Yi Chuan Xue Bao, 2004 Nov, 31(11), 1316 - 20 Phylogenetic analysis indicates bacteria-to-apicoplast lateral gene transfer; Zhu XY; Apicomplexan protozoa contains a highly reduced plastid-like organelle termed apicoplast . Data from clpC gene in apicoplast and their homologs in other plastids and bacteria were used to reconstruct phylogeny of apicoplast . Trees were reconstructed using neighbor-joining, minimum evolution, maximum parsimony and maximum likelihood . The reconstructions robustly support the monophyly of apicoplast and B . burgdorferi . This result underpins the mixture-genome hypotheses of apicoplast, furthermore, provides a new insight into the origin of this mixture genome. Dev Biol (Basel), 2000, 102, 115 - 23 Inactivation of viruses, bacteria, protozoa and leukocytes in platelet and red cell concentrates; Corash L; Despite the increased safety of blood achieved through continued improvements in donor testing, concern remains about the safety of blood components . Transfusion of cellular components has been implicated in transmission of viral, bacterial, and protozoan diseases . While it is commonly recognized that hepatitis B virus, hepatitis C virus, cytomegalovirus, and the retroviruses, such as human immunodeficiency virus and the human lymphotrophic viruses can be transmitted through cellular components, other pathogens are emerging as potentially significant transfusion-associated infectious agents . For example, transmission of protozoan infections due to trypanosomes and babesia have been reported . In addition to viral and protozoal infectious agents, bacterial contamination of platelet and red cell concentrates continues to be reported and may be an under-reported transfusion complication . More importantly, new infectious agents, such as HIV, may periodically enter the donor population before they can be identified . During the past decade a number of methods to inactivate infectious pathogens in blood components have been investigated . This technology is now in the clinical trial phase. Ned Tijdschr Geneeskd, 2004 Dec 25, 148(52), 2590 - 4 {Van Leeuwenhoek's discovery of bacteria: a look too far ahead}; James J; During the 17th century microscopy was practised at the Royal Society in London by the curator Robert Hooke (1635-1703) . He made use of the compound microscope (with uncorrected lenses) and published a book describing the most varied observations of botanical and animal specimens, among which he introduced the concept of 'cellula', observed in botanical material . The useful magnification was limited to 30-40 times . During the same period, the passionate amateur Anthonie van Leeuwenhoek in Delft (1632-1723) was engaged in microscopy, using a so-called simple microscope which was difficult to use but could be applied--albeit with a greater effort--at a much larger aperture so that magnifications in the range of 75-150 times were feasible . Using these self-made instruments, Van Leeuwenhoek was able to observe and describe bacteria, but this could not be confirmed at the Royal Society . It took 15o years before the compound microscope reached this level and bacteria were recognized as pathogenic organisms. Appl Environ Microbiol, 2005 Jan, 71(1), 580 - 6 Molecular characterization of resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in petroleum-contaminated soil; Meguro N et al.; PCR assays for analyzing resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in soil were developed . Sequence analysis of amplicons showed that the PCR successfully retrieved transporter gene fragments from soil . Most of the genes retrieved from petroleum-contaminated soils formed a cluster (cluster PCS) that was distantly related to known transporter genes . Competitive PCR showed that the abundance of PCS genes is increased in petroleum-contaminated soil. Appl Environ Microbiol, 2005 Jan, 71(1), 423 - 7 Effect of direct electric current on the cell surface properties of phenol-degrading bacteria; Luo Q et al.; The change in cell surface properties in the presence of electric currents is of critical concern when the potential to manipulate bacterial movement with electric fields is evaluated . In this study, the effects of different direct electric currents on the cell surface properties involved in bacterial adhesion were investigated by using a mixed phenol-degrading bacterial culture in the exponential growth phase . The traits investigated were surface hydrophobicity (measured by adherence to n-octane), net surface electrostatic charge (determined by measurement of the zeta potential), and the cell surface shape and polymers (determined by scanning electron microscope analysis) . The results showed that a lower current (less than 20 mA) induced no significant changes in the surface properties of phenol-degrading bacteria, that an electric current of 20 mA could increase the surface hydrophobicity and flatten the cell shape, and that a higher current (40 mA) could increase the surface extracellular substances and the net negative surface electrostatic charge . The results also revealed that the electric current effects on cell hydrophobicity varied with the suspending medium . We suggest that an electric current greater than 20 mA is not suitable for use in manipulation of the movement of the phenol-degrading bacteria, although such a current might favor the electrophoretic movement of the bacterial species. Rocz Akad Med Bialymst, 2004, 49 Suppl 1, 216 - 8 Cytotoxic lymphocytes (CD8+) in the antrum mucosa in children with chronic Helicobacter pylori-related inflammation before and after bacteria eradication; Maciorkowska E et al.; The authors assessed the expression of cytotoxic CD8 lymphocytes in the antrum mucosa of children with chronic Helicobacter pylori-related inflammation, before and after bacteria eradication . Biopsy specimens of gastric mucosa were evaluated in specimens, collected from 59 H . pylori-positive patients (Group I), 29 patients after H . pylori infection (Group II) and 18 H . pylori-negative children (Group III) . The obtained specimens were assessed for infection and inflammation and the expression of CD8+ lymphocytes was estimated, using monoclonal antibodies . The number of CD8+ lymphocytes in the mucosa was counted . The results of the study showed an increase in the expression of CD8+ lymphocytes in children with H . pylori infection, in comparison to the values in children after bacteria eradication . The increased expression of CD8+ lymphocytes correlated with the severity degree of antrum gastritis. Trends Biotechnol, 2005 Jan, 23(1), 6 - 8 Bacteria and phytoremediation: new uses for endophytic bacteria in plants; Newman LA et al.; The use of plants and bacterial to clean up environmental pollutants has gained momentum in past years . A limitation to phytoremediation of solvents has been toxicity of the compounds to plants, and the uncertainty as to the fate of many of the compounds . In a recent study, engineered endophytes have been shown to increase plant tolerance to toluene, and to decrease the transpiration of toluene to the atmosphere . This type of work has the potential to increase the use of phytoremediation by decreasing toxicity and increasing degradation of toxins. Inflamm Bowel Dis, 2004 Nov, 10(6), 811 - 23 Interleukin 10-deficient mice exhibit defective colonic Muc2 synthesis before and after induction of colitis by commensal bacteria; Schwerbrock NM et al.; Germ-free (GF) interleukin 10-deficient (IL-10) mice develop chronic colitis after colonization by normal enteric bacteria . Muc2 is the major structural component of the protective colonic mucus . Our aim was to determine whether primary or induced aberrations in Muc2 synthesis occur in GF IL-10 mice that develop colitis after bacterial colonization . GF IL-10 and wild-type mice were colonized with commensal bacteria for various intervals up to 6 weeks . Colitis was quantified by histologic score and IL-12 secretion . Muc2 synthesis, total level of Muc2, and Muc2 sulfation were measured quantitatively . GF IL-10 mice showed 10-fold lower Muc2 synthesis and Muc2 levels compared with GF wild-type mice, but Muc2 sulfation was not different . When bacteria were introduced, IL-10 mice developed colitis, whereas wild-type mice remained healthy . Muc2 synthesis was unchanged in wild-type mice, but IL-10 mice showed a peak increase in Muc2 synthesis 1 week after bacterial introduction, returning to baseline levels after 2 weeks . Total Muc2 levels decreased 2-fold in wild-type mice but remained at stable low levels in IL-10 mice . Upon introducing bacteria, Muc2 sulfation increased 2-fold in wild-type mice, whereas in IL-10 mice Muc2 sulfation decreased 10-fold . In conclusion, a primary defect in colonic Muc2 synthesis is present in IL-10 mice, whereas bacterial colonization and colitis in these mice led to reduced Muc2 sulfation . These quantitative and structural aberrations in Muc2 in IL-10 mice likely reduce the ability of their mucosa to cope with nonpathogenic commensal bacteria and may contribute to their susceptibility to develop colitis. Toxicon, 2005 Feb, 45(2), 129 - 37 Structural features common to intracellularly acting toxins from bacteria; Menetrey J et al.; This mini-review focuses on structural features shared by bacterial intracellularly-acting toxins . These complex proteins adopt an A(n)B(m) assembly . B(m) is a cellular-uptake machinery that delivers the enzymatic A(n) component, where it specifically modifies an intracellular eukaryotic cell target . In this nomenclature, the m index reflects the mono- or oligomeric (homo or hetero) state of the B component and the n index indicates the number of A molecules that concomitantly bind to B(m) . A structural analysis of the available 3D structures suggests that each of the A molecules that constitute the A(n) component can be divided into A(link) and A(enz) sub-domains, with A(link) specifically linking the enzymatically active A(enz) domain to a given B(m) . This module-based A(n)B(m) assembly seems decisive for natural intracellularly-acting toxins to be potent and for the success of engineered toxins. Infect Immun, 2005 Jan, 73(1), 485 - 93 CXCR3 and its ligands participate in the host response to Bordetella bronchiseptica infection of the mouse respiratory tract but are not required for clearance of bacteria from the lung; Widney DP et al.; Intranasal inoculation of mice with Bordetella bronchiseptica produces a transient pneumonia that is cleared over several weeks in a process known to require both neutrophils and lymphocytes . In this study, we evaluated the roles of the chemokines MIG (CXCL9), IP-10 (CXCL10), and I-TAC (CXCL11) and their common receptor, CXCR3 . Following bacterial inoculation, message expression of interleukin-1 (IL-1), IL-6, and the neutrophil-attracting chemokines KC, LIX, and MIP-2 was rapidly induced, with maximal expression found at 6 h . In contrast, message expression of gamma interferon, MIG, IP-10, and I-TAC peaked at 2 days . Expression of all of these chemokines and cytokines returned to near baseline by 5 days, despite the persistence of high levels of live bacteria at this time . Induced MIG, IP-10, and I-TAC protein expression was localized in areas of inflammation at 2 to 3 days and was temporally associated with increased levels of CXCR3(+) lymphocytes in bronchoalveolar lavage fluid . There was no increase in mortality in mice lacking CXCR3 . However, the clearance of bacteria from the lung and trachea was delayed, and the recruitment of lymphocytes and NK cells was slightly decreased, for CXCR3(-/-) mice relative to CXCR3(+/+) mice . We conclude that the CXCR3 receptor-ligand system contributes to pulmonary host defense in B . bronchiseptica infection by recruiting lymphocytes and NK cells into the lung. J Exp Bot . 2004 Dec 20; {Epub ahead of print} Accumulation and remobilization of amino acids during senescence of detached and attached leaves: in planta analysis of tryptophan levels by recombinant luminescent bacteria; Soudry E et al.; The process of leaf senescence is biochemically characterized by the transition from nutrient assimilation to nutrient remobilization . The nutrient drain by developing vegetative and reproductive structures has been implicated in senescence induction . The steady-state levels of amino acids in senescing leaves are dependent on the rate of their release during protein degradation and on the rate of efflux into growing structures . To determine the possible regulatory role of amino acid content in leaf senescence, an in planta non-destructive, semi-quantitative method for the analysis of endogenous levels of free amino acids has been developed . The method is based on in vivo bioluminescence of amino acid-requiring strains of recombinant Escherichia coli carrying the lux gene . The luminescence signal was found to be proportional to the levels of added exogenous tryptophan and to the free amino acid levels in the plant tissues analysed . During the senescence of tobacco flowers and of detached leaves of oats and Arabidopsis, a progressive increase in the levels of free amino acids was monitored . By contrast to the detached leaves, the attached oat leaves displayed a decrease in the levels of free amino acids during senescence . In Arabidopsis, both the attached and detached leaves exhibited a similar pattern of gradual increase in amino acid content during senescence . The differences between the sink-source balance of the two species and the possible relationships between amino acid content and leaf senescence are discussed. Chem Biol, 2004 Dec, 11(12), 1602 - 4 Catching bacteria with sugar; Mahal LK; In this issue of Chemistry & Biology, Disney and Seeberger exploit bacterial targeting of host cell surface sugars during pathogenesis to create a simple diagnostic carbohydrate microarray for the detection of bacteria in complex biological mixtures {1}. Nucleic Acids Res, 2005 Jan 1, 33 Database Issue, D164 - 8 PSORTdb: a protein subcellular localization database for bacteria; Rey S et al.; Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets . PSORTdb is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions . The dataset of experimentally verified information (approximately 2000 proteins) was manually curated by us and represents the largest dataset of its kind . Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors . The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes . Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins . Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats . Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources . PSORTdb is freely available under GNU General Public License. Water Res, 2005 Jan, 39(1), 257 - 263 Contribution of drinking water to the weekly intake of heterotrophic bacteria from diet in the United States; Stine SW et al.; The goal of this study was to assess the relative contribution of heterotrophic bacteria from various sources in the normal diet of an average person in the United States, due to concerns regarding the potential health implications of such bacteria in household tapwater . A literature search was conducted to determine the concentration of heterotrophic plate count (HPC) bacteria in drinking water, as well as foods common to the American diet . Food items were also obtained in Tucson, AZ to further evaluate the consumption of HPC and total coliform bacteria . This was compared to a recent study on HPC bacteria in tapwater with and without POU devices mounted on the tap in Tucson, AZ households . It was determined that only 0.048-4.5% of the average consumer's total heterotrophic bacteria intake is derived from drinking water . Thus, HPC bacteria in drinking water do not represent a significant exposure of total HPC bacteria in the average diet of consumers in the United States. Mutat Res, 2005 Jan 6, 569(1-2), 3 - 11 Stress responses and genetic variation in bacteria; Foster PL; Under stressful conditions mechanisms that increase genetic variation can bestow a selective advantage . Bacteria have several stress responses that provide ways in which mutation rates can be increased . These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases . Adaptive mutation appears to be process by which cells can respond to selective pressure specifically by producing mutations . In Escherichia coli strain FC40 adaptive mutation involves the following inducible components: (i) a recombination pathway that generates mutations; (ii) a DNA polymerase that synthesizes error-containing DNA; and (iii) stress responses that regulate cellular processes . In addition, a subpopulation of cells enters into a state of hypermutation, giving rise to about 10% of the single mutants and virtually all of the mutants with multiple mutations . These bacterial responses have implications for the development of cancer and other genetic disorders in higher organisms. Clin Anat, 2005 Jan, 18(1), 64 - 7 Recovery of periodontopathogenic bacteria from embalmed human cadavers; Wood N et al.; There is recent interest in recovery of periodontopathogenic bacteria from arterial and bronchial tissues to identify a link between periodontal and cardiovascular or pulmonary diseases . This interest could provide a useful clinical correlation exercise for gross anatomy . Our objective was to perform a feasibility study to determine whether these bacteria could be recovered from two sites within eight (4 dentate, 4 edentulous) human embalmed cadavers from an anatomical dissection laboratory . Bacterial samples were collected from the right coronary artery and the right superior secondary bronchus and assayed for the presence and concentrations of the DNA of A . actinomycetemcomitans, E . corrodens, C . rectus, P . intermedia, P . gingivalis, B . forsythus, T . denticola, and F . nucleatum . Frequencies were compared using a Kruskal-Wallis H-test . Correlations between the presence of teeth, bacterial species, and site were determined by a Spearman's rho correlation test . A . actinomycetemcomitans and B . forsythus frequencies were different between the sites in edentulous subjects (P <0.05); the frequency of B . forsythus was different in dentate and edentulous subjects at the bronchus site (P <0.05) . Numerous significant correlations were identified between strains of bacteria, site, and presence of teeth . Thus, it is possible for the DNA of periodontopathogenic bacteria to be recovered from human embalmed cadavers . Collection and identification of these bacteria from these cadavers could be a useful clinical correlation exercise for dental students in a gross anatomy class. Biophys J . 2004 Dec 13; {Epub ahead of print} A Minimal Generic Model of Bacteria-Induced Intracellular Ca2+ Oscillations in Epithelial Cells; Oxhamre C et al.; The toxin alpha-hemolysin expressed by uropathogenic Escherichia coli bacteria was recently shown as the first pathophysiologically relevant protein to induce oscillations of the intracellular Ca(2+) concentration in target cells . Here, we propose a generic three-variable kinetic model describing the Ca(2+) oscillations induced in single rat renal epithelial cells by this toxin . The predicted response of cells exposed to the toxin is in good agreement with the results of experiments(P . Uhlen et al., 2000 . Nature . 405:694-697). Nature, 2004 Dec 9, 432(7018), 750 - 3 A taxa-area relationship for bacteria; Horner-Devine MC et al.; A positive power-law relationship between the number of species in an area and the size of that area has been observed repeatedly in plant and animal communities . This species-area relationship, thought to be one of the few laws in ecology, is fundamental to our understanding of the distribution of global biodiversity . However, such a relationship has not been reported for bacteria, and little is known regarding the spatial distribution of bacteria, relative to what is known of plants and animals . Here we describe a taxa-area relationship for bacteria over a scale of centimetres to hundreds of metres in salt marsh sediments . We found that bacterial communities located close together were more similar in composition than communities located farther apart, and we used the decay of community similarity with distance to show that bacteria can exhibit a taxa-area relationship . This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition. Comp Biochem Physiol B Biochem Mol Biol, 2004 Dec, 139(4), 705 - 11 Fatty acid composition of aquatic insect larvae Stictochironomus pictulus (Diptera: Chironomidae): evidence of feeding upon methanotrophic bacteria; Kiyashko SI et al.; Larvae of the chironomid Stictochironomus pictulus were collected from Lake Biwa, central Japan . Both the fatty acid composition of the total lipid fraction and the carbon stable isotope ratios of whole larvae were determined . Larvae showed delta(13)C values of -57.4 per thousand to -62.4 per thousand, similar to the values of methane recorded from the lake sediments . A high level of monounsaturated fatty acids (MUFAs; approximately 50% of total fatty acids) and an extremely low level of n-3 series polyunsaturated fatty acids (PUFAs) in the total lipids of S . pictulus indicated a predominantly bacterial nutrition for this species . Moreover, chironomid tissues contained large amounts of the Type I methanotroph group-specific fatty acid, 16:1(n-8) (approximately 8% of total fatty acids) . This is the first time such a fatty acid biomarker has been described from freshwater invertebrates . The data suggest that S . pictulus larvae directly feed upon methanotrophic bacteria. FEBS Lett, 2004 Dec 3, 578(1-2), 26 - 30 Pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria; Misra HS et al.; Transgenic Escherichia coli expressing pyrroloquinoline-quinone (PQQ) synthase gene from Deinococcus radiodurans showed superior survival during Rose Bengal induced oxidative stress . Such cells showed significantly low levels of protein carbonylation as compared to non-transgenic control . In vitro, PQQ reacted with reactive oxygen species with rate constants comparable to other well known antioxidants, producing non-reactive molecular products . PQQ also protected plasmid DNA and proteins from the oxidative damage caused by gamma-irradiation in solution . The data suggest that radioprotective/oxidative stress protective ability of PQQ in bacteria may be consequent to scavenging of reactive oxygen species per se and induction of other free radical scavenging mechanism. Appl Environ Microbiol, 2004 Dec, 70(12), 7487 - 96 Novel, attached, sulfur-oxidizing bacteria at shallow hydrothermal vents possess vacuoles not involved in respiratory nitrate accumulation; Kalanetra KM et al.; Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif . There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater . Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date . Attached filaments, ranging in diameter from 4 to 100 microm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole . A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 microm or more . Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera Beggiatoa, Thioploca, and Thiomargarita) and no nonvacuolate genera . However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate . It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments. Appl Environ Microbiol, 2004 Dec, 70(12), 7311 - 20 Comparison of proteolytic activities produced by entomopathogenic Photorhabdus bacteria: strain- and phase-dependent heterogeneity in composition and activity of four enzymes; Marokhazi J et al.; Twenty strains (including eight phase variant pairs) of nematode-symbiotic and insect-pathogenic Photorhabdus bacteria were examined for the production of proteolytic enzymes by using a combination of several methods, including gelatin liquefaction, zymography coupled to native and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and activity measurement with two chromogen substrate types . Four protease activities (approximately 74, approximately 55, approximately 54, and approximately 37 kDa) could be separated . The N-terminal sequences of three of the proteases were determined, and a comparison with sequences in databases allowed identification of these proteases as HEXXH metallopeptidases . Thus, the 74-kDa protease (described formerly as Php-B {J . Marokhazi, G . Koczan, F . Hudecz, L . Graf, A . Fodor, and I . Venekei, Biochem . J . 379:633-640, 2004) is an ortholog of OpdA, a member the thimet oligopeptidase family, and the 55-kDa protease is an ortholog of PrtA, a HEXXH+H peptidase in clan MB (metzincins), while the 37-kDa protease (Php-C) belongs to the HEXXH+E peptidases in clan MA . The 54-kDa protease (Php-D) is a nonmetalloenzyme . PrtA and Php-C were zymographically detected, and they occurred in several smaller forms as well . OpdA could not be detected by zymography . PrtA, Php-C, and Php-D were secreted proteases; OpdA, in contrast, was an intracellular enzyme . OpdA activity was found in every strain tested, while Php-D was detected only in the Brecon/1 strain . There was significant strain variation in the secretion of PrtA and Php-C activities, but reduced activity or a lack of activity was not specific to secondary-phase variants . The presence of PrtA, OpdA, and Php-C activities could be detected in the hemolymph of Galleria melonella larvae 20 to 40 h postinfection . These proteases appear not to be directly involved in the pathogenicity of Photorhabdus, since strains or phase variants lacking any of these proteases do not show reduced virulence when they are injected into G . melonella larvae. BMC Evol Biol . 2004 Nov 30;4(1):52. Host resistance does not explain variation in incidence of male-killing bacteria in Drosophila bifasciata; Veneti Z et al.; BACKGROUND: Selfish genetic elements that distort the sex ratio are found widely . Notwithstanding the number of records of sex ratio distorters, their incidence is poorly understood . Two factors can prevent a sex ratio distorter from invading: inability of the sex ratio distorter to function (failure of mechanism or transmission), and lack of drive if they do function (inappropriate ecology for invasion) . There has been no test to date on factors causing variation in the incidence of sex ratio distorting cytoplasmic bacteria . We therefore examined whether absence of the male-killing Wolbachia infection in D . bifasciata in Hokkaido island of Japan, in contrast to the presence of infection on the proximal island of Honshu, was associated with failure of the infection to function properly on the Hokkaido genetic background . RESULTS: The male-killer both transmitted and functioned well following introgression to each of 24 independent isofemale inbred lines carrying Hokkaido genetic backgrounds . This was maintained even under stringent conditions of temperature . We therefore reject the hypothesis that absence of infection is due to its inability to kill males and transmit on the Hokkaido genetic background . Further trap data indicates that D . bifasciata may occur at different densities in Hokkaido and Honshu populations, giving some credence to the idea that ecological differentiation could be important . CONCLUSIONS: The absence of the infection from the Hokkaido population is not caused by failure of the male-killer to function on the Hokkaido genetic background. Gene Expr Patterns, 2004 Dec, 5(2), 167 - 70 Wolbachia bacteria, the cause for false vesicular staining pattern in Drosophila melanogaster; Cho KO; Majority of fly laboratory strains is infected with Wolbachia, intracellular rickettsial-type symbiotic bacteria widespread in various organisms including insects and nematodes . To make the matter worse, I found that certain antisera used for fly immunocytochemistry can recognize Wolbachia bacteria in addition to their own antigens, due to impurity in the antisera generated against the recombinant fusion proteins frequently used as antigens . Thus, combinatorial use of contaminated antisera and Wolbachia-infected flies can result in serious misinterpretations, which can be avoided by curing laboratory strains of Wolbachia. Cell Mol Biol (Noisy-le-grand), 2004 Jul, 50(5), 553 - 61 Psychrophilic versus psychrotolerant bacteria--occurrence and significance in polar and temperate marine habitats; Helmke E et al.; The numerical dominance and ecological role of psychrophilic bacteria in bottom sediments, sea ice, surface water and melt pools of the polar oceans were investigated using isolates, colony forming units (CFU) and metabolic activities . All sediment samples of the Southern Ocean studied showed a clear numerical dominance of cold-loving bacteria . In Arctic sediments underlying the influence of cold polar water bodies psychrophiles prevailed also but they were less dominant in sediments influenced by the warm Atlantic Water . A predominance of psychrophiles was further found in consolidated Antarctic sea ice as well as in multiyear Arctic sea ice and in melt pools on top of Arctic ice floes . A less uniform adaptation response was, however, met in polar surface waters . In the very northern part of the Fram Strait (Arctic Ocean) we found bacterial counts and activities at 1 degree C exceeding those at 22 degrees C . In surface water of the Weddell Sea (Southern Ocean) psychrophiles also dominated numerically in early autumn but the dominance declined obviously with the onset of winter-water and a decrease of chlorphyll a . Otherwise in surface water of the Southern Ocean CFUs were higher at 22 degrees C than at 1 degree C while activities were vice versa indicating at least a functional dominance of psychrophiles . Even in the temperate sediments of the German Bight true psychrophiles were present and a clear shift towards cold adapted communities in winter observed . Among the polar bacteria a more pronounced cold adaptation of Antarctic in comparison with Arctic isolates was obtained . The results and literature data indicate that stenothermic cold adapted bacteria play a significant role in the global marine environment . On the basis of the temperature response of our isolates from different habitats it is suggested to expand the definition of Morita in order to meet the cold adaptation strategies of the bacteria in the various cold habitats. J Environ Sci (China), 2004, 16(5), 856 - 9 Isolation and characterization of deodorizing bacteria for organic sulfide malodor; Jiang AX et al.; Strain JII screened out from different odor origins can efficiently degrade methyl mercaptan and ethanethiol whereas has no ability to remove dimethyl sulfide . The results indicated that the strain JII breaks only the C-SH bond . The optimum temperature and pH of JII are 20-30 degrees C and 6.0-8.3 respectively . A systematic identification method-16S rDNA gene sequence comparison, for deodorizing bacteria was carried out . The 16S rDNA gene sequence analysis of strain JII showed the highest level of 97% homology to Rape rhizosphere. Mikrobiol Z, 2004 Sep-Oct, 66(5), 84 - 9 {Phytopathogenic bacteria in two-spore white button mushroom culture} {Phylogenetic analysis of facultative methylotrophic bacteria of Methylobacterium genus} {No authors listed} Phylogenetic analysis of Methylobacterium genus species using analysis of nucleotide sequence of 16S rRNA genes has shown that Methylobacterium zatmanii and M . rhodesianum possess high-level similarity with M . extorquens (99.4-98.8%), and M . fujisawaense and M . radiotolerans--with M . mesophilicum (98.9-97.8%) . These species are also similar as to their phenotypical properties and their total DNAs have also close similarity . Thus, the right of M . zatmanii, M . rhodesianum, M . fujisawaense and M . radiotolerans species for existence needs confirmation . Some phenotypical properties which were assummed as a basis for formation of certain species of the genus Methylobacterium (radioresistance, e.g.) cannot serve as the differentiating characteristic of this genus species . High resistance to gamma- and UV-radiation is a specific sign of representatives of Methylobacterium genus. Prikl Biokhim Mikrobiol, 2004 Sep-Oct, 40(5), 536 - 43 {Conversion of androstenedione and androstadienedione by sterol-degrading bacteria}; Molecular adaptation in plant hemoglobin et al.; CNRS UMR 5171--Genome, Populations, Interactions, Adaptation, Universite Montpellier, 2--CC63, Place E Bataillon, 34095 Montpellier, FranceThe evolutionary history of the hemoglobin gene family in angiosperms is unusual in that it involves two mechanisms known for potentially generating molecular adaptation: gene duplication and among-species interaction . In plants able to achieve symbiosis with nitrogen-fixing bacteria, class 2 hemoglobin is expressed at high concentrations in nodules and appears to be a key factor for the achievement and regulation of the symbiotic exchange . In this study, we make use of codon models of DNA sequence evolution with the goal of determining the nature of the selective forces which have driven the evolution of this gene . Our results suggest that adaptive evolution occurred during the period of time following the duplication event (functional divergence) and that a change in the selective pressures arose in class 2 hemoglobin in relation to the acquisition of a symbiotic function. Biochem Biophys Res Commun, 2004 Dec 17, 325(3), 739 - 43 Quantum dot-antibody and aptamer conjugates shift fluorescence upon binding bacteria; Dwarakanath S et al.; CdSe/ZnS quantum dots (QDs) exhibited fluorescence emission blue shifts when conjugated to antibodies or DNA aptamers that are bound to bacteria . The intensity of the shifted emission peak increased with the number of bound bacteria . Curiously, the emission was consistently shifted to approximately 440-460 nm, which is distinctly different from the major component of the natural fluorescence spectrum of these QDs . This minor emission peak can grow upon conjugation to antibodies or aptamers and subsequent binding to bacterial cell surfaces . We hypothesize that the wavelength shift is due to changes in the chemical environment of the QD conjugates when they encounter the bacterial surface and may be due to physical deformation of the QD that changes the quantum confinement state . Regardless of the mechanism, these remarkable emission wavelength shifts of greater than 140 nm in some cases strongly suggest new applications for QD-receptor conjugates. Scand J Immunol, 2004 Nov, 60(5), 477 - 85 Modulation of cytokine release by differentiated CACO-2 cells in a compartmentalized coculture model with mononuclear leucocytes and nonpathogenic bacteria; Parlesak A et al.; To further investigate the interaction between human mononuclear leucocytes {peripheral blood mononuclear cells (PBMC)} and enterocytes, the effect of a confluent layer of differentiated CACO-2 cells on cytokine kinetics during challenge with bacteria in a compartmentalized coculture model was investigated . Nonpathogenic Escherichia coli were added either to the apical or the basolateral compartment of this transwell cell culture system, the latter of which contained human leucocytes . The synthesis of tumour necrosis factor (TNF-alpha) and interleukin (IL)-12 was significantly suppressed by CACO-2 cells when leucocytes were stimulated directly with bacteria . This suppression was not paralleled by changes in the production of IL-10, IL-6 and transforming growth factor (TGF)-beta . When the bacteria were applied apically to the CACO-2 cell layer, the production of TNF-alpha, IL-12, IL-1beta, IL-8, IL-6, IL-10, TGF-beta and interferon-gamma was pronouncedly lower as compared to the bacterial stimulation of leucocytes beneath the CACO-2 cells . In the latter experiments, IL-6, IL-8 and TNF-alpha were the cytokines being mostly induced by apical addition of E . coli . Quantitative mRNA expression analysis revealed that IL-8 gene expression was equally induced in both CACO-2 and PBMC after apical stimulation with bacteria . Of note, bacteria-stimulated CACO-2 cells produced little or no cytokines in the absence of leucocytes, supporting the concept of leucocyte-epithelial cell cross-talk in modulating cytokine responses in the gut mucosa. Curr Opin Genet Dev, 2004 Dec, 14(6), 627 - 33 Genomic changes following host restriction in bacteria; Moran NA et al.; Many genomic sequences have been recently published for bacteria that can replicate only within eukaryotic hosts . Comparisons of genomic features with those of closely related bacteria retaining free-living stages indicate that rapid evolutionary change often occurs immediately after host restriction . Typical changes include a large increase in the frequency of mobile elements in the genome, chromosomal rearrangements mediated by recombination among these elements, pseudogene formation, and deletions of varying size . In anciently host-restricted lineages, the frequency of insertion sequence elements decreases as genomes become extremely small and strictly clonal . These changes represent a general syndrome of genome evolution, which is observed repeatedly in host-restricted lineages from numerous phylogenetic groups . Considerable variation also exists, however, in part reflecting unstudied aspects of the population structure and ecology of host-restricted bacterial lineages. Leukemia . 2004 Nov 04; {Epub ahead of print} A novel approach to identify antigens recognized by CD4 T cells using complement-opsonized bacteria expressing a cDNA library; van de Corput L et al.; In patients with hematological malignancies receiving HLA-matched stem cell transplantation, T cells specific for minor histocompatibility antigens play a major role in graft rejection, induction of graft-versus-host disease and beneficial graft-versus-leukemia reactivity . Several human minor histocompatibility antigens recognized by T cells have been identified, but only two are presented by HLA class II molecules . In search of an efficient approach to identify antigenic peptides processed through the HLA class II pathway, we constructed a cDNA library in bacteria that were induced to express proteins . Bacteria were opsonized with complement to enforce receptor-mediated uptake by Epstein-Barr virus immortalized B cells that were subsequently used as antigen-presenting cells . This approach was validated with an HLA class II-restricted antigen encoded by gene DBY . We were able to identify bacteria expressing DBY diluted into a 300-fold excess of bacteria expressing a nonrelevant gene . Screening of a bacterial library using a DBY-specific CD4 T cell clone resulted in the isolation of several DBY cDNAs . We propose this strategy for a rapid identification of HLA class II-restricted antigenic peptides recognized by CD4 T cells.Leukemia advance online publication, 4 November 2004; doi:10.1038/sj.leu.2403583. Adv Microb Physiol, 2004, 49, 131 - 74 Stress responsive bacteria: biosensors as environmental monitors; Cheng Vollmer A et al.; The delicate and dynamic balance of the physiological steady state and its maintenance is well characterized by studies of bacterial stress response . Through the use of genetic analysis, numerous stress regulons, their physiological regulators and their biochemical processes have been delineated . In particular, transcriptionally activated stress regulons are subjects of study and application . These regulons include those that respond to macromolecular damage and toxicity as well as to nutrient starvation . The convenience of reporter gene fusions has allowed the creation of biosensor strains, resulting from the fusion of stress-responsive promoters with a variety of reporter genes . Such cellular biosensors are being used for monitoring dynamic systems and can report the presence of environmental stressors in real time . They provide a greater range of sensitivity, e.g . to sub-lethal concentrations of toxicants, than the simple assessment of cell viability . The underlying physiological context of the reporter strains results in the detection of bioavailable concentrations of both toxicants and nutrients . Culture conditions and host strain genotypes can be customized so as to maximize the sensitivity of the strain for a particular application . Collections of specific strains that are grouped in panels are used to diagnose targets or mode of action for unknown toxicants . Further application in massive by parallel DNA and gene fusion arrays greatly extends the information available for diagnosis of modes of action and may lead to development of novel high-throughput screens . Future studies will include more panels, arrays, as well as single reporter cell detection for a better understanding of the population heterogeneity during stress response . New knowledge of physiology gained from further studies of novel systems, or using innovative methods of analysis, will undoubtedly yield still more useful and informative environmental biosensors. BMC Biotechnol . 2004 Oct 30;4(1):27. Mucosal delivery of anti-inflammatory IL-1Ra by sporulating recombinant bacteria; Porzio S et al.; BACKGROUND: Mucosal delivery of therapeutic protein drugs or vaccines is actively investigated, in order to improve bioavailability and avoid side effects associated with systemic administration . Orally administered bacteria, engineered to produce anti-inflammatory cytokines (IL-10, IL-1Ra), have shown localised ameliorating effects in inflammatory gastro-intestinal conditions . However, the possible systemic effects of mucosally delivered recombinant bacteria have not been investigated . RESULTS: B . subtilis was engineered to produce the mature human IL-1 receptor antagonist (IL-1Ra) . When recombinant B . subtilis was instilled in the distal colon of rats or rabbits, human IL-1Ra was found both in the intestinal lavage and in the serum of treated animals . The IL-1Ra protein in serum was intact and biologically active . IL-1-induced fever, neutrophilia, hypoglycemia and hypoferremia were inhibited in a dose-dependent fashion by intra-colon administration of IL-1Ra-producing B . subtilis . In the mouse, intra-peritoneal treatment with recombinant B . subtilis could inhibit endotoxin-induced shock and death . Instillation in the rabbit colon of another recombinant B . subtilis strain, which releases bioactive human recombinant IL-1beta upon autolysis, could induce fever and eventually death, similarly to parenteral administration of high doses of IL-1beta . CONCLUSIONS: A novel system of controlled release of pharmacologically active proteins is described, which exploits bacterial autolysis in a non-permissive environment . Mucosal administration of recombinant B . subtilis causes the release of cytoplasmic recombinant proteins, which can then be found in serum and exert their biological activity in vivo systemically. Ying Yong Sheng Tai Xue Bao, 2004 Jul, 15(7), 1241 - 4 {Introdoction of bioluminescence genes into silicate-dissolving bacteria strain NBT}; He L et al.; In this study, silicate-dissolving bacteria NBT strain was grown with 0.25% maltose as carbon source, and the rifampicin-resistance was generated by ultraviolet mutagenesis and streak naturalized to 200 microg x ml(-1) . Through triparental cross, the luxAB genes were introduced into NBT-R200 at the help of pRK2013 . The luminescence activity of the hybrid strain was tested, which indicated that all colonies had a high luminescence activity and kanamycin-, tetracyctine-and rifampicin-resistance . The NBT-R200 cells prepared from initial logarithmic growth phage were more likely to be sensitive to foreign DNA, and the maximum translocation frequency was up to 6.70 x 10(-5) . In addition, the optimal mating ratio was 1:1:1 . The potassium release ability from feldspar and the luminescence of luxAB genes marked silicate-dissolving bacteria RL85 strain were stable, and hence, the RL85 was available to rhizosphere microecology researches. Bioessays, 2004 Nov, 26(11), 1209 - 16 An intracellular actin motor in bacteria? Graumann PL, Defeu Soufo HJ. Actin performs structural as well as motor-like functions in eukaryotic cells . Orthologues of actin have also been identified in bacteria, where they perform an essential function during cell growth . Bacterial actins are implicated in the maintenance of rod-shaped cell morphology, and appear to form a cytoskeletal structure, localising as helical filaments underneath the cell membrane . Recently, a plasmid-borne actin orthologue has been shown to perform a mitotic-like function during segregation of a plasmid, and chromosomally encoded actin proteins were found to play an important role in chromosome segregation . Based on the findings that actin filaments are dynamic structures in two bacterial species, we propose that actins perform motor functions rather than a purely structural role in bacteria . We suggest that an intracellular motor exists in bacteria that could be derived from an ancestral actin motor that was present in cells early in evolution. Appl Opt, 2004 Oct 1, 43(28), 5295 - 302 Rapid optically based measurements of diameter and length for spherical or rod-shaped bacteria in vivo; Van De Merwe WP et al.; The application in light scattering of the Mueller matrix ratio (S34)/(S11) for determining average particle size is extended to a large size parameter range for spherical or randomly oriented rod-shaped particles such as micro-organisms . It is shown that combining the graph of this ratio with a Coulter counter measurement of particle volume gives results in agreement with microscopic measurements . Thus this combination provides a method to measure particle diameter and width simultaneously in real time for elongated particles such as bacteria, which are measured in vivo with this method . An approximate empirical formula is developed to estimate the motion of the extrema in the graph of the oscillating matrix ratio as size changes occur . This formula is also shown to be consistent with wavelength changes. Adv Biophys, 2004, 38, 81 - 96 Cell death promoted by homologous DNA interaction from bacteria to humans; Kusano K; Pairing between homologous DNA controls cellular functions including double-strand break repair, mitotic recombination, and progression of DNA replication forks, as well as chiasma formation during meiosis . Here I summarize that homologous interaction could promote the cell killing in bacteria, yeast, and multicellular organisms . The mechanisms of cell killing are categorized into two types: (1) the killing due to the accumulation of extrachromosomal DNA; (2) the killing induced by Holliday junction structures . I propose that the mechanisms of such killing function as novel apoptotic pathways in the cells carrying severe DNA damages to eliminate such damages from cell population. Mol Microbiol, 2004 Nov, 54(3), 598 - 603 Why is transcription coupled to translation in bacteria? Gowrishankar J, Harinarayanan R. Active mechanisms exist to prevent transcription that is uncoupled from translation in the protein-coding genes of bacteria, as exemplified by the phenomenon of nonsense polarity . Bacterial transcription-translation coupling may be viewed as one among several co-transcriptional processes, including those for mRNA processing and export in the eukaryotes, that operate in the various life forms to render the nascent transcript unavailable for formation of otherwise deleterious R-loops in the genome. J Clin Periodontol, 2004 Nov, 31(11), 985 - 90 Longitudinal stability of serum immunoglobulin G responses to periodontal bacteria; Papapanou PN et al.; BACKGROUND: The value of seroepidemiology in the study of periodontal infections has not been adequately explored . This study examined serum immunoglobulin (IgG) responses to periodontal bacteria in patients with periodontitis and periodontitis-free individuals over a 30-month period . METHODS: Eighty-nine patients with chronic periodontitis and 42 control subjects with no deep periodontal pockets and no or minimal attachment loss (30-72 years old, 43% men) were included . Patients were examined at baseline, after completed periodontal therapy 4 months post-baseline, and at 30 months, and controls, at baseline and 30 months . IgG antibodies to 19 periodontal species were determined by checkerboard immunoblotting . RESULTS: On average, patients displayed at baseline up to 800-fold higher titers than controls to all but three species . Over the 30-month period, titers remained stable at low levels in controls . In patients, periodontal conditions improved from a baseline mean probing depth of 3.6 mm, bleeding on probing of 62% and an average of 21.5 pockets of=6 mm/person, to 2.5 mm mean pocket depth, 30% bleeding on probing, and 1.2 deep pockets, at 30 months . Over time, antibody titers showed a modest decline in patients, but remained significantly elevated at 30 months in comparison with controls . Antibody-level changes over time were not significantly different between subjects that did and did not receive adjunctive systemic antibiotics . CONCLUSIONS: Conspicuous differences in IgG titers to periodontal bacteria exist between periodontitis patients and periodontally healthy controls . Despite successful periodontal therapy, titers remained elevated over a 30-month period, suggesting that serology may mark the history of past periodontal infection . (c) Blackwell Munksgaard, 2004 Crit Rev Microbiol, 2004, 30(3), 197 - 204 Decontamination techniques of pathogen bacteria in meat and poultry; Dincer AH et al.; Means of controlling or even improving the safety of food products is to decontaminate the carcasses or products during or at the end of the production line . The decontamination of meat and poultry can help to reduce human foodborne infections . However, process hygiene to prevent contamination should never be neglected . Some techniques of decontaminating raw meat and poultry meat products are discussed in this review. J Microbiol Methods, 2004 Dec, 59(3), 427 - 31 Simplified sample preparation using frame spotting method for direct counting of total bacteria by fluorescence microscopy; Maruyama F et al.; A new preparation method for direct counting of bacteria in liquid samples with fluorescence microscope was developed using a glass slide coated with 3-aminopropyltriethoxy silane and ring-shaped polyester seal as a retainer . The experimental steps of this method were spotting samples onto the coated slides with the seal, drying under vacuum, staining with SYBR Green II, drying and covering with immersion oil and coverslip to allow counting . This simplified method provided consistent results when compared with the conventional filtration method for fluorescence microscopy, and is rapid, inexpensive and reproducible. J Microbiol Methods, 2004 Dec, 59(3), 423 - 5 "Paraffin wax-overlay of pour plate", a method for the isolation and enumeration of purple non-sulfur bacteria; Archana A et al.; A modification of pour plate technique with an overlay of wax was used for isolation and enumeration of purple non-sulfur bacteria (PNSB) with equal efficiency as that of agar shake culture . The total count of PNSB ranged from 10(5)-10(8) CFU g dry soil(-1) and belonged to the genera of Rhodobacter, Rhodopseudomonas, Rhodocista and Rubrivivax. J Am Chem Soc, 2004 Oct 20, 126(41), 13343 - 6 Detection of bacteria with carbohydrate-functionalized fluorescent polymers; Disney MD et al.; Many pathogens that infect humans use cell surface carbohydrates as receptors to facilitate cell-cell adhesion . The hallmark of these interactions is their multivalency, or the simultaneous occurrence of multiple interactions . We have used a carbohydrate-functionalized fluorescent polymer, which displays many carbohydrate ligands on a single polymer chain, to allow for multivalent detection of pathogens . Incubation of a mannose-functionalized polymer with Escherichia coli yields brightly fluorescent aggregates of bacteria . These results show that carbohydrate-functionalized fluorescent polymers are a versatile detection method for bacteria . Future design of detectors for other pathogens only requires information on the carbohydrates bound by the organisms, which has been exhaustively reported in the literature. J Appl Toxicol, 2004 Sep-Oct, 24(5), 343 - 8 Water toxicity detection by a panel of stress-responsive luminescent bacteria; Pedahzur R et al.; A panel of Escherichia coli strains harbouring different stress-responsive promoters fused to a lux reporter system was used to assess the potential toxicity of 17 unknown model water samples . Using liquid cultures, nine out of 14 toxic samples were properly identified as toxic, whereas five were false negatives . All three non-toxic controls were identified correctly (no false positives) . Two strains containing promoter-lux fusions were also tested when immobilized onto fibre-optic tips . One genotoxic sample and six toxic samples were correctly identified in this manner . The potential advantages and limitations in the use of genetically engineered bacteria as biosensors for water toxicity are discussed in view of these results . Copyright (c) 2004 John Wiley & Sons, Ltd. Adv Biophys, 2004, 38(Complete), 81 - 96 Cell death promoted by homologous DNA interaction from bacteria to humans; Kusano K; Pairing between homologous DNA controls cellular functions including double-strand break repair, mitotic recombination, and progression of DNA replication forks, as well as chiasma formation during meiosis . Here I summarize that homologous interaction could promote the cell killing in bacteria, yeast, and multicellular organisms . The mechanisms of cell killing are categorized into two types: (1) the killing due to the accumulation of extrachromosomal DNA; (2) the killing induced by Holliday junction structures . I propose that the mechanisms of such killing function as novel apoptotic pathways in the cells carrying severe DNA damages to eliminate such damages from cell population. J Biochem Mol Biol, 2004 Jul 31, 37(4), 487 - 92 Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M . smegmatis: identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species; Sahu K et al.; The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M . smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms . Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons . The second major explanatory axis differentiates the genes according to their genome type . A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxz1 identified 21 codons, which are statistically over represented in the former group of genes . Further analysis found that the Bxz1- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxz1 . In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxz1 . This analysis predicts for the first time that the Bxz1-specific tRNA species modulates the optimal expression of its proteins during development. Appl Environ Microbiol, 2004 Oct, 70(10), 6333 - 6 Stabilization of oil-water emulsions by hydrophobic bacteria; Dorobantu LS et al.; Formation of oil-water emulsions during bacterial growth on hydrocarbons is often attributed to biosurfactants . Here we report the ability of certain intact bacterial cells to stabilize oil-in-water and water-in-oil emulsions without changing the interfacial tension, by inhibition of droplet coalescence as observed in emulsion stabilization by solid particles like silica. Appl Environ Microbiol, 2004 Oct, 70(10), 6306 - 8 Intestinal mucus alters the ability of probiotic bacteria to bind aflatoxin B1 in vitro; Gratz S et al.; Several probiotics are known to bind aflatoxin B(1) (AFB(1)) to their surfaces and to adhere to intestinal mucus . In this study, preincubation of two probiotic preparations with either AFB(1) or mucus reduced the subsequent surface binding of mucus and AFB(1), respectively, in a strain-dependent manner. Appl Environ Microbiol, 2004 Oct, 70(10), 6272 - 81 Bloom of filamentous bacteria in a mesotrophic lake: identity and potential controlling mechanism; Pernthaler J et al.; Ephemeral blooms of filamentous bacteria are a common phenomenon in the water column of oligo- to mesotrophic lakes . It is assumed that the appearance of such morphotypes is favored by selective predation of bacterivorous protists and that filter-feeding zooplankton plays a major role in suppressing these bacteria . The phylogenetic affiliation of the important bloom-forming filamentous bacteria in freshwaters is presently unknown . Here we report the identification of dominant members of a filamentous bacterial assemblage during a bloom of such morphotypes in a mesotrophic lake . By molecular cloning and fluorescence in situ hybridization with specific oligonucleotide probes, up to 98% of filamentous cells in lake water could be assigned to a clade of almost identical (99% similarity) 16S rRNA gene sequence types, the cosmopolitan freshwater LD2 cluster . For a period of less than 1 week, members of the LD2 clade constituted >40% of the total bacterial biomass, potentially favored by high grazing of planktivorous protists . This is probably the most pronounced case of dominance by a single bacterioplankton species ever observed in natural freshwaters . In enclosures artificially stocked with the metazoan filter feeder Daphnia, bacteria related to the LD2 clade formed a significantly larger fraction of filaments than in enclosures where Daphnia had been removed . However, in the presence of higher numbers of Daphnia individuals, the LD2 bacteria, like other filaments, were eventually eliminated both in enclosures and in the lake . This points at the potential importance of filter-feeding zooplankton in controlling the occurrence and species composition of filamentous bacterial morphotypes in freshwater plankton. Eur J Vasc Endovasc Surg, 2004 Nov, 28(5), 553 - 8 Detection and localization of periodontopathic bacteria in abdominal aortic aneurysms; Kurihara N et al.; OBJECTIVES: We examined a possible link between periodontal disease and abdominal aortic aneurysm (AAA) by studying resected aneurysmal specimens from AAA patients for the presence of periodontopathic bacteria . DESIGN: Prospective case control study . MATERIAL AND METHODS: Thirty-two AAA patients were enrolled in the study . Periodontitis was classified according to the probing depth of periodontal pocket . Thirty-two aneurysmal walls, 16 mural thrombi, 5 atherosclerotic occlusive aorta and 5 control arterial tissue, were examined for 7 periodontal bacteria using polymerase chain reaction (PCR) method . The localization of the bacteria in the aneurysmal/atherosclerotic wall was determined by thromboendarterectomy . RESULTS: All patients had periodontal disease, and most cases were severe . PCR examination of the aneurysmal specimens showed that 86% were positive for periodontal bacterial DNA . No bacteria were detected in the control specimens . The bacteria were found in both the intimal/medial layer and the adventitial layer of the aneurysmal wall but only in intimal/medial layer of the atherosclerotic occlusive aorta . CONCLUSION: Periodontopathic bacteria were present in a high percentage of specimens of diseased arteries from AAA patients and were found throughout the whole aneurysmal wall . These bacteria may play a role in the development of AAAs and/or contribute to weakening the aneurysmal wall. Parasitol Today, 1993 May, 9(5), 179 - 83 Modification of arthropod vector competence via symbiotic bacteria; Beard CB et al.; Some of the world's most devastating diseases are transmitted by arthropod vectors . Attempts to control these arthropods are currently being challenged by the widespread appearance of insecticide resistance . It is therefore desirable to develop alternative strategies to complement existing methods of vector control . In this review, Charles Beard, Scott O'Neill, Robert Tesh, Frank Richards and Serap Aksoy present an approach for introducing foreign genes into insects in order to confer refractoriness to vector populations, ie . the inability to transmit disease-causing agents . This approach aims to express foreign anti-parasitic or anti-viral gene products in symbiotic bacteria harbored by insects . The potential use of naturally occurring symbiont-based mechanisms in the spread of such refractory phenotypes is also discussed. Environ Sci Technol, 2004 Sep 1, 38(17), 4596 - 602 Electrokinetic transport of PAH-degrading bacteria in model aquifers and soil; Wick LY et al.; An investigation of the mobility, viability, and activity of polycyclic aromatic hydrocarbon (PAH) degrading bacteria in an electric field is presented . Bench-scale model aquifers were used to test electrophoresis and electroosmosis as potential mechanisms for bacterial dispersion in contaminated sites . Glass beads, alluvial sand from Lake Geneva, and historically polluted clayey soil were used as packing materials . The green-fluorescent protein labeled PAH-degrading bacteria Sphingomonas sp . L138 and Mycobacterium frederiksbergense LB501TG were used as test organisms because of the known differing physicochemical surface and adhesion properties of the corresponding wild-type strains . No adverse effects of the electric current on bacterial viability and PAH-degradation were observed in the system chosen . Up to 90% of the weakly negatively charged and moderately adhesive cells of strain L138 were transported by electroosmosis, whereas 0-20% were transported by electrophoresis . By contrast, poor electrokinetic transport of strongly charged and highly adhesive cells of M . frederiksbergense LB501TG occurred in the different model aquifers . Treatment of bacteria with the nonionic surfactant Brij35 resulted in up to 80% enhanced electrokinetic dispersion of both strains . Our findings demonstrate that electroosmosis may be a valuable mechanism to transport bacteria in the subsurface with transport efficiencies heavily depending on the retention of the bacteria by the solid phase. Biofizika, 2004 Jul-Aug, 49(4), 653 - 8 {A discrepancy between the experimental and theoretical data on energy migration from B800 to B850 in LH-2 antennary complexes in purple bacteria}; Spurious rise in the automated platelet count because of bacteria; Department of Pathology, Christian Medical College and Hospital, Ludhiana-141 008, Punjab, India . n_kakkar@satyam.net.in The era of automation in haematology, although improving the accuracy and precision of results, has also introduced the laboratory haematologist to a vast array of spurious parameters . The identification of these results is important so that inappropriate management decisions are avoided . The case presented here illustrates a spuriously raised automated platelet count resulting from bacterial overgrowth in the blood sample. FEMS Microbiol Rev, 2004 Jun, 28(3), 353 - 76 Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation; Dubbs JM et al.; For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions . These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis . After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes . Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms . Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways . Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport . The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific . For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance . From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved. Ecotoxicol Environ Saf, 2004 Nov, 59(3), 349 - 69 Environmental impact of heavy metals from dredged and resuspended sediments on phytoplankton and bacteria assessed in in situ mesocosms; Nayar S et al.; Past and on-going reclamation, dredging, construction and shipping activities impact Ponggol Estuary, located on the northeastern coast of Singapore . Tin, lead, nickel, cadmium, and copper in particulate and dissolved fractions and sediments ranged from ND (undetectable)-92 ppm, ND-303.2 ppm, ND-2818.4 ppm, ND-74.4 ppm and ND-1117.7 ppm, respectively . Intensive dredging activity during the monitoring period may have led to the resuspension and bioavailability of particulate metals . This was tested by the exposure of phytoplankton and bacteria in mesocosms to previously measured environmental levels of heavy metals and the contaminated sediments with the highest heavy metal concentrations from one of the impacted sites . The results showed significant copper toxicity to phytoplankton and autotrophic bacteria, followed by nickel and lead at all concentrations tested . Enhanced rates of heterotrophic bacterial production and total bacterial abundance were observed in treatments with higher metal concentrations . Among the various treatments, particulate and sediment metal concentrations were significantly different from those of the control . Mesocosms using contaminated sediments with the highest metal concentrations compared with the control showed a bioavailability of metals that resulted in the inhibition of phytoplankton and autotrophic bacteria . High concentrations of copper (5.52-11.35 mg L(-1)) and nickel (2.42-2.71 mg L(-1)) observed in the aqueous phase of treatment mesocosms, and attributed to release from the contaminated sediments could account for the toxicity to phytoplankton and autotrophic bacteria. Curr Microbiol, 2004 Oct, 49(4), 300 - 7 Phylogenetic analyses and diterpenoid production by marine bacteria of the genus Saprospira; Mincer TJ et al.; The relationship between 16S rRNA gene sequence-derived phylogeny and the bacterial production of diterpenoids from 18 isolates of marine bacteria belonging to the genus Saprospira was determined . Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified 16S rRNA genes of these isolates indicated four distinct phylotypes . The terpenoid metabolite profiles of each phylotype, determined by liquid chromatography mass spectrometry (LCMS) and nuclear magnetic resonance (NMR) analyses, indicated that diterpenoid production was restricted to phylotype A, which included the type specimen S . grandis Gross, and the sole member of the closely related phylotype B . The discovery of two new neoverrucosane diterpenoids produced by phylotype B has also been documented. IEEE Trans Nanobioscience, 2003 Sep, 2(3), 146 - 9 Exposure of magnetic bacteria to simulated mobile phone-type RF radiation has no impact on mortality; Cranfield CG et al.; The interaction of mobile phone RF emissions with biogenic magnetite in the human brain has been proposed as a potential mechanism for mobile phone bioeffects . This is of particular interest in light of the discovery of magnetite in human brain tissue . Previous experiments using magnetite-containing bacteria exposed directly to emissions from a mobile phone have indicated that these emissions might be causing greater levels of cell death in these bacterial populations when compared to sham exposures . A repeat of these experiments examining only the radio frequency (RF) global system for mobile communication (GSM) component of the mobile phone signal in a well-defined waveguide system (REFLEX), shows no significant change in cell mortality compared to sham exposures . A nonmagnetite containing bacterial cell strain (CC-26) with similar genotype and phenotype to the magnetotactic bacteria was used as a control . These also showed no significant change in cell mortality between RF and sham exposed samples . Results indicate that the RF components of mobile phone exposure do not appear to be responsible for previous findings indicating cell mortality as a result of direct mobile phone exposure . A further mobile phone emission component that should be investigated is the 2-Hz magnetic field pulse generated by battery currents during periods of discontinuous transmission. J Microbiol Methods, 2004 Nov, 59(2), 189 - 98 Enumeration of soil bacteria with the green fluorescent nucleic acid dye Sytox green in the presence of soil particles; Klauth P et al.; Total counts in soils are usually determined using fluorescent dyes, such as DAPI or Sybr green, due to fluorescence enhancement if they are bound to nucleic acids . Unfortunately, these commonly used dyes stain soil particles as well . Therefore, besides fluorescence enhancement, sufficient spectral differentiation is also required . We present a new procedure that overcomes the problems of visualising bacteria on surfaces in soil and avoids the separation of soil particles to a large extent . Spectral differentiation between bacteria and soil matrix is achieved by using Sytox green and a suboptimal excitation wavelength . Bacteria exhibit a bright green fluorescence, while soil particles fluoresce blue or red . Slight homogenisation and sedimentation of the sand and coarse silt that were too big for microscopic investigations were the only separation steps required . We compared the proposed Sytox green staining with Sybr green staining . The recovery of Sybr green-stained cells amounted to 38%, whereas in samples stained by Sytox green 81% of the spiked cells were counted . Sytox green can also be combined with fluorescence in situ hybridisation (FISH) using deep red dyes such as Cy5. Science, 2004 Sep 10, 305(5690), 1612 - 5 Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria; Kim HJ et al.; Siderophores are extracellular iron-binding compounds that mediate iron transport into many cells . We present evidence of analogous molecules for copper transport from methane-oxidizing bacteria, represented here by a small fluorescent chromopeptide (C45N12O14H62Cu, 1216 daltons) produced by Methylosinus trichosporium OB3b . The crystal structure of this compound, methanobactin, was resolved to 1.15 angstroms . It is composed of a tetrapeptide, a tripeptide, and several unusual moieties, including two 4-thionyl-5-hydroxy-imidazole chromophores that coordinate the copper, a pyrrolidine that confers a bend in the overall chain, and an amino-terminal isopropylester group . The copper coordination environment includes a dual nitrogen- and sulfur-donating system derived from the thionyl imidazolate moieties . Structural elucidation of this molecule has broad implications in terms of organo-copper chemistry, biological methane oxidation, and global carbon cycling. J Microbiol, 2004 Jun, 42(2), 87 - 93 Genetic and phenotypic diversity of (R/S)-mecoprop {2-(2-methyl-4-chlorophenoxy)propionic acid}-degrading bacteria isolated from soils; Lim JS et al.; Twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated . Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genus Sphingomonas . Ten different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 12 isolates . The isolates were found to be able to utilize the chiral herbicide mecoprop as a sole source of carbon and energy . While seven of the isolates were able to degrade both (R)- and (S)-mecoprop, four isolates exhibited enantioselective degradation of the (S)-type and one isolate could degrade only the (R)-enantiomer . All of the isolates were observed to possess plasmid DNAs . When certain plasmids were removed from isolates MP11, MP15, and MP23, those strains could no longer degrade mecoprop . This compelling result suggests that plasmid DNAs, in this case, conferred the ability to degrade the herbicide . The isolates MP13, MP15, and MP24 were identified as the same strain; however, they exhibited different plasmid profiles . This indicates that these isolates acquired different mecoprop-degradative plasmids in different soils through natural gene transfer. J Biol Chem, 2004 Nov 12, 279(46), 47699 - 703 Epub 2004 Sep 07. Bacteria binding by DMBT1/SAG/gp-340 is confined to the VEVLXXXXW motif in its scavenger receptor cysteine-rich domains; Bikker FJ et al.; The scavenger receptor cysteine-rich (SRCR) proteins form an archaic group of metazoan proteins characterized by the presence of SRCR domains . These proteins are classified in group A and B based on the number of conserved cysteine residues in their SRCR domains, i.e . six for group A and eight for group B . The protein DMBT1 (deleted in malignant brain tumors 1), which is identical to salivary agglutinin and lung gp-340, belongs to the group B SRCR proteins and is considered to be involved in tumor suppression and host defense by pathogen binding . In a previous study we used nonoverlapping synthetic peptides covering the SRCR consensus sequence to identify a 16-amino acid bacteria-binding protein loop (peptide SRCRP2; QGRVEVLYRGSWGTVC) within the SRCR domains . In this study, using overlapping peptides, we pinpointed the minimal bacteria-binding site on SRCRP2, and thus DMBT1, to an 11-amino acid motif (DMBT1 pathogen-binding site 1 or DMBT1pbs1; GRVEVLYRGSW) . An alanine substitution scan revealed that VEVL and Trp are critical residues in this motif . Bacteria binding by DMBT1pbs1 was different from the bacteria binding by the macrophage receptor MARCO in which an RXR motif was critical . In addition, the homologous consensus sequences of a number of SRCR proteins were synthesized and tested for bacteria binding . Only consensus sequences of DMBT1 orthologues bound bacteria by this motif. Appl Environ Microbiol, 2004 Sep, 70(9), 5708 - 13 Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments; Webster G et al.; Phylogenetic analysis of 16S rRNA gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division JS1 . Primers for PCR amplification of partial 16S rRNA genes that target the JS1 division were developed and used to detect JS1 sequences in DNA extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments. Appl Environ Microbiol, 2004 Sep, 70(9), 5651 - 8 Metabolic primers for detection of (Per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences; Bender KS et al.; Natural attenuation of the environmental contaminant perchlorate is a cost-effective alternative to current removal methods . The success of natural perchlorate remediation is dependent on the presence and activity of dissimilatory (per)chlorate-reducing bacteria (DPRB) within a target site . To detect DPRB in the environment, two degenerate primer sets targeting the chlorite dismutase (cld) gene were developed and optimized . A nested PCR approach was used in conjunction with these primer sets to increase the sensitivity of the molecular detection method . Screening of environmental samples indicated that all products amplified by this method were cld gene sequences . These sequences were obtained from pristine sites as well as contaminated sites from which DPRB were isolated . More than one cld phylotype was also identified from some samples, indicating the presence of more than one DPRB strain at those sites . The use of these primer sets represents a direct and sensitive molecular method for the qualitative detection of (per)chlorate-reducing bacteria in the environment, thus offering another tool for monitoring natural attenuation . Sequences of cld genes isolated in the course of this project were also generated from various DPRB and provided the first opportunity for a phylogenetic treatment of this metabolic gene . Comparisons of the cld and 16S ribosomal DNA (rDNA) gene trees indicated that the cld gene does not track 16S rDNA phylogeny, further implicating the possible role of horizontal transfer in the evolution of (per)chlorate respiration. Appl Environ Microbiol, 2004 Sep, 70(9), 5426 - 33 Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria; Pernthaler A et al.; We developed for Bacteria in environmental samples a sensitive and reliable mRNA fluorescence in situ hybridization (FISH) protocol that allows for simultaneous cell identification by rRNA FISH . Samples were carbethoxylated with diethylpyrocarbonate to inactivate intracellular RNases and pretreated with lysozyme and/or proteinase K at different concentrations . Optimizing the permeabilization of each type of sample proved to be a critical step in avoiding false-negative or false-positive results . The quality of probes as well as a stringent hybridization temperature were determined with expression clones . To increase the sensitivity of mRNA FISH, long ribonucleotide probes were labeled at a high density with cis-platinum-linked digoxigenin (DIG) . The hybrid was immunocytochemically detected with an anti-DIG antibody labeled with horseradish peroxidase (HRP) . Subsequently, the hybridization signal was amplified by catalyzed reporter deposition with fluorochrome-labeled tyramides . p-Iodophenylboronic acid and high concentrations of NaCl substantially enhanced the deposition of tyramides and thus increased the sensitivity of our approach . After inactivation of the antibody-delivered HRP, rRNA FISH was performed by following routine protocols . To show the broad applicability of our approach, mRNA of a key enzyme of aerobic methane oxidation, particulate methane monooxygenase (subunit A), was hybridized with different types of samples: pure cultures, symbionts of a hydrothermal vent bivalve, and even sediment, one of the most difficult sample types with which to perform successful FISH . By simultaneous mRNA FISH and rRNA FISH, single cells are identified and shown to express a particular gene . Our protocol is transferable to many different types of samples with the need for only minor modifications of fixation and permeabilization procedures. Environ Microbiol, 2004 Oct, 6(10), 1061 - 9 Quantifying 3H-thymidine incorporation rates by a phylogenetically defined group of marine planktonic bacteria (Bacteriodetes phylum); van Mooy BA et al.; The rate of {(3)H-methyl} thymidine ((3)H-TdR) incorporation into DNA has been applied extensively to measure cell production by bacterial communities in aquatic environments . Here we describe a method to quantify (3)H-TdR incorporation by specific, phylogenetically defined members of the bacterial community . The method involves selectively capturing DNA from targeted groups of bacteria and then quantifying its (3)H radioactivity . The method was applied to measure (3)H-TdR incorporation by the members of the phylum Bacteriodetes whose members, which include the Cytophaga-Flavobacter cluster, are ubiquitous in coastal waters . (3)H-labelled DNA from Bacteriodetes was selectively biotinylated in PCR-like reactions that contained a Bacteriodetes-specific 16S rRNA gene primer, thermostable DNA polymerase and biotinylated dUTP . The biotinylated DNA was then captured on streptavidin-coated beads and its (3)H radioactivity determined by scintillation counting . We have termed this method 'selective nucleic acid polymerase-biotinylation and capture' or 'SNAP-BAC' . Internal (33)P-labelled DNA standards were used to quantify the recovery of (3)H-labelled DNA from the SNAP-BAC reactions . The method was verified by successfully targeting Bacteriodetes in simple laboratory mixtures of (3)H-labelled DNA extracted from pure cultures of Bacteriodetes and gamma-proteobacteria . Field application of this method in Puget Sound and off the Washington coast determined that Bacteriodetes were responsible for 56 +/- 17% and 32 +/- 5% of community (3)H-TdR incorporation (1.3 +/- 0.3 and 9.9 +/- 1.7 pmol l(-1) h(-1)) at these two locations. Arch Microbiol, 2004 Oct, 182(4), 265 - 76 Epub 2004 Sep 01. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria; Frigaard NU et al.; Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria . However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically . This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus . The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx . aurantiacus, and gene inactivation studies in Chl . tepidum . Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly . In agreement with its facultative anaerobic nature, Cfx . aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions . The Chl . tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo . J Environ Sci Health A Tox Hazard Subst Environ Eng, 2004, 39(8), 2081 - 92 Regrowth evaluation of coliform bacteria injured by low chlorine doses using selective and nonselective media; Rizzo L et al.; In this study, the repairing capacity of coliform bacteria injured by chlorine is determined . Chlorine doses from 0.014 to 0.070mg L(-1) were used in according to frequency (up to 38%) of chlorine concentrations detected in a drinking water distribution network, adopted as case study . m-Endo (selective) and m-T7 (nonselective) cultivation media are used . Bacterial regrowth was detected up to 0.035 mgL(-1) of chlorine for 4h of incubation . The coliform bacteria were not able to regrowth when the dose of chlorine increased to 0.07 mgL(-1) . Bacterial regrowth increased by increasing C:N ratio from 1:40 to 11:40 . m-T7 (nonselective) medium allowed to detect bacterial regrowth also for lower incubation periods . Chlorine doses higher than 0.2 mg L(-1) dose at water source with a low total organic carbon (TOC) content are recommended to control bacterial regrowth in the distribution network. J Biomol Tech, 2004 Sep, 15(3), 191 - 8 Proteomic analysis of novel marine bacteria using MALDI and ESI mass spectrometry; Stapels MD et al.; The objective of this study was to develop a mass spectrometric protocol to search for proteins related to phototrophy in marine bacteria . The genes that produce proteins involved in conversion of light into energy have been detected by cloning-sequencing from some of these bacteria, but it was previously unknown if these proteins were actually expressed . Attaining this study's goal was complicated by the fact that the samples consisted of miniscule cell pellets, which yielded small amounts of very complex mixtures of proteins . Sample preparation and analysis were tailored to optimize the probability of detecting the proteins of interest . It has been reported that using both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) to analyze a mixture of peptides leads to the identification of more peptides that either technique alone . In order to exploit this complementarity between ESI and MALDI for proteomic analysis, samples were analyzed using both ionization techniques . With correct choices in sample preparation and ionization process, biologically relevant proteins can be identified out of small samples containing whole proteomes . Med Hypotheses, 2004, 63(4), 731 - 9 Is mad cow disease caused by a bacteria? Broxmeyer L. Transmissible spongioform enchephalopathies (TSE's), include bovine spongiform encephalopathy (also called BSE or "mad cow disease"), Creutzfeldt-Jakob disease (CJD) in humans, and scrapie in sheep . They remain a mystery, their cause hotly debated . But between 1994 and 1996, 12 people in England came down with CJD, the human form of mad cow, and all had eaten beef from suspect cows . Current mad cow diagnosis lies solely in the detection of late appearing "prions", an acronym for hypothesized, gene-less, misfolded proteins, somehow claimed to cause the disease . Yet laboratory preparations of prions contain other things, which could include unidentified bacteria or viruses . Furthermore, the rigors of prion purification alone, might, in and of themselves, have killed the causative virus or bacteria . Therefore, even if samples appear to infect animals, it is impossible to prove that prions are causative . Manuelidis found viral-like particles, which even when separated from prions, were responsible for spongiform STE's . Subsequently, Lasmezas's study showed that 55% of mice injected with cattle BSE, and who came down with disease, had no detectable prions . Still, incredibly, prions, are held as existing TSE dogma and Heino Dringer, who did pioneer work on their nature, candidly predicts "it will turn out that the prion concept is wrong." Many animals that die of spongiform TSE's never show evidence of misfolded proteins, and Dr . Frank Bastian, of Tulane, an authority, thinks the disorder is caused by the bacterial DNA he found in this group of diseases . Recently, Roels and Walravens isolated Mycobacterium bovis it from the brain of a cow with the clinical and histopathological signs of mad cow . Moreover, epidemiologic maps of the origins and peak incidence of BSE in the UK, suggestively match those of England's areas of highest bovine tuberculosis, the Southwest, where Britain's mad cow epidemic began . The neurotoxic potential for cow tuberculosis was shown in pre-1960 England, where one quarter of all tuberculous meningitis victims suffered from Mycobacterium bovis infection . And Harley's study showed pathology identical to "mad cow" from systemic M . bovis in cattle, causing a tuberculous spongiform encephalitis . In addition to M . bovis, Mycobacterium avium subspecies paratuberculosis (fowl tuberculosis) causes Johne's disease, a problem known and neglected in cattle and sheep for almost a century, and rapidly emerging as the disease of the new millennium . Not only has M . paratuberculosis been found in human Crohn's disease, but both Crohn's and Johne's both cross-react with the antigens of cattle paratuberculosis . Furthermore, central neurologic manifestations of Crohn's disease are not unknown . There is no known disease which better fits into what is occurring in Mad Cow and the spongiform enchephalopathies than bovine tuberculosis and its blood-brain barrier penetrating, virus-like, cell-wall-deficient forms . It is for these reasons that future research needs to be aimed in this direction . Proc Natl Acad Sci U S A, 2004 Aug 31, 101(35), 12974 - 9 Epub 2004 Aug 20. Drosophila lifespan enhancement by exogenous bacteria; Brummel T et al.; We researched the lifespan of Drosophila under axenic conditions compared with customary procedure . The experiments revealed that the presence of bacteria during the first week of adult life can enhance lifespan, despite unchanged food intake . Later in life, the presence of bacteria can reduce lifespan . Certain long-lived mutants react in different ways, indicating an interplay between bacteria and longevity-enhancing genes . Mikrobiologiia, 2004 May-Jun, 73(3), 377 - 87 {An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups}; Spiridonova EM et al.; Based on the analysis of GenBank nucleotide sequences of the cbbL and cbbM genes, coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC), the key enzyme of the Calvin cycle, a primer system was designed that allows about 800-bp-long fragments of these genes to be PCR-ampliflied in various photo- and chemotrophic bacteria . The efficiency of the designed primer system in detection of RuBPC genes was demonstrated in PCR with DNA of taxonomically diverse bacteria possessing RuBPC genes with a known primary structure . Nucleotide sequences of RuBPC gene fragments of bacteria belonging to the genera Acidithiobacillus . Ectothiorhodospira, Magnetospirillum, Methylocapsa, Thioalkalispira, Rhodobacter, and Rhodospirillum were determined to be deposited with GenBank and to be translated into amino acid sequences and subjected to phylogenetic analysis. Immunology, 2004 Sep, 113(1), 15 - 22 Improving M cell mediated transport across mucosal barriers: do certain bacteria hold the keys? Man AL, Prieto-Garcia ME, Nicoletti C. Specialized microfold (M) cells of the follicle-associated epithelium (FAE) of the mucosal-associated lymphoid tissue (MALT) in gut and the respiratory system play an important role in the genesis of both mucosal and systemic immune responses by delivering antigenic substrate to the underlying lymphoid tissue where immune responses start . Although it has been shown that dendritic cells (DC) also have the ability to sample antigens directly from the gut lumen, M cells certainly remain the most important antigen-sampling cell to be investigated in order to devise novel methods to improve mucosal delivery of biologically active compounds . Recently, novel information on the interactions between bacteria and FAE have come to light that unveil further the complex cross-talk taking place at mucosal interfaces between bacteria, epithelial cells and the immune system and which are central to the formation and function of M cells . In particular, it has been shown that M cell mediated transport of antigen across the FAE is improved rapidly by exposure to certain bacteria, thus opening the way to identify new means to achieve a more effective mucosal delivery . Here, these novel findings and their potential in mucosal immunity are analysed and discussed, and new approaches to improve antigen delivery to the mucosal immune system are also proposed. J Biol Chem, 2004 Oct 22, 279(43), 44250 - 7 Epub 2004 Aug 11. Human platelet dense granules contain polyphosphate and are similar to acidocalcisomes of bacteria and unicellular eukaryotes; Ruiz FA et al.; Inorganic polyphosphate (polyP) has been identified and measured in human platelets . Millimolar levels (in terms of Pi residues) of short chain polyP were found . The presence of polyP of approximately 70-75 phosphate units was identified by 31P NMR and by urea-polyacrylamide gel electrophoresis of platelet extracts . An analysis of human platelet dense granules, purified using metrizamide gradient centrifugation, indicated that polyP was preferentially located in these organelles . This was confirmed by visualization of polyP in the dense granules using 4',6-diamidino-2-phenylindole and by its release together with pyrophosphate and serotonin upon thrombin stimulation of intact platelets . Dense granules were also shown to contain large amounts of calcium and potassium and both bafilomycin A1-sensitive ATPase and pyrophosphatase activities . In agreement with these results, when human platelets were loaded with the fluorescent calcium indicator Fura-2 acetoxymethyl ester to measure their intracellular Ca2+ concentration ({Ca2+}i), they were shown to possess a significant amount of Ca2+ stored in an acidic compartment . This was indicated by the following: 1) the increase in {Ca2+}i induced by nigericin, monensin, or the weak base, NH4Cl, in the nominal absence of extracellular Ca2 and 2) the effect of ionomycin, which could not take Ca2+ out of acidic organelles and was more effective after alkalinization of this compartment by the previous addition of nigericin, monensin, or NH4Cl . All of these characteristics of the platelet dense granules, together with their known acidity and high density (both by weight and by electron microscopy), are similar to those of acidocalcisomes (volutin granules, polyP bodies) of bacteria and unicellular eukaryotes . The results suggest that acidocalcisomes have been conserved during evolution from bacteria to humans. J Investig Allergol Clin Immunol, 2004, 14(2), 149 - 53 Skin reactivity to autologous bacteria isolated from respiratory tract of patients with obstructive pulmonary disease; Halasa J et al.; Bacterial flora of various strains was isolated from sputum and in some cases from BAL fluid of 75 patients with obstructive pulmonary disease experiencing dyspnea symptoms accompanying infections of respiratory tract . Among strains recognized traditionally as pathogenic in respiratory tract, we also isolated various strains typically called "normal oropharyngeal flora", "physiologic" or "non-pathogenic" bacteria . Those latter strains used in the skin tests in autologous manner for each patient had the property of provoking early (15 min) and late (24-48h) reactions . Early reactivity resembles that induced in the tests with airborn allergens . This suggests a potentially important role of those currently ignored strains in pathogenesis of obstructive pulmonary disease. Hua Xi Kou Qiang Yi Xue Za Zhi, 2004 Jun, 22(3), 198 - 200 {The effect of left bacteria in the root canal on prognosis of the root canal therapy}; He JM et al.; OBJECTIVE: To study the effect of the left bacteria on the root canal therapy . METHODS: 50 single-rooted teeth with chronic apical periodontitis were divided into two groups, one was instrumented with step-back technique and 2.5%NaOCl ultrasonic irrigation for 3 min, then filled with Thermafil . Samples were taken after instrumentation to culture . The other was treated with traditional RCT at three visits . RESULTS: In 24 months the apical radiolucency were greatly reduced in all cases . There weren't significant relationship among the postoperative pain and the left bacteria, the degree of the obturation or the pre-operative symptoms (P > 0.05) . CONCLUSION: The effect of left bacteria in root canal filled with Thermafil wasn't observed. J Reprod Immunol, 2004 Jun, 62(1-2), 111 - 24 Male genital tract infection: an influence of leukocytes and bacteria on semen; Sanocka D et al.; We have studied the oxidative status of 155 semen samples, 95 originating from healthy individuals and 60 from infertile patients, which were subdivided into two groups: (a) normozoospermic with genitourinary tract infection (GTI); and (b) with pathological spermiogram and GTI . Several phases of infection were observed: with bacterial presence only, bacteria and leukocytes, and leukocytes only, following the routine inflammatory pattern . Leukocyte numbers, bacterial strains, pro- and anti-oxidants, and selected pro-inflammatory cytokines (IL-1 beta, IL-6, IL-8 and TNF-alpha) were studied . Additionally, two oxido-sensitive indices were created (SOD/XO and CAT/XO) in order to follow particular phases of semen infection in two subgroups of patients . Different patterns of activities of pro- and anti-oxidant substances, as well as cytokines, were observed in the studied populations . It was reflected mainly by elevated XO activity in a group of patients with a pathological spermiogram while, in a group of patients with GTI and normozoospermia, xanthine oxidase was normal . In the latter group, oxido-sensitive indices were elevated in favour of anti-oxidants; similarly, this occurred with IL-6 levels in comparison to healthy controls . It appears therefore that normozoospermic semen recovers better after infection than pathological semen . Perhaps, IL-6 secretion might be helpful in the observed recovery? Radiats Biol Radioecol, 2004 May-Jun, 44(3), 324 - 7 {The radioadaptation condition at various stages of transition process, induced by gamma-irradiation in bacteria Escherichia coli JM 101}; Mikheev AN et al.; The dynamics of transition process caused by gamma-irradiation in bacterial Escherichia coli JM 101 culture was investigated . The bacteria radiostability at different phases of this process was defined . The received results testified to phase gamma-irradiation doze dependent character of bacteria population reaction . It was shown, that the increase of bacteria cell radioresistance occured at the postradiation restoration stage, whereas at the inhibition stage the radioresistance decreased. Prikl Biokhim Mikrobiol, 2004 May-Jun, 40(3), 261 - 9 {Stressors, stress reactions, and survival of bacteria (a review)}; Vorob'eva LI; Recent data on the molecular mechanisms of stress responses of bacteria are reviewed, with emphasis on their reactions to a variety of stressors (heat, oxidation, cold, osmotic shock, etc.) . Mechanisms underlying the phenomenon of sensoring are discussed . It is shown that cross-resistance to stressors and cell-to-cell communication of bacteria, mediated by chemical metabolites, affect their survival in food products . Stress-antiagonizing activity of bacteria is discussed in relation to food product biotechnology. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi, 2004 Feb 28, 22(1), 50 - 3 {Relationship between the Demodex and bacteria infection in human rosacea}; Hu Q et al.; OBJECTIVE: To understand the relationship between Demodex and bacteria infection in rosacea (brandy nose), and to find effective means for the treatment . METHODS: Cellophane tape was used to detect Demodex on the nasolabial grooves and the face; sebum and tissue on face was scraped and cultured to examine bacteria under microscope . The hospital-made anti-rosacea lotion was used on the affected part two times a day for 7 days . RESULTS: It was found that 193 (74.2%) of 260 cases with rosacea were infected by Demodex and 209 (80.4%) of the patients were infected by bacteria . The overall effective rate of the treatment for rosacea was 73.5% . CONCLUSION: Bacteria infection in rosacea is an important factor inducing rosacea . The curative effect of the anti-rosacea lotion is good. Nat Prod Rep, 2004 Aug, 21(4), 519 - 38 Epub 2004 Jul 06. Metabolites from symbiotic bacteria; Piel J; This review describes natural products that are shown or suspected to be synthesized by symbiotic bacteria.It includes 349 references and covers the literature in this field through 2003. Eur J Nutr . 2004 Aug 4; {Epub ahead of print} The antioxidative effect of the bacteria Dienococcus radiophilus against LDL lipid peroxidation; Lavy A et al.; BACKGROUND . Lipid peroxidation is an important process in the development of atherosclerosis . Thus agents with antioxidant properties may play an important role in the inhibition of atherosclerosis . OBJECTIVES . In this study we aimed to show that the lipid extract of the bacteria Deinococcus radiophilus (leDR) has antioxidant properties against LDL oxidation . RESULTS . This antioxidant effect was shown in both transition metal ion and free radical generating systems . We also showed that leDR can protect LDL from UV light-induced oxidative damage . The antioxidative capacity of leDR is partly due to copper ion chelation . CONCLUSION . We conclude that some specific bacteria constituent has the ability to inhibit LDL oxidation and, thus, to attenuate atherogenesis. Electrophoresis, 2004 Jul, 25(14), 2282 - 91 Capillary electrophoresis of biological particles: viruses, bacteria, and eukaryotic cells; Kremser L et al.; A review about the application of electrophoretic methods in the capillary format for the investigation of large biological assemblies like viruses, bacteria, yeast or entire mammalian cells is given . These entities are of a size ranging between some nanometers and tens of micrometers . They can form colloidal solutions or dispersions and move under the influence of an electric field . They are separated by zone electrophoresis according to their different electrophoretic velocity, and characterized by the electrophoretic mobility, which is easily determinable in free solution in capillaries or in other microdevices . As the charge of these particles, when being amphoteric, is pH-dependent, isoelectric focusing can also be carried out and the capillary format is increasingly being employed for their separation and determination of pI values . Furthermore, interactions with ligands can be assessed by various modes of affinity capillary electrophoresis . Capillary zone electrophoresis has thus become a valuable tool for investigation of large macromolecular assemblies in the field of biochemistry, clinical chemistry, toxicology, and nutrition chemistry amongst many others. Environ Toxicol, 2004 Aug, 19(4), 445 - 8 Acute toxicity investigations of ester-based lubricants by using biotests with algae and bacteria; Michel K et al.; Although ester-based lubricants are ecologically acceptable due to their good biodegradability, there are still some environmental ecotoxicological impacts that have to be considered . Information on the acute ecotoxicological behavior of lubricants is obtained in this work using several single species bioassays . In previous studies it was observed that lubricating fluids containing additives for the enhancement of their technical performance were more problematic than base fluids especially with respect to algae growth inhibition . In order to clarify the influence of additives, the anti-wear additive tri-n-butyl phosphate was tested . It was very toxic to algae though not to bacteria . Additionally, a mixture of this additive with a base fluid is characterized . Despite the high toxicity of the single additive, the water extract of the mixture of tri-n-butyl phosphate with hydraulic base fluid caused almost no toxicity . Therefore, tri-n-butyl phosphate cannot explain the effect observed for the toxicity of water extracts of the commercially available lubricants . Colloids Surf B Biointerfaces, 2004 May 1, 35(1), 41 - 4 Enhanced affinochromism of polydiacetylene monolayer in response to bacteria by incorporating CdS nano-crystallites; Zhang Y et al.; By incorporating bio-specific receptors, such as p-10,12-pentacosadiyne-1-N-(3,6,9-trioxaundecylamide)-alpha-D-mannopyranoside (MPDA), into 10,12-pentacosadiyonic acid (PDA) monolayer, the MPDA/PDA monolayer underwent affinochromatic transition in response to the bacteria binding to the receptor . Here, we described a new method to study the membrane/macromolececular interaction between Escherichia coli (E . coli) and mannose and its relative affinochromism by modifying MPDA/PDA with CdS nano-crystallites (MPDA/PDA-CdS) . CdS not only triggered the strong tropism of the bacteria but also reduced the rigidity of the MPDA/PDA backbone, resulting in the enhanced affinochromism . This discovery might be of significance in basic biophysical studies of membrane/macromolececular and designing novel biosensor. Arch Environ Health, 2003 Aug, 58(8), 538 - 42 Summary of the 5th International Conference on Bioaerosols, Fungi, Bacteria, Mycotoxins, and Human Health; Kilburn KH; Risk assessment of bioaerosols indoors has been summarized in terms of human health effects (e.g., allergy, infection, and irritation), but neurotoxicity has been a topic of heated debate <fseif@esceng.com> . However, this debate has been resolved rather clearly by evidence presented at this conference (and at the 21st Annual International Symposium on Man and His Environment in Healt