Bacteriological

Org Lett, 2004 Sep 2, 6(18), 3043 - 6
Synthesis of LuxS inhibitors targeting bacterial cell-cell communication; Alfaro JF et al.; {reaction: see text} Quorum sensing is a process by which bacteria sense cell density . This cell-cell communication process is mediated by autoinducers . A cross-species messenger, autoinducer-2 (AI-2) is produced from S-ribosyl-L-homocysteine by the LuxS enzyme . A proposed mechanism for LuxS is an aldose-ketose isomerization of S-ribosylhomocysteine followed by a beta-elimination . We report here the synthesis of two substrate analogues, S-anhydroribosyl-L-homocysteine and S-homoribosyl-L-cysteine, which prevent the initial and final step of the mechanism, respectively.

Biotechnol Bioeng, 2004 Sep 20, 87(6), 687 - 94
Single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (ALDH2) gene using bacterial magnetic particles based on dissociation curve analysis; Maruyama K et al.; Single nucleotide polymorphism (SNP) detection for aldehyde dehydrogenase 2 (ALDH2) gene based on DNA thermal dissociation curve analysis was successfully demonstrated using an automated system with bacterial magnetic particles (BMPs) by developing a new method for avoiding light scattering caused by nanometer-size particles when using commercially available fluorescent dyes such as FITC, Cy3, and Cy5 as labeling chromophores . Biotin-labeled PCR products in ALDH2, two allele-specific probes (Cy3-labeled detection probe for ALDH2*1 and Cy5-labeled detection probe for ALDH2*2), streptavidin-immobilized BMPs (SA-BMPs) were simultaneously mixed . The mixture was denatured at 70 degrees C for 3 min, cooled slowly to 25 degrees C, and incubated for 10 min, allowing the DNA duplex to form between Cy3- or Cy5-labeled detection probes and biotin-labeled PCR products on SA-BMPs . Then duplex DNA-BMP complex was heated to 58 degrees C, a temperature determined by dissociation curve analysis and a dissociated single-base mismatched detection probe was removed at the same temperature under precise control . Furthermore, fluorescence signal from the detection probe was liberated into the supernatant from completely matched duplex DNA-BMP complex by heating to 80 degrees C and measured . In the homozygote target DNA (ALDH2*1/*1 and ALDH2*2/*2), the fluorescence signals from single-base mismatched were decreased to background level, indicating that mismatched hybridization was efficiently removed by the washing process . In the heterozygote target DNA (ALDH2*1/*2), each fluorescence signals was at a similar level . Therefore, three genotypes of SNP in ALDH2 gene were detected using the automated detection system with BMPs .

Med Sci Monit, 2004 Sep, 10(9), PI99 - PI103 Epub 2004 Aug 20.
Efficacy of a topical suspension of bacterial antigens for the management of recurrent eczema in children; Mora R et al.; BACKGROUND: The aim of this study was to compare the efficacy and safety of a topical suspension of bacterial antigens for the management of recurrent eczema in children . MATERIAL/METHODS: Eighty pediatric patients, aged between 2 and 6 years, with a history of recurrent external auditory eczema, were enrolled in this study . Congenital immune deficiencies, treatment with corticosteroids, immunostimulant or immunosuppressive agents in the past 6 months, and bronchopulmonary disease were considered as exclusion criteria . The patients were randomized to receive topical suspension of bacterial antigens (Lantigen B) (Group A) or placebo (physiological solution) (Group B) . The efficacy parameters were evaluated before, at the end of, and one year after the beginning of the therapy . All the children underwent clinical examinations, blood test, skin prick tests (SPT), and clinical evaluation using the clinical score proposed by Rajka and Langeland, considering the intensity, extent, and course of lesions . RESULTS: In Group A, using the statistical Wilcoxon test, we saw an improvement in the clinical items measured . It is important to consider that the patients were allowed to receive concomitant medications to treat acute episodes, which may have partially contributed to the positive results obtained . CONCLUSIONS: A topical suspension of bacterial antigens was significantly more effective than placebo in the treatment of recurrent eczema in children.

BJOG, 2004 Sep, 111(9), 982 - 8
Randomised treatment trial of bacterial vaginosis to prevent post-abortion complication; Miller L et al.; OBJECTIVE: To evaluate the efficacy of metronidazole to reduce post-abortion complications among women with bacterial vaginosis . DESIGN: A randomised, double-blind placebo-controlled trial . SETTING: An American outpatient abortion facility between April 1999 and June 2000 . SAMPLE: Women presenting for surgical abortion were screened for bacterial vaginosis using a pH and amines card test . METHODS: Women positive for elevated pH and amines on a self-collected vaginal discharge sample were randomised to 1000 mg oral metronidazole before abortion followed by 500 mg twice daily or placebo . All randomised women were also dispensed 100 mg doxycycline to take twice daily for seven days . MAIN OUTCOME MEASURES: Data were collected by phone, daily diary or visit and scored from 0 to 7 for post-abortion complications . Intention-to-treat analyses were completed prior to unblinding . RESULTS: Of 1764 women screened by card test, 638 (36%) were positive . Of these, 393 were randomised . Follow up data were available for 253 (64%) of these women . A complication score of 3 or more occurred in 21% of women assigned to metronidazole, compared with 19% in those assigned placebo (RR 1.1, 95% CI 0.7-1.9) . Among 153 women with Gram stain confirmation for bacterial vaginosis, there was a similar lack of benefit with treatment (RR 1.6, 95% CI 0.9-3.0) . No individual symptom or sign was statistically different between groups even for second trimester procedures . CONCLUSION: Among women undergoing abortion and diagnosed with bacterial vaginosis, oral metronidazole, in conjunction with doxycycline, did not reduce post-abortion complications.

J Am Chem Soc, 2004 Sep 1, 126(34), 10598 - 602
Presentation and detection of azide functionality in bacterial cell surface proteins; Link AJ et al.; An improved protocol for copper-catalyzed triazole formation on the bacterial cell surface is described . Addition of highly pure CuBr to cells treated with azidohomoalanine (2) leads to ca . 10-fold more extensive cell surface labeling than previously observed . This highly active catalyst allows detection of the methionine analogues azidoalanine (1), azidonorvaline (3), and azidonorleucine (4) in cell surface proteins . Azidoalanine was previously believed to be silent with regard to the cellular protein synthesis machinery .

J Biol Chem, 2004 Oct 29, 279(44), 46008 - 13 Epub 2004 Aug 23.
A unifying model for the role of polyamines in bacterial cell growth, the polyamine modulon; Yoshida M et al.; We reported previously that the synthesis of specific proteins such as OppA, Cya, and RpoS (sigma(38)), which are important for cell growth and viability, is stimulated by polyamines at the level of translation . In this study we found that the synthesis of FecI and Fis was also stimulated by polyamines at the level of translation . The FecI and Fis proteins enhance the expression of mRNAs that are involved in iron uptake and energy metabolism and the expression of rRNA and some tRNAs . The Shine-Dalgarno (SD) sequence of their mRNAs was not obvious or was not located at the usual position . When the SD sequences were created at the normal position on these mRNAs, protein synthesis was no longer influenced by polyamines . Thus, the common characteristic of these mRNAs was to have a weak or ineffective SD sequence . We propose that a group of genes whose expression is enhanced by polyamines at the level of translation be referred to as a "polyamine modulon." By DNA microarray, we found that 309 of 2,742 mRNA species were upregulated by polyamines . Among the 309 up-regulated genes, transcriptional enhancement of at least 58 genes might be attributable to increased levels of the transcription factors Cya, RpoS, FecI, and Fis, which are all organized in the polyamine modulon . This unifying molecular mechanism is proposed to underlie the physiological role of polyamines in controlling the growth of Escherichia coli.

Biophys J, 2004 Nov, 87(5), 3137 - 47 Epub 2004 Aug 23.
Permeation properties of an engineered bacterial OmpF porin containing the EEEE-locus of Ca2+ channels; Miedema H et al.; The selectivity filter of the bacterial porin OmpF carries a small net charge close to -1 e and is therefore only slightly cation-selective . Calcium channels, on the other hand, contain four negatively charged glutamates, the EEEE-locus, and are among the most selective cation channels known . We aimed to turn the essentially nonselective OmpF into a Ca2+-selective channel . To that end, two additional glutamates (R42E and R132E) were introduced in the OmpF constriction zone that already contains D113 and E117 . Mutant OmpF containing this DEEE-locus has a high Ca2+ over Cl- selectivity and a Na+ current with a strongly increased sensitivity to 1 mM Ca2+ . The charge/space competition model, initially applied to the L-type Ca2+ channel, identifies the fixed charge and filter volume as key determinants of ion selectivity, with the precise atomic arrangement having only second-order effects . By implication, the reproduction of fixed charge and filter volume should transform two channels into channels of similar selectivity, even if the two belong to entirely different ion channel families, as is the case for OmpF and the L-type Ca2+ channel . The results presented here fit quite well in the framework of charge/space competition theory.

Biophys J, 2004 Nov, 87(5), 3010 - 22 Epub 2004 Aug 23.
Circular dichroism of carotenoids in bacterial light-harvesting complexes: experiments and modeling; Georgakopoulou S et al.; In this work we investigate the origin and characteristics of the circular dichroism (CD) spectrum of rhodopin glucoside and lycopene in the light-harvesting 2 complex of Rhodopseudomonas acidophila and Rhodospirillum molischianum, respectively . We successfully model their absorption and CD spectra based on the high-resolution structures . We assume that these spectra originate from seven interacting transition dipole moments: the first corresponds to the 0-0 transition of the carotenoid, whereas the remaining six represent higher vibronic components of the S2 state . From the absorption spectra we get an estimate of the Franck-Condon factors of these transitions . Furthermore, we investigate the broadening mechanisms that lead to the final shape of the spectra and get an insight into the interaction energy between carotenoids . Finally, we examine the consequences of rotations of the carotenoid transition dipole moment and of deformations in the light-harvesting 2 complex rings . Comparison of the modeled carotenoid spectra with modeled spectra of the bacteriochlorophyll QY region leads to a refinement of the modeling procedure and an improvement of all calculated results . We therefore propose that the combined carotenoid and bacteriochlorophyll CD can be used as an accurate reflection of the overall structure of the light-harvesting complexes.

FEMS Immunol Med Microbiol, 2004 Sep 1, 42(1), 139 - 45
Interleukin 1-beta responses to bacterial toxins and sudden infant death syndrome; Moscovis SM et al.; We tested the hypothesis that significantly higher IL-1beta responses to toxic shock syndrome toxin (TSST) noted for parents of sudden infant death syndrome (SIDS) infants might be due in part to genetic factors such as the IL-1beta (C-511T) and IL-1RN (T+2018C) single nucleotide polymorphisms (SNP) . The first objective was to assess the distribution of these polymorphisms among SIDS infants, parents of SIDS infants and controls, and two ethnic groups: Aboriginal Australians who have a high incidence of SIDS; and Bangladeshis who in Britain have a low incidence of SIDS compared with Europeans . The second objective was to assess IL-1beta responses to endotoxin and toxic shock syndrome toxin (TSST) from leukocytes of smokers and non-smokers in relation to these polymorphisms . There were major differences in the distributions of the IL-1beta (C-511T) SNP between Europeans and Bangladeshis (p=0.00) and between Europeans and Aboriginal Australians (p=0.00); however, they were similar for the Bangladeshi and Aboriginal Australian subjects . The allele frequency distribution of the IL-1RN (T+2018C) SNP for the Aboriginal Australians was statistically different from the European group (p=0.00), but it was not different from the Bangladeshi group (p=0.09) . Compared with controls of European origin, there were no significant differences in the distribution of these polymorphisms among SIDS infants or parents of SIDS infants . For the IL-1beta (C-511T) SNP, the highest IL-1beta responses to endotoxin were obtained with leukocytes of non-smokers with the heterozygous CT genotype . Smokers had significantly lower levels of IL-1beta in response to endotoxin (p=0.01) and these differences were significant for donors with the wild type CC (p=0.00) and CT (p=0.03) genotypes . Similar patterns were observed for IL-1beta responses to TSST, but the differences were not significant . For the IL-1RN (T+2018C) SNP, the highest IL-1beta responses to endotoxin were obtained with leukocytes from non-smoker donors with the wildtype TT genotype and significantly lower responses were found with leukocytes from donors with the TC genotype (p=0.02) . The responses of smokers were lower but the differences were significant only for donors with the TT genotype (p=0.00) . Similar patterns were observed for IL-1beta responses to TSST, but the differences were not significant . IL-1beta responses to both endotoxin and TSST were increased for the small number of smokers with the TT genotype of the IL-1beta (C-511T) SNP . The TT genotype of the IL-1beta (C-511T) was found predominantly among Aboriginal Australian and Bangladeshi individuals but only a small proportion of Europeans . Smokers with the AA genotype of the IL-10 (G-1082A) SNP which is found predominantly among these two groups had significantly lower levels of IL-10 responses . If cigarette smoke enhances pro-inflammatory responses and reduces anti-inflammatory responses in individuals with these genotypes, this might partly explain the increased susceptibility of Aboriginal Australian infants to infections and SIDS.

FEMS Immunol Med Microbiol, 2004 Sep 1, 42(1), 42 - 7
Common bacterial toxins and physiological vulnerability to sudden infant death: the role of deleterious genetic mutations; Morris JA; The common bacterial toxin hypothesis of sudden infant death syndrome (SIDS) is consistent with the epidemiological features of the condition including the age distribution, seasonal incidence, association with prone sleeping and with exposure to tobacco smoke . The hypothesis is supported by experimental evidence but there are two barriers to its acceptance: the speed of onset does not fit with conventional concepts of an infective process; furthermore, the hypothesis appears to offer a single explanation for what is regarded as a multifactorial disease . Concepts from information theory are used to explore these objections . Complex physiological systems process information and need a high level of redundancy to minimise error . Models show that deleterious mutations in such a system will interact synergistically . Environmental perturbations are most likely to cause failure (sudden death) in systems with several mutations . Models also indicate that mutation rates will pose a limit to the size of the functioning genome and, therefore, increased complexity in evolution depends on using old genes in new combinations rather than the chance appearance of new genes . The idea that we share our genes with the rest of creation (same genes but different combinations) leads to the following conjecture: for every receptor controlling the flow of information across a cell membrane there will be a bacterially coded molecule that can switch it off or on . Based on this premise, bacterial toxaemia could cause sudden death, merely the time it takes for a molecule to associate with or dissociate from its receptor . Regardless of the number of physiological systems involved in SIDS, the age distribution will have a unimodal peak corresponding to the age range during which infant serum IgG reaches its nadir . In this way, the two barriers to the common bacterial toxin hypothesis can be overcome: one explanation but multiple bacteria and toxins acting with variable speed on multiple target systems.

Clin Lab Med, 2004 Sep, 24(3), 627 - 49, vi
Emerging intracellular bacterial infections; Katz B et al.; Human infections by intracellular bacteria have been recognized for many years, but much of what we know about the pathogenesis of these diseases and their etiologic organisms has emerged within the past few years as a result of improved molecular-based means for their detection and classification . New insights concerning the epidemiology and pathogenesis of intracellular bacterial infections and methods for the detection of Chlamydophila pneumoniae, Ehrlichia chaffeensis, Anaplasma phagocytophilum, and Rickettsia species have made an impact on how we view them as agents of human disease . Emerging evidence suggesting a possible intracellular existence for another organism, Mycoplasma pneumoniae, may explain how this organism interacts with the host to induce chronic inflammatory conditions of the respiratory tract.

Biochem J, 2004 Dec 1, 384(Pt 2), 385 - 90
Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli; Hytonen VP et al.; Chicken avidin is a highly popular tool with countless applications in the life sciences . In the present study, an efficient method for producing avidin protein in the periplasmic space of Escherichia coli in the active form is described . Avidin was produced by replacing the native signal sequence of the protein with a bacterial OmpA secretion signal . The yield after a single 2-iminobiotin-agarose affinity purification step was approx . 10 mg/l of virtually pure avidin . Purified avidin had 3.7 free biotin-binding sites per tetramer and showed the same biotin-binding affinity and thermal stability as egg-white avidin . Avidin crystallized under various conditions, which will enable X-ray crystallographic studies . Avidin produced in E . coli lacks the carbohydrate chains of chicken avidin and the absence of glycosylation should decrease the non-specific binding that avidin exhibits towards many materials {Rosebrough and Hartley (1996) J . Nucl . Med . 37, 1380-1384} . The present method provides a feasible and inexpensive alternative for the production of recombinant avidin, avidin mutants and avidin fusion proteins for novel avidin-biotin technology applications.

Clin Exp Immunol, 2004 Sep, 137(3), 460 - 8
Correlation of virulence, lung pathology, bacterial load and delayed type hypersensitivity responses after infection with different Mycobacterium tuberculosis genotypes in a BALB/c mouse model; Dormans J et al.; One of the most intriguing aspects of tuberculosis is that the outcome of an infection with M . tuberculosis (TB) is highly variable between individuals . The possibility of differences in virulence between M . tuberculosis strains or genotypes has only recently been studied . There is evidence of multifactorial genetic predisposition in humans that influences the susceptibility to tuberculosis . A better understanding of differences in virulence between M . tuberculosis genotypes could be important with regard to the efforts at TB control and the development of improved antituberculosis vaccines . Survival, lung pathology, bacterial load and delayed type hypersensitivity (DTH) responses of BALB/c mice after intratracheal infection with any of 19 different M . tuberculosis complex strains of 11 major genotype families were studied . The results indicate that among genetically different M . tuberculosis strains a very broad response was present with respect to virulence, pathology, bacterial load and DTH . 'Low'-responders were the H37Rv, Canetti, Beijing-1 strains, while Beijing-2,3, Africa-2 and Somalia-2 strains were 'high'-responders . A severe pathological response correlates with a high mortality and a high CFU counts in lungs, but poorly with the degree of the DTH response.

Pediatr Res, 2004 Nov, 56(5), 804 - 9 Epub 2004 Aug 19.
Evaluation of IL-8-concentrations in plasma and lysed EDTA-blood in healthy neonates and those with suspected early onset bacterial infection; Orlikowsky TW et al.; Plasma IL-8 is a diagnostic parameter of early-onset bacterial infection (EOBI) in neonates but has a short half-life . The detergent-lysed whole-blood (DLWB) IL-8 consists of both extracellular and cell-bound IL-8 . The objective of this study was to investigate kinetics of plasma and DLWB IL-8 in healthy newborns and those with suspected EOBI and to test the hypothesis that determination of DLWB IL-8 results in higher sensitivity for EOBI detection . Sixty-one neonates with clinical and serologic signs of EOBI composed the study group; 188 neonates with risk factors but without EOBI served as control subjects . IL-8 concentrations were determined in plasma and DLWB . In the control group, DLWB IL-8 concentrations were 280-fold higher (9599 pg/mL; SD 4433) up to 24 h post partum than corresponding plasma levels (34.2 pg/mL; SD 18.1) . The sensitivity of DLWB versus plasma IL-8 for EOBI was 0.97 versus 0.71 after 6 h and 0.70 versus 0.32 after 24 h . Corresponding values for specificity were 0.95 versus 0.90 after 6 h and 0.92 versus 0.99 after 24 h . After 24 h, the negative predictive value for DLWB versus plasma IL-8 was 0.80 versus 0.66 . DLWB IL-8 showed a higher sensitivity for EOBI within 6 h after first clinical suspicion than plasma IL-8 . It also remained elevated longer . Our results suggest that DLWB IL-8 results in a higher sensitivity for EOBI.

Mol Biol Evol, 2004 Nov, 21(11), 2172 - 81 Epub 2004 Aug 18.
The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola; Gomez-Valero L et al.; Reduction of the genome size in endosymbiotic bacteria is the main feature linked to the adaptation to a host-associated lifestyle . We have analyzed the fate of the nonfunctional DNA in Buchnera aphidicola, the primary endosymbiont of aphids . At least 164 gene losses took place during the recent evolution of three B . aphidicola strains, symbionts of the aphids Acyrthosiphon pisum (BAp), Schizaphis graminum (BSg), and Baizongia pistacia (BBp) . A typical pattern starts with the inactivation of a gene, which produces a pseudogene, and is followed by the progressive loss of its DNA . Our results show that during the period from the separation of the Aphidinae and Pemphiginae lineages (86-164 MYA) to the divergence of BAp and BSg (50-70 MYA) the half-life of a pseudogene was 23.9 Myr . For the remaining periods of evolution, the ranges of values obtained for this parameter are of the same order of magnitude . These results have revealed that a gene inactivated during B . aphidicola evolution requires 40-60 Myr to become almost completely disintegrated . Moreover, we have shown a positive correlation between the decrease in the GC content and the DNA loss for these nonfunctional DNA regions . When gene losses are classified, based on the detection of a pseudogene or otherwise of an absent gene in the modern B . aphidicola genomes, we have observed a drastic reduction of DNA length in the latter versus the former relative to the functional gene . Finally, we have also detected a slight reduction in size of the intergenic regions in the three B . aphidicola strains, when they are compared with the size of the close relative Escherichia coli.

JAMA, 2004 Aug 18, 292(7), 852 - 8
Small intestinal bacterial overgrowth: a framework for understanding irritable bowel syndrome; Lin HC; CONTEXT: Irritable bowel syndrome (IBS), which affects 11% to 14% of the population, is a puzzling condition with multiple models of pathophysiology including altered motility, visceral hypersensitivity, abnormal brain-gut interaction, autonomic dysfunction, and immune activation . Although no conceptual framework accounts for all the symptoms and observations in IBS, a unifying explanation may exist since 92% of these patients share the symptom of bloating regardless of their predominant complaint . EVIDENCE ACQUISITION: Ovid MEDLINE was searched through May 2004 for relevant English-language articles beginning with those related to bloating, gas, and IBS . Bibliographies of pertinent articles and books were also scanned for additional suitable citations . EVIDENCE SYNTHESIS: The possibility that small intestinal bacterial overgrowth (SIBO) may explain bloating in IBS is supported by greater total hydrogen excretion after lactulose ingestion, a correlation between the pattern of bowel movement and the type of excreted gas, a prevalence of abnormal lactulose breath test in 84% of IBS patients, and a 75% improvement of IBS symptoms after eradication of SIBO . Altered gastrointestinal motility and sensation, changed activity of the central nervous system, and increased sympathetic drive and immune activation may be understood as consequences of the host response to SIBO . CONCLUSIONS: The gastrointestinal and immune effects of SIBO provide a possible unifying framework for understanding frequent observations in IBS, including postprandial bloating and distension, altered motility, visceral hypersensitivity, abnormal brain-gut interaction, autonomic dysfunction, and immune activation.

Indian J Environ Health, 2003 Jul, 45(3), 209 - 12
Effect of holding time and temperature on bacterial counts; Ahammed MM; Water samples of different pollution levels were collected from four different sources, viz., a canal, an open dug well, a deep tube well, and a drinking water tap, stored at refrigerator (4-5 degrees C) and ambient (28-30 degrees C) temperatures, and analysed at 0, 6, 12, 24 and 48 hours in order to find the effect of holding time and temperature on bacterial counts . The samples were analysed for total coliforms and for heterotrophic plate counts (HPC) . Results of the study indicate significant reduction in the coliform counts in all the water samples tested at both ambient and refrigerator temperatures . However, the rate of decline was much less in refrigerated samples compared to that in samples stored at ambient temperature . Further, the rate of decline was dependent on the source of water . After 48 hours of storage at ambient temperature, canal water samples showed the sharpest decline of 82% in coliform counts, and water samples from open dug well showed the least decline of 51% . While HPCs of the samples held at refrigerator temperature did not show significant changes with time, those samples held at ambient temperature increased upon storage . Up to 12 hours of storage, there was no significant changes in bacterial counts in any type of water at both the temperatures, which suggests that water samples can be stored at ambient temperatures for 12 hours without significantly affecting the coliform counts.

Anesteziol Reanimatol, 2004 May-Jun, (3), 43 - 5
{Prevention and treatment of bacterial infection by the recombinant human granulocytic colony-stimulating factor in newborns}; Structure of alanine dehydrogenase from Archaeoglobus: active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin; Biotechnology Division of the National Institute of Standards and Technology, Gaithersburg, MD 20899-8312, USA . travis.gallagher@nist.gov

The hyperthermophilic archaeon Archaeoglobus fulgidus contains an L-Ala dehydrogenase (AlaDH, EC 1.4.1.1) that is not homologous to known bacterial dehydrogenases and appears to represent a previously unrecognized archaeal group of NAD-dependent dehydrogenases . The gene (Genbank; TIGR AF1665) was annotated initially as an ornithine cyclodeaminase (OCD) on the basis of strong homology with the mu crystallin/OCD protein family . We report the structure of the NAD-bound AF1665 AlaDH (AF-AlaDH) at 2.3 A in a C2 crystal form with the 70 kDa dimer in the asymmetric unit, as the first structural representative of this family . Consistent with its lack of homology to bacterial AlaDH proteins, which are mostly hexameric, the archaeal dimer has a novel structure . Although both types of AlaDH enzyme include a Rossmann-type NAD-binding domain, the arrangement of strands in the C-terminal half of this domain is novel, and the other (catalytic) domain in the archaeal protein has a new fold . The active site presents a cluster of conserved Arg and Lys side-chains over the pro-R face of the cofactor . In addition, the best ordered of the 338 water molecules in the structure is positioned well for mechanistic interaction . The overall structure and active site are compared with other dehydrogenases, including the AlaDH from Phormidium lapideum . Implications for the catalytic mechanism and for the structures of homologs are considered . The archaeal AlaDH represents an ancient and previously undescribed subclass of Rossmann-fold proteins that includes bacterial ornithine and lysine cyclodeaminases, marsupial lens proteins and, in man, a thyroid hormone-binding protein that exhibits 30% sequence identity with AF1665.

Trends Genet, 2004 Sep, 20(9), 413 - 6
GroEL and the maintenance of bacterial endosymbiosis; Fares MA et al.; Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria . The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift . However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations . We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome.

J Biotechnol, 2004 Sep 9, 112(3), 313 - 22
Bacterial expression of biologically active recombinant musarmin 1 from bulbs of Muscari armeniacum L . and Miller; Antolin P et al.; Musarmins are type 1 ribosome-inactivating proteins with N-glycosidase activity on the 28 S rRNA that are present in bulbs of Muscari armeniacum L . and Miller at rather low concentrations . In the present work, a cDNA fragment coding for musarmin 1 was sub-cloned and expressed in Escherichia coli . The recombinant protein (rMU1) was synthesised as a polypeptide of 295 amino acids that was delivered to the periplasm and processed . Recombinant musarmin 1 present in the periplam has two forms: insoluble with a molecular mass of 29,423 and soluble with a molecular mass of 29,117 because of a small proteolytic shortening with respect to the insoluble one, presumably in the C-terminal . The yield of protein homogeneous by polyacrylamide gel electrophoresis was 23mgl-1 of bacterial culture . The recombinant musarmin 1 forms isolated from both the soluble and the insoluble (upon refolding) fractions retained full translational inhibitory and 28 S rRNA N-glycosidase activities as compared with the native protein . The recombinant protein displayed great stability towards trypsin, collagenase, rat plasma and rat liver protein extract, but was sensitive to the action of papain and proteinase K . The easy availability and full activity of the recombinant musarmin 1 makes it a good candidate for the preparation of immunotoxins for targeted therapy and for the construction of transgenic plants expressing it as antipathogenic agent.

Scand J Infect Dis, 2004, 36(6-7), 523 - 4
Chron's disease, rare association with selective IgA immunodeficiency, and development of life-threatening bacterial infections; Manfredi R et al.; Life-threatening necrotizing fasciitis and relapsing Lemierre syndrome associated with Fusobacterium necrophorum septicaemia occurred in young adults with a moderate Chron's disease and a missed profound IgA deficiency . This unexpected association of a chronic bowel inflammatory syndrome with prominent IgA abnormalities and severe bacterial infection deserves careful attention by physicians faced with young patients with Chron's disease.

Clin Infect Dis, 2004 Jul 15, 39(2), 206 - 17 Epub 2004 Jul 02.
Serum procalcitonin and C-reactive protein levels as markers of bacterial infection: a systematic review and meta-analysis; Simon L et al.; A meta-analysis was performed to evaluate the accuracy of determination of procalcitonin (PCT) and C-reactive protein (CRP) levels for the diagnosis of bacterial infection . The analysis included published studies that evaluated these markers for the diagnosis of bacterial infections in hospitalized patients . PCT level was more sensitive (88% {95% confidence interval {CI}, 80%-93%} vs . 75% {95% CI, 62%-84%}) and more specific (81% {95% CI, 67%-90%} vs . 67% {95% CI, 56%-77%}) than CRP level for differentiating bacterial from noninfective causes of inflammation . The Q value for PCT markers was higher (0.82 vs . 0.73) . The sensitivity for differentiating bacterial from viral infections was also higher for PCT markers (92% {95% CI, 86%-95%} vs . 86% {95% CI, 65%-95%}); the specificities were comparable (73% {95% CI, 42%-91%} vs . 70% {95% CI, 19%-96%}) . The Q value was higher for PCT markers (0.89 vs . 0.83) . PCT markers also had a higher positive likelihood ratio and lower negative likelihood ratio than did CRP markers in both groups . On the basis of this analysis, the diagnostic accuracy of PCT markers was higher than that of CRP markers among patients hospitalized for suspected bacterial infections.

J Perinatol, 2004 Dec, 24(12), 735 - 42
Prospective validation of a perinatal bacterial vaginosis screening risk score; Pastore LM et al.; OBJECTIVE: Prospectively validate an antenatal bacterial vaginosis (BV) risk score at two public health department obstetrics clinics . STUDY DESIGN: Women (n=409) entering prenatal care received a BV risk score (range 0 to 16) at their first visit and at 24 to 28 weeks' gestation . BV was measured with Gram-stained vaginal smears . Normal discharge was used as a surrogate for being asymptomatic . RESULTS: Approximately half of the women scored > or =3 at each assessment . In total 29% had true BV at the first assessment (13% at the second assessment) . The BV risk score (> or =3) had 91% sensitivity and 63% specificity, and the BV risk score (> or =5) had 88% sensitivity and 76% specificity . Among true cases, 42% were asymptomatic, of which 77% had risk scores > or =3 . All symptomatic BV cases had risk scores > or =3 . CONCLUSION: In practice, the risk score identified both asymptomatic and symptomatic cases . Asymptomatic women are of particular interest because they are not screened for BV under current practice guidelines.

Environ Microbiol, 2004 Sep, 6(9), 921 - 7
Targeting modular polyketide synthases with iteratively acting acyltransferases from metagenomes of uncultured bacterial consortia; Piel J et al.; Bacterial type I polyketide synthases (PKSs) produce a wide range of biomedically important secondary metabolites . These enzymes possess a modular structure that can be genetically re-engineered to yield novel drug candidates not found in nature . Recently, we have reported the putative pederin PKS from an uncultured bacterial symbiont of Paederus fuscipes beetles . It belongs to an architecturally unusual PKS group, the members of which contain iteratively acting acyltransferases that are not integrated into the PKS modules but are encoded by isolated genes . As these systems are rare, often contain additional unusual features and are of smaller size than regular PKSs, the development of a method for the targeted isolation of new group members would be of great interest . Here, we present a phylogenetic approach to identify these systems rapidly in highly complex metagenomic DNA samples . To demonstrate its practical value, we located two pederin-type PKS systems putatively involved in the biosynthesis of antitumour polyketides in the metagenomic DNA of beetles, sponges and their uncultivated bacterial symbionts.

Dev Dyn, 2004 Sep, 231(1), 199 - 203
Creation of a transgenic mouse for hair-cell gene targeting by using a modified bacterial artificial chromosome containing Prestin; Tian Y et al.; We made a transgenic mouse that expresses Cre recombinase activity in inner ear hair cells by using a modified bacterial artificial chromosome containing Prestin . Cre recombinase activity was restricted to inner and outer hair cells, a subset of vestibular hair cells, spiral and vestibular ganglia in the inner ear, and a subset of cells in the testis, epididymis, and ear bone . This mouse will be useful for hair-cell-specific gene targeting.

Mol Cell, 2004 Aug 13, 15(3), 389 - 98
Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities; Betat H et al.; Bacterial poly(A) polymerases (PAP) and tRNA nucleotidyltransferases are highly similar in sequence but display different activities: whereas tRNA nucleotidyltransferase catalyzes the addition of CCA to 3' ends of tRNAs, PAP adds poly(A) tails to a variety of transcripts . Using domain substitution experiments, we show that these enzymes follow a modular concept: exchange of N- and C-terminal regions leads to chimeric enzymes with unexpected activities, indicating that tRNA nucleotidyltransferase carries an "anchor domain" in the C-terminal section that restricts polymerization to three nucleotides . A 27 amino acid region was identified that determines whether poly(A) or CCA is synthesized by the enzyme chimeras . Sequence alignments suggest that the catalytic cores of both enzymes carry identical components involved in nucleotide recognition and incorporation . This seems to be the prerequisite for the observed reprogramming of the catalytic center of PAP to incorporate a sequence of defined length and composition instead of long stretches of A residues.

J Gastroenterol Hepatol, 2004 Sep, 19(9), 988 - 93
Hypergastrinemia after Helicobacter pylori infection is associated with bacterial load and related inflammation of the oxyntic corpus mucosa; Chuang CH et al.; BACKGROUND AND AIM: Helicobacter pylori infection causes hypergastrinemia . This study aimed to determine the association between serum gastrin and the severity of H . pylori-related gastric histology . METHODS: A total of 458 dyspeptic patients were included in this study after the absence of gastric malignancy was confirmed using endoscopy . The gastric specimens of each patient were collected from the antrum and corpus for the analysis of H . pylori-related histology changes by updated Sydney's system . Before endoscopy, the fasting blood samples were collected for gastrin analysis . RESULTS: The H . pylori-infected patients had higher gastrin levels than those without infection (P = 0.01) . Gastrin levels were related to H . pylori density and acute and chronic inflammation scores in the corpus mucosa (P < 0.05), but not in the antral mucosa (P = NS) . Gastrin levels were also not related to the presence of gastric atrophy . Multivariate regression showed that the gastrin level was only related to acute corpus inflammation . However, in the patients without infection, the gastrin level was also associated with acute corpus inflammation . Nevertheless, the patients with denser H . pylori infection were more likely to have acute corpus gastritis than those with lighter H . pylori infection, and thus presented with higher gastrin levels (P < 0.05) . CONCLUSIONS: The increased level of gastrin of serum after H . pylori infection was associated with acute inflammation in the gastric corpus mucosa, but not in the antral mucosa . Denser H . pylori infection causes more severe corpus gastritis and thus may lead to a higher fasting level of gastrin of serum.

J Environ Biol, 2004 Jan, 25(1), 93 - 8
Toxicological evaluation of bacterial decolourised anaerobically treated distillery effluent with common duckweed (Lemna minor); Chandra R et al.; Duckweed (Lemna minor) a small vascular plant, grows rapidly, is sensitive to a wide variety of toxicants and is easy to culture . A method is described that measures duckweed frond growth, chlorophyll, protein and biomass content as indicator of growth inhibition . The physico-chemical analysis of anaerobically treated distillery effluent revealed high BOD (28,000 mg/l), COD (52,400 mg/l) and dark brown colour (180,000 Co . Pt.) . This effluent showed high toxicity to Lemna minor after 96 h of exposure in laboratory condition . EC50 of the fronds for chlorophyll, protein and biomass was found to be 25%, however, the bacterial decolourised effluent showed reduction of BOD (87.50%), COD (84.50%) and colour (76%) . Further the toxicity evaluation with Lemna minor showed toxicity reduction up to 63% for all tested parameters . The EC50 noted for chlorophyll, protein and biomass was 100% concentration of decolourised effluent.

Toxicon, 2004 Sep 1, 44(3), 243 - 9
No evidence for an endosymbiotic bacterial origin of tetrodotoxin in the newt Taricha granulosa; Lehman EM et al.; Tetrodotoxin (TTX) is a potent neurotoxin which is known to occur in numerous taxa, including newts . The origin of TTX is unknown, but production by symbiotic bacteria is suspected for some groups . Using PCR primers that specifically amplify 16S rRNA genes of bacteria, we examined tissues from rough-skin newts, Taricha granulosa, for the presence of bacteria which may produce TTX . No amplification of bacterial DNA was seen in samples taken from skin, liver, gonads or oviposited eggs-tissues known to contain TTX . Amplification of bacterial DNA was seen only in samples taken from newt intestines, a tissue with low concentrations of TTX . These results indicate that symbiotic bacteria are unlikely to be the source of TTX in newts.

Acta Crystallogr D Biol Crystallogr, 1997 Mar, 53(Pt 2), 213 - 6
Crystallization and preliminary X-ray crystallographic and electron microscopic study of a bacterial DNA helicase (RSF1010 RepA); Roleke D; Helicases are ATP-driven enzymes essential for DNA unwinding . The broad host range plasmid RSFI010 harbours a gene (repA) encoding for one of the smallest known oligomeric helicases, RepA, a homo-hexamer with 30 kDa subunits . Electron micrographs indicate that the overall shape of RepA resembles a hexagon with globular monomers at the corners, diameter 140 A, and a central channel . Below pH 6, the molecules aggregate into tubular structures . The enzyme has been purified and crystallized using the hanging-drop vapour-diffusion method with polyethyleneglycol monomethylether as precipitating agent . The crystals exhibit the monoclinic space group P2(1) with unit-cell parameters a = 105.8, b = 180.3, c = 115.4 A, beta = 95.2 degrees, and diffract to 3.5 A resolution using rotating-anode Cu Kalpha radiation . Assuming two 180 kDa molecules per asymmetric unit, the volume per unit weight is V(m) = 3.06 A Da(-1), equivalent to a solvent content of 60% . A self-rotation search indicates that the sixfold axis of the hexamer is parallel to the ac plane and inclined at about 2 degrees to the c axis . The two hexamers are oriented head-to-head with point-group symmetry D(6).

Commun Agric Appl Biol Sci, 2003, 68(2 Pt A), 141 - 5
Growth enhancement of ETBE-degrading bacterial consortium with various carbon sources; Bekri M et al.; In this study, we evaluated Ethyl tert-Butyl Ether (ETBE)-degrading consortia growths in the presence of diverse carbon sources (alcohols, alkanes, ether compounds and carbohydrates) . In a second step, we studied the consortium ability to maintain its ETBE degradation activity after growing on these carbon sources in presence or in absence of ETBE . The results indicate that the bacterial growth of ETBE-degrading consortia is enhanced three times more with addition of ethanol than with ETBE alone, while maintaining its ability to degrade ETBE . The bacterial yield growth rate was 0.504 d(-1) when growing on ETBE alone, 1.728 d(-1) on both ETBE and ethanol and 2.856 d(-1) on ethanol alone . Both ETBE and ethanol are completely degraded at 8.33 mg L(-1) h(-1) and 18.55 mg L(-1) h(-1) respectively for an initial OD of 0.4 . The frequency of ethanol addition, as growth co-substrate, was studied to preserve the ETBE-degrading capacity of the consortium, and to observe the stability of the genetic character of the ether degradation.

Pediatr Infect Dis J, 2004 Aug, 23(8), 719 - 25
Topically applied sunflower seed oil prevents invasive bacterial infections in preterm infants in Egypt: a randomized, controlled clinical trial; Darmstadt GL et al.; BACKGROUND: Because the therapeutic options for managing infections in neonates in developing countries are often limited, innovative approaches to preventing infections are needed . Topical therapy with skin barrier-enhancing products may be an effective strategy for improving neonatal outcomes, particularly among preterm, low birth weight infants whose skin barrier is temporarily but critically compromised as a result of immaturity . METHODS: We tested the impact of topical application of sunflower seed oil 3 times daily to preterm infants <34 weeks gestational age at the Kasr El-Aini neonatal intensive care unit at Cairo University on skin condition, rates of nosocomial infections and mortality . RESULTS: Treatment with sunflower seed oil (n = 51) resulted in a significant improvement in skin condition (P = 0.037) and a highly significant reduction in the incidence of nosocomial infections (adjusted incidence ratio, 0.46; 95% confidence interval, 0.26-0.81; P = 0.007) compared with infants not receiving topical prophylaxis (n = 52) . There were no reported adverse events as a result of topical therapy . CONCLUSIONS: Given the low cost (approximately .20 dollars for a course of therapy) and technologic simplicity of the intervention and the effect size observed in this study, a clinical trial with increased numbers of subjects is indicated to evaluate the potential of topical therapy to reduce infections and save newborn lives in developing countries.

Appl Environ Microbiol, 2004 Aug, 70(8), 4921 - 9
"Candidatus Endobugula glebosa," a specific bacterial symbiont of the marine bryozoan Bugula simplex; Lim GE et al.; The bryozoans Bugula neritina and Bugula simplex harbor bacteria in the pallial sinuses of their larvae as seen by electron microscopy . In B . neritina, the bacterial symbiont has been characterized as a gamma-proteobacterium, "Candidatus Endobugula sertula." "Candidatus E . sertula" has been implicated as the source of the bryostatins, polyketides that provide chemical defense to the host and are also being tested for use in human cancer treatments . In this study, the bacterial symbiont in B . simplex larvae was identified by 16S rRNA-targeted PCR and sequencing as a gamma-proteobacterium closely related to and forming a monophyletic group with "Candidatus E . sertula." In a fluorescence in situ hybridization, a 16S ribosomal DNA probe specific to the B . simplex symbiont hybridized to long rod-shaped bacteria in the pallial sinus of a B . simplex larva . The taxonomic status "Candidatus Endobugula glebosa" is proposed for the B . simplex larval symbiont . Degenerate polyketide synthase (PKS) primers amplified a gene fragment from B . simplex that closely matched a PKS gene fragment from the bryostatin PKS cluster . PCR surveys show that the symbiont and this PKS gene fragment are consistently and uniquely associated with B . simplex . Bryostatin activity assays and chemical analyses of B . simplex extracts reveal the presence of compounds similar to bryostatins . Taken together, these findings demonstrate a symbiosis in B . simplex that is similar and evolutionarily related to that in B . neritina.

Appl Environ Microbiol, 2004 Aug, 70(8), 4848 - 54
Influence of humic substances on bacterial and viral dynamics in freshwaters; Anesio AM et al.; Bacterial and viral abundances were measured in 24 lakes with dissolved organic carbon (DOC) concentrations ranging from 3 to 19 mg of C liter(-1) . In addition, a laboratory experiment was performed to test the effects of different sources of carbon (i.e., glucose and fulvic acids) and nutrients on the dynamics of viruses and bacteria . In the lake survey, no correlation was found between virus abundance and DOC concentration, yet there was a significant positive correlation between bacterial abundance and DOC concentration . A negative correlation was found between the virus-to-bacteria ratio and DOC level . These results are in agreement with our findings in the laboratory, where virus counts were significantly lower in treatments with fulvic acid additions than in a control (mean, 67.4% +/- 6.5% of the control) . Virus counts did not differ significantly among the control and treatments with glucose, indicating that it was the type of organic carbon and not quantity which had an impact on viruses . Results from this study suggest that the way viruses control bacterial assemblages in humic lakes is different from the mechanism in clear water systems.

Appl Environ Microbiol, 2004 Aug, 70(8), 4582 - 7
Enhanced arsenic accumulation in engineered bacterial cells expressing ArsR; Kostal J et al.; The metalloregulatory protein ArsR, which offers high affinity and selectivity toward arsenite, was overexpressed in Escherichia coli in an attempt to increase the bioaccumulation of arsenic . Overproduction of ArsR resulted in elevated levels of arsenite bioaccumulation but also a severe reduction in cell growth . Incorporation of an elastin-like polypeptide as the fusion partner to ArsR (ELP153AR) improved cell growth by twofold without compromising the ability to accumulate arsenite . Resting cells overexpressing ELP153AR accumulated 5- and 60-fold-higher levels of arsenate and arsenite than control cells without ArsR overexpression . Conversely, no significant improvement in Cd(2+) or Zn(2+) accumulation was observed, validating the specificity of ArsR . The high affinity of ArsR allowed 100% removal of 50 ppb of arsenite from contaminated water with these engineered cells, providing a technology useful to comply with the newly approved U.S . Environmental Protection Agency limit of 10 ppb . These results open up the possibility of using cells overexpressing ArsR as an inexpensive, high-affinity ligand for arsenic removal from contaminated drinking and ground water.

Mikrobiyol Bul, 2004 Jan-Apr, 38(1-2), 27 - 32
{Determination of serologic markers against bacterial atypical pneumonia agents in pneumonia patients}; Pinar A et al.; Approximately one third of all community acquired pneumonia cases are caused by Legionella pneumophila, Mycoplasma pneumoniae and Chlamydophila pneumoniae (previously, Chlamydia pneumoniae) which are known as bacterial atypical pneumonia agents . Serological tests are used commonly for laboratory diagnosis of these agents . The aim of this study was to evaluate the causative role of bacterial atypical pneumonia agents in clinically diagnosed pneumonia patients . Acute and convalescent serum samples were collected from a total of 65 clinically diagnosed adult pneumonia patients in order to evaluate IgM and IgG positivities against L . pneumophila, M . pneumoniae and C . pneumoniae . IgM and IgG were evaluated by enzyme immunoassay (ELISA) for L . pneumophila and M . pneumoniae, and by indirect fluorescent antibody (IFA) method for C . pneumoniae . In acute serum samples, 4 (6.2%) M . pneumoniae IgM positivity in addition to 3 (4.6%) L . pneumophila IgG, 3 (4.6%) M . pneumoniae IgG and 62 (95.4%) C . pneumoniae IgG positivity were detected . In convelescent serum samples, 3 (4.6%) L . pneumophila, 1 (1.5%) M . pneumoniae, 3 (4.6%) C . pneumoniae IgM positivity and 4 (6.2%) L . pneumophila with 1 (1.5%) M . pneumoniae IgG positivity were detected in addition to acute sample positivities . According to these serological data, totally 16 (24.6%) of the patients were infected by bacterial atypical pneumonia agents . These results show that bacterial atypical pneumonia agents are important etiological factors for community acquired pneumonia.

Rev Mal Respir, 2004 Jun, 21(3 Pt 1), 539 - 47
{Tobacco smoke and risk of bacterial infection}; Trosini-Desert V et al.; INTRODUCTION: Tobacco smoke is a proven risk factor for bacterial infection . STATE OF THE ART: In adults without COPD, smoking is associated with a significant increase in the relative risk (RR) of pneumonia (RR=2.97; 95% CI 1.52-5.81), S pneumoniae pneumonia (RR=2.50; 95% IC 1.50-5.10), Legionella infection (RR=3.75; 95% CI 2.17-6.17) . Smoking has clearly been shown to be associated with an increased risk of tuberculosis (RR=2.60; 95% CI 2,20-3,20), and also with increased incidence of post-operative infections . In young children whose parents smoke, passive exposure to tobacco smoke is associated with an increased relative risk of seasonal infections (RR=1.7; CI 95% 1.55-1.91) and recurrent otitis media (RR=1.48; 95% CI 1.08-2.04) . Passive smoking also increases risk of pneumonia in adults (RR=2.5; CI 95% 1.2-5.1) . Plausible explanations of the increased risk of infection in active or passive smokers include increased bacterial adherence, decrease of lung and nasal clearance, and changes in the immune response . CONCLUSIONS: Exposure to tobacco smoke approximately doubles the risk of infection . This increased burden of infection has significant healthcare cost implications . Each infectious episode in an individual should prompt an attempt at smoking cessation.

Cytometry, 2004 Aug, 60A(2), 165 - 72
Green fluorescent protein-propidium iodide (GFP-PI) based assay for flow cytometric measurement of bacterial viability; Lehtinen J et al.; BACKGROUND: Several staining protocols have been developed for flow cytometric analysis of bacterial viability . One promising method is dual staining with the LIVE/DEAD BacLight bacterial viability kit . In this procedure, cells are treated with two different DNA-binding dyes (SYTO9 and PI), and viability is estimated according to the proportion of bound stain . SYTO9 diffuses through the intact cell membrane and binds cellular DNA, while PI binds DNA of damaged cells only . This dual-staining method allows effective separation between viable and dead cells, which is far more difficult to achieve with single staining . Although SYTO9-PI dual staining is practical for various bacterial viability analyses, the method has a number of disadvantages . Specifically, the passage of SYTO9 through the cell membrane is a slow process, which is significantly accelerated when the integrity of the cell membrane is disrupted . As a result, SYTO9 binding to DNA is considerably enhanced . PI competes for binding sites with SYTO9 and may displace the bound dye . These properties diminish the reliability of the LIVE/DEAD viability kit . In this study, we investigate an alternative method for measuring bacterial viability using a combination of green fluorescent protein (GFP) and PI, with a view to improving data reliability . METHODS: Recombinant Escherichia coli cells with a plasmid containing the gene for jellyfish GFP were stained with PI, and green and red fluorescence were measured by FCM . For comparison, cells containing the plasmid from which gfp was removed were stained with SYTO9 and PI, and analyzed by FCM . Viability was estimated according to the proportion of green and red fluorescence . In addition, bioluminescence and plate counting (other methods to assess viability) were used as reference procedures . RESULTS: SYTO9-PI dual staining of bacterial cells revealed three different cell populations: living, compromised, and dead cells . These cell populations were more distinct when the GFP-PI combination was used instead of dual staining . No differences in sensitivity were observed between the two methods . However, substitution of SYTO9 with GFP accelerated the procedure . Bioluminescence and plate counting results were in agreement with flow cytometric viability data . CONCLUSIONS: In bacterial viability analyses, the GFP-PI combination provided better distinction between current viability stages of E . coli cells than SYTO9-PI dual staining . Additionally, the overall procedure was more rapid . No marked differences in sensitivity were observed.

Emerg Radiol, 2002 Dec, 9(6), 317 - 9 Epub 2002 Nov 30.
Bacterial aortitis resulting in rapid development of infective "mycotic" aneurysm; Shu KE et al.; Aortitis and aneurysms with an infective etiology, though uncommon, must be recognized at imaging so that early medical and surgical intervention can improve survival . We report a case in which serial CT scans illustrate the short-interval development of an infective "mycotic" aneurysm resulting from bacterial aortitis.

Nucleic Acids Res, 2004 Aug 02, 32(13), 4071 - 80 Print 2004.
Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V; Hitchcock TM et al.; Oxanine (O) is a deamination product derived from guanine with the nitrogen at the N1 position substituted by oxygen . Cytosine, thymine, adenine, guanine as well as oxanine itself can be incorporated by Klenow Fragment to pair with oxanine in a DNA template with similar efficiency, indicating that oxanine in DNA may cause various mutations . As a nucleotide, deoxyoxanosine may substitute for deoxyguanosine to complete a primer extension reaction . Endonuclease V, an enzyme known for its enzymatic activity on uridine-, inosine- and xanthosine-containing DNA, can cleave oxanosine-containing DNA at the second phosphodiester bond 3' to the lesion . Mg2+ or Mn2+, and to a small extent Co2+ or Ni2+, support the oxanosine-containing DNA cleavage activity . All four oxanosine-containing base pairs (A/O, T/O, C/O and G/O) were cleaved with similar efficiency . The cleavage of double-stranded oxanosine-containing DNA was approximately 6-fold less efficient than that of double-stranded inosine-containing DNA . Single-stranded oxanosine-containing DNA was cleaved with a lower efficiency as compared with double-stranded oxanosine-containing DNA . A metal ion enhances the binding of endonuclease V to double-stranded and single-stranded oxanosine-containing DNA 6- and 4-fold, respectively . Hypothetic models of oxanine-containing base pairs and deaminated base recognition mechanism are presented.

Microbiology, 2004 Aug, 150(Pt 8), 2497 - 502
Cyclic di-GMP as a bacterial second messenger; D'Argenio DA et al.; Environmental signals trigger changes in the bacterial cell surface, including changes in exopolysaccharides and proteinaceous appendages that ultimately favour bacterial persistence and proliferation . Such adaptations are regulated in diverse bacteria by proteins with GGDEF and EAL domains . These proteins are predicted to regulate cell surface adhesiveness by controlling the level of a second messenger, the cyclic dinucleotide c-di-GMP . Genetic evidence suggests that the GGDEF domain acts as a nucleotide cyclase for c-di-GMP synthesis while the EAL domain is a good candidate for the opposing activity, a phosphodiesterase for c-di-GMP degradation.

Trends Biochem Sci, 2004 Aug, 29(8), 392 - 5
BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases; Ginalski K et al.; Using sequence similarity searches and top-of-the-range fold-recognition methods, we have identified a novel family of bacterial transglutaminase-like cysteine proteinases (BTLCPs) with an invariant Cys-His-Asp catalytic triad and a predicted N-terminal signal sequence . This family of previously uncharacterized hypothetical proteins encompasses sequences of unknown function from DUF920 (in the Pfam database) and COG3672 . BTLCPs are predicted to possess the papain-like cysteine proteinase fold and catalyze post-translational protein modification through transamidase, acetylase or hydrolase activity . Inspection of neighboring genes encoding BTLCPs suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity.

Genome, 2004 Aug, 47(4), 764 - 8
Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes; Pagel J et al.; Soybean (Glycine max L . Merr.) is presumed to be an ancient polyploid based on chromosome number and multiple RFLP fragments in genetic mapping . Direct cytogenetic observation of duplicated regions within the soybean genome has not heretofore been reported . Employing fluorescence in situ hybridization (FISH) of genetically anchored bacterial artificial chromosomes (BACs) in soybean, we were able to observe that the distal ends of molecular linkage group E had duplicated regions on linkage groups A2 and B2 . Further, using fiber-FISH, it was possible to measure the molecular size and organization of one of the duplicated regions . As FISH did not require repetitive DNA for blocking fluorescence signals, we assume that the 200-kb genome region is relatively low in repetitive sequences . This observation, along with the observation that the BACs are located in distal euchromatin regions, has implications for genome structure/evolution and the approach used to sequence the soybean genome.

Am J Obstet Gynecol, 2004 Jun, 190(6), 1582 - 7; discussion 1587-9
Fetal fibronectin and bacterial vaginosis are associated with preterm birth in women who are symptomatic for preterm labor; Stevens AO et al.; OBJECTIVE: The purpose of this study was to codify the relationship between bacterial vaginosis/fetal fibronectin and preterm labor/birth . STUDY DESIGN: In this prospective study, 185 women who were symptomatic for preterm labor were assessed for bacterial vaginosis and fetal fibronectin . RESULTS: These women comprised 4 groups: group A (n=23 women; +bacterial vaginosis/+fetal fibronectin); group B (n=31 women; -bacterial vaginosis/+fetal fibronectin); group C (n=47 women; +bacterial vaginosis/-fetal fibronectin); and group D (n=84 women; -bacterial vaginosis/-fetal fibronectin) . The time interval from gestational age at testing until delivery was significantly shorter for groups A and B versus groups C and D (P < or =.05 and P <.001, respectively) . Similarly, delivery at <32 weeks of gestation was increased in group B (26%) compared with groups A (9%), C (2%), and D (5%; P <.009; odds ratio, 165.90; 95% CI, 30.02, 916.08) . CONCLUSION: Women who are symptomatic for preterm labor should be considered for fetal fibronectin and bacterial vaginosis testing.

Am J Obstet Gynecol, 2004 Jun, 190(6), 1504 - 8; discussion 3A
A polymorphism in the promoter region of TNF and bacterial vaginosis: preliminary evidence of gene-environment interaction in the etiology of spontaneous preterm birth; Macones GA et al.; OBJECTIVE: The rarer of 2 alleles of a polymorphism in the promoter of the tumor necrosis factor alpha gene (TNF) has been associated with spontaneous preterm birth following preterm premature rupture of the fetal membranes in some populations . The aim of this study was to assess if the presence of symptomatic bacterial vaginosis amplifies the risk of spontaneous preterm birth in those with a "susceptible" TNF genotype . STUDY DESIGN: A case-control study was performed at our institution . Cases (n=125) were defined as women who delivered before 37 weeks as a result of ruptured membranes or preterm labor, while control subjects (n=250) were defined as women who delivered after 37 weeks . DNA was collected from maternal blood and analyzed for the TNF genotype . Information on symptomatic bacterial vaginosis and other risk factors for preterm birth was obtained by review of the antenatal record . Multiple logistic regression was also used to test the interaction between bacterial vaginosis, the TNF genotype, and preterm birth . RESULTS: Maternal carriers of the rarer allele (TNF-2) were at a significantly increased risk of spontaneous preterm birth {odds ratio (OR) 2.7, 95% CI 1.7-4.5} . The association between TNF-2 and preterm birth was modified by the presence of bacterial vaginosis, such that those with a "susceptible" genotype and bacterial vaginosis had increased odds of preterm birth compared with those who did not (OR 6.1, 95% CI 1.9-21.0) . CONCLUSION: This study provides preliminary evidence that an interaction between genetic susceptibilities (ie, TNF-2 carriers) and environmental factors (ie, bacterial vaginosis) is associated with an increased risk of spontaneous preterm birth.

Biochim Biophys Acta, 2004 Jul 23, 1658(1-2), 50 - 7
Probing light-induced conformational transitions in bacterial photosynthetic reaction centers embedded in trehalose-water amorphous matrices; Francia F et al.; The coupling between electron transfer and protein dynamics has been studied in photosynthetic reaction centers (RC) from Rhodobacter sphaeroides by embedding the protein into room temperature solid trehalose-water matrices . Electron transfer kinetics from the primary quinone acceptor (Q(A)(-)) to the photoxidized donor (P(+)) were measured as a function of the duration of photoexcitation from 20 ns (laser flash) to more than 1 min . Decreasing the water content of the matrix down to approximately 5x10(3) water molecules per RC causes a reversible four-times acceleration of P(+)Q(A)(-) recombination after the laser pulse . By comparing the broadly distributed kinetics observed under these conditions with the ones measured in glycerol-water mixtures at cryogenic temperatures, we conclude that RC relaxation from the dark-adapted to the light-adapted state and thermal fluctuations among conformational substates are hindered in the room temperature matrix over the time scale of tens of milliseconds . When the duration of photoexcitation is increased from a few milliseconds to the second time scale, recombination kinetics of P(+)Q(A)(-) slows down progressively and becomes less distributed, indicating that even in the driest matrices, during continuous illumination, the RC is gaining a limited conformational freedom that results in partial stabilization of P(+)Q(A)(-) . This behavior is consistent with a tight structural and dynamical coupling between the protein surface and the trehalose-water matrix.

Int J Syst Evol Microbiol, 2004 Jul, 54(Pt 4), 1151 - 6
Identification of the bacterial endosymbionts of the marine ciliate Euplotes magnicirratus (Ciliophora, Hypotrichia) and proposal of 'Candidatus Devosia euplotis'; Vannini C et al.; This paper reports the identification of bacterial endosymbionts that inhabit the cytoplasm of the marine ciliated protozoon Euplotes magnicirratus . Ultrastructural and full-cycle rRNA approaches were used to reveal the identity of these bacteria . Based on analysis of 16S rRNA gene sequences, evolutionary trees were constructed; these placed the endosymbiont in the genus Devosia in the alpha-Proteobacteria . The validity of this finding was also shown by fluorescence in situ hybridization with a Devosia-specific oligonucleotide probe . Differences at the 16S rRNA gene level (which allowed the construction of a species-specific oligonucleotide probe) and the peculiar habitat indicate that the endosymbiont represents a novel species . As its cultivation has not been successful to date, the provisional name 'Candidatus Devosia euplotis' is proposed . The species- and group-specific probes designed in this study could represent convenient tools for the detection of 'Candidatus Devosia euplotis' and Devosia-like bacteria in the environment.

Heart Vessels, 2004 Jul, 19(4), 179 - 82
Mid-term results of mitral valve repair for complicated active bacterial endocarditis in high-risk patients; Cebi N et al.; Mitral valve repair in endocarditis achieves a competent valve and prevents septic embolization and acute left ventricular failure, in which operative mortality could be increased . Early and mid-term results were examined to establish whether emergency mitral valve repair offers an advantage in complicated active endocarditis . Ten patients with complicated active native valve endocarditis underwent mitral valve repair . The mean age was 45.8 +/- 18.5 years; two patients were female (20%) . All patients had severe mitral regurgitation, which combined in one patient with mitral valve stenosis . New York Heart Association (NYHA) functional class was IV in all patients . The macroscopically infected tissue with vegetation in all patients was excised . Multiple techniques were required to achieve valve competence . There was one (10%) hospital death in a patient with persistent congestive heart failure, and a reoperation in another (10%) after 2 years . Mean follow-up was 32.1 +/- 12.7 months (range 1-45 months) and was complete . There were no late deaths, recurrent endocarditis, or thromboembolic events . Seven patients (77.7%) were in NYHA functional class I, and two (22.2%) were in class II . Mitral valve repair in complicated active bacterial endocarditis limited to leaflet tissues has a low operative mortality and valve-related morbidity, with promising mid-term survival in high-risk patients.

Res Vet Sci, 2004 Dec, 77(3), 189 - 95
Detection of bacterial DNA in synovial fluid from horses with infectious synovitis; Pille F et al.; Standard culturing techniques are often unrewarding in confirming diagnosis of synovial infection in the equine patient . Several human studies report the use of sensitive polymerase chain reaction (PCR) techniques for the detection of bacterial involvement in acute synovitis . However, successful extraction of bacterial DNA directly from clinical samples from horses without prior culture has not been reported yet . The goal of this study was to develop a sensitive and reliable method for molecular detection and identification of bacterial species in synovial fluid from horses with infectious synovitis . Synovial fluid samples from 6 horses with culture confirmed synovial infection were used for broad range 16S rRNA gene PCR . Synovial aspirates of 2 healthy horses were used as negative controls . Following extraction and purification of synovial fluid DNA, all samples were processed by touchdown PCR . Amplicons were detected by reverse line blot hybridisation and visualised with chemiluminescence . Pathogen-specific detection of 16S rRNA gene sequences was successful in all 6 synovial fluid samples . No bacterial DNA was detected in the aspirates from the negative control horses using touchdown PCR followed by 25 additional cycles of amplification . The identity of the pathogens was confirmed by DNA sequencing of the amplicons . It can be concluded that broad range 16S rRNA gene PCR followed by reverse line blot hybridisation is a promising technique for detection of bacterial DNA in synovial fluid samples . Further research should aim at the detection of bacterial DNA in synovial fluid samples suspected of infection but having negative culture results . When the 16S PCR proves to be reliable and more sensitive than standard culturing techniques, it may become a powerful tool in the diagnosis of synovial infection.

Trends Microbiol, 2004 Aug, 12(8), 366 - 72
Bacterial linguistic communication and social intelligence; Ben Jacob E et al.; Bacteria have developed intricate communication capabilities (e.g . quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability . We propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to collectively maintain linguistic communication: self and shared interpretations of chemical cues, exchange of chemical messages (semantic) and dialogues (pragmatic) . Meaning-based communication permits colonial identity, intentional behavior (e.g . pheromone-based courtship for mating), purposeful alteration of colony structure (e.g . formation of fruiting bodies), decision-making (e.g . to sporulate) and the recognition and identification of other colonies - features we might begin to associate with a bacterial social intelligence . Such a social intelligence, should it exist, would require going beyond communication to encompass unknown additional intracellular processes to generate inheritable colonial memory and commonly shared genomic context.

Biomaterials, 2005 Feb, 26(4), 419 - 31
Bacterial cellulose as a potential scaffold for tissue engineering of cartilage; Svensson A et al.; Tissue constructs for cartilage with native mechanical properties have not been described to date . To address this need the bacterial cellulose (BC) secreted by Gluconacetobacter xylinus (= Acetobacter xylinum) was explored as a novel scaffold material due to its unusual material properties and degradability . Native and chemically modified BC materials were evaluated using bovine chondrocytes . The results indicate that unmodified BC supports chondrocyte proliferation at levels of approximately 50% of the collagen type II substrate while providing significant advantages in terms of mechanical properties . Compared to tissue culture plastic and calcium alginate, unmodified BC showed significantly higher levels of chondrocyte growth . Chemical sulfation and phosphorylation of the BC, performed to mimic the glucosaminoglycans of native cartilage, did not enhance chondrocyte growth while the porosity of the material did affect chondrocyte viability . The BC did not induce significant activation of proinflammatory cytokine production during in vitro macrophage screening . Hence, unmodified BC was further explored using human chondrocytes . TEM analysis and RNA expression of the collagen II from human chondrocytes indicated that unmodified BC supports proliferation of chondrocytes . In addition, ingrowth of chondrocytes into the scaffold was verified by TEM . The results suggest the potential for this biomaterial as a scaffold for tissue engineering of cartilage.

Cell Microbiol, 2004 Sep, 6(9), 849 - 65
Simultaneous analysis of host and pathogen interactions during an in vivo infection reveals local induction of host acute phase response proteins, a novel bacterial stress response, and evidence of a host-imposed metal ion limited environment; Motley ST et al.; A fundamental goal in the study of infections is to understand the dynamic interplay between host and pathogen; however, direct in vivo interrogation of this disease process via transcriptional profiling has been lacking . Here we describe the development and application of novel bacterial RNA amplification technology to simultaneously identify key elements of both host and pathogen responses in a murine infection model . On the bacterial side, we found induction of an unusual pattern of stress response genes, a response to host-induced metal ion limitation, and a failure to achieve stationary phase in vivo . On the mammalian side, we observed the surprising induction of several genes encoding acute phase response proteins including hepcidin, haptoglobin, complement C3 and metallothionein 1 at the site of infection, as well as other mediators of innate immunity . Thus, our results reveal host-pathogen cross-talk not predicted by previous in vitro analyses and provide the framework to eavesdrop on a broad array of host-pathogen interactions in vivo . As described here, the comprehensive examination of host-pathogen interactions during an infection is critical to the discovery of novel approaches for intervention not predicted by current models.

Acta Crystallogr D Biol Crystallogr, 2004 Aug, 60(Pt 8), 1429 - 31 Epub 2004 Jul 21.
Expression, crystallization and crystallographic analysis of DegS, a stress sensor of the bacterial periplasm; Grininger M et al.; Regulated proteolysis is a key event in transmembrane signalling between intercellular compartments . In Escherichia coli, a protein DegS has been identified as being a periplasmic stress sensor for unfolded or misfolded outer membrane proteins (OMPs) . Activation of DegS initiates a proteolytic cascade which results in the transcription of periplasmic genes under sigmaE control, most importantly chaperones and proteases . DegS has been cloned and expressed as full-length protein and in an N-terminally truncated form . Both proteins were tested for crystallization and two forms of well diffracting crystals of the truncated form were obtained . Crystals of form I diffract to 3.5 A and belong to space group P2(1)3, while crystals of form II diffract to 2.2 A and belong to space group I23 . Crystals of form II were soaked with a consensus peptide representing the C-termini of outer membrane proteins and data to 2.4 A resolution were collected . Molecular-replacement trials using a homologous protease domain indicate the presence of two molecules in the asymmetric unit of crystal form I . The correctness of the molecular-replacement solution was verified by identifying radiation-damage-induced structural changes.

Biotechnol Lett, 2004 Jun, 26(12), 1007 - 11
Toxicity and degradation of metal-complexed cyanide by a bacterial consortium under sulfate-reducing conditions; Quan ZX et al.; Free cyanide at 1 mm decreased the initial sulfate reduction rate of a batch culture of granular sludge from 0.3 to 0.14 mmol d(-1) g(-1) SS (suspended solid), whereas 0.5 mm cyanide had a minimal effect (0.25 mmol d(-1) g(-1) SS) . The order of toxicity of metal-complexed cyanides to the sludge was as follows: zinc-complexed cyanide (most toxic) > free cyanide = nickel-complexed cyanide > copper-complexed cyanide (least toxic), which also corresponds well with the order of the stability (dissociation) constants of the metal-cyanide complexes . A consortium degrading cyanide was enriched using nickel cyanide as the sole nitrogen source . This consortium completely removed 0.5 mm of nickel-complexed cyanide under sulfate-reducing conditions in 11 d . Analysis of clone library of 16S rRNA genes shows that the consortium was composed of three major phylotypes including Desulfovibrio.

J Biol Chem, 2004 Sep 24, 279(39), 40470 - 4 Epub 2004 Jul 20.
Demethylation of 3-methylthymine in DNA by bacterial and human DNA dioxygenases; Koivisto P et al.; Rare DNA lesions that are chemically stable and refractory to repair may add disproportionately to the accumulation of mutations in long lived cells . 3-Methylthymine is a minor lesion that is induced by DNA-methylating agents and for which no repair process has been described previously . Here we demonstrate that this lesion can be directly demethylated in vitro by bacterial and human DNA dioxygenases . The Escherichia coli AlkB and human ABH3 proteins repaired 3-methylthymine in both single-stranded and double-stranded polydeoxynucleotides, whereas the human ABH2 protein preferred a duplex substrate . Thus, the known substrates of these enzymes now include 3-methylthymine in DNA, as well as 1-methyladenine and 3-methylcytosine, which all have structurally similar sites of alkylation . Repair of 3-methylthymine by AlkB and ABH3 was optimal at pH 6, but inefficient . At physiological pH, 3-methylthymine, which is a minor methylated lesion, was more slowly repaired than the major lesion generated in single-stranded DNA, 3-methylcytosine . Our data suggest that 3-methylthymine residues in DNA will be repaired inefficiently in vivo and therefore may occur at a low steady-state level, but the residues should not gradually accumulate to high levels in long lived cells .

Nucl Med Commun, 2004 Aug, 25(8), 819 - 23
Dual time point 2-{18F}fluoro-2'-deoxyglucose positron emission tomography in chronic bacterial osteomyelitis; Sahlmann CO et al.; OBJECTIVE: Quantitative dual time point imaging with {F}fluorodeoxyglucose positron emission tomography (F-FDG PET) has recently been found to be more accurate than single time point scanning in the discrimination between benign lesions and malignancy in various conditions . In our study we investigated glucose metabolism in chronic bacterial osteomyelitis (COM) by using F-FDG PET and a dual time protocol . METHODS: Seventeen non-diabetic patients with histopathologically proven COM and four non-diabetic patients with malignant bone disease were prospectively investigated with dual time F-FDG PET . All lesions were detected by their increased F-FDG uptake 30 and 90 min after injection of 370 MBq of F-FDG . The maximum and mean lesional standardized uptake values (SUV(max) and SUV(mean) after 30 and 90 min were determined . RESULTS: The median SUV(max) and SUV(mean) values of all osteomyelitic lesions at 30 min were 1.85 (range, 0.45-3.45) and 1.1 (range, 0.21-1.99), respectively . The median SUV(max) and SUV(mean) values of all malignant lesions at 30 min were 3.19 (range, 2.31-4.7) and 2.82 (range, 2.4-3.71), respectively . At 90 min the median SUV(max) and SUV(mean) of all osteomyelitic lesions were 1.78 (range, 0.4-2.93) and 1.1 (range, 0.18-1.72), respectively . At the same time point the median SUV(max) and SUV(mean) of all malignant lesions were 4.1 (range, 3.52-5.32) and 3.34 (range, 2.81-4.12), respectively . In osteomyelitis the SUV(max) and SUV(mean) between 30 and 90 min post-injection remained stable or decreased in 16/17 patients . In these patients a median decrease of 6% for SUV(max) (range, 1-31%) and a median decrease of 8.5% for SUV(mean) (range, 0-24%) was observed . Changes of SUV(max) and SUV(mean) between 30 and 90 min were highly significant (P<0.05) . In one patient SUV(max) and SUV(mean) increased over the time . The histology of this patient revealed multiple foreign body granulomas in addition to a mononuclear infiltrate . In malignant lesions the SUV(max) and SUV(mean) between 30 and 90 min post-injection increased . CONCLUSION: Our preliminary results indicate that dynamic dual time point F-FDG PET provides a characteristic pattern in chronic osteomyelitis similar to inflammatory processes in other locations . This pattern may be of value in the differentiation between COM and malignant bone lesions.

J Biol Chem, 2004 Oct 22, 279(43), 45162 - 74 Epub 2004 Jul 20.
Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates; Austin MB et al.; In bacteria, a structurally simple type III polyketide synthase (PKS) known as 1,3,6,8-tetrahydroxynaphthlene synthase (THNS) catalyzes the iterative condensation of five CoA-linked malonyl units to form a pentaketide intermediate . THNS subsequently catalyzes dual intramolecular Claisen and aldol condensations of this linear intermediate to produce the fused ring tetrahydroxynaphthalene (THN) skeleton . The type III PKS-catalyzed polyketide extension mechanism, utilizing a conserved Cys-His-Asn catalytic triad in an internal active site cavity, is fairly well understood . However, the mechanistic basis for the unusual production of THN and dual cyclization of its malonyl-primed pentaketide is obscure . Here we present the first bacterial type III PKS crystal structure, that of Streptomyces coelicolor THNS, and identify by mutagenesis, structural modeling, and chemical analysis the unexpected catalytic participation of an additional THNS-conserved cysteine residue in facilitating malonyl-primed polyketide extension beyond the triketide stage . The resulting new mechanistic model, involving the use of additional cysteines to alter and steer polyketide reactivity, may generally apply to other PKS reaction mechanisms, including those catalyzed by iterative type I and II PKS enzymes . Our crystal structure also reveals an unanticipated novel cavity extending into the "floor" of the traditional active site cavity, providing the first plausible structural and mechanistic explanation for yet another unusual THNS catalytic activity: its previously inexplicable extra polyketide extension step when primed with a long acyl starter . This tunnel allows for selective expansion of available active site cavity volume by sequestration of aliphatic starter-derived polyketide tails, and further suggests another distinct protection mechanism involving maintenance of a linear polyketide conformation.

Transfusion, 2004 Aug, 44(8), 1166 - 73
Detection of bacterial contamination of platelet components: six years' experience with the BacT/ALERT system; Munksgaard L et al.; BACKGROUND: Hemovigilance has shown that bacteria cause more fatalities than other infections together . Surveillance for detection of bacteria in platelets (PLTs) was initiated . Concomitantly, the storage period for PLTs was extended from 5 to 7 days to reduce cost . STUDY DESIGN AND METHODS: Analysis was performed of all cases of a positive signal in a screening procedure for contaminated PLTs taking into account results of confirmative cultures and results of culture from blood components including bacteria strains . Records were assessed from patients transfused with blood components issued before the screening culture became positive . RESULTS: Samples were collected from 22,057 PLT units . An initial reaction was seen in 84 (0.38%) . Growth was confirmed in 70 of these . Of the associated PLT units, 26 had been issued or outdated at the time when the culture was found to be reactive, in 27 bacteria were found, and in 17 cultures were negative . The bacteria found were mainly from normal skin flora . Sixty-six patients received 75 blood components issued before the screening system alarmed . None of these patients had a transfusion reaction reported . The outdating fell to less than 5 percent . CONCLUSION: A screening system for detection of bacterial contamination was implemented without increase in cost owing to extension of storage time to 7 days . Transfusion of several contaminated blood components was prevented.

Prostate, 2004 Sep 1, 60(4), 282 - 8
Application of serum PSA to identify acute bacterial prostatitis in patients with fever of unknown origin or symptoms of acute pyelonephritis; Hara N et al.; BACKGROUND: Exclusion of prostatitis in screening for prostate cancer (Cap) is a matter of concern in the prostate-specific antigen (PSA) era . Yet, the identification of acute bacterial prostatitis (ABP), intentionally utilizing PSA in patients with pyrexia has been scarcely reported . METHODS: In total, 39 men, who presented at our department with a fever higher than 38.3 degrees C, were randomly selected . We investigated the fraction of patients who had serum PSA levels higher than 4.0 ng/ml and categorized them according to an initial diagnosis of pyelonephritis, ABP, other urogenital infections, and fever of unknown origin (FUO) . RESULTS: Six of nine cases initially diagnosed as pyelonephritis, presented with elevated PSA levels between 9.5 and 75.1 ng/ml . All six cases of clinically diagnosed prostatitis had PSA elevated between 4.1 and 13.6 ng/ml . In 8 of 18 FUO cases, PSA was elevated between 5.1 and 77.0 ng/ml . PSA levels significantly correlated with age (P < 0.005) . All 20 patients with elevated PSA received antibiotics, and serum PSA was significantly reduced in all cases (P < 0.001) together with the alleviation of fever and normalization of CRP . CONCLUSIONS: PSA is a prompt and steady diagnostic tool for identifying ABP that might be missed or misdiagnosed . We recommend the measurement of PSA in cases not only with urologic infection but also puzzling pyrexia.

Turk J Gastroenterol, 2004 Mar, 15(1), 34 - 8
Comparison of cefotaxime and ofloxacin in treatment of spontaneous bacterial peritonitis; Taskiran B et al.; BACKGROUND/AIMS: Gold-standard treatment of spontaneous bacterial peritonitis currently involves 3rd generation cephalosporins . To evaluate the efficacy of ofloxacin in this infection, we compared a combined therapy with intravenous and oral ofloxacin to intravenous cefotaxime . METHODS: Thirty cirrhotic patients with spontaneous bacterial peritonitis were assigned to receive either intravenous (1 g/12 h) cefotaxime for 7 days (n=17) or intravenous (200 mg/12 h) ofloxacin for 2 days followed by oral (200 mg/12 h) ofloxacin for 5 days (n=13) . All cases had community-acquired spontaneous bacterial peritonitis . RESULTS: The infection resolution rate on the 7th day of therapy was 82.4% in the cefotaxime group and 92.3% in the ofloxacin group . Hospital survival rates were 82.4% and 100%, respectively . CONCLUSIONS: Oral ofloxacin after a short course of intravenous ofloxacin is effective in the treatment of uncomplicated spontaneous bacterial peritonitis . This regimen may allow physicians to treat these patients as outpatients as soon as their intravenous therapy is completed.

Int Rev Cytol, 2004, 236, 181 - 249
Bacterial endocytobionts of ciliophora and their interactions with the host cell; Fokin SI; Ciliates may be hosts for numerous bacteria, which can occupy almost all cellular compartments of the protists . About 200 ciliate species are recorded as hosts of different intracellular bacteria, being a small part of the diversity for such types of endocytobiosis in nature . In the Paramecium genus alone close to 60 types of bacteria adapted for intracellular life are known . In this review extensive material concerning the variety of endocytobionts, their categories, and their interaction with host cells is presented . Special attention is paid to endocytobiosis in Paramecium with highly infectious bacteria Holospora, bacteria of the Caedibacter and Polynucleobacter genera, methanogenic bacteria, and "xenosomes" as well as to life cycles and strategies of bacterial endonucleobionts . The above model bacteria and their interactions with hosts have not been exhaustively studied . A number of unsolved problems concerning their interactions within an endocytobiotic system and their ecological implications remain to be studied.

Ecotoxicol Environ Saf, 2004 Sep, 59(1), 127 - 32
Effect of fungicide iprodione on soil bacterial community; Wang YS et al.; The effect of the fungicide iprodione on soil bacterial communities was studied by treating two kinds of soils with different concentrations of iprodione . Degradation rates of iprodione in sterile and unsterile soils were also investigated . Residues of iprodione were measured by using high-performance liquid chromatography (HPLC) and a change of bacterial communities was performed with denaturing gradient gel electrophoresis (DGGE) by counting the 16S rDNA band on DGGE patterns . The degradation rate of iprodione was slower in sterile soil than in unsterile soil in both Da-Hu sandy loam and Kuan-Shi loam . After treatment with fungicide, soil bacterial communities were changed and recovered rapidly to the original status when incubated at a lower temperature (15 degrees C) and a lower iprodione concentration (5 microg/g) . At the same temperature but with more iprodione (50 microg/g) added, the soil bacterial community increases slowly and regains the original status slowly . However, when incubated at the higher temperature (30 degrees C), the soil bacterial community is more complex than that at the lower temperature . The response of the soil bacterial community to the iprodione is faster at the higher than at the lower temperature . At 30 degrees C and with 50 microg/g iprodione, the amounts of soil bacterial communities increased quickly but cannot be reduced to the original status after incubation for 23 days .

Traffic, 2004 Aug, 5(8), 561 - 70
Chlamydia--host cell interactions: recent advances on bacterial entry and intracellular development; Dautry-Varsat A et al.; Bacteria of the Chlamydiales order are very successful intracellular organisms that grow in human and animal cells, and even in amoebae . They fulfill several essential functions to enter their host cells, establish an intracellular environment favorable for their multiplication and exit the host cell . They multiply in a unique organelle called the inclusion, which is isolated from the endocytic but not the exocytic pathway . A combination of host cell factors and of proteins secreted by the bacteria, from within the inclusion, contribute to the establishment and development of this inclusion . Here we review recent data on the entry mechanisms and maturation of the inclusion .

Indian J Exp Biol, 2004 Jun, 42(6), 558 - 61
Immune haemolymph proteins in response to bacterial infection and identification of a putative bacteria binding protein in malaria vector Anopheles stephensi; Dixit RK et al.; Induction of haemolymph proteins in mosquito A . stephensi due to wounding or bacterial infection (E . coli) was analyzed using SDS-PAGE . Wounding response of pupa revealed subsequent induction of two polypeptides (21 and 74 kDa) . Two other polypeptides (44 and 57 kDa) were induced commonly in both pupa and adult female haemolymph upon bacterial infection . In vitro binding assay revealed identification of 44 kDa, a putative bacterial binding protein, a more relevant protein for further elucidation of molecular mechanism involved in host parasite interactions.

World J Gastroenterol, 2004 Aug 1, 10(15), 2228 - 31
Early diagnosis of bacterial and fungal infection in chronic cholestatic hepatitis B; Wu XZ et al.; AIM: To investigate the early diagnostic methods of bacterial and fungal infection in patients with chronic cholestatic hepatitis B . METHODS: One hundred and one adult in-patients with chronic hepatitis B were studied and divided into 3 groups: direct bilirubin (DBil)/total bilirubin (TBil) > or = 0.5, without bacterial and fungal infection (group A, n=38); DBil/TBil <0.5, without bacterial and fungal infection (group B, n=23); DBil/TBil> or = 0.5, with bacterial or fungal infection (group C, n=40) . The serum biochemical index and pulse rate were analyzed . RESULTS: Level of TBil, DBil, alkaline phosphatase (ALP) and DBil/ALP in group A increased compared with that in group B . The level of ALP in group C decreased compared with that in group A, whereas the level of TBil, DBil and DBil/ALP increased (ALP: 156+/-43, 199+/-68, respectively, P<0.05; TBil: 370+/-227, 220+/-206, respectively, P<0.01; DBil: 214+/-143, 146+/-136, respectively, P<0.01; DBil/ALP: 1.65+/-1.05, 0.78+/-0.70, respectively, P<0.001) . The level of DBil and infection affected DBil/ALP . Independent of the effect of DBil, infection caused DBil/ALP to rise (P<0.05) . The pulse rate in group A decreased compared with that in group B (63.7+/-6.4, 77.7+/-11.4, respectively, P<0.001), and the pulse rate in group C increased compared with that in group A (81.2+/-12.2, 63.7+/-6.4, respectively, P<0.001) . The equation (infection=0.218 pusle rate +1.064 DBil/ALP -16.361), with total accuracy of 85.5%, was obtained from stepwise logistic regression . Pulse rate (> or =80/min) and DBil/ALP (> or =1.0) were used to screen infection . The sensitivity was 62.5% and 64.7% respectively, and the specificity was 100% and 82.8% respectively . CONCLUSION: Bacterial and fungal infection deteriorate jaundice and increase pulse rate, decrease serum ALP and increase DBil/ALP . Pulse rate, DBil/ALP and the equation (infection=0.218 pusle rate+1.064 DBil/ALP-16.361) are helpful to early diagnosis of bacterial and fungal infection in patients with chronic cholestatic hepatitis B.

Shock, 2004 Aug, 22(2), 180 - 5
N(omega)-nitro-L-arginine methyl ester effects on neutrophil function and bacterial clearance; Stehr SN et al.; Nitric oxide synthase (NOS) inhibitors are considered promising as a therapeutic option in severe septic shock . The aim of this study was to investigate the effects of N-nitro-L-arginine methyl ester (L-NAME) application on neutrophil (PMN) respiratory burst, phagocytosis, and elimination of Escherichia coli from blood and tissue in rabbits . Twenty-eight female chinchilla rabbits were randomized to a treatment and control group . To quantify the bacterial clearance process, 10 colony forming units (CFU) of E . coli were injected intravenously into anesthetized rabbits . Animals in the L-NAME group had a significantly higher mortality compared with controls . NOS inhibition resulted in a significant delay of bacterial clearance (P < 0.001) . These findings correlated with a significant augmentation of all organ E . coli findings (P = 0.002-0.035) . PMN phagocytosis activity was notably reduced by L-NAME treatment during the experimental observation . Neutrophil burst, on the other hand, was amplified by NOS inhibition (P = 0.008) . Our findings point to an interference with the PMN-dependent immune mechanisms after L-NAME treatment . The augmented PMN burst reaction could be a compensatory mechanism, potentially leading to tissue damage . Therefore, in this model, we find sufficient evidence pointing to a possible cause for the deleterious effect of early nonselective NOS inhibition in critically ill patients.

J Proteome Res, 2004 May-Jun, 3(3), 463 - 8
Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes; Zeghouf M et al.; A vector system is described that combines reliable, very low level, regulated protein expression in human cells with two affinity purification tags (Sequential Peptide Affinity, or SPA, system) . By avoiding overproduction of the target protein, this system allows for the efficient purification of natural protein complexes and their identification by mass spectrometry . We also present an adaptation of the SPA system for the efficient purification and identification of protein complexes in E . coli and, potentially, other bacteria.

FEBS Lett, 2004 Jul 16, 570(1-3), 171 - 4
Temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers; Pokkuluri PR et al.; We have determined the first de novo position of the secondary quinone QB in the Rhodobacter sphaeroides reaction center (RC) using phases derived by the single wavelength anomalous dispersion method from crystals with selenomethionine substitution . We found that in frozen RC crystals, QB occupies primarily the proximal binding site . In contrast, our room temperature structure showed that QB is largely in the distal position . Both data sets were collected in dark-adapted conditions . We estimate that the occupancy of the QB site is 80% with a proximal: distal ratio of 4:1 in frozen RC crystals . We could not separate the effect of freezing from the effect of the cryoprotectants ethylene glycol or glycerol . These results could have far-reaching implications in structure/function studies of electron transfer in the acceptor quinone complex because the above are the most commonly used cryoprotectants in spectroscopic experiments.

Spine, 2004 Jul 15, 29(14), E298 - 9
A case with cauda equina syndrome due to bacterial meningitis of anterior sacral meningocele; Bal S et al.; STUDY DESIGN: A case of a patient with anterior sacral meningocele that was misdiagnosed as perianal abscess is presented . After the transrectal aspiration, the patient developed meningitis and cauda equina syndrome . OBJECTIVE: To report a rare case of anterior sacral meningocele in which primary presentation was mimicking perianal abscess . SUMMARY AND BACKGROUND DATA: Anterior sacral meningocele is a rare example of spinal dysraphism . It is created by a herniation of a dural sac through a defect in the sacral wall . It is usually asymptomatic until later decades . Most of the presenting symptoms are related to the pelvic organs . In the management of anterior sacral meningocele, surgical treatment is necessary . METHODS: The reported case is that of a 35-year-old female with cauda equina syndrome due to bacterial meningitis of the anterior sacral meningocele . At the beginning, she presented signs and symptoms resembling perianal abscess . She was misdiagnosed as anorectal abscess according to the computed tomography findings . The patient then underwent transrectal aspiration . Following the aspiration, meningitis and cauda equina syndrome were developed . Meningitis was treated with the appropriate antibiotics, and the patient underwent rehabilitation for paraplegia and bladder and bowel incontinence . RESULTS: Following the rehabilitation program, the patient has recovered completely within 8 months . CONCLUSION: This case represents a rare example of anterior sacral meningocele in which the patient was misdiagnosed as perianal abscess . Meningitis either iatrogenic or spontaneous may occur during the course of anterior sacral meningocele . Once it has occurred, it may result in severe morbidity and mortality . However, our case had been treated effectively, and she had regained her health with rehabilitation program.

RNA, 2004 Aug, 10(8), 1225 - 35 Epub 2004 Jul 09.
A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1; Leger M et al.; HIV-1 uses a programmed -1 ribosomal frameshift to produce the precursor of its enzymes . This frameshift occurs at a specific slippery sequence followed by a stimulatory signal, which was recently shown to be a two-stem helix, for which a three-purine bulge separates the upper and lower stems . In the present study, we investigated the response of the bacterial ribosome to this signal, using a translation system specialized for the expression of a firefly luciferase reporter . The HIV-1 frameshift region was inserted at the beginning of the coding sequence of the luciferase gene, such that its expression requires a -1 frameshift . Mutations that disrupt the upper or the lower stem of the frameshift stimulatory signal or replace the purine bulge with pyrimidines decreased the frameshift efficiency, whereas compensatory mutations that re-form both stems restored the frame-shift efficiency to near wild-type level . These mutations had the same effect in a eukaryotic translation system, which shows that the bacterial ribosome responds like the eukaryote ribosome to the HIV-1 frameshift stimulatory signal . Also, we observed, in contrast to a previous report, that a stop codon immediately 3' to the slippery sequence does not decrease the frameshift efficiency, ruling out a proposal that the frameshift involves the deacylated-tRNA and the peptidyl-tRNA in the E and P sites of the ribosome, rather than the peptidyl-tRNA and the aminoacyl-tRNA in the P and A sites, as commonly assumed . Finally, mutations in 16S ribosomal RNA that facilitate the accommodation of the incoming aminoacyl-tRNA in the A site decreased the frameshift efficiency, which supports a previous suggestion that the frameshift occurs when the aminoacyl-tRNA occupies the A/T entry site.

Nucleic Acids Res, 2004 Jun 24, 32(11), 3418 - 26 Print 2004.
Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships; Rigali S et al.; Transcription factors (TFs) of bacterial helix-turn-helix superfamilies exhibit different effector-binding domains (EBDs) fused to a DNA-binding domain with a common feature . In a previous study of the GntR superfamily, we demonstrated that classifying members into subfamilies according to the EBD heterogeneity highlighted unsuspected and accurate TF-binding site signatures . In this work, we present how such in silico analysis can provide prediction tools to discover new cis/trans relationships . The TF-binding site consensus of the HutC/GntR subfamily was used to (i) predict target sites within the Streptomyces coelicolor genome, (ii) discover a new HutC/GntR regulon and (iii) discover its specific TF . By scanning the S.coelicolor genome we identified a presumed new HutC regulon that comprises genes of the phosphotransferase system (PTS) specific for the uptake of N-acetylglucosamine (PTS(Nag)) . A weight matrix was derived from the compilation of the predicted cis-acting elements upstream of each gene of the presumed regulon . Under the assumption that TFs are often subject to autoregulation, we used this matrix to scan the upstream region of the 24 HutC-like members of S.coelicolor . orf SCO5231 (dasR) was selected as the best candidate according to the high score of a 16 bp sequence identified in its upstream region . Our prediction that DasR regulates the PTS(Nag) regulon was confirmed by in vivo and in vitro experiments . In conclusion, our in silico approach permitted to highlight the specific TF of a regulon out of the 673 orfs annotated as 'regulatory proteins' within the genome of S.coelicolor.

J Biotechnol, 2004 Aug 5, 111(3), 291 - 5
Development of an efficient enzymatic production of gamma-D-glutamyl-L-tryptophan (SCV-07), a prospective medicine for tuberculosis, with bacterial gamma-glutamyltranspeptidase; Suzuki H et al.; Gamma-D-Glutamyl-L-tryptophan (SCV-07) is a prospective medicine for the treatment of tuberculosis, according to the phase two clinical trial . Because gamma-D-glutamyl-L-tryptophan has several reactive groups in its molecule, consists of D- and L-amino acids, and is connected by gamma-glutamyl linkage, its chemical synthesis is complicated . An efficient enzymatic method to synthesize gamma-D-glutamyl-L-tryptophan from D-glutamine and L-tryptophan employing bacterial gamma-glutamyltranspeptidase was developed . The optimum reaction conditions were 50 mM D-glutamine, 50 mM L-tryptophan, and 0.2 U ml(-1) gamma-glutamyltranspeptidase, pH 9-9.5, and incubation at 37 degrees C for 5 h . After a 5 h incubation, 33 mM gamma-D-glutamyl-L-tryptophan was obtained, the conversion rate being 66% . The product was purified by Dowex 1 x 8 column and was considered to be gamma-D-glutamyl-L-tryptophan.

Vaccine, 2004 Jul 29, 22(21-22), 2761 - 8
Maturation of dendritic cells by bacterial immunomodulators; Spisek R et al.; Dendritic cells (DC) become fully functional upon maturation by various stimuli . We tested whether an immunostimulatory effect of clinically used immunomodulators (Luivac, Biostim, Ribomunyl, Imudon, Bronchovaxom) is caused by direct DC activation . We found that Luivac, Biostim and Ribomunyl have a very high DC stimulatory potential in vitro . The level of DC activation was comparable or higher than DC maturation induced by standard maturation stimuli, Poly (I:C) or lipopolysaccharide . Treated DC had activated phenotype, reduced phagocytic activity and they induced the proliferation of allogeneic T lymphocytes . These results are important for understanding the physiology of action of these widely prescribed agents . Administration of bacterial immunomodulators should be considered with care to avoid the potential risk of inducing an autoimmune disease . They could also be used as well-defined maturating agents in the protocols used for the ex vivo production of DC-based vaccines for clinical trials.

Eur J Radiol, 2004 Aug, 51(2), 102 - 13
Radiology of bacterial pneumonia; Vilar J et al.; Bacterial pneumonia is commonly encountered in clinical practice . Radiology plays a prominent role in the evaluation of pneumonia . Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio . CT should be used in unresolved cases or when complications of pneumonia are suspected . The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications . The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification . Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment . Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent . Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities . Nosocomial Pneumonia (NP) occurs in hospitalised patients . The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis . The role of imaging in NP is limited but decisive . The most valuable information is when the chest radiographs are negative and rule out pneumonia . The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion . Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias . In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings.

Bioorg Med Chem, 2004 Aug 1, 12(15), 4067 - 74
A bacterial selection for the directed evolution of pyruvate aldolases; Griffiths JS et al.; A novel bacterial in vivo selection for pyruvate aldolase activity is described . Pyruvate kinase deficient cells, which lack the ability to biosynthetically generate pyruvate, require supplementation of exogenous pyruvate when grown on ribose . Supplementation with pyruvate concentrations as low as 50 microM rescues cell growth . A known substrate of the KDPG aldolases, 2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (KHPB), also rescues cell growth, consistent with retroaldol cleavage by KDPG aldolase and rescue through pyruvate release . An initial round of selection against 2-keto-4-hydroxyoctonate (KHO), a nonsubstrate for wild-type aldolase, produced three mutants with intriguing alterations in protein sequence . This selection system allows rapid screening of mutant enzyme libraries and facilitates the discovery of enzymes with novel substrate specificities.

Curr Opin Immunol, 2004 Aug, 16(4), 506 - 10
Heat-shock proteins and the host-pathogen interaction during bacterial infection; Stewart GR et al.; Heat-shock proteins (HSPs) are expressed at high levels by bacterial pathogens during adaptation to intracellular survival . Both host and pathogen heat-shock proteins contribute to immunity by receptor-mediated activation of the innate immune response and by participation in the presentation of antigens for the adaptive immune response . Manipulation of these interactions presents a potential route to improved control of infection by vaccination or immunotherapy.

Phys Rev E Stat Nonlin Soft Matter Phys . 2004 May;69(5 Pt 1):051904 . Epub 2004 May 12.
Phase transition of traveling waves in bacterial colony pattern; Wakano JY et al.; Depending on the growth condition, bacterial colonies can exhibit different morphologies . Many previous studies have used reaction diffusion equations to reproduce spatial patterns . They have revealed that nonlinear reaction term can produce diverse patterns as well as nonlinear diffusion coefficient . Typical reaction term consists of nutrient consumption, bacterial reproduction, and sporulation . Among them, the functional form of sporulation rate has not been biologically investigated . Here we report experimentally measured sporulation rate . Then, based on the result, a reaction diffusion model is proposed . One-dimensional simulation showed the existence of traveling wave solution . We study the wave form as a function of the initial nutrient concentration and find two distinct types of solution . Moreover, transition between them is very sharp, which is analogous to phase transition . The velocity of traveling wave also shows sharp transition in nonlinear diffusion model, which is consistent with the previous experimental result . The phenomenon can be explained by separatrix in reaction term dynamics . Results of two-dimensional simulation are also shown and discussed.

Phys Rev E Stat Nonlin Soft Matter Phys . 2004 Jun;69(6 Pt 2):066109 . Epub 2004 Jun 04.
Postcollapse dynamics of self-gravitating Brownian particles and bacterial populations; Sire C et al.; We address the postcollapse dynamics of a self-gravitating gas of Brownian particles in D dimensions in both canonical and microcanonical ensembles . In the canonical ensemble, the postcollapse evolution is marked by the formation of a Dirac peak with increasing mass . The density profile outside the peak evolves self-similarly with decreasing central density and increasing core radius . In the microcanonical ensemble, the postcollapse regime is marked by the formation of a "binarylike" structure surrounded by an almost uniform halo with high temperature . These results are consistent with thermodynamical predictions in astrophysics . We also show that the Smoluchowski-Poisson system describing the collapse of self-gravitating Brownian particles in a strong-friction limit is isomorphic to a simplified version of the Keller-Segel equations describing the chemotactic aggregation of bacterial populations . Therefore, our study has direct applications in this biological context.

Cell, 2004 Jul 9, 118(1), 57 - 68
Single processing center models for human Dicer and bacterial RNase III; Zhang H et al.; Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins . Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer . Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed . We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing . Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs . Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.

J Gastroenterol Hepatol, 2004 Aug, 19(8), 904 - 9
Small bowel bacterial overgrowth is a common cause of chronic diarrhea; Teo M et al.; BACKGROUND AND AIMS: Often a cause for chronic non-specific diarrhea (> or =3 stools per day for more than 4 weeks) is not identified . Small bowel bacterial overgrowth (SBO) can occur without morphological damage and remains difficult to diagnose . Often diarrhea is treated empirically with antibiotics with a good response . The aims of the present study were first to investigate the prevalence of SBO in a consecutive series of patients with chronic diarrhea and second to compare the utility of duodenal fluid culture and (14)C-d-xylose breath/lactulose test in diagnosing SBO . METHODS: In the first study, the cause of chronic diarrhea was prospectively diagnosed in 87 subjects . In the second study, tests of SBO were compared in 18 subjects with chronic diarrhea and 15 subjects with reflux oesophagitis used as control subjects . Duodenal fluid was aspirated at endoscopy and cultured and later a (14)C-d-xylose breath/lactulose test was performed . RESULTS: In the first study, SBO was present in 48% of those with chronic diarrhea . In the second study, the diarrhea group had an average (range) stool frequency of 5.5 (3-10) per day and had normal duodenal biopsies . A total of 33%, 50%, 67% of subjects had SBO by duodenal culture alone, by a (14)C-d-xylose breath/lactulose test alone and by a combination of both tests, respectively . In the control group, 0%, 13% and 13% had SBO by duodenal culture alone, by (14)C-d-xylose breath/lactulose test alone and by combination of tests, respectively . CONCLUSION: Small bowel bacterial overgrowth is a common (33-67%) cause of chronic diarrhea .

Biophys J, 2004 Jul, 87(1), 656 - 61
Placing single-molecule T4 lysozyme enzymes on a bacterial cell surface: toward probing single-molecule enzymatic reaction in living cells; Hu D et al.; The T4 lysozyme enzymatic hydrolyzation reaction of bacterial cell walls is an important biological process, and single-molecule enzymatic reaction dynamics have been studied under physiological condition using purified Escherichia coli cell walls as substrates . Here, we report progress toward characterizing the T4 lysozyme enzymatic reaction on a living bacterial cell wall using a combined single-molecule placement and spectroscopy . Placing a dye-labeled single T4 lysozyme molecule on a targeted bacterial cell wall by using a hydrodynamic microinjection approach, we monitored single-molecule rotational motions during binding, attachment to, and dissociation from the cell wall by tracing single-molecule fluorescence intensity time trajectories and polarization . The single-molecule attachment duration of the T4 lysozyme to the cell wall during enzymatic reactions was typically shorter than the photobleaching time under physiological conditions . Applying single-molecule fluorescence polarization measurements to characterize the binding and motions of the T4 lysozyme molecules, we observed that the motions of wild-type and mutant T4 lysozyme proteins are essentially the same whether under an enzymatic reaction or not . The changing of the fluorescence polarization suggests that the motions of the T4 lysozyme are associated with orientational rotations . This observation also suggests that the T4 lysozyme binding-unbinding motions on cell walls involve a complex mechanism beyond a single-step first-order rate process.

Biophys J, 2004 Jul, 87(1), 256 - 67
Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1; Domene C et al.; The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potassium (Kir) channels . The conformational dynamics of the selectivity filter of Kir channels are of some interest in the context of possible permeation and gating mechanisms for this channel . Molecular dynamics simulations of KirBac have been performed on a 10-ns timescale, i.e., comparable to that of ion permeation . The results of five simulations (total simulation time 50 ns) based on three different initial ion configurations and two different model membranes are reported . These simulation data provide evidence for limited (<0.1 nm) filter flexibility during the concerted motion of ions and water molecules within the filter, such local changes in conformation occurring on an approximately 1-ns timescale . In the absence of K(+) ions, the KirBac selectivity filter undergoes more substantial distortions . These resemble those seen in comparable simulations of other channels (e.g., KcsA and KcsA-based homology models) and are likely to lead to functional closure of the channel . This suggests filter distortions may provide a mechanism of K-channel gating in addition to changes in the hydrophobic gate formed at the intracellular crossing point of the M2 helices . The simulation data also provide evidence for interactions of the "slide" (pre-M1) helix of KirBac with phospholipid headgroups.

Biophys J, 2004 Jul, 87(1), 75 - 80
Localization and extinction of bacterial populations under inhomogeneous growth conditions; Lin AL et al.; The transition from localized to systemic spreading of bacteria, viruses, and other agents is a fundamental problem that spans medicine, ecology, biology, and agriculture science . We have conducted experiments and simulations in a simple one-dimensional system to determine the spreading of bacterial populations that occurs for an inhomogeneous environment under the influence of external convection . Our system consists of a long channel with growth inhibited by uniform ultraviolet (UV) illumination except in a small "oasis", which is shielded from the UV light . To mimic blood flow or other flow past a localized infection, the oasis is moved with a constant velocity through the UV-illuminated "desert" . The experiments are modeled with a convective reaction-diffusion equation . In both the experiment and model, localized or extinct populations are found to develop, depending on conditions, from an initially localized population . The model also yields states where the population grows everywhere . Further, the model reveals that the transitions between localized, extended, and extinct states are continuous and nonhysteretic . However, it does not capture the oscillations of the localized population that are observed in the experiment.

BMC Bioinformatics . 2004 Jul 07;5(1):90.
Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns; Reva ON et al.; BACKGROUND: Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail . In this paper we analyzed oligonucleotide usage (OU) biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages . RESULTS: Two global features were analyzed: pattern skew (PS) and variance of OU deviations normalized by mononucleotide content of the sequence (OUV) . OUV reflects the strength of OU biases and taxonomic signals . PS denotes asymmetry of OU in direct and reverse DNA strands . A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands . Five of the 155 bacterial chromosomes have anomalously high PS, of which the chromosomes of Xylella fastidiosa 9a5c and Prochlorococcus marinus MIT9313 exhibit extreme PS values suggesting an intermediate unstable state of these two genomes . CONCLUSIONS: Strand symmetry as indicated by minimal PS is a universally conserved feature of complete bacterial genomes that results from the matching mutual compensation of local OU biases on both replichors while OUV is more a taxon specific feature . Local events such as inversions or the incorporation of genome islands are balanced by global changes in genome organization to minimize PS that may represent one of the leading evolutionary forces driving bacterial genome diversification.

J Appl Microbiol, 2004, 97(2), 246 - 55
Physiological characterization of Mycobacterium sp . strain 1B isolated from a bacterial culture able to degrade high-molecular-weight polycyclic aromatic hydrocarbons; Dandie CE et al.; AIM: The aim of this study was to further characterize a bacterial culture (VUN 10,010) capable of benzo{a}pyrene cometabolism . METHODS AND RESULTS: The bacterial culture, previously characterized as a pure culture of Stenotrophomonas maltophilia (VUN 10,010), was found to also contain another bacterial species (Mycobacterium sp . strain 1B), capable of degrading a similar range of PAH substrates . Analysis of its 16S rRNA gene sequence and growth characteristics revealed the strain to be a fast-growing Mycobacterium sp., closely related to other previously isolated PAH and xenobiotic-degrading mycobacterial strains . Comparison of the PAH-degrading characteristics of Mycobacterium sp . strain 1B with those of S . maltophilia indicated some similarities (ability to degrade phenanthrene and pyrene), but some differences were also noted (S . maltophilia able to degrade fluorene, but not fluoranthene, whereas Mycobacterium sp . strain 1B can degrade fluoranthene, but not fluorene) . Unlike the S . maltophilia culture, there was no evidence of benzo{a}pyrene degradation by Mycobacterium sp . strain 1B, even in the presence of other PAHs (ie pyrene) as co-metabolic substrates . Growth of Mycobacterium sp . strain 1B on other organic carbon sources was also limited compared with the S . maltophilia culture . CONCLUSIONS: This study isolated a Mycobacterium strain from a bacterial culture capable of benzo{a}pyrene cometabolism . The Mycobacterium strain displays different PAH-degrading characteristics to those described previously for the PAH-degrading bacterial culture . It is unclear what role the two bacterial strains play in benzo{a}pyrene cometabolism, as the Mycobacterium strain does not appear to have endogenous benzo{a}pyrene degrading ability . SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes the isolation and characterization of a novel PAH-degrading Mycobacterium strain from a PAH-degrading culture . Further studies utilizing this strain alone, and in combination with other members of the consortium, will provide insight into the diverse roles different bacteria may play in PAH degradation in mixed cultures and in the environment.

Br J Haematol, 2004 Jul, 126(2), 252 - 4
Neutrophil CD177 (NB1 gp, HNA-2a) expression is increased in severe bacterial infections and polycythaemia vera; Gohring K et al.; The NB1 glycoprotein (CD177, HNA-2a antigen) is exclusively expressed on human neutrophils . As the clinical significance of CD177 expression is unknown, we investigated its expression in healthy individuals before and after stimulation with granulocyte colony-stimulating factor (G-CSF), in patients with rheumatoid arthritis, viral hepatitis, severe bacterial infections and polycythaemia vera . Expression was quantitatively determined by flow cytometry and by real time polymerase chain reaction . Only G-CSF-stimulated individuals and patients with severe bacterial infections and polycythaemia showed a significantly (P < 0.001) increased CD177 expression compared with healthy individuals, indicating that neutrophil CD177 expression can increase significantly in certain clinical conditions.

Folia Med Cracov, 2003, 44(1-2), 5 - 25
{Disturbances of cerebral perfusion in patients with bacterial meningoencephalitis}; Garlicki A et al.; The investigations were done in acute and reconvalescent phase in 34 patients with bacterial meningoencephalitis . Neurologic condition, degree of the brain injury on the basis of Glasgow Coma Scale (GCS), protein level and pleocytosis in cerebrospinal fluid (CSF), and regional cerebral blood flow on dynamic computed tomography (CT) were assessed . The brain blood flow was measured in the white matter of the frontal and occipital horns of lateral ventricles, symmetrically in both hemispheres . Statistically significant reduction of the brain perfusion in acute phase of illness was improved . In reconvalescent phase normalisation of the brain blood supply was observed . 56% of patients had changes of consciousness . There was no significant correlation between these symptoms and parameters describing blood supply . The rest of patients had neurologic abnormalities: seizure, pyramidal syndrome, injury of the central nerves due to the reduction of blood flow in selected regions of the brain . Patients who aggregated low GCS score had high inflow of the blood . In patients who were in better condition, inflow was smaller . High pleocytosis in CSF was associated with small blood inflow and perfusion in investigated regions of the brain . Whereas high protein concentration correlated with higher inflow and increase in regional perfusion . We consider, that the brain blood supply correlate with intensification of inflammatory response in CSF.

Curr Opin Plant Biol, 2004 Aug, 7(4), 429 - 33
Plant responses to bacterial quorum sensing signals; Bauer WD et al.; Bacterial infection of plants often depends on the exchange of quorum sensing signals between nearby bacterial cells . It is now evident that plants, in turn, 'listen' to these bacterial signals and respond in sophisticated ways to the information . Plants also secrete compounds that mimic the bacterial signals and thereby confuse quorum sensing regulation in bacteria.

Pol J Vet Sci, 2004, 7(2), 77 - 81
Studies on the efficacy of different adjuvants in live stock specific bacterial vaccines for turkeys against Bordetella infection and onset of antibody titers in respect to the age of the turkey poults; Glunder G et al.; For evaluating the influence of the age of the vaccinated birds on the development of antibodies, five groups of turkey poults were inoculated subcutaneously at day 1, 7, 10, 14 and 21 of life with vaccine containing inactivated Bordetella avium and Freund's incomplete adjuvant . No matter which vaccine schedule was used, serum antibodies with the ELISA were first detected at the 28th day of life and increased continuously until the 49th day, when it exhibited either a peak or a plateau . Aluminium hydroxide, Freund's complete and incomplete adjuvant and a mineral oil-arlacel-tween-mixture being permitted adjuvants (appendix II EWG 2377/90) and the adjuvant Gerbu 100 were evaluated for their suitability . Turkeys were vaccinated at the age of three weeks and examined clinically as well as serologically up to the 11th week . Humoral antibodies were detected quantitatively using an ELISA for IgG and a microagglutination test for IgM and qualitatively using immunodiffusion . The damage at the application site was rated by measurement of the swelling of the tissue . In the 10th week, the animals were infected with the agent for challenge . The serological examination for IgG antibodies in the ELISA both treatments with Freund's adjuvants resulted in high titers, which differed significantly from the unvaccinated control after 21 days . IgM could be detected from day 7 onwards in all vaccinated groups and showed the highest titers when aluminium hydroxide was used as adjuvant . In the immunodiffusion assay, precipitating antibodies could be found from the first week after vaccination onwards . There was no correlation between the occurrence of precipitating antibodies and ELISA titers . The measurements of the swelling of the tissue in the beginning showed the largest swellings in the animals injected with Freund's incomplete adjuvant and differed significantly from the unvaccinated control . In the 10th week, the animals were infected with Bordetella avium for challenge . In comparison to the unvaccinated animals, all vaccinated turkeys, no matter which adjuvant was used, showed a distinct and significant reduction of the reisolation rate.

Przegl Lek, 2004, 61(2), 102 - 4
{Chronic bacterial infection as a risk factor for atherogenesis . The role of heat shock protein}; Rabczynski M et al.; There is an increasing number of evidence of correlation between bacterial infection and atherosclerosis . Heat shock proteins as a possible factor connecting an inflammation reaction inducted by infection and development of the early atherosclerotic lesions is postulated.

Przegl Lek, 2004, 61(2), 78 - 85
{Concentration of proinflammatory cytokines (TNF-alpha, IL-8) in the cerebrospinal fluid and the course of bacterial meningitis}; Bociaga-Jasik M et al.; Bacterial meningitis is still associated with high mortality rate and severe neurological sequels . The aim of the study was to assess correlation between concentration of proinflammatory cytokines (TNF-alpha, IL-1 beta, IL-8) in the cerebrospinal fluid (CSF) and patient condition described on the basis of Glasgow Coma Scale (GCS), changes in the CSF (pleocytosis, protein and glucose level), mortality rate and occurrence of neurological complications . 42 patients with bacterial meningitis have been analysed . Control group consisted of 25 patients with viral meningitis and 23 patients without meningitis . In analysed group with bacterial meningitis the correlation between number of scores aggregated by patients in GCS and outcome has been observed . Concentration of TNF-alpha, IL-1 beta, IL-8 in CSF of patient with bacterial meningitis was significantly higher (mean value; 705.2 pg/ml, 401.1 pg/ml and 1696.0 pg/ml) than in control group (viral meningitis: 7.93 pg/ml, 31.89 pg/ml, 405.28 pg/ml, without meningitis: 0.38 pg/ml, 2.55 pg/ml, 32.56 pg/ml) . Negative correlation between concentration of investigated cytokines in the CSF of patient with bacterial meningitis and GCS has been observed . Furthermore TNF-alpha and IL-8 levels correlated with pleocytosis, and protein and glucose levels, whereas IL-1 beta correlated with pleocytosis and protein level in CSF . Connection between TNF-alpha and IL-1 beta but not IL-8 level and outcome of bacterial meningitis has been observed . High TNF-alpha in the CSF (median value 953 pg/ml) was associated with significant risk of patient death . IL-1 beta has been better prognostic indicator . Patients who developed neurological sequels had median value of IL-1 beta level 401.3 pg/ml, and those who died had 585.9 pg/ml vs 244.7 pg/ml in the group who survived without any complications . Analysis of the ROC curve-revealed, that concentration of IL-1 beta > or = 289.9 pg/ml with 88.9% sensitivity and 67.7% specifity differentiate cases who at risk for death . For TNF-alpha the cut-off was > or = 538.9 pg/ml . The sensitivity for determined critical point was 77%, and specificity was 68.7% . Our investigation confirm that TNF alpha, IL-1 beta, IL-8 are useful in differential diagnosis of neuroinfections . Assessment of patients with bacterial meningitis on the basis of GCS is helpful to establish prognosis, and CGS seems to correlate with the intensity of inflammation in the CSF . High concentration of TNF-alpha, and IL-1 beta in the CSF are associated with the risk of patient death during the course of bacterial meningitis, but IL-1 beta has been the better prognostic marker.

Adv Exp Med Biol, 2004, 547, 83 - 9
The intricate workings of a bacterial epigenetic switch; Hernday A et al.; Bacteria have developed epigenetic mechanisms to control the reversible Off-to-On switching of cell surface structures such as pyelonephritis-associated pili (PAP) . The pap pili switch is primarily controlled by the global regulator leucine-responsive regulatory protein (Lrp), the local regulator PapI, and DNA adenine methylase (Dam) . There are two sets of binding sites for Lrp in the pap regulatory region: promoter proximal sites 1,2,3 and promoter distal sites 4,5,6 . The pilin promoter proximal (GATCprox) and distal (GATCdist) targets for Dam are located within Lrp binding sites 2 and 5, respectively . In the Off state, Lrp binds cooperatively to sites 1,2,3 overlapping the papBA pilin promoter, shutting off pilin transcription, and blocking methylation of GATCprox . Binding of Lrp at sites 1,2,3, together with methylation of GATCdist, reduces the affinity of Lrp for sites 4,5,6, preventing simultaneous binding of Lrp at sites 4,5,6 upstream . Switching to the phase . On state requires the environmentally regulated PapI co-regulator, which increases the affinity of Lrp for sites 5 and 2 . PapI binds specifically to Lrp-pap DNA complexes via binding with Lrp as well as contact with DNA sequences within pap sites 5 and 2 . Directionality in switching from Off to On appears to be due to methylation of GATCprox, which prevents formation of the PapI-Lrp-pap site 2 ternary complex . A switch model is presented in which DNA replication is proposed to play a critical role by generating a hemimethylated GATCdist site and displacing Lrp from sites 1,2,3 . This facilitates methylation of GATCprox and binding of PapI-Lrp to sites 4,5,6, with subsequent activation of pap transcription . The first gene product of the pap operon, PapB, positively regulates papI transcription, resulting in a positive feedback loop that helps maintain the On state . The pap switch is environmentally regulated by a number of factors including the CpxAR two-component regulatory system, the Histone-like nucleoid structuring protein H-NS, and cAMP-Catabolite Gene Activator Protein (CAP), which all involve binding of regulatory binding proteins to pap DNA sequences with subsequent alteration of PapI and Lrp binding . The Pap switch mechanism, with interesting variations, is conserved among a number of enteric bacteria, controlling expression of many unrelated pili-adhesin complexes.

Nucleic Acids Res, 2004 Jun 30, 32(11), 3456 - 61 Print 2004.
Substrate specificities of bacterial and human AlkB proteins; Falnes PO et al.; Methylating agents introduce cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) residues into nucleic acids, and it was recently demonstrated that the Escherichia coli AlkB protein and two human homologues, hABH2 and hABH3, can remove these lesions from DNA by oxidative demethylation . Moreover, AlkB and hABH3 were also found to remove 1-meA and 3-meC from RNA, suggesting that cellular RNA repair can occur . We have here studied the preference of AlkB, hABH2 and hABH3 for single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), and show that AlkB and hABH3 prefer ssDNA, while hABH2 prefers dsDNA . This was consistently observed with three different oligonucleotide substrates, implying that the specificity for single-stranded versus double-stranded DNA is sequence independent . The dsDNA preference of hABH2 was observed only in the presence of magnesium . The activity of the enzymes on single-stranded RNA (ssRNA), double-stranded RNA (dsRNA) and DNA/RNA hybrids was also investigated, and the results generally confirm the notion that while AlkB and hABH3 tend to prefer single-stranded nucleic acids, hABH2 is more active on double-stranded substrates . These results may contribute to identifying the main substrates of bacterial and human AlkB proteins in vivo.

Obstet Gynecol, 2004 Jul, 104(1), 114 - 9
Natural history of bacterial vaginosis and intermediate flora in pregnancy and effect of oral clindamycin; Ugwumadu A et al.; OBJECTIVE: We sought to describe the natural history of abnormal vaginal flora in pregnancy and estimate the efficacy of oral clindamycin in eradicating it and preventing relapse . METHODS: This was a subanalysis of a randomized trial of oral clindamycin for abnormal vaginal flora in pregnancy . All 494 enrolled women were asked to provide a vaginal smear 2 weeks after treatment and every second participant to provide further smears at 20, 24, 28, 32, and 36 weeks of gestation . We used Nugent score of Gram-stained smears to assess the cure rate among the clindamycin group and the rate of spontaneous resolution among the placebo group . RESULTS: Posttreatment smears were available for 462 women (231 in each of the clindamycin and placebo arms) . The prevalence of abnormal flora posttreatment was 10% (22 of 231) in the clindamycin group compared with 93% (214 of 231) in the placebo group (P <.001) . Two hundred nineteen women obtained 4 weekly smears; slides for 84 women were lost, and results were available for 135 women (69 clindamycin, 66 placebo) . In the clindamycin group, the prevalence of abnormal flora was 15% at 20 weeks of gestation and 17% at 36 weeks of gestation compared with 69% at 20 weeks of gestation and 43% at 36 weeks of gestation in the placebo group . CONCLUSION: Oral clindamycin eradicated abnormal flora in 90% of treated pregnant women and maintained a normal flora in two thirds of women throughout pregnancy . Almost one third of untreated women in our study had spontaneous resolution of abnormal flora by 20 weeks of gestation . Because previous research has shown that spontaneous resolution does not modify the risk of preterm birth, early screening is essential.

FEBS Lett, 2004 Jul 2, 569(1-3), 351 - 8
Structural analysis of DegS, a stress sensor of the bacterial periplasm; Zeth K; Regulated proteolysis is a key event in transmembrane signalling between intracellular compartments . In Escherichia coli the membrane-bound protease DegS has been identified as the periplasmic stress sensor for unfolded outer membrane proteins (OMPs) . DegS inititates a proteolytic cascade resulting in the release of sigmaE the transcription factor of periplasmic genes . The crystal structure of DegS protease reported at 2.2 A resolution reveals a trimeric complex with the monomeric protease domain in an inhibited state followed by the inhibitory PDZ domain . Noteably, domain architecture and communication of DegS are remarkably to homologous proteins known to date . Here the domain interface is mechanically locked by three intradomain salt bridges . Co-crystallisation trials in the presence of a 10-residue activating peptide did not result in significant structural intradomain shifts nor distortions in the crystal packing . These observations imply a mode of activation indicative of peptide-induced structural shifts imposed to the protease domain rather than disturbing the PDZ-protease interface.

FEBS Lett, 2004 Jul 2, 569(1-3), 229 - 34
A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C; Rigden DJ; In eukaryotes some surface proteins are attached to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor . A GPI-specific phospholipase D (GPI-PLD) activity has been characterized and implicated in the regulation of anchoring, thereby influencing the dispersal of anchored proteins or their maintenance on the cell surface, and possibly in cell signalling . Despite its biological and medical importance, little is known of the structure of GPI-PLD . Here, a distant relationship between the catalytic domains of GPI-PLD and some bacterial phospholipases C is demonstrated . A model of the GPI-PLD catalytic site sheds light on catalysis and highlights possibilities for design of improved and more specific GPI-PLD inhibitors . The databases contain hitherto unnoticed close homologues of GPI-PLD from yeast and Dictyostelium discoideum.

Zhonghua Gan Zang Bing Za Zhi, 2004 Jun, 12(6), 350 - 2
{Diagnosis and therapy of 186 spontaneous bacterial peritonitis patients with end-stage liver disease}; Zhou Z et al.; OBJECTIVE: To improve the diagnosis and treatment level of spontaneous bacterial peritonitis (SBP) in the patients with advanced liver disease, get better curative effect and prognosis . METHODS: Registered the body temperature, symptoms and signs in the abdomen, and blood routine test, the polymorphonuclear (PMN) cell count, and ascites culture in the patients with cirrhosis and fulminant hepatitis . These patients were given supporting therapies including use plasma and albumin as well as antibiotics treatment according to drug sensitivity or empiric . Changes of the body temperature, symptoms and signs were used to evaluate the effect of therapy . RESULTS: 186 of 275 inward patients with end-stage liver disease during this period were considered as SBP by ascites culture or clinical experience with various degree symptoms and signs such as pain, distention, higher tension and touch pain in the abdomen . Infective rate was 67.6% . Among them 138 patients had abnormal body temperature more than 37.4 degrees C . 106 patients with leukocyte count in the peripheral blood more than 10 x 10(9)/L; 137 patients with PMN more than 80% in differential cell count; 103 patients with PMN more than 250/mm(3) in ascites . Only 29 patients were culture positive . 82 patients were cured, 17 patients with improvement, 18 patients with inefficacy or deterioration . 42 patients died of hepatic-renal failure and 27 patients died because of upper alimentary tract bleeding, respectively . CONCLUSION: Signs and symptoms of SBP were atypical in the patients with end-stage liver disease . Ascites culture positive rate was not high . Early diagnosis and proper use antibiotics according to culture and empirics were important to increase effect and improve prognosis

J Neuroimmunol, 2004 Jul, 152(1-2), 78 - 82
Inflammatory response during bacterial meningitis is unchanged in Fas- and Fas ligand-deficient mice; Paul R et al.; Fas (CD95) and Fas ligand (FasL, CD95L) have been implicated to be involved in the acute inflammatory response by attracting neutrophils and regulating their survival . Increased levels of soluble Fas and FasL are found in cerebrospinal fluid (CSF) samples of patients with bacterial meningitis but not in controls . Functional FasL (gld)- or Fas (lpr)-deficient mice were used to assess their role in the pathophysiology of pneumococcal meningitis . Induction of meningitis in wild-type (WT) mice caused an increase in CSF white blood cell (WBC) count, intracranial pressure (ICP), and vessel permeability, paralleled by a worse clinical status at 24 h . The inflammatory response was accompanied by elevated levels of IL-1beta, MMP-2, and MMP-9 in the brain . Neither gld- nor lpr-mice showed significant differences in the above-mentioned pneumococci-induced pathophysiological alterations . These results indicate that Fas and FasL are not essential in the regulation of the acute inflammatory response during pneumococcal meningitis.

Vet Microbiol, 2004 Jul 14, 101(3), 177 - 86
Bacterial growth during the early phase of infection determines the severity of experimental Escherichia coli mastitis in dairy cows; Kornalijnslijper JE et al.; The aim of this study was to investigate the importance of bacterial growth for the severity of experimental Escherichia coli mastitis, indirectly expressed as the area under the curve of bacterial counts in milk over time . The association of pre-infusion somatic cell count and post-infusion influx of inflammatory cells in milk with severity of infection was also examined . Bacterial growth was studied through culture in milk samples (in vitro) and through monitoring of bacterial counts in milk during the early phase of infection (in vivo) in 36 cows . Individual variation in bacterial counts was more than 2 x 10(2)-fold after 6 h of in vitro incubation, and more than 8 x 10(2)-fold 6 h after intramammary infusion . In vitro growth in milk was not associated with in vivo growth during the early phase of infection, nor with severity of E . coli mastitis . Somatic cell count before experimental E . coli mastitis was negatively associated with in vivo bacterial growth during the early phase of infection (R2 = 0.28), but was not associated with severity of E . coli mastitis (R2 = 0.06) . In vivo bacterial growth during the early phase of infection (positive association; R2 = 0.41), together with influx of inflammatory cells in milk, expressed as mean hourly increase of somatic cell count between 6 and 12 h post-infusion (negative association; R2 = 0.11), are major determinants for the severity of experimental E . coli mastitis (R2 = 0.56).

Biochemistry, 2004 Jul 6, 43(26), 8322 - 32
NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system; Di Lello P et al.; Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently detoxify both ionic and organomercurial compounds . The organomercurial lyase (MerB) catalyzes the protonolysis of the carbon-mercury bond resulting in the formation of ionic mercury and a reduced hydrocarbon . The ionic mercury {Hg(II)} is subsequently reduced to the less reactive elemental mercury {Hg(0)} by a specific mercuric reductase (MerA) . To better understand MerB's unique enzymatic activity, we used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the free enzyme . MerB is characterized by a novel protein fold consisting of three noninteracting antiparallel beta-sheets surrounded by six alpha-helices . By comparing the NMR data of free MerB and the MerB/Hg/DTT complex, we identified a set of residues that likely define a Hg/DTT binding site . These residues cluster around two cysteines (C(96) and C(159)) that are crucial to MerB's catalytic activity . A detailed analysis of the structure revealed the presence of an extensive hydrophobic groove adjacent to this Hg/DTT binding site . This extensive hydrophobic groove has the potential to interact with the hydrocarbon moiety of a wide variety of substrates and may explain the broad substrate specificity of MerB.

J Biotechnol, 2004 Jul 15, 111(2), 191 - 201
Off-line monitoring of bacterial stress response during recombinant protein production using an optical biosensor; Vostiar I et al.; A surface plasmon resonance (SPR) biosensor was used to monitor the profiles of the heat-shock protein (DnaK) and the expression of a heterologous protein to map the dynamics of the cellular stress response in Escherichia coli . As expression system was used an E . coli strain overproducing human recombinant superoxide dismutase (rhSOD) . Expression of DnaK showed complex patterns differing with strength of induction . The strong up-regulation of DnaK expression was observed in all cultivations which over-produced of rhSOD . Similar patterns were not observed in non-induced reference cultures . Differences in DnaK concentration profiles were correlated with induction strength . Presented data, carried out in shake flask and glucose limited fed-batch cultivation, show a good consistency with previously published transcriptional profiling results and provide complementary information to understand stress response related to overproduction of recombinant protein . The study also demonstrates the feasibility of using the SPR as a two channel protein array for monitoring of intracellular components.

Bioinformatics, 2004 Nov 22, 20(17), 3128 - 36 Epub 2004 Nov 22.
Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens; Satten GA et al.; MOTIVATION: Application of mass spectrometry in proteomics is a breakthrough in high-throughput analyses . Early applications have focused on protein expression profiles to differentiate among various types of tissue samples (e.g . normal versus tumor) . Here our goal is to use mass spectra to differentiate bacterial species using whole-organism samples . The raw spectra are similar to spectra of tissue samples, raising some of the same statistical issues (e.g . non-uniform baselines and higher noise associated with higher baseline), but are substantially noisier . As a result, new preprocessing procedures are required before these spectra can be used for statistical classification . RESULTS: In this study, we introduce novel preprocessing steps that can be used with any mass spectra . These comprise a standardization step and a denoising step . The noise level for each spectrum is determined using only data from that spectrum . Only spectral features that exceed a threshold defined by the noise level are subsequently used for classification . Using this approach, we trained the Random Forest program to classify 240 mass spectra into four bacterial types . The method resulted in zero prediction errors in the training samples and in two test datasets having 240 and 300 spectra, respectively.

J Anim Sci, 2004 Jun, 82(6), 1725 - 31
Effects of combining three fungal phytases with a bacterial phytase on plasma phosphorus status of weanling pigs fed a corn-soy diet; Stahl CH et al.; The objective of this study was to determine possible synergistic effects of supplementing one of three fungal phytases: Aspergillus fumitagus PhyA (AFP),A . niger PhyA (ANP), or Peniophora lyci phytase (PLP) with an Escherichia coli AppA phytase (EP) in diets for pigs . Three experiments, each lasting for 4 wk, were conducted with a total of 106 weanling pigs (5 wk old) . The corn-soybean meal basal diet (BD) contained no supplemental inorganic P . In Exp . 1, 35 pigs (8.6 +/- 1.0 kg BW) were fed (as-fed basis) BD + AFP at 750 U/ kg of feed, BD + inorganic P (0.2% P), or BD + PLP at 500, 750, or 1,000 U/kg feed . Pigs fed BD + AFP or BD + 0.2% P had higher (P < 0.05) plasma inorganic P concentrations than those fed BD + PLP at the end of the trial (wk 4) . In Exp . 2, 35 pigs (8.1 +/- 0.9 kg BW) were fed BD + AFP, EP, PLP, a 1:1 mix of AFP:EP, or a 1:1 mix of PLP:EP at 500 U/kg . Pigs fed the AFP:EP mixture had growth performance and plasma measures similar to those fed either enzyme alone . Pigs fed the PLP:EP mixture had lower (P < 0.05) plasma alkaline phosphatase activity than those fed BD + PLP . Pigs fed BD + PLP had lower (P < 0.05) plasma inorganic P concentrations than pigs fed BD + EP, and higher (P < 0.05) plasma alkaline phosphatase activity than all other groups at wk 4 . In Exp . 3, 36 pigs (9.1 +/- 1.2 kg BW) were fed BD + ANP, EP, or a 1:1 mix of ANP:EP at 500 U/kg feed . Pigs fed the two enzymes together had lower (P < 0.05) plasma inorganic P concentration than those fed BD + EP and lower (P < 0.05) plasma alkaline phosphatase activity than pigs fed BD + ANP at wk 4 . In conclusion, although the four phytases showed different effects on plasma P status of weanling pigs, there was no synergistic effect between any of the three fungal phytases and the bacterial phytase on the plasma measures or growth performance under the conditions of the present study.

Sex Transm Dis, 2004 Jul, 31(7), 433 - 6
Predictors of bacterial vaginosis in adolescent women who douche; Schwebke JR et al.; OBJECTIVE: Risk factors for bacterial vaginosis (BV) include douching and sexual activity, although the exact cause of BV is unknown . GOAL: The goal of this study was to determine the relative significance of douching as a risk factor for BV . STUDY DESIGN: Two hundred fifty adolescent women who regularly douched were enrolled into a randomized douching intervention trial . Behavioral questionnaires and testing for sexually transmitted diseases and BV were performed . Associations between baseline characteristics and behaviors were compared for teens who were BV-positive and BV-negative at baseline . RESULTS: Positive correlates of BV included multiple partners, recent sexual intercourse, douching after menses, recent douching, and gonorrhea . Of these, douching after menses showed the strongest association (odds ratio, 5.11; 95% confidence interval, 1.99-13.15) in a multivariate analysis . CONCLUSIONS: Douching after menses was strongly correlated with BV; however, difficulty remains in trying to evaluate douching and sexual behavior independently.

Biosci Biotechnol Biochem, 2004 Jun, 68(6), 1216 - 20
ATP amplification for ultrasensitive bioluminescence assay: detection of a single bacterial cell; Satoh T et al.; We developed an ultrasensitive bioluminescence assay of ATP by employing (i) adenylate kinase (ADK) for converting AMP + ATP to two molecules of ADP, (ii) polyphosphate (polyP) kinase (PPK) for converting ADP back to ATP (ATP amplification), and (iii) a commercially available firefly luciferase . A highly purified PPK-ADK fusion protein efficiently amplified ATP, resulting in high levels of bioluminescence in the firefly luciferase reaction . The present method, which was approximately 10,000-fold more sensitive to ATP than the conventional bioluminescence assay, allowed us to detect bacterial contamination as low as one colony-forming unit (CFU) of Escherichia coli per assay.

Plasmid, 2004 Jul, 52(1), 13 - 30
Replication of a unit-copy plasmid F in the bacterial cell cycle: a replication rate function analysis; Morrison PF et al.; For stability, the replication of unit-copy plasmids ought to occur by a highly controlled process . We have characterized the replication dynamics of a unit-copy plasmid F by a replication rate function defined as the probability per unit age interval of the cell cycle that a plasmid will initiate replication . Analysis of baby-machine data {J . Bacteriol . 170 (1988) 1380; J . Bacteriol . 179 (1997) 1393} by stochastics that make no detailed reference to underlying mechanism revealed that this rate function increased monotonically over the cell cycle with rapid increase near cell division . This feature is highly suggestive of a replication control mechanism that is designed to force most plasmids to replicate before cells undergo division . The replication rate function is developed anew from a mechanistic model incorporating the hypotheses that initiators are limiting and that steric hindrance of origins by handcuffing control initiation of replication . The model is based on correctly folded initiator protein monomers arising from an inactive dimer pool via chaperones in limiting amounts, their random distribution to high affinity sites (iterons) at the origin (ori) and an outside locus (incC), the statistical mechanics of bound monomer participation in pairing the two loci (cis-handcuffing), and initiation probability as proportional to the number of non-handcuffed ori-saturated plasmids . Provided cis-handcuffing is present, this model closely accounts for the shape of the replication rate function derived from experiment, and reproduces the observation that replication occurs throughout the cell cycle . Present concepts of iteron-based molecular mechanisms thus appear capable of yielding a quantitative description of unit-copy-number plasmid replication dynamics.

J Mol Biol, 2004 Jul 9, 340(3), 513 - 24
The bacterial protein-translocation complex: SecYEG dimers associate with one or two SecA molecules; Tziatzios C et al.; In bacteria, the Sec-protein transport complex facilitates the passage of most secretory and membrane proteins across and into the plasma membrane . The core complex SecYEG forms the protein channel and engages either ribosomes or the ATPase SecA, which drive translocation of unfolded polypeptide chains through the complex and into the periplasmic space . Escherichia coli SecYEG forms dimers in membranes, but in detergent solution the population of these dimers is low . However, we find that stable dimers can be assembled by the addition of a monoclonal antibody . Normally, a stable SecYEG-SecA complex can only form on isolated membranes or on reconstituted proteo-liposomes . The antibody-stabilised SecYEG dimer binds one SecA molecule in detergent solution . In the presence of AMPPNP, a non-hydrolysable analogue of ATP, a complex forms containing one antibody and two each of SecYEG and SecA . SecYEG monomers or tetramers do not associate to a significant degree with SecA . The observed variability in the stoichiometry of SecYEG and SecA association and its nucleotide modulation may be important and necessary for the protein translocation reaction .

J Mol Biol, 2004 Jul 9, 340(3), 405 - 18
Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR; Smirnova IA et al.; The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes . To optimise the sensitivity of the biosensor for such compounds we have chosen a rational design of the inducer-binding cavity based on knowledge of the three-dimensional structure of DntR . We report two crystal structures of DntR with acetate (resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms), respectively, occupying the inducer-binding cavity . These structures allow for the construction of models of DntR in complex with salicylate (Kd approximately or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR with enhanced specificity for dinitrotoluenes . In both crystal structures DntR crystallises as a homodimer with a "head-to-tail" arrangement of monomers in the asymmetric unit . Analysis of the crystal structure has allowed the building of a full-length model of DntR in its biologically active homotetrameric form consisting of two "head-to-head" dimers . The implications of this model for the mechanism of transcription regulation by LysR proteins are discussed .

Cell, 2004 Jun 25, 117(7), 850 - 1
Catching some Zs: a new protein for spatial regulation of bacterial cytokinesis; Margolin W; Prior to its duplication, the bacterial nucleoid exerts local negative control over assembly of the cytokinetic Z ring to prevent potential cutting of the chromosome . In this issue of Cell, Wu and Errington show that a specific nucleoid-associated protein mediates this nucleoid occlusion effect, providing the first mechanistic insight into this key spatial regulatory system.

J Obstet Gynaecol Res, 2004 Jun, 30(3), 230 - 6
Analysis of the prevalence of bacterial vaginosis and Chlamydia trachomatis infection in 6083 pregnant women at a hospital in Otaru, Japan; Shimano S et al.; AIM: Our aims were to evaluate the prevalence of bacterial vaginosis (BV), Chlamydia trachomatis (C . trachomatis) infection and Mobiluncus spp . infection among pregnant women in Otaru, Hokkaido, Japan according to the month and year of the first prenatal visit, and to evaluate their risk factors . METHODS: Six thousand and eighty-three pregnant women who were seen consecutively at our hospital between 1993 and 2000, were enrolled in the study . Vaginal and endocervical swabs were subjected to Gram stain and detection of C . trachomatis . Univariate and multivariate methods were used to investigate the association between each infection and potential risk factors including age, gravidity, parity, history of dilatation and curettage (D & C), and history of natural abortion . RESULTS: The annual rate of BV increased from 13.6% in 1993 to 21.4% in 2000 . The annual rate of C . trachomatis infection was relatively constant . The prevalence of bacterial vaginosis, C . trachomatis infection and Mobiluncus spp . infection over the 8-year period was 18.2%, 4.2%, and 4.1%, respectively . The prevalence of the three infections was significantly higher among teenagers and among women with a history of D & C . The prevalence of C . trachomatis and Mobiluncus spp . infections was significantly higher among women with no history of delivery . BV was not associated with parity on multivariate analysis . The monthly prevalence of BV was significantly higher in May than in December, and the monthly prevalence of C . trachomatis infection was high in August . CONCLUSION: The differences in the annual and monthly infection patterns between BV and C . trachomatis infection suggest that the etiologies of the two infections differ.

Plant Cell, 2004 Jul, 16(7), 1801 - 11 Epub 2004 Jun 18.
An Arabidopsis homolog of the bacterial cell division inhibitor SulA is involved in plastid division; Raynaud C et al.; Plastids have evolved from an endosymbiosis between a cyanobacterial symbiont and a eukaryotic host cell . Their division is mediated both by proteins of the host cell and conserved bacterial division proteins . Here, we identified a new component of the plastid division machinery, Arabidopsis thaliana SulA . Disruption of its cyanobacterial homolog (SSulA) in Synechocystis and overexpression of an AtSulA-green fluorescent protein fusion in Arabidopsis demonstrate that these genes are involved in cell and plastid division, respectively . Overexpression of AtSulA inhibits plastid division in planta but rescues plastid division defects caused by overexpression of AtFtsZ1-1 and AtFtsZ2-1, demonstrating that its role in plastid division may involve an interaction with AtFtsZ1-1 and AtFtsZ2-1.

Res Microbiol, 2004 Jun, 155(5), 370 - 5
Evolution of bacterial diversity and the origins of modularity; Rainey PB et al.; A characteristic feature of all organisms is modular organisation: the tendency for groups of genes to interact in such a way as to limit the extent of pleiotropic effects among characters belonging to different functional complexes . While the implications of modularity for the evolution of variability have been much discussed the evolutionary origins remain obscure . Here we develop a model, with special reference to signal transduction cascades of bacteria, which predicts that in the face of ecological opportunity and lateral gene transfer, selection will favour modular genome architectures because such architectures minimise the pleiotropic effects associated with accommodation of potentially beneficial foreign DNA.

Adv Exp Med Biol, 2003, 527, 85 - 9
Increased mRNA expression of kynurenine pathway enzymes in human placentae exposed to bacterial endotoxin; Manuelpillai U et al.; Intra-amniotic bacterial infection is a major risk factor for cerebral impairment in infants that are born pre-term however, the causal pathways are largely unknown . Whether placental derived, neuroactive kynurenine metabolites play any role in fetal cerebral damage during episodes of intra-amniotic infection is presently unknown . In this preliminary study, we explored if kynurenine metabolites may be involved, examining if mRNAs of enzymes involved in tryptophan catabolism through the kynurenine pathway (KP) were expressed in the placenta and if their expression was co-ordinately altered with exposure to bacterial infection . We found that placentae from healthy women at term and those with clinical signs of amniotic fluid bacterial infection pre-term expressed mRNAs of the KP enzymes, with higher expression overall in the infected group . Significant increases in indoleamine 2,3-dioxygenase (IDO), tryptophan dioxygenase (TDO) and kynureninase (KYNase) expression were detected in association with infection . These findings suggest that tryptophan may be constitutively degraded through the KP in the human placenta . Whether higher concentrations of placental derived kynurenine metabolites enter the fetus during episodes of infection and their physiological roles if any remains to be elucidated.

Mol Membr Biol, 2004 May-Jun, 21(3), 183 - 91
The structure and function of bacterial light-harvesting complexes; Law CJ et al.; The harvesting of solar radiation by purple photosynthetic bacteria is achieved by circular, integral membrane pigment-protein complexes . There are two main types of light-harvesting complex, termed LH2 and LH1, that function to absorb light energy and to transfer that energy rapidly and efficiently to the photochemical reaction centres where it is trapped . This mini-review describes our present understanding of the structure and function of the purple bacterial light-harvesting complexes.

J Drug Target, 2003, 11(8-10), 531 - 8
Protective immunity induced by DNA-library immunization against an intracellular bacterial infection; Leclercq SY et al.; DNA-based immunization has shown to be a viable alternative approach to induce protective immunity against Brucella abortus infection . However, the use of a unique gene may not be sufficient to induce full protection . Therefore, a new strategy based on library immunization has been described to improve the level of protection against different pathogens and to identify new protective genes . In the present study, a B . abortus library was subcloned into the mammalian expression vector pCMV-Ubi . This plasmid was designed to create a fusion between the gene of interest with ubiquitin . The analysis of this Brucella-library showed approximately 72% of clones containing inserts with an average size of 500-2000 bp . Further, homology searches were performed using the BLASTn program, and all sequenced clones showed homology with Brucella genes, as expected . BALB/c mice immunised intramuscularly with the Brucella genomic expression library showed a strong specific total IgG antibody response to a Brucella protein extract, with production of IgG1 and IgG2a isotypes . Regarding cellular immunity, high levels of IFN-gamma and no IL-4 were detected in primed mouse splenocytes and partial protection against infection was reached in animals vaccinated with the Brucella library compared to the control group.

Vet Clin North Am Food Anim Pract, 2004 Jul, 20(2), 363 - 77, vii
Bacterial meningitis and encephalitis in ruminants; Fecteau G et al.; The clinical aspects of bacterial meningitis in neonates are described in this article . Specific types of meningitis affecting adult cattle are also described . Other conditions occurring less frequently,such as frontal sinusitis and brain abscess, are discussed.

Curr Biol, 2004 Jun 22, 14(12), R486 - 7
Bacterial chemosensing: cooperative molecular logic; Wolanin PM et al.; Bacterial chemotaxis is mediated by transmembrane receptors that bind attractant and repellent chemicals and control an intracellular protein kinase . Each cell contains thousands of receptor subunits that form a tightly packed array at one pole . Recent studies of bacterial behavior have begun to reveal the molecular logic of this sensory architecture.

BMJ, 2004 Jul 24, 329(7459), 206 - 10 Epub 2004 Jun 16.
Predicting bacterial cause in infectious conjunctivitis: cohort study on informativeness of combinations of signs and symptoms; Rietveld RP et al.; OBJECTIVE: To find an efficient set of diagnostic indicators that are optimally informative in the diagnosis of a bacterial origin of acute infectious conjunctivitis . DESIGN: Cohort study involving consecutive patients . Results of index tests and reference standard were collected independently from each other . SETTING: 25 Dutch health centres . PARTICIPANTS: 184 adults presenting with a red eye and either (muco)purulent discharge or glued eyelid(s), not wearing contact lenses . MAIN OUTCOME MEASURES: Probability of a positive bacterial culture, given different combinations of index test results; area under receiver operating characteristics curve . RESULTS: Logistic regression analysis showed optimal diagnostic discrimination for the combination of early morning glued eye(s), itch, and a history of conjunctivitis . The first of these indicators increased the likelihood of a bacterial cause, whereas the other two decreased it . The area under the receiver operating characteristics curve for this combination of symptoms was 0.74 (95% confidence interval 0.63 to 0.80) . The overall prevalence of bacterial involvement of 32% could be lowered to 4% or raised to 77%, depending on the pattern of index test results . CONCLUSION: A bacterial origin of complaints indicative of acute infectious conjunctivitis can be made much more likely or unlikely by the answers to three simple questions posed during clinical history taking (possibly by telephone) . These results may have consequences for more targeted prescription of ocular antibiotics.

J Endotoxin Res, 2004, 10(3), 175 - 84
Bacterial endotoxin modifies heat shock factor-1 activity in RAW 264.7 cells: implications for TNF-alpha regulation during exposure to febrile range temperatures; Singh IS et al.; Recent studies have identified heat shock factor (HSF)-1, the predominant heat/stress-stimulated transcriptional activator of heat shock protein genes as a repressor of certain cytokine genes, including TNF-alpha and IL-1beta . We previously showed that exposing macrophages to febrile-range temperature (FRT; 39.5 degrees C) activates HSF-1 to a DNA binding form that does not activate heat shock protein gene transcription, but apparently represses TNF-alpha and IL-1beta transcription . Prewarming macrophages to 39.5 degrees C for 30 min prior to stimulation with bacterial lipopolysaccharide (LPS) does not change the induction of TNF-alpha transcription, but markedly reduces its duration . This raised the question of how TNF-alpha transcription could occur at all in the presence of activated HSF-1 . We used RAW 264.7 cells to test the hypothesis that macrophage activation triggers a transient reversal of HSF-1-mediated repression, thereby allowing induction of TNF-alpha transcription . Electrophoretic mobility shift assays revealed that LPS triggers a transient inactivation of HSF-1 that temporally correlates with TNF-alpha transcription and was associated with a transient increase in HSF-1 molecular weight, a decrease in its pI, and appearance of HSF-1 phosphorylating activity . The serine/threonine phosphatase inhibitor, calyculin A, blocked the inhibitory affect of FRT on LPS-induced TNF-alpha generation and prevented the re-activation of HSF-1 . We propose that LPS stimulation of FRT-exposed macrophages stimulates a sequential phosphorylation and dephosphorylation of HSF-1, causing a cycle of inactivation and reactivation of HSF-1 repressor activity that allows a temporally-limited period of gene transcription.

Asian Pac J Allergy Immunol, 2003 Dec, 21(4), 223 - 30
An open-label, prospective study of an oral polyvalent bacterial lysate (Luivac) in the treatment of recurrent respiratory tract infections in Thai patients; Jareoncharsri P et al.; An open-label, non-comparative study was performed in the Department of Otolaryngology, Siriraj Hospital, Bangkok, Thailand, to assess the safety, tolerability, acceptability and efficacy of an oral polyvalent bacterial lysate (Luivac) in the treatment of recurrent respiratory tract infections (RTIs) in Thai patients . Thirty-three patients were included in this study, 18 males and 15 females, with a mean age of 34.0 +/- 14.7 years . The mean number of RTIs during the 12-month period preceding the study was 9.5 per patient . During the study each patient received one tablet of Luivac daily for 28 days followed by a treatment-free period of 28 days . This was followed with another 28 days on Luivac, after which there was a 28-day treatment-free follow-up period . This study lasted 4 months with five scheduled patient visits (V1-V5) . Laboratory studies were done at baseline (V1) and after treatment (V4), which included complete blood count and serum immunoglobulins (IgA, IgE, IgG and IgM) . The incidence of all adverse events was 15.2% and no case was related to the studied drug . There were no clinical relevant changes in laboratory parameters after treatment . The reduction rate of RTIs per month at the end of the study period was 63.5% when compared to the average RTIs rate per month during the 12 months preceding the study . A comparison of the first study period (V1-V3) and the second study period (V3-V5) showed a reduction in duration of RTIs (23.1%), in the clinical infection score (17.5%), in the number of antibiotics used (2.1%), in the number of symptomatic treatments (3.5%), and in the number of days absent from school or work (50.0%) . Overall tolerability and acceptability were assessed as very good and good in 96.8% of the patients . This study suggests that oral polyvalent bacterial lysate (Luivac) was safe and also showed a tendency to be effective in preventing RTIs in Thai patients with or without risk factors for recurrent RTIs . Other clinical advantages were reduction in the severity and duration of infection as well as in reduction of the cost of treatment and the number of days absent from school or work.

Mikrobiologiia, 2004 Mar-Apr, 73(2), 248 - 57
{Bacterial processes of the methane cycle in the bottom sediments of Baikal lake}; Dagurova OP et al.; The activity of methanogenic and methanotrophic bacteria was evaluated in bottom sediments of Lake Baikal . Methane concentration in Baikal bottom sediments varied from 0.0053 to 81.7 ml/dm3 . Bacterial methane was produced at rates of 0.0004-534.7 microliters CH4/(dm3 day) and oxidized at rates of 0.005-1180 microliters CH4/(dm3 day) . Peak methane production and oxidation were observed in Frolikha Bay near a methane vent . Methane was emitted into water at rates of 49.2-4340 microliters CH4/(m2 day) . Rates of bacterial methane oxidation in near-bottom water layers ranged from 0.002 to 1.78 microliters/(1 day) . Methanogens and methanotrophs were found to play an important role in the carbon cycle through all layers of sediments, particularly in the areas of methane vent and gas-hydrate occurrence.

Curr Opin Microbiol, 2004 Jun, 7(3), 314 - 20
Bacterial genomes pave the way to novel vaccines; Meinke A et al.; The availability of complete genome sequences of pathogens has dramatically changed the scope for developing improved and novel vaccines by increasing the speed of target identification . Genomics-based technologies have many advantages, compared to conventional approaches, which are time-consuming and usually identify only abundant antigens that are expressible under in vitro culture conditions . This review focuses on recent reports of genomics-based strategies that can be applied to most pathogens and that exploit genome sequence information in alliance with adjunct technologies, including bioinformatics, expression analyses, random mutagenesis or protein/peptide-based selection methods . Despite the caveats that are associated with the individual approaches, these technologies have already made major contributions to the identification and selection of novel vaccine candidates to combat bacterial infections.

Curr Opin Microbiol, 2004 Jun, 7(3), 277 - 82
Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection; Hinton JC et al.; The understanding of bacterial pathogenesis is dependent on techniques that elucidate the underlying genetic and biochemical mechanisms . To study the mechanism of bacterial survival and proliferation within host cells we need accurate tools that tell us what is occurring within the infecting organism . It has now become possible to determine the transcriptional status of in vivo-derived bacteria at the level of the whole genome . Such expression profiles serve as a monitor of the host cell environment as well as an indicator of the bacterial adaptation to its intracellular niche . Here, we review the methods used to produce microarray data for defining the bacterial intracellular transcriptome, and examine the pitfalls in extracting bacterial RNA from the infected host compartment.

Curr Opin Genet Dev, 2004 Apr, 14(2), 126 - 32
Structure and segregation of the bacterial nucleoid; Wu LJ; In bacteria, chromosome segregation and DNA replication occur concurrently and there is no clear equivalent of a eukaryote mitotic spindle . Chromosome segregation can be viewed as a two-step process . As the first step, the origin of replication regions are segregated actively, probably by a mechanism involving an as yet unidentified motor protein or proteins, and held in position . The second step is the separation and migration of the rest of the chromosome probably driven by forces generated from various cellular processes such as DNA replication, transcription and transertion.

Pediatr Infect Dis J, 2004 Jun, 23(6), 511 - 7
Differentiating acute bacterial meningitis from acute viral meningitis among children with cerebrospinal fluid pleocytosis: a multivariable regression model; Bonsu BK et al.; BACKGROUND: Although accurate models for predicting acute bacterial meningitis exist, most have narrow application because of the specific variables selected for them . In this study, we estimate the accuracy of a simple new model with potentially broader applicability . METHODS: On the basis of previous reports, we created a reduced multivariable logistic regression model for predicting bacterial meningitis that relies on age (years) (AGE), cerebrospinal fluid (CSF), total protein (TP) and total neutrophil count (TNC) alone . Data were from children ages 1 month-18 years diagnosed with acute enteroviral or bacterial meningitis whose initial CSF revealed >7 white blood cells/mm . A fractional polynomial model was specified and validated internally by the bootstrap procedure . The area under the receiver operating characteristic curve (discrimination: criterion standard, >0.7), the Hosmer-Lemeshow deciles-of-risk statistic (calibration: criterion standard, P > 0.05) and sensitivity-specificity pairs at prespecified probability thresholds of the model were computed . RESULTS: We identified 60 children with bacterial meningitis and 82 with enteroviral meningitis . At an area under the receiver operating characteristic curve of 0.97, our model represented by the equation: log odds of bacterial meningitis = 0.343 - 0.003 TNC - 34.802 TP + 21.991 TP - 0.345 AGE, was highly accurate when differentiating between bacterial and enteroviral meningitis . The model fit the data well (Hosmer-Lemeshow statistic; P ={r} 0.53) . At probability cutoffs between 0.1 and 0.4, the model had sensitivity values between 98 and 92% and specificity values between 62 and 94% . CONCLUSIONS: Among children with CSF pleocytosis, a prediction model based exclusively on age, CSF total protein and CSF neutrophils differentiates accurately between acute bacterial and viral meningitis.

J Virol, 2004 Jul, 78(13), 7004 - 15
Production of high-titer Epstein-Barr virus recombinants derived from Akata cells by using a bacterial artificial chromosome system; Kanda T et al.; An Epstein-Barr virus (EBV) genome in Burkitt's lymphoma-derived cell line Akata was cloned into a bacterial artificial chromosome (BAC) vector . The BAC clone, designated AK-BAC, was rapidly and precisely modified by means of efficient homologous recombination in Escherichia coli . This system was used to produce recombinant EBVs with transgenes . An expression cassette of green fluorescent protein (GFP) was inserted into AK-BAC, and the resultant BAC clone, AK-BAC-GFP, was transfected into Akata cells . We found that transfected BAC plasmids efficiently formed episomes in EBV-positive Akata cells . Mixtures of wild-type and AK-BAC-GFP viruses were then produced and used to infect EBV-negative Akata cells . We obtained cell clones that harbored only AK-BAC-GFP but no wild-type episome . These cell clones produced infectious viruses after stimulating virus production, and the recombinant viruses of AK-BAC-GFP efficiently immortalized primary B lymphocytes . We further revised the method so that any kind of cDNA could be rapidly inserted into the unique I-PpoI site that had been artificially introduced into AK-BAC . The AK-BAC system will have a broad range of applications, such as genetic analyses of various viral gene products and development of viral vectors for human gene therapy.

Biochem Biophys Res Commun, 2004 Jul 9, 319(4), 1088 - 95
Bacterial heat shock protein 60 may increase epithelial cell migration through activation of MAP kinases and inhibition of alpha6beta4 integrin expression; Zhang L et al.; Exogenous heat shock proteins may modify cell behavior of infected epithelium . The effect of heat shock protein 60 (hsp60) of Actinobacillus actinomycetemcomitans and Escherichia coli, and human recombinant hsp60 on migration of HaCaT skin keratinocytes was studied using the Boyden chamber assay . Hsp60 from different species increased cell migration by two- to fivefold and this effect was inhibited by ERK inhibitor PD 98059, p38 inhibitor SB 203580, and a function-blocking epidermal growth factor receptor (EGFR) antibody . Hsp60 reduced the expression of alpha6-integrin mRNA and its protein levels on the cell surface but had no effect on the expression of beta4, beta1, alpha1, alpha5 or alphav integrin subunits . Hsp60 also significantly inhibited cell adhesion to laminin-5, a ligand of alpha6beta4 integrin . These results suggest that exogenous hsp60 released from bacteria or inflammatory cells may promote epithelial cell migration through activation of EGFR and MAP kinases, and inhibition of alpha6beta4 integrin expression.

Gene, 2004 Jun 23, 335, 73 - 88
Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer; Iyer LM et al.; Comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria . DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta-beta' module (BBM) 1 domain in the beta' subunit, and a distinct helical module in the sigma subunit . The DdRp subunits of remaining bacteria, which comprise Group II, lack these inserts, although some additional inserted domains are present in individual lineages . The separation of bacteria into Group I and Group II is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution . A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group I, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II . The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events . Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium.

J Vet Sci, 2004 Jun, 5(2), 111 - 7
Comparative antibody response of five recombinant antigens in related to bacterial shedding levels and development of serological diagnosis based on 35 kDa antigen for Mycobacterium avium subsp . paratuberculosis; Shin SJ et al.; Eighty-five complex (85A, 85B and 85C), 35-kDa and superoxide dismutase (SOD) were cloned, expressed and purified as antigens in an enzyme-linked immunosorbent assay (ELISA) to compare the serological reactivity of cows with different shedding levels of Mycobacterium avium subsp . paratuberculosis (MPT) . Antibody responses to all recombinant antigens positively increased depending on shedding levels . In particular, antibody responses to the 35 kDa were higher than those to the others in all shedder groups . Also, the mean of O . D . values among Ag 85 complex, 85B showed slightly higher response than others with high sensitivity and specificity in all shedder groups . In receiver operating characteristic (ROC) curve analysis, the result of 35 kDa ELISA yielded an area under the curve value of 0.945 (95% confidence interval = 0.895 . 0.996), which indicated that this 35 kDa is more accurate indicator of MPT infection than other antigens . At the cut-off point recommended by the ROC curve analysis, the sensitivity and specificity of 35 kDa ELISA were higher than those of other antigens with 93.3% and 86.4%, respectively . Finally, a commercially available ELISA kit was used to clarify 200 positive and 200 negative sera . We then re-tested these serum samples with our ELISA test using the 35-kDa antigens . 35 kDa ELISA and commercial kit showed almost similar results in ROC curve analysis even though two of positive sera in commercial kit were negative in 35 kDa ELISA . The sera, which showed difference in the comparison with commercial ELISA kit, they also did not react with 35 kDa in Western blot . These results suggest that a 35-kDa based ELISA can be useful for detecting MPT infection.

Plant Physiol Biochem, 2004 May, 42(5), 451 - 5
Differential expression of 10 sweetpotato peroxidase genes in response to bacterial pathogen, Pectobacterium chrysanthemi; Jang IC et al.; To understand the function of each peroxidase (POD, EC 1.11.1.7) in terms of biotic stress, changes in POD specific activity and expression of 10 POD genes were investigated in four cultivars of sweetpotato (Ipomoea batatas) after infection with Pectobacterium chrysanthemi . POD specific activity (units mg(-1) protein) increased from 16 h after inoculation (HAI) in three varieties . POD activities of two cultivars, Shinwhangmi and White Star, reached a maximum level at 24 HAI by about three times compared to mock treatment (MT), and then decreased, whereas those of Zami and Yulmi continuously increased until 36 HAI . Native gel analysis revealed that one POD isoenzyme with a high electrophoretic mobility significantly increased in response to pathogen infection in all cultivars . Additionally, 10 POD genes displayed differential expression patterns upon bacterial infection by northern analysis . Several POD genes such as swpa2, swpa3, swpa4, swpa5, swpb1 were induced upon bacterial infection, but other genes were not . Particularly, swpa4 gene was markedly expressed in response to bacterial infection in four different cultivars, suggesting that this gene has a stress-inducible promoter . These results indicate that some specific POD isoenzymes are involved in defense in relation to pathogenesis of P . chrysanthemi in sweetpotato plants .

J Invest Dermatol, 2004 Jul, 123(1), 87 - 92
Diabetes prolongs the inflammatory response to a bacterial stimulus through cytokine dysregulation; Naguib G et al.; Diabetes has been identified as an important risk factor for infection . But relatively little is known about how diabetes alters the inflammatory response to bacteria . The objective of this study was to investigate how diabetes affects host-bacteria interactions by focusing on the inflammatory response in a connective tissue setting . Diabetic (db/db) and control (db/+) mice were inoculated with Porphyromonas gingivalis, a pathogen associated with bite wounds and periodontal disease . The response was measured histologically or by the expression of inflammatory cytokines . By quantitative histologic analysis, there was little difference between the diabetic and control mice on day 1 . On day 3, however, the inflammatory infiltrate had subsided in the control group, whereas it had not in the diabetic group (p<0.05) . Similar results were noted at the molecular level by the persistent expression of tumor necrosis factor-alpha (TNF-alpha) and the chemokines MCP-1 and MIP-2 . The importance of TNF in this process was demonstrated by reversal of the prolonged chemokine expression by specific inhibition of TNF with Enbrel . These results indicate that cytokine dysregulation associated with prolonged TNF expression represents a mechanism through which bacteria may induce a more damaging inflammatory response in diabetic individuals.

Clin Transplant, 2004, 18 Suppl 11, 44 - 9
An autopsy case of bacterial septic shock 12 years following ABO-incompatible renal transplantation; Okamoto M et al.; We report the case of an ABO-incompatible kidney transplant recipient who died suddenly following a good transplant course of 12 years . For 10 years after transplantation, the graft function had been stable (s-Cr: 1.0-1.5 mg/dL), although chronic hepatitis C had developed, with elevation of transaminase . In the 11th year, he was admitted into the hospital with low-grade fever and general fatigue . Jaundice and anaemia progressed, and he died 2 months after admission . The autopsy diagnosis was: (1) post-renal transplantation state, (2) phlegmonous enterocolitis with septic infarction, (3) cellulitis and necrotic myositis, and (4) sepsis . The transplanted kidney graft showed well-preserved glomeruli and tubules, corresponding to chronic allograft nephropathy (CAN) grade Iota (ci1, ct1, cv1), according to the Banff classification . The pathological changes observed in this long-surviving ABO-incompatible kidney graft were similar to those of an ABO-compatible graft, although its degree was milder.

Can J Gastroenterol, 2004 Jun, 18(6), 381 - 6
Clinical presentation and prevalence of spontaneous bacterial peritonitis in patients with cryptogenic cirrhosis and features of metabolic syndrome; Sorrentino P et al.; BACKGROUND: Nonalcoholic steatohepatitis (NASH) may progress to cirrhosis . The prevalence and clinical relevance that spontaneous bacterial peritonitis may have in complicating ascites due to NASH-related cirrhosis have yet to be defined . METHODS: Among 611 cases of cirrhosis-associated ascites, 45 patients with cryptogenic cirrhosis were retrospectively identified . Of these, 36 patients and a control group of subjects with viral- associated ascites were followed up and compared in a case control study . Information on the onset of ascites, with or without spontaneous bacterial peritonitis, history of risk factors for multimetabolic syndrome, and serological and ascitic laboratory data were compared between groups . RESULTS: Spontaneous bacterial peritonitis occurred significantly more often in patients with cryptogenic cirrhosis than in equally symptomatic viral controls . The prevalence of obesity, diabetes and spontaneous bacterial peritonitis was significantly higher in patients with cryptogenic cirrhosis . Although liver function was similar in both groups, cryptogenic cirrhosis patients had lower aminotransferase levels . Multivariate analysis identified diabetes, juvenile obesity and spontaneous bacterial peritonitis as independent factors associated with ascites due to cryptogenic cirrhosis . CONCLUSIONS: Features suggestive of NASH are more frequently observed in patients with ascites and cryptogenic cirrhosis than in age- and sex-matched ascitic patients with well-defined viral etiology . Ascites may be a presenting symptom of NASH-related cirrhosis, and affected patients have a twofold greater risk of spontaneous bacterial peritonitis.

Annu Rev Biochem, 2004, 73, 991 - 1018
Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s; Pylypenko O et al.; Cytochrome P450 enzymes are heme-containing monooxygenases that are named after an absorption band at 450 nm when complexed with carbon monoxide . They catalyze a wide variety of reactions and are unique in their ability to hydroxylate nonactivated hydrocarbons . P450 enzymes are involved in numerous biological processes, which include the biosynthesis of lipids, steroids, antibiotics, and the degradation of xenobiotics . In line with the variety of reactions catalyzed, the size of their substrates varies significantly . Some P450s have open active sites (e.g., BM3), and some have shielded active sites that open only transiently (e.g., P450cam), whereas others bind the substrate only when attached to carrier proteins (e.g., Oxy proteins) . Structural aspects of both organic and gaseous ligand binding and electron transfer are described.

Ann Trop Paediatr, 2004 Jun, 24(2), 133 - 40
Intensive care needs of children with acute bacterial meningitis: a developing country perspective; Singhi SC et al.; In view of very limited availability of paediatric intensive care (PIC) facilities in developing countries, it is important to define priorities and recognise children who might benefit most from PIC . The objective of this retrospective, descriptive analysis was to identify the clinical indicators for intensive care in children with acute bacterial meningitis (ABM) . The study included 220 children aged between 1 month and 12 years with ABM admitted to the paediatric services of an urban, tertiary-care, teaching hospital in northern India from July 1993 to December 1996 . Of these, 88 were transferred to the PICU by the primary physician, 59% were comatose (Glasgow coma score <8), 44% had raised intracranial pressure (ICP), 24% were in shock and 42% had respiratory distress/failure . Seizures occurred during their illness in 64 children, 34 of whom had refractory status epilepticus . Endotracheal intubation was needed in 29 and ventilatory support in 19 children . Most of the life support measures were required during the initial 48 hours . Nineteen (22%) children died, 16 of whom were comatose on admission . Multiple system involvement was associated with higher mortality . There were no deaths among the children who were not transferred to the PICU . Children with ABM who have a Glasgow coma score <8, clinical signs of raised ICP, refractory status epilepticus, shock and/or respiratory compromise should be prioritised to receive PIC.

Environ Microbiol, 2004 Jul, 6(7), 754 - 9
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins; Santos SR et al.; Molecular characterizations of bacteria often employ ribosomal DNA (rDNA) to establish the identity and relationships among organisms, but the use of rRNA sequences can be problematic as the result of alignment ambiguities caused by indels, the lack of informative characters, and varying functional constraints over the molecule . Although protein-coding regions have been used as an alternative to rRNA, there is neither consensus among the genes examined nor ways to rapidly obtain sequence information for such genes from uncharacterized bacterial species . To standardize the set of protein-coding loci assayed in bacterial genomes, we examined over 100 widely distributed genes to identify sets of universal primers for use in the PCR amplification of protein coding regions that are common to virtually all bacteria . From this set, we developed primer sets that each target of 10 genes spanning an array of genomic locations and functional categories . Although many of the primers contain sequence degeneracies that aid in targeting genes across diverse taxa, most are adequate for direct sequencing of amplification products, thereby eliminating intermediate cloning before sequence determination . We foresee the analysis of these protein-coding regions as being complementary to ribosomal DNA for answering questions pertaining to bacterial identification, classification, phylogenetics and evolution.

Environ Microbiol, 2004 Jul, 6(7), 745 - 53
Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability; Luna GM et al.; We investigated vertical distribution and depth-related patterns (from 670 to 2,570 metres) of bacterial diversity in sediment samples collected along a transect in the warm deep Mediterranean sea . Analyses of bacterial diversity were compared with the abundance of benthic bacteria, their metabolically active fraction and the substrates potentially available for their growth . The number of active bacteria was dependent upon the availability of organic substrate in the sediment deriving from phytopigment inputs from the photic layer . The T-RFLP analysis revealed that the surface layers of all sediments analysed were dominated by the same ribotypes, but clear shifts in bacterial community structure were observed in deeper sediment layers . High values of bacterial diversity (expressed as D, H') and evenness (as J) were observed at all stations (a total of 61 ribotypes was identified), and as a result of the large fraction of rare ribotypes (c . 35%), the overall bacterial diversity in the deep sea region investigated was among the highest reported so far in literature . Biodiversity parameters did not display any relationship with water depth, but ribotype richness was related with the number and percentage of active bacteria, suggesting a coupling between organic inputs stimulating bacterial growth and deep-sea bacterial diversity.

Environ Microbiol, 2004 Jul, 6(7), 733 - 44
Top-down impact of bacterivorous nematodes on the bacterial community structure: a microcosm study; De Mesel I et al.; The influence of bacterivorous nematodes (Diplolaimelloides meyli, Diplolaimelloides oschei, Diplolaimella dievengatensis, Panagrolaimus paetzoldi) on the development of a bacterial community growing on decaying cordgrass detritus was studied in laboratory microcosm experiments . Cordgrass leaves were incubated on a sediment surface with a natural bacterial mixture containing bacteria from sediment, cordgrass detritus and habitat water . The four nematode species were applied separately to the microcosms; controls remained without nematodes . Samples were taken seven times over a 65-day period . The bacterial community structure was analysed by means of DGGE of the 16S rRNA genes . Multi Dimensional Scaling showed grouping of the samples per treatment . Analysis of Similarities indicated that the differences between treatments were significantly larger than differences within treatments . Our results suggest that nematodes can have a significant structuring top-down influence on the 'pool' of bacteria growing on the detritus, even at low densities . Dissimilarities were similar between all treatments . Differences in bacterial community composition within the treatments with monhysterids (D . meyli, D . oschei and D . dievengatensis) can be explained by species-specific food preferences . Panagrolaimus paetzoldi on the other hand feeds unselectively, and thus affects the bacterial community differently . A top-down effect of the nematodes on the diversity of the bacterial community was only evident under high grazing pressure, i.e . in the presence of P . paetzoldi.

Epidemiol Mikrobiol Imunol, 2004, 53(2), 81 - 5
{Type III bacterial secretion systems and their relation to virulence}; Hostacka A et al.; Newer data on type III secretion systems (SST systems) associated with virulence in gramnegative bacteria are summarized . The focus is on substrates of SST systems (effector proteins), recognition of type III secretion signals, structural components of SST systems and their genetic determination.

Microbiology, 2004 Jun, 150(Pt 6), 1965 - 72
Effects of high hydrostatic pressure on bacterial cytoskeleton FtsZ polymers in vivo and in vitro; Ishii A et al.; Some rod-shaped bacteria, including Escherichia coli, exhibit cell filamentation without septum formation under high-hydrostatic-pressure conditions, indicating that the cell-division process is affected by hydrostatic pressure . The effects of elevated pressure on FtsZ-ring formation in E . coli cells were examined using indirect immunofluorescence microscopy . Elevated pressure of 40 MPa completely inhibited colony formation of E . coli cells under the cultivation conditions used, and the cells exhibited obviously filamentous shapes . In the elongated cells, normal cell-division processes appeared to be inhibited, because no FtsZ rings were observed by indirect immunofluorescent staining . In addition, it was observed that hydrostatic pressure dissociated the E . coli FtsZ polymers in vitro . These results suggest that high hydrostatic pressure directly affects cell survival and morphology through the dissociation of the cytoskeletal frameworks.

Microbiology, 2004 Jun, 150(Pt 6), 1609 - 27
The replication-related organization of bacterial genomes; Rocha EP; The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division . Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes . Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions . These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome . When asymmetries or gradients increase in some genomes, e.g . due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases . As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation . Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division . Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.

J Clin Microbiol, 2004 Jun, 42(6), 2566 - 72
Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora; Ott SJ et al.; The composition of the human intestinal flora is important for the health status of the host . The global composition and the presence of specific pathogens are relevant to the effects of the flora . Therefore, accurate quantification of all major bacterial populations of the enteric flora is needed . A TaqMan real-time PCR-based method for the quantification of 20 dominant bacterial species and groups of the intestinal flora has been established on the basis of 16S ribosomal DNA taxonomy . A PCR with conserved primers was used for all reactions . In each real-time PCR, a universal probe for quantification of total bacteria and a specific probe for the species in question were included . PCR with conserved primers and the universal probe for total bacteria allowed relative and absolute quantification . Minor groove binder probes increased the sensitivity of the assays 10- to 100-fold . The method was evaluated by cross-reaction experiments and quantification of bacteria in complex clinical samples from healthy patients . A sensitivity of 10(1) to 10(3) bacterial cells per sample was achieved . No significant cross-reaction was observed . The real-time PCR assays presented may facilitate understanding of the intestinal bacterial flora through a normalized global estimation of the major contributing species.

Appl Environ Microbiol, 2004 Jun, 70(6), 3758 - 60
Bacterial strains isolated from different niches can exhibit different patterns of adhesion to substrata; Bakker DP et al.; Various mechanisms have been demonstrated to be operative in bacterial adhesion to surfaces, but whether bacterial adhesion to surfaces can ever be captured in one generally valid mechanism is open to question . Although many papers in the literature make an attempt to generalize their conclusions, the majority of studies of bacterial adhesion comprise only two or fewer strains . Here we demonstrate that three strains isolated from a medical environment have a decreasing affinity for substrata with increasing surface free energy, whereas three strains from a marine environment have an increasing affinity for substrata with increasing surface free energy . Furthermore, adhesion of the marine strains related positively with substratum elasticity, but such a relation was absent in the strains from the medical environment . This study makes it clear that strains isolated from a given niche, whether medical or marine, utilize different mechanisms in adherence, which hampers the development of a generalized theory for bacterial adhesion to surfaces.

Zhongguo Wei Zhong Bing Ji Jiu Yi Xue, 2004 Jun, 16(6), 345 - 7
{Defensin-5 and Matrilysin mRNA expression in the intestine of scalded rats and its relation to bacterial translocation}; Yang HM et al.; OBJECTIVE: To investigate the effect of burn injury on the expression of rat defensin-5 (RD-5) and Matrilysin mRNA in the intestine of scalded rats and to determine its relation to bacterial translocation . METHODS: Thirty-two Wistar rats were divided randomly into sham injury group (n=8) and burn group (n=24) . Rats of the burn group were subjected to 30% total body surface area (TBSA) full-thickness scald injury . At 8, 24 and 72 hours after the injury, the animals (n=8 at each time point) were sacrificed and ileum was sampled for the determination of the expression of RD-5 mRNA and Matrilysin mRNA with reverse transcription-polymerase chain reaction (RT-PCR) technique . Cultures of mesenteric lymph nodes (MLN), liver, spleen and lung were carried out at 24 hours after the injury to assess the rate of bacterial translocation to visceral organs,and the morphological changes in ileal Paneth cells were observed . RESULTS: The expression of RD-5 mRNA was significantly up-regulated at 8 hours when compared with control group . It was down-regulated sharply at 24 hours but was still higher than control group, and at 72 hours it was down-regulated to a level lower than control . On the contrary, the expression of Matrilysin mRNA was up-regulated continuously to 72 hours, and it was significantly higher than control . Bacterial translocation rate was significantly higher in rats of the burn group at 24 hours (58.3%) than in control group (8.3%, P<0.01), but there were no obvious morphological changes in ileal Paneth cells at the same time point . CONCLUSION: The expressions of both RD-5 mRNA and Matrilysin Mrna are up-regulated in the early stage after the injury, but their time phases are different . The phenomenon might imply that there is a host protective response against bacterial translocation.

Biochem Cell Biol, 2004 Jun, 82(3), 407 - 12
An analysis of mismatched duplex DNA unzipping through a bacterial nanopore; Sutherland TC et al.; A 50-base Guide strand was synthesized that consisted of a central 10-base probe sequence flanked by two tracts of 20 adenine residues . Target sequences of 10 bases containing up to three mismatches were prepared and hybridized to the Guide strand in 1 M KCl . The transport of these constructs through single alpha-hemolysin pores was analysed by measuring the current blockade as a function of time . Complementary dsDNA takes significantly longer (840 +/- 60 micro s) to pass through the pore than a sequence of the same length containing a single (590 +/- 45 micro s) and a double (270 +/- 50 micro s) mismatch . Constructs involving three mismatches were indistinguishable from Guide ssDNA transport (120 +/- 30 micro s) . The results suggest that dsDNA must unzip as it is transported through the nanopore . Duplexes containing mismatches unzip more quickly and can be distinguished from those with perfect complementarity.

Shock, 2004 Apr, 21(4), 364 - 9
Bacterial DNA and RNA induce rat cardiac myocyte contraction depression in vitro; Paladugu B et al.; Sepsis and septic shock, the systemic immunologic and pathophysiologic response to overwhelming infection, are associated with perturbation of a variety of metabolic cell pathways and with multiple organ failure (MOF) including cardiac depression . This depression has been attributed to the effect of several circulating and locally produced proinflammatory mediators . Recent data suggest that bacterial nucleic acids can produce profound systemic inflammatory responses characterized by circulatory shock in intact animals . In this study, bacterial DNA and RNA derived from pathogenic clinical S . aureus and E . coli isolates are shown to induce early concentration-dependent depression of maximum extent and peak velocity of contraction of electrically paced neonatal rat ventricular myocytes in culture . Significant but more modest depression was generated by a nonpathogenic E . coli isolate . Pretreatment with a DNase or RNase abrogated this effect . Further, synthetic, double-stranded RNA (dsRNA) also induced concentration-dependent depression of myocyte contraction, with the effect also being prevented by pretreatment with RNase . These data suggest that bacterial DNA and RNA may contribute to myocardial depression during bacterial sepsis and septic shock.

Eur Surg Res, 2004 May-Jun, 36(3), 136 - 41
Beneficial effects of recombinant platelet-activating factor acetylhydrolase and BN 52021 on bacterial translocation in cerulein-induced pancreatitis; Bedirli A et al.; BACKGROUND: Bacterial translocation (BT) has been suggested to be responsible for the high incidence of infections occurring after acute pancreatitis (AP) . The aim of this study was to investigate the effects of the platelet-activating factor (PAF) inactivator, recombinant PAF-acetylhydrolase (rPAF-AH), and the PAF receptor antagonist, BN 52021, in AP . METHODS: Forty-eight male Wistar rats were divided into 4 groups: the sham group received saline intraperitoneally every hour for 6 h; the control group received cerulein 50 g/kg i.p . every hour for 6 h; the rPAF-AH group received AP plus rPAF-AH (5 mg/kg i.v . bolus), and the BN52021 group received AP plus BN 52021 (5 mg/kg i.v . bolus) . The animals were sacrificed 12 h after the first cerulein injection . RESULTS: Supramaximal cerulein stimulation induced an increase in serum pancreatic enzymes, interleukin (IL)-6, pancreatic edema, and produced histologic evidence of AP . Compared with the control group, the addition of PAF receptor antagonists had a significant effect on serum pancreatic enzymes, pancreatic edema, and the histologic score of the pancreatitis . AP caused significant increases in BT in mesenteric lymph nodes (MLNs), pancreas, liver, spleen and blood . Compared with the control group, both rPAF-AH and BN 52021 decreased BT in the pancreas and blood . In addition, rPAF-AH decreased BT in the MLNs . We also found that PAF receptor antagonists suppressed the elevation in IL-6 levels . CONCLUSION: PAF antagonists attenuated the severity of experimental AP and reduced pancreatitis-induced BT to distant sites .

Proc Natl Acad Sci U S A, 2004 Jun 22, 101(25), 9257 - 62 Epub 2004 Jun 03.
Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication; Viollier PH et al.; The chromosomal origin and terminus of replication are precisely localized in bacterial cells . We examined the cellular position of 112 individual loci that are dispersed over the circular Caulobacter crescentus chromosome and found that in living cells each locus has a specific subcellular address and that these loci are arrayed in linear order along the long axis of the cell . Time-lapse microscopy of the location of the chromosomal origin and 10 selected loci in the origin-proximal half of the chromosome showed that during DNA replication, as the replisome sequentially copies each locus, the newly replicated DNA segments are moved in chronological order to their final subcellular destination in the nascent half of the predivisional cell . Thus, the remarkable organization of the chromosome is being established while DNA replication is still in progress . The fact that the movement of these 10 loci is, like that of the origin, directed and rapid, and occurs at a similar rate, suggests that the same molecular machinery serves to partition and place many, if not most, chromosomal loci at defined subcellular sites.

Science, 2004 Jul 9, 305(5681), 222 - 7 Epub 2004 Jun 03.
The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure; Case RB et al.; Condensins are conserved proteins containing SMC (structural maintenance of chromosomes) moieties that organize and compact chromosomes in an unknown mechanism essential for faithful chromosome partitioning . We show that MukBEF, the condensin in Escherichia coli, cooperatively compacts a single DNA molecule into a filament with an ordered, repetitive structure in an adenosine triphosphate (ATP) binding-dependent manner . When stretched to a tension of approximately 17 piconewtons, the filament extended in a series of repetitive transitions in a broad distribution centered on 45 nanometers . A filament so extended and held at a lower force recondensed in steps of 35 nanometers or its multiples; this cycle was repeatable even in the absence of ATP and free MukBEF . Remarkably, the pattern of transitions displayed by a given filament during the initial extension was identical in every subsequent extension . Hence, after being deformed micrometers in length, each filament returned to its original compact structure without the addition of energy . Incubation with topoisomerase I increased the rate of recondensation and allowed the structure to extend and reform almost reversibly, indicating that supercoiled DNA is trapped in the condensed structure . We suggest a new model for how MukBEF organizes the bacterial chromosome in vivo.

Acta Paediatr, 2004 May, 93(5), 648 - 53
Whole blood interleukin 8 and plasma interleukin 8 levels in newborn infants with suspected bacterial infection; Franz AR et al.; AIM: To evaluate a new micro-method technique for measurement of interleukin 8 in detergent-lysed whole blood (whole blood IL-8) applicable to capillary blood sampling as a test for bacterial infections in neonates . METHODS: Whole blood IL-8 was measured at the first suspicion of infection along with IL-8 determined in plasma (plasma IL-8), C-reactive protein and blood cultures in 154 consecutive newborn infants with clinical signs of bacterial infection . Only 20 microl of whole blood were required for the new assay . RESULTS: Blood culture-proven infections were diagnosed in six infants and clinical infection (defined as a combination of clinical and laboratory signs) in 20 infants . 1000 pg/ml was determined as the suitable threshold for whole blood IL-8 by ROC-curve analysis . At that threshold, whole blood IL-8 detected blood culture-proven infections with a sensitivity of 83% and a specificity of 67% . The areas under the ROC curves were similar for whole blood IL-8 and plasma IL-8 . CONCLUSIONS: Compared with plasma IL-8, whole blood IL-8 offers the advantages that measurements of whole blood IL-8 require a smaller blood sample volume and are not altered by haemolysis . The diagnostic accuracy of whole blood IL-8 remains to be studied in more detail in the future.

Eur J Intern Med, 2004 Apr, 15(2), 89 - 92
Accuracy of chest sonography and polymorphonuclear elastase in the assessment of bacterial pleural effusion; Aleman C et al.; Background: The relationship between chest sonography findings and inflammatory markers for assessing bacterial pleural effusion is not well established . We decided to study the accuracy of chest sonography in determining the nature of bacterial pleural effusion and its relationship with polymorphonuclear elastase (PMN-E) results . Methods: Pleural sonography and PMN-E were evaluated in a prospective study of 144 consecutive patients with pleural effusion of various etiologies: 25 complicated parapneumonic, 18 uncomplicated parapneumonic, 33 tuberculous, 17 malignant, 12 transudates, and 39 of unknown etiology . The sonographer distinguished between anechoic and septated pattern . The relationship between sonographic appearance and inflammatory markers was evaluated . Results: All of the complicated parapneumonic, 11 uncomplicated parapneumonic, and 28 tuberculous effusions were septated . Septated pattern and PMN-E value were independent predictors of infectious pleural disease (p <0.05) . The simultaneous presence of a septated pattern and a PMN-E higher than 100 microg/l had a sensitivity of 79.1% and a specificity of 91.1% for the diagnosis of bacterial effusions . Conclusions: PMN-E level and the sonographic pattern of pleural fluid may be useful in the diagnosis of bacterial pleural effusions.

Ann Transplant, 2003, 8(4), 10 - 5
Immune changes in lymph nodes after skin grafting . I . Effects of bacterial antigens; Cakala M et al.; Transplantation of skin brings about response of the regional lymph nodes . Lymph node cells (B and T lymphocytes, dendritic cells, imigrating monocytes, high endothelial venous cells) respond to three types of antigens: allogeneic, bacterial and self-antigens . Allogeneic reaction is induced by contact of antigen presenting cells (APC) with donor antigens . Bacteria penetrate rejecting graft epidermis and travel along lymphatics to the nearest lymph node . Rejecting graft debris is phagocytized by macrophages and dendritic cells and transported to lymph nodes . These different type antigens induce different reaction of node cells . In this review we present data from literature and own studies on the effect of bacteria normally residing on skin surface on lymph node after penetration of epidermis . Further reviews will be dealing with the response of lymph nodes to allo- and autoantigens.

Pediatr Blood Cancer, 2004 Jul, 43(1), 85 - 7
Mondini dysplasia and recurrent bacterial meningitis in a girl with relapsing Langerhans cell histiocytosis; Kitazawa K et al.; We report a case of a girl with Langerhans cell histiocytosis (LCH) of multifocal bone disease, who developed recurrent bacterial meningitis and unilateral sensorineural hearing loss during the relapsing course of the disease . Mondini dysplasia, a congenital inner ear anomaly, was suspected by high resolution computed tomographic scan and the dysplasia with cerebrospinal fluid leakage was confirmed by surgery in the ipsilateral ear showing hearing loss . Although rare, congenital inner ear anomalies such as Mondini dysplasia should be kept in mind in pediatric patients with hearing impairment and/or recurrent bacterial meningitis during chemotherapy for various types of neoplasms including LCH .

J Mol Microbiol Biotechnol, 2004, 7(1-2), 5 - 17
Self-assembly and type III protein export of the bacterial flagellum; Minamino T et al.; The bacterial flagellum is a supramolecular structure consisting of a basal body, a hook and a filament . Most of the flagellar components are translocated across the cytoplasmic membrane by the flagellar type III protein export apparatus in the vicinity of the flagellar base, diffuse down the narrow channel through the nascent structure and self-assemble at its distal end with the help of a cap structure . Flagellar proteins synthesized in the cytoplasm are targeted to the export apparatus with the help of flagellum-specific chaperones and pushed into the channel by an ATPase, whose activity is controlled by its regulator to enable the energy of ATP hydrolysis to be efficiently coupled to the translocation reaction . The export apparatus switches its substrate specificity by monitoring the state of flagellar assembly in the cell exterior, allowing this huge and complex macromolecular assembly to be built efficiently by a highly ordered and well-regulated assembly process .

Curr Microbiol, 2004 Jun, 48(6), 424 - 7
Roles of poly(3-hydroxybutyrate) depolymerase and 3HB-oligomer hydrolase in bacterial PHB metabolism; Sugiyama A et al.; Many poly-3-hydroxybutyrate (PHB)-degrading enzymes have been studied . But biological roles of 3HB-oligomer hydrolases (3HBOHs) and how PHB depolymerases (PHBDPs) and 3HBOHs cooperate in PHB metabolism are not fully elucidated . In this study, several PHBDPs and 3HBOHs from three types of bacteria were purified, and their substrate specificity, kinetic properties, and degradation products were investigated . From the results, PHBDP and 3HBOH seemed to play a role in PHB metabolism in three types of bacteria, as follows: (A) In Ralstonia pickettii T1, an extracellular PHBDP degrades extracellular PHB to various-sized 3HB-oligomers, which an extracellular 3HBOH hydrolyzes to 3HB-monomers . (B) In Acidovorax sp . SA1, an extracellular PHBDP hydrolyzes extracellular PHB to small 3HB-oligomers (dimer and trimer), which an intracellular 3HBOH efficiently degrades to 3HB in the cell . (C) In Ralstonia eutropha H16, an intracellular 3HBOH helps in the degradation of intracellular PHB inclusions by PHBDP.

Histol Histopathol, 2004 Jul, 19(3), 907 - 14
Role of intestinal bacterial flora in oral tolerance induction; Tanaka K et al.; In healthy individuals, the immune responses against foods cannot be induced . This phenomenon is known as oral tolerance . We observed that the oral tolerance was impaired in germfree mice, and that Th2-dependent antibodies such as IgE could be thus induced by an orally given antigen . As a result, the germfree mouse was considered to be a good animal model for allergic disorder . When germfree mice were mono-associated with such bacteria as E.coli and B . infantis, then oral tolerance was restored in these gnotobiotes to a level similar to that observed in SPF mice . Thus, these bacterias seemed to be important in oral tolerance induction . In addition, the probiotics using these bacteria may be a useful material for the treatment of allergic disorders.

Anal Chem, 2004 Jun 1, 76(11), 3012 - 7
Monitoring of bacterial contamination in food samples using capillary zone electrophoresis; Palenzuela B et al.; A capillary electrophoresis method with UV detection is proposed for the identification and quantitation of bacterial contamination in food samples . The electrophoretic separation relies on the differential mobility of bacteria in the capillary . Electrophoretic resolution is improved by using calcium and myoinositol hexakisphosphate as specific ions that interact with the bacterial surface changing its electrical properties and electrophoretic mobility . The proposed method allows the effective separation of eight different types of bacteria in only 25 min . It was successfully used to detect the presence of bacteria in contaminated food . The precision of the analysis of real spiked samples ranges from 3.3 to 7.0%, and the overall analysis time is 7 h, which is much shorter than the 24-48 h typically required for plate counts . The validity of the method was established by comparison with the standard plate counting method.

Eur J Gastroenterol Hepatol, 2004 Jun, 16(6), 571 - 7
Nitric oxide in ascitic fluid is an independent predictor of the development of renal impairment in patients with cirrhosis and spontaneous bacterial peritonitis; Such J et al.; BACKGROUND/AIMS: Cirrhotic patients with spontaneous bacterial peritonitis show a marked activation of the cytokine cascade, and cytokines induce the synthesis of nitric oxide in vitro . Our aim was to assess whether patients with ascitic fluid infection show increased levels of nitric oxide, and whether this is related to the development of renal impairment . METHODS: Retrospective analysis of prospectively collected specimens from 168 patients with cirrhosis and presence of sterile or infected ascitic fluid . Routine biochemical data together with nitric oxide metabolites, tumour necrosis factor and interleukin-6 were measured . Univariate and multivariate analyses were performed to identify factors related to the development of renal impairment . RESULTS: Patients with infected ascites showed increased serum and ascitic-fluid levels of nitric oxide metabolites and cytokines compared with patients with sterile ascites . A significant direct correlation was observed between serum and ascitic fluid nitric oxide metabolite levels . Multivariate analysis identified ascitic-fluid nitric oxide metabolites as an independent predictor of renal impairment . CONCLUSIONS: The increased serum and ascitic fluid nitric oxide found in patients with infected ascites might induce a deterioration of the increased peripheral vasodilation found in this setting, leading to the development of renal impairment in a series of patients with spontaneous bacterial peritonitis.

J Biol Chem, 2004 Jul 30, 279(31), 32212 - 8 Epub 2004 May 27.
Tuning a nitrate reductase for function . The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties; Jepson BJ et al.; Bacterial cytoplasmic assimilatory nitrate reductases are the least well characterized of all of the subgroups of nitrate reductases . In the present study the ferredoxin-dependent nitrate reductase NarB of the cyanobacterium Synechococcus sp . PCC 7942 was analyzed by spectropotentiometry and protein film voltammetry . Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB . Analysis of dithionite-reduced enzyme by low temperature EPR revealed at 10 K the presence of a signal that is characteristic of a {4Fe-4S}(1+) cluster . EPR-monitored potentiometric titration of NarB revealed that this cluster titrated as an n = 1 Nernstian component with a midpoint redox potential (E(m)) of -190 mV . EPR spectra collected at 60 K revealed a Mo(V) signal termed "very high g" with g(av) = 2.0047 in air-oxidized enzyme that accounted for only 10-20% of the total molybdenum . This signal disappeared upon reduction with dithionite, and a new "high g" species (g(av) = 1.9897) was observed . In potentiometric titrations the high g Mo(V) signal developed over the potential range of -100 to -350 mV (E(m) Mo(6+/5+) = -150 mV), and when fully developed, it accounted for 1 mol of Mo(V)/mol of enzyme . Protein film voltammetry of NarB revealed that activity is turned on at potentials below -200 mV, where the cofactors are predominantly {4Fe-4S}(1+) and Mo(5+) . The data suggests that during the catalytic cycle nitrate will bind to the Mo(5+) state of NarB in which the enzyme is minimally two-electron-reduced . Comparison of the spectral properties of NarB with those of the membrane-bound and periplasmic respiratory nitrate reductases reveals that it is closely related to the periplasmic enzyme, but the potential of the molybdenum center of NarB is tuned to operate at lower potentials, consistent with the coupling of NarB to low potential ferredoxins in the cell cytoplasm.

Genetics, 2004 May, 167(1), 9 - 20
Phenotypic plasticity in bacterial plasmids; Turner PE; Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence . Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15 . One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density . I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture . Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities . The results can be explained by phenotypic plasticity in traits governing plasmid transfer . As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase . Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade . I discuss adaptive vs . nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments.

Mol Microbiol, 2004 Jun, 52(5), 1475 - 85
Characterization of the MerD protein from Ralstonia metallidurans CH34: a possible role in bacterial mercury resistance by switching off the induction of the mer operon; Champier L et al.; MerD and MerR from Tn4378 found in Ralstonia metallidurans CH34 were purified to homogeneity after overexpression in Escherichia coli . Using electrophoretic mobility shift assays and footprinting experiments, we found that MerD cannot bind to DNA . However, in vitro MerD can form a ternary complex in association with merOP and MerR . The presence of MerD in this complex was demonstrated by Western analysis with antibodies to MerD . To our knowledge, this is the first description of such a ternary complex between MerD-MerR and DNA . The formation and stability of this ternary complex are dependent on the relative concentration of the two proteins and modulated by the presence of mercury . We postulate that MerD could displace Hg-bound MerR from the mer operator to allow new synthesis of metal-free MerR able to switch off the induction of the mer genes when the external mercury is exhausted . This could fully explain how MerD can be a co-regulator repressing the induction of the mer operon.

Theor Appl Genet, 2004 Sep, 109(5), 1041 - 50 Epub 2004 May 26.
Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping; Wu CC et al.; Two plant-transformation-competent large-insert binary clone bacterial artificial chromosome (hereafter BIBAC) libraries were previously constructed for soybean cv . Forrest, using BamHI or HindIII . However, they are not well suited for clone-based genomic sequencing due to their larger ratio of vector to insert size (27.6 kbp:125 kbp) . Therefore, we developed a larger-insert bacterial artificial chromosome (BAC) library for the genotype in a smaller vector (pECBAC1), using EcoRI . The BAC library contains 38,400 clones; about 99.1% of the clones have inserts; the average insert size is 157 kbp; and the ratio of vector to insert size is much smaller (7.5 kbp:157 kbp) . Colony hybridization with probes derived from several chloroplast and mitochondrial genes showed that 0.89% and 0.45% of the clones were derived from the chloroplast and mitochondrial genomes, respectively . Considering these data, the library represents 5.4 haploid genomes of soybean . The library was hybridized with six RFLP marker probes, 5S rDNA and 18S-5.8S-25S rDNA, respectively . Each RFLP marker hybridized to about six clones, and the 5S and 18S-5.8S-25S rDNA probes collectively hybridized to 402 BACs--about 1.05% of the clones in the library . The BAC library complements the existing soybean Forrest BIBAC libraries by using different restriction enzymes and vector systems . Together, the BAC and BIBAC libraries encompass 13.2 haploid genomes, providing the most comprehensive clone resource for a single soybean genotype for public genome research . We show that the BAC library has enhanced the development of the soybean whole-genome physical map and use of three complementary BAC libraries improves genome physical mapping by fingerprint analysis of most of the clones of the library . The rDNA-containing clones were also fingerprinted to evaluate the feasibility of constructing contig maps of the rDNA regions . It was found that physical maps for the rDNA regions could not be readily constructed by fingerprint analysis, using one or two restriction enzymes . Additional data to fingerprints and/or different fingerprinting methods are needed to build contig maps for such highly tandem repetitive regions and thus, the physical map of the entire soybean genome.

Pharmacology, 2004 Jul, 71(3), 128 - 34
Effects of melatonin on impaired neurogenic and endothelial relaxations by bacterial lipopolysaccharide in the mouse corpus cavernosum; Kumcu EK et al.; We investigated whether bacterial lipopolysaccharide treatment causes any neuronal and vascular hyporeactivity in mouse cavernous tissue and also whether melatonin has any restorative effect on this possible neuronal and vascular hyporesponsiveness . Lipopolysaccharide treatment attenuated contractions in response to phenylephrine . Treatment with the inducible nitric oxide synthase inhibitor aminoguanidine or melatonin restored the hypocontractility of the cavernous smooth muscle to phenylephrine . Relaxant responses of corpus cavernosum precontracted by phenylephrine to acetylcholine or electrical field stimulation were significantly impaired in mice treated with bacterial lipopolysaccharide . Treatment with aminoguanidine or melatonin could prevent the impairment of the neuronal and endothelial relaxations . There was no significant difference between control and lipopolysaccharide-treated groups in the contractile response to high-dose KCl and in the relaxant response to papaverine . In conclusion, bacterial lipopolysaccharide treatment caused a neuronal and endothelial dysfunction in the mouse corpus cavernosum . A possible increased oxidative activity in the cavernous tissue may be a major reason for the impairment of relaxant responses and hypocontracility of tissue . The restorative effects of melatonin on this hyporeactivity may depend on its antioxidant properties and partly on its inhibitory action on the inducible nitric oxide synthase production .

Biochim Biophys Acta, 2004 Jun 1, 1699(1-2), 173 - 82
Effects of mutagenesis of residue 221 on the properties of bacterial and mitochondrial elongation factor EF-Tu; Hunter SE et al.; During protein biosynthesis, elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to the A-site of ribosomes . This factor is highly conserved throughout evolution . However, several key residues differ between bacterial and mammalian mitochondrial EF-Tu (EF-Tu(mt)) . One such residue is Ser221 (Escherichia coli numbering) . This residue is conserved as a Ser or Thr in the bacterial factors but is present as Pro269 in EF-Tu(mt) . Pro269 reorients the loop containing this residue and shifts the adjoining beta-strand in EF-Tu(mt) compared to that of E . coli EF-Tu potentially altering the binding pocket for the acceptor stem of the aa-tRNA . Pro269 was mutated to a serine residue (P269S) in EF-Tu(mt) . For comparison, the complementary mutation was created at Ser221 in E . coli EF-Tu (S221P) . The E . coli EF-Tu S221P variant is poorly expressed in E . coli and the majority of the molecules fail to fold into an active conformation . In contrast, EF-Tu(mt) P269S is expressed to a high level in E . coli . When corrected for the percentage of active molecules, both variants function as effectively as their respective wild-type factors in ternary complex formation using E . coli Phe-tRNA(Phe) and Cys-tRNA(Cys) . They are also active in A-site binding and in vitro translation assays with E . coli Phe-tRNA(Phe) . In addition, both variants are as active as their respective wild-type factors in ternary complex formation, A-site binding and in vitro translation assays using mitochondrial Phe-tRNA(Phe).

Lancet, 2004 May 22, 363(9422), 1689 - 97
Role of toll-like receptor 4 in protection by bacterial lipopolysaccharide in the nasal mucosa of atopic children but not adults; Tulic MK et al.; BACKGROUND: Exposure to bacterial products in early life could protect against development of atopy . We examined the effect of bacterial lipopolysaccharide on allergic inflammation and expression of cytokines and lipopolysaccharide receptor (toll-like receptor 4 TLR4) in nasal mucosa of 15 atopic children and ten atopic adults . METHODS: Explanted mucosa was cultured with allergen with or without lipopolysaccharide (0.1 mg/L) for 24 h . Immunocytochemistry and in-situ hybridisation were used to phenotype the cells and cytokines . FINDINGS: In explants from atopic children, lipopolysaccharide prevented allergen-induced T-helper type 2 (Th2) inflammation and upregulated Th1 cytokine reactivity and expression . These effects were blocked by antibody to interleukin 10 . In children but not in adults, lipopolysaccharide caused increases of three times in T-cell reactivity, five times in T-cell proliferation, and four times in expression of interleukin 10 compared with mucosa stimulated with allergen alone . This difference in response was mirrored by lipopolysaccharide-induced increases in TLR4 reactivity in children but not adults . TLR4 receptor was expressed by CD3-positive T cells, and TLR4-positive cells contained interleukin 10 . Lipopolysaccharide increased expression of cells positive for both CD3 and TLR4; both TLR4 and interleukin 10; and both CD4 and CD25 . INTERPRETATION: Lipopolysaccharide inhibits allergic inflammation in nasal mucosa of atopic children by skewing local immune responses from Th2 to Th1 and upregulating production of interleukin 10 . These effects are mediated by TLR4 . Our results emphasise an important difference between adults and children in their ability to respond to bacterial products . These differences could have a role in normal maturation of the immune system.

Ann Plast Surg, 2004 Mar, 52(3), 276 - 9; discussion 279-80
Quantifying bacterial bioburden during negative pressure wound therapy: does the wound VAC enhance bacterial clearance?
Weed T, Ratliff C, Drake DB.
The bacterial colonization of a wound is a recognized detrimental factor in the multifactorial process of wound healing . The harmful effects on wound healing are recognized to correspond to a level of > 10(5) colonies of bacteria per gram of tissue . Negative pressure wound therapy has become an accepted treatment modality for acute and chronic wounds with accelerated healing rates observed . It has been previously reported that this therapy enhances bacterial clearance, which may account for the wound healing effects noted . We retrospectively reviewed 25 patients' charts undergoing Wound VAC (Vacuum Assisted Closure Device; KCI International, San Antonio, TX) therapy with serial quantitative cultures and found that there is not a consistent effect of bacterial clearance with the Wound VAC . Furthermore, bacterial colonization increased significantly with Wound VAC therapy and remained in a range of 10(4)-10(6) . Despite this finding, the beneficial effects of this treatment modality on wound healing were noted in most cases.

BMC Gastroenterol . 2004 May 22;4(1):10.
Partially responsive celiac disease resulting from small intestinal bacterial overgrowth and lactose intolerance; Ghoshal UC et al.; BACKGROUND: Celiac disease is a common cause of chronic diarrhea and malabsorption syndrome all over the world . Though it was considered uncommon in India in past, it is being described frequently recently . Some patients with celiac disease do not improve despite gluten free diet (GFD) . A study described 15 cases of celiac disease unresponsive to GFD in whom small intestinal bacterial overgrowth (SIBO) or lactose intolerance was the cause for unresponsiveness . CASE PRESENTATION: During a three-year period, 12 adult patients with celiac disease were seen in the Luminal Gastroenterology Clinic in a tertiary referral center in northern India . Two of these 12 patients (16.6%), who did not fully respond to GFD initially, are presented here . Unresponsiveness resulted from SIBO in one and lactose intolerance in the other . The former patient responded to antibiotics and the latter to lactose withdrawal in addition to standard GFD . CONCLUSION: In patients with celiac disease partially responsive or unresponsive to GFD, SIBO and lactose intolerance should be suspected; appropriate investigations and treatment for these may result in complete recovery.

Biotechnol Appl Biochem, 2004 Jun, 39(Pt 3), 293 - 301
Uniformly oriented bacterial F0F1-ATPase immobilized on a semi-permeable membrane: a step towards biotechnological energy transduction; Bhattacharya S et al.; The immobilization of F(0)F(1)-ATPase in uniform orientation is reported . The biotinylated and histidine-tagged subunits of the bacterial F(0)F(1)-ATPase complex were used for immobilization of the complex on artificial semi-permeable membranes resulting in 88+/-7.8 and 72+/-5.2% coupling of the enzymes . The immobilized enzymes retained over 90% activity . The immobilized ATPase/synthase was used for generation of ATP from ADP and P(i) at the expense of electrochemical potential energy . The re-usability, ratio of amount of enzyme immobilized to enzymic activity conferred on the membranes, ATP synthesized by assembled system and suitability of ATP generated for use in coupled enzymic reactions were determined.

Cell Cycle, 2004 Jun, 3(6), 752 - 5 Epub 2004 Jun 14.
Regulation of mammalian cell growth and death by bacterial redox proteins: relevance to ecology and cancer therapy; Yamada T et al.; Recent evidence indicates that bacterial redox proteins such as cupredoxins and cytochromes, that are normally involved in electron transfer during respiration, can enter mammalian cells and induce either apoptosis or inhibition of cell cycle progression . Such proteins have also been shown to demonstrate a good deal of specificity for entry and induction of cytotoxic effects in cancer cells, allowing both in vitro cell death and in vivo inhibition of cancer progression . An alteration in the hydrophobicity of the bacterial redox proteins can lead to a switch from apoptosis to growth arrest and vice versa through modulation of the intracellular levels of tumor suppressors . The preferential entry and cytotoxicity of these redox proteins in cancer cells raises interesting questions about the presence of other bacterial proteins that may affect cell cycle at the G(2)/M phase, thereby potentially arresting cancer growth . The intracellular localization of the bacterial redox proteins in nonpathogenic soil bacteria similarly raises questions about their possible role in allowing various nonpathogenic soil bacteria to defend themselves from environmental predators by inducing cytotoxicity when engulfed in large numbers . A new role of the redox proteins in soil bacteria in maintaining an ecological balance among the predators and preys is proposed.

J Mol Microbiol Biotechnol, 2003, 6(3-4), 191 - 205
Bioinformatic analyses of the bacterial L-ascorbate phosphotransferase system permease family; Hvorup R et al.; The tripartite L-ascorbate permease of Escherichia coli is the first functionally characterized member of a large family of enzyme II complexes (SgaTBA, encoding enzymes IIC, IIB and IIA) of the bacterial phosphotransferase system (PTS) . We here report bioinformatic analyses of these proteins . Forty-five homologous systems from a wide variety of bacteria were identified, but no homologues were found in archaea or eukaryotes . These systems fell into five structural types: (1) IIC, IIB and IIA are encoded by distinct genes; (2) IIC and IIB are encoded by distinct genes, but the IIA-encoding gene is absent; (3) IIC and IIB are encoded by a fused gene, but IIA is a distinct gene product; (4) IIA and IIB are fused, but IIC is encoded by a distinct gene, and (5) IIC and IIB are encoded by distinct genes, but IIA is fused to a transcriptional regulator . Phylogenetic analyses revealed that gene fusion/splicing events have occurred repeatedly during the evolutionary divergence of family members, although no evidence for shuffling of constituents between systems was obtained . The SgaTBA family proved to be distantly related to the GatCBA family of PTS permeases, and this family was also analyzed . In contrast to the SgaTBA family, no gene splicing/fusion has occurred during the evolutionary divergence of GatCBA family members as each domain is always encoded by a distinct gene . However, GatC homologues were identified in organisms that lack other PTS proteins, suggesting a transport mechanism not coupled to substrate phosphorylation . Topological analyses suggest that in contrast to all other PTS permeases, IIC proteins of the Sga and Gat families exhibit 12 transmembrane alpha-helical segments and are distantly related to secondary carriers . Like many secondary carriers, GatC (IIC) homologues could be shown to have arisen by an ancient intragenic duplication event . These results suggest that the Sga and Gat families of PTS permeases comprise a small superfamily in which the transmembrane IIC domains evolved independently of all other known PTS permeases .

J Immunol, 2004 Jun 1, 172(11), 6858 - 65
Bacterial ghosts are an efficient delivery system for DNA vaccines; Ebensen T et al.; Mass implementation of DNA vaccines is hindered by the requirement of high plasmid dosages and poor immunogenicity . We evaluated the capacity of Mannheimia haemolytica ghosts as delivery system for DNA vaccines . In vitro studies showed that bacterial ghosts loaded with a plasmid carrying the green fluorescent protein-encoding gene (pEGFP-N1) are efficiently taken up by APC, thereby leading to high transfection rates (52-60%) . Vaccination studies demonstrated that ghost-mediated delivery by intradermal or i.m . route of a eukaryotic expression plasmid containing the gene coding for beta-galactosidase under the control of the CMV immediate early gene promoter (pCMVbeta) stimulates more efficient Ag-specific humoral and cellular (CD4(+) and CD8(+)) immune responses than naked DNA in BALB/c mice . The use of ghosts also allows modulating the major Th response from a mixed Th1/Th2 to a more dominant Th2 pattern . Intravenous immunization with dendritic cells loaded ex vivo with pCMVbeta-containing ghosts also resulted in the elicitation of beta-galactosidase-specific responses . This suggests that dendritic cells play an important role in the stimulation of immune responses when bacterial ghosts are used as a DNA delivery system . Bacterial ghosts not only target the DNA vaccine construct to APC, but also provide a strong danger signal, acting as natural adjuvants, thereby promoting efficient maturation and activation of dendritic cells . Thus, bacterial ghosts constitute a promising technology platform for the development of more efficient DNA vaccines.

Eur J Biochem, 2004 Jun, 271(11), 2093 - 100
Bacterial IscU is a well folded and functional single domain protein; Adinolfi S et al.; Iron-sulfur clusters are widely represented in most organisms, but the mechanism of their formation is not fully understood . Of the two main proteins involved in cluster formation, NifS/IscS and NifU/IscU, only the former has been well studied from a structural point of view . Here we report an extensive structural characterization of Escherichia coli IscU . We show by a variety of physico-chemical techniques that E . coli IscU construct can be expressed to high purity as a monomeric protein, characterized by an alphabeta fold with high alpha-helix content . The high melting temperature and the reversibility of the thermal unfolding curve (as measured by CD spectroscopy) hint at a well ordered stable fold . The excellent dispersion of cross peaks in the (1)H-(15)N correlation spectrum is consistent with these observations . Monomeric E . coli IscU is able to provide a scaffold for Iron-sulfur cluster assembly, but has no direct interaction with either Fe(II) or Fe(III) ions, suggesting the need of further partners to achieve a stable interaction.

J Bacteriol, 2004 Jun, 186(11), 3525 - 30
Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores; Frenkiel-Krispin D et al.; Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults . A family of highly conserved spore-specific DNA-binding proteins, termed alpha/beta-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance . The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex . By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the alpha/beta-type SASP family . The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch . The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices . By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the alpha/beta-type SASP.

Proc Natl Acad Sci U S A, 2004 May 25, 101(21), 7919 - 24 Epub 2004 May 17.
A new activity for an old enzyme: Escherichia coli bacterial alkaline phosphatase is a phosphite-dependent hydrogenase; Yang K et al.; Genetic analysis indicates that Escherichia coli possesses two independent pathways for oxidation of phosphite (Pt) to phosphate . One pathway depends on the 14-gene phn operon, which encodes the enzyme C-P lyase . The other pathway depends on the phoA locus, which encodes bacterial alkaline phosphatase (BAP) . Transposon mutagenesis studies strongly suggest that BAP is the only enzyme involved in the phoA-dependent pathway . This conclusion is supported by purification and biochemical characterization of the Pt-oxidizing enzyme, which was proven to be BAP by N terminus protein sequencing . Highly purified BAP catalyzed Pt oxidation with specific activities of 62-242 milliunits/mg and phosphate ester hydrolysis with specific activities of 41-61 units/mg . Surprisingly, BAP catalyzes the oxidation of Pt to phosphate and molecular H2 . Thus, BAP is a unique Pt-dependent, H2-evolving hydrogenase . This reaction is unprecedented in both P and H biochemistry, and it is likely to involve direct transfer of hydride from the substrate to water-derived protons.

Klin Mikrobiol Infekc Lek, 2004 Apr, 10(2), 68 - 72
{Chronic obstructive pulmonary disease--acute bacterial exacerbations}; Kasak V; COPD (Chronic obstructive pulmonary disease) belongs to leading causes of morbidity and mortality worldwide and results in substantial and everincreasing medical, social and economic burden . The same applies to the Czech Republic as well . To combat the disease the Global Initiative for Obstructive Lung Disease (GOLD) has been founded in collaboration with the World Health Organization (WHO) . GOLD guideline was published in April 2001 and its Czech version appeared in November 2001 . The prevention and management of acute exacerbations of COPD forms one of the basic chapters of the document . A COPD exacerbation is defined as sustained worsening of the patient's condition compared to the stable state and beyond normal day-to-day variations that is acute in onset and may warrant additional treatment in a patient with known COPD . COPD exacerbations can be triggered by both an acute infection (viral or bacterial) and noninfectious cause (air pollution events, cold weather, interruption of regular treatment) . Accurate diagnosis and assessment of the severity of COPD exacrbation, adequate therapy including rational application of antibiotics, accurate indication for hospitalization and timely admission to an intensive care unit decrease the COPD -associated mortality.

Anal Chem, 2004 May 15, 76(10), 2902 - 9
Living bacterial cell array for genotoxin monitoring; Kuang Y et al.; A biosensor composed of a high-density living bacterial cell array was fabricated by inserting bacteria into a microwell array formed on one end of an imaging fiber bundle . The size of each microwell allows only one cell to occupy each well . In this biosensor, E . coli cells carrying a recA::gfp fusion were used as sensing components for genotoxin detection . Each fiber in the array has its own light pathway, enabling thousands of individual cell responses to be monitored simultaneously with both spatial and temporal resolution . The biosensor was capable of performing cell-based functional sensing of a genotoxin with high sensitivity and short incubation times (1 ng/mL mitomycin C after 90 min) . Dose-response curves for several genotoxins were obtained . The biosensors demonstrated an active sensing lifetime of more than 6 h and a shelf lifetime of two weeks.

Protist, 2004 Mar, 155(1), 105 - 15
Diverse eukaryotes have retained mitochondrial homologues of the bacterial division protein FtsZ; Kiefel BR et al.; Mitochondrial fission requires the division of both the inner and outer mitochondrial membranes . Dynamin-related proteins operate in division of the outer membrane of probably all mitochondria, and also that of chloroplasts--organelles that have a bacterial origin like mitochondria . How the inner mitochondrial membrane divides is less well established . Homologues of the major bacterial division protein, FtsZ, are known to reside inside mitochondria of the chromophyte alga Mallomonas, a red alga, and the slime mould Dictyostelium discoideum, where these proteins are likely to act in division of the organelle . Mitochondrial FtsZ is, however, absent from the genomes of higher eukaryotes (animals, fungi, and plants), even though FtsZs are known to be essential for the division of probably all chloroplasts . To begin to understand why higher eukaryotes have lost mitochondrial FtsZ, we have sampled various diverse protists to determine which groups have retained the gene . Database searches and degenerate PCR uncovered genes for likely mitochondrial FtsZs from the glaucocystophyte Cyanophora paradoxa, the oomycete Phytophthora infestans, two haptophyte algae, and two diatoms--one being Thalassiosira pseudonana, the draft genome of which is now available . From Thalassiosira we also identified two chloroplast FtsZs, one of which appears to be undergoing a C-terminal shortening that may be common to many organellar FtsZs . Our data indicate that many protists still employ the FtsZ-based ancestral mitochondrial division mechanism, and that mitochondrial FtsZ has been lost numerous times in the evolution of eukaryotes.

Water Res, 2004 May, 38(9), 2432 - 8
Changes in phosphorus removing performance and bacterial community structure in an enhanced biological phosphorus removal reactor; Okunuki S et al.; A lab-scale-enhanced biological phosphorus removal (EBPR) reactor was operated for 204 days to investigate the correlation between phosphorus removing performance and bacterial community structure . The phosphorus removing performance was good from day 1 to 92 and from day 172 to 204 . However, the removal activity was in a deteriorated state from day 93 to 171 . From day 69 (2 weeks before the beginning of the deterioration) to 118 (2 weeks after the beginning of the deterioration), sludge P content decreased . The amounts of ubiquinone-8 and menaquinone-8 (H(4)) decreased during this period while the amount of ubiquinone-10 increased . The comparison of these changes and the general attribution of each quinone to the bacterial phylogenetic groups suggested that beta proteobacteria and Actinobacteria contributed to EBPR positively, and that alpha proteobacteria were related to this EBPR deterioration . Glycogen accumulating organisms (GAOs) are considered to detrimentally affect EBPR ability by outcompeting the phosphorus accumulating organisms by using aerobically synthesized glycogen as the energy source to assimilate organic substrates anaerobically to form polyhydroxyalkanoates . However, in this research, there was nearly no substrate uptake during the anaerobic period at the middle of the deteriorated performance period . This suggests that the deterioration observed in this research does not agree with the GAOs inhibition model . In this research, the excess P release at the anaerobic period was concluded to cause the deterioration.

Environ Microbiol, 2004 Jun, 6(6), 552 - 67
Bacterial signal transduction network in a genomic perspective; Galperin MY; Bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters . The complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies . Comparative studies revealed certain general trends in the organization of diverse signalling systems . These include (i) modular structure of signalling proteins; (ii) common organization of signalling components with the flow of information from N-terminal sensory domains to the C-terminal transmitter or signal output domains (N-to-C flow); (iii) use of common conserved sensory domains by different membrane receptors; (iv) ability of some organisms to respond to one environmental signal by activating several regulatory circuits; (v) abundance of intracellular signalling proteins, typically consisting of a PAS or GAF sensor domains and various output domains; (vi) importance of secondary messengers, cAMP and cyclic diguanylate; and (vii) crosstalk between components of different signalling pathways . Experimental characterization of the novel domains and domain combinations would be needed for achieving a better understanding of the mechanisms of signalling response and the intracellular hierarchy of different signalling pathways.

J Fish Dis, 2004 May, 27(5), 267 - 76
Effects of the wood extractive betulinol and 17beta-oestradiol on reproduction in zebrafish, Danio rerio (Hamilton)--complications due to a bacterial infection; Christianson-Heiska I et al.; Zebrafish were exposed to the wood extractive betulinol (5 microg L(-1)) and to 17beta-oestradiol (E2, 0.27 microg L(-1)) for 8 weeks in an attempt to study the possible endocrine-disrupting activity of betulinol . Females exposed to betulinol showed increased spawning intensity, while males exposed to betulinol and E2 had increased incidences of structural alterations in the testes . However, histological examination of the fish revealed that they were infected by acid-fast bacteria suspected to be Mycobacterium sp . despite a careful examination of their health state prior to the onset of the experiment . Fish exposed to betulinol and E2 showed more serious consequences of the bacterial infection than control fish indicating that the test chemicals had weakened the immune defence of the fish . When the exposure was repeated with healthy fish, an increase in the proportion of spermatogonia was seen in the testes of betulinol-treated males . A similar alteration, although not statistically significant, was also seen in the first experiment . However, no increase in the incidences of structural alterations in the testes was seen in betulinol- and E2-treated fish in the second experiment . Our study indicates that betulinol might have an endocrine-disrupting effect in zebrafish, but the increase in incidences of structural alterations in the testes might have been caused by a synergistic action between the test compounds and the bacterial infection . Our study stresses the importance of carefully checking the health of experimental fish, not only prior to the onset of an experiment but also upon termination of the experiment, in order to avoid misinterpretation of the results.

Hum Pathol, 2004 May, 35(5), 536 - 45
Histologic correlates of viral and bacterial infection of the placenta associated with severe morbidity and mortality in the newborn; Satosar A et al.; The purpose of this study was to correlate the histologic features of the placenta with the in situ detection of viral or bacterial nucleic acids in cases of severe morbidity and mortality in the neonatal period . The criteria for the cases were either fetal or neonatal death (11 cases with autopsy material available in 8 cases) or idiopathic severe respiratory distress or central nervous system-related symptoms at birth (49 cases) . Controls included 11 placentas from births with no morbidity and 6 placentas that were associated with severe neonatal morbidity of known etiology (trisomy, ruptured uterus, prolapsed cord) . The 77 placental tissues were analyzed with a consensus bacterial probe and for a wide variety of viral infections . An infectious cause was found in 46/60 (76%) of cases; these were distributed as follows: enterovirus, 23 cases (22 were coxsackie virus); bacterial (consensus probe), 15 cases; cytomegalovirus (CMV), 4 cases; herpes simplex virus (HSV), 2 cases; parvovirus, 2 cases . The infectious agents localized primarily to Hofbauer cells and trophoblasts . In each of the 8 cases for which autopsy material was available, the same infectious agent that was detected in the placenta was also detected in the autopsy material (spleen, heart, central nervous system, or lungs) . No infectious agent was detected in any of the 17 controls . Viral inclusions (only evident for DNA viruses) and stem vessel vasculitis were the 2 histologic findings that were associated with infectious disease in the placenta (P = 0.025) . These data show that infection of the villi is highly associated with neonatal morbidity and mortality and that the histologic findings are, in most cases, nonspecific for infection.

Gut, 2004 Jun, 53(6), 860 - 4
Bacterial DNA activates cell mediated immune response and nitric oxide overproduction in peritoneal macrophages from patients with cirrhosis and ascites; Frances R et al.; BACKGROUND AND AIMS: Translocation of intestinal bacteria to ascitic fluid is probably the first step in the development of episodes of spontaneous bacterial peritonitis in patients with cirrhosis . We have recently reported the detection of bacterial DNA in blood and ascitic fluid from patients with advanced cirrhosis, what we consider as molecular evidence of bacterial translocation . Several studies have shown the immunogenic role of bacterial DNA in vitro, and we hypothesised that the presence of bacterial DNA could activate the type I immune response in peritoneal macrophages from these patients, leading to greater cytokine synthesis (interleukin (IL)-2 and IL-12, tumour necrosis factor alpha, and interferon gamma) and effector molecules such as nitric oxide . METHODS: Peritoneal macrophages obtained from patients with cirrhosis and culture negative non-neutrocytic ascitic fluid were collected and characterised by flow cytometry . Inducible nitric oxide synthase, nitric oxide levels, and cytokine production were measured by immunoenzymometric assays in basal and harvested conditions according to the presence/absence of bacterial DNA . RESULTS: The ability of peritoneal macrophages to synthesise nitric oxide and levels of all cytokines were significantly increased in patients with bacterial DNA . There was a positive correlation between inducible nitric oxide synthase and nitric oxide levels . CONCLUSIONS: The presence of bacterial DNA in patients with decompensated cirrhosis is associated with marked activation of peritoneal macrophages, as evidenced by nitric oxide synthesising ability, together with enhanced cytokine production.

Gut, 2004 Jun, 53(6), 782 - 4
Early events in spontaneous bacterial peritonitis; Runyon BA; Insight into the very early events in the pathogenesis of spontaneous bacterial peritonitis.

J Agric Food Chem, 2004 May 19, 52(10), 3115 - 9
Method for bacterial expression and purification of sesame cystatin via artificial oil bodies; Peng CC et al.; A method was developed for production of sesame cystatin, a thermostable cysteine protease inhibitor . Sesame cystatin was first expressed in Escherichia coli as an insoluble recombinant protein fused to oleosin, a unique structural protein of seed oil bodies, by a short hydrophilic linker peptide . Stable artificial oil bodies were constituted with triacylglycerol, phospholipid, and the insoluble oleosin-cystatin fusion protein . After centrifugation, the oleosin-cystatin fusion protein was exclusively found in the artificial oil bodies . Proteolytic cleavage with papain, a cysteine protease effectively inhibited by cystatin, separated soluble cystatin from oleosin that was firmly embedded in the artificial oil bodies . After recentrifugation, papain that coexisted with cystatin in the collected supernatant was denatured by incubating at 55 degrees C for 30 min . The insoluble denatured papain was removed by one more centrifugation, and the expressed cystatin of high yield and purity was harvested simply by concentrating the ultimate supernatant . Comparable inhibitory activity toward papain was observed between the expressed cystatin and the native one purified from sesame seeds . This method is presumably applicable to production of other protease inhibitors whose target proteases are economically available.

Probl Tuberk Bolezn Legk, 2004, (2), 33 - 5
{Non-bacterial recurrent respiratory tuberculosis}; Il'ina TIa et al.; The diagnostic and clinical features of recurrent respiratory tuberculosis with negative sputum tests and the efficiency of its therapy were studied in 98 patients . Such recurrences were found to form 30% of all the recurrences . They were more frequently detected by referral rates . Due to difficulties in X-ray diagnosis, the activity of a process should be previously evaluated in patients before their registration . The timely detection of a relapse requires a longer (3-4 years) post-treatment follow-up in a group of cured tuberculosis . The proportion of late relapses was twice higher than that of early relapses occurring after the treatment recommended by the WHO . The vast majority of patients were found to factors, mainly social, that increase the risk of (recurrent) tuberculosis . Patients with alcoholism require compulsory treatment . The efficiency of therapy for abacillary relapses was less than that of therapy for the same processes in first detected patients.

J Biol Chem, 2004 Jul 16, 279(29), 30781 - 90 Epub 2004 May 10.
Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor; Paetzel M et al.; We report here the crystallographic and biophysical analysis of a soluble, catalytically active fragment of the Escherichia coli type I signal peptidase (SPase Delta2-75) in complex with arylomycin A2 . The 2.5-A resolution structure revealed that the inhibitor is positioned with its COOH-terminal carboxylate oxygen (O45) within hydrogen bonding distance of all the functional groups in the catalytic center of the enzyme (Ser90 O-gamma, Lys145 N-zeta, and Ser88 O-gamma) and that it makes beta-sheet type interactions with the beta-strands that line each side of the binding site . Ligand binding studies, calorimetry, fluorescence spectroscopy, and stopped-flow kinetics were also used to analyze the binding mode of this unique non-covalently bound inhibitor . The crystal structure was solved in the space group P4(3)2(1)2 . A detailed comparison is made to the previously published acyl-enzyme inhibitor complex structure (space group: P2(1)2(1)2) and the apo-enzyme structure (space group: P4(1)2(1)2) . Together this work provides insights into the binding of pre-protein substrates to signal peptidase and will prove helpful in the development of novel antibiotics.

Brain Res Mol Brain Res, 2004 May 19, 124(2), 159 - 64
Bacterial DNA induced iNOS expression through MyD88-p38 MAP kinase in mouse primary cultured glial cells; Hosoi T et al.; To study the role of bacterial DNA in the immune function of the brain, we examined the effect of CpG-DNA on the inducible nitric oxide synthase (iNOS) expression in mouse primary cultured glial cells . The expression of Toll-like receptor 9 (TLR9), the receptor of bacterial DNA, was detected by RT-PCR . We observed an increase in iNOS mRNA 6 h after CpG-DNA application . The expression of iNOS protein peaked at 12 h and declined thereafter . CpG-DNA increased p38 mitogen-activated protein kinase (MAPK) activation in primary cultured glial cells . SB203580, a specific inhibitor of p38 MAP kinase, inhibited the CpG-DNA-induced iNOS expression . Moreover, CpG-DNA failed to activate p38 MAP kinase and iNOS induction in the primary cultured glial cells prepared from myeloid differentiation factor 88 (MyD88) deficient mice . Therefore, it is suggested that functional receptor for bacterial DNA exists in primary cultured glial cells and CpG-DNA induces iNOS expression via the MyD88-p38 MAP kinase-dependent mechanisms . Thus, the present results point to the important role of bacterial DNA by acting on glial cells to operate brain immune function.

Microb Cell Fact . 2004 May 7;3(1):4.
Protein quality control in the bacterial periplasm; Miot M et al.; The proper functioning of extracytoplasmic proteins requires their export to, and productive folding in, the correct cellular compartment . All proteins in Escherichia coli are initially synthesized in the cytoplasm, then follow a pathway that depends upon their ultimate cellular destination . Many proteins destined for the periplasm are synthesized as precursors carrying an N-terminal signal sequence that directs them to the general secretion machinery at the inner membrane . After translocation and signal sequence cleavage, the newly exported mature proteins are folded and assembled in the periplasm . Maintaining quality control over these processes depends on chaperones, folding catalysts, and proteases . This article summarizes the general principles which control protein folding in the bacterial periplasm by focusing on the periplasmic maltose-binding protein.

J Clin Microbiol, 2004 May, 42(5), 2264 - 7
Presence of bacterial phage-like DNA sequences in commercial Taq DNA polymerase reagents; Newsome T et al.; Many studies have reported the presence of bacterial DNA contamination in commercial Taq DNA polymerase reagents . This is the first report of the presence of phage-like DNA sequences in certain commercial Taq DNA polymerase reagents . Precautions are needed when using amplification reagents with exogenous DNAs.

J Biotechnol, 2004 Mar 4, 108(2), 153 - 9
Rapid and sensitive detection of 17beta-estradiol in environmental water using automated immunoassay system with bacterial magnetic particles; Tanaka T et al.; A fully automated immunoassay of 17beta-estradiol (E2) was performed using anti-E2 monoclonal antibody immobilized on bacterial magnetic particles (AntiE2-BMPs) and alkaline phosphatase-conjugated E2 (ALP-E2) . E2 concentration in environmental water samples was evaluated by decrease in luminescence based on competitive reaction . A linear correlation between the luminescence intensity and E2 concentration was obtained between 0.5 and 5 ppb . The minimum detectable concentration of E2 was 20 ppt . All measurement steps were done within 0.5 h . The analysis of environmental water samples by a commercially available ELISA kit and the BMP-based immunoassay gave good correlation plots with a correlation efficient of 0.992 . These results suggest that the fully automated system using the BMP-based immunoassay has some advantages in the high rapidity and sensitivity of the measurement . This system will enable us to determine low E2 concentrations without sample condensation.

Biofizika, 2004 Mar-Apr, 49(2), 199 - 211
{Mechanism of charge separation and their stabilization in bacterial reaction centers}; Iakovlev AG et al.; The nuclear wavepacket formed by 20-fs excitation on the P* potential energy surface in native and mutant (YM210W and YM210L) reaction centers of Rhodobacter (Rb.) sphaeroides and Chloroflexus (C.) aurantiacus RCs was found to be reversibly transferred to the P+BA- surface at 120, 380, and 640-fs delays (monitored by measurements of BA- absorption at 1020-1028 nm) . The reaction centers of YM210W(L) mutant show the most simple pattern of fs oscillations with a period of 230 fs in stimulated emission from P* and in the product P+BA- . The mechanisms of the electron transfer pathway between P* and BA and of the stabilization of the state P+BA- in bacterial reaction centers are discussed.

Nature, 2004 May 6, 429(6987), 92 - 6
Integrating high-throughput and computational data elucidates bacterial networks; Covert MW et al.; The flood of high-throughput biological data has led to the expectation that computational (or in silico) models can be used to direct biological discovery, enabling biologists to reconcile heterogeneous data types, find inconsistencies and systematically generate hypotheses . Such a process is fundamentally iterative, where each iteration involves making model predictions, obtaining experimental data, reconciling the predicted outcomes with experimental ones, and using discrepancies to update the in silico model . Here we have reconstructed, on the basis of information derived from literature and databases, the first integrated genome-scale computational model of a transcriptional regulatory and metabolic network . The model accounts for 1,010 genes in Escherichia coli, including 104 regulatory genes whose products together with other stimuli regulate the expression of 479 of the 906 genes in the reconstructed metabolic network . This model is able not only to predict the outcomes of high-throughput growth phenotyping and gene expression experiments, but also to indicate knowledge gaps and identify previously unknown components and interactions in the regulatory and metabolic networks . We find that a systems biology approach that combines genome-scale experimentation and computation can systematically generate hypotheses on the basis of disparate data sources.

Nature, 2004 May 6, 429(6987), 79 - 82
Nitration of a peptide phytotoxin by bacterial nitric oxide synthase; Kers JA et al.; Nitric oxide (NO) is a potent intercellular signal in mammals that mediates key aspects of blood pressure, hormone release, nerve transmission and the immune response of higher organisms . Proteins homologous to full-length mammalian nitric oxide synthases (NOSs) are found in lower multicellular organisms . Recently, genome sequencing has shown that some bacteria contain genes coding for truncated NOS proteins; this is consistent with reports of NOS-like activities in bacterial extracts . Biological functions for bacterial NOSs are unknown, but have been presumed to be analogous to their role in mammals . Here we describe a gene in the plant pathogen Streptomyces turgidiscabies that encodes a NOS homologue, and we reveal its role in nitrating a dipeptide phytotoxin required for plant pathogenicity . High similarity between bacterial NOSs indicates a general function in biosynthetic nitration; thus, bacterial NOSs constitute a new class of enzymes . Here we show that the primary function of Streptomyces NOS is radically different from that of mammalian NOS . Surprisingly, mammalian NO signalling and bacterial biosynthetic nitration share an evolutionary origin.

Otol Neurotol, 2004 May, 25(3), 302 - 7
Evidence of subtle auditory deficit in a group of patients recovered from bacterial meningitis; Mulheran M et al.; OBJECTIVES: Sensorineural hearing loss of greater than 30 dB hearing loss occurs in up to 30% of patients after acute bacterial meningitis . This study investigated whether postbacterial meningitic patients with no apparent clinical sensorineural hearing loss had any evidence of more subtle subclinical cochlear deficit . DESIGN: Prospective case-controlled clinical trial . SETTING: Departments of Otolaryngology in Leicester and Nottingham, England, UK . PATIENTS: Fifty-eight controls and 20 postbacterial meningitic patients aged between 18 and 38 years were screened by a questionnaire and tympanometry to exclude hearing loss attributable to other causes . All participants fell below the 90th percentile pure-tone audiometry threshold of the Lutman and Davis UK data sets . MAIN OUTCOME MEASURES: In both ears, standard (0.25-8 kHz) pure-tone audiometry, high-frequency pure-tone audiometry (10-16 kHz), and distortion product otoacoustic emissions at 2, 4, and 6 kHz were measured . RESULTS: Mean thresholds over the range of standard pure-tone audiometry (analyzed independently) for the postbacterial meningitic patients were significantly elevated at most frequencies (p < 0.05-p < 0.001) between 4 and 7 dB in both ears above control group values . There was no evidence of significant high-frequency threshold elevation (10-16 kHz) . The mean iso-distortion product values at 2, 4, and 6 kHz were elevated in both ears in the meningitis group; significantly so (p < 0.05-p < 0.01) at all three frequencies in the right ear and at 4 kHz in the left . CONCLUSIONS: Postbacterial meningitic patients with hearing below the 90th percentile range had a slight but significant subclinical threshold elevation over the standard pure-tone audiometry . This may reflect a real effect of the infection at the level of the cochlea, or it may be attributable to a mild residual cognitive defect . The moderate increases in iso-distortion product values are more likely to be real and reflect an effect on outer hair cell function in response to lower stimulus intensities.

J Immunol, 2004 May 15, 172(10), 6345 - 53
Intracellular bacterial infection-induced IFN-gamma is critically but not solely dependent on Toll-like receptor 4-myeloid differentiation factor 88-IFN-alpha beta-STAT1 signaling; Rothfuchs AG et al.; Infection of murine bone marrow-derived macrophages (BMMphi) with Chlamydia pneumoniae induces IFN-alphabeta-dependent IFN-gamma secretion that leads to control of the intracellular bacterial growth . Enhanced growth of C . pneumoniae in Toll-like receptor (TLR) 4(-/-) and myeloid differentiation factor (MyD) 88(-/-) (but not TLR2(-/-), TLR6(-/-), or TLR9(-/-)) BMMphi is shown in this study . Reduced accumulation of IFN-alpha and IFN-gamma mRNA was also observed in TLR4(-/-)- and MyD88(-/-)-infected cells . IL-1R and IL-18R signaling did not account for differences between MyD88(-/-) and wild-type BMMphi . Surprisingly, infection-induced NF-kappaB activation as well as TNF-alpha, IL-1, or IL-6 mRNA expression were all normal in TLR4(-/-) and MyD88(-/-) cells . Phosphorylation of the transcription factor STAT1 during bacterial infection is IFN-alphabeta dependent, and necessary for increased IFN-gamma mRNA accumulation and chlamydial growth control . Signaling through common cytokine receptor gamma-chain and RNA-dependent protein kinase both mediated IFN-alphabeta-dependent enhancement of IFN-gamma mRNA levels . Accumulation of IFN-gamma mRNA and control of C . pneumoniae growth required NF-kappaB activation . Such NF-kappaB activation was independent of IFN-alphabeta, STAT1, and RNA-dependent protein kinase . In summary, C . pneumoniae-induced IFN-gamma expression in BMMphi is controlled by a TLR4-MyD88-IFN-alphabeta-STAT1-dependent pathway, as well as by a TLR4-independent pathway leading to NF-kappaB activation.

Genome Biol . 2004;5(5):R37 . Epub 2004 Apr 05.
Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data; Baerends RJ et al.; Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences . Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map . Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values . The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.

BMC Bioinformatics . 2004 May 05;5(1):52.
GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes; Celamkoti S et al.; BACKGROUND: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases . In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing . GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes . It was originally developed for comparing virus, mitochondrion and chloroplast genomes . This is now extended to small bacterial genomes of sizes less than 2 Mb . RESULTS: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca . 580 kb to 1.83 Mb) archived in the NCBI GenBank database . It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes . Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools . This can be displayed at the protein level using GeneOrder3.0 . Whole genome alignments of genes are presented in both a table and a dot plot . This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences . CONCLUSIONS: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." Availability: and http://pasteur.atcc.org:8050/GeneOrder3.0.

J Endocrinol, 2004 May, 181(2), 207 - 21
Role of the hypothalamic-pituitary-adrenal axis, glucocorticoids and glucocorticoid receptors in toxic sequelae of exposure to bacterial and viral products; Webster JI et al.; The hypothalamic-pituitary-adrenal (HPA) axis is activated during many bacterial and viral infections, resulting in an increase in circulating glucocorticoid levels . This HPA axis activation and glucocorticoid response are critical for the survival of the host, as demonstrated by the fact that removal of the HPA axis (by adrenalectomy or hypophysectomy) or glucocorticoid receptor (GR) blockade enhances the severity of the infection and in some cases enhances the mortality rate . Replacement with a synthetic glucocorticoid reverses these effects by reducing the severity of the infection and provides protection against lethal effects . In addition, some bacteria and viral infections have been shown to affect the GR directly . These have been described and the implications of such an effect discussed.

J Am Chem Soc, 2004 May 12, 126(18), 5690 - 8
Inhibitors of ADP-ribosylating bacterial toxins based on oxacarbenium ion character at their transition states; Zhou GC et al.; The bacterial exotoxins, cholera toxin (CT), pertussis toxin (PT), and diphtheria toxin (DT), interfere with specific host proteins to cause tissue damage for their respective infections . The common toxic mechanism for these agents is mono-ADP-ribosylation of specific amino acids in G(s)(alpha), G(i)(alpha), and eEF-2 proteins, respectively, by the catalytic A chains of the toxins (CTA, PTA, and DTA) . In the absence of acceptor proteins, these toxins also act as NAD(+)-N-ribosyl hydrolases . The transition-state structures for NAD(+) hydrolysis and ADP-ribosylation reactions have oxacarbenium ion character in the ribose . We designed and synthesized analogues of NAD(+) to resemble their oxacarbenium ion transition states . Inhibitors with oxacarbenium mimics replacing the NMN-ribosyl group of NAD(+) show 200-620-fold increased affinity in the hydrolytic and N-ribosyl transferase reactions catalyzed by CTA . These analogues are also inhibitors for the hydrolysis of NAD(+) by PTA with K(i) values of 24-40 microM, but bind with similar affinity to the NAD(+) substrates . Inhibition of the NAD(+) hydrolysis and ADP-ribosyl transferase reactions of DTA gave K(i) values from 19 to 48 microM . Catalytic rate enhancements by the bacterial exotoxins are small, and thus transition-state analogues cannot capture large energies of activation . In the cases of DTA and PTA, analogues known to resemble the transition states bind with approximately the same affinity as substrates . Transition-state analogue interrogation of the bacterial toxins indicates that CTA gains catalytic efficiency from modest transition-state stabilization, but DTA and PTA catalyze ADP-ribosyl transferase reactions more from ground-state destabilization . pH dependence of inhibitor action indicated that both neutral and cationic forms of transition-state analogues bind to DTA with similar affinity . The origin of this similarity is proposed to reside in the cationic nature of NAD(+) both as substrate and at the transition state.

Chromosome Res, 2004, 12(3), 251 - 62
Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti); Xu HL et al.; We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China . This library contains a total of 136 320 BAC clones . The average insert size of BAC clones was estimated to be 148 kb . The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed . Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage . By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library . A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys . Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library . This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates . The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.

J Biol Chem, 2004 Jul 16, 279(29), 30722 - 30 Epub 2004 Apr 29.
Identification of the mitochondrial ATP-Mg/Pi transporter . Bacterial expression, reconstitution, functional characterization, and tissue distribution; Fiermonte G et al.; The mitochondrial carriers are a family of transport proteins that, with a few exceptions, are found in the inner membranes of mitochondria . They shuttle metabolites, nucleotides, and cofactors through this membrane and thereby connect and/or regulate cytoplasm and matrix functions . ATP-Mg is transported in exchange for phosphate, but no protein has ever been associated with this activity . We have isolated three human cDNAs that encode proteins of 458, 468, and 489 amino acids with 66-75% similarity and with the characteristic features of the mitochondrial carrier family in their C-terminal domains and three EF-hand Ca(2+)-binding motifs in their N-terminal domains . These proteins have been overexpressed in Escherichia coli and reconstituted into phospholipid vesicles . Their transport properties and their targeting to mitochondria demonstrate that they are isoforms of the ATP-Mg/Pi carrier described in the past in whole mitochondria . The tissue specificity of the three isoforms shows that at least one isoform was present in all of the tissues investigated . Because phosphate recycles via the phosphate carrier in mitochondria, the three isoforms of the ATP-Mg/Pi carrier are most likely responsible for the net uptake or efflux of adenine nucleotides into or from the mitochondria and hence for the variation in the matrix adenine nucleotide content, which has been found to change in many physiopathological situations.

Fish Shellfish Immunol, 2004 Apr, 16(4), 461 - 74
Efficacy of cellular vaccines and genetic adjuvants against bacterial kidney disease in chinook salmon (Oncorhynchus tshawytscha); Rhodes LD et al.; DNA adjuvants and whole bacterial cell vaccines against bacterial kidney disease (BKD) were tested in juvenile chinook salmon . Whole cell vaccines of either a nonpathogenic Arthrobacter spp . or an attenuated Renibacterium salmoninarum strain provided limited prophylactic protection against acute intraperitoneal challenge with virulent R . salmoninarum, and the addition of either synthetic oligodeoxynucleotides or purified R . salmoninarum genomic DNA as adjuvants did not increase protection . However, a combination of both whole cell vaccines significantly increased survival among fish naturally infected with R . salmoninarum, and the surviving fish treated with the combination vaccine exhibited reduced levels of bacterial antigens in the kidney . This is the first demonstration of a potential therapeutic effect of a whole cell vaccine against BKD.

Cancer Genet Cytogenet, 2004 May, 151(1), 36 - 51
Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme; Cowell JK et al.; Identification of genetic losses and gains is valuable in analysis of brain tumors . Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci . These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells . Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment . These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region . Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested . We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa . Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa . In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies . There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample . CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture . CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells . This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence . CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.

Biosci Biotechnol Biochem, 2004 Apr, 68(4), 894 - 902
Characterization of murine grancalcin specifically expressed in leukocytes and its possible role in host defense against bacterial infection; Liu F et al.; Such phagocytic leukocytes as macrophages and neutrophils are the key cellular components of innate immunity . The actin cytoskeleton is essential for their recruitment and activation in infected tissues . We have previously identified p65/L-plastin with Ca(2+)-, calmodulin-, and beta-actin-binding domains in macrophages . In order to further investigate the p65/L-plastin-involved cellular functions, we cloned the cDNA for murine grancalcin, a possible binding partner of p65/L-plastin . According to the sequence, grancalcin is a member of the penta-EF-hand protein family . We prepared recombinant (r) grancalcin for functional studies and found that it exhibited Ca(2+)-dependent precipitation . High-titer antibodies against the protein enabled us to detect intracellular grancalcin . A flow cytometric analysis revealed grancalcin to be highly expressed in macrophages and neutrophils . The protein was particularly abundant in those cells recovered from bacteria-infected sites . Immunohistochemical studies clarified that grancalcin was translocated to the actin cytoskeleton in macrophages upon exposure to bacterial lipopolysaccharide . These findings suggest that grancalcin plays a key role in leukocyte-specific functions that are responsible for host defense.

Biosci Biotechnol Biochem, 2004 Apr, 68(4), 873 - 80
Enhanced resistance to blast fungus and bacterial blight in transgenic rice constitutively expressing OsSBP, a rice homologue of mammalian selenium-binding proteins; Sawada K et al.; The rice Oryza sativa selenium-binding protein homologue (OsSBP) gene encodes a homologue of mammalian selenium-binding proteins, and it has been isolated as one of the genes induced by treating a plant with a cerebroside elicitor from rice blast fungus . The possible role of OsSBP in plant defense was evaluated by using a transgenic approach . Plants overexpressing OsSBP showed enhanced resistance to a virulent strain of rice blast fungus as well as to rice bacterial blight . The expression of defense-related genes and the accumulation of phytoalexin after infection by rice blast fungus were accelerated in the OsSBP overexpressors . A higher level of H(2)O(2) accumulation and reduced activity of such scavenging enzymes as ascorbate peroxidase and catalase were seen when the OsSBP-overexpressing plants were treated with the protein phosphatase 1 inhibitor, calyculin A . These results suggest that the upregulation of OsSBP expression conferred enhanced tolerance to different pathogens, possibly by increasing plant sensitivity to endogenous defense responses . Additionally, the OsSBP protein might have a role in modulating the defense mechanism to biotic stress in rice.

Stroke, 2004 Jun, 35(6), 1333 - 9 Epub 2004 Apr 29.
Cerebral blood flow and metabolism during infusion of norepinephrine and propofol in patients with bacterial meningitis; Moller K et al.; BACKGROUND AND PURPOSE: In patients with severe bacterial meningitis, norepinephrine is often infused to increase mean arterial pressure (MAP) . This increases cerebral blood flow (CBF), but it is unknown if this increase is caused by impaired cerebral autoregulation or by a cerebral effect of norepinephrine through increased cerebral metabolism . The latter possibility implies a CBF-metabolism coupling . This has not been studied during meningitis . We studied the effect of norepinephrine and propofol on CBF and oxidative metabolism in patients with severe bacterial meningitis . METHODS: In seven patients with pneumococcal meningitis and 7 healthy subjects, norepinephrine was infused intravenously; patients also underwent intravenous propofol infusion . Global CBF was measured by the Kety-Schmidt technique; cerebral oxidative metabolism and net flux of norepinephrine and epinephrine were calculated from measured arterial-to-jugular venous concentration differences (a-vD) . RESULTS: During norepinephrine infusion, MAP increased from a median value of 79 (range, 70 to 89) to 99 (98 to 129) mm Hg in patients, and from 87 (72 to 103) to 123 (112 to 132) mm Hg in controls . CBF increased in patients (51 {48 to 60} to 59 {54 to 77} mL/100 g per minute) but remained unchanged in controls . The cerebral metabolic rate of oxygen (CMRO2) decreased in patients and remained unchanged in controls . No cerebral net flux of norepinephrine or epinephrine was found at any time in the 2 groups . During propofol infusion, CMRO2, and the a-vDO2 decreased whereas CBF was unchanged . CONCLUSIONS: In patients with severe bacterial meningitis, norepinephrine increases both MAP and CBF but not CMRO2, indicating impaired autoregulation . Propofol reduces CBF relatively less than cerebral metabolism, suggesting a resetting of the CBF-CMRO(2) relationship.

Carcinogenesis, 2004 Sep, 25(9), 1727 - 33 Epub 2004 Apr 29.
Aldehydic DNA lesions in calf thymus DNA and HeLa S3 cells produced by bacterial quinone metabolites of fluoranthene and pyrene; Zielinska-Park J et al.; There is increasing concern that compounds formed during the chemical or biological transformation of pollutants in the environment may be more detrimental to human and environmental health than the original pollutant . In this study, two bacterial transformation products of polycyclic aromatic hydrocarbons (PAHs), pyrene-4,5-quinone (P45Q) and fluoranthene-2,3-quinone (F23Q), were evaluated for mutagenicity by measuring aldehydic DNA lesions (ADL) in calf thymus DNA and HeLa S3 cells . Both quinones caused oxidative DNA damage in vitro through a copper-mediated redox cycle and subsequent production of reactive oxygen species (ROS) . Hydrogen peroxide and copper were essential for causing oxidative DNA damage and glutathione (GSH) prevented DNA damage from F23Q better than from P45Q . In experiments using HeLa cells, F23Q decreased cell viability, but did not produce measurable levels of ADL or base oxidation . To test the hypothesis that DNA damage was being prevented by conjugation of F23Q with GSH, GSH-depleted cells were treated with both quinones . GSH depletion did not increase the toxicity of F23Q or cause it to oxidize DNA . Treatment of HeLa cells with metal chelators did not decrease F23Q toxicity . It is therefore possible that F23Q affected cell viability through a ROS-independent mechanism, either by conjugation with essential cellular proteins or through cellular or mitochondrial membrane damage, which precluded oxidation of DNA . In contrast, P45Q caused both ADL and base oxidation in cells . Neocuproine reduced the amount of ADL caused by P45Q, indicating that copper was still important for the intracellular generation of damaging oxidants . P45Q is a novel metabolite and its effects on DNA have not been investigated previously . This study exemplifies the importance of considering not only primary environmental pollutants, but also their biologically or chemically generated transformation products.

Int J STD AIDS, 2004 May, 15(5), 285 - 8
Cover up or cool it? Sexual intercourse during therapy for bacterial sexually transmitted infections--a discussion of evidence for efficacy of condom use preventing transmission during an acute bacterial STI; Lee JD et al.; Effective treatment of sexually transmitted infections (STIs) such as gonorrhoea and chlamydia needs sexual behaviour modification, in addition to antibiotics, to protect the index patient and their sexual partner from re-infection during treatment . This may mean advice to avoid sex, or to use condoms for intercourse, until all current sexual partners have completed treatment . This article discusses the effectiveness of condoms as re-infection protection during therapy of gonorrhoea and chlamydial infection . Indirect evidence from studies on primary prevention indicates that, although physically, condoms are impermeable to STI pathogens, the risk of failure depends on the experience of the user and the frequency of use . Health care workers may over-estimate the protective value of condoms in this situation . Patients should be made aware of the risk of infection present, even in experienced condom users, if they choose to continue protected sexual intercourse during therapy for acute bacterial STIs.

Rontgenpraxis, 2003, 55(3), 99 - 102
{Mesenteric ossification in CT indicates sclerosing peritonitis in chronic bacterial infection and pancreatitis}; Kirchner J et al.; Sclerosing peritonitis already has been described as a serious complication of the continuous ambulatory peritoneal dialysis . But different other affections of the peritoneum such as chronic bacterial peritonitis and pancreatitis may result in sclerosing peritonitis, too . The symptom is characterised by thickened small bowel walls and peritoneal membranes as well as peritoneal calcifications which can be shown in computed tomography . We demonstrate two cases of peritoneal ossifications due to peritonitis and pancreatitis.

Biophys J, 2004 May, 86(5), 3204 - 10
Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament; Flynn TC et al.; Certain motile bacteria employ rotating flagella for propulsion . The relative flexibility of two key components of the flagellum, filament and hook, is partially responsible for the mechanistic workings of this motor . A new computational method, the quantized elastic deformational model, was employed in this article to calculate the dimensionless twist/bend ratio (EI/GJ) of the filament and hook, providing a quantitative means to compare their relative stiffness . Both ratios were much <1.0, an average of 0.0440 for the filament and 0.0512 for the hook, indicating that within each structure bending is favored over twisting . These two ratios, along with previous experimental measurements, allowed us to propose a theoretical Young's modulus (E) between 10(6) and 10(7) dyn/cm(2) for the hook . This value is orders of magnitude smaller than experimentally determined Young's moduli of the filament, hence in agreement with empirical evidence linking compliance in the flagellum mainly to the hook.

FEBS Lett, 2004 Apr 30, 564(3), 234 - 8
New insights into the structure and oligomeric state of the bacterial multidrug transporter EmrE: an unusual asymmetric homo-dimer; Ubarretxena-Belandia I et al.; EmrE is a small multidrug transporter that contains 110 amino acid residues that form four transmembrane alpha-helices . The three-dimensional structure of EmrE has been determined from two-dimensional crystals by electron cryo-microscopy . EmrE is an asymmetric homo-dimer with one substrate molecule bound in a chamber accessible laterally from one leaflet of the lipid bilayer . Evidence from substrate binding analyses and analytical ultracentrifugation of detergent-solubilised EmrE shows that the minimum functional unit for substrate binding is a dimer . However, it is possible that EmrE exists as a tetramer in vivo and plausible models are suggested based upon analyses of two-dimensional crystals.

J Mol Biol, 2004 May 14, 338(5), 863 - 75
ATP-dependent transcriptional activation by bacterial PspF AAA+protein; Schumacher J et al.; Transcription activation by bacterial sigma(54)-dependent enhancer-binding proteins (EBPs) requires their tri-nucleotide hydrolysis to restructure the sigma(54) RNA polymerase (RNAP) . EBPs share sequence similarity with guanine nucleotide binding-proteins and ATPases associated with various cellular activities (AAA) proteins, especially in the mononucleotide binding P-loop fold . Using the phage shock protein F (PspF) EBP, we identify P-loop residues responsible for nucleotide binding and hydrolysis, consistent with their roles in other P-loop NTPases . We show the refined low-resolution structure of an EBP, PspF, revealing a hexameric ring organisation characteristic of AAA proteins . Functioning of EBPs involves ATP binding, higher oligomer formation and ATP hydrolysis coupled to the restructuring of the RNAP . This is thought to be a highly coordinated multi-step process, but the nucleotide-driven mechanism of oligomerisation and ATP hydrolysis is little understood . Our kinetic and structural data strongly suggest that three PspF dimers assemble to form a hexamer upon nucleotide binding . During the ATP hydrolysis cycle, both ATP and ADP are bound to oligomeric PspF, in line with a sequential hydrolysis cycle . We identify a putative R-finger, and show its involvement in ATP hydrolysis . Substitution of this arginine residue results in nucleotide-independent formation of hexameric rings, structurally linking the putative R-finger and, by inference, a specific nucleotide interaction to the control of PspF oligomerisation.

Plasmid, 2004 May, 51(3), 162 - 78
Segregation of the yeast plasmid: similarities and contrasts with bacterial plasmid partitioning; Jayaram M et al.; The high copy yeast plasmid 2 microm circle, like the well-studied low copy bacterial plasmids, utilizes two partitioning proteins and a cis-acting 'centromere'-like sequence for its stable propagation . Functionally, though, the protein and DNA constituents of the two partitioning systems are quite distinct . Key events in the yeast and bacterial segregation pathways are plasmid organization, localization, replication, 'counting' of replicated molecules and their distribution to daughter cells . We suggest that the two systems facilitate these common logistical steps by adapting to the physical, biochemical, and mechanical contexts in which the host chromosomes segregate .

Poult Sci, 2004 Apr, 83(4), 624 - 37
Immune modulation of the pulmonary hypertensive response to bacterial lipopolysaccharide (endotoxin) in broilers; Wideman RF et al.; The lungs of broilers are constantly challenged with lipopolysaccharide (LPS, endotoxin) that can activate leukocytes and trigger thromboxane A2 (TxA2)- and serotonin (5HT)-mediated pulmonary vasoconstriction leading to pulmonary hypertension . Among broilers from a single genetic line, some individuals respond to LPS with large increases in pulmonary arterial pressure, whereas others fail to exhibit any response to the same supramaximal dose of LPS . This extreme variability in the pulmonary hypertensive response to LPS appears to reflect variability in the types or proportions of chemical mediators released by leukocytes . Our research has confirmed that TxA2 and 5HT are potent pulmonary vasoconstrictors in broilers and that broilers hatched and reared together consistently exhibit pulmonary hypertension after i.v . injections of TxA2 or 5HT . Previous in vitro studies conducted using macrophages from different lines of chickens demonstrated innate variability in the LPS-stimulated induction of nitric oxide synthase (iNOS) followed by the onset of an LPS-refractory state . The NOS enzyme converts arginine to citrulline and nitric oxide (NO) . It is known that NO produced by endothelial NOS serves as a key modulator of flow-dependent pulmonary vasodilation, and it is likely that NO generated by iNOS also contributes to the pulmonary vasodilator response . Accordingly, it is our hypothesis that the pulmonary hypertensive response to LPS in broilers is minimal when more vasodilators (NO, prostacyclin) than vasoconstrictors (TxA2, 5HT) are generated during an LPS challenge . Indeed, inhibiting NO production through pharmacological blockade of NOS with the inhibitor Nomega-nitro-L-arginine methyl ester modestly increased the baseline pulmonary arterial pressure and dramatically increased the pulmonary hypertensive response to LPS in all broilers evaluated . Innate differences in the effect of LPS on the pulmonary vasculature may contribute to differences in susceptibility of broilers to pulmonary hypertension syndrome (ascites).

Sex Transm Dis, 2004 May, 31(5), 301 - 4
Associations among human leukocyte antigen (HLA) class II DQ variants, bacterial sexually transmitted diseases, endometritis, and fertility among women with clinical pelvic inflammatory disease; Ness RB et al.; BACKGROUND: We investigated associations between HLA class II DQ alleles, chlamydial and gonococcal cervicitis, endometritis, and infertility among women with pelvic inflammatory disease (PID) . METHODS: Ninety-two women with clinical signs and symptoms of mild-to-moderate PID, enrolled in the PEACH Study, were evaluated . For all HLA class II DQ alleles with a prevalence of 10% or greater in the population, we assessed demographics, cervical infections, endometrial pathology, and fertility outcomes . RESULTS: Chlamydial cervicitis, gonococcal cervicitis, endometritis, and infertility were all more common among women carrying the DQA *0301 allele after adjustment for race . Endometritis and infertility were somewhat less common (or pregnancy more common) among women carrying the DQA *0501 and DQB *0402 alleles . CONCLUSION: Among women with signs and symptoms of PID, carriage of the DQA *0301, DQA *0501, and DQB *0402 alleles altered the occurrence of lower genital tract infection, upper genital tract inflammation, and infertility.

Science, 2004 Apr 23, 304(5670), 596 - 600
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD; Budanov AV et al.; Acting as a signal, hydrogen peroxide circumvents antioxidant defense by overoxidizing peroxiredoxins (Prxs), the enzymes that metabolize peroxides . We show that sestrins, a family of proteins whose expression is modulated by p53, are required for regeneration of Prxs containing Cys-SO(2)H, thus reestablishing the antioxidant firewall . Sestrins contain a predicted redox-active domain homologous to AhpD, the enzyme catalyzing the reduction of a bacterial Prx, AhpC . Purified Hi95 (sestrin 2) protein supports adenosine triphosphate-dependent reduction of overoxidized PrxI in vitro, indicating that unlike AhpD, which is a disulfide reductase, sestrins are cysteine sulfinyl reductases . As modulators of peroxide signaling and antioxidant defense, sestrins constitute potential therapeutic targets.

BJOG, 2004 May, 111(5), 409 - 22
The accuracy of various tests for bacterial vaginosis in predicting preterm birth: a systematic review; Honest H et al.; OBJECTIVE: To determine the accuracy with which various types of tests for bacterial vaginosis predict spontaneous preterm birth in pregnant women . DATA SOURCES: Studies were identified without language restrictions through nine different databases, and manual searching of bibliographies of known primary and review articles . STUDY SELECTION AND DATA EXTRACTION: There are four different bacterial vaginosis testing methods: Gram staining tests using either Nugent's or Spiegel's criteria, and gas liquid chromatography are laboratory based, and the fourth method uses clinical (Amsel's) criteria to diagnose bacterial vaginosis . Two reviewers independently selected studies and extracted data on their characteristics, quality and accuracy . Accuracy data were used to form 2 x 2 contingency tables of the bacterial vaginosis test results with spontaneous preterm birth as the reference standard . DATA SYNTHESIS: Data on asymptomatic women and women with symptoms of threatened preterm labour were analysed separately . Data were pooled to produce summary estimates of likelihood ratios for positive (LR+) and negative (LR-) test results for the various types of tests . RESULTS: There were 18 primary articles, involving altogether 17,868 women . There was unexplained heterogeneity in the meta-analyses of the accuracy results, which requires caution in their interpretation . Meta-analyses of studies testing asymptomatic women in the second trimester showed that clinical criteria had a LR+ of 0.98 (95% confidence interval 0.59 to 1.6) and a LR- of 1.00 (0.93 to 1.1), Gram staining (Nugent's criteria) had a LR+ of 1.6 (1.4 to 1.9) and a LR- of 0.9 (0.8 to 0.9), and Gram staining (Spiegel's criteria) had a LR+ of 2.4 (1.4 to 4.9) and a LR- of 0.81 (0.64 to 1.0) . Among symptomatic women, Gram staining (Spiegel's criteria) had a LR+ of 1.3 (1.0 to 1.6) and LR- of 0.9 (0.7 to 1.0) . CONCLUSION: There was a lack of difference in the accuracy of the various bacterial vaginosis tests for predicting preterm birth in both asymptomatic and symptomatic women of threatened preterm labour.

Infect Immun, 2004 May, 72(5), 2679 - 88
Intranasal immunization with a colloid-formulated bacterial extract induces an acute inflammatory response in the lungs and elicits specific immune responses; Rial A et al.; Nonspecific stimulation of lung defenses by repeated oral administration of immunomodulators, such as bacterial extracts, has shown potential for the prevention of respiratory tract infections . Here, we show that intranasal (i.n.) immunization with a bacterial extract formulated as a colloid induces an acute inflammatory response in the lungs characterized by increased production of CCL and CXCL chemokines and a major influx of dendritic cells (DCs) and neutrophils, with a higher proportion of DCs showing an activated phenotype (high CD80/CD86 expression) . Cytokine levels measured in bronchoalveolar-lavage samples showed a small increase in the production of tumor necrosis factor alpha and similar levels of the other cytokines measured (interleukin 10 {IL-10}, IL-12, and gamma interferon {IFN-gamma}) in immunized mice compared with control mice . However, the recall response of primed animals after antigenic challenge induced increased expression of IL-12 and IFN-gamma mRNAs in lung homogenates . Overall, all these effects were not due to the lipopolysaccharide content in the bacterial extract . Furthermore, we found that three i.n . doses administered 2 to 3 weeks apart were enough to elicit long-lasting specific serum immunoglobulin G (IgG) and secretory IgA antibody responses . Assessment of IgG subclasses showed a balanced pattern of IgG1-IgG2a responses . The serum total IgE concentrations were also elevated in immunized mice 2 weeks after the third dose, but they significantly decreased soon afterwards . Our results suggest that simple formulations of bacterial extracts administered i.n . are highly immunogenic, eliciting local and systemic immune responses, and may serve as the basis for cost-effective immunotherapies for the prevention and treatment of respiratory infections.

Mol Microbiol, 2004 May, 52(3), 725 - 33
Rv1818c-encoded PE_PGRS protein of Mycobacterium tuberculosis is surface exposed and influences bacterial cell structure; Delogu G et al.; Identification of the novel PE multigene family was an unexpected finding of the genomic sequencing of Mycobacterium tuberculosis . Presently, the biological role of the PE and PE_PGRS proteins encoded by this unique family of mycobacterial genes remains unknown . In this report, a representative PE_PGRS gene (Rv1818c/PE_PGRS33) was selected to investigate the role of these proteins . Cell fractionation studies and fluorescence analysis of recombinant strains of Mycobacterium smegmatis and M . tuberculosis expressing green fluorescent protein (GFP)-tagged proteins indicated that the Rv1818c gene product localized in the mycobacterial cell wall, mostly at the bacterial cell poles, where it is exposed to the extracellular milieu . Further analysis of this PE_PGRS protein showed that the PE domain is necessary for subcellular localization . In addition, the PGRS domain, but not PE, affects bacterial shape and colony morphology when Rv1818c is overexpressed in M . smegmatis and M . tuberculosis . Taken together, the results indicate that PE_PGRS and PE proteins can be associated with the mycobacterial cell wall and influence cellular structure as well as the formation of mycobacterial colonies . Regulated expression of PE genes could have implications for the survival and pathogenesis of mycobacteria within the human host and in other environmental niches.

Lab Chip, 2002 Nov, 2(4), 207 - 12 Epub 2002 Nov 07.
Bacterial chromosome extraction and isolation; Prinz C et al.; We have used diffusive mixing and dielectrophoretic trapping to lyse Escherichia coli cells in a microfabricated environment and trap the E . coli chromosome . We characterize the conditions needed for efficient lysis of the cells, and conditions needed for the dielectrophoretic trapping of the chromatin without the trapping of cytoplasmic proteins.

Biochim Biophys Acta, 2004 Apr 12, 1655(1-3), 388 - 99
The bacterial cytochrome cbb3 oxidases; Pitcher RS et al.; Cytochrome cbb(3) oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory heme-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) . Expression of cytochrome cbb(3) oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain N(2) fixation . We review recent progress in the biochemical characterisation of these distinctive oxidases that lays the foundation for understanding the basis of their proposed high affinity for oxygen, an apparent degeneracy in their electron input pathways and whether or not they acquired the ability to pump protons independently of other HCOs.

J Mol Biol, 2004 May 7, 338(4), 683 - 93
Study of the functional interaction of the 900 Tetraloop of 16S ribosomal RNA with helix 24 within the bacterial ribosome; Belanger F et al.; The 900 tetraloop that caps helix 27 of 16S ribosomal RNA (rRNA) is amongst the most conserved regions of rRNA . This tetraloop forms a GNRA motif that docks into the minor groove of three base-pairs at the bottom of helix 24 of 16S rRNA in the 30S subunit . Both the tetraloop and its receptor in helix 24 contact the 23S rRNA, forming the intersubunit bridge B2c . Here, we investigated the interaction between the 900 tetraloop and its receptor by genetic complementation . We used a specialized ribosome system in combination with an in vivo instant evolution approach to select mutations in helix 24 compensating for a mutation in the 900 tetraloop (A900G) that severely decreases ribosomal activity, impairing subunit association and translational fidelity . We selected two mutants where the G769-C810 base-pair of helix 24 was substituted with either U-A or C x A . When these mutations in helix 24 were investigated in the context of a wild-type 900 tetraloop, the C x A but not the U-A mutation severely impaired ribosome activity, interfering with subunit association and decreasing translational fidelity . In the presence of the A900G mutation, both mutations in helix 24 increased the ribosome activity to the same extent . Subunit association and translational fidelity were increased to the same level . Computer modeling was used to analyze the effect of the mutations in helix 24 on the interaction between the tetraloop and its receptor . This study demonstrates the functional importance of the interaction between the 900 tetraloop and helix 24.

J Pediatr Psychol, 2004 Mar, 29(2), 67 - 81
Cognitive and executive function 12 years after childhood bacterial meningitis: effect of acute neurologic complications and age of onset; Anderson V et al.; OBJECTIVES: This study investigated long-term neurobehavioral outcome from childhood bacterial meningitis, with particular focus on the influence of acute neurologic complications and age at illness . METHODS: This prospective, longitudinal study compared survivors of childhood bacterial meningitis (n = 109) with grade- and gender-matched controls (n = 96) selected from the target children's schools 12 years post-illness, in order to identify residual deficits in intellectual, academic, and executive ability . RESULTS: Results showed that at 12 years post-illness, children with a history of meningitis were at greater risk of impairment in each of these domains . However, development was shown to keep pace with that exhibited by healthy controls, suggesting no deterioration in function with time since illness . While prediagnosis symptom duration and acute neurologic complications were not predictors of 12-year outcome, meningitis before 12 months of age was significantly related to poorer performance on tasks requiring language and executive skills . CONCLUSIONS: These findings suggest that while the overall impact of meningitis may be relatively general and mild, younger age at illness is predictive of neurobehavioral outcome . There was no evidence of progressive deterioration postmeningitis, with comparison of results from 7 to 12 years post-illness demonstrating significant "catch-up" in aspects of executive function.

J Mol Biol, 2004 Feb 27, 336(4), 871 - 87
Evolution of protein superfamilies and bacterial genome size; Ranea JA et al.; We present the structural annotation of 56 different bacterial species based on the assignment of genes to 816 evolutionary superfamilies in the CATH domain structure database . These assignments have enabled us to analyse the recurrence of specific superfamilies within and across the genomes . We have selected the superfamilies that have a very broad representation and therefore appear to be universally distributed in a significant number of bacterial lineages . Occurrence profiles of these universally distributed superfamilies are compared with genome size in order to estimate the correlation between superfamily duplication and the increase in proteome size . This distinguishes between those size-dependent superfamilies where frequency of occurrence is highly correlated with increase in genome size, and size-independent superfamilies where no correlation is observed . Consideration of the size correlation and the ratio between the mean and the standard deviations for all the superfamily profiles allows more detailed subdivisions and classification of superfamilies . For example, within the size-independent superfamilies, we distinguished a group that are distributed evenly amongst all the genomes . Within the size-dependent superfamilies we differentiated two groups: linearly distributed and non-linearly distributed . Functional annotation using the COG database was performed for all superfamilies in each of these groups, and this revealed significant differences amongst the three sets of superfamilies . Evenly distributed, size-independent domains are shown to be involved primarily in protein translation and biosynthesis . For the size-dependent superfamilies, linearly distributed superfamilies are involved mainly in metabolism, and non-linearly distributed superfamily domains are involved principally in gene regulation.

Environ Pollut, 1997, 96(2), 161 - 71
Effects of bacterial inoculum and moisture adjustment on composting of pig manure; Tiquia SM et al.; Spent litter (a mixture of partially composted pig manure and sawdust) was taken from pig pens employing the pig-on-litter system with and without the addition of a commercial bacterial product (Odor control (OC)-organic fertilizers (OF)) . A duplicate series of windrows was set up with spent litter which contained the bacterial product and a further duplicate series was set up with spent litter which did not contain the bacterial product . All four sets had their initial moisture content adjusted to 60% but one of each duplicate pair had its moisture content adjusted to 60% during the entire period of further composting in windrows . The rate of further (windrow) composting was significantly different in the litter which contained no bacterial product and which only had its moisture content adjusted at the beginning of the experiment . Decomposition was incomplete in this set even after day 91 . In the three other sets, the rate of decomposition was faster and the spent litter became stabilised by day 56 . This result suggests that if the bacterial product has been added during the initial pig-on-litter composting process, moisture adjustment during further (windrow) composting is not important . Conversely, if moisture was adjusted during further composting, the addition of bacterial product during initial pig-on-litter composting would be of no value . Such a finding is of remarkable significance in the further composting of spent litter since this indicates that the process could be run on a much more economical basis.

Biosens Bioelectron, 2004 Jun 15, 19(11), 1429 - 37
Optical tweezers based force measurement system for quantitating binding interactions: system design and application for the study of bacterial adhesion; Fallman E et al.; An optical force measurement system for quantitating forces in the pN range between micrometer-sized objects has been developed . The system was based upon optical tweezers in combination with a sensitive position detection system and constructed around an inverted microscope . A trapped particle in the focus of the high numerical aperture microscope-objective behaves like an omnidirectional mechanical spring in response to an external force . The particle's displacement from the equilibrium position is therefore a direct measure of the exerted force . A weak probe laser beam, focused directly below the trapping focus, was used for position detection of the trapped particle (a polystyrene bead) . The bead and the condenser focus the light to a distinct spot in the far field, monitored by a position sensitive detector . Various calibration procedures were implemented in order to provide absolute force measurements . The system has been used to measure the binding forces between Escherichia coli bacterial adhesins and galabiose-functionalized beads.

Environ Pollut, 2000 May, 108(2), 291 - 5
Acute and chronic impacts caused by aromatic hydrocarbons on bacterial communities at Boa Viagem and Forte do Rio Branco Beaches, Guanabara Bay, Brazil; Crapez MA et al.; The bacterial community presented significantly different hydrocarbonoclastic activity under acute and chronic impacts . Benzoic acid, toluene, benzene and xylene were used in final concentrations of 5, 10 and 15 mM and bacterial biomass was quantified through protein dosage . Under acute impact, the highest biomass percentages occurred between the 11th and 14th days; under chronic impact, between the 20th and 29th days . Under acute and chronic impacts, the bacterial biomass presented higher nutritional specialization at Boa Viagem Beach, using the aromatic hydrocarbons up to a concentration of 15 mM . Under acute impact, the concentration of the hydrocarbons constituted a critical factor for the bacterial flora from Forte do Rio Beach, because biomass increases only occurred in concentrations of 5 mM; under chronic impact, the aromatic hydrocarbons induced the specialization and increased bacterial biomass for 15 mM toluene . Benzoic acid (15 mM) was used by the bacteria from Boa Viagem and Forte do Rio Branco Beaches.

Environ Pollut, 1993, 79(2), 153 - 62
Bacterial degradation of acetone in an outdoor model stream; Rathbun RE et al.; Diurnal variations of the acetone concentration in an outdoor model stream were measured with and without a nitrate supplement to determine if the nitrate supplement would stimulate bacterial degradation of the acetone . Acetone loss coefficients were computed from the diurnal data using a fitting procedure based on a Lagrangian particle model . The coefficients indicated that bacterial degradation of the acetone was occurring in the downstream part of the stream during the nitrate addition . However, the acetone concentrations stabilized at values considerably above the limit of detection for acetone determination, in contrast to laboratory respirometer studies where the acetone concentration decreased rapidly to less than the detection limit, once bacterial acclimation to the acetone had occurred . One possible explanation for the difference in behavior was the limited 6-hour residence time of the acetone in the model stream.

Environ Pollut, 1994, 85(2), 175 - 84
Major factors influencing bacterial leaching of heavy metals (Cu and Zn) from anaerobic sludge; Couillard D et al.; Anaerobically digested sewage sludges were treated for heavy metal removal through a biological solubilization process called bacterial leaching (bioleaching) . The solubilization of copper and zinc from these sludges is described in this study: using continuously stirred tank reactors with and without sludge recycling at different mean hydraulic residence times (1, 2, 3 and 4 days) . Significant linear equations were established for the solubilization of zinc and copper according to relevant parameters: oxygen reduction potential (ORP), pH and residence time ( {Formula: see text} ) . Zinc solubilization was related to the residence time with a {Formula: see text} (explained variance) of 0.82 . Considering only {Formula: see text} days explained variance of 0.31 and 0.24 were found between zinc solubilization as a function of ORP and pH indicating a minor importance of those two factors for this metal in the range of pH and ORP experimented . Cu solubilization was weakly correlated to mean hydraulic residence time ( {Formula: see text} ), while it was highly correlated to ORP ( {Formula: see text} ) and pH ( {Formula: see text} ) considering only {Formula: see text} of 2 and 3 days in the case of pH and ORP . The ORP dependence of Cu solubilization has been clearly demonstrated in this study . In addition to this, the importance of the substrate concentration for Cu solubilization has been confirmed . The hypothesis of a biological solubilization of Cu by the indirect mechanism has been supported . The results permit, under optimum conditions, the drawing of linear equations which will allow prediction of metal solubilization efficiencies from the parameters pH (Cu), ORP (Cu) and residence time (Cu and Zn), during the treatment . The linear regressions will be a useful tool for routine operation of the process.

Shock, 2004 May, 21(5), 452 - 7
Enhanced interferon-gamma production and bacterial clearance in the liver of splenectomized mice in the models of Escherichia coli injection or intestinal obstruction; Ikuta S et al.; Although several studies have reported that splenectomy increases susceptibility to bacterial infections, other reports have indicated that splenectomy does not induce such susceptibility . To clarify this discrepancy, we studied the effects of splenectomy in the models of lipopolysaccharide (LPS) or Escherichia coli challenge and intestinal obstruction, focusing on cytokine production and bacterial clearance in the liver . Using C57BL/6 mice at 4 weeks after splenectomy or a sham operation, either LPS or E . coli was injected or an intestinal obstruction was made to examine the mortality, serum cytokine levels, cytokine production of the liver mononuclear cells (MNCs), and bacterial clearance in the liver . As a result, no differences were observed in survival rates after LPS or E . coli challenge between the mice with and without splenectomy . However, in a model of intestinal obstruction, splenectomized mice survived significantly longer than the sham-operated mice . Liver MNCs from splenectomized mice produced a significantly larger amount of interferon-gamma compared with those from sham-operated mice . Furthermore, bacterial counts in the liver at 2 h after E . coli injection and at 24 h after intestinal obstruction were significantly decreased in splenectomized mice compared with sham-operated mice . In conclusion, splenectomy does not impair host defense against bacteria infection provided that recovery is sufficient to allow compensatory processes in the liver to occur.

Science, 2004 May 14, 304(5673), 983 - 7 Epub 2004 Apr 15.
Oscillating global regulators control the genetic circuit driving a bacterial cell cycle; Holtzendorff J et al.; A newly identified cell-cycle master regulator protein, GcrA, together with the CtrA master regulator, are key components of a genetic circuit that drives cell-cycle progression and asymmetric polar morphogenesis in Caulobacter crescentus . The circuit drives out-of-phase temporal and spatial oscillation of GcrA and CtrA concentrations, producing time- and space-dependent transcriptional regulation of modular functions that implement cell-cycle processes . The CtrA/GcrA regulatory circuit controls expression of polar differentiation factors and the timing of DNA replication . CtrA functions as a silencer of the replication origin and GcrA as an activator of components of the replisome and the segregation machinery.

Bioinformatics, 2004 Nov 1, 20(16), 2832 - 3 Epub 2004 Apr 15.
A System for Automated Bacterial (genome) Integrated Annotation--SABIA; Almeida LG et al.; A web-based software suite, SABIA (System for Automated Bacterial Integrated Annotation), is described that provides a comprehensive computational support for the assembly and annotation of whole bacterial genomes from the data derived from sequencing projects . AVAILABILITY: Both SABIA and supplementary materials are available at http://www.sabia.lncc.br

J Heart Valve Dis, 2004 Mar, 13(2), 217 - 27
Bacterial endocarditis complicating mitral annular calcification: a clinical and echocardiographic study; Eicher JC et al.; BACKGROUND AND AIM OF THE STUDY: Although described in a number of necropsy studies, endocarditis on mitral annular calcification (MAC) has rarely been reported during life . The study aim was to assess the frequency and specific features of bacterial endocarditis complicating MAC . METHODS: Data relating to 62 cases of infective endocarditis of the native mitral valve diagnosed with multiplane transesophageal echocardiography (TEE) over a five-year period were collected prospectively . RESULTS: Among 62 patients, 15 (24%) had vegetations originating from a calcified mitral annulus (group 1), while 47 had classic leaflet endocarditis (group 2) . Group 1 patients differed significantly from group 2 patients with regard to: (i) higher incidence of diabetes mellitus and cancers; (ii) initial clinical presentation, with febrile coma or meningoencephalitis in 53% of cases; (iii) echocardiographic features, with significantly greater vegetations, presence of calcium-dense echoes within the vegetation, high frequency of ring abscess, and high frequency of para-annular ventriculoatrial leakage; and (iv) poorer clinical outcome, with 53% in-hospital mortality . CONCLUSION: MAC appears to be an underestimated predisposing factor for a particularly severe type of bacterial endocarditis . The use of multiplane TEE should improve current knowledge of this disease.

Genesis, 2004 Apr, 38(4), 195 - 9
Generation of Pax2-Cre mice by modification of a Pax2 bacterial artificial chromosome; Ohyama T et al.; The Pax2 gene is expressed in the developing otocyst, kidney, and midbrain-hindbrain boundary . We generated Pax2-Cre transgenic lines by modification of a Pax2 bacterial artificial chromosome (BAC) . In one Pax2-Cre line, Cre mRNA starts to be expressed in the otic placode at the late presomite stage . R26R reporter mouse analysis revealed that the Cre expression is sufficient to delete the loxP-flanked sequences in most of the cells in the inner ear . Reporter-positive cells are also detected in other Pax2-expressing tissues such as midbrain, cerebellum, olfactory bulb, and kidney, suggesting that these cells are the descendants of Pax2-expressing cells in these tissues and that Pax2-Cre transgenic mice can delete genes efficiently in these tissues .

Nat Rev Microbiol, 2004 Mar, 2(3), 241 - 9
DNA uptake during bacterial transformation; Chen I et al.; Naturally competent bacteria are able to take up exogenous DNA and undergo genetic transformation . The transport of DNA from the extracellular milieu into the cytoplasm is a complex process, and requires proteins that are related to those involved in the assembly of type IV pili and type II secretion systems, as well as a DNA translocase complex at the cytoplasmic membrane . Here, we will review the current knowledge of DNA transport during transformation.

Bioorg Med Chem Lett, 2004 May 3, 14(9), 2275 - 7
Two new bacterial DNA primase inhibitors from the plant Polygonum cuspidatum; Hegde VR et al.; The 70% aqueous methanolic extract of the Peruvian plant Polygonum cuspidatum sp . was found to contain two novel phenolic saccharides 1 and 2, which were identified as inhibitors of the bacterial DNA primase enzyme . Structures of these two compounds were established based on high resolution NMR studies . Compound 1 and 2 inhibited the primase enzyme with an IC(50) of 4 and 5 microM, respectively.

J Appl Microbiol, 2004, 96(5), 1057 - 66
Production of exopolysaccharides by Antarctic marine bacterial isolates; Mancuso Nichols CA et al.; AIMS: This study was undertaken to examine and characterize Antarctic marine bacterial isolates and the exopolysaccharides (EPS) they produce in laboratory culture . METHODS AND RESULTS: Two EPS-producing bacterial strains CAM025 and CAM036 were isolated from particulate material sampled from seawater and sea ice in the southern ocean . Analyses of 16S rDNA sequences placed these isolates in the genus Pseudoalteromonas . In batch culture, both strains produced EPS . The yield of EPS produced by CAM025 was 30-fold higher at -2 and 10 degrees C than at 20 degrees C . Crude chemical analyses showed that these EPS were composed primarily of neutral sugars and uronic acids with sulphates . Gas chromatographic analysis of monosaccharides confirmed these gross compositional findings and molar ratios of monosaccharides revealed differences between the two EPS . CONCLUSIONS: The EPS produced by Antarctic bacterial isolates examined in this study appeared to be polyanionic and, therefore, 'sticky' with respect to cations such as trace metals . SIGNIFICANCE AND IMPACT OF THE STUDY: As the availability of iron as a trace metal is of critical importance in the southern ocean where it is know to limit primary production, the role of these bacterial EPS in the Antarctic marine environment has important ecological implications.

Vox Sang, 2004 Apr, 86(3), 178 - 82
Relative values of the interventions of diversion and improved donor-arm disinfection to reduce the bacterial risk from blood transfusion; McDonald CP et al.; BACKGROUND AND OBJECTIVES: The aim of this study was to demonstrate the efficiency of diverting the initial 20-ml donation from the collection bag and of an improved donor-arm disinfection procedure in reducing bacterial contamination in blood . MATERIALS AND METHODS: Donations were collected in bags specially manufactured for the study . These bags incorporated two satellite pouches into each of which 20 ml of blood was collected . Blood initially flowed into sample pouch P1, representing a diversion pouch . Pouch P2 was then filled with 20 ml of blood, which allowed us to sample the collection bag after diversion was complete . Blood then flowed into the standard collection bag . The contents of the pouches were aerobically and anaerobically cultured on the BacT/ALERT automated culture system for 7 days . Two procedures were investigated in the study (each involving 1409 blood donations): one analysed the current disinfection procedure; and the other analysed an improved donor-arm disinfection procedure . RESULTS: The use of diversion alone resulted in a 47% reduction in contamination, and improved donor-arm disinfection alone resulted in a 57% reduction in contamination . Diversion plus improved donor-arm disinfection produced a predicted 77% reduction in contamination . CONCLUSIONS: The study validates diversion and an improved donor-arm disinfection procedure . In combination, these two interventions produced a substantial reduction in contamination . These procedures are to be introduced by the English National Blood Service to enhance the safety of the blood supply.

Vox Sang, 2004 Apr, 86(3), 157 - 63
Transfusion-transmitted bacterial infection: risks, sources and interventions; Wagner SJ; Records of the transmission of bacterial infections by transfusion date back to the beginning of organized blood banking . Despite tremendous strides in preventing viral infection through careful donor screening and viral testing, there has been little improvement in reducing the risk of bacterial sepsis since the introduction of closed collection systems . Based on the French Haemovigilance study, the British Serious Hazards of Transmission (SHOT) study and fatality reports to the United States Food and Drug Administration, the risk of clinically apparent sepsis exceeds the risk of HIV, HBV, and HCV transmission . Sources of contamination include the skin, blood, disposables, and the environment . Potential interventions to reduce transfusion-associated bacterial sepsis include improvements to donor arm preparation, diversion of the first aliquot of whole blood, introduction of bacterial testing and/or implementation of pathogen reduction methods.

Genes Dev, 2004 Mar 15, 18(6), 715 - 27
Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain; Paul R et al.; Pole development is coordinated with the Caulobacter crescentus cell cycle by two-component signaling proteins . We show that an unusual response regulator, PleD, is required for polar differentiation and is sequestered to the cell pole only when it is activated by phosphorylation . Dynamic localization of PleD to the cell pole provides a mechanism to temporally and spatially control the signaling output of PleD during development . Targeting of PleD to the cell pole is coupled to the activation of a C-terminal guanylate cyclase domain, which catalyzes the synthesis of cyclic di-guanosine monophosphate . We propose that the local action of this novel-type guanylate cyclase might constitute a general regulatory principle in bacterial growth and development.

Environ Sci Technol, 2004 Mar 15, 38(6), 1777 - 85
Bacterial adhesion and transport in porous media: role of the secondary energy minimum; Redman JA et al.; The adhesion of a well-characterized Escherichia coli bacterial strain to quartz sediment grains in the presence of repulsive electrostatic interactions is systematically examined . An increase in the ionic strength of the pore fluid results in an increase in bacterial attachment, despite DLVO calculations indicating a sizable electrostatic energy barrier to deposition . Bacterial deposition is likely occurring in the secondary energy minimum, which DLVO calculations indicate increases in depth with ionic strength . A decrease in the ionic strength of the pore fluid--thereby eliminating the secondary energy minimum--resulted in release of the majority of previously deposited bacteria, suggesting that these cells were deposited reversibly in the secondary minimum . Additionally, bacterial attachment to a quartz surface in a radial stagnation point flow system was absent at ionic strengths less than 0.01 M and resulted in attachment efficiencies over an order of magnitude lower than in the packed-bed column experiments at higher ionic strengths . Because of the hydrodynamics in the radial stagnation point flow system, this observation supports our conclusion that the majority of bacterial deposition in the packed bed occurs in a secondary energy minimum.

Science, 2004 Apr 9, 304(5668), 242 - 8
Bacterial invasion: the paradigms of enteroinvasive pathogens; Cossart P et al.; Invasive bacteria actively induce their own uptake by phagocytosis in normally nonphagocytic cells and then either establish a protected niche within which they survive and replicate, or disseminate from cell to cell by means of an actin-based motility process . The mechanisms underlying bacterial entry, phagosome maturation, and dissemination reveal common strategies as well as unique tactics evolved by individual species to establish infection.

Curr Opin Pulm Med, 2004 May, 10(3), 183 - 8
Imaging features of bacterial respiratory infections in AIDS; Aviram G et al.; PURPOSE OF REVIEW: Although an emphasis has historically been placed on nonbacterial, opportunistic respiratory infections in HIV-infected individuals, it is increasingly important for clinicians to be familiar with the spectrum of bacterial respiratory infections that may occur in this population . RECENT FINDINGS: Bacterial pneumonia and acute bronchitis are currently the most common causes of respiratory disease in HIV-infected individuals in developed countries . Moreover, these infections are frequently the first clinical manifestation of HIV infection . Among patients with sustained CD4 cell count >200 cells/microL, the discontinuation of Pneumocystis carinii pneumonia prophylaxis is not associated with an increased risk of bacterial pneumonia . The most common radiographic pattern of bacterial pneumonia is focal consolidation, which typically presents in either a segmental or lobar distribution . In cases in which the chest radiograph is inconclusive, high-resolution chest CT has a very high accuracy for detecting pyogenic small airways disease and for distinguishing between P . carinii pneumonia and other lung infections including bacterial infection . SUMMARY: Knowledge of the characteristic imaging and clinical features of bacterial respiratory infections can enhance their timely diagnosis and treatment.

J Clin Microbiol, 2004 Apr, 42(4), 1402 - 8
Use of quantitative 16S ribosomal DNA detection for diagnosis of central vascular catheter-associated bacterial infection; Warwick S et al.; Many central vascular catheters (CVCs) are removed unnecessarily because current diagnostic methods for CVC-associated infection are unreliable . A quantitative PCR assay using primers and probe targeted to bacterial 16S ribosomal DNA was used to measure the levels of bacterial DNA in blood samples drawn through the CVC in a population of patients receiving intravenous nutrition . Bacterial DNA concentrations were raised in 16 of 16 blood samples taken during episodes of probable bacterial CVC-associated infection . Bacterial DNA concentrations were raised in 4 of 29 episodes in which bacterial CVC-associated infection was unlikely . The use of this technique has the potential to substantially reduce the unnecessary removal of CVCs.

J Periodontol, 2004 Feb, 75(2), 292 - 6
Bacterial adhesion on commercially pure titanium and zirconium oxide disks: an in vivo human study; Scarano A et al.; BACKGROUND: Little is known about the mechanisms of bacterial interaction with implant materials in the oral cavity . A correlation between plaque accumulation and progressive bone loss around implants has been reported . Bacterial adhesion shows a direct positive correlation with surface roughness . Other surface characteristics also seem to be extremely important with regard to plaque formation . Different adhesion affinities of bacteria have been reported for different materials . The aim of this study was to characterize the percentage of surface covered by bacteria on commercially pure titanium and zirconium oxide disks . METHODS: Ten patients participated in this study . A removable acrylic device was adapted to the molar-premolar region, and commercially pure titanium (control) and zirconium oxide (test) disks were glued to the buccal aspect of each device . The surface roughness of titanium and test specimens was similar . After 24 hours, all disks were removed and processed for scanning electron microscopy, for the evaluation of the portion of surface covered by bacteria . RESULTS: In control specimens, the area covered by bacteria was 19.3% +/- 2.9; in test specimens, the area was 12.1% +/- 1.96 . The disk surface covered by bacteria on test specimens was significantly lower than that of control specimens (P = 0.0001) . CONCLUSION: Our results demonstrate that zirconium oxide may be a suitable material for manufacturing implant abutments with a low colonization potential.

Theor Appl Genet, 2004 Apr, 108(6), 1047 - 55 Epub 2004 Jan 23.
Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum; Coaker GL et al.; Two quantitative trait loci (QTL) from Lycopersicon hirsutum, Rcm 2.0 and Rcm 5.1, control resistance to Clavibacter michiganensis subsp . michiganensis ( Cmm) . To precisely map both loci, we applied interval mapping techniques to 1,056 individuals in three populations exhibiting F(2) segregation . Based on a 1-LOD confidence interval, Rcm 2.0 mapped to a 14.9-cM interval on chromosome 2 and accounted for 25.7-34.0% of the phenotypic variation in disease severity . Rcm 5.1 mapped to a 4.3-cM interval on chromosome 5 and accounted for 25.8-27.9% of the phenotypic variation . Progeny testing of recombinant plants narrowed the QTL location for Rcm 2.0 to a 4.4-cM interval between TG537-TG091 and to a 2.2-cM interval between CT202-TG358 for Rcm 5.1 . A population of 750 individuals exhibiting F(2) segregation was used to detect epistasis between both loci using ANOVA and orthogonal contrasts ( P=0.027), suggesting that resistance was determined by additive gene action and an additive-by-additive epistatic interaction . A partial diallel mating design was used to confirm epistasis, advance superior genotypes, randomize genetic backgrounds, and create recombination opportunities . This crossing scheme created a more balanced population ( n=112) containing the nine F(2) genotypic classes . Parents in the diallel were selected from the previous population based on resistance, genotype at the Rcm 2.0 and Rcm 5.1 loci, and horticultural traits . A replicated trial using the diallel population confirmed additive-by-additive epistasis ( P<0.0001) . These results validate the gene action, intra -locus interaction, and map position of two loci controlling resistance to Cmm.

Neuroinformatics, 2004, 2(1), 59 - 70
Probable epitopes: Relationships between myelin basic protein antigenic determinants and viral and bacterial proteins; Klee L et al.; Nature holds numerous viral and bacterial proteins with regions of similarity to myelin basic protein antigenic determinants . Bioinformatic technology, including sequence similarity searches, may allow for the detection of biochemical and biophysical relationships between these peptides . Understanding these relationships is essential to understanding immune-mediated disease and, consequently, may be used to elucidate the etiology of pathological demyelinating diseases such as multiple sclerosis . Studies of experimental autoimmune encephalomyelitis have been used to identify antigenic determinants . We have used these determinants to search available databases of viral and bacterial proteins . Our results indicate numerous viral and bacterial protein segments with probabilistic sequence similarity to myelin basic protein antigenic determinants.

J Immunol, 2004 Apr 15, 172(8), 5024 - 33
Helicobacter pylori-specific antibodies impair the development of gastritis, facilitate bacterial colonization, and counteract resistance against infection; Akhiani AA et al.; In recent years, Abs have been considered a correlate rather than an effector of resistance against Helicobacter pylori infection . However, it is still poorly understood to what extent Ab production correlates with gastric immunopathology . Here we report that Abs not only are dispensable for protection, but they are detrimental to elimination of the bacteria and appear to impair gastric inflammatory responses . We found that the initial colonization with H . pylori bacteria was normal in the B cell-deficient (microMT) mice, whereas at later times (>8 wk) most of the bacteria were cleared, concomitant with the development of severe gastritis . In contrast, wild-type (WT) mice exhibited extensive bacterial colonization and only mild gastric inflammation, even at 16 wk after inoculation . Oral immunizations with H . pylori lysate and cholera toxin adjuvant stimulated comparable levels of protection in microMT and WT mice . The level of protection in both strains correlated well with the severity of the postimmunization gastritis . Thus, T cells were responsible for the gastritis, whereas Abs, including potentially host cell cross-reactive Abs, were not involved in causing the gastritis . The T cells in micro MT and WT mice produced high and comparable levels of IFN-gamma to recall Ag at 2 and after 8 wk, whereas IL-4 was detected after 8 wk only, indicating that Th1 activity dominated the early phase of protection, whereas later a mixed Th1 and Th2 activity was seen.

Mol Microbiol, 2004 Apr, 52(2), 385 - 98
Bacterial mitosis: partitioning protein ParA oscillates in spiral-shaped structures and positions plasmids at mid-cell; Ebersbach G et al.; The par2 locus of Escherichia coli plasmid pB171 encodes oscillating ATPase ParA, DNA binding protein ParB and two cis-acting DNA regions to which ParB binds (parC1 and parC2) . Three independent techniques were used to investigate the subcellular localization of plasmids carrying par2 . In cells with a single plasmid focus, the focus located preferentially at mid-cell . In cells with two foci, these located at quarter-cell positions . In the absence of ParB and parC1/parC2, ParA-GFP formed stationary helices extending from one end of the nucleoid to the other . In the presence of ParB and parC1/parC2, ParA-GFP oscillated in spiral-shaped structures . Amino acid substitutions in ParA simultaneously abolished ParA spiral formation, oscillation and either plasmid localization or plasmid separation at mid-cell . Therefore, our results suggest that ParA spirals position plasmids at the middle of the bacterial nucleoid and subsequently separate them into daughter cells.

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