Bacteria

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 Health and Disease, Dallas, Texas, June 2003) which showed that neurotoxicity, as well as pulmonary and immune dysfunction, can result from exposure to molds in the indoor environment . Toxicity is apparent, and confirming studies are being published . For more information regarding the conference, visit <For details on the research summarized herein, please contact the presenting authors via their e-mail addresses . This reference system should aid in the dissemination of information that is current but not yet published.

Clin Microbiol Rev, 2004 Jul, 17(3), 581 - 611, table of contents
Phase and antigenic variation in bacteria; van der Woude MW et al.; Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively . This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy . This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation . The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature . The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete . From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations . The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed . Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity . Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.

Bioinformatics, 2004 Dec 12, 20(18), 3336 - 45 Epub 2004 Jul 09.
DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria; Wang Y et al.; MOTIVATION: It has been speculated that CpG dinucleotide deficiency in genomes is a consequence of DNA methylation . However, this hypothesis does not adequately explain CpG deficiency in bacteria . The hypothesis based on DNA structure constraint as an alternative explanation was therefore examined . RESULTS: By comparing real bacterial genomes and Markov artificial genomes in the second order, we found that the core structure of a restricted pattern, the TTCGAA pattern, was under represented in low GC content bacterial genomes regardless of CpG dinucleotide level . This is in contrast to the AACGTT pattern, indicating that the counterselection is context-dependent . Further study discovered nine underrepresented patterns that were supposed to be capable of inducing DNA structure constraint . In summary, most of them are in TTCGNA and TTCGAN patterns in both DNA strands . An explanation is also proposed for the strong correlation between GC content and CpG deficiency . The result of random sequence simulation showed that the occurrences of these patterns were correlated with GC content, as well as the percentage of CpG dinucleotides being trapped in these patterns . Finally, we suggest that the degree of counter-selection against these restricted patterns could be influenced by global GC content of a genome.

Bioresour Technol, 2004 Nov, 95(2), 151 - 8
Characteristics of anaerobic ammonia removal by a mixed culture of hydrogen producing photosynthetic bacteria; Takabatake H et al.; It is known that the presence of ammonia inhibits hydrogen production by photosynthetic bacteria . In order to avoid it, a two-step process containing ammonia removal and hydrogen production was investigated in this study . Firstly, the effects of carbonate presence on ammonia removal by photosynthetic bacteria were investigated by the vial tests because it is known that the uptake of volatile fatty acids (VFAs) sometimes requires carbonate . The results of them showed that the presence of carbonate promoted the uptake of VFAs and ammonia . Especially, the uptake of propionate and/or butyrate required the presence of carbonate . The results of the batch experiments of two-step hydrogen production showed that the depletion of ammonia triggered hydrogen evolution . Herein, the presence of albumin did not inhibit hydrogen evolution and preferably it increased the hydrogen production rate . And the VFA-C/NH4-N ratio in substrate fed into two-step hydrogen production process should be more than 6.0.

Biochim Biophys Acta, 2004 Jul 13, 1679(1), 80 - 5
Characterization of a novel selenium methyltransferase from freshwater bacteria showing strong similarities with the calicheamicin methyltransferase; Ranjard L et al.; A novel group of Se-methyltransferases is presented . The genetic determinant, named mmtA, which revealed this group was isolated from selenite and selenate-resistant freshwater bacteria . E . coli expressing mmtA and grown with a Se supplement emitted dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe) . Phylogenetic analysis divided MmtA-like bacterial sequences into two clusters, one grouping MmtA with S- and O-methyltransferases, and one grouping UbiE C-methyltransferases . Se methylation by some of these MmtA phyletic neighbours was investigated .

Appl Environ Microbiol, 2004 Jul, 70(7), 4411 - 4
Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and Archaea in the deep ocean; Teira E et al.; The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K . This modification resulted in about twofold-higher detection rates for Archaea in deep waters . Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42% versus 32% of 4',6'-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up l-aspartic acid (19% versus 10%).

Appl Environ Microbiol, 2004 Jul, 70(7), 4387 - 9
Evidence for acyl homoserine lactone signal production in bacteria associated with marine sponges; Taylor MW et al.; We report for the first time the production of acyl homoserine lactones (AHLs) by bacteria associated with marine sponges . Given the involvement of AHLs in bacterial colonization of many higher organisms, we speculate that such quorum sensing signals could play a part in interactions between sponges and the dense bacterial communities living within them.

Appl Environ Microbiol, 2004 Jul, 70(7), 4363 - 6
Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria; Schoenborn L et al.; Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture . In contrast, members of Acidobacteria, Verrucomicrobia, and Gemmatimonadetes and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media . We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.

Appl Environ Microbiol, 2004 Jul, 70(7), 4053 - 63
Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria; Schleheck D et al.; Parvibaculum lavamentivorans DS-1(T) utilized the commercial surfactant linear alkylbenzenesulfonate (LAS) (20 congeners with C(10) to C(13) side chains) as a carbon and energy source by shortening the side chain, and sulfophenylcarboxylates (SPCs) and similar compounds (e.g., alpha,beta-unsaturated SPCs {SPC-2Hs}) were excreted with quantitative recovery of the sulfophenyl moiety . 2-(4-Sulfophenyl)decane (2-C10-LAS) was converted largely to 3-(4-sulfophenyl)butyrate (3-C4-SPC), as were 2-C12-LAS and 2-C14-LAS; the other products were 5-C6-SPC (SPC+2C) and 3-C4-SPC-2H . 2-C11-LAS was converted largely to 4-C5-SPC with the corresponding SPC+2C and SPC-2H; similarly, 3-C12-LAS yielded 4-C6-SPC with the corresponding SPC+2C and SPC-2H . This pattern of products confirmed that LAS is degraded by omega-oxygenation and chain shortening through beta-oxidation . At least nine major SPCs were formed from commercial LAS . The novel isolates Comamonas testosteroni SPB-2 and KF-1 utilized 3-C4-SPC; Delftia acidovorans SPH-1 utilized 4-C6-SPC enantioselectively . The substrate-dependent oxygen uptake of whole cells of strain SPB-2 indicated that there was inducible oxygenation of 3-C4-SPC and of 4-sulfophenol in whole cells of the strains of C . testosteroni during growth with 3-C4-SPC or 4-sulfophenol . The degradative pathways apparently involved 4-sulfocatechol and 4-sulfocatechol 1,2-dioxygenase . Strain SPB-2 and strain DS-1(T) grew together in LAS-salts medium, and only seven of the nine major SPCs were recovered . Strain SPB-2 utilized 3-C4-SPC, 3-C5-SPC, and 3-C4-SPC-2H . Strain SPH-1 grew together with strain DS-1(T) in LAS-salts medium, and a different set of seven major SPCs was recovered . Strain SPH-1 utilized 4-C6-SPC, 4-C5-SPC, 4-C6-SPC-2H, and 4-C5-SPC-2H . A three-member community consisting of strains DS-1(T), SPB-2, and SPH-1 utilized four major SPCs . We inferred that this community mineralized the major SPCs derived from 8 of the 20 LAS congeners.

J Theor Biol, 2004 Aug 7, 229(3), 361 - 9
Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?
Amzallag GN.
Adaptive changes in bacteria are generally considered to result from random mutations selected by the environment . This interpretation is challenged by the non-randomness of genomic changes observed following ageing or starvation in bacterial colonies . A theory of adaptive targeting of sequences for enzymes involved in DNA transactions is proposed here . It is assumed that the sudden leakage of cAMP consecutive to starvation induces a rapid drop in the ATP/ADP ratio that inactivates the homeostasis in control of the level of DNA supercoiling . This phase change enables the emergence of local modifications in chromosome topology in relation to the missing metabolites, a first stage in expression of an adaptive status in which DNA transactions are induced . The nonlinear perspective proposed here is homologous to that already suggested for adaptation of pluricellular organisms during their development . In both cases, phases of robustness in regulation networks for genetic expression are interspaced by critical periods of breakdown of the homeostatic regulations during which, through isolation of nodes from a whole network, specific changes with adaptive value may locally occur.

Curr Opin Plant Biol, 2004 Aug, 7(4), 384 - 90
Cysteine proteases in phytopathogenic bacteria: identification of plant targets and activation of innate immunity; Hotson A et al.; Phytopathogenic bacteria use the type-III secretion system (TTSS) to inject effector proteins into plant cells, presumably to colonize their hosts . The function of these proteins inside plant cells has remained a mystery for years . The recent discovery that the effectors XopD, AvrXv4, AvrPphB, and AvrRpt2 have cysteine protease functions reveals that the proteolysis of host substrates is an important strategy employed by pathogens to alter plant physiology . Moreover, the characterization of these proteases and their targets provides new insight to mechanisms of bacterial virulence and the activation of plant immunity.

J Endod, 2004 Jul, 30(7), 518 - 22
Evaluation of the whole genome DNA-DNA hybridization technique to identify bacteria in histological sections of periradicular lesions; Chan S et al.; Whole genome DNA-DNA hybridization has been used to identify bacteria in periradicular lesions partly because there is no amplification of the bacteria, therefore, minor contaminants are not detected . There are, however, potential pitfalls with this technique, including inability to distinguish dead bacteria, cross-reactions of species within a genus, and inability to detect species present in low numbers because of loss of DNA during extraction and purification . Alternatively, inadequate extraction and purification of DNA could result in false positives . Therefore, controls are required to monitor DNA loss, DNA cross-reactions, and DNA of pure cultures mixed with bacteria-free tissue to monitor for false positives.We determined that the quality of DNA extracted from histological sections of periradicular lesions is excellent for DNA-DNA hybridization . Although lesions contain large numbers of bacteria, histological sections through lesions barely contain sufficient quantity of bacteria for such analysis . This was confirmed by histological observation of sparsely distributed bacteria within lesions . Furthermore, we found that the bacteria are not distributed evenly throughout periradicular lesions, in numbers or species.

J Neuropathol Exp Neurol, 2004 Jun, 63(6), 610 - 7
Apoptosis of hippocampal neurons in organotypic slice culture models: direct effect of bacteria revisited; Gianinazzi C et al.; Neurons of the hippocampal dentate gyrus selectively undergo programmed cell death in patients suffering from bacterial meningitis and in experimental models of pneumococcal meningitis in infant rats . In the present study, a membrane-based organotypic slice culture system of rat hippocampus was used to test whether this selective vulnerability of neurons of the dentate gyrus could be reproduced in vitro . Apoptosis was assessed by nuclear morphology (condensed and fragmented nuclei), by immunochemistry for active caspase-3 and deltaC-APP, and by proteolytic caspase-3 activity . Co-incubation of the cultures with live pneumococci did not induce neuronal apoptosis unless cultures were kept in partially nutrient-deprived medium . Complete nutrient deprivation alone and staurosporine independently induced significant apoptosis, the latter in a dose-response way . In all experimental settings, apoptosis occurred preferentially in the dentate gyrus . Our data demonstrate that factors released by pneumococci per se failed to induce significant apoptosis in vitro . Thus, these factors appear to contribute to a multifactorial pathway, which ultimately leads to neuronal apoptosis in bacterial meningitis.

J Pharmacol Sci, 2004 Jun, 95(2), 153 - 7
Proof of the mysterious efficacy of ginseng: basic and clinical trials: metabolic activation of ginsenoside: deglycosylation by intestinal bacteria and esterification with fatty acid; Hasegawa H; Orally ingested ginsenoside passes through the stomach and small intestine without decomposition by either gastric juice or liver enzymes into the large intestine, where ginsenoside is deglycosylated by colonic bacteria followed by transit to the circulation . Colonic bacteria cleave the oligosaccharide connected to the aglycone stepwise from the terminal sugar to afford the major metabolites, 20S-protopanaxadiol 20-O-beta-D-glucopyranoside (M1) and 20S-protopanaxatriol (M4) . These metabolites are further esterified with fatty acids . The resultant fatty-acid conjugates are still active molecules that are sustained longer in the body than parental metabolites . Accumulating evidence strongly suggests that ginsenoside is a prodrug that is activated in the body by intestinal bacterial deglycosylation and fatty acid esterification.

Syst Appl Microbiol, 2004 May, 27(3), 334 - 42
RRNA and dnaK relationships of Bradyrhizobium sp . nodule bacteria from four papilionoid legume trees in Costa Rica; Parker MA; Enzyme electrophoresis and sequencing of rRNA and dnaK genes revealed high genetic diversity among root nodule bacteria from the Costa Rican trees Andira inermis, Dalbergia retusa, Platymiscium pinnatum (Papilionoideae tribe Dalbergieae) and Lonchocarpus atropurpureus (Papilionoideae tribe Millettieae) . A total of 21 distinct multilocus genotypes {ETs (electrophoretic types)} was found among the 36 isolates analyzed, and no ETs were shared in common by isolates from different legume hosts . However, three of the ETs from D . retusa were identical to Bradyrhizobium sp . isolates detected in prior studies of several other legume genera in both Costa Rica and Panama . Nearly full-length 16S rRNA sequences and partial 23S rRNA sequences confirmed that two isolates from D . retusa were highly similar or identical to Bradyrhizobium strains isolated from the legumes Erythrina and Clitoria (Papilionoideae tribe Phaseoleae) in Panama . rRNA sequences for five isolates from L . atropurpureus, P . pinnatum and A . inermis were not closely related to any currently known strains from Central America or elsewhere, but had affinities to the reference strains Bradyrhizobium japonicum USDA 110 (three isolates) or to B . elkanii USDA 76 (two isolates) . A phylogenetic tree for 21 Bradyrhizobium strains based on 603 bp of the dnaK gene showed several significant conflicts with the rRNA tree, suggesting that genealogical relationships may have been altered by lateral gene transfer events.

Res Microbiol, 2004 Jun, 155(5), 387 - 98
Regulation of transposition in bacteria; Nagy Z et al.; Mobile genetic elements (MGEs) play a central role in the evolution of bacterial genomes . Transposable elements (TE: transposons and insertion sequences) represent an important group of these elements . Comprehension of the dynamics of genome evolution requires an understanding of how the activity of TEs is regulated and how their activity responds to the physiology of the host cell . This article presents an overview of the large range of, often astute, regulatory mechanisms, which have been adopted by TEs . These include mechanisms intrinsic to the element at the level of gene expression, the presence of key checkpoints in the recombination pathway and the intervention of host proteins which provide a TE/host interface . The multiplicity and interaction of these mechanisms clearly illustrates the importance of limiting transposition activity and underlines the compromise that has been reached between TE activity and the host genome . Finally, we consider how TE activity can shape the host genome.

J Zoo Wildl Med, 2004 Mar, 35(1), 15 - 9
Treatment with omeprazole, metronidazole, and amoxicillin in captive South African cheetahs (Acinonyx jubatus) with spiral bacteria infection and gastritis; Lane E et al.; Six captive cheetahs (Acinonyx jubatus) with severe gastritis diagnosed by gastric endoscopy and mucosal histopathology were treated with omeprazole, metronidazole, and amoxicillin for 3 wk . Endoscopic biopsies were performed before therapy, immediately after treatment, and 3, 7, and 19 mo after treatment . Macroscopic appearance of the stomach, histologic scoring of gastric inflammation, and the presence or absence of spiral bacteria were recorded . Spiral bacteria were absent histologically immediately after treatment but reappeared in endoscopic biopsies by 3 mo after treatment . Gastritis scores fluctuated widely during the trial but improved in five of six cheetahs by 3 mo after treatment . By 19 mo after treatment, scores were close to the pretreatment scores . Therapy with omeprazole, amoxicillin, and metronidazole was associated with temporary improvement in the degree and distribution of gastritis in some cheetahs with gastritis, suggesting that treatment may be warranted once severe gastric inflammation has been diagnosed.

Lett Appl Microbiol, 2004, 39(1), 55 - 9
Interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria Xylella fastidiosa, causal agent of citrus-variegated chlorosis; Lacava PT et al.; AIMS: To isolate endophytic bacteria and Xylella fastidiosa and also to evaluate whether the bacterial endophyte community contributes to citrus-variegated chlorosis (CVC) status in sweet orange (Citrus sinensis {L.} Osbeck cv . Pera) . METHODS AND RESULTS: The presence of Xylella fastidiosa and the population diversity of culturable endophytic bacteria in the leaves and branches of healthy, CVC-asymptomatic and CVC-symptomatic sweet orange plants and in tangerine (Citrus reticulata cv . Blanco) plants were assessed, and the in vitro interaction between endophytic bacteria and X . fastidiosa was investigated . There were significant differences in endophyte incidence between leaves and branches, and among healthy, CVC-asymptomatic and CVC-symptomatic plants . Bacteria identified as belonging to the genus Methylobacterium were isolated only from branches, mainly from those sampled from healthy and diseased plants, from which were also isolated X . fastidiosa . CONCLUSIONS: The in vitro interaction experiments indicated that the growth of X . fastidiosa was stimulated by endophytic Methylobacterium extorquens and inhibited by endophytic Curtobacterium flaccumfaciens . SIGNIFICANCE AND IMPACT OF THE STUDY: This work provides the first evidence of an interaction between citrus endophytic bacteria and X . fastidiosa and suggests a promising approach that can be used to better understand CVC disease.

Antonie Van Leeuwenhoek, 2000 Apr, 77(3), 251 - 62
Isolation and characterization of alkaliphilic, chemolithoautotrophic, sulphur-oxidizing bacteria; Sorokin DY et al.; Alkaliphilic sulphur-oxidizing bacteria were isolated from samples from alkaline environments including soda soil and soda lakes . Two isolates, currently known as strains AL 2 and AL 3, were characterized . They grew over a pH range 8.0-10.4 with an optimum at 9.5-9.8 . Both strains could oxidize thiosulphate, sulphide, polysulphide, elemental sulphur and tetrathionate . Strain AL 3 more actively oxidized thiosulphate and sulphide, while isolate AL 2 had higher activity with elemental sulphur and tetrathionate . Isolate AL 2 was also able to oxidize trithionate . The pH optimum for thiosulphate and sulphide oxidation was between 9-10 . Some activity remained at pH 11, but was negligible at pH 7 . Metabolism of tetrathionate by isolate AL 2 involved initial anaerobic hydrolysis to form sulphur, thiosulphate and sulphate in a sequence similar to that in other colourless sulphur-oxidizing bacteria . Sulphate was produced by both strains . During batch growth on thiosulphate, elemental sulphur and sulphite transiently accumulated in cultures of isolates AL 2 and AL 3, respectively . At lower pH values, both strains accumulated sulphur during sulphide and thiosulphate oxidation . Both strains contained ribulose bisphosphate carboxylase . Thiosulphate oxidation in isolate AL 3 appeared to be sodium ion-dependent . Isolate AL 2 differed from AL 3 by its high GC mol % value (65.5 and 49.5, respectively), sulphur deposition in its periplasm, the absence of carboxysomes, lower sulphur-oxidizing capacity, growth kinetics (lower growth rate and higher growth yield) and cytochrome composition.

Environ Microbiol, 2004 Jul, 6(7), 686 - 98
High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria; Klepac-Ceraj V et al.; The biogeochemistry of North Atlantic salt marshes is characterized by the interplay between the marsh grass Spartina and sulphate-reducing bacteria (SRB), which mineralize the diverse carbon substrates provided by the plants . It was hypothesized that SRB populations display high diversity within the sediment as a result of the rich spatial and chemical structuring provided by Spartina roots . A 2000-member 16S rRNA gene library, prepared with delta-proteobacterial SRB-selective primers, was analysed for diversity patterns and phylogenetic relationships . Sequence clustering detected 348 16S rRNA sequence types (ribotypes) related to delta-proteobacterial SRB, and it was estimated that a total of 623 ribotypes were present in the library . Similarity clustering showed that approximately 46% of these sequences fell into groups with < 1% divergence; thus, microheterogeneity accounts for a large portion of the observable genetic diversity . Phylogenetic comparison revealed that sequences most frequently recovered were associated with the Desulfobacteriaceae and Desulfobulbaceae families . Sequences from the Desulfovibrionaceae family were also observed, but were infrequent . Over 80% of the delta-proteobacterial ribotypes clustered with cultured representatives of Desulfosarcina, Desulfococcus and Desulfobacterium genera, suggesting that complete oxidizers with high substrate versatility dominate . The large-scale approach demonstrates the co-existence of numerous SRB-like sequences and reveals an unexpected amount of microdiversity.

Microbiology, 2004 Jun, 150(Pt 6), 1881 - 91
Phototrophic utilization of taurine by the purple nonsulfur bacteria Rhodopseudomonas palustris and Rhodobacter sphaeroides; Novak RT et al.; Taurine metabolism by two phototrophically grown purple nonsulfur bacteria enrichment isolates has been examined . Rhodopseudomonas palustris (strain Tau1) grows with taurine as a sole electron donor, sulfur and nitrogen source during photoautotrophic growth . Rhodobacter sphaeroides (strain Tau3) grows on the compound as sole electron donor, sulfur and nitrogen source, and partial carbon source, in the presence of CO(2) during photoheterotrophic growth . Both organisms utilize an inducible taurine-pyruvate aminotransferase and a sulfoacetaldehyde acetyltransferase . The products of this metabolism are bisulfite and acetyl phosphate . Bisulfite ultimately was oxidized to sulfate, but this was not an adequate source of electrons for photometabolism . Experiments using either {U-(14)C}taurine or (14)CO(2) demonstrated that Rb . sphaeroides Tau3 assimilated the carbon from approximately equimolar amounts of taurine and exogenous CO(2) . The taurine-carbon assimilation was not diminished by excess non-radioactive bicarbonate . Malate synthase (but not isocitrate lyase) was induced in these taurine-grown cells . It is concluded that assimilation of taurine carbon occurs through an intermediate other than CO(2) . Similar labelling experiments with Rp . palustris Tau1 determined that taurine is utilized only as an electron donor for the reduction of CO(2), which contributes all the cell carbon . Photoautotrophic metabolism was confirmed in this organism by the absence of either malate synthase or isocitrate lyase in taurine+CO(2)-grown cells . Culture collection strains of these two bacteria did not utilize taurine in these fashions.

Mini Rev Med Chem, 2004 Jun, 4(5), 461 - 76
Description, distribution, activity and phylogenetic relationship of ribosome-inactivating proteins in plants, fungi and bacteria; Girbes T et al.; Ribosome-Inactivating Proteins (RIPs) are enzymes that trigger the catalytic inactivation of ribosomes and other substrates . They are present in a large number of plants and have been found also in fungi, algae and bacteria . RIPs are currently classified as type 1, those formed by a single polypeptide chain with the enzymatic activity, and type 2, those formed by 2 types of chains, i.e . A chains equivalent to a type 1 RIPs and B chains with lectin activity . Type 2 RIPs usually contain the formulae A-B, (A-B)2 and less frequent (A-B)4 and polymeric forms of type 2 RIPs lectins . RIPs are broadly distributed in plants, and are present also in fungi, bacteria, at least in one alga; recently RIP-type activity has been described in mammalian tissues . The highest number of RIPs has been found in Caryophyllaceae, Sambucaceae, Cucurbitaceae, Euphorbiaceae, Phytolaccaceae and Poaceae . However there are no systematic screening studies to allow generalisations about occurrence . The most known activity of RIPs is the translational inhibitory activity, which seems a consequence of a N-glycosidase on the 28 S rRNA of the eukaryotic ribosome that triggers the split of the A(4324) (or an equivalent base in other ribosomes), which is key for translation . This activity seems to be part of a general adenine polynucleotide glycosylase able to act on several substrates other than ribosomes, such as tRNA, mRNA, viral RNA and DNA . Other enzymatic activities found in RIPs are lipase, chitinase and superoxide dismutase . RIPs are phylogenetically related . In general RIPs from close families share good amino acid homologies . Type 1 RIPs and the A chains of type 2 RIPs from Magnoliopsida (dicotyledons) are closely related . RIPs from Liliopsida (monocotyledons) are at the same time closely related and distant from Magnoliopsida . Concerning the biological roles played by RIPs there are several hypotheses, but the current belief is that they could play significant roles in the antipathogenic (viruses and fungi), stress and senescence responses . In addition, roles as antifeedant and storage proteins have been also proposed . Future research will approach the potential biological roles played by RIPs and their use as toxic effectors in the construction of immunotoxins and conjugates for target therapy.

Chembiochem, 2004 Jun 7, 5(6), 804 - 10
Bacteria displaying interleukin-4 mutants stimulate mammalian cells and reflect the biological activities of variant soluble cytokines; Krause S et al.; We describe a novel procedure that allows the rapid determination of cytokine activity on cells that express their cognate receptor . The four-helix bundle cytokine interleukin-4 (IL-4) was inducibly expressed as a fusion with the E . coli outer-membrane protein intimin, such that IL-4 was presented on the surfaces of the bacteria . Expression and accessibility of the cytokine on the cell exteriors were monitored by Western blotting and fluorescence microscopy, making use of two epitopes flanking the IL-4 component of the fusion protein . To demonstrate the biological activity of the immobilized cytokine, a Ba/F3-derived cell line stably transfected with both the bipartite human IL-4 receptor and an IL-4-specific luciferase reporter gene construct was employed . Bacterial cells displaying interleukin-4 elicited a specific, dose-dependent response in the reporter cells . Two variants of IL-4 with previously characterized (partial) antagonistic properties were also expressed as membrane-bound fusion proteins and were tested for their activity in the immobilized state . In comparison with bacteria displaying wild-type IL-4, E . coli clones presenting variants IL-4 Y124G and Y124D showed diminished or abolished activity, respectively, on murine reporter cells . The relative signaling potencies of the immobilized IL-4 variants thus closely mirror the agonistic properties of the corresponding soluble cytokines . This approach should be generally applicable for the mutational analysis of numerous signal mediators that trigger cellular responses through dimerization of transmembrane receptors.

Biochemistry, 2004 Jun 8, 43(22), 7003 - 16
Interactions stabilizing the structure of the core light-harvesting complex (LH1) of photosynthetic bacteria and its subunit (B820); Parkes-Loach PS et al.; Reconstitution experiments with a chemically synthesized core light-harvesting (LH1) beta-polypeptide analogue having 3-methylhistidine instead of histidine in the position that normally donates the coordinating ligand to bacteriochlorophyll (Bchl) have provided the experimental data needed to assign to B820 one of the two possible alphabeta.2Bchl pairs that are observed in the crystal structure of LH2 from Phaeospirillum (formerly Rhodospirillum) molischianum, the one with rings III and V of Bchl overlapping . Consistent with the assigned structure, experimental evidence is provided to show that significant stabilizing interactions for both the subunit complex (B820) and LH1 occur between the N-terminal regions of the alpha- and beta-polypeptides . On the basis of the results with the chemically synthesized polypeptides used in this study, along with earlier results with protease-modified polypeptides, mutants, and chemically synthesized polypeptides, the importance of a stretch of 9-13 amino acids at the N-terminal end of the alpha- and beta-polypeptides is underscored . A progressive loss of interaction with the LH1 beta-polypeptide was found as the first three N-terminal amino acids of the LH1 alpha-polypeptide were removed . The absence of the N-terminal formylmethionine (fMet), or conversion of the sulfur in this fMet to the sulfoxide, resulted in a decrease in LH1 formation . In addition to the removal of fMet, removal of the next two amino acids also resulted in a decrease in K(assoc) for B820 formation and nearly eliminated the ability to form LH1 . It is suggested that the first three amino acids (fMetTrpArg) of the LH1 alpha-polypeptide of Rhodospirillum rubrum form a cluster that is most likely involved in close interaction with the side chain of His -18 (see Figure 1 for numbering of amino acids) of the beta-polypeptide . The results provide evidence that the folding motif of the alpha- and beta-polypeptides in the N-terminal region observed in crystal structures of LH2 is also present in LH1 and contributes significantly to stabilizing the complex.

Trends Microbiol, 2004 Jun, 12(6), 264 - 70
Evolutionary significance of stress-induced mutagenesis in bacteria; Tenaillon O et al.; Mutagenesis is often increased in bacterial populations as a consequence of stress-induced genetic pathways . Analysis of the molecular mechanisms involved suggests that mutagenesis might be increased as a by-product of the stress response of the organism . By contrast, computer simulations and analyses of stress-inducible phenotypes among natural isolates of Escherichia coli suggest that stress-induced mutagenesis (SIM) could be the result of selection because of the beneficial mutations that such a process can potentially generate . Regardless of the nature of the selective pressure acting on SIM, it is possible that the resulting increased genetic variability plays an important role in bacterial evolution.

Mol Gen Mikrobiol Virusol, 2004, (2), 3 - 10
{Bacteria of Bartonella genus: characteristics, pathogenicity factors and methods of molecular-genetic investigation}; Il'ina TS et al.; Bartonella bacteria are an agent of a variety of human and animal diseases whose etiology used to be unknown . The survey contains a description of the above bacteria with the established pathogenicity factors and with the molecular and genetic approaches to studies of genes' functions and of their regulation being in the focus of attention . Modern methods related with the genus-specific and species-specific determination and identification of Bartonella bacteria are discussed.

J Basic Microbiol, 2004, 44(3), 178 - 84
Effects of hydrogen peroxide on light emission by various strains of marine luminescent bacteria; Katsev AM et al.; Light-emitting bacteria are the most abundant and widespread luminescent organisms . Most species of such bacteria live in marine environments . However, until recently, biological role of bacterial luminescence remained unknown . Recent studies indicated that light produced in bacterial cells may stimulate DNA repair . Therefore, it is not surprising that agents that cause DNA damage induce expression of lux genes . Moreover, it was proposed previously that bacterial luciferases may be involved in detoxification of reactive oxygen species . Recently, this hypothesis was confirmed experimentally . Here we investigated effects of hydrogen peroxide on light emission by various strains of luminescent bacteria . We found that luminescence of strains with luciferase of fast kinetics of reaction decreased at considerably lower concentrations of H2O2 than that of strains with luciferase of the slow kinetics . The action (either direct or indirect) of luciferases as anti-oxidants seemed to be independent of activity of catalase, which was found to be different in various strains . Therefore, it seems that luciferases of the slow kinetics are more efficient in detoxification of reactive oxygen species than those of the fast kinetics .

Proc Natl Acad Sci U S A, 2004 Jun 8, 101(23), 8643 - 8 Epub 2004 May 24.
An actin-like gene can determine cell polarity in bacteria; Gitai Z et al.; Achieving proper polarity is essential for cellular function . In bacteria, cell polarity has been observed by using both morphological and molecular markers; however, no general regulators of bacterial cell polarity have been identified . Here we investigate the effect on cell polarity of two cytoskeletal elements previously implicated in cell shape determination . We find that the actin-like MreB protein mediates global cell polarity in Caulobacter crescentus, although the intermediate filament-like CreS protein influences cell shape without affecting cell polarity . MreB is organized in an axial spiral that is dynamically rearranged during the cell cycle, and MreB dynamics may be critical for the determination of cell polarity . By examining depletion and overexpression strains, we demonstrate that MreB is required both for the polar localization of the chromosomal origin sequence and the dynamic localization of regulatory proteins to the correct cell pole . We propose that the molecular polarity inherent in an actin-like filament is translated into a mechanism for directing global cell polarity.

Infect Immun, 2004 Jun, 72(6), 3113 - 9
Experimental pneumococcal meningitis: impaired clearance of bacteria from the blood due to increased apoptosis in the spleen in Bcl-2-deficient mice; Wellmer A et al.; Necrotic and apoptotic neuronal cell death can be found in pneumococcal meningitis . We investigated the role of Bcl-2 as an antiapoptotic gene product in pneumococcal meningitis using Bcl-2 knockout (Bcl-2(-/-)) mice . By using a model of pneumococcal meningitis induced by intracerebral infection, Bcl-2-deficient mice and control littermates were assessed by clinical score and a tight rope test at 0, 12, 24, 32, and 36 h after infection . Then mice were sacrificed, the bacterial titers in blood, spleen, and cerebellar homogenates were determined, and the brain and spleen were evaluated histologically . The Bcl-2-deficient mice developed more severe clinical illness, and there were significant differences in the clinical score at 24, 32, and 36 h and in the tight rope test at 12 and 32 h . The bacterial titers in the blood were greater in Bcl-2-deficient mice than in the controls (7.46 +/- 1.93 log CFU/ml versus 5.16 +/- 0.96 log CFU/ml {mean +/- standard deviation}; P < 0.01) . Neuronal damage was most prominent in the hippocampal formation, but there were no significant differences between groups . In situ tailing revealed only a few apoptotic neurons in the brain . In the spleen, however, there were significantly more apoptotic leukocytes in Bcl-2-deficient mice than in controls (5,148 +/- 3,406 leukocytes/mm2 versus 1,070 +/- 395 leukocytes/mm2; P < 0.005) . Bcl-2 appears to counteract sepsis-induced apoptosis of splenic lymphocytes, thereby enhancing clearance of bacteria from the blood.

Int J Food Microbiol, 2004 May 1, 92(3), 265 - 74
Heterotrophic plate count bacteria--what is their significance in drinking water?
Allen MJ, Edberg SC, Reasoner DJ.
While the literature documents the universal occurrence of heterotrophic plate count (HPC) bacteria in soils, foods, air, and all sources of water, there is a lingering question as to whether this group of organisms may signal an increased health risk when elevated populations are present in drinking water . This paper reviews the relevant literature on HPC bacteria in drinking water, the lack of clinical evidence that elevated populations or specific genera within the HPC flora pose an increased health risk to any segment of the population, and the appropriate uses of HPC data as a tool to monitor drinking water quality changes following treatment . It finds no evidence to support health-based regulations of HPC concentrations .

Zhonghua Yi Xue Za Zhi, 2004 Apr 2, 84(7), 559 - 63
{High efficient generation of recombinant adenovirus containing human Fas gene using a method of homologous recombination in bacteria}; Lu F et al.; OBJECTIVE: To generate recombinant adenovirus with human Fas gene and transfect the Fas gene into keloid-derived fibroblasts to take place of the dysfunctional Fas gene, reconstruct the blocked Fas signal . METHODS: We used a new bacterial homologous recombination system (Ad-Easy system) to construct recombinant adenovirus vector . Fas gene was cut down from the PMD-T-Fas plasmid and then transferred to track plasmid . Recombination was successfully completed in bacteria BJ5183 and recombinant adenovirus was produced in 293 cells . Then we infected keloid derived fibroblasts and compared the expression of Fas protein . Finally, we detected the function of newly produced Fas protein . RESULTS: We successfully constructed the recombinant adenovirus with Fas gene and detected its highly expressed Fas protein in infected keloid derived fibroblasts . Obvious apoptosis was also detected in infected keloid derived fibroblasts exposed to FasMcab . CONCLUSION: (1) The recombinant adenovirus with Fas gene can transfect the Fas gene into keloid-derived fibroblasts and highly improved the expression of Fas protein . The newly expressed Fas gene can reconstruct the blocked Fas signal . (2) The correlation between keloid and Fas gene was further proved and it may paves a sound foundation for further gene therapy in keloid.

Clin Diagn Lab Immunol, 2004 May, 11(3), 473 - 82
Study of humoral immunity to commensal oral bacteria in human infants demonstrates the presence of secretory immunoglobulin A antibodies reactive with Actinomyces naeslundii genospecies 1 and 2 ribotypes; Cole MF et al.; The mouths of three human infants were examined from birth to age 2 years to detect colonization of Actinomyces naeslundii genospecies 1 and 2 . These bacteria did not colonize until after tooth eruption . The diversity of posteruption isolates was determined by ribotyping . Using immunoblotting and enzyme-linked immunosorbent assay, we determined the reactivity of secretory immunoglobulin A (SIgA) antibodies in saliva samples collected from each infant before and after colonization against cell wall proteins from their own A . naeslundii strains and carbohydrates from standard A . naeslundii genospecies 1 and 2 strains . A . naeslundii genospecies 1 and 2 carbohydrate-reactive SIgA antibodies were not detected in any saliva sample . However, SIgA antibodies reactive with cell wall proteins were present in saliva before these bacteria colonized the mouth . These antibodies could be almost completely removed by absorption with A . odontolyticus, a species known to colonize the human mouth shortly after birth . However, after colonization by A . naeslundii genospecies 1 and 2, specific antibodies were induced that could not be removed by absorption with A . odontolyticus . Cluster analysis of the patterns of reactivity of postcolonization salivary antibodies from each infant with antigens from their own strains showed that not only could these antibodies discriminate among strains but antibodies in saliva samples collected at different times showed different reactivity patterns . Overall, these data suggest that, although much of the salivary SIgA antibodies reactive with A . naeslundii genospecies 1 and 2 are directed against genus-specific or more broadly cross-reactive antigens, species, genospecies, and possibly strain-specific antibodies are induced in response to colonization.

J Eukaryot Microbiol, 2004 Mar-Apr, 51(2), 139 - 44
Algicidal bacteria in the sea and their impact on algal blooms; Mayali X et al.; Over the past two decades, many reports have revealed the existence of bacteria capable of killing phytoplankton . These algicidal bacteria sometimes increase in abundance concurrently with the decline of algal blooms, suggesting that they may affect algal bloom dynamics . Here, we synthesize the existing knowledge on algicidal bacteria interactions with marine eukaryotic microalgae . We discuss the effectiveness of the current methods to characterize the algicidal phenotype in an ecosystem context . We briefly consider the literature on the phylogenetic identification of algicidal bacteria, their interaction with their algal prey, the characterization of algicidal molecules, and the enumeration of algicidal bacteria during algal blooms . We conclude that, due to limitations of current methods, the evidence for algicidal bacteria causing algal bloom decline is circumstantial . New methods and an ecosystem approach are needed to test hypotheses on the impact of algicidal bacteria in algal bloom dynamics . This will require enlarging the scope of inquiry from its current focus on the potential utility of algicidal bacteria in the control of harmful algal blooms . We suggest conceptualizing bacterial algicidy within the general problem of bacterial regulation of algal community structure in the ocean.

Microbiology, 2004 May, 150(Pt 5), 1301 - 13
NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria; Dedysh SN et al.; The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB) . This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds . Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus BEIJERINCKIA: To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined . For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB . The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent . The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features . First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group . From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching . Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98.5 and 96.6 %, respectively) than would be expected from their 16S rRNA-based relationships . Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition . This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M . acidiphila B2 and Beijerinckia spp . are capable of active growth on nitrogen-free media under fully aerobic conditions.

J Org Chem, 2004 May 14, 69(10), 3530 - 7
Total synthesis of petrobactin and its homologues as potential growth stimuli for Marinobacter hydrocarbonoclasticus, an oil-degrading bacteria; Gardner RA et al.; A modular synthesis was developed to access petrobactin, a catechol-containing siderophore isolated from Marinobacter hydrocarbonoclasticus . A range of petrobactin homologues with differing dihydroxybenzamide motifs and in one case an increased number of carbons in the polyamine backbone were also synthesized . As such, these systems represent new isomeric probes to study iron transport properties in M . hydrocarbonoclasticus . The synthesis of petrobactin and its homologues and the first biological study of how these agents influence the growth of Mycobacterhydrocarbonoclasticus are reported . New synthetic methods were developed to overcome issues (imide formation) encountered in earlier syntheses . Both the (1)H and (13)C NMR of petrobactin were consistent with the recently revised structure showing that petrobactin in fact contains a 3,4-dihydroxybenzene motif rather than a 2,3-dihydroxybenzene motif . The preliminary biological studies suggested that using the native petrobactin 1b for M . hydrocarbonoclasticus-specific growth stimulation may be a poor strategy for oil-spill cleanup.

Am J Gastroenterol, 2004 May, 99(5), 905 - 6
A role for bacteria in celiac disease?
Sollid LM, Gray GM.
The finding of rod-shaped bacteria attached to the small intestinal epithelium of some untreated and treated celiac-disease patients, but not to the epithelium of healthy controls, ignites the notion that bacteria may be involved in the pathogenesis of celiac disease . This editorial discusses this possibility in relation to the current understanding of the molecular basis of this disorder.

Circulation, 2004 Jun 8, 109(22), 2801 - 6 Epub 2004 May 03.
Innate immune recognition of invasive bacteria accelerates atherosclerosis in apolipoprotein E-deficient mice; Gibson FC 3rd et al.; BACKGROUND: Infectious diseases have emerged as potential risk factors for cardiovascular disease (CVD) . Epidemiological studies support a connection between periodontal disease, a chronic inflammatory disease of the supporting tissues of the teeth, and CVD . METHODS AND RESULTS: To directly test the connection between periodontal disease and atherosclerosis, apoE-/- mice were orally challenged with the periodontal disease pathogen Porphyromonas gingivalis or an invasion-impaired P gingivalis fimbriae-deficient mutant (FimA-) . Both wild-type P gingivalis and the FimA- mutant were detected in blood and aortic arch tissue of apoE-/- mice by PCR after challenge . ApoE-/- mice challenged with wild-type P gingivalis presented with increased atherosclerotic plaque and expressed the innate immune response markers Toll-like receptor (TLR)-2 and TLR-4 in aortic tissue . Despite detection of the FimA- mutant in the blood and in aortic arch tissue, apoE-/- mice challenged with the FimA- mutant did not present with periodontal disease, upregulation of TLRs, or accelerated atherosclerosis . Furthermore, we demonstrate that immunization to control P gingivalis-elicited periodontal disease concomitantly prevents P gingivalis-accelerated atherosclerosis . CONCLUSIONS: We conclude that invasive P gingivalis accelerates atherosclerosis.

Plasmid, 2004 May, 51(3), 246 - 55
Improvement of pCVD442, a suicide plasmid for gene allele exchange in bacteria; Philippe N et al.; Allelic exchange experiments allow investigation of the functions of many unknown genes identified during the sequencing of entire genomes . Isogenic strains differing by only specific mutations can be constructed . Among other tools, suicide plasmids are widely used for this task . They present many advantages because they leave no scars on the chromosome, and therefore allow combining several mutations in the same genetic background . While using the previously described pCVD442 suicide plasmid {Infect . Immun . 59 (1991) 4310}, we found untargeted recombination events due to the presence of an IS1 element on this plasmid . The plasmid was therefore improved by removal of the IS1 element . We also replaced the bla gene of pCVD442, conferring ampicillin resistance, by the cat gene conferring chloramphenicol resistance, leading to the new suicide plasmid pDS132 . The plasmid was entirely sequenced . We demonstrate that this new vector can be easily used to introduce various types of mutations into different genetics backgrounds: removal of IS elements, introduction of point mutations or deletions . It can be introduced into bacterial strains by either transformation or conjugation .

Dig Dis Sci, 2004 Feb, 49(2), 228 - 36
Esophageal bacteria and Barrett's esophagus: a preliminary report; Osias GL et al.; The objective of this study was to investigate if esophageal bacteria are associated with Barrett's esophagus (BE) . This study was comprised of a retrospective (Part 1) and a subsequent prospective (Part 2) study . In Part 1, Gram stains were performed on esophageal biopsy specimens obtained in 47 patients . Bacteria were quantitated from 0 to 4 . In Part 2, Gram stains and cultured bacterial counts of esophageal biopsies were obtained in 18 GERD patients (9 with BE and 9 without BE) . Part 1 results were as follows . Bacteria were found in 37 of 47 esophageal biopsies . Quantitative bacterial stain scores for BE (2.5 +/- 0.2) were higher than for non-BE (1.5 +/- 0.3; P = 0.02) . The quantitative bacterial stain scores correlated with increasing severity of dysplasia (r = 0.37, P = 0.028) . In Part 2, bacteria were found in 8 of 18 esophageal biopsies by Gram stain (6 of 9 patients with BE vs . 2 of 9 non-BE) . The distal esophageal bacterial stain scores in BE patients (1.6 +/- 0.5) were higher than in those without BE (0.4 +/- 0.3; P = 0.07) . Patients on proton pump inhibitors tended to have higher bacterial stain scores (1.2 +/- 0.4) than patients who were not (0.7 +/- 0.3; P = 0.45) . Bacterial colony counts were similar in patients with BE compared to those without BE . In conclusion, bacteria in esophageal biopsies were detected more often in BE than non-BE . Increasing bacterial stain scores were associated with metaplasia and increasing dysplasia . Esophageal bacteria, possibly related to stasis or gastric acid suppression therapy, may play a role in the pathogenesis of BE and dysplasia.

Mikrobiol Z, 2004 Jan-Feb, 66(1), 10 - 8
{Pigments of green sulfur bacteria isolated from reservoirs of Iavoriv sulfur deposit}; Baran IM et al.; The enormous amount of hydrogen sulfide (up to 11 mg/ml) is present in the Yavoriv sulfur deposit reservoirs owing to sulfur reductive bacteria activity . As a consequence the ecological situation is badly affected and requires recovering . The biological H2S decomposition by photosynthetic sulfur bacteria, which use the hydrogen sulfide as electron donor during photosynthesis, can be one of the possible ways of this toxic substance destruction . The qualitative and quantitative analysis of photosynthetic pigments composition that derived from green photosynthesizing sulfur bacteria from reservoirs of Yavoriv sulfur deposit is carried out . It was fixed that Pelodictyon sp., Chlorobium sp . and isolated consortia "Pelochromatium sp." contain the bacteriochlorophyll c and d . All the isolated cultures contained bacteriochlorophyll a in trace amounts . The obtained photosynthetic pigments (bacteriochlorophylls, carotenoids) were recognized by their absorption spectra in the visible and far-red region and by their quantity . The difference was not essential . All investigated cultures of isolated bacteria contain some carotenoid the Chlorobium sp . and obtained consortia possesses isorenieratene . The absorption maxima of extracted pigments from young cultures of isolated green sulfur bacteria are more definitely displayed than those from old cultures . Investigations of phototrophic sulfur bacteria were carried out in Ukraine up to now . Ecological problem that occurred in the Yavoriv sulfur deposit as a result of the deposit exploitation caused a necessity of the investigation of photosynthetic sulfur bacteria and bacterial photosynthesis mechanism . The photosynthetic pigments nature identification will promote the fast and precise identification of the new forms of photosynthetic sulfur bacteria and will extend our knowledge about their role in the anoxygenic photosynthesis.

Phys Rev E Stat Nonlin Soft Matter Phys . 2004 Mar;69(3 Pt 1):032902 . Epub 2004 Mar 31.
Low-lying excited states of light-harvesting system II in purple bacteria; Zhao Y et al.; The low-lying excited states of a B850 ring of Rhodospirillum (Rs.) molischianum are determined accurately by a semiempirical INDO/S method . Results obtained are found to fit extremely well with a Frenkel exciton model with long-range dipolar interactions, and the spatial size of the electron-hole pair is confirmed to fall predominantly within one bacteriochlorophyll with a small leakage to its nearest neighbors . More importantly, the nearest neighbor exciton coupling constants are found to be close to those evaluated directly from dimers, and thus, an existing discrepancy between calculated results of dimers and B850 rings has been resolved.

Gene, 2004 Apr 14, 330, 169 - 76
Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria; Brochier C et al.; The initiation factor 5A (IF-5A) of archaea and eukaryotes undergoes an unusual post-translational modification consisting of the transformation of a specific conserved lysine residue into the amino acid hypusine . This occurs in a two-step reaction catalysed by the enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase . Bacteria do not have IF-5A but only a very distant homologue, the elongation factor P (EF-P) . Consequently, all bacteria appeared to also lack genes with significant homology to DHS genes . However, we have carried out BLAST searches and found DHS-like genes in a number of bacterial species . The phylogenetic analysis of these sequences strongly suggests that they have been acquired from archaea by horizontal gene transfer (HGT) . Our analysis also suggests, although with weaker support, that a single HGT event from archaea, followed by several HGT between bacterial species, accounts for the patchy distribution of DHS-like genes in bacteria . The activity of these genes in bacteria is enigmatic, since we have not found any evidence of interaction between this protein and the bacterial EF-P . Nevertheless, we cannot discard that it exists, since it appears that the interaction between the DHS and its natural substrate, the IF-5A, is rather weak . This is exemplified by the fact that, in archaea, the complex evolutionary history of the DHS is not paralleled by that of the IF-5A, indicating that these proteins do not follow a perfect co-evolution.

J Virol Methods, 2004 Jun 15, 118(2), 131 - 9
Continuous-flow UVC irradiation: a new, effective, protein activity-preserving system for inactivating bacteria and viruses, including erythrovirus B19; Caillet-Fauquet P et al.; Despite the increasing number of screening tests being introduced, ensuring the inactivation of blood-borne pathogens in blood-derived therapeutic material is a major concern . Dynamic continuous-flow UVC irradiation is a new way to inactivate a large range of pathogens without adding any photosentizers . The efficacy of different methods was evaluated against the following viruses: murine parvovirus MVMp, human B19, the encephalomyocarditis virus (EMC, a picornavirus used as a model for model for hepatitis A virus), and bovine herpes virus type 1 (BHV, a model for enveloped viruses such as hepatitis B virus) . We show that continuous-flow UVC irradiation is very effective, particularly against resistant pathogens (e.g . parvoviruses and bacteria) at UVC doses preserving protein activity . It may be applicable to newly emerging related viruses or variants.

Biochemistry, 2004 Apr 20, 43(15), 4421 - 30
Toward delineating the structure and function of the particulate methane monooxygenase from methanotrophic bacteria; Chan SI et al.; The particulate methane monooxygenase (pMMO) is a complex membrane protein complex that has been difficult to isolate and purify for biochemical and biophysical characterization because of its instability in detergents used to solubilize the enzyme . In this perspective, we summarize the progress recently made toward obtaining a purified pMMO-detergent complex and characterizing the enzyme in pMMO-enriched membranes . The purified pMMO is a multi-copper protein, with ca . 15 copper ions sequestered into five trinuclear copper clusters: two for dioxygen chemistry and alkane hydroxylation (catalytic or C-clusters) and three to provide a buffer of reducing equivalents to re-reduce the C-clusters following turnover (electron transfer or E-clusters) . The enzyme is functional when all the copper ions are reduced . When the protein is purified under ambient aerobic conditions in the absence of a hydrocarbon substrate, only the C-clusters are oxidized; there is an apparent kinetic barrier for electron transfer from the E-cluster copper ions to the C-clusters under these conditions . Evidence is provided in support of both C-clusters participating in the dioxygen chemistry, but only one C-cluster supporting alkane hydroxylation . Acetylene modification of the latter C-cluster in the hydrophobic pocket of the active site lowers or removes the kinetic barrier for electron transfer from the E-clusters to the C-clusters so that all the copper ions could be fully oxidized by dioxygen . A model for the hydroxylation chemistry when a hydrocarbon substrate is bound to the active site of the hydroxylation C-cluster is presented . Unlike soluble methane monooxygenase (sMMO), pMMO exhibits limited substrate specificity, but the hydroxylation chemistry is highly regioselective and stereoselective . In addition, the hydroxylation occurs with total retention of configuration of the carbon center that is oxidized . These results are consistent with a concerted mechanism involving direct side-on insertion of an active singlet "oxene" from the activated copper cluster across the "C-H" bond in the active site . Finally, in our hands, both the purified pMMO-detergent complex and pMMO-enriched membranes exhibit high NADH-sensitive as well as duroquinol-sensitive specific activity . A possible role for the two reductants in the turnover of the enzyme is proposed.

Proc Natl Acad Sci U S A, 2004 Mar 30, 101(13), 4560 - 5 Epub 2004 Mar 19.
Human IL-23-producing type 1 macrophages promote but IL-10-producing type 2 macrophages subvert immunity to (myco)bacteria; Verreck FA et al.; Macrophages (Mphi) play a central role as effector cells in immunity to intracellular pathogens such as Mycobacterium . Paradoxically, they also provide a habitat for intracellular bacterial survival . This paradoxical role of Mphi remains poorly understood . Here we report that this dual role may emanate from the functional plasticity of Mphi: Whereas Mphi-1 polarized in the presence of granulocyte-Mphi colony-stimulating factor promoted type 1 immunity, Mphi-2 polarized with Mphi colony-stimulating factor subverted type 1 immunity and thus may promote immune escape and chronic infection . Importantly, Mphi-1 secreted high levels of IL-23 (p40/p19) but no IL-12 (p40/p35) after (myco)bacterial activation . In contrast, activated Mphi-2 produced neither IL-23 nor IL-12 but predominantly secreted IL-10 . Mphi-1 required IFN-gamma as a secondary signal to induce IL-12p35 gene transcription and IL-12 secretion . Activated dendritic cells produced both IL-12 and IL-23, but unlike Mphi-1 they slightly reduced their IL-23 secretion after addition of IFN-gamma . Binding, uptake, and outgrowth of a mycobacterial reporter strain was supported by both Mphi subsets, but more efficiently by Mphi-2 than Mphi-1 . Whereas Mphi-1 efficiently stimulated type 1 helper cells, Mphi-2 only poorly supported type 1 helper function . Accordingly, activated Mphi-2 but not Mphi-1 down-modulated their antigen-presenting and costimulatory molecules (HLA-DR, CD86, and CD40) . These findings indicate that (i) Mphi-1 and Mphi-2 play opposing roles in cellular immunity and (ii) IL-23 rather than IL-12 is the primary type 1 cytokine produced by activated proinflammatory Mphi-1 . Mphi heterogeneity thus may be an important determinant of immunity and disease outcome in intracellular bacterial infection.

Anal Bioanal Chem, 1996 Mar, 354(5-6), 636 - 40
Synthesis, structure, spectra and redox activities of model compounds for methanogenic bacteria; Pandiyan T et al.; Synthetically accessible benzimidazoles have been synthesized and the benzimidazole ligands were complexed with nickel(II) nitrate . A nickel(II) complex of N,N'-bis(benzimidazole-2-ylethyl)ethylenediamine was crystallized in single-crystal form and the structure was investigated by X-ray crystallography . The structure of the complex is bicapped axial coordinated octahedral . Ni(bbes)(2+)(2){bbes=bis(benzimidazole-2-ylethyl)sulfide} exhibits broad low energy bands in electronic spectra and high redox potential in cyclic voltammetry (CV) rather than Ni(enbzim)(2+) {enbzim =N,N'-bis(benzimidazol-2-ylethyl)ethylenediamine}, where high energy well separated bands were observed in the visible region and a more negative redox potential was detected in CV . Experimental studies show that an increasing amount of pi-orbital interaction with the Ni(2+)ion, irrespective of chelate ring may favour the higher redox potential . The higher redox potential of methanogenic bacterial {Ni(II)/Ni(I)} than nickel compounds is one of the main factors for the degradation of organic biodegradable compounds and the further transformation to methane.

Anal Bioanal Chem, 1996 Mar, 354(5-6), 566 - 70
Toxicity of cadmium species on luminescent bacteria; Villaescusa I et al.; The toxicity of cadmium compounds against luminescent bacteria has been measured using the Microtox(R) toxicity bioassay and has been related to the cadmium species . Since the Microtox(R) test is carried out in NaCl (2%) and cadmium forms stable chloro complexes, NaNO(3) and NaClO(4) have been tested successfully as alternative to sodium chloride to provide the adequate osmotic protection of the bacteria . The influence of medium and ionic strength as well as different exposure times on EC(50) values has been evaluated.

Appl Environ Microbiol, 2004 Apr, 70(4), 2342 - 8
Urease-encoding genes in ammonia-oxidizing bacteria; Koper TE et al.; Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth . We sequenced the urease operons from two AOB, the beta-proteobacterium Nitrosospira sp . strain NpAV and the gamma-proteobacterium Nitrosococcus oceani . In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively . Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani . Southern analyses revealed two copies of ureC in the Nitrosospira sp . strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani . The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB . In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several beta-proteobacterial AOB . Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision . UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences . The UreC proteins from beta-proteobacterial AOB formed a distinct monophyletic group . Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other beta-proteobacteria . Instead, it appears that urease in beta-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of gamma- and beta-proteobacteria that was initiated before their divergence during speciation . Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from beta-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB . These gene sequences are the first publicly available for ure genes from autotrophic AOB.

Appl Environ Microbiol, 2004 Apr, 70(4), 2186 - 92
Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay; Short SM et al.; The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay . By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002 . Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10(7) gene copies . The maximum number of 907h22 gene copies detected was approximately 140 ml(-1) and the maximum number of 912h4 gene copies detected was approximately 340 ml(-1) . Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002 . Overall, the 907h22 phylotype was most abundant at the mid-bay station . Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay . Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.

Curr Opin Microbiol, 2004 Apr, 7(2), 185 - 91
Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?
Jenal U.
The cyclic nucleotide cyclic di-guanosine-monophosphate (c-diGMP) was recognized in the 1980s as a signaling compound that is involved in controlling the condensation of glucose moieties into cellulose polymers . More recent data from several different bacterial species now suggest that c-diGMP might have a general role as secondary messenger in modulating bacterial growth on surfaces by regulating cellular adhesion components and preparing cells for cell-cell and cell-surface interactions.

J Biotechnol, 2004 Apr 8, 109(1-2), 45 - 52
Bacteria co-transformed with recombinant proteins and chaperones cloned in independent plasmids are suitable for expression tuning; de Marco A et al.; The efficient over-expression of several recombinant proteins in the same bacterial cell is usually prevented due to metabolic limitations . Nevertheless, the possibility to co-produce high amounts of the sub-units of a complex or to express a wide set of chaperones and foldases could be technologically very useful . We developed a system based on three vectors . Two are under IPTG regulation and enable the recombinant expression of six chaperones, the third one is arabinose-inducible and harbours the sequence for the target protein . In such a way the independent induction and the level of expression of both chaperones and target protein is possible . The data show that the expression leakage from pET vectors was prevented by the introduction of further plasmids in the cell and that the recombinant proteins compete for their expression . In fact, the high rate induction of one of them could switch off the accumulation of the other recombinant proteins . The first information was used to maximise the expression of toxic proteins while the cross-inhibition among recombinant proteins was exploited to modulate and optimise the target protein expression and to induce the chaperone-assisted in vivo re-folding of aggregated target protein.

Curr Microbiol, 2004 Feb, 48(2), 130 - 4
Isolation of carotenoid-deficient mutant from alkylated dibenzothiophene desulfurizing nocardioform bacteria, Gordonia sp . TM414; Matsui T et al.; The dibenzothiophene-desulfurizing nocardioform bacteria, Gordonia sp . TM414, was isolated from oil-contaminated soil . To avoid coloration of the oil layer after the desulfurization reaction, which could decrease the quality of the oil, two colorless knock-out mutants, TPc and TPd, were isolated by using a broad-host-range transposon complex . Genomic sequence analysis revealed that the same gene was disrupted in these mutants and that the transposon-inserted gene was assigned as the gene for phytoene desaturase, crt I . The crt I mutants also showed desulfurization activity comparable to that of the parent strain in a model-oil/aqueous bi-phasic reaction, suggesting that the carotenoid production is not responsible for the bi-phasic desulfurization reaction that requires hydrophobic substrate incorporation from the organic phase.

Biosci Biotechnol Biochem, 2004 Mar, 68(3), 746 - 8
The evolution of the phenylacetic acid degradation pathway in bacteria; Abe-Yoshizumi R et al.; The phenylacetic acid (PhAc) degradation pathway becomes an interesting model for the catabolism of aromatic compounds . To determine the molecular basis for this environmentally important process, we did a phylogenic analysis based on the PhAc CoA ligase gene . It suggests that the PhAc CoA ligase genes are distributing widely and subject to frequent lateral gene transfer within and across bacterial phylum.

J Biol Chem, 2004 May 21, 279(21), 22145 - 51 Epub 2004 Mar 23.
Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria; Mosbahi K et al.; We have shown previously that the 134-residue endonuclease domain of the bacterial cytotoxin colicin E9 (E9 DNase) forms channels in planar lipid bilayers (Mosbahi, K., Lemaitre, C., Keeble, A . H., Mobasheri, H., Morel, B., James, R., Moore, G . R., Lea, E . J., and Kleanthous, C . (2002) Nat . Struct . Biol . 9, 476-484) . It was proposed that the E9 DNase mediates its own translocation across the cytoplasmic membrane and that the formation of ion channels is essential to this process . Here we describe changes to the structure and stability of the E9 DNase that accompany interaction of the protein with phospholipid vesicles . Formation of the protein-lipid complex at pH 7.5 resulted in a red-shift of the intrinsic protein fluorescence emission maximum (lambda(max)) from 333 to 346 nm . At pH 4.0, where the E9 DNase lacks tertiary structure but retains secondary structure, DOPG induced a blue-shift in lambda(max), from 354 to 342 nm . Changes in lambda(max) were specific for anionic phospholipid vesicles at both pHs, suggesting electrostatics play a role in this association . The effects of phospholipid were negated by Im9 binding, the high affinity, acidic, exosite inhibitor protein, but not by zinc, which binds at the active site . Fluorescence-quenching experiments further demonstrated that similar protein-phospholipid complexes are formed regardless of whether the E9 DNase is initially in its native conformation . Consistent with these observations, chemical and thermal denaturation data as well as proteolytic susceptibility experiments showed that association with negatively charged phospholipids destabilize the E9 DNase . We suggest that formation of a destabilizing protein-lipid complex pre-empts channel formation by the E9 DNase and constitutes the initial step in its translocation across the Escherichia coli inner membrane.

FEBS Lett, 2004 Mar 12, 561(1-3), 11 - 21
Class III nucleotide cyclases in bacteria and archaebacteria: lineage-specific expansion of adenylyl cyclases and a dearth of guanylyl cyclases; Shenroy AR et al.; The Class III nucleotide cyclases are found in bacteria, eukaryotes and archaebacteria . Our survey of the bacterial and archaebacterial genome and plasmid sequences identified 193 Class III cyclase genes in only 29 species, of which we predict the majority to be adenylyl cyclases . Interestingly, several putative cyclase genes were found to have non-conserved substrate specifying residues . Ancestors of the eukaryotic C1-C2 domain containing soluble adenylyl cyclases as well as the protist guanylyl cyclases were found in bacteria . Diverse domains were fused to the cyclase domain and phylogenetic analysis indicated that most proteins within a single cluster have similar domain compositions, emphasising the ancient evolutionary origin and versatility of the cyclase domain.

J Struct Biol, 2004 Apr-May, 146(1-2), 79 - 89
Chaperone networks in bacteria: analysis of protein homeostasis in minimal cells; Wong P et al.; The prevention of aberrant behavior of proteins is fundamental to cellular life . Protein homeostatic processes are present in cells to stabilize protein conformations, refold misfolded proteins, and degrade proteins that might be detrimental to the cell . Molecular chaperones and proteases perform a major role in these processes . In bacteria, the main cytoplasmic components involved in protein homeostasis include the chaperones trigger factor, DnaK/DnaJ/GrpE, GroEL/GroES, HtpG, as well as ClpB and the proteases ClpXP, ClpAP, HslUV, Lon, and FtsH . Based on recent genome sequencing efforts, it was surprising to find that the Mycoplasma, a genus proposed to include a minimal form of cellular life, do not contain certain major members of the protein homeostatic network, including GroEL/GroES . We propose that, in mycoplasmas, there has been a fundamental shift towards favoring processes that promote protein degradation rather than protein folding . The arguments are based on two different premises: (1) the regulation of stress response in Mycoplasma and (2) the unique characteristics of the Mycoplasma proteome.

Acta Paediatr Suppl, 2004 Feb, 93(444), 4 - 5
The role of intrauterine bacteria in brain injury; Sullivan MH et al.; Organisms appear to be present in human fetal membranes without any apparent impact on pregnancy maintenance or the fetal brain . A clear link between chorioamnionitis and fetal brain damage suggests that tissue responses at the feto-maternal interface may be the key determinant of whether preterm labour and brain damage occur.

Endocrinology, 2004 Jun, 145(6), 2997 - 3003 Epub 2004 Mar 19.
Diabetes alters the response to bacteria by enhancing fibroblast apoptosis; Liu R et al.; Diabetics suffer from both more frequent bacterial infections and greater consequences of infection . However, bacteria-induced tissue destruction and the subsequent response in diabetics have received relatively little attention . To investigate this issue, we inoculated the scalp of control or db/db diabetic mice, with the pathogen Porphyromonas gingivalis, which causes connective tissue destruction in humans . Both bacteria-induced cytokine expression and tissue loss were similar in diabetic and control mice . However, there was a significantly higher rate of fibroblast-specific apoptosis in the diabetic group, which was measured as cells that were double positive for the terminal deoxynucleotidyltransferase-mediated deoxy-UTP nick end labeling assay and expression of vimentin . The higher rate of fibroblast apoptosis could be explained in the diabetic group by enhanced levels of activated caspase-3 . Apoptosis was evident during the peak healing period and coincided with reduced numbers of fibroblasts, diminished collagen I and III expression, and significantly reduced formation of new connective tissue matrix in diabetic mice . Thus, diabetes may impair the healing response to bacteria-induced connective tissue loss by increasing the number of caspase-3-activated fibroblasts, leading to greater apoptosis and reduced numbers of fibroblastic cells.

Plant Cell, 2004 Apr, 16(4), 933 - 44 Epub 2004 Mar 18.
A nonsymbiotic root hair tip growth phenotype in NORK-mutated legumes: implications for nodulation factor-induced signaling and formation of a multifaceted root hair pocket for bacteria; Esseling JJ et al.; The Medicago truncatula Does not Make Infections (DMI2) mutant is mutated in the nodulation receptor-like kinase, NORK . Here, we report that NORK-mutated legumes of three species show an enhanced touch response to experimental handling, which results in a nonsymbiotic root hair phenotype . When care is taken not to induce this response, DMI2 root hairs respond morphologically like the wild type to nodulation factor (NF) . Global NF application results in root hair deformation, and NF spot application induces root hair reorientation or branching, depending on the position of application . In the presence of Sinorhizobium meliloti, DMI2 root hairs make two-dimensional 180 degrees curls but do not entrap bacteria in a three-dimensional pocket because curling stops when the root hair tip touches its own shank . Because DMI2 does not express the promoter of M . truncatula Early Nodulin11 (ENOD11) coupled to beta-glucuronidase upon NF application, we propose a split in NF-induced signaling, with one branch to root hair curling and the other to ENOD11 expression.

Prikl Biokhim Mikrobiol, 2004 Jan-Feb, 40(1), 62 - 5
{Sulfur metabolism enzymes in thermoacidophilus bacteria Sulfobacillus sibiricus}; Krasil'nikova EN et al.; Sulfur oxygenase, sulfite oxidase, adenylyl sulfate reductase, rhodanase, sulfur:Fe(III) oxidoreductase, and sulfite:Fe(III) oxidoreductase were found in cells of aerobic thermoacidophilic bacteria Sulfobacillus sibiricus strains N1 and SSO . Enzyme activity was revealed in cells grown on the medium with elemental sulfur or in the presence of various sulfide elements and concentrates of sulfide ores . The activity of sulfur-metabolizing enzymes depended little on the degree of aeration during bacterial growth.

Anal Chem, 2004 Mar 15, 76(6), 1571 - 9
Dielectrophoretic concentration and separation of live and dead bacteria in an array of insulators; Lapizco-Encinas BH et al.; Insulator-based (electrodeless) dielectrophoresis (iDEP) is an innovative approach in which the nonuniform electric field needed to drive DEP is produced by insulators, avoiding problems associated with the use of electrodes . Live and dead Escherichia coli were concentrated and selectively released by applying stepped DC voltages across a microchannel containing an array of insulating posts etched in glass . The only electrodes present were two platinum wires placed in the inlet and outlet reservoirs, producing mean electric fields of up to 200 V/mm across the insulators . The cells were labeled with Syto 9 and propidium iodide and imaged through a fluorescent microscope . Cell trapping and release were controlled by modifying the relative responses of electrokinesis and DEP by adjusting the magnitude of the applied voltage . Dead cells were observed to have significantly lower dielectrophoretic mobility than live cells, whereas the electrokinetic mobilities of live and dead cells were indistinguishable . The locations of the bands of differentially trapped cells were consistent with predictions . In addition, cells were selectively trapped and concentrated against backgrounds of 1- and 0.2-microm carboxylate-modified polystyrene particles . This first application of iDEP for simultaneous live/dead bacteria separation and concentration illustrates its potential as a front-end method for bacterial analysis.

Zhongguo Zhong Yao Za Zhi, 2003 Sep, 28(9), 842 - 4
{A comparison of the protective activity of liver injury induced by D-galact-osamine between huangqin-tang and their metabolites by human intestinal bacteria}; Zuo F et al.; OBJECTIVE: To compare the protective activity of liver injury induced by D-galactosamine (GalN) between Huangqin-Tang and their metabolites by human intestinal bacteria(HIB) . METHOD: The liver injuries in conventional and pseudo-germfree mice were induced by GalN . After oral administration of Huangqin-Tang and their metabolites mixtures by HIB, the serum transaminase (ALT and AST) activities were detected . RESULT: In conventional mice, large and medium doses (20 and 10 g.kg-1) of Huangqin-Tang decoction significantly reduced the increase of serum ALT activity after 18 h GalN treatment . In pseudo-germfree mice, metabolites significantly reduced the ALT levels . However, Huangqing-Tang didn't affect the ALT levels in this kind of mice . To all of the animals, AST levels remained the same after oral Huangqin-tang or their metabolites . CONCLUSION: The metabolism by intestinal bacteria plays a role in pharmacological effects of constituents of Chinese herbal medicine . The metabolites of the constituents by intestinal bacteria were the real active components in vivo.

Comp Biochem Physiol C Toxicol Pharmacol, 2003 Dec, 136(4), 337 - 42
cDNA cloning and expression of bacteria-induced Hdd11 gene from eri-silkworm, Samia cynthia ricini; Bao Y et al.; A cDNA clone encoding Hdd11 protein, a bacteria-induced protein of unknown function, was isolated from fat body of immunized Samia cynthia ricini larvae based on suppression subtractive hybridization . The cDNA encodes a 167 amino acid residue open reading frame with an 18 residue predicted signal peptide . The deduced amino acid sequence showed 54% and 55% identity with Hdd11 proteins from Hyphantria cunea and Manduca sexta, respectively . Expression of the gene was undetectable in naive larvae when measured by Northern blot hybridization, but strongly induced in fat body after injecting bacterial cells or peptidoglycan into the larvae . The mRNA expression in the fat body was detected as early as 3 h post injection, reached peak levels at 12 h and continued for further 60 h at significant levels . The transcript was detected at very low levels in midgut, hemocytes and malpighian tubules.

Clin Microbiol Infect, 2004 Mar, 10(3), 220 - 3
Evaluation of an automated complement-fixation test (Seramat) for diagnosis of acute respiratory infections caused by viruses and atypical bacteria; de Ory F et al.; The complement-fixation test (CFT) permits low-cost screening of serum samples for different agents within a single assay, and is a useful tool for the serological diagnosis of acute respiratory infections . This study evaluated the automated Seramat CFT system with 160 paired serum samples taken from 80 patients with acute respiratory infection in comparison with in-house CFTs against a panel of agents, including influenza A and B, adenovirus, respiratory syncitial virus, cytomegalovirus, Mycoplasma pneumoniae, Coxiella burnetti and Chlamydia spp., and in comparison with indirect immunofluorescence (IIF) against Legionella pneumophila . Overall, the Seramat system identified 75 (88.2%) of the 85 seroconversions recognised by in-house CFTs or IIF . In comparison to the in-house CFTs, the correlation was 89.2% (66/74) . For L . pneumophila, the Seramat system detected nine (81.8%) of the 11 cases diagnosed by IIF . The Seramat system also identified eight additional seroconversions that were not detected by the in-house assays; none of these seroconversions was detected by the in-house assay on retesting . The Seramat system represents a significant technical improvement that may enable many clinical laboratories to use the CFT as a routine diagnostic tool.

Proc Natl Acad Sci U S A, 2004 Mar 16, 101(11), 3765 - 9 Epub 2004 Mar 03.
Universality and flexibility in gene expression from bacteria to human; Ueda HR et al.; Highly parallel experimental biology is offering opportunities to not just accomplish work more easily, but to explore for underlying governing principles . Recent analysis of the large-scale organization of gene expression has revealed its complex and dynamic nature . However, the underlying dynamics that generate complex gene expression and cellular organization are not yet understood . To comprehensively and quantitatively elucidate these underlying gene expression dynamics, we have analyzed genome-wide gene expression in many experimental conditions in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Mus musculus, and Homo sapiens . Here we demonstrate that the gene expression dynamics follows the same and surprisingly simple principle from E . coli to human, where gene expression changes are proportional to their expression levels, and show that this "proportional" dynamics or "rich-travel-more" mechanism can regenerate the observed complex and dynamic organization of the transcriptome . These findings provide a universal principle in the regulation of gene expression, show how complex and dynamic organization can emerge from simple underlying dynamics, and demonstrate the flexibility of transcription across a wide range of expression levels.

Insect Biochem Mol Biol, 2004 Jan, 34(1), 89 - 100
Beta-1,3-glucan recognition protein-2 (betaGRP-2)from Manduca sexta; an acute-phase protein that binds beta-1,3-glucan and lipoteichoic acid to aggregate fungi and bacteria and stimulate prophenoloxidase activation; Jiang H et al.; We have isolated and characterized a new beta-1,3-glucan recognition protein that is present in Manduca sexta cuticle and hemolymph . This 52 kDa protein, designated betaGRP-2, is 57% identical in sequence to betaGRP-1 from larval hymolymph of the same insect . BetaGRP-2 differs from betaGRP-1 in its absence of the naive larvae before the wandering stage begins . Transcription of the betaGRP-2 was up-regulated in larvae challenged with yeast or bacteria . BetaGRP-2 contains a region with sequence similarity to several glucanases but lacks glucanase activity . It aggregates yeasts and bacteria to, perhaps, limit the spread of invading cells and ensure a localized defense reaction . BetaGRP-2 binds laminarin and lipoteichoic acid, but not lipopolysaccharide . Laminarin-triggered prophenoloxidase activation was greatly enhanced in the induced larval hemolymph supplemented with purified betaGRP-2 . Complementing other studies on pattern recognition molecules in M . sexta, these results indicate that a complex system of protein sensors is an integral component of the insect immune system and that different recognition molecules have overlapping binding specificity and functions.

Rev Argent Microbiol, 2003 Oct-Dec, 35(4), 175 - 82
Birth of the domains Bacteria, Archaea and Eucarya and of major taxa within them: a hypothesis; Zorzopulos J; A hypothesis to explain how the birth of the Bacteria, Archaea and Eucarya domains and of major taxa within them took place is presented . It is proposed that the birth of each domain was an independent event consisting in the genetic isolation of a particular cell from a very diverse pool of "primitive cells" . Cells within this pool have a dynamic pattern of cell fusion followed by mostly illegitimate DNA recombination . It is postulated that genetic isolation was achieved: a) by evolution of the peptidoglycan layer in Bacteria, b) by evolution of a glycoproteic cell wall in Archaea, and c) by evolution of the nuclear membrane in Eucarya . It is also postulated that, within each domain, branching was a consequence of sporadic events of fusion between two cells of different phylogenetic lineages, followed by mostly illegitimate DNA recombination and cell wall regeneration . The two fusing cells may have belonged to the same domain, to different domains or even one may have belonged to one of the domains and the other to the pool of "primitive cells" . In this last case, new complex phenotypes, previously absent from all the domains, were suddenly introduced in one of them (e.g.: photosynthesis in Bacteria, methanogenesis in Archaea) . A corollary of this theory is that genes should have a phylogenetic tree with defined nodes while organisms are characterized by discontinuities instead of nodes.

Appl Environ Microbiol, 2004 Feb, 70(2), 1008 - 16
Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil; Okano Y et al.; Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact . In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture . Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult . A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil . This assay has a detection limit of 1.3 x 10(5) cells/g of dry soil . The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate . AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application . AOB populations in amended treatments increased from an initial density of approximately 4 x 10(6) cells/g of dry soil to peak values (day 7) of 35 x 10(6) and 66 x 10(6) cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively . The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 x 10(9) and 2.2 x 10(9) cells/g of soil, regardless of the ammonia concentration . A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field . AOB population size increased from 8.9 x 10(6) to 38.0 x 10(6) cells/g of soil by day 39 . Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study . Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h(-1) cell(-1) and decreased with time in both microcosms and the field . Growth yields were 5.6 x 10(6), 17.5 x 10(6), and 1.7 x 10(6) cells/mol of NH4+ in the 1.5 and 7.5 mM microcosm treatments and the field study, respectively . In a second field experiment, AOB population size was significantly greater in annually fertilized versus unfertilized soil, even though the last ammonium application occurred 8 months prior to measurement, suggesting a long-term effect of ammonium fertilization on AOB population size.

Appl Environ Microbiol, 2004 Feb, 70(2), 745 - 51
Stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria; Londry KL et al.; We examined the potential use of natural-abundance stable carbon isotope ratios of lipids for determining substrate usage by sulfate-reducing bacteria (SRB) . Four SRB were grown under autotrophic, mixotrophic, or heterotrophic growth conditions, and the delta13C values of their individual fatty acids (FA) were determined . The FA were usually 13C depleted in relation to biomass, with Deltadelta13C(FA - biomass) of -4 to -17 per thousand; the greatest depletion occurred during heterotrophic growth . The exception was Desulfotomaculum acetoxidans, for which substrate limitation resulted in biomass and FA becoming isotopically heavier than the acetate substrate . The delta13C values of FA in Desulfotomaculum acetoxidans varied with the position of the double bond in the monounsaturated C16 and C18 FA, with FA becoming progressively more 13C depleted as the double bond approached the methyl end . Mixotrophic growth of Desulfovibrio desulfuricans resulted in little depletion of the i17:1 biomarker relative to biomass or acetate, whereas growth with lactate resulted in a higher proportion of i17:1 with a greater depletion in 13C . The relative abundances of 10Me16:0 in Desulfobacter hydrogenophilus and Desulfobacterium autotrophicum were not affected by growth conditions, yet the Deltadelta13C(FA - substrate) values of 10Me16:0 were considerably greater during autotrophic growth . These experiments indicate that FA delta13C values can be useful for interpreting carbon utilization by SRB in natural environments.

Appl Environ Microbiol, 2004 Feb, 70(2), 675 - 8
Observing growth and division of large numbers of individual bacteria by image analysis; Elfwing A et al.; We describe a method that enabled us to observe large numbers of individual bacterial cells during a long period of cell growth and proliferation . We designed a flow chamber in which the cells attached to a transparent solid surface . The flow chamber was mounted on a microscope equipped with a digital camera . The shear force of the flow removed the daughter cells, making it possible to monitor the consecutive divisions of a single cell . In this way, kinetic parameters and their distributions, as well as some physiological characteristics of the bacteria, could be analyzed based on more than 1,000 single-cell observations . The method which we developed enabled us to study the history effect on the distribution of the lag times of single cells.

Biochim Biophys Acta, 2004 Jan 28, 1660(1-2), 80 - 92
Stability and solubility of integral membrane proteins from photosynthetic bacteria solubilized in different detergents; Odahara T; As a first step toward the establishment of practical guidelines for the search for crystallization conditions, stability and solubility were examined for integral membrane proteins from photosynthetic bacteria in the presence of different detergents . The results obtained from their stability provided practical information on the proper choice of detergent type in the preparation process and the subsequent crystallization experiment . In addition, the determination of a solubility diagram provided a practical method for quantifying the correct choice of detergent concentration and for setting up the suitable precipitant concentration in the crystallization experiment.

Biochim Biophys Acta, 2004 Jan 28, 1660(1-2), 53 - 65
Overcoming the toxicity of membrane peptide expression in bacteria by upstream insertion of Asp-Pro sequence; Montigny C et al.; Transmembrane (TM) peptides often induce toxic effects when expressed in bacteria, probably due to membrane destabilization . We report here that in the case of the TM domains of hepatitis C virus (HCV) E1 and E2 envelope proteins, which are both particularly toxic for the bacteria, the insertion of the Asp-Pro (DP) sequence dramatically reduced their toxicities and promoted their expressions when produced as glutathione S-transferase (GST) GST-DP-TM chimeras . Subcellular fractionation showed that these chimeras co-sediment with the membrane fraction and contain active GST that could be solubilized with a mild detergent . Surprisingly, immuno-gold electron microscopy clearly showed that such chimeras are not localized in the membrane but in the cytosol . We thus postulate that they likely form proteo-lipidic aggregates, which prevent the bacteria from toxicity by sequestering the TM part of the chimeras . The reduction of toxicity in the presence of the Asp-Pro sequence is possibly due to Asp's negative charge that probably disadvantages the binding of the TM peptides to the membrane . In addition, the structural features of Pro residue could promote the formation of chimera aggregates.

Mol Microbiol, 2004 Jan, 51(2), 395 - 405
Nucleoid restructuring in stationary-state bacteria; Frenkiel-Krispin D et al.; The textbook view of the bacterial cytoplasm as an unstructured environment has been overturned recently by studies that highlighted the extent to which non-random organization and coherent motion of intracellular components are central for bacterial life-sustaining activities . Because such a dynamic order critically depends on continuous consumption of energy, it cannot be perpetuated in starved, and hence energy-depleted, stationary-state bacteria . Here, we show that, at the onset of the stationary state, bacterial chromatin undergoes a massive reorganization into ordered toroidal structures through a process that is dictated by the intrinsic properties of DNA and by the ubiquitous starvation-induced DNA-binding protein Dps . As starvation proceeds, the toroidal morphology acts as a structural template that promotes the formation of DNA-Dps crystalline assemblies through epitaxial growth . Within the resulting condensed assemblies, DNA is effectively protected by means of structural sequestration . We thus conclude that the transition from bacterial active growth to stationary phase entails a co-ordinated process, in which the energy-dependent dynamic order of the chromatin is sequentially substituted with an equilibrium crystalline order.

J Environ Monit, 2004 Feb, 6(2), 113 - 20 Epub 2004 Jan 06.
Viable fungi and bacteria in personal exposure samples in relation to microenvironments; Toivola M et al.; Personal exposures to viable fungi and bacteria were compared with the concentrations being assessed by stationary samplers in home and workplace microenvironments . A random sample of 81 elementary school teachers in eastern Finland performed two 24-hour measurement periods in wintertime . Concentrations and prevalences of viable fungi and bacteria on the collection filters were determined by cultivation method . The geometric mean concentration was 3-12 cfu m(-3) for total viable fungi, 0.6-3.7 cfu m(-3) for Penicillium and mainly under 1 cfu m(-3) for other fungi . The samples with higher fungal concentrations also had higher diversity of fungi than samples with lower concentrations . The total number of fungal genera recovered was 39 for personal, 34 for home and 23 for work samples . The variation in concentration of Penicillium explained even 25-95% of the variations of total fungal concentration in personal exposure, home and workplace environments . There was an association between personal exposure and home concentration of viable fungi and between personal exposure and home and work concentrations of viable bacteria . Personal exposure and home concentrations of fungi were higher in rural areas than in urban areas . Our results also indicate that presence of a certain fungus in a microenvironment does not necessarily mean similar findings in personal exposure samples.

J Anim Sci, 2004 Jan, 82(1), 250 - 61
Evaluation of methods to reduce bacteria concentrations in spray-dried animal plasma and its effects on nursery pig performance; DeRouchey JM et al.; Four experiments with 1,040 weanling pigs (17 +/- 2 d of age at weaning) were conducted to evaluate the effects of spray-dried animal plasma source, drying technique, and methods of bacterial reduction on nursery pig performance . In Exp . 1, 180 barrows and gilts (initial BW 5.9 +/- 1.8 kg) were used to compare effects of animal plasma, animal plasma source, drying technique (spray-dried or freeze-dried), and plasma irradiation in nursery pig diets . From d 0 to 10, pigs fed diets containing irradiated spray-dried animal plasma had increased ADG and ADFI (P < 0.05) compared with pigs fed diets containing nonirradiated spray-dried animal plasma . Pigs fed irradiated animal plasma Sources 1 and 2 were similar in ADG and ADFI, but pigs fed animal plasma Source 1 had greater ADG (P < 0.05) than pigs fed animal plasma Source 2 and pigs not fed plasma . Pigs fed freeze-dried animal plasma had growth performance similar (P > 0.36) to pigs fed spray-dried animal plasma . Overall (d 0 to 24), pigs fed irradiated spray-dried animal plasma were heavier (P < 0.05) than pigs fed no animal plasma, whereas pigs fed nonirradiated spray-dried plasma were intermediate . In Exp . 2, 325 barrows and gilts (initial BW 5.8 +/- 1.7 kg) were used to compare the effects of irradiation or formaldehyde treatment of animal plasma and formaldehyde treatment of the whole diet . Pigs fed diets containing irradiated animal plasma had greater ADG (P < 0.05) than pigs fed nonirradiated plasma . Pigs fed formaldehyde-treated plasma had greater ADG and ADFI (P < 0.05) than pigs fed diets with either nonirradiated plasma or whole diet treated with formaldehyde . In Exp . 3 (360 barrows and gilts; initial BW 6.3 +/- 2.7 kg) and Exp . 4 (175 barrows and gilts; initial BW 6.1 +/- 1.7 kg), the irradiation of feed (high bacteria) and food-grade (low bacteria) animal plasma in nursery pig diets was examined . Pigs fed irradiated feed-grade plasma Product 2 had increased ADG (P < 0.05) compared with pigs fed nonirradiated plasma Product 2 and pigs fed the control diet without plasma . In Exp . 3 and 4, pigs fed irradiated food-grade plasma had growth performance similar to pigs fed nonirradiated food-grade plasma (P > 0.12) . These studies indicate that bacterial reduction of feed-grade, but not food-grade animal plasma, improves nursery pig performance.

Biophys J, 2004 Feb, 86(2), 1082 - 8
Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering; Hong X et al.; The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively . The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell . The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 A, a long axis of 110 A, and a short axis of 85 A . After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 A, a long axis of 80 A, and a short axis of 55 A . In contrast to the cylindrical crystal structure with a height of 40 A and a diameter of 68 A, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59-consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules.

J Microbiol Methods, 2004 Feb, 56(2), 151 - 9
A disintegration method for direct counting of bacteria in clay-dominated sediments: dissolving silicates and subsequent fluorescent staining of bacteria; Boenigk J; The masking of bacteria by abundant microparticles of the clay and silt fraction and cell losses due to sonication hampered direct enumeration of bacteria in sediments dominated by fine sediments . These problems can be circumvented by dissolving silicate fine particles using hydrofluoric acid and subsequent staining of bacteria by DTAF . The developed disintegration method partly replaces mechanical separation of bacteria from sediment particles by chemical disintegration of the silicates . Recovery efficiency ranged from 90% to 111% for different clays and clay-dominated sediments . Especially for the analysis of fine sediments and clays, this method circumvents both strong dilution of the sediment sample and harsh sonication . The method can also therefore be used in sediments where particle abundance is several orders of magnitude higher than bacterial abundance and simple dilution would not suffice in reliably counting bacteria.

J Mol Evol, 2004 Jan, 58(1), 19 - 29
Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota; Vaughan S et al.; The FtsZ protein is a polymer-forming GTPase which drives bacterial cell division and is structurally and functionally related to eukaryotic tubulins . We have searched for FtsZ-related sequences in all freely accessible databases, then used strict criteria based on the tertiary structure of FtsZ and its well-characterized in vitro and in vivo properties to determine which sequences represent genuine homologues of FtsZ . We have identified 225 full-length FtsZ homologues, which we have used to document, phylum by phylum, the primary sequence characteristics of FtsZ homologues from the Bacteria, Archaea, and Eukaryota . We provide evidence for at least five independent ftsZ gene-duplication events in the bacterial kingdom and suggest the existence of three ancestoral euryarchaeal FtsZ paralogues . In addition, we identify "FtsZ-like" sequences from Bacteria and Archaea that, while showing significant sequence similarity to FtsZs, are unlikely to bind and hydrolyze GTP.

Mol Genet Genomics, 2004 Mar, 271(2), 180 - 8 Epub 2004 Jan 22.
Asymmetrically acting lycopene beta-cyclases (CrtLm) from non-photosynthetic bacteria; Tao L et al.; Carotenoids have important functions in photosynthesis, nutrition, and protection against oxidative damage . Some natural carotenoids are asymmetrical molecules that are difficult to produce chemically . Biological production of carotenoids using specific enzymes is a potential alternative to extraction from natural sources . Here we report the isolation of lycopene beta-cyclases that selectively cyclize only one end of lycopene or neurosporene . The crtLm genes encoding the asymmetrically acting lycopene beta-cyclases were isolated from non-photosynthetic bacteria that produced monocyclic carotenoids . Co-expression of these crtLm genes with the crtEIB genes from Pantoea stewartii (responsible for lycopene synthesis) resulted in the production of monocyclic gamma-carotene in Escherichia coli . The asymmetric cyclization activity of CrtLm could be inhibited by the lycopene beta-cyclase inhibitor 2-(4-chlorophenylthio)-triethylamine (CPTA) . Phylogenetic analysis suggested that bacterial CrtL-type lycopene beta-cyclases might represent an evolutionary link between the common bacterial CrtY-type of lycopene beta-cyclases and plant lycopene beta- and epsilon-cyclases . These lycopene beta-cyclases may be used for efficient production of high-value asymmetrically cyclized carotenoids.

FEMS Microbiol Lett, 2004 Jan 15, 230(1), 63 - 71
Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica); Michaud L et al.; A set of 146 Antarctic marine isolates from the Ross Sea was characterized by a combination of molecular techniques in order to determine the degree of inter- and intraspecific variability . Isolates were analyzed by amplified rDNA restriction analysis (ARDRA) using the tetrameric enzyme AluI, resulting in 52 different groups, corresponding to at least 52 different bacterial species, indicating a high degree of interspecific variability . The phylogenetic position of bacteria belonging to some ARDRA groups was obtained by sequencing of 16S rDNA . Random amplified polymorphic DNA (RAPD) analysis, carried out on the largest ARDRA groups, revealed a high intraspecific genetic variability, too . The analysis of plasmid content revealed the existence of horizontal gene transfer between strains belonging to the same and to different species . A comparison of the whole body of morphological, physiological and biochemical data was finally carried out.

J Endotoxin Res, 2003, 9(6), 390 - 4
Immunopathogenesis of Onchocerca volvulus keratitis (river blindness): a novel role for TLR4 and endosymbiotic Wolbachia bacteria; Hise AG et al.; Infection with the parasitic nematode Onchocerca volvulus is associated with inflammation of the skin and cornea that can lead to blindness . Corneal damage is thought to occur as a result of the host inflammatory responses to degenerating microfilariae in the eye . We have utilized a murine model of corneal inflammation (keratitis) to investigate the immune and inflammatory responses associated with river blindness . Soluble extracts of O . volvulus, a filarial species that contains the endosymbiont bacteria Wolbachia or Acanthocheilonema viteae (a nematode not naturally infected with the bacteria) were injected into mouse corneas . Inflammatory responses and corneal changes were measured . We demonstrated a major role for endosymbiont Wolbachia bacteria and Toll-like receptor 4 (TLR4) in the pathogenesis of ocular onchocerciasis.

Biosci Biotechnol Biochem, 2003 Dec, 67(12), 2668 - 73
Protein profile of symbiotic bacteria Mesorhizobium loti MAFF303099 in mid-growth phase; Kajiwara H et al.; Expressed proteins in cultured symbiotic bacteria (Mesorhizobium loti MAFF303099) in the mid-growth phase were proteomically analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and capillary high-performance liquid chromatography coupled with an ion-trap mass spectrometry (MS) . The genome sequence data of M . loti were used to identify the analyzed proteins . We identified 114 of the 127 proteins analyzed on 2D-PAGE gel with some microheterogenities which were caused by post-translational modifications.

J Bacteriol, 2004 Feb, 186(3), 740 - 9
Rhodobacter capsulatus nifA1 promoter: high-GC -10 regions in high-GC bacteria and the basis for their transcription; Richard CL et al.; It was previously shown that the Rhodobacter capsulatus NtrC enhancer-binding protein activates the R . capsulatus housekeeping RNA polymerase but not the Escherichia coli RNA polymerase at the nifA1 promoter . We have tested the hypothesis that this activity is due to the high G+C content of the -10 sequence . A comparative analysis of R . capsulatus and other alpha-proteobacterial promoters with known transcription start sites suggests that the G+C content of the -10 region is higher than that for E . coli . Both in vivo and in vitro results obtained with nifA1 promoters with -10 and/or -35 variations are reported here . A major conclusion of this study is that alpha-proteobacteria have evolved a promiscuous sigma factor and core RNA polymerase that can transcribe promoters with high-GC -10 regions in addition to the classic E . coli Pribnow box . To facilitate studies of R . capsulatus transcription, we cloned and overexpressed all of the RNA polymerase subunits in E . coli, and these were reconstituted in vitro to form an active, recombinant R . capsulatus RNA polymerase with properties mimicking those of the natural polymerase . Thus, no additional factors from R . capsulatus are necessary for the recognition of high-GC promoters or for activation by R . capsulatus NtrC . The addition of R . capsulatus sigma(70) to the E . coli core RNA polymerase or the use of -10 promoter mutants did not facilitate R . capsulatus NtrC activation of the nifA1 promoter by the E . coli RNA polymerase . Thus, an additional barrier to activation by R . capsulatus NtrC exists, probably a lack of the proper R . capsulatus NtrC-E . coli RNA polymerase (protein-protein) interaction(s).

Appl Spectrosc, 2004 Jan, 58(1), 33 - 40
Surface-enhanced Raman spectroscopy as a tool for probing specific biochemical components in bacteria; Zeiri L et al.; Treatment of bacteria with silver yields intense and highly specific surface-enhanced Raman spectroscopy (SERS) spectra from various cellular chemical components located in the vicinity of the silver colloids . In particular, we demonstrate an extreme sensitivity to flavin components associated with the cell envelope and to their state of oxidation . Different spectra, possibly associated with DNA, carboxylates, and perhaps phosphates, are obtained from the soluble interior fraction of the cell.

Int Dent J, 2003 Dec, 53(6 Suppl 1), 391 - 7
The effect of a toothpaste containing 2% zinc citrate/0.3% Triclosan on the glycolysis of plaque bacteria ex vivo after food intake; Adams SE et al.; OBJECTIVE: To develop an ex vivo plaque pH method to assess the efficacy of a new zinc citrate/Triclosan formulation . METHODS: Study (1) focussed on method development . Study (2) examined the effect of a toothpaste containing 2% zinc citrate/0.3% Triclosan on the pH of plaque after product use and consumption of pizza . Study (3) investigated the effect of the same formulation and a fluoride toothpaste on the pH of plaque without an 'eating occasion' . The pH of plaque samples was measured over 10 minutes in the presence of glucose . RESULTS: The test product significantly reduced the amount of acid produced 30 minutes (p = 0.0035) and 3 hours (p = 0.0018) after brushing (study (2)) . In study (3) use of the test product significantly reduced the amount of acid produced 3 hours after brushing (p = 0.0023) . No significant benefit was found for the fluoride toothpaste . CONCLUSION: An ex vivo plaque pH method has been developed which can detect changes in acid produced following brushing with different toothpastes . A toothpaste containing 2% zinc citrate/0.3% Triclosan significantly reduced the total acid produced for at least 3 hours after product use . Moreover it has been demonstrated that this effect is detectable even after eating.

Microbiol Res, 2003, 158(4), 363 - 9
Fluctuation of endophytic bacteria and phytoplasmosis in elm trees; Mengoni A et al.; A total of 658 heterotrophic bacterial colonies isolated from phloem tissues of roots and branches in four months (April, June, September and December) from two elm plants, one of which affected by phytoplasmosis, were typed by means of ARDRA . This analysis revealed the existence of a high degree of variability within the community and was able to detect 84 different ARDRA groups . The Analysis of Molecular Variance was applied to ARDRA patterns to analyze the differentiation between communities isolated from the various samplings . Data obtained were compared with those from a previous work (Mocali et al . 2003) . Results indicated that plants with symptoms of phytoplasmosis showed marked alterations in the extent of the fluctuations of the community along the seasons in the different plant organs.

Mol Biol (Mosk), 2003 Nov-Dec, 37(6), 989 - 98
{Thermostability of alkaline phosphatase of Meithermus ruber bacteria: cloning of the gene, expression in Escherichia coli cells and biochemical characterization of the recombinant protein}; Iurchenko IuV et al.; The Meiothermus ruber alkaline phosphatase gene was cloned, expressed in Escherichia coli cells, and sequenced . The enzyme precursor, including the putative signal peptide, was shown to consist of 503 residues (deduced molecular mass 54,229 Da) . The recombinant enzyme showed the maximal activity at 60-65 degrees C and pH 11.0 and had K(m) = 0.055 mM as estimated with p-nitrophenyl phosphate (pNPP) . The enzyme proved to be moderately thermostable, retaining 50% activity after 6 h incubation at 60 degrees C and being completely inactivated in 2 h at 80 degrees C . In substrate specificity assays, the highest enzymic activity was observed with pNPP and dATP . Vanadate, inorganic phosphate, and SDS inhibited M . ruber alkaline phosphatase, while thiol-reducing agents had virtually no effect . The enzymic activity strongly depended on exogenous Mg2+ and declined in the presence of EDTA.

Appl Environ Microbiol, 2004 Jan, 70(1), 332 - 9
Successful predation of filamentous bacteria by a nanoflagellate challenges current models of flagellate bacterivory; Wu QL et al.; Current models suggest that (i) filamentous bacteria are protected against predation by nanoflagellates, (ii) prey size is positively correlated with prey-predator contact probability, and (iii) contact probability is mainly responsible for size-selective predation by interception-feeding flagellates . We used five strains of filamentous bacteria and one bacterivorous nanoflagellate, Ochromonas sp . strain DS, to test these assumptions . The five strains, including one spirochete and four Betaproteobacteria strains, were isolated by the filtration-acclimatization method . All five strains possess flexible cells, but they differ in average cell length, which ranged from 4.5 to 13.7 micro m . High-resolution video microscopy was used to measure contact, capture, and ingestion rates, as well as selectivity of the flagellate feeding . Growth and feeding experiments with satiating and nonsatiating food conditions, as well as experiments including alternative well-edible prey, were performed . In contrast to predictions by current models, the flagellate successfully consumed all the tested filamentous strains . The ingestion rate was negatively correlated with bacterial length . On the other hand, the lengths of the filamentous bacteria were not positively correlated to the contact rate and capture rate but were negatively correlated to ingestion efficiency . In experiments including alternative nonfilamentous prey, the flagellates showed negative selection for filamentous bacteria, which was independent of food concentration and is interpreted as a passive selection . Our observations indicate that (i) size alone is not sufficient to define a refuge for filamentous bacteria from nanoflagellate predation and (ii) for the investigated filamentous bacteria, prey-predator contact probability could be more influenced by factors other than the prey size.

Protein Expr Purif, 2004 Feb, 33(2), 326 - 31
Improved production of recombinant fibroblast growth factor 7 (FGF7/KGF) from bacteria in high magnesium chloride; Luo Y et al.; Because of specificity for both heparin/heparan sulfate and the receptor complex on epithelial cells relative to other fibroblast growth factor (FGF) homologues, there is considerable interest in clinical and commercial applications of FGF7 (also called keratinocyte growth factor or KGF) that require large quantities at reasonable cost . Production of recombinant FGF7 from bacteria suffers from lower yields and recovery relative to FGF1 and FGF2 . Fusion of FGF7 at the N-terminus with glutathione-S-transferase (GST) followed by removal of GST by proteolysis while bound to natural ligand heparin improved the intrinsically low yields from Escherichia coli hosts to 3.2 mg per liter per OD(600), which was still only 10% of that for FGF1 . Yield of the GST-FGF7 fusion product was improved to about 17 mg per liter per OD(600) in strain BL21(DE3)pLysS by inclusion of 10-100mM magnesium chloride (MgCl(2)) in the culture medium . This improved by about five times the yields of fully active 54ser-FGF7 after proteolytic excision of the GST portion from GST-FGF7 immobilized on heparin-Sepharose . This simple enhancement improves the cost-effectiveness of production of recombinant FGF7 in bacteria for clinical and commercial applications.

Cell Microbiol, 2004 Feb, 6(2), 97 - 104
The role of endosymbiotic Wolbachia bacteria in filarial disease; Hise AG et al.; In this review, we describe the pathogenic role of Wolbachia endosymbiotic bacteria in filarial diseases, focusing on the host innate immune responses to filarial and Wolbachia products . A description of the host pathogen recognition and early inflammatory responses including TLR4-mediated signalling, chemokine and cytokine responses and inflammatory cell recruitment is provided from human studies and from animal models of filarial disease . Finally, the impact of the discovery and characterization of Wolbachia on filarial research and treatment programmes is discussed.

Trends Microbiol, 2004 Jan, 12(1), 37 - 43
Evolution of minimal-gene-sets in host-dependent bacteria; Klasson L et al.; Several attempts have been made to identify the minimal set of genes that is required for life using computational approaches or studies of deletion mutants . These experiments resemble those already performed by nature; a few hundred million years ago an ancestor of Escherichia coli was domesticated by aphids, which resulted in the elimination of 70-75% of the original bacterial genome . Amazingly, the small genomes of these imprisoned bacteria are more stable than those of their free-living relatives . Minimal-gene-sets that have evolved naturally are largely species-specific, with the exception of a small set of core genes that are required for information processing . Comparative genomics of host-dependent bacteria have shown that minimal-gene-sets can persist in nature for tens of millions of years provided that the environment is rich in nutrients, that the host population size is large and that there is a strong host-level selection for bacterial gene functions.

J Cell Biol, 2004 Jan 5, 164(1), 19 - 24 Epub 2003 Dec 29.
The Omp85 family of proteins is essential for outer membrane biogenesis in mitochondria and bacteria; Gentle I et al.; Integral proteins in the outer membrane of mitochondria control all aspects of organelle biogenesis, being required for protein import, mitochondrial fission, and, in metazoans, mitochondrial aspects of programmed cell death . How these integral proteins are assembled in the outer membrane had been unclear . In bacteria, Omp85 is an essential component of the protein insertion machinery, and we show that members of the Omp85 protein family are also found in eukaryotes ranging from plants to humans . In eukaryotes, Omp85 is present in the mitochondrial outer membrane . The gene encoding Omp85 is essential for cell viability in yeast, and conditional omp85 mutants have defects that arise from compromised insertion of integral proteins like voltage-dependent anion channel (VDAC) and components of the translocase in the outer membrane of mitochondria (TOM) complex into the mitochondrial outer membrane.

Crit Rev Biochem Mol Biol, 2003, 38(6), 471 - 95
Metabolism of inorganic N compounds by ammonia-oxidizing bacteria; Arp DJ et al.; Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite . Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations . Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron . Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies . Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria . NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction . NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains . Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow . Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.

Gut, 2004 Jan, 53(1), 91 - 8
Systemic antibodies towards mucosal bacteria in ulcerative colitis and Crohn's disease differentially activate the innate immune response; Furrie E et al.; BACKGROUND AND AIMS: The mucosa in ulcerative colitis (UC) is replete with antibody producing plasma B cells and polymorphonuclear leucocytes (PMN) . This combination of effector cells requires a crosslinking antigen to evoke an antibody driven PMN inflammatory response via their Fc receptors . The stimulus for activation is thought to be commensal bacteria colonising the gut mucosa . The aim of this investigation was to compare the principal culturable bacterial populations on the rectal mucosa of UC patients, and to determine whether specific antibodies towards these bacteria can activate infiltrating PMN through opsonisation . This would provide an explanation for this chronic inflammatory condition . METHODS: Bacteria colonising rectal tissue were characterised using chemotaxonomic techniques . Systemic antibody responses were measured against total antigens and surface antigens of these organisms in UC and Crohn's disease (CD) patients, together with healthy controls . Antibody enhancement of the respiratory burst in PMN was also investigated, against a range of mucosal isolates . RESULTS: Distinct differences were observed in some bacterial populations in UC biopsies, which were generally reflected in antibody responses towards these organisms . UC patients had higher IgG responses to surface antigens, primarily IgG1, whereas the response in CD was mainly IgG2 . Antibodies from UC patients greatly enhanced the respiratory burst in PMN, in response to individual bacterial species . CONCLUSIONS: Changes in mucosal bacteria, and a switch from internal to surface antigen/antibody reactivity of a predominantly IgG1 type, leads to greater opsonisation of the respiratory burst in PMN, providing a mechanism for maintaining the inflammatory state in UC.

FEMS Microbiol Lett, 2003 Dec 12, 229(2), 271 - 6
Detection and sequencing of the microcystin LR-degrading gene, mlrA, from new bacteria isolated from Japanese lakes; Saito T et al.; mlrA is the only microcystin-degrading gene detected in Sphingomonas sp . MJ-PV . The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database . We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2 . These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively . On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp . strains employing hemi-nested polymerase chain reaction detection using two primer sets . Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species . We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas.

Genome Res, 2004 Jan, 14(1), 44 - 53 Epub 2003 Dec 12.
Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids; Rispe C et al.; We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative . We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the genomic changes following symbiosis . We identified clear strand asymmetries, distribution biases (putative high-expression genes were found more often on the leading strand), and a residual slight codon bias within each strand . Amino acid usage was strongly biased in putative high-expression genes, characterized by avoidance of aromatic amino acids, but above all by greater conservation and resistance to AT enrichment . Despite the almost complete loss of codon bias and heavy mutational pressure, selective forces are still strong at nonsynonymous sites of a fraction of the genome . However, Buchnera from Baizongia pistaciae appears to have suffered a stronger symbiotic syndrome than the two other species.

Carbohydr Res, 2003 Nov 14, 338(23), 2491 - 502
Biosynthesis and assembly of Group 1 capsular polysaccharides in Escherichia coli and related extracellular polysaccharides in other bacteria; Whitfield C et al.; Extracellular and capsular polysaccharides (EPSs and CPSs) are produced by a wide range of bacteria, including important pathogens of humans, livestock, and plants . These polymers are major surface antigens and serve a variety of roles in virulence, depending on the biology of the producing organism . In addition to their importance in disease, some EPSs also have industrial applications as gelling and emulsifying agents . An understanding of the processes involved in the synthesis and regulation of CPSs and EPSs therefore potentially contributes to an understanding of the disease state, surface expression of protective antigens, and modulation of polymer structure to give defined physical properties . Escherichia coli has provided important model systems for EPS and CPS biosynthesis . Here we describe current knowledge concerning assembly of the Group 1 CPSs of E . coli and the conservation of similar mechanisms in other bacteria.

J Biol Inorg Chem, 2004 Mar, 9(2), 145 - 51 Epub 2003 Dec 11.
Incorporation of either molybdenum or tungsten into formate dehydrogenase from Desulfovibrio alaskensis NCIMB 13491; EPR assignment of the proximal iron-sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate-reducing bacteria; Brondino CD et al.; We report the characterization of the molecular properties and EPR studies of a new formate dehydrogenase (FDH) from the sulfate-reducing organism Desulfovibrio alaskensis NCIMB 13491 . FDHs are enzymes that catalyze the two-electron oxidation of formate to carbon dioxide in several aerobic and anaerobic organisms . D . alaskensis FDH is a heterodimeric protein with a molecular weight of 126+/-2 kDa composed of two subunits, alpha=93+/-3 kDa and beta=32+/-2 kDa, which contains 6+/-1 Fe/molecule, 0.4+/-0.1 Mo/molecule, 0.3+/-0.1 W/molecule, and 1.3+/-0.1 guanine monophosphate nucleotides . The UV-vis absorption spectrum of D . alaskensis FDH is typical of an iron-sulfur protein with a broad band around 400 nm . Variable-temperature EPR studies performed on reduced samples of D . alaskensis FDH showed the presence of signals associated with the different paramagnetic centers of D . alaskensis FDH . Three rhombic signals having g-values and relaxation behavior characteristic of {4Fe-4S} clusters were observed in the 5-40 K temperature range . Two EPR signals with all the g-values less than two, which accounted for less than 0.1 spin/protein, typical of mononuclear Mo(V) and W(V), respectively, were observed . The signal associated with the W(V) ion has a larger deviation from the free electron g-value, as expected for tungsten in a d(1) configuration, albeit with an unusual relaxation behavior . The EPR parameters of the Mo(V) signal are within the range of values typically found for the slow-type signal observed in several Mo-containing proteins belonging to the xanthine oxidase family of enzymes . Mo(V) resonances are split at temperatures below 50 K by magnetic coupling with one of the Fe/S clusters . The analysis of the inter-center magnetic interaction allowed us to assign the EPR-distinguishable iron-sulfur clusters with those seen in the crystal structure of a homologous enzyme.

Dermatology, 2003, 207(4), 362 - 6
Bacteria ingestion by blowfly larvae: an in vitro study; Lerch K et al.; BACKGROUND: Maggot debridement therapy is the medical use of live fly larvae for cleaning chronic and infected wounds, removing devitalized tissue and decreasing the risk of infection . Maggot-derived proteins are able to kill bacteria, and proteolytic enzymes are responsible for the liquefying of necrotic tissue . OBJECTIVE: The aim of this study is to investigate bacterial ingestion by larvae roaming free on bacterial agar, compared to those larvae contained within vinyl bags . METHODS: Free-roaming sterile larvae of Lucilla sericata and larvae contained in vinyl bags were fed on Escherichia coli producing green fluorescent protein (GFP) . The time interval to the onset of fluorescent maggots was determined . At different time intervals, maggots were sacrificed, washed in sterile saline, sagittally cut in frozen sections and examined under a microscope with UV light . RESULTS: After feeding on GFP-labelled E . coli, maggots roaming free on bacterial lawn agar demonstrated fluorescence after 3 min, maggots entrapped in vinyl bags after 25 min . In the sagittal frozen sections, the highest fluorescent intensity was detected in the larvae's rostral part of the alimentary tract, the crop and the anterior midgut . CONCLUSION: In an in vitro setting, digestion and ingestion of whole or disintegrated bacteria is accomplished within minutes . The vinyl bag's permeable membrane clearly causes a delay of this process .

Int J Syst Evol Microbiol, 2003 Nov, 53(Pt 6), 1893 - 900
Gene sequences useful for predicting relatedness of whole genomes in bacteria; Zeigler DR; Thirty-two protein-encoding genes that are distributed widely among bacterial genomes were tested for the potential usefulness of their DNA sequences in assigning bacterial strains to species . From publicly available data, it was possible to make 49 pairwise comparisons of whole bacterial genomes that were related at the genus or subgenus level . DNA sequence identity scores for eight of the genes correlated strongly with overall sequence identity scores for the genome pairs . Even single-gene alignments could predict overall genome relatedness with a high degree of precision and accuracy . Predictions could be refined further by including two or three genes in the analysis . The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.

Environ Microbiol, 2003 Nov, 5(11), 1064 - 70
Effect of growth temperature on cellular fatty acids in sulphate-reducing bacteria; Konneke M et al.; The effect of growth temperature on the cellular fatty acid composition of sulphate-reducing bacteria (SRB) was studied in 12 species belonging to eight genera including psychrophiles and mesophiles . Most of these species were of marine origin . The investigated SRB with the exception of four Desulfobacter species exhibited only a minor increase in the proportion of cis-unsaturated fatty acids (by < or = 5% per 10 degrees C) when the growth temperature was decreased; psychrophiles maintained their typically high content of cis-unsaturated fatty acids (around 75% of total fatty acids) nearly constant . The four Desulfobacter species, however, increased the proportion of cis-unsaturated among total fatty acids significantly (by > or =14% per 10 degrees C; measured in late growth phase) with decreasing growth temperature . The ratio between unsaturated and saturated fatty acids in Desulfobacter species changed not only with the growth temperature, but also with the growth state in batch cultures at constant temperature . Changes of cellular fatty acids were studied in detail with D . hydrogenophilus, the most psychrotolerant (growth range 0-35 degrees C) among the mesophilic SRB examined . Desulfobacter hydrogenophilus also formed cis-9,10-methylenehexadecanoic acid (a cyclopropane fatty acid) and 10-methylhexadecanoic acid . At low growth temperature (12 degrees C), the relative amount of these fatty acids was at least threefold lower; this questions the usefulness of 10-methylhexadecanoic acid as a reliable biomarker of Desulfobacter in cold sediments.

J Leukoc Biol, 2004 Feb, 75(2), 240 - 3 Epub 2003 Nov 21.
Rapid and extensive membrane reorganization by dendritic cells following exposure to bacteria revealed by high-resolution imaging; Salter RD et al.; Using live cell imaging, we demonstrate that immature dendritic cells (DC) derived from human peripheral blood monocytes undergo pronounced morphologic changes in vitro within minutes of exposure to unopsonized Escherichia coli, developing extensive membrane veils that efficiently capture additional bacteria . Internalization does not occur in the veils, but instead, bacteria are transported to the central region of the cell, where they sink directly into the plasma membrane . In contrast, exposure to polystyrene beads does not induce notable changes in cell morphology, and DC do not efficiently capture beads when introduced alone or mixed with bacteria . Long dendritic processes were also visualized in some cells that allowed capture of clumps of bacteria at a distance of more than 100 microm . These results demonstrate that immature DC can distinguish between inert particles and bacteria and alter their shape and phagocytic capacity in response to the latter.

FEBS Lett, 2003 Nov 27, 555(1), 35 - 9
The structural basis of light-harvesting in purple bacteria; Cogdell RJ et al.; A typical purple bacterial photosynthetic unit consists of two types of light-harvesting complex (LH1 and LH2) together with a reaction centre . This short review presents a description of the structure of the LH2 complex from Rhodopseudomonas acidophila, which has recently been improved to a resolution of 2.0 A {Papiz et al., J . Mol . Biol . 326 (2003) 1523-1538} . We show how this structure has helped to reveal the details of the various excitation energy transfer events in which it is involved.

J Reprod Med, 2003 Oct, 48(10), 775 - 9
Prevalence of Mycoplasma bacteria in amniotic fluid at the time of genetic amniocentesis using the polymerase chain reaction; Markenson GR et al.; OBJECTIVE: To use the polymerase chain reaction (PCR) to detect the presence of bacteria and Mycoplasma in amniotic fluid at the time of genetic amniocentesis and to assess their relationship to amniotic fluid interleukin-6 (IL-6) concentration and preterm delivery . STUDY DESIGN: A prospective study was performed on 78 asymptomatic pregnancies presenting for genetic amniocentesis . Amniotic fluid samples were analyzed by PCR for the detection of bacterial 16S ribosomal RNA, by PCR/enzyme-linked immunosorbent assay (ELISA) for Mycoplasma and by ELISA analysis for IL-6 concentration . RESULTS: All 78 samples were analyzed, and bacterial RNA was detected in 18% of them . However, no sample tested positive for Mycoplasma . The mean IL-6 concentration was 435 pg/mL . There was no difference in IL-6 levels or gestational age between bacteria-positive and -negative groups . CONCLUSION: Amniotic fluid may not be sterile in the midtrimester, yet the presence of bacteria, as detected by PCR, does not always result in an inflammatory response or adverse perinatal outcome.

J Math Biol, 2003 Dec, 47(6), 518 - 46 Epub 2003 Jun 12.
Cell balance equation for chemotactic bacteria with a biphasic tumbling frequency; Chen KC et al.; Alt's three-dimensional cell balance equation characterizing the chemotactic bacteria was analyzed under the presence of one-dimensional spatial chemoattractant gradients . Our work differs from that of others who have developed rather general models for chemotaxis in the use of a non-smooth anisotropic tumbling frequency function that responds biphasically to the combined temporal and spatial chemoattractant gradients . General three-dimensional expressions for the bacterial transport parameters were derived for chemotactic bacteria, followed by a perturbation analysis under the planar geometry . The bacterial random motility and chemotaxis were summarized by a motility tensor and a chemotactic velocity vector, respectively . The consequence of invoking the diffusion-approximation assumption and using intrinsic one-dimensional models with modified cellular swimming speeds was investigated by numerical simulations . Characterizing the bacterial random orientation after tumbles by a turn angle probability distribution function, we found that only the first-order angular moment of this turn angle probability distribution is important in influencing the bacterial long-term transport.

J Biol Chem, 2004 Feb 20, 279(8), 6385 - 94 Epub 2003 Nov 14.
Aerobic and anaerobic Mg-protoporphyrin monomethyl ester cyclases in purple bacteria: a strategy adopted to bypass the repressive oxygen control system; Ouchane S et al.; Two different mechanisms for Mg-protoporphyrin monomethyl ester (MgPMe) cyclization are shown to coexist in Rubrivivax gelatinosus and are proposed to be conserved in all facultative aerobic phototrophs: an anaerobic mechanism active under photosynthesis or low oxygenation, and an aerobic mechanism active only under high oxygenation conditions . This was confirmed by analyzing the bacteriochlorophyll accumulation in the wild type and in three mutant strains grown under low or high aeration . A mutant lacking the acsF gene is photosynthetic, exhibits normal bacteriochlorophyll accumulation under low oxygenation and anaerobiosis, and accumulates MgPMe under high oxygenation . The photosynthesis-deficient bchE mutant produces bacteriochlorophyll only under high oxygenation and accumulates MgPMe under low oxygenation and anaerobiosis . The double knockout mutant is devoid of photosystem and accumulates MgPMe under both conditions indicating the involvement of the two enzymes at the same step of the biosynthesis pathway . Oxygen-mediated expression of bchE was studied in the wild type and in a regulatory mutant . The reverse transcriptase-PCR and the bchE promoter activity results demonstrate that the expression of the bchE gene is oxygen-independent and suggest that it is rather the enzyme activity that should be oxygen-sensitive . No obvious sequence similarities were found between oxygen-dependent AcsF and the oxygen-independent anaerobic Mg-protoporphyrin monomethylester cyclase (BchE) enzymes . However, common to all BchE proteins is the conserved CXXX-CXXC sequence . This motif is essential for 4Fe-4S cluster formation in many anaerobic enzymes . Expression and purification of BchE were achieved, and the UV-visible spectral analyses confirmed the presence of an active 4Fe-4S cluster in this protein . The use of different classes of enzymes catalyzing the same reaction under different oxygen growth conditions appears to be a common feature of different biosynthetic pathways, and the benefit of possessing both aerobic and anaerobic systems is discussed.

Electrophoresis, 2003 Nov, 24(21), 3815 - 20
Hybrid microdevice electrophoresis of peptides, proteins, DNA, viruses, and bacteria in various separation media, using UV-detection; Vegvari A et al.; Recently we described the design of a hybrid microdevice for micro(nano)electrophoresis and electrochromatography, discussed its advantages and disadvantages compared to conventional microdevices and presented a few applications with low-molecular-weight samples . In this paper, we demonstrate the broad application range of this device using UV-based analyses of (i) peptides by free-zone electrophoresis and electrophoresis in a recently introduced gel (polyacrylamide cross-linked with allyl-beta-cyclodextrin), (ii) proteins by electrophoretic molecular-sieving in a polymer solution supplemented with SDS, (iii) DNA fragments by electrophoresis in the above gel, (iv) virus particles in this gel, as well as in free buffer and (v) bacteria in free buffer . To illustrate the advantages of the hybrid microdevice we can mention that electrophoresis of proteins in a polymer-containing buffer, supplemented with sodium dodecyl sulfate (SDS), in a 4.30 (2.75) cm long channel gave a resolution similar to that in conventional capillary electrophoresis in a 23.5 (18.6) cm long capillary and analysis times which were 15-fold shorter.

J Microbiol Methods, 2003 Dec, 55(3), 801 - 5
Use of 3-hydroxyphenylacetylene for activity-dependent, fluorescent labeling of bacteria that degrade toluene via 3-methylcatechol; Kauffman ME et al.; 3-hydroxyphenylacetylene (3-HPA) served as a novel, activity-dependent, fluorogenic and chromogenic probe for bacterial enzymes known to degrade toluene via meta ring fission of the intermediate, 3-methylcatechol . By this direct physiological analysis, cells grown with an aromatic substrate to induce the synthesis of toluene-degrading enzymes were fluorescently labeled.

J Microbiol Methods, 2003 Dec, 55(3), 697 - 708
Amplified functional DNA restriction analysis to determine catechol 2,3-dioxygenase gene diversity in soil bacteria; Junca H et al.; To determine phylogenetic diversity of a functional gene from strain collections or environmental DNA amplifications, new and fast methods are required . Catechol 2,3-dioxygenase (C23O) subfamily I.2.A genes, known to be of crucial importance for aromatic degradation, were used as a model to adapt the amplified ribosomal DNA restriction analysis to functional genes . Sequence data of C23O genes from 13 reference strains, representing the main branches of the C23O family I.2.A phylogeny, were used for simulation of theoretical restriction patterns . Among other restriction enzymes, Sau3A1 theoretically produce characteristic profiles from each subfamily I.2.A member and their similarities reassembled the main divergent branches of C23O gene phylogeny . This enzyme was used to perform an amplified functional DNA restriction analysis (AFDRA) on C23O genes of reference strains and 19 isolates . Cluster analyses of the restriction fragment profiles obtained from isolates showed patterns with distinct similarities to the reference strain profiles, allowing to distinguish four different groups . Sequences of PCR fragments from isolates were in close agreement with the phylogenetic correlations predicted with the AFDRA approach . AFDRA thus provided a quick assessment of C23O diversity in a strain collection and insights of its gene phylogeny affiliation among known family members . It cannot only be easily applied to a vast number of isolates but also to define the predominant polymorphism of a functional gene present in environmental DNA extracts . This approach may be useful to differentiate functional genes also for many other gene families.

Surgery, 2003 Oct, 134(4), 574 - 80; discussion 580-1
Enterocyte apoptosis and barrier function are modulated by SIgA after exposure to bacteria and hypoxia/reoxygenation; Diebel LN et al.; BACKGROUND: Secretory immunoglobulin A (SIgA) is the principal immune defense against luminal pathogens at gut mucosal surfaces . It also has anti-inflammatory activities that may be important for the maintenance of mucosal surface integrity . Enterocyte apoptosis (Apo) is increased after challenge with invasive bacteria and ischemia-reperfusion insults . Increased Apo also has been associated with impaired intestinal barrier function . However, the impact of SIgA on enterocyte apoptosis and mucosal barrier integrity after challenge with commensal bacteria and ischemia-reperfusion is unknown . METHODS: Caco2 intestinal epithelial cell monolayers were subjected to 21% O(2) (control) or 95% N(2)/15% CO(2) (hypoxic) conditions for 90 minutes, followed by 21% O(2) . Escherichia coli and SIgA were added in subsets . Caco2 cell Apo was identified by flow cytometry and barrier function indexed by permeability to dextran-fluorescein isothiocyanate . RESULTS: There were no differences in the percentage of Apo Caco2 cells after exposure to either bacteria or hypoxic-reoxygenation versus control . There was a significant increase in Apo after the combined bacteria/hypoxia-reoxygenation challenge . SIgA abrogated the Apo response and preserved barrier function after this combined challenge . CONCLUSION: Modulation of enterocyte Apo by SIgA may serve to maintain intestinal barrier function and thereby decrease the systemic inflammatory response after clinical conditions associated with gut ischemia-reperfusion insults.

Zhongguo Wei Zhong Bing Ji Jiu Yi Xue, 2003 Nov, 15(11), 666 - 8
{Prospective study of systemic inflammatory response syndrome of patients with nosocomial G- bacteria infection}; Dong CM et al.; OBJECTIVE: To study the characteristics of systemic inflammatory response syndrome (SIRS) of inpatients with nosocomial G- bacteria infection in order to find on effective treatment . METHODS: Eighty-two inpatients of SIRS with lower respiratory tract infection with G- bacteria were studied prospectively until discharge or death . They were divided into two groups: observation group (42 cases) and control group (40 cases) . Bacteria culture of sputum and drug sensitivity was performed . Routine treatment was carried out in the control group, and rhubarb and antibiotics with lower endotoxin releasing property were given to the observation group . The course of SIRS, the incidence of MODS, and the mortality were compared . RESULTS: The duration with SIRS in observation group and control group was respectively (6.2+/-1.3) days and (7.4+/-1.2) days, u=3.91, P<0.05; the incidence of MODS was 11.4 percent and 32.3 percent, respectively, chi(2)=4.27, P<0.05 . The mortality rates of the patients with SIRS in two groups were 8.6 percent and 29.0 percent, respectively . CONCLUSION: The results indicated that the treatment with rhubarb could obviously reduce the duration of SIRS compared with routine method . The same is true in the incidence of MODS and mortality rate.

Prog Nucleic Acid Res Mol Biol, 2003, 75, 293 - 320
The roles and regulation of potassium in bacteria; Epstein W; Potassium is the major intracellular cation in bacteria as well as in eucaryotic cells . Bacteria accumulate K+ by a number of different transport systems that vary in kinetics, energy coupling, and regulation . The Trk and Kdp systems of enteric organisms have been well studied and are found in many distantly related species . The Ktr system, resembling Trk in many ways, is also found in many bacteria . In most species two or more independent saturable K(+)-transport systems are present . The KefB and KefC type of system that is activated by treatment of cells with toxic electrophiles is the only specific K(+)-efflux system that has been well characterized . Pressure-activated channels of at least three types are found in bacteria; these represent nonspecific paths of efflux when turgor pressure is dangerously high . A close homolog of eucaryotic K+ channels is found in many bacteria, but its role remains obscure . K+ transporters are regulated both by ion concentrations and turgor . A very general property is activation of K+ uptake by an increase in medium osmolarity . This response is modulated by both internal and external concentrations of K+ . Kdp is the only K(+)-transport system whose expression is regulated by environmental conditions . Decrease in turgor pressure and/or reduction in external K+ rapidly increase expression of Kdp . The signal created by these changes, inferred to be reduced turgor, is transmitted by the KdpD sensor kinase to the KdpE-response regulator that in turn stimulates transcription of the kdp genes . K+ acts as a cytoplasmic-signaling molecule, activating and/or inducing enzymes and transport systems that allow the cell to adapt to elevated osmolarity . The signal could be ionic strength or specifically K+ . This signaling response is probably mediated by a direct sensing of internal ionic strength by each particular system and not by a component or system that coordinates this response by different systems to elevated K+.

Appl Environ Microbiol, 2003 Nov, 69(11), 6703 - 14
Diversity and activity of methanotrophic bacteria in different upland soils; Knief C et al.; Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB) . MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase . MB commonly detected in soils were closely related to Methylocaldum spp., Methylosinus spp., Methylocystis spp., or the "forest sequence cluster" (USC alpha), which has previously been detected in upland soils and is related to pmoA sequences of type II MB (Alphaproteobacteria) . As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected . This novel "upland soil cluster gamma" (USC gamma) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils . To identify active MB, four selected soils were incubated with (13)CH(4) at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry . Incorporation of (13)C into PLFAs characteristic for methanotrophic Gammaproteobacteria was observed in all soils in which USC gamma sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs . A pattern of labeled PLFAs typical for methanotrophic Alphaproteobacteria was obtained for a sample in which only USC alpha sequences were detected . The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.

Appl Opt, 2003 Oct 20, 42(30), 6184 - 91
Detection of bacteria by time-resolved laser-induced breakdown spectroscopy; Morel S et al.; A laser-induced breakdown spectroscopy technique for analyzing biological matter for the detection of biological hazards is investigated . Eight species were considered in our experiment: six bacteria and two pollens in pellet form . The experimental setup is described, then a cumulative intensity ratio is proposed as a quantitative criterion because of its linearity and reproducibility . Time-resolved laser-induced breakdown spectroscopy (TRELIBS) exhibits a good ability to differentiate among all these species, whatever the culture medium, the species or the strain . Thus we expect that TRELIBS will be a good candidate for a sensor of hazards either on surfaces or in ambient air.

Ying Yong Sheng Tai Xue Bao, 2003 Jul, 14(7), 1161 - 4
{Effects of marine bacteria on the growth and toxin production of red-tide algae under different pH and salinities}; Su J et al.; The effects of strain S10 isolated from sediments of Xiamen Western Sea Area on the growth and paralytic shellfish poison (PSP) production of Alexandrium tamarense at different pH and salinities were studied . The results showed that the alga grew well at pH 6-8 and at salinity of 20-34 . The toxicity of A . tamarense varied markedly at different pH and salinities: it decreased with increasing pH, while increased with salinity and reached its peak value at the salinity of 30, and then declined . The strain S10 inhibited the growth and the PSP production of A . tamarense at different pH and salinities . It had the best inhibitory function on the growth of A . tamarense at pH 7 and salinity of 34 . The best inhibitory function on the PSP production of A . tamarense was at pH 7, but this inhibitory function was not related to salinity.

Astrobiology, 2003 Summer, 3(2), 263 - 70
Magnetotactic bacteria on Earth and on Mars; McKay CP et al.; Continued interest in the possibility of evidence for life in the ALH84001 Martian meteorite has focused on the magnetite crystals . This review is structured around three related questions: is the magnetite in ALH84001 of biological or non-biological origin, or a mixture of both? does magnetite on Earth provide insight to the plausibility of biogenic magnetite on Mars? could magnetotaxis have developed on Mars? There are credible arguments for both the biological and non-biological origin of the magnetite in ALH84001, and we suggest that more studies of ALH84001, extensive laboratory simulations of non-biological magnetite formation, as well as further studies of magnetotactic bacteria on Earth will be required to further address this question . Magnetite grains produced by bacteria could provide one of the few inorganic traces of past bacterial life on Mars that could be recovered from surface soils and sediments . If there was biogenic magnetite on Mars in sufficient abundance to leave fossil remains in the volcanic rocks of ALH84001, then it is likely that better-preserved magnetite will be found in sedimentary deposits on Mars . Deposits in ancient lakebeds could contain well-preserved chains of magnetite clearly indicating a biogenic origin.

Lipids, 2003 Aug, 38(8), 885 - 7
Phospholipid FA of piezophilic bacteria from the deep sea; Fang J et al.; Phospholipid FA (PLFA) profiles were determined on four piezophilic bacteria from the deep sea: Moritella japonica DSK1, Shewanella violacea DSS12, S . benthica DB6705, and S . benthica DB21MT-2 . The total concentrations of PLFA were higher in strains grown at low pressure (DSK1, 10 MPa, 27.0 mg/g dry wt cells; DSS12, 50 MPa, 24.0 mg/g), and lower in strains grown at high pressure (DB6705, 85 MPa, 1.9 mg/g; DB21MT-2, 100 MPa, 3.0 mg/g) . The piezophilic bacteria were characterized by a high abundance of unsaturated FA (62-73% of total FA) . In particular, PUFA were detected in all piezophiles examined . Moritella japonica DSK1 produced 22:6n-3 (DHA), whereas the three Shewanella strains produced 20:5n-3 (EPA) with trace amounts of DHA . The detection of low levels of the medium-chain-length PUFA 18:2n-6 and 18:3 (DSK1) and 20:2 (DB6705 and DB21MT-2) suggests that the biosynthesis of EPA and DHA may be regulated by the formation and desaturation of di- and tri-unsaturated FA.

Ukr Biokhim Zh, 2003 Mar-Apr, 75(2), 94 - 8
{Effect of surface-active substances on bioluminescence intensity of bacteria}; Katsev AM et al.; The study of sensitivity of luminous bacteria isolated from the Black and Azov seas to surfactants from various classes was carried out . It was shown that cationic surfactants had a strong inhibition effect on bacterial luminescence in contrast to anionic and in particular nonionic surfactants . To increase the luminous bacteria sensitivity to the action of OP-10 (nonionic surfactant) and ABS (anionic surfactant), which are widely used in industry, several approaches have been developed . They include modulation of bacterial sensitivity by the additives of cationic substances, use of luminous bacteria at a logarithmic stage of growth, realization of biotesting at low pH = 5.5 . The use of these approaches allows to lower effective concentrations of OP-10 and ABS, which caused a decrease of bioluminescence by 50%, 3-200 times and opens perspectives for the use of the bioluminescent method to study these surfactants toxicity on the principle of biosensorics.

Ukr Biokhim Zh, 2003 May-Jun, 75(3), 99 - 103
{Effect of mycotoxin T-2 on bioluminescence intensity of bacteria}; Katsev AM et al.; The acute and chronic toxicity of T-2 was studied by bioluminescent method with the use of two strains of luminous bacteria--P . phosphorum Sq3 u V . fischeri F1 as biological objects . It was shown that in acute experiments after 10 min incubation of bacteria in the presence of T-2 the bioluminescence inhibition on the 50% level was observed at the toxin concentration equal to 12 mg/mL . In chronic experiments such a level of bioluminescence inhibition was registered after 16 hours incubation at the toxin concentration of 18 mg/mL . T-2 toxicity was also investigated in the presence of different serum albumin concentrations . It decreases with the increase of albumin concentration at the short term of incubation (5 min) of the mixture to be analyzed . In case of the longer term of incubation (up to 30 min) of this mixture T-2 toxicity was restored . Probably, it is a result of destruction of protein-toxin complex, which is, evidently, reversible and may be characterized by some index . It is necessary to emphasize that the sensitivity of T-2 analysis increases under the decrease of pH value up to lower bacterial physiological level, i.e . to 5-5.5 . The revealed abilities of T-2 toxin effect on the intensity of bacterial bioluminescence may be used under the development of instrumental analytical approach on the basis of biosensor technology for testing this toxin in the environment . Taking into account the analysis simplicity and rapidity, such analytical device may have a perspective for wide practical application.

Curr Opin Microbiol, 2003 Oct, 6(5), 482 - 9
Identifying global regulators in transcriptional regulatory networks in bacteria; Martinez-Antonio A et al.; The machinery for cells to take decisions, when environmental conditions change, includes protein-DNA interactions defined by transcriptional factors and their targets around promoters . Properties of global regulators are revised attempting to reach diagnostic explicit criteria for their definition and eventual future computational identification . These include among others, the number of regulated genes, the number and type of co-regulators, the different sigma-classes of promoters and the number of transcriptional factors they regulate, the size of the evolutionary family they belong to, and the variety of conditions where they exert their control . As a consequence, global versus local regulation can be identified, as shown for Escherichia coli and eventually in other genomes.

J Food Prot, 2003 Oct, 66(10), 1935 - 48
Methods for rapid separation and concentration of bacteria in food that bypass time-consuming cultural enrichment; Benoit PW et al.; The rapid detection of pathogenic organisms that cause foodborne illnesses is needed to insure food safety . Conventional methods for the detection of pathogens in foods are time-consuming and labor-intensive . New advanced rapid methods (i.e., polymerase chain reaction, DNA probes) are more sensitive and selective than conventional techniques, but many of these tests are inhibited by food components, rendering them dependent on slow cultural enrichment . The need for alternative methods that will rapidly separate and concentrate bacteria directly from food samples, thereby reducing the time required for these new rapid detection techniques, is evident . Separation and concentration methods extract target bacteria from interfering food components and/or concentrate bacteria to detectable levels . This review describes several methods used to separate and/or concentrate bacteria in food samples . Several methods discussed here, including centrifugation and immunomagnetic separation, have been successfully used, individually and in combination, to rapidly separate and/or concentrate bacteria from food samples in less time than is required for cultural enrichment.

Biotechnol Lett, 2003 Sep, 25(18), 1563 - 9
Molecular detection and direct enumeration of methanogenic Archaea and methanotrophic Bacteria in domestic solid waste landfill soils; Chen AC et al.; Methane oxidizing and producing activities of cover soil (10, 30 cm depth) and burial waste (1, 3 m depth) were evaluated: top cover soil (10 cm) had the highest methane oxidizing activity, while 1 m depth buried waste showed the highest methane producing potential . All the sequences of the 1 m sample were found to be closely related to 16S rDNAs of mainly hydrogenotrophic methanogens known, such as genera Methanosarcina, Methanoculleus, and Methanobacterium . We developed a modified fluorescence in situ hybridization (FISH) direct counting method for landfill samples, resulting in the detection of approx . 1% of total cells as archaeal cells (presumably methanogens) . However, probe-positive cells could not be found with probes for methanotrophs by the methods.

Biodegradation, 2003 Oct, 14(5), 347 - 55
Effective bead preparation of coimmobilized methanogenic and methanotrophic bacteria for tetrachloroethene degradation; Sung-In Y et al.; Three types of coimmobilized methanogenic and methanotrophic bacterial beads--Ca-alginate, Ba-alginate, and Ca-alginate chitosan--were used for tetrachloroethene (PCE) degradation . For the purpose of effective preparation of coimmobilized bacterial beads, the diameter and broken-loading of beads were measured . The activity tests to find the optimal bacteria concentration in the bead were performed . It was found that Ba-alginate beads had superiority in bacterial growth and the degree of strength of beads from the diameter and broken-loading tests . Also, it was shown that it is most effective to add 200 mL of methanogens into 500 mL of 2% alginate solution and 20 mL of methanotrophs into 500 mL to 2% alginate solution . When methanogens and methanotrophs were applied with the Ba-alginate bead in the actual dechlorination of PCE, the biological PCE dechlorination rate was 92%, and there was highly effective degradation of PCE based on the coimmobilized bead . Additionally, relation to the diameter (X) and broken-loading (Y) of the Ba-alginate bead was derived following equation, Y = 438.02 exp(-1.4815 X).

J Exp Med, 2003 Oct 20, 198(8), 1253 - 63
Lipopolysaccharide or whole bacteria block the conversion of inflammatory monocytes into dendritic cells in vivo; Rotta G et al.; Monocytes can develop into dendritic cells (DCs) that migrate to lymph nodes (LNs) and present antigens to T cells . However, we find that this differentiation is blocked when monocytes accumulate subcutaneously in response to bacteria or lipopolysaccharide (LPS) . The inhibition of DC differentiation is mediated by the bacteria and in conjunction with inflammatory cells recruited at the site of injection . Inhibition of migratory DC development was reversed in Toll-like receptor (TLR)4-mutated mice when LPS, but not whole bacteria, was injected, suggesting that TLR4 is one but not the only mediator of the inhibition . The block imposed by bacteria was partly relieved by the absence of interleukin (IL)-12 p40, but not by individual absence of several cytokines involved in DC differentiation or in inflammation, i.e., IL-6, IL-10, IL-12 p35, and interferon gamma . Consistent with the inability of monocytes to yield migrating DCs, and the finding that other DCs had limited access to particulate or bacterial antigens, these antigens were weakly presented to T cells in the draining LN . These results illustrate that bacteria-associated signals can have a negative regulatory role on adaptive immunity and that local innate responses for containment of infectious bacteria can at least initially supersede development of adaptive responses.

Zh Mikrobiol Epidemiol Immunobiol, 2003 Sep-Oct, (5), 121 - 6
{Acidic stress in bacteria}; Basnak'ian IA; Information on acidic stress in bacteria, studied not only on the phenomenological, but also molecular and genetic levels, are systematized . Acidic stress in bacteria, appearing as the result of the acidification of the medium, is characterized by many events on the level of gene regulation . An increased expression of some genes and a decreased expression of others result in growth deceleration, quantitative and qualitative changes in the synthesis of proteins . Some of the newly synthesized proteins ensure the survival of bacteria in a medium with higher acidity and their protection from other stresses . The applied importance of acidic stress is relevant to some aspects of biotechnology, immunobiology and medicine.

Pediatr Surg Int, 2003 Dec, 19(11), 699 - 702 Epub 2003 Oct 15.
Bacteria ascend to liver from the bilioenteric conduit after choledochojejunostomy in the cholestatic rat; Hsieh CS et al.; The high incidence of postoperative cholangitis in children with clinical restoration of bile flow after Roux-Y choledochojejunostomy (RYCJ) assumed the concept of a direct ascending cholangitis caused by pathogens in the intestine, into the intrahepatic bile duct via the porta hepatis . It is also well known that jaundiced animals (patients) are more susceptible to infections of the bile ducts following the procedure of bilioenteric anastomosis . An animal experiment was conducted to compare quantitative bacterial cultures of the choledochojejunostomy area and the liver 24 hours after Escherichia coli (ATCC 25922) or sterile normal saline was injected into the bilioenteric conduit (BEC), following RYCJ in rats with or without the proceeding bile duct ligation . A significant increase of E . coli of the same strain (ATCC 25922), that we injected into the BEC, was proved with pulse-field gel electrophoresis (PFGE) and shown in the liver of the jaundiced rats receiving E . coli (ATCC 25922), compared to that in the nonjaundiced rats with normal saline treatment . It is concluded that bacteria often ascend early to the liver from the BEC following RYCJ . This ascending cholangitis model might be produced for further studies.

Naturwissenschaften, 2003 Oct, 90(10), 449 - 51 Epub 2003 Aug 23.
Transmission of ice-nucleating active bacteria from a prey reduces cold hardiness of a predator (Araneae: Theridiidae); Tanaka K et al.; The influence of ice-nucleating active (INA) bacteria on cold hardiness of the house spider, Achaearanea tepidariorum, was determined by measuring the supercooling point (SCP) of hatchlings given either INA-bacteria-fed or bacteria-free prey (Drosophila melanogaster) . Spiders that had eaten INA-bacteria-fed flies showed higher SCPs than those fed on bacteria-free flies . Through feeding, INA bacteria in the prey reduce the cold hardiness of spiders . This fact should be taken into account before using INA agents as a means of pest management.

Dtsch Tierarztl Wochenschr, 2003 Sep, 110(9), 394 - 7
{Total count of bacteria in the air of three different laying hen housing systems}; Saleh M et al.; Bacteria in the air of animal housing is assumed to have an impact on the health of the humans and the animals in them and on the environment . The bacterial count in poultry housing systems is particularly high in comparison to those of pigs and cattle . Little is known about the bacteria in the air of new laying hen housing systems . We therefore made simple, simultaneous measurements in the air of three different systems (enriched cages, AK; conventional battery cages, BK; aviary, VOL), in the unheated scratching area of the VOL, and in the outside air over a period of one year (24-h samples were taken about once a month using polycarbonate filters) in order to determine the general bacterial count (using blood agar) . The highest concentrations of bacteria were found all year long in the VOL, followed by the BK and the AK . In the VOL, there were on average 2.16 and 0.56 x 10(6) colony forming units (cfu)/m3 in the winter and summer, respectively; 0.25 and 0.38 in the BK; and 0.39 and 0.12 in the AK . These preliminary results show that air quality considerations should be included in the development and implementation of new housing systems, as should the impact on the respiratory system of the humans and animals in them and on the environment, because high concentrations of air contamination in the housing generally also lead to high emissions into the vicinity of the facility, the significance of which cannot always be estimated, as has recently been shown for antibiotics in the exhaust air from animal housing.

Appl Microbiol Biotechnol, 2004 Feb, 63(5), 520 - 6 Epub 2003 Oct 11.
Collagenolytic proteases from bacteria; Watanabe K; Collagen degradation occurs during various physiological and pathological conditions . However, only a limited number of proteases with unique characteristics can trigger collagen degradation . Until recently, practical applications of collagenolytic proteases from bacteria had not been considered because their functions in bacteria are closely related to pathogenicity . However, bacterial collagenolytic proteases have many interesting and useful features . This review focuses on the collagenolytic proteases from bacteria, in particular their molecular properties and practical applications.

Biotechnol Adv, 1993, 11(2), 199 - 217
Protoplast fusion: a tool for intergeneric gene transfer in bacteria; Gokhale DV et al.; Protoplasts can be isolated from bacterial cells by digestion of the cell wall with the help of lysozyme in presence of osmotic stabilizers . Fusion of protoplasts can be induced by chemical fusogens like polyethylene glycol . The electrofusion technique has been reported in bacteria in which the fusion frequency is much higher than that obtained by PEG induced protoplast fusion . This technology allows recombination to take place not only between related species but also between unrelated genera and is of great potential in the breeding and improvement of industrial strains . This review includes the information and developments on the protoplast fusion in bacteria with special reference to genetic recombination by protoplast fusion between phylogenetically unrelated bacteria.

Biotechnol Adv, 1988, 6(2), 135 - 50
Monoclonal antibodies against bacteria; Macario AJ et al.; Highlights are presented of most recent work in which monoclonal antibodies have been instrumental in the study of bacteria and their products . Topics summarized pertain to human and veterinary medicines, dentistry, phytopathology, ichthyology, and bacterial ecophysiology, differentiation, evolution and methanogenic biotechnology.

J Vet Diagn Invest, 2003 Sep, 15(5), 465 - 9
16S ribosomal RNA sequence-based identification of veterinary clinical bacteria; Cai H et al.; This study evaluated 16S rRNA gene sequence analysis methods as tools for identification of 22 phenotypically difficult to identify veterinary clinical bacterial isolates in a veterinary diagnostic laboratory . The study compared 16S rRNA gene sequencing and conventional phenotypic identification methods . Using 16S rRNA full-gene sequencing, 95% (21/22) of the isolates were identified to the genus level and 86% (19/22) to the species level . The conventional or commercially available manual identification phenotypic characterization methods presumptively identified 91% (20/22) of the isolates to the genus level and 1 isolate to the species level . However, only 55% (12/22) or 4.5% (1/22) of the phenotypic identifications were correct at the genus or species level when they were compared with the 16S rRNA full-gene sequencing . This study also compared 16S rRNA full-gene and partial-gene sequencing . The results demonstrated that the best 16S rRNA gene-sequencing approach is full-gene sequencing because it gives the most precise species identification . Sequencing of the variable regions 1, 2, and 3 of the 16S rRNA gene could be used for tentative identification because the ability of this sequencing to identify bacteria to the genus level is similar to that of the 16S rRNA full-gene sequencing . This method identified only 14% (3/22) isolates differently to the species level compared with the 16S rRNA full gene sequence . Sequencing of the variable regions 7, 8, and 9 is not recommended because it gives more ambiguous identifications . The cost of a 16S RNA full-gene-sequencing analysis was Can 160 dollars and Can 60 dollars for a partial 16S rRNA gene sequence, i.e., sequencing of variable regions 1, 2, and 3 or variable regions 7, 8 and 9.

Antonie Van Leeuwenhoek, 2003, 84(2), 99 - 107
Differential pulse polarography: a method for the direct study of biosorption of metal ions by live bacteria from mixed metal solutions; Savvaidis I et al.; The technique of differential pulse polarography is shown here to be applicable to the monitoring directly the biosorption of metal ions from solution by live bacteria from mixed metal solutions . Biosorption of Cd(II), Zn(II) and Ni(II) by P . cepacia was followed using data obtained at the potential which is characteristic of the metal ion in the absence and presence of cells . Hepes buffer (pH 7.4, 50 mM) was used as a supporting electrolyte in the polarographic chamber and metal ion peaks in the presence of cells of lower amplitude were obtained due to metal-binding by the cells . Well defined polarographic peaks were obtained in experiments involving mixtures of metal ions of Cd(II)-Zn(II), Cu(II)-Zn(II), Cu(II)-Cd(II) and Cd(II)-Ni(II) . Biosorption of Cd(II), Zn(II) increased with solution pH . The method was also tested as a rapid technique for assessing removal of metal ions by live bacteria and the ability of the polarographic technique in measuring biosorption of metal ions from mixed metal solutions is demonstrated . Cu(II) was preferentially bound and removal of metals was in the order Cu(II) > Ni(II) > Zn(II), Cd(II) by intact cells of P . cepacia.

J Microbiol Methods, 2003 Nov, 55(2), 393 - 7
Application of Amido black staining to enumerating bacteria grown on membrane filters; Inatomi K; A method to detect and enumerate bacterial colonies grown on membrane filters (MF) was described . The colonies were stained with an ethanolic solution of 0.1% Amido black 10B . The procedure yielded the rapid detection of colonies as compared to a conventional plate counting method.

Endocrinology, 2004 Jan, 145(1), 447 - 52 Epub 2003 Oct 02.
Diabetes causes decreased osteoclastogenesis, reduced bone formation, and enhanced apoptosis of osteoblastic cells in bacteria stimulated bone loss; He H et al.; The most common cause of inflammatory bone loss is periodontal disease . After bacterial insult, inflammation induces bone resorption, which is followed by new reparative bone formation . Because diabetics have a higher incidence and more severe periodontitis, we examined mechanisms by which diabetes alters the response of bone to bacterial challenge . This was accomplished with db/db mice, which naturally develop type 2 diabetes . After inoculation of bacteria osteoclastogenesis and bone resorption was measured . Both parameters were decreased in the diabetic group . Diabetes also suppressed reparative bone formation measured histologically and by the expression of osteocalcin . The impact of diabetes on new bone formation coincided with the effect of diabetes on apoptosis of bone-lining cells . Within 5 d of bacterial challenge, apoptosis declined in the wild-type animals yet remained significantly higher in the diabetic group . Thus, diabetes may cause a net loss of bone because the suppression of bone formation is greater than the suppression of bone resorption . The uncoupling of bone formation and resorption may be due in part to prolonged apoptosis of bone lining cells.

Eur J Clin Microbiol Infect Dis, 2003 Oct, 22(10), 628 - 31 Epub 2003 Oct 01.
Identification of bacteria recovered from clinical specimens by 16S rRNA gene sequencing; Kiratisin P et al.; The sequence of the 16S rRNA gene has been used extensively for phylogenetic classification, identification, and genotypic typing of bacteria . Identification of bacterial isolates by 16S rRNA gene sequencing, though generally performed in reference laboratories, has been recently introduced for routine use in clinical laboratories to identify isolates that cannot be identified by conventional methods . Described in this report is the use of 16S rRNA gene sequencing to identify uncommon bacteria, or bacteria with unusual phenotypic properties, with four brief case presentations to illustrate its clinical application . The feasibility, usefulness and limitations of performing this approach in the clinical laboratory are also discussed.

J Contam Hydrol, 2003 Oct, 66(1-2), 1 - 23
Effect of dissolved organic matter and bacteria on contaminant transport in riverbank filtration; Kim SB et al.; A mathematical model for the transport of hydrophobic organic contaminants in an aquifer under simplistic riverbank filtration conditions is developed . The model considers a situation where contaminants are present together with dissolved organic matter (DOM) and bacteria . The aquifer is conceptualized as a four-phase system: two mobile colloidal phases, an aqueous phase, and a stationary solid phase . An equilibrium approach is used to describe the interactions of contaminants with DOM, bacteria, and solid matrix . The model is composed of bacterial transport equation and contaminant transport equation . Numerical simulations are performed to examine the contaminant transport behavior in the presence of DOM and bacteria . The simulation results illustrate that contaminant transport is enhanced markedly in the presence of DOM and bacteria, and the impact of DOM on contaminant mobility is greater than that of bacteria under examined conditions . Sensitivity analysis demonstrates that the model is sensitive to changes of three lumped parameters: K+1 (total affinity of stationary solid phase to contaminants), K+2 (total affinity of DOM to contaminants), and K+3 (total affinity of bacteria to contaminants) . In a situation where contaminants exist simultaneously with DOM and bacteria, contaminant transport is mainly affected by a ratio of K+1/K+2/K+3, which can vary with changes of equilibrium distribution coefficient of contaminants and/or colloidal concentrations . In riverbank filtration, the influence of DOM and bacteria on the transport behavior of contaminants should be accounted to accurately predict the contaminant mobility.

Biofizika, 2003 Jul-Aug, 48(4), 673 - 7
{Species specificity and reaction of bacteria to a 50 GHz magnetic field}; Lob'yshev VI et al.; The growth of cultures of bacteria with different lipid content of cell membranes in response to a 40 min exposure to alternating magnetic field of 50 Hz, 18 mT was studied . Three important phenomena were revealed . A species specificity of responses of bacteria to the magnetic field, including both inhibition and activation, was observed . The changes in the kinetics of growth of bacterial culture correlate with the type of membrane lipid complex . The information on the exposure to magnetic field is memorized by the previously exposed distilled water, which makes itself evident in responses much more intensive than the responses of the same cultures exposed immediately in the culture medium.

Biofizika, 2003 Jul-Aug, 48(4), 648 - 55
{Initial stage of coupling electron and proton transport in the vicinity of the secondary quinone in photosynthesis of bacteria and plants}; Belousov RV et al.; The coupling of electron and proton transport in the vicinity of the secondary quinone QB in the reaction center of bacteria and photosystem II of higher plants was investigated . The energy levels and wave functions of the proton in the system QB--histidine L 190 were calculated . It was shown that the proton of histidine forms a hydrogen bond with the doubly reduced quinone QB2- . A new scheme of proton transport through histidine L 190 and its coupling with electron transport was proposed.

Zhonghua Shao Shang Za Zhi, 2003 Aug, 19(4), 229 - 32
{Influence of intra-abdominal hypertension on the intestinal permeability and endotoxin/bacteria translocation in rabbits}; Cheng JT et al.; OBJECTIVE: To observe different degrees of intra-abdominal pressure and different duration on the intestinal permeability and endotoxin/bacteria translocation in rabbit model, so as to explore the mechanism of the development of abdominal compartment syndrome (ACS) and MODS . METHODS: Rabbit model of intra-abdominal hypertension was established by injection of gaseous nitrogen into the peritoneal cavity . Thirty-nine New Zealand white rabbits were employed in the study . The change in intestinal permeability was determined by fluorescein isothiocyanate dextran (FITC-D) and two kinds of molecular probes of type II horseradish peroxidase (HRP-II) . The effects of intra-abdominal hypertension on the endotoxin/bacteria translocation were also detected . RESULTS: The contents of FITC-D and HRP-II in portal veins increased evidently (P < 0.01) when intra-abdominal pressure (IAP) was higher than 20 mmHg . The endotoxin (ET) content in portal vein in rabbits with IAP of 10 mmHg for 1, 2 and 4 hours exhibited no difference compared with that in normal control, while the ET content increased obviously after 1 hour with IAP of 20 mmHg and increased thereafter along with the prolongation of IAP, and increase in pressure . The bacterial translocation rates were 33.3%, 66.7% and 100% when IAP was maintained at 20 mmHg for 1, 2 and 4 hours, respectively, and there was evidence of bacterial translocation to the liver . The rate of bacterial translocation to intestinal mesenteric lymph nodes was 100% when IAP was 30 mmHg for 1 and 2 hours . There was no bacterial translocation to the spleen in all experimental rabbits . CONCLUSION: Intestinal mucosal permeability increased significantly with increased endotoxin content in portal vein when IAP was higher than 20 mmHg . At the sane time, the bacteria could be translocate to intestinal mesenteric lymph nodes and liver, which might be constitute one of the important factors leading to the development of ACS and MODS.

Biotechnol Lett, 2003 Sep, 25(17), 1385 - 95
Protein aggregation in recombinant bacteria: biological role of inclusion bodies; Villaverde A et al.; Protein aggregation is an ordinary consequence of thermal stress . In recombinant bacteria, the over-expression of plasmid-encoded genes triggers transcription of heat-shock genes and other stress responses and often results in the aggregation of the encoded protein as inclusion bodies . The formation of these deposits represents a major obstacle for the production of biologically active polypeptides and restricts the spectrum of protein products being available for the industrial-biomedical market . Inclusion body formation was formerly considered to occur passively by the irretrievable deposition of partially-folded intermediates . Increasing evidence, however, indicates that protein aggregation in bacteria occurs as a reversible process deeply integrated in the cell mechanisms for coping with thermal stress, and that inclusion bodies are structurally dynamic structures . Inclusion body formation might actually be supported by the cellular machinery that when operated under specific stress conditions, transiently stores misfolded polypeptides until they could be further processed: either refolded or proteolysed . A better understanding of protein aggregation in cell physiology could allow not only inclusion body formation to be minimized more efficiently for a higher soluble yield, but also to comprehend in detail the intricacy of cell mechanisms committed to handling the misfolding danger.

J AOAC Int, 2003 Jul-Aug, 86(4), 719 - 21
Impedance method for rapid detection of total counts of bacteria and fungi in bottled purified water; Ji-Cheng H et al.; A study was conducted to compare the current conventional method and the impedance method for rapid detection of total counts of bacteria and fungi in bottled purified water . The results indicated that the corresponding detection rate for the 2 methods was 94.5 and 90.4%, respectively . The detection time was shortened from 48 h (bacteria) and 5 days (fungi) to 14.5 and 44 h, respectively . Moreover, for more serious contamination, less time was needed . The impedance method predicted a positive sample within 11.3 h (bacteria) and 27.1 h (fungi) . Therefore, the impedance method was found to be a rapid, accurate method.

Odontology, 2003 Sep, 91(1), 13 - 8
Intracellular production and extracellular release of oxygen radicals by PMNs and oxidative stress on PMNs during phagocytosis of periodontopathic bacteria; Katsuragi H et al.; In this study we investigated intracellular and extracellular oxygen radical production by polymorphonuclear leukocytes (PMNs) during the phagocytosis of periodontopathic bacteria . In in vitro assays, bacteria of the species Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, and Fusobacterium nucleatum were phagocytosed at 37 degrees C for 4 h by purified peripheral human PMNs from healthy subjects (n = 6) . Superoxide production during phagocytosis was determined by flow cytometry and with a fluorescence/luminescence microplate reader . After phagocytosis, oxidative stress was determined by flow cytometry . Both the intracellular and extracellular oxygen radical production by PMNs phagocytosing F . nucleatum was significantly greater than that of PMNs phagocytosing P . gingivalis and A . actinomycetemcomitans ( P < 0.01 by the Mann-Whitney test) . Moreover, after 4 h of incubation, the oxidative stress of PMNs phagocytosing F . nucleatum was significantly greater than that of PMNs phagocytosing P . gingivalis and A . actinomycetemcomitans . We conclude that a high level of superoxide production by PMNs may damage not only periodontopathic bacteria but also PMNs themselves, and may be correlated with the destruction of periodontal tissue.

Proc Natl Acad Sci U S A, 2003 Sep 30, 100(20), 11394 - 9 Epub 2003 Sep 22.
Conserved pathways within bacteria and yeast as revealed by global protein network alignment; Kelley BP et al.; We implement a strategy for aligning two protein-protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and complexes . Using this approach we show that the protein-protein interaction networks of two distantly related species, Saccharomyces cerevisiae and Helicobacter pylori, harbor a large complement of evolutionarily conserved pathways, and that a large number of pathways appears to have duplicated and specialized within yeast . Analysis of these findings reveals many well characterized interaction pathways as well as many unanticipated pathways, the significance of which is reinforced by their presence in the networks of both species.

Biotechnol Adv, 2003 Aug, 21(5), 383 - 93
Phytoremediation: synergistic use of plants and bacteria to clean up the environment; Glick BR; Phytoremediation is a relatively new approach to removing contaminants from the environment . It may be defined as the use of plants to remove, destroy or sequester hazardous substances from the environment . Unfortunately, even plants that are relatively tolerant of various environmental contaminants often remain small in the presence of the contaminant . To remedy this situation, plant growth-promoting bacteria that facilitate the proliferation of various plants especially under environmentally stressful conditions may be added to the roots of plants . These bacteria have been selected to lower the level of growth-inhibiting stress ethylene within the plant and also to provide the plant with iron from the soil . The net result of adding these bacteria to plants is a significant increase in both the number of seeds that germinate and the amount of biomass that the plants are able to attain, making phytoremediation in the presence of plant growth-promoting bacteria a much faster and more efficient process.

J Nucl Med Technol, 2003 Sep, 31(3), 170 - 2
133Xe contamination found in internal bacteria filter of xenon ventilation system; Hackett MT et al.; OBJECTIVE: We report on (133)Xe contamination found in the reusable internal bacteria filter of our xenon ventilation system . METHODS: Internal bacteria filters (n = 6) were evaluated after approximately 1 mo of normal use . The ventilation system was evacuated twice to eliminate (133)Xe in the system before removal of the filter . Upon removal, the filter was monitored using a survey meter with an energy-compensated probe and was imaged on a scintillation camera . The filter was monitored and imaged over several days and was stored in a fume hood . RESULTS: Estimated (133)Xe activity in each filter immediately after removal ranged from 132 to 2,035 kBq (3.6-55.0 micro Ci), based on imaging . Initial surface radiation levels ranged from 0.4 to 4.5 micro Sv/h (0.04-0.45 mrem/h) . The (133)Xe activity did not readily leave the filter over time (i.e., time to reach half the counts of the initial decay-corrected image ranged from <6 to >72 h) . The majority of the image counts (approximately 70%) were seen in 2 distinctive areas in the filter . They corresponded to sites where the manufacturer used polyurethane adhesive to attach the fiberglass filter medium to the filter housing . CONCLUSION: (133)Xe contamination within the reusable internal bacteria filter of our ventilation system was easily detected by a survey meter and imaging . Although initial activities and surface radiation levels were low, radiation safety practices would dictate that a (133)Xe-contaminated bacteria filter be stored preferably in a fume hood until it cannot be distinguished from background before autoclaving or disposal.

Orig Life Evol Biosph, 2003 Feb, 33(1), 53 - 74
Survivability of bacteria ejected from icy surfaces after hypervelocity impact; Burchell MJ et al.; Both the Saturnian and Jovian systems contain satellites with icy surfaces . If life exists on any of these icy bodies (in putative subsurface oceans for example) then the possibility exists for transfer of life from icy body to icy body . This is an application of the idea of Panspermia, wherein life migrates naturally through space . A possible mechanism would be that life, here taken as bacteria, could become frozen in the icy surface of one body . If a high-speed impact occurred on that surface, ejecta containing the bacteria could be thrown into space . It could then migrate around the local region of space until it arrived at a second icy body in another high-speed impact . In this paper we consider some of the necessary steps for such a process to occur, concentrating on the ejection of ice bearing bacteria in the initial impact, and on what happens when bacteria laden projectiles hit an icy surface . Laboratory experiments using high-speed impacts with a light gas gun show that obtaining icy ejecta with viable bacterial loads is straightforward . In addition to demonstrating the viability of the bacteria carried on the ejecta, we have also measured the angular and size distribution of the ejecta produced in hypervelocity impacts on ice . We have however been unsuccessful at transferring viable bacteria to icy surfaces from bacteria laden projectiles impacting at hypervelocities.

Guang Pu Xue Yu Guang Pu Fen Xi, 2003 Apr, 23(2), 340 - 1
{Analyses of cell coloring matter and degradation products of anthraquinone dye decolorization bacteria XL-1 using ultraviolet absorption spectroscopy}; Dong XL et al.; The species of cell coloring matter of anthraquinone dye decolorization bacteria XL-1, degradation reaction degrees, and the changes of molecule structure of degradation products were studied using ultraviolet absorption spectroscopy . The results indicate that the bacteria cells contain bacteria chlorophyll a and like-carotene . Its molecular structure changed evidently during the degradation process, the conjugate structure was destroyed, and new intermediate products were created.

Yao Xue Xue Bao, 2003 May, 38(5), 321 - 4
{Platelet phospholipase A2 mRNA content changes and cDNA cloning in rat blood with bacteria infection}; Liu TT et al.; AIM: To explore the changes of rat platelet phospholipase A2 (PLA2) mRNA content in bacteria infected rat and study the cDNA and amino acid sequences of the PLA2 structure to lay a good foundation for the development of new antibiotics . METHODS: The PLA2 mRNA level in blood was determined by RT-PCR . The DNA sequence was cloned and analyzed . RESULTS: After injection of bacteria in rats, the mRNA level of PLA2 in blood increased markedly . The cDNA and amino acid sequence were highly homologous to other PLA2 cDNA from different tissues of the rat . CONCLUSION: Platelet PLA2 in blood responded quickly to bacteria infection in gene level . Therefore, the PLA2 protein was produced increasingly which was shown to control the infection with bacteria . Although there are little difference between PLA2 cDNA cloned from blood and other sources in DNA and amino acid sequences, the catalytic site for enzymatic activity and basic structure are identical.

Appl Environ Microbiol, 2003 Sep, 69(9), 5693 - 8
Reevaluation of production of paralytic shellfish toxin by bacteria associated with dinoflagellates of the Portuguese coast; Martins CA et al.; Paralytic shellfish toxins (PSTs) are potent neurotoxins produced by certain dinoflagellate and cyanobacterial species . The autonomous production of PSTs by bacteria remains controversial . In this study, PST production by two bacterial strains, isolated previously from toxic dinoflagellates, was evaluated using biological and analytical methods . Analyses were performed under conditions determined previously to be optimal for toxin production and detection . Our data are inconsistent with autonomous bacterial PST production under these conditions, thereby challenging previous findings for the same strains.

Appl Environ Microbiol, 2003 Sep, 69(9), 5414 - 22
Mercury methylation independent of the acetyl-coenzyme A pathway in sulfate-reducing bacteria; Ekstrom EB et al.; Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems . Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production . The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species . To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities . Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway . So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury . Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth . However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition) . Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B(12) in some and perhaps many incomplete-oxidizing SRB strains.

J Colloid Interface Sci, 2003 Oct 1, 266(1), 60 - 7
Specific surface chemical interactions between hydrous ferric oxide and iron-reducing bacteria determined using pK(a) spectra; Smith DS et al.; A modified regularized least squares pK(a) spectrum approach is applied to determine disassociation constants and proton binding site concentrations on bacteria, hydrous ferric oxide (HFO), and bacteria/HFO composite surfaces . This involves fitting experimental acid-base titration data to a continuous binding site model for a chemically heterogeneous surface with a variety of reactive groups yielding a pK(a) spectrum . The modified parameter fitting method optimizes simultaneously for both smoothness of the pK(a) spectrum and goodness of fit, whereas other methods optimize for goodness of fit given a fixed smoothness factor . Uncertainty estimates in pK(a) spectra were made by taking the mean and standard deviation of the spectra from replicate titration data . Titration of Shewanella putrefaciens strain CN32, a facultative iron-reducing bacterial species, demonstrate five types of binding sites consistent with known cell surface groups on bacteria, with mean pK(a) values of 3.62, 4.97, 6.92, 8.22, and 9.97 . Composite surfaces formed by precipitation of HFO onto bacteria surfaces were also titrated . These surfaces no longer yielded low pK(a) sites in pK(a) spectra, indicating that ferric iron interacts with the bacteria via carboxylic (low pK(a)) sites during precipitation . In addition, mechanically mixed HFO bacterial samples also showed removal of carboxylic binding sites, suggesting that solid phase HFO interacts directly with carboxylic sites on bacterial cells . Moreover, the pK(a) spectra for HFO bacterial composites were not dependent on how the composite was formed; the mechanically mixed or surface-precipitated samples exhibited very similar binding site distributions . The determined pK(a) spectra imply that the overall binding mechanism for bacteria interactions with HFO involve carboxylic groups on the bacteria binding to the most basic sites on the HFO surface in approximately 1:1 stoichiometry.

Proc Natl Acad Sci U S A, 2003 Nov 25, 100 Suppl 2, 14549 - 54 Epub 2003 Aug 29.
Chemical communication among bacteria; Taga ME et al.; Cell-cell communication in bacteria is accomplished through the exchange of chemical signal molecules called autoinducers . This process, called quorum sensing, allows bacteria to monitor their environment for the presence of other bacteria and to respond to fluctuations in the number and/or species present by altering particular behaviors . Most quorum-sensing systems are species- or group-specific, which presumably prevents confusion in mixed-species environments . However, some quorum-sensing circuits control behaviors that involve interactions among bacterial species . These quorum-sensing circuits can involve both intra- and interspecies communication mechanisms . Finally, anti-quorumsensing strategies are present in both bacteria and eukaryotes, and these are apparently designed to combat bacteria that rely on cell-cell communication for the successful adaptation to particular niches.

Presse Med, 2003 Jul 12, 32(24), 1111 - 5
{Early and late nosocomial broncho-pulmonary diseases in intensive care . Comparative study of risk factors and of causing bacteria}; Nseir S et al.; OBJECTIVES: Determine the risk factors and germs responsible for early-onset (E) and late-onset (L) nosocomial broncho-pulmonary infections (NBPI), in order to improve preventive strategies and the choice of initial antibiotherapy . METHODS: An observational prospective study conducted in an intensive care unit of 30 beds, from March 1993 to September 1999 . The patients presenting with an ENBPI and those with an LNBPI were compared with patients without NBPI using univariate and then multivariate analysis . RESULTS: 517 (14%) of early-onset NBPI were diagnosed, but the majority of NBPI were late-onset (87%) . Multiresistant bacteria predominated . The similarity in the germs responsible for the early and late onset forms of NBPI was probably related to the large number of patients transferred from other departments (82%) and having already received antibiotics before their admission to the intensive care unit (49%) . Multivariate analysis identified anti-ulcer and long term corticosteroid treatments as common risk factors for early and late onset forms of NBPI, digestive failure, tracheotomy and kidney failure as risk factors for ENBPI and the number of antibiotics used in intensive care and the duration of mechanical ventilation as factors of risk for LNBPI . CONCLUSION: The limited use of antibiotics and anti-ulcer agents could improve the prevention of early and late onset forms of NBPI . The distinction in intensive care between the two forms of NBPI must be emphasized by the notion of prior hospitalization.

Proc Natl Acad Sci U S A, 2003 Sep 16, 100(19), 10806 - 11 Epub 2003 Aug 28.
Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles; Nesbo CL et al.; Group I introns are common in the 23 rRNA genes of mitochondria and chloroplasts . Often, they encode "homing endonucleases," which target highly conserved gene sequences and drive interorganellar intron mobility, even across species and genus lines . Most bacterial 23S rRNA genes show these same endonuclease-sensitive target sequences . However, only two bacterial 23S rRNA genes are known to contain group I introns: that of Simkania negevensis {Everett, K . D., Kahane, S., Bush, R . M . & Friedman, M . G . (1999) J . Bacteriol . 181, 4734-4740}, where the intron is not spliced and probably limits growth, and that of Coxiella burnetii {Seshadri, R., et al . (2003) Proc . Natl . Acad . Sci . USA 100, 5455-5460}, where no direct evidence of splicing exists . Both bacteria are intracellular parasites and might have acquired introns from eukaryotic hosts . Here we provide direct evidence for splicing, and evolutionary evidence for mobility, of group I introns in the 23S rRNA genes of several free-living hyperthermophilic bacteria of the genus Thermotoga . These bacteria do not live closely with eukaryotes, but phylogenetic analyses suggest that their introns were also acquired from eukaryotic (probably algal) organelles . In vivo, their introns must be spliced at temperatures approaching 90 degrees C, making them the most thermostable natural ribozymes so far described . We demonstrate that at least some of these introns can also self-splice in vitro.

Photochem Photobiol, 2003 Aug, 78(2), 114 - 23
Inter- and intraspecific variation in excited-state triplet energy transfer rates in reaction centers of photosynthetic bacteria; Laible PD et al.; In protein-cofactor reaction center (RC) complexes of purple photosynthetic bacteria, the major role of the bound carotenoid (C) is to quench the triplet state formed on the primary electron donor (P) before its sensitization of the excited singlet state of molecular oxygen from its ground triplet state . This triplet energy is transferred from P to C via the bacteriochlorophyll monomer B(B) . Using time-resolved electron paramagnetic resonance (TREPR), we have examined the temperature dependence of the rates of this triplet energy transfer reaction in the RC of three wild-type species of purple nonsulfur bacteria . Species-specific differences in the rate of transfer were observed . Wild-type Rhodobacter capsulatus RCs were less efficient at the triplet transfer reaction than Rhodobacter sphaeroides RCs, but were more efficient than Rhodospirillum rubrum RCs . In addition, RCs from three mutant strains of R . capsulatus carrying substitutions of amino acids near P and B(B) were examined . Two of the mutant RCs showed decreased triplet transfer rates compared with wild-type RCs, whereas one of the mutant RCs demonstrated a slight increase in triplet transfer rate at low temperatures . The results show that site-specific changes within the RC of R . capsulatus can mimic interspecies differences in the rates of triplet energy transfer . This application of TREPR was instrumental in defining critical energetic and coupling factors that dictate the efficiency of this photoprotective process.

J Theor Biol, 2003 Oct 7, 224(3), 277 - 83
The ancestor of the Bacteria domain was a hyperthermophile; Di Giulio M; Brochier and Philippe have recently re-analysed the phylogeny of ribosomal RNA using only multiple alignment positions with no phylogenetic noise . They conclude that the first branch of divergence in the Bacteria domain comprises Planctomycetales and not hyperthermophile bacteria as in classic phylogeny . In the present paper I examine the robustness of their conclusions . (1) A site-by-site reading of the RNA alignments of Brochier and Philippe seems to suggest that the number of nucleotide positions used in their analysis is not sufficiently high and their phylogenetic analysis is consequently not robust . Furthermore, (2) a different method for selecting positions with no phylogenetic noise from the rRNA alignment relocates the Aquificales and the Thermotogales as the first lines of divergence in the Bacteria domain, and sets Planctomycetales as the third branch of divergence in the phylogenetic tree built from these selected positions . These findings consolidate the hypothesis that the ancestor of the Bacteria domain was a hyperthermophile and, more generally, that the last universal common ancestor might also have been one.

Micron, 2003, 34(6-7), 339 - 44
X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100 nm resolution; Thieme J et al.; Visualization of the spatial arrangement of bacteria and other colloids permits to describe relevant soil parameters like porosity or nutrient storage capacity . Major advantages of X-ray microscopy for these investigations are the much higher spatial resolution compared to visible light microscopy and its ability to study colloidal structures directly in aqueous media . To obtain information about the three-dimensional structure of the microhabitats formed by bacteria and other soil colloids, tomography based on X-ray microscopy images with about 45 nm resolution was performed . Tomographic reconstructions presented in this paper clearly reveal the spatial arrangement of bacteria and other soil colloids which cannot be obtained from two-dimensional projections . The results show that X-ray nanotomography is a very powerful tool for examining the three-dimensional structure of flocs of colloidal particles.

J Comp Pathol, 2003 Aug-Oct, 129(2-3), 154 - 60
Experimental infection of mice with tightly coiled spiral bacteria ("Candidatus Helicobacter suis") originating from the pig stomach; Park JH et al.; Mice (n=34) were inoculated orally with a gastric homogenate from a pig infected with tightly coiled spiral bacteria (TCSB) . In mice killed in pairs at 16 intervals up to 108 weeks post-inoculation (pi), TCSB were invariably found, mainly in the mucosal surface, gastric pits, intercellular spaces, cytoplasm of surface epithelial cells, and lumina of gastric glands . Histopathologically, infiltration of lymphocytes and plasma cells was seen from 8 weeks pi onwards, gradually increasing as infection progressed . From 64 weeks pi onwards, the formation of large follicles was observed in the lamina propria and submucosa, together with severe necrosis of surface epithelial cells . Glandular epithelial cells in the fundic mucosa were markedly dysplastic and intruded through the basement membrane into the submucosal layer . Common antigenicity between TCSB and Helicobacter pylori was demonstrated by Western blotting, ELISA, and immunohistochemistry . The sequence of the 16S rDNA fragment of 374 bp showed 100% homology with the 16S rRNA gene of "Candidatus Helicobacter suis" . Experimental infection of the gastric mucosa of mice with TCSB was closely associated with chronic gastritis and dysplastic lesions.

Biomol Eng, 2003 Jul, 20(4-6), 311 - 6
Marine bacteria associated with sponge as source of cyclic peptides; De Rosa S et al.; Two bacteria associated with the marine sponge Ircinia variabilis were isolated using commercial and experimental media . The use of media containing marine derived proteins improved the growth of both isolated bacteria, showing that marine bacteria need of marine derived proteins for a better growth . The composition of free and total fatty acids of both strains cultivated under different carbon source was investigated . Several diketopiperazines were isolated from both bacteria and the hypothesis of their role in the bacterial-spongy interaction is discussed.

Transfusion, 2003 Sep, 43(9), 1276 - 85
Detection of bacteria in WBC-reduced PLT concentrates using percent oxygen as a marker for bacteria growth; Ortolano GA et al.; BACKGROUND: The risk of receiving a PLT concentrate (PC) contaminated with bacteria may be 1000-fold greater than that of pathogenic viral transmission, yet surveillance for this risk is not generally practiced . A novel bacteria detection system (BDS) that overcomes the limitations of current systems is described . The BDS monitors percent oxygen (%O2) in air above aliquots of PCs that have been filtered to remove the confounding effect of respiring PLTs and residual WBCs . STUDY DESIGN AND METHODS: One-day-old WBC-reduced whole-blood-derived PCs (WBPCs) were inoculated with bacteria at 100 to 500 CFU per mL . After 30 minutes, 2- to 3-mL aliquots were processed through a PLT-reducing filter into a sample pouch containing sodium polyanethol sulfonate and entrained air . After incubation at 35 degrees C for at least 24 hours, the %O2 was measured within the pouch . Noninoculated WBC-reduced WBPCs (n = 155), confirmed free of bacteria by routine culture, were tested in a like manner . Results from the latter group of WBC-reduced WBPCs were used to distinguish contaminated from noncontaminated units . RESULTS: After a 24-hour incubation at 35 degrees C, 195 (96.5%) of the 202 sample pouches obtained from inoculated units were detected by the BDS . After an additional 6 hours at room temperature, those that remained and were tested were found positive . None of the noninoculated controls produced a positive reading . CONCLUSION: The BDS is easy to use and provides good levels of sensitivity and specificity.

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