J Biol Chem . 2005 Jan 14; {Epub ahead of print} Evolution of mitochondrial oxa proteins from bacterial YidC: Inherited and acquired functions of a conserved protein insertion machinery; Preuss M et al.; Members of the Oxa1/YidC family are involved in the biogenesis of membrane proteins . In bacteria, YidC catalyzes the insertion and assembly of proteins of the inner membrane . Mitochondria of animals, fungi, and plants harbour two distant homologues of YidC: Oxa1 and Cox18/Oxa2 . Oxa1 plays a pivotal role in the integration of mitochondrial translation products into the inner membrane of mitochondria . It contains a C-terminal ribosome-binding domain which physically interacts with mitochondrial ribosomes to facilitate the cotranslational insertion of nascent membrane proteins . The molecular function of Cox18/Oxa2 is not well understood . Employing a functional complementation approach with mitochondria-targeted versions of YidC we show that YidC is able to functionally replace both Oxa1 and Cox18/Oxa2 . However, to integrate mitochondrial translation products into the inner membrane of mitochondria, the ribosome-binding domain of Oxa1 has to be appended onto YidC . On the contrary, the fusion of the ribosome-binding domain onto YidC prevents its ability to complement COX18 mutants suggesting an indispensable post-translational activity of Cox18/Oxa2 . Our observations suggest that during evolution of mitochondria from their bacterial ancestors the two descendents of YidC functionally segregated in order to perform two distinct activities, one co-translational and one post-translational. Clin Microbiol Rev, 2005 Jan, 18(1), 195 - 204 Bacterial contamination of blood components; Brecher ME et al.; Blood for transfusion is a potential source of infection by a variety of known and unknown transmissible agents . Over the last 20 years, astounding reductions in the risk of viral infection via allogeneic blood have been achieved . As a result of this success, bacterial contamination of blood products has emerged as the greatest residual source of transfusion-transmitted disease . This paper summarizes the current status of detection, prevention, and elimination of bacteria in blood products for transfusion. Biochim Biophys Acta, 2005 Jan 18, 1721(1-3), 27 - 36 Epub 2004 Nov 04. Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways; Hudson AO et al.; With the aim of elucidating how plants synthesize lysine, extracts prepared from corn, tobacco, Chlamydomonas and soybean were tested and found to lack detectable amounts of N-alpha-acyl-l,l-diaminopimelate deacylase or N-succinyl-alpha-amino-epsilon-ketopimelate-glutamate aminotransaminase, two key enzymes in the central part of the bacterial pathway for lysine biosynthesis . Corn extracts missing two key enzymes still carried out the overall synthesis of lysine when provided with dihydrodipicolinate . An analysis of available plant DNA sequences was performed to test the veracity of the negative biochemical findings . Orthologs of dihydrodipicolinate reductase and diaminopimelate epimerase (enzymes on each side of the central pathway) were readily found in the Arabidopsis thaliana genome . Orthologs of the known enzymes needed to convert tetrahydrodipicolinate to diaminopimelic acid (DAP) were not detected in Arabidopsis or in the plant DNA sequence databases . The biochemical and reinforcing bioinformatics results provide evidence that plants may use a novel variant of the bacterial pathways for lysine biosynthesis. Chembiochem . 2005 Jan 13; {Epub ahead of print} Structure and Biosynthesis of Myxochromides S(1-3) in Stigmatella aurantiaca: Evidence for an Iterative Bacterial Type I Polyketide Synthase and for Module Skipping in Nonribosomal Peptide Biosynthesis; Wenzel SC et al.; The myxobacterium Stigmatella aurantiaca DW4/3-1 harbours an astonishing variety of secondary metabolic gene clusters, at least two of which were found by gene inactivation experiments to be connected to the biosynthesis of previously unknown metabolites . In this study, we elucidate the structures of myxochromides S(1-3), novel cyclic pentapeptide natural products possessing unsaturated polyketide side chains, and identify the corresponding biosynthetic gene locus, made up of six nonribosomal peptide synthetase modules . By analyzing the deduced substrate specificities of the adenylation domains, it is shown that module 4 is most probably skipped during the biosynthetic process . The polyketide synthase MchA harbours only one module and is presumably responsible for the formation of the variable complete polyketide side chains . These data indicate that MchA is responsible for an unusual iterative polyketide chain assembly. World J Surg . 2005 Jan 6; {Epub ahead of print} Bacterial Translocation: Not a Clinically Relevant Phenomenon in Colorectal Cancer; Takesue Y et al.; The aim of this study was to identify the risk factors for bacterial translocation and to determine the clinical significance of bacterial translocation in patients with colorectal cancer . Mesenteric lymph node sampling was performed to identify the presence of bacterial translocation in 75 patients with colorectal cancer undergoing laparotomy . Bacterial translocation was identified in 29 patients (39%), with the most common organism being Escherichia coli (31%) . Three factors for bacterial translocation were identified, including a preoperative low peripheral lymphocyte count, metastasis to lymph nodes, and invasion depth (= T3) . Stepwise regression analysis, however, selected only = T3 {odds ratio (OR) 4.0, 95% confidence interval (CI) 1.2-13.5} . Altogether, 35% of patients with bacterial translocation developed septic complications, compared with 20% in patients without bacterial translocation . In the multivariate analysis, bacterial translocation was not an independent risk factor for infection, with an OR of 1.8 (95% CI 0.56-5.96) . Systemic inflammatory response syndrome developed on the first day in 62% of patients with bacterial translocation, compared with 50% of patients without bacterial translocation . Adjusting for the other factors, bacterial translocation was not a significant risk factor in the occurrence of systemic inflammatory response syndrome after surgery (OR 1.1, 95% CI 0.37-3.29) . We concluded that n patients with colorectal cancers bacterial translocation does occur and is increased in patients with deep invasion . However, it appears to be of no clinical significance. J Microbiol, 2004 Dec, 42(4), 357 - 60 Bacterial aggregates formation after addition of glucose in Lake Baikal water; Spiglazov LP et al.; For determining the process of bacterial aggregation, glucose was added into water from Lake Baikal which had been stored for seven months . In the presence of a higher concentration of glucose, the abundance of single bacteria and aggregates were higher, but the biovolumes of both bacteria were similar . Theses results mean that both free-living and aggregated bacteria have similar maximum sizes and that aggregates are forming with available organic materials . With available organic materials, the biovolume of aggregates becomes larger. Eur J Gastroenterol Hepatol, 2005 Jan, 17(1), 45 - 51 Intracellular cytokine expression in peritoneal monocyte/macrophages obtained from patients with cirrhosis and presence of bacterial DNA; Frances R et al.; BACKGROUND: The detection of bacterial DNA in serum and ascitic fluid from patients with cirrhosis and ascites is interpreted as molecular evidence of intestinal bacterial translocation and considered sufficient to activate the cellular immune response . In vitro studies on ascitic fluid culture have shown a close relationship between the synthesis of several cytokines and nitric oxide and the presence of bacterial DNA . Since different cell types give rise to cytokines, flow cytometry becomes a powerful tool to discriminate between populations involved in a bacterial challenge . OBJECTIVE: To study the pre-activation status of macrophage/monocyte population ex vivo according to the presence of bacterial DNA . PATIENTS: Patients with cirrhosis and culture-negative, non-neutrocytic ascites, with or without the presence of bacterial DNA in blood and ascitic fluid were studied . METHODS: Flow cytometry analysis of intracellular cytokine expression in monocyte/macrophages from ascitic fluid was performed in basal conditions and after 12 h of cell stimulation adding lypopolysaccharide . RESULTS: Monocyte/macrophages from patients with bacterial DNA showed a significantly higher production of interleukin-6 and tumor necrosis factor alpha in basal conditions than that in cells from patients without the presence of bacterial DNA . The addition of lipopolysaccharide produced a non-significant increment in the expression of these cytokines in patients with the presence of bacterial DNA, while this increment became significant in the other group of patients . CONCLUSIONS: Bacterial translocation in patients with cirrhosis and ascites increases the basal intracellular cytokine expression, reducing its functional reserve capability. J Environ Qual, 2005 Jan-Feb, 34(1), 217 - 26 Bacterial diversity in selenium reduction of agricultural drainage water amended with rice straw; Siddique T et al.; Bacterial reduction of the Se oxyanions selenate {Se(VI)} and selenite {Se(IV)} to elemental selenium {Se(0)} is an important biological process in removing Se from drainage water . This study was conducted to characterize the molecular diversity of bacterial populations involved in Se reduction of drainage water amended with rice (Oryza sativa L.) straw and also to monitor the bacterial community shifts during the course of the study . Selenate was removed in the drainage water by the bacteria 5 to 6 d after addition of rice straw . Six Se(VI)- and 32 Se(IV)-reducing bacteria were isolated from rice straw containing sterilized drainage water . Three Se(VI)- and two Se(IV)-reducing bacteria were also isolated from the drainage water . Identification of Se(VI)- and Se(IV)-reducing bacteria by 16S rDNA sequence analysis showed a broad phylogenetic diversity in Se-reducing assemblages . Three major phyla (Proteobacteria, Actinobacteria, and Firmicutes) of bacterial domain with numerous classes, orders, and families constituted the Se-reducing bacterial community . We documented changes in the composition of bacterial assemblages in the drainage water amended with rice straw using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA . The Shannon-Weaver index (H') revealed higher bacterial diversity at Day 6 in the sterilized and Day 4 in the nonsterilized drainage water amended with rice straw . The results of this study suggest that rice straw, a good source of carbon and energy, harbors a wide range of bacteria useful in Se reduction and may be used in removing Se from drainage water. J Am Acad Nurse Pract, 2004 Dec, 16(12), 555 - 60 A descriptive correlational study of bacterial vaginosis in pregnancy and its association with preterm birth: implications for advanced practice nurses; Mascagni JR et al.; PURPOSE: To expand on prior (often contradictory) research implicating maternal infection as a cause of preterm birth, specifically exploring whether bacterial vaginosis (BV) in pregnancy caused preterm birth in a sample of 103 women in a rural Mississippi obstetric-gynecologic clinic . DATA SOURCES: This descriptive correlational study explored the relationship between BV and preterm birth, using retrospective chart data from a purposive sample of 103 women (for a power level of 95%) from one rural obstetric-gynecologic clinic . CONCLUSIONS: Contrary to the majority of published research, this study did not find a positive correlation between BV and preterm birth . This unexpected result raises questions, particularly given that the preponderance (86%) of women who tested positive for BV during their pregnancy were African American, a population in which both BV and preterm birth are more prevalent . IMPLICATIONS FOR PRACTICE: Whether to screen for BV in pregnancy is a clinically important question not only in terms of the health of mother and child but also in terms of responsible use of resources . Clear findings supporting beneficial health results for screening would dictate screening regardless of the cost . But research continues to lack consensus on the efficacy of BV screening during pregnancy in preventing adverse pregnancy outcomes . In this study, as in some of the literature, the risk of preterm birth did not correlate positively with BV during pregnancy . In the absence of that correlation, cost gains importance . Nurse practitioners (NPs) must use resources wisely, including time, laboratory tests, and medications . Although some specialists recommend screening or treating all pregnant patients for BV, the current practice of not screening or treating all pregnant patients seems warranted until definitive findings establish a conclusive correlation between BV and preterm birth. Clin Gastroenterol Hepatol, 2005 Jan, 3(1), 85 - 9 The role of likelihood ratio in clinical diagnosis: Applicability in the setting of spontaneous bacterial peritonitis; Sierra F et al.; Despite imperfect clinical information and uncertainty about clinical course and outcome, the clinician's main task is to make reasonable decisions about patient care . The clinical history and physical examination typically provide information that is useful for making a diagnosis; however, we still rely on laboratory and radiologic tests to confirm a diagnosis in most cases . Understanding the operative characteristic of a test is of key importance because it can change the probability that a patient has a disease before the result of a test is known . This operative characteristic, better known as the likelihood ratio (LR), is a global assessment of the information provided by a test . The LR allows calculating the odds that a patient has a disease after a test is performed . In this article, we explain the meaning of the LR, how it works, and the applicability of this tool in the setting of a challenging scenario in clinical practice, spontaneous bacterial peritonitis. J Mol Biol, 2005 Feb 4, 345(5), 937 - 55 Epub 2004 Dec 16. Conformational analysis of invariant Peptide sequences in bacterial genomes; Prakash T et al.; The functional significance of evolutionarily conserved motifs/patterns of short regions in proteins is well documented . Although a large number of sequences are conserved, only a small fraction of these are invariant across several organisms . Here, we have examined the structural features of the functionally important peptide sequences, which have been found invariant across diverse bacterial genera . Ramachandran angles (varphi,psi) have been used to analyze the conformation, folding patterns and geometrical location (buried/exposed) of these invariant peptides in different crystal structures harboring these sequences . The analysis indicates that the peptides preferred a single conformation in different protein structures, with the exception of only a few longer peptides that exhibited some conformational variability . In addition, it is noticed that the variability of conformation occurs mainly due to flipping of peptide units about the virtual C(alpha)cdots, three dots, centeredC(alpha) bond . However, for a given invariant peptide, the folding patterns are found to be similar in almost all the cases . Over and above, such peptides are found to be buried in the protein core . Thus, we can safely conclude that these invariant peptides are structurally important for the proteins, since they acquire unique structures across different proteins and can act as structural determinants (SD) of the proteins . The location of these SD peptides on the protein chain indicated that most of them are clustered towards the N-terminal and middle region of the protein with the C-terminal region exhibiting low preference . Another feature that emerges out of this study is that some of these SD peptides can also play the roles of "fold boundaries" or "hinge nucleus" in the protein structure . The study indicates that these SD peptides may act as chain-reversal signatures, guiding the proteins to adopt appropriate folds . In some cases the invariant signature peptides may also act as folding nuclei (FN) of the proteins. Environ Microbiol, 2005 Jan, 7(1), 78 - 87 Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments; Denaro R et al.; Summary The distribution of bacterial communities terminal restriction fragment length polymorphism (T-RFLP) fingerprint patterns was evaluated at three proximal hydrocarbon-contaminated sites located within the harbour of Messina . In order to analyse the short-term variability of the individual terminal restriction fragment (T-RF) patterns, water samples were collected at the three sites on three occasions within 3 months (T(0), T(90) and T(91)) . Four sample sizes, from 50 to 1000 ml for each collected sample, were analysed separately (36 total analysed samples) to evaluate the relationship between the sample size and the bacterial diversity estimates . The dominant T-RF groups mostly belonged to signatures of putative hydrocarbon-degrading bacteria, as revealed by the virtual analysis of the obtained bands . In order to test whether significant differences were occurring between the analysed samples, the Kruskal-Wallis non-parametric test was applied to the T-RF data set . Neither significant influence of the sample size nor short spatial variability within the three sampled sites was detected for each sampling time . On the contrary, significant temporal changes in the diversity of the bacterial communities were observed . These results were confirmed by the non-metric multidimensional scales (nMDS) analysis of the whole set of samples, which indicated three main groups corresponding to the three different sampling times . In summary, the T-RFLP technique, although a polymerase chain reaction-based method, proved to be a suitable technique for monitoring polluted marine environments, typically characterized by low diversity and high relative abundances of a few dominant groups. J Asthma, 2004, 41(8), 863 - 8 Atypical bacterial pneumonia and asthma risk; Sutherland ER et al.; The role of respiratory infections in asthma is poorly understood . Atypical bacteria Mycoplasma pneumoniae and Chlamydia pneumoniae are present in the lower airways of approximately 50% of asthmatics . This study tested the hypothesis that early life community-acquired pneumonia caused by Mycoplasma pneumoniae or Chlamydia pneumoniae is associated with increased asthma prevalence . Thirty-five subjects with a history of community-acquired pneumonia (22 due to atypical bacteria, 13 due to nonatypical pathogens) were evaluated by questionnaire 7-9 years after the episode of pneumonia . Subjects with a history of either typical or atypical pneumonia demonstrated increased asthma prevalence . Current or past asthma prevalence was 55% in subjects with atypical bacterial pneumonia and 61.5% in subjects with nonatypical bacterial pneumonia . Significant between-group differences were not demonstrated with regard to asthma prevalence (risk ratio=0.89; 95% confidence interval=0.49-1.61), current bronchodilator use {1.18 (0.44-3.17)}, and family history of atopy {1.18 (0.73-1.91)}, or asthma {1.63 (0.68-3.88)} . These data suggest that atypical bacterial pneumonia confers a risk of asthma similar to that seen with nonatypical bacterial pneumonia . Prospective studies are warranted to more fully evaluate the importance of atypical bacterial pneumonia as an asthma risk factor. Eur J Clin Invest, 2005 Jan, 35(1), 13 - 6 Identification of different bacterial DNAs in human coronary arteries; Lehtiniemi J et al.; Abstract Background Various studies have suggested a link between infection, atherosclerosis and coronary artery disease . We studied whether bacterial DNA is present in coronary specimens obtained from left anterior descending coronary arteries of subjects having sudden deaths of cardiovascular and other causes, as verified by an autopsy . Materials and methods Coronary specimens were obtained from five subjects who died of sudden coronary causes and five controls . Broad-range 16-s rDNA PCR (Br-PCR) amplification, cloning and sequencing were used to detect bacterial rDNA . Results Bacterial rDNA sequences of oral pathogens were detected from the coronary samples in all cases regardless of the cause of death . Conclusions Br-PCR is a powerful method to detect bacterial rDNA . By this method we were able to detect wide palette of oral bacteria from coronary tissues . Our findings suggest that atheromas may act as mechanical sieves collecting bacteria from the circulation . Eur J Clin Invest 2005; 35 (1): 13-16. J Antibiot (Tokyo), 2004 Oct, 57(10), 639 - 46 A-503083 A, B, E and F, novel inhibitors of bacterial translocase I, produced by Streptomyces sp . SANK 62799; Muramatsu Y et al.; Novel nucleoside antibiotics were isolated from the cultured broth of the strain classified as Streptomyces sp . SANK 62799 . The strain produced four novel capuramycin derivatives designated as A-503083 A, B, E and F . Their structures were elucidated as 2'-O-carbamoyl derivatives of A-500359 A, B (capuramycin), E and F, respectively . A-503083 A, B, E and F inhibited bacterial phospho-N-acetylmuramyl-pentapeptide-translocase (translocase I: EC 2.7.8.13) with IC50 values of 0.024, 0.038, 0.135 and 17.9 microM, respectively. Res Microbiol, 2005 Jan-Feb, 156(1), 1 - 6 Bacterial conjugation: a potential tool for genomic engineering; Llosa M et al.; Bacterial conjugation is a mechanism for horizontal DNA transfer with potential for universal DNA delivery . The conjugal machinery can be separated into three functional modules: the relaxosome, the coupling protein, and a type IV protein secretion system . Module interchangeability among different conjugative systems opens up the possibility of "a la carte" engineering of DNA delivery into virtually any cell type. Rev Med Chil, 2004 Oct, 132(10), 1217 - 20 {Malignant middle cerebral artery territory infarct in one patient with bacterial meningitis}; Lopez MG et al.; The mortality of acute bacterial meningitis (BM) has remained stable in the last decades in spite of the use of new antibiotics, probably due to vascular complications . We report a 68-year-old woman with BM who had a malignant infarction of left middle cerebral artery territory 72 hours after admission to the hospital . The patient experienced a bad evolution and died four days after admission . The arterial involvement in patients with BM is explained by vasospasm of large arteries and vasculitis of small arteries . The medical treatment of a malignant middle cerebral artery infarct has a high mortality. Plant Mol Biol, 2004 Nov, 56(4), 555 - 61 Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz); Tomkins J et al.; Pest and disease problems are important constraints of cassava production and host plant resistance is the most efficient method of combating them . Breeding for host plant resistance is considerably slowed down by the crop's biological constraints of a long growth cycle, high levels of heterozygosity and a large genetic load . More efficient methods such as gene cloning and transgenesis are required to deploy resistance genes . To facilitate the cloning of resistance genes, bacterial artificial chromosome (BAC) library resources have been developed for cassava . Two libraries were constructed from the cassava clones, TMS 30001, resistant to the cassava mosaic disease (CMD) and the cassava bacterial blight (CBB), and MECU72, resistant to cassava white fly . The TMS30001 library has 55 296 clones with an insert size range of 40-150 kb with an average of 80 kb, while the MECU72 library consists of 92 160 clones and an insert size range of 25-250 kb average of 93 kb . Based on a genome size of 772 Mb, the TMS30001 and MECU72 libraries have a 5 and 11.3 haploid genome equivalents and a 95 and 99 chance of finding any sequence, respectively . To demonstrate the potential of the libraries, the TMS30001 library was screened by southern hybridization using a cassava analog (CBB1) of the Xa21 gene from rice that maps to a region containing a QTL for resistance to CBB as probe . Five BAC clones that hybridized to CBB1 were isolated and a Hind III fingerprint revealed 2-3 copies of the gene in individual BAC clones . A larger scale analysis of resistance gene analogs (RGAs) in cassava has also been conducted in order to understand the number and organization of RGAs . To scan for gene and repeat DNA content in the libraries, end-sequencing was performed on 2301 clones from the MECU72 library . A total of 1705 unique sequences were obtained with an average size of 715 bp . Database homology searches using BLAST revealed that 458 sequences had significant homology with known proteins and 321 with transposable elements . The use of the library in positional cloning of pest and disease resistance genes is discussed. Mol Cell, 2005 Jan 7, 17(1), 113 - 20 Suppression of Homologous and Homeologous Recombination by the Bacterial MutS2 Protein; Pinto AV et al.; In addition to their role in DNA repair, recombination events are associated with processes aimed at providing the genetic variability needed for adaptation and evolution of a population . In bacteria, recombination is involved in the appearance of new variants by allowing the incorporation of exogenous DNA or the reshuffling of endogenous sequences . Here we show that HpMutS2, a protein belonging to the MutS2 family in Helicobacter pylori, is not involved in mismatch repair but inhibits homologous and homeologous recombination . Disruption of HpmutS2 leads to an increased efficiency of exogenous DNA incorporation . HpMutS2 has a selective affinity for DNA structures mimicking recombination intermediates with no specificity for homoduplex DNA or mismatches . The purified protein has an ATPase activity stimulated by the same DNA structures . Finally, we show that HpMutS2 inhibits DNA strand exchange reactions in vitro . Thus, MutS2 proteins are candidates for controlling recombination and therefore genetic diversity in bacteria. Anal Chem, 2005 Jan 1, 77(1), 327 - 34 Microfluidic immunoassay for bacterial toxins with supported phospholipid bilayer membranes on poly(dimethylsiloxane); Phillips KS et al.; We report a heterogeneous immunoassay for cholera toxin (CT) using supported bilayer membranes (SBMs) in a poly(dimethylsiloxane) (PDMS) microfluidic device . Phosphatidylcholine membranes assembled on plasma-oxidized PDMS by vesicle fusion bring about favorable surface properties, such as improved wettability and protein resistance . Contact angle measurements show that the lipid membranes can preserve hydrophilic surfaces for hours, whereas untreated substrates rapidly undergo hydrophobic recovery . Fluorescence recovery after photobleaching performed in situ reveals that the membranes have relatively high lateral mobility . Experimental data-fitting to theoretical models yields diffusion coefficients of 1.8 +/- 0.7 microm(2)/s on PDMS and 3.4 +/- 0.8 microm(2)/s on glass . Fluorescence studies utilizing tagged proteins show that SBMs reduce nonspecific adsorption of avidin and BSA on PDMS by 2-3 orders of magnitude, as compared to that on plasma oxidized surfaces . SBMs and their protein-resistant properties are not significantly affected by long flow times, indicating good membrane stability . These studies increase our understanding of the relationship between molecular level interactions and membrane properties, allowing for development of a rapid heterogeneous immunoassay for CT in PDMS microchips with cell surface receptor molecules . Using optimized sample injection and buffer washing conditions, microfluidic immunoassay of CT is complete within 25 min, and a dynamic range over 3 orders of magnitude with a detection limit of 8 fmol of toxin is achieved. Anal Biochem, 2005 Jan 15, 336(2), 300 - 4 Quantitative nonisotopic nitrocellulose filter binding assays: bacterial manganese superoxide dismutase-DNA interactions; Czerwinski JD et al.; Nitrocellulose filter binding assays (NCFBAs) have been used for many years to qualitatively and quantitatively determine protein-nucleic acid affinities . While this technique can be robust thermodynamically and fairly simple to perform, the requirement of radiolabeled nucleic acids (typically (32)P) has several major drawbacks . Some disadvantages are the short half-life of (32)P, the inherent safety concerns, and the cost of working with radioisotopes . Another drawback is that over time the beta emissions cause fragmentation of the nucleic acids . We have modified standard NCFBAs by developing a quantitative nonisotopic chemiluminescent method using biotin-labeled DNA and a dual-filter format . The biotin tag is detected on both nitrocellulose and positively charged nylon membranes by conventional streptavidin-conjugated alkaline phosphatase recognition systems . Quantitation of the photon emissions is simplified by use of a cooled charge-coupled device camera, although exposure to X-ray film and quantitation by densitometry could also be employed . The binding affinity of bacterial manganese superoxide dismutase to nonsequence-specific DNA has been quantitated previously by standard NCFBAs . We have replicated parts of a published binding study using identical solution conditions and the nonisotopic method that we have developed . We provide quantitative agreement between the isotopic and the nonisotopic methods. Biosci Biotechnol Biochem, 2004 Dec, 68(12), 2451 - 6 Analysis of Bacterial Glucose Dehydrogenase Homologs from Thermoacidophilic Archaeon Thermoplasma acidophilum: Finding and Characterization of Aldohexose Dehydrogenase; Nishiya Y et al.; The NADP(+)-preferring glucose dehydrogenase from thermoacidophilic archaeon Thermoplasma acidophilum has been characterized, and its crystal structure has been determined (Structure, 2:385-393, 1994) . Its sequence and structure are not homologous to bacterial NAD(P)(+)-dependent glucose dehydrogenases, and its molecular weight is also quite defferent . On the other hand, three functionally unknown genes with homologies to bacterial NAD(P)(+)-dependent glucose dehydrogenases have been sequenced as part of the T . acidophilum genome project (gene names: Ta0191, Ta0747, and Ta0754 respectively) . We expressed two genes of three, Ta0191 and Ta0754, in Escherichia coli, and purified the gene products to homogeneity . Dehydrogenase activities were thereby detected from the purified proteins . The Ta0754 gene product exhibited aldohexose dehydrogenase activity, and the Ta0191 gene product exhibited weak 2-deoxyglucose dehydrogenase activity . No aldohexose dehydrogenase gene has been isolated, while the enzyme was reported in 1968 . This is the first report of the gene and primary structure . The purified Ta0754 gene product, designated AldT, was characterized . The enzyme AldT effectively catalyzed the oxidation of various aldohexoses, especially D-mannose . Lower activities on D-2-deoxyglucose, D-xylose, D-glucose, and D-fucose were detected although no activities were shown on other aldohexoses or additional sugars . As a cofactor, NAD(+) was much more suitable for the activity than NADP(+) . The NAD(+)-preferring dehydrogenase most effectively reacting to D-mannose is for the first time . AldT was most active at pH 10 and above 70 degrees C, and completely stable up to 60 degrees C after incubation for 15 min . Other enzymatic properties were also investigated. J Biol Chem . 2004 Dec 23; {Epub ahead of print} The bacterial ATPase SecA functions as a monomer In protein translocation; Or E et al.; The ATPase SecA drives the post-translational translocation of proteins through the SecY channel in the bacterial inner membrane . SecA is a dimer which can dissociate into monomers under certain conditions . To address the functional importance of the monomeric state, we generated an E . coli SecA mutant that is almost completely monomeric (>99%), consistent with predictions from the crystal structure of B . subtilis SecA . In vitro, the monomeric derivative retained significant activity in various assays and in vivo, it sustained 85% of the growth rate of wild type cells and reduced the accumulation of precursor proteins in the cytoplasm . Disulfide cross-linking in intact cells showed that mutant SecA is monomeric and that even its parental dimeric form is dissociated . Our results suggest that SecA functions as a monomer during protein translocation in vivo. Infect Immun, 2005 Jan, 73(1), 657 - 60 Relative contributions of innate and acquired host responses to bacterial control and arthritis development in Lyme disease; Wang X et al.; TLR2(-/-)/scid double-mutant mice were infected with B . burgdorferi to assess the relative importance of acquired and innate host defenses . Although spirochete levels at 4 weeks were lower in TLR2(-/-) mice than in TLR2(-/-)/scid mice, the increased arthritis severity of TLR2 (Toll-like receptor 2)-deficient mice was reduced by the presence of the scid mutation. Surgery, 2005 Jan, 137(1), 85 - 91 Apoptosis inhibition plays a greater role than necrosis inhibition in decreasing bacterial translocation in experimental intestinal transplantation; Azuara D et al.; BACKGROUND: During small-bowel transplantation, necrosis and apoptosis are involved in the destruction of intestinal epithelial cells . This study was conducted to assess which mode of cell death plays a greater role as a trigger of the bacterial translocation (BT) associated with intestinal transplantation . METHODS: The following experimental groups were studied: sham, Tx (intestinal transplantation), Tx + poly (ADP-ribose) synthetase (PARS) inhibitor 3-aminobenzamide (3-AB), and Tx + caspase inhibitor Z-VAD-fmk . Histological analysis, caspase-3 activity, DNA fragmentation, and BT were measured in tissue samples after transplantation . RESULTS: During intestinal transplantation, apoptosis and necrosis both increased, showing graft injury and high levels of BT . Rats treated with 3-AB showed histological protection of the transplanted graft and a tendency toward lower BT despite the existence of high apoptosis levels . The rats treated with Z-VAD showed histological protection of the transplanted graft and decreased levels of caspase-3 and DNA fragmentation . The Tx + Z-VAD group showed the lowest levels of BT in all tissues . CONCLUSIONS: In small intestinal transplantation, both apoptosis and cell necrosis give rise to histological injury and BT . Apoptosis inhibition and necrosis inhibition treatments protect intestinal grafts from ischemia/reperfusion injury; Z-VAD supplementation has a greater effect on BT prevention than does administration of the PARS inhibitor 3-AB. J Biol Chem . 2004 Dec 21; {Epub ahead of print} Two heme binding sites are involved in the regulated degradation of the bacterial iron response regulator (Irr) protein; Yang J et al.; The iron response regulator (Irr) protein from Bradyrhizobium japonicum is a conditionally stable protein that degrades in response to cellular iron availability . This turnover is heme-dependent, and rapid degradation involves heme binding to a heme regulatory motif (HRM) of Irr . Here, we show that Irr confers iron-dependent instability on glutathione S-transferase (GST) when fused to it . Analysis of Irr-GST derivatives with C-terminal truncations of Irr implicated a second region necessary for degradation other than the HRM, and showed that the HRM was not sufficient to confer instability on GST . The HRM-defective mutant IrrC29A degraded in the presence of iron, but much more slowly than the wild type protein . This slow turnover was heme-dependent as discerned by the stability of Irr in a heme-defective mutant strain . Whereas the HRM of purified recombinant Irr binds ferric (oxidized) heme, a second site that binds ferrous (reduced) heme was identified based on spectral analysis of truncation and substitution mutants . A mutant in which histidines 117 to 119 were changed to alanines severely diminished ferrous, but not ferric, heme binding . Introduction of these substitutions in an Irr-GST fusion stabilized the protein in vivo in the presence of iron . We conclude that normal iron-dependent Irr degradation involves two heme binding sites, and that both redox states of heme are required for rapid turnover. Bioinformatics . 2004 Dec 21; {Epub ahead of print} Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection; Guthke R et al.; MOTIVATION: The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions . We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks . The proposed approach is based on both, microarray data and available biological knowledge . RESULTS: The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series) . The number of clusters was optimized using various evaluation criteria . For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge . Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes . For the construction of hypothetical network structures Singular Value Decomposition (SVD) based methods and a here newly introduced heuristic Network Generation Method were compared . It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Eur J Neurol, 2005 Jan, 12(1), 67 - 9 Fulminant acute disseminated encephalomyelitis mimicking acute bacterial menigoencephalitis; Harloff A et al.; Most patients with acute disseminated encephalomyelitis (ADEM) recover quickly under corticosteroid treatment and have a favourable long-term prognosis . We report on a young woman with acute onset of an extensive and solitary white-matter lesion in the left hemisphere . Fever, high pleocytosis and elevated protein in cerebrospinal fluid initially suggested bacterial meningoencephalitis . The patient died from brain herniation despite maximal conservative therapy . Histological changes in necropsy were consistent with the diagnosis ADEM . Treatment options of fulminant ADEM are discussed. Lett Appl Microbiol, 2005, 40(1), 12 - 8 The influence of environmental adaptation on bacterial genome structure; Fadiel A et al.; Abstract a . fadiel, s . lithwick and f . naftolin . 2004.Aims: Researchers have long been puzzled by the diversity of life . Now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa . The aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches . Methods and Results: Coding sequences from three phylogenetically related bacterial species namely Mycoplasma genitalium, M . pneumoniae and Ureaplasma urealyticum were subject to in depth sequence analyses . M . genitalium and M . pneumoniae both belong to the genus Mycoplasma while U . urealyticum is a member of the genus Ureaplasma . However, M . genitalium and U . urealyticum are urogenital pathogens while M . pneumoniae is a respiratory pathogen . Complete transcriptomes were downloaded from NCBI for each species, and were subject to in silico investigation using in-house software, and public sequence analysis tools . Clear similarities in transcriptome structure were identified among the functionally similar species M . genitalium and U . urealyticum while no such relationship was identified among the phylogenetically related species M . genitalium and M . pneumoniae . Conclusions: It is plausible to conclude that, in these bacterial species, environmental stimuli might be more influential in shaping sequence signatures than phylogenetic relationships . Significance and Impact of the Study: This study suggests that molecular signatures within the transcriptomes of the species examined are likely to be a product of evolutionary adaptation to diverse environmental ecological stimuli, and not a result of common phylogeny. J Comp Neurol, 2005 Feb 7, 482(2), 123 - 41 Glycinergic neurons expressing enhanced green fluorescent protein in bacterial artificial chromosome transgenic mice; Zeilhofer HU et al.; Although glycine is a major inhibitory transmitter in the mammalian CNS, the role of glycinergic neurons in defined neuronal circuits remains ill defined . This is due in part to difficulties in identifying these cells in living slice preparations for electrophysiological recordings and visualizing their axonal projections . To facilitate the morphological and functional analysis of glycinergic neurons, we generated bacterial artificial chromosome (BAC) transgenic mice, which specifically express enhanced green fluorescent protein (EGFP) under the control of the promotor of the glycine transporter (GlyT) 2 gene, which is a reliable marker for glycinergic neurons . Neurons expressing GlyT2-EGFP were intensely fluorescent, and their dendrites and axons could be visualized in great detail . Numerous positive neurons were detected in the spinal cord, brainstem, and cerebellum . The hypothalamus, intralaminar nuclei of the thalamus, and basal forebrain also received a dense GlyT2-EGFP innervation, whereas in the olfactory bulb, striatum, neocortex, hippocampus, and amygdala positive fibers were much less abundant . No GlyT2-EGFP-positive cell bodies were seen in the forebrain . On the subcellular level, GlyT2-EGFP fluorescence was colocalized extensively with glycine immunoreactivity in somata and dendrites and with both glycine and GlyT2 immunoreactivity in axon terminals, as shown by triple staining at all levels of the neuraxis, confirming the selective expression of the transgene in glycinergic neurons . In slice preparations of the spinal cord, no difference between the functional properties of EGFP-positive and negative neurons could be detected, confirming the utility of visually identifying glycinergic neurons to investigate their functional role in electrophysiological studies . J . Comp . Neurol . 482:123-141, 2005 . (c) 2004 Wiley-Liss, Inc. Biochemistry, 2004 Dec 28, 43(51), 16487 - 96 Carotenoid-induced cooperative formation of bacterial photosynthetic LH1 complex; Fiedor L et al.; A simple reconstitution technique has been developed and then applied to prepare a series of light-harvesting antenna 1 (LH1) complexes with a programmed carotenoid composition, not available from native photosynthetic membranes . The complexes were reconstituted with different C(40) carotenoids, having two structural parameters variable: the functional side groups and the number of conjugated C-C double bonds, systematically increasing from 9 to 13 . The complexes, differing only in the type of carotenoid, bound to an otherwise identical bacteriochlorophyll-polypeptide matrix, can serve as a unique model system in which the relationship between the carotenoid character and the functioning of pigment-protein complexes can be investigated . The reconstituted LH1 complexes resemble the native antenna, isolated from wild-type Rhodospirillum rubrum, but their coloration is entirely determined by carotenoid . Along with the increase in its conjugation size, the carotenoid absorption transitions gradually shift to the red . Thus, the extension of the conjugation size of the antenna carotenoids provides a mechanism for the spectral tuning of light harvesting in the visible part of the spectrum . The carotenoids in the reconstitution system promote the LH1 formation and seem to bind and transfer the excitation energy specifically only to a species with characteristically red-shifted absorption and emission maxima, apparently, due to a cooperative effect . Monitoring the LH1 formation by steady-state absorption and fluorescence spectroscopies reveals that in the presence of carotenoids it proceeds without spectrally resolved intermediates, leading directly to B880 . The effect of the carotenoid is enhanced when the pigment contains the hydroxy or methoxy side groups, implying that, in parallel to hydrophobic interactions and pi-pi stacking, other interactions are also involved in the formation and stabilization of LH1. J Infect Dis, 2005 Jan 15, 191(2), 299 - 306 Epub 2004 Dec 09. 16alpha-Bromoepiandrosterone restores T helper cell type 1 activity and accelerates chemotherapy-induced bacterial clearance in a model of progressive pulmonary tuberculosis; Hernandez-Pando R et al.; BALB/c mice with pulmonary tuberculosis develop a T helper cell type 1 response that peaks at 3 weeks, temporarily controlling bacterial growth . Then bacterial proliferation recommences, accompanied by increasing interleukin (IL)-4 levels and decreasing interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, and inducible nitric oxide synthase (iNOS) levels . These changes mimic those in the human disease . In a previous study, administration of dehydroepiandrosterone (DHEA) beginning on day 60 after infection reversed these changes and protected the mice . However, DHEA is suboptimal for human use, partly because it is readily metabolized into sex steroids . 16alpha-Bromoepiandrosterone (EpiBr; 16alpha -bromo-5alpha -androstan-3beta-ol-17-one) is a synthetic adrenal steroid derivative that does not enter sex steroid pathways . In the present study, when tuberculous BALB/c mice were treated with EpiBr 3 times/week beginning on day 60, inhibition of bacterial proliferation and increased expression of TNF-alpha, IFN-gamma, and iNOS were observed, although decreased expression of IL-4 was also observed . Moreover, when given as an adjunct to conventional chemotherapy, EpiBr enhanced bacterial clearance . Trials for the use of EpiBr in the treatment of human tuberculosis are now justified. Nucleic Acids Res, 2005 Jan 1, 33 Database Issue, D325 - 8 VFDB: a reference database for bacterial virulence factors; Chen L et al.; Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century . Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the mechanisms of the disease processes at the molecular level over the last decades . To facilitate future research, it becomes necessary to form a database collectively presenting the virulence factors (VFs) of various medical significant bacterial pathogens . The aim of virulence factor database (VFDB) is to provide such a source for scientists to rapidly access to current knowledge about VFs from various bacterial pathogens . VFDB is comprehensive and user-friendly . One can search VFDB by browsing each genus or by typing keywords . Furthermore, a BLAST search tool against all known VF-related genes is also available . VFDB provides a unified gateway to store, search, retrieve and update information about VFs from various bacterial pathogens. Pediatr Neurol, 2005 Jan, 32(1), 72 - 74 Diagnosis of bacterial cerebellitis: Diffusion imaging and proton magnetic resonance spectroscopy; Jaggi RS et al.; Diffusion-weighted imaging and in vivo proton magnetic resonance spectroscopy ((1)H magnetic resonance spectroscopy) have demonstrated great potential in differentiating intracranial lesions of various pathologies . This report describes a case of a 12-year-old child with cerebellitis and subdural empyema that manifested presence of succinate, acetate, lactate, and amino acids on in vivo (1)H magnetic resonance spectroscopy from a large area of restricted diffusion in the vermis on diffusion-weighted imaging, a finding specific for bacteria-induced infection . The child made a complete clinical and imaging recovery on conservative management. J Biotechnol, 2005 Jan 12, 115(1), 11 - 21 Electronic microarray analysis of 16S rDNA amplicons for bacterial detection; Barlaan EA et al.; Electronic microarray technology is a potential alternative in bacterial detection and identification . However, conditions for bacterial detection by electronic microarray need optimization . Using the NanoChip electronic microarray, we investigated eight marine bacterial species . Based on the 16S rDNA sequences of these species, we constructed primers, reporter probes, and species-specific capture probes . We carried out two separate analyses for longer (533bp) and shorter (350 and 200bp) amplified products (amplicons) . To detect simultaneously the hybridization signals for the 350- and 200-bp amplicons, we designed a common reporter probe from an overlapping sequence within both fragments . We developed methods to optimize detection of hybridization signals for processing the DNA chips . A matrix analysis was performed for different bacterial species and complementary capture probes on electronic microarrays . Results showed that, when using the longer amplicon, not all bacterial targets hybridized with the complementary capture probes, which was characterized by the presence of false-positive signals . However, with the shorter amplicons, all bacterial species were correctly and completely detected using the constructed complementary capture probes. Clin Exp Immunol, 2005 Jan, 139(1), 43 - 7 Influence of age and duration of infection on bacterial load and immune responses to Helicobacter pylori infection in a murine model; Minoura T et al.; Summary Using a murine model, we previously showed that Helicobacter pylori infects and colonizes offspring via maternal transmission during the nursing period . The aim of this study was to investigate the influence of age and duration of infection on inflammatory and immune responses to H . pylori in infant and adult mice . During the breast-feeding period, the number of bacteria was significantly suppressed in 1-week-old mice infected with H . pylori at an early stage of nursing, compared with adult mice, suggesting that breast-milk induces such low colonization . In addition, these mice had weaker gastric inflammation, especially Th1 cytokine and humoral responses than in mice infected with H . pylori after weaning in spite of elevated levels of Th1 cytokines . Although infant mice showed low inflammatory responses against H . pylori, they produced H . pylori-specific antibodies following vaccination with oral or parenteral adjuvant . Our results suggest the importance of age at the time of primary infection on bacterial load, gastric inflammation and humoral responses in a murine model of H . pylori infection. Ginekol Pol, 2004 Sep, 75(9), 733 - 40 {Bacterial vaginosis}; Ostaszewska-Puchalska I et al.; Bacterial vaginosis (BV) is one of the most common lower genital tract infections among women of childbearing age . This paper is a survey of literature data concerning epidemiology, pathogenesis, clinical and laboratory diagnostic criteria of this clinical syndrome. FEMS Microbiol Lett, 2004 Dec 15, 241(2), 129 - 134 Displaying the relatedness among isolates of bacterial species - the eBURST approach; Spratt BG et al.; Determining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species . In many cases, a bifurcating tree can be positively misleading . The recently described program eBURST can be used with multilocus data to define groups or clonal complexes of related isolates derived from a common ancestor, the patterns of descent linking them together, and the ancestral genotype . eBURST has recently been extensively updated to include additional tools for exploring the relationships between isolates . We discuss the advantages of this approach and describe its use to explore patterns of descent within clonal complexes identified using multilocus sequence typing. Mol Plant Microbe Interact, 2004 Dec, 17(12), 1376 - 84 Relationship between avirulence gene (avrA) diversity in Ralstonia solanacearum and bacterial wilt incidence; Robertson AE et al.; Bacterial wilt, caused by Ralstonia solanacearum, is a serious disease of tobacco in North and South Carolina . In contrast, the disease rarely occurs on tobacco in Georgia and Florida, although bacterial wilt is a common problem on tomato . We investigated whether this difference in disease incidence could be explained by qualitative characteristics of avirulence gene avrA in the R . solanacearum population in the southeastern United States . Sequence analysis established that wild-type avrA has a 792-bp open reading frame . Polymerase chain reaction (PCR) amplification of avrA from 139 R . solanacearum strains generated either 792-bp or approximately 960-bp DNA fragments . Strains that elicited a hypersensitive reaction (HR) on tobacco contained the 792-bp allele, and were pathogenic on tomato and avirulent on tobacco . All HR-negative strains generated a approximately 960-bp DNA fragment, and wilted both tomato and tobacco . The DNA sequence of avrA in six HR-negative strains revealed the presence of one of two putative miniature inverted-repeat transposable elements (MITEs): a 152-bp MITE between nucleotides 542 and 543, or a 170-bp MITE between nucleotides 461 and 462 or 574 and 575 . Southern analysis suggested that the 170-bp MITE is unique to strains from the southeastern United States and the Caribbean . Mutated avrA alleles were present in strains from 96 and 75% of North and South Carolina sites, respectively, and only in 13 and 0% of the sites in Georgia and Florida, respectively . Introduction of the wildtype allele on a plasmid into four HR-negative strains reduced their virulence on both tobacco and tomato . Inactivation of avrA in an HR-positive, avirulent strain, resulted in a mutant that was weakly virulent on tobacco . Thus, the incidence of bacterial wilt of tobacco in the southeastern United States is partially explained by which avrA allele dominates the local R . solanacearum population. Alcohol, 2004 Jul, 33(3), 199 - 208 Impaired intestinal immunity and barrier function: a cause for enhanced bacterial translocation in alcohol intoxication and burn injury; Choudhry MA et al.; Alcohol intoxication is being recognized increasingly as the major factor in pathogenesis after burn injury . Findings from multiple studies support the suggestion that, in comparison with burn-injured patients who sustained injury in the absence of alcohol intoxication, burn-injured patients who sustained injury under the influence of alcohol exhibit higher rates of infection and are more likely to die . Thus, infection becomes the primary cause of death in burn-injured patients . Because the intestine is considered to be a major source of bacteria, studies in experimental animals have been designed to examine whether alcohol intoxication before burn injury enhances bacterial translocation from the intestine . Results of these studies have shown a several-fold increase in bacterial translocation from the intestine in the group of animals receiving combined insult of alcohol intoxication and burn injury compared with findings for the groups receiving either insult alone . Alcohol intoxication and burn injury independent of each other have also been shown to cause an increase in bacterial translocation . The gastrointestinal tract normally maintains a physical mucosal and immunologic barrier that provides an effective defense in keeping bacteria within the intestinal lumen . However, in injury conditions these defense mechanisms are impaired . Intestinal bacteria consequently gain access to extraintestinal sites . Intestine-derived bacteria are implicated in causing systemic infection and in subsequent multiple organ dysfunction in both immunocompromised patients and patients with injury, such as burn and trauma . In this article, we discuss three potential mechanisms that are likely to contribute to the increase in bacterial translocation in alcohol intoxication and burn injury: (1) increase in bacterial growth in the intestine, (2) physical disruption of mucosal barrier of the intestine, and (3) suppression of the immune defense in the intestine. Bioinformatics, 2003 Sep 1, 19(13), 1707 - 9 Intergenic sequence inspector: searching and identifying bacterial RNAs; Pichon C et al.; Intergenic Sequence Inspector (ISI) is a program that helps in identifying bacterial ribonucleic acids (RNAs).It automatically extracts, selects and visualizes candidate intergenic regions (IGRs) that bear conservations between phylogenetically related species, displaying sequence and structural signatures of RNA genes encompassing putative promoters, terminators, RNA secondary structure predictions and the G+C percent of the selected sequences . ISI is intentionally modular to analyze various bacterial genomes according to their intrinsic specificities and to the available data . ISI provides a sum of information to the user who can evaluate whether or not an IGR is susceptible to express RNAs. Eur Cell Mater, 2004 Dec 07, 8, 37 - 57; discussion 37-57 Concise review of mechanisms of bacterial adhesion to biomaterials and of techniques used in estimating bacteria-material interactions; Katsikogianni M et al.; This article reviews the mechanisms of bacterial adhesion to biomaterial surfaces, the factors affecting the adhesion, the techniques used in estimating bacteria-material interactions and the models that have been developed in order to predict adhesion . The process of bacterial adhesion includes an initial physicochemical interaction phase and a late molecular and cellular one . It is a complicated process influenced by many factors, including the bacterial properties, the material surface characteristics, the environmental factors, such as the presence of serum proteins and the associated flow conditions . Two categories of techniques used in estimating bacteria-material interactions are described: those that utilize fluid flowing against the adhered bacteria and counting the percentage of bacteria that detach, and those that manipulate single bacteria in various configurations which lend themselves to more specific force application and provide the basis for theoretical analysis of the receptor-ligand interactions . The theories that are reviewed are the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the thermodynamic approach and the extended DLVO theory . Over the years, significant work has been done to investigate the process of bacterial adhesion to biomaterial surfaces, however a lot of questions still remain unanswered. Am J Obstet Gynecol, 2004 Dec, 191(6), 1898 - 906 Intravaginal metronidazole gel versus metronidazole plus nystatin ovules for bacterial vaginosis: a randomized controlled trial; Sanchez S et al.; OBJECTIVE: We compared metronidazole 0.75% gel (containing 37.5 mg metronidazole per dose) with ovules containing metronidazole 500 mg and nystatin 100,000 U, for intravaginal treatment of bacterial vaginosis (BV) . STUDY DESIGN: In a single-blinded trial, symptomatic women with BV by both Amsel and Nugent criteria were randomly assigned to gel or ovules, once nightly for 5 nights, and asked to return 3 times after treatment . Analyses were intent-to-treat . RESULTS: Of 151 women with BV by both criteria at enrollment, 138 (91%) returned at least once . Product limit estimates for persistence or recurrence of BV at 14, 42, and 104 days were 20% (95% CI 10%-29%), 38% (95% CI 25%-48%), and 52% (95% CI 37%-63%) after gel treatment, and 4% (95% CI 0%-9%), 17% (95% CI 7%-26%), and 33% (95% CI 21%-46%) after ovule treatment ( P = .01) . Among women without BV at first follow-up, subsequent intercourse without condoms independently predicted subsequent recurrence ( P </= .01) . CONCLUSION: Metronidazole/nystatin ovules were significantly more effective than metronidazole gel . Unprotected sex predicted recurrence after initial improvement. J Neuroimmunol, 2005 Jan, 158(1-2), 40 - 9 STAT3 activation and c-FOS expression in the brain following peripheral administration of bacterial DNA; Sako K et al.; To study the role of bacterial DNA in the brain function, we investigated signal transducer and activator of transcription 3 (STAT3) activation and c-FOS expression in the brain by immunohistochemistry in response to peripheral administration of CpG-DNA . CpG-DNA induced phospho-STAT3-immunoreactive cells and c-FOS-positive cells in several brain regions in a different manner . Phospho-STAT3-immunoreactive cells were observed in the circumventricular organs where the blood-brain barrier is weak . On the other hand, CpG-DNA increased c-FOS-positive cells in the paraventricular nucleus of the hypothalamus, and the nucleus of the tractus solitarius (NTS) and the area postrema . Unilateral cervical vagotomy did not modify CpG-DNA-induced c-FOS expression in the NTS, indicating that CpG-DNA-induced activation of the NTS is independent of the afferent vagus nerve input originating from the subdiaphragmatic organs . On the other hand, Toll-like receptor 9 mRNA was expressed in the nodose ganglion . Therefore, it is possible that CpG-DNA activates afferent vagus nerve through the nodose ganglion which subsequently activates the NTS . Present observations represented that peripheral CpG-DNA induced immune event in the brain, and that not only c-FOS but also phosphorylation of STAT3 can be a useful indicator for evaluation of neuro-immune interaction. J Immunol, 2004 Dec 15, 173(12), 7490 - 6 IL-27 signaling compromises control of bacterial growth in mycobacteria-infected mice; Pearl JE et al.; Resistance to tuberculosis (TB) is dependent on the induction of Ag-specific CD4 Th1 T cells capable of expressing IFN-gamma . Generation of these T cells is dependent upon IL-12p70, yet other cytokines have also been implicated in this process . One such cytokine, IL-27, augments differentiation of naive T cells toward an IFN-gamma-producing phenotype by up-regulating the transcription factor T-bet and promoting expression of the IL-12Rbeta2 chain allowing T cells to respond to IL-12p70 . We show that the components of IL-27 are induced during TB and that the absence of IL-27 signaling results in an altered disease profile . In the absence of the IL-27R, there is reduced bacterial burden and an increased lymphocytic character to the TB granuloma . Although the number of Ag-specific CD4 IFN-gamma-producing cells is unaffected by the absence of the IL-27R, there is a significant decrease in the level of mRNA for IFN-gamma and T-bet within the lungs of infected IL-27R(-/-) mice . Ag-specific CD4 T cells in the lungs of IL-27R(-/-) also produce less IFN-gamma protein per cell . The data show that expression of IL-27 during TB is detrimental to the control of bacteria and that although it does not affect the number of cells capable of producing IFN-gamma it does reduce the ability of CD4 T cells to produce large amounts of IFN-gamma . Because IFN-gamma is detrimental to the survival of effector T cells, we hypothesize that the reduced IFN-gamma within the IL-27R(-/-) lung is responsible for the increased accumulation of lymphocytes within the mycobacterial granuloma. J Immunol, 2004 Dec 15, 173(12), 7401 - 5 TLR2 recognizes a bacterial lipopeptide through direct binding; Vasselon T et al.; The TLRs play an important role in the initiation of cellular innate immune responses to a wide range of bacterial products, including LPS and lipoproteins . Although rapid progress has been made on signaling functions of activated TLRs, the molecular mechanisms that lead to TLR activation are still poorly understood . We report in this study that the extracellular domain of TLR2 interacts directly with synthetic bacterial lipopeptide (sBLP), a potent analog of bacterial lipoproteins . Using fluorescently labeled sBLP complexed to soluble recombinant CD14 (rsCD14), we observed specific binding of sBLP to the surface of cells expressing TLR2 transgenes and to a recombinant soluble form of the TLR2 ectodomain . TLR2-mediated binding of sBLP at the cell surface did not require prior induction of intracellular signals . In addition, using a chimeric TLR2/TLR4 construct, we showed that the leucine-rich region of TLR2 carries the specificity for binding of the agonist and for initiating signaling . Specific binding of fluorescent sBLP to purified sTLR2 required sCD14 . However, sCD14 was not part of the complex formed by soluble TLR2 and sBLP . Together, these data provide evidence that TLR2 recognizes sBLP through direct binding. Rev Esp Enferm Dig, 2004 Nov, 96(11), 796 - 800 Amebic liver abscess with bacterial superinfection in a patient with no epidemiologic risk factors; Sachez Pobre P et al.; The amebic liver abscess is uncommon in developed countries like Spain, but the incidence is increasing probably due to the migratory movements of the population . We report a case of an amebic abscess, initially unsuspected due to the absence of epidemiologic risk factors and the negative serology for amebiasis, in the early stages of the disease. Berl Munch Tierarztl Wochenschr, 2004 Nov-Dec, 117(11-12), 464 - 71 {Bacterial pathogen associated molecular pattern and superantigens indirectly induce the accelerated death of bovine neutrophilic granulocytes}; Schuberth HJ et al.; Pathogen associated molecular patterns (PAMPs) and bacterial superantigens have many effects on mononuclear cells (MNC) and macrophages . Influences on neutrophilic granulocytes (PMN), especially by non methylated CpG motifs, gained less attention . Here we investigated whether PAMPs and the superantigen SEA have a direct or indirect influence on the survival rate of bovine PMN . Different CpG motifs, a reverse GpC motif, Lipopolysaccharide (LPS) and SEA did not result in a loss of viability of pure PMN . In the presence of MNC or in vitro generated macrophages (MdM), however, they induced an accelerated dying of PMN . The simultaneous stimulation of MNC/MdM with combinations of CpG motifs and LPS or SEA resulted in an additive or over additive effect: compared to control set ups, only 28-36% of the PMN remained viable in SEA/CpG stimulated MNC/PMN cocultures . Comparing autologous with allogeneic MNC/PMN or MdM/PMN cocultures, it showed up that not only the stimulated MNC or MdM population but also the individual reaction state of the PMN have an influence on the degree of PMN dying . Taken together, CpG motifs and other PAMPs as well as superantigens act in concert to reduce indirectly the viability of neutrophilic granulocytes and hence the functional capacity of an important effector cell population. Proc Natl Acad Sci U S A, 2004 Dec 21, 101(51), 17873 - 8 Epub 2004 Dec 06. Reversed voltage-dependent gating of a bacterial sodium channel with proline substitutions in the S6 transmembrane segment; Zhao Y et al.; Members of the voltage-gated-like ion channel superfamily have a conserved pore structure . Transmembrane helices that line the pore (M2 or S6) are thought to gate it at the cytoplasmic end by bending at a hinge glycine residue . Proline residues favor bending of alpha-helices, and substitution of proline for this glycine (G219) dramatically stabilizes the open state of a bacterial Na(+) channel NaChBac . Here we have probed S6 pore-lining residues of NaChBac by proline mutagenesis . Five of 15 proline-substitution mutants yielded depolarization-activated Na(+) channels, but only G219P channels have strongly negatively shifted voltage dependence of activation, demonstrating specificity for bending at G219 for depolarization-activated gating . Remarkably, three proline-substitution mutations on the same face of S6 as G219 yielded channels that activated upon hyperpolarization and inactivated very slowly . Studies of L226P showed that hyperpolarization to -147 mV gives half-maximal activation, 123 mV more negative than WT . Analysis of combination mutations and studies of block by the local anesthetic etidocaine favored the conclusion that hyperpolarization-activated gating results from opening of the cytoplasmic gate formed by S6 helices . Substitution of multiple amino acids for L226 indicated that hyperpolarization-activated gating was correlated with a high propensity for bending, whereas depolarization-activated gating was favored by a low propensity for bending . Our results further define the dominant role of bending of S6 in determining not only the voltage dependence but also the polarity of voltage-dependent gating . Native hyperpolarization-activated gating of hyperpolarization- and cyclic nucleotide-gated (HCN) channels in animals and KAT channels in plants may involve bending at analogous S6 amino acid residues. Biochem Biophys Res Commun, 2005 Jan 14, 326(2), 290 - 7 Mutational study of the bacterial hemoglobin distal heme pocket; Verma S et al.; Ligand binding experiments on three mutants in the distal heme pocket of Vitreoscilla hemoglobin (GlnE7His, ProE8Ala, and GlnE7His,ProE8Ala) were used to probe the role of GlnE7 and ProE8 in the pocket's unusual structure . The oxygen dissociation constants for the wild type, E8Ala mutant, and E7His mutant proteins were 4.5, 4.7, and 1.7microM, respectively; the K(d) for the double mutant was not determinable by our technique . Visible-Soret spectra of the carbonyl and cyanyl forms and FT-IR of the carbonyl form of the E8 mutant were similar to those of the wild type; the opposite was true for the GlnE7His and GlnE7His,ProE8Ala mutants, which also differed from wild type in the visible-Soret spectra of their oxidized forms . Models of the effects of the mutations on distal pocket structure were consistent with the experimental findings, particularly the larger effects of the GlnE7His change. Curr Opin Struct Biol, 2004 Dec, 14(6), 731 - 40 Structural insights into bacterial modulation of the host cytoskeleton; Stebbins CE; Many bacterial pathogens manipulate the host cell cytoskeleton during infection . Such cytoskeletal modulation can occur at several points of contact between the pathogen and the host, and involves extracellular receptors, intracellular signal transduction and cytoskeletal proteins themselves . The field of bacterial pathogenesis has progressed dramatically over the past decade, such that structural knowledge is both timely and essential for a full appreciation of the biology at the pathogen-host interface . Several recent examples involving bacterial proteins that target actin, Rho family GTPases and extracellular receptors have contributed to a structural understanding of eukaryotic cytoskeletal modulation by pathogens. Arch Biochem Biophys, 2005 Jan 1, 433(1), 240 - 54 Bacterial defenses against oxidants: mechanistic features of cysteine-based peroxidases and their flavoprotein reductases; Poole LB; Antioxidant defenses include a group of ubiquitous, non-heme peroxidases, designated the peroxiredoxins, which rely on an activated cysteine residue at their active site to catalyze the reduction of hydrogen peroxide, organic hydroperoxides, and peroxynitrite . In the typical 2-Cys peroxiredoxins, a second cysteinyl residue, termed the resolving cysteine, is also involved in intersubunit disulfide bond formation during the course of catalysis by these enzymes . Many bacteria also express a flavoprotein, AhpF, which acts as a dedicated disulfide reductase to recycle the bacterial peroxiredoxin, AhpC, during catalysis . Mechanistic and structural studies of these bacterial proteins have shed light on the linkage between redox state, oligomeric state, and peroxidase activity for the peroxiredoxins, and on the conformational changes accompanying catalysis by both proteins . In addition, these studies have highlighted the dual roles that the oxidized cysteinyl species, cysteine sulfenic acid, can play in eukaryotic peroxiredoxins, acting as a catalytic intermediate in the peroxidase activity, and as a redox sensor in regulating hydrogen peroxide-mediated cell signaling. Biochemistry, 2004 Dec 14, 43(49), 15633 - 42 Alpha-glucan recognition by a new family of carbohydrate-binding modules found primarily in bacterial pathogens; Lammerts van Bueren A et al.; TmPul13, a family 13 glycoside hydrolase from Thermotoga maritima, is a four-module protein having pullulanase activity; the three N-terminal modules are of unknown function while the large C-terminal module is likely the catalytic module . Dissection of the functions of the three unknown modules revealed that the 100 amino acid module at the extreme N-terminus of TmPul13 comprises a new family of carbohydrate-binding modules (CBM) that a bioinformatic analysis shows are most frequently found in pullulanase-like sequences from bacterial pathogens . Detailed binding studies of this isolated CBM, here called TmCBM41, reveals a preference for alpha-(1,4)-linked glucans, but occasional alpha-(1,6)-linked glucose residues, such as those found in pullulan, are tolerated . UV difference, isothermal titration calorimetry, and analytical ultracentrifugation binding studies suggest that maltooligosaccharides longer than four glucose residues are able to bind two TmCBM41 molecules per oligosaccharide when sugar concentrations are below the CBM concentration . This is explained in terms of an equilibrium expression involving the formation of both a 1 to 1 sugar to CBM complex and a 1 to 2 sugar to CBM complex (i.e., a CBM dimer ligated by an oligosaccharide) . The presence of an alpha-(1-6) linkage in the oligosaccharide appears to prevent this phenomenon. Med Oral Patol Oral Cir Bucal, 2004, 9 Suppl, 34 - 6; 32-4 Bacterial infections of pulp and periodontal origin; Gonzalez-Moles MA et al.; The anatomical and structural characteristics of the pulp make this structure prone to altering as a result of, for instance, periodontal conditions (proximity), iatrogenic alterations, infections and involvement of vascular and nerve structures (it is surrounded by hard tissues that prevent expansion), to name just a few . Pulpitis is a process that courses with pain of varying intensity that allows us to determine the location of the lesion in clinical terms . Its evolution varies and may even progress to pulpar necrosis that in turn, produces neuritis-like pain . Diagnosis is established by means of clinical symptomatology and supported by X-rays, palpation of tissues at painful sites, application of electrical stimuli, heat, etc . Periodontitis is a bacterial infection originating in the apex . The most important form is the so-called acute apical periodontitis that arises as a result of a prior episode of pulpitis . It is characterized by acute pain located in the tooth, accompanied by the feeling of having a long-tooth . The patient refers being unable to chew on that side; there may be painful mobility of the tooth and an outflow of pus that alleviates symptoms . X-rays do not provide a lot of information, but may attest to a widening of the apical space . This pathology may disseminate to surrounding tissues, leading to conditions of considerable severity. Curr Drug Targets Infect Disord, 2004 Dec, 4(4), 303 - 9 Advances in adjuvant therapy against acute bacterial meningitis; Pomar V et al.; Death and co-morbidity derived from acute bacterial meningitis remain unacceptably high and are mainly related to immune-mediated cerebral dysfunction . Cerebral edema, hydrocephalus and ischaemic cerebrovascular events are severe complications that eventually occur following the activation of a complex network of cytokines, chemokines, proteases and oxidants released after cerebrospinal fluid infection . The caspase pathway appears to play a central role in the induction and amplification of the host inflammatory response . Such overactive immune reactions induce brain cell damage but, importantly, they may potentially be blocked . Several agents have been developed aiming to counteract the deleterious effects of such immune imbalance . These drugs are candidates to become adjuvant therapy against acute bacterial meningitis in the future, in addition to dexamethasone . We review the current state-of-art of bacterial meningitis adjuvant therapy, including caspase inhibitors, antioxidants, poly (ADP-ribose) polymerase inhibitors, inhibitors of lipid peroxidation and metalloproteinase inhibitors. Nature, 2004 Dec 2, 432(7017), 622 - 5 A candidate NAD+ transporter in an intracellular bacterial symbiont related to Chlamydiae; Haferkamp I et al.; Bacteria living within eukaryotic cells can be essential for the survival or reproduction of the host but in other cases are among the most successful pathogens . Environmental Chlamydiae, including strain UWE25, thrive as obligate intracellular symbionts within protozoa; are recently discovered relatives of major bacterial pathogens of humans; and also infect human cells . Genome analysis of UWE25 predicted that this symbiont is unable to synthesize the universal electron carrier nicotinamide adenine dinucleotide (NAD+) . Compensation of limited biosynthetic capacity in intracellular bacteria is usually achieved by import of primary metabolites . Here, we report the identification of a candidate transporter protein from UWE25 that is highly specific for import of NAD+ when synthesized heterologously in Escherichia coli . The discovery of this candidate NAD+/ADP exchanger demonstrates that intact NAD+ molecules can be transported through cytoplasmic membranes . This protein acts together with a newly discovered nucleotide transporter and an ATP/ADP translocase, and allows UWE25 to exploit its host cell by means of a sophisticated metabolic parasitism. Otolaryngol Head Neck Surg, 2004 Dec, 131(6), 871 - 6 Bacterial tracheitis reexamined: is there a less severe manifestation? Salamone FN, Bobbitt DB, Myer CM, Rutter MJ, Greinwald JH Jr. OBJECTIVE: Bacterial tracheitis (BT) is a condition that can cause fatal airway obstruction . We evaluated our experience with BT over a 10-year period . STUDY DESIGN: Retrospective review of patients treated for BT between 1991 and 2001 . RESULTS: Ninety-four cases were evaluated . The mean patient age was 7.9 years . At presentation, 60% were afebrile, and the mean WBC count was 10.8 x 10(3)/mm3 . Only 53% of patients required intubation . Younger children were more likely to require this intervention . S . aureus was the most commonly cultured bacteria, while isolation of M . catarrhalis was associated with a higher intubation rate . A pathologic virus was isolated in 64% of the 34 cultures performed . Only 9 patients were described as "toxic," and 6 presented in respiratory extremis . There were no deaths . CONCLUSION AND SIGNIFICANCE: A subset of patients with tracheal membranes has a less severe clinical appearance . Nonetheless, these patients require debridement and aggressive medical treatment . We propose that the term "exudative tracheitis" (ET) better describes this entity . Older patients who are less systemically ill and rapidly respond to local and systemic therapy are characteristic of ET . EBM RATING: C. Nucleic Acids Res, 2004, 32(21), 6260 - 7 Print 2004. Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins; Falnes PO; The Escherichia coli AlkB protein repairs 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions in DNA and RNA by oxidative demethylation, a reaction requiring ferrous iron and 2-oxoglutarate as cofactor and co-substrate, respectively . Here, we have studied the activity of AlkB proteins on 3-methylthymine (3-meT) and 1-methylguanine (1-meG), two minor lesions which are structurally analogous to 1-meA and 3-meC . AlkB as well as the human AlkB homologues, hABH2 and hABH3, were all able to demethylate 3-meT in a DNA oligonucleotide containing a single 3-meT residue . Also, 1-meG lesions introduced by chemical methylation of tRNA were efficiently removed by AlkB . Unlike 1-meA and 3-meC, nucleosides or bases corresponding to 1-meG or 3-meT did not stimulate the uncoupled, AlkB-mediated decarboxylation of 2-oxoglutarate . Our data show that 3-meT and 1-meG are repaired by AlkB, but indicate that the recognition of these substrates is different from that in the case of 1-meA and 3-meC. Environ Sci Technol, 2004 Nov 1, 38(21), 5656 - 64 Cd and proton adsorption onto bacterial consortia grown from industrial wastes and contaminated geologic settings; Borrok DM et al.; To model the effects of bacterial metal adsorption in contaminated environments, results from metal adsorption experiments involving individual pure stains of bacteria must be extrapolated to systems in which potentially dozens of bacterial species are present . This extrapolation may be made easier because bacterial consortia from natural environments appear to exhibit similar metal binding properties . However, bacteria that thrive in highly perturbed contaminated environments may exhibit significantly different adsorptive behavior . Here we measure proton and Cd adsorption onto a range of bacterial consortia grown from heavily contaminated industrial wastes, groundwater, and soils . We model the results using a discrete site surface complexation approach to determine binding constants and site densities for each consortium . The results demonstrate that bacterial consortia from different contaminated environments exhibit a range of total site densities (approximately a 3-fold difference) and Cd-binding constants (approximately a 10-fold difference) . These ranges for Cd binding constants may be small enough to suggest that bacteria-metal adsorption in contaminated environments can be described using relatively few "averaged" bacteria-metal binding constants (in conjunction with the necessary binding constants for competing surfaces and ligands) . However, if additional precision is necessary, modeling parameters must be developed separately for each contaminated environment of interest. Appl Environ Microbiol, 2004 Dec, 70(12), 7070 - 7 Bacterial life and dinitrogen fixation at a gypsum rock; Boison G et al.; The organisms of a bluish-green layer beneath the shards of a gypsum rock were characterized by molecular techniques . The cyanobacterial consortium consisted almost exclusively of Chroococcidiopsis spp . The organisms of the shards expressed nitrogenase activity (C2H2 reduction) aerobically and in light . After a prolonged period of drought at the rock, the cells were inactive, but they resumed nitrogenase activity 2 to 3 days after the addition of water . In a suspension culture of Chroococcidiopsis sp . strain PCC7203, C2H2 reduction required microaerobic conditions and was strictly dependent on low light intensities . Sequencing of a segment of the nitrogenase reductase gene (nifH) indicated that Chroococcidiopsis possesses the alternative molybdenum nitrogenase 2, expressed in Anabaena variabilis only under reduced O2 tensions, rather than the widespread, common molybdenum nitrogenase . The shards apparently provide microsites with reduced light intensities and reduced O2 tension that allow N2 fixation to proceed in the unicellular Chroococcidiopsis at the gypsum rock, unless the activity is due to minute amounts of other, very active cyanobacteria . Phylogenetic analysis of nifH sequences tends to suggest that molybdenum nitrogenase 2 is characteristic of those unicellular or filamentous, nonheterocystous cyanobacteria fixing N2 under microaerobic conditions only. Surgeon, 2003 Apr, 1(2), 63 - 75 Inflammatory bowel disease: dysfunction of GALT and gut bacterial flora (I); Chandran P et al.; Gut-associated lymphoid tissue (GALT) is the largest lymphoid organ in the body . This is not surprising considering the huge load of antigens (Ags) from food and commensal bacteria with which it interacts on a daily basis . Gut-associated lymphoid tissue has to recognise and allow the transfer of beneficial Ags whilst concurrently dealing with and successfully removing putative and overtly harmful Ags . This distinctive biological feature of GALT is believed to be crucial to good health . Deregulation or dysfunction of GALT is thought to predispose to inflammatory bowel diseases (IBD) such as ulcerative colitis and Crohn's disease . The exact mechanism(s) underlying the pathogenesis of IBD is (are) poorly understood and the immunological defects in GALT are poorly documented . Advances in immunology have highlighted the importance of dendritic cells (DCs), which are the key Ag presenting cells in tissues and lymphoid compartments . Their crucial role in GALT, in health and disease is discussed in this review . Interaction of DCs with T cells in the gut produces a subset of T lymphocytes, which have immunosuppressive function . Inappropriate Ag uptake and presentation to naive T cells in mesenteric lymph nodes may lead to T cell tolerance in GALT . These various complex factors in the gut are discussed and their possible relevance to IBD evaluated. Environ Sci Technol, 2004 Nov 15, 38(22), 5925 - 31 Uncertainty analysis in a mechanistic model of bacterial regrowth in distribution systems; Digiano FA et al.; The first generation of mechanistic models of bacterial regrowth in distribution systems (DS) provides insight into cause-and-effect relationships . However, the state of knowledge about the processes included in these models is insufficient to warrant deterministic predictions . Even if the process descriptions are reasonable, the uncertainty in values of key system constants limits predictions of bacterial growth . A new mechanistic model was developed to incorporate the accepted knowledge of physical, chemical, and biological processes with the hydraulic features in order to capture the unsteady state behavior of the DS . Sensitivitytesting showed that the extent of bacterial regrowth was affected mainly by the rate constants for chlorine decay reactions in bulk water and on the pipe wall and by the maximum growth rate constant of attached bacteria . A simple hypothetical network was used to evaluate the effects of uncertainty in these three system constants by running 100 Monte Carlo simulations . Cumulative probability plots showed a wide range of predictions for concentrations of bacteria and chlorine in bulk water at various nodes in the DS . The magnitude of these concentrations and the range of values were greatly affected by water residence time to each node . Once the chlorine residual is depleted, bacterial growth is mainly influenced by the amount of substrate available . However, high values of the coefficients for the maximum growth rate of attached bacteria, the chlorine decay in bulk water, and the chlorine decay by wall reaction did not necessarily lead to the maximum bacterial growth at a given location. Nat Rev Mol Cell Biol, 2004 Dec, 5(12), 1024 - 37 Making sense of it all: bacterial chemotaxis; Wadhams GH et al.; Bacteria must be able to respond to a changing environment, and one way to respond is to move . The transduction of sensory signals alters the concentration of small phosphorylated response regulators that bind to the rotary flagellar motor and cause switching . This simple pathway has provided a paradigm for sensory systems in general . However, the increasing number of sequenced bacterial genomes shows that although the central sensory mechanism seems to be common to all bacteria, there is added complexity in a wide range of species. Acta Microbiol Immunol Hung, 2004, 51(3), 249 - 61 Studies on bacterial conjugational crosses via model populations . II . Genetic studies; Alfoldi L; Model populations, simulating progenies obtained from Escherichia coli Hfr x F- crosses, are generated . Linkage relations and exchange frequencies are expressed in these populations in complex, in some cases, even paradoxical manner . It is demonstrated that the origin of the complexities is located in the particular allelic configuration of the genotypes, characteristic for all exconjugant and selected populations. Acta Microbiol Immunol Hung, 2004, 51(3), 239 - 47 Studies on bacterial conjugational crosses via model populations . I . The model populations; Alfoldi L; A procedure is presented in which model populations, simulating progenies obtained from Escherichia coli Hfr x F- crosses, are generated . The procedure seems to be appropriate for visualizing hidden features of the genetic analysis, which are not detected by the conjugational crosses. Surgeon, 2003 Jun, 1(3), 125 - 36 Inflammatory bowel disease: dysfunction of GALT and gut bacterial flora (II); Chandran P et al.; The precise cause(s) of Crohn's disease and ulcerative colitis are unknown . From animal models and human studies it is well established that gut bacterial flora are essential for inducing the bowel inflammation . Animal models, when kept in a germ-free environment, do not develop colitis until the gut flora is reconstituted . It is not clear whether the bacterial antigens (Ags) from the normal flora or some other pathogenic bacterial Ags induce/propagate the inflammatory process in inflammatory bowel disease (IBD) . Despite extensive research it has not been possible to identify any specific bacteria or virus as a credible cause of IBD . Recent understanding of quorum sensing molecules (QSMs) secreted by bacteria helps to explain the community behaviour in bacterial species . When QSMs reach a defined concentration, they activate bacterial proliferation and a number of virulence genes . Also, these molecules have been found to modulate the immune system to the advantage of the gut bacteria . They have not been well studied, however, in the gut . Inappropriate secretion of QSMs may alter the gut-associated lymphoid tissue (GALT) and, thereby, deregulate the immune tolerance normally present . Usefulness of probiotics and their immune modulating effects are being increasingly reported . Probiotics are also being used in the treatment of IBD . The interaction between the epithelial cells and the gut flora is very important as this is the first line of contact; this interaction may determine the induction of tolerance and mucosal integrity or immune activity, tissue inflammation and abnormal permeability . The latter is documented in patients with IBD and their healthy relatives . This may be an important factor in disruption of mucosal integrity and GALT dysfunction. J Reprod Med, 2004 Oct, 49(10), 781 - 6 Clinical variability of bacterial vaginosis and trichomoniasis; Brown D Jr; Bacterial vaginosis and trichomoniasis are two of the most commonly encountered vaginal diseases . Although risk factors for both vaginal conditions have been identified, there continues to be lack of knowledge in regard to their role in association with other sexually transmitted diseases . Vaginal pH is an essential ingredient in the defense and control of the vaginal environment . The alteration of pH with the sequelae of such pregnancy complications as preterm delivery, preterm labor and premature rupture of the membranes; amniotic fluid infection; postpartum endometritis and surgical infections; and the role of bacterial vaginosis are discussed . Treatment modalities in both the nonpregnant and pregnant woman, as well as treatment of resistant cases of both vaginal conditions, are recommended. J Microbiol Methods, 2005 Jan, 60(1), 55 - 62 A rapid microplate method for quantifying inhibition of bacterial adhesion to eukaryotic cells; Acord J et al.; Adhesion of bacteria to the mucosal epithelial cell surface is the first step in infection, and studies have shown that inhibition of this step may be useful therapeutically . To test compounds that may prevent bacterial binding to a number of epithelial cell lines, we have developed a high-throughput adhesion assay using a microtitre plate system and bacteria that have been modified to express firefly luciferase . This method has proved to be a sensitive, rapid, and reproducible system for screening antiadhesive agents for their effects on bacterial adhesion. J Microbiol Methods, 2005 Jan, 60(1), 41 - 6 Activity-dependent fluorescent labeling of bacterial cells expressing the TOL pathway; Clingenpeel SR et al.; 3-Ethynylbenzoate (3EB) functions as a novel, activity-dependent, fluorogenic, and chromogenic probe for bacterial strains expressing the TOL pathway, which degrade toluene via conversion to benzoate, followed by meta ring fission of the intermediate catechol . This direct physiological analysis allows the fluorescent labeling of cells whose toluene-degrading enzymes have been induced by an aromatic substrate. Nihon Kokyuki Gakkai Zasshi, 2004 Oct, 42(10), 871 - 4 {Study of administration times and clinical efficacy of carbapenems in the treatment of moderate community-acquired bacterial pneumonia}; Okimoto N et al.; The half-lives of carbapenems are about 1 hour . It was expected that increasing the daily frequency of administration would improve the clinical effects . We therefore studied the clinical effects of increasing the daily administration frequency of meropenem in the treatment of community-acquired bacterial pneumonia . The subjects were patients with moderate community-acquired bacterial pneumonia who were aged less than 75 years . They were divided into a BID group (28 patients receiving 0.5 g morning and evening) and a TID group (27 patients receiving 0.25 g in the morning and about midday, and 0.5 g in the evening), and the clinical effects were reviewed prospectively . Clinical efficacy on the third day was 78.6% in the BID group and 85.2% in the TID group, and over-all clinical efficacy was 89.3% in the BID group and 88.9% in the TID group . Administration periods were 12.8 +/- 4.2 days in the BID group and 10.9 +/- 3.4 days in the TID group . These results show no statistically significant difference, and suggest that the excellent clinical effect of administration of MEPM 0.5 g twice a day on moderate community-acquired bacterial pneumonia is not improved by administration three times a day. Can J Gastroenterol, 2004 Nov, 18(11), 677 - 80 Deadaption and readaptation with lactose, but no cross-adaptation to lactulose: a case of occult colonic bacterial adaptation; Szilagyi A et al.; The standard 3 h breath hydrogen (3hBH2) test distinguishes lactose maldigesters from lactose digesters . However, multiple factors impact on BH2 and care is needed to exclude a priori variables . When these factors are controlled, a negative BH2 test implies lactase persistent status or lactase nonpersistent status with colonic adaptation . A case of a Sicilian man who tested negative (lactase persistent status confirmed) on an initial 50 g lactose challenge is described . It was observed that he consumed 28.1 g lactose/day before testing . He subsequently underwent five additional challenge tests in the course of the next 10 months . In four tests the dose intake of lactose was varied upon instruction, and in the fifth test a 30 g lactulose challenge was carried out . It was demonstrated that on radically decreasing lactose intake, a full lactase nonpersistent status was unmasked . Output of 3hBH2 varied inversely with daily lactose intake . Finally, at a time when he was readapted to lactose, there was no discernible adaptation to lactulose challenge . It was concluded that 'occult' colonically adapted subjects may contribute to negative BH2 tests . There is a relationship between variation in lactose intake and the results of BH2 testing . Finally, there was no cross-adaptation to lactulose challenge when lactose was used as the adapting sugar. Thorax, 2004 Dec, 59(12), 1057 - 62 Protective role of metallothionein in acute lung injury induced by bacterial endotoxin; Takano H et al.; BACKGROUND: Metallothionein (MT) is a protein that can be induced by inflammatory mediators and participate in cytoprotection . However, its role in inflammation remains to be established . A study was undertaken to determine whether intrinsic MT protects against acute inflammatory lung injury induced by bacterial endotoxin in MT-I/II knock out (-/-) and wild type (WT) mice . METHODS: MT (-/-) and WT mice were given vehicle or lipopolysaccharide (LPS, 125 microg/kg) intratracheally and the cellular profile of the bronchoalveolar lavage (BAL) fluid, pulmonary oedema, lung histology, expression of proinflammatory molecules, and nuclear localisation of nuclear factor-kappaB (NF-kappaB) in the lung were evaluated . RESULTS: MT (-/-) mice were more susceptible than WT mice to lung inflammation, especially to lung oedema induced by intratracheal challenge with LPS . After LPS challenge, MT deficiency enhanced vacuolar degeneration of pulmonary endothelial cells and type I alveolar epithelial cells and caused focal loss of the basement membrane . LPS treatment caused no significant differences in the enhanced expression of proinflammatory cytokines and chemokines nor in the activation of the NF-kappaB pathway in the lung between the two genotypes . Lipid peroxide levels in the lungs were significantly higher in LPS treated MT (-/-) mice than in LPS treated WT mice . CONCLUSIONS: Endogenous MT protects against acute lung injury related to LPS . The effects are possibly mediated by the enhancement of pulmonary endothelial and epithelial integrity, not by the inhibition of the NF-kappaB pathway. J Am Soc Echocardiogr, 2004 Dec, 17(12), 1315 - 6 Coronary artery fistula presenting as bacterial endocarditis; Kasravi B et al.; Coronary artery fistula is often considered to be a benign and rare congenital anomaly . It is usually an incidental finding encountered during routine cardiac catheterization . We report a case of a patient presenting with endocarditis involving a large coronary artery fistula connecting an aneurysmal circumflex coronary artery to the coronary sinus . The diagnosis was initially made by echocardiography and confirmed by cardiac catheterization . In addition, we briefly discuss the literature on management of this coronary anomaly. Curr Opin Biotechnol, 2004 Dec, 15(6), 530 - 7 Bacterial ghosts--biological particles as delivery systems for antigens, nucleic acids and drugs; Tabrizi CA et al.; Despite the exponential rate of discovery of new antigens and DNA vaccines resulting from modern molecular biology and proteomics, the lack of effective delivery technology is a major limiting factor in their application . The bacterial ghost system represents a platform technology for antigen, nucleic acid and drug delivery . Bacterial ghosts have significant advantages over other engineered biological delivery particles, owing to their intrinsic cellular and tissue tropic abilities, ease of production and the fact that they can be stored and processed without the need for refrigeration . These particles have found both veterinary and medical applications for the vaccination and treatment of tumors and various infectious diseases. Mol Biol Rep, 2004 Sep, 31(3), 159 - 64 Mammalian apoptosis-inducing protein, HAP, induces bacterial cell death; Gan M et al.; In attempting to produce the HAP, endoplasmic reticulum (ER) targeted apoptosis-inducing protein, as a GST-fusion protein we found that the expression of HAP, but not GST alone, induced bacterial cell death . The HAP protein inhibited the bacterial growth within 30 min after inducting HAP expression . The transmission electron microscopic examination revealed that the morphology of the bacterial cells expressing hap was changed dramatically: unusually elongated phenotype compared with those of controls and finally leading to cell death . The lethality of HAP was relieved by the addition of vitamin E as a reducing agent and under anaerobic growth conditions . These results suggest that a trace amount of HAP induces bacterial cell death and the death is related with reactive oxygen species (ROS). Urologiia, 2004 Sep-Oct, (5), 31 - 4 {Naiz (nimesulid) in combined treatment of patients with chronic bacterial prostatitis with chronic pelvic pain syndrome}; Long-term survival of dialysis patients with bacterial endocarditis in the United States; Department of Internal Medicine, Hennepin County Medical Center and University of Minnesota, Minneapolis, MN, USABACKGROUND: The incidence of bacterial endocarditis is much greater in long-term dialysis patients compared with the general population, and chronic kidney disease has been postulated as an independent host-related risk factor . Limited data are available on the long-term survival of dialysis patients with endocarditis . METHODS: Dialysis patients hospitalized for bacterial endocarditis between 1977 and 2000 were studied retrospectively using data from the US Renal Data System database . Long-term survival was estimated by means of the life-table method . A Cox proportional hazards model was used to identify the impact of demographic characteristics and comorbidity on outcome . RESULTS: A total of 13,130 dialysis patients with bacterial endocarditis were identified . The in-hospital mortality rate for the entire cohort was 23.5% . Survival rates at 1, 2, 3, and 5 years were 45.9%, 33.3%, 24.3%, and 14.7% for patients hospitalized between 1977 and 1991 and 41.0%, 29.1%, 20.6%, and 10.9% for those hospitalized between 1992 and 1996, respectively . Survival rates at 1, 2, and 3 years were 38.4%, 25.3%, and 18.3% for patients hospitalized between 1997 and 2000, respectively . The most powerful independent predictors of all-cause death were age, diabetes as cause of end-stage renal disease, and cerebrovascular accident or transient ischemic attack as a comorbid condition . CONCLUSION: Dialysis patients with bacterial endocarditis have poor long-term survival, even in the current treatment era, with survival rates changing little in the past 2 decades . Additional studies are needed to identify risk-reduction measures and develop additional treatment strategies for dialysis patients with endocarditis. J Exp Biol, 2004 Dec 1, 207(Pt 25), 4479 - 88 Bacterial lipopolysaccharide (LPS) modulates corticotropin-releasing hormone (CRH) content and release in the brain of juvenile and adult tilapia (Oreochromis mossambicus; Teleostei); Pepels PP et al.; Although immune endocrine interactions in teleost fish have been shown to involve adrenocorticotropin hormone (ACTH) and cortisol, the involvement of corticotropin-releasing hormone (CRH) has not been demonstrated . The present study investigates whether treatment with bacterial endotoxin (lipopolysaccharide, LPS) modulates brain CRH contents or in vitro CRH release in tilapia (Oreochromis mossambicus) . 10 days LPS (Escherichia coli) exposure of juvenile tilapia (4.5 weeks post hatch) via the ambient water increased brain CRH and alpha-MSH content, whereas cortisol contents were not increased . This indicates that the elevation of brain CRH levels were not secondary to activation of HPI-axis . Adult tilapia were treated for 6 days with LPS (intraperitoneally) and were sampled before and after 24 h of confinement . Overall LPS pre-treatment modified the reaction of tilapia to the additional stressor of 24 h confinement, as interactions between LPS treatment and confinement were observed at the level of the hypothalamus (diencephalic CRH content), the pituitary (CRH and alpha-MSH content) and in plasma glucose levels . In vitro, LPS pre-treatment abolished CRH release from telencephalic tissues induced by norepinephrine, one of the CRH secretagogues released during stress in vivo . This effect might be a mechanism of action through which LPS in vivo abolished the up-regulation of telencephalic CRH induced by confinement stress . Our results provide evidence that the role of CRH in immune-endocrine interactions is a phylogenetically old mechanism, and we here demonstrate that LPS molecules are able to locally modulate CRH release in the central nervous system. Biophys J . 2004 Nov 19; {Epub ahead of print} Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane; Murzyn K et al.; Phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) are the main lipid components of the inner bacterial membrane . A computer model for such a membrane was built of palmitoyloleoylPE (POPE) and palmitoyloleoylPG (POPG) in the proportion 3:1, and sodium ions (Na+) to neutralize the net negative charge on each POPG (POPE-POPG bilayer) . The bilayer was simulated for 25 ns . A final 10-ns trajectory fragment was used for analyses . In the bilayer interfacial region, POPEs and POPGs interact readily with one another via intermolecular hydrogen (H) bonds and water bridges . POPE is the main H bond donor in either PEPE or PEPG H bonds; PGPG H bonds are rarely formed . Almost all POPEs are H bonded and/or water bridged to either POPE or POPG but PE-PG links are favored . In effect, the atom packing in the near-the-interface regions of the bilayer core is tight . Na+ does not bind readily to lipids and inter-lipid links via Na+ are not numerous . Although POPG and POPE comprise one bilayer, their bilayer properties differ . The average surface area per POPG is larger and the average vertical location of the POPG phosphate group is lower than those of POPE . Also, the alkyl chains of POPG are more ordered and less densely packed than the POPE chains . The main conclusion of this study is that in the PE-PG bilayer PE interacts more strongly with PG than PE . This is a likely molecular level event behind a regulating mechanism developed by the bacteria to control its membrane permeability and stability consisting in changes of the relative PG to PE concentration in the membrane. Curr Opin Microbiol, 2004 Dec, 7(6), 572 - 8 Spatial complexity of mechanisms controlling a bacterial cell cycle; Viollier PH et al.; Cell cycle progression in Caulobacter is governed by a multilayered regulatory network linking chromosome replication with polar morphogenesis and cell division . Temporal and spatial regulation have emerged as the central themes, with the abundance, activity and subcellular location of key structural and regulatory proteins changing over the course of the cell cycle . An additional layer of complexity was recently uncovered, showing that each segment of the chromosome is located at a specific cellular position both during and after the completion of DNA replication, raising the possibility that this positioning contributes to temporal and spatial control of gene expression. Chem Biol, 2004 Nov, 11(11), 1553 - 9 Bacterial biosynthesis of cadmium sulfide nanocrystals; Sweeney RY et al.; Semiconductor nanocrystals, which have unique optical and electronic properties, have potential for applications in the emerging field of nanoelectronics . To produce nanocrystals cheaply and efficiently, biological methods of synthesis are being explored . We found that E . coli, when incubated with cadmium chloride and sodium sulfide, have the capacity to synthesize intracellular cadmium sulfide (CdS) nanocrystals . The nanocrystals are composed of a wurtzite crystal phase with a size distribution of 2-5 nm . Nanocrystal biosynthesis increased about 20-fold in E . coli cells grown to stationary phase compared to late logarithmic phase . Our results highlight how different genetic and physiological parameters can enhance the formation of nanocrystals within bacterial cells. Chem Biol, 2004 Nov, 11(11), 1543 - 52 bryA: an unusual modular polyketide synthase gene from the uncultivated bacterial symbiont of the marine bryozoan Bugula neritina; Hildebrand M et al.; "Candidatus Endobugula sertula," the uncultivated bacterial symbiont of Bugula neritina, is the proposed source of the bryostatin family of anticancer compounds . We cloned a large modular polyketide synthase (PKS) gene complex from "Candidatus Endobugula sertula" and characterized one gene, bryA, which we propose is responsible for the initial steps of bryostatin biosynthesis . Typical PKS domains are present . However, acyltransferase domains are lacking in bryA, and beta-ketoacyl synthase domains of bryA cluster with those of PKSs with discrete, rather than integral, acyltransferases . We propose a model for biosynthesis of the bryostatin D-lactate starter unit by the bryA loading module, utilizing atypical domains homologous to FkbH, KR, and DH . The bryA gene product is proposed to synthesize a portion of the pharmacologically active part