Microbial

Arch AIDS Res, 1992, 6(3), 177 - 82
Bacterial vaginosis associated with G vaginallis / Mobiluncus sp: ultrastructural parameters; Villegas-castrejon H et al.; PIP: Physicians at the National Institute of Perinatology in Mexico City, Mexico used a Carl-Zeiss EM 10C electron microscope to examine genital secretion samples from 10 pregnant women (15-38 weeks' gestation) who had been diagnosed with Mobiluncus species and Gardnerella vaginalis infections to illustrate the form and structure of bacteria responsible for bacterial vaginosis . They were concerned that these bacteria induce preterm labor and premature rupture of membranes (PL/PROM) . These bacteria have been present in the genital tract of 30% of pregnant women with a thick whitish discharge who have attended the Institute's prenatal outpatient clinic . Physicians noted on the microscope slides that bacteria surrounded vaginal squamous epithelial cells (clue cells) . Numerous gardnerella-like bacteria surrounded elongated squamous epithelial cells with many plasma projections . An extensive area of lysis existed around the bacteria in the cytoplasm of many squamous epithelial cells with intact membrane and nonexistent microfilaments . This finding indicated that the bacteria invade and destroy the cells . Plasma membrane projections almost completely surrounded the gardnerella-like bacteria in certain areas . Since this study strengthened the theory that G . vaginalis enters the vaginal squamous epithelial cells, researchers should conduct more studies to determine its role in PL/PROM .

Biofizika, 2002 Jul-Aug, 47(4), 595 - 9
{Similarities in periodical structures in the position of nucleotides in regions of initiation of replication of bacterial genomes}; Kravatskaia GI et al.; The regions of initiation of replication of some bacterial genomes were studied by the method of Fourier matrix analysis . A generalized spectral portrait of the primary structures of E . coli-like regions of initiation of replication in bacteria was obtained, which reflects the features of their structural and functional organization . It contains well-pronounced peaks that correspond to the periods T = 2, 11, 17, 27, 86-105 of nucleotides . The peaks corresponding to T = 9, 13, 14, 18, 19, 33-35, 45-47, 74-85, 106-110 are less pronounced . The uniqueness of the Fourier spectrum corresponding to the region of initiation of replication of E . coli oriC was considered by the example of the complete genome of E . coli . Some regions of the E . coli genome were identified that differ from oriC in the primary structure but have Fourier spectra resembling the spectrum of oriC . A number of these regions are alternative points of initiation of replication in sdrA(rnh) mutants of E . coli, the others are localized in yet unidentified regions of the E . coli genome but are capable, in our opinion, to participate in the initiation of replication . Thus, from the similarity of spectral portraits of different regions of the genome, it was possible to reveal several regions that have similar functions, i.e., are involved in initiation of replication.

Biol Reprod, 2002 Oct, 67(4), 1337 - 41
Intrauterine bacterial inoculation induces labor in the mouse by mechanisms other than progesterone withdrawal; Hirsch E et al.; We tested the hypothesis that progesterone (P(4)) withdrawal is the primary mechanism by which intrauterine bacteria induce preterm labor in mice . CD-1 mice on Day 14.5 of a 19- to 20-day gestation were subjected to one of four treatments: 1) intrauterine injection of sterile medium, 2) intrauterine injection of 10(6) heat-killed Escherichia coli bacteria, 3) intrauterine injection of 10(9) heat-killed E . coli, or 4) ovariectomy . Mice were then killed at four time points from 0.75 to 11 h after surgery for serum collection . Separately, animals were pretreated either with s.c . P(4) or with vehicle 2 h before ovariectomy or high-dose bacterial inoculation . Ovariectomy led to a rapid fall in serum P(4) levels of 60% by 1 h and 81% by 8 h compared with levels in controls (P < 0.001) . In contrast, intrauterine inoculation with 10(9) bacteria led to a more modest decline in P(4) of only 28% by 8 h (P = 0.24, which was no different from that of 10(6) bacteria, an inoculum below the threshold for preterm delivery) . Despite significantly lower levels of P(4) in the ovariectomy group, time to delivery was significantly shorter with 10(9) bacteria intrauterine (24 +/- 5.6 h vs . 19 +/- 3.6 h, P = 0.03) . Pretreatment with 1.5 mg P(4) per mouse prolonged the interval to delivery following both ovariectomy and high-dose bacteria, in association with pharmacologically elevated serum P(4) levels . In contrast, physiologic P(4) supplementation (0.375 mg/mouse) prolonged gestation only in the ovariectomy group . We conclude that withdrawal of endogenous P(4) is not the primary cause of labor following intrauterine bacterial inoculation in mice.

Circulation, 2002 Sep 24, 106(13), 1659 - 63
Serum immunoglobulin G antibodies to chlamydial heat shock protein 60 but not to human and bacterial homologs are associated with coronary artery disease; Mahdi OS et al.; BACKGROUND: Evidence for an association between Chlamydia pneumoniae infection and coronary artery disease (CAD) has been reported by numerous studies, cross-reactive heat shock protein (Hsp) antibody responses have been causally linked to CAD, and the severity of chlamydial disease pathogenesis correlates with Hsp serology . Our aim was to determine if chlamydial Hsp (cHsp) antibody responses are predictive of CAD . METHODS AND RESULTS: Patients were recruited in a case-control study: 250 cases had angiographically significant CAD (stenosis > or =70%), and 250 controls had normal coronary arteries (stenosis <10%) . Serum immunoglobulin G reactivity to Hsp10 and Hsp60 antigens (chlamydial, Escherichia coli, and human), and C pneumoniae whole organisms were measured by ELISA . Univariate analysis confirmed that classical CAD risk factors were predictors of CAD . Univariate analysis showed that cHsp60 (P= 0.001, OR 3.9), cHsp10 (P=0.045, OR 3.8), E coli Hsp60 (P=0.04, OR 1.5) and C pneumoniae (P=0.03, OR 1.8) ELISA optical density (OD) values were significantly different between cases and controls . Multivariate analysis found that only upper-quintile cHsp60 seroreactivity remained a significant predictor of CAD after controlling for classical CAD risk factors and seroreactivity to the other antigens (cHsp60 OD, P=0.005, OR 3.9 per OD unit; cHsp60 quintile, 5 versus 1 to 4; P=0.01, OR 2.1) . CONCLUSIONS: The presence of elevated anti-cHsp60 immunoglobulin G antibodies, but not anti-human or anti-E coli homologs, was independently associated with CAD . This finding argues against previous suggestions that cross-reactive or autoimmune Hsp60 responses may contribute to disease progression . High anti-cHsp60 antibody response appears to identify the subset of patients with chlamydial infection and significant CAD.

Neurosci Lett, 2002 Sep 27, 330(3), 270 - 4
The bacterial chaperonin GroEL requires GroES to reduce aggregation and cell death in a COS-7 cell model of Huntington's disease; Carmichael J et al.; Huntington's disease (HD) is caused by expansions of more than 35 CAG repeats in the HD gene . These repeats are translated into a long polyglutamine tract that confers a deleterious gain-of-function on the mutant protein . Intraneuronal inclusions comprising mutant huntingtin are found in HD patient brains . Here we show that the bacterial chaperonin GroEL can reduce aggregation of mutant huntingtin in COS-7 cells and requires GroES for efficient activity, analogous to what has been described in bacteria . The reduction in aggregation of mutant huntingtin by GroEL/GroES was associated with protection against polyglutamine-induced cell death .

Eur J Obstet Gynecol Reprod Biol, 2002 Oct 10, 105(1), 64 - 6
Local treatment of bacterial vaginosis with a bioadhesive metronidazole tablet; Voorspoels J et al.; OBJECTIVES: Oral metronidazole is still the drug of choice in the treatment of bacterial vaginosis . Yet, side effects have been reported, and dosage as well as duration of therapy are still controversial . This study presents a possible alternative treatment using a single dose of metronidazole administered in a vaginal bioadhesive tablet . STUDY DESIGN: Double blind, randomised, placebo-controlled trial . SUBJECTS: The 116 patients were allocated to placebo; metronidazole 100; 250; 500mg in a 1:1:1:1 ratio . RESULTS: A cure rate of 64% was obtained with a single 100mg dose of metronidazole formulated in a bioadhesive vaginal tablet compared to a cure rate of 29% in the placebo group . The cure rates with the higher doses were similar 61.5% for 250mg dose and 68% for the 500mg dose . No side effects were reported . CONCLUSIONS: Treatment of bacterial vaginosis with a single application of 100mg metronidazole in a bioadhesive vaginal tablet was found to be a valid alternative . Further research in relation to tablet shaping and optimal dose finding might increase the cure rate.

Mikrobiologiia, 2002 Jul-Aug, 71(4), 437 - 44
{Aspects of cellular biology of the bacterial stationary phase: programmed cell death and regulation by guanosine tetraphosphate}; Golovlev EL; The paper discusses (1) programmed cell death, the phenomenon typical of the stationary phase of bacteria occurring under unfavorable conditions, (2) its pleiotropic regulation by guanosine tetraphosphate, and (3) the conception of "addiction module," a specific genetic system responsible for the cell choice between survival and death under unfavorable conditions . The shortcomings of the proposed interpretation of the problem at hand are considered and the necessity of their further investigation is substantiated.

J Immunol, 2002 Oct 1, 169(7), 3934 - 9
IL-1 receptor-associated kinase and low molecular weight GTPase RhoA signal molecules are required for bacterial lipopolysaccharide-induced cytokine gene transcription; Chen LY et al.; Proinflammatory cytokines such as IL-1, TNF, IL-6, and IL-8 are produced by leukocytes in response to bacteria or bacterial components . A great deal has been learned during the past few years about the synthesis and release of proinflammatory cytokines by leukocytes; however, relatively little is known about the intracellular events that lead to leukocyte proinflammatory cytokine gene transcription . This study examined the signal transduction pathway of IL-8 induction by bacterial LPS . Stimulation of monocytes with LPS rapidly activated RhoA, and pretreatment of monocytes with a RhoA inhibitor, C3 transferase exoenzyme, effectively blocked LPS-induced IL-8 gene expression . Overexpression of dominant negative RhoA (T19N) or IL-1R-associated kinase completely inhibited LPS-stimulated reporter gene expression . Induction of IL-8 was also inhibited by dominant negative IkappaB kinase and myeloid differentiation protein (MyD88) . These results indicate that RhoA and IL-1R-associated kinase are novel signal transducers for LPS-induced Toll-like receptor 4-mediated proinflammatory cytokine synthesis in human monocytes.

Avian Dis, 2002 Jul-Sep, 46(3), 605 - 12
Studies on the bacterial etiology of airsacculitis of broilers in northern and middle Jordan with special reference to Escherichia coli, Ornithobacterium rhinotracheale, and Bordetella avium; El-Sukhon SN et al.; A total of 100 poultry farms in northern and middle areas of Jordan were sampled to investigate the bacteria associated with airsacculitis in broiler chickens . Of 170 bacterial isolates, 88.2% were identified as Escherichia coli, 8.8% as Ornithobacterium rhinotracheale, and 3% as Bordetella avium . Fourteen serotypes of E . coli were identified among 66 typeable isolates and the remainder were untypeable . The most prevalent serotypes were O1, O8, and O78 . The main serotype of O . rhinotracheale was serotype A . Experimental inoculation of O . rhinotracheale via intravenous, intratracheal, and intra-air sac routes resulted in growth retardation, thickening in the air sacs, arthritis, and liver necrosis . Reisolation of O . rhinotracheale from the air sacs, liver, trachea, heart, and spleen at day 7 postinoculation confirmed its role . In vitro susceptibility testing revealed that E . coli isolates were sensitive to gentamicin and colistin, O . rhinotracheale to tetracyline, and B . avium to most of the nine antibiotics examined.

Plant Cell, 1995 Jan, 7(1), 29 - 42
Coordinated Activation of Programmed Cell Death and Defense Mechanisms in Transgenic Tobacco Plants Expressing a Bacterial Proton Pump; Mittler R et al.; In plants, programmed cell death is thought to be activated during the hypersensitive response to certain avirulent pathogens and in the course of several differentiation processes . We describe a transgenic model system that mimics the activation of programmed cell death in higher plants . In this system, expression of a bacterial proton pump in transgenic tobacco plants activates a cell death pathway that may be similar to that triggered by recognition of an incompatible pathogen . Thus, spontaneous lesions that resemble hypersensitive response lesions are formed, multiple defense mechanisms are apparently activated, and systemic resistance is induced in the absence of a pathogen . Interestingly, mutation of a single amino acid in the putative channel of this proton pump renders it inactive with respect to lesion formation and induction of resistance to pathogen challenge . This transgenic model system may provide insights into the mechanisms involved in mediating cell death in higher plants . In addition, it may also be used as a general agronomic tool to enhance disease protection.

Genetics, 2002 Sep, 162(1), 129 - 34
A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus; Srinivasan J et al.; To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems . Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species . In the nematode Pristionchus pacificus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans . However, substantial changes in gene function between P . pacificus and C . elegans limit the use of candidate gene approaches in studying P . pacificus mutations . To facilitate map-based cloning of mutations in P . pacificus, we constructed a BAC-based genetic linkage map . A BAC library of 13,440 clones was generated and completely end sequenced . By comparing BAC end and EST sequences between the "wild-type" strain P . pacificus var . California and the polymorphic strain P . pacificus var . Washington, 133 single-stranded conformational polymorphisms were identified . These markers were tested on a meiotic mapping panel of 46 randomly picked F(2) animals after a cross of the two strains, providing the first genetic linkage map of P . pacificus . A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene.

Biotechnol Appl Biochem, 2002 Oct, 36(Pt 2), 85 - 8
Guide DNA technique in bacterial ribonuclease P reaction for effective processing of tRNA precursor; Tanaka T et al.; Previously, we found that a small (approx . 20-mer) DNA hybridizing to the 5'-leader region of a tRNA precursor enhances the cleavage efficiency in bacterial ribonuclease P reaction . We named this technique the 'guide DNA technique' . Detailed analyses showed that the length of the guide DNA, concentration of the guide DNA and the hybridizing position affected the cleavage efficiency: for an effective cleavage reaction, guide DNA should be designed to hybridize to the region on the cleavage site, should be 20 bases or more in length and should be of high concentration . The presence of a 5'-flanking region in the DNA did not affect the cleavage reaction . The guide DNA technique is a useful tool for effective preparation of mature tRNA molecules in vitro.

Mol Biol Rep, 2002, 29(1-2), 21 - 6
Flux control of the bacterial phosphoenolpyruvate:glucose phosphotransferase system and the effect of diffusion; Francke C et al.; We analyzed the role of diffusion and cell size on the flux control properties of the glucose-PTS of Escherichia coli, in silicon cells under various metabolic conditions . To our surprise, the influence of the concentration of phosphoryl-donor PEP on the distribution of control was small . We found for cells of bacterial size that PTS-flux control was mainly located in processes taking place in the membrane and that diffusion hardly controlled the flux (< 2.8 %) . Enlargement of the cells shifted the control from membrane to cytoplasm and from process rates to diffusion rates, the latter now having a total control of about 38 % . In the presence of glucose, nearly all diffusion flux control resided in the component that links the cytoplasmic processes to those in the membrane.

Protein Sci, 2002 Oct, 11(10), 2512 - 21
Bacterial expression and membrane targeting of the rat complement regulator Crry: a new model anticomplement therapeutic; Fraser DA et al.; Inappropriate or unregulated activation of complement can contribute to pathology in inflammatory diseases . Previous studies have shown that soluble recombinant regulators of complement are effective in animal models and some human diseases . However, limitations include cost, rapid clearance, and unwanted systemic effects . To avoid some of these problems, bacterial expression of regulators has been optimized and methods for the addition of a membrane-targeting moiety to the complement regulator developed . When administered directly to sites of inflammation, membrane-targeted human regulators are retained and inhibit complement-activation locally . To test the efficacy of membrane-targeted complement regulators in vivo, we have undertaken the expression and membrane targeting of the rat-complement regulator Crry . A soluble recombinant form of Crry, containing only the first four short consensus repeats, was expressed in a mammalian expression system and shown to be functional as a fluid phase regulator . To generate the quantities required for testing in vivo, Crry was expressed in bacteria and refolded successfully . Refolded protein had full-complement regulatory activity in vitro . Attachment of a membrane address tag conferred membrane-binding capacity and greatly increased complement regulatory function in vitro . This novel anticomplement agent can now be applied to rat models of arthritis and other inflammatory diseases.

Rev Esp Cardiol, 2002 Sep, 55(9), 988 - 90
{Tricuspid stenosis after pacemaker implantation without evidence of bacterial endocarditis . A case report}; Garrote C et al.; Tricuspid stenosis related to endocardial pacemaker leads is uncommon . We report the case of a patient with severe tricuspid stenosis documented 15 years after the implantation of a permanent DDD pacemaker for symptomatic congenital heart block . The atrial and ventricular leads both had a loop at the level of the tricuspid valve that may have caused endothelial damage and, eventually, tricuspid stenosis.

Anal Chem, 2002 Sep 1, 74(17), 4410 - 6
On-probe digestion of bacterial proteins for MALDI-MS; Harris WA et al.; On-probe digestion combined with MALDI mass spectrometry is studied as a rapid method for the analysis and identification of bacterial proteins . The use of trypsin adsorbed to the probe surface reduces the digestion time from hours to minutes . A high amount of trypsin must be applied to the probe for the successful digestion of bacterial proteins . Mass spectra of the digest contain a number of low-mass digest fragments . Several components of a B . subtilis bacterial digest can be identified through postsource decay and database searching.

EMBO J, 2002 Sep 16, 21(18), 4763 - 73
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation; Erzberger JP et al.; The initiation of DNA replication is a key event in the cell cycle of all organisms . In bacteria, replication initiation occurs at specific origin sequences that are recognized and processed by an oligomeric complex of the initiator protein DnaA . We have determined the structure of the conserved core of the Aquifex aeolicus DnaA protein to 2.7 A resolution . The protein comprises an AAA+ nucleotide-binding fold linked through a long, helical connector to an all-helical DNA-binding domain . The structure serves as a template for understanding the physical consequences of a variety of DnaA mutations, and conserved motifs in the protein suggest how two critical aspects of origin processing, DNA binding and homo-oligomerization, are mediated . The spatial arrangement of these motifs in DnaA is similar to that of the eukaryotic-like archaeal replication initiation factor Cdc6/Orc1, demonstrating that mechanistic elements of origin processing may be conserved across bacterial, archaeal and eukaryotic domains of life.

J Appl Microbiol, 2002, 93(4), 656 - 67
An arsenic(III)-oxidizing bacterial population: selection, characterization, and performance in reactors; Battaglia-Brunet F et al.; AIMS: To select an autotrophic arsenic(III)-oxidizing population, named CASO1, and to evaluate the performance of the selected bacteria in reactors . METHODS AND RESULTS: An As(III)-containing medium without organic substrate was used to select CASO1 from a mining environment . As(III) oxidation was studied under batch and continuous conditions . The main organisms present in CASO1 were identified with molecular biology tools . CASO1 exhibited significant As(III)-oxidizing activity between pH 3 and 8 . The optimum temperature was 25 degrees C . As(III) oxidation was still observed in the presence of 1000 mg l(-1) As(III) . In continuous culture mode, the As(III) oxidation rate reached 160 mg l(-1) h(-1) . The CASO1 consortium contains at least two organisms - strain b3, which is phylogenetically close to Ralstonia picketii, and strain b6, which is related to the genus Thiomonas . The divergence in 16S rDNA sequences between b6 and the closest related organism was 5.9%, suggesting that b6 may be a new species . CONCLUSIONS: High As(III)-oxidizing activity can be obtained without organic nutrient supply, using a bacterial population from a mining environment . SIGNIFICANCE AND IMPACT OF THE STUDY: The biological oxidation of arsenite by the CASO1 population is of particular interest for decontamination of arsenic-contaminated waste or groundwater.

Biochem Cell Biol, 2002, 80(4), 415 - 20
Screening regulatory sequences from bacterial artificial chromosome DNA of alpha- and beta-globin gene clusters; Zhang S et al.; In the forthcoming postgenomic era, identification of regulatory DNA sequences is becoming increasingly important for characterizing DNA-binding proteins and for elucidating the regulatory mechanisms of gene expression . Presently, there lack efficient methods to broadly screen and identify DNA regulatory elements on a large scale . We established herein an efficient strategy to screen regulatory sequences from bacterial artificial chromosome (BAC) DNAs containing human alpha- and beta-globin gene clusters based on polymerase chain reaction and electrophoretic mobility shift assay (EMSA) techniques without purified transcription factors . Twenty-three subclones derived from alpha-BAC DNA by bulk EMSA selection retained the ability to bind nuclear proteins of K562 cells when retested by EMSA . In 19 clones sequenced, 14 are identical to those registered in GenBank and five have one base difference . All of the 24 randomly picked beta-BAC clones showed specific binding with nuclear proteins of K562 cells . In 11 clones sequenced, eight are identical to those registered in GenBank and three have one base difference . This approach could be particularly powerful if combined with other systematic methods for identifying cis-regulatory DNA elements.

Plant Physiol, 1994 Jun, 105(2), 473 - 482
Plant Expression of a Bacterial Cytochrome P450 That Catalyzes Activation of a Sulfonylurea Pro-Herbicide; O'Keefe DP et al.; The Streptomyces griseolus gene encoding herbicide-metabolizing cytochrome P450SU1 (CYP105A1) was expressed in transgenic tobacco (Nicotiana tabacum) . Because this P450 can be reduced by plant chloroplast ferredoxin in vitro, chloroplast-targeted and nontargeted expression were compared . Whereas P450SU1 antigen was found in the transgenic plants regardless of the targeting, only those with chloroplast-directed enzyme performed P450SU1-mediated N-dealkylation of the sulfonylurea 2-methylethyl-2,3-dihydro-N-{(4,6-dimethoxypyrimidin-2-yl)aminocarbonyl}-1, 2-benzoisothiazole- 7-sulfonamide-1,1-dioxide (R7402) . Chloroplast targeting appears to be essential for the bacterial P450 to function in the plant . Because the R7402 metabolite has greater phytotoxicity than R7402 itself, plants bearing active P450SU1 are susceptible to injury from R7402 treatment that is harmless to plants without P450SU1 . Thus, P450SU1 expression and R7402 treatment can be used as a negative selection system in plants . Furthermore, expression of P450SU1 from a tissue-specific promoter can sequester production of the phytotoxic R7402 metabolite to a single plant tissue . In tobacco expressing P450SU1 from a tapetum-specific promoter, treatment of immature flower buds with R7402 caused dramatically lowered pollen viability . Such treatment could be the basis for a chemical hybridizing agent.

Plant Physiol, 1994 Jan, 104(1), 153 - 159
Aminomethylenediphosphonate: A Potent Type-Specific Inhibitor of Both Plant and Phototrophic Bacterial H+-Pyrophosphatases; Zhen RG et al.; The suitability of different pyrophosphate (PPi) analogs as inhibitors of the vacuolar H+-translocating inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) of tonoplast vesicles isolated from etiolated hypocotyls of Vigna radiata was investigated . Five 1,1-diphosphonates and imidodiphosphate were tested for their effects on substrate hydrolysis by the V-PPase at a substrate concentration corresponding to the Km of the enzyme . The order of inhibitory potency (apparent inhibition constants, Kiapp values, {mu}M, in parentheses) of the compounds examined was aminomethylenediphosphonate (1.8) > hydroxymethylenediphosphonate (5.7) {almost equal to} ethane-1-hydroxy-1,1-diphosphonate (6.5) > imidodiphosphate (12) > methylenediphosphonate (68) >> dichloromethylenediphosphonate (>500) . The specificity of three of these compounds, aminomethylenediphosphonate, imidodiphosphate, and methylenediphosphonate, was determined by comparing their effects on the V-PPase and vacuolar H+-ATPase from Vigna, plasma membrane H+-ATPase from Beta vulgaris, H+-PPi synthase of chromatophores prepared from Rhodospirillum rubrum, soluble PPase from Saccharomyces cerevisiae, alkaline phosphatase from bovine intestinal mucosa, and nonspecific monophosphoesterase from Vigna at a PPi concentration equivalent to 10 times the Km of the V-PPase . Although all three PPi analogs inhibited the plant V-PPase and bacterial H+-PPi synthase with qualitatively similar kinetics, whether substrate hydrolysis or PPi-dependent H+-translocation was measured, neither the vacuolar H+-ATPase nor plasma membrane H+-ATPase nor any of the non-V-PPase-related PPi hydrolases were markedly inhibited under these conditions . It is concluded that 1, 1-diphosphonates, in general, and aminomethylenediphosphonate, in particular, are potent type-specific inhibitors of the V-PPase and its putative bacterial homolog, the H+-PPi synthase of Rhodospirillum.

Trop Med Int Health, 2002 Sep, 7(9), 722 - 31
Clinical predictors of bacterial meningitis in infants and young children in The Gambia; Weber MW et al.; BACKGROUND: Bacterial meningitis is an important cause of childhood morbidity and mortality world-wide . In the developing world, where the burden of acute meningitis and its long-term sequelae are especially high, staff with limited training at primary health care facilities must be able to recognize the symptoms and signs of meningitis, so that suspected cases can be referred urgently to hospitals . METHODS: Children who presented with possible invasive bacterial infection to health facilities in The Gambia, West Africa, between 1993 and 1995 were investigated in a standardized manner and clinical findings were documented . Bacterial meningitis was defined as the growth of bacteria from the cerebrospinal fluid . Clinical findings were compared between cases of meningitis and other children . RESULTS: Of 2097 children between 2 months and 3 years of age investigated, 51 had a confirmed diagnosis of bacterial meningitis . In multivariate analysis using a model adjusting for age but not including respiratory signs, the variables associated independently with meningitis were appearance of being very sick (odds ratio for meningitis vs . no meningitis or no lumbar puncture performed (OR) 4.1, 95% CI 1.5-11.1), being lethargic or unconscious (OR 5.2, 95% CI 2.1-13), a stiff neck (OR 29.3, 95% CI 12.2-70.3), a bulging fontanel (OR 3.2, 95% CI 1.2-8.5) and reduced feeding as a prompted complaint (OR 2.9, 95% CI 1.3-6.7) . A combination model of a history of convulsions, or being lethargic or unconscious, or having a stiff neck, as used in the WHO-Integrated Management of Childhood Illness (IMCI) guidelines, had a sensitivity of 98% and a specificity of 72% to predict meningitis . CONCLUSIONS: A combination of a limited number of signs is sufficient to predict meningitis with high sensitivity, without a large number of children who do not have meningitis being unnecessarily referred.

Phys Rev Lett . 2002 Sep 9;89(11):118102 . Epub 2002 Aug 23.
Periodic chirality transformations propagating on bacterial flagella; Coombs D et al.; When a helical bacterial flagellum, clamped at one end, is placed in an external flow, it has been observed that regions of the flagellum transform to the opposite chirality, and travel as pulses down the length of the filament, the process repeating periodically {H . Hotani, J . Mol . Biol . 156, 791 (1982)}} . We propose a theory for this phenomenon based on a treatment of the flagellum as an elastic object with multiple stable configurations . The simplest possible implementation of the model accurately reproduces key features seen in experiment.

Biol Chem, 2002 Jun, 383(6), 945 - 60
The bacterial regulatory protein H-NS--a versatile modulator of nucleic acid structures; Schroder O et al.; The small DNA binding protein H-NS is attracting broad interest for its profound involvement in the regulation of bacterial physiology . It is involved in the regulation of many genes in response to a changing environment and functions in the adaptation to many different kinds of stress . Many H-NS-controlled genes, including the hns gene itself, are further linked to global regulatory networks . H-NS thus plays a key role in maintaining bacterial homeostasis under conditions of a rapidly changing environment . In this review we summarize recent results from combined biochemical and biophysical efforts which have yielded new insights into the three-dimensional structure and function of H-NS . The protein consists of two distinct domains separated by an unstructured linker region, and the structural details available today have helped to understand how these domains may interact with each other or with ligand molecules . Functional studies have, in addition, revealed mechanistic clues for the various H-NS activities, like temperature- or growth phase-dependent regulation . Important elements for the specific regulatory activities of H-NS comprise different modes of DNA binding, protein oligomerization, the competition with other regulators and the fact that the topology of the target DNA is modulated during complex formation . The distinctive ability to recognize nucleic acid structures in combination with other proteins also explains H-NS-dependent post-transcriptional activities where the interaction with defined RNA structures and the interference with RNA/protein complexes during mRNA translation are crucial for regulation . Thus, protein/protein interactions, in combination with the recognition and modulation of nucleic acid structures, are key elements of the different mechanisms which make H-NS such a versatile regulator.

Med Sci Monit, 2002 Sep, 8(9), BR345 - 53
Repeated intravenous doses of all-trans-retinoyl beta-D-glucuronide is not effective in the treatment of bacterial bronchopneumonia in lambs but is devoid of gross and acute toxicity; Gallup JM et al.; BACKGROUND: All-trans-retinoyl beta-D-glucuronide, a water-soluble glucuronic acid conjugate of all-trans-retinoic acid, has demonstrated high biological activity and low toxicity in most in vitro and in vivo models . Since the reparative effects of retinoids on epithelium are well-known, our aim was to study the effect(s) of intravenously-administered all-trans-retinoyl beta-D-glucuronide in lambs with chronic bacterial bronchopneumonia . MATERIAL/METHODS: Two groups of lambs were inoculated intrabronchially with either pyrogen-free saline or Mannheimia haemolytica . Thirty-three days later, lambs were injected four times at five-day intervals with 2 mL of 116 mM all-trans-retinoyl beta-D-glucuronide (6.0-9.3 mmol/kg or 2.86-4.42 mg/kg animal body weight) in dimethyl sulfoxide, or dimethyl sulfoxide alone . Animal behavior and signs of clinical illness were logged daily . Lung and liver samples were assessed for histopathology, while serum and liver samples were extracted for retinoids and analyzed by reversed-phase gradient high-performance liquid chromatography . RESULTS: Repeated injections of highly concentrated all-trans-retinoyl beta-D-glucuronide did not cause changes in appetite, activity or other behaviors nor did it cause histologic lesions in liver and lung . However, it had no effect on resolution of lung lesions resultant of chronic Mannheimia haemolytica bronchopneumonia . CONCLUSIONS: Repeated intravenous administration of high amounts of all-trans-retinoyl beta-D-glucuronide to lambs did not elicit signs of gross or microscopic toxicity . However, administering all-trans-retinoyl beta-D-glucuronide too late in the progression of bacterial pneumonia is thought to be the main reason for its lack of effect in this model . A retinoid lactone derivative was detected in sheep serum and liver several days after treatment.

J Hepatol, 2002 Oct, 37(4), 463 - 70
Bacterial infection in cirrhosis impairs coagulation by a heparin effect: a prospective study; Montalto P et al.; BACKGROUND: Bacterial infections have been postulated as a trigger for variceal bleeding in cirrhotic patients, and impair coagulation evaluated by thrombelastography (TEG) . Endogenous heparinoids have been detected after variceal bleeding and during liver transplantation in some cirrhotics using heparinase-modified-TEG . AIM: To assess if bacterial infection is associated with endogenous heparinoids in cirrhotics, thus impairing coagulation . METHODS: Native and heparinase-modified-TEG (cleavage of heparin and heparan-sulphate) was performed in 60 cirrhotics (Grade A, 2; B, 30; C, 28): 30 infected {septicaemia, 6 (culture positive); 6 (culture negative); spontaneous bacterial peritonitis, 10; chest infection, 4; others, 4}, 30 not infected, and five infected patients without liver diseases, comparing TEG parameters r, alpha, and ma . Eight cirrhotics were studied before and after infection . The diagnosis of presence and type of infection was based on international standard criteria . RESULTS: A significant heparin effect was found only in infected cirrhotics (28 of 30) with significant changes in r (P=0.0003), alpha (P<0.0001), and ma (P<0.0001), but in none of those not infected . This effect completely reversed in the eight evaluated after resolution of infection . There was no heparin effect in infected non-cirrhotics . CONCLUSIONS: A heparin effect was only found in cirrhotic patients with infection, further confirming that infection significantly modifies coagulation in cirrhotic patients.

Biomacromolecules, 2002 Sep-Oct, 3(5), 1071 - 7
Studies on comonomer compositional distribution of bacterial poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)s and thermal characteristics of their factions; Feng L et al.; The comonomer-unit compositional distributions have been investigated for bacterial poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) {P(3HB-co-3HH)} samples with 3HH unit content of 13.8, 18.0, 22.0, and 54.0 mol % . They were comonomer compositionally fractionated using chloroform/n-heptane mixed solvent at ambient temperature . The fractionation of P(3HB-co-18.0 mol %3HH) and P(3HB-co-22.0 mol % 3HH), which could not be carried out effectively at room temperature, were refractionated at 70 degrees C in the mixed solvent . Fractions with different 3HH unit content in a wide range (from 4.4 to 80.7 mol %) were obtained . By use of these fractions with narrow compositional distribution, the comonomer composition dependence of thermal properties was investigated by differential scanning calorimetry . The melting point (T(m)) and heat of fusion (DeltaH) decreased as the 3HH unit content increased in the range of low 3HH content (<40 mol %), while they increased as the 3HH unit content increased in the high 3HH content range (>70 mol %) . The minimum T(m) and DeltaH values were found to exist at 3HH unit content of about 60 mol % . The glass transition temperature (T(g)) decreased linearly with the increase of 3HH unit content . The values of T(m), DeltaH, and T(g) of P(3HB-co-3HH)s were compared with those of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxybutyrate-co-3-hydroxypropionate), and poly(3-hydroxybutyrate-co-4-hydroxybutyrate), and the effects of comonomer types on the thermal properties were revealed.

Biomacromolecules, 2002 Sep-Oct, 3(5), 1057 - 64
One-step synthesis of amphiphilic diblock copolymers from bacterial poly({R}-3-hydroxybutyric acid); Ravenelle F et al.; Catalyzed transesterification in the melt is used to produce diblock copolymers of poly({R}-3-hydroxybutyric acid), PHB, and monomethoxy poly(ethylene glycol), mPEG, in a one-step process . Bacterial PHB of high molecular weight is depolymerized by consecutive and partly simultaneous reactions: pyrolysis and transesterification . The formation of diblocks is accomplished by the nucleophilic attack from the hydroxyl end-group of the mPEG catalyzed by bis(2-ethylhexanoate) tin . The resulting diblock copolymers are amphiphilic and self-assemble into sterically stabilized colloidal suspensions of PHB crystalline lamellae.

Eur J Gynaecol Oncol, 2002, 23(4), 366 - 8
Absence of bacterial growth in the culture from the epidural catheter of a patient with endometrial carcinoma and febrile neutropenia: a case report and review of the literature; Pirbudak L et al.; Infection is a potentially serious complication of long-term epidural (EP) catheterization in cancer patients . Although the use of epidural opioid analgesia is an effective and safe means for pain relief in terminally ill patients, these patients are in need of monitorization for possible infection . This is the first report in which EP catheter cultivation has been assessed in an immunocompromised and febrile neutropenic endometrial cancer patient.

Acta Neurochir (Wien), 2002 Jun, 144(6), 601 - 8; discussion 608-9
Cerebral physiological and biochemical changes during vasogenic brain oedema induced by intrathecal injection of bacterial lipopolysaccharides in piglets; Gardenfors A et al.; BACKGROUND: The objective of the study was to evaluate biochemical and physiological changes in an experimental model of vasogenic brain oedema utilising techniques also used in routine neurointensive care . METHOD: 32 piglets were randomised to control or experimental group . The latter received an intrathecal injection of lipopolysaccharide (LPS) from E . coli (LPS group) . Intracranial pressure (ICP)and mean arterial pressure (MAP) were measured continuously . Intracerebral microdialysis was used for analysing interstitial levels of glucose, pyruvate, lactate, glutamate, glycerol and urea every 30 min . Repeated calculations of mean hemispheric CBF were performed utilising an extracranial scintillation detector and Intra-carotid injection of (133)Xe . Cerebral specific gravity was measured and the brains were fixed for histological examinations.FINDINGS: After LPS injection ICP increased reaching a plateau phase after 4-7 hours and CBF increased by 46% . Histological examination showed inflammation with pronounced extravasation of granulocytes . A significant decrease in brain specific gravity (p =0.022) was obtained . LPS caused a significant decrease in cerebral interstitial concentration of glucose (p = 0.0035), and significant increases in lactate concentration (p = 0.002) and lactate/pyruvate ratio (p = 0.0017) . A small but significant increase in glutamate was obtained (p = 0.0219) . Glycerol did not change significantly . INTERPRETATION: Intrathecal LPS caused an inflammatory reaction with extravasation of granulocytes, increased blood-brain barrier permeability and cerebral oedema . Biochemical analyses indicate increased glycolysis but no signs of cell membrane degradation.

Med Sci Monit, 2001 May, 7 Suppl 1, 169 - 74
Influence of HBV or HCV associated chronic liver diseases on the course and outcome of purulent, bacterial meningoencephalitis; Kepa L et al.; BACKGROUND: Aim of the study was evaluation of HBV or HCV associated chronic liver diseases (HBV or HCV CHLD) influence on the course and outcome of purulent, bacterial meningoencephalitis (PBME), without symptoms of sepsis . MATERIAL AND METHODS: Between 1995-99 there were 8 patients with PBME, with chronic HBV (5 subjects) or HCV (3 subjects) infection, treated in our centre; mean age 43 years . Str . pneumoniae and N . meningitidis were etiologic factors of PBME in 25% and 12.5% of patients, respectively . In 62.5% of cases etiology of PBME remained unknown . In 2 patients HBV or HCV CHLD was diagnosed before PBME (1 case--chronic active hepatitis, 1 case--postinflammatory liver cirrhosis) . During hospitalization due to PBME in 4 patients liver cirrhosis was diagnosed on the base of clinical picture and laboratory results, in 2 patients chronic hepatitis B or C was subject to further diagnostic procedures . RESULTS: In 7 subjects (87.5%) significant increase of AlAT and AspAT activity was recorded during acute phase of neuroinfection as compared to results preceding the hospitalization (to 300-400 U/l) . Together with recovery from PBME decrease of aminotransferases activity was noted . In 1 fatal case high AlAT and AspAT activity was observed for the whole time of the disease . In 2 other patients with liver cirrhosis, classified into class A of Child-Turcott-Pugh classification at the beginning of PBME, after transient insignificant aminotransferases increase sudden decompensation of liver functions during recovery from PBME was observed . Both patients died due to haemorrhage from esophageal varices . In all patients with PBME and HBV or HCV CHLD inflammatory parameters of cerebrospinal fluid were increased for longer than average time . It was the reason of longer hospital stay . The influence of HBV or HCV CHLD on PBME outcome was not observed . CONCLUSIONS: 1 . In patients with PBME concomitant HBV or HCV CHLD may exert negative influence on the course of neuroinfection and extend the period of hospitalization . 2 . The increase of aminotransferases activity in these patients may suggest other hepatotropic virus superinfection and require further diagnostics . 3 . In the case of HBV or HCV associated postinflammatory liver cirrhosis PBME may be connected with rapid liver disease progression and even the death of a patient.

Chembiochem, 2002 Sep 2, 3(9), 874 - 86
Aspartyl phosphonates and phosphoramidates: the first synthetic inhibitors of bacterial aspartate-semialdehyde dehydrogenase; Cox RJ et al.; The synthesis of methylene phosphonate, difluoromethylene phosphonate and phosphoramidate analogues of aspartyl phosphate, together with reduced analogues, is described . These compounds were shown to be effective inhibitors of aspartate-semialdehyde dehydrogenase (ASA-DH) from Escherichia coli . However, despite the structural similarity of the compounds, different patterns of inhibition were observed, indicative of two phases of recognition and binding . Correlation between measured inhibition constants with pK(a) values supports the theory that binding at the phosphate binding site is optimised for singly ionised phosphate analogues.

Pediatr Pulmonol, 2002 Oct, 34(4), 324 - 8
Recurrent unilateral bacterial pneumonias and interstitial fibrosis associated with pulmonary vein atresia: successful treatment with endovascular stent implantation; Sacco O et al.; A variety of pulmonary vascular disorders, such as hemangiomatosis, telangectasia, and veno-occlusive disease, may be involved in the pathogenesis of interstitial lung diseases . We describe the case of a girl with recurrent bacterial pneumonia and progressive interstitial fibrosis affecting the right lung . Morphologic evaluation of the lung biopsy showed structural changes of the vessel walls suggesting pulmonary hypertension . The echocardiogram showed the presence of centripetal blood flow in the right pulmonary artery from the periphery of the lung to the heart . A selective right angiography demonstrated the presence of pulmonary venous obstruction at the veno-atrial junction, successfully treated by endovascular stent implantation during cardiac catheterization .

Comput Med Imaging Graph, 2002 Sep-Oct, 26(5), 327 - 32
Diffusion MRI in Rasmussen's encephalitis, herpes simplex encephalitis, and bacterial meningoencephalitis; Sener RN; Three patients with Rasmussen's encephalitis, herpes simplex type 1 encephalitis, and bacterial meningoencephalitis are included in this study . Echo-planar diffusion MRI was acquired with the trace protocol at 1.5 T . b= 1000 s/mm(2) images, and apparent diffusion coefficient (ADC) maps were studied with respect to lesion identification . ADC values were also studied, and compared to those of 25 normals . In Rasmussen's encephalitis b= 1000 s/mm(2) images were uninformative while ADC maps had superior information . In herpes simplex type 1 encephalitis both b= 1000 s/mm(2) images, and ADC maps had diagnostic information . In meningoencephalitis b= 1000 s/mm(2) images had superior information, especially with respect to early cerebritis while ADC maps were negative . In conclusion, diffusion MRI provided useful imaging data on different types of encephalitis, either on b= 1000 s/mm(2) images or on ADC maps, or on both.

Mol Reprod Dev, 2002 Oct, 63(2), 161 - 7
Position-independent and tissue-specific expression of porcine whey acidic protein gene from a bacterial artificial chromosome in transgenic mice; Rival-Gervier S et al.; Silencing of transgenes is a frequent event after the random integration of foreign DNA in the host genome following microinjection . Long genomic fragments are expected to contain all the regulatory elements necessary to induce an appropriate expression of transgenes . A bacterial artificial chromosome containing the porcine wap gene with approximately 145 and 5 kb of 5'- and 3'-flanking sequences, respectively, was microinjected into fertilized mouse ovocytes . In the six transgenic lines studied, expression was strictly specific to the mammary gland of lactating animals and was position-independent . Levels of exogenous porcine wap mRNA per copy compared favorably with the porcine wap mRNA yield in the mammary gland of a 9-day lactating pig . These findings suggest that this insert contained most if not all of the cis-acting elements involved in the full specific expression of the porcine wap gene . These elements constitute good candidates for directing the optimized expression of protein recombinant-encoding genes in the mammary gland of lactating animals .

Clin Infect Dis, 2002 Sep 15, 35(6), 678 - 83 Epub 2002 Aug 23.
Prospective evaluation of a model of prediction of invasive bacterial infection risk among children with cancer, fever, and neutropenia; Santolaya ME et al.; A risk prediction model for invasive bacterial infection (IBI) was prospectively evaluated among children presenting with cancer, fever, and neutropenia . The model incorporated assessment of 5 previously identified risk factors: serum level of C-reactive protein (CRP) >/=90 mg/L, hypotension, identification of relapse of leukemia as the cancer type, platelet count of </=50,000 platelets/mm(3), and recent receipt of chemotherapy {16} . Children were uniformly evaluated at enrollment and were classified as having high or low risk for IBI according to a model that considers the number and type of variables present . Of the 263 febrile episodes evaluated during a 17-month period, 140 (53%) were in IBI-positive children . The sensitivity, specificity, and positive and negative predictive values of the model were 92%, 76%, 82%, and 90%, respectively . Identification of these 5 risk factors during the first 24 h of hospitalization was helpful in discriminating between children with a high or low risk for IBI.

Anal Biochem, 2002 Aug 15, 307(2), 322 - 9
Fluorescent assay for polymerization of purified bacterial FtsZ cell-division protein; Trusca D et al.; Septum formation in Escherichia coli is a complex cascade of interactions among cell-division proteins . The tubulin-like FtsZ division protein localizes to the division site and serves a cytoskeletal role during septum formation . A novel fluorescent-based 96-well format filter assay has been developed to measure the polymerization of FtsZ . A mixture of monomers and aggregates (38 to approximately 200 KDa in range) of purified wild-type FtsZ and a fluorescently tagged derivative of FtsZ protein in stoichiometric ratio passes through a 0.2-microm filter membrane, while polymerized FtsZ is retained on the filter . Addition of the SulA protein to the assay leads to rapid disassembly of existing FtsZ polymers, demonstrating its natural regulatory effect on FtsZ under the assay conditions . This assay is sensitive (requiring 2 microM FtsZ or less) and facilitates high-throughput screening of factors affecting FtsZ polymerization.

Biochem J, 2002 Dec 1, 368(Pt 2), 483 - 94
The first biantennary bacterial secondary cell wall polymer and its influence on S-layer glycoprotein assembly; Steindl C et al.; The cell surface of Aneurinibacillus thermoaerophilus DSM 10155 is covered with a square surface (S)-layer glycoprotein lattice . This S-layer glycoprotein, which was extracted with aqueous buffers after a freeze-thaw cycle of the bacterial cells, is the only completely water-soluble S-layer glycoprotein to be reported to date . The purified S-layer glycoprotein preparation had an overall carbohydrate content of 19% . Detailed chemical investigations indicated that the S-layer O-glycans of previously established structure accounted for 13% of total glycosylation . The remainder could be attributed to a peptidoglycan-associated secondary cell wall polymer . Structure analysis was performed using purified secondary cell wall polymer-peptidoglycan complexes . NMR spectroscopy revealed the first biantennary secondary cell wall polymer from the domain Bacteria, with the structure alpha-L-Glc p NAc-(1-->3)-beta-L-Man p NAc-(1-->4)-beta-L-Gal p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->3)-beta-L-Man p NAc-(1-->4)-beta-L-Gal p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->4)-{alpha-L-Glc p NAc-(1-->3)-beta-L-Man p NAc-(1-->4)-beta-L-Gal p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->3)-beta-L-Man p NAc-(1-->4)-beta-L-Gal p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->3)}-beta-L-Man p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->3)-beta-L-Man p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->3)-alpha-L-Glc p NAc-(1-->O)-PO(2)(-)-O-PO(2)(-)-(O-->6)-MurNAc- (where MurNAc is N -acetylmuramic acid) . The neutral polysaccharide is linked via a pyrophosphate bond to the C-6 atom of every fourth N -acetylmuramic acid residue, in average, of the A1gamma-type peptidoglycan . In vivo, the biantennary polymer anchored the S-layer glycoprotein very effectively to the cell wall, probably due to the doubling of motifs for a proposed lectin-like binding between the polymer and the N-terminus of the S-layer protein . When the cellular support was removed during S-layer glycoprotein isolation, the co-purified polymer mediated the solubility of the S-layer glycoprotein in vitro . Initial crystallization experiments performed with the soluble S-layer glycoprotein revealed that the assembly property could be restored upon dissociation of the polymer by the addition of poly(ethylene glycols) . The formed two-dimensional crystalline S-layer self-assembly products exhibited the same lattice symmetry as observed on intact bacterial cells.

Hepatology, 2002 Sep, 36(3), 679 - 86
Bacterial motif DNA as an adjuvant for the breakdown of immune self-tolerance to pyruvate dehydrogenase complex; Jones DE et al.; Bacterial DNA containing unmethylated CpG dinucleotide motifs is immunostimulatory to mammals, skewing CD4(+) T-cell responses toward the Th1 phenotype . Autoreactive T-cell responses seen in primary biliary cirrhosis (PBC) are typically of the Th1 phenotype, raising the possibility that bacterial DNA might play a role in the generation of pathologic autoimmunity . We therefore studied the effects of CpG motif-containing oligodeoxynucleotides (ODN) on responses to pyruvate dehydrogenase complex (PDC, the autoantigen in PBC) in a murine model . Sensitization of SJL/J mice with non-self-PDC has been shown to result in induction of autoreactive T-cell responses to PDC sharing characteristics with those seen in patients with PBC . Administration of CpG ODN to SJL/J mice at the time of sensitization with PDC resulted in a significant skewing of splenic T-cell response to self-PDC, with significant augmentation of the Th1 cytokine response (interleukin {IL} 2 and interferon {IFN} gamma) and reduction of the Th2 response (IL-4 and IL-10) . In fact, CpG ODN seemed to be more effective at biasing the response phenotype and as effective at inducing liver histologic change as complete Freund's adjuvant (CFA), the standard adjuvant used for induction of Th1 responses in murine autoimmune and infectious immunity models . In conclusion, our findings raise the possibility that bacteria play a role in the development of autoimmunity (in PBC at least) through the potential of their DNA to shift the T-cell responses toward the phenotype associated with autoimmune damage . Moreover, this study suggests caution in the therapeutic use of CpG ODN as vaccine adjuvants.

J Infect Dis, 2002 Sep 15, 186(6), 769 - 73 Epub 2002 Aug 28.
Association of hypercoagulable states and increased platelet adhesion and aggregation with bacterial colonization of intravenous catheters; Musher D et al.; Bacterial adherence to intravenous catheters may be mediated, in part, by adherence to coagulation proteins and platelets . The possibility that catheter infection is associated with gene polymorphisms that cause hypercoagulability or increased platelet stickiness was examined . Among patients with infected catheters, there was no increase in the frequency of polymorphisms that increase coagulability, including factor V Leiden R506G, factor II (prothrombin) G20210A, and methylenetetrahydrofolate reductase C677T, compared with control subjects . The incidence of polymorphisms of the platelet beta(3) integrin among patients with infected catheters was also similar to that among control subjects . The C/D heterozygote of the variable number tandem repeat polymorphism and the C/T heterozygote of the KO polymorphism of glycoprotein Ibalpha were more frequent among patients with infected catheters than they were among control subjects . In a small proportion of patients, a genetic predisposition to platelet stickiness may be associated with infection of intravenous catheters, but in the majority, a recognized genetic tendency to hypercoagulability or platelet stickiness does not underlie infection.

Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 2002 Sep, 34(5), 533 - 43
Methods for structural and functional analysis of an RNA hexamer of bacterial virus phi29 DNA packaging motor; Guo PX; During multiplication and maturation, the lengthy genomic DNA of dsDNA viruses is translocated with remarkable velocity into a limited space within the procapsid and packaged to crystalline density . A viral DNA-packaging motor accomplishes this energy consuming motion task . An RNA molecule of bacterial virus phi29 has been found to be a vital component of the DNA-packaging motor . Six pRNAs form a hexagonal complex to gear the DNA translocating machine using a mechanism similar to the driving of a bolt with a hex nut . Sequential action of six RNA molecules to drive the motor is similar to the consecutive firing of six cylinders of a car engine . This article reviews the structure of pRNA to demonstrate that its structure plays a vital role in its function, and focuses on methods and unique approaches that lead to the elucidation of pRNA structure.

EMBO J, 2002 Sep 2, 21(17), 4470 - 9
Dissociation of the dimeric SecA ATPase during protein translocation across the bacterial membrane; Or E et al.; The ATPase SecA mediates post-translational translocation of precursor proteins through the SecYEG channel of the bacterial inner membrane . We show that SecA, up to now considered to be a stable dimer, is actually in equilibrium with a small fraction of monomers . In the presence of membranes containing acidic phospholipids or in certain detergents, SecA completely dissociates into monomers . A synthetic signal peptide also affects dissociation into monomers . In addition, conversion into the monomeric state can be achieved by mutating a small number of residues in a dimeric and fully functional SecA fragment . This monomeric SecA fragment still maintains strong binding to SecYEG in the membrane as well as significant in vitro translocation activity . Together, the data suggest that the SecA dimer dissociates during protein translocation . Since SecA contains all characteristic motifs of a certain class of monomeric helicases, and since mutations in residues shared with the helicases abolish its translocation activity, SecA may function in a similar manner.

Mol Divers, 2000, 5(3), 117 - 26
Identification of peptides that neutralize bacterial endotoxins using beta-hairpin conformationally restricted libraries; Gonzalez-Navarro H et al.; Bacterial endotoxins are the major mediator of septic shock; therefore, endotoxin-neutralizing molecules could have biomedical applications . The septic shock cascade relies in a series of molecular recognition processes . The large contact-surface described for the interacting macromolecules, in most cases, prevents the identification of small molecules that could modulate such recognition events . Here we report on a beta-hairpin conformationally restricted combinatorial library that has been generated and screened towards the identification of new peptides that neutralize bacterial endotoxins . Starting with a de novo designed linear peptide that shows a beta-hairpin structure population of around 30%, (Ramirez-Alvarado, M., Blanco, F . J . and Serrano, L . Nat . Struc . Biol., 7, 604-612 (1996)), we selected four positions to build up a combinatorial library of 20(4) sequences . Deconvolution of the library reduced such a sequence complexity to 8 defined sequences . The newly identified peptides have a biological activity equivalent to that reported for peptides derived from natural endotoxin-binding proteins.

Proc Natl Acad Sci U S A, 2002 Sep 17, 99(19), 12415 - 20 Epub 2002 Aug 26.
Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells; Domi A et al.; The ability to manipulate the vaccinia virus (VAC) genome, as a plasmid in bacteria, would greatly facilitate genetic studies and provide a powerful alternative method of making recombinant viruses . VAC, like other poxviruses, has a linear, double-stranded DNA genome with covalently closed hairpin ends that are resolved from transient head-to-head and tail-to-tail concatemers during replication in the cytoplasm of infected cells . Our strategy to construct a nearly 200,000-bp VAC-bacterial artificial chromosome (BAC) was based on circularization of head-to-tail concatemers of VAC DNA . Cells were infected with a recombinant VAC containing inserted sequences for plasmid replication and maintenance in Escherichia coli; DNA concatemer resolution was inhibited leading to formation and accumulation of head-to-tail concatemers, in addition to the usual head-to-head and tail-to-tail forms; the concatemers were circularized by homologous or Cre-loxP-mediated recombination; and E . coli were transformed with DNA from the infected cell lysates . Stable plasmids containing the entire VAC genome, with an intact concatemer junction sequence, were identified . Rescue of infectious VAC was consistently achieved by transfecting the VAC-BAC plasmids into mammalian cells that were infected with a helper nonreplicating fowlpox virus.

Int J STD AIDS, 2002 Aug, 13(8), 559 - 63
Diagnosis of bacterial vaginosis on self-collected vaginal tampon specimens; Sturm PD et al.; A vaginal tampon specimen was previously shown to be suitable for the molecular diagnosis of non-ulcerative sexually transmitted infections (STIs) . Different tampon fluid preparations were evaluated for the diagnosis of bacterial vaginosis (BV) . Women with pregnancy related problems were enrolled . Two observers evaluated the different tampon fluid preparations and vaginal smears collected during speculum examination using the Nugent score . Using the Amsel criteria, 21% of the 84 women enrolled were diagnosed with BV . Results of the tampon fluid preparations and vaginal smears showed excellent agreement for both observers (Spearman >0.80) . The overall sensitivity and specificity was 91.7% (95% CI: 81.6-96.5) and 79.3% (95% CI: 67.2-87.8), respectively, using the Amsel criteria as reference standard . The tampon provides a specimen for the combined diagnosis of non-ulcerative STIs and BV . This non-invasively collected specimen may facilitate self-initiated testing and population-based studies as well as longitudinal studies that are necessary to gain insight in the epidemiology of BV related to STIs and HIV.

Clin Sci (Lond), 2002 Aug, 103 Suppl 48, 90S - 93S
Characterization of PgPepO, a bacterial homologue of endothelin-converting enzyme-1; Carson JA et al.; PgPepO is a homologue of endothelin-converting enzyme-1 (ECE-1), with which it shares 31% identity . PgPepO was isolated from the periodontal pathogen Porphyromonas gingivalis . Recent studies have suggested a link between periodontal and cardiovascular disease, and several groups have suggested that bacterial and viral infections may contribute to the latter . P . gingivalis possesses the ability to invade, and multiply within, aortic endothelial cells and has been localized to atherosclerotic plaques . PgPepO was expressed and purified to homogeneity and we have begun detailed functional analysis, in terms of substrate preference and inhibitor specificity, in order to provide active-site comparisons with other members of the neprilysin (NEP)/ECE family . PgPepO possesses similar substrate specificity to ECE-1 and has been shown to cleave big endothelin-1 (big ET-1), big ET-2 and big ET-3, converting the substrates into their respective mature endothelin peptides . Substance P, angiotensin I, angiotensin II and neurotensin are all cleaved at multiple sites by PgPepO and the kinetics of these reactions have been compared . The potent vasoconstrictor urotensin II is not hydrolysed by PgPepO . Cleavage of bradykinin by PgPepO occurs at the Pro(7)-Phe(8) bond and is inhibited by the NEP and ECE-1 inhibitor phosphoramidon in a pH-dependent fashion (IC(50) =10 microM at pH 7.0) but not by thiorphan, an NEP-specific inhibitor . PgPepO activity is completely inhibited by EDTA . Characterization of this enzyme is important in elucidating possible links between periodontal pathogens and cardiovascular disorders such as atherosclerosis, and provides an opportunity to gain structural information on a bacterial protein with striking similarity to human ECE-1.

Prog Urol, 2002 Jun, 12(3), 479 - 81
{Focal bacterial nephritis: diagnosis and treatment}; Ameur A et al.; Focal bacterial nephritis or lobar nephronia represents an acute localized non-liquefactive infection of the kidney caused by bacterial infection . This is an uncommon form of pyelonephritis that can affect both adults and children . Imaging techniques, particularly CT scan, are necessary for diagnosis and to distinguish it from other conditions (abscess or renal masses) that require a different treatment . The authors describe a case of acute lobar nephronia in a 24-year-old man.

Proc Natl Acad Sci U S A, 2002 Sep 3, 99(18), 11605 - 10 Epub 2002 Aug 20.
Reactions of cysteines substituted in the amphipathic N-terminal tail of a bacterial potassium channel with hydrophilic and hydrophobic maleimides; Li J et al.; Single cysteine-substitution mutants of KcsA, a K(+) channel from Streptomyces lividans, were expressed in Escherichia coli, and inner membranes were isolated . The rate constants for the reactions of these cysteines with three maleimides of increasing hydrophobicity, 4-(N-maleimido)phenyltrimethylammonium, N-phenylmaleimide, and N-(1-pyrenyl)maleimide, were determined by back titration of the remaining cysteines with methoxypolyethylene glycol-2-pyridine disulfide (M(r) 3,000) and quantitation of the fraction of gel-shifted KcsA as a function of reaction time . The patterns of the rate constants for the reactions of all three reagents with eight consecutive cysteines in the partially lipid-immersed amphipathic N-terminal tail helix were the same, with cysteines on the hydrophilic side of the helix reacting faster than Cys on the hydrophobic side . The results are consistent with the tail helix lying with its long axis in the lipid-water interface and with the orientation of the helix fluctuating around this axis . The patterns of the rate constants for the three reagents were similar to the pattern of the probabilities that the substituted cysteines were exposed to water, based on the sum of the free energies of transfer from water to octanol of all of the residues exposed to lipid in each orientation of the helix.

J Biol Chem, 2002 Oct 25, 277(43), 40567 - 74 Epub 2002 Aug 19.
Shiga-like toxin inhibition of FLICE-like inhibitory protein expression sensitizes endothelial cells to bacterial lipopolysaccharide-induced apoptosis; Erwert RD et al.; Shiga-like toxin (SLT) has been implicated in the pathogenesis of hemolytic uremic syndrome and its attendant endothelial cell (EC) injury . Key serotypes of Escherichia coli produce SLT-1 in addition to another highly pro-inflammatory molecule, lipopolysaccharide (LPS) . It has previously been established that SLT-1 induces EC apoptosis and that LPS enhances this effect . LPS alone has no affect on human EC viability, and the mechanism for this enhancement remains unknown . In the present report, we demonstrate that SLT-1 sensitizes EC to LPS-induced apoptosis . Pretreatment with SLT-1 sensitized EC to LPS-induced apoptosis, whereas pretreatment with LPS did not influence SLT-1-induced apoptosis . SLT-1 exposure resulted in decreased expression of FLICE-like inhibitory protein (FLIP), an anti-apoptotic protein that has previously been shown to block LPS-induced apoptosis . This SLT-1-mediated decrease in FLIP expression preceded the onset of apoptosis elicited by SLT-1 alone or in combination with LPS . SLT-1-mediated decrements in FLIP expression correlated in a dose- and time-dependent manner with sensitization to LPS-induced apoptosis . Finally, transient or stable overexpression of FLIP protected against LPS enhancement of SLT-1-induced apoptosis, and this protection corresponded with sustained expression of FLIP . Together, these data suggest that SLT-1 sensitizes EC to LPS-induced apoptosis by inhibiting FLIP expression.

Zhonghua Nei Ke Za Zhi, 2002 Jul, 41(7), 459 - 61
Small bowel bacterial overgrowth and endotoxemia in cirrhosis; Wang J et al.; OBJECTIVE: To investigate the incidence of the small bowel bacterial overgrowth in cirrhotics and analyze the correlation among small bowel bacterial overgrowth (SBBO), plasma endotoxin level and plasma interleukin-2(IL-2), interleukin-6(IL-6), or tumor necrosis factor alpha(TNF-alpha) level . METHODS: Small bowel bacterial overgrowth in 71 cirrhotics was test by glucose hydrogen breath test (GHBT); plasma endotoxin in cirrhotics was measured with limilus lysate test; and plasma cytokine (IL-2, IL-6 and TNF-alpha) was measured with a solid-phase enzyme-linked immunosorbent assay; the incidence of SBBO in those 71 cirrhotics was investigated and the correlation between plasma endotoxin level and plasma IL-2, IL-6, or TNF-alpha level was analysed . RESULTS: (1)Positive GHBT were observed in 18 of 71 icrrhotics(25.3%); (2) Plasma endotoxin, IL-2, IL-6 and TNF-alpha levels were significantly higher in those cirrhotic patients with positive GHBT than in those with negative GHBT {(0.715 +/- 0.229) Eu/L versus (0.379 +/- 0.223) Eu/L, (19.15 +/- 4.60) ng/L versus (9.41 +/- 6.69) ng/L, (93.29 +/- 27.37) ng/L versus (53.22 +/- 28.31) ng/L, (42.18 +/- 16.91) ng/L versus (27.72 +/- 17.06) ng/L, respectively; P < 0.01}; (3) A significant correlation was observed between the level of plasma endotoxin and the level of plasma IL-2(r = 0.894, P < 0.001), IL-6(r = 0.857, P < 0.001) or TNF-alpha( r = 0.845,P < 0.001)in cirrhotics; CONCLUSIONS: (1)Plasma endotoxin, IL-2, IL-6,and TNF-alpha levels are increased in cirrhotic patients with SBBO, which suggests SBBO in cirrhotics may exasperated endotoxeamia;(2)Plasma endotoxin level in cirrhotics may stimulate some kinds of immune activated cells to produce IL-2, IL-6 and TNF-alpha, which may deteriorated cirrhosis or the complications.

Nephron, 2002 Sep, 92(1), 213 - 5
Acute focal bacterial nephritis: report of four cases; Montejo M et al.; Focal acute bacterial nephritis is a localized bacterial infection of the kidney presenting as an inflammatory mass not containing drainable pus . The further distinction between acute focal bacterial nephritis and other renal masses is aided by the appropriate use of renal sonography and computed tomography . We report 4 cases with this entity .

Proc Natl Acad Sci U S A, 2002 Sep 3, 99(18), 11611 - 5 Epub 2002 Aug 19.
Dynamic and clustering model of bacterial chemotaxis receptors: structural basis for signaling and high sensitivity; Kim SH et al.; Bacterial chemotaxis receptors can detect a small concentration gradient of attractants and repellents in the environment over a wide range of background concentration . The clustering of these receptors to form patches observed in vivo and in vitro has been suspected as a reason for the high sensitivity, and such wide dynamic range is thought to be due to the resetting of the receptor sensitivity threshold by methylation/demethylation of the receptors . However, the mechanisms by which such high sensitivity is achieved and how the methylation/demethylation resets the sensitivity are not well understood . A molecular modeling of an intact bacterial chemotaxis receptor based on the crystal structures of a cytoplasmic domain and a periplasmic domain suggests an interesting clustering of three dimeric receptors and a two-dimensional, close-packed lattice formation of the clusters, where each receptor dimer contacts two other receptor dimers at the cytoplasmic domain and two yet different receptor dimers at the periplasmic domain . This interconnection of the receptors to form a patch of receptor clusters suggests a structural basis for the high sensitivity of the bacterial chemotaxis receptors . Furthermore, we present crystallographic data suggesting that, in contrast to most molecular signaling by conformational changes and/or oligomerization of the signaling molecules, the changes in dynamic property of the receptors on ligand binding or methylation may be the language of the signaling by the chemotaxis receptors . Taken together, the changes of the dynamic property of one receptor propagating mechanically to many others in the receptor patch provides a plausible, simple mechanism for the high sensitivity and the dynamic range of the receptors.

Eur J Clin Pharmacol, 2002 Aug, 58(5), 321 - 2 Epub 2002 Jun 25.
Bacterial pneumonia can increase serum concentration of clozapine; Raaska K et al.; Concentrations of serum clozapine, C-reactive protein (CRP) and alpha1 acid glycoprotein were greatly increased during a bacterial pneumonia in a 53-year-old woman . As the pneumonia subsided, and CRP and alpha1 acid glycoprotein normalised, serum clozapine concentration also decreased to the previous level . An increased serum clozapine and a lowered N-desmethylclozapine to clozapine ratio during the infection suggest a decreased cytochrome P(450) (CYP)1A2 activity . Cytokine-mediated CYP1A2 suppression is discussed.

J Biol Chem, 2002 Nov 1, 277(44), 41489 - 96 Epub 2002 Aug 14.
Molecular cloning of a novel chaperone-like protein induced by rhabdovirus infection with sequence similarity to the bacterial extracellular solute-binding protein family 5; Cho WJ et al.; Previously we demonstrated that a novel stress protein is induced in fish cells by the infection of a fish rhabdovirus (Cho W . J., Cha, S . J., Do, J . W., Choi, J . Y., Lee, J . Y., Jeong, C . S., Cho, K . J., Choi, W . S., Kang, H . S., Kim, H . D., and Park, J . W . (1997) Biochem . Biophys . Res . Commun . 233, 316-319) . In this paper, we present the molecular cloning and characterization of a gene encoding this protein named virus-inducible stress protein (VISP) . The VISP was purified partially by immunoprecipitation using a monoclonal antibody against the VISP and further purified by the electroelution from a SDS-PAGE gel . The protein was subjected to internal protein sequencing, and the sequence of three peptides was determined . Degenerate oligonucleotides based on the three peptide sequences were used to screen a cDNA library from rhabdovirus-infected CHSE-214 fish cells, and a cDNA of a 2193-bp open reading frame encoding the VISP with 730 amino acid residues (M(r) = 79.84) was identified . Whereas the nucleotide sequence of VISP shows no similarity with other genes in the GenBank(TM), the amino acid sequence of the VISP has similarity with the bacterial extracellular solute-binding protein family 5 (SBP_bac_5) that is proposed to have chaperone activity . Thus, we explored whether the VISP also had chaperone-like activity . Purified recombinant VISP expressed in Escherichia coli promoted the functional folding of alpha-glucosidase after urea denaturation and also prevented thermal aggregation of alcohol dehydrogenase . These results suggest that the VISP has amino acid sequence similarity with SBP_bac_5 and that it has chaperone activity that may play a role in virus infection.

Proc Natl Acad Sci U S A, 2002 Sep 3, 99(18), 11772 - 7 Epub 2002 Aug 14.
Identification of the binding sites of regulatory proteins in bacterial genomes; Li H et al.; We present an algorithm that extracts the binding sites (represented by position-specific weight matrices) for many different transcription factors from the regulatory regions of a genome, without the need for delineating groups of coregulated genes . The algorithm uses the fact that many DNA-binding proteins in bacteria bind to a bipartite motif with two short segments more conserved than the intervening region . It identifies all statistically significant patterns of the form W(1)N(x)W(2), where W(1) and W(2) are two short oligonucleotides separated by x arbitrary bases, and groups them into clusters of similar patterns . These clusters are then used to derive quantitative recognition profiles of putative regulatory proteins . For a given cluster, the algorithm finds the matching sequences plus the flanking regions in the genome and performs a multiple sequence alignment to derive position-specific weight matrices . We have analyzed the Escherichia coli genome with this algorithm and found approximately 1,500 significant patterns, which give rise to approximately 160 distinct position-specific weight matrices . A fraction of these matrices match the binding sites of one-third of the approximately 60 characterized transcription factors with high statistical significance . Many of the remaining matrices are likely to describe binding sites and regulons of uncharacterized transcription factors . The significance of these matrices was evaluated by their specificity, the location of the predicted sites, and the biological functions of the corresponding regulons, allowing us to suggest putative regulatory functions . The algorithm is efficient for analyzing newly sequenced bacterial genomes for which little is known about transcriptional regulation.

Curr Opin Biotechnol, 2002 Jun, 13(3), 234 - 7
Disruption of bacterial quorum sensing by other organisms; Bauer WD et al.; Higher plants and algae produce compounds that mimic quorum sensing: signals used by bacteria to regulate the expression of many genes and behaviors . Similarly, various bacteria can stimulate, inhibit or inactivate quorum sensing in other bacteria . These discoveries offer new opportunities to manipulate bacterial quorum sensing in applications relevant to medicine, agriculture and the environment.

Physiol Biochem Zool, 2002 May-Jun, 75(3), 273 - 82
The influence of bacterial lipopolysaccharide on the thermoregulation of the box turtle Terrapene carolina; do Amaral JP et al.; Ectotherms can adjust their thermoregulatory set points in response to bacterial infection; the result may be similar to endothermic fever . We examined the influence of dose on the set point of body temperature (T(b)) in Terrapene carolina . After acclimating postprandial turtles to 20 degrees C, we injected them with two doses of bacterial endotoxin (LPS; lipopolysaccharide from Escherichia coli), 0.0025 or 0.025 mg LPS/g nonshell body mass, or with reptilian saline (control group) . We placed the animals singly in linear thigmothermal gradients and recorded their T(b)'s for 48 h . The turtles showed dose-influenced thermal selection . Turtles injected with the high dose had T(b)'s significantly higher than control turtles, whereas low-dose turtles had T(b)'s significantly lower than control turtles . Also, there was a low daily effect on the T(b) of the turtles injected with the high dose . High-dose turtles had significantly higher T(b)'s than the control turtles during the first day but not during the second . Our results support the prediction of Romanovsky and Szekely that an infectious agent may elicit opposite thermoregulatory responses depending on quality and quantity of the agent and the host health status.

Proc Natl Acad Sci U S A, 2002 Aug 20, 99(17), 10994 - 1001 Epub 2002 Aug 13.
FAST CARS: engineering a laser spectroscopic technique for rapid identification of bacterial spores; Scully MO et al.; Airborne contaminants, e.g., bacterial spores, are usually analyzed by time-consuming microscopic, chemical, and biological assays . Current research into real-time laser spectroscopic detectors of such contaminants is based on e.g., resonance fluorescence . The present approach derives from recent experiments in which atoms and molecules are prepared by one (or more) coherent laser(s) and probed by another set of lasers . However, generating and using maximally coherent oscillation in macromolecules having an enormous number of degrees of freedom is challenging . In particular, the short dephasing times and rapid internal conversion rates are major obstacles . However, adiabatic fast passage techniques and the ability to generate combs of phase-coherent femtosecond pulses provide tools for the generation and utilization of maximal quantum coherence in large molecules and biopolymers . We call this technique FAST CARS (femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman spectroscopy), and the present article proposes and analyses ways in which it could be used to rapidly identify preselected molecules in real time.

Br Med Bull, 2002, 62, 113 - 23
Vaccines against human enteric bacterial pathogens; Dougan G et al.; The development of vaccines against enteric bacterial pathogens presents a challenge because of the large number of pathogens capable of causing disease and the requirement to induce immunity that is effective in the gut . A new generation of enteric vaccines based either on live or non-living antigens delivered orally or by injection are reaching the clinic in the early phases of evaluation . However, considerable technical barriers have to be overcome before these vaccines reach the general population.

Cell Microbiol, 2002 Aug, 4(8), 541 - 56
Effect of Nramp1 on bacterial replication and on maturation of Mycobacterium avium-containing phagosomes in bone marrow-derived mouse macrophages; Frehel C et al.; Pathogenic mycobacteria prevent maturation of the phagosomes in which they reside inside macrophages and this is thought to be a major strategy allowing them to survive and multiply within macrophages . The molecular basis for this inhibition is only now beginning to emerge with the molecular characterization of the phagosome membrane enclosing these pathogens . We have used here several electron microscopy approaches in combination with counts of bacterial viability to analyse how expression of Nramp1 at the phagosomal membrane may influence survival of Mycobacterium avium and affect its ability to modulate the fusogenic properties of the phagosome in which it resides . The experiments were carried out in bone marrow-derived macrophages from wild-type 129sv (Nramp1(G169)) mice and from isogenic 129sv carrying a null mutation at Nramp1 (Nramp(1-/-)) following infection with a virulent strain of M . avium . We show here that Nramp1 expression has a bacteriostatic effect and that abrogation of Nramp1 restores the bacteria's capacity to replicate within macrophages . The combined analyses of the acquisition of endocytic contents markers delivered to early endosomes and/or lysosomes either prior to or after phagocytic uptake showed that in Nramp1-positive macrophages, M . avium was unable to prevent phagosome maturation and fusion with lysosomes but that in Nramp1-negative macrophages this capacity was restored . Several hypotheses are proposed to explain how Nramp1 could affect survival of M . avium . We also propose how the present observations could relate to the model according to which mycobacteria can prevent phagosome maturation by establishing a tight interaction with constituents of the phagosome membrane . Furthermore, these results show the importance of the choice of macrophages used as a model to study intracellular survival strategies of pathogens.

Biochemistry, 2002 Aug 20, 41(33), 10426 - 38
Identification of A-minor tertiary interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping; Soukup JK et al.; The A-minor motifs appear to be the most ubiquitous helix packing elements within RNA tertiary structures . These motifs have been identified throughout the ribosome and almost every other tertiary-folded RNA for which structural information is available . These motifs utilize the packing of the donor adenosine's N1, N3, and/or 2'-OH against the 2'-OHs and minor groove edge of the acceptor base pair . The ability to identify biochemically which adenosines form A-minor motifs and which base pairs they contact is an important experimental objective . Toward this goal, we report the synthesis and transcriptional incorporation of 5'-O-(1-thio)-3-deazaadenosine triphosphate and its use in Nucleotide Analogue Interference Mapping (NAIM) and Nucleotide Analogue Interference Suppression (NAIS) . This analogue makes it possible for the first time to explore the functional importance of the N3 imino group of adenosine in RNA polymers . Interference analysis of the group I self-splicing introns from Tetrahymena and Azoarcus indicates that A-minor motifs are integral to the helix packing interactions that define the 5'-splice site of the intron . Specifically, Azoarcus A58 in the J4/5 region contacts the G.U wobble pair at the cleavage site in the P1 helix, and Azoarcus A167 in the J8/7 region contacts the C13-G37 base pair in the P2 helix . Both of these structural features are conserved between the eukaryotic and bacterial introns . These results suggest that nucleotide analogue interference patterns can identify and distinguish A-minor interactions in RNA tertiary structure, particularly the most prevalent type I and type II varieties . Furthermore, clustering of 3-deazaadenosine interferences is suggestive of A patches, in which a series of consecutive A-minor motifs mediate helix packing . Biochemical identification of these interactions may provide valuable constraints for RNA structure prediction.

Biochemistry, 2002 Aug 20, 41(33), 10382 - 9
The purine nucleoside phosphorylase from Trichomonas vaginalis is a homologue of the bacterial enzyme; Munagala N et al.; Trichomonas vaginalis is a parasitic protozoan and the causative agent of trichomoniasis . Its primary purine salvage system, consisting of a purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase, presents potential targets for designing selective inhibitors as antitrichomonial drugs because of lack of de novo synthesis of purine nucleotides in this organism . cDNA encoding T . vaginalis PNP was isolated by complementation of an Escherichia coli strain deficient in PNP and expressed, and the recombinant enzyme was purified to apparent homogeneity . It bears only 28% sequence identity with that of human PNP but 57% identity with the E . coli enzyme . Gel filtration showed the enzyme in a hexameric form, similar to the bacterial PNPs . Steady-state kinetic analysis of T . vaginalis PNP-catalyzed reactions gave K(m)'s of 31.5, 59.7, and 6.1 microM for inosine, guanosine, and adenosine in the nucleosidase reaction and 45.6, 35.9, and 12.3 microM for hypoxanthine, guanine, and adenine in the direction of nucleoside synthesis . This substrate specificity appears to be similar to that of bacterial PNPs . The catalytic efficiency of this enzyme with adenine as substrate is 58-fold higher than that with either hypoxanthine or guanine, representing a distinct disparity with the mammalian PNPs, which have negligible activity with either adenine or adenosine . The kinetic mechanism of T . vaginalis PNP-catalyzed reactions, determined by product inhibition and equilibrium isotope exchange, was by random binding of substrates (purine base and ribose 1-phosphate) with ordered release of the purine nucleoside first, followed by inorganic phosphate . Formycin A, an analogue of adenosine known as an inhibitor of E . coli PNP without any effect on mammalian PNPs, was shown to inhibit T . vaginalis PNP with a K(is) of 2.3 microM by competing with adenosine . T . vaginalis PNP thus belongs to the family of bacterial PNPs and constitutes a target for antitrichomonial chemotherapy.

J Cereb Blood Flow Metab, 2002 Aug, 22(8), 988 - 96
Triptans reduce the inflammatory response in bacterial meningitis; Hoffmann O et al.; Severe headache and meningism provide clear evidence for the activation of trigeminal neurotransmission in meningitis . The authors assessed the antiinflammatory potential of 5HT1B/D/F receptor agonists (triptans), which inhibit the release of proinflammatory neuropeptides from perivascular nerve fibers . In a 6-hour rat model of pneumococcal meningitis, zolmitriptan and naratriptan reduced the influx of leukocytes into the cerebrospinal fluid, and attenuated the increase of regional cerebral blood flow . Elevated intracranial pressure as well as the brain water content at 6 hours was reduced by triptans . These effects were partially reversed by a specific 5HT1D as well as by a specific 5HT1B receptor antagonist . Meningitis caused a depletion of calcitonin gene-related peptide (CGRP) and substance P from meningeal nerve fibers, which was prevented by zolmitriptan and naratriptan . In line with these findings, patients with bacterial meningitis had significantly elevated CGRP levels in the cerebrospinal fluid . In a mouse model of pneumococcal meningitis, survival and clinical score at 24 hours were significantly improved by triptan treatment . The findings suggest that, besides mediating meningeal nociception, meningeal nerve fibers contribute to the inflammatory cascade in the early phase of bacterial meningitis . Adjunctive treatment with triptans may open a new therapeutic approach in the acute phase of bacterial meningitis.

Int J STD AIDS, 2002 Jul, 13(7), 449 - 52
Bacterial vaginosis in climacteric and menopausal women; Taylor-Robinson D et al.; The objective was to determine how frequently an abnormal vaginal flora occurred in women attending a menopause clinic and whether any abnormality might be related to a particular risk factor . Women completed a questionnaire on their gynaecological, sexual and medical history . Whether they were perimenopausal or postmenopausal was determined on the basis of symptomatology, duration of amenorrhoea and on a follicle-stimulating hormone (FSH) assay when clinically indicated . A speculum examination of the vagina was undertaken, at which time a smear of vaginal secretion was Gram stained and the bacterial flora graded as follows: grade 1, normal; grade 2, intermediate, and grade 3, bacterial vaginosis (BV) . Of 100 women examined, 44 had grade 1 flora, 17 had grade 2 flora and 18 had BV . An apparent absence of, or very scanty, vaginal bacteria in which grading was not possible was found in 21 women . Women with BV had had more sexual partners than the others, but otherwise there were no discernible factors associated with the occurrence of BV . Women with vaginal atrophy were more likely to have an apparent absence of vaginal bacteria, but a few had BV.

J Mol Diagn, 2002 Aug, 4(3), 144 - 9
Rapid detection of IgH/BCL2 rearrangement in follicular lymphoma by interphase fluorescence in situ hybridization with bacterial artificial chromosome probes; Jiang F et al.; Follicular lymphomas (FLs) can be difficult to diagnose on aspirated specimens since the architectural pattern is not present . FLs characteristically have rearrangements in the IgH and BCL2 genes resulting from the reciprocal t(14;18) (q32; q21) translocation . Because of the dispersed distribution of breakpoints, fluorescence in situ hybridization (FISH) using genomic probes that span or flank the breakpoints is ideal for detecting this rearrangement in fine-needle aspiration (FNA) biopsies . To develop a set of probes, a bacterial artificial chromosome library was screened and the clones were mapped by fiber FISH . The probes were produced by the direct incorporation of fluorochrome-labeled nucleotides . The colocalization base FISH assay was applied to Cytospin preparations from FNA biopsies of lymph nodes from 26 patients with FL and 10 patients without FL . In those with FL, the percentage of cells with at least one IgH/BCL2 fusion signal ranged from 22% to 100% (mean, 63%), which was statistically significantly higher than that in FL-negative samples (mean, 2.7%) . The probes demonstrated a significantly lower cutoff value (7%) in normal controls and effectively reduced the false-positive rate in FL-negative cases . These results were confirmed with fiber FISH assays on the same specimens . This interphase FISH assay is rapid and reliable for detecting rearrangements in the IGH/BCL2 gene, thereby aiding in the diagnosis of FL on FNA biopsy specimens.

Nature, 2002 Aug 8, 418(6898), 662 - 5
Three-dimensional structure of the bacterial protein-translocation complex SecYEG; Breyton C et al.; Transport and membrane integration of polypeptides is carried out by specific protein complexes in the membranes of all living cells . The Sec transport path provides an essential and ubiquitous route for protein translocation . In the bacterial cytoplasmic membrane, the channel is formed by oligomers of a heterotrimeric membrane protein complex consisting of subunits SecY, SecE and SecG . In the endoplasmic reticulum membrane, the channel is formed from the related Sec61 complex . Here we report the structure of the Escherichia coli SecYEG assembly at an in-plane resolution of 8 A . The three-dimensional map, calculated from two-dimensional SecYEG crystals, reveals a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG . The monomeric complex contains 15 transmembrane helices . In the centre of the dimer we observe a 16 x 25 A cavity closed on the periplasmic side by two highly tilted transmembrane helices . This may represent the closed state of the protein-conducting channel.

Proc Natl Acad Sci U S A, 2002 Aug 20, 99(17), 11055 - 60 Epub 2002 Aug 07.
Interactions between lipids and bacterial reaction centers determined by protein crystallography; Camara-Artigas A et al.; The structure of the reaction center from Rhodobacter sphaeroides has been solved by using x-ray diffraction at a 2.55-A resolution limit . Three lipid molecules that lie on the surface of the protein are resolved in the electron density maps . In addition to a cardiolipin that has previously been reported {McAuley, K . E., Fyfe, P . K., Ridge, J . P., Isaacs, N . W., Cogdell, R . J . & Jones, M . R . (1999) Proc . Natl . Acad . Sci . USA 96, 14706-14711}, two other major lipids of the cell membrane are found, a phosphatidylcholine and a glucosylgalactosyl diacylglycerol . The presence of these three lipids has been confirmed by laser mass spectroscopy . The lipids are located in the hydrophobic region of the protein surface and interact predominately with hydrophobic amino acids, in particular aromatic residues . Although the cardiolipin is over 15 A from the cofactors, the other two lipids are in close contact with the cofactors and may contribute to the difference in energetics for the two branches of cofactors that is primarily responsible for the asymmetry of electron transfer . The glycolipid is 3.5 A from the active bacteriochlorophyll monomer and shields this cofactor from the solvent in contrast to a much greater exposed surface evident for the inactive bacteriochlorophyll monomer . The phosphate atom of phosphatidylcholine is 6.5 A from the inactive bacteriopheophytin, and the associated electrostatic interactions may contribute to electron transfer rates involving this cofactor . Overall, the lipids span a distance of approximately 30 A, which is consistent with a bilayer-like arrangement suggesting the presence of an "inner shell" of lipids around membrane proteins that is critical for membrane function.

Auris Nasus Larynx, 2002 Jul, 29(3), 241 - 5
Immunoreactivity for myeloperoxidase (MPO) in the vestibule after the injection of bacterial lipopolysaccharide into the middle ear; Watanabe K et al.; OBJECTIVE: In this study, the effect of endotoxin on the vestibule of the ear of guinea pigs was immunohistochemically examined . METHODS: Bacterial lipopolysaccharide was injected into the middle ear transtympanically . After 48 h, the animals were sacrificed by intracardiac perfusion of fixative; then, the temporal bones were removed and processed for immunohistochemical staining with the anti-myeloperoxidase antibody . RESULTS: Myeloperoxidase could be detected after 48 h in the sensory epithelium and the dark cell area . CONCLUSION: It is reported that radical oxygen species, which are cytotoxic, are detected under inflammatory conditions . Our results suggest that myeloperoxidase and reactive oxygen species are involved in vestibular dysfunction under inflammation.

Theor Popul Biol, 2002 Jun, 61(4), 503 - 7
Preferential orientation of natural lambdoid prophages and bacterial chromosome organization; Campbell AM; All known lambdoid prophages of Escherichia coli have the same orientation with respect to direction of chromosomal replication . This includes 12 prophages that are replicated in one direction and five in the other . Among candidate explanations, the most amenable to experimental study is an effect on dif site function in assuring chromosomal segregation . This is but one of numerous examples of strand bias in the E . coli genome, all of which may interact with one another .

Shock, 2002 Aug, 18(2), 148 - 51
The effects of pentoxifylline on bacterial translocation after intestinal obstruction; Kocdor MA et al.; Bacterial translocation (BT) occurs mainly in preseptic conditions such as intestinal obstruction, trauma, and burn, and the underlying mechanisms are still unclear . Pentoxifylline (PTX) is a derivative of methyl xanthine and has several beneficial effects in sepsis . We investigated the effects of PTX on a rat BT model . Simple intestinal obstruction (IO) was choosen to create high BT rates . Rats were divided in to five groups of 10 rats . Either 50 mg/kg PTX or placebo (3 mg/100 g saline) was administered subcutaneously following IO, either by single injection or twice with a 12-h interval . All rats were sacrificed 12 or 24 h after the procedure, and mesenteric lymph nodes (MLN), liver, and blood samples were obtained under aseptic conditions for bacterial cultures . The samples were obtained 12 h following IO in the first two groups, and the same samples were obtained 24 h after IO in last three groups . Groups IV and V were the PTX treatment groups . PTX was re-injected 12 h after IO only in group IV . As a result, BT rates in MLNs and liver were found to be significantly low, blood specimens remained sterile in PTX-pretreated and -treated rats, and BT rates were high in control groups and group V (once treatment late specimen group) . We conclude that simple intestinal obstruction causes BT, and PTX reduces BT in rats with IO during the first 12-h period if PTX is given once immediately following IO . PTX reduces BT during the first 24-h after IO provided that is injected twice with a 12-h interval . More experimental studies are need to explain the exact mechanism of this beneficial effect.

Endocrine, 2002 Jun, 18(1), 13 - 20
Bacterial lipopolysaccharide-induced coordinate downregulation of arginine vasopressin receptor V3 and corticotropin-releasing factor receptor 1 messenger ribonucleic acids in the anterior pituitary of endotoxemic steers; Qahwash IM et al.; AVP and CRF are potent stimulators of pituitary ACTH secretion in cattle . Actions of AVP and CRF at the anterior pituitary are mediated by AVP receptor V3 (V3) and CRF receptor 1 (CRFR1) . The primary objective of these studies was to determine the effect of systemic inflammatory stress on V3 and CRFR1 mRNAs in the bovine anterior pituitary . Holstein steers (n = 20) were injected with 200 ng/kg bacterial lipopolysaccharide (LPS) and tissues collected 0, 2, 4, 12, and 24 h later . All animals responded to LPS administration with an increase in body temperature, plasma ACTH, and cortisol (p < 0.05) . Abundance of anterior pituitary V3 mRNA was decreased at 2, 4, and 12 h following LPS administration (p < 0.05) and returned to basal by 24 h . A similar temporal regulation of pituitary CRFR1 mRNA (p < 0.05), but not pituitary pro-opiomelanocortin (POMC) mRNA, was observed following LPS administration . Similar downregulation of CRFR1 mRNA was not observed in other brain regions following LPS administration (cerebellum, hypothalamus) . Our results indicate that V3 and CRFR1 mRNAs are coordinately downregulated in the anterior pituitary during systemic inflammatory stress . Decreased AVP and CRF receptor expression may help regulate the pituitary-adrenal response to stress.

Oral Dis, 2002, 8 Suppl 2, 80 - 7
Oral fungal and bacterial infections in HIV-infected individuals: an overview in Africa; Hodgson TA et al.; Oral opportunistic infections developing secondary to human immunodeficiency virus (HIV) infection have been reported from the early days of the epidemic and have been classified by both the EC-Clearinghouse and the World Health Organisation (WHO) . Among the fungal infections, oral candidiasis, presenting in African HIV-infected patients has been sporadically documented . We review the literature with respect to candidal carriage, oral candidiasis prevalence and the predictive value of oral candidiasis for a diagnosis of underlying HIV disease in African HIV-infected patients . The use of oral candidiasis as a marker of disease progression, the species of yeasts isolated from the oral cavity in Africa and the resistance of the yeasts to antifungal agents and treatment regimens are discussed . Orofacial lesions as manifestations of the systemic mycoses are rarely seen in isolation and few cases are reported in the literature from Africa . In spite of the high incidence of noma, tuberculosis, chronic osteomyelitis and syphilis in Africa, surprisingly there have been very few reported cases of the oral manifestations of these diseases in HIV-positive individuals . Orofacial disease in HIV-infected patients is associated with marked morbidity, which is compounded by malnutrition . The authors indicate specific research areas, initially directed at the most effective management strategies, which would complete data in this important area.

Kaohsiung J Med Sci, 2002 Apr, 18(4), 164 - 70
Improving Gram-stained reproducible result by further adding clue cells in diagnosing bacterial vaginosis; Lin DP et al.; The reproducibility of interpretation in diagnosing bacterial vaginosis may be enhanced by adding pus cells and clue cells into two different criteria, developed by Spiegel et al . and Nugent et al . The purpose of study was designed to find out which parameter was more reproducible . 100 patients were collected with the diagnosis of bacterial vaginosis as an experimental group, while the other 100 patients who were with routine Papanicolaou smears in gynecologic clinic the collected as a control group . Two slides, including the original and reproducible ones, were obtained from vaginal smears for each patient . Three technicians read the slides randomly by using two different criteria, plus pus cells and clue cells . This showed the agreement for clue cells is the best method regardless of experimental group or control group (Kappa values between 0.708 and 1.000) . The intra-observer agreement for the diagnosis of bacterial vaginosis by the method of Nugent et al . is superior to the method of Spiegel et al . Our data show the comparison of Amsel criteria versus Nugent criteria for the diagnosis of bacterial vaginosis with sensitivity of 88.9%, specificity of 55.4%, negative positive value of 62.1%, and positive predictive value of 85.8% . Moreover, our data also demonstrate the comparison of Amsel criteria versus the diagnosis either based on Nugent criteria or the presence of clue cells with sensitivity of 95.7%, specificity of 56.7%, negative positive value of 81.2%, and positive predictive value of 87.1% . The results demonstrate further adding score of the clue cells can enhance the reproducible diagnosis of bacterial vaginosis, which is superior to the methods of Nugent et al . and Spiegel et al.

Otolaryngol Head Neck Surg, 2002 Jul, 127(1), 1 - 6
Short treatment durations for acute bacterial rhinosinusitis: Five days of gemifloxacin versus 7 days of gemifloxacin; Ferguson BJ et al.; OBJECTIVE: The primary objective of this study was to demonstrate the clinical and radiologic efficacy of 5 days compared with 7 days of gemifloxacin therapy in the treatment of acute bacterial rhinosinusitis (ABRS) . STUDY DESIGN: In this prospective, double-blind, multicenter, parallel-group study, adult patients presenting with ABRS were randomized to receive gemifloxacin 320 mg once daily for either 5 days (n = 218) or 7 days (n = 203) . RESULTS: For the primary efficacy end point, clinical response to therapy at follow-up, 5 days of therapy with gemifloxacin was as effective as 7 days of therapy (per-protocol population; treatment difference 0.44%; 95% confidence interval {CI}, -6.54 to 7.41) . Five and 7 days of treatment with gemifloxacin were well tolerated . CONCLUSION AND SIGNIFICANCE: The clinical efficacy of gemifloxacin 320 mg daily for 5 days is at least as good as the efficacy of gemifloxacin 320 mg daily for 7 days in the treatment of ABRS.

Environ Microbiol, 2002 Aug, 4(8), 477 - 81
nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass; Hamelin J et al.; Rhizosphere associative dinitrogen fixation could be a valuable source of nitrogen in many nitrogen limited natural ecosystems, such as the rhizosphere of Molinia coerulea, a hemicryptophytic perennial grass naturally occurring in contrasted oligonitrophilic soils . The diversity of the dinitrogen-fixing bacteria associated with this environment was assessed by a cloning-sequencing approach on the nifH gene directly amplified from environmental DNA extracts . Seventy-seven randomly picked clones were analysed . One type of NifH sequence was dominant in both roots and surrounding soil, and represented 56% of all retrieved sequences . This cluster included previously described environmental clones and did not contain any NifH sequences similar to cultivated diazotrophs . The predominance of few NifH sequence types in the roots and the rhizosphere of Molinia coerulea indicate that the plant environment mediates a favourable niche for such dinitrogen-fixing bacteria.

Biotechnol Prog, 2002 Jul-Aug, 18(4), 686 - 93
Nonlinear dynamics of regulation of bacterial trp operon: model analysis of integrated effects of repression, feedback inhibition, and attenuation; Xiu ZL et al.; The trp operon encodes the five genes for the enzymes required to convert chorismate to tryptophan, and its switching on and off is controlled by both feedback repression and attenuation in response to different levels of tryptophan in the cell . Repression of the operon occurs when tryptophan concentration is high, and attenuation fine-tunes the transcription level at a lower cellular concentration of tryptophan . An extended mathematical model is established in this study to describe the switching on and off of the trp operon by considering the integrated effects of repression and attenuation . The influences of cell growth rate on the biosynthesis of tryptophan, stability and dynamic behavior of the trp operon are investigated . Sustained oscillations of tryptophan levels are predicted from the regulated turning on and off of the trp operon . It is interesting to note that during such oscillations the regulation of transcription displays a kind of "on" and "off" state in terms of gene expression, indicating the existence of a genetic circuit or switch in the regulation of the trp operon . Time lags between transcription and translation are also predicted and may explain the occurrence of such oscillation phenomenon.

Water Res, 2002 May, 36(10), 2561 - 70
Hydrogeochemical controls on the organic matter and bacterial ecology of a small freshwater wetland in the New Jersey Pine Barrens; Maurice PA et al.; This study investigated the effects of variable ground-water/surface-water exchange and photoinduced processes on longitudinal patterns in dissolved organic matter (DOM) and bacterial communities in a small first-order stream in the New Jersey Pine Barrens . DOM concentration, along with DOM weight average molecular weight (Mw) and absorptivity (epsilon280, an estimator of aromaticity), and bacterial cell counts all decreased from the stream and hyporheic zone into the shallow aquifer in a ground-water recharge zone . Further downstream, influx of ground water into the stream resulted in a lower Mw DOM pool and was accompanied by decreased cell counts . The observed effect of this ground-water discharge on bacterial numbers may be direct, if discharge temporarily dilutes cell counts, or indirect, if changes in DOM concentration and properties control the bacterial community . In either case, this study suggested the importance of considering ground-water-surface-water exchange in studies of longitudinal changes in the bacterial communities of streams.

Dis Aquat Organ, 2002 Jun 21, 50(1), 1 - 8
Usefulness of dead shrimp specimens in studying the epidemiology of white spot syndrome virus (WSSV) and chronic bacterial infection; Mohan CV et al.; This paper describes the utility of dead shrimp samples in epidemiological investigations of the white spot syndrome virus (WSSV) and chronic bacterial infections . A longitudinal observational study was undertaken in shrimp farms in Kundapur, Karnataka, India, from September 1999 to April 2000 to identify risk factors associated with outbreaks of white spot disease (WSD) in cultured Penaeus monodon . As a part of the larger study, farmers were trained to collect and preserve dead and moribund shrimp (when observed) during the production cycle . At the end of the production cycle, 73 samples from 50 ponds had been collected for histopathology and 55 samples from 44 ponds for PCR . Intranuclear viral inclusion bodies diagnostic of WSSV infection were detected in dead samples from 32 ponds (64 %) . Samples of dead shrimp from 18 ponds (36%) showed no histopathological evidence of WSSV infection . However, of these, samples from 13 ponds (26%) showed clear evidence of shell, oral, enteric and systemic chronic inflammatory lesions (CIL) in the form of haemocytic nodules, typical of bacterial infection . Samples from 5 ponds (10%) were negative for both WSSV and CIL . Samples from 8 ponds had dual WSSV and CIL, although both WSSV and CIL were only observed in the same shrimp from 1 pond . Useful information was obtained from these shrimp despite the presence of post-mortem changes . Samples from 19 ponds (43%) tested positive for WSSV by 1-step PCR and samples from an additional 10 ponds (22.7%) were positive by 2-step nested PCR . Samples from 15 ponds (34.1%) were negative for WSSV by 2-step nested PCR . There was moderate to substantial agreement between PCR and histopathology in the diagnosis of WSSV infection in dead shrimp . WSSV infection in dead shrimp was significantly associated with crop failures as defined by a shorter length of the production cycle (<90 d) and lower average weight at harvest (<22 g) . WSSV infection was also associated with lower survival (<50%), but this was not significant . Ponds with CIL did not experience any crop failures, and the presence of CIL was significantly associated with successful crops . The study demonstrates that samples of dead shrimp can provide useful information for disease surveillance and epidemiological investigations of WSSV and chronic bacterial infections.

Cell, 2002 Jul 12, 110(1), 1 - 4
Dancing with the host; flow-dependent bacterial adhesion; Isberg RR et al.; Most bacteria that colonize eukaryotes must bind directly to host cells to establish a replicative niche . In enteric bacteria, adhesion to host cells is often promoted by a lectin found on surface-localized pili . Some pili promote efficient adhesion only when they are subjected to shear stress, as found during the flow of blood over endothelium or mucous over the surface of the epithelium.

Kaohsiung J Med Sci, 2002 Mar, 18(3), 121 - 6
Clinical application of serum C-reactive protein measurement in the detection of bacterial infection in patients with liver cirrhosis; Lin ZY et al.; A significant proportion of patients with cirrhosis can demonstrate elevated serum C-reactive protein (CRP) values which are not stimulated by bacterial infection . This may limit the clinical application of CRP determination in patients with cirrhosis . Therefore, we designed this prospective study to clarify whether serum CRP value could be used as an indicator of bacterial infection in patients with cirrhosis or not . A total of 129 sessions of admission (bacterial infection 46, bacterial infection and gastrointestinal hemorrhage 5, gastrointestinal hemorrhage 24, other causes 54) from 94 patients with cirrhosis were studied . Serum CRP value was determined on admission . The normal range of CRP value was < 6 micrograms/ml . The serum CRP values obtained on admission ranged from 3 to 232 micrograms/ml in patients with bacterial infection, 17 to 178 micrograms/ml in patients with bacterial infection and hemorrhage, < 1 to 44 micrograms/ml in patients with gastrointestinal hemorrhage, and < 1 to 54 micrograms/ml in patients with other causes of admission . Using the normal upper limit of CRP value as a cut-off value did not differentiate those patients with from those without bacterial infection . However, using the CRP value of 20 micrograms/ml which was obtained from receiver-operating characteristic curves could differentiate between two groups of patients (sensitivity 80.39%, specificity 80.77%, accuracy 80.62%) . In conclusion, serum CRP determination can be used in the detection of bacterial infection in patients with cirrhosis . However, a new cut-off value should be applied.

J Clin Microbiol, 2002 Aug, 40(8), 3057 - 9
DNA hybridization test: rapid diagnostic tool for excluding bacterial vaginosis in pregnant women with symptoms suggestive of infection; Witt A et al.; This prospective comparative study evaluated a DNA hybridization test (Affirm VPIII) as an alternative to Gram stain for the diagnosis of bacterial vaginosis . We examined vaginal smears from 1,725 pregnant women between the 12th and 36th weeks of gestation with clinical signs of vaginal infection . The DNA hybridization test compared well with Gram stain and can be used as a rapid diagnostic tool to exclude bacterial vaginosis.

Biotechnol Appl Biochem, 2002 Aug, 36(Pt 1), 41 - 5
Development of an optimized, simple chemically defined medium for bacterial cellulose production by Acetobacter sp . A9 in shaking cultures; Heo MS et al.; The genus Acetobacter can synthesize cellulose when grown in an undefined medium containing glucose . By using the technique of the omission of a single medium component, an optimized and simple chemically defined medium was developed to support cellulose production by Acetobacter sp . A9 in shaking culture . It contained 4.0% (w/v) glucose, 0.2% (w/v) (NH(4))(2)SO(4), 0.25% (w/v) KH(2)PO(4), 0.3% (w/v) Na(2)HPO(4).12H(2)O, 0.05% (w/v) MgSO(4).7H(2)O, 0.0002% (w/v) FeSO(4).7H(2)O, 0.00025% (w/v) H(3)BO(3), 0.00006% (w/v) nicotinamide, 0.00025% (w/v) inositol and 1.4% (v/v) ethanol . A maximum cellulose concentration of around 8 g/l was achieved after 9 days of cultivation at 200 rev./min . The production of cellulose by Acetobacter sp . A9 was greater in simplified synthetic medium than in complex medium (Hestrin and Schramm medium) conventionally used for Acetobacter strains.

Am J Reprod Immunol, 2002 May, 47(5), 257 - 64
Correlation of local interleukin-1beta levels with specific IgA response against Gardnerella vaginalis cytolysin in women with bacterial vaginosis; Cauci S et al.; PROBLEM: Mucosal immune system activation may represent a critical determinant of adverse sequelae correlated with bacterial vaginosis, as HIV sexual transmission, upper genital tract infections, cervicitis, endometritis, postsurgical infections, and adverse pregnancy outcomes as preterm delivery (PTD), low birth weight (LBW) . METHOD OF STUDY: Levels of interleukin-1beta (IL-1beta), anti-Gardnerella vaginalis hemolysin (Gvh) IgA, pH, Nugent score, and number of leukocytes were measured in vaginal fluids of 60 fertile women with bacterial vaginosis and of 64 healthy controls . RESULTS: Vaginal IL-1beta levels were nearly 13-fold higher in women with bacterial vaginosis (BV) and were associated with anti-Gvh IgA response . IL-1beta was positively correlated with leukocyte counts in the smear both in healthy and bacterial vaginosis positive women . CONCLUSIONS: Induction of the proinflammatory cytokine IL-1beta may be a necessary event to elicit an innate immune response to control anaerobic genital tract infections . High levels of vaginal IL-1beta are associated with mounting of an antigen-specific mucosal immune response in women with bacterial vaginosis . Parallel induction of innate and adaptive immune response may be associated with protection from ascent of micro-organisms to the upper genital tract, and from acquiring viral infection through the vaginal tract.

J Biol Chem, 2002 Oct 4, 277(40), 37456 - 63 Epub 2002 Jul 29.
The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing; Ederth J et al.; Regulation of RNA polymerase during initiation, elongation, and termination of transcription is mediated in part by interactions with intrinsic regulatory signals encoded in the RNA and DNA that contact the enzyme . These interactions include contacts to an 8-9-bp RNA:DNA hybrid within the active-site cleft of the enzyme, contacts to the melted nontemplate DNA strand in the vicinity of the hybrid, contacts to exiting RNA upstream of the hybrid, and contacts to approximately 20 bp of duplex DNA downstream of the active site . Based on characterization of an amino acid substitution (G1161R) and a deletion (Delta1149-1190) in the jaw domain of the bacterial RNA polymerase largest subunit (beta'), we report here that contacts of the jaw domain to downstream DNA at the leading edge of the transcription complex contribute to regulation during all three phases of transcription . The results provide insight into the role of the jaw domain-downstream DNA contact in transcriptional initiation and pausing and suggest possible explanations for the previously reported isolation of the jaw mutants based on reduced ColEI plasmid replication.

Appl Environ Microbiol, 2002 Aug, 68(8), 4061 - 6
Molecular breeding of transgenic rice plants expressing a bacterial chlorocatechol dioxygenase gene; Shimizu M et al.; The cbnA gene encoding the chlorocatechol dioxygenase gene from Ralstonia eutropha NH9 was introduced into rice plants . The cbnA gene was expressed in transgenic rice plants under the control of a modified cauliflower mosaic virus 35S promoter . Western blot analysis using anti-CbnA protein indicated that the cbnA gene was expressed in leaf tissue, roots, culms, and seeds . Transgenic rice calluses expressing the cbnA gene converted 3-chlorocatechol to 2-chloromucote efficiently . Growth and morphology of the transgenic rice plants expressing the cbnA gene were not distinguished from those of control rice plants harboring only a Ti binary vector . It is thus possible to breed transgenic plants that degrade chloroaromatic compounds in soil and surface water.

Arch Biochem Biophys, 2002 Aug 15, 404(2), 227 - 33
Conservation of the free energy change of the alkaline isomerization in mitochondrial and bacterial cytochromes c; Battistuzzi G et al.; The thermodynamic parameters of the alkaline transition for oxidized native yeast iso-1 cytochrome c and Rhodopseudomonas palustris cytochrome c(2) (cytc(2)) have been determined through direct electrochemistry experiments carried out at variable pH and temperature and compared to those for horse and beef heart cytochromes c . We have found that both transition enthalpy and entropy are remarkably species dependent, following the order R . palustris cytc(2) >> beef (horse) heart cytc>yeast iso-1 cytc . Considering the high homology at the heme-protein interface in the native species, this variability is likely to be mainly determined by differences in the structural and solvation properties and the relative abundance of the various alkaline conformers . Notably, changes in transition enthalpy and entropy among these cytochromes c are compensative and result in small variations in the free energy change of the process (which amounts approximately to +50 kJ mol(-1)) and consequently in the apparent pK(a) value . This compensation indicates that solvent reorganization effects play an important role in the thermodynamics of the transition . This mechanism is functional to ensure a relatively high pK(a) value for the alkaline transition, which is needed to preserve His,Met ligation to the heme iron in cytochrome c at physiological pH and temperature, hence the E(o) value required for the biological function .

Biochemistry, 2002 Aug 6, 41(31), 10021 - 5
Exploring the energy landscape for Q(A)(-) to Q(B) electron transfer in bacterial photosynthetic reaction centers: effect of substrate position and tail length on the conformational gating step; Xu Q et al.; The ability to initiate reactions with a flash of light and to monitor reactions over a wide temperature range allows detailed analysis of reaction mechanisms in photosynthetic reaction centers (RCs) of purple bacteria . In this protein, the electron transfer from the reduced primary quinone (Q(A)(-)) to the secondary quinone (Q(B)) is rate-limited by conformational changes rather than electron tunneling . Q(B) movement from a distal to a proximal site has been proposed to be the rate-limiting change . The importance of quinone motion was examined by shortening the Q(B) tail from 50 to 5 carbons . No change in rate was found from 100 to 300 K . The temperature dependence of the rate was also measured in three L209 proline mutants . Under conditions where Q(B) is in the distal site in wild-type RCs, it is trapped in the proximal site in the Tyr L209 mutant {Kuglstatter, A., et al . (2001) Biochemistry 40, 4253-4260} . The electron transfer slows at low temperature for all three mutants as it does in wild-type protein, indicating that conformational changes still limit the reaction rate . Thus, Q(B) movement is unlikely to be the sole, rate-limiting conformational gating step . The temperature dependence of the reaction in the L209 mutants differs somewhat from wild-type RCs . Entropy-enthalpy compensation reduces the difference in rates and free energy changes at room temperature.

Cell Mol Biol (Noisy-le-grand), 2002 Jul, 48(5), 521 - 4
Radiation induced-like effects of four home bleaching agents used for tooth whitening: effects on bacterial cultures with different capabilities of repairing deoxyribonucleic acid (DNA) damage; Zouain-Ferreira SL et al.; "Home bleaching" methods are commonly used in dentistry to correct tooth discoloration . This technique employs carbamide peroxide, in several concentrations, where the active component is hydrogen peroxide . In patients undertaking this treatment, this exposure can cause biological effects mainly due to the activity of hydrogen peroxide . Hydrogen peroxide is associated with effects induced by chemical (natural and synthetic substances) and physical agents (ionizing radiations) . We have evaluated the cytotoxic effects of four commercial dental bleaching agents: Insta-Brite, Karisma, Opalescence and Whiteness . We have studied the effects of these agents on the survival of different E . coli strains with various capabilities to repair damages on the deoxyribonucleic acid (DNA): AB1157 (wild type), AB2463 (recA) and BW9091 (xthA) . To determine the effect of the bleaching agents on the survival of E . coli AB1157, AB2463 and BW9091, cultures in exponential growth-phase were incubated with the bleaching agent or with 0.9% NaCl, as a control . After plating, the survival fractions were determined . The bleaching agents tested decreased the survival fractions of all strains studied and the E . coli BW9091 was the most sensitive and, moreover, these bleaching agents are capable of inducing damage to the DNA molecule . In conclusion, our results indicate that dental bleaching agents can generate biological effects like the ionizing radiations, and we suggest that dental professionals involved in bleaching to correct tooth discoloration, should control the clinical environment strictly, thus preventing contact between the oral mucosa/gingival tissues and the bleaching agents.

Phys Rev Lett . 2002 Jul 15;89(3):038101 . Epub 2002 Jul 01.
Model for mutation in bacterial populations; Donangelo R et al.; We describe the evolution of E . coli populations through a Bak-Sneppen-type model which incorporates random mutations . We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model reproduces the measures of mean fitness relative to that of a common ancestor, performed for over 10,000 bacterial generations.

Nutr Rev, 2002 Jul, 60(7 Pt 1), 201 - 8
Subtyping of bacterial foodborne pathogens; Wiedmann M; Phenotype-based and DNA-based subtyping methods allow for differentiation of bacterial isolates beyond the species and subspecies level . Bacterial subtyping methods not only have improved our ability to detect and track foodbome disease outbreaks, but also represent tools to track sources of bacterial contamination throughout the food system . The use of subtyping methods furthermore provides an opportunity to better understand the population genetics, epidemiology, and ecology of different foodbome pathogens . The last 5 years have seen tremendous advancement in the development of sensitive, rapid, automated, and increasingly easy-to-use molecular subtyping methods for a variety of different bacterial foodborne pathogens . This review will highlight key aspects of different subtyping methods for bacterial foodborne pathogens and provide examples of their applications in public health, food safety, epidemiology, and population genetics . Molecular subtyping and characterization methods may also facilitate the development of a novel framework for tracking, preventing, and regulating foodborne bacterial diseases, which is based on evolutionary relationships and genetic characteristics rather than traditional species definitions.

Annu Rev Microbiol, 2002, 56, 457 - 87 Epub 2002 Jan 30.
What are bacterial species?
Cohan FM.
Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species . The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species . Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct . In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes . These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection . These ecotypes can be discovered by several universal sequence-based approaches . These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species . A named bacterial species is thus more like a genus than a species.

Annu Rev Cell Dev Biol, 2002, 18, 315 - 44 Epub 2002 Apr 02.
Bacterial toxins that modify the actin cytoskeleton; Barbieri JT et al.; Bacterial pathogens utilize several strategies to modulate the organization of the actin cytoskeleton . Some bacterial toxins catalyze the covalent modification of actin or the Rho GTPases, which are involved in the control of the actin cytoskeleton . Other bacteria produce toxins that act as guanine nucleotide exchange factors or GTPase-activating proteins to modulate the nucleotide state of the Rho GTPases . This latter group of toxins provides a temporal modulation of the actin cytoskeleton . A third group of bacterial toxins act as adenylate cyclases, which directly elevate intracellular cAMP to supra-physiological levels . Each class of toxins gives the bacterial pathogen a selective advantage in modulating host cell resistance to infection.

J Biotechnol, 2002 Jun 13, 96(1), 3 - 12
Construction and deconstruction of bacterial inclusion bodies; Carrio MM et al.; Bacterial inclusion bodies (IBs) are refractile aggregates of protease-resistant misfolded protein that often occur in recombinant bacteria upon gratuitous overexpression of cloned genes . In biotechnology, the formation of IBs represents a main obstacle for protein production since even favouring high protein yields, the in vitro recovery of functional protein from insoluble deposits depends on technically diverse and often complex re-folding procedures . On the other hand, IBs represent an exciting model to approach the in vivo analysis of protein folding and to explore aggregation dynamics . Recent findings on the molecular organisation of embodied polypeptides and on the kinetics of inclusion body formation have revealed an unexpected dynamism of these protein aggregates, from which polypeptides are steadily released in living cells to be further refolded or degraded . The close connection between in vivo protein folding, aggregation, solubilisation and proteolytic digestion offers an integrated view of the bacterial protein quality control system of which IBs might be an important component especially in recombinant bacteria.

Arch Biochem Biophys, 2002 Jul 15, 403(2), 237 - 48
Bacterial expression of the molybdenum domain of assimilatory nitrate reductase: production of both the functional molybdenum-containing domain and the nonfunctional tungsten analog; Pollock VV et al.; Assimilatory NADH:nitrate reductase (EC 1.6.6.1), a complex molybdenum-, cytochrome b(557)- and FAD-containing protein, catalyzes the regulated and rate-limiting step in the utilization of inorganic nitrogen by higher plants . To facilitate structure/function studies of the individual molybdenum center, we have developed bacterial expression systems for the heterologous production of the 541 residue amino-terminal, molybdenum center-containing domain of spinach nitrate reductase either as a six-histidine-tagged variant or as a glutathione-S-transferase-tagged fusion protein . Expression of the his-tagged molybdenum domain in Escherichia coli BL21(DE3) cells under anaerobic conditions yielded a 55-kDa domain with a specific activity of 1.5 micromol NO(3)(-) consumed/min/nmol enzyme and with a K(mapp)(NO(3)(-)) of 8 mciroM . In contrast, expression of the molybdenum domain as a GST-tagged fusion protein in E . coli TP1000(MobA(-) strain) cells under aerobic conditions yielded an 85-kDa fusion protein with a specific activity of 10.8 micromol NO(3)(-) consumed/min/nmol enzyme and with a K(mapp)(NO(3)(-)) of 12 microM . Fluorescence analysis indicated that both forms of the molybdenum domain contained the cofactor, MPT, although the MPT content was higher in the GST-fusion domain . Inductively coupled plasma mass spectrometric analysis of both the his-tagged and GST-fusion protein domain samples indicated Mo/protein ratios of 0.44 and 0.93, respectively, confirming a very high level of Mo incorporation in the GST-fusion protein . Expression of the GST-fusion protein in TP1000 cells in the presence of elevated tungsten concentrations resulted in an 85-kDa fusion protein that contained MPT but which was devoid of nitrate-reducing activity . Partial reduction of the molybdenum domain resulted in the generation of an axial Mo(V) EPR species with g values of 1.9952, 1.9693, and 1.9665, respectively, and exhibiting superhyperfine coupling to a single exchangeable proton, analogous to that previously observed for the native enzyme . In contrast, the tungsten-substituted MPT-containing domain yielded a W(V) EPR species with g values of 1.9560, 1.9474, and 1.9271, respectively, with unresolved superhyperfine interaction . NADH:nitrate reductase activity could be reconstituted using the GST-molybdenum domain fusion protein in the presence of the recombinant forms of the spinach nitrate reductase' flavin- and heme-containing domains.

J Mol Biol, 2002 Aug 2, 321(1), 7 - 20
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors; Mirny LA et al.; Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes . Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs . We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition . Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design . Assuming conservation of specificity among orthologs and different specificity of paralogs, we identify residues that correlate with this grouping by specificity . The method is taking advantage of complete genomes to find multiple orthologs and paralogs . The central part of this method is a procedure to compute statistical significance of the predictions . The procedure is based on a simple statistical model of protein evolution . When applied to a large family of bacterial transcription factors, our method identified 12 residues that are presumed to determine the protein-DNA and protein-ligand recognition specificity . Structural analysis of the proteins and available experimental results strongly support our predictions . Our results suggest new experiments aimed at rational re-design of specificity in bacterial transcription factors by a minimal number of mutations.

Am J Trop Med Hyg, 2002 Mar, 66(3), 234 - 7
Polymerase chain reaction-based identification and genotyping of Anopheles mosquitoes with a 96-pin bacterial replicator; Rafferty CS et al.; A simple method for rapid identification of large numbers of Anopheles mosquitoes was developed based on polymerase chain reaction (PCR) amplification of the rDNA intergenic spacer and internal transcribed spacer 2 . By means of previously described primers for the Anopheles gambiae and An . quadrimaculatus species complexes, rDNA was amplified simultaneously from 96 whole mosquitoes or parts . No homogenization or individual DNA preparation was necessary, and transfer of 96 samples to PCR reactions was performed simultaneously with a bacterial replicator . Control reactions indicate that the level of cross-contamination is negligible, and false-negative findings are rare . The method was tested on larvae, pupae, adult heads, whole adult males and females, and single tarsi . All parts except tarsi provided satisfactory template . Fresh, ethanol-preserved, dried, and frozen adults were also tested with similar results . The method was also tested for amplification of a single-copy gene, white . Results were generally positive, although some false-negative findings were observed . This method allows rapid analysis of large numbers of mosquitoes without robotic equipment and should enable rapid and extensive PCR analysis of field-collected samples and laboratory specimens.

Indian J Med Res, 2002 Feb, 115, 55 - 8
Association of tumour necrosis factor alpha & malnutrition with outcome in children with acute bacterial meningitis; Hemalatha R et al.; BACKGROUND & OBJECTIVES: Tumour necrosis factor alpha (TNF alpha) is implicated in the pathogenesis of acute bacterial meningitis (ABM) . However, we do not know if the nutritional status influences the concentration of TNF alpha in the CSF in children with ABM . The present study evaluates the association between malnutrition and TNF alpha detectability in CSF and the outcome from ABM in children . METHODS: A total of 120 children aged 1-5 yr diagnosed as ABM, based on the standard criteria of CSF changes were recruited for the study . A CSF sample was collected at the time of admission . TNF alpha was measured by ELISA and CSF culture was done by standard technique . Nutritional status was assessed by anthropometry . Outcome was measured by clinical examination . RESULTS: Of the 120 children, 20 died, 36 developed complications and 64 children recovered without sequelae . TNF alpha was detectable in 94 (78.3%) CSF samples, with a range of 32 to 1714 pg/ml . TNF alpha detectability was not associated with either nutritional status or with death and sequelae . However, death and sequelae were significantly (P = 0.01) associated with malnutrition . INTERPRETATION & CONCLUSION: CSF TNF alpha was not associated with nutritional status . However, malnutrition was associated with adverse outcome due to ABM in children.

Rev Gastroenterol Peru, 2000 Jan, 20(1), 49 - 52
{BACTERIAL PERITONITIS HIGH VOLUMEN LAVAGE TREATMENT}; Durand Lopez C; OBJECTIVE: To better define appropriate management of patients with disseminated purulent peritonitis using GREAT VOLUME PERITONEAL LAVAGE (GVPL).DESIGN : Prospective, comparative study.SETTING : "JOSE CASIMIRO ULLOA" Emergency Hospital, Lima Per .PATIENTS: 50 adult patients with disseminated purulent peritonitis plus feces in peritoneal cavity, which were operated using GVPL . Previously we evaluated 100 cases of the same disease operated without GVPL, in order to compare with our new results . INTERVENTION: All patients received pre-operative antibiotics, exploratory laparotomy was done to solve the cause of peritonitis, using a mean of 26 liters (20-42) of sterile lukewarm water for peritoneal lavage, to retire the pus and the fibrin adhered to intestinal surface.MAIN OUTCOME MEASURES: GVPL may be a definitive surgical solution for cases of disseminated purulent peritonitis.RESULTS: The 50 patients treated with GVPL were operated only one time and did not present post-operative surgical complication, the hospital stay was diminished.The 100 patients operated before we started this study presented 3% mortality, 81% morbidity and 19% were re-operated . CONCLUSIONS: GVPL method is the best surgical way to cure patients with disseminated purulent peritonitis.

Sci STKE . 2002 Jul 23;2002(142):PL11.
Analysis of phosphorylation-dependent protein-protein interactions using a bacterial two-hybrid system; Shaywitz AJ et al.; Phosphorylation-dependent protein-protein interactions provide the foundation for a multitude of intracellular signal transduction pathways . One of the goals of signal transduction research is to more precisely understand the nature of these phosphorylation-dependent interactions . Here, we describe a bacterial two-hybrid assay that allows for the rapid, efficient analysis of phosphorylation-dependent protein-protein interactions . In this system, the interacting protein domains are provided as fusion proteins in Escherichia coli . cells that contain a eukaryotic kinase . Specific phosphorylation of one of the fused protein domains results in a protein-protein interaction that can be detected as a change in the expression of a reporter gene . We also describe how this system can be modified to permit the use of cDNA libraries to identify either novel binding partners for a phosphorylated substrate or novel kinases that can induce a specific protein-protein interaction.

J Biol Chem, 2002 Sep 27, 277(39), 36640 - 5 Epub 2002 Jul 22.
The core of the bacterial translocase harbors a tilted transmembrane segment 3 of SecE; Veenendaal AK et al.; The bacterial translocase mediates the translocation and membrane integration of proteins . The integral membrane proteins SecY and SecE are conserved core subunits of the translocase . Previous cysteine-scanning studies showed that the transmembrane segment (TMS) 3 of SecE contacts TMS 2 and 7 of SecY, and TMS 3 of another SecE . We now demonstrate that SecE also contacts TMS 10 of SecY . Combining all available cysteine-scanning mutagenesis data, a three-dimensional model has been built in which the positions of the helices that form the central core of the bacterial translocase are mapped . Remarkably, this model reveals that TMS 3 of SecE is strongly tilted relative to SecY.

Gene, 2002 Jun 26, 293(1-2), 205 - 11
Two-dimensional display and whole genome comparison of bacterial pathogen genomes of high G+C DNA content; Malloff CA et al.; High-resolution comparison of bacterial genomes facilitates the identification of the genetic changes responsible for clinically relevant phenotypes . For this purpose we have established a method for the display and comparison of high G+C bacterial genomes in two dimensions . Here we describe the application of two-dimensional bacterial genomic display to resolve the genomes of Bordetella pertussis, Mycobacterium avium and Mycobacterium tuberculosis, and its utility in strain comparison and detection of insertion and substitution mutations.

Genetics, 2002 Jul, 161(3), 1101 - 12
Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation; Garigan D et al.; The genetic analysis of life span has revealed many interesting genes and pathways; however, our understanding of aging has been limited by the lack of a way to assay the aging process itself . Here we show that the tissues of aging worms have a characteristic appearance that is easy to recognize and quantify using Nomarski optics . We have used this assay to determine whether life-span mutations affect the rate of aging, to identify animals that age more rapidly than normal, and to infer the cause of death in C . elegans . Mutations that reduce insulin/IGF-1 signaling double the life span of C . elegans, and we find that tissue decline is slowed in these mutants . Thus this endocrine system appears to influence the rate at which tissues age . This effect extends even to the germline, which is the only mitotically active tissue in the adult . We find that Nomarski microscopy also allows a ready distinction between short-lived mutants that age more rapidly than normal and those that are simply sick, and we have identified an RNAi clone that confers a dramatic rapid-aging phenotype . This clone encodes the C . elegans heat-shock factor (HSF), a transcription factor that regulates the response to heat and oxidative stress . This suggests that heat-shock proteins, many of which act as chaperones, may function in normal animals to slow the rate of aging . Finally, we have identified a cause of death of C . elegans: namely, proliferating bacteria . This suggests that increased susceptibility to bacterial infections contributes to mortality in these animals, just as it does in humans.

Genetics, 2002 Jul, 161(3), 945 - 56
Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability; Slechta ES et al.; In the genetic system of Cairns and Foster, a nongrowing population of an E . coli lac frameshift mutant appears to specifically accumulate Lac(+) revertants when starved on medium including lactose (adaptive mutation) . This behavior has been attributed to stress-induced general mutagenesis in a subpopulation of starved cells (the hypermutable state model) . We have suggested that, on the contrary, stress has no direct effect on mutability but favors only growth of cells that amplify their leaky mutant lac region (the amplification mutagenesis model) . Selection enhances reversion primarily by increasing the mutant lac copy number within each developing clone on the selection plate . The observed general mutagenesis is attributed to a side effect of growth with an amplification-induction of SOS by DNA fragments released from a tandem array of lac copies . Here we show that the S . enterica version of the Cairns system shows SOS-dependent general mutagenesis and behaves in every way like the original E . coli system . In both systems, lac revertants are mutagenized during selection . Eliminating the 35-fold increase in mutation rate reduces revertant number only 2- to 4-fold . This discrepancy is due to continued growth of amplification cells until some clones manage to revert without mutagenesis solely by increasing their lac copy number . Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process) . These observations support the amplification mutagenesis model.

Eur J Biochem, 2002 Jul, 269(14), 3578 - 86
A critical motif for oligomerization and chaperone activity of bacterial alpha-heat shock proteins; Studer S et al.; Oligomerization into multimeric complexes is a prerequisite for the chaperone function of almost all alpha-crystallin type heat shock proteins (alpha-Hsp), but the molecular details of complex assembly are poorly understood . The alpha-Hsp proteins from Bradyrhizobium japonicum are suitable bacterial models for structure-function studies of these ubiquitous stress proteins . They fall into two distinct classes, A and B, display chaperone activity in vitro and form oligomers of approximately 24 subunits . We constructed 19 derivatives containing truncations or point mutations within the N- and C-terminal regions and analyzed them by gel filtration, citrate synthase assay and coaffinity purification . Truncation of more than the initial few amino acids of the N-terminal region led to the formation of distinct dimeric to octameric structures devoid of chaperone activity . In the C-terminal extension, integrity of an isoleucine-X-isoleucine (I-X-I) motif was imperative for alpha-Hsp functionality . This I-X-I motif is one of the characteristic consensus motifs of the alpha-Hsp family, and here we provide experimental evidence of its structural and functional importance . alpha-Hsp proteins lacking the C-terminal extension were inactive, but still able to form dimers . Here, we demonstrate that the central alpha-crystallin domain alone is not sufficient for dimerization . Additional residues at the end of the N-terminal region were required for the assembly of two subunits.

Nat Struct Biol, 2002 Aug, 9(8), 591 - 6
X-ray snapshots of quinone cofactor biogenesis in bacterial copper amine oxidase; Kim M et al.; The quinone cofactor TPQ in copper amine oxidase is generated by posttranslational modification of an active site tyrosine residue . Using X-ray crystallography, we have probed the copper-dependent autooxidation process of TPQ in the enzyme from Arthrobacter globiformis . Apo enzyme crystals were anaerobically soaked with copper; the structure determined from this crystal provides a view of the initial state: the unmodified tyrosine coordinated to the bound copper . Exposure of the copper-bound crystals to oxygen led to the formation of freeze-trapped intermediates; structural analyses indicate that these intermediates contain dihydroxyphenylalanine quinone and trihydroxyphenylalanine . These are the first visualized intermediates during TPQ biogenesis in copper amine oxidase.

J Biol Chem, 2002 Sep 27, 277(39), 36068 - 75 Epub 2002 Jul 19.
Induction of bacterial lipoprotein tolerance is associated with suppression of toll-like receptor 2 expression; Wang JH et al.; Tolerance to bacterial cell wall components including lipopolysaccharide (LPS) may represent an essential regulatory mechanism during bacterial infection . Two members of the Toll-like receptor (TLR) family, TLR2 and TLR4, recognize the specific pattern of bacterial cell wall components . TLR4 has been found to be responsible for LPS tolerance . However, the role of TLR2 in bacterial lipoprotein (BLP) tolerance and LPS tolerance is unclear . Pretreatment of human THP-1 monocytic cells with a synthetic bacterial lipopeptide induced tolerance to a second BLP challenge with diminished tumor necrosis factor-alpha and interleukin-6 production, termed BLP tolerance . Furthermore, BLP-tolerized THP-1 cells no longer responded to LPS stimulation, indicating a cross-tolerance to LPS . Induction of BLP tolerance was CD14-independent, as THP-1 cells that lack membrane-bound CD14 developed tolerance both in serum-free conditions and in the presence of a specific CD14 blocking monoclonal antibody (MEM-18) . Pre-exposure of THP-1 cells to BLP suppressed mitogen-activated protein kinase phosphorylation and nuclear factor-kappaB activation in response to subsequent BLP and LPS stimulation, which is comparable with that found in LPS-tolerized cells, indicating that BLP tolerance and LPS tolerance may share similar intracellular pathways . However, BLP strongly enhanced TLR2 expression in non-tolerized THP-1 cells, whereas LPS stimulation had no effect . Furthermore, a specific TLR2 blocking monoclonal antibody (2392) attenuated BLP-induced, but not LPS-induced, tumor necrosis factor-alpha and interleukin-6 production, indicating BLP rather than LPS as a ligand for TLR2 engagement and activation . More importantly, pretreatment of THP-1 cells with BLP strongly inhibited TLR2 activation in response to subsequent BLP stimulation . In contrast, LPS tolerance did not prevent BLP-induced TLR2 overexpression . These results demonstrate that BLP tolerance develops through down-regulation of TLR2 expression.

J Microbiol Methods, 2002 Oct, 51(2), 217 - 26
A probabilistic neural network approach for modeling and classification of bacterial growth/no-growth data; Hajmeer M et al.; In this paper, we propose to use probabilistic neural networks (PNNs) for classification of bacterial growth/no-growth data and modeling the probability of growth . The PNN approach combines both Bayes theorem of conditional probability and Parzen's method for estimating the probability density functions of the random variables . Unlike other neural network training paradigms, PNNs are characterized by high training speed and their ability to produce confidence levels for their classification decision . As a practical application of the proposed approach, PNNs were investigated for their ability in classification of growth/no-growth state of a pathogenic Escherichia coli R31 in response to temperature and water activity . A comparison with the most frequently used traditional statistical method based on logistic regression and multilayer feedforward artificial neural network (MFANN) trained by error backpropagation was also carried out . The PNN-based models were found to outperform linear and nonlinear logistic regression and MFANN in both the classification accuracy and ease by which PNN-based models are developed.

J Toxicol Environ Health A, 2002 Jul 26, 65(14), 961 - 76
The temporal relationship between bacterial lipopolysaccharide and monocrotaline exposures influences toxicity: shift in response from hepatotoxicity to nitric oxide-dependent lethality; Yee SB et al.; Liver injury from a variety of hepatotoxicants, including the food-borne phytotoxin monocrotaline (MCT), can be augmented by exposure to a noninjurious dose of the inflammagen bacterial lipopolysaccharide (LPS) . In a previous study, a nontoxic dose of LPS given 4 h after MCT resulted in synergistic hepatotoxicity within 12-18 h . This study was designed to determine whether temporal differences in MCT and LPS exposure affect toxicity . When LPS (3.4 x 10(6) EU/kg; iv) was given one hour before MCT (100 mg/kg; ip), hepatotoxicity developed between 4 and 8 h after MCT administration, and mortality was much greater than when LPS was administered 4 h after MCT . To explore this difference, the temporal relationship between LPS and MCT exposure (7.4 x 10(6) EU/kg and 100 mg/kg, respectively) was altered . Twenty-four-hour survival was high in animals that received LPS 4 h before (86%) or after (88%) MCT, but it decreased markedly when LPS was administered 1 h before MCT (17%) . Using this latter dosing regimen, animals became moribund as early as 4 h after MCT administration . Since liver injury was similar from regimens that differed greatly in mortality, death appeared to result from extrahepatic causes . To explore a role for nitric oxide (NO)-induced shock in this regimen, animals were treated with aminoguanidine (AG), an inhibitor of inducible NO synthase, prior to administration of LPS given an hour before MCT . In the cotreated animals, AG significantly attenuated mortality and decreased plasma nitrate/nitrite concentrations, markers of NO biosynthesis . Hence, the primary target of toxicity from MCT and LPS cotreatment appeared to shift from the liver to an extrahepatic site or sites as exposure to these agents occurred closer together temporally . NO appears to be causally involved in the deaths of animals treated with LPS 1 h before MCT.

Trends Genet, 2002 Jul, 18(7), 335 - 7
Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes; Ochman H; A substantial fraction of hypothetical open reading frames (ORFs) in completely sequenced bacterial genomes are short, suggesting that many are not genes but random stretches of DNA . Although it is not feasible to authenticate the coding capacity of all such regions experimentally, comparisons of ORFs in related genomes can expose those that encode functional proteins.

Phytochemistry, 2002 Aug, 60(7), 691 - 702
(+)-(10R)-Germacrene A synthase from goldenrod, Solidago canadensis; cDNA isolation, bacterial expression and functional analysis; Prosser I et al.; Profiling of sesquiterpene hydrocarbons in extracts of goldenrod, Solidago canadensis, by GC-MS revealed the presence of both enantiomers of germacrene D and lesser amounts of germacrene A, alpha-humulene, and beta-caryophyllene . A similarity-based cloning strategy using degenerate oligonucleotide primers, based on conserved amino acid sequences in known plant sesquiterpene synthases and RT-PCR, resulted in the isolation of a full length sesquiterpene synthase cDNA . Functional expression of the cDNA in E . coli, as an N-terminal thioredoxin fusion protein using the pET32b vector yielded an enzyme that was readily purified by nickel-chelate affinity chromatography . Chiral GC-MS analysis of products from of (3)H- and (2)H-labelled farnesyl diphosphate identified the enzyme as (+)-(10R)-germacrene A synthase . Sequence analysis and molecular modelling was used to compare this enzyme with the mechanistically related epi-aristolochene synthase from tobacco.

Photochem Photobiol, 2002 Jul, 76(1), 1 - 11
Coexistence of domains with distinct order and polarity in fluid bacterial membranes; Vanounou S et al.; In this study we sought the detection and characterization of bacterial membrane domains . Fluorescence generalized polarization (GP) spectra of laurdan-labeled Escherichia coli and temperature dependencies of both laurdan's GP and fluorescence anisotropy of 1,3-diphenyl-1,3,5-hexatriene (DPH) (rDPH) affirmed that at physiological temperatures, the E . coli membrane is in a liquid-crystalline phase . However, the strong excitation wavelength dependence of rlaurdan at 37 degrees C reflects membrane heterogeneity . Time-resolved fluorescence emission spectra, which display distinct biphasic redshift kinetics, verified the coexistence of two subpopulations of laurdan . In the initial phase, <50 ps, the redshift in the spectral mass center is much faster for laurdan excited at the blue edge (350 nm), whereas at longer time intervals, similar kinetics is observed upon excitation at either blue or red edge (400 nm) . Excitation in the blue region selects laurdan molecules presumably located in a lipid domain in which fast intramolecular relaxation and low anisotropy characterize laurdan's emission . In the proteo-lipid domain, laurdan motion and conformation are restricted as exhibited by a slower relaxation rate, higher anisotropy and a lower GP value . Triple-Gaussian decomposition of laurdan emission spectra showed a sharp phase transition in the temperature dependence of individual components when excited in the blue but not in the red region . At least two kinds of domains of distinct polarity and order are suggested to coexist in the liquid-crystalline bacterial membrane: a lipid-enriched and a proteolipid domain . In bacteria with chloramphenicol (Cam)-inhibited protein synthesis, laurdan showed reduced polarity and restoration of an isoemissive point in the temperature-dependent spectra . These results suggest a decrease in membrane heterogeneity caused by Cam-induced domain dissipation.

J Neuropathol Exp Neurol, 2002 Jul, 61(7), 605 - 13
Cerebral vasculature is the major target of oxidative protein alterations in bacterial meningitis; Schaper M et al.; We have previously shown that antioxidants such as a-phenyl-tert-butyl nitrone or N-acetylcysteine attenuate cortical neuronal injury in infant rats with bacterial meningitis, suggesting that oxidative alterations play an important role in this disease . However, the precise mechanism(s) by which antioxidants inhibit this injury remain(s) unclear . We therefore studied the extent and location of protein oxidation in the brain using various biochemical and immunochemical methods . In cortical parenchyma, a trend for increased protein carbonyls was not evident until 21 hours after infection and the activity of glutamine synthetase (another index of protein oxidation) remained unchanged . Consistent with these results, there was no evidence for oxidative alterations in the cortex by various immunohistochemical methods even in cortical lesions . In contrast, there was a marked increase in carbonyls, 4-hydroxynonenal protein adducts and manganese superoxide dismutase in the cerebral vasculature . Elevated lipid peroxidation was also observed in cerebrospinal fluid and occasionally in the hippocampus . All of these oxidative alterations were inhibited by treatment of infected animals with N-acetylcysteine or alpha-phenyl-tert-butyl nitrone . Because N-acetylcysteine does not readily cross the blood-brain barrier and has no effect on the loss of endogenous brain antioxidants, its neuroprotective effect is likely based on extraparenchymal action such as inhibition of vascular oxidative alterations.

Genesis, 2002 Jul, 33(3), 125 - 30
Targeting mammary epithelial cells using a bacterial artificial chromosome; Wintermantel TM et al.; We describe the generation of transgenic mouse lines expressing Cre recombinase in epithelial cells of the lactating mammary gland . As an expression vector, we used a P1-derived bacterial artificial chromosome (PAC) which harbors the gene for the secretory milk protein, whey acidic protein (Wap) . Using homologous recombination in E . coli, the PAC was modified to carry the improved coding sequence of Cre recombinase (iCre) . Transgenic lines carrying the WAPiCre PAC express Cre recombinase efficiently in the majority of mammary epithelial cells upon lactation . Of only four transgenic lines produced, three express Cre recombinase to a high efficiency . LoxP-flanked DNA sequences are recombined in virtually all epithelial cells of WAPiCre transgenic mice at lactation day 3 .

Biophys J, 2002 Aug, 83(2), 733 - 9
A mathematical explanation of an increase in bacterial swimming speed with viscosity in linear-polymer solutions; Magariyama Y et al.; Bacterial swimming speed is sometimes known to increase with viscosity . This phenomenon is peculiar to bacterial motion . Berg and Turner (Nature . 278:349-351, 1979) indicated that the phenomenon was caused by a loose, quasi-rigid network formed by polymer molecules that were added to increase viscosity . We mathematically developed their concept by introducing two apparent viscosities and obtained results similar to the experimental data reported before . Addition of polymer improved the propulsion efficiency, which surpasses the decline in flagellar rotation rate, and the swimming speed increased with viscosity.

Anal Biochem, 2002 Jul 15, 306(2), 314 - 22
Bacterial expression of in vivo-biotinylated aequorin for direct application to bioluminometric hybridization assays; Verhaegen M et al.; We have constructed a plasmid suitable for bacterial expression of in vivo-biotinylated photoprotein aequorin . The biotin tag facilitates the isolation of aequorin from crude cell extract and the direct complexation of aequorin with streptavidin for the development of highly sensitive hybridization assays, thereby avoiding the need for chemical crosslinking . The plasmid contains a biotin-acceptor coding sequence fused to an apoaequorin gene . The birA gene, encoding biotin protein ligase (BPL), is inserted downstream of the apoaequorin sequence . BPL biotinylates, posttranslationally, the acceptor domain at a unique position . Functional aequorin is generated by incubating the lysate with coelenterazine and is purified by using a monomeric avidin column that allows elution under nondenaturing conditions . The biotinylated aequorin is complexed with streptavidin and used as a reporter molecule in a hybridization assay . The assay entails immobilization of an oligonucleotide probe on microtiter wells followed by hybridization with a denatured DNA target labeled with biotin through PCR . Streptavidin-biotinylated aequorin is used for quantification of the hybrids . Luminescence is measured in the presence of excess Ca(2+) . The analytical range extends from 80 amol of target DNA per well (with a signal-to-background ratio of 2.1) up to 40 fmol per well . The coefficient of variation is about 6% . In vivo-biotinylated aequorin produced from 1 liter of culture is sufficient for 300,000 hybridization assays.

Curr Biol, 2002 Jun 25, 12(12), R427 - 8
Bacterial evolution: chromosome arithmetic and geometry; Ochman H; Recent sequencing projects have characterized bacterial genomes that are organized onto elements of various sizes, shapes and numbers . Aside from its biological relevance and curiosity, this diversity calls into question the way that we define bacterial chromosomes.

Proc R Soc Lond B Biol Sci, 2001 Jan 7, 268(1462), 61 - 9
The social evolution of bacterial pathogenesis; Smith J; Many of the genes responsible for the virulence of bacterial pathogens are carried by mobile genetic elements that can be transferred horizontally between different bacterial lineages . Horizontal transfer of virulence-factor genes has played a profound role in the evolution of bacterial pathogens, but it is poorly understood why these genes are so often mobile . Here, I present a hypothetical selective mechanism maintaining virulence-factor genes on horizontally transmissible genetic elements . For virulence factors that are secreted extracellularly, selection within hosts may favour mutant 'cheater' strains of the pathogen that do not produce the virulence factor themselves but still benefit from factors produced by other members of the pathogen population within a host . Using simple mathematical models, I show that if this occurs then selection for infectious transmission between hosts favours pathogen strains that can reintroduce functional copies of virulence-factor genes into cheaters via horizontal transfer, forcing them to produce the virulence factor . Horizontal gene transfer is thus a novel mechanism for the evolution of cooperation . I discuss predictions of this hypothesis that can be tested empirically and its implications for the evolution of pathogen virulence.

Eur J Oral Sci, 2002 Jun, 110(3), 212 - 7
Actinobacillus actinomycetemcomitans proportion of subgingival bacterial flora in relation to its clonal type; Lakio L et al.; We investigated whether certain Actinobacillus actinomycetemcomitans clones occur in elevated proportions in subgingival flora, and if the proportions relate to other bacteria in the samples . A total of 121 A . actinomycetemcomitans strains from 121 patients with periodontitis were serotyped and 60 strains were also genotyped . The 121 strains were divided into three groups and the 60 strains into two groups according proportion of A . actinomycetemcomitans . The samples from the 60 patients with genotyped strains were cultured for five other species . Among the 121 strains, serotype b occurred significantly more frequently in the high- (n = 14, proportions > 5%, mean = 18.09, SD = 20.07%) than low- (n = 49, proportions < or = 0.1%), mean = 0.04, SD = 0.03%) or intermediate-proportion groups (n = 58, proportions > 0.5%, mean = 1.31, SD = 1.24%) . Genotype 3 occurred significantly more frequently in samples with low A . actinomycetemcomitans proportions (n = 28, < or = 0.1%, mean = 0.04, SD = 0.03%) than in those with high proportions (n = 32, > 0.1%, mean = 5.70, SD = 14.60%) . No differences were seen in the detection frequencies or proportions of the five bacterial species between the samples with low or high A . actinomycetemcomitans proportions . The results indicate that certain clonotypes of A . actinomycetemcomitans may preferentially occur as low proportions, suggesting their controlled growth . Conversely, some serotype b clones may have a competitive advantage in subgingival flora.

Vet Microbiol, 2002 Aug 2, 88(1), 1 - 12
Porcine reproductive-respiratory syndrome virus infection predisposes pigs for respiratory signs upon exposure to bacterial lipopolysaccharide; Labarque G et al.; This study examined whether an infection with porcine reproductive and respiratory syndrome virus (PRRSV) potentiates respiratory signs upon exposure to bacterial lipopolysaccharides (LPS) . Five-week-old conventional pigs were inoculated intratracheally with the Lelystad strain of PRRSV and received 5 days later one or two intratracheal LPS administrations . The necessary controls were included . After LPS administration, pigs were intensively monitored for clinical signs . Additionally, some pigs were euthanatized after a second LPS administration for broncho-alveolar cell analysis and virological examinations of the lungs . Broncho-alveolar lavage (BAL) cells were counted and differentiated . Lung suspensions and BAL fluids were titrated for PRRSV . Exposure of pigs to PRRSV only resulted in a fever for time periods ranging from 1 to 5 days and slight respiratory signs . Exposure of pigs to LPS only resulted in general signs, characterized by fever and depression, but respiratory signs were slight or absent . PRRSV-LPS exposed pigs, on the other hand, developed severe respiratory signs upon LPS exposure, characterized by tachypnoea, abdominal breathing and dyspnoea . Besides respiratory signs, these pigs also showed enhanced general signs, such as fever and depression . Lung neutrophil infiltration was similar in non-infected and PRRSV-infected pigs upon LPS exposure . PRRSV quantities were similar in lungs and BAL fluids of pigs infected with PRRSV only and PRRSV-LPS exposed pigs . These data show a clear synergism between PRRSV and LPS in the induction of respiratory signs in conventional pigs . The synergism was observed in 87% of the pigs . So, it can be considered as reproducible and may be used to test the efficacy of preventive and therapeutic measures.

Biochemistry, 2002 Jul 23, 41(29), 9132 - 8
Effect of binding of Cd2+ on bacterial reaction center mutants: proton-transfer uses interdependent pathways; Gerencser L et al.; In bacterial reaction center of Rhodobacter sphaeroides, Cd2+ binds in stoichiometric amount to the protein . In the wild type, this results into a notable decrease of the rates of electron-transfer between the two quinone acceptors after the first (kAB(1)) and second flash (kAB(2)) . We have studied these effects in two single mutants, L209PY and L209PF . L209Pro is situated in a protein region rich in hydrogen-bond networks involving water molecules . We show that (1) the combined effects of Cd2+ binding and point mutations have a cumulative consequence in the two mutants, decreasing very substantially the observed rates of electron-transfer . Interestingly, the {Cd2+} titration curves of kAB(2) in the L209PY and L209PF mutants are nearly superimposable to those previously reported for the M17DN and L210DN mutants (Paddock, M . L., Feher, G., and Okamura, M . Y . (2000) Proc . Natl . Acad . Sci U.S.A . 97, 1548-1553) . These observations suggest a common effect of all of these mutations (L209, M17, L210) on the protonation state of the histidine cluster to which Cd2+ binds; (2) in the L209PY mutant, the pH titration curves of kAB(1), kAB(2), and k(H)(+), the proton-transfer rate at the second flash, are systematically downshifted by 1.5-2 pH units in the presence of 300 microM Cd2+, similarly to the wild type RCs (Gerencser, L., and Maroti, P . (2001) Biochemistry 40, 1850-1860) . We propose that Cd2+ binding influences the electrostatics of interdependent ways of proton penetration within the protein, involving at least, directly or indirectly, L209P, L210D, and M17D, probably in conjunction with hydrogen-bonded connected water molecules.

Chem Res Toxicol, 2002 Jul, 15(7), 943 - 9
Genotoxicity of trivalent chromium in bacterial cells . Possible effects on DNA topology; Plaper A et al.; Trivalent chromium is a metal required for proper sugar and fat metabolism . However, it has been suggested that it causes DNA damage in in vitro test systems, although in vivo toxicity has not yet been proved . In the present study, the effect of Cr3+ on bacterial cells was tested with the Pro-Tox (C) assay, and its cellular uptake was measured with flame atomic absorption spectroscopy . The potential genotoxicity of Cr3+ was further examined by the study of its influence on a bacterial type II topoisomerase . Cr3+ was shown to cause DNA damage and inhibit topoisomerase DNA relaxation activity, probably by preventing the formation of the covalent link between enzyme and double helix . In addition, Cr3+ decreases the viability and/or proliferation rate of eukaryotic cells such as murine B16 melanoma cells and human MCF-10A neoT ras-transformed human epithelial cells . The possible implication for Cr3+ intake by humans is discussed.

BJOG, 2002 Jun, 109(6), 714 - 7
Rates of bacterial vaginosis in women undergoing in vitro fertilisation for different types of infertility; Wilson JD et al.; OBJECTIVE: To assess whether the rate of bacterial vaginosis (BV) is higher in women with tubal factor infertility compared with those with other causes of infertility . DESIGN: Cross-sectional study . SETTING: Assisted conception unit of a teaching hospital in Leeds . POPULATION: Consecutive women undergoing in vitro fertilisation . METHODS: Women undergoing in vitro fertilisation (IVF) had a vaginal smear taken at the time of their egg collection . The smear was Gram-stained and graded as normal, intermediate or BV . MAIN OUTCOME MEASURES: The presence of bacterial vaginosis and the causes of infertility . RESULTS: A total of 749 women were included . The vaginal smears were normal in 63.6%, intermediate in 12.1%, and BV in 24.3% . The rates of BV in women with different types of infertility were 36.4% in tubal factor, 15.6% in male factor, 33.3% in anovulation, 12.5% in endometriosis and 18.9% in unexplained infertility . After controlling for the effects of age and smoking using a multivariate logistic regression model, women with tubal infertility were significantly more likely to have BV than women with endometriosis OR 3.63 (95% CI 1.52-8.67); male factor OR 2.98 (95% CI 1.80-4.90); and unexplained infertility OR 2.20 (95% CI 1.35-3.59) . The adjusted figures for the increase of BV in women with anovulation were: endometriosis OR 3.77 (95% CI 1.28-11.08); male factor OR 3.09 (95% CI 1.37-6.96); and unexplained infertility OR 2.29 (95% CI 1.02-5.12) . CONCLUSIONS: Women with tubal infertility were three times more likely to have BV than women with endometriosis, male factor or unexplained infertility . These findings support the association between BV, pelvic inflammatory disease (PID) and tubal damage but do not help distinguish between cause and effect . Women with anovulation were also three times more likely to have BV than women with endometriosis or male factor infertility, supporting suggestions of hormonal influence on vaginal flora.

Nat Struct Biol, 2002 Aug, 9(8), 597 - 600
Three-dimensional structure of a bacterial oxalate transporter; Hirai T et al.; The major facilitator superfamily (MFS) represents one of the largest classes of evolutionarily related membrane transporter proteins . Here we present the three-dimensional structure at 6.5 A resolution of a bacterial member of this superfamily, OxlT . The structure, derived from an electron crystallographic analysis of two-dimensional crystals, reveals that the 12 helices in the OxlT molecule are arranged around a central cavity, which is widest at the center of the membrane . The helices divide naturally into three groups: a peripheral set comprising helices 3, 6, 9 and 12; a second set comprising helices 2, 5, 8 and 11 that faces the central substrate transport pathway across most of the length of the membrane; and a third set comprising helices 1, 4, 7 and 10 that participate in the pathway either on the cytoplasmic side (4 and 10) or on the periplasmic side (1 and 7) . Overall, the architecture of the protein is remarkably symmetric, providing a compelling molecular explanation for the ability of such transporters to carry out bi-directional substrate transport.

Arterioscler Thromb Vasc Biol, 2002 Jul 1, 22(7), 1075 - 80
Aspirin inhibits Chlamydia pneumoniae-induced nuclear factor-kappa B activation, cytokine expression, and bacterial development in human endothelial cells; Tiran A et al.; OBJECTIVE: Chlamydia pneumoniae has been associated with atherosclerosis . Infection of vascular endothelial cells with C pneumoniae increases the expression of proatherogenic cytokines mediated by nuclear factor (NF)-kappaB, a transcription factor . The present study was designed to test the effect of aspirin on C pneumoniae-induced NF-kappaB activation, interleukin expression, and bacterial development in cultured human endothelial cells . METHODS AND RESULTS: Aspirin, its metabolite salicylic acid, and 2 other unrelated NF-kappaB inhibitors showed a strong concentration-dependent inhibitory effect on chlamydial growth, indicated by the reduction of bacterial inclusions and the titer of infectious progeny . Involvement of the transcription factor NF-kappaB was confirmed by electrophoretic mobility shift assay and by transfection experiments with appropriate decoy oligodeoxynucleotides . Attenuation of the C pneumoniae-induced activation of NF-kappaB by aspirin also reduced the secretion of interleukin-6 and interleukin-8, indicating efficient inhibition of NF-kappaB gene expression . Reduction of chlamydial growth was not caused by apoptosis of the host cell, as determined by monitoring characteristic chromatin condensation . CONCLUSIONS: These data provide evidence that NF-kappaB-mediated gene activation represents a crucial step in the developmental cycle of C pneumoniae . Aspirin exerts an anti-chlamydial effect that is due to the inhibition of C pneumoniae-induced NF-kappaB activation, which might account for some of the cardioprotective activity of aspirin.

Syst Biol, 2001 Aug, 50(4), 513 - 24
Bacterial species and speciation; Cohan FM; Bacteria are profoundly different from eukaryotes in their patterns of genetic exchange . Nevertheless, ecological diversity is organized in the same way across all of life: individual organisms fall into more less discrete clusters on the basis of their phenotypic, ecological, and DNA sequence characteristics . Each sequence cluster in the bacterial world appears to correspond to an "ecotype," defined as a population of cells in the same ecological niche, which would all be out-competed by any adaptive mutant coming from the population . Ecotypes, so defined, share many of the dynamic properties attributed to eukaryotic species: genetic diversity within an ecotype is limited by a force of cohesion (in this case, periodic selection); different ecotypes are free to diverge without constraint from one another; and ecotypes are ecologically distinct . Also, ecotypes can be discovered and classified as DNA sequence clusters, even when we are ignorant of their ecology . Owing to the rarity and promiscuity of bacterial genetic exchange, speciation in the bacterial world is expected to be much less constrained than in the world of animals and plants.

Cytometry, 2002 Jun 1, 48(2), 93 - 6
Use of SYTOX green dye in the flow cytometric analysis of bacterial phagocytosis; Gaforio JJ et al.; BACKGROUND: Fluorescein isothiocyanate (FITC) is used widely to label the targets used in flow cytometric phagocytosis assays . Unfortunately, the fluorescence intensity of phagocytosed FITC-labeled targets is influenced by changes in intracellular pH level, making quantitative measurements with this fluorophore problematic . We describe the use of SYTOX green nucleic acid stain to measure phagocytosis by flow cytometry . METHODS: Suspensions of isopropyl alcohol-permeabilized Escherichia coli DH5alpha were stained with the SYTOX green dye and then incubated with resident peritoneal macrophages . The samples were analyzed by flow cytometry and phagocytosis was determined by gating the cells . RESULTS: Results are expressed as percentage of phagocyte-associated green fluorescent cells . The validity of the method was shown by the effects of a phagocytosis inhibitor (incubation at 4 degrees C) or enhancer (gamma interferon {IFN- gamma} treatment) being accurately assessed with this assay . CONCLUSIONS: The method described was reproducible and provides an advantageous alternative to the use of FITC to label bacteria for the flow cytometric measurement of target uptake by phagocytic cells .

Eur J Immunol, 2002 Jul, 32(7), 2084 - 92
CpG motifs of bacterial DNA exacerbate colitis of dextran sulfate sodium-treated mice; Obermeier F et al.; Inflammatory bowel disease (IBD) is characterized by a dysregulated intestinal immune response with elevated levels of the Th1 cytokines TNF, IL-12 and IFN-gamma . The luminal flora has been implicated as a major factor contributing to the initiation and perpetuation of chronic intestinal inflammation by as yet unknown mechanisms . Bacterial DNA contains unmethylated cytosine-guanosine dinucleotides (CpG) which strongly activate Th1-mediated immune responses . To test whether these CpG-motifs contribute to intestinal inflammation we treated mice with dextran-sulfate-sodium (DSS)-induced acute or chronic colitis for 5 days with CpG-containing oligodeoxynucleotides (CpG-ODN) . Colonic inflammation was assessed by histological scoring . Colonic cytokine RNA was quantified by reverse transcription-PCR and cytokine secretion from mesenterial lymph node cells by ELISA . In chronic colitis, CpG-ODN treatment severely aggravated inflammation by 50% . Colonic expression of IFN-gamma and TNF was elevated (200- and 150-fold, respectively) and IFN-gamma and IL-12 secretion from lymph node cells was increased 5,000- and 8-fold, respectively, compared to GpG-ODN-treated controls . Similar effects were obtained in acute colitis . In conclusion, CpG-motifs of bacterial DNA have proinflammatory activity by strengthening the Th1 arm of immunity in DSS-induced colitis, and might therefore play a significant role in the initiation and perpetuation of inflammation in IBD.

J Nephrol, 2002 May-Jun, 15(3), 297 - 301
Differential diagnosis of bacterial infection and inflammatory response in kidney diseases using procalcitonin; Sitter T et al.; BACKGROUND: Early diagnosis of bacterial infection in renal patients remains difficult . Common laboratory parameters, such as white blood cell (WBC) count, erythrocyte sedimentation rate, and C-reactive protein (CRP) may be affected by the underlying disease, uremia or its extracorporeal treatment, or by immunosuppressive drugs . Procalcitonin (PCT) may be useful for the detection of systemic bacterial infections in patients with end-stage renal disease (ESRD) undergoing renal replacement therapy, but elevated PCT concentrations have also been found in a significant number of uremic patients without signs of infection . METHODS: We tested whether measurements of PCT levels help distinguish the chronic inflammation in renal diseases from invasive bacterial infections . Serum levels of PCT were compared with the corresponding serum C-reactive protein (CRP) concentrations and WBC counts in 197 patients with different stages of renal disease: Group I) 32 patients with chronic renal failure (serum creatinine 2-6 mg/dL); group II) 31 patients with a functioning renal transplant receiving standard immunosuppressive regimens; group III) 76 clinically stable patients with ESRD undergoing hemodialysis (HD); group IV) 23 patients with chronic renal failure (CRF) due to systemic autoimmune disease; group V) 35 patients with proven systemic bacterial infection and CRF . RESULTS: PCT levels were within the normal range (< 0.5 ng/mL) in patients with CRF and renal transplant patients without any clinical evidence of bacterial infection, regardless of the degree of renal failure and the underlying disorders . In 22 out of 76 stable HD patients, PCT levels were above the upper limit of normal, but 97% of these values were below the proposed cut-off for chronic HD patients of < 1.5 ng/mL . CRP levels were elevated in 17 of 32 patients with CRF (mean +/- SD: 0.57 +/- 0.49 mg/dL), in 10 of 31 renal transplant patients (0.41 +/- 0.55 mg/dL), in 16 of 23 patients with autoimmune disorders (2.78 +/- 3.21 mg/dL) and in 42 of 76 patients treated by HD (0.64 +/- 0.58 mg/dL) . In patients with CRF and systemic bacterial infections, both PCT and CRP were markedly elevated (PCT 61.50 +/- 115.4 ng/mL, CRP 14.50 +/- 10.36 mg/dL), but in contrast to PCT, CRP values overlapped in infected and non-infected patients . CONCLUSIONS: Our data indicate that PCT levels are not significantly affected by loss of renal function, immunosuppressive agents or autoimmune disorders . Thus, significantly elevated PCT concentrations offer good sensitivity and specificity for the early diagnosis of systemic bacterial infection in patients with CRF or patients with ESRD treated by HD . CRP concentrations may be useful indicators for inflammation in patients with renal diseases, but have low specificity for the diagnosis of bacterial infection.

J Nephrol, 2002 May-Jun, 15(3), 255 - 62
Hospitalizations for bacterial pneumonia after renal transplantation in the United States; Tveit DJ et al.; PURPOSE: Bacterial pneumonia has been cited as the leading cause of infectious death in renal transplant recipients but has not been studied in a national transplant population . SUBJECT AND METHODS: Retrospective analysis of the incidence, risk factors and mortality of hospitalized bacterial pneumonia (ICD9 Code 481.x486.x) for 33,479 renal transplant recipients in the United States Renal Data System transplanted from 1 July 1994-30 June 1997 . RESULTS: Among all transplant recipients, 4.7% were hospitalized for a primary discharge diagnosis of pneumonia in the study period (2.86 episodes per 100 person years) . 9.9% had bronchoscopy and 4.8% had open lung biopsy . A specific etiology was not identified in 72.5% of patients . The hospitalization rate for pneumonia and hazard for mortality due to hospitalized pneumonia were both constant over time . In logistic regression analysis, pneumonia prior to transplant (odds ratio 1.73, 95% confidence interval, 1.32-2.26), older recipient age, diabetes, delayed graft function, rejection (occurring at any time after transplant during the time of the study), duration of pre-transplant dialysis, and positive recipient cytomegalovirus serology were associated with pneumonia . In Cox Regression, hospitalization for pneumonia was associated with greater risk of mortality (hazard ratio 1.64, 95% CI, 1.42-1.89) . CONCLUSIONS: Renal transplant recipients with a previous history of pneumonia are at increased risk for subsequent pneumonia, which is associated with substantially decreased patient survival . Given the low rate of specific etiologies identified in this study, invasive diagnosis may be underutilized in this population.

Curr Womens Health Rep, 2001 Aug, 1(1), 14 - 9
Bacterial vaginosis and other asymptomatic vaginal infections in pregnancy; Carey JC et al.; Preterm birth is a common cause of neonatal morbidity and mortality . Many asymptomatic genital infections have been associated with preterm birth, but attempts to determine a causal relationship between specific infections and preterm birth have been disappointing . Treatment trials of specific infections have generally failed to show a positive effect, and in some trials have shown a deleterious effect . Although there is a strong association between the presence of bacterial vaginosis and Trichomonas vaginalis in pregnancy and preterm birth, randomized treatment trials have failed to show a benefit of treatment of these organisms . Treatment of asymptomatic bacterial vaginosis or T . vaginalis to prevent preterm birth is not warranted.

J Clin Lab Anal, 2002, 16(4), 187 - 93
Superiority of a functional leukocyte adhesiveness/aggregation test over the white blood cell count to discriminate between mild and significant inflammatory response in patients with acute bacterial infections; Rogowski O et al.; Electronic cell counters may underestimate the white blood cell count (WBCC) in the presence of aggregated leukocytes . In the present study we focused on the possibility of using a functional, as opposed to an anatomic, count to circumvent this eventual underestimation . A model of bacterial infection was used because of the importance of leukocytosis in the physician's clinical decision-making process . There were 35 patients with low C-reactive protein (CRP) concentrations (0.5-4.9 mg/dL), 45 with intermediate (5-9.9 mg/dL), and 120 with relatively high (>10 mg/dL) CRP concentrations . A significant (P=0.008) difference was noted between the state of leukocyte adhesiveness/aggregation in the peripheral blood of individuals with low CRP concentrations (3.5%+/-4.3%) and those with high CRP concentrations (7.4%+/-8%), while there was no significant difference in the respective number of WBCs per cubic millimeter (cmm) (11,600 +/- 5,500 and 14,000 +/- 7,200, respectively) . We raise the possibility that a functional test might be superior over an anatomic count in patients with acute bacterial infection and a significant acute phase response .

Mutagenesis, 2002 Jul, 17(4), 321 - 9
Comparison of the computer programs DEREK and TOPKAT to predict bacterial mutagenicity . Deductive Estimate of Risk from Existing Knowledge . Toxicity Prediction by Komputer Assisted Technology; Cariello NF et al.; The performance of two computer programs, DEREK and TOPKAT, was examined with regard to predicting the outcome of the Ames bacterial mutagenicity assay . The results of over 400 Ames tests conducted at Glaxo Wellcome (now GlaxoSmithKline) during the last 15 years on a wide variety of chemical classes were compared with the mutagenicity predictions of both computer programs . DEREK was considered concordant with the Ames assay if (i) the Ames assay was negative (not mutagenic) and no structural alerts for mutagenicity were identified or (ii) the Ames assay was positive (mutagenic) and at least one structural alert was identified . Conversely, the DEREK output was considered discordant if (i) the Ames assay was negative and any structural alert was identified or (ii) the Ames assay was positive and no structural alert was identified . The overall concordance of the DEREK program with the Ames results was 65% and the overall discordance was 35%, based on over 400 compounds . About 23% of the test molecules were outside the permissible limits of the optimum prediction space of TOPKAT . Another 4% of the compounds were either not processable or had indeterminate mutagenicity predictions; these molecules were excluded from the TOPKAT analysis . If the TOPKAT probability was (i) > or =0.7 the molecule was predicted to be mutagenic, (ii) < or =0.3 the compound was predicted to be non-mutagenic and (iii) between 0.3 and 0.7 the prediction was considered indeterminate . From over 300 acceptable predictions, the overall TOPKAT concordance was 73% and the overall discordance was 27% . While the overall concordance of the TOPKAT program was higher than DEREK, TOPKAT fared more poorly than DEREK in the critical Ames-positive category, where 60% of the compounds were incorrectly predicted by TOPKAT as negative but were mutagenic in the Ames test . For DEREK, 54% of the Ames-positive molecules had no structural alerts and were predicted to be non-mutagenic . Alternative methods of analyzing the output of the programs to increase the accuracy with Ames-positive compounds are discussed.

Insect Biochem Mol Biol, 2002 Aug, 32(8), 829 - 37
A protein from the cabbage looper, Trichoplusia ni, regulated by a bacterial infection is homologous to 3-dehydroecdysone 3beta-reductase; Lundstrom A et al.; During the screening of immune-regulated genes from the cabbage looper, Trichoplusia ni, a 3-dehydroecdysone 3beta-reductase homologue (DERH) was cloned . In the course of development, 3-dehydroecdysone 3beta-reductase mediates the conversion of 3-dehydroecdysone (3dE) secreted from the prothoracic glands to ecdysone (E), which is subsequently converted to 20-hydroxyecdysone (20E), the major insect molting hormone . The cloned gene is upregulated in fat body during development and is strongly induced after the larva is challenged with bacteria . The gene codes for a 308 amino acid residue protein which shows 42.5% identity to Spodoptera littoralis 3-dehydroecdysone 3beta-reductase . Using the baculovirus expression system, the recombinant DERH was expressed . The purified protein mediates the reduction of 3-dehydromakisterone A to makisterone A, and requires NADPH as a cofactor . Western blots using an antiserum to T . ni DERH revealed the presence of the protein in larval hemolymph and integument . The data indicate that the protein is regulated developmentally and is induced after a challenge with bacteria . Immunohistochemical studies localized the enzyme exclusively in the epidermis and the cuticle.

Cell, 2002 Jun 28, 109(7), 913 - 23
Bacterial adhesion to target cells enhanced by shear force; Thomas WE et al.; Surface adhesion of bacteria generally occurs in the presence of shear stress, and the lifetime of receptor bonds is expected to be shortened in the presence of external force . However, by using Escherichia coli expressing the lectin-like adhesin FimH and guinea pig erythrocytes in flow chamber experiments, we show that bacterial attachment to target cells switches from loose to firm upon a 10-fold increase in shear stress applied . Steered molecular dynamics simulations of tertiary structure of the FimH receptor binding domain and subsequent site-directed mutagenesis studies indicate that shear-enhancement of the FimH-receptor interactions involves extension of the interdomain linker chain under mechanical force . The ability of FimH to function as a force sensor provides a molecular mechanism for discrimination between surface-exposed and soluble receptor molecules.

Microbes Infect, 2002 Jul, 4(9), 915 - 26
Structural and functional analyses of bacterial lipopolysaccharides; Caroff M et al.; Bacterial lipopolysaccharides (LPSs) are powerful immunomodulators in infected hosts, and may cause endotoxic shock . Most of them share a common architecture but vary considerably in structural motifs from one genus, species, and strain to another . Cells of the innate immune response recognize evolutionarily conserved LPS molecular patterns of endotoxins and structural details thereby greatly influencing their response.

J Am Chem Soc, 2002 Jul 17, 124(28), 8445 - 51
A quantum chemistry study of binding carotenoids in the bacterial light-harvesting complexes; Wang Y et al.; Carotenoids play the dual function of light harvesting and photoprotection in photosynthetic organisms . Despite their functional importance, the molecular basis for binding of carotenoids in the photosynthetic proteins is poorly understood . We have discovered that all carotenoids are surrounded either by aromatic residues or by chlorophylls in all known crystal structures of the photosynthetic pigment-protein complexes . The intermolecular pi-pi stacking interactions between carotenoids and the surrounding aromatic residues in the light-harvesting complex II (LH-II) of Rhodospirillum molischianum were analyzed by high level ab initio electronic structure calculations . Intermolecular interaction energies were calculated with the second-order Moller-Plesset perturbation method (MP2) using the modified 6-31G*(0.25) basis set with diffuse d-polarization by Hobza and co-workers . The MP2/6-31G*(0.25) calculations yield a total stabilization energy of -15.66 kcal/mol between the carotenoid molecule and the four surrounding aromatic residues (alpha-Trp-23, beta-Phe-20, beta-Phe-24, beta-Phe-27) . It is thus concluded that pi-pi stacking interactions between carotenoids and the aromatic residues play an essential role in binding carotenoids in the LH-II complex of Rhodospirillum molischianum . The physical nature of the pi-pi stacking interactions was further analyzed, and the dispersion interactions were found to be the dominant intermolecular attraction force . There is also a substantial electrostatic contribution to the overall intermolecular stabilization energy.

J Biol Chem, 2002 Nov 1, 277(44), 42325 - 33 Epub 2002 Jul 05.
Dual recognition of the bacterial chemoreceptor by chemotaxis-specific domains of the CheR methyltransferase; Shiomi D et al.; Adaptation to persisting stimulation is required for highly sensitive detection of temporal changes of stimuli, and often involves covalent modification of receptors . Therefore, it is of vital importance to understand how a receptor and its cognate modifying enzyme(s) modulate each other through specific protein-protein interactions . In the chemotaxis of Escherichia coli, adaptation requires methylation of chemoreceptors (e.g . Tar) catalyzed by the CheR methyltransferase . CheR binds to the C-terminal NWETF sequence of a chemoreceptor that is distinct from the methylation sites . However, little is known about how CheR recognizes its methylation sites or how it is distributed in a cell . In this study, we used comparative genomics to demonstrate that the CheR chemotaxis methyltransferase contains three structurally and functionally distinct modules: (i) the catalytic domain common to a methyltransferase superfamily; (ii) the N-terminal domain; and (iii) the beta-subdomain of the catalytic domain, both of which are found exclusively in chemotaxis methyltransferases . The only evolutionary conserved motif specific to CheR is the positively charged face of helix alpha2 in the N-terminal domain . The disulfide cross-linking analysis suggested that this face interacts with the methylation helix of Tar . We also demonstrated that CheR localizes to receptor clusters at cell poles via interaction of the beta-subdomain with the NWETF sequence . Thus, the two chemotaxis-specific modules of CheR interact with distinct regions of the chemoreceptor for targeting to the receptor cluster and for recognition of the substrate sites, respectively.

Lett Appl Microbiol, 2002, 35(2), 157 - 61
Optimization of carbon and nitrogen sources for phytase production by Mitsuokella jalaludinii, a new rumen bacterial species; Lan GQ et al.; AIMS: The effects of different carbon and nitrogen sources on phytase production by Mitsuokella jalaludinii were evaluated and the optimization of rice bran (RB) and soybean milk (SM) concentrations in the medium for phytase production was also determined . METHODS AND RESULTS: Replacement of glucose, cellobiose and starch in MF1 medium by RB or palm kernel cake and replacement of trypticase peptone and yeast extract in the medium by SM or enzymatic digested soybean milk significantly increased the phytase production by M . jalaludinii . The optimal concentrations of RB and SM in the medium for phytase production were 15% RB and 20% SM or 20% RB and 10% SM or 20% RB and 20% SM and the phytase activities in the media were 12.53, 12.93 and 12.75 U g-1 culture broth, respectively . CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The high production of phytase by M . jalaludinii warrants further research to increase its yield by genetic manipulation for commercial application.

Mol Microbiol, 2002 Jul, 45(1), 17 - 29
The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation; Woldringh CL; Many recent reviews in the field of bacterial chromosome segregation propose that newly replicated DNA is actively separated by the functioning of specific proteins . This view is primarily based on an interpretation of the position of fluorescently labelled DNA regions and proteins in analogy to the active segregation mechanism in eukaryotic cells, i.e . to mitosis . So far, physical aspects of DNA organization such as the diffusional movement of DNA supercoil segments and their interaction with soluble proteins, leading to a phase separation between cytoplasm and nucleoid, have received relatively little attention . Here, a quite different view is described taking into account DNA-protein interactions, the large variation in the cellular position of fluorescent foci and the compaction and fusion of segregated nucleoids upon inhibition of RNA or protein synthesis . It is proposed that the random diffusion of DNA supercoil segments is transiently constrained by the process of co- transcriptional translation and translocation (transertion) of membrane proteins . After initiation of DNA replication, a bias in the positioning of transertion areas creates a bidirectionality in chromosome segregation that becomes self-enhanced when neighbouring genes on the same daughter chromosome are expressed . This transertion-mediated segregation model is applicable to multifork replication during rapid growth and to multiple chromosomes and plasmids that occur in many bacteria.

Biomacromolecules, 2002 Jul-Aug, 3(4), 828 - 34
Enzymatic hydrolysis of bacterial poly(3-hydroxybutyrate-co-3-hydroxypropionate)s by poly(3-hydroxyalkanoate) depolymerase from Acidovorax Sp . TP4; Wang Y et al.; Enzymatic degradability has been investigated for a series of bacterial poly(3-hydroxybutyrate-co-3-hydroxypropionate)s (P(3HB-co-3HP)s) with 3-hydroxypropionate (3HP) unit contents from 11 to 86 mol % as well as poly(3-hydroxybutyrate) (P(3HB)) and chemosynthesized poly(3-hydroxypropionate) (P(3HP)) . The behavior of degradation by two types of extracellular poly(3-hydroxyalkanoate) (PHA) depolymerases purified from Ralstonia pikettii T1 and Acidovorax Sp . TP4, defined respectively as PHA depolymerase types I and II according to the position of the lipase box in the catalytic domain, were compared in relation to the thermal properties and crystalline structures of the PHA samples elucidated by differential scanning calorimetry and wide-angle X-ray diffraction . The degradation products were characterized by high-performance liquid chromatography and one- (1D) and two-dimension (2D) (1)H NMR spectroscopy . It was found that the PHA depolymerase of Acidovorax Sp . TP4 showed degradation behavior different from that shown by depolymerase of R . pikettii T1 . PHA depolymerase from Acidovorax Sp . TP4 degraded the P(3HB-co-3HP) films with lower crystallinity in higher rates than those with higher crystallinity, no matter what kinds of crystalline structures they formed . In contrast, PHA depolymerase from R . pikettii T1 degraded P(3HB-co-3HP) films forming P(3HB) crystalline structure in higher rates than those forming P(3HP)s . The increase in amorphous nature of the P(3HB-co-3HP) films with P(3HB)-homopolymer-like crystalline structure increases and then decreases the rate of degradation by depolymerase from R . pikettii T1 . The 3-hydroxybutyrate (3HB) monomer was produced as a major product by the hydrolysis of P(3HB) film by PHA depolymerase from Acidovorax Sp . TP4 . The P(3HB-co-3HP) films could be degraded into 3HB and 3-hydroxypropionate (3HP) monomer at last, indicating that the catalytic domain of the enzyme recognized at least two monomeric units as substrates . While the PHA depolymerase from R . pikettii T1 hydrolyzed P(3HB) film into 3HB dimer as a major product, and the catalytic domain recognized at least three monomeric units . The degradation behavior of P(3HB-co-3HP) films by the PHA depolymerase of Acidovorax Sp . TP4 could be distinguished from that by the depolymerase of R . pikettii T1.

Dent Mater, 2002 Sep, 18(6), 470 - 8
Bacterial microleakage and pulp inflammation associated with various restorative materials; Murray PE et al.; OBJECTIVES: Many restorative materials are claimed to be successful in preventing bacterial microleakage and minimizing pulp inflammation . However, information regarding the in vivo performance of materials in comparison with each other is limited . The aim of this study was to evaluate and compare the pulp response of nine restorative materials when placed in non-exposed monkey cavities.METHODS: 279 standardized non-exposed Class V cavities, were prepared into buccal dentin . Cavities were restored with a number of materials in the following categories: Zinc oxide eugenol (ZnOE), Calcium hydroxide {Ca(OH)(2)}, zinc phosphate (ZP), Resin-modified glass ionomer (RMGI), Composite resin (CR), Bonded amalgam (BA), Gutta-percha (GP), Compomer and Silicate . Pulp tissues were collected and evaluated at short, intermediate and long-term intervals according to ISO guidelines; employing histomorphometric analysis, Spearman's rho and ANOVA statistics . Pulp responses were categorized according to FDI, ISO and ADA standards . Bacteria were detected using McKay stains.RESULTS: Pulp inflammation was found to be correlated to bacterial microleakage around the restoration (p < or =0.0001) . The frequency of bacterial microleakage was found to vary between restorative materials (p < or =0.0001) . In rank order of preventing bacterial microleakage from best to the worst; RMGI (100%), BA (88%), ZnOE (86%), CR (80%), GP (64%), Ca(OH)(2) (58%), compomer (42%), silicate (36%) and ZP (0%).SIGNIFICANCE: The most effective restorative materials to prevent bacterial microleakage and pulp injury from inflammatory activity were RMGI, BA, ZnOE and CR restorations.

J Nutr, 2002 Jul, 132(7), 2028 - 32
Bacterial infection affects protein synthesis in primary lymphoid tissues and circulating lymphocytes of rats; Papet I et al.; Bacterial infection alters whole-body protein homeostasis . Although immune cells are of prime importance for host defense, the effect of sepsis on their protein synthesis rates is poorly documented . We analyzed protein synthesis rates in rat primary lymphoid tissues and circulating lymphocytes after infection . Male Sprague-Dawley rats were studied 1, 2, 6 or 10 d after an intravenous injection of live Escherichia coli . Control healthy rats consumed food ad libitum (d 0) or were pair-fed to infected rats . Protein synthesis was quantified using a flooding dose of L-(4,4,4-(2)H(3))valine . Sepsis induced a delayed increase in total blood leukocytes and a rapid and persistent inversion of the counts . Basal fractional rates of protein synthesis (ks) were 117, 73 and 29%/d in bone marrow, thymus and circulating lymphocytes, respectively . Pair-feeding strongly depressed the absolute protein synthesis rates (ASR) of bone marrow (d 2 and 10) and thymus (d 2-10) . The infection per se increased bone marrow, thymus and circulating lymphocyte ks but at various postinfection times . It decreased bone marrow (d 1) and thymus (d 1 and 2) ASR but increased lymphocyte (d 2 and 10) and bone marrow (d 10) ASR . Our results reflect the deleterious effect of anorexia on primary lymphoid tissues . The host defense against bacterial infection exhibited time- and tissue-dependent modifications of protein synthesis, indicating that blood lymphocyte protein data are not representative of the immune system as a whole . Optimization of nutritional supports would be facilitated by including protein synthesis measurements of the immune system.

J Nutr, 2002 Jul, 132(7), 2019 - 27
Nutritional regulation of porcine bacterial-induced colitis by conjugated linoleic acid; Hontecillas R et al.; Excessive intake of saturated fatty acids and/or linoleic acid favors the induction of an array of lipid mediators and cytokines enhancing inflammatory responses . Conversely, dietary supplementation with (n-3) fatty acids or vitamin D ameliorates inflammation and autoimmune diseases . Although it was well accepted that conjugated linoleic acid (CLA) prevented diseases with a common inflammatory pathogenesis (i.e., cancer and atherosclerosis), no studies were available on the roles of CLA in mucosal inflammation . The present study was designed to investigate the anti-inflammatory actions and molecular mechanisms underlying the regulation of colonic health by CLA . We hypothesized that colonic inflammation can be ameliorated by dietary CLA supplementation . To test this hypothesis, inflammation of the colonic mucosa was triggered by challenging pigs fed either soybean oil-supplemented or CLA-supplemented diets with an enteric bacterial pathogen (i.e., Brachyspira hyodysenteriae) . Immunoregulatory cytokines and peroxisome proliferator-activated receptor-gamma (PPAR-gamma) mRNA expression were assayed in colonic lymph nodes and colon of pigs . Colonic mucosal lesions and lymphocyte subset distribution were evaluated by histology and immunohistochemistry . Supplementation of CLA in the diet before the induction of colitis decreased mucosal damage; maintained cytokine profiles (i.e., interferon-gamma and interleukin-10) and lymphocyte subset distributions (i.e., CD4+ and CD8+), resembling those of noninfected pigs; enhanced colonic expression of PPAR-gamma; and attenuated growth failure . Therefore, CLA fed preventively before the onset of enteric disease attenuated inflammatory lesion development and growth failure.

Genome Res, 2002 Jul, 12(7), 1080 - 90
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history; Daubin V et al.; It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data . For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology . In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms . Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny . This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny . We then used this core of genes to infer a tree . This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.

J Mol Biol, 2002 Jul 12, 320(3), 645 - 61
Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates; Erlandsen H et al.; Structure determination of bacterial homologues of human disease-related proteins provides an efficient path to understanding the three-dimensional fold of proteins that are associated with human diseases . However, the precise locations of active-site residues are often quite different between bacterial and human versions of an enzyme, creating significant differences in the biological understanding of enzyme homologs . To study this hypothesis, phenylalanine hydroxylase from a bacterial source has been structurally characterized at high resolution and comparison is made to the human analog . The enzyme phenylalanine hydroxylase (PheOH) catalyzes the hydroxylation of l-phenylalanine into l-tyrosine utilizing the cofactors (6R)-l-erythro-5,6,7,8 tetrahydrobiopterin (BH(4)) and molecular oxygen . Previously determined X-ray structures of human and rat PheOH, with a sequence identity of more than 93%, show that these two structures are practically identical . It is thus of interest to compare the structure of the divergent Chromobacterium violaceum phenylalanine hydroxylase (CvPheOH) ( approximately 24% sequence identity overall) to the related human and rat PheOH structures . We have determined crystal structures of CvPheOH to high resolution in the apo-form (no Fe-added), Fe(III)-bound form, and 7,8-dihydro-l-biopterin (7,8-BH(2)) plus Fe(III)-bound form . The bacterial enzyme displays higher activity and thermal melting temperature, and structurally, differences are observed in the N and C termini, and in a loop close to the active-site iron atom . (c) 2002 Elsevier Science Ltd.

Mol Cell Proteomics, 2002 Mar, 1(3), 243 - 52
Analysis of mammalian peroxin interactions using a non-transcription-based bacterial two-hybrid assay; Fransen M et al.; In recent years, substantial progress has been made in the identification of proteins involved in peroxisome biogenesis . However, with the exception of the peroxisome-targeting signal receptors and the receptor docking proteins, the function of most of these proteins, called peroxins, remains largely unknown . One step toward elucidating the function of a protein is to identify its interacting partners . We have used a non-transcription-based bacterial two-hybrid system to analyze the interactions among a set of 12 mammalian peroxins and a yeast protein three-hybrid system to investigate whether proteins that interact with the same peroxin and have overlapping binding sites cooperate or compete for this site . Here we report a detailed interaction map of these peroxins and demonstrate that (i) farnesylation, and not the CAAX motif, of Pex19p strongly enhances its affinity for Pex13p; (ii) the CAAXmotif, and not farnesylation, of Pex19p strongly enhances its affinity for Pex11pbeta; and (iii) the C(3)HC(4) RING (really interesting new gene) finger domain of Pex12p does not alter the binding properties of Pex5p for the C-terminal peroxisome-targeting signal PTS1 . Finally, we show that the Pex5p-Pex13p interaction is bridged by Pex14p and that the latter molecule exists predominantly as a dimer in vivo . Collectively, as demonstrated in this work with peroxins, these results indicate that the bacterial two-hybrid system is an attractive complementary approach to the conventional transcription-based yeast two-hybrid system for studying protein-protein interactions.

J Biol Chem, 2002 Aug 9, 277(32), 28380 - 3 Epub 2002 Jun 27.
A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids; Takahashi Y et al.; The assembly of iron-sulfur (Fe-S) clusters is mediated by complex machinery . In several proteobacteria, this process involves ISC (Fe-S cluster assembly) machinery composed of at least six components also conserved in mitochondria from lower to higher eukaryotes . In nitrogen-fixing bacteria, another system, termed NIF (nitrogen fixation), is required for the maturation of nitrogenase . Here we report the identification of a third system, designated the SUF machinery, the components of which are encoded in Escherichia coli by an unassigned operon, sufABCDSE . We have analyzed spontaneous pseudorevertants isolated from a mutant strain lacking all the components of the ISC machinery . The suppressor mutations in the revertants have been localized to the regulatory region of the suf operon; overexpression of this operon restores the growth phenotypes and activity of Fe-S proteins in mutant cells lacking ISC . Disruption of the suf operon alone does not cause any major defects, but synthetic lethality was observed when both the isc and suf operons were inactivated . These results indicate that proteins encoded by the suf operon participate in the ISC-independent minor pathway for the assembly of Fe-S clusters . The genes homologous to sufBC are present in a wide range of bacteria, Archaea, and plastids, suggesting that this type of system is almost ubiquitous in nature.

J Biol Chem, 2002 Sep 6, 277(36), 32538 - 45 Epub 2002 Jun 26.
Bacterial surface association of heat-labile enterotoxin through lipopolysaccharide after secretion via the general secretory pathway; Horstman AL et al.; Heat-labile enterotoxin (LT) is an important virulence factor expressed by enterotoxigenic Escherichia coli . The route of LT secretion through the outer membrane and the cellular and extracellular localization of secreted LT were examined . Using a fluorescently labeled receptor, LT was found to be specifically secreted onto the surface of wild type enterotoxigenic Escherichia coli . The main terminal branch of the general secretory pathway (GSP) was necessary and sufficient to localize LT to the bacterial surface in a K-12 strain . LT is a heteromeric toxin, and we determined that its cell surface localization was mediated by the its B subunit independent of an intact G(M1) ganglioside binding site and that LT binds lipopolysaccharide and G(M1) concurrently . The majority of LT secreted into the culture supernatant by the GSP in E . coli associated with vesicles . Only a mutation in hns, not overexpression of the GSP or LT, caused an increase in vesicle yield, supporting a specific vesicle formation machinery regulated by the nucleoid-associated protein HNS . We propose a model in which LT is secreted by the GSP across the outer membrane, secreted LT binds lipopolysaccharide via a G(M1)-independent binding region on its B subunit, and LT on the surface of released outer membrane vesicles interacts with host cell receptors, leading to intoxication . These data explain a novel mechanism of vesicle-mediated receptor-dependent delivery of a bacterial toxin into a host cell.

Proc Natl Acad Sci U S A, 2002 Jun 25, 99(13), 8536 - 41
Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR; Camarero JA et al.; Bacterial sigma factors combine with the catalytic core RNA polymerase to direct the process of transcription initiation through sequence-specific interactions with the -10 and -35 elements of promoter DNA . In the absence of core RNA polymerase, the DNA-binding function of sigma is autoinhibited by its own N-terminal 90 amino acids (region 1.1), putatively by a direct interaction with conserved region 4.2, which binds the -35 promoter element . In the present work, this mechanism of autoinhibition was studied by using a combination of NMR spectroscopy and segmental isotopic labeling of a sigma70-like subunit from Thermotoga maritima . Our data argue strongly against a high-affinity interaction between these two domains . Instead we suggest that autoinhibition of DNA binding occurs through an indirect steric and/or electrostatic mechanism . More generally, the present work illustrates the power of segmental isotopic labeling for probing molecular interactions in large proteins by NMR.

Sex Transm Infect, 2002 Apr, 78 Suppl 1, i139 - 44
Geographical variations in the epidemiology of bacterial sexually transmitted infections in Manitoba, Canada; Elliott LJ et al.; Feasible epidemiological approaches are required to make a better assessment of the stage of an epidemic and to monitor its transition through various phases . Application of the Lorenz curve and Gini coefficient to summarise the inequality in STD incidence rates between jurisdictions in Manitoba, Canada, was found to provide useful insights into the concentration of these epidemics over time and thus their transition through epidemic phases . Further exploration of the statistical properties of these and other indices of inequality and their potential application to STD epidemiology is warranted . New epidemiological tools are also required for better monitoring of the impact of prevention and control activities and to inform the content of these activities.

Protein Eng, 2002 Jun, 15(6), 493 - 502
Rational design of green fluorescent protein mutants as biosensor for bacterial endotoxin; Goh YY et al.; Enhanced green fluorescent protein (EGFP) was selected as a signalling scaffold protein for design of a fluorescent biosensor for bacterial endotoxin {or lipopolysaccharide (LPS)} . Virtual mutagenesis was utilized to model EGFP variants containing binding sites for LPS and lipid A (LA), the bioactive component of LPS . Cationic amphipathic sequences of five alternating basic and hydrophobic residues were introduced to beta-sheets located on the surface of EGFP barrel, in the vicinity of the chromophore . Computational methods were employed to predict binding affinity of Escherichia coli LA, to the models of virtual EGFP mutants . DNA mutant constructs of five predicted best binding EGFP variants were expressed in COS-1 cells . The EGFP-mutant proteins exhibited differential expression and variable degrees of fluorescence yield at 508 nm . The EGFP mutants showed a range of LA binding affinities that corresponded to the computational predictions . LPS/LA binding to the mutants caused concentration-dependent fluorescence quenching . The EGFP mutant, G10 bearing LPS/LA amphipathic binding motif in the vicinity of the chromophore (YLSTQ(200-204)-->KLKTK) captured LA with a dissociation constant of 8.5 microm . G10 yielded the highest attenuation of fluorescence intensity in the presence of LPS/LA and demonstrated capability in fluorescence-mediated quantitative detection of LPS in endotoxin-contaminated samples . Thus, the EGFP mutant can form the basis of a novel fluorescent biosensor for bacterial endotoxin.

Ann N Y Acad Sci, 2002 Jun, 967, 476 - 81
A novel Mammalian homologue of a bacterial citrate-metabolizing enzyme; Soderberg C et al.; Mammals metabolize citrate to acetyl-CoA and oxaloacetate via the enzyme, ATP:citrate lyase . Bacteria lack this enzyme, but have the ability to cleave citrate in the form of citryl-CoA in an analogous manner using a structurally distinct enzyme . We have identified a novel mammalian gene that shows significant amino acid sequence homology to the bacterial CitE gene product that is responsible for cleavage of citryl-CoA . We propose that this gene encodes an enzyme that catalyzes cleavage of substrates related to CoA esters of citrate or an analogous intermediary metabolite . The product of this novel gene may represent a component of an unknown metabolic pathway in mammals.

J Pediatr Surg, 2002 Jul, 37(7), 1081 - 7; discussion 1081-7
Heparin-binding EGF-like growth factor preserves crypt cell proliferation and decreases bacterial translocation after intestinal ischemia/reperfusion injury; Xia G et al.; BACKGROUND/PURPOSE: Heparin-binding epidermal growth factor (EGF)-like growth factor (HB-EGF), a known mitogenic, chemotactic, and cytoprotective growth factor for epithelial cells, was examined to see whether it could protect intestinal barrier function and decrease bacterial translocation (BT) after ischemia/reperfusion (I/R) injury . METHODS: In vitro, tight junctional integrity of intestinal epithelial cells (IEC-6) cells was evaluated by measuring transepithelial electric resistance (TEER), and monolayer permeability was evaluated by translocation of Escherichia coli C25 . In vivo, crypt cell proliferation was assessed by 5-bromodeoxyuridine incorporation with calculation of a proliferative index (PI), and BT was evaluated by culture of mesenteric lymph nodes . RESULTS: In vitro, anoxia damaged tight junctional integrity and increased permeability of IEC-6 cell monolayers, events that were reversed completely by treatment of the cells with HB-EGF . Twenty-four hours after I/R injury in vivo, crypt cell proliferation index (PI) decreased significantly from 35.6 +/- 4.5 to 17.8 +/- 3.4 . Administration of HB-EGF preserved crypt cell activity with PI of 34.9 +/- 4.1, similar to that of normal ileum . None of the normal or sham-operated animals showed BT, whereas BT occurred in 87.5% of I/R-injured rats . In animals exposed to I/R but treated with HB-EGF, BT was decreased significantly to 12.5% . CONCLUSION: HB-EGF preserves proliferation of crypt cells, maintains integrity of epithelial cells, and subsequently decreases enteric BT after I/R injury .

J Chromatogr A, 2002 May 10, 955(2), 229 - 36
Reversed-phase high-performance liquid chromatography method for the determination of prolactin in bacterial extracts and in its purified form; Soares CR et al.; Reversed-phase high-performance liquid chromatography methodology for the determination of human prolactin (hPRL) in bacterial periplasmic space or in purified preparations has been developed . The technique, based on the high hydrophobicity of the hPRL molecule, allows its separation from the bulk of bacterial proteins . The precision for periplasmic shock fluid analysis was characterized by relative standard variations of 3-7% for intra-day and of 3-25% for inter-day determinations . Accuracy, evaluated by recovery tests, was of the order of 90%, a calibration curve being constructed with the use of a lyophilized osmotic shock fluid extract, which provided a stable, readily prepared internal reference . Sensitivity was of the order of 0.5 microg of hPRL . The methodology developed also provided a tool for comparing the hydrophobicity of glycosylated and non-glycosylated prolactin molecules obtained from several different species and of different preparations of native or biosynthetic human prolactin.

Toxicol Sci, 2002 Jul, 68(1), 220 - 5
Bacterial lipopolysaccharide exposure alters aflatoxin B(1) hepatotoxicity: benchmark dose analysis for markers of liver injury; Luyendyk JP et al.; Aflatoxin B(1) (AFB(1)) is a fungal toxin that causes both acute hepatotoxicity and hepatocellular carcinoma in humans and experimental animals . Previous studies demonstrated that a small, noninjurious dose of bacterial lipopolysaccharide (LPS) augments the hepatotoxicity of AFB(1) through activation of inflammatory cells and production of soluble inflammatory mediators (Barton et al., 2000b, 2001) . This study was conducted to examine the effect of LPS on the dose-response relationship for AFB(1)-induced liver injury . Male Sprague-Dawley rats (250-350g) were treated with AFB(1) (0.1 mg/kg-6.3 mg/kg, ip) and 4 h later with a noninjurious dose of E . coli LPS (7.4 x 10(6) EU/kg, iv) . Twenty-four h after AFB(1) administration, hepatic parenchymal cell injury was estimated from elevations in serum alanine aminotransferase and aspartate aminotransferase activities . Injury to intrahepatic bile ducts was evaluated from increased serum gamma-glutamyl transferase and alkaline phosphatase activities . Based on benchmark dose (BMD) analysis, the AFB(1) BMD for parenchymal cell injury was decreased 10-fold by LPS cotreatment, whereas AFB(1) BMDs for bile duct injury were decreased nearly 20-fold . The data suggest that concurrent inflammation renders the liver considerably more sensitive to the hepatotoxic effects of AFB(1).

Am J Med Sci, 2002 Jun, 323(6), 299 - 315
Bacterial pathogens as biological weapons and agents of bioterrorism; Greenfield RA et al.; Bacterial pathogens have been identified as agents that have been, or could be, used as weapons of biological warfare and/or biological terrorism . These agents are relatively easily obtained, prepared, and dispersed, either as weapons of mass destruction or for more limited terrorist attacks . Although phylogenetically diverse, these agents all have the potential for aerosol dissemination . Physicians in the United States and most of the developed world have never encountered most of these agents and the diseases they produce . Public health programs must be prepared, and individual primary care providers must be able to recognize, diagnose, treat, and prevent infection with these agents.

Lik Sprava, 2002, (2), 20 - 2
{Bacterial infections complicating gastrointestinal diseases in victims of the Chernobyl catastrophe}; Danylash MM et al.; Overall 303 patients with digestive diseases who had been exposed to adverse factors because of the Chernobyl accident were examined . Of these 124 subjects (40.9%) had degree II-III dysbacteriosis of the large intestine that is believed to develop in the wake of disordered immunity, cholesecretion, and bilification as well as of decline in the enzyme-excretory function of the pancreas.

Eur J Biochem, 2002 Jun, 269(12), 3005 - 13
Mycobacterium tuberculosis FprA, a novel bacterial NADPH-ferredoxin reductase; Fischer F et al.; The gene fprA of Mycobacterium tuberculosis, encoding a putative protein with 40% identity to mammalian adrenodoxin reductase, was expressed in Escherichia coli and the protein purified to homogeneity . The 50-kDa protein monomer contained one tightly bound FAD, whose fluorescence was fully quenched . FprA showed a low ferric reductase activity, whereas it was very active as a NAD(P)H diaphorase with dyes . Kinetic parameters were determined and the specificity constant (kcat/Km) for NADPH was two orders of magnitude larger than that of NADH . Enzyme full reduction, under anaerobiosis, could be achieved with a stoichiometric amount of either dithionite or NADH, but not with even large excess of NADPH . In enzyme titration with substoichiometric amounts of NADPH, only charge transfer species (FAD-NADPH and FADH2-NADP+) were formed . At NADPH/FAD ratios higher than one, the neutral FAD semiquinone accumulated, implying that the semiquinone was stabilized by NADPH binding . Stabilization of the one-electron reduced form of the enzyme may be instrumental for the physiological role of this mycobacterial flavoprotein . By several approaches, FprA was shown to be able to interact productively with {2Fe-2S} iron-sulfur proteins, either adrenodoxin or plant ferredoxin . More interestingly, kinetic parameters of the cytochrome c reductase reaction catalyzed by FprA in the presence of a 7Fe ferredoxin purified from M . smegmatis were determined . A Km value of 30 nm and a specificity constant of 110 microM(-1) x s(-1) (10 times greater than that for the 2Fe ferredoxin) were determined for this ferredoxin . The systematic name for FprA is therefore NADPH-ferredoxin oxidoreductase.

Protein Expr Purif, 2002 Jun, 25(1), 166 - 73
Bacterial expression and in vitro refolding of a single-chain fv antibody specific for human plasma apolipoprotein B-100; Lee MH et al.; From the cloned heavy and light chains of a murine monoclonal antibody (mAbB23) which is specific for human apolipoprotein (apo) B-100 of plasma low-density lipoproteins, a vector was designed for expression of a single-chain antibody (scFv) of mAbB23 in Escherichia coli . The expression vector was constructed so that the scFv gene (V(L)-linker-V(H)) was expressed under the control of the T7 promoter . The inclusion body of scFv was isolated from E . coli lysate and solubilized in 6 M guanidine-hydrochloride without reducing agents, followed by refolding through slow dilution into refolding buffer . After complete removal of the remaining denaturant by dialysis, the soluble scFv was purified through an apo B-100-coupled affinity column, and an active fraction, which had an antigen-binding activity comparable with that of native Fab, was easily obtained . The expression and in vitro refolding of scFv resulted in production of an active molecule in a yield of 15-20 mg per 1-liter flask cultivation .

Protein Expr Purif, 2002 Jun, 25(1), 124 - 33
Bacterial expression of a natively folded extracellular domain fusion protein of the hFSH receptor in the cytoplasm of Escherichia coli; Lobel L et al.; We have expressed the extracellular domain of the hFSH receptor as a fusion protein with thioredoxin in the cytoplasm of an Escherichia coli strain that contains mutations in both the thioredoxin reductase and the glutathione reductase genes . The chimeric protein isolated following induction of expression was purified in a soluble form and binds hFSH with an affinity approximating that of native receptor . This truncated form of the receptor displays the same specificity as intact receptor and does not bind hCG . The protein is expressed at levels that exceed 5 mg/L in the bacterial cytoplasm . Expression of the properly folded extracellular domain of the hFSH receptor in the cytoplasm of E . coli allows the facile and economical purification of large quantities of material . This will facilitate the determination of the structure of the hormone-binding domain of this glycoprotein receptor as well as the production of epitope-specific antibodies .

Virchows Arch, 2002 Jun, 440(6), 627 - 34 Epub 2002 Feb 19.
Leukotriene A(4)-hydrolase expression and leukotriene B(4) levels in chronic inflammation of bacterial origin: immunohistochemistry and reverse-phase high-performance liquid chromatography analysis of oral mucosal epithelium; Eberhard J et al.; Chronic inflammation of the oral epithelium of bacterial origin is associated with elevated leukotriene B(4) (LTB(4)) levels . We investigated leukotriene A(4) (LTA(4))-hydrolase expression and LTB(4) levels in oral epithelium in relation to the clinical disease manifestation and immunohistopathology and LTA(4)-hydrolase expression in cultured oral keratinocytes . In 11 patients, three different types of biopsy specimens of the oral mucosa tissues were examined . Each sample was divided, and one-half was analysed using immunohistochemistry with antibodies to LTA(4)-hydrolase, CD1a, CD3, CD19, macrophages/monocytes and granulocytes . The other half of the sample was homogenised and analysed using reverse-phase high-performance liquid chromatography to determine LTB(4) levels . We found strong LTA(4)-hydrolase expression in basal cells of the oral epithelium from tissue samples that appeared clinically healthy; however, histologically a mild chronic inflammation was observed . In contrast, patients with symptoms of an inflammation of the oral mucosa showed only weak LTA(4)-hydrolase staining of the epithelial cell layers, but strong immunoreactivity in endothelial and invading inflammatory cells . LTB(4) levels were elevated in inflamed tissues compared with non-inflamed controls . Most significantly, there was a strong association between the immunohistochemical detection of the enzyme, LTB(4) levels, cellular infiltration and the clinical disease manifestations . In vitro experiments indicated that LTA(4)-hydrolase expression may be induced by bacterial contamination . This study suggests that LTA(4)-hydrolase expression and elevated LTB(4) levels in oral mucosal epithelium are integral parts of the induction and progression of chronic inflammatory reactions . Epithelial cells may participate in early stages of inflammation as a source of LTB(4).

J Microbiol Methods, 2002 Sep, 51(1), 119 - 21
Bacterial DNA decontamination for reverse transcription polymerase chain reaction (RT-PCR); Wang G et al.; For RT-PCR, removal of contaminating genomic DNA in RNA samples using manganese sulfate was more effective than magnesium . DNA contamination was removed in 3 microg of nucleic acid using 10 U of RNase-free DNase I in 10-microl reaction volumes . The digestion procedure was compatible with commercial RNA extraction kits and was suitable for RT-PCR assay.

J Microbiol Methods, 2002 Sep, 51(1), 83 - 93
Significance of electrophoretic mobility distribution to bacterial transport in granular porous media; Dong H; A method is developed to obtain the electrophoretic mobility distribution of colloidal particles by microelectrophoresis . The results demonstrate that for small particles (< 1 microm), the experimental mobility distribution must be deconvoluted to remove the effect of the random Brownian motion so that the electrophoretic mobility distribution can be obtained . For bacteria-sized particles (on the order of 1 microm or larger), the random Brownian motion is not significant, and the experimental mobility distribution represents the electrophoretic mobility distribution . The significance of the electrophoretic mobility distribution to bacterial transport is demonstrated through comparison between experimental and theoretical values of collision efficiency . Using the extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the electrophoretic mobility distribution of bacteria is transformed to the distribution of collision efficiencies . For strain Comamonas sp . DA001, the predicted collision efficiency values span orders of magnitude, indicating that variation of surface charge density in a monoclonal bacterial population is a cause for the orders of magnitude variation of experimentally determined collision efficiencies . However, despite the fact that the predicted and experimental alpha distributions overlap, the match is not adequate . This inadequacy is ascribed to inability to probe heterogeneity of bacterial surface hydrophobicity, and the inability of the DLVO theory to quantitatively model particle deposition.

J Vet Med Sci, 2002 May, 64(5), 419 - 22
Bacterial lipopolysaccharide induces mRNA expression of an IkappaB MAIL through toll-like receptor 4; Kitamura H et al.; Molecule possessing ankyrin-repeats induced by lipopolysaccharide (MAIL) is a nuclear IkappaB protein recently identified as a molecule appearing in immunocompetent organs after administration of bacterial lipopolysaccharide (LPS) . Participation of Toll-like receptor (TLR) 4, which is a major form of LPS receptors, in the LPS-induced MAIL expression was investigated . When a human myelomonocytic cell line U937 was treated with phorbol 12-myristate 13-acetate for 3 days, the LPS-induced MAIL expression was much potentiated in parallel with an increase in TLR4 expression . The MAIL induction was attenuated when the cells were treated with a neutralizing antibody against TLR4 . The in vivo induction of MAIL in the spleen was smaller in mice having a missense mutation of the Tlr4 gene than in normal control mice . These results collectively indicate that TLR4 contributes, at least in part, MAIL induction after LPS stimulation.

Alcohol Clin Exp Res, 2002 Jun, 26(6), 864 - 74
Epidermal growth factor protects the liver against alcohol-induced injury and sensitization to bacterial lipopolysaccharide; Deaciuc IV et al.; BACKGROUND: Whereas the role of proinflammatory cytokines in the pathogenesis of alcoholic liver disease has been at the forefront of investigation, a possible role for anti-inflammatory cytokines in this disease has received little attention . This study investigated (1) the hepatic protective effect of an anti-inflammatory cytokine, epidermal growth factor (EGF), against deleterious effects of alcohol and sensitization to bacterial lipopolysaccharide (LPS), and (2) the possible mechanisms that underlie such protection . METHODS: Male C57BL/6 mice were fed a Lieber-DeCarli liquid diet that contained alcohol or an isocaloric replacement for 6 weeks . The animals then were treated daily with human EGF for 7 days (5 microg/mouse), after which they were injected with either LPS (1 mg/kg of body weight) or vehicle and killed 8 hr later . Blood and liver were analyzed for plasma aminotransferase activity, liver histology, liver apoptotic nuclei, mRNA of several cytokines (tumor necrosis factor {TNF}-alpha, interleukin {IL}-1beta, IL-6, and IL-10), apoptotic ligands (TRAIL), cytokine receptors (TNFRp55), pro- and antiapoptotic regulators/adaptors (Fas receptor, FasL, FADD, TRADD, RIP, Bak, Bax, Bcl-X, Bcl-2 and Bcl-w), and caspase-8 . RESULTS: Alcohol increased plasma aminotransferase activity and sensitized the liver to the effects of LPS, such as polymorphonuclear infiltration, occurrence of necrotic foci and microabscesses, and increased apoptosis . These changes were associated with elevated mRNA expression of proapoptotic regulators/adaptors . EGF either counteracted or markedly blunted most of these effects . EGF did not affect liver mRNA expression of TNF-alpha, IL-1beta, IL-6, and IL-10, which suggested that these cytokines were not involved in EGF protective effect . EGF protection was mediated by down-regulation of apoptosis through suppression of proapoptotic gene expression . CONCLUSIONS: EGF protects the liver against both alcohol-induced liver damage and liver sensitization to bacterial LPS through down-regulation of apoptosis.

Cell Microbiol, 2002 Jun, 4(6), 329 - 39
Bacterial infection of a model insect: Photorhabdus luminescens and Manduca sexta; Silva CP et al.; Invertebrates, including insects, are being developed as model systems for the study of bacterial virulence . However, we understand little of the interaction between bacteria and specific invertebrate tissues or the immune system . To establish an infection model for Photorhabdus, which is released directly into the insect blood system by its nematode symbiont, we document the number and location of recoverable bacteria found during infection of Manduca sexta . After injection into the insect larva, P . luminescens multiplies in both the midgut and haemolymph, only later colonizing the fat body and the remaining tissues of the cadaver . Bacteria persist by suppressing haemocyte-mediated phagocytosis and culture supernatants grown in vitro, as well as plasma from infected insects, suppress phagocytosis of P . luminescens . Using GFP-labelled bacteria, we show that colonization of the gut begins at the anterior of the midgut and proceeds posteriorly . Within the midgut, P . luminescens occupies a specific niche between the extracellular matrix and basal membrane (lamina) of the folded midgut epithelium . Here, the bacteria express the gut-active Toxin complex A (Tca) and an RTX-like metalloprotease PrtA . This close association of the bacteria with the gut, and the production of toxins and protease, triggers a massive programmed cell death of the midgut epithelium.

Res Microbiol, 2002 May, 153(4), 191 - 7
Growth mechanism of the bacterial flagellar filament; Yonekura K et al.; The growth of the bacterial flagellar filament occurs at its distal end by self-assembly of flagellin transported from the cytoplasm through the narrow central channel of the flagellum . The cap at the growing end is essential for its growth, remaining stably attached while permitting the flagellin insertion . The structure of the cap-filament analyzed by electron cryomicroscopy suggested a cap rotation mechanism to promote the flagellin self-assembly.

Carbohydr Res, 2002 Jun 12, 337(12), 1145 - 53
Molecular interactions in bacterial cellulose composites studied by 1D FT-IR and dynamic 2D FT-IR spectroscopy; Kacurakova M et al.; Specific strain-induced orientation and interactions in three Acetobacter cellulose composites: cellulose (C), cellulose/pectin (CP) and cellulose/xyloglucan (CXG) were characterized by FT-IR and dynamic 2D FT-IR spectroscopies . On the molecular level, the reorientation of the cellulose fibrils occurred in the direction of the applied mechanical strain . The cellulose-network reorientation depends on the composition of the matrix, including the water content, which lubricates the motion of macromolecules in the network . At the submolecular level, dynamic 2D FT-IR data suggested that there was no interaction between cellulose and pectin in CP and that they responded independently to a small amplitude strain, while in CXG, cellulose and xyloglucan were uniformly strained along the sample length.

FEBS Lett, 2002 Apr 24, 517(1-3), 1 - 6
Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucleotidyl transferase superfamily; Russell RB et al.; Similarities between protein three-dimensional structures can reveal evolutionary and functional relationships not apparent from sequence comparison alone . Here we report such a similarity between the metabolic enzymes histidine phosphocarrier protein kinase (HPrK) and phosphoenolpyruvate carboxykinase (PCK), suggesting that they are evolutionarily related . Current structure classifications place PCK and other P-loop containing nucleotidyl-transferases into different folds . Our comparison of both HPrK and PCK to other P-loop containing proteins reveals that all share a common structural motif consisting of an alphabeta segment containing the P-loop flanked by an additional beta-strand that is adjacent in space, but far apart along the sequence . Analysis also shows that HPrK/PCK differ from other P-loop containing structures no more than they differ from each other . We thus suggest that HPrK and PCK should be classified with other P-loop containing proteins, and that all probably share a common ancestor that probably contained a simple P-loop motif with different protein segments being added or lost over the course of evolution . We used the structure-based sequence alignment containing residues specific to HPrK/PCK to identify additional members of this P-loop containing family.

J Biol Chem, 2002 Aug 23, 277(34), 30463 - 8 Epub 2002 Jun 11.
Human neutrophils use the myeloperoxidase-hydrogen peroxide-chloride system to chlorinate but not nitrate bacterial proteins during phagocytosis; Rosen H et al.; The generation of extracellular oxidants by neutrophils has been widely investigated, but knowledge about the chemical reactions that occur in the phagolysosome, the cellular compartment that kills pathogens, is more limited . One important pathway may involve the production of potent halogenating agents such as hypochlorous acid (HOCl) by the myeloperoxidase-hydrogen peroxide-halide system . However, explorations of the oxidation chemistry of phagolysosomes have been hampered by the organelle's inaccessibility . To overcome this limitation, we recovered Escherichia coli that had been internalized by human neutrophils . We then analyzed the bacterial proteins for 3-chlorotyrosine, a stable marker of damage by HOCl . Mass spectrometric analysis revealed that levels of 3-chlorotyrosine in E . coli proteins increased markedly after the bacteria were internalized by human neutrophils . This increase failed to occur in E . coli exposed to neutrophils deficient in NADPH oxidase or myeloperoxidase, implicating H(2)O(2) and myeloperoxidase in the halogenation reaction . The extent of protein chlorination by normal neutrophils paralleled bacterial killing . Our observations support the view that the phagolysosome of human neutrophils uses the myeloperoxidase-hydrogen peroxide-chloride system to chlorinate bacterial proteins . In striking contrast, human neutrophils failed to nitrate bacterial proteins unless the medium was supplemented with 1 mm nitrite, and the level of nitration was low . Protein chlorination associated with bacterial killing was unaffected by the presence of nitrite in the medium . Nitration required NADPH oxidase but appeared to be independent of myeloperoxidase, suggesting that neutrophils can nitrate proteins through a pathway that requires nitrite but is independent of myeloperoxidase.

Biomaterials, 2002 Jul, 23(13), 2761 - 6
In vitro degradation of chitosan by bacterial enzymes from rat cecal and colonic contents; Zhang H et al.; The degradative activities of extracellular and cell-associated portions of rat cecal and colonic enzymes, whose activities are comparable to that in the human colon, against five chitosan samples were characterized . The effects of the molecular weight (MW) and degree of deacetylation (DD) of chitosan on its susceptibility to degradation were investigated . In addition, the degradation function of rat bacterial enzymes was compared to that of a commercially available almond emulsin beta-glucosidase that contains a chitinase . The results show that rat bacterial enzymes had the ability to degrade chitosan with extracellular enzymes exhibiting a more profound effect than did cell-associated enzymes . The reaction to bacterial enzymes degradation was dependent on both the MW and DD of the chitosan sample . Those samples with a lower MW and lower DD were more susceptible substrates . A similar degradation function of rat bacterial enzymes and of almond emulsin beta-glucosidase on chitosan was revealed, which indicates that almond emulsin beta-glucosidase might be able to be used as an in vitro enzyme system to predict the large intestinal degradation of chitosan.

Curr Opin Microbiol, 2002 Jun, 5(3), 288 - 95
Bacterial detoxification of organophosphate nerve agents; Raushel FM; Bacterial enzymes have been isolated that catalyze the hydrolysis of organophosphate nerve agents with high-rate enhancements and broad substrate specificity . Mutant forms of these enzymes have been constructed through rational redesign of the active-site binding pockets and random mutagenesis to create protein variants that are optimized for the detoxification of agricultural insecticides and chemical warfare agents . In this review, the catalytic properties of two bacterial enzymes, phosphotriesterase and organophosphorus anhdrolase, are examined for their ability to hydrolyze organophosphate nerve agents.

J Commun Dis, 1984 Mar, 16(1), 30 - 7
Immunodiagnosis of bacterial meningitis; Ichhpujani RL et al.; The quest for the search of rapid, cheap, easy to perform and highly sensitive and specific tests has resulted into the introduction and application of various new tests for the diagnosis of bacterial meningitis . Most of these tests are based on immunological principles, viz . counter-immunoelectrophoresis, latex agglutination test, co-agglutination, radio-immunoassay, haemagglutination inhibition as well as study of immune profile of cerebrospinal fluid . Apart from these certain non-immunological tests viz . Limulus amoebecyte lysate test, gas liquid chromatography, nitroblue tetrazolium dye reduction test have also been evaluated to make the laboratory diagnosis of this important clinical entity rapid and more reliable . These tests have been discussed and their current status presented.

Nat Struct Biol, 2002 Jul, 9(7), 544 - 52
Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM; Fromme JC et al.; MutM is a bacterial 8-oxoguanine glycosylase responsible for initiating base-excision repair of oxidized guanine residues in DNA . Here we report five different crystal structures of MutM-DNA complexes that represent different steps of the repair reaction cascade catalyzed by the protein and also differ in the identity of the base opposite the lesion (the 'estranged' base) . These structures reveal that the MutM active site performs the multiple steps of base-excision and 3' and 5' nicking with minimal rearrangement of the DNA backbone.

J Mol Biol, 2002 May 3, 318(3), 889 - 900
Interactions between bacterial flagellar axial proteins in their monomeric state in solution; Furukawa Y et al.; The axial structure of the bacterial flagellum is composed of many different proteins, such as hook protein and flagellin, and each protein forms a short or long axial segment one after another in a well-defined order along the axis . Under physiological conditions, most of these proteins are stable in the monomeric state in solution, and spontaneous polymerization appears to be suppressed, as demonstrated clearly for flagellin, probably to avoid undesirable self-assembly in the cytoplasmic space . However, no systematic studies of the possible associations between monomeric axial proteins in solution have been carried out . We therefore studied self and cross-association between hook protein, flagellin and three hook-associated proteins, HAP1, HAP2 and HAP3, in all possible pairs, by gel-filtration and analytical centrifugation, and found interactions in the following two cases only . Flagellin facilitated HAP3 aggregation into beta-amyloid-like filaments, but without stable binding between the two . Addition of HAP3 to HAP2 resulted in disassembly of preformed HAP2 decamers and formation of stable HAP2-HAP3 heterodimers . HAP2 missing either of its disordered terminal regions did not form the heterodimer, whereas HAP3 missing either of its disordered terminal regions showed stable heterodimer formation . This polarity in the heterodimer interactions suggests that the interactions between HAP2 and HAP3 in solution are basically the same as those in the flagellar axial structure . We discuss these results in relation to the assembly mechanism of the flagellum . (c) 2002 Elsevier Science Ltd.

Int J Syst Evol Microbiol, 2002 May, 52(Pt 3), 777 - 87
Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission; Ragan MA et al.; If open reading frames (ORFs) have been transmitted primarily by vertical descent, the distributional profile of orthologues of each ORF should be congruent with the organismal tree or a subtree thereof . Distributional patterns not reconciled parsimoniously with tree-like descent and loss are prima facie evidence of lateral gene transfer . Herein, a rigorous criterion for recognizing ORF distributions is described and implemented; it does not require the inference of phylogenetic trees, nor does it assume any specific tree . Because lineage-specific differences in rates of sequence change can also generate unexpected distributional patterns, rate artefacts were controlled for by requiring pairwise matches between ORFs to exceed a rigorous inclusion threshold, but absence of a match was assessed against a more-permissive exclusion threshold . Applying this dual-threshold criterion to cross-domain and cross-phylum distributional patterns for ORFs in 23 bacterial genomes, a relative abundance of ORFs was observed that find a match in exactly seven other bacterial phyla; 94-99% of these ORFs also find matches among the Archaea and/or Eukarya . In the larger (and some smaller) bacterial genomes, ORFs that find matches in exactly one other bacterial phylum are also relatively abundant, but fewer of these have non-bacterial homologues; most of their matches within the Bacteria are to the Proteobacteria and/or Firmicutes, which cannot be sister lineages to all bacteria . ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes.

Can Fam Physician, 2002 May, 48, 877 - 8
Bacterial vaginosis during pregnancy . Should we screen for and treat it?
Einarson A, Koren G.
QUESTION: Some of my patients have been diagnosed with bacterial vaginousis (BV) during pregnancy; some have symptoms, others do not . Should I be treating them, and if so, with what? Also, should I be screening all my pregnant pateints for BV? ANSWER: There appears to be no benefit to screening or treating pregnant women with an average risk of BV . It is not even clear that treating pregnant women at high risk of BV is beneficial . If you decide to treat, the drugs of choice are oral or intravaginal gel metronidazole or oral clindamycin . Both these drugs are safe to use throughout pregnancy.

Nephron, 2002 Jun, 91(2), 203 - 9
Hospitalizations for bacterial endocarditis after initiation of chronic dialysis in the United States; Abbott KC et al.; AIMS: Bacterial endocarditis is a significant cause of morbidity and mortality but has not been studied in a national population of end-stage renal disease patients . METHODS: 327,993 dialysis patients in the United States Renal Data System initiated from 1 January 1992 to 30 June 1997 were analyzed in a historical cohort study of hospitalized bacterial endocarditis (ENDO, ICD9 Code 421.x) . Renal transplant recipients were excluded . RESULTS: Hemodialysis patients had an age-adjusted incidence ratio for ENDO of 17.86 (95% confidence interval, 6.62-48.90) and peritoneal dialysis patients 10.54 (95% CI, 0.71- 158.13, not statistically significant) compared to the general population in 1996 (the National Hospital Discharge Survey) . 6.1% of patients with ENDO underwent valve replacement surgery . In multivariate analysis, hemodialysis (vs . peritoneal dialysis), earlier year of dialysis, cardiac disease, and lower serum creatinine and albumin were associated with increased risk of ENDO . In Cox regression analysis, patients with ENDO had increased mortality, relative risk 1.48 (95% CI 1.45-1.73) . CONCLUSIONS: Patients on chronic dialysis were at increased risk for ENDO compared to the general population . The risk for peritoneal dialysis patients was not statistically significant, possibly due to the smaller numbers of patients on this modality . Hemodialysis (vs . peritoneal dialysis) and comorbidities were the strongest risk factors for ENDO identified .

J Mol Biol, 2002 Apr 26, 318(2), 219 - 36
The tubulin ancestor, FtsZ, draughtsman, designer and driving force for bacterial cytokinesis; Addinall SG et al.; We discuss in this review the regulation of synthesis and action of FtsZ, its structure in relation to tubulin and microtubules, and the mechanism of polymerization and disassembly (contraction) of FtsZ rings from a specific nucleation site (NS) at mid cell . These topics are considered in the light of recent immunocytological studies, high resolution structures of some division proteins and results indicating how bacteria may measure their mid cell point . (c) 2002 Elsevier Science Ltd.

Arch Biochem Biophys, 2002 Jun 1, 402(1), 38 - 50
Synthesis and bacterial expression of a gene encoding the heme domain of assimilatory nitrate reductase; Barber MJ et al.; Assimilatory NADH:nitrate reductase (EC 1.6.6.1), a complex Mo-pterin-, cytochrome b(557)-, and FAD-containing protein, catalyzes the regulated and rate-limiting step in the utilization of inorganic nitrogen by higher plants . A codon-optimized gene has been synthesized for expression of the central cytochrome b(557)-containing fragment, corresponding to residues A542-E658, of spinach assimilatory nitrate reductase . While expression of the full-length synthetic gene in Escherichia coli did not result in significant heme domain production, expression of a Y647* truncated form resulted in substantial heme domain production as evidenced by the generation of "pink" cells . The histidine-tagged heme domain was purified to homogeneity using a combination of NTA-agarose and size-exclusion FPLC, resulting in a single protein band following SDS-PAGE analysis with a molecular mass of approximately 13 kDa . MALDI-TOF mass spectrometry yielded an m/z ratio of 12,435 and confirmed the presence of the heme prosthetic group (m/z=622) while cofactor analysis indicated a 1:1 heme to protein stoichiometry . The oxidized heme domain exhibited spectroscopic properties typical of a b-type cytochrome with a visible Soret maximum at 413 nm together with epr g-values of 2.98, 2.26, and 1.49, consistent with low-spin bis-histidyl coordination . Oxidation-reduction titrations of the heme domain indicated a standard midpoint potential (E(o)') of -118 mV . The isolated heme domain formed a 1:1 complex with cytochrome c with a K(A) of 7 microM (micro=0.007) and reconstituted NADH:cytochrome c reductase activity in the presence of a recombinant form of the spinach nitrate reductase flavin domain, yielding a k(cat) of 1.4 s(-1) and a K(m app) for cytochrome c of 9 microM . These results indicate the efficient expression of a recombinant form of the heme domain of spinach nitrate reductase that retained the spectroscopic and thermodynamic properties characteristic of the corresponding domain in the native spinach enzyme.

Int Microbiol, 2001 Dec, 4(4), 203 - 8
Speciation of termite gut protists: the role of bacterial symbionts; Dolan MF; At least 12 termite gut protists have been named because of their bacterial symbionts . Dozens more species are diagnosed by epi- and endosymbionts and more still have regular bacterial associations referred to in their species description . Molecular systematic studies have begun to identify these bacteria, but the ecological relations with their protist bionts are still unknown . Recent findings of acetogenic spirochetes in termite guts may explain the peculiar arrangement of spirochetes on some of these protists . Other bacteria function as motility or chemotactic symbionts of these protists . The size and shape of the parabasal body, a Golgi complex, are morphological characters of the Parabasalia (trichomonads, hypermastigids) that may be influenced by regular, heritable epi- and endosymbiotic bacteria.

Int J Food Microbiol, 2002 Jun 25, 76(3), 207 - 14
Estimating the precision of serial dilutions and viable bacterial counts; Hedges AJ; The propagation of error in serial dilutions was investigated theoretically and by means of computer simulations . The principal aim of the study was, given only the pipette manufacturer's specification, to estimate the variance of any step in a dilution series both of pure solutions and of homogeneous bacterial suspensions by means of simple formulae . The study was extended to include bacterial plate counts by both the standard and the Miles and Misra methods . It was found that such estimation was possible and that the distributions approximated the normal sufficiently for the construction of confidence intervals (Cls) by the usual method . Such intervals can be regarded as minima which could be inflated by other, possibly undetermined, factors . It is suggested that laboratories could construct tables such as that reported here for pipettes and methods in common use to facilitate estimation . While replication of the final sampling step of a plate count increases the precision of estimation, averaging across dilutions may decrease precision and is not recommended for the standard pour-plate count.

Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 2001, 33(3), 331 - 334
Improvement of Bacterial Two Hybrid System; Liao GX et al.; Bacterial two-hybrid system is a newly developed method for studying protein-protein interactions, especially for effects of the environmental factors on the interaction . In our studies of the effect of NH(4)( ) or oxygen on the NifL-NifA interaction, it was found that E.coli strain DHP1 cya(-), when transformed by T18-NifL together with T25-NifA, exhibited high activity of beta-galactosidase in the presence of NH(4)( ), and appeared as red colonies when grown in MacConkey/maltose agar . This indicated the direct interaction of NifL and NifA . However,similar phenomena were also shown in the case of the DHP1 cya(-) strain harboring T18-NifL or T25-NifL alone, respectively, without its interacting counterpart T25-NifA or T18-NifA . In this paper, a brief method is presented to detect the protein-protein interaction using direct assay of the adenylate cyclase, thus minimizing the false positives produced by the beta-galactosidase activity assay or MacConkey/maltose agar plating.

J Virol, 2002 Jul, 76(13), 6660 - 8
Construction and manipulation of an infectious clone of the bovine herpesvirus 1 genome maintained as a bacterial artificial chromosome; Mahony TJ et al.; The complete genome of bovine herpesvirus 1 (BoHV-1) strain V155 has been cloned as a bacterial artificial chromosome (BAC) . Following electroporation into Escherichia coli strain DH10B, the BoHV-1 BAC was stably propagated over multiple generations of its host . BAC DNA recovered from DH10B cells and transfected into bovine cells produced a cytopathic effect which was indistinguishable from that of the parent virus . Analysis of the replication kinetics of the viral progeny indicated that insertion of the BAC vector into the thymidine kinase gene did not affect viral replication . Specific manipulation of the BAC was demonstrated by deleting the gene encoding glycoprotein E by homologous recombination in DH10B cells facilitated by GET recombination . These studies illustrate that the propagation and manipulation of herpesviruses in bacterial systems will allow for rapid and accurate characterization of BoHV-1 genes . In turn, this will allow for the full utilization of BoHV-1 as a vaccine vector.

Orbit, 1998 Dec, 17(4), 227 - 235
Bacterial infections of the orbit; van Dissel JT et al.; This review of the literature on orbital infections focusses on bacterial infections of the preseptal space, subperiosteal abscesses, orbital phlegmon and orbital abscesses . The need for a timely diagnosis of and multidisciplinary approach to treatment of these infections, which may lead to life-threatening complications, is emphasized .

J Biol Chem, 2002 Aug 23, 277(34), 30976 - 83 Epub 2002 Jun 04.
Crystal structure of bacterial morphinone reductase and properties of the C191A mutant enzyme; Barna T et al.; The crystal structure of the NADH-dependent bacterial flavoenzyme morphinone reductase (MR) has been determined at 2.2-A resolution in complex with the oxidizing substrate codeinone . The structure reveals a dimeric enzyme comprising two 8-fold beta/alpha barrel domains, each bound to FMN, and a subunit folding topology and mode of flavin-binding similar to that found in Old Yellow Enzyme (OYE) and pentaerythritol tetranitrate (PETN) reductase . The subunit interface of MR is formed by interactions from an N-terminal beta strand and helices 2 and 8 of the barrel domain and is different to that seen in OYE . The active site structures of MR, OYE, and PETN reductase are highly conserved reflecting the ability of these enzymes to catalyze "generic" reactions such as the reduction of 2-cyclohexenone . A region of polypeptide presumed to define the reducing coenzyme specificity is identified by comparison of the MR structure (NADH-dependent) with that of PETN reductase (NADPH-dependent) . The active site acid identified in OYE (Tyr-196) and conserved in PETN reductase (Tyr-186) is replaced by Cys-191 in MR . Mutagenesis studies have established that Cys-191 does not act as a crucial acid in the mechanism of reduction of the olefinic bond found in 2-cyclohexenone and codeinone.

Genes Cells, 2002 May, 7(5), 509 - 19
Bacterial SsrA system plays a role in coping with unwanted translational readthrough caused by suppressor tRNAs; Ueda K et al.; BACKGROUNDS: Bacterial SsrA RNA (also known as tmRNA or 10Sa RNA) mediates the addition of a short peptide tag to the C-terminus of the nascent polypeptide when a ribosome is stalled at the 3' end of an mRNA lacking a stop codon . This process, called trans-translation, rescues the stalled ribosome and ensures degradation of tagged polypeptides by ATP-dependent proteases . To fully understand the physiological roles of SsrA RNA, it is essential to know how endogenous mRNA targets for the SsrA system are generated in cells . The aim of the present study is to examine how translational readthrough by suppressor tRNAs affects trans-translation in Escherichia coli . RESULTS: We demonstrated that SsrA tagging of bulk cellular proteins was significantly enhanced by an ochre or an amber suppressor tRNA . Western blot analysis of proteins produced from specific genes possessing a Rho-independent terminator revealed that readthrough at the normal stop codon leads to an efficient tagging and proteolysis of the extended proteins . Size analyses of both protein and mRNA suggested that tagging of extended proteins occurs because ribosome passing through the normal stop codon presumably reach the 3' end of mRNA defined by the transcription terminator hairpin . The inhibitory effect of ssrA mutation on cell growth was markedly amplified in cells with an ochre suppressor tRNA . CONCLUSION: The present finding suggests that the SsrA system contributes to scavenge errors and/or problems caused by translational readthrough that occurs typically in the presence of a suppressor tRNA.

Annu Rev Biochem, 2002, 71, 71 - 100 Epub 2001 Nov 09.
The bacterial RecA protein and the recombinational DNA repair of stalled replication forks; Lusetti SL et al.; The primary function of bacterial recombination systems is the nonmutagenic repair of stalled or collapsed replication forks . The RecA protein plays a central role in these repair pathways, and its biochemistry must be considered in this context . RecA protein promotes DNA strand exchange, a reaction that contributes to fork regression and DNA end invasion steps . RecA protein activities, especially formation and disassembly of its filaments, affect many additional steps . So far, Escherichia coli RecA appears to be unique among its nearly ubiquitous family of homologous proteins in that it possesses a motorlike activity that can couple the branch movement in DNA strand exchange to ATP hydrolysis . RecA is also a multifunctional protein, serving in different biochemical roles for recombinational processes, SOS induction, and mutagenic lesion bypass . New biochemical and structural information highlights both the similarities and distinctions between RecA and its homologs . Increasingly, those differences can be rationalized in terms of biological function.

J Bone Joint Surg Br, 2002 May, 84(4), 486 - 8
Do warming blankets increase bacterial counts in the operating field in a laminar-flow theatre?
Sharp RJ, Chesworth T, Fern ED.
Patient warming systems are used routinely to prevent hypothermia under anaesthesia . Airflow from warming blankets may potentially influence bacterial counts either by pumping 'dirty air' from floor level to the operating area or by blowing the patients' skin cells into the operating field from airflow under the blanket . Using slit-air sampling we analysed the air quality within a laminar-flow theatre at a simulated operating site . We assessed the effect of 'high shedding of skin' under the blanket using volunteer patients with psoriasis . We also simulated general theatre activity outside the laminar-flow area in order to determine whether the bacterial counts in the operating field were affected . No colonies were grown in any of the groups tested and our results suggest that the patient warming system does not influence bacterial counts at the operating site in an ultraclean air-ventilated theatre, even with patients who have high shedding of skin cells.

Wiad Lek, 2002, 55(1-2), 51 - 5
{The value of determining vaginal secretion reaction (pH) as a screening test of bacterial vaginosis}; Manka W et al.; The reaction of vaginal fluid was performed in 386 women admitted to the Outpatient Clinic . In 120 (31.09%) cases pH value was more than 4.5 . The frequency of abnormal results grew with the age of patients; lower percentage was observed in pregnant women, more educated ones and nulliparas . Much lower diagnostic specificity of the vaginal fluid reaction was noticed in postmenopausal women what was confirmed in the test on the presence of aromatic amines and clue cells in microscopic examination . The correct reaction (it means pH lower than 4.5) practically exclude the bacterial vaginosis.

Calcif Tissue Int, 2002 Jul, 71(1), 53 - 8 Epub 2002 Jun 04.
Interferon-gamma production changes in parallel with bacterial lipopolysaccharide induced bone resorption in mice: an immunohistometrical study; Moriyama H et al.; It has been reported that bacterial lipopolysaccharide (LPS) induces alveolar bone resorption and that the host immune system, especially activated T cells, plays a crucial role in osteoclastogenesis . On the other hand, interferon-gamma (IFN-g), which is produced by activated T cells, suppresses bone resorption both in vitro and in vivo . Thus, the question arises as to whether or not IFN-g production increases with increasing bone resorption . We previously demonstrated that repeated injections of Escherichia coli LPS into mouse gingiva causes osteoclast formation in alveolar bone . In the present study we observed changes in the IFN-g production of infiltrating cells in concurrence with bone resorption . Mice were repeatedly injected with 5 mg LPS 26 times every 48 hours . After the 16th injection, when the alveolar bone resorption reached a plateau, the concentration of LPS was altered (25 mg LPS or PBS alone) . The level of bone resorption became significantly elevated, and the number of IFN-g- and interleukin-1 beta (IL-1b)-bearing cells also increased significantly in relation to bone resorption within the 25 mg LPS-injected group . On the other hand, few tartrate-resistant acid phosphatase positive cells, or IFN-g- and IL-1b-bearing cells, were seen in the PBS-injected group . These results suggest that alteration in IFN-g-bearing cells might play a role in counterbalancing LPS-induced bone resorption resulting from osteoclast activating cytokines such as IL-1b.

Nat Rev Genet, 2002 Jun, 3(6), 462 - 73
Redefining bacterial populations: a post-genomic reformation; Joyce EA et al.; Sexual reproduction and recombination are essential for the survival of most eukaryotic populations . Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked . The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria . These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level . Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host pathogen relationships.

Clin Pediatr (Phila), 2002 May, 41(4), 239 - 47
Is care in alternative settings safe for infants with possible serious bacterial infection?
Brayer AF, Conners GP, Kaur T, McConnochie KM.
Febrile infants are frequently hospitalized for possible serious bacterial illness (SBI) . Potential to replace hospitalization of selected febrile infants with care in alternative settings was assessed by estimating risk for deterioration and by determining resource use . Lower and upper bound estimates for the number of infants admitted to a tertiary care hospital from 1994 to 1998 for possible SBI were 537 and 836, respectively . Detailed record reviews were conducted for febrile infants among this group, who, on the basis of positive blood or cerebrospinal cultures, were considered most likely to have SBI . No infant with a positive blood culture who was eligible for alternative setting care (ASC) deteriorated . Ninety-five percent confidence interval for the worst-case (assuming denominator of 537) estimate of risk for deterioration was 0% to 0.56% . Most resource use was compatible with ASC . Alternative setting care for selected febrile infants is both safe and feasible.

Przegl Lek, 2001, 58(12), 1055 - 8
{The role of cytokines in bacterial meningitis}; Bociaga-Jasik M et al.; Bacterial meningitis is the serious infection of the central nervous system (CNS), and stimulated by bacteria inflammatory host response has crucial role in its pathogenesis . The most important elements of this response are cytokines, especially tumor necrosis factor (TNF-alpha), interleukin-1 beta (IL-1 beta), interleukin-6 (IL-6), interleukin-8 (IL-8), and interleukin-10 (IL-10), which have antiinflammatory activity . Production of cytokines in the CNS triggers a cascade of inflammatory mediators . Better understanding of mechanisms which take place during the course of the bacterial meningitis can be useful in differential diagnosis, prognosis and treatment of this disease . Investigations on the role of cytokines in the bacterial meningitis, have great therapeutic implications, and can result in introduction to the treatment antiinflammatory drugs, which can help to reduce mortality rate and number of complications.

S Afr Med J, 2002 Mar, 92(3), 231 - 4
Preterm labour--is bacterial vaginosis involved?
Odendaal HJ, Popov I, Schoeman J, Smith M, Grove D.
OBJECTIVE: To assess the efficacy of treatment of bacterial vaginosis (BV) using metronidazole to reduce preterm labour in primigravidae and multigravidae with previous midtrimester abortion or preterm labour . DESIGN: Randomised controlled trial . SETTING: Tertiary academic hospital . METHOD: Two different groups of patients were screened for BV at the first antenatal visit, namely primigravidae and high-risk multigravidae who had had a previous midtrimester abortion or preterm delivery . Patients where BV was diagnosed clinically or on Gram's stain of a smear taken from the posterior vaginal fornix, received either 400 mg metronidazole, or 100 mg vitamin C orally twice daily for 2 days . The Gram's stain was repeated after 4 weeks . If BV was found again, treatment with the same drug was repeated . OUTCOME MEASURES: Preterm delivery, birth weight and perinatal deaths . RESULTS: One thousand and five patients entered the study, but 40 were excluded for various reasons and 10 were lost to follow-up . There were 464 primigravidae, of whom 150 (32%) had BV . Except for the 5-minute Apgar score, no significant differences were found between primigravidae negative for BV and those who received either metronidazole or vitamin C . There were 491 high-risk multigravidae, of whom 127 (26%) had BV . The mean gestational age in the BV-negative group was 37 weeks, in contrast to 37.4 weeks in the vitamin C group and 35.6 weeks in the metronidazole group . Birth weights in these three groups were 2,752 g, 2,759 g and 2,475 g respectively, significantly less (P = 0.0109) in the metronidazole group in comparison with the BV-negative group . Delivery before 37 weeks occurred in 29% of high-risk multigravidae with no BV but in 24% of those who took vitamin C and in 43% who took metronidazole . Differences were significant between the BV-negative and metronidazole groups (P = 0.0231) and also between the metronidazole and vitamin C groups (P = 0.0274) . Delivery before 28 weeks occurred in 4% of the high-risk multigravidae with no BV but in 10% of those with BV who took metronidazole . The difference was significant (P = 0.0430) . Analysis for maximum likelihood estimates for preterm labour identified only previous preterm labour or midtrimester abortion as risk factors . CONCLUSION: Metronidazole does not seem to reduce the prevalence of preterm labour when given for BV before 26 weeks' gestation.

Indian J Med Res, 2001 Dec, 114, 192 - 8
Estimation of vacuolating cytotoxin secreted by different strains of Helicobacter pylori using bead enzyme-linked immunosorbent assay & its correlation with bacterial genotype; Datta S et al.; BACKGROUND & OBJECTIVES: A highly sensitive bead enzyme-linked immunosorbent assay was applied for the quantitative determination of vacuolating cytotoxin (VacA) released in the culture supernatant of 40 well characterized Helicobacter pylori strains in order to clarify the significance of allelic combination of the vacA gene as the predictor of the level of toxin secretion and also to determine the most appropriate genotype of H . pylori associated with high VacA release . Attempts were also made for the detection of VacA in the gastric juice of patients for the rapid diagnosis of H . pylori infection . METHODS: The genotypes of 40 H . pylori strains cultured from the gastric biopsy samples were determined by specific PCRs . The cell-free culture supernatant of the strains as well as the gastric juice of the patients were used for bead-ELISA and the purified VacA from the H . pylori strain ATCC49503 was used as positive control . RESULTS: Ninety per cent of the strains with vacAs1m1 allele combination secrete on an average 146.4 ng/ml of VacA while the corresponding value was 19.1 ng/ml for s1m2 strains . None of the s2m2 as well as the ice negative H . pylori strains produced detectable VacA in the medium while strains expressed the toxin irrespective of the presence or absence of cagA gene . Fifteen of 22 gastric juice samples yielded positive bead-ELISA results . INTERPRETATION & CONCLUSION: vacAs1, vacAm1 and iceA1 could be considered as the determinants of high VacA secretion . Also, the detection of VacA by bead-ELISA in the gastric juice could be considered as an alternative approach in the diagnosis of H . pylori infection.

Microb Ecol, 2000 Apr, 39(3), 186 - 196
16S rRNA Targeted Probes for the Identification of Bacterial Strains Isolated from Cultures of the Toxic Dinoflagellate Alexandrium tamarense; Groben R et al.; A BSTRACTBacteria have been implicated in the production of paralytic shellfish poison (PSP) toxins, which are normally associated with bloom-forming algal species, specifically toxic dinoflagellate algae . To clarify the role that these bacteria may play in the production of PSP toxins, it is desirable to identify and localize the bacteria associated with the dinoflagellates . 16S rRNA-targeted probes offer the possibility for both, and thus, probes have been made to putatively toxigenic bacteria isolated from the PSP-related dinoflagellate Alexandrium tamarense and tested for their specificity in dot blot and in situ hybridization experiments.

Microb Ecol, 2001 Jul, 42(1), 69 - 79
Short-Term Responses of the Natural Planktonic Bacterial Community to the Changing Water Properties in an Estuarine Environment: Ectoenzymatic Activity, Glucose Incorporation, and BiomassProduction; Cunha MA et al.; The possibility that two principal bacterial communities expressing different levels of heterotrophic activity might coexist in an estuarine ecosystem (Ria de Aveiro, Portugal) and could quickly respond to tidal fluctuations of environmental factors was experimentally tested in diffusion chambers by swapping the dissolved components of the natural water between the two communities and comparing their reactivity against the unaltered controls . The results for ectoenzymatic activity (Leu-aminopeptidase and b-glucosidase), glucose incorporation and biomass production after transference of the marine bacterial community to brackish water showed maxima in the range of 241-384% of the control values . The opposite transference of the brackish-water bacterial community to marine water produced maximal decreases to 0.14-0.58% of the control values . In a reverse experiment, designed as the return to the initial conditions after 2 hours of the first exposure, the marine community rapidly re-acquired the characteristic low profile of activity . Contrastingly, the negative effects of 2 hours of exposure to marine water on the activity of the brackish water bacteria persisted, at least for 4 hours, after return to their own water . The apparent short-term irreversibility of the decline in activity of the brackish water bacteria when exposed to marine water, in parallel with the quick and reversible positive response of the marine water bacteria to the brackish water, suggests the development of two distinct bacterioplankton communities adapted to the environmental conditions prevailing at distinct sections of the estuary . The reactivity to environmental changes demonstrated by the two communities allows the prediction of estuarine profiles of bacterial activity steeper than those expected from the conservative transport of bacterial cells associated with tidal currents.

Microb Ecol, 2001 Jul, 42(1), 46 - 55
Composition and Activity of Marine Alkane-Degrading Bacterial Communities in the Transition from Suboxic to Anoxic Conditions; Berthe-Corti L et al.; The impact of the oxygen supply rate (OSR) on the metabolic activity and on the composition of hexadecane-degrading bacterial communities in a quasi-anoxic milieu (nominal DOT = 0%) was studied in continuous cultures containing intertidal sediment . The dilution rate was kept constant at 0.035 h-1 . The OSR was stepwise reduced from 3.5 mmol O2 L-1 h-1 to 0.06 mmol O2 L-1 h-1 . Activity was determined by analyzing the respiration quotient (RQ) and the rates of hexadecane degradation (QHex), of hexadecane mineralization, and of protein production (PPR) . The community composition and size were investigated by fluorescence in situ hybridization (FISH), by dilution plating (colony forming units or CFU), and by most probable number (MPN) . The culture showed an aerobic hexadecane metabolism down to an OSR of 0.35 mmol O2 L-1 h-1 . Below this OSR, anaerobic metabolism was initiated . The relationship among the RQ, PPR, QHex, and the OSR can be approximated by hyperbola (Michaelis-Menten kinetics) . We suggest that the metabolic adaptation of the culture to low OSRs is due to regulation of protein expression and enzyme activity . Reducing the OSR resulted in minor but significant changes in the concentration of different physiological and phylogenetic groups . This means that, in addition to protein expression and activity regulation, the adaptation of the population to low OSRs is due to changes in the community composition.

Am J Respir Cell Mol Biol, 2002 Jun, 26(6), 680 - 4
Protease-activated receptor-2 activating peptide SLIGRL inhibits bacterial lipopolysaccharide-induced recruitment of polymorphonuclear leukocytes into the airways of mice; Moffatt JD et al.; Protease-activated receptor-2 (PAR2) acts as a receptor for trypsin and trypsin-like enzymes . The role of this receptor in airway inflammation is uncertain . In this study we assessed the effect of activation of PAR2 following intranasal administration of the peptide activator of PAR2, SLIGRL, over 72 h in mice . The extent of immune cell infiltration into the airways and activities of matrix metalloprotease-2 (MMP-2) and MMP-9 were assessed in bronchoalveolar lavage (BAL) by differential cell counts and gelatin zymography, respectively . SLIGRL did not cause a change in the number or types of cells retrieved in BAL at any time point and did not alter the levels of MMP-2 and MMP-9 present in BAL . In contrast, similar intranasal administration of bacterial lipopolysaccharide (LPS) caused a large influx of neutrophilic polymorphonuclear leukocytes, which was associated with increased MMP-2 at 3 h only and MMP-9 activity from 3-72 h . Simultaneous administration of SLIGRL and LPS transiently potentiated increased MMP-9 activity at 3 h but markedly inhibited neutrophil influx and elevated MMP-2 activity at 3 h . These findings suggest that PAR2 agonists may be useful therapeutic molecules in pulmonary inflammatory diseases.

Biochim Biophys Acta, 2002 Apr 22, 1554(1-2), 36 - 47
Selective perturbation of the second electron transfer step in mutant bacterial reaction centers; Schenkl S et al.; In order to specifically perturb the primary electron acceptor B(A) -- a monomeric bacteriochlorophyll (BChl) a -- involved in bacterial photosynthetic charge separation (CS), the protein environment of B(A) in the reaction center (RC) of Rhodobacter sphaeroides was modified by site-directed mutagenesis . Isolated RCs were characterized by redox titrations, low temperature optical spectroscopy, ENDOR/TRIPLE resonance spectroscopy and femtosecond time-resolved spectroscopy . Two mutations were studied: In the GS(M203) mutant a serine is introduced near the ring E keto group of B(A), while in FY(L146) a phenylalanine near the ring A acetyl group of B(A) is replaced by tyrosine . In all mutations the oxidation potential of the primary electron donor P as well as the electronic structure of both the P(*+) radical cation and the radical anion of the secondary electron acceptor, H(A)(*-), are not significantly altered compared to the wild type (WT), while changes of the optical absorption spectra at 77 K in the BChl Q(X) and Q(Y) regions are observed . The GS(M203) mutation only leads to a minor retardation of the CS reactions at room temperature, whereas for FY(L146) significant deviations from the native electron transfer (ET) rates could be detected: In addition to a faster first (2.9 ps) and a slower second (1 ps) ET step, a new 8-ps time constant was found in the FY(L146) mutant, which can be ascribed to a fraction of RCs with slowed down secondary ET . The results allow us to address the functional role of the acetyl group of B(A) and question the role of the free energy changes as the main determining factor of ET rates in RCs . It is concluded that structural rearrangements alter the electronic coupling between the pigments and thereby influence the rate of fast CS.

Vaccine, 2002 Jun 21, 20(21-22), 2671 - 9
Epidermal powder immunization using non-toxic bacterial enterotoxin adjuvants with influenza vaccine augments protective immunity; Chen D et al.; The non-toxic B subunit of cholera toxin (CTB) and E . coli heat-labile toxin mutant proteins with reduced toxicity (LTR72) or no toxicity (LTK63) were used as adjuvants for epidermal powder immunization (EPI) with an influenza vaccine . When administered by EPI, CTB, LTR72 and LTK63 significantly augmented antibody responses to the influenza vaccine and protection against a lethal challenge in a mouse model . The antigen dose could be reduced by 125-fold . These adjuvants were well-tolerated both locally and systemically following EPI . These results suggest that EPI with influenza vaccine and a non-toxic bacterial enterotoxin hold promise for human vaccination.

Proc Natl Acad Sci U S A, 2002 May 28, 99(11), 7323 - 8
Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics; van Nimwegen E et al.; Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be clustered into regulons . Using the assumption that regulatory sites can be represented as samples from weight matrices (WMs), we derive a unique probability distribution for assignments of sites into clusters . Our algorithm, "PROCSE" (probabilistic clustering of sequences), uses Monte Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters . The algorithm internally determines the number of clusters from the data and assigns significance to the resulting clusters . We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from WMs when these WMs are unknown . Our analysis suggests that the set of all putative sites for a single genome (e.g., Escherichia coli) is largely inadequate for clustering . When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible . We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E . coli.

J Lipid Res, 2002 Jun, 43(6), 952 - 9
Bacterial lipopolysaccharide induces expression of ABCA1 but not ABCG1 via an LXR-independent pathway; Kaplan R et al.; Two ATP-binding cassette transporter proteins, ABCA1 and ABCG1, may mediate an active efflux of cellular cholesterol and phospholipids . They are ubiquitously expressed and are subject to regulation by cholesterol loading or by treatment with agents that activate the nuclear hormone receptor LXR . Earlier studies in both primates and non-primates reported that treatment with endotoxin (bacterial lipopolysaccharide, LPS) reduces plasma levels of HDL cholesterol . To determine if such HDL reduction correlates with a change in ABCA1 or ABCG1 expression, their expressions were measured in THP-1 monocytes and mice treated with LPS . LPS treatment leads to a rapid, dose-dependent increase of ABCA1 but not ABCG1 mRNA expression . Analysis of mouse livers showed that LPS treatment decreases expression of CYP7A, another target gene of LXR . When THP-1 cells were transfected with the ABCA1 promoter construct (-928 to +101 bp), promoter activity was significantly increased by treatment of 22(R)-hydroxycholesterol but not by LPS . Together, these studies show that LPS regulates ABCA1 expression through an LXR-independent mechanism . Further studies showed that treatment with Rhodobacter sphaeroiders LPS, an LPS antagonist, or PD169316, a specific p38 MAP kinase inhibitor, prevented the induction of ABCA1 by LPS . Therefore, this suggests that both transport of LPS from the plasma membrane to an intracellular site and activation of p38 MAP kinase are involved in the LPS-mediated induction of ABCA1.

J Microbiol Methods, 2002 Aug, 50(3), 291 - 7
Can composition and structural features of oligonucleotides contribute to their wide-scale applicability as random PCR primers in mapping bacterial genome diversity?
Limansky AS, Viale AM.
Among current genotypic methodologies, random amplification of polymorphic DNA (RAPD or AP-PCR) represents a widely employed assay for the evaluation of bacterial genomic diversity . A common bottleneck of this technique, however, is represented by the screening of useful informative primers to discriminate among isolates of a particular bacterial species . In an attempt to simplify this process, we evaluated here the utility of degenerate oligonucleotides to act as informative AP-PCR primers . For this purpose, a number of features (G+C contents, degeneracy rate, modifications at the 5' end) of related degenerate primers was tested for their effects in the generation of informative arrays from a set of bacterial genomes . Our results indicate that a combination of a wide base composition and a common palindromic structure at the 5' end of the sequences that compose the degenerate primers tested here beneficially resulted for the generation of informative arrays aimed to evaluate the bacterial genome heterogeneity.

Environ Microbiol, 2002 May, 4(5), 277 - 86
Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments; Inagaki F et al.; A depth profile of naturally occurring bacterial community structures associated with the deep-sea cold seep push-core sediment in the Japan Trench at a depth of 5343 m were evaluated using molecular phylogenetic analyses of RNA reverse transcription-PCR (RT-PCR) amplified 16S crDNA fragments . A total of 137 clones of bacterial crDNA (complimentary rDNA) phylotypes (phylogenetic types) obtained at three different depths (2-4, 8-10 and 14-16 cm) were identified in partial crDNA sequencings . crDNA phylotypes from the cold seep sediment were dominantly composed of delta- and epsilon-Proteobacteria (36% and 42% respectively) . Phylotype analysis of crDNA clone libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the majority of bacterial components shifted from delta- Proteobacteria to epsilon-Proteobacteria with increasing depth . Among the delta-proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant . Almost all sequences of crDNA belonging to epsilon-Proteobacteria were affiliated with the same cluster (epsilon-CSG: epsilon-proteobacterial cold seep group), and were closely related with rDNA sequences from deep-sea hydrothermal vent environments.

Biochem J, 2002 Sep 1, 366(Pt 2), 565 - 71
Nucleotide binding to human uncoupling protein-2 refolded from bacterial inclusion bodies; Jekabsons MB et al.; Experiments were performed to test the hypothesis that recombinant human uncoupling protein-2 (UCP2) ectopically expressed in bacterial inclusion bodies binds nucleotides in a manner identical with the nucleotide-inhibited uncoupling that is observed in kidney mitochondria . For this, sarkosyl-solubilized UCP2 inclusion bodies were treated with the polyoxyethylene ether detergent C12E9 and hydroxyapatite . Protein recovered from hydroxyapatite chromatography was approx . 90% pure UCP2, as judged by Coomassie Blue and silver staining of polyacrylamide gels . Using fluorescence resonance energy transfer, N-methylanthraniloyl-tagged purine nucleoside di- and tri-phosphates exhibited enhanced fluorescence with purified UCP2 . Dissociation constants determined by least-squares non-linear regression indicated that the affinity of UCP2 for these fluorescently tagged nucleotides was 3-5 microM or perhaps an order of magnitude stronger, depending on the model used . Competition experiments with {8-14C}ATP demonstrated that UCP2 binds unmodified purine and pyrimidine nucleoside triphosphates with 2-5 microM affinity . Affinities for ADP and GDP were approx . 10-fold lower . These data indicate that: UCP2 (a) is at least partially refolded from sarkosyl-solubilized bacterial inclusion bodies by a two-step treatment with C12E9 detergent and hydroxyapatite; (b) binds purine and pyrimidine nucleoside triphosphates with low micromolar affinity; (c) binds GDP with the same affinity as GDP inhibits superoxide-stimulated uncoupling by kidney mitochondria; and (d) exhibits a different nucleotide preference than kidney mitochondria.

Prof Nurse, 2001 Oct, 17(2), 100 - 2
Prevention, treatment and outcomes of bacterial meningitis in childhood; Bedford H; Meningitis is more likely to occur in childhood that at any other age . Preventive measures, in the form of vaccination programmes targeted at certain at-risk age groups, have drastically reduced the incidence in recent years . Early identification of symptoms remains vital in order to prevent mortality and reduce the likelihood of long-term effects.

Acta Anaesthesiol Scand, 2002 May, 46(5), 567 - 78
Cerebral blood flow, oxidative metabolism and cerebrovascular carbon dioxide reactivity in patients with acute bacterial meningitis; Moller K et al.; BACKGROUND: The optimal arterial carbon dioxide tension (P(a)CO(2)) in patients with acute bacterial meningitis (ABM) is unknown and controversial . The objective of this study was to measure global cerebral blood flow (CBF), cerebrovascular CO(2) reactivity (CO(2)R), and cerebral metabolic rates (CMR) of oxygen (O(2)), glucose (glu), and lactate (lac), in patients with ABM and compare the results to those obtained in healthy volunteers . METHODS: We studied 19 patients (17 of whom were sedated) with ABM and eight healthy volunteers (controls) . CBF was measured during baseline ventilation and hyperventilation with single-photon emission computed tomography (SPECT) (14 patients) and/or the Kety-Schmidt technique (KS) (11 patients and all controls) . In KS studies, CMR was measured by multiplying the arterial to jugular venous concentration difference (a-v D) by CBF . RESULTS: CBF did not differ significantly among groups, although a larger variation was seen in patients than in controls . CO(2)R was not significantly different among groups . At baseline, patients had significantly lower a-v DO(2), CMR(O(2)), CMR(glu), and CMR(lac) than controls . CMR(O(2)) did not change between hyperventilation compared to baseline ventilation, whereas CMR(glu) increased . CONCLUSION: In patients with acute bacterial meningitis, we found variable levels of CBF and cerebrovascular CO(2) reactivity, a low a-v DO(2), low cerebral metabolic rates of oxygen and glucose, and a cerebral lactate efflux . In these patients, a ventilation strategy guided by jugular bulb oximetry and/or repeated CBF measurements may be more optimal in terms of cerebral oxygenation than a strategy aiming at identical levels of P(a)CO(2) for all patients.

Novartis Found Symp, 2002, 245, 193 - 203; discussion 203-6, 261-4
Electron diffraction of a bacterial ClC-type chloride channel; Pirruccello MM et al.; ClC-type Cl- channels, as two-pore homodimers, display an architecture unprecedented in selective ion channels, yet little is known regarding their mechanisms of selectivity and gating . In contrast to the great successes with K+ channels, a decade of mutagenic analysis has revealed little about the structure and function of the ClCs: even the number of ion-conducting pores per complex is controversial . Thus, for these proteins direct structural information is particularly important . We have formed two-dimensional crystals of a bacterial CIC homologue, and are analysing their structure using cryo-electron microscopy of glucose-embedded specimens . Here we report the measurement of electron diffraction patterns from these crystals . Unfettered by the imaging limitations of the electron microscope, the diffraction patterns reveal ordering of the crystals to at least 3.8 A resolution, suggesting that they can be used to generate an atomic model of the protein . We present an improved projection structure of the channel at 6.5 A using amplitude data derived from four electron diffraction patterns, with crystallographic statistics comparable to those reported for other high-quality two-dimensional crystals.

Cir Pediatr, 2002 Jan, 15(1), 29 - 33
{Tissue antioxidant capacity and bacterial translocation in parenteral nutrition . Experimental study}; Eizaguirre I et al.; Alterations in the antioxidant system (AS) has been observed during total parenteral nutrition (TPN) . Light exposure or changes in the composition of TPN may affect this deleterious effect . On the other hand, bacterial translocation (BT) is frequent under TPN and may be related to AS . The aim of the study was to determine the adverse effect of standard and glutamine-enriched (GE) TPN, with or without light exposure, on the AS, and its relationship to BT . Forty-nine adult Wistar rats underwent central venous cannulation and were randomly assigned to one of five groups: Sham (n = 16): chow and water ad libitum and saline i.v . TPN (n = 10): had standard TPN . TPN(-) (n = 8): standard TPN without light-exposure . GTPN (n = 8): GE TPN . GTPN(-) (n = 7): GE TPN without light exposure . After 10 days, glutation reduced (GSH) was determined in liver and kidney . Mesenteric lymph nodes, peripheral and portal blood samples were cultured for BT . Comparing to Sham rats, TPN groups had statistically significant lower GSH levels, but there were no differences between standard or GE groups nor with or without light exposure groups . Sham animals had 12% BT . Significantly higher BT (p < 0.05) was found in TPN rats: 70% in TPN group, 88% in TPN(-) group, 86% in GTPN(-) animals and only 50% in GTPN group (p = 0.06 vs TPN group) . To conclude: 1 . TPN reduces antioxidant capacity and induces BT . 2 . Glutamine supplementation or light protection do not improve tissue antioxidant capacity under TPN . 3 . Glutamine supplementation tends to reduce BT only in the presence of light . 4 . Absence of light exposure does not improve BT TPN-related.

Mikrobiologiia, 2002 Mar-Apr, 71(2), 237 - 9
{Evaluation of the hydrophobicity of bacterial cells by measuring their adherence to chloroform drops}; Serebriakova EV et al.; A simple method for measuring the hydrophobicity of bacterial cells is proposed, which is based on the spectrophotometric evaluation of cell adherence to chloroform drops in a biphasic water-chloroform mixture.

Microb Ecol, 2001 Oct, 42(3), 416 - 426
Factors Influencing Bacterial Production in a Shallow Estuarine System; Almeida MA et al.; The bacterioplankton of the marine and brackish water zones of the complex system Ria de Aveiro was characterized as profiles of bacterial abundance and biomass productivity . During the warm season, total bacteria ranged from 0.2 to 8.5 x 109 cells L-1 and active bacteria number from 0.1 to 3.1 x 109 cells L-1 . Total and active bacterial numbers were, on average, three times higher in brackish than in marine water . Bacterial productivity on different dates and different tides in the marine zone varied from 0.05 to 4.5 mg C L-1 h-1 . Here the average productivity (1.1 mg C L-1 h-1) was 3.5 times less than in brackish water (average 3.8 mg C L-1 h-1; range 0.7-14.2 mg C L-1 h-1) . Specific productivity varied from 0.05 to 2.61 fg C cell-1 h-1, a range that was similar throughout the ecosystem . However, specific productivity per active cell was 19% higher in brackish water . Bacterial production variation was best explained by the number of active bacteria, which, in turn, was highly associated with total bacterial number, temperature, and particulate organic carbon . In the marine zone, bacterial production was also influenced by depth and salinity . In the brackish zone, the set of independent variables explained a smaller percentage of bacterial production variation than in marine zone, suggesting greater importance of other variables . In the marine zone, and mainly near low tide, productivity was significantly higher (average 3.3 times) at the surface (down to 0.5 m) than in the deeper layers of the water column . This stratification of bacterial productivity was linked to the increased specific productivity per active cell, as no modification in the proportion of active cells in the population could be detected . The vertical profile of bacterial production in the deeper zone of this estuarine ecosystem, in which no clear salinity or thermal stratification occurs throughout the tidal cycle, seemed to reflect a biochemical stratification generated by increased phytoplankton exudation and/or by photochemical transformation of semilabile or recalcitrant organic compounds . Shallower water masses tend to blur this surface effect . The relative importance of photochemical transformation in the pattern of estuarine bacterial production will therefore tend to vary with the bathymetry of the system.

Microb Ecol, 2001 Dec, 42(4), 586 - 597
Ecophysiological Characterization of Rhizosphere Bacterial Communities at Different Root Locations and Plant Developmental Stages of Cucumber Grown on Rockwool; Folman LB et al.; Bacterial communities from the rhizosphere of cucumber were characterized with respect to growth rates and carbon source utilization, in order to develop a selection strategy for biocontrol agents against Pythium aphanidermatum . Rhizosphere samples were collected from different root regions (root tips, the root base, and the intermediate region where lateral roots emerge) and developmental stages (the seedling, vegetative, and generative stage) from plants cultivated on reused rockwool . By colony counts on 1/10 strength TSA on subsequent days after plating, percentages of fast- and slow-growing isolates (i.e., forming visible colonies within 2 days, or after 3 or more days, respectively) were determined for each rhizosphere sample . At all plant developmental stages, root tips had the highest percentages of fast growing isolates, and root bases the lowest . During plant growth, the relative amounts of slowly growing bacteria increased . Community-level carbon source utilization was determined for the different rhizosphere samples with Biolog GN plates . Principal component analysis showed that rhizosphere samples from different developmental stages and root locations had distinct carbon source utilization patterns . Communities from root tips of seedlings showed the highest utilization of several monosaccharides . Communities from tips and intermediate regions of plants in the vegetative stage utilized relatively many amino acids and several organic acids, and in the generative stage, more di- and polysaccharides were used . Root base samples scored low with respect to carbon source utilization, except for some disaccharides . From the different rhizosphere samples, 826 bacteria, randomly collected from 1/10 strength TSA plates, were screened on the utilization of 9 carbon sources . The 9 selected carbon sources were chosen because they are reported to occur in the rhizosphere, to be used by the zoospores of Pythium in the infection process, or appeared to be discriminant in the analysis of community-level carbon source utilization performed in this study . It appeared that monosaccharides (glucose and fucose), amino acids (alanine and asparagine), and organic acids (galacturonic, succinic, and linoleic acid) were used for growth mainly by bacteria from the root tips, and to a lesser extent from the intermediate region, of young plants . Disaccharides were predominantly utilized by isolates from plants in the vegetative stage . Overall, the results indicated that growth rates and carbon source utilization reflect the adaptation of bacteria to the rhizosphere environment . The possibility of using these characteristics to screen for rhizosphere competent biocontrol agents that compete for substrates with P . aphanidermatum is discussed.

Microb Ecol, 2001 Dec, 42(4), 549 - 561
Measuring Bacterial Production in Deep-Sea Sediments using 3H-Thymidine Incorporation: Ecological Significance; Dixon JL et al.; Bacteria play a major role in the decomposition of organic matter arriving at the deep-sea floor, and hence there is a need to determine accurate rates of bacterial production associated with sediment particles . However, sediment-based procedures are not well defined and sampling deep-sea sediments is technically difficult, time consuming, and expensive, often only producing relatively small amounts of undisturbed sediment for analysis . We describe and test a small-scale method (requiring 0.25 ml sediment) for the examination of bacterial production in deep-sea calcium carbonate rich sediments . Time course experiments showed variation in the period of linear {3H}thymidine uptake between 1 and 3 hr depending on station depth . The average concentration of natural thymidine in deep-sea sediments was 0.61 nmol per 0.5 ml slurry sample . Isotope dilution was significant, ranging between 26 and 51% . There was substantial small-scale (0.2-1.0 m) variation in deep-sea benthic bacterial {3H}thymidine incorporation rates (39%) . Deep-sea surficial sediment bacterial production (assuming zero isotope dilution due to its potential high variability) in surficial sediments of the deep NE Atlantic varied between 0.014 and 0.48 mg C g-1 d-1 (mean = 0.23 mg C g-1 d-1) over 3 locations of depths between 1,092 and 3,572 m and at 3 times . Bacterial biomass varied between 1.1 and 12 mg C g-1 (mean = 6.1 mg C g-1) . Bacterial growth rate estimates in these deep-sea sediments varied between 0.003 and 0.13 d-1 (mean = 0.050 d-1) giving doubling times of 5.3-216 d (mean = 44.5 d); which are similar to those of bacteria inhabiting waters in the upper mixed layer (2-<40 m) of the water column (2.6-57.8 d) . comparison with shallow and coastal sea sediments (0.13-116 d) indicates that deep-sea sediment bacteria in the NE Atlantic are able to grow at rates similar to those in shallow sediment systems given sufficient food . However, the range is broader for deep-sea sediment bacteria, which may indicate a more "feast" and "fast" life than their counterparts in shallower environments . waters >2,000 m cover 60% of the Earth's surface; thus bacterial production in deep-sea sediments must contribute an important fraction of oceanic and global bacterial production . It is therefore important to establish an accurate method of measuring bacterial production so that the full roles and controls of bacteria from this environment can be determined.

Genetics, 2002 May, 161(1), 345 - 53
A molecular cytogenetic map of sorghum chromosome 1 . Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes; Islam-Faridi MN et al.; We used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum . Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH) . Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR) . The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map . In addition, the order of several tightly linked molecular markers was clarified by FISH analysis . The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1 . The centromere and NOR were located in a large heterochromatic region that spans approximately 60% of chromosome 1 . In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome . Variation in recombination frequency among euchromatic chromosomal regions also was apparent . The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions . The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific "paints" from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping . Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application of genomic resources, cloning, transgene localization, development of plant "chromonomics," germplasm introgression, and marker-assisted breeding . In combination with previously reported work, the results indicate that a sorghum cytogenomics system would be partially applicable to other gramineous genera.

J Med Microbiol, 2002 Jun, 51(6), 459 - 67
Spot the difference: applications of subtractive hybridisation to the study of bacterial pathogens; Winstanley C; Comparison of DNA from virulent strains of bacterial pathogens with DNA from less virulent or avirulent close relatives allows the identification of those genomic regions that are present only in virulent strains . Such regions are often associated with pathogenicity islands (PIs) and their characterisation can lead to a greater understanding of the pathogenesis of infectious diseases . There is now a large database of bacterial genomic sequences that provides useful reference information with which to compare the genomes of strains that exhibit variations in virulence or host preferences . Subtractive hybridisation (SH) and its sister method, suppression subtractive hybridisation (SSH), are techniques designed to identify those regions present in one genome but absent from another . The application of these techniques has led to the identification of PIs, mobile genetic elements and variations in virulence gene expression in a range of bacterial pathogens.

Appl Biochem Biotechnol, 2002 Spring, 98-100, 383 - 94
Effect of single active-site cleft mutation on product specificity in a thermostable bacterial cellulase; Rignall TR et al.; Mutation of a single active-site cleft tyrosyl residue to a glycyl residue significantly changes the mixture of products released from phosphoric acid-swollen cellulose (PSC) by EIcd, the catalytic domain of the endoglucanase-I from Acidothermus cellulolyticus . The percentage of glucose in the product stream is almost 40% greater for the Y245G mutant (and for an additional double mutant, Y245G/Q204A) than for the wild type enzyme . Comparisons of results for digestion PSC and of pretreated yellow poplar suggest that the observed shifts in product specificity are connected to the hydrolysis of a more easily digestible fraction of both substrates . A model is presented that relates the changes in product specificity to a mutation-driven shift in indexing of the polymeric substrate along the extended binding-site cleft.

Am J Physiol Gastrointest Liver Physiol, 2002 Jun, 282(6), G937 - 47
Gut-associated lymphoid T cell suppression enhances bacterial translocation in alcohol and burn injury; Choudhry MA et al.; The mechanism of alcohol-mediated increased infection in burn patients remains unknown . With the use of a rat model of acute alcohol and burn injury, the present study ascertained whether acute alcohol exposure before thermal injury enhances gut bacterial translocation . On day 2 postinjury, we found a severalfold increase in gut bacterial translocation in rats receiving both alcohol and burn injury compared with the animals receiving either injury alone . Whereas there were no demonstrable changes in intestinal morphology in any group of animals, a significant increase in intestinal permeability was observed in ethanol- and burn-injured rats compared with the rats receiving either injury alone . We further examined the role of intestinal immune defense by determining the gut-associated lymphoid (Peyer's patches and mesenteric lymph nodes) T cell effector responses 2 days after alcohol and burn injury . Although there was a decrease in the proliferation and interferon-gamma by gut lymphoid T cells after burn injury alone; the suppression was maximum in the group of rats receiving both alcohol and burn injuries . Furthermore, the depletion of CD3(+) cells in healthy rats resulted in bacterial accumulation in mesenteric lymph nodes; such CD3(+) cell depletion in alcohol- and burn-injured rats furthered the spread of bacteria to spleen and circulation . In conclusion, our data suggest that the increased intestinal permeability and a suppression of intestinal immune defense in rats receiving alcohol and burn injury may cause an increase in bacterial translocation and their spread to extraintestinal sites.

Bioinformatics, 2002 Apr, 18(4), 641 - 3
DOLOP--database of bacterial lipoproteins; Madan Babu M et al.; Bacterial lipoproteins and lipid modification are gaining importance owing to their essential nature, roles in pathogenesis and interesting commercial applications . We have created an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details . Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility . AVAILABILITY: The website called Database Of bacterial LipOProteins (DOLOP) is available at along with additional information on the biosynthetic pathway, supplementary material and other related figures.

Protein Sci, 2002 Jun, 11(6), 1472 - 81
Site-directed spin labeling of a bacterial chemoreceptor reveals a dynamic, loosely packed transmembrane domain; Barnakov A et al.; We used site-directed spin labeling and electron paramagnetic resonance spectroscopy to investigate dynamics and helical packing in the four-helix transmembrane domain of the homodimeric bacterial chemoreceptor Trg . We focused on the first transmembrane helix, TM1, particularly on the nine-residue sequence nearest the periplasm, because patterns of disulfide formation between introduced cysteines had identified that segment as the region of closest approach among neighboring transmembrane helices . Along this sequence, mobility and accessibility of the introduced spin label were characteristic of loosely packed or solvent-exposed side chains . This was also the case for eight additional positions around the circumference and along the length of TM1 . For the continuous nine-residue sequence near the periplasm, mobility and accessibility varied only modestly as a function of position . We conclude that side chains of TM1 that face the interior of the four-helix domain interact with neighboring helices but dynamic movement results in loose packing . Compared to transmembrane segments of other membrane proteins reconstituted into lipid bilayers and characterized by site-directed spin labeling, TM1 of chemoreceptor Trg is the most dynamic and loosely packed . A dynamic, loosely packed chemoreceptor domain can account for many experimental observations about the transmembrane domains of chemoreceptors.

J Virol, 2002 Jun, 76(12), 6185 - 96
Efficient infection by a recombinant Kaposi's sarcoma-associated herpesvirus cloned in a bacterial artificial chromosome: application for genetic analysis; Zhou FC et al.; Kaposi's sarcoma-associated herpesvirus (KSHV) is etiologically associated with Kaposi's sarcoma and several other malignancies . The lack of an efficient infection system has impeded the understanding of KSHV-related pathogenesis . A genetic approach was used to isolate infectious KSHV . Recombinant bacteria artificial chromosome (BAC) KSHV containing hygromycin resistance and green fluorescent protein (GFP) markers was generated by homologous recombination in KSHV-infected BCBL-1 cells . Recombinant KSHV genomes from cell clones that were resistant to hygromycin, expressed GFP, and produced infectious virions after induction with tetradecanoyl phorbol acetate (TPA) were rescued in Escherichia coli and reconstituted in 293 cells . Several 293 cell lines resulting from infection with recombinant virions induced from a full-length recombinant KSHV genome, named BAC36, were obtained . BAC36 virions established stable latent infection in 293 cells, harboring 1 to 2 copies of viral genome per cell and expressing viral latent proteins, with approximately 0.5% of cells undergoing spontaneous lytic replication, which is reminiscent of KSHV infection in Kaposi's sarcoma tumors . TPA treatment induced BAC36-infected 293 cell lines into productive lytic replication, expressing lytic proteins and producing virions that efficiently infected normal 293 cells with a approximately 50% primary infection rate . BAC36 virions were also infectious to HeLa and E6E7-immortalized human endothelial cells . Since BAC36 can be efficiently shuttled between bacteria and mammalian cells, it is useful for KSHV genetic analysis . The feasibility of the system was illustrated through the generation of a KSHV mutant with the vIRF gene deleted . This cellular model is useful for the investigation of KSHV infection and pathogenesis.

J Biol Chem, 2002 Aug 2, 277(31), 27682 - 8 Epub 2002 May 15.
Functional design of bacterial mechanosensitive channels . Comparisons and contrasts illuminated by random mutagenesis; Okada K et al.; MscS and MscL are mechanosensitive channels found in bacterial plasma membranes that open large pores in response to membrane tension . These channels function to alleviate excess cell turgor invoked by rapid osmotic downshock . Although much is known of the structure and molecular mechanisms underlying MscL, genes correlating with MscS activity have only recently been identified . Previously, it was shown that eliminating the expression of Escherichia coli yggB removed a major portion of MscS activity . YggB is distinct from MscL by having no obvious structural similarity . Here we have reconstituted purified YggB in proteoliposomes and have successfully detected MscS channel activity, confirming that purified YggB protein encodes MscS activity . Additionally, to define functional regions of the channel protein, we have randomly mutagenized the structural gene and isolated a mutant that evokes a gain-of-function phenotype . Physiological experiments demonstrate that the mutated channel allows leakage of solutes from the cell, suggesting inappropriate channel opening . Interestingly, this mutation is analogous in position and character to mutations yielding a similar phenotype in MscL . Hence, although MscS and MscL mechanosensitive channels are structurally quite distinct, there may be analogies in their gating mechanisms.

Sci STKE . 2002 May 14;2002(132):PE25.
Information processing in bacterial chemotaxis; Stock JB et al.; Motile bacteria respond to attractants and repellents in their environment by changing their movement . Stock et al . describe the similarities of the bacterial chemotaxis signaling system to eukaryotic signaling cascades . Also included is a discussion of how the ordered signaling complex of the receptor, the kinase CheA, and the kinase regulator CheW can be thought of as a primitive "probrain" to allow the integration of signals to produce the optimal cellular response.

Mol Microbiol, 2002 May, 44(4), 947 - 56
Bacterial conjugative transfer: visualization of successful mating pairs and plasmid establishment in live Escherichia coli; Lawley TD et al.; We used the LacO/GFP-LacI system to label and visualize the IncP beta plasmid R751 fluorescently during conjugative transfer between live donor and recipient bacteria . Comparisons of R751 in conjugative and non-conjugative conditions have allowed us to identify key localizations and movements associated with the initiation of conjugative transfer in the donor and the establishment of R751 in the recipient . A survey of successful mating pairs demonstrates that close physical contact between donor and recipient bacteria is required for DNA transfer and that regions of intimate contact can occur at any location on the donor or recipient cell membrane . The transferred DNA is positioned at the characteristic centre or quarter-cell position after conversion to a double-stranded molecule in the recipient cell . Initial duplication of plasmids often results in an asymmetric distribution of plasmid foci . Symmetric localization (either at centre or at 1/4 and 3/4 cell lengths) occurs only after a significant lag, presumably reflecting the time required to synthesize the plasmid-encoded partitioning proteins.

Environ Microbiol, 2002 Apr, 4(4), 193 - 203
A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology; McDonald IR et al.; Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments . They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions . The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria . This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495 . These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the alpha-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments . An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions . This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments . These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.

J Biol Chem, 2002 Jul 19, 277(29), 26066 - 73 Epub 2002 May 02.
The function of the {4Fe-4S} clusters and FAD in bacterial and archaeal adenylylsulfate reductases . Evidence for flavin-catalyzed reduction of adenosine 5'-phosphosulfate; Fritz G et al.; The iron-sulfur flavoenzyme adenylylsulfate (adenosine 5'-phosphosulfate, APS) reductase catalyzes reversibly the 2-electron reduction of APS to sulfite and AMP, a key step in the biological sulfur cycle . APS reductase from one archaea and three different bacteria has been purified, and the molecular and catalytic properties have been characterized . The EPR parameters and redox potentials (-60 and -520 mV versus NHE) have been assigned to the two {4Fe-4S} clusters I and II observed in the three-dimensional structure of the enzyme from Archaeoglobus fulgidus (Fritz, G., Roth, A., Schiffer, A., Buchert, T., Bourenkov, G., Bartunik, H . D., Huber, H., Stetter, K . O., Kroneck, P . M . H., and Ermler, U . (2002) Proc . Natl . Acad . Sci . U . S . A . 99, 1836-1841) . Sulfite binds to FAD to form a covalent FAD N(5)-sulfite adduct with characteristic UV/visible spectra, in accordance with the three-dimensional structure of crystalline enzyme soaked with APS . UV/visible monitored titrations reveal that the substrates AMP and APS dock closely to the FAD cofactor . These results clearly document that FAD is the site of the 2-electron reduction of APS to sulfite and AMP . Reaction of APS reductase enzyme with sulfite and AMP leads to partial reduction of the {4Fe-4S} centers and formation of the anionic FAD semiquinone . Thus, both {4Fe-4S} clusters function in electron transfer and guide two single electrons from the protein surface to the FAD catalytic site.

J Biol Chem, 2002 Aug 2, 277(31), 27622 - 8 Epub 2002 May 10.
The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids . DNA, RNA, and their hybrids; Balandina A et al.; HU, a major component of the bacterial nucleoid, shares properties with histones, high mobility group proteins (HMGs), and other eukaryotic proteins . HU, which participates in many major pathways of the bacterial cell, binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates . Here we demonstrate that HU binds to double-stranded DNA, double-stranded RNA, and linear DNA-RNA duplexes with a similar low affinity . In contrast to this nonspecific binding to total cellular RNA and to supercoiled DNA, HU specifically recognizes defined structures common to both DNA and RNA . In particular HU binds specifically to nicked or gapped DNA-RNA hybrids and to composite RNA molecules such as DsrA, a small non-coding RNA . HU, which modulates DNA architecture, may play additional key functions in the bacterial machinery via its RNA binding capacity . The simple, straightforward structure of its binding domain with two highly flexible beta-ribbon arms and an alpha-helical platform is an alternative model for the elaborate binding domains of the eukaryotic proteins that display dual DNA- and RNA-specific binding capacities.

Phys Rev E Stat Nonlin Soft Matter Phys . 2002 Apr;65(4 Pt 1):040903 . Epub 2002 Apr 10.
Role of body rotation in bacterial flagellar bundling; Powers TR; In bacterial chemotaxis, E . coli cells drift up chemical gradients by a series of runs and tumbles . Runs are periods of directed swimming, and tumbles are abrupt changes in swimming direction . Near the beginning of each run, the rotating helical flagellar filaments that propel the cell form a bundle . Using resistive-force theory, we show that the counterrotation of the cell body necessary for torque balance is sufficient to wrap the filaments into a bundle, even in the absence of the swirling flows produced by each individual filament.

Indian J Pediatr, 2002 Mar, 69(3), 219 - 21
Interleukin-8 levels in children with bacterial, tuberculous and aseptic meningitis; Yilmaz E et al.; OBJECTIVE: lnterleukin-8 (IL-8) is produced in monocytes and vascular endothelial cells in response to stimulation with bacteria or lipopolysaccharides, and is released from these cells into blood stream or tissue fluid . METHODS: Cerebrospinal fluid (CSF) levels of interleukin-8 in 56 children with nonbacterial, bacterial and tuberculous meningitis (TBM), and in 15 control subjects were analyzed to evaluate the involvement of this cytokine in the pathogenesis acute bacterial meningitis and their discriminative value between different etiologies of meningitis . The kinetics of IL-8 concentrations during the course of bacterial meningitis was also evaluated in patients . IL-8 levels were significantly higher in bacterial and TBM than in aseptic meningitis and in control subjects (p < 0.0001) . RESULTS: There was no difference in the levels of IL-8 between the non-bacterial meningitis and control groups . The analysis of the kinetics of production of IL-8 in patients with bacterial meningitis showed that the SSF concentrations of this cytokine decreased to undetectable values in recovery stage . Conversely in patients with TBM the concentrations of IL-8 were elevated in two weeks after beginning the specific treatment . CONCLUSION: The results suggest that determining IL-8 levels may be useful in the differential diagnosis.

Chemosphere, 2002 Feb, 46(7), 961 - 74
Chemical and bacterial changes during laboratory conditioning of formulated and natural sediments; Verrhiest GJ et al.; Within the framework of toxicity testing using formulated sediment, a conditioning treatment prior to toxic contamination has been examined . This preliminary step enables the bacterial colonisation of the sediment, the initiation of organic matter degradation, and the establishment of stable biological and physico-chemical conditions . The treatment involved in keeping the formulated sediment under water in conditions similar to that chosen for toxicity tests . The behaviour of a formulated sediment was compared with a natural sediment . The monitoring of physico-chemical and biological parameters of sediment and water column was carried out over a 30-day incubation in two laboratories . The parameters of pH and redox, dissolved organic carbon (DOC), NH4 and NO2, total organic carbon (TOC) were measured . The bacterial community was characterised by the determination of bacterial density, in total bacteria number or colony forming units (CFU), several exoenzymatic activities (P-glucosidase, xylosidase, leucine-amino-peptidase phosphatase and sulfatase activities), and three gas productions (CO2, N2O and CH4) . The same experiment was carried out with a natural sediment . A 10- to 15-day conditioning allowed a physico-chemical stabilisation and corresponded to kinetic changes in hydrolysis activities . As compared to data of the natural sediment, the biological activity of the formulated sediment showed a different dynamic with lower activity levels . For both sediments, an important decrease of activities levels was observed after 15 days because of a substrate limitation . The work showed that a preliminary conditioning treatment of a formulated sediment provides the stabilisation of parameters that can affect toxicant bioavailability . Additional research is needed to determine the real influence of conditioning on the bioavailability of contaminants . The possible advisability of organic matter input, to maintain the sediment bacterial activity, has to be studied.

Water Res, 2002 Mar, 36(6), 1469 - 82
Comparison of bacterial regrowth in distribution systems using free chlorine and chloramine: a statistical study of causative factors; Zhang W et al.; Bacterial regrowth was investigated over a 15-month period in distribution systems (DSs) of Durham and Raleigh in North Carolina . These two water utilities were chosen because they are adjacent to one another, have similar service area characteristics, and treat surface waters of similar characteristics with conventional processes (coagulation-sedimentation and dual-media filtration) . The finished waters have similar chemical quality and regrowth potential as measured by assimilable organic carbon (AOC) . The major difference in treatment is the choice of final disinfectants (chlorine in Durham and chloramine in Raleigh) . Ten sampling sites (monthly sampling) were chosen in each system to give wide geographic coverage and correspondingly, a wide range of water residence times . Significant losses were observed in both chlorine and chloramine residual in the DSs that produced bacterial regrowth as measured by heterotrophic plate count (HPC) . The frequency distributions for log HPC (133 observations from Durham and 135 observations from Raleigh) were statistically the same in the chlorinated and chloraminated DSs . A correlation analysis indicated that disinfectant residual is the most important factor determining HPC level . However, the resulting R2 value for a non-linear regression model that also included AOC, temperature, and pH as independent variables was less than 0.7 . Bacterial regrowth as measured by HPC, is dependent upon a complex interaction of chemical, physical, and operational parameters that may not be captured by such a simple statistical relationship.

Reprod Nutr Dev, 2001 Sep-Oct, 41(5), 413 - 24
Cereal supplementation modified the fibrolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta; Martin C et al.; 4 ruminally cannulated cows were fed a forage diet (93% hay + 7% straw) and a mixed diet (33 % hay + 7% straw + 40% barley) in a 2 x 2 crossover experimental design . In sacco degradation of forage, fibrolytic activities (polysaccharidases and glycosidases) of the solid-associated bacteria (SAB), and distribution of the 3 main cellulolytic bacterial species (Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens) were determined for both diets . Barley supplementation decreased the hay degradation rate and mainly the polysaccharidase activities of the SAB (30% on average) . The sum of rRNA of the 3 cellulolytic bacterial species represented on average 17% of the total bacterial signal and R . albus was the dominant cellulolytic bacterial species of the 3 studied . Barley supplementation did not modify the proportion of the 3 cellulolytic bacteria attached to plant particles . The negative effect of barley on the ruminal hay degradation rate is due to a decrease in fibrolytic activity of the SAB, and not to a modification of the balance of the three cellulolytic bacterial species examined.

J Infect Dis, 2002 May 15, 185(10), 1476 - 82 Epub 2002 Apr 30.
The granulocyte colony-stimulating factor response after intrapulmonary and systemic bacterial challenges; Quinton LJ et al.; In contrast to many cytokines such as tumor necrosis factor (TNF)-alpha, we hypothesized that, after an intrapulmonary bacterial challenge, lung-derived granulocyte colony-stimulating factor (G-CSF) would subsequently enter the systemic circulation . BALB/c mice were given Escherichia coli or saline, either intratracheally or intravenously . Four hours after intratracheal E . coli administration, bronchoalveolar lavage fluid (BALF) and plasma G-CSF concentrations increased, compared with concentrations in phosphate-buffered saline-treated controls . Lung G-CSF messenger RNA (mRNA) increased to 586+/-229 copies G-CSF mRNA/ng ribosomal RNA (rRNA) from the values in control animals (<0.5 copies/ng rRNA) . In contrast, G-CSF mRNA was not increased in the extrapulmonary tissues examined (liver, spleen, and kidney) in mice challenged with intratracheal E . coli (<1 copy/ng rRNA) . Intravenous E . coli increased plasma G-CSF and TNF-alpha, but neither cytokine was detected in BALF . These data show that, after an intrapulmonary infection, both lung and circulating G-CSF increase and that the lung is the likely source.

J Infect Dis, 2002 May 15, 185(10), 1395 - 400 Epub 2002 Apr 30.
Intra-abdominal bacterial infection reactivates latent pulmonary cytomegalovirus in immunocompetent mice; Cook CH et al.; Critically ill surgery patients are susceptible to pulmonary reactivation of latent cytomegalovirus (CMV), but what triggers this reactivation is unknown . Immunosuppression and bacterial sepsis are thought to stimulate reactivation of CMV, and in this study it was hypothesized that immunosuppressive effects of surgery with or without concomitant bacterial infection may reactivate latent CMV . Mice infected with CMV were allowed to develop latent infections . Latently infected mice underwent a laparotomy with cecal ligation and puncture (CLP; n=30), a laparotomy alone (sham; n=10), or no surgery (control; n=5) . Lung tissue homogenates were evaluated for viral activity, and, 2 and 3 weeks after CLP, lungs of 7 of 7 and 5 of 5 mice, respectively, showed reactivation of latent CMV . In contrast, lungs from all sham-operated animals and controls showed no viral reactivation . These findings demonstrate that surgery with subsequent intra-abdominal bacterial infection reactivated CMV in lungs of latently infected mice . The mechanism of this reactivation is unknown but likely involves cytokines induced by sepsis.

Genomics, 2002 May, 79(5), 625 - 7
The misidentification of bacterial genes as human cDNAs: was the human D-1 tumor antigen gene acquired from bacteria?
Skaar EP, Seifert HS.
The initial analysis of the draft copy of the human genome sequence revealed the presence of several genes that were proposed to have been directly transferred from bacteria . We investigated the human D-1 antigen as a potential lateral transfer event . We report that although the human D-1 antigen seems to be an excellent candidate for lateral transfer, it is a contaminating bacterial sequence present in a human cDNA library that was included in the human genome analysis . Furthermore, several other genes present in the publicly available databases that were included in the analysis of the human genome are also likely contaminating bacterial sequences present in cDNA libraries.

Dig Dis Sci, 2002 Apr, 47(4), 929 - 34
Bacterial translocation and intestinal morphological findings in jaundiced rats; Sileri P et al.; The susceptibility to sepsis in obstructive jaundice may be related to bacterial translocation (BT) from the gastrointestinal tract . We evaluated BT to visceral organs and morphological changes of the intestinal mucosa in a rat model of obstructive jaundice . Animals were randomly divided into two groups: in group A the common bile duct was tied and divided, while group B had the bile duct mobilized but not tied . After seven days, peritoneal swabs and liver, spleen, pancreas, lung, mesenteric lymph nodes (MLN), cecum, and terminal ileum biopsies were obtained for cultures . Light and electron microscopy were performed on intestinal samples . The TUNEL assay was performed to detect apoptosis . Data were analyzed using Fisher exact test and Student t test . Bile duct obliteration resulted in an increased incidence of BT . Seven days after duct obliteration, BT to the peritoneal cavity was evident in 37.5% of the animals in group A and 25% in group B . The respective BT rates for the two groups were: 42.8% vs 37.5% to MLN, 71.4% vs 25% to liver, 42.8% vs 12.5% to spleen, 28.6% vs 0% to pancreas and 14.3% vs 0% to lungs . Despite a trend, this was not statistically significant . Cecal counts did not differ statistically among the groups, while ileal counts were significantly higher in jaundiced rats (P < 0.05) . Structural and ultrastructural abnormalities were evident only in the mucosa of the terminal ileum of jaundiced rats . Apoptosis was significantly increased in the terminal ileum of jaundiced rats (P < 0.002) . This study suggests the possible association of biliary obstruction and BT . The nonspecific physical injury observed may contribute to breakdown of gastrointestinal barrier function thus promoting BT.

Anal Chem, 2002 Apr 15, 74(8), 1805 - 10
Arrays of self-assembled monolayers for studying inhibition of bacterial adhesion; Qian X et al.; This paper describes a simple and convenient method for the rapid screening of potential inhibitors of bacterial adhesion and for the quantitative evaluation of the efficacy of the inhibitors using arrays of self-assembled monolayers (SAMs) of alkanethiolates on gold that are presented on a 96-well microtiter plate . The SAMs present mixtures of alpha-D-mannopyranoside (a ligand that promotes the adhesion of uropathogenic Escherichia coli by binding to the FimH proteins on the tip of type 1 pili), and tri(ethylene glycol) moieties (organic groups that resist nonspecific adsorption of proteins and cells) . The SAMs provide surfaces for studies of adhesion of uropathogenic E . coli to specific ligands; they also provide excellent resistance to nonspecific adhesion . Using arrays of mannoside-presenting SAMs, inhibitors of bacterial adhesion were easily screened by observing the number of bacteria that adhered to the surface of the SAMs in the presence of inhibitor . The potency of the inhibitor was quantified by measuring the percentage of inhibition as a function of the concentration of the inhibitor . The properties of SAMs, when combined with the convenience and standardization of a microtiter plate, make arrays of SAMs a versatile tool that can be applied to high-throughput screening of inhibitors of bacterial, viral, and mammalian cell adhesion and of strongly binding ligands for proteins.

Microb Ecol, 2002 Jan, 43(1), 119 - 33 Epub 2002 Jan 23.
Longitudinal and vertical trends of bacterial limitation by phosphorus and carbon in the Mediterranean Sea; Van Wambeke F et al.; The effect of phosphate (P), nitrate (N), and organic carbon (C, glucose) enrichment on heterotrophic bacterial production was examined along two longitudinal transects covering the whole Mediterranean Sea during June and September 1999 . During these cruises, integrated bacterial production ranged from 11 to 349 mgC m(-2) d(-1) for the 0-150 m layer . P was found to stimulate bacterial production (BP) in 13 out of 18 experiments, in the eastern and in the western Mediterranean Sea . Organic carbon stimulation of bacterial production was observed at two stations in the Alboran Sea, where the highest bacterial production was recorded (216 and 349 mg C m(-2) d(-1)) and in the Sicily Strait . Maximum rates of alkaline phosphatase (AP) increased from the Alboran to the Levantine Sea whereas AP turnover time decreased . Moreover, alkaline phosphatase activity was not systematically reduced following additions of P . In cases of P limitation, however, the alkaline phosphatase activity to bacterial production ratio was severely reduced in the P and NPC enrichments . Generally, the addition of the limiting factor--whether P or C--had a synchronous stimulating effect on bacterial production and ectoaminopeptidase activity and induced a decline in the amino acid respiration percentage . At two selected stations in the eastern and northwestern Mediterranean, response to enrichment was tested on vertical profiles . Bacteria shifted from P to C limitation at a depth where soluble reactive phosphorus was still undetectable, but corresponding to a strong increase in alkaline phosphatase turnover time . Our results showed that values of AP turnover time lower than 100 h corresponded to situations of P limitation of bacterial production.

J Biol Chem, 2002 Jul 5, 277(27), 24243 - 51 Epub 2002 Apr 30.
Novel mode of interference with nuclear factor of activated T-cells regulation in T-cells by the bacterial metabolite n-butyrate; Diakos C et al.; The transcription factor nuclear factor of activated T-cells (NF-AT) plays an essential role in the activation of many early immune response genes . A dynamic equilibrium between calcineurin and cellular kinases controls its phosphorylation and thus regulates its activity by determining its subcellular localization . Here, we demonstrate that T-cell activation in the presence of the bacterial metabolite n-butyrate, which leads to inhibition of interleukin-2 transcription, is characterized by the maintenance of the activity of counter-regulatory kinases glycogen synthase kinase 3 and protein kinase A as well as persistence of intracellular cAMP levels, whereas calcium response and mitogen-activated protein kinase activation were indistinguishable from cells stimulated in the absence of n-butyrate . Nuclear binding of NF-AT was decreased but other transcription factors implicated in interleukin-2 expression such as AP1 and nuclear factor kappaB were unaffected . The effect on NF-AT binding appeared to be the result of increased nuclear export because the export inhibitor leptomycin B completely restored nuclear binding of NF-AT . We, therefore, provide first evidence for interference with NF-AT regulation alternative to the currently understood inhibition of nuclear import . This mechanism might represent a bacterial strategy to subvert host defense, which could be of particular clinical importance in the gastrointestinal tract where high amounts of n-butyrate are physiologically present.

Biochim Biophys Acta, 2002 Apr 1, 1596(1), 28 - 35
The receptor docking segment and S-adenosyl-L-homocysteine bind independently to the methyltransferase of bacterial chemotaxis; Yi X et al.; To mediate adaptation to stimuli, the methyltransferase (CheR) catalyzes methyl group transfer from S-adenosyl-L-methionine (SAM) to glutamyl residues in the transmembrane receptors of the bacterial chemosensory signaling pathway . The interaction between receptors and CheR occurs at two sites: a methylation site-active site interaction, and a 'docking' site interaction that is separated both from the methylation sites and the CheR active site . It is not certain if the docking site interaction functions merely to localize the transferase in close proximity to the methylation sites, or if it also increases CheR catalytic activity . Isothermal titration calorimetry experiments are conducted to test for allosteric interactions between the docking and active sites on CheR, which are expected to be present if docking activates CheR . The binding parameters (DeltaG, DeltaH, DeltaS) of a substrate analog of SAM, S-adenosyl-L-homocysteine (SAH), are measured both in the absence and presence of saturating concentrations of a pentapeptide (NWETF) that defines the docking receptor docking segment . SAH binding is unaffected by the presence of saturating NWETF, providing evidence that an allosteric activation of CheR does not take place upon docking, and thus supports the idea that the CheR-NWETF interaction merely functions to localize CheR near the sites of methylation.

Mol Cell, 2002 Apr, 9(4), 698 - 700
RfaH, a bacterial transcription antiterminator; Santangelo TJ et al.; The bacterial transcription antiterminator RfaH has been shown to act, in a purified biochemical system, by binding both RNA polymerase and the nontemplate strand of DNA at the regulatory site ops.

Eur J Gastroenterol Hepatol, 2002 Feb, 14(2), 189 - 90
Recurrent bacterial cholangitis due to a juxtapapillary diverticulum; van Nieuwkoop C et al.; We present a patient with recurrent bacterial cholangitis . Endoscopic retrograde cholangiopancreatography did not show evidence for choledocholithiasis or obstructing abnormalities of the common bile duct . However, a juxtapapillary diverticulum was situated at the edge of the papilla of Vater . We postulate that a juxtapapillary diverticulum can obstruct biliary flow due to its anatomical relation with the papilla, which may predispose to bacterial cholangitis . This might be prevented by sphincterotomy of the papilla.

Biochemistry, 2002 May 7, 41(18), 5807 - 15
Double mutant studies identify electrostatic interactions that are important for docking cytochrome c2 onto the bacterial reaction center; Tetreault M et al.; Cytochrome c2 (cyt) is the mobile electron donor to the reaction center (RC) in photosynthetic bacteria . The electrostatic interactions involved in the dynamics of docking of cyt onto the RC were examined by double mutant studies of the rates of electron transfer between six modified Rhodobacter sphaeroides RCs in which negatively charged acid residues were replaced with Lys and five modified Rhodobacter capsulatus Cyt c2 molecules in which positively charged Lys residues were replaced with Glu . We measured the second-order rate constant, k2, for electron transfer from the reduced cyt to the oxidized primary donor on the RC, which reflects the energy of the transition state for the formation of the active electron transfer complex . Strong interactions were found between Lys C99 and Asp M184/Glu M95, and between Lys C54 and Asp L261/Asp L257 . The interacting residues were found to be located close to each other in the recently determined crystal structure of the cyt-RC complex {Axelrod, H., et al . (2002) J . Mol . Biol . (in press)} . The interaction energies were approximately inversely proportional to the distances between charges . These results support earlier suggestions {Tetreault, M., et al . (2001) Biochemistry 40, 8452-8462} that the structure of the transition state in solution resembles the structure of the cyt-RC complex in the cocrystal and indicate that specific electrostatic interactions facilitate docking of the cyt onto the RC in a configuration optimized for both binding and electron transfer . The specific interaction between Asp M184 and Lys C99 may help to nucleate short-range hydrophobic contacts.

Thorax, 2002 May, 57(5), 438 - 41
Differentiation of bacterial and viral pneumonia in children; Virkki R et al.; BACKGROUND: A study was undertaken to investigate the differential diagnostic role of chest radiographic findings, total white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and serum C reactive protein (CRP) in children with community acquired pneumonia of varying aetiology . METHODS: The study population consisted of 254 consecutive children admitted to hospital with community acquired pneumonia diagnosed between 1993 and 1995 . WBC, ESR, and CRP levels were determined on admission . Seventeen infective agents (10 viruses and seven bacteria) were searched for . Chest radiographs were retrospectively and separately reviewed by three paediatric radiologists . RESULTS: A potential causative agent was found in 215 (85%) of the 254 cases . Bacterial infection was found in 71% of 137 children with alveolar infiltrates on the chest radiograph, while 72% of the 134 cases with a bacterial pneumonia had alveolar infiltrates . Half of the 77 children with solely interstitial infiltrates on the chest radiograph had evidence of bacterial infection . The proportion of patients with increased WBC or ESR did not differ between bacterial and viral pneumonias, but differences in the CRP levels of >40 mg/l, >80 mg/l, and >120 mg/l were significant although the sensitivity for detecting bacterial pneumonia was too low for use in clinical practice . CONCLUSIONS: Most children with alveolar pneumonia, especially those with lobar infiltrates, have laboratory evidence of a bacterial infection . Interstitial infiltrates are seen in both viral and bacterial pneumonias.

J Biol Chem, 2002 Jul 5, 277(27), 24204 - 11 Epub 2002 Apr 26.
Identification of a novel transporter for dicarboxylates and tricarboxylates in plant mitochondria . Bacterial expression, reconstitution, functional characterization, and tissue distribution; Picault N et al.; A cDNA from Arabidopsis thaliana and four related cDNAs from Nicotiana tabacum that we have isolated encode hitherto unidentified members of the mitochondrial carrier family . These proteins have been overexpressed in bacteria and reconstituted into phospholipid vesicles . Their transport properties demonstrate that they are orthologs/isoforms of a novel mitochondrial carrier capable of transporting both dicarboxylates (such as malate, oxaloacetate, oxoglutarate, and maleate) and tricarboxylates (such as citrate, isocitrate, cis-aconitate, and trans-aconitate) . The newly identified dicarboxylate-tricarboxylate carrier accepts only the single protonated form of citrate (H-citrate2-) and the unprotonated form of malate (malate2-) and catalyzes obligatory, electroneutral exchanges . Oxoglutarate, citrate, and malate are mutually competitive inhibitors, showing K(i) close to the respective K(m) . The carrier is expressed in all plant tissues examined and is largely spread in the plant kingdom . Furthermore, nitrate supply to nitrogen-starved tobacco plants leads to an increase in its mRNA in roots and leaves . The dicarboxylate-tricarboxylate carrier may play a role in important plant metabolic functions requiring organic acid flux to or from the mitochondria, such as nitrogen assimilation, export of reducing equivalents from the mitochondria, and fatty acid elongation.

Ann Pharm Fr, 2002 Jan, 60(1), 38 - 43
{Inactivation of bacterial spores by high hydrostatic pressure}; Delacour H et al.; High pressure biotechnology was developed in Japan in the 90's . This new technology has been used in several domains, including chemical synthesis, food industry, physical chemistry of proteins . Moreover, it could be used instead of heat or chemical treatment for inactivation of pathogenic micro-organisms . Hydrostatic pressures ranging from 100 to 300 MPa cause the inactivation of viruses, parasites, yeast and bacteria . However, bacterial spores are particularly resistant and their inactivation by high hydrostatic pressure can be achieved in combination with synergistic treatments (heat, chemicals and ultrasound).

Kansenshogaku Zasshi, 2002 Mar, 76(3), 185 - 7
{Diagnosis of bacterial pneumonia by serum beta-globulin demarcation}; Okimoto N et al.; We studied whether the consolidation whose serum beta-globulin demarcation showed more than 12% was bacterial pneumonia or not . The materials were the patients with fever (> or = 37 degrees C) and the consolidation on chest-X ray film, the value of serum beta-globulin demarcation was more than 12% from 1995 to 2000 . There were 5 cases with drug-induced pneumonitis, 5 cases with BOOP, 2 cases with eosinophilic pneumonia, 1 case with lung cancer (adenocarcinoma), and 1 case with interstitial pneumonia with dermatomyositis . No one had bacterial pneumonia . These results suggested the consolidation with fever whose serum beta-globulin demarcation showed more than 12% was not bacterial pneumonia.

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