species, however, have operons encoding multiple putative chemosensory pathways, some including putative cytoplasmic receptors . In-genome fusions to single or multiple genes encoding components of two chemosensory pathways in Rhodobacter sphaeroides, cheOp2 and cheOp3, revealed that while sensory transducing proteins associated with transmembrane receptors and encoded on cheOp2 were targeted to the cell poles, the proteins associated with putative cytoplasmic receptors and encoded on cheOp3 were all targeted to a cytoplasmic cluster . No proteins were localized to both sites . These data show that bacteria target components of related pathways to different sites in the cell, presumably preventing direct cross-talk between the different pathways, but allowing a balanced response between extracellular and cytoplasmic signals . It also indicates that there is intracellular organization in bacterial cells, with specific proteins targeted and localized to cytoplasmic regions.

Plant J, 2003 Nov, 36(3), 353 - 65
ERECTA, an LRR receptor-like kinase protein controlling development pleiotropically affects resistance to bacterial wilt; Godiard L et al.; Bacterial wilt, one of the most devastating bacterial diseases of plants worldwide, is caused by Ralstonia solanacearum and affects many important crop species . We show that several strains isolated from solanaceous crops in Europe are pathogenic in different accessions of Arabidopsis thaliana . One of these strains, 14.25, causes wilting symptoms in A . thaliana accession Landsberg erecta (Ler) and no apparent symptoms in accession Columbia (Col-0) . Disease development and bacterial multiplication in the susceptible Ler accession depend on functional hypersensitive response and pathogenicity (hrp) genes, key elements for bacterial pathogenicity . Genetic analysis using Ler x Col-0 recombinant inbred lines showed that resistance is governed by at least three loci: QRS1 (Quantitative Resistance to R . solanacearum) and QRS2 on chromosome 2, and QRS3 on chromosome 5 . These loci explain about 90% of the resistance carried by the Col-0 accession . The ERECTA gene, which encodes a leucine-rich repeat receptor-like kinase (LRR-RLK) and affects development of aerial organs, is dimorphic in our population and lies close to QRS1 . Susceptible Ler plants transformed with a wild-type ERECTA gene, and the LER line showed increased disease resistance to R . solanacearum as indicated by reduced wilt symptoms and impaired bacterial growth, suggesting unexpected cross-talk between resistance and developmental pathways.

Clin Microbiol Infect, 2003 Nov, 9(11), 1142 - 7
Spread of Stenotrophomonas maltophilia colonization in a pediatric intensive care unit detected by monitoring tracheal bacterial carriage and molecular typing; Lanotte P et al.; In our pediatric intensive care unit in Tours (France), intubated and ventilated inpatients are systematically monitored for tracheal bacterial colonization twice a week . This led us to detect five patients colonized with Stenotrophomonas maltophilia over a 4-month period . Molecular typing of the isolates using random amplified polymorphism DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) confirmed that four of the five isolates were genetically related . The strict isolation of carriers and improvements in hygiene measures stopped the spread . This systematic strategy prevented pulmonary nosocomial infections or allowed their early detection . Moreover, it has made it possible to assess the efficiency of care practices continuously.

J Theor Biol, 2003 Dec 21, 225(4), 493 - 6
DNA-membrane interactions can localize bacterial cell center; Rabinovitch A et al.; In actively growing bacterial cells, the DNA exerts stress on the membrane, in addition to the turgor caused by osmotic pressure . This stress is applied through coupled transcription/translation and insertion of membrane proteins (so-called "transertion" process) . In bacillary bacteria, the strength of this interaction varies along cell length with a minimum at its midpoint, and hence can locate the cell's equator for the assembly of the FtsZ-ring.

Biosens Bioelectron, 2003 Dec 15, 19(4), 325 - 30
Development and evaluation of an automated workstation for single nucleotide polymorphism discrimination using bacterial magnetic particles; Tanaka T et al.; We designed an automated workstation for magnetic particle-based single nucleotide polymorphism (SNP) discrimination of ALDH genotypes . Bacterial magnetic particles (BMPs) extracted from Magnetospirillum magneticum AMB-1 were used as DNA carriers . The principle for SNP discrimination in this study was based on fluorescence resonance energy transfer (FRET) between FITC (donor) and POPO-3 (acceptor) bound to double-stranded DNA . The workstation is equipped with a 96-way automated pipetter which collects and dispenses fluids as it moves in x- and z-directions . The platform contains a disposable tip rack station, a reagent vessel serving as a stock for POPO-3 and FITC-labeled probes and a reaction station for a 96-well microtiter plate . BMPs were collected by attaching a neodymium iron boron sintered (Nd-Fe-B) magnet on the bottom of the microtiter plate . This system permits the simultaneous heating and magnetic separation of 96 samples per assay . The genotypes ALDH2*1 and ALDH2*2 were discriminated by calculating the relative fluorescence intensities on BMPs.

FEMS Microbiol Lett, 2003 Nov 7, 228(1), 45 - 9
Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes; Coenye T et al.; The availability of a large number of completely sequenced bacterial genomes allows the rapid and reliable determination of intragenomic sequence heterogeneity of 16S rRNA genes . In the present study we assessed the intragenomic sequence heterogeneity of 16S rRNA genes in 55 bacterial genomes, representing various phylogenetic groups . The total number of rRNA operons in genomes included ranged from 2 to 13 . The maximum number of nucleotides that were different between any pair of 16S rRNA genes within a genome ranged from 0 to 19 . The corresponding minimal similarity ranged from 100 to 98.74% . This indicates that the intragenomic heterogeneity between multiple 16S rRNA operons in these genomes is rather limited and is unlikely to have a profound effect on the classification of taxa . Among the multiple copies of the 16S rRNA genes present in the genomes included, 199 mutations were counted with transitions being the dominant type of mutations over the total length of the 16S rRNA gene . Most heterogeneity occurred in variable regions V1, V2, and V6.

Biosens Bioelectron, 2003 Nov 30, 19(3), 249 - 59
Chemisorptions of bacterial receptors for hydrophobic amino acids and sugars on gold for biosensor applications: a surface plasmon resonance study of genetically engineered proteins; Luck LA et al.; This paper demonstrates potential applications of two periplasmic receptor proteins from E . coli as sensing elements for biosensors using the surface plasmon resonance (SPR) technique . These molecules, namely the aspartate to cysteine mutant of the leucine-specific receptor (LS-D1C) and the glutamine to cysteine mutant of the D-glucose/D-galactose receptor (GGR-Q26C) proteins, are chemisorbed on a thin (approximately 40 nm) Au film in neutral K2HPO4 buffers . Using angle and time resolved SPR measurements; we show that adsorption behaviors of both proteins are dominated by diffusion-free second order Langmuir kinetics . We also show that the protein-modified Au films exhibit measurable SPR shifts upon binding to their respective target ligands . According to these SPR data, the kinetics of ligand binding for both LS-D1C and GGR-Q26C are governed by irreversible first order diffusion limited Langmuir model . The utility of the SPR technique for studying reactions of biological molecules is further illustrated in this work.

Genome, 2003 Oct, 46(5), 870 - 8
Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers; Nilmalgoda SD et al.; A BAC library of hexaploid wheat was constructed using the spring wheat cultivar Triticum aestivum L . 'Glenlea' . Fresh shoot tissue from 7- to 10-day-old seedlings was used to obtain HMW DNA . The library was constructed using the HindIII site of pIndigoBAC-5 and the BamHI site of pIndigoBAC-5 and pECBAC1 . A total of 12 ligations were used to construct the entire library, which contains over 650 000 clones . Ninety-six percent of the clones had inserts . The insert size ranged from 5 to 189 kb with an average of 79 kb . The entire library was gridded onto 24 high-density filters using a 5 x 5 array . A subset of these membranes was hybridized with two intergenic chloroplast probes and the percentage of clones containing chloroplast DNA (cpDNA) was calculated to be 2.2% . The genome coverage was estimated to be 3.1 x haploid genome equivalents, giving a 95.3% probability of identifying a clone corresponding to any wheat DNA sequence . BAC pools were constructed and screened using markers targeting the Glu-B1 locus (1BL), the hardness loci (5AS, 5BS, 5DS), the leaf rust resistance locus Lr1 (5DL), and the major fusarium head blight QTL locus located on 3BS . These markers were either locus-specific amplicons or microsatellites . A total of 49 BAC clones were identified for 14 markers giving an average of 3.5 clones/marker, thereby corroborating the estimated 3.1x genome coverage . An example using the gene encoding the HMW glutenin Bx7 is illustrated.

Hepatobiliary Pancreat Dis Int, 2002 Feb, 1(1), 150 - 4
Early intrajejunal nutrition: bacterial translocation and gut barrier function of severe acute pancreatitis in dogs; Qin HL et al.; OBJECTIVE: To evaluate the effect of early intrajejunal nutrition in attenuating bacterial and/or endotoxin translocation and improving gut barrier function of severe acute pancreatitis (SAP) in dogs . METHODS: 15 dogs were divided into parenteral nutrition (PN) group (7 dogs) and early intrajejunal nutrition (EIN) group (8) . EIN was delivered nutrients via a needle jejunostomy catheter feeding at 48 h after operation . SAP model was induced by injecting 1 ml/kg of combined solution of 5% sodium taurocholate and 8000-10 000 BAEE units trypsin/ml into the pancreas via the pancreatic duct . Systemic blood samples were obtained before and 1, 3, 5, 7 d following SAP, and cultured by aerobic as well as anaerobic bacterial growth . Systemic plasma and portal vein endotoxin levels were quantified by the chromogenic limulus amebocyte lysate (LAL) technique . Portal vein blood and specimens of tissue from the mesenteriolum and mesocolon lymph nodes, lung, pulmonary portal lymph nodes, pancreatitistissue and periopancreas tissue were adopted before the experiment was finished . Aliquots of the homogenata were cultured as blood mentioned above to determine the magnitude of the bacteria . DNA, protein and the villi, the thickness of mucosa, and the whole bowel wall of the ileum and transverse colon were measured . RESULTS: The study showed that the levels of systemic plasma endotoxin and the magnitude of bacterial translocation to the portal and systemic blood and distant organ were reduced significantly in the EIN group as compared with the TPN group . The contents of Protein and DNA, the height of villi, the thickness of mucosa and whole bowel wall of the ileum and transverse colon in the EIN group were higher than those in the PN group . CONCLUSION: Our results suggested that EIN is safe and effective to be adopted by intrajejunal delivery of nutrients in SAP, decreases the occurrence of gut bacterial translocation, and improves the gut barrier function.

Bioresour Technol, 2004 Feb, 91(3), 243 - 8
Stimulation of bacterial decolorization of an azo dye by extracellular metabolites from Escherichia coli strain NO3; Chang JS et al.; This study provides an attempt to use the extracellular metabolites of a dye-decolorizing strain, Escherichia coli strain NO3, as a biostimulator to entice E . coli strain NO3 into a beneficial mode of metabolism for an economically feasible decolorization . Addition of supernatants containing metabolites from growth and decolorization cultures triggered an enhancement of decolorization rates . Although extracellular metabolites play a crucial role for stimulating decolorization, they still cannot enable decolorization alone without involvement of biodecolorizers (E . coli strain NO3) . Substantial decreases in oxidation-reduction potential to negative levels were observed during anaerobic decolorization in the presence of the metabolites . Results of repeated batch cultures also showed that serial acclimation of E . coli strain NO3 significantly increased decolorization capability . Supplements of metabolites seem to derepress glucose inhibition on decolorization by E . coli strain NO3 . The metabolites produced from higher dye-concentration decolorization led to more enhancement of the bacterial decolorization.

J Microbiol Methods, 2003 Dec, 55(3), 755 - 62
Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens; Francois P et al.; Microarrays have emerged as potential tools for bacterial detection and identification . Given their high parallelism, they might represent a breakthrough in current diagnostic methods, provided they can be coupled to simplified labeling protocols and detected with adequate sensitivities . We describe here a technique to directly label total bacterial RNA, thus avoiding the multiple steps and possible biases associated with enzymatic amplification (e.g . PCR) . We have then compared the performances of one white-light source and two laser-based fluorescence scanners for detection reliability and sensitivity . Our study reveals that nanoparticle-labeled bacterial RNA generates reproducible resonance light scattering signals that are at least 50 times more intense than state-of-the-art confocal-based fluorescence signals.

Eur J Heart Fail, 2003 Oct, 5(5), 609 - 14
Invasive assessment of bacterial endotoxin and inflammatory cytokines in patients with acute heart failure; Peschel T et al.; AIMS: To test the hypothesis that during acute heart failure endotoxin might be increased in hepatic veins as a sign of bacterial or endotoxin translocation from the bowel into the blood stream . METHODS AND RESULTS: In patients with acute heart failure (NYHA IV; n=17) levels of endotoxin, soluble (s) CD14, tumor necrosis factor alpha (TNFalpha and interleukin 6 (IL6)) were measured in blood drawn from an antecubital vein on admission and compared with age-matched patients with stable chronic heart failure (n=21) and healthy volunteers (n=9) . All levels were systemically elevated during acute heart failure (all P<0.05); once patients were stable enough to undergo cardiac catheterization, endotoxin was found to be significantly higher in hepatic veins (0.62+/-0.05 EU/ml) than left ventricles (0.46+/-0.04 EU/ml; P<0.05), whereas sCD14, TNFalpha and IL6 were not different between these sites . At follow-up (29+/-6 days) endotoxin but not sCD14, TNFalpha or IL-6 was significantly lower as compared to baseline (P<0.05) . CONCLUSIONS: Higher levels of endotoxin in hepatic veins as compared to the left ventricle during acute heart failure are suggestive of bacterial or endotoxin translocation from the bowel into the blood stream . This may lead to new treatment strategies . The lack of difference in TNFalpha levels between the pulmonary artery and the left ventricle sheds doubt on the heart as a source of systemically elevated TNFalpha levels.

Trends Microbiol, 2003 Nov, 11(11), 527 - 35
The outs and ins of bacterial type IV secretion substrates; Ding Z et al.; Bacteria use type IV secretion systems (T4SS) to translocate macromolecular substrates destined for bacterial, plant or human target cells . The T4SS are medically important, contributing to virulence-gene spread, genome plasticity and the alteration of host cellular processes during infection . The T4SS are ancestrally related to bacterial conjugation machines, but present-day functions include (i) conjugal transfer of DNA by cell-to-cell contact, (ii) translocation of effector molecules to eukaryotic target cells, and (iii) DNA uptake from or release to the extracellular milieu . Rapid progress has been made toward identification of type IV secretion substrates and the requirements for substrate recognition.

Clin Tech Small Anim Pract, 2003 Aug, 18(3), 193 - 8
Bacterial corneal diseases in dogs and cats; Ollivier FJ; Corneal diseases are very common in small animals . Corneal disease associated with bacterial agents is frequent in the dog and maybe less frequent in the cat . The medical history, important steps of the ophthalmic examination, and the ophthalmic diagnostic tests that are relevant in such corneal conditions are outlined . Bacterial corneal diseases in dogs and cats are most commonly considered in one of two categories--bacterial ulcerative keratitis and corneal abscesses . The clinical aspects of these two entities as well as the therapeutic strategies available for general practitioners and ophthalmologists are discussed . Ulcerative keratitis is frequent; it represents the most common ocular diseases in dogs and cats . Because some of these corneal ulcers can be very severe, progress rapidly, and therefore are sight threatening, the crucial steps of their diagnosis and management are stressed . The use of a magnification system, fluorescein dye, and corneal cytology and culture, if indicated, is necessary for diagnosis at an early stage of the disease . The treatment of bacterial ulcerative keratitis should eradicate the infection, reduce or stop the corneal destruction and support the corneal structures, control the uveal reaction and the pain associated with it, and minimize the scarring . The prognosis depends on the stage and the severity of the corneal ulceration, the etiology of the condition, and the therapeutic choice . A close follow-up of animals with corneal ulceration is highly recommended because corneal ulcers can progress rapidly.

Exp Physiol, 2003 Nov, 88(6), 747 - 54
Influence of pregnancy on plasma cytokines and the febrile response to intraperitoneal administration of bacterial endotoxin in rats; Fofie AE et al.; Rats have an attenuated febrile response to exogenous (e.g . bacterial endotoxin) and endogenous pyrogen (e.g . interleukin-1beta) near the term of pregnancy, the mechanism of which is unknown . The present experiments were carried out on 71 non-pregnant and 181 pregnant Sprague-Dawley rats to determine if basal levels of the endogenous antipyretic substance, interleukin-1 receptor antagonist (IL-1ra), change relative to interleukin-1beta (IL-1beta) throughout gestation . Furthermore, we have constructed complete Escherichia coli lipopolysaccharide (LPS) dose-core temperature response curves in non-pregnant and pregnant rats on days 10, 15 and 20 of gestation (term of gestation approximately 21 days) to determine if the attenuated febrile response near the term of pregnancy results from a simple shift of the dose-response relationship or results from a dampening of the overall dose-response relationship . Basal IL-1beta, as determined by ELISA on trunk blood from non-pregnant and pregnant rats on days 10, 15 and 20 of gestation (d10, d15, d20), did not change significantly during pregnancy . Basal IL-1ra, however, was increased significantly in d15 rats as compared to non-pregnant, and d10 and d20 rats . The attenuated febrile response near the term of pregnancy, as determined by biotelemetry, did not result from a simple shift of the E . coli LPS dose-core temperature response curve but rather a dampening of the overall dose-response relationship . The febrile responses to EC(50) and EC(100) doses of E . coli LPS were preceded by a period of hypothermia, and were delayed and attenuated near the term of pregnancy as compared to that observed early in pregnancy and in non-pregnant rats . Our data provide evidence that pregnant rats are more sensitive to the hypothermia-producing effects of E . coli LPS than are non-pregnant rats and allow us to speculate that elevated basal IL-1ra may play a role in mediating the attenuated febrile response to pyrogen on day 15 but not on day 20 of gestation in rats.

Nucleic Acids Res, 2003 Nov 15, 31(22), 6409 - 18
A DNA translocation motif in the bacterial transcription--repair coupling factor, Mfd; Chambers AL et al.; The bacterial transcription-repair coupling factor, Mfd, is a superfamily II helicase that releases transcription elongation complexes stalled by DNA damage or other obstacles . Transcription complex displacement is an ATP-dependent reaction that is thought to involve DNA translocation without the strand separation associated with classical helicase activity . We have identified single amino acid substitutions within Mfd that disrupt the ability of Mfd to displace RNA polymerase but do not prevent ATP hydrolysis or binding to DNA . These substitutions, or deletion of the C-terminal 209 residues of Mfd, abrogate the ability of Mfd to increase the efficiency of roadblock repression in vivo . The substitutions fall in a region of Mfd that is homologous to the 'TRG' motif of RecG, a protein that catalyses ATP-dependent translocation of Holliday junctions . Our results define a translocation motif in Mfd and suggest that Mfd and RecG couple ATP hydrolysis to translocation of DNA in a similar manner.

Appl Environ Microbiol, 2003 Nov, 69(11), 6399 - 404
Use of bacterial gamma-glutamyltranspeptidase for enzymatic synthesis of gamma-D-glutamyl compounds; Suzuki H et al.; An enzymatic method for synthesizing various gamma-D-glutamyl compounds efficiently and stereospecifically involving bacterial gamma-glutamyltranspeptidase (EC 2.3.2.2) with D-glutamine as a gamma-glutamyl donor was developed . With D-glutamine as a gamma-glutamyl donor instead of L-glutamine in gamma-glutamyltaurine synthesis, by-products such as gamma-glutamylglutamine and gamma-glutamyl-gamma-glutamyltaurine were not synthesized and the yield of gamma-glutamyltaurine dramatically increased from 25 to 71% . It was also shown that the purification could be simplified without these gamma-glutamyl by-products . The possibility of synthesizing various gamma-D-glutamyl compounds was also shown.

Virus Res, 2003 Nov, 97(2), 57 - 63
Cloning of biologically active genomes from a Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus isolate by using a bacterial artificial chromosome; Wang H et al.; Purification of genotypes from baculovirus isolates provides understanding of the diversity of baculoviruses and may lead to the development of better pesticides . Here, we report the cloning of different genotypes from an isolate of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) by using a bacterial artificial chromosome (BAC) . A transfer vector (pHZB10) was constructed which contained an Escherichia coli mini-F replicon cassette within the upstream and downstream arms of HaSNPV polyhedrin gene . Hz2e5 cells were co-transfected with wild-type HaSNPV DNA and pHZB10 to generate recombinant viruses by homologous recombination . The DNA of budded viruses (BVs) was used to transform E . coli . One of the bacmid colonies, HaBacHZ8, has restriction enzyme digestion profiles similar to an in vivo cloned strain HaSNPV-G4, the genome of which has been completely sequenced . For testing the oral infectivity, the polyhedrin gene of HaSNPV was reintroduced into HaBacHZ8 to generate the recombinant bacmid HaBacDF6 . The results of one-step growth curves, electron microscopic examination, protein expression analysis and bioassays indicated that HaBacDF6 replicated as well as HaSNPV-G4 in vitro and in vivo . The biologically functional HaSNPV bacmids obtained in this research will facilitate future studies on the function genomics and genetic modification of HaSNPV.

Transgenic Res, 2003 Oct, 12(5), 631 - 4
Expression of green fluorescent protein from bacterial and plastid promoters in tobacco chloroplasts; Newell CA et al.; The expression of the green fluorescent protein reporter gene (gfp) from the bacterial trc and plastid rrn and psbA promoters has been compared in transplastomic tobacco plants produced by microprojectile bombardment . The homoplasmic nature of the regenerated plants was confirmed by Southern blot analysis . Northern blot analysis indicated that plants expressing gfp from the rrn promoter contained 3-fold more gfp RNA than plants containing the psbA promoter and 12-fold more than plants with the trc promoter . Immunoblot analysis and fluorescence spectroscopy indicated that plants expressing gfp from the rrn promoter contained approximately 90-fold more green fluorescent protein (GFP) than plants containing the psbA or trc promoters . This study demonstrates that the bacterial trc promoter is significantly weaker than the plastid rrn promoter for expression of gfp in tobacco chloroplasts.

Transgenic Res, 2003 Oct, 12(5), 577 - 86
Induction of H2O2 in transgenic rice leads to cell death and enhanced resistance to both bacterial and fungal pathogens; Kachroo A et al.; Oxidative burst, mediated by hydrogen peroxide (H2O2), has been recognized as a key component of plant defense response during an incompatible interaction . To determine if elevated levels of H2O2 lead to cell death, activation of defense genes and enhanced resistance to diverse pathogens, transgenic rice plants expressing a fungal glucose oxidase gene (GOX) were generated using both constitutive and inducible expression systems . Constitutive or wound/pathogen-induced expression of GOX also allowed us to determine the effectiveness of these systems in conferring long lasting resistance to various pathogens . Both constitutive and wound/pathogen-induced expression of GOX lead to increases in the endogenous levels of H2O2, which in turn caused cell death . Elevated levels of H2O2 also activated the expression of several defense genes and these transgenic plants showed enhanced resistance to both bacterial and fungal pathogens . In comparison to inducible expression, constitutive expression of GOX resulted in 3-10-fold higher levels of the GOX transcript and the corresponding enzymatic activity . Such increased levels of GOX, which would result in elevated levels of H2O2, caused improper seed set and decreased seed viability in transgenic plants constitutively expressing GOX . Our results suggest that pathogen inducible expression of heterologous genes may be a practical and robust way of generating broad spectrum disease resistance.

DNA Repair (Amst), 2003 Nov 21, 2(11), 1273 - 4
Excision repair--its bacterial beginnings; Cleaver JE; Nucleotide excision repair was first reported in 1964 by Setlow and Carrier and by Boyce and Howard-Flanders . These two reports clearly defined the existence in bacteria of a repair process that physically removed damaged sites, pyrimidine dimers, from the DNA in the form of acid-soluble fragments . These reports were the starting point for subsequent development of the whole field of DNA excision point.

Gastroenterology, 2003 Nov, 125(5), 1388 - 97
Bacterial colonization leads to the colonic secretion of RELMbeta/FIZZ2, a novel goblet cell-specific protein; He W et al.; BACKGROUND & AIMS: Goblet cells are highly polarized exocrine cells found throughout the small and large intestine that have a characteristic morphology due to the accumulation of apical secretory granules . These granules contain proteins that play important physiologic roles in cellular protection, barrier function, and proliferation . A limited number of intestinal goblet cell-specific proteins have been identified . In this study, we investigate the expression and regulation of RELMbeta, a novel colon-specific gene . METHODS: The regulation of RELMbeta messenger RNA expression was determined in LS174T, Caco-2, and HT-29 cell lines in response to stimulation with interleukin 13 and lipopolysaccharide . Quantitative reverse-transcription polymerase chain reaction, immunoblots, and immunohistochemistry were used to examine the expression of RELMbeta in BALB/c and C.B17.SCID mice housed in conventional, germ-free, and gnotobiotic environments . RESULTS: Messenger RNA for RELMbeta is restricted to the undifferentiated, proliferating colonic epithelium . Immunohistochemistry shows that this protein is expressed in goblet cells located primarily in the distal half of the colon and cecum with lower levels detectable in the proximal colon . High levels of RELMbeta can be detected in the stool of mice and humans, where it exists as a homodimer under nonreducing conditions . Interestingly, the secretion of RELMbeta is dramatically reduced in germ-free mice . Furthermore, introduction of germ-free mice into a conventional environment results in enhanced expression and robust secretion of RELMbeta within 48 hours . CONCLUSIONS: These studies define a new goblet cell-specific protein and provide the first evidence that colon-specific gene expression can be regulated by colonization with normal enteric bacteria.

Plant Cell Rep, 2004 Mar, 22(8), 569 - 75 Epub 2003 Nov 01.
Use of asymmetric somatic hybridization for transfer of the bacterial blight resistance trait from Oryza meyeriana L . to O . sativa L . ssp . japonica; Yan CQ et al.; Bacterial blight is one of the major diseases affecting rice productivity . To improve the resistance of cultivated rice to bacterial blight, we introduced a bacterial blight resistance trait from Oryza meyeriana, a wild rice species, into an elite japonica rice cultivar (Dalixiang) using asymmetric somatic hybridization . One hundred and thirty-two independent lines were regenerated . The hybrid plants possessed several morphological features of the donor species, O . meyeriana . Random amplified polymorphic DNA analysis revealed that hybrid plants exhibited banding patterns derived from their parental genotypes . For the majority of the hybrids, resistance to bacterial blight pathogens was intermediate to that observed for O . meyeriana and O . sativa (cv . Dalixiang) . Four of the hybrid lines exhibited a high bacterial blight resistance, but it was less than that observed for O . meyeriana . These results demonstrate that O . meyeriana can be used as a good genetic source for improving bacterial blight resistance in commercial rice cultivars through asymmetric somatic hybridization.

Appl Opt, 2003 Oct 20, 42(30), 6174 - 8
Laser-induced breakdown spectroscopy used to detect palladium and silver metal dispersed in bacterial cellulose membranes; Martin M et al.; The technique of laser-induced breakdown spectroscopy has been used for the first time to our knowledge for the identification of metals such as palladium and silver that were dispersed in bacterial cellulose membranes . These results for palladium-dispersed films have been correlated to a calibration curve obtained by use of atomic absorption spectroscopy and were found to be in good agreement . The experiments were conducted by use of wet and dry metal-doped membranes . The metal peaks obtained with a dry membrane are greater than five times higher in signal-to-background ratio than when metals are detected by a hydrated membrane . The advantage of this laser-based technique is that minimal sample handling and sample preparation are needed and measurements are completed in real time (a few seconds) . Hence this technique can be used for the detection of metals in dry membranes that would be used in the construction of electrode assemblies.

Mol Biol (Mosk), 2003 Sep-Oct, 37(5), 916 - 23
{Biosynthesis of mini-antibodies to human ferritin in plant and bacterial producers}; Semeniuk EG et al.; A recombinant scFv antibody against human spleen ferritin was expressed as a barstar-fused protein in Escherichia coli and in Nicotiana tabacum plants and suspension cell cultures . As demonstrated by immunoblotting with antibarstar antibodies, direction of the recombinant protein to the endomembrane system of plant cells ensured its stability and solubility . Production of the recombinant protein did not differ between parental transgenic plants and their first-generation progeny . Fusion with barstar allowed not only immunochemical detection of the recombinant scFv antibody, but also their purification from the plant material by affinity chromatography with barnase-His6 immobilized on a metal-affinity carrier.

Mol Biol (Mosk), 2003 Sep-Oct, 37(5), 834 - 42
{Search for alternative secondary structures of RNA, regulating expression of bacterial genes}; Liubetskaia EV et al.; Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence . Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria . The attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted.

Rev Neurol, 2003 Oct 16-31, 37(8), 722 - 5
{Spastic tetraparesis as a sequela of bacterial meningitis}; T-Barros SV et al.; AIMS: The aim of this study is to demonstrate the incidence of spastic tetraparesis (ST) in meningitis patients in the paediatric ICU, together with the associated variables, and establish comparisons with the existing literature . PATIENTS AND METHODS: We reviewed the medical records of patients who presented symptoms of meningitis and required hospital treatment in the Paediatric ICU at the Hospital de Clinicas de Porto Alegre, between January 1985 and June 2001 . In addition to the diagnosis of meningitis and the incidence of ST as a complication, we also examined the aetiological agent, sex, age at the moment of hospital admittance, length of time spent in hospital and treatment given in each case . RESULTS AND DISCUSSION . An incidence of 15.1% was found for cerebral palsy in the 112 cases of bacterial meningitis that were followed up clinically . In the patients with ST, the time spent in hospital was longer, and the frequency of seizures, intracranial hypertension and the protein concentration levels in CSF were higher (p<0.05).

FEMS Microbiol Lett, 2003 Oct 24, 227(2), 243 - 7
Anaplasma phagocytophilum major surface protein-2 (Msp2) forms multimeric complexes in the bacterial membrane; Park J et al.; Anaplasma phagocytophilum 44-kDa major surface protein-2 (Msp2) mediates partial neutrophil adhesion and interactions . Since A . phagocytophilum 44-kDa monoclonal antibodies also react with 160- and 100-kDa bands, a putative adhesin complex was studied . After separate excision/immunoprecipitation of these three bands, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) resolved each into three bands again with increased 44-kDa protein under reducing conditions suggesting oligomerization of Msp2 44-kDa monomers . With 9 M urea, each separately excised band was resolved only into 44-kDa monomers with three different pIs . With protein cross-linking, immunoblots showed four additional bands and increased high molecular mass band intensity, suggesting homo- and hetero-polymerization with other A . phagocytophilum proteins . Recognition of Msp2 complexes facilitates understanding of A . phagocytophilum-neutrophil adhesion.

Surg Infect (Larchmt), 2003 Fall, 4(3), 281 - 7
Bacterial agents used for bioterrorism; Horn JK; BACKGROUND: Bacterial pathogens and their products are potential agents of biological terrorism and biological warfare . These agents can be deployed through simple aerosol delivery systems and thereby cause widespread disease and death . METHODS: This report is a review of bacterial species that have been employed for development of biological terrorism, relying on a system for classification of their threat developed by the Centers for Disease Control . RESULTS: Physicians must understand how to recognize early signs and symptoms caused by bacterial agents . Clinical findings often seen on presentation are emphasized along with a summary of therapeutic approaches . CONCLUSIONS: Initiation of immediate therapy and supportive care provides the best chance for survival from these potentially lethal and devastating infections . A high index of suspicion must be maintained, especially in the setting of a sudden influx of cases with what are often relatively nonspecific symptoms.

Nature, 2003 Oct 30, 425(6961), 917 - 25
A gene expression atlas of the central nervous system based on bacterial artificial chromosomes; Gong S et al.; The mammalian central nervous system (CNS) contains a remarkable array of neural cells, each with a complex pattern of connections that together generate perceptions and higher brain functions . Here we describe a large-scale screen to create an atlas of CNS gene expression at the cellular level, and to provide a library of verified bacterial artificial chromosome (BAC) vectors and transgenic mouse lines that offer experimental access to CNS regions, cell classes and pathways . We illustrate the use of this atlas to derive novel insights into gene function in neural cells, and into principal steps of CNS development . The atlas, library of BAC vectors and BAC transgenic mice generated in this screen provide a rich resource that allows a broad array of investigations not previously available to the neuroscience community.

Biosci Biotechnol Biochem, 2003 Oct, 67(10), 2294 - 6
The protein component of bacterial ribonuclease P flickers the metal ion response to the substrate shape preference of the ribozyme; Ando T et al.; The substrate shape specificity of the Escherichia coli ribonuclease P (RNase P) ribozyme depends on the concentration of magnesium ion . At 10 mM or more, it can cleave a hairpin substrate as well as a cloverleaf pre-transfer RNA (tRNA) . The results showed, however, that the holo enzyme cleaved the hairpin substrate at low concentrations of magnesium ion . Considering that the homologous E . coli tRNAs are resistant to internal cleavage by the RNase P, the phenomena suggest that this catalytic activity might take part in the removing the mis-folded RNAs in the cell.

Int J Neurosci, 2003 Nov, 113(11), 1497 - 504
Evaluation of antioxidant status in children with acute bacterial meningitis and encephalitis; Caksen H et al.; Antioxidant status was investigated in children with acute bacterial meningitis and encephalitis to investigate the possible role of free radicals in children with meningitis and encephalitis . Our study included 16 children with acute bacterial meningitis, 13 with encephalitis, and 17 control subjects . Serum ceruloplasmin, uric acid, albumin, bilirubin superoxide dismutase (SOD), catalase, and glutathione peroxidase (GPx) levels were studied in all subjects within 6 h of admission . There was a statistically significant difference between the groups for all parameters except for serum uric acid . All antioxidant activities except for albumin level were increased in the study groups . Albumin level was higher in the control group than those of meningitis and encephalitis groups . When the values of meningitis and encephalitis were compared, there was a statistically significant difference between the groups for serum SOD, GPx, ceruloplasmin, and albumin . In conclusion, our study showed that serum SOD, GPx, catalase, and ceruloplasmin were higher in children with acute bacterial meningitis and serum SOD, GPx, catalase, ceruloplasmin, and total bilirubin levels were increased in children with encephalitis . These findings suggest that antioxidant status was almost similar in both acute bacterial meningitis and encephalitis conditions in childhood.

Mol Cell Biol, 1982 Dec, 2(12), 1628 - 32
Expression of bacterial beta-galactosidase in animal cells; An G et al.; A recombinant plasmid containing the gene for bacterial beta-galactosidase, situated close to the simian virus 40 early promoter, has been constructed . Transfection of CHO, L, and COS-1 cells with this plasmid led to the expression and appearance of the enzyme . Using this system, we have developed a series of promoter cloning vehicles capable of accepting promoter signals for animal genes.

J Exp Med, 2003 Nov 3, 198(9), 1349 - 60 Epub 2003 Oct 27.
Plasticity of repetitive DNA sequences within a bacterial (Type IV) secretion system component; Aras RA et al.; DNA rearrangement permits bacteria to regulate gene content and expression . In Helicobacter pylori, cagY, which contains an extraordinary number of direct DNA repeats, encodes a surface-exposed subunit of a (type IV) bacterial secretory system . Examining potential DNA rearrangements involving the cagY repeats indicated that recombination events invariably yield in-frame open reading frames, producing alternatively expressed genes . In individual hosts, H . pylori cell populations include strains that produce CagY proteins that differ in size, due to the predicted in-frame deletions or duplications, and elicit minimal or no host antibody recognition . Using repetitive DNA, H . pylori rearrangements in a host-exposed subunit of a conserved bacterial secretion system may permit a novel form of antigenic evasion.

J Biol Chem, 2004 Jan 16, 279(3), 2231 - 41 Epub 2003 Oct 27.
Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage; Lamontagne B et al.; Bacterial double-stranded RNA-specific RNase III recognizes the A-form of an RNA helix with little sequence specificity . In contrast, baker yeast RNase III (Rnt1p) selectively recognizes NGNN tetraloops even when they are attached to a B-form DNA helix . To comprehend the general mechanism of RNase III substrate recognition, we mapped the Rnt1p binding signal and directly compared its substrate specificity to that of both Escherichia coli RNase III and fission yeast RNase III (PacI) . Rnt1p bound but did not cleave long RNA duplexes without NGNN tetraloops, whereas RNase III indiscriminately cleaved all RNA duplexes . PacI cleaved RNA duplexes with some preferences for NGNN-capped RNA stems under physiological conditions . Hydroxyl radical footprints indicate that Rnt1p specifically interacts with the NGNN tetraloop and its surrounding nucleotides . In contrast, Rnt1p interaction with GAAA-capped hairpins was weak and largely unspecific . Certain duality of substrate recognition was exhibited by PacI but not by bacterial RNase III . E . coli RNase III recognized RNA duplexes longer than 11 bp with little specificity, and no specific features were required for cleavage . On the other hand, PacI cleaved long, but not short, RNA duplexes with little sequence specificity . PacI cleavage of RNA stems shorter than 27 bp was dependent on the presence of an UU-UC internal loop two nucleotides upstream of the cleavage site . These observations suggest that yeast RNase IIIs have two recognition mechanisms, one that uses specific structural features and another that recognizes general features of the A-form RNA helix.

Curr Opin Chem Biol, 2003 Oct, 7(5), 586 - 91
Molecular mechanisms of bacterial quorum sensing as a new drug target; Suga H et al.; Bacterial quorum sensing evolved as a means for bacterial communities to rapidly and coordinately change genome expression patterns in response to environmental cues . Each cell in a community produces and responds to a signaling molecule called an autoinducer that serves as an indicator of the population density . A high concentration of autoinducer is associated with a large, often confined population, which requires altered gene expression for survival . Quorum sensing is one mechanism through which a bacterial population receives input from the environment and elicits an appropriate response . Because many pathogens require quorum sensing to produce virulence factors in response to association with a human host, the signaling pathway is a target for design of small-molecule inhibitors.

Biotechniques, 2003 Oct, 35(4), 796 - 807
Parameters influencing high-efficiency transfection of bacterial artificial chromosomes into cultured mammalian cells; Montigny WJ et al.; Although bacterial artificial chromosomes (BACs) provide a well-characterized resource for the analysis of large chromosomal domains, low transfection rates have proven a significant limitation for their use in cell culture models . Using TP53 BAC clones that contain expression cassettes for enhanced green fluorescent protein or red fluorescent protein, we have examined conditions that promote BAC transfection in hamster, human, and mouse cell lines . Atomic force microscopy shows that BAC transfection efficiency correlates with the generation of small, highly condensed but dispersed lipid: BAC DNA transfection complexes . BAC DNA purity and concentration are critical for good transfection; debris from purification columns induces the formation of large aggregates that do not gain entry into the cell, and DNA concentrations must be optimized to promote intramolecular condensation rather than intermolecular linking, which also causes aggregation and diminished transfection efficiency . The expression of both markers and genes within BACs initially occurs at lower levels than observed with plasmids, requiring 3-5 days to evaluate the transfection results . We also show that BACs can be co-transfected with other BACs, which provides for increased experimental flexibility.

Eur J Immunol, 2003 Nov, 33(11), 3164 - 74
Bacterial DNA activates human neutrophils by a CpG-independent pathway; Trevani AS et al.; Bacterial DNA stimulates macrophages, monocytes, B lymphocytes, NK cells, and dendritic cells in a CpG-dependent manner . In this work we demonstrate that bacterial DNA, but not mammalian DNA, induces human neutrophil activation as assessed by L-selectin shedding, CD11b upregulation, and stimulation of cellular shape change, IL-8 secretion, and cell migration . Induction of these responses is not dependent on the presence of unmethylated CpG motifs, as neutrophil stimulatory properties were neither modified by CpG-methylation of bacterial DNA nor reproduced by oligonucleotides bearing CpG motifs . We found that human neutrophils express Toll-like receptor (TLR) 9 mRNA . However, as expected for a CpG-independent mechanism, activation does not involve a TLR9-dependent signaling pathway; neutrophil stimulation was not prevented by immobilization of bacterial DNA or by wortmannin or chloroquine, two agents that inhibit TLR9 signaling . Of note, both single-stranded and double-stranded DNA were able to induce activation, suggesting that neutrophils might be activated by bacterial DNA at inflammatory foci even in the absence of conditions required to induce DNA denaturation . Our findings provide the first evidence that neutrophils might be alerted to the presence of invading bacteria through recognition of its DNA via a novel mechanism not involving CpG motifs.

Hepatology, 2003 Nov, 38(5), 1210 - 8
Systemic, renal, and hepatic hemodynamic derangement in cirrhotic patients with spontaneous bacterial peritonitis; Ruiz-del-Arbol L et al.; Spontaneous bacterial peritonitis (SBP) is frequently associated with renal failure . This study assessed if systemic and hepatic hemodynamics are also affected by this condition . Standard laboratory tests, tumor necrosis factor alpha (TNF-alpha) in plasma and ascitic fluid, plasma renin activity (PRA) and norepinephrine (NE), and systemic and hepatic hemodynamics were determined in 23 patients with SBP at diagnosis and after resolution of infection . Eight patients developed renal failure during treatment . At diagnosis of infection, patients developing renal failure showed significantly higher values of TNF-alpha, blood urea nitrogen (BUN), PRA and NE, peripheral vascular resistance, and hepatic venous pressure gradient (HVPG) and lower cardiac output than patients not developing renal failure . During treatment, a significant reduction in cardiac output and arterial pressure and increase in PRA and NE, HVPG, and Child-Pugh score were observed in the first group but not in the second . Peripheral vascular resistance remained unmodified in both groups . Changes in PRA and NE correlated inversely with changes in arterial pressure and directly with changes in BUN, Child-Pugh score, and HVPG . Five patients in the renal failure group developed encephalopathy, and 6 died . In the group without renal failure, none of the patients developed encephalopathy or expired . In conclusion, patients with SBP frequently develop a rapidly progressive impairment in systemic hemodynamics, leading to severe renal and hepatic failure, aggravation of portal hypertension, encephalopathy, and death . This occurs despite rapid resolution of infection and is associated with an extremely poor prognosis.

Am J Pathol, 2003 Nov, 163(5), 1961 - 8
Interleukin-12-independent down-modulation of cockroach antigen-induced asthma in mice by intranasal exposure to bacterial lipopolysaccharide; Lundy SK et al.; Several studies have shown that exposure to bacterial lipopolysaccharide (LPS) can either prevent or inhibit asthma in humans and laboratory rodents . Much emphasis has been placed on the role of cytokines and chemokines in the establishment and maintenance of allergic airway disease . Therefore, it is of interest to study the role of LPS in affecting airway pathology and lung cytokine and chemokine responses in the maintenance phase of asthma . Increasing doses of LPS were administered into the airways of mice presensitized with cockroach allergen (CRAg), then allergic airway disease parameters were assessed after CRAg challenge . Airway hyperresponsiveness after antigen challenge decreased at the highest dose of LPS tested, which was accompanied by a decrease in airway and lung eosinophils . However, a dramatic increase in lung inflammation because of neutrophil influx was observed . Measurement of cytokines in lungs of LPS-treated, CRAg-sensitized mice indicated that interleukin (IL)-12 levels were increased by LPS treatment in a dose-dependent manner, as were levels of several inflammatory chemokines . In contrast, levels of IL-4, IL-13, IL-5, and IL-10 were reduced in whole lung homogenates only of high-dose LPS-treated mice . Intranasal administration of neutralizing anti-IL-12 at the time of high-dose LPS challenge reduced lung IL-12, interferon-gamma, CXCL9, and CXCL10 but did not affect levels of the other chemokines or Th2-type cytokines, and did not restore AHR . These findings suggest that the amelioration of airway hyperresponsiveness observed in LPS-treated, CRAg-sensitized mice is coincident with an immune deviation of the lung inflammatory response, independent of IL-12.

J Endotoxin Res, 2003, 9(5), 331 - 5
Receptor cluster formation during activation by bacterial products; Triantafilou M et al.; The recognition of bacterial products, such as lipopolysaccharide (LPS) by the innate immune system lead to a strong pro-inflammatory response that can eventually lead to fatal sepsis syndrome in humans . Although CD14 and TLR4 have been identified as the key molecules involved in LPS-induced signal transduction, accumulating evidence indicates that multiple receptors are also involved . Our group has recently identified a cluster of receptors, involving heat-shock proteins 70 and 90, chemokine receptor 4 as well as growth differentiation factor 5, that are formed following LPS stimulation . In addition, we present data demonstrating that these molecules associate with TLR4 and accumulate in membrane microdomains following LPS ligation . Our results suggest that the entire bacterial recognition is based around the recruitment of multiple signalling molecules, in addition to CD14 and TLRs, within the lipid rafts . We propose that different combinational associations of receptors within activation clusters determine the different responses to a variety of bacterial stimuli.

Cornea, 2003 Nov, 22(8), 746 - 53
Culture plate temperature and delayed incubation effect on bacterial recovery; Rudometkin NJ et al.; PURPOSE: To discover if initial culturing conditions (plate temperature and time delay to incubation) adversely influence the recovery of organisms associated with bacterial keratitis . METHODS: The rate of temperature equilibration of culture plates taken from a refrigerator and placed in an incubator and left on the desk was evaluated with a digital thermometer . A standard inoculum for each of five organisms (S . aureus, S . pneumoniae, P . aeruginosa, E . aerogenes, K . oxytoca) isolated from human bacterial keratitis was spread evenly on blood agar plates at refrigerator (Tcold; 4 degrees C), room (Troom; 24 degrees C), and incubator (Twarm; 37 degrees C) temperatures . The plates were then kept at room temperature for 0, 1, 3, 5, and 8 hours before overnight incubation at 37 degrees C (S . pneumoniae under microaerophilic conditions), and the number of colony-forming units was counted . RESULTS: Cold plates took at least 15 minutes in an incubator to attain room temperature, and up to an hour when left on the desk . Increased organism recovery was found comparing both Twarm and Troom plates (6.2 to 24.8% and 7.0 to 14.7%, respectively, P<0.001) to Tcold plates for all organisms except S . pneumoniae (P=0.057) . Comparing Twarm plates to Troom plates demonstrated an increased recovery (P<0.001) for S . aureus . Delayed incubation resulted in decreased recovery for S . pneumoniae (P<0.001) . CONCLUSIONS: Culture plates should preferably be warmed at least to room temperature before inoculation, as well as promptly incubated to increase bacterial recovery from cases of septic keratitis.

Science, 2003 Oct 24, 302(5645), 650 - 4
A new class of bacterial RNA polymerase inhibitor affects nucleotide addition; Artsimovitch I et al.; RNA polymerase (RNAP) is the central enzyme of gene expression . Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure . We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism . These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis . CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site . We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.

Vaccine, 2003 Nov 7, 21(31), 4539 - 44
Bacterial otitis media: a new non-invasive rat model; Tonnaer EL et al.; This study describes the development of a physiological rat model for otitis media . The model is based on the assumption that bacteria, intranasally introduced into the nasopharynx, will be transferred into the middle ear cavity during swallowing provided that the ambient air pressure is higher than the middle ear pressure . This model demonstrates that small pressure changes, generated in a pressure cabin under controlled conditions, can be used as driving force for the transfer of bacteria into the middle ear cavity resulting in bilateral otitis media . Because invasive techniques or biochemical agents are not applied, this model is suited to investigate immunological aspects of otitis media, including the effects of vaccination.

Protein Sci, 2003 Nov, 12(11), 2588 - 96
The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG; Stevens SY et al.; The Hsp70 family of molecular chaperones participates in a number of cellular processes, including binding to nascent polypeptide chains and assistance in protein (re)folding and degradation . We present the solution structure of the substrate binding domain (residues 393-507) of the Escherichia coli Hsp70, DnaK, that is bound to the peptide NRLLLTG and compare it to the crystal structure of DnaK(389-607) bound to the same peptide . The construct discussed here does not contain the alpha-helical domain that characterizes earlier published peptide-bound structures of the Hsp70s . It is established that removing the alpha-helical domain in its entirety does not affect the primary interactions or structure of the DnaK(393-507) in complex with the peptide NRLLLTG . In particular, the arch that protects the substrate-binding cleft is also formed in the absence of the helical lid . 15N-relaxation measurements show that the peptide-bound form of DnaK(393-507) is relatively rigid . As compared to the peptide-free state, the peptide-bound state of the domain shows distinct, widespread, and contiguous differences in structure extending toward areas previously defined as important to the allosteric regulation of the Hsp70 chaperones.

Infect Immun, 2003 Nov, 71(11), 6420 - 5
Modulation of the bovine delayed-type hypersensitivity responses to defined mycobacterial antigens by a synthetic bacterial lipopeptide; Whelan AO et al.; The use of defined protein and peptide antigens can overcome specificity limitations of purified protein derivatives in the detection of bovine tuberculosis when the antigens are used in blood-based tests . Since the use of these specific antigens as skin test reagents could have practical advantages, we investigated the potential of Mycobacterium bovis-specific antigens to stimulate delayed-type hypersensitivity (DTH) responses in cattle experimentally infected with M . bovis . A cocktail of the recombinant antigens ESAT-6, MPB83, and MPB64 failed to stimulate in vivo DTH in cattle that had been experimentally infected with M . bovis despite the fact that the antigens were recognized in vitro by the same animals . However, it was possible to stimulate antigen-specific bovine DTH responses by using ESAT-6 in combination with a synthetic bacterial lipopeptide . This lipopeptide stimulated the release of the proinflammatory cytokine tumor necrosis factor alpha from monocyte-derived bovine dendritic cells in vitro, thereby providing a possible mechanism for its DTH-enhancing properties.

Curr Opin Microbiol, 2003 Oct, 6(5), 512 - 8
Tracing the evolution of gene loss in obligate bacterial symbionts; Moran NA; The gamma-proteobacterial symbionts of insects are a model group for comparative studies of genome reduction . The phylogenetic proximity of these reduced genomes to the larger genomes of well-studied free-living bacteria has enabled reconstructions of the process by which genes and DNA are lost . Three genome sequences are now available for Buchnera aphidicola . Analyses of Buchnera genomes in comparison with those of related enteric bacteria suggest that extensive changes including large deletions, repetitive element proliferation and chromosomal rearrangements occurred initially, followed by extreme stasis in gene order and slow decay of additional genes . This pattern appears to be characteristic of symbiont evolution.

Hepatogastroenterology, 2003 Sep-Oct, 50(53), 1700 - 3
Outcome of patients with inconsistent results from 13C-urea breath test and bacterial culture at the time of assessment of Helicobacter pylori eradication therapy in Japan; Nagahara Y et al.; BACKGROUND/AIMS: At the assessment of eradication therapy of Helicobacter pylori, the results of 13C-urea breath test and other methods such as bacterial culture are occasionally inconsistent . In this study, we examined the outcomes of inconsistent results . METHODOLOGY: Four hundred and four patients with peptic ulcer who were H . pylori-positive and who had completed eradication therapy were studied . Bacterial culture, rapid urease tests and 13C-urea breath test were performed between one and three months after the end of the therapy . The cut-off value for the 13C-urea breath test used originally in this study was 2.5 per mil . We investigated the outcome of inconsistent results by following up the patients every 6 to 12 months . RESULTS: At the initial assessment of eradication therapy, we observed inconsistent results with bacterial culture and 13C-urea breath test in 43 of 404 patients . Most of them (40 of 43) were culture-negative but urea breath test-positive, and the majority became negative for both tests . Based on the follow-up results, the optimum value for 13C-urea breath test at the assessment of eradication therapy was found to be 3.5 per mil . CONCLUSIONS: We found that outcomes of inconsistent results were variable, indicating the importance of the follow-up of patients after eradication therapy of H . pylori.

Hepatogastroenterology, 2003 Sep-Oct, 50(53), 1542 - 6
Short and long-term effects of bacterial translocation due to obstructive jaundice on liver damage; Sakrak O et al.; BACKGROUND/AIMS: The present study was conducted to determine if obstructive jaundice promotes bacterial translocation and to evaluate the changes in hepatic histopathology in patients with benign biliary obstruction . METHODOLOGY: Between January 1996 and January 1998, 19 patients treated for benign biliary obstruction were studied . Fourteen patients with symptomatic cholelithiasis were taken as the control group . Patient characteristics, preoperative and post-operative laboratory tests with an interval of 7 days were recorded . In all patients, bile and mesenteric lymph nodes samples were taken for bacterial growth and histopathologic changes were studied on the liver excised during surgery . RESULTS: In the control group, bacterial growth was observed in the bile and mesenteric lymph nodes cultures in one (7.1%) and two patients (14.3%), respectively . In the study group, 8 patients (42%) had positive bile cultures and 12 patients (63.2%) had positive mesenteric lymph nodes cultures, respectively . Histopathologic examination of the liver revealed significant increase in the rate of periductal and portal fibrosis in the jaundiced patients, compared with control group (p < 0.001) . Postoperative complications in the study group were wound infection (3 cases), renal failure (2 cases), ARDS (1 cases) and intraabdominal abscess (1 cases) . In the control group, one patient had wound infection and one had atelectasis . Two patients with jaundice died of multiple organ failure and respiratory failure . In long-term follow-up (mean 17 months), when sclerosing cholangitis and secondary biliary cirrhosis developed in one patient each in the study group, no long-term complication occurred in the control group . CONCLUSIONS: Our clinical results demonstrate that extrahepatic biliary obstruction promotes bacterial translocation and this process is an important cause of morbidity and mortality in patients with jaundice . Also, obstructive jaundice subsequently leads to significant functional and morphological damage in the liver.

Hepatogastroenterology, 2003 Sep-Oct, 50(53), 1415 - 8
Bone mineral density in patients with small intestinal bacterial overgrowth; Stotzer PO et al.; BACKGROUND/AIMS: Malabsorption has long been recognized as a cause of osteopenia, and mild forms of osteopenia are present in many gastrointestinal disorders . The aim of this study was to determine if osteopenia is common in patients with small intestinal bacterial overgrowth . METHODOLOGY: Bone mineral density was measured in fourteen patients with small intestinal bacterial overgrowth . Patients with obvious structural predisposing conditions such as previous gastric operations, small bowel strictures and small bowel diverticula, were excluded . Measurements were made in the distal right radius and ulna, in the hip and in the spine . The results were compared to those of a reference population . Radiographs of the spine were assessed for evidence of vertebral fractures . Blood samples were analyzed for serum concentrations of 25-hydroxyvitamin-D3 and 1,25-dihydroxyvitamin-D3, alkaline phosphatase activity, ionized calcium, intact parathyroid hormone and osteocalcin . All patients completed a questionnaire concerning, inter alia, previous fractures, past and current diseases, tobacco smoking and medication . RESULTS: Patients with small intestinal bacterial overgrowth had significantly low bone density in the femoral neck (p < 0.01) and in the lumbar spine (p < 0.05), compared to a reference population . Six of 14 (43%) patients had had fractures . CONCLUSIONS: Patients with small intestinal bacterial overgrowth have low bone mineral density . In patients with osteopenia of unknown origin, small intestinal bacterial overgrowth should be considered.

Biol Proced Online, 2003, 5, 123 - 135 Epub 2003 May 1.
Shotgun Phage Display - Selection for Bacterial Receptins or other Exported Proteins; Jacobsson K et al.; Shotgun phage display cloning involves construction of libraries from randomly fragmented bacterial chromosomal DNA, cloned genes, or eukaryotic cDNAs, into a phagemid vector . The library obtained consists of phages expressing polypeptides corresponding to all genes encoded by the organism, or overlapping peptides derived from the cloned gene . From such a library, polypeptides with affinity for another molecule can be isolated by affinity selection, panning . The technique can be used to identify bacterial receptins and identification of their minimal binding domain, and but also to identify epitopes recognised by antibodies . In addition, after modification of the phagemid vector, the technique has also been used to identify bacterial extracytoplasmic proteins.

Can J Microbiol, 2003 Jul, 49(7), 418 - 24
Mechanisms of cadmium resistance in anaerobic bacterial enrichments degrading pentachlorophenol; Kamashwaran SR et al.; The mechanisms of heavy-metal resistance used by adapted sulfidogenic and methanogenic enrichments degrading pentachlorophenol in the presence of cadmium (Cd) were studied . The enrichment cultures adapted to and readily tolerated bioavailable Cd concentrations up to 50 ppm while degrading an equal concentration of pentachlorophenol . Both cultures removed >95% of the Cd from solution . Transmission electron micrographs revealed (i) . the presence of electron-dense particles surrounding the cells in the sulfidogenic enrichments and (ii) . the unusual clumping of cells and the presence of an exopolymer in the methanogenic enrichments . Energy dispersive X-ray analysis showed that the sulfidogenic enrichments removed Cd by extracellular precipitation of cadmium sulfide, while the methanogenic enrichment culture removed Cd by extracellular sequestration of Cd into the exopolymer.

J Pharm Biomed Anal, 2003 Jul 14, 32(3), 495 - 503
Estimation of uncertainty in kinetic-colorimetric assay of bacterial endotoxins; Haishima Y et al.; The relative standard deviation (R.S.D.) of measurements is estimated in the kinetic-colorimetric assay of bacterial endotoxins without recourse to the usual repeated experiments . The measurements are the slopes of kinetic curves and two major factors are considered to cause the uncertainty of the measurements: (1) the pipetting of the sample and color development reagent; and (2) noise in the detection unit . The measurement R.S.D . is formulated as a function of endotoxin concentration . Two parameters (S.D . of the pipetted volumes and S.D . of the detector noise) are also required in the uncertainty equation, but no arbitrary coefficients are included . Since the S.D . values for pipettes and detector noise can be determined independently of the endotoxin assays, the measurement R.S.D . can be estimated by the above equation without repeating the assays . However, the calibration curve is necessary . The theoretical estimation is shown to be in good agreement with the experimental R.S.D . (n = 12) over a wide concentration range.

Appl Microbiol Biotechnol, 2004 Apr, 64(2), 199 - 205 Epub 2003 Oct 15.
Utilization of the buffering capacity of corn steep liquor in bacterial cellulose production by Acetobacter xylinum; Noro N et al.; Acetobacter xylinum BPR2001 produces water-insoluble bacterial cellulose (BC) . Using a pH sensor for the accurate control of pH, which is one of the most critical factors for efficient BC production, is difficult especially in a baffled shake-flask and an airlift reactor . The buffering capacity of corn steep liquor (CSL) was estimated by measuring beta (buffering capacity) values in advance and was used to maintain the pH within the optimal range during the production of BC . When CSL was added to either a shake-flask, a stirred-tank reactor or an airlift reactor, BC production was almost the same as that in cultivations where pH was controlled manually or by a pH sensor.

Theor Appl Genet, 2004 Feb, 108(4), 663 - 9 Epub 2003 Oct 16.
Construction of a HindIII Bacterial Artificial Chromosome library and its use in identification of clones associated with disease resistance in chickpea; Rajesh PN et al.; A chickpea ( Cicer arietinum L.) Bacterial Artificial Chromosome (BAC) library from germplasm line, FLIP 84-92C, was constructed to facilitate positional cloning of disease resistance genes and physical mapping of the genome . The BAC library has 23,780 colonies and was calculated to comprise approximately 3.8 haploid-genome equivalents . Studies on 120 randomly chosen clones revealed an average insert size of 100 kb and no empty clones . Colony hybridization using the RUBP carboxylase large subunit as a probe resulted in a very low percentage of chloroplast DNA contamination . Two clones with a combined insert size of 200 kb were isolated after the library was screened with a Sequence Tagged Microsatellite Site (STMS) marker, Ta96, which is tightly linked to a gene ( Foc3) for resistance to fusarium wilt caused by Fusarium oxysporum Schlechtend.: Fr . f . sp . ciceris (Padwick) race 3 at a genetic distance of 1 cM . Also, these two clones were analyzed with several resistance gene analog (RGA) markers . End sequencing of these clones did not identify repetitive sequences . The development of the BAC library will facilitate isolation of Foc3 and allow us to perform physical mapping of this genomic region where additional R genes against other races of the wilt causing pathogen are positioned.

Cancer Res, 2003 Oct 1, 63(19), 6350 - 6
Coexpression of Helicobacter pylori's proteins CagA and HspB induces cell proliferation in AGS gastric epithelial cells, independently from the bacterial infection; De Luca A et al.; Adenocarcinoma of the stomach is the second most common cause of cancer mortality in the world . The purpose of this study was to evaluate the potential role in carcinogenesis of two secreted Helicobacter pylori's proteins, CagA and HspB, both shown to increase the risk of gastric carcinoma in patients infected with H . pylori-positive strain . The effects of these two proteins on cell kinetics and the ability to selectively affect the expression of cell cycle-related proteins by transfection of a human gastric epithelial cell line (AGS) were analyzed . Using a genomic library of H . pylori, we isolated and cloned CagA and HspB . The effects of the overexpression of these proteins on cell growth were analyzed in AGS cells by immunoblots, proliferation assay, and flow cytometry . Coexpression of CagA and HspB in AGS cells in the first 48 h caused an increase of the level of E2F transcription factor, cyclin D3, and phosphorylated retinoblastoma protein, all involved in the G(1)-S checkpoint of the cell cycle . Consistently, an increase of cell proliferation, corresponding to an augment of the fraction of the cells in the S-G(2)-M phase of the cell cycle, was also demonstrated . Moreover, an increase of c-jun protein levels, but not of c-fos, was also found after coexpression of CagA and HspB . All these data suggest that CagA and HspB, independently from the bacterial infection, have a direct effect on the cell growth of the gastric cells acting on the G(1)-S checkpoint of the cell cycle.

Rapid Commun Mass Spectrom, 2003, 17(20), 2260 - 6
Electrospray ion-trap multistage mass spectrometry for characterisation of co-monomer compositional distribution of bacterial poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) at the molecular level; Adamus G et al.; We report an electrospray ionisation multistage mass spectrometry (ESI-MSn) method that utilises molecular mass information for determination of sequence distribution and chemical structure of mass-selected macromolecules of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) biopolyester, PHBH . On the basis of ESI-MSn studies of PHBH oligomers obtained by partial alkaline depolymerisation of natural PHBH containing 13-14 mol% of hydroxyhexanoate (HH) units, the microstructure of this bacterial copolyester was assessed up to the level of 28 repeat units . The subtle structural details of the PHBH were evaluated based on sequencing of individual macromolecular ions thus showing the utility of this technique for the analysis of biological copolyester macromolecules . It was confirmed that both HH and hydroxybutyrate (HB) units of the PHBH copolymer are randomly distributed .

Eur J Obstet Gynecol Reprod Biol, 2003 Nov 10, 111(1), 83 - 7
New technology for diagnosis of bacterial vaginosis; Chaim W et al.; OBJECTIVE: To replace clinical diagnosis of bacterial vaginosis (BV) with a new and rapid analytical method based on ion mobility spectrometry (IMS) . IMS is an instrumental technique for identifying compounds and determining their concentrations, based on measurement of the velocity of ions drifting through air at atmospheric pressure under the influence of an electric field . The technique is particularly sensitive to amines taking less than 2 min . STUDY DESIGN: Clinical examination of 174 samples determined 22 BV-positive and 152 BV-negative samples . IMS analyzed and recorded biogenic amine emanation mobility spectra of the 174 samples of vaginal discharge from duplicate swabs . RESULTS: IMS confirmed 21 (true positive BV) samples with 1 false negative (21/22, sensitivity=95.5%) . Out of 152 samples, 150 were confirmed true BV-negative with 2 false positive samples (specificity=98.7%), PPV: 91.3%, NPV: 100% . CONCLUSIONS: The diagnostic procedure shows high accuracy and is technically simple and rapid . The trimethylamine level becomes an index of severity of the infection.

Burns, 2003 Nov, 29(7), 733 - 8
Bacterial toxicosis/toxic shock syndrome as a contributor to morbidity in children with burn injuries; Brown AP et al.; When a child with a thermal injury suddenly becomes unwell, it is often difficult to obtain an accurate diagnosis in the early stages of the illness . Out of 71 children admitted to our burns unit over a 15-month period, 13 became acutely toxic . Most of the cases had relatively small burns and the exact reason for their sudden deterioration was not apparent in the immediate stages . Several children required admission to the intensive therapy unit and there was one death . The number of children experiencing this significant morbidity over a relatively short period of time prompted us to perform a detailed retrospective study to ascertain the exact cause of the deterioration and to identify any patterns in their presenting signs and symptoms.There was considerable variation in the clinical picture of the children who developed the toxicosis, however, several features were frequently observed which resembled those seen in the toxic shock syndrome (TSS) . In order to be more specific, we applied the criteria for TSS as defined by the Centres for Disease Control (CDC) to each of the 13 children . All of the criteria were noted in six children and the majority in the other seven . This was a much higher incidence than we would normally have expected . The clinical features of children with TSS are not always easy to distinguish from those observed in other illnesses . We therefore explored the possibility of alternative diagnoses that may have caused the toxicosis in these children.The mortality associated with TSS can be high, especially if there is a delay in recognition and subsequent management of the disease . Clinicians should be alerted to the fact that TSS is probably more prevalent than previously thought and should practise with a high index of suspicion in any child with a burn whose clinical condition suddenly deteriorates.

Microbes Infect, 2003 Oct, 5(12), 1149 - 58
Fascination with bacteria-triggered cell death: the significance of Fas-mediated apoptosis during bacterial infection in vivo; Menaker RJ et al.; Increasing evidence indicates that bacterial pathogens have developed mechanisms to modulate the apoptotic signaling cascade of host cells and thereby cause disease . The Fas death receptor pathway is one of the most extensively investigated apoptotic signaling pathways . In this review we discuss the role of Fas signaling during the interplay between bacterial pathogens and the host in vivo.

Zhonghua Gan Zang Bing Za Zhi, 2003 Sep, 11(9), 539 - 41
{Effects of cisapride on intestinal bacterial and endotoxin translocation in cirrhotic rats}; Zhang SC et al.; OBJECTIVES: To further investigate the effects of cisapride on intestinal bacterial overgrowth (IBO), bacterial and endotoxin translocation, intestinal transit and permeability in cirrhotic rats . METHODS: 25 normal control rats, 25 cirrhotic rats, 20 cirrhotic rats received saline, and 20 cirrhotic rats treated with cisapride were included in the study . All animals were assessed with many variables including bacterial and endotoxin translocation, IBO, intestinal transit and permeability . RESULTS: Bacterial translocation was found in 48%(12/25) cirrhotic rats and none of control rats . Among the 20 rats with IBO, there were 11 rats with bacterial translocation (BT) while only one rats occurred BT out of the 5 rats without IBO . Cirrhotic rats with IBO had a significantly higher rate of endotoxin translocation, higher intestinal permeability and longer intestinal transit than those without IBO . BT of a specific organism was always associated with IBO of that organism . Compared with the placebo group, cisapride-treated rats had lower rates of bacterial and endotoxin translocation and IBO, which had close relationship with shorter intestinal transit and lower permeability . CONCLUSION: Endotoxin and bacterial translocation in cirrhotic rats may be the result of IBO and higher permeability . IBO may be the result of longer transit . Cisapride which can accelerate intestinal transit and improve intestinal permeability is helpful in preventing and treating intestinal bacterial and endotoxin translocation.

Pediatr Surg Int, 2003 Oct, 19(8), 573 - 7 Epub 2003 Oct 09.
Pathogenesis of neonatal necrotizing enterocolitis: a study of the role of intraluminal pressure, age and bacterial concentration; Chan KL et al.; The pathogenesis of neonatal necrotizing enterocolitis (NEC) is unknown . Intestinal dilatation and preferred occurrence of NEC at sites of bacterial overgrowth (colon and ileum) are common findings . The study attempted to produce NEC with increasing intraluminal pressures and bacterial concentrations in two different aged groups of rats . First, 10-cm terminal ileum segments were isolated with intact vascular pedicles in 1-and 3-month-old rats, and a dose of 10(11) E . coli in 1 ml was injected into each segment . Intraluminal pressure was sustained for 1 h at 150, 100, 50 and 0 cmH(2)0, respectively, in four experimental groups ( n=6) . The isolated loop was then returned to the abdominal cavity and assessed grossly for NEC after 24 h . Histological examination was performed by a pathologist (KWC) who was blinded to the procedures . Second, the procedure was repeated with doses of 10(8), 10(5) and 0 bacteria/ml ( n=6) at intraluminal pressure of 100 cmH(2)0 in 1-month-old rats . Third, in another experimental group, oxygenation of the pedicled loop was assessed by oximetry as the intraluminal pressure increased and the findings were correlated with aortic blood pressure . The blood pressures (mean+/-SD) for 3- and 1-month-old rats were 110+/-6 and 72+/-4 mmHg, respectively . Hypoxia (<50% oxygen saturation) of the bowel was detected when the intraluminal pressure exceeded the mean blood pressure . The relative incidences of NEC in the bowel with intraluminal pressure above and below mean blood pressure were 100% (6/6) vs . 4% (1/24; P<0.05) in 3-month-old rats, and 100% (12/12) vs . 11% (2/18; P<0.05) in 1-month-old rats . There was no occurrence of NEC in bowel injected with 10(5) E . coli/ml and less at 100 cm intraluminal pressure . Increased intraluminal pressure results in bowel hypoxia and in the presence of adequate bacterial concentration predisposes to the development of NEC . Young age is associated with a lower threshold for increased intraluminal pressure leading to NEC.

Pediatr Infect Dis J, 2003 Oct, 22(10), 895 - 903
Procalcitonin in pediatric emergency departments for the early diagnosis of invasive bacterial infections in febrile infants: results of a multicenter study and utility of a rapid qualitative test for this marker; Fernandez Lopez A et al.; BACKGROUND: Procalcitonin (PCT) is a potentially useful marker in pediatric Emergency Departments (ED) . The basic objectives of this study were to assess the diagnostic performance of PCT for distinguishing between viral and bacterial infections and for the early detection of invasive bacterial infections in febrile children between 1 and 36 months old comparing it with C-reactive protein (CRP) and to evaluate the utility of a qualitative rapid test for PCT in ED . METHODS: Prospective, observational and multicenter study that included 445 children who were treated for fever in pediatric ED . Quantitative and qualitative plasma values of PCT and CRP were correlated with the final diagnosis . To obtain the qualitative level of PCT the BRAHMS PCT-Q rapid test was used . RESULTS: Mean PCT and CRP values in viral infections were 0.26 ng/ml and 15.5 mg/l, respectively . The area under the curve obtained for PCT in distinguishing between viral and bacterial infections was 0.82 (sensitivity, 65.5%; specificity, 94.3%; optimum cutoff, 0.53 ng/ml), whereas for CRP it was 0.78 (sensitivity, 63.5%; specificity, 84.2%; optimum cutoff, 27.5 mg/l) . PCT and CRP values in invasive infections (PCT, 24.3 ng/ml; CRP 96.5 mg/l) were significantly higher than those for noninvasive infections (PCT, 0.32 ng/ml; CRP, 23.4 mg/l) . The area under the curve for PCT was 0.95 (sensitivity, 91.3%; specificity, 93.5%; optimum cutoff, 0.59 ng/ml), significantly higher (P < 0.001) than that obtained for CRP (0.81) . The optimum cutoff value for CRP was >27.5 mg/l with sensitivity and specificity of 78 and 75%, respectively . In infants in whom the evolution of fever was <12 h (n = 104), the diagnostic performance of PCT was also greater than that of CRP (area under the curve, 0.93 for PCT and 0.69 for CRP; P < 0.001) . A good correlation between the quantitative values for PCT and the PCT-Q test was obtained in 87% of cases (kappa index, 0.8) . The sensitivity of the PCT-Q test (cutoff >0.5 ng/ml) for detecting invasive infections and differentiating them from noninvasive infections was 90.6%, with a specificity of 83.6% . CONCLUSIONS: PCT offers better specificity than CRP for differentiating between the viral and bacterial etiology of the fever with similar sensitivity . PCT offers better sensibility and specificity than CRP to differentiate between invasive and noninvasive infection . PCT is confirmed as an excellent marker in detecting invasive infections in ED and can even make early detection possible of invasive infections if the evolution of the fever is <12 h . The PCT-Q test has a good correlation with the quantitative values of the marker.

Protein Expr Purif, 2003 Oct, 31(2), 188 - 96
Bacterial production and purification of SGPI-1 and SGPI-2, two peptidic serine protease inhibitors from the desert locust, Schistocerca gregaria; Simonet G et al.; The last decade, a new serine protease inhibitor family has been described in arthropods . Eight members were purified from the locusts Locusta migratoria (LMPI-1-2 and HI) and Schistocerca gregaria (SGPI-1-5) and 11 additional locust peptides were identified by cDNA cloning . Furthermore, the light chain of the 155-kDa heterodimeric protease inhibitor pacifastin, from the freshwater crayfish Pacifastacus leniusculus, was found to be composed of nine consecutive inhibitory domains (PLDs) . These domains share a pattern of 6 conserved cysteine residues (Cys-Xaa(9-12)-Cys-Asn-Xaa-Cys-Xaa-Cys-Xaa(2-3)-Gly-Xaa(3-4)-Cys-Thr-Xaa3-Cys) with the locust inhibitors . So far, for most of the PLD-related peptides the biological functions remain obscure . To obtain sufficient amounts of material to perform physiological experiments, we have optimised the production of SGPI-1-2 via a bacterial (Escherichia coli) expression system . The cDNA sequences encoding these peptides were inserted in the pMAL-2pX vector, downstream of the gene encoding the maltose-binding protein (including a signal peptide) . As a consequence, both peptides were expressed as fusion proteins (2-3 mg/l) and targeted to the periplasmic space . Following a one-step affinity purification, both fusion proteins were successfully cleaved by Factor Xa and after a methanol extraction, it took only one additional RP-HPLC run to purify both peptides to homogeneity . Finally, the formation of the disulphide bridges and the biological activity of the recombinant peptides were verified by mass spectrometry and a spectrophotometric protease inhibitor assay, respectively.

Biotechnol Adv, 1990, 8(1), 185 - 205
Bacterial haloperoxidases and their role in secondary metabolism; Van Pee KH; Bacteria produce a large number of different halogenated secondary metabolites . Haloperoxidases are believed to be the enzymes responsible for the halogenation reaction . Two classes of haloperoxidases, heme and nonheme, were isolated from different bacteria and their role in the biosynthesis of halogenated secondary metabolites was investigated . Two genes of bacterial haloperoxidases were cloned and can now be used to produce large quantities of the enzymes.

Biotechnol Adv, 1984, 2(2), 347 - 55
Bacterial degradation of ammonium lignosulfonate; Ammar E et al.; Bacterial strains were selected for their capacity to assimilate and to transform ammonium-lignosulfonate . Modification of the methyl content and of low molecular weight alkyl functions were demonstrated by gas-chromatography and HLPC analysis . Most of these strains completely degraded simple phenolic compounds related to lignosulfonate without inhibition by the carbohydrates present in the liquor . Further investigation suggested that the enzymes involved in the fission of the aromatic nuclei were constitutive in the strains tested.

J Urol, 2003 Nov, 170(5), 2053 - 6
Prospective analysis of 16S rDNA as a highly sensitive marker for bacterial presence in Peyronie's disease plaques; Hauck EW et al.; PURPOSE: Previous studies have implicated an infectious agent induced pathogenesis in Peyronie's disease . To our knowledge an association with venereal diseases or other infectious diseases has not been demonstrated to date, although Peyronie's disease is an inflammatory disorder . In case of an infectious origin of the disorder bacteria or at least their fragments should occur in the plaque . We investigated prospectively the occurrence of 16S rDNA as a highly sensitive marker for the presence of bacteria in inflammatory processes . MATERIALS AND METHODS: In 19 patients with idiopathic Peyronie's disease biopsy of the tunica albuginea was sampled . A total of 16 men with no evidence of Peyronie's disease served as the control group . In these men tissue from the tunica albuginea was obtained during penile prosthesis implantation for erectile dysfunction or during a Nesbit procedure for congenital penile curvature . Screening for bacterial DNA was performed prospectively using a polymerase chain reaction targeting bacterial 16S rDNA . RESULTS: In the tunica albuginea specimen 16S rDNA was not detectable in patients with Peyronie's disease or in the control group . CONCLUSIONS: The results of this study do not indicate an association between Peyronie's disease and bacterial infection.

Appl Environ Microbiol, 2003 Oct, 69(10), 6268 - 71
An alternative efficient procedure for purification of the obligate intracellular fish bacterial pathogen Piscirickettsia salmonis; Henriquez V et al.; Piscirickettsia salmonis is an obligate intracellular bacterial pathogen of salmonid fish and the etiological agent of the aggressive disease salmonid rickettsial syndrome . Today, this disease, also known as piscirickettsiosis, is the cause of high mortality in net pen-reared salmonids in southern Chile . Although the bacteria can be grown in tissue culture cells, genetic analysis of the organism has been hindered because of the difficulty in obtaining P . salmonis DNA free from contaminating host cell DNA . In this report, we describe a novel procedure to purify in vitro-grown bacteria with iodixanol as the substrate to run differential centrifugation gradients which, combined with DNase I digestion, yield enough pure bacteria to do DNA analysis . The efficiency of the purification procedure relies on two main issues: semiquantitative synchrony of the P . salmonis-infected Chinook salmon embryo (CHSE-214) tissue culture cells and low osmolarity of iodixanol to better resolve bacteria from the membranous structures of the host cell . This method resulted in the isolation of intact piscirickettsia organisms and removed salmon and mitochondrial DNA effectively, with only 1.0% contamination with the latter.

Crit Rev Oral Biol Med, 2003, 14(5), 331 - 44
Molecular genetic analysis of the virulence of oral bacterial pathogens: an historical perspective; Kuramitsu HK; This review will focus on the impact of molecular genetic approaches on elucidating the bacterial etiology of oral diseases from an historical perspective . Relevant results from the pre- and post-recombinant DNA periods will be highlighted, including the roles of gene cloning, mutagenesis, and nucleotide sequencing in this area of research . Finally, the impact of whole-genome sequencing on deciphering the virulence mechanisms of oral pathogens, along with new approaches to control these organisms, will be discussed.

J Biol Chem, 2003 Dec 26, 278(52), 52710 - 23 Epub 2003 Oct 06.
A DNA pairing-enhanced conformation of bacterial RecA proteins; Haruta N et al.; The RecA proteins of Escherichia coli (Ec) and Deinococcus radiodurans (Dr) both promote a DNA strand exchange reaction involving two duplex DNAs . The four-strand exchange reaction promoted by the DrRecA protein is similar to that promoted by EcRecA, except that key parts of the reaction are inhibited by Ec single-stranded DNA-binding protein (SSB) . In the absence of SSB, the initiation of strand exchange is greatly enhanced by dsDNA-ssDNA junctions at the ends of DNA gaps . This same trend is seen with the EcRecA protein . The results lead to an expansion of published hypotheses for the pathway for RecA-mediated DNA pairing, in which the slow first order step (observed in several studies) involves a structural transition to a state we designate P . The P state is identical to the state found when RecA is bound to double-stranded (ds) DNA . The structural state present when the RecA protein is bound to single-stranded (ss) DNA is designated A . The DNA pairing model in turn facilitates an articulation of three additional conclusions arising from the present work . 1) When a segment of a RecA filament bound to ssDNA is forced into the P state (as RecA bound to the ssDNA immediately adjacent to dsDNA-ssDNA junction), the segment becomes "pairing enhanced." 2) The unusual DNA pairing properties of the D . radiodurans RecA protein can be explained by postulating this protein has a more stringent requirement to initiate DNA strand exchange from the P state . 3) RecA filaments bound to dsDNA (P state) have directly observable structural changes relative to RecA filaments bound to ssDNA (A state), involving the C-terminal domain.

J Microbiol Methods, 2003 Nov, 55(2), 471 - 4
Consecutive analysis of bacterial PCR samples on a single electronic microarray; Zimmermann K et al.; For routine mass screening, the use of microarrays is hampered because one chip can only analyze one sample . 16S rRNA gene PCR products of several bacterial strains or mixtures thereof were consecutively loaded on a single electronic microarray and successfully analyzed using probes specific for the bacterial strains.

J Microbiol Methods, 2003 Nov, 55(2), 411 - 8
Rapid screening method for quantitation of bacterial cell lipids from whole cells; Izard J et al.; Although specific lipids in bacteria can be quantitated, there is still a need to quantitate the total lipid content of a bacterial sample . The sulfo-phospho-vanillin reaction for quantitation of bacterial lipids has significant advantages over traditional methods for screening of engineered mutant strains . In this report we show that this methodology can be used directly on whole cell or homogenized biological material, without any extraction step . The cell components, and most of the reagents used for cell extraction, that were tested did not interfere with the reaction . The screening is based on the observation of physiologic variations using ratios of relative amounts: lipid/DNA and lipid/protein . Our results show that significant differences in those ratios can be detected when there is a modification of the phospholipid content of the cell . The sample manipulation required is minimal and could be automated . Used as a primary screening and/or characterization of engineered mutant strain, the test may lead to further investigation of the nature and distribution of lipids in the cell.

J Hosp Infect, 2003 Oct, 55(2), 92 - 7
The addition of a mobile ultra-clean exponential laminar airflow screen to conventional operating room ventilation reduces bacterial contamination to operating box levels; Friberg S et al.; A mobile screen producing ultra-clean exponential laminar airflow (LAF) was investigated as an addition to conventional turbulent/mixing operating room (OR) ventilation (16 air changes/h) . The evaluation was performed in a small OR (50 m(3)) during 60 standardized operations for groin hernia including mesh implantation . The additional ventilation was used in 50 of the operations . The LAF passed from the foot-end of the OR table over the instrument and surgical area . Strict hygiene OR procedures including tightly woven and non-woven OR clothing were used . Sedimentation rates were recorded at the level of the patients' chests (N=60) (i.e . the air had passed the surgical team) and in the periphery of the OR . In addition bacterial air contamination was studied above the patients' chests in all 10 operations without the additional LAF and in 12 with the LAF . The screen reduced the mean counts of sedimenting bacteria (cfu/m(2)/h) on the patients' chests from 775 without the screen to 355 (P=0.0003) . The screen also reduced the mean air counts of bacteria (cfu/m(3)) above the patients' chests from 27 to 9 (P=0.0001) . No significant differences in mean sedimentation rates (cfu/m(2)/h) existed in the periphery of the OR where 628 without and 574 with screen were recorded . During the follow-up period of six months no surgical site infections were detected . In conclusion when the mobile LAF screen was added to conventional OR ventilation the counts of aerobic airborne and sedimenting bacteria-carrying particles downstream of the surgical team were reduced to the levels achieved with complete ultra-clean LAF OR ventilation (operating box).

Biochemistry, 2003 Oct 14, 42(40), 11726 - 35
Bacterial expression, characterization, and disulfide bond determination of soluble human NTPDase6 (CD39L2) nucleotidase: implications for structure and function; Ivanenkov VV et al.; The ectonucleoside triphosphate diphosphohydrolases (NTPDases) control extracellular nucleotide concentrations, thereby modulating many important biological responses, including blood clotting and pain perception . NTPDases1-4 are oligomeric integral membrane proteins, whereas NTPDase5 (CD39L4) and NTPDase6 (CD39L2) are soluble monomeric enzymes, making them more amenable to thorough structural and functional analyses than the membrane-bound forms . Therefore, we report here the bacterial expression, refolding, purification, and biochemical characterization of the soluble portion of human NTPDase6 . Consistent with the enzyme expressed in mammalian cells, this recombinant NTPDase6 efficiently hydrolyzes GDP, IDP, and UDP (specific activity of approximately 50000 micromol mg(-1) h(-1)), with slower hydrolysis of CDP, ITP, GTP, CTP, ADP, and UTP and virtually no hydrolysis of ATP . The K(m) for GDP (130 +/- 30 microM) is similar to that determined for the soluble rat NTPDase6 expressed in mammalian cells . The secondary structure of the refolded enzyme was determined by circular dichroism to be 33% alpha-helix, 18% beta-sheet, and 49% random coil, consistent with the secondary structure predicted from the amino acid sequence of soluble NTPDase6 . Four of the five cysteine residues in the soluble NTPDase6 are highly conserved among all the NTPDases, while the fifth residue is not . Mutation of this nonconserved cysteine resulted in an enzyme very similar to wild type in its enzymology and secondary structure, indicating that this cysteine exists as a free sulfhydryl and is not essential for structure or function . The disulfide pairing of the other four cysteine residues was determined as Cys(249)-Cys(280) and Cys(340)-Cys(354) by HPLC and mass spectral analysis of tryptic peptides . Due to conservation of these cysteine residues, these two disulfide bonds are likely to exist in all NTPDases . A structural model for NTPDase6, incorporating these and other findings obtained with other NTPDases, is proposed.

Proc Natl Acad Sci U S A, 2003 Nov 25, 100 Suppl 2, 14543 - 8 Epub 2003 Oct 03.
A genomic perspective on nutrient provisioning by bacterial symbionts of insects; Moran NA et al.; Many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients . The best studied such association is that between aphids and Buchnera aphidicola, which produces essential amino acids that are rare in the phloem sap diet . Genomic studies of Buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts . Despite evolutionary reduction of genome size, involving loss of most ancestral genes, Buchnera retains capabilities for biosynthesis of all essential amino acids . In contrast, most genes duplicating amino acid biosynthetic capabilities of hosts have been eliminated . In Buchnera of many aphids, genes for biosynthesis of leucine and tryptophan have been transferred from the chromosome to distinctive plasmids, a feature interpreted as a mechanism for overproducing these amino acids through gene amplification . However, the extent of plasmid-associated amplification varies between and within species, and plasmid-borne genes are sometimes fewer in number than single copy genes on the (polyploid) main chromosome . This supports the broader interpretation of the plasmid location as a means of achieving regulatory control of gene copy number and/or transcription . Buchnera genomes have eliminated most regulatory sequences, raising the question of the extent to which gene expression is moderated in response to changing demands imposed by host nutrition or other factors . Microarray analyses of the Buchnera transcriptome reveal only slight changes in expression of nutrition-related genes in response to shifts in host diet, with responses less dramatic than those observed for the related nonsymbiotic species, Escherichia coli.

Res Microbiol, 2003 Oct, 154(8), 531 - 8
DNA repair by bacterial AlkB proteins; Falnes PO et al.; The Escherichia coli AlkB protein is an iron- and 2-oxoglutarate-dependent oxygenase, repairing 1-methyladenine and 3-methylcytosine lesions in DNA . AlkB homologues are present in a number of bacterial species, and some bacteria have two different AlkB proteins . AlkB also repairs lesions in RNA, and the biological significance of RNA repair is discussed.

Annu Rev Microbiol, 2003, 57, 551 - 77
The bacterial RecA protein as a motor protein; Cox MM; The bacterial RecA protein plays a central role in the repair of stalled replication forks, double-strand break repair, general recombination, induction of the SOS response, and SOS mutagenesis . The major activity of RecA in DNA metabolism is the promotion of DNA strand exchange reactions . RecA is the prototype for a ubiquitous family of proteins but exhibits a few activities that some of its eukaryotic, archaeal, and viral homologs appear to lack . In particular, the bacterial RecA protein possesses an apparent motor function that is not evident in the reactions promoted by the eukaryotic Rad51 protein . This motor may be needed only in a subset of the DNA metabolism contexts in which RecA protein functions . Models for the coupling of DNA strand exchange to ATP hydrolysis are examined.

Annu Rev Microbiol, 2003, 57, 487 - 516
Archeal DNA replication: eukaryal proteins in a bacterial context; Grabowski B et al.; Genome sequences of a number of archaea have revealed an apparent paradox in the phylogenies of the bacteria, archaea, and eukarya, as well as an intriguing set of problems to be resolved in the study of DNA replication . The archaea, long thought to be bacteria, are not only different enough to merit their own domain but also appear to be an interesting mosaic of bacterial, eukaryal, and unique features . Most archaeal proteins participating in DNA replication are more similar in sequence to those found in eukarya than to analogous replication proteins in bacteria . However, archaea have only a subset of the eukaryal replication machinery, apparently needing fewer polypeptides and structurally simpler complexes . The archaeal replication apparatus also contains features not found in other organisms owing, in part, to the broad range of environmental conditions, some extreme, in which members of this domain thrive . In this review the current knowledge of the mechanisms governing DNA replication in archaea is summarized and the similarities and differences of those of bacteria and eukarya are highlighted.

Berl Munch Tierarztl Wochenschr, 2003 Sep-Oct, 116(9-10), 373 - 80
{Establishment and use of infectious bacterial artificial chromosome (BAC) DNA clones of animal herpesviruses}; Osterrieder N et al.; Since the first description of the cloning und mutagenesis of a herpesviral genome in 1997, a number of herpesviral DNA's have been cloned as bacterial artificial chromosomes (BACs) . Herpesvirus BAC's are established by introduction of a mini F origin of replication into the viral genome, which can as such be maintained und manipulated in Escherichia coli as a single copy extrachromosomal DNA . Herpesvirus DNA's cloned as BAC's are accessible to the DNA repair und mutagenesis apparatus encoded by E . coli, which can be exploited for the generation und subsequent analysis of virus mutants . One of the advantages of BAC cloning und mutagenesis is that it is independent of virus growth in cultured cells, thereby minimizing the risk of compensatory mutations . Here we summarize BAC's that have been established for Herpesviruses of livestock, among them Bovine Herpesvirus Type 1 (BHV-1), Equine Herpesvirus Type 1 (EHV-1), Marek's Disease Virus (MDV), Pseudorabies Virus (PRV) . Special emphasis is put on the exploitation of herpesviral BAC's for the analysis of virus replication und vaccine developments.

J Biol Chem, 2003 Dec 19, 278(51), 51543 - 8 Epub 2003 Oct 01.
DNA lesion recognition by the bacterial repair enzyme MutM; Fromme JC et al.; MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA . The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA . The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition . MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom . The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis . Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.

Phys Rev E Stat Nonlin Soft Matter Phys . 2003 Aug;68(2 Pt 1):021925 . Epub 2003 Aug 29.
Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics; D'Orsogna MR et al.; Motivated by observations of the dynamics of Myxococcus xanthus, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis . Cells are constrained to move in one dimension, but release a chemical chemoattractant at a steady state . The bacteria sense the chemical that they produce . The probability of direction reversals is modeled as a function of both the absolute level of chemoattractant sensed directly under each cell as well as the gradient sensed across the length of the cell . If the chemical does not degrade or diffuse rapidly, the one-dimensional trajectory depends on the entire past history of the trajectory . We derive the corresponding Fokker-Planck equations, use an iterative mean-field approach that we solve numerically for short times, and perform extensive Monte Carlo simulations of the model . Cell positional distributions and the associated moments are computed in this feedback system . Average drift and mean squared displacements are found . Crossover behaviors among different diffusion regimes are found.

Chembiochem, 2003 Oct 6, 4(10), 1041 - 8
Evaluation of bacterial RNase P RNA as a drug target; Willkomm DK et al.; RNA has gained increasing importance as a therapeutic target . However, so far mRNAs rather than stable cellular RNAs have been considered in such studies . In bacteria, the tRNA-processing enzyme RNase P has a catalytic RNA subunit . Fundamental differences in structure and function between bacterial and eukaryotic RNase P, and its indispensability for cell viability make the bacterial enzyme an attractive drug target candidate . Herein we describe two approaches utilized to evaluate whether the catalytic RNA subunit of bacterial RNase P is amenable to inactivation by antisense-based strategies . In the first approach, we rationally designed RNA hairpin oligonucleotides targeted at the tRNA 3'-CCA binding site (P15 loop region) of bacterial RNase P RNA by attempting to include principles derived from the natural CopA-CopT antisense system . Substantial inactivation of RNase P RNA was observed for Type A RNase P RNA (such as that in Escherichia coli) but not for Type B (as in Mycoplasma hyopneumoniae) . Moreover, only an RNA oligonucleotide (Eco 3') complementary to the CCA binding site and its 3' flanking sequences was shown to be an efficient inhibitor . Mutation of Eco 3' and analysis of other natural RNase P RNAs with sequence deviations in the P15 loop region showed that inhibition is due to interaction of Eco 3' with this region and occurs in a highly sequence-specific manner . A DNA version of Eco 3' was a less potent inhibitor . The potential of Eco 3' to form an initial kissing complex with the P15 loop did not prove advantageous . In a second approach, we tested a set of oligonucleotides against E . coli RNase P RNA which were designed by algorithms developed for the selection of suitable mRNA targets . This approach identified the P10/11-J11/12 region of bacterial RNase P RNA as another accessible region . In conclusion, both the P15 loop and P10/11-J11/12 regions of Type A RNase P RNAs seem to be promising antisense target sites since they are easily accessible and sufficiently interspersed with nonhelical sequence elements, and oligonucleotide binding directly interferes with substrate docking to these two regions.

Med Sci Monit, 2003 Oct, 9(10), CR426 - 31
Serum procalcitonin concentration as a negative predictor of serious bacterial infection in acute sickle cell pain crisis; Scott LK et al.; BACKGROUND: A pilot study was designed to determine if serum procalcitonin levels would assist in the diagnosis of severe bacterial infections in patients presenting to an emergency department (ED) with acute sickle cell pain crisis and evidence of acute inflammatory response . MATERIAL/METHODS: Prospective single cohort study evaluating measured procalcitonin levels in patients with sickle cell pain crisis and evidence of acute inflammation . Acute inflammation was defined as fever (>38 degrees C) and/or elevation in the white blood cell count (>4000 above baseline) and tachycardia (heart rate >100) . Procalcitonin was measured using a semi-quantitative monoclonal antibody test . Patients were followed clinically to determine if procalcitonin has predictive value in excluding severe bacterial infections . RESULTS: Twenty four subjects were enrolled and completed the study . Sixteen had levels 0.5 ng/ml or less, two had levels 0.5 to 2 ng/ml, one had a level of 2 but less than 10 ng/ml, and four had levels 10 ng/ml or greater . All subjects with documented infections at presentation had procalcitonin levels > or =2.0 ng/ml . The sensitivity of the test in this study sample was 1, and the specificity was 0.95 (95% CI, 0.75-0.99) . CONCLUSIONS: A serum procalcitonin less than 2 ng/ml appears to have good negative predictive value in excluding serious bacterial infections in patients that present with acute sickle cell pain crisis and evidence of acute inflammatory response . Further study is needed to investigate if procalcitonin has positive predictive value in identifying patients with serious bacterial infections in this patient population.

Prikl Biokhim Mikrobiol, 2003 Jul-Aug, 39(4), 435 - 7
{Participation of beta-carotene in antioxidant defense of bacterial cells}; Gessler NN et al.; The effect of recombinant beta-carotene on the resistance of E . coli culture to menadione and paraquat was studied . The presence of beta-carotene in the E . coli cell significantly prevented an increase in the activity of superoxide dismutase induced by redox mediators but had no effect on the culture growth . The findings suggested the involvement of beta-carotene in the cell defense against oxidative stress.

Curr Opin Cell Biol, 2003 Oct, 15(5), 633 - 9
Bacterial pathogenesis: exploiting cellular adherence; Boyle EC et al.; Cell adhesion molecules, such as integrins, cadherins, the immunoglobulin superfamily of cell adhesion molecules and selectins, play important structural roles and are involved in various signal transduction processes . As an initial step in the infectious process, many bacterial pathogens adhere to cell adhesion molecules as a means of exploiting the underlying signaling pathways, entering into host cells or establishing extracellular persistence . Often, bacteria are able to bind to cell adhesion molecules by mimicking or acting in place of host cell receptors or their ligands . Recent studies have contributed to our understanding of bacterial adherence mechanisms and the consequences of receptor engagement; they have also highlighted alternative functions of cell adhesion molecules.

Langenbecks Arch Chir Suppl Kongressbd, 1998, 115(Suppl I), 31 - 2
{Extent of bacterial contamination is a derminant fur microvascular damage in soft tissue infection}; Kraft C et al.; With the use of intravital microscopy, we demonstrate that the extent of bacterial contamination is a determinant for the microvascular response and consecutively the microvascular injury . The model of bacterial soft tissue infection used, ideally allows to study the influence of foreign materials on microvascular immune response.

Biochemistry, 2003 Oct 7, 42(39), 11555 - 60
Determination of the B820 subunit size of a bacterial core light-harvesting complex by small-angle neutron scattering; Wang ZY et al.; The B820 subunit is an integral pigment-membrane protein complex and can be obtained by both dissociation of the core light-harvesting complex (LH1) in photosynthetic bacteria and reconstitution from its component parts in the presence of n-octyl beta-D-glucopyranoside (OG) . Intrinsic size of the B820 subunit from Rhodospirillum rubrum LH1 complex was measured by small-angle neutron scattering in perdeuterated OG solution and evaluated by Guinier analysis . Both the B820 subunits prepared by dissociation of LH1 and reconstitution from apopolypeptides and pigments were shown to have a molecular weight of 11,400 +/- 500 and radius of gyration of 11.0 +/- 1.0 A, corresponding to a heterodimer consisting of one pair of alphabeta-polypeptides and two bacteriochlorophyll a molecules . Molecular weights of micelles formed by OG alone in solutions were determined in a range from 30,000 to 50,000 over concentrations of 1-5% (w/v), and thus are much larger than that of the B820 subunit . Similar measurement on the pigment-depleted apopolypeptides revealed highly heterogeneous behavior in the OG solutions, indicating that aggregates with various sizes were formed . The result provides evidence that bacteriochlorophyll a molecules play a crucial role in stabilizing and maintaining the B820 subunits in the dimeric state in solution . Further measurements on individual alpha- and beta-polypeptides exhibited a marked difference in aggregation property between the two polypeptides . The alpha-polypeptides appear to be uniformly dissolved in OG solution in a monomeric form, whereas the beta-polypeptides favor a self-associated form and tend to form large aggregates even in the presence of detergent . The difference in aggregation tendency was discussed in relation to the different behavior between alpha- and beta-polypeptides in reconstitution with bacteriochlorophyll a molecules.

Biofizika, 2003 Jul-Aug, 48(4), 678 - 82
{Specificity of bacterial response to variation of isotopic composition of water}; Nikitin DI et al.; Culture growth of bacteria with different membrane lipid composition was studied in liquid media with different isotope content of water . The concentration of deuterium in water was varied from 0.01 to 90% . It was shown that large concentrations of deuterium cause the inhibition of all cultures except Deinococcus radiodurans, the most stable living cell . Two cultures, Methylobacterium organophilum and Hyphomonas jannaschiana, showed a pronounced activation at a deuterium concentration of 0.01% . At higher deuterium concentrations, the inhibition of culture growth was observed . The strains Renobacter vacuolatum, Arcocella aquatica NO502 and Caulobacter crescentus did not show any significant effect at low concentrations of deuterium.

Med Pediatr Oncol, 2003 Nov, 41(5), 436 - 43
Identification of children presenting with fever in chemotherapy-induced neutropenia at low risk for severe bacterial infection; Ammann RA et al.; BACKGROUND: Febrile neutropenia (FN) remains a frequent complication in pediatric oncology, requiring emergency hospitalization and empirical broad spectrum antibiotics . The distinction of patients at high versus low risk for severe bacterial infection (SBI) is not fully established . The purpose of this study was to define a rule predicting the risk to develop SBI in children and adolescents with FN, based on information accessible at presentation . PROCEDURE: Information accessible within 2 hr from presentation was collected retrospectively on all pediatric cancer patients presenting with FN from 1993 to 2001 in a single institution . Patients with established SBI at presentation were excluded . After univariate analyses, two multivariate models predicting the risk of SBI were constructed and their performance evaluated using crossvalidation . RESULTS: An SBI developed in 106 (37%) of 285 episodes of 111 children . The logistic regression model outperformed the decision tree model in predicting SBI . It was based on seven variables: bone marrow involvement, no clinical signs of viral infection, high level of C-reactive protein, high hemoglobin, low leukocyte count, presence of central venous catheter, and diagnosis of pre-B-cell leukemia . At 96% sensitivity, the crossvalidated specificity was 26%, and the negative predictive value 91% . CONCLUSIONS: Combining selected information accessible at presentation, SBI in FN can be predicted with clinically useful specificity maintaining very high sensitivity . Induction therapy and absence of clinical signs of viral infection were identified as new predictors of SBI . The results of this study need confirmation and refinement in prospective studies, aiming at more selective management of FN in pediatric oncology .

Science, 2003 Sep 26, 301(5641), 1874 - 7
A bacterial cell-cycle regulatory network operating in time and space; McAdams HH et al.; Transcriptional regulatory circuits provide only a fraction of the signaling pathways and regulatory mechanisms that control the bacterial cell cycle . The CtrA regulatory network, important in control of the Caulobacter cell cycle, illustrates the critical role of nontranscriptional pathways and temporally and spatially localized regulatory proteins . The system architecture of Caulobacter cell-cycle control involves top-down control of modular functions by a small number of master regulatory proteins with cross-module signaling coordinating the overall process . Modeling the cell cycle probably requires a top-down modeling approach and a hybrid control system modeling paradigm to treat its combined discrete and continuous characteristics.

Plant Physiol, 2003 Oct, 133(2), 589 - 96 Epub 2003 Sep 25.
Functional expression of a bacterial heavy metal transporter in Arabidopsis enhances resistance to and decreases uptake of heavy metals; Lee J et al.; Large parts of agricultural soil are contaminated with lead (Pb) and cadmium (Cd) . Although most environments are not heavily contaminated, the low levels observed nonetheless pose a high risk of heavy metal accumulation in the food chain . Therefore, approaches to develop plants with reduced heavy metal uptake are important . Recently, many transgenic plants with increased heavy metal resistance and uptake of heavy metals were developed for the purpose of phytoremediation . However, to reduce heavy metal in the food chain, plants that transfer less heavy metals to the shoot are required . We tested whether an Escherichia coli gene, ZntA, which encodes a Pb(II)/Cd(II)/Zn(II) pump, could be useful for developing plants with reduced heavy metal content . Yeast cells transformed with this gene had improved resistance to Pb(II) and Cd(II) . In Arabidopsis plants transformed with ZntA, ZntA was localized at the plasma membrane and improved the resistance of the plants to Pb(II) and Cd(II) . The shoots of the transgenic plants had decreased Pb and Cd content . Moreover, the transgenic protoplasts showed lower accumulation of Cd and faster release of preloaded Cd than wild-type protoplasts . These results show that a bacterial transporter gene, ZntA, can be functionally expressed in plant cells, and that that it may be useful for the development of crop plants that are safe from heavy metal contamination.

Comp Biochem Physiol A Mol Integr Physiol, 2003 Oct, 136(2), 409 - 16
Prostaglandins, not lipoxygenase products, mediate insect microaggregation reactions to bacterial challenge in isolated hemocyte preparations; Phelps PK et al.; Nodulation is the predominant cellular defense reaction to bacterial challenge in insects . Eicosanoids mediate several steps in the nodulation process, including formation of hemocyte microaggregations . Isolated hemocyte preparations synthesize and secrete eicosanoids, which mediate hemocytic immune reactions . Two major groups of eicosanoids are prostaglandins (products of cyclooxygenase pathways) and various products of lipoxygenase pathways . In this study, we test the hypothesis that prostaglandins, but not lipoxygenase products, mediate hemocyte microaggregation reactions in response to bacterial challenge . Our results indicate that isolated hemocyte preparations pretreated with the cyclooxygenase inhibitors indomethacin and naproxen yielded fewer microaggregates than untreated control groups (3.7 x 10(5) microaggregates/ml hemolymph vs . 11.0 x 10(5) microaggregates/ml hemolymph) . These inhibitors influence hemocyte microaggregate formation in a dose-dependent manner in treatments ranging from 0 to 200 microM . The lipoxygenase inhibitors esculetin and caffeic acid did not impact the formation of microaggregates in this system . The influence of the phospholipase A(2) inhibitor dexamethasone was reversed by amending experimental (dexamethasone-treated) preparations with prostaglandin H(2), but not prostaglandin D(2), prostaglandin E(2), nor 5(S)-hydroperoxy-6E,8Z,11Z,14Z-eicosatetraenoic acid, a product of the lipoxygenase pathway . We infer that prostaglandins are the primary mediators of microaggregation reactions to bacterial challenge in insect hemocyte preparations.

Eur J Biochem, 2003 Oct, 270(19), 4016 - 25
A pathway through interferon-gamma is the main pathway for induction of nitric oxide upon stimulation with bacterial lipopolysaccharide in mouse peritoneal cells; Matsuura M et al.; Production of nitric oxide (NO) in response to bacterial lipopolysaccharide (LPS) was investigated using cultures of mouse peritoneal exudate cells (PEC) and the macrophage cell line RAW264.7 . In the presence of anti-(interferon-gamma) (IFN-gamma), NO production was markedly suppressed in the PEC culture but not in the RAW264.7 culture . In the PEC culture, LPS induced both IFN-gamma production and activation of IFN response factor-1, which leads to the gene expression of inducible NO synthase, but neither was induced in the culture of RAW264.7 cells . In addition to anti-(IFN-gamma), antibodies against interleukin (IL)-12 and IL-18 showed a suppressive effect on LPS-induced NO production in the PEC culture, and these antibodies in synergy showed strong suppression . Stimulation of the PEC culture with IL-12 or IL-18 induced production of IFN-gamma and NO, and these cytokines, in combination, exhibited marked synergism . Stimulation of the culture with IFN-gamma induced production of NO, but not IL-12 . The macrophage population in the PEC, prepared as adherent cells, responded well to LPS for IL-12 production, but weakly for production of IFN-gamma and NO . The macrophages also responded well to IFN-gamma for NO production . For production of IFN-gamma by stimulation with LPS or IL-12 + IL-18, nonadherent cells were required in the PEC culture . Considering these results overall, the indirect pathway, through the production of intermediates (such as IFN-gamma-inducing cytokines and IFN-gamma) by the cooperation of macrophages with nonadherent cells, was revealed to play the main role in the LPS-induced NO production pathway, as opposed to the direct pathway requiring only a macrophage population.

Nucleic Acids Res Suppl, 2003, (3), 281 - 2
Recognition of tRNA bottom half by bacterial ribonuclease P; Nagai Y et al.; Bacterial ribonuclease P (RNase P) contains a catalytic RNA that cleaves precursor tRNA to form the 5'-end of mature tRNA . Bacterial RNase P mainly recognizes the acceptor stem and T arm modules of tRNA molecules . The region consisting of T arm, acceptor stem and 3' CCA motif in the tRNA is generally termed "top half", and the region consisting of the others, anticodon arm, extra loop and D arm, is called "bottom half" . The stems in the top half contribute to recognition, but effects of the bottom half have not been elucidated . To study the effects of the bottom half on the RNase P recognition, we have synthesized several mutant substrates that have the bottom half on different positions along the top half stem . Most of these mutants were cleaved by Escherichia coli RNase P precisely at the expected position, but the cleavage efficiencies were very different especially at low Mg2+ concentration . We also found that RNase P holoenzyme prefered somewhat mutated tRNA precursor to the wild-type tRNA precursor.

Nucleic Acids Res Suppl, 2003, (3), 275 - 6
Revisiting the substrate recognition of bacterial ribonuclease P: in the view of the recognition of the base N73 in the substrate; Tanaka T et al.; The RNA subunit of bacterial ribonuclease P (RNase P) is a ribozyme which can cleave a canonical cloverleaf tRNA precursor and a hairpin RNA with a CCA-3' tag sequence as its substrate . At high concentration of Mg ion, the substrate shape preference of the ribozyme becomes broader to accept a hairpin shape RNA . In hairpin RNA cleavage reactions, we found that the base interaction between the base U294 of E . coli ribozyme and the base N73 of the substrate RNA did not obey the response according to the Watson-Crick type interaction which is usually observed in the interaction between the base U294 of ribozyme and the base N73 of tRNA precursor.

Water Sci Technol, 2003, 48(2), 53 - 60
Use of image analysis to determine algal and bacterial biomass in a high rate algal pond following Percoll fractionation; Cromar NJ et al.; This paper reports the results of work to allow a more accurate enumeration, and gravimetric determination, of the relative proportions of algae and bacteria within the floccular matrix present in a High Rate Algal Pond (HRAP) . Methodology involving a combination of physical and chemical treatments was used and the resulting material was separated using density gradient centrifugation . The "fractions" were analysed using microscopical image analysis . Each "fraction" was categorised as containing bacteria only, algae only or an association of bacteria and algae, the relative proportions of which were then determined by image analysis to enable a "true" gravimetric determination of the algal and bacterial components of HRAP biomass for the first time . The biomass from HRAPs operated both outdoors and in a glasshouse was examined over complete operational seasons to investigate environmental effects as well as possible effects of variation in COD loading rate and retention time on cell biovolumes and cell quotients . In this study, the accurate assessment of both algal and bacterial biomass, determined as cell volume or dry matter, in addition to measurement of carbon and nitrogen has enabled the calculation of cell quotients . This allows a direct comparison between these values obtained from a nutrient-rich system and those published values obtained from systems with various nutrient status . Conversion factors obtained may also be of value for deriving inputs for computer models for the design and operation of high rate algal ponds.

J Cardiovasc Pharmacol, 2003 Oct, 42(4), 477 - 83
Novel anticoagulant activity of polyamino acid offsets bacterial endotoxin-induced extrinsic hypercoagulation: downregulation of monocytic tissue factor-dependent FVII activation; Chu AJ et al.; The extrinsic hypercoagulation often resulting from sepsis could contribute to disseminated intravascular coagulation and cardiovascular complications . The effective prevention and intervention remained largely complex and unclear . In a cell model of human leukemia THP-1 monocytes following bacterial endotoxin (LPS) exposure, we show the novel anticoagulant ability of polyamino acid (polyAA) to suppress the extrinsic hypercoagulation . LPS-induced monocytic tissue factor (mTF) procoagulation was readily offset by poly-L-lysine (PLK), poly-L-arginine (PLR), or poly-L-ornithine (POR) included in single-stage clotting assays . IC50 was estimated at 0.35, 0.30, or 0.58 microM for PLR, POR, or PLK, respectively, whereas, poly-L-asparatic acid (PLD) remained ineffective . In a separate approach, inclusion of cationic polyAA in human plasma significantly prolonged prothrombin time, confirming the depressed extrinsic coagulation . In chromogenic assays dissecting the extrinsic pathway, we further determined the inhibitory site(s) . PLK, PLR, or POR significantly inhibited LPS-induced FVII activation, which was consistent with the diminished FVIIa formation shown on Western blotting analysis . In contrast, polyAA did not show any additional effect on either FVIIa/FXa amidolytic activities or mTF/FVIIa-catalyzed FX activation . Nor did polyAA show any effect on FVII activation directly catalyzed by FXa . Taken together, PLK, PLR, or POR preferentially inhibited mTF-dependent FVII activation, accounting for their novel anticoagulant activities . PolyAA might present the specific antagonists to arrest the extrinsic hypercoagulation following inflammation.

J Clin Epidemiol, 2003 Sep, 56(9), 862 - 6
Self-collected versus provider-collected vaginal swabs for the diagnosis of bacterial vaginosis: an assessment of validity and reliability; Nelson DB et al.; Bacterial vaginosis (BV) in pregnancy is related to numerous adverse events; however, the validity of different methods of vaginal swab collection to diagnosis BV among pregnant women is unclear . This study examines the validity of self-collected compared with provider-collected vaginal swabs and describes the intra-rater and inter-rater reliability of BV assessment among a sample of pregnant women early in gestation . Gram-stain evaluation of vaginal samples using the Nugent criteria was conducted to determine the overall and morphotype-specific BV scores . We found strong validity for the overall and morphotype-specific scores comparing self-collected swabs to provider-collected swabs . In addition, we found excellent overall and morphotype-specific inter-rater reliability and excellent intra-rater reliability in our sample . These study results support the use of self-collected vaginal swabs for diagnosing BV and document the reliability of BV assessment among pregnant women.

Annu Rev Plant Biol, 2003, 54, 207 - 33
From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule; Ball SG et al.; Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway . Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway . This multiplicity does not coincide with any functional redundancy, as each form has seemingly acquired a distinctive and conserved role in starch metabolism . Comparisons of phenotypes generated by debranching enzyme-defective mutants in Escherichia coli and plants suggest that enzymes previously thought to be involved in polysaccharide degradation have been recruited during evolution to serve a particular purpose in starch biosynthesis . Speculations have been made that link this recruitment to the appearance of semicrystalline starch in photosynthetic eukaryotes . Besides the common core pathway, other enzymes of malto-oligosaccharide metabolism are required for normal starch metabolism . However, according to the genetic and physiological system under study, these enzymes may have acquired distinctive roles.

Nat Immunol, 2003 Oct, 4(10), 957 - 64 Epub 2003 Sep 21.
Sustained exposure to bacterial antigen induces interferon-gamma-dependent T cell receptor zeta down-regulation and impaired T cell function; Bronstein-Sitton N et al.; T cell antigen receptor zeta chain down-regulation and impaired in vitro T cell function have been described in cancer and autoimmune and infectious diseases . However, the immunological basis for this phenomenon is unknown . Sustained exposure to antigen and chronic systemic inflammation, factors shared by the various pathologies, might account for this phenomenon . We developed an in vivo experimental system that mimics these conditions and show that sustained exposure of mice to bacterial antigens was sufficient to induce T cell antigen receptor zeta chain down-regulation and impair T cell function, provided an interferon-gamma-dependent T helper type 1 immune response developed . This indicates zeta chain down-regulation could be a physiological response that attenuates an exacerbated immune response . However, it can act as a 'double-edged sword', impairing immune responses to chronic diseases.

Ann Surg, 2003 Sep, 238(3), 401 - 10; discussion 410-1
Use of intracellular cytokine staining and bacterial superantigen to document suppression of the adaptive immune system in injured patients; Murphy T et al.; OBJECTIVE: To determine the percentages of major T lymphocyte subsets in the circulating peripheral blood mononuclear cell population in patients with major traumatic injury at early and late time points and to determine the expression of coreceptors and cytokine production by these T cell subsets . SUMMARY BACKGROUND DATA: Prior studies suggest that serious injury in humans suppresses the adaptive immune system as revealed by diminished proliferation and altered cytokine production in response to polyclonal T cell activation . However, the contribution of individual cell types to this immune dysfunction has not been well characterized . METHODS: The percentage of circulating CD4+ and CD8+ T cells and the relative density of CD4 and CD8 coreceptor expression was determined by flow cytometry in 17 consecutive trauma patients (injury severity score > 20) within 24 hours of injury and at day 7 . Intracellular expression of the cytokines interleukin 2 (IL-2), interferon gamma (IFNgamma), IL-4, and IL-10 were also studied after stimulation with bacterial superantigen (SEB) . Patients were compared with age- and sex-matched controls and to themselves for differences between early and late cytokine expression . RESULTS: The percentage of circulating CD4+ and CD8+ T cells was decreased versus controls at day 1 and further decreased by day 7 following injury . CD4 and CD8 cell surface expression was also decreased at days 1 and 7 . CD4+ T cells in injured patients responded to SEB activation with decreased expression of IFNgamma and IL-2 on day 1 versus controls (P < 0.05) and of all 4 cytokines by day 7 (P < 0.05), while CD8+ T cells showed diminished expression of IFNgamma and IL-2 only at both time points . When day 1 and day 7 cytokine expression results were compared in the same patients, CD4+ T cells showed diminished expression of IFNgamma, IL-2, and IL-4 by day 7 (P < 0.05), but maintained expression of IL-10 . CD8 T cells showed diminished expression of IFNgamma only . CONCLUSIONS: Severe injury induces a loss of circulating CD4+ and CD8+ T lymphocytes and diminished coreceptor expression by these cells . Both T cell subsets show progressive loss of immunostimulatory cytokine production with maintenance of potentially suppressive IL-10 production . These events may have negative consequences for host defense.

Proc Natl Acad Sci U S A, 2003 Sep 30, 100(20), 11255 - 60 Epub 2003 Sep 19.
Computational design of a Zn2+ receptor that controls bacterial gene expression; Dwyer MA et al.; The control of cellular physiology and gene expression in response to extracellular signals is a basic property of living systems . We have constructed a synthetic bacterial signal transduction pathway in which gene expression is controlled by extracellular Zn2+ . In this system a computationally designed Zn2+-binding periplasmic receptor senses the extracellular solute and triggers a two-component signal transduction pathway via a chimeric transmembrane protein, resulting in transcriptional up-regulation of a beta-galactosidase reporter gene . The Zn2+-binding site in the designed receptor is based on a four-coordinate, tetrahedral primary coordination sphere consisting of histidines and glutamates . In addition, mutations were introduced in a secondary coordination sphere to satisfy the residual hydrogen-bonding potential of the histidines coordinated to the metal . The importance of the secondary shell interactions is demonstrated by their effect on metal affinity and selectivity, as well as protein stability . Three designed protein sequences, comprising two distinct metal-binding positions, were all shown to bind Zn2+ and to function in the cell-based assay, indicating the generality of the design methodology . These experiments demonstrate that biological systems can be manipulated with computationally designed proteins that have drastically altered ligand-binding specificities, thereby extending the repertoire of genetic control by extracellular signals.

J Microbiol Methods, 2003 Oct, 55(1), 311 - 4
Application of a disposable transparent filtration membrane to the infrared spectroscopic discrimination among bacterial species; Mossoba MM et al.; This study describes the application of filtration, infrared spectroscopy, and multivariate analysis to the identification of 10 foodborne bacterial species . The bacteria were applied by filtration to a disposable optical membrane that is transparent to infrared radiation . The filtration step was rapid (2 min) . Observed cellular infrared spectra were unique and were used to discriminate among the different species . A dataset for the 10 bacterial species investigated was successfully used to correctly identify unknowns included in the dataset.

J Microbiol Methods, 2003 Oct, 55(1), 91 - 7
Comprehensive detection of bacterial populations by PCR amplification of the 16S-23S rRNA spacer region; Gonzalez N et al.; PCR amplification of the spacer region between the 16S and 23S rRNA genes is commonly employed for the analysis of bacterial communities . In this analysis, the intergenic spacers are amplified by PCR using primers complementary to conserved regions in the 3' 16S rDNA and 5' 23S rDNA . By this method, the observation of every bacterial population may be limited by several causes . To explore the extent of bacterial populations overlooked by this method, we have used an empirical approach . In a sample containing about 50 colonies, we tested the capability to amplify by PCR the spacers from each colony . We also examined the ability to observe the spacers from each colony in the product obtained after amplification of the DNA extracted from the whole sample, as it is usually performed by this method . Contrarily to our expectations that a significant fraction of colonies would not yield amplification products, spacers were successfully amplified from every colony of two different samples examined . Overall, our results suggest that in spite of well-based theoretical limitations, the analysis of bacterial communities by amplification of the spacer regions can render a comprehensive representation of the more abundant bacterial clades in the sample.

Am J Gastroenterol, 2003 Sep, 98(9), 1970 - 5
Does bacterial gastroenteritis predispose people to functional gastrointestinal disorders? A prospective, community-based, case-control study; Parry SD et al.; OBJECTIVES: Irritable bowel syndrome (IBS) might develop after gastroenteritis . Most previous studies of this relationship have been uncontrolled, and little is known regarding other functional gastrointestinal disorders (FGIDs) after gastroenteritis . The primary aim of this study was to determine the frequency of IBS, functional dyspepsia, or functional diarrhea 6 months after bacterial gastroenteritis . METHODS: This was a prospective, community-based, case-control study . Cases had proven bacterial gastroenteritis, and controls were community-based . FGIDs were diagnosed with the use of self-completed Rome II modular questionnaires administered at baseline, 3, and 6 months . Subjects with prior FGIDs were excluded . The primary endpoint was the presence of one of the three specific FGIDs at 6 months . RESULTS: A total of 500 cases and 705 controls were identified . Of the 500 cases, 265 (53%) consented, but only 128 cases and 219 community controls who consented were eligible . At 6 months, 108 cases and 206 controls returned the questionnaire . FGIDs were diagnosed in significantly more cases (n = 27, 25%) than controls (n = 6, 2.9%) (OR = 11.11, 95% CI = 4.42-27.92) . IBS was diagnosed in 18 cases (16.7%) and four controls (1.9%) (OR = 10.1, 95% CI = 3.32-30.69); functional diarrhea in six cases (5.6%) and no controls . Functional dyspepsia was uncommon in both cases and controls . Similar findings were found at 3 months, with 29% of cases and 2.9% of controls having an FGID . CONCLUSIONS: Symptoms consistent with IBS and functional diarrhea occur more frequently in people after bacterial gastroenteritis compared with controls, even after careful exclusion of people with pre-existing FGIDs . The frequency is similar at 3 and 6 months . Our findings support the existence of postinfectious IBS and give an accurate estimate of its frequency.

Radiat Environ Biophys, 2003 Oct, 42(3), 189 - 92 Epub 2003 Sep 11.
Gamma-radiation dose-rate effects on DNA damage and toxicity in bacterial cells; Min J et al.; In order to investigate the relationship between radiation dose-rate and bacterial DNA damage as well as general cellular toxicity, two recombinant Escherichia coli strains, DPD2794 and GC2 were used . Following gamma-ray irradiation, these bioluminescent bacteria showed quantitative stress responses in terms of DNA damage and general toxicity depending on the dose rates of energy deposition, i.e . dose-rate of radiation . In addition, an inverse relationship was found, at lower dose rates between 0.5 and 1 Gy/h and a parabolic relationship at dose rates between 0.5 and 2.6 Gy/h.

Appl Microbiol Biotechnol, 2003 Dec, 63(2), 115 - 27 Epub 2003 Sep 16.
Bacterial heme biosynthesis and its biotechnological application; Frankenberg N et al.; Proteins carrying a prosthetic heme group are vital parts of bacterial energy conserving and stress response systems . They also mediate complex enzymatic reactions and regulatory processes . Here, we review the multistep biosynthetic pathway of heme formation including the enzymes involved and reaction mechanisms . Potential biotechnological implications are discussed.

Alcohol, 2003 Jul, 30(3), 183 - 91
Effects of ethanol on gut-associated lymphoid tissues in a model of bacterial translocation: a possible role of apoptosis; Souza HS et al.; Chronic ethanol intake has been shown to be associated with immune suppression and impairment of epithelial barrier function . We investigated the effects of ethanol on intestinal immunity and its relation to bacterial translocation (BT) . Male Wistar rats were assigned to one of three groups and received respective diets for 28 days . The ethanol-fed group {(EG); n=11} received a liquid diet containing 5% {volume/volume (vol./vol.)} ethanol; a pair-fed group {(PFG); n=11} received an isocaloric diet without ethanol; and a third (control) group {(CG); n=11} received water and chow ad libitum . On experimental day 29, animals in the EG and the PFG underwent distal ileum ligature and small intestine inoculation of a tetracycline-resistant Escherichia coli strain (TcR E . coli R6), by means of gastric intubation, followed by duodenal ligature . One hour after inoculation, mesenteric lymph nodes, right lobe of liver, spleen, and left kidney were excised for bacterial studies . Sections of jejunum and colon were immunostained, with the use of antibodies against immunoglobulin (Ig) A, T cells, macrophages, and proliferating cell nuclear antigen (PCNA) . Apoptosis was determined by the terminal deoxynucleotidyltransferase TdT-mediated dUDP-biotin nick end labeling (TUNEL) method . Bacterial translocation rates were greater in the PFG compared with findings for the EG . Lamina propria of the jejunum of the EG showed a reduction in the densities of IgA+ cells and T cells compared with findings for the PFG and the CG . Colonic lamina propria of the EG showed reduced densities of IgA+ cells and macrophages compared with findings for the PFG and the CG . Apoptotic index was increased in the EG compared with findings for the PFG and the CG, in both jejunum and colon . Proliferation index was not significantly different among groups . Results of the current study show that chronic ethanol ingestion led to a reduction of cellular and humoral components of the intestinal mucosa, possibly by cell loss as a result of ethanol-induced apoptosis . The reduced rates of BT observed after chronic ethanol intake seem to indicate that factors irrespective of immune function might be involved in BT inhibition.

Curr Biol, 2003 Sep 16, 13(18), R705 - 7
Bacterial shape: growing off this mortal coil; Margolin W; Members of the actin-like MreB family of proteins localize as a helical filament in bacteria and are important for determining cylindrical cell shape . Recent results show that new cell wall biosynthesis occurs along a helical track dependent on one of these actin homologs, providing new insights into bacterial cell growth, division and shape.

J Drug Target, 2003 Apr, 11(3), 151 - 61
Sealed bacterial ghosts--novel targeting vehicles for advanced drug delivery of water-soluble substances; Paukner S et al.; The purpose of the present study was to develop a drug delivery model for water soluble drug substances using the bacterial ghost platform technology . Bacterial ghosts are non-denatured bacterial cell envelopes that are produced by the plasmid encoded gene E mediated lysis . We present a novel method to fill and seal bacterial ghosts for the application as a drug delivery system for fluid, non-anchored substances . E . coli ghosts were filled with the reporter substance calcein and sealed by fusion with membrane vesicles . By flow cytometry and fluorescence microscopy it was shown that bacterial ghosts can be filled with calcein, and that the bacterial ghosts can be sealed by restoring the membranes integrity . The adherence and uptake studies showed that almost all murine macrophages and a lower proportion of human colorectal adenocarcinoma cells took up fluorescence labeled bacterial ghosts . Moreover, these cells also took up effectively sealed E . coli ghosts filled with calcein, which then was released within the cells . Therefore, we propose bacterial ghosts as alternative drug delivery and release vehicles for advanced cell targeting.

Biotechnol Appl Biochem . 2003 Sep 17; {Epub ahead of print}
Uniformly oriented immobilized bacterial F 0F 1 ATPase on semi-permeable membrane: A step towards biotechnological energy transduction; Bhattacharya S et al.; The immobilization of F 0F 1 #45 ATPase in uniform orientation is reported . The biotinylated and histidine tagged subunits of bacterial F 0F 1 ATPase complex was used for immobilization of the complex on artificial semi-permeable membranes resulting in 88 #177 7.8 and 72 #177 5.2 percent coupling of the enzymes on a protein basis . The immobilized enzymes retained over 90 percent activity . The immobilized ATPase/synthase was used for generation of ATP from ADP and inorganic phosphate at the expense of electrochemical potential energy . The reusability, ratio of amount of enzyme immobilized to enzymatic activity conferred on the membranes, ATP synthesized by assembled system, and suitability of ATP generated for use in coupled enzymatic reactions were determined.

Pharmacoeconomics, 2003, 21(14), 1053 - 68
Prevention of recurrent rhinopharyngitis in at-risk children in France: a cost-effectiveness model for a nonspecific immunostimulating bacterial extract (OM-85 BV); Pessey JJ et al.; OBJECTIVE: To estimate the pharmacoeconomic impact for the French Social Security System of preventing recurrent acute rhinopharyngitis (RARP) in at-risk children with OM-85 BV, an immunostimulating agent indicated for the prevention of recurrences . DESIGN: A decision-analysis model . The probability of progression of the infection and of its associated care, the principal direct costs linked to them, and the effectiveness of OM-85 BV were established or calculated by reviewing the available literature (published between 1984 and 2000) . Four experts validated the parameters and the model . RESULTS: For the French Social Security System, the mean direct cost for an acute rhinopharyngitis (ARP) infection was 49.39 Euro(2000 values) . By using OM-85 BV prevention, 1.52 infections were prevented in 6 months saving 67.83 Euro on the costs of care for the recurrently infected child . Sensitivity analyses confirmed the robustness of the model and indicated a saving of between 6.28 Euro and 303.64 Euro in direct costs for each individual treated preventively . Threshold analyses showed that OM-85 BV prophylaxis is economically profitable if more than 0.15 infections are prevented and if direct costs of care of an ARP are greater than 4.78 Euro . CONCLUSION: Non-specific immunotherapy should be considered for the child at risk of RARP and administered in addition to other recommended measures . The economic savings for the community of using a medication for which the clinical effectiveness has been demonstrated should also be taken into account in assessing its usefulness.

J Biol Chem, 2003 Nov 21, 278(47), 46826 - 31 Epub 2003 Sep 15.
Four inteins and three group II introns encoded in a bacterial ribonucleotide reductase gene; Liu XQ et al.; A bacterial ribonucleotide reductase gene was found to encode four inteins and three group II introns in the oceanic N2-fixing cyanobacterium Trichodesmium erythraeum . The 13,650-bp ribonucleotide reductase gene is divided into eight extein- or exon-coding sequences that together encode a 768-amino acid mature ribonucleotide reductase protein, with 83% of the gene sequence encoding introns and inteins . The four inteins are encoded on the second half of the gene, and each has conserved sequence motifs for a protein-splicing domain and an endonuclease domain . These four inteins, together with known inteins, define five intein insertion sites in ribonucleotide reductase homologues . Two of the insertion sites are 10 amino acids apart and next to key catalytic residues of the enzyme . Protein-splicing activities of all four inteins were demonstrated in Escherichia coli . The four inteins coexist with three group II introns encoded on the first half of the same gene, which suggests a breakdown of the presumed barrier against intron insertion in this bacterial conserved protein-coding gene.

An Pediatr (Barc), 2003 Sep, 59(3), 246 - 51
{Interleukin-6 and tumor necrosis factor-alpha as markers of vertically-transmitted neonatal bacterial infection}; Rite Gracia S et al.; INTRODUCTION: Neonatal infection is a major cause of morbidity in the neonatal period . Several parameters have been used to assess neonatal sepsis . C-reactive protein (CRP) shows high specificity for bacterial infections, but an increase in CRP is often not detected until 12 to 24 hours after onset of the infection . OBJECTIVE: To evaluate the usefulness of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) in the early diagnosis of vertically-transmitted neonatal bacterial infection . METHODS: Thirty-four newborns admitted to the neonatal intensive care unit with an initial diagnosis of respiratory distress were included . Twelve newborns presented the criteria for clinical sepsis or pneumonia (group I) and six had positive blood culture . The remaining patients did not present the clinical criteria for infection (group II) . IL-6, TNF-alpha, CRP levels and the ratio between immature and mature neutrophil count were assessed at 8.8 +/- 7.3 hours of life . In 17 patients the same parameters were assessed at 67.4 +/- 24.8 hours of life . The statistical analysis was performed using the Mann-Whitney test . The sensitivity and specificity of these markers were assessed . RESULTS: No differences were found in the perinatal features of either group . Analysis of markers of infection revealed the following significant differences: ratio between immature and mature neutrophil count: (0.25 +/- 0.21 vs 0.12 +/- 0.09; p=0.048), CRP first determination (1.4 +/- 0.8 mg/dL vs 1 +/- 0.5 mg/dL; p=0.036), CRP second determination: (3.8 +/- 1.8 mg/dL vs 1.4 +/- 1.1 mg/dL; p=0.008), IL-6 first determination: (582.2 +/- 810.5 pg/mL vs 31.3 +/- 24.2 pg/mL; p=0.000) . Sensitivity/specificity (%): ratio between immature and mature neutrophil count: 41.6/83.6; CRP first determination: 16.6/90.9; CRP second determination: 83.3/87.5; IL-6 (optimum cut-off value: 55 pg/mL): 100/72.7, and TNF-alpha: 16.6/85 . CONCLUSIONS: IL-6 determination in the first hours of life is a more sensitive early marker of neonatal infection than other classical markers because of its early elevation . Like CRP, early TNF-alpha determination has high specificity but low sensitivity.

Clin Exp Immunol, 2003 Oct, 134(1), 32 - 7
Childhood Helicobacter pylori infection in a murine model: maternal transmission and eradication by systemic immunization using bacterial antigen-aluminium hydroxide; Minoura T et al.; In humans, transmission of Helicobacter pylori is thought to occur largely during childhood . Infected mothers are generally considered to be the main source of the pathogen . However, little is known about when and how often maternal transmission of H . pylori occurs during childhood . In the present study, we examined these issues in an experimental murine model . Pregnant C57BL/6 mice, infected experimentally with H . pylori, delivered and nursed their litters . The stomachs of the infants were isolated and assessed for transmission of H . pylori . We also investigated the effect of systemic immunization using H . pylori antigen-aluminium hydroxide (AlOH) with regard to providing anti-H . pylori immunity and eradicating the maternally transmitted bacteria in infants . Polymerase chain reaction (PCR) was used to examine the presence of transmitted bacteria and their eradication . Maternal transmission of H . pylori varied widely during the nursing period, but almost all litters showed bacterial transmission at 2 weeks postpartum . Systemic immunization with bacterial antigen-AlOH eradicated the bacteria in most litters; this immunization induced a local decrease of Th2 cytokines and a local increase of Th1 cytokines in the gastric tissue, as determined by ELISA . Our results indicate that our H . pylori vaccine provides not only protection, but also eradication of the already transmitted H . pylori.

Biochemistry, 2003 Sep 23, 42(37), 10923 - 30
Hydrogen exchange in a bacterial cytochrome c: a fingerprint of the cytochrome c fold; Bartalesi I et al.; The hydrogen exchange rates of backbone amides in a minimal (71 amino acid long) monoheme cytochrome c were determined as a function of pH in the absence and in the presence of guanidinium chloride . These data permitted the identification of units undergoing the opening reaction that precedes hydrogen exchange through a common mechanism . The opening units broadly correlate with the secondary structure elements of the protein . It is found that, despite the significant difference in primary sequence, the distribution of the opening units within the three-dimensional structure of the cytochrome studied here closely resembles that determined in mitochondrial c-type cytochromes . It is proposed that the observed distribution represents a fingerprint of the cytochrome c fold and has a role in directing the folding/unfolding of the protein.

Ying Yong Sheng Tai Xue Bao, 2003 Jun, 14(6), 1012 - 4
{A review on modelling bacterial transport in soils}; Li G et al.; Most studies on bacterial transport in soils were carried out in columns under controlled conditions, and the results were various, reflecting the need of standardizing the method . Other methods were also used in conjunction with microscopy to examine the transport at pore scale . Mathematical models based on convection-dispersion equation were developed to simulate bacterial transport . Within specific limits, these models could simulate the major behaviors of bacterial transport . However, they neglected some parameters such as the growth and death of bacteria . The theoretical development, experimental size, scale exchange and modeling for predicting bacterial transport at field scale should be further studied.

Crit Care Med, 2003 Aug, 31(8), 2126 - 30
Bacterial filters in respiratory circuits: an unnecessary cost?
Lorente L, Lecuona M, Malaga J, Revert C, Mora ML, Sierra A.
OBJECTIVE: To evaluate the efficacy of bacterial filters (BF) to decrease pneumonia associated with mechanical ventilation (MV) . DESIGN: Prospective, randomized study . SETTING: A 24-bed medicosurgical intensive care unit in a 650-bed tertiary hospital . PATIENTS: A total of 230 patients who needed MV for >24 hrs . INTERVENTIONS: A total of 114 patients were ventilated with BF and 116 without BF . MEASUREMENTS: Throat swab and tracheal aspirate were taken at the moment of admission and twice a week until discharge . We considered the following infectious events: pneumonia, respiratory infection, which comprises pneumonia or tracheobronchitis, and respiratory colonization-infection complex, which comprises respiratory infection or colonization . All infectious events were classified as endogenous or exogenous based on throat flora . MAIN RESULTS: Both groups of patients (ventilated with and without filters) were similar in age, sex, Acute Physiology and Chronic Health Evaluation II score, diagnostic group, days of MV, and mortality . There was no difference in the percentage of patients who developed pneumonia (24.56% with BF and 21.55% without BF), respiratory infection (33.33% vs . 28.44%), or colonization-infection (42.10% vs . 43.96%) . The number of infectious events per 1000 days of MV were also similar in both groups: pneumonia (17.41 with BF and 16.26 without BF), respiratory infection (24.62 vs . 21.48), and colonization-infection (36.63 vs . 36) . There were also no differences in incidence of infectious events by MV duration . Likewise, we did not find any differences in the number of exogenous events per 1000 days of MV: pneumonia, 2.40 with BF vs . 1.74 without BF; colonization-infection, 4.20 vs . 4.05 . CONCLUSIONS: Bacterial filters in ventilation circuits neither reduce the prevalence of respiratory infections associated with MV nor decrease exogenous infectious events; thus, their usage is not necessary.

Mol Plant Microbe Interact, 2003 Sep, 16(9), 827 - 34
Production of substances by Medicago truncatula that affect bacterial quorum sensing; Gao M et al.; Earlier work showed that higher plants produce unidentified compounds that specifically stimulate or inhibit quorum sensing (QS) regulated responses in bacteria . The ability of plants to produce substances that affect QS regulation may provide plants with important tools to manipulate gene expression and behavior in the bacteria they encounter . In order to examine the kinds of QS active substances produced by the model legume M . truncatula, young seedlings and seedling exudates were systematically extracted with various organic solvents, and the extracts were fractionated by reverse phase C18 high-performance liquid chromatography . M . truncatula appears to produce at least 15 to 20 separable substances capable of specifically stimulating or inhibiting responses in QS reporter bacteria, primarily substances that affect QS regulation dependent on N-acyl homoserine lactone (AHL) signals . The secretion of AHL QS mimic activities by germinating seeds and seedlings was found to change substantially with developmental age . The secretion of some mimic activities may be dependent upon prior exposure of the plants to bacteria.

Eur J Obstet Gynecol Reprod Biol, 2003 Oct 10, 110(2), 149 - 52
Treatment of asymptomatic bacterial vaginosis to prevent pre-term delivery: a randomised trial; Guaschino S et al.; OBJECTIVES: To evaluate the efficacy of clindamycin vaginal cream 2% once daily for 7 days in prolonging pregnancy . STUDY DESIGN: Randomised clinical trial of 112 women between 14 and 25 weeks of gestation with diagnosis of asymptomatic bacterial vaginosis were enrolled in a multicenter randomised trial and assigned to active or no treatment . A total of 55 women were assigned to clindamycin and 57 to no treatment . MAIN OUTCOME MEASURE: frequency of pre-term delivery . RESULTS: The rates of pre-term delivery was 12.2% in the clindamycin group and 15.7% in the no treatment group (P=0.78) . Birth weight was <2500 g in three and seven babies, respectively, in the two groups (P=0.32) . Mean gestational ages at birth were 38.9 and 39.2 (P=0.52), respectively, in the clindamycin and no treatment groups . CONCLUSIONS: The results of this study suggest that treating asymptomatic bacterial vaginosis does neither markedly prolong pregnancy nor increase birthweight.

J Immunol Methods, 2003 Aug, 279(1-2), 233 - 49
Rapid site-directed mutagenesis of chemokines and their purification from a bacterial expression system; Wain JH et al.; Chemokines are a family of small chemoattractant cytokines implicated in the recruitment and migration of leukocytes from the blood into tissues during disease and routine immune homeostasis . Although there are many similarities in the structure and function of certain chemokines, the importance of many residues in the function of these proteins is yet to be determined, and studies from related chemokines have shown that similar sequences may play different roles in each protein . The migration-inducing capacity of many chemokines is thought to involve the cell surface glycosaminoglycan (GAG), heparan sulphate (HS), which may assist in the formation of an immobilised chemokine gradient within inflamed tissues . To examine the heparan sulphate binding ability of the CC chemokine monocyte chemoattractant protein (MCP)-3 and its importance in chemotactic migration, we have identified and mutated conserved basic residues within the mature MCP-3 protein to the neutral amino acid alanine using a novel inverse polymerase chain reaction (I-PCR) method that rapidly generates essentially 100% mutational efficiency due to decreased requirements for template DNA and an alkaline denaturation step; this increased mutational efficiency reduces both screening time and sequencing costs . We also describe an optimised method for the expression of soluble, correctly folded MCP-3 in a bacterial system using nickel affinity columns and reverse-phase fast protein liquid chromatography (RP-FPLC), and achieve purified yields of up to 0.4 mg/l of initial culture medium after 5 h of induction . These optimised methods could work equally well for any small circular plasmid (< or =4.5 kb) incorporating a polyhistidine tag.

Lett Appl Microbiol, 2003, 37(4), 344 - 8
The effects of treating bovine hide with steam at subatmospheric pressure on bacterial numbers and leather quality; McEvoy JM et al.; AIMS: To examine the effect of subatmospheric steam treatment on total viable counts (TVCs) on bovine hide and on the quality of derived leather . METHODS AND RESULTS: Pieces of bovine hide were heated to 75 degrees C (+/-2 degrees C) (n = 3) or 80 degrees C (+/-2 degrees C) (n = 3) for periods of 1, 10 or 20 s by the application of steam at subatmospheric pressure in a laboratory scale apparatus . Treated hide pieces and untreated controls were tanned and the quality of leather was assessed . Treatment at 80 degrees C (T80) reduced the TVC on hide pieces by 2.95 (1 s), 3.33 (10 s) and 3.99 (20 s) log10 CFU cm-2 (P > 0.05) . Treatment at 75 degrees C (T75) reduced the TVC on hide pieces by 1.87 (1 s), 2.51 (10 s) and 2.56 (20 s) log10 CFU cm-2 (P > 0.05) . The grain on all treated hides was damaged resulting in sueding on derived leather . Sueding was observed on 100% of surfaces from T80-treated samples and on 18 (1 s) to 84% (20 s) of the surfaces of T75 samples . CONCLUSIONS: The magnitude of TVC reductions achieved using T75 and T80 could limit the impact and scale of contamination transfer to the carcass during dehiding . However, because of the sueding observed on derived leather, it is unlikely that either T75 or T80 would be a commercially valid operation during routine slaughter operations . SIGNIFICANCE AND IMPACT OF THE STUDY: Hide decontamination would provide an important critical control point for beef processing, however there are currently no commercially available treatments.

Cell Microbiol, 2003 Oct, 5(10), 681 - 93
Recognition of the cellular beta1-chain integrin by the bacterial AfaD invasin is implicated in the internalization of afa-expressing pathogenic Escherichia coli strains; Plancon L et al.; The afa operons from Escherichia coli associated with extra-intestinal and intestinal infections have been characterized and the AfaD protein has been shown to be involved in the low internalization of laboratory strains expressing the afa-3 operon . The aim of this study was to determine the role of the AfaD invasin during the interaction of pathogenic E . coli with epithelial cells . We show that AfaD is implicated in the entry of a clinical isolate into both HeLa and undifferentiated Caco-2 cells . Once in the cytoplasm of these cells, the bacteria formed inclusions in which they were able to survive for at least 72 h . Internalization assays using polystyrene beads coated with His6-tagged purified AfaD (rAfaD) demonstrated that this invasin mediates entry into cells derived from various tissues (intestine and urothelium) that are targets for afa-positive strains . Consistent with the previous observation that an antibody blockade involving anti-alpha5beta1 integrin abolishes bacterial internalization, we show here that the entry of rAfaD-coated beads was dependent on the production and accessibility of beta1 integrins on the cells . The AfaD proteins belong to a family of invasins that are at least 45% identical . Despite their differences, the recombinant rAfaD-III and rAfaD-VIII proteins both bound to beta1 integrins . Our results suggest that beta1 integrin is a common receptor for AfaD invasins and that additional AfaD-type-specific receptors exist.

Biotechnol Bioeng, 2003 Oct 20, 84(2), 151 - 9
Binding and reversibility of Thermobifida fusca Cel5A, Cel6B, and Cel48A and their respective catalytic domains to bacterial microcrystalline cellulose; Jung H et al.; The binding and reversibility of Thermobifida fusca intact Cel5A, Cel5B, and Cel48A and their corresponding catalytic domains (CDs) to bacterial microcrystalline cellulose (BMCC) were studied at 5 degrees C . The binding of the intact cellulases and of corresponding CDs to BMCC was irreversible in all regions: Langmuir binding (region I), interstice penetration (region II), and interstice saturation (region III) . The three cellulose binding domains (CBMs) bind reversibly in "region I" although their respective CDs do not . The irreversible binding of these enzymes in the Langmuir region does not satisfy the Langmuir assumption; however, the overall fit of the Interstice Saturation model, which includes binding in MBCC interstices as well as on the freely accessible surface (Jung et al., 2002a) is good . The main limitation of the model is that it does not explicitly address a mechanism for forming the enzyme-substrate complex within the active site of the CDs .

Clin Diagn Lab Immunol, 2003 Sep, 10(5), 808 - 12
Effect of bacterial flora on postimmunization gastritis following oral vaccination of mice with Helicobacter pylori heat shock protein 60; Yamaguchi H et al.; In order to assess the efficacy of oral Helicobacter pylori heat shock protein 60 (HSP60) as a vaccine, protection against H . pylori infection in specific-pathogen-free (SPF) C57BL/6 and germfree (GF) IQI mice was examined . Prophylactic oral vaccination of these two strains of mice with either H . pylori HSP60 or Escherichia coli GroEL inhibited H . pylori colonization by 90 to 95% at 3 weeks postinfection (p.i.) . However, these mice were only partially protected because bacterial loads increased in all animals at 10 weeks p.i . Anti-H . pylori HSP60 immunoglobulin G was detected in serum at 3 weeks p.i . in mice vaccinated with either H . pylori HSP60 or GroEL . Significant increases in the gastritis scores were observed only in SPF mice immunized with H . pylori HSP60 . These results indicate that oral vaccination with H . pylori HSP60 has partial protective effects on subsequent H . pylori infection but also induces postimmunization gastritis . However, GF mice immunized with H . pylori HSP60 did not suffer from severe gastritis . Therefore, the presence of bacterial flora appears to contribute to the induction of postimmunization gastritis.

Protein Expr Purif, 2003 Sep, 31(1), 140 - 8
Bacterial expression, purification, and characterization of rat kidney-type mitochondrial glutaminase; Kenny J et al.; The human gene that encodes the kidney-type glutaminase (KGA) spans 84-kb, contains 19 exons, and encodes two alternatively spliced mRNAs . Various segments of the rat KGA cDNA were PCR amplified and cloned into a bacterial expression vector to determine whether the N- and C- terminal ends of the glutaminase protein were essential for activity . A recombinant glutaminase, lacking the coding sequence contained in exon 1, was found to be fully active . In contrast, proteins that lacked sequences from exons 1 and 2 and exons 1-3 were inactive . An additional construct that corresponded to the sequence encoded by exons 2-14 also retained full activity . Both of the fully active, truncated proteins were purified to apparent homogeneity using an incorporated N-terminal His(6)-tag and Ni(2+)-affinity chromatography . The K(M) values for glutamine of the native and recombinant forms of glutaminase were nearly identical . However, the two truncated forms of the glutaminase exhibit the characteristic phosphate activation profile only when dialyzed into a buffer lacking phosphate . Dialysis versus 10mM Tris-phosphate was sufficient to form an active tetramer . Thus, the deleted N-terminal sequence may contribute to the phosphate-dependent oligomerization and activation of the native glutaminase.

Obstet Gynecol, 2003 Sep, 102(3), 527 - 34
Clinical and cervical cytokine response to treatment with oral or vaginal metronidazole for bacterial vaginosis during pregnancy: a randomized trial; Yudin MH et al.; OBJECTIVE: To compare the efficacy of oral versus vaginal metronidazole treatment in pregnant women with bacterial vaginosis, and to compare cytokine profiles (interleukin-1beta, -6, and -8) in the cervical secretions of these women before and after treatment . METHODS: Pregnant women with bacterial vaginosis diagnosed both by Gram stain and clinical criteria were randomized to receive oral (n=52) or vaginal (n=50) metronidazole therapy . Cervical specimens for cytokine analysis and vaginal fluid for evaluation of bacterial vaginosis were obtained at baseline and 4 weeks after treatment . RESULTS: There was no significant difference in therapeutic cure rates (defined as a Gram stain score of 0-3 and the absence of all four clinical signs of bacterial vaginosis) between the two groups (71% and 70% for the oral and vaginal groups, respectively, P=1.0) . Cervical levels of interleukin-1beta, -6, and -8 were significantly lower after treatment among the 72 women cured of bacterial vaginosis (P<.001, P=.001, and P=.02, respectively) but not among women who failed to respond to therapy . For interleukin-1beta and -6, a significant decrease in cytokine level was observed in both the oral and vaginal treatment groups . CONCLUSION: One week of oral metronidazole and 5 days of intravaginal metronidazole are equally efficacious for treatment of bacterial vaginosis during pregnancy . The decrease in cervical interleukin-1beta, -6, and -8 levels among women who established a normal flora after treatment but not among those with persistent bacterial vaginosis suggests a direct linkage between vaginal flora abnormalities and elevated cervical levels of interleukin-1beta, -6, and -8.

Proc Natl Acad Sci U S A, 2003 Sep 16, 100(19), 11127 - 32 Epub 2003 Sep 05.
Localization of a bacterial protein in starch granules of transgenic maize kernels; Chikwamba RK et al.; The B subunit of Escherichia coli heat labile enterotoxin (LT-B) is a potent oral immunogen with potential for use as a vaccine, a carrier molecule to deliver antigens to gut-associated lymphoid tissues, and possibly an adjuvant to make coadministered vaccines more effective . LT-B produced in plants was shown to be functional and immunogenic in animals and humans . In this work, we show that maize-derived LT-B is strongly associated with starch granules in endosperm . Using immunogold labeling/electron microscopy, cell fractionation, and protein analysis techniques, we observed that LT-B protein could be detected both internally and externally in starch granules . This strong association confers an effective copurification of the antigen with the starch fraction of maize kernels, thermostability desirable in maize processing, and resistance to peptic degradation in simulated gastric fluid digests, an important attribute for an orally delivered antigen.

Biomacromolecules, 2003 Sep-Oct, 4(5), 1362 - 71
Structure and properties of a bacterial polysaccharide named Fucogel; Guetta O et al.; The chemical structure of a polysaccharide named Fucogel was characterized and the position of acetylation was identified by NMR . A conformational analysis was performed on this 3-sugar repeating unit . From this, the persistence length, characterizing the stiffness of the polysaccharide, was determined and the role of the presence of acetyl group, reducing the stiffness, was pointed out . The helical conformations were also predicted, one of these being in agreement with X-ray data obtained on a similar polysaccharide . Experimental characterization of the native and deacetylated polysaccharides was developed . SEC experiments allowed us to determine the molar mass and the persistence length on the deacetylated polysaccharide . The value is in good agreement with that predicted from the molecular modeling . Microcalorimetry, rheology, and fluorescence spectroscopy demonstrated respectively that no helical conformation exists in solution but that loose interchain interactions due to the acetyl substituents exist in dilute solutions.

Appl Environ Microbiol, 2003 Sep, 69(9), 5070 - 8
Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete; Campbell BJ et al.; The deep-sea polychaete Alvinella pompejana colonizes tubes on the sides of black smoker chimneys along the East Pacific Rise . A diverse, yet phylogenetically constrained episymbiotic community is obligately associated with its dorsal surface . The morphologically and phylogenetically distinct dominant episymbionts have not yet been cultured, and there are no clearly defined roles for these bacteria in this symbiosis . A large insert fosmid library was screened for the presence of the two dominant phylotypes . Two fosmids, 35.2 and 38 kb, containing phylotype-specific 16S ribosomal DNA sequences were fully sequenced . Each fosmid had a gene encoding ATP citrate lyase, a key enzyme in the reverse tricarboxylic acid (rTCA) cycle, a CO(2) fixation pathway . A selection of episymbiont communities from various geographic locations and vent sites were screened for the presence, diversity, and expression (via reverse transcription-PCR) of the ATP citrate lyase gene . Our results indicate that the ATP citrate lyase gene is not only a consistent presence in these episymbiont communities but is also expressed . Phylogenetically distinct forms of ATP citrate lyase were also found associated with and expressed by bacteria extracted from the tubes of A . pompejana . Utilizing PCR with degenerate primers based on a second key enzyme in the rTCA cycle, 2-oxoglutarate:acceptor oxidoreductase, we also demonstrated the persistent presence and expression of this gene in the episymbiont community . Our results suggest that members of both the episymbiont and the surrounding free-living communities display a chemolithoautotrophic form of growth and therefore contribute fixed carbon to other organisms in the vent community.

ANZ J Surg, 2003 Sep, 73(9), 722 - 6
Effects of ursodeoxycholic acid, glutamine and polyclonal immunoglobulins on bacterial translocation in common bile duct ligated rats; Aldemir M et al.; BACKGROUND: The present study was conducted to investigate the effects of ursodeoxycholic acid (UDCA), glutamine and i.v . polyclonal immunoglobulins (IVIG) on the bacterial translocation (BT) and intestinal integrity of obstructive jaundice (OJ) in an animal model . METHODS: Fifty rats were randomized into five groups containing 10 rats each . All procedures were performed aseptically under general anaesthesia using intramuscular ketamine (25 mg/kg) . The abdomen was opened and the common bile duct was identified, mobilized, doubly ligated using 5-0 silk and divided . In group 1 (the 'sham' group), the rats had a similar incision followed by mobilization of the common bile duct (CBD), without ligation or division . In group 2 rats, only common bile duct ligation (CBDL) was performed . In group 3, CBDL was performed and UDCA was administered by orogastric intubation once daily . In group 4 rats, CBDL was performed and glutamine was given by orogastric intubation once daily . Therapeutic substances were started orally on the day CBDL was fulfilled and were continued for 7 days . In group 5, IVIG was administrated via a femoral vein catheter just before CBDL . The animals were killed at the end of the 7th day, and serum levels of total bilirubin (TB), alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and gamma-glutamyl transpeptidase (GGT) were measured . Mesenteric lymph nodes (MLN), liver, spleen and blood were cultured . The terminal ileum specimens were examined histopathologically . RESULTS: Bacterial translocation significantly increased in the MLN and spleen of rats in group 2 as compared to groups 3, 4 and 5 (P < 0.05, P = 0.001, P = 0.001, respectively) . The BT of the liver in group 2 was significantly higher than that of group 5 (P < 0.05) . In the blood, the BT was significantly higher in group 2 than groups 3, 4 and 5 (P < 0.05) . The bacterial counts, colony-forming units per gram tissue (cfu/g), were found significantly higher in MLN, liver and spleen of rats in group 2 than those of groups 3, 4 and 5 (P = 0.000) . The average villus height in the group 4 was significantly higher than that of groups 2, 3 and 5 (P = 0.000) . CONCLUSION: The present experimental study has demonstrated that the administration of glutamine, UDCA and IVIG reduce the incidence of BT and additionally glutamine preserves intestinal mucosal integrity.

Emerg Med J, 2003 Sep, 20(5), 479 - 82
A preliminary investigation into bacterial contamination of Welsh emergency ambulances; Nigam Y et al.; OBJECTIVES: The objective of this regional study across Wales was to perform a preliminary examination of Welsh emergency vehicles to determine levels of bacterial contamination . METHODS: Specific sites within emergency vehicles were swabbed, before and after vehicle cleaning, over a 12 month period, on a monthly basis . All swabs were sent to pathology laboratories for culturing and analysis . RESULTS: Results showed that most sites within emergency vehicles across Wales were contaminated with a range of bacterial species before vehicle cleaning . After vehicle cleaning, many sites in vehicles were still contaminated, and some sites that were previously uncontaminated, became freshly contaminated as a result of cleaning methods used . CONCLUSIONS: The authors conclude that the Welsh emergency vehicles examined exhibited an unacceptable level of bacterial contamination . This finding should be carefully considered and all attempts must be made to tackle the problem of vehicle cleanliness and infection control.

Contraception, 2003 Aug, 68(2), 105 - 9
Follow-up of users of intrauterine device with and without bacterial vaginosis and other cervicovaginal infections; Ferraz do Lago R et al.; This study aimed to assess the prevalence of bacterial vaginosis (BV) and other cervicovaginal infections, as well as the incidence of complications among new users of IUD, 1 and 6 months after its insertion, in the City of Campinas, Brazil . A total of 223 women who had a TCu-380A IUD inserted from May through November 2001, were included in the study . After the IUD insertion all women were scheduled to two additional visits: after 1 month and after 6 months, when they were interviewed and a pelvic examination was performed, along with a collection of specimens from the vagina and the endocervix for laboratory testing . The Nugent's criterion was used for the BV diagnosis . They were also evaluated with regard to presence of complications possibly related to IUD insertion and use, i.e., abnormal bleeding, dysmenorrhea, expulsion and pelvic inflammatory disease . The prevalence of cervicovaginal infections was 29.1%, BV being the most frequent (19.7%) . Dysmenorrhea was more frequent among women with BV than among women without BV (p = 0.03) . A trend of abnormal bleeding being more frequent among women with BV was also found . In conclusion, BV after 1 month of IUD insertion was not associated with IUD complications, with the exception of dysmenorrhea.

Am Surg, 2003 Aug, 69(8), 679 - 86; discussion 686-7
Natural killer cell activation primes macrophages to clear bacterial infection; Scott MJ et al.; Natural killer (NK) cells are major cytokine producers during bacterial sepsis, but their precise role is undefined . This study investigates the effect of NK cell depletion with and without prior activation on macrophage function and bacterial clearance during cecal ligation and puncture . Two different NK cell-depleting antibodies were used: anti-asialo-GM1 (GM1), a nonactivating antibody, and anti-NK1.1 (NK1.1), an NK cell-activating antibody . C57BL/6 mice were NK depleted with either GM1 or NK1.1 by intraperitoneal injection 7 and 3 days before experimentation . Control animals received isotype immunoglobulin G . Depletion was confirmed by flow cytometry . Bacterial levels in peritoneal washout, blood, and liver were determined 4 hours after cecal ligation and puncture . Macrophage activation was measured by phagocytosis ability and by production of nitric oxide and interleukin-6 . Depletion with GM1 resulted in significantly higher bacterial levels at 4 hours, whereas depletion with NK1.1 had the opposite effect of significantly decreasing bacterial levels . Macrophage phagocytosis ability was significantly increased in mice depleted with NK1.1 compared with those mice depleted with GM1 . We conclude that activation of NK cells improves bacterial clearance by priming macrophages to help clear a subsequent bacterial challenge . Macrophages are less able to clear bacteria when NK cells are depleted without activation . NK cells are therefore important in bacterial clearance through interactions with macrophages.

J Clin Invest, 2003 Sep, 112(5), 648 - 51
Dendritic cells and the intestinal bacterial flora: a role for localized mucosal immune responses; Uhlig HH et al.; Mammals coexist in an overall symbiotic relationship with a complex array of commensal bacterial flora that colonizes the gastrointestinal tract . These intestinal bacteria interface with cells of the mucosal immune system, including DCs . Here we discuss mechanisms of interaction between intestinal bacteria and DCs and the role of localized gastrointestinal immune responses.

Genome Biol . 2003;4(9):R57 . Epub 2003 Aug 21.
The source of laterally transferred genes in bacterial genomes; Daubin V et al.; BACKGROUND: Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome . These genes are usually A+T-rich, arguing either that there is a bias towards acquiring genes from donor organisms having low G+C contents or that genes acquired from organisms of similar genomic base compositions go undetected in these analyses . RESULTS: By examining the genome contents of closely related, fully sequenced bacteria, we uncovered genes confined to a single genome and examined the sequence features of these acquired genes . The analysis shows that few transfer events are overlooked by compositional analyses . Most observed lateral gene transfers do not correspond to free exchange of regular genes among bacterial genomes, but more probably represent the constituents of phages or other selfish elements . CONCLUSIONS: Although bacteria tend to acquire large amounts of DNA, the origin of these genes remains obscure . We have shown that contrary to what is often supposed, their composition cannot be explained by a previous genomic context . In contrast, these genes fit the description of recently described genes in lambdoid phages, named 'morons' . Therefore, results from genome content and compositional approaches to detect lateral transfers should not be cited as evidence for genetic exchange between distantly related bacteria.

Mol Biol Evol, 2003 Dec, 20(12), 2091 - 6 Epub 2003 Aug 29.
Neutral mutations and neutral substitutions in bacterial genomes; Ochman H; Molecular evolutionary biologists usually assess the underlying spectrum of mutations within a bacterial genome by examining substitutions that occur at sites believed to be under no selective constraints . Alternatively, bacterial mutation rates can also be estimated in a variety of experimental systems . The two classes of changes occurring in DNA sequences-i.e., mutations and neutral substitutions-are, in theory, identical; however, the rates and patterns of mutations in bacteria, as inferred from sequence comparisons, often differ significantly from those derived experimentally . These differences have resulted in conflicting interpretations of the nonselective forces that affect mutation rates.

Anal Chem, 2003 Jun 1, 75(11), 2746 - 52
Analysis of whole bacterial cells by flow field-flow fractionation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; Lee H et al.; The purpose of this study is to develop a novel bacterial analysis method by coupling the flow field-flow fractionation (flow FFF) separation technique with detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry . The composition of carrier liquid used for flow FFF was selected based on retention of bacterial cells and compatibility with the MALDI process . The coupling of flow FFF and MALDI-TOF MS was demonstrated for P . putida and E . coli . Fractions of the whole cells were collected after separation by FFF and further analyzed by MALDI-MS . Each fraction, collected over different time intervals, corresponded to different sizes and possibly different growth stages of bacteria . The bacterial analysis by flow FFF/MALDI-TOF MS was completed within 1 h with only preliminary optimization of the process.

J Biol Chem, 2003 Dec 12, 278(50), 50671 - 81 Epub 2003 Aug 28.
An N-terminal segment of the active component of the bacterial genotoxin cytolethal distending toxin B (CDTB) directs CDTB into the nucleus; Nishikubo S et al.; Cytolethal distending toxin (CDT), produced by Actinobacillus actinomycetemcomitans, is a putative virulence factor in the pathogenesis of periodontal diseases . It is a cell cycle specific inhibitor at the G2/M transition . CDTB, one of the subunits of the CDT holotoxin, is implicated in a genotoxic role after entering the target cells, whereby chromosomal damage induces checkpoint phosphorylation cascades . CDTB microinjected into the cytoplasm was shown to localize in the nucleus and induce chromatin collapse . To investigate the molecular mechanism involved in nuclear transport of CDTB, we used transient expression and microinjection of a CDTB-green fluorescent protein (GFP) fusion protein . After microinjection, His-tagged CDTB-GFP entered the nucleus in 3-4 h . Leptomycin B did not increase the speed of entry of the fusion protein, suggesting that the relatively slow entry of the fusion protein is not due to the CRM1-dependent nuclear export of the protein . Nuclear localization of the CDTBGFP was temperature-dependent . An in vitro transport assay demonstrated that the nuclear localization of CDTB is mediated by active transport . An assay using transient expression of a series of truncated CDTB-GFP fusion proteins revealed that residues 48-124 constitute the minimum region involved in nuclear transport of CDTB . A domain swapping experiment of the region involved in nuclear transport of CDTB with an SV40 T nuclear localization signal indicated that CDTB is composed of two domains, an N-terminal domain for nuclear transport and a C-terminal active domain . Our results strongly suggest that nuclear localization of CDTB is required for the holotoxin to induce cytodistension and cell cycle block . This is the first demonstration that a bacterial toxin possessing a unique domain for nuclear transport is transferred to the animal cell nucleus by active transport.

Mol Ther, 2003 Sep, 8(3), 495 - 500
Minicircle DNA vectors devoid of bacterial DNA result in persistent and high-level transgene expression in vivo; Chen ZY et al.; The loss of transgene expression has been a major obstacle to the development of nonviral vectors for the treatment of human diseases . We previously demonstrated that bacterial DNA linked to a mammalian expression cassette resulted in transcriptional silencing of the transgene in vivo . To confirm these studies and develop a means to produce a robust DNA vector that is not silenced in vivo, we developed a phage phiC31 integrase-mediated intramolecular recombination technology to prepare minicircle vector DNA devoid of the bacterial backbone and then compared the transgene expression profile of the minicircle with different molecular forms of plasmid DNAs in mice . We demonstrate that minicircular DNAs devoid of bacterial sequences expressed 45- and 560-fold more serum human factor IX and alpha1-antitrypsin, respectively, compared to standard plasmid DNAs transfected into mouse liver . Our data suggest that minicircles are capable of expressing high and persistent levels of therapeutic products in vivo and have a great potential to serve as episomal vectors for the treatment of a wide variety of diseases.

Anal Sci, 2003 Aug, 19(8), 1183 - 5
Cationic liposomes enhanced firefly bioluminescent assay of bacterial ATP in the presence of an ATP extractant; Nakata N et al.; Cationic liposomes composed of two components, diethylaminoethyl-carbamoyl cholesterol and phosphatidylcholine, were applied to an enhancer for a firefly bioluminescent (BL) assay of bacterial ATP in the presence of an ATP extractant . Trichloroacetic acid (TCA), which inhibits the activity of luciferase, was used as an ATP extractant . Cationic liposomes enhanced the BL intensity as long as luciferase was active . The detection limits for cell numbers of Escherichia coli extracts in the presence of cationic liposomes and in water alone were 199 and 897 colony forming units ml(-1), respectively . The sensitivity for bacterial ATP in the presence of cationic liposomes was improved by a factor of 2.5 times compared to that in the presence of diethylaminoethyl-dextran.

Biophys J, 2003 Sep, 85(3), 1851 - 70
Charge recombination and protein dynamics in bacterial photosynthetic reaction centers entrapped in a sol-gel matrix; Kriegl JM et al.; Many proteins can be immobilized in silica hydrogel matrices without compromising their function, making this a suitable technique for biosensor applications . Immobilization will in general affect protein structure and dynamics . To study these effects, we have measured the P(+)Q(A)(-) charge recombination kinetics after laser excitation of Q(B)-depleted wild-type photosynthetic reaction centers from Rhodobacter sphaeroides in a tetramethoxysilane (TMOS) sol-gel matrix and, for comparison, also in cryosolvent . The nonexponential electron transfer kinetics observed between 10 and 300 K were analyzed quantitatively using the spin boson model for the intrinsic temperature dependence of the electron transfer and an adiabatic change of the energy gap and electronic coupling caused by protein motions in response to the altered charge distributions . The analysis reveals similarities and differences in the TMOS-matrix and bulk-solvent samples . In both preparations, electron transfer is coupled to the same spectrum of low frequency phonons . As in bulk solvent, charge-solvating protein motions are present in the TMOS matrix . Large-scale conformational changes are arrested in the hydrogel, as evident from the nonexponential kinetics even at room temperature . The altered dynamics is likely responsible for the observed changes in the electronic coupling matrix element.

Biophys J, 2003 Sep, 85(3), 1406 - 20
Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states; Faraldo-Gomez JD et al.; FhuA is one of the more complex members of the superfamily of bacterial outer membrane proteins . Its primary function is to provide a binding site on the outer membrane surface for siderophores, such as ferrichrome, and subsequently to facilitate their energy-dependent transport across the membrane, presumably powered by the TonB-ExbBD protein complex that resides in the cytoplasmic membrane . Crystal structures of FhuA with and without a bound ferrichrome molecule have provided some clues as to the initial stages of the siderophore transport mechanism . In the current study, we have employed 10-ns duration molecular dynamics simulations of FhuA and of the FhuA-ferrichrome complex, both embedded in a phospholipid bilayer, to probe the short timescale dynamics of this integral membrane protein, and to explore possible mechanistic implications of this dynamic behavior . Analysis of the dynamics of the protein suggests that the extracellular loops move as relatively rigid entities relative to the transmembrane beta-barrel . Comparison of the two simulations (with and without bound ferrichrome) revealed some ligand-induced changes in loop mobility . Specifically, loop L8 appears to be involved in a mechanism whereby the binding site is gated closed upon ligand binding . Analysis of the dynamics of water molecules within the core of the FhuA protein provided no evidence for a water-permeable protopore through which the ferrichrome might pass without a major perturbation of the FhuA protein . Overall, these simulations support the proposal that binding of ferrichrome initiates a signaling mechanism that ultimately leads to the TonB-mediated partial or total removal of the core domain from the beta-barrel, thus opening up a permeable pore . These simulations are among the longest that have been performed on a complex membrane protein . However, a simple analysis of sampling reveals that the description of protein motions is far from complete.

Clin Exp Rheumatol, 2003 Jul-Aug, 21(4), 497 - 9
Systemic lupus erythematosus-like autoimmune abnormalities induced by bacterial infection; Tomita H et al.; Recent evidence has revealed that bacterial DNA can promote several of the autoimmune abnormalities observed in systemic lupus erythematosus (SLE), and a possible pathogenic role in the induction of SLE has been highlighted . We have recently encountered patients in whom bacterial infection (septicemia) triggered the production of several autoantibodies . This seems to be interesting with respect to the consideration of the relationship between SLE and bacterial infection.

J Theor Biol, 2003 Oct 7, 224(3), 377 - 83
Bacterial debris-an ecological mechanism for coexistence of bacteria and their viruses; Rabinovitch A et al.; A model of bacteria and phage survival is developed based on the idea of shielding by bacterial debris in the system . This model is mathematically formulated by a set of four nonlinear difference equations for susceptible bacteria, contaminated bacteria, bacterial debris and phages . Simulation results show the possibility of survival, and domains of existence of stable and unstable solutions

Mol Microbiol, 2003 Sep, 49(5), 1377 - 90
A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase; Hatzixanthis K et al.; A group of bacterial exported proteins are synthesized with N-terminal signal peptides containing a SRRxFLK 'twin-arginine' amino acid motif . Proteins bearing twin-arginine signal peptides are targeted post-translationally to the twin-arginine translocation (Tat) system which transports folded substrates across the inner membrane . In Escherichia coli, most integral inner membrane proteins are assembled by a co-translational process directed by SRP/FtsY, the SecYEG translocase, and YidC . In this work we define a novel class of integral membrane proteins assembled by a Tat-dependent mechanism . We show that at least five E . coli Tat substrate proteins contain hydrophobic C-terminal transmembrane helices (or 'C-tails') . Fusions between the identified transmembrane C-tails and the exclusively Tat-dependent reporter proteins TorA and SufI render the resultant chimeras membrane-bound . Export-linked signal peptide processing and membrane integration of the chimeras is shown to be both Tat-dependent and YidC-independent . It is proposed that the mechanism of membrane integration of proteins by the Tat system is fundamentally distinct from that employed for other bacterial inner membrane proteins.

Evolution Int J Org Evolution, 2003 Jul, 57(7), 1535 - 42
Host growth conditions regulate the plasticity of horizontal and vertical transmission in Holospora undulata, a bacterial parasite of the protozoan Paramecium caudatum; Kaltz O et al.; A parasite might be prohibited from investing simultaneously in horizontal (infection of new hosts) and vertical (infection of the current host's offspring) transmission because of developmental, physiological, or evolutionary costs and constraints . Rather, these constraints may select for adaptive phenotypic plasticity, where the parasite uses the transmission pathway that maximizes transmission in the current ecological and epidemiological conditions . By varying environmental conditions for the host's replication, we investigated the plasticity of vertical and horizontal transmission of Holospora undulata, a micronucleus-specific bacterial parasite of the protozoan Paramecium caudatum . We observed a negative correlation between the host's growth rate and the parasite's investment in horizontal transmission . In rapidly dividing hosts, the parasite remained in the reproductive stage and was passed on vertically to the daughter nuclei during mitotic division of the Paramecium . In contrast, at low or negative growth rates of the host, the parasite's reproductive forms differentiated into infectious forms, the agents of horizontal transmission . Furthermore, in treatments that were initiated with a high proportion of individuals harboring horizontally transmitted infectious forms, rapid replication resulted in a switch back from predominantly horizontal to almost exclusively vertical transmission . These results suggest a trade-off between the efficacies of vertical and horizontal transmission, with the parasite switching to horizontal transmission only if conditions for host replication, and thus vertical transmission, deteriorate.

J Biol Chem, 2003 Nov 7, 278(45), 44913 - 20 Epub 2003 Aug 22.
A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome; Robert F et al.; In this study, we used site-directed mutagenesis to disrupt an interaction that had been detected between ribosomal proteins S7 and S11 in the crystal structure of the bacterial 30 S subunit . This interaction, which is located in the E site, connects the head of the 30 S subunit to the platform and is involved in the formation of the exit channel through which passes the 30 S-bound messenger RNA . Neither mutations in S7 nor mutations in S11 prevented the incorporation of the proteins into the 30 S subunits but they perturbed the function of the ribosome . In vivo assays showed that ribosomes with either mutated S7 or S11 were altered in the control of translational fidelity, having an increased capacity for frameshifting, readthrough of a nonsense codon and codon misreading . Toeprinting and filter-binding assays showed that 30 S subunits with either mutated S7 or S11 have an enhanced capacity to bind mRNA . The effects of the S7 and S11 mutations can be related to an increased flexibility of the head of the 30 S, to an opening of the mRNA exit channel and to a perturbation of the proposed allosteric coupling between the A and E sites . Altogether, our results demonstrate that S7 and S11 interact in a functional manner and support the notion that protein-protein interactions contribute to the dynamics of the ribosome.

J Endotoxin Res, 2003, 9(4), 237 - 43
Bacterial LPS and CpG DNA differentially induce gene expression profiles in mouse macrophages; Gao JJ et al.; Bacterial DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent immune stimulating agent that holds strong promise in the treatment of many disorders . Studies have established that CpG DNA triggers an immune response through activated expression of genes in immune cells including macrophages . To dissect further the molecular mechanism(s) by which CpG DNA activates the immune system, we studied macrophage gene expression profiles in response to CpG DNA using microarray technology . Since CpG DNA is reported to use the TLR9 receptor that shares homology with the TLR4 receptor used by bacterial lipopolysaccharide (LPS), we also evaluated gene expression profiles in macrophages stimulated by LPS versus CpG DNA . Both CpG DNA and LPS modulate expression of a large array of genes . However, LPS modulated the expression of a much greater number of genes than did CpG DNA and all genes induced or repressed by CpG DNA were also induced or repressed by LPS . These data indicate that the CpG DNA signaling pathway through TLR9 activates only a subset of genes induced by the LPS TLR4 signaling pathway.

Clin Imaging, 2003 Sep-Oct, 27(5), 304 - 6
Calcific cerebral arterial embolization in the setting of bacterial endocarditis superimposed on prior rheumatic aortic valvular disease; Thompson DB et al.; Stroke from a calcific cerebral artery embolus demonstrated by noncontrast computed tomography (CT) is rare . Although the ability of CT to demonstrate early acute cerebral emboli is limited, in the uncommon event of a calcific cerebral embolus, CT can easily visualize the embolized material . We present an unusual case of calcific cerebral arterial embolization to the proximal middle cerebral artery and illustrate the usefulness of CT in diagnosing this rare entity in conjunction with important predisposing clinical factors.

Genetics, 2003 Aug, 164(4), 1279 - 89
Associations between inverted repeats and the structural evolution of bacterial genomes; Achaz G et al.; The stability of the structure of bacterial genomes is challenged by recombination events . Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure . First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable . Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes . Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats . Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats . Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance . Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria . These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

Genetics, 2003 Aug, 164(4), 1271 - 7
Bacterial evolution through the selective loss of beneficial Genes . Trade-offs in expression involving two loci; Zinser ER et al.; The loss of preexisting genes or gene activities during evolution is a major mechanism of ecological specialization . Evolutionary processes that can account for gene loss or inactivation have so far been restricted to one of two mechanisms: direct selection for the loss of gene activities that are disadvantageous under the conditions of selection (i.e., antagonistic pleiotropy) and selection-independent genetic drift of neutral (or nearly neutral) mutations (i.e., mutation accumulation) . In this study we demonstrate with an evolved strain of Escherichia coli that a third, distinct mechanism exists by which gene activities can be lost . This selection-dependent mechanism involves the expropriation of one gene's upstream regulatory element by a second gene via a homologous recombination event . Resulting from this genetic exchange is the activation of the second gene and a concomitant inactivation of the first gene . This gene-for-gene expression tradeoff provides a net fitness gain, even if the forfeited activity of the first gene can play a positive role in fitness under the conditions of selection.

J Med Assoc Thai, 2003 Jun, 86 Suppl 2, S379 - 84
Single hydrogen peroxide vaginal douching versus single-dose oral metronidazole for the treatment of bacterial vaginosis: a randomized controlled trial; Chaithongwongwatthana S et al.; OBJECTIVE: To compare the effectiveness of single hydrogen peroxide vaginal douching and a single oral dose of metronidazole for the treatment of bacterial vaginosis . METHOD: A randomized trial was performed at the outpatient clinic in King Chulalongkorn Memorial Hospital . 142 patients diagnosed as having bacterial vaginosis were randomly allocated into two groups . The subjects in the first group were douched with 20 milliliters of 3 per cent hydrogen peroxide and received an oral placebo . The subjects in the second group received oral metronidazole 2 grams orally and were douched with a placebo . The cure rate in each group was assessed using Amsel's criteria 2 weeks after treatment . RESULT: The cure rate in the subjects treated with hydrogen peroxide douching was lower than the cases who received oral metronidazole (62.5% versus 78.6%, p-value = 0.036) . Rate of gastrointestinal side effects in metronidazole group was higher than in the hydrogen peroxide group (48.6% versus 13.9%, p-value < 0.001) . CONCLUSION: Single hydrogen peroxide vaginal douching was less effective than a single oral dose of metronidazole in the treatment of bacterial vaginosis.

BMC Microbiol . 2003 Aug 16;3(1):18.
The dynamic behavior of bacterial macrofibers growing with one end prevented from rotating: variation in shaft rotation along the fiber's length, and supercoil movement on a solid surface toward the constrained end; Mendelson NH et al.; BACKGROUND: Bacterial macrofibers twist as they grow, writhe, supercoil and wind up into plectonemic structures (helical forms the individual filaments of which cannot be taken apart without unwinding) that eventually carry loops at both of their ends . Terminal loops rotate about the axis of a fiber's shaft in contrary directions at increasing rate as the shaft elongates . Theory suggests that rotation rates should vary linearly along the length of a fiber ranging from maxima at the loop ends to zero at an intermediate point . Blocking rotation at one end of a fiber should lead to a single gradient: zero at the blocked end to maximum at the free end . We tested this conclusion by measuring directly the rotation at various distances along fiber length from the blocked end . The movement of supercoils over a solid surface was also measured in tethered macrofibers . RESULTS: Macrofibers that hung down from a floating wire inserted through a terminal loop grew vertically and produced small plectonemic structures by supercoiling along their length . Using these as markers for shaft rotation we observed a uniform gradient of initial rotation rates with slopes of 25.6 degrees /min . mm . and 36.2 degrees /min . mm . in two different fibers . Measurements of the distal tip rotation in a third fiber as a function of length showed increases proportional to increases in length with constant of proportionality 79.2 rad/mm . Another fiber tethered to the floor grew horizontally with a length-doubling time of 74 min, made contact periodically with the floor and supercoiled repeatedly . The supercoils moved over the floor toward the tether at approximately 0.06 mm/min, 4 times faster than the fiber growth rate . Over a period of 800 minutes the fiber grew to 23 mm in length and was entirely retracted back to the tether by a process involving 29 supercoils . CONCLUSIONS: The rate at which growing bacterial macrofibers rotated about the axis of the fiber shaft measured at various locations along fibers in structures prevented from rotating at one end reveal that the rate varied linearly from zero at the blocked end to maximum at the distal end . The increasing number of twisting cells in growing fibers caused the distal end to continuously rotate faster . When the free end was intermittently prevented from rotating a torque developed which was relieved by supercoiling . On a solid surface the supercoils moved toward the end permanently blocked from rotating as a result of supercoil rolling over the surface and the formation of new supercoils that reduced fiber length between the initial supercoil and the wire tether . All of the motions are ramifications of cell growth with twist and the highly ordered multicellular state of macrofibers.

Stroke, 2003 Sep, 34(9), 2126 - 31 Epub 2003 Aug 14.
Impact of viral and bacterial burden on cognitive impairment in elderly persons with cardiovascular diseases; Strandberg TE et al.; BACKGROUND AND PURPOSE: Inflammation and infectious etiology have been implicated in the pathogenesis of dementia . We sought to investigate whether the seropositivity of common infections was associated with cognitive function . METHODS: Viral burden (seropositivity for herpes simplex virus type 1 {HSV-1}, herpes simplex virus type 2 {HSV-2}, or cytomegalovirus {CMV}) and bacterial burden (Chlamydia pneumoniae and Mycoplasma pneumoniae) were related to cognitive status and its impairment among 383 home-dwelling elderly with cardiovascular diseases (mean age, 80 years) . The Mini-Mental State Examination (MMSE) and its changes and the Clinical Dementia Rating (CDR) were used to define cognitive impairment . RESULTS: At baseline, 0 to 1, 2, and 3 positive titers toward viruses were found in 48 (12.5%), 229 (59.8%), and 106 individuals (27.7%), respectively . MMSE points decreased with increasing viral burden (P=0.03) . At baseline, 58 individuals (15.1%) had cognitive impairment, which after adjustments was significantly associated with seropositivity for 3 viruses (hazard ratio, 2.5; 95% CI, 1.3 to 4.7) . MMSE score decreased in 150 (43% of 348) during 12-month follow-up . After adjustment for MMSE score at baseline and with 0 to 1 seropositivities as reference (1.0), the hazard ratios were 1.8 (95% CI, 0.9 to 3.6) and 2.3 (95% CI, 1.1 to 5.0) for 2 and 3 seropositivities, respectively . The prevalence of possible or definite dementia according to CDR also increased with viral burden . No significant associations were observed between bacterial burden and cognition . CONCLUSIONS: Viral pathogen burden of HSV and CMV was associated with cognitive impairment in home-dwelling elderly persons with cardiovascular diseases . The results need to be tested in larger databases, but they may offer a preventable cause of cognitive decline.

Biomol Eng, 2003 Jul, 20(4-6), 305 - 9
Single nucleotide mismatch analysis using oligonucleotide probes synthesized on bacterial magnetic particle; Ota H et al.; An approach to analyze mismatches using short and specific oligonucleotide probes directly synthesized on bacterial magnetic particles (BMPs) by phosphoramidite methods was exploited . Approximately 126 molecules of 4-mer oligonucleotides/particle were synthesized on BMPs with high reaction efficiencies . Hybridization between FITC-labeled oligonucleotides and chemically synthesized oligonucleotides on BMPs was performed . Perfect matched and mismatched hybridizations were successfully discriminated by using the oligonucleotide probes on BMPs.

Leuk Lymphoma, 2003 Jul, 44(7), 1247 - 8
Atypical hemophagocytic lymphohistiocytosis following bacterial tonsillitis in acute lymphoblastic leukemia; Kakihara T et al.; We report a rare case of a cute lymphoblasticleukemia (ALL) who developed dyspnea, neurological disturbance with illusions, pancytopenia, phagocytosis and coagulation disturbances following bacterial tonsillitis . The values of soluble interleukin-2 receptor (sIL-2R), IL-6 and IL-8 were also elevated . Her clinicolaboratory findings were similar to hemophagocytic lymphohistiocytosis (HLH), which is a cytokine disease induced by activated T cells and macrophages . Atypical HLH following bacterial tonsillitis should be kept in mind in leukemia patients.

J Biochem Biophys Methods, 2003 Aug 29, 57(2), 87 - 103
Fluorescent probes for bacterial cytoplasmic membrane research; Trevors JT; Fluorescent methods in biological and medical research are extremely useful at the cellular and molecular levels . This is due to sensitive and affordable detection equipment and a variety of specific and more general fluorescent probes, and analytical procedures . In this article, I examine the use of fluorescence membrane probes to study the fluidity (membrane polarization) of the bacterial cytoplasmic membrane, central to energy transduction, ion and nutrient transport and diffusion of water and gases.

FEBS Lett, 2003 Aug 14, 549(1-3), 26 - 30
The diverse bacterial origins of the Arabidopsis polyamine biosynthetic pathway; Illingworth C et al.; We functionally identified the last remaining step in the plant polyamine biosynthetic pathway by expressing an Arabidopsis thaliana agmatine iminohydrolase cDNA in yeast . Inspection of the whole pathway suggests that the arginine decarboxylase, agmatine iminohydrolase, N-carbamoylputrescine amidohydrolase route to putrescine in plants was inherited from the cyanobacterial ancestor of the chloroplast . However, the rest of the pathway including ornithine decarboxylase and spermidine synthase was probably inherited from bacterial genes present in the original host cell, common ancestor of plants and animals, that acquired the cyanobacterial endosymbiont . An exception is S-adenosylmethionine decarboxylase, which may represent a eukaryote-specific enzyme form.

Cell, 2003 Aug 8, 114(3), 335 - 45
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase; Opalka N et al.; Bacterial GreA and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase . The structure of Escherichia coli core RNA polymerase bound to GreB was determined by cryo-electron microscopy and image processing of helical crystals to a nominal resolution of 15 A, allowing fitting of high-resolution RNA polymerase and GreB structures . In the resulting model, the GreB N-terminal coiled-coil domain extends 45 A through a channel directly to the RNA polymerase active site . The model leads to detailed insights into the mechanism of Gre factor activity that explains a wide range of experimental observations and points to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNA polymerase active site to catalyze the cleavage reaction . Mutational studies confirm that these positions are critical for Gre factor function.

Biochemistry, 2003 Aug 19, 42(32), 9626 - 32
Mechanism of proton transfer inhibition by Cd(2+) binding to bacterial reaction centers: determination of the pK(A) of functionally important histidine residues; Paddock ML et al.; The bacterial photosynthetic reaction center (RC) uses light energy to catalyze the reduction of a bound quinone molecule Q(B) to quinol Q(B)H(2) . In RCs from Rhodobacter sphaeroides the protons involved in this process come from the cytoplasm and travel through pathways that involve His-H126 and His-H128 located near the proton entry point . In this study, we measured the pH dependence from 4.5 to 8.5 of the binding of the proton transfer inhibitor Cd(2+), which ligates to these surface His in the RC and inhibits proton-coupled electron transfer . At pH <6, the negative slope of the logarithm of the dissociation constant, K(D), versus pH approaches 2, indicating that, upon binding of Cd(2+), two protons are displaced; i.e., the binding is electrostatically compensated . At pH >7, K(D) becomes essentially independent of pH . A theoretical fit to the data over the entire pH range required two protons with pK(A) values of 6.8 and 6.3 (+/-0.5) . To assess the contribution of His-H126 and His-H128 to the observed pH dependence, K(D) was measured in mutant RCs that lack the imidazole group of His-H126 or His-H128 (His --> Ala) . In both mutant RCs, K(D) was approximately pH independent, showing that Cd(2+) does not displace protons upon binding in the mutant RCs, in contrast to the native RC in which His-H126 and His-H128 are the predominant contributors to the observed pH dependence of K(D) . Thus, Cd(2+) inhibits RC function by binding to functionally important histidines.

Photochem Photobiol Sci, 2003 Jul, 2(7), 759 - 66
Listening to the blue: the time-resolved thermodynamics of the bacterial blue-light receptor YtvA and its isolated LOV domain; Losi A et al.; YtvA is a bacterial flavo-protein related to plant phototropin . The photochemistry of YtvA and of its isolated LOV domain (YtvA-LOV) has been characterized by optical, mass spectrometric and photocalorimetric methods . The energy content (E390) of the FMN-C4a-thiol photoadduct (YtvA390 and YtvA-LOV390) and its structural volume change (deltaV390), with respect to the parent state, have been determined by means of Laser Induced Optoacoustic Spectroscopy (LIOAS) . The high value of E390, 136 and 115 kJ mol(-1), respectively, ensures a large driving force for the dark recovery to the unphotolyzed state and points to a strained conformation of the protein or/and the chromophore in the photoadduct . The value of deltaV390 is significantly different for the two proteins, deltaV390 = -12.5 ml mol(-1) in YtvA and -17.2 ml mol(-1) in YtvA-LOV . The kinetics of the dark recovery reaction for YtvA-LOV is slower than for full-length YtvA, with taurec = 3900 and 2600 s at 25 degrees C, respectively, and shows a different temperature dependence . A similarly slow kinetics can be induced in YtvA by high ionic strength . Minor differences are observed in the fluorescence and photoadduct formation quantum yield . The overall stability is higher for YtvA than for YtvA-LOV . The data as a whole are indicative of an interaction between the two domains of YtvA, most probably mediated by electrostatic interactions that renders the full-length protein a compact and more rigid unit . The results reported here support the idea that the formation of the photoadduct changes the dynamics of the protein, depending on the conformational flexibility of the parent state . Flashing of the photoadduct induces a negligible deltaV, with 96% of the excitation energy dissipated as heat in <20 ns, indicating that the photoadduct does not undergo a photocycle on the LIOAS time scale, or that the photoinduced reactions occur with very low yield.

Biotechnol Bioeng, 2003 Oct 5, 84(1), 96 - 102
Single-nucleotide polymorphism analysis using fluorescence resonance energy transfer between DNA-labeling fluorophore, fluorescein isothiocyanate, and DNA intercalator, POPO-3, on bacterial magnetic particles; Nakayama H et al.; To develop an analytical system for single-nucleotide polymorphisms (SNPs), the fluorescence resonance energy transfer (FRET) technique was employed on a bacterial magnetic particle (BMP) surface . A combination of fluorescein isothiocyanate (FITC; excitation 490 nm/emission 520 nm) labeled at the 5' end of DNA and an intercalating compound (POPO-3, excitation 534 nm/emission 570 nm) was used to avoid the interference from light scattering caused by nanoparticles . After hybridization between target DNA immobilized onto BMPs and FITC-labeled probes, fluorescence from POPO-3, which was excited by the energy from the FITC, was detected . The major homozygous (ALDH2*1), heterozygous (ALDH2*1/*2), and minor homozygous (ALDH2*2) genotypes in the blood samples were discriminated by this method . The assay described herein allows for a simple and rapid SNP analysis using a fully automated system .

Gene, 2003 Jul 17, 312, 151 - 63
Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events; Gophna U et al.; Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts . The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella . Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs . Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another . The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted . A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes . It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Neuroradiology, 2003 Sep, 45(9), 634 - 9 Epub 2003 Aug 08.
Diffusion-weighted imaging in acute bacterial meningitis in infancy; Jan W et al.; Bacterial meningitis is frequently fatal or leads to severe neurological impairment . Complications such as vasculitis, resulting in infarcts, should be anticipated and dealt with promptly . Our aim was to demonstrate the complications of meningitis by diffusion weighted imaging (DWI) in patients who deteriorated despite therapy . We studied 13 infants between the ages of 1 day and 32 months who presented with symptoms ranging from fever and vomiting to seizures, encephalopathy and coma due to bacterial meningitis, performing MRI, including DWI, 2-5 days after presentation . Multiple infarcts were found on DWI in 12 of the 13, most commonly in the frontal lobes (in 10) . Global involvement was seen in four children, three of whom died; the fourth had a very poor outcome . In one case abnormalities on DWI were due to subdural empyemas . We diagnosed vasculitis in three of five patients studied with MRA . We think DWI an important part of an MRI study in infants with meningitis . Small cortical or deep white-matter infarcts due to septic vasculitis can lead to tissue damage not easily recognized on routine imaging and DWI can be used to confirm that extra-axial collections represent empyemas.

Pesqui Odontol Bras, 2003 Jan-Mar, 17(1), 17 - 23 Epub 2003 Aug 05.
Effectiveness of low cost toothbrushes, with or without dentifrice, in the removal of bacterial plaque in deciduous teeth; Parizotto SP et al.; The main objective of this study was to compare the effectiveness of a low cost toothbrush ("monoblock") to that of a conventional toothbrush with and without addition of dentifrice with respect to the removal of dental plaque . Thirty-two 4- to 6-year-old children took part in this study: they were evaluated under four experimental conditions defined by the combinations of the values of two factors, toothbrush (conventional or monoblock) and use of dentifrice (with or without) . The effectiveness of the treatments was defined in terms of the reduction of a bacterial plaque index evaluated before and after toothbrushing . No statistically significant differences were detected between the two types of toothbrushes with respect to the reduction of the bacterial plaque index . Similarly, there were no statistical evidences that the use of dentifrice improves the mechanical control of dental plaque . These results are important from a public health point of view, specially in developing countries, where the dissemination of educational and preventive techniques of low cost are fundamental.

Science, 2003 Aug 8, 301(5634), 829 - 32
Phylogenetics and the cohesion of bacterial genomes; Daubin V et al.; Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification . Lateral gene transfer is considered the primary explanation for discordance among gene phylogenies and as an obstacle to reconstructing the tree of life . We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes . Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree.

Science, 2003 Aug 8, 301(5634), 780 - 5
Bacterial chromosome dynamics; Sherratt DJ; Bacterial chromosomes are highly compacted structures and share many properties with their eukaryote counterparts, despite not being organized into chromatin or being contained within a cell nucleus . Proteins conserved across all branches of life act in chromosome organization, and common mechanisms maintain genome integrity and ensure faithful replication . The principles that underlie chromosome segregation in bacteria and eukaryotes share similarities, although bacteria segregate DNA as it replicates and lack a eukaryote-like mitotic apparatus for segregating chromosomes . This may be because the distances that newly replicated bacterial chromosomes move apart before cell division are small as compared to those in eukaryotes . Bacteria specify positional information, which determines where cell division will occur and which places the replication machinery and chromosomal loci at defined locations that change during cell cycle progression.

Nucleic Acids Res, 2003 Aug 15, 31(16), 4822 - 7
The bacterial transposon Tn7 causes premature polyadenylation of mRNA in eukaryotic organisms: TAGKO mutagenesis in filamentous fungi; Lo C et al.; TAGKO is a Tn7-based transposition system for genome wide mutagenesis in filamentous fungi . The effects of transposon insertion on the expression of TAGKO alleles were examined in Magnaporthe grisea and Mycosphaerella graminicola . Northern analysis showed that stable, truncated transcripts were expressed in the TAGKO mutants . Mapping of the 3'-ends of TAGKO cDNAs revealed that they all contain Tn7 end sequences, regardless of the transposon orientation . Polyadenylation signals characteristic of eukaryotic genes, preceded by stop codons in all frames, are located in both ends of the bacterial transposon . Thus, TAGKO transcripts are prematurely polyadenylated, and truncated proteins are predicted to be translated in the fungal mutants . Depending on the extent of protein truncation, TAGKO mutations in HPD4 (encoding p-hydroxyphenylpyruvate dioxygenase) resulted in tyrosine sensitivity in the two fungi . Similarly, a particular M.grisea CBS1 (encoding cystathionine beta-synthase) TAGKO cDNA failed to complement cysteine auxotrophy in a yeast CBS mutant . TAGKO, therefore, represents a useful tool for in vivo study of truncated gene products in filamentous fungi.

J Biol Chem, 2003 Oct 17, 278(42), 40640 - 6 Epub 2003 Aug 06.
Two-stage binding of SecA to the bacterial translocon regulates ribosome-translocon interaction; Zito CR et al.; The bacterial translocon interacts with both SecA-bound preproteins and nascent chain-ribosome complexes during Sec and signal recognition particle-dependent protein translocation, respectively . In their inactive state, translocons are saturated with ribosomes and SecA protein, reflecting the inherent affinity of these components for one another . We found that SecA and ribosomes are bound simultaneously and noncompetitively to a common set of inactive translocons . Furthermore, we demonstrate that at a later stage in binding, SecA possesses a ribosome-translocon dissociation activity that is coupled to its ATP-dependent membrane insertion and retraction cycle that drives protein translocation . This novel activity is presumably important in the commitment of the translocon to the Sec-dependent pathway . These results also provide a rationale for the compatibility and regulation of multiple protein translocation pathways that each makes distinct demands on a common translocon core.

Am J Gastroenterol, 2003 Aug, 98(8), 1844 - 8
Validation of automated blood cell counter for the determination of polymorphonuclear cell count in the ascitic fluid of cirrhotic patients with or without spontaneous bacterial peritonitis; Angeloni S et al.; OBJECTIVES: Polymorphonuclear (PMN) cell count in ascitic fluid is the most useful test for the diagnosis of spontaneous bacterial peritonitis (SBP) . We evaluated the validity of an automated blood cell counter for the PMN determination in ascitic fluid by comparing it with the traditional hematologic method with a light microscope in a manual counting chamber . METHODS: A total of 130 ascitic fluid samples were collected from 74 consecutive cirrhotics . The agreement between the two techniques was assessed according to Bland and Altman's method . The sensitivity, specificity, and positive and negative predictive values of the automated blood cell counter were calculated by considering the diagnosis of SBP as a PMN count > or = 250 cells/mm(3), determined by the manual method as the "gold standard." RESULTS: The mean PMN counts assessed by the manual method and the automated blood cell counter were 124 +/- 301 cells/mm(3) and 130 +/- 339 cells/mm(3), respectively (p = 0.89, ns) . The mean +/- SD of the difference between manual and automated measurements was 6 +/- 61 cells/mm(3), whereas the limits of agreement were +127 cells/mm(3) (95% CI = +108 to +147) and -115 cells/mm(3) (95%CI = -96 to -135) . SBP was diagnosed in 11 patients . All but one were correctly identified with the automated blood cell counter, with a sensitivity of 94% and a specificity of 100%; positive and negative predictive values were 100% and 99.1%, respectively . CONCLUSIONS: The manual method and the automated blood cell counter have a good agreement in the PMN determination in ascitic fluid, and the automated blood cell counter is a reliable tool for rapid diagnosis of SBP.

Biochem Pharmacol, 2003 Aug 1, 66(3), 405 - 14
Interaction of polyhalogenated compounds of appropriate configuration with mammalian or bacterial CYP enzymes . Increased bilirubin and uroporphyrinogen oxidation in vitro; Pons N et al.; Polyhalogenated compounds, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin, are associated with toxic Uroporphyria and cause alleviation of jaundice in the Gunn rat . These effects have been attributed to a microsomal oxidation of uroporphyrinogen and bilirubin for which supportive evidence has been obtained in vitro . CYP1A1 required planar polyhalogenated biphenyls for these oxidative reactions, while CYP1A2 was capable of oxidation in their absence.We have now used rat CYP1A1 and confirmed with the pure enzyme that increased bilirubin oxidation was caused by the addition of 3,4,3',4'-tetrachlorobiphenyl . CYP1A2 was more active than CYP1A1 at oxidizing bilirubin in presence of NADPH alone and reacted to addition of 3,4,3',4'-tetrachlorobiphenyl with a depression rather than a stimulation of bilirubin oxidation.We have also tested a bacterial enzyme, CYP102 . Dodecanoic acid and its polyhalogenated analogue (perfluorododecanoic acid) both stimulated NADPH oxidation by CYP102, but only the perfluoro analogue stimulated markedly bilirubin oxidation . The analogue exhibited much greater potency than the normal substrate in stimulating NADPH and bilirubin oxidation and also showed greater affinity for CYP102, as measured by the binding constant, Ks . The molar stoichiometry ratio between NADPH and O(2) consumption was 1 in the case of the substrate, but approximated 2 with the perfluoro analogue . We conclude that halogenated substrate analogues can interact with different CYPs to increase production of oxidative species, probably by an uncoupling mechanism . A role of the ferryl-oxygen intermediate is suggested in the oxidation of biologically important molecules, with possible implications for the therapy of jaundice and for toxic oxidative reactions, such as uroporphyria and cancer.

Genomics, 2003 Sep, 82(3), 378 - 89
High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis; Luo MC et al.; We have developed an automated, high-throughput fingerprinting technique for large genomic DNA fragments suitable for the construction of physical maps of large genomes . In the technique described here, BAC DNA is isolated in a 96-well plate format and simultaneously digested with four 6-bp-recognizing restriction endonucleases that generate 3' recessed ends and one 4-bp-recognizing restriction endonuclease that generates a blunt end . Each of the four recessed 3' ends is labeled with a different fluorescent dye, and restriction fragments are sized on a capillary DNA analyzer . The resulting fingerprints are edited with a fingerprint-editing computer program and contigs are assembled with the FPC computer program . The technique was evaluated by repeated fingerprinting of several BACs included as controls in plates during routine fingerprinting of a BAC library and by reconstruction of contigs of rice BAC clones with known positions on rice chromosome 10.

Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2003 Feb, 25(1), 56 - 9
{Isolation of a HBV-PreS2 epitope from a random peptide library displayed on the bacterial flagellin}; Xin ZT et al.; OBJECTIVE: To establish an improved procedure for isolation and identification of epitopes from a random peptide library displayed on the bacterial surface . METHODS: Epitopes were screened from FliTrx random peptide library by a monoclonal antibody 3B9 against HBV-PreS2 protein . The enrichment was monitored in each round . Higher affinity clones were obtained by increasing the washing strength and randomly selected for sequencing and Western blot analysis . RESULTS: Clones specifically binding to antibody were enriched in each round . Ten sequences were obtained from sixteen sequenced clones, seven of them contained the common motif RXRGXY with high homogeneity to 135-140 amio acids in HBV-PreS protein and have positive results in Western blot analysis . The other three sequences have no typical motif RXRGXY and showed different Western blot results . CONCLUSIONS: It's easy and quick to drive epitopes from a random peptide library displayed on the bacterial surface.

Br J Surg, 2003 Aug, 90(8), 981 - 8
Colonic anastomotic strength and matrix metalloproteinase activity in an experimental model of bacterial peritonitis; de Hingh IH et al.; BACKGROUND: Clinical studies report conflicting results on the safety of primary intestinal anastomoses in the presence of peritonitis, and comprehensive experimental data are lacking . The present study investigated whether the strength of experimental colonic anastomoses is affected if surgery is performed in the presence of pre-existing bacterial peritonitis . METHODS: Colonic anastomoses were constructed in Wistar rats 24 h after caecal ligation and puncture or a sham procedure . Anastomotic strength was assessed by measuring breaking strength and bursting pressure during the first 5 days after operation . Anastomotic hydroxyproline levels were measured and matrix metalloproteinase (MMP) activity was analysed by quantitative gelatin zymography . RESULTS: Anastomotic strength was lowered in the presence of bacterial peritonitis but in a minor and transient way . The breaking strength was lower only immediately after construction of the anastomosis (- 15 per cent, P = 0.011) and the bursting pressure only on the third postoperative day (- 33 per cent, P = 0.038); no anastomotic dehiscence was observed . At 3 days after operation increased levels of MMP activity were observed but anastomotic hydroxyproline content was not affected by bacterial peritonitis . CONCLUSION: The influence of bacterial peritonitis on the development of anastomotic strength is limited . This experimental finding lends support to recent clinical studies that have demonstrated the feasibility of constructing a primary anastomosis under these conditions .

Microb Ecol, 2003 Nov, 46(4), 391 - 405 Epub 2003 Aug 14.
Temporal patterns in bacterial communities in three temperate lakes of different trophic status; Yannarell AC et al.; Despite considerable attention in recent years, the composition and dynamics of lake bacterial communities over annual time scales are poorly understood . This study used automated ribosomal intergenic spacer analysis (ARISA) to explore the patterns of change in lake bacterial communities in three temperate lakes over 2 consecutive years . The study lakes included a humic lake, an oligotrophic lake, and a eutrophic lake, and the epilimnetic bacterial communities were sampled every 2 weeks . The patterns of change in bacterial communities indicated that seasonal forces were important in structuring the behavior of the bacterial communities in each lake . All three lakes had relatively stable community composition in spring and fall, but summer changes were dramatic . Summertime variability was often characterized by recurrent drops in bacterial diversity . Specific ARISA fragments derived from these lakes were not constant among lakes or from year to year, and those fragments that did recur in lakes in different years did not exhibit the same seasonal pattern of recurrence . Nonetheless, seasonal patterns observed in 2000 were fairly successful predictors of the rate of change in bacterial communities and in the degree of autocorrelation of bacterial communities in 2001 . Thus, seasonal forces may be important structuring elements of these systems as a whole even if they are uncoupled from the dynamics of the individual system components.

Intensive Care Med, 2003 Nov, 29(11), 1967 - 73 Epub 2003 Aug 06.
Acute community-acquired bacterial meningitis in adults admitted to the intensive care unit: clinical manifestations, management and prognostic factors; Flores-Cordero JM et al.; OBJECTIVE: To study the clinical features, management and prognostic factors associated with adverse clinical outcome in a series of patients with acute community-acquired bacterial meningitis admitted to the intensive care unit (ICU) . DESIGN AND SETTING: Descriptive, prospective study at two ICUs of a university hospital over a 6-year period . PATIENTS: Sixty-four episodes in 62 adults with acute community-acquired bacterial meningitis admitted to the ICU . RESULTS: Most of the patients (95.3%) were admitted to the ICU presenting with altered mental status (the median value of Glasgow Coma Scale (GCS) was 11) . Overall mortality rate was 10.9% (7 patients) and 11 (17.1%) developed adverse clinical outcome (death or severe neurologic deficit) . The features associated with adverse clinical outcome were: age over 50 years, seizures or focal neurologic signs at admission, a GCS score of 10 or less and an APACHE II score more than 13 at admission to the ICU . Only the severity of the disease determined according to the APACHE II scale was independently associated with adverse clinical outcome after a multivariate analysis was performed (adjusted odds ratio =8.74; 95% CI =1.70-44.77; p=0.009) . All patients were empirically treated with third-generation cephalosporins and dexamethasone was used in 40 cases (62.5%) . Ten patients (15.6%) received mannitol, nine of them after a transcranial Doppler sonography recording had been performed . CONCLUSIONS: In adult patients with acute community-acquired bacterial meningitis admitted to the ICU, the overall severity of the disease within 24 h of admission may be the major indicator of adverse in-hospital clinical outcome.

Nature, 2003 Aug 7, 424(6949), 643 - 50
Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy; Yonekura K et al.; The bacterial flagellar filament is a helical propeller for bacterial locomotion . It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling . The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization . Here we report a complete atomic model of the R-type filament by electron cryomicroscopy . A density map obtained from image data up to 4 A resolution shows the feature of alpha-helical backbone and some large side chains . The atomic model built on the map reveals intricate molecular packing and an alpha-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament.

Expert Rev Vaccines, 2003 Jun, 2(3), 417 - 36
Bioinformatics: how it is being used to identify bacterial vaccine candidates; Zagursky RJ et al.; Genomic sequencing has provided a tremendous amount of information that can be useful in vaccine target identification . The sheer volume of information available necessitates the use of new research disciplines and techniques . Using bioinformatics, researchers sift through available data to identify appropriate candidates for biological analysis . This review provides an overview of available bioinformatic techniques for vaccine candidate identification and a few examples of how these techniques are being applied to specific bacterial pathogens.

Nucleic Acids Res Suppl, 2002, (2), 271 - 2
Regulation of bacterial RNase P ribozyme reaction by divalent cation and guide DNA; Ando T et al.; The RNA subunit of bacterial ribonuclease P (RNase P) is a ribozyme which can cleave a canonical cloverleaf tRNA precursor and a hairpin RNA with a CCA-3' tag sequence as its substrate . With high concentration of Mg ion, the ribozyme as well as holo enzyme internally cleaves certain tRNAs in vitro . We denoted this unusual reaction as hyperprocessing . By controlling magnesium ion concentration for the reaction and also by forcing the RNA shape with external guide DNAs, we could regulate the hyperprocessing reaction by the bacterial RNase P enzymes . These techniques will lead the RNase P ribozyme to more designable and more applicable RNA-cleaving enzyme.

Sex Transm Infect, 2003 Aug, 79(4), 332 - 5
Predictors of the prevalence of bacterial STI among young disadvantaged Indigenous people in north Queensland, Australia; Miller GC et al.; OBJECTIVE: To identify sexually transmitted infections in rural and remote Indigenous communities in north eastern Australia and examine factors that may influence prevalence . METHODS: A cross sectional survey of 26 Aboriginal and Torres Strait Islander communities in northern Queensland was carried out . 3313 people (2862 Indigenous) aged 15 years and over resident in participating communities during the period March 1998 to December 2000 . The main outcome measures were community and population prevalence of chlamydia and gonorrhoea and independently associated risk factors . RESULTS: A total of 238 cases of chlamydia, 66 cases of gonorrhoea, and 37 cases of co-infection were detected among Indigenous participants . Prevalence of chlamydia and/or gonorrhoea ranged from 23.0% among 15-19 year olds to 3.5% among those 40 years and older . In the adjusted analysis younger age, female sex, lower socioeconomic status, the use of alcohol and tobacco, and the structure of community health services were independently associated with a higher prevalence of bacterial STI . CONCLUSION: This study highlights the need for improved STI control in north Queensland Indigenous communities through strategies to improve the reach and accessibility of primary healthcare services.

Appl Environ Microbiol, 2003 Aug, 69(8), 4421 - 30
A new bacterial steroid degradation gene cluster in Comamonas testosteroni TA441 which consists of aromatic-compound degradation genes for seco-steroids and 3-ketosteroid dehydrogenase genes; Horinouchi M et al.; In Comamonas testosteroni TA441, testosterone is degraded via aromatization of the A ring, which is cleaved by the meta-cleavage enzyme TesB, and further degraded by TesD, the hydrolase for the product of TesB . TesEFG, encoded downstream of TesD, are probably hydratase, aldolase, and dehydrogenase for degradation of 2-oxohex-4-enoicacid, one of the products of TesD . Here we present a new and unique steroid degradation gene cluster in TA441, which consists of ORF18, ORF17, tesI, tesH, ORF11, ORF12, and tesDEFG . TesH and TesI are 3-ketosteroid-Delta(1)-dehydrogenase and 3-ketosteroid-Delta(4)(5alpha)-dehydrogenase, respectively, which work in the early steps of steroid degradation . ORF17 probably encodes the reductase component of 9alpha-hydroxylase for 1,4-androstadiene-3,17-dione, which is the product of TesH in testosterone degradation . Gene disruption experiments showed that these genes are necessary for steroid degradation and do not have any isozymes in TA441 . By Northern blot analysis, these genes were shown to be induced when TA441 was incubated with steroids (testosterone and cholic acid) but not with aromatic compounds {phenol, biphenyl, and 3-(3-hydroxyphenyl)propionic acid}, indicating that these genes function exclusively in steroid degradation.

Mikrobiologiia, 2003 May-Jun, 72(3), 414 - 8
{Bacterial motion in porous media}; Zaval'skii LIu et al.; The motion of chemotactically different Escherichia coli C600, cheB287, and AW405 cells was studied using a column packed with silica gel . The model chemotaxis of bacteria in porous media seems to be adequate to natural bacterial chemotaxis in soils . The porous structure of silica gel prevents interfering convective flows . Silica gel columns make it possible to separate bacterial cells differing in motility and chemotaxis . Relevant physical phenomena are discussed . The concept of fast and slow chemotaxis is considered.

Curr Opin Immunol, 2003 Aug, 15(4), 456 - 60
Vaccines for parasitic and bacterial diseases; Reed SG et al.; The first decade of the millennium should mark the beginning of a new era in vaccine development, reaping the rewards of advances in genome characterization, antigen identification, understanding the molecular bases of protective immune responses, and adjuvant design and development . Advances in all of these areas have culminated in vaccine candidates entering clinical testing . These include vaccines against two of humankind's oldest and deadliest diseases, tuberculosis and malaria . Several vaccine candidates for each of these diseases will be tested in humans during the next few years . A candidate vaccine for leishmaniasis, an infection that has taught us much about T-cell regulation of protection and disease in animal models, has been developed and is now in the clinic . There are indications both in animal models and in patients that vaccines may be used not only to protect but also to treat leishmania infections.

FEMS Immunol Med Microbiol, 2003 Aug 18, 38(1), 71 - 9
Osteoclast differentiation by human osteoblastic cell line SaOS-2 primed with bacterial lipid A; Asai Y et al.; We examined the responses of human osteoblastic cell line SaOS-2 to bacterial lipid A, a bioactive center of lipopolysaccharide, during osteoclast differentiation of human peripheral blood mononuclear cells (PBMC) . SaOS-2 cells expressed mRNA for Toll-like receptor (TLR) 4, MD-2, CD14, and myeloid differentiation factor 88, whereas they failed to express mRNA for TLR2 . Escherichia coli-type synthetic lipid A (compound 506) induced cytokine mRNA expression and nuclear factor (NF)-kappaB activation in SaOS-2 cells . Compound 506 also increased the expression of receptor activator of NF-kappaB ligand . Further, cells primed with compound 506 augmented the differentiation of PBMC into osteoclastic cells, and the effect was inhibited by anti-TLR4 monoclonal antibody . These findings suggest that the TLR signaling cascade in osteoblastic cells is involved in regulating the function of osteoclastogenesis.

J Mol Biol, 2003 Aug 15, 331(3), 541 - 56
Mapping the active sites of bacterial translation initiation factor IF3; Petrelli D et al.; IF3C is the C-terminal domain of Escherichia coli translation initiation factor 3 (IF3) and is responsible for all functions of this translation initiation factor but for its ribosomal recycling . To map the number and nature of the active sites of IF3 and to identify the essential Arg residue(s) chemically modified with 2,3-butanedione, the eight arginine residues of IF3C were substituted by Lys, His, Ser and Leu, generating 32 variants that were tested in vitro for all known IF3 activities . The IF3-30S subunit interaction was inhibited strongly by substitutions of Arg99, Arg112, Arg116, Arg147 and Arg168, the positive charges being important at positions 116 and 147 . The 70S ribosome dissociation was affected by mutations of Arg112, Arg147 and, to a lesser extent, of Arg99 and Arg116 . Pseudo-initiation complex dissociation was impaired by substitution of Arg99 and Arg112 (whose positive charges are important) and, to a lesser extent, of Arg116, Arg129, Arg133 and Arg147, while the dissociation of non-canonical 30S initiation complexes was preserved at wild-type levels in all 32 mutants . Stimulation of mRNA translation was reduced by mutations of Arg116, Arg129 and, to a lesser extent, of Arg99, Arg112 and Arg131 whereas inhibition of non-canonical mRNA translation was affected by substitutions of Arg99, Arg112, Arg168 and, to a lesser extent, Arg116, Arg129 and Arg131 . Finally, repositioning the mRNA on the 30S subunit was affected weakly by mutations of Arg133, Arg131, Arg168, Arg147 and Arg129 . Overall, the results define two active surfaces in IF3C, and indicate that the different functions of IF3 rely on different molecular mechanisms involving separate active sites.

Biochemistry, 2003 Aug 12, 42(31), 9374 - 82
Investigating the interfacial binding of bacterial phosphatidylinositol-specific phospholipase C; Wehbi H et al.; The interactions of PI-PLC with nonsubstrate zwitterionic {phosphatidylcholine (PC)} and anionic {phosphatidylmethanol (PMe), phosphatidylserine, phosphatidylglycerol, and phosphatidic acid} interfaces that affect the catalytic activity of PI-PLC have been examined . PI-PLC binding is strongly coupled to vesicle curvature and is tighter at acidic pH for all of the phospholipids examined . PI-PLC binds to small unilamellar vesicles (SUVs) of anionic lipids with much higher affinity (K(d) is 0.01-0.07 microM for a site consisting of n = 100 +/- 25 lipids when analyzed with a Langmuir adsorption isotherm) than to zwitterionic PC SUVs (K(d) is 5-20 microM and n = 8 +/- 3) . The binding to PC surfaces is dominated by hydrophobic interactions, while binding to anionic surfaces is dominated by electrostatic interactions . The contributions of specific cationic side chains and hydrophobic groups at the rim of the alpha beta-barrel to zwitterionic and anionic vesicle binding have been assessed with mutagenesis . The results are used to explain how PC activates the enzyme for both phosphotransferase and cyclic phosphodiesterase activities.

Chin Med Sci J, 2000 Mar, 15(1), 20 - 3
The transmembrane signal transduction in HEp-2 cells induced by bacterial adherence; Guan Y et al.; In order to understand the role of transmembrane signal transduction of host cells in the early steps of infection, the adherence of E . coli to HEp-2 cells and the change of activity of phospholipase C-gamma (PLC-gamma) induced by the adherence were investigated . The adherence of enteropathogenic E . coli (EPEC), strain E . 7, induced a significant increase of inositol-triphosphat (IP-3) level in HEp-2 cells . The adherence of the bacteria and the increase of IP-3 was kinetically correlated . Whereas the increase of IP3 level induced by the adherence of the control strain EPEC (H511), a non-piliated strain, was much meager than that by E7, a piliated strain . The results highlighted an important role of transmembrane signals like 1P-3 in the pathogenesis of EPEC.

Chin Med Sci J, 2001 Mar, 16(1), 46 - 8
Epidermal growth factor prevents increased permeability and bacterial translocation in rats with acute pancreatitis; Chen D et al.; OBJECTIVE: To evaluate the effects of epidermal growth factor (EGF) on intestinal permeability and bacterial translocation in rats with acute pancreatitis during total parenteral nutrition (TPN) . METHODS: Thirty-two male Sprague-Dawley rats that underwent injection of 3.5% sodium taurocholate solution into the pancreatic duct were randomly divided into one of the following two groups: (1) received only TPN (control group) or (2) received TPN with EGF at a dose of 0.2 mg x kg(-1) x day(-1) (Egf group) . On fifth day of total parenteral nutrition, samples from mesenteric lymph nodes, pancreas, liver and spleen were harvested for cultures . Water, protein and DNA content in jejunal mucosa were determined . D-xylose and fluorescein isothiocyanate (FTC)-dextran were instilled into the lumen of a ligated segament of small intestine . Thirty minutes later, superior mesenteric vein D-xylose and plasma FITC-dextran concentration were measured . RESULTS: Positive cultures in liver and spleen, as well as FITC-dextran concentration in the Egf group were significantly lower than in the control group . Protein and DNA content in jejunal mucosa in the Egf group were significantly higher than in the control group . CONCLUSION: The results indicate that EGF may prevent increased intestinal permeability and bacterial translocation in rats with acute pancreatitis during TPN.

Probl Tuberk Bolezn Legk, 2003, (5), 28 - 31
{Long-term results of surgical treatment of pulmonary tuberculosis wtih respect to the extent of bacterial isolation and to drug resistance of Mycobacterium tuberculosis}; El'kin AV et al.; The remote postoperative results were followed up for as long as up to 10 years . It was established in case of abacillary patients that the frequency rate of relapses was minimal ranging from 3.6% in the group of patients operated for tuberculosis and caseous-necrotic tuberculosis to 11.5% in fibrous-cavernous tuberculosis . Patients with bacterial discharge, primarily of the extensive nature, had more often relapses (19.4% in operated patients for caseous-necrotic tuberculosis and 31.7% in patients operate for fibrous-cavernous tuberculosis) . Drug resistance (DR) of Mycobacterium tuberculosis (MBT) to three and more anti-TB preparations essentially increase a possibility of relapses in all clinical forms of tuberculosis with maximum threat being in patients with fibrous-cavernous lesions (36%) . As for the repeatedly operated patients for postoperative relapses involving DR MBT to isoniazid and rifampicin, only slightly above 50% of them survived 5 years after surgery; the index of the 5-year survival was 33% among the patients with DR to 4 and more drugs.

Int J Eat Disord, 2003 Sep, 34(2), 269 - 72
Reduced febrile response to bacterial infection in anorexia nervosa patients; Birmingham CL et al.; OBJECTIVE: To report a reduced febrile response to bacterial infections in anorexia nervosa (AN) patients . METHOD: Four cases were obtained from a retrospective review of charts from the St . Paul's Hospital Eating Disorders Program (Vancouver, Canada) . The patients had died or had been admitted to the hospital for treatment of a bacterial infection . In addition, one case was obtained from the Royal Prince Alfred Hospital (Sydney, Australia) . RESULTS: All patients suffered a bacterial infection during the course of AN . None of the patients had a temperature higher than 37 degrees C during the infectious illness . DISCUSSION: The absence of fever in AN may delay the diagnosis of bacterial infection and may be a marker of an impaired immune response . Therefore, alternative methods of investigation are necessary in patients with AN suspected of having a bacterial infection .

Sex Transm Dis, 2003 Aug, 30(8), 645 - 9
Bacterial vaginosis in pregnancy: diagnosis and treatment practices of physicians in San Diego, California, 1999; Callahan DB et al.; BACKGROUND: Treating symptomatic bacterial vaginosis (BV) early in pregnancy may decrease preterm birth (PTB) . Understanding how physicians manage BV is important for the development of interventions . GOAL: The goal was to determine the extent of knowledge and behaviors of physicians related to the diagnosis, treatment, and medical effects of BV in pregnant and nonpregnant patients . STUDY DESIGN: This was a cross-sectional survey . RESULTS: The study group consisted of 208 physicians who provided gynecologic care, including 102 (49%) who provided care to pregnant patients . Only 65% believed that there was a strong causal association between BV and PTB . Physicians who believed that BV causes PTB were much more likely to optimally manage vaginal infections (43% versus 7%) . Only 12% of physicians prescribed oral metronidazole or clindamycin during the first trimester of pregnancy to treat BV . CONCLUSION: Physicians should be aware of the relation between symptomatic BV and PTB, seek a specific diagnosis for symptoms of vaginitis, use standard criteria to diagnose BV, and treat BV with effective regimens early in pregnancy.

J Am Acad Dermatol, 2003 Aug, 49(2 Suppl Case Reports), S177 - 9
Tinea capitis in adult women masquerading as bacterial pyoderma; Martin ES et al.; Tinea capitis is generally thought to be a common disease in children but not in adults . Adults with tinea capitis generally present with scale and alopecia . We report 3 adults with inflammatory tinea capitis caused by Trichophyton tonsurans that resembled a bacterial infection . Of these patients, 2 were initially given a diagnosis of bacterial pyoderma . All patients were successfully treated with oral antifungal agents . One patient had significant eosinophilia that resolved with treatment . We conclude that tinea capitis should remain in the differential diagnosis of adults with alopecia and pyoderma-like presentations . A biopsy specimen was helpful in making the diagnosis in 2 of the 3 patients, but fungal culture confirmed the diagnosis in all cases.

Ann Surg, 2003 Aug, 238(2), 249 - 57
Hypertonic saline enhances host response to bacterial challenge by augmenting receptor-independent neutrophil intracellular superoxide formation; Shields CJ et al.; OBJECTIVE: This study sought to determine whether hypertonic saline (HTS) infusion modulates the host response to bacterial challenge . METHODS: Sepsis was induced in 30 Balb-C mice by intraperitoneal injection of Escherichia coli (5 x 107 organisms per animal) . In 10 mice, resuscitation was performed at 0 and 24 hours with a 4 mL/kg bolus of HTS (7.5% NaCl), 10 animals received 4 mL/kg of normal saline (0.9% NaCl), and the remaining animals received 30 mL/kg of normal saline . Samples of blood, spleen, and lung were cultured at 8 and 36 hours . Polymorphonucleocytes were incubated in isotonic or hypertonic medium before culture with E . coli . Phagocytosis was assessed by flow cytometry, whereas intracellular bacterial killing was measured after inhibition of phagocytosis with cytochalasin B . Intracellular formation of free radicals was assessed by the molecular probe CM-H(2)DCFDA . Mitogen-activated protein (MAP) kinase p38 and ERK-1 phosphorylation, and nuclear factor kappa B (NFkappaB) activation were determined . Data are represented as means (SEM), and an analysis of variance test was performed to gauge statistical significance . RESULTS: Significantly reduced bacterial culture was observed in the animals resuscitated with HTS when compared with their NS counterparts, in blood (51.8 +/- 4.3 vs . 82.0 +/- 3.3 and 78.4 +/- 4.8, P = 0.005), lung (40.0 +/- 4.1 vs . 93.2 +/- 2.1 and 80.9 +/- 4.7, P = 0.002), and spleen (56.4 +/- 3.8 vs . 85.4 +/- 4.2 and 90.1 +/- 5.9, P = 0.05) . Intracellular killing of bacteria increased markedly (P = 0.026) and superoxide generation was enhanced upon exposure to HTS (775.78 +/- 23.6 vs . 696.57 +/- 42.2, P = 0.017) despite inhibition of MAP kinase and NFkappaB activation . CONCLUSIONS: HTS significantly enhances intracellular killing of bacteria while attenuating receptor-mediated activation of proinflammatory cascades.

Nucleic Acids Res, 2003 Aug 1, 31(15), 4434 - 40
DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery; Witte G et al.; Single-stranded DNA binding (SSB) protein binds to single-stranded DNA (ssDNA) at the lagging strand of the replication fork in Escherichia coli cells . This protein is essential for the survival of the E.coli cell, presumably because it shields the ssDNA and holds it in a suitable conformation for replication by DNA polymerase III . In this study we undertook a biophysical analysis of the interaction between the SSB protein of E.coli and the chi subunit of DNA polymerase III . Using analytical ultracentrifugation we show that at low salt concentrations there is an increase in the stability in the physical interaction between chi and an EcoSSB/ssDNA complex when compared to that of chi to EcoSSB alone . This increase in stability disappeared in high salt conditions . The sedimentation of an EcoSSB protein lacking its C-terminal 26 amino acids remains unchanged in the presence of chi, showing that chi interacts specifically with the C-terminus of EcoSSB . In DNA melting experiments we demonstrate that chi specifically enhances the ssDNA stabilization by EcoSSB . Thus, the binding of EcoSSB to chi at the replication fork prevents premature dissociation of EcoSSB from the lagging strand and thereby enhances the processivity of DNA polymerase III.

J Virol, 2003 Aug, 77(16), 8712 - 8
Replication-competent bacterial artificial chromosomes of Marek's disease virus: novel tools for generation of molecularly defined herpesvirus vaccines; Petherbridge L et al.; Marek's disease (MD), a highly infectious disease caused by an oncogenic herpesvirus, is one of the few herpesvirus diseases against which live attenuated vaccines are used as the main strategy for control . We have constructed bacterial artificial chromosomes (BACs) of the CVI988 (Rispens) strain of the virus, the most widely used and effective vaccine against MD . Viruses derived from the BAC clones were stable after in vitro and in vivo passages and showed characteristics and growth kinetics similar to those of the parental virus . Molecular analysis of the individual BAC clones showed differences in the structure of the meq gene, indicating that the commercial vaccine contains virus populations with distinct genomic structures . We also demonstrate that, contrary to the published data, the sequence of the L-meq of the BAC clone did not show any frameshift . Virus stocks derived from one of the BAC clones (clone 10) induced 100 percent protection against infection by the virulent strain RB1B, indicating that BAC-derived viruses could be used with efficacies similar to those of the parental CVI988 vaccines . As a DNA vaccine, this BAC clone was also able to induce protection in 6 of 20 birds . Isolation of CVI988 virus from all of these six birds suggested that immunity against challenge was probably dependent on the reconstitution of the virus in vivo and that such viruses are also as immunogenic as the in vitro-grown BAC-derived or parental vaccine viruses . Although the reasons for the induction of protection only in a proportion of birds (33.3%) that received the DNA vaccine are not clear, this is most likely to be related to the suboptimal method of DNA delivery . The construction of the CVI988 BAC is a major step towards understanding the superior immunogenic features of CVI988 and provides the opportunity to exploit the power of BAC technology for generation of novel molecularly defined vaccines.

Biochemistry, 2003 Aug 5, 42(30), 9147 - 52
Functional asymmetry of the human Na+/glucose transporter (hSGLT1) in bacterial membrane vesicles; Quick M et al.; The functional characteristics of the forward and reverse transport modes of the human Na(+)/glucose transporter (hSGLT1) were investigated using plasma membrane vesicles of E . coli expressing the recombinant transporter . Correctly and inverse-oriented vesicles were employed to measure the initial rates of methyl-alpha-D-glucose uptake, under zero-trans conditions, as a function of Na(+), sugar, and phlorizin concentrations and membrane potential . This approach enabled the analysis of the two faces of hSGLT1 in parallel, revealing the reversibility of Na(+)/sugar cotransport . While the key characteristics of secondary active sugar transport were maintained in both modes, namely, Na(+) and voltage dependence, the kinetic properties of the two sides indicated a functional asymmetry of the transporter . That is, the apparent affinity for sugar and driver cation Na(+) exhibited a difference of more than 1 order of magnitude between the two modes . Furthermore, the selectivity pattern of ligands and the interaction of the transporter with the competitive inhibitor phlorizin were different . Whereas the high-affinity substrates, D-glucose and D-galactose, inhibited uptake of radioactive sugar tracer at their physiological concentrations (10 mM) in the forward reaction, they were poor inhibitors even at high concentrations in the reverse transport mode . Taken together, these results confirm the successful employment of E . coli to express and characterize a human membrane protein (hSGLT1), elucidating the functional asymmetry of this cotransporter.

Eur J Immunol, 2003 Jul, 33(7), 1934 - 40
Differential acquired immune responsiveness to bacterial lipoproteins in Lyme disease-resistant and -susceptible mouse strains; Ganapamo F et al.; We investigated the effect of Borrelia burgdorferi lipoproteins (outer surface protein A) and the synthetic lipohexapeptide tripalmitoyl-S-glyceryl-Cys-Ser-4(Lys) (Pam3-Cys) on isolated lymph node (LN) cells from Lyme disease-susceptible (C3H/HeJ) and -resistant (C57BL/6J) mice . Mice were either infected with B . burgdorferi for 1 week or left uninfected . Lipoprotein-stimulated LN cells from infected C3H/HeJ mice produced significantly higher levels of the inflammatory cytokines IL-6 and IFN-gamma than did cells from C57BL/6J mice . Cells from uninfected mice did not respond . No TNF-alpha or IL-1beta were produced by LN cells from infected mice of either strain in response to lipoprotein or B . burgdorferi spirochetes . Unlike with IL-6 or IFN-gamma, LN cells from either strain failed to produce IL-10 in response to lipoproteins . However, the LN cells were able to produce this cytokine in response to B . burgdorferi spirochetes or after incubation with phorbol-12-myristate-13-acetate/ionomycin, anti-CD3 antibody alone or anti-CD3 combined with anti-CD28 antibodies . Addition of exogenous IL-10 to lipopeptide-stimulated cultures significantly reduced IFN-gamma and IL-6 production in a dose-dependent fashion . This inhibition was more effective with cells from disease-resistant C57BL/6J mice than with cells from disease-susceptible C3H/HeJ mice . The proclivity to disease of the C3H/HeJ mouse could be simultaneously based on the phenomena of enhanced inflammatory responsiveness to lipoproteins and diminished ability to respond to IL-10 . An investigation of the determinants of these two phenomena could be used as a blueprint to elucidate the pathogenesis of Lyme disease in humans.

Clin Infect Dis, 2003 Aug 1, 37(3), 319 - 25 Epub 2003 Jul 15.
Association between acquisition of herpes simplex virus type 2 in women and bacterial vaginosis; Cherpes TL et al.; A longitudinal cohort study of sexually active women 18-30 years of age was conducted to identify variables associated with the acquisition of herpes simplex virus type 2 (HSV-2) infections . Six hundred seventy HSV-2-seronegative women were followed up at 4-month intervals for 1 year; acquisition of HSV-2 antibodies was detected in 32 of these women . Black race, < or =12 years of education, having a new sex partner, and bacterial vaginosis (BV) were associated with HSV-2 seroconversion on univariate analysis . Antecedent HSV-1 infection was not protective against HSV-2 acquisition . After controlling for other identified risk factors in multivariable models, the diagnosis of BV remained associated with an increased risk of acquiring HSV-2 infection (hazard ratio, 2.1; 95% confidence interval, 1.0-4.5; P=.05) . In this study, the population attributable risk of BV for HSV-2 seroconversion was 21% . Additional studies are needed to determine whether screening and treatment of BV could reduce susceptibility to the acquisition of HSV-2 in women.

Appl Microbiol Biotechnol, 2003 Aug, 62(2-3), 268 - 73 Epub 2003 Mar 15.
Quantitative detection of crystalline lysine supplementation in poultry feeds using a rapid bacterial bioluminescence assay; Zabala Diaz IB et al.; Lysine is an essential amino acid for both humans and animals; and it is usually the first or second limiting amino acid in most formulated diets . In order to estimate the lysine content in feeds and feed sources, rapid amino acid bioassays have been developed . The objective of this work is to assess a rapid assay for lysine supplementation in chicken feeds, using a luminescent Escherichia coli lysine-auxotrophic strain, to avoid prior thermal sterilization . An E . coli lysine auxotroph carrying a plasmid with lux genes was used as the test organism . The lysine assay was conducted using depleted auxotrophic cells in lysine samples . Luminescence was measured with a Dynex MLX luminometer after addition of the aldehyde substrate . Growth response (monitored as optical density at 600 nm) and light emission response of the assay E . coli strain were monitored to generate standard curves . Bioluminescent analysis of feed samples indicated that the method works well in the presence of a complex feed matrix . Comparison of both optical density and luminescent-based methods indicated that, when the assay takes place under optimal conditions, both methodologies correlated well ( r(2)=0.99) . Except for the 0.64% lysine-supplemented feed, estimates for lysine based on the bacterial assay were over 80% (82-97%) of the theoretical values . Animal data showed that the bacterial bioluminescent method correlated well with the chick bioassay when diets with different levels of lysine supplementation were assayed for lysine bioavailability ( r(2)=0.97) . Luminescent methodology coupled with a bacterial growth assay is a promising technique to assess lysine availability in supplemented animal feeds.

Hepatology, 2003 Aug, 38(2), 452 - 9
Increased carbon monoxide production in patients with cirrhosis with and without spontaneous bacterial peritonitis; De las Heras D et al.; Carbon monoxide, a product of the heme-oxygenase (HO) pathway, is an important endogenous vasoactive substance . Production of CO has not been assessed in human cirrhosis . The aim of this study was to assess production of CO in patients with cirrhosis with and without spontaneous bacterial peritonitis (SBP) . CO concentration in the exhaled air and blood carboxyhemoglobin (COHb) levels, as estimates of total HO activity, were determined in 16 healthy subjects, 32 noninfected cirrhotic patients (20 with ascites), and 19 patients with SBP, all nonsmokers . Noninfected cirrhotic patients had a CO concentration in the exhaled air and COHb levels significantly higher compared with values of healthy subjects (2.3 +/- 0.2 ppm vs . 0.7 +/- 0.1 ppm and 1.0% +/- 0.1% vs . 0.6% +/- 0.1%, respectively; P <.05 for both) . Patients with ascites had the highest values . Both CO concentration in the exhaled air and COHb levels were very high in patients with SBP (5.6 +/- 0.6 ppm and 1.9% +/- 0.2%; P <.01 vs . the other 2 groups) and decreased slowly after resolution of the infection, reaching values similar to those of noninfected patients 1 month after SBP . In patients with SBP, there was a significantly direct correlation between CO and plasma renin activity (PRA) (r = 0.71, P <.001) . In conclusion, these results support the existence of increased CO production in human cirrhosis, which further increases in the setting of SBP . Increased CO production may participate in the disturbance of circulatory function that occurs during severe bacterial infections in cirrhosis.

Ostomy Wound Manage, 2003 Jul, 49(7A Suppl), 8 - 12
Bacterial toxins and wound healing; Ovington L; Infection--a factor commonly related to delayed closure for many chronic and acute wounds--is associated with relatively high levels of bacteria in viable tissues . But bacteria also can delay wound healing at lower levels before tissue invasion via toxin secretion either directly from viable cells (exotoxins) or as a result of cell lysis (endotoxins) . These toxins tend to cause local necrosis and disrupt the delicate balance of critical mediators such as cytokines and proteases necessary for healing progression . Therefore, toxin control or absorption is a potentially valuable adjunct to any infection control modality . A long-standing method of controlling toxins of many types is the use of high surface area adsorbents, such as activated charcoal . Recent data suggest that activated charcoal may offer specific advantages in topical wound management through its effects on bacterial toxins.

Inhal Toxicol, 2000, 12 Suppl 4, 227 - 46
Pulmonary inflammatory response to inhaled ultrafine particles is modified by age, ozone exposure, and bacterial toxin; Elder AC et al.; Epidemiological studies demonstrate associations between increasing levels of ambient particles and morbidity in the elderly with cardiopulmonary disease . Such findings have been challenged partly because particles may not act alone to cause these effects . We hypothesized that carbonaceous ambient ultrafine particles and ozone can act together to induce greater oxidative stress and inflammation in the lung than when administered alone and that these effects would be amplified in the compromised, aging lung . Two models of a compromised lung were used: endotoxin priming and old-age emphysema (TSK mice) . Young (10 wk) and old (22 mo) male F344 rats and male TSK mice (14-17 mo) were exposed to ultrafine carbon particles (count median diameter 25 nm, 110 micrograms/m3) and to ozone (1 ppm) alone and in combination for 6 h . Inhalation of low-dose endotoxin (70 and 7.5 units estimated alveolar deposited dose in rats and mice, respectively) was used to model respiratory-tract infection . Cellular and biochemical lavage parameters and oxidant release from lung lavage cells were assessed 24 h after exposure . Inflammatory cell influx into the alveolar space was observed for both species and age groups: The combination of inhaled ultrafine carbon and ozone after endotoxin priming resulted in the greatest increase in lavage-fluid neutrophils . In general, the unstimulated and stimulated release of reactive oxygen species (ROS) from lavage inflammatory cells correlated well with the neutrophil response . There were significant effects of carbon particles as well as a consistent interaction between carbon and ozone as determined by analysis of variance (ANOVA) . However, this interaction was in the opposite direction in young rats versus old rats and old TSK mice: Carbon and ozone interacted such that ROS activity was depressed in young rats, whereas it was enhanced in old rats and old TSK mice, indicating age-dependent functional differences in elicited pulmonary inflammatory cells . These results demonstrate that ultrafine carbonaceous particles inhaled for short periods of time can induce significant pulmonary inflammation and oxidative stress that are modified by age, copollutants, and a compromised respiratory tract.

J Insect Physiol, 2003 Aug, 49(8), 795 - 803
Adipokinetic hormone enhances nodule formation and phenoloxidase activation in adult locusts injected with bacterial lipopolysaccharide; Goldsworthy G et al.; Interactions between the locust endocrine and immune systems have been studied in vivo in relation to nodule formation and activation of the prophenoloxidase cascade in the haemolymph . Injection of bacterial lipopolysaccharide (LPS) extracted from Escherichia coli induces nodule formation in larval and adult locusts but does not increase phenoloxidase activity in the haemolymph . Nodule formation starts rapidly after injection of LPS and is virtually complete within 8 h, nodules occurring mainly associated with the dorsal diaphragm on either side of the heart, but sometimes with smaller numbers associated with the ventral diaphragm on either side of the nerve cord . Co-injection of adipokinetic hormone-I (Lom-AKH-I) with LPS stimulates greater numbers of nodules to be formed in larval and adult locusts, and activates phenoloxidase in the haemolymph of mature adults but not of nymphs . The effect of co-injection of Lom-AKH-I with LPS on nodule formation is seen at low doses of hormone; only 0.4 pmol of Lom-AKH-I per adult locust is needed to produce a 50% increase in the number of nodules formed . When different components of LPS from the E . coli Rd mutant are tested, the mono- and the diphosphoryl Lipid A components have similar effects to the intact LPS . Remarkably, detoxified LPS activates phenoloxidase in the absence of Lom-AKH-I, although co-injection with hormone does enhance this response . Both diphosphoryl Lipid A and detoxified LPS induce a level of nodule formation that is enhanced by co-injection of Lom-AKH-I, but monophosphoryl Lipid A does not initiate nodule formation even when injected with hormone . Co-injection of a water-soluble inhibitor of eicosanoid synthesis, diclofenac (2-{(2, 6-dichlorophenyl)amino} benzeneacetic acid), reduces nodule formation in response to injections of LPS (both in the absence and presence of hormone) in a dose-dependent manner, but does not prevent activation of phenoloxidase in adult locusts . It is shown that nodule formation and activation of the prophenoloxidase in locust haemolymph can both be enhanced by Lom-AKH-I, but it is argued that these processes involve distinct mechanisms in which eicosanoid synthesis is important for nodule formation, but not for the increased phenoloxidase activity.

J Insect Physiol, 2003 Aug, 49(8), 739 - 46
Molecular evidence for the expression of angiotensin converting enzyme in hemocytes of Locusta migratoria: stimulation by bacterial lipopolysaccharide challenge; Macours N et al.; The presence of angiotensin converting enzyme (ACE) in insects has been reported many times, but numerous questions about the functional role of this enzyme in insects remain . Here we show by RT-PCR experiments that ACE has a wide tissue distribution in Locusta migratoria, suggesting diverse roles for this enzyme in the locust . Immune challenge through injection of bacterial lipopolysaccharides resulted in a tenfold increase of ACE gene transcripts in the hemocytes and is suggestive for a role of ACE in the cellular defense of the locust . However, phenotypic knockout experiments with the ACE inhibitor captopril showed that ACE is not essential for the efficient clearance of injected E . coli bacteria.

IUBMB Life, 2003 Apr-May, 55(4-5), 205 - 12
Parallels in genome evolution in mitochondria and bacterial symbionts; Burger G et al.; Mitochondria, the energy-producing organelles of the eukaryotic cell, originate from an endosymbiotic alpha-proteobacterium . These organelles are believed to have arisen only once in evolutionary history, but despite their common ancestry, mitochondrial DNAs vary extensively throughout eukaryotes in genome architecture and gene content . New insights into early mitochondrial genome evolution come from the investigation of primitive mitochondriate eukaryotes, as well as the comparison between mitochondria and intracellular bacterial symbionts.

Pediatr Neurol, 2003 May, 28(5), 365 - 9
Absolute neutrophil count in aseptic and bacterial meningitis related to time of lumbar puncture; Straussberg R et al.; Previous studies have demonstrated that during the first 24 hours of illness caused by aseptic meningitis, polymorphonuclear cells predominate in cerebrospinal fluid and decline afterward . To test the hypothesis that the absolute neutrophil count and percentage of polymorphonuclear cells in cerebrospinal fluid of bacterial meningitis patients are elevated and sustained after 24 hours compared with that of patients with aseptic meningitis . Seventy-two patients with aseptic meningitis and 13 with bacterial meningitis participated . All patients with aseptic meningitis and four patients with bacterial meningitis were followed-up prospectively . The patients were enrolled in four groups according to the interval between onset of symptoms and performance of the lumbar puncture (<12 hours, 12-24 hours, 24-36 hours, and >36 hours) . In aseptic meningitis the mean absolute neutrophil count was 182, 164, 79, and 68 cells/mm(3), respectively (P = 0.025) . In bacterial meningitis the absolute neutrophil count was 28, 1,466, 5,853, and 235 cells/mm(3), respectively . The mean percentage of polymorphonuclear cells in aseptic meningitis was 49%, 46%, 40%, and 26%, respectively (P = 0.038); in bacterial meningitis, 70%, 83%, 81%, and 58%, respectively . The findings suggest that the absolute neutrophil count and the polymorphonuclear cell percentage in cerebrospinal fluid have different kinetics in aseptic vs . bacterial meningitis.

Biochim Biophys Acta, 2003 Jul 30, 1649(2), 146 - 53
Using O-(n-alkyl)-N-(N,N'-dimethylethyl)phosphoramidates to investigate the role of Ca2+ and interfacial binding in a bacterial phospholipase D; Oh MK et al.; O-(n-alkyl)-N-(N,N'-dimethylethyl)phosphoramidates (n=6, 8, and 10; CnPNC) were synthesized and characterized as inhibitors of phospholipase D (PLD) activity toward phosphatidylcholine presented as monomers, micelles, and bilayers . Detailed studies with recombinant Streptomyces chromofuscus PLD, a Ca(2+)-activated enzyme that does not show large changes in catalytic activity toward the same substrate as a monomer or micelle, showed that the longer the inhibitor chain length, the more potent CnPNC is as a competitive inhibitor toward all the substrates . However, the physical state of the inhibitor did affect the maximum inhibition attainable . For a fixed concentration of diC4PC (monomer substrate), CnPNC inhibition reached a maximum around the CMC of the inhibitor; the inhibition was reduced at higher inhibitor concentrations, in part caused by the lower solubility of the aggregated inhibitor . With diC4PC as the substrate and using concentrations of C10PNC that were below its CMC, the Ki for C10PNC was 0.030+/-0.003 mM, approximately 13-fold less than the Km for substrate . Aggregated substrates showed significant inhibition of PLD by CnPNC, although as the substrate chain length increased, inhibition by a given CnPNC was diminished . With POPC vesicles, the apparent Ki for C10PNC was 0.030 of the apparent Km . The availability of these inhibitors allowed us to show that PC analogues can bind to the active site of S . chromofuscus PLD in the absence of Ca2+ . Once bound at the active site, the inhibitor does not significantly affect the divalent ion-dependent partitioning of the enzyme to PC surfaces . Of the two other PLD enzymes examined, cabbage PLD, but not Streptomyces sp . PMF, was able to catalyze the cleavage of the P-N bond . Differential susceptibility of PLDs to these phosphoramidates may eventually be useful in studying PLD isozymes in cells.

Scand J Infect Dis, 2003, 35(5), 341 - 3
Spontaneous bacterial peritonitis caused by Brucella melitensis; Gencer S et al.; This report presents a case of blood and ascitic fluid culture-proven spontaneous bacterial peritonitis caused by Brucella melitensis in a 67-y-old male with congestive heart failure . Ten cases of reported previously brucella peritonitis are reviewed, 3 of which were ascitic fluid culture negative.

J Immunol, 2003 Aug 1, 171(3), 1393 - 400
Repetitive elements in mammalian telomeres suppress bacterial DNA-induced immune activation; Gursel I et al.; Bacterial DNA contains immunostimulatory CpG motifs that trigger an innate immune response capable of promoting host survival following infectious challenge . Yet CpG-driven immune activation may also have deleterious consequences, ranging from autoimmune disease to death . We find that repetitive elements present at high frequency in mammalian telomeres, but rare in bacteria, down-regulate CpG-induced immune activation . Suppressive activity correlates with the ability of telomeric TTAGGG repeats to form G-tetrads . Colocalization of CpG DNA with Toll-like receptor 9 in endosomal vesicles is disrupted by these repetitive elements, although cellular binding and uptake remain unchanged . These findings are the first to establish that specific host-derived molecules can down-regulate the innate immune response elicited by a TLR ligand.

Dig Liver Dis, 2003 Jul, 35(7), 503 - 6
Is spontaneous bacterial peritonitis an inducer of vasopressin analogue side-effects? A case report; Vaccaro F et al.; In recent years, the use of vasopressin analogues in the treatment of hepatorenal syndrome has become an effective therapeutic strategy leading to improved survival and often allowing the completion of liver transplantation . Terlipressin, in particular, has proven to be safe and effective . Due to the limited number of patients treated so far, it is, however, difficult to draw any definite conclusions on the optimal dosage and on the occurrence of side-effects in these patients . The case is reported of an ascitic cirrhotic patient who developed spontaneous bacterial peritonitis followed by a type-I hepatorenal syndrome . Treatment with terlipressin boluses (0.5 mg/4 h) associated with albumin infusion was then started . The course of the disease was monitored by clinical and laboratory means . After 10 boluses of terlipressin, rectorrhagia and severe ischaemic complications involving the skin of the abdomen, lower limbs, scrotus, and penis, occurred . These ischaemic complications improved after terlipressin withdrawal, while renal failure evolved leading to the patient's death . This case report shows that, in patients with type-I hepatorenal syndrome, the use of terlipressin, even at low dosages, may induce life-threatening ischaemic complications and, moreover, suggests that the recent occurrence of spontaneous bacterial peritonitis, even if properly treated, may significantly increase the risk of major ischaemic complications.

Int J STD AIDS, 2003 Jul, 14(7), 448 - 50
Does bacterial vaginosis alter the sensitivity of screening tests for Chlamydia trachomatis? An analysis of patient characteristics; Hussey J et al.; The aim of this study was to assess if patient characteristics could influence the sensitivity of enzyme immunoassay (EIA) testing used for chlamydia screening . Our cohort consisted of 56 patients who were known polymerase chain reaction-positive for chlamydia, but with variable EIA results . Characteristics analysed included those already known to influence the EIA (menstruation, pregnancy, difficult examination) and those suspected from clinical observation (including presence of symptoms or signs, coexistent gonorrhoea, duration from last sexual exposure) . An unexpected finding was that significantly more cases of bacterial vaginosis were found in those chlamydia EIA-negative compared to those with positive results . We postulate that an enzyme produced in bacterial vaginosis, proline aminopeptidase, may cause destruction of the chlamydial cell wall, therefore affecting the EIA adversely . Further research is needed to explore this hypothesis.

Int J Med Microbiol, 2003 Jun, 293(2-3), 123 - 31
Inhibition of allergic disorders by infection with bacteria or the exposure to bacterial products; Trujillo C et al.; The incidence, severity, and mortality rate of allergic diseases, such as asthma, atopic dermatitis and rhinitis is increasing in the developed nations of the world, despite the use of steroids and other drugs . The reason for this development is unknown, but has been speculated to be due to a steady decline in infectious diseases . This view is supported by recent epidemiological and experimental findings showing that bacterial infections have the capacity to inhibit the development of allergic disorders . In addition, the exposure to bacterial products such as lipopolysaccharide (LPS) or bacterial DNA is also associated with a decrease in allergen-specific Th2 responses . Although the immunological mechanisms responsible for these protective effects are ill defined, recent publications indicate that they are associated with the induction of Th1 or T regulatory responses . This review focuses on experimental and epidemiological studies addressing the question if bacterial infections or the exposure to bacterial products can inhibit the development of allergic responses.

J Mol Microbiol Biotechnol, 2003, 5(4), 225 - 9
Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb; Ponomarev VA et al.; PriB is a proteobacterial protein that is involved in the pre-primosomal step of DNA replication and, unexpectedly, is encoded with a ribosomal protein operon . Detailed sequence comparisons and analysis of operon organization show that PriB evolved from the single-stranded DNA-binding (Ssb) via gene duplication with subsequent rapid sequence diversification . Duplication of the SSB gene was accompanied by a genome rearrangement which resulted in one of the paralogs retaining the original position, whereas the other was relocated . The functional specialization of the resulting paralogs apparently proceeded in an unexpected fashion: the original Ssb function remained with the relocated paralog, whereas the one within the ribosomal protein operon acquired a new, specialized function in replication .

Syst Appl Microbiol, 2003 Jun, 26(2), 302 - 11
Characterisation of the bacterial community associated with early stages of Great Scallop (Pecten maximus), using denaturing gradient gel electrophoresis (DGGE); Sandaa RA et al.; Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA was used to characterise and compare bacterial communities associated with scallop larvae (Pecten maximus), in different production units in a shellfish hatchery . Water and larvae samples were collected from three different aquaculture systems; stagnant, flow-through and a flow- through system with seawater treated with ozone . Samples were also collected from different algal cultures, inlet tanks and water pipes leading to the different aquaculture systems . Clear differences were seen between the bacterial community associated with the larvae and in the water from the different aquaculture systems . However, there were high similarities in the community composition between different water samples and between larvae samples collected at different time periods, indicating a high stability in the bacterial communities . Fifty three percent of the sequences from these samples were similar to 16S rRNA gene sequences of members of the gamma-subclass of the Proteobacteria . The different algal cultures had different bacterial communities, however 73 percent of the sequences were similar to 16S rRNA gene sequences of members of the alpha-subclass of the Proteobacteria . Differences in the DGGE profiles were also seen between the samples taken from the inlet tanks and water pipes, indicating a change in the bacterial community composition as the water passed through the pipes . To our knowledge this is the first study investigating bacterial communities associated with Great Scallop larvae in different aquaculture systems including noncultured components.

Am J Obstet Gynecol, 2003 Jul, 189(1), 139 - 47
Bacterial vaginosis as a risk factor for preterm delivery: a meta-analysis; Leitich H et al.; OBJECTIVE: We performed a meta-analysis to evaluate bacterial vaginosis as a risk factor for preterm delivery . STUDY DESIGN: Selection criteria were (1) . the data appeared in original, published English-language reports of prospective studies or control groups of clinical trials that included women at <37 weeks of gestation with intact amniotic membranes, (2) . all the women had to have been screened for bacterial vaginosis that was diagnosed by either clinical criteria or criteria that were based on Gram stain findings, and (3) . the outcomes were preterm delivery, spontaneous abortion, maternal or neonatal infection, and perinatal death . RESULTS: Eighteen studies with results for 20,232 patients were included . Bacterial vaginosis increased the risk of preterm delivery >2-fold (odds ratio, 2.19; 95% CI, 1.54-3.12) . Higher risks were calculated for subgroups of studies that screened for bacterial vaginosis at <16 weeks of gestation (odds ratio, 7.55; 95% CI, 1.80-31.65) or at <20 weeks of gestation (odds ratio, 4.20; 95% CI, 2.11-8.39) . Bacterial vaginosis also significantly increased the risk of spontaneous abortion (odds ratio, 9.91; 95% CI, 1.99-49.34) and maternal infection (odds ratio, 2.53; 95% CI, 1.26-5.08) . No significant results were calculated for the outcome of neonatal infection or perinatal death . CONCLUSION: Bacterial vaginosis, early in pregnancy, is a strong risk factor for preterm delivery and spontaneous abortion.

Ann N Y Acad Sci, 2003 Jun, 990, 182 - 90
Genetic diversity of bacterial agents detected in ticks removed from asymptomatic patients in northeastern Italy; Sanogo YO et al.; A total of 360 ticks were removed from 353 asymptomatic subjects in Belluno Province, Italy and surrounding areas, from 1998 to 2001 . Ticks were identified as Ixodes ricinus (357), Ixodes hexagonus (1), Rhipicephalus sanguineus (1), and Ixodes ventalloi (1) . Tick DNA was investigated by PCR and subsequent sequencing of amplified products to identity associated bacterial agents . Primers targeting different genes of Rickettsia (gltA and OmpA), Borrelia (16S rDNA, rpoB), Francisella (16S rDNA), and all genera members of the Anaplasmataceae (16S rDNA), were used . DNA of bacterial agents was identified in 28 Ixodes ricinus specimens (7.8%) . Rickettsia helvetica was detected in 7 ticks . Rickettsia sp . IRS4 and Borrelia afzelii was detected in 4 ticks each . B . garinii and B . valaisiana were identified in one tick each . Anaplasma phagocytophilum, the agent of human granulocytic ehrlichiosis, was identified in 1 specimen of I . ricinus . A new Ehrlichia sp . ("Candidatus Ehrlichia walkerii", sp . nov.) was identified in 10 I . ricinus specimens.

Am J Cardiol, 2003 Jul 15, 92(2), 188 - 93
Elevated circulating levels of inflammatory cytokines and bacterial endotoxin in adults with congenital heart disease; Sharma R et al.; Chronic heart failure is a state of immune activation, and endotoxin is a potential trigger for cytokine production . Our aim was to study whether immune activation and endotoxemia occur in adults with congenital heart disease . We prospectively measured tumor necrosis factor (TNF)-alpha, soluble TNF receptors (sTNFR-1, sTNFR-2), interleukin-6, interleukin-10, endotoxin, and soluble CD14 levels in 52 consecutive adults with congenital heart disease (age 34 +/- 2 years {mean +/- SEM}) and 18 healthy controls (age 31 +/- 1 years) . A variety of congenital heart lesions were studied: single ventricle physiology (n = 15), systemic right ventricle (n = 7), tetralogy of Fallot (n = 20), and "other" congenital heart disease (n = 10) . Patients were subgrouped into asymptomatic (New York Heart Association {NYHA} class I, n = 11), mild (NYHA class II, n = 30), and moderate/severe (NYHA class III/IV, n = 11) categories . Patients had elevated TNF and interleukin-6 levels compared with controls (TNF 2.8 vs 2.1 pg/ml, p <0.05; interleukin-6 8.5 vs 5.7 pg/ml, p <0.001) . TNF levels were higher in patients with moderate/severe symptoms compared with patients who were asymptomatic or had mild symptoms (p <0.05) . Soluble TNFR-1 levels related directly to the degree of systemic ventricular impairment (p <0.05) . There were no significant differences in sTNFR-1, sTNFR-2, interleukin-10, or sCD14 levels between patients and controls . Endotoxin levels were greater in patients with congenital heart disease versus controls (0.40 vs 0.26 endotoxin units/ml, p <0.0001) . Thus, adults with congenital heart disease have elevated levels of inflammatory cytokines and bacterial endotoxin, which relate to functional status . Congenital heart disease in adults may be amenable to novel anti-inflammatory therapies in selected patients.

J Cell Biochem, 2003 Jul 1, 89(4), 848 - 61
Gene expression in human neutrophils during activation and priming by bacterial lipopolysaccharide; Tsukahara Y et al.; Circulating neutrophils play a key role both in the systemic inflammatory response and in complications of bacterial infection such as septic shock and septic multiple organ dysfunction syndrome . We have analyzed gene expression patterns in human neutrophils stimulated by E . coli lipopolysaccharide (LPS), with or without prior exposure to LPS, using differential display and oligonucleotide chip techniques . We identified 307 genes that were activated or repressed after treatment with LPS at 10 ng/ml and 385 genes after LPS at 100 ng/ml, compared with untreated neutrophils . The two sets included many transcription factors, cytokines, chemokines, interleukins, and surface antigens, as well as members of the toll-like receptor, Rel/NF-kappaB, and immune mediator gene families . Time course analysis showed that the early and late neutrophil responses to LPS share some common mechanisms, but many changes in gene expression are transient or late to develop . Neutrophils also showed a priming response to LPS, in which 97 genes significantly changed expression on re-exposure to lower dose LPS and were analyzed by unsupervised hierarchical clustering . These findings indicate that the neutrophil is a transcriptionally active cell responsive to environmental stimuli and capable of a complex series of both early and late changes in gene expression . Supplementary material for this article can be found on the Journal of Cellular Biochemistry website .

Gene Ther, 2003 Aug, 10(15), 1258 - 67
Bacterial virus phi29 pRNA as a hammerhead ribozyme escort to destroy hepatitis B virus; Hoeprich S et al.; The DNA-packaging pRNA of bacterial virus phi29, which forms dimers and then hexamers, contains two independent tightly self-folded domains . Circularly permuted pRNAs were constructed without impacting pRNA folding . Connecting the pRNA 5'/3' ends with variable sequences did not disturb its folding and function . These unique features, which help prevent two common problems - exonuclease degradation and misfolding in the cell, make pRNA an ideal vector to carry therapeutic RNAs . A pRNA-based vector was designed to carry hammerhead ribozymes that cleave the hepatitis B virus (HBV) polyA signal . The chimeric HBV-targeting ribozyme was connected to the pRNA 5'/3' ends as circularly permuted pRNA . Two cis-cleaving ribozymes were used to flank and process the chimeric ribozyme . The hammerhead ribozyme including its two arms for HBV targeting was able to fold correctly while escorted by the pRNA . The chimeric ribozyme cleaved the polyA signal of HBV mRNA in vitro almost completely . Cell culture studies showed that the chimeric ribozyme was able to enhance the inhibition of HBV replication when compared with the ribozyme not escorted by pRNA, as demonstrated by Northern blot and e-antigen assays . pRNA could also carry another hammerhead ribozyme to cleave other RNA substrate . These findings suggest that pRNA can be used as a vector for imparting stability to ribozymes, antisense, and other therapeutic RNA molecules in vivo.

Klin Med (Mosk), 2003, 81(5), 15 - 22
{Spontaneous bacterial peritonitis: a clinical variant of ascites-peritonitis: diagnosis and treatment}; Pavlov ChS; The lecture deals with diagnosis, prevention and treatment of spontaneous bacterial peritonitis (SBP) . The choice of treatment groups is described according to recommendations of the International Ascitis Club (IAC) . Algorithm of SBP examination for different SBP forms, the disease course characteristics and factors of prognosis are provided.

Bioinformatics, 2003, 19 Suppl 1, i34 - 43
Predicting bacterial transcription units using sequence and expression data; Bockhorst J et al.; MOTIVATION: A key aspect of elucidating gene regulation in bacterial genomes is identifying the basic units of transcription . We present a method, based on probabilistic language models, that we apply to predict operons, promoters and terminators in the genome of Escherichia coli K-12 . Our approach has two key properties: (i) it provides a coherent set of predictions for related regulatory elements of various types and (ii) it takes advantage of both DNA sequence and gene expression data, including expression measurements from inter-genic probes . RESULTS: Our experimental results show that we are able to predict operons and localize promoters and terminators with high accuracy . Moreover, our models that use both sequence and expression data are more accurate than those that use only one of these two data sources.

Rev Gastroenterol Peru, 2003 Apr-Jun, 23(2), 111 - 4
{Small intestine bacterial overgrowth in patients with chronic diarrhea and normal control subjects}; Torres Lam R et al.; The purpose of this study was to investigate the prevalence and meaning of small intestine bacterial overgrowth (SIBO) in patients with chronic diarrhea and normal control subjects.To that effect, a hydrogen breath test was performed using lactulose on 54 patients with chronic diarrhea and 16 normal control subjects . The presence of SIBO was defined as an increase in the hydrogen concentration, of > 20 parts per million above the basal value in any of the breath tests after the ingestion of lactulose . In addition, the logarithms of the areas under the hydrogen concentration curves were calculated.SIBO was present in two (12.5%) of the 16 normal control subjects . The frequency of SIBO was higher in patients with chronic diarrhea (24.1%) than in the normal control subjects; however, this difference was not statistically significant (p:0.27) . Finally, the mean + sd of the logarithms of the areas under the hydrogen concentration curves was significantly higher in patients with chronic diarrhea (6.485 + 0.751) than in normal control subjects (6.135 + 0.500) (p<0.05).The results obtained show that SIBO occurs in a certain percentage of the population, without presenting diarrhea . For SIBO to produce diarrhea, it probably requires some additional characteristics . However, it is worth it to suspect and investigate for SIBO in all chronic diarrhea cases.

Digestion, 2003, 67(3), 129 - 37
Patients with chronic renal failure have abnormal small intestinal motility and a high prevalence of small intestinal bacterial overgrowth; Strid H et al.; BACKGROUND/AIMS: Gastrointestinal (GI) symptoms are common among patients with chronic renal failure (CRF) . The pathogenesis of these symptoms is probably multifactorial . Our aims were to assess gastric and small intestinal motility and the prevalence of small intestinal bacterial overgrowth (SIBO) in order to clarify possible pathophysiological mechanisms behind these symptoms in CRF patients . METHODS: Twenty-two patients with CRF, 12 with GI symptoms and 10 without GI symptoms underwent antroduodenojejunal manometry . All patients with GI symptoms had diarrhea and half of them had abdominal pain, nausea and/or early satiety . Symptoms were unexplained by conventional investigations . Interdigestive motility was recorded for 5 h and postprandially for 1 h . Samples for culture from the small intestine were obtained through the manometry catheter . Results were compared with 34 healthy controls . RESULTS: On manometry, 11 CRF patients demonstrated neuropathic-like abnormalities, with no significant difference between the patients with (7/12) and without (4/10) GI symptoms . SIBO was seen in 8 CRF patients (36%), 3 with and 5 without GI symptoms (p = 0.15) . Six of eleven (55%) of the CRF patients with neuropathic-like abnormalities had SIBO, compared to 2/11 (18%) in those without abnormalities on conventional analysis (p = 0.07) . The propagation velocity of phase III was significantly faster in CRF patients with GI symptoms compared to CRF patients without symptoms and healthy controls (21.4 (16.4-54.7) vs . 8.1 (4.6-9.6) and 10.8 (7.2-21.6) cm/min, p = 0.007 and p = 0.019, respectively) . We found a higher proportion of retrograde pressure waves in late phase II in the proximal duodenum in patients with and without GI symptoms, than in healthy controls (29 (17-38) and 16 (14-42) vs . 8 (0-24)%, p < 0.0001 and p = 0.0005, respectively) . The number of long clusters during the fasting recording was higher in both patient groups than in controls (9 (5-21) and 11 (7-15) vs . 4 (2-9)/5, p = 0.046 and p = 0.002, respectively) . CONCLUSION: In the small intestine, abnormal motility and bacterial overgrowth are common in patients with chronic renal failure . These alterations correlate poorly with GI symptoms, but disturbed intestinal motility might explain diarrhea in some of these patients .

J Biol Chem, 2003 Sep 26, 278(39), 37160 - 8 Epub 2003 Jul 09.
Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase; Lacour S et al.; The alternative sigma factor sigmaS, mainly active in stationary phase of growth, recognizes in vitro a -10 promoter sequence almost identical to the one for the main sigma factor, sigma70, thus raising the problem of how specific promoter recognition by sigmaS-RNA polymerase (EsigmaS) is achieved in vivo . We investigated the promoter features involved in selective recognition by EsigmaS at the strictly sigmaS-dependent aidB promoter . We show that the presence of a C nucleotide as first residue of the aidB -10 sequence (-12C), instead of the T nucleotide canonical for sigma70-dependent promoters, is the major determinant for selective recognition by EsigmaS . The presence of the -12C does not allow formation of an open complex fully proficient in transcription initiation by Esigma70 . The role of -12C as specific determinant for promoter recognition by EsigmaS was confirmed by sequence analysis of known EsigmaS-dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes . We propose that EsigmaS, unlike Esigma70, can recognize both C and T as the first nucleotide in the -10 sequence . Additional promoter features such as the presence of a C nucleotide at position -13, contributing to open complex formation by EsigmaS, and a TG motif found at the unusual -16/-15 location, possibly contributing to initial binding to the promoter, also represent important factors for sigmaS-dependent transcription . We propose a new sequence, TG(N)0-2CCATA(c/a)T, as consensus -10 sequence for promoters exclusively recognized by EsigmaS.

Bioorg Med Chem Lett, 2003 Aug 4, 13(15), 2527 - 30
Synthesis and in vitro evaluation of novel small molecule inhibitors of bacterial arylamine N-acetyltransferases (NATs); Brooke EW et al.; The synthesis and inhibitory activity of a series of 5-substituted-(1,1-dioxo-2,3-dihydro-1H-1 lambda(6)-benzo{e}{1,2}thiazin-4-ylidene)-thiazolidine-2,4-dione derivatives as competitive inhibitors of recombinant bacterial arylamine-N-acetyltransferases (NATs) are described . The most potent NAT inhibitors are those that contain planar hydrophobic substituents on the sultam nitrogen.

Dev Cell, 2003 Jul, 5(1), 4 - 5
Cell walls, cell shape, and bacterial actin homologs; Egelman EH; The synthesis of the peptidoglycan layer, one of the key determinants of cell shape in B . subtilis, has been shown by Daniel and Errington to occur in a helical pattern . This pattern is generated by the actin homolog Mbl.

J Biol Chem, 2003 Sep 19, 278(38), 36148 - 56 Epub 2003 Jul 08.
Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes; Walter W et al.; We have previously shown that nucleosomes act as a strong barrier to yeast RNA polymerase II (Pol II) in vitro and that transcription through the nucleosome results in the loss of an H2A/H2B dimer . Here, we demonstrate that Escherichia coli RNA polymerase (RNAP), which never encounters chromatin in vivo, behaves similarly to Pol II in all aspects of transcription through the nucleosome in vitro . The nucleosome-specific pausing pattern of RNAP is comparable with that of Pol II . At physiological ionic strength or lower, the nucleosome blocks RNAP progression along the template, but this barrier can be relieved at higher ionic strength . Transcription through the nucleosome by RNAP results in the loss of an H2A/H2B dimer, and the histones that remain in the hexasome retain their original positions on the DNA . The results were similar for elongation complexes that were assembled from components (oligonucleotides and RNAP) and elongation complexes obtained by initiation from the promoter . The data suggest that eukaryotic Pol II and E . coli RNAP utilize very similar mechanisms for transcription through the nucleosome . Thus, bacterial RNAP can be used as a suitable model system to study general aspects of chromatin transcription by Pol II . Furthermore, the data argue that the general elongation properties of polymerases may determine the mechanism used for transcription through the nucleosome.

J Surg Res, 2003 May 15, 111(2), 209 - 14
Bacterial translocation after cirrhotic liver resection: a clinical investigation of 181 patients; Yeh DC et al.; BACKGROUND: Cirrhotic patients are usually associated with a high susceptibility to infection . Although bacterial translocation from gut mucosa to mesenteric lymph node (MLN) and systemic circulation is a well-known phenomenon after hepatectomy, its role in cirrhotic patients remains unclear . MATERIALS AND METHODS: MLN was harvested for bacterial culture before and after liver resection in 181 cirrhotic patients . The characteristics and postoperative courses of patients with positive and negative bacterial culture for MLN after hepatectomy were compared . Postoperative systemic antibiotics were administered if infectious complications occurred . RESULTS: No bacteria were cultured in MLN before hepatectomy . Bacterial translocation (BT) to MLN after hepatectomy occurred in 36 patients (BT group) . After multivariate analysis, intraoperative blood transfusion was the only independent factor that influenced bacterial translocation rates after cirrhotic liver resection . BT group patients also had higher infectious and overall complication rates, with a longer postoperative hospital stay . Among the cultured bacteriae from infected sites in BT group patients with infectious complications, only 2 patients (12.5%) had totally different bacterial species to those cultured from MLNs . CONCLUSIONS: Bacterial translocation more often occurred after liver resection in cirrhotic patients who received intraoperative blood transfusion . Such patients had higher postoperative infectious and overall complication rates . Thus, avoidance of intraoperative blood transfusion is mandatory for cirrhotic liver resection.

J Mol Biol, 2003 Jul 18, 330(4), 641 - 9
Folding of DsbB in mixed micelles: a kinetic analysis of the stability of a bacterial membrane protein; Otzen DE; Measuring the stability of integrated membrane proteins under equilibrium conditions is hampered by the nature of the proteins' amphiphilic environment . While intrinsic fluorescence is a useful probe for structural changes in water-soluble proteins, the fluorescence of membrane proteins is sensitive to changes in lipid and detergent composition . As an attempt to overcome this problem, I present a kinetic analysis of the folding of a membrane protein, disulfide bond reducing protein B (DsbB), in a mixed micelle system consisting of varying molar ratios of sodium dodecyl sulfate (SDS) and dodecyl maltoside (DM) . This analysis incorporates both folding and unfolding rates, making it possible to determine both the stability of the native state and the process by which the protein folds . Refolding and unfolding occur on the second to millisecond timescale and involve only one relaxation phase, when monitored by conventional stopped-flow . The kinetic data indicate that denaturation occurs around 0.3 mole fraction of SDS, in agreement with CD analysis and acrylamide quenching data . The rate constants have been fit to a three-state folding scheme involving the SDS-denatured state, the native state and an unfolding intermediate that accumulates only under unfolding conditions at high mole fractions of SDS . The stability of DsbB is around 4.4 kcal/mol in DM, and this is halved upon reduction of the two periplasmic disulfide bonds, and is sensitive to mutagenesis . With the caveat that kinetic data are always open to alternative interpretations, time-resolved studies in mixed micelles provide a useful approach to measure membrane protein stability over a wide range of concentrations of SDS and DM, as well as a framework for the future characterization of the DsbB folding mechanism.

Curr Opin Biotechnol, 2003 Jun, 14(3), 319 - 25
Monitoring bacterial pathogens in the environment: advantages of a multilayered approach; Pickup RW et al.; The application of advanced and highly sensitive molecular techniques to the detection of specific bacteria in the freshwater environment is limited, in the first instance, by sampling strategy and sample quality . Further combinations of molecular methods and techniques from apparently unrelated disciplines will ultimately shape the monitoring techniques of the future.

Arch Gerontol Geriatr, 2003 Jan-Feb, 36(1), 49 - 55
Bacterial endocarditis of oral etiology in an elderly population; Tomas Carmona I et al.; The aim of this study was to analyze the prevalence and characteristics of bacterial endocarditis (BE) of oral origin in a group of elderly people . A retrospective study of 115 BE clinical records was performed, focusing on the demographic and predisposing features, as well as on the analytical and clinical variables . Twenty-two of the 115 cases were excluded as they were detected in intravenous drug users . Of the remaining 93 cases, 54.8% were diagnosed in patients older than 60 years of age (group A) and 45.2% in patients younger than 60 years (group B) . There were 16 cases (17.2%) of oral origin; 4 BE cases mainly associated with tooth extractions were found in group A and 12 BE (most of them related with odontogenic abscesses) in group B . Within group A, 1 patient (25%) had not an underlying cardiac condition versus 5 cases (41.6%) in group B . Even though the prevalence of BE of oral origin in patients older than 60 is low, the high frequency of cardiopathies, poor oral health and high number of dental procedures shown by the old population makes them a risk group for BE of oral origin.

Can J Gastroenterol, 2003 Jun, 17 Suppl B, 13B - 17B
Role of bacterial overgrowth in the stomach as an additional risk factor for gastritis; Naylor G et al.; Gastric bacteria can either be ingested or ascend from the distal bowel; however, their survival is usually limited by gastric acidity and motility . A reduction in gastric acid can result in bacterial overgrowth in the stomach and proximal small bowel, and the number of organisms rises as the intragastric pH rises . The increased risk of noncardia gastric cancer seen in patients with hypochlorhydria may be explained by an excess of nitrites and N-nitroso compounds (NOCs) . These compounds are found in the diet of populations with a high gastric cancer risk, but can also be produced by the organisms that exist in the hypochlorhydria stomach . It has long been hypothesized that nitrites and NOCs act as one of the triggers in the atrophy-metaplasia-dysplasia-carcinoma path . However, although indirect data have linked the premalignant changes of metaplasia and dysplasia to NOCs, direct measurement of gastric nitrites and NOCs has not confirmed such a link . The role of Helicobacter pylori in bacterial overgrowth is mainly as a cause of hypochlorhydria resulting from atrophic gastritis, leading to a reduction in the parietal cell mass . Acid-suppressing drugs can result in bacterial overgrowth and increased nitrites and NOCs, although there is no current evidence for an increased risk of gastric cancer in patients taking them . One explanation is that the stomach appears to be colonized by different organisms than those in patients with hypochlorhydria for other reasons . There is some evidence that bacterial overgrowth per se can cause gastric inflammation in mice; however, although in humans the degree of gastric inflammation is greater when overgrowth is more prominent this may simply reflect the greater degree of hypochlorhydria in patients with a more severe H pylori-induced inflammation.

J Biomol Screen, 2003 Apr, 8(2), 157 - 63
Development and use of a high-throughput bacterial DNA gyrase assay to identify mammalian topoisomerase II inhibitors with whole-cell anticancer activity; Roychoudhury S et al.; A high-throughput screen (HTS) was developed and used to identify inhibitors of bacterial DNA gyrase . Among the validated hits were 53 compounds that also inhibited mammalian topoisomerase II with IC(50) values of <12.5 micro g/mL for 51 of them . Using computational methods, these compounds were subjected to cluster analysis to categorize them according to their chemical and structural properties . Nine compounds from different clusters were tested for their whole-cell inhibitory activity against 3 cancer cell lines-NCI-H460 (lung), MCF7 (breast), and SF-268 (CNS)-at a concentration of 100 micro M . Five compounds inhibited cell growth by >50% for all 3 cell lines tested . These compounds were tested further against a panel of 53 to 57 cell lines representing leukemia, melanoma, colon, CNS, ovarian, renal, prostate, breast, and non-small cell lung cancers . In this assay, PGE-7143417 was found to be the most potent compound, which inhibited the growth of all the cell lines by 50% at a concentration range of 0.31 to 2.58 micro M, with an average of 1.21 micro M . An additional 17 compounds were also tested separately against a panel of 10 cell lines representing melanoma, colon, lung, mammary, ovarian, prostate, and renal cancers . In this assay, 4 compounds-PGE-3782569, PGE-7411516, PGE-2908955, and PGE-3521917-were found to have activity with concentrations for 50% cell growth inhibition in the 0.59 to 3.33, 22.5 to 59.1, 7.1 to >100, and 24.7 to >100 micro M range.

Biosci Biotechnol Biochem, 2003 Jun, 67(6), 1405 - 9
A T42M substitution in bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) generates enzymes with increased resistance to glyphosate; He M et al.; Mutants of class I enolpyruvylshikimate 3-phosphate synthase (EPSPS) with resistance to glyphosate were produced in a previous study using the staggered extension process with aroA genes from S . typhimurium and E . coli . Two of these mutants shared a common amino acid substitution, T42M, near the hinge region between the large globular domains of EPSPS . Using site-directed mutagenisis, we produced the T42M mutants without the other amino acid changes of the original mutants . The T42M substitution alone produced enzymes with a 9- to 25-fold decreased K(m){PEP} and a 21- to 26-fold increased K(i){glyphosate} compared to the wild-type enzymes . These results provide more testimony for the powerful approach for protein engineering by the combination of directed evolution and rational design.

J Clin Microbiol, 2003 Jul, 41(7), 3336 - 8
Comparison of genotyping Helicobacter pylori directly from biopsy specimens and genotyping from bacterial cultures; Park CY et al.; PCR for vacA and cagA genotypes of Helicobacter pylori using DNA isolated from infected gastric biopsy specimens was approximately equal to genotyping using bacterial DNA from cultures . Inconsistent results were associated with low H . pylori density in biopsies . A higher proportion of mixed infection was found when biopsies were used.

Anal Biochem, 2003 Aug 1, 319(1), 171 - 6
A continuous coupled enzyme assay for bacterial malonyl-CoA:acyl carrier protein transacylase (FabD); Molnos J et al.; Bacterial malonyl-CoA:acyl carrier protein transacylase catalyzes the transfer of a malonyl moiety from malonyl-CoA to the free thiol group of the phosphopantetheine arm of acyl carrier protein . Malonyl-ACP, the product of this enzymatic reaction, is the key building block for de novo fatty acid biosynthesis . Here, we describe a continuous enzyme assay based on the coupling of the malonyl-CoA:acyl carrier protein transacylase reaction to alpha-ketoglutarate dehydrogenase (KDH) . KDH-dependent consumption of the coenzyme A generated by malonyl-CoA:acyl carrier protein transacylase is accompanied by a reduction of nicotinamide adenine dinucleotide, oxidized (NAD(+)) to nicotinamide adenine dinucleotide, reduced . The rate of NAD(+) reduction is continuously monitored as a change in fluorescence using a microtiter plate reader . We show that this coupled enzyme assay is amenable to routine chemical compound screening.

Mol Cell Biochem, 2003 May, 247(1-2), 83 - 94
Inhibition of oxygen radical formation by methylene blue, aspirin, or alpha-lipoic acid, prevents bacterial-lipopolysaccharide-induced fever; Riedel W et al.; Phagocytic cells contain NADPH oxidase that they use for host defense by catalyzing the production of superoxide . Bacterial lipopolysaccharide (LPS) has been found to stimulate NADPH oxidase in mobile and sessile macrophages and microglia . It also evokes fever in homeothermic animals and men, a reaction mediated by central nervous system (CNS) activities . The purpose of the present study was to determine whether reactive oxygen species are involved in LPS-induced fever . In rabbits we found that plasma hydroperoxide levels increased and catalase activity decreased 15 min after LPS injection and that fever started with a similar latency, while plasma levels of tumor necrosis factor-alpha (TNFalpha) increased 30 min after the injection . Treating rabbits with methylene blue or aspirin did not affect TNFalpha secretion but prevented the LPS-induced rise of hydroperoxides and the inactivation of catalase, abolishing fever . Incubation of human blood with nitroblue tetrazolium and LPS increased the number of formazan-positive neutrophils from 10 +/- 5 to 52 +/- 9% . Adding LPS to blood preincubated with either methylene blue, alpha-lipoic acid, or aspirin respectively decreased the number of formazan-positive neutrophils to 0.9 +/- 0.8, 0.8 +/- 0.9, or 2.0 +/- 0.9%, disclosing the antioxidant capacity of these drugs . Systemic application of 80 mg/kg alpha-lipoic acid elicited heat-loss reactions within 15 min and decreased core temperature by 2.2 +/- 0.3 degrees C within 2 h . Alpha-lipoic acid applied 45 min after LPS induced antipyresis within 15 min, and this antipyresis was associated with a decrease of elevated hydroperoxide levels and restoration of catalase activity . Our results show that fever is prevented when the production of reactive oxygen species is blocked and that an elevated body temperature returns to normal when oxygen radical production decreases . Estimation of plasma dihydrolipoic acid (DHLA) levels following injection of 80 mg/kg alpha-lipoic acid in afebrile and febrile rabbits revealed that this acid is converted into DHLA, which in afebrile rabbits increased the plasma DHLA concentration from 2.22 +/- 0.26 microg/ml to peak values of 8.60 +/- 2.28 microg/ml DHLA within 30 min and which in febrile rabbits increased it from 0.84 +/- 0.22 microg/ml to peak values of 3.90 +/- 0.94 microg/ml within 15 min . Methylene blue, aspirin, and alpha-lipoic acid, which all cross the blood-brain barrier, seem to act not only on peripheral tissues but also on the CNS . Brain structures that have been shown to sense oxidative stress are vicinal thiol groups attached to the NMDA subtype of glutamate receptor . Their reduction by thiol-reducing drugs like dithiothreitol or DHLA has been found to increase glutamate-mediated neuronal excitability, while the opposite effect has been observed after their oxidation . Because we found that systemic application of alpha-lipoic acid in the afebrile state elicits hypothermia and in the febrile state is antipyretic, we think this type of NMDA receptor is involved in thermoregulation and that oxidation of its thiol groups induces fever . It appears that temperature homeostasis can be maintained only if the redox homeostasis of the brain is guaranteed.

J Biol Chem, 2003 Sep 19, 278(38), 36522 - 30 Epub 2003 Jul 01.
How bacterial ribosomal protein L20 assembles with 23 S ribosomal RNA and its own messenger RNA; Raibaud S et al.; In bacteria, the expression of ribosomal proteins is often feedback-regulated at the translational level by the binding of the protein to its own mRNA . This is the case for L20, which binds to two distinct sites of its mRNA that both resemble its binding site on 23 S rRNA . In the present work, we report an NMR analysis of the interaction between the C-terminal domain of L20 (L20C) and both its rRNA- and mRNA-binding sites . Changes in the NMR chemical shifts of the L20C backbone nuclei were used to show that the same set of residues are modified upon addition of either the rRNA or the mRNA fragments, suggesting a mimicry at the atomic level . In addition, small angle x-ray scattering experiments, performed with the rRNA fragment, demonstrated the formation of a complex made of two RNAs and two L20C molecules . A low resolution model of this complex was then calculated using (i) the rRNA/L20C structure in the 50 S context and (ii) NMR and small angle x-ray scattering results . The formation of this complex is interesting in the context of gene regulation because it suggests that translational repression could be performed by a complex of two proteins, each interacting with the two distinct L20-binding sites within the operator.

Appl Environ Microbiol, 2003 Jul, 69(7), 3798 - 808
Determination of in situ bacterial growth rates in aquifers and aquifer sediments; Mailloux BJ et al.; Laboratory and field-scale studies with stained cells were performed to monitor cell growth in groundwater systems . During cell division, the fluorescence intensity of the protein stain 5-(and 6-)-carboxyfluorescein diacetate succinimidyl ester (CFDA/SE) for each cell is halved, and the intensity can be tracked with a flow cytometer . Two strains of bacteria, Comamonas sp . strain DA001 and Acidovorax sp . strain OY-107, both isolated from a shallow aquifer, were utilized in this study . The change in the average generation or the average fluorescence intensity of the CFDA/SE-stained cells could be used to obtain estimates of doubling times . In microcosm experiments, the CFDA/SE-based doubling times were similar to the values calculated by total cell counting and were independent of cell concentration . Intact and repacked sediment core experiments with the same bacteria indicated that changes in groundwater chemistry were just as important as growth rates in determining planktonic cell concentrations . The growth rates within the sediment cores were similar to those calculated in microcosm experiments, and preferential transport of the daughter cells was not observed . The experiments indicated that the growth rates could be determined in systems with cell losses due to other phenomena, such as attachment to sediment or predation . Application of this growth rate estimation method to data from a field-scale bacterial transport experiment indicated that the doubling time was approximately 15 days, which is the first known direct determination of an in situ growth rate for bacteria in an aquiferPublication Types:

Evaluation Studies

What Is Biofilm?, What Is Botulism?, What Is Bioreactor?, What Is Fermentation?, What Is Water Purification?, o, Microbiology, i, Microorganism, a, Bacteriology, s, Microorganisms, r, Microbe, c, Pseudomonas aeruginosa, e, Enterococci, s, Phage, r, Antibiotics, o, Growth media, e, Thermophiles, a, Salmonella typhimurium, e, Cephalosporin, a, Staphylococcus, s, Streptococcal, e, Streptococci, i, Bactericidal, o, Pseudomonas aeruginosa, n, Escherichia coli, o, Enterobacteriacea, r, Microorganism, o, Bacillus subtilis, e, Cryptococci, e, Lactobacillus, n, Streptococci, e, Streptococci

Scientific Publications - Work Done by Microbiology Reader Bioscreen C
Agricultural Microbiology Anaerobic Microbiology Antimicrobial Susceptibility Artificial Atmosphere Bioassay of Antibiotics Biofilm Microbiology Bioreactor Technology Biotechnology Cell Biology Clinical Microbiology Environmental Microbiology Experiments with Yeast	Fermentation Food Microbiology Functional Genomics Gene Technology Growth Media Development Growth Rate and Lag Time Industrial Microbiology Medical/Pharmaceutical Field Microbiological Assay Microbiological Research Microbiology of Cosmetics go to a specific theme...	Military Microbiology Molecular Microbiology Mutagenicity and Genotoxicity Oral Microbiology Patents Postantibiotic Studies Soil Microbiology Spore Microbiology Veterinary Microbiology Waste/Wastewater Treatment Water Microbiology Wine Microbiology

� 2005 Transgalactic Ltd (manufacturer of Bioscreen C software) | Privacy Statement | P.O. Box 1393, 00101 Helsinki, Finland, phone: +358 9 85172920, fax: +358 9 8749481, e-mail: microbiology@bionewsonline.com

Last modified: May 25, 2005