Hum Reprod Update, 1999 Jul-Aug, 5(4), 373 - 85 Hypothesis on the role of sub-clinical bacteria of the endometrium (bacteria endometrialis) in gynaecological and obstetric enigmas; Viniker DA; Unexplained infertility, recurrent abortion, dysfunctional uterine bleeding, pelvic pain, premenstrual syndrome, premature labour, placental insufficiency and pre-eclampsia are examples of common obstetric and gynaecological problems that frequently defy adequate explanation . Bacterial vaginosis, a non-inflammatory condition, is associated with premature labour, but antibiotics administered topically provide less effective prophylaxis than those administered orally . This would indicate that bacterial vaginosis might be a marker for significant genital tract bacteria, but some pathology is dependent on micro-organisms ascending out of reach of topical antibiotics . The author was led to consider the hypothesis that micro-organisms, possibly those associated with bacterial vaginosis, surreptitiously inhabit the uterine cavity (bacteria endometrialis) where they are culprits of some common gynaecological and obstetric enigmas . The objective of this review is to provide an initial theoretical examination of this hypothesis . Bacteria in the endometrium have been associated with infertility . Antiphospholipids have been linked to recurrent miscarriage and pre-eclampsia and with infections including Mycoplasma . Pre-eclampsia might be explained by an exaggerated host response to intrauterine micro-organisms or bacterial toxins . The hypothesis that one common factor, bacteria endometrialis, could provide a plausible explanation for a variety of obstetric and gynaecological mysteries is particularly intriguing . There is sufficient evidence to justify further investigation. Microbiology, 1999 Aug, 145 ( Pt 8), 2043 - 50 Helicobacter pylori VacA cytotoxin associated with the bacteria increases epithelial permeability independently of its vacuolating activity; Pelicic V et al.; Polarized epithelial monolayers of Madin-Darby canine kidney (MDCK) cells were used to study the pathogenicity of Helicobater pylori, with an emphasis on the effect of VacA . The adherence of H . pylori to MDCK monolayers resulted in a decrease in trans-epithelial resistance (TER) across the cell monolayer . Isogenic vacA mutants did not lower the TER, demonstrating that the effect is strictly linked to the action of the toxin . A similar effect was observed with all VacA-producing strains, including those producing m2 toxins that are inactive in the vacuolating assay . In contrast to that seen with purified toxin, TER decrease was not enhanced by acid pH, which may indicate that the toxin associated to the bacterial surface is possibly in a monomeric state and therefore does not require a pH-induced conformation to be active . These data raise the possibility that one role of VacA in ulcerogenesis may consist of increasing the paracellular permeability of the gastric epithelium. Biochemistry, 1999 Aug 24, 38(34), 11115 - 21 Conformation of bacteriochlorophyll molecules in photosynthetic proteins from purple bacteria; Lapouge K et al.; Fourier transform near-infrared resonance Raman spectroscopy can be used to obtain information on the bacteriochlorophyll a (BChl a) molecules responsible for the redmost absorption band in photosynthetic complexes from purple bacteria . This technique is able to distinguish distortions of the bacteriochlorin macrocycle as small as 0.02 A, and a systematic analysis of those vibrational modes sensitive to BChl a macrocycle conformational changes was recently published {Naveke et al . (1997) J . Raman Spectrosc . 28, 599-604} . The conformation of the two BChl a molecules constituting the primary electron donor in bacterial reaction centers, and of the 850 and 880 nm-absorbing BChl a molecules in the light-harvesting LH2 and LH1 proteins, has been investigated using this technique . From this study it can be concluded that both BChl a molecules of the primary electron donor in the photochemical reaction center are in a conformation close to the relaxed conformation observed for pentacoordinate BChl a in diethyl ether . In contrast, the BChl a molecules responsible for the long-wavelength absorption transition in both LH1 and LH2 antenna complexes are considerably distorted, and furthermore there are noticeable differences between the conformations of the BChl molecules bound to the alpha- and beta-apoproteins . The molecular conformations of the pigments are very similar in all the antenna complexes investigated. Arch Oral Biol, 1999 Aug, 44(8), 665 - 70 Negative correlation between oral malodour and numbers and activities of sulphate-reducing bacteria in the human mouth; Willis CL et al.; The majority of cases of oral malodour are thought to be due to bacterial activities in the mouth, but many of the bacterial species responsible have not been identified . Volatile sulphide compounds have been proposed as constituents of oral malodour . Therefore, the relation between intensity of odour and numbers of bacteria in the mouth that are sulphide-producing from sulphate was investigated . Numbers of such dissimilatory sulphate-reducing bacteria (SRB) and sulphide reduction rates were evaluated in samples from different oral sites in relation to measures of oral malodour . Results showed that sulphate-reducing bacterial numbers and activities were negatively correlated with malodour, as determined by organoleptic assessment and measurement with a sulphide-monitoring instrument, the Halimeter . The data indicate that sulphide produced by oral SRB may not be an important contributor to oral malodour . A rather poor correlation was observed between Halimetric and organoleptic values, indicating that these methods may measure different aspects of oral malodour intensity. J Ind Microbiol Biotechnol, 1999 Jun, 22(6), 582 - 589 Use of nitrate to control sulfide generation by sulfate-reducing bacteria associated with oily waste; Londry K et al.; Sulfide is a toxic and corrosive product of sulfate-reducing bacteria that can accumulate in oily waste streams to nuisance levels . Sludge associated with an oily waste stream was collected from a settling tank and used to assess sulfide generation activities . Methanogenesis was a predominant process in sludge in the absence of sulfate, and was suppressed by nitrate . Sulfate reduction and sulfide formation were evident when sulfate was available . Nitrate diminished sulfate reduction and prevented sulfide accumulation under freshwater, brackish, and saltwater conditions . Sodium-, potassium-, and calcium nitrate were equally effective in curtailing sulfide formation . The effects of nitrate on sulfate depletion were concentration-dependent, with 50 mM nitrate diminishing sulfate reduction, yet as little as 16 mM nitrate prevented sulfide accumulation . Sulfide was oxidized in nitrate-reducing incubations, and accumulation of sulfur or sulfate was observed . Nitrate reduction was accompanied by production of nitrite and nitrous oxide, which probably helped prevent sulfate reduction in extended incubations . Our results suggest that nitrate amendments control the formation of sulfide in oily waste streams both by preventing sulfate reduction and by stimulating anaerobic sulfide oxidation. J Mol Biol, 1999 Aug 27, 291(4), 745 - 59 Shutdown in protein synthesis due to the expression of mini-genes in bacteria; Dincbas V et al.; Mutants of Escherichia coli partially deficient in peptidyl-tRNA hydrolase are killed by the expression of certain very short open reading frames (mini-genes), encoded by the wild-type bar regions of phage lambda . According to the current hypothesis, protein synthesis is shut off, and the host cells die, after essential tRNA species become sequestered due to abnormal translation termination (drop-off) of mini-gene-encoded peptides as peptidyl-tRNA . Here we study variants of bar mini-genes, both in vivo and in vitro, in order to identify the structural elements that influence this inhibition of protein synthesis . Three parameters were measured during the expression of these variants: the rates of normal translation termination, peptidyl-tRNA dissociation from the ribosome and hydrolysis of peptidyl-tRNA by peptidyl-tRNA hydrolase were measured . Previous observations that RRF, EF-G and RF3 stimulated drop-off were confirmed and extended; stimulation by these factors can reach 30-fold . Both factor-stimulated and spontaneous drop-off depended on the nature of the stop signal . The degree of inhibition of cell growth following induction of mini-gene expression could be accounted for in terms of a toxicity index comprising the three parameters above . Inhibition was greatly reduced in cells lacking RF3 . Mini-genes with more efficient Shine/Dalgarno sequences killed cells even with normal peptidyl-tRNA hydrolase activity . It is proposed that the retranslation by ribosomes of mini-gene transcripts with efficient ribosome binding (Shine/Dalgarno) sequences strongly contributes to the inhibitory effects of mini-gene expression on protein synthesis . FEMS Immunol Med Microbiol, 1999 Aug 1, 25(1-2), 221 - 6 Sudden infant death syndrome and Canadian Aboriginals: bacteria and infections; Wilson CE; Aboriginal populations in Canada, America and Australia have higher incidences of sudden infant death syndrome (SIDS) than non-Aboriginal groups . Canadian Aboriginal populations (known also as first nation, native or Indian) experience infant morbidity/mortality rates 3-7 times that of non-Aboriginals, with upper track respiratory infection and SIDS recorded as the leading causes . The aim of this investigation was to examine the home environment of Aboriginal infants, particularly during winter months when respiratory tract infections and SIDS are more common . Environmental bacteria, fungi and air particulates were examined in the residences of Aboriginal infants during visits to individual homes on an Aboriginal reserve . The physical histories of SIDS victims were gathered from medical files . Air and surfaces were sampled by agar strips which were processed by a commercial laboratory . The levels of fungi, bacteria and air particulate rates recorded in the reserve homes of Aboriginal infants registered levels considered to be detrimental to the health of the inhabitants . Such extreme levels could contribute to the high incidence of respiratory disease and SIDS experienced by Canadian Aboriginal infants. Microb Ecol, 1999 Aug, 38(2), 136 - 145 Temporal and Vertical Difference in Factors Limiting Growth Rate of Heterotrophic Bacteria in Lake Biwa; Gurung TB et al.; > Abstract Dilution bioassays were performed to examine the seasonal and vertical difference in the relative importance of factors limiting growth of heterotrophic bacteria in Lake Biwa . The lake water diluted by 0.2 microm lake filtrate (1:6.6) was enriched either with glucose (C), inorganic phosphorus (P), ammonium nitrogen (N), amino acids (AA), or a combination of these, and incubated for 2 days at the depths where lake water was collected (2.5, 20 and 30 m depths) . Experiments showed that at 2.5 m, P was the most deficient resource for bacterial growth, but the magnitude of P limitation depended on water temperature . Among others, amino acids showed a slight but significant stimulation of bacterial growth rates during the fall . At 20 and 30 m, however, growth stimulation by resource addition was rarely detected . Vertically reciprocal translocation experiments revealed that the growth rate was limited by low temperature rather than resource supply at the greater depths . The results support a simple view that bacterial growth rate is basically regulated by water temperature, but high growth rate is not realized in summer because of resource depletion . The present study suggests that both temperature and P supply play a crucial role in biogeochemical cycling of organic matter in Lake Biwa through the bacterial growth rate.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p136.html Biofizika, 1999 May-Jun, 44(3), 503 - 4 {Oscillation in the number of bacteria during starvation}; Vakhitov TIa; Factors stimulating the increase in the numbers of Escherichia coli bacteria and accelerating their death were studied . It was shown that oscillations in the numbers of viable bacteria are due to periodic changes in the activity of these two factors, which do not coincide in phase . The oscillations in cell numbers occur only at particular cell concentrations. Curr Opin Microbiol, 1998 Feb, 1(1), 109 - 14 Protein signaling via type III secretion pathways in phytopathogenic bacteria; Mudgett MB et al.; Progress in the genetic and biochemical dissection of the hrp-encoded type III secretion pathway has revealed new mechanisms by which phytopathogenic bacteria infect plants . The suggestion that bacterial gene products are 'delivered to' and 'perceived by' plants cells has fundamentally changed the way in which plant-bacterial interactions are now being viewed. Planta, 1999 Aug 12, 209(2), 259 - 263 Rhizosphere bacteria enhance the accumulation of selenium and mercury in wetland plants; de Souza MP et al.; The role of rhizosphere bacteria in facilitating Se and Hg accumulation in two wetland plants, saltmarsh bulrush (Scirpus robustus Pursh) and rabbitfoot grass (Polypogon monspeliensis (L.) Desf.), was studied . Ampicillin-amended plants (i.e., with inhibited rhizosphere bacteria) supplied with Na(2)SeO(4) or HgCl(2) had significantly lower concentrations of Se and Hg, respectively, in roots than plants without ampicillin . These results were confirmed by inoculating axenic saltmarsh bulrush plants with bacteria isolated from the rhizosphere of plants collected from the field; these plants accumulated significantly more Se and Hg compared to axenic controls . Therefore, rhizosphere bacteria can increase the efficiency of Se and Hg phytoremediation by promoting the accumulation of Se and Hg in tissues of wetland plants. Proc Natl Acad Sci U S A, 1999 Aug 3, 96(16), 8873 - 8 A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea; Komori K et al.; The Holliday junction is an essential intermediate of homologous recombination . RecA of Bacteria, Rad51 of Eukarya, and RadA of Archaea are structural and functional homologs . These proteins play a pivotal role in the formation of Holliday junctions from two homologous DNA duplexes . RuvC is a specific endonuclease that resolves Holliday junctions in Bacteria . A Holliday junction-resolving activity has been found in both yeast and mammalian cells . To examine whether the paradigm of homologous recombination apply to Archaea, we assayed and found the activity to resolve a synthetic Holliday junction in crude extract of Pyrococcus furiosus cells . The gene, hjc (Holliday junction cleavage), encodes a protein composed of 123 amino acids, whose sequence is not similar to that of any proteins with known function . However, all four archaea, whose total genome sequences have been published, have the homologous genes . The purified Hjc protein cleaved the recombination intermediates formed by RecA in vitro . These results support the notion that the formation and resolution of Holliday junction is the common mechanism of homologous recombination in the three domains of life. Appl Environ Microbiol, 1999 Aug, 65(8), 3407 - 12 Determination of abundance and biovolume of bacteria in sediments by dual staining with 4',6-diamidino-2-phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics; Kuwae T et al.; We measured the abundance and biovolume of bacteria in intertidal sediments from Tokyo Bay, Japan, by using a dual-staining technique (4',6-diamidino-2-phenylindole and acridine orange) and several dispersion techniques (ultrasonic cleaner, ultrasonic sonicator, and tissue homogenizer) . Dual staining reduced serious background fluorescence, particularly when used for silt-, clay-, and detritus-rich sediments, and allowed us to distinguish bacteria from other objects during both counting and sizing . Within the studied samples, the number of bacterial cells ranged from 0.20 x 10(9) to 3 . 54 x 10(9) g of wet sediment(-1) . With the cleaner and sonicator treatments, the bacterial numbers for all of the sites initially increased with dispersion time and then became constant . For the homogenizer treatments, the highest bacterial numbers were observed with the shortest (0.5- to 2-min) treatments, and the counts then declined steeply as the homogenization time increased, indicating that cell destruction occurred . The cleaner treatment had the possibility of insufficient dispersion of bacteria for fine-grain sediments . Within the studied samples, the bacterial biovolume ranged from 0.07 to 0.22 microm(3) . With the cleaner and sonicator treatments, the biovolume peaked during the shorter dispersion time . This pattern was caused not by cell destruction but by the incremental portion of dispersed small cells . We concluded that with the cleaner and sonicator treatments, the longer dispersion time reflected the real size spectrum and was preferable for accurate estimation of mean bacterial biovolumes. Int J Syst Bacteriol, 1999 Jul, 49 Pt 3, 1241 - 6 Studies on the phylogenetic relationships of melanogenic marine bacteria: proposal of Marinomonas mediterranea sp . nov; Solano F et al.; The polyphenol oxidase (PPO) activities of the marine melanogenic strains MMB-1T and 2-40 were compared . Both contained a multifunctional PPO able to oxidize a wide range of substrates . In spite of this similarity, phylogenetic studies based on 16S rRNA sequences showed that these strains are not closely related . Strain 2-40 is not related to any previously described genus . On the basis of these studies and morphological and physiological characteristics, it is proposed that strain MMB-1T (= CECT 4803T = ATCC 700492T) represents a new species in the genus Marinomonas, Marinomonas mediterranea sp . nov. Rev Med Univ Navarra, 1998 Oct-Dec, 42(4), 183 - 7 {Intestinal bacteria overgrowth in chronic hepatopathies}; Casafont F et al.; Intestinal bacterial overgrowth (IBD) is very frequent in patients with chronic hepatopathies . Causes of IBO, although not entirely known, principally are: the hepatopathy, the alcoholism and the alterations produced by these two factors, such as achylia (and above all hypochlorhydria), decrease in the secretion of IgA, and malnutrition . On the other hand, the IBO increases the severity of the hepatopathy and frequently produces a bacterial peritonitis . All these data suggest that the IBO play an important role increasing the hepatopathy severity and consequently is a factor to bear in mind. Int J Biol Macromol, 1999 Jun-Jul, 25(1-3), 303 - 6 PHA production, from bacteria to plants; Valentin HE et al.; The genes encoding the polyhydroxyalkanoate (PHA) biosynthetic pathway in Ralstonia eutropha (3-ketothiolase, phaA or bktB; acetoacetyl-CoA reductase, phaB; and PHA synthase, phaC) were engineered for plant plastid targeting and expressed using leaf (e35S) or seed-specific (7s or lesquerella hydroxylase) promoters in Arabidopsis and Brassica . PHA yields in homozygous transformants were 12-13% of the dry mass in homozygous Arabidopsis plants and approximately 7% of the seed weight in seeds from heterozygous canola plants . When a threonine deaminase was expressed in addition to bktB, phaB and phaC, a copolyester of 3-hydroxybutyrate and 3-hydroxyvalerate was produced in both Arabidopsis and Brassica. Arch Latinoam Nutr, 1999 Mar, 49(1), 72 - 5 {Thermoresistance of acid producing psychrotrophic bacteria isolated from milk}; Alfenas Rde C; An acidificant psychrotrophic bacteria was isolated from raw milk from Bromocresol Purple Agar medium, after incubation at 7 degrees C, for 10 days . Cells from the culture, at the beginning of the stationary phase, were inoculated sterilized in powder milk, reconstituted at 12% of total solids, resulting in approximately 10(8) cells per milliliter . Portions of 3 ml of inoculated milk were transferred to borosilicate tubes and were submitted to cells resistance determination at 62, 70, 75 and 80 degrees C, by the TDT tube method . The survival curves at the respective temperatures and the curve of thermal death were drawn . The bacteria presented a D75 degrees C value of 0.15 minutes and z = 8.7 degrees C . Treatments LTLT and HTST of pasteurization promoted 5.27 and 0.53 decimal reductions in the number of available bacteria cells, respectively . The conclusion of this study was that the isolated bacteria is destroyed only by the treatment LTLT of pasteurization. J Chromatogr A, 1999 May 28, 843(1-2), 287 - 300 Carbohydrate profiling of bacteria by gas chromatography-mass spectrometry and their trace detection in complex matrices by gas chromatography-tandem mass spectrometry; Fox A; Bacterial cellular polysaccharides are composed of a variety of sugar monomers . These sugars serve as chemical markers to identify specific species or genera or to determine their physiological status . Some of these markers can also be used for trace detection of bacteria or their constituents in complex clinical or environmental matrices . Analyses are performed, in our hands, employing hydrolysis followed by the alditol acetate derivatization procedure . Substantial improvements have been made to sample preparation including simplification and computer-controlled automation . For characterization of whole cell bacterial hydrolysates, sugars are analyzed by gas chromatography-mass spectrometry (GC-MS) . Simple chromatograms are generated using selected ion monitoring (SIM) . Using total ion GC-MS, sugars can be readily identified . In more complex clinical and environmental samples, markers for bacteria are present at sufficiently low concentrations that more advanced instrumentation, gas chromatography-tandem mass spectrometry (GC-MS-MS), is preferred for optimal analysis . Using multiple reaction monitoring, MS-MS is used (replacing more conventional SIM) to ignore extraneous chromatographic peaks . Triple quadrupole and ion trap GC-MS-MS instruments have both been used successfully . Absolute chemical identification of sugar markers at trace levels is achieved, using MS-MS, by the product spectrum. Biotechnol Bioeng, 1999 Aug 20, 64(4), 478 - 83 Inhibitory effect of iron-oxidizing bacteria on ferrous-promoted chalcopyrite leaching Hiroyoshi N, Hirota M, Hirajima T, Tsunekawa M. It is generally accepted that iron-oxidizing bacteria, Thiobacillus ferrooxidans, enhance chalcopyrite leaching . However, this article details a case of the bacteria suppressing chalcopyrite leaching . Bacterial leaching experiments were performed with sulfuric acid solutions containing 0 or 0.04 mol/dm3 ferrous sulfate . Without ferrous sulfate, the bacteria enhance copper extraction and oxidation of ferrous ions released from chalcopyrite . However, the bacteria suppressed chalcopyrite leaching when ferrous sulfate was added . This is mainly due to the bacterial consumption of ferrous ions which act as a promoter for chalcopyrite oxidation with dissolved oxygen . Coprecipitation of copper ions with jarosite formed by the bacterial ferrous oxidation also causes the bacterial suppression of copper extraction . Genomics, 1999 Jul 1, 59(1), 18 - 23 A human nucleobase transporter-like cDNA (SLC23A1): member of a transporter family conserved from bacteria to mammals; Hogue DL et al.; A family of related polytopic membrane proteins that mediate the transport of nucleobases has been extended to Homo sapiens by the cloning of a full-length human cDNA that encodes a nucleobase transporter-like protein . The protein is predicted to contain 11-14 transmembrane-spanning regions, exhibits 20-28% overall sequence identity to fungal and bacterial transporters, and contains a conserved signature motif found in this family . Fluorescence in situ hybridization localized the gene (HGMW-approved symbol SLC23A1) to human chromosome 20p13 . Human nucleobase transporter-like mRNA was present in all tissues examined, with lower levels found in heart, skeletal muscle, and ovary . Expression of the 60-kDa cDNA-encoded protein was demonstrated by an in vitro transcription-translation approach . The identification of this nucleobase transporter-like protein will allow the further elucidation of the interaction of human cells with physiological nucleobases and pharmacologically important drugs such as 5-F-uracil, dideoxynucleosides, and acyclic nucleosides . J Microbiol Methods, 1999 Jul, 37(1), 77 - 86 LIVE/DEAD BacLight : application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water; Boulos L et al.; A rapid epifluorescence staining method using the LIVE/DEAD Bacterial Viability Kit (BacLight) was applied to estimate both viable and total counts of bacteria in drinking water . BacLight is composed of two nucleic acid-binding stains: SYTO 9 and propidium iodide . SYTO 9 penetrates all bacterial membranes and stains the cells green, while propidium iodide only penetrates cells with damaged membranes, and the combination of the two stains produces red fluorescing cells . Optimal incubation conditions were found to be 15 to 20 min, at room temperature in the dark . Total (red + green) and viable (green) cells can hence be counted simultaneously . Factors affecting the staining procedure were tested (addition of glutaraldehyde, staining time, chlorine impact) . In the absence of stress, BacLight viable counts were comparable and to 5-cyano-2,3-ditolyl tetrazolium (CTC) counts . BacLight total counts were comparable to acridine orange counts (differing by <0.1 log/ml) . However, the increase in environmental stresses (chlorine, growth rate or temperature) induced a decrease in viability that was more pronounced for CTC and plate counts than for BacLight viable counts. Biochim Biophys Acta, 1999 Jun 30, 1412(2), 149 - 72 Uphill energy transfer in LH2-containing purple bacteria at room temperature Trissl HW, Law CJ, Cogdell RJ. Uphill energy transfer in the LH2-containing purple bacteria Rhodopseudomonas acidophila, Rhodopseudomonas palustris, Rhodobacter sphaeroides, Chromatium vinosum and Chromatium purpuratum was studied by stationary fluorescence spectroscopy at room temperature upon selective excitation of the B800 pigments of LH2 and the B880 pigments of LH1 at 803 nm and 900 nm, respectively . The resulting fluorescence spectra differed significantly at wavelengths shorter than the fluorescence maximum but agreed at longer wavelengths . The absorption spectra of the species studied were decomposed into five bands at approx . 800, 820, 830, 850 and 880 nm using the shapes of the absorption spectra of the LH1-RC only species Rhodospirillum rubrum and the isolated B800-850 complex from Rps . acidophila strain 10050 as guide spectra . This allowed a quantification of the number of pigments in each pigment group and, consequently, the antenna size of the photosynthetic unit assuming 36 bacteriochlorophyll a molecules in an LH1-RC complex . In most of the LH2-containing purple bacterial strains the number of LH2 rings per LH1-RC was less than the idealized number of eight (Papiz et al., Trends Plant Sci . 1 (1996) 198-206), which was achieved only by C . purpuratum . Uphill energy transfer was assayed by comparing the theoretical fluorescence spectrum obtained from a Boltzmann equilibrium with the measured fluorescence spectrum obtained by 900 nm excitation . The good match of both spectra in all the purple bacteria studied indicates that uphill energy transfer occurs practically up to its thermodynamically maximal possible extent . All strains studied contained a small fraction of either poorly connected or unconnected LH2 complexes as indicated by higher fluorescence yields from the peripheral complexes than predicted by thermal equilibration or kinetic modeling . This impedes generally the quantitative analysis of blue-excited fluorescence spectra. Trends Genet, 1999 Jul, 15(7), 273 - 7 Cell fate and organogenesis in bacteria; Kaiser D; Intercellular signaling through the Notch receptor and its ligands leads to the spatial differentiation of cell fate in vertebrates and invertebrates . In Myxococcus xanthus, fruiting-body development requires the transmission of a cell-bound intercellular signal by the protein called C-factor, which is functionally equivalent to the eukaryotic Notch ligands . Functional parallels between these two signaling systems include strong positive and negative feedback, and a consequent role in spatial differentiation . Consideration of these parallels enables us to make testable experimental predictions about Notch and C-signaling. J Invest Dermatol, 1999 Jun, 112(6), 910 - 8 Human epidermal differentiation complex in a single 2.5 Mbp long continuum of overlapping DNA cloned in bacteria integrating physical and transcript maps; South AP et al.; Terminal differentiation of keratinocytes involves the sequential expression of several major proteins which can be identified in distinct cellular layers within the mammalian epidermis and are characteristic for the maturation state of the keratinocyte . Many of the corresponding genes are clustered in one specific human chromosomal region 1q21 . It is rare in the genome to find in such close proximity the genes belonging to at least three structurally different families, yet sharing spatial and temporal expression specificity, as well as interdependent functional features . This DNA segment, termed the epidermal differentiation complex, contains 27 genes, 14 of which are specifically expressed during calcium-dependent terminal differentiation of keratinocytes (the majority being structural protein precursors of the cornified envelope) and the other 13 belong to the S100 family of calcium binding proteins with possible signal transduction roles in the differentiation of epidermis and other tissues . In order to provide a bacterial clone resource that will enable further studies of genomic structure, transcriptional regulation, function and evolution of the epidermal differentiation complex, as well as the identification of novel genes, we have constructed a single 2.45 Mbp long continuum of genomic DNA cloned as 45 p1 artificial chromosomes, three bacterial artificial chromosomes, and 34 cosmid clones . The map encompasses all of the 27 genes so far assigned to the epidermal differentiation complex, and integrates the physical localization of these genes at a high resolution on a complete NotI and SalI, and a partial EcoRI restriction map . This map will be the starting resource for the large-scale genomic sequencing of this region by The Sanger Center, Hinxton, U.K. Ital J Gastroenterol Hepatol, 1999 Apr, 31(3), 244 - 6 Crohn's disease: the case for bacteria; Prantera C et al.; At the present time, there is no convincing indication that Crohn's disease is a bacterial disease, although an association with mycobacteria has been hypothesised for many years . The hypothesis that bacteria could be the cause, or at least an important concause of Crohn's disease is supported by several experimental and clinical observations: animals kept in a germ-free environment fail to develop intestinal inflammation; bacteria are the cause of human and animal intestinal diseases similar to Crohn's disease; luminal content is necessary for causing gut lesions; and, moreover, antibiotics are successfully used in the treatment of Crohn's disease . Bradford Hill criteria recently used to assess a causal relationship for Helicobacter pylori and peptic ulcer can be applied for establishing or excluding a causality between mycobacteria and Crohn's disease . Of these criteria, only biological plausibility, coherence and analogy are satisfied . However, failure to identify a specific pathogen does not exclude a possible role for bacteria in causing Crohn's disease lesions and symptoms . Pathogenic or commensal enteric bacteria could overinfect the primary lesions, leading to chronic intestinal inflammation in genetically susceptible hosts . Another possibility is that components of the normal intestinal flora could acquire pathogenic characteristics. Proc Natl Acad Sci U S A, 1999 Jun 22, 96(13), 7348 - 51 Mutation, recombination, and incipient speciation of bacteria in the laboratory; Vulic M et al.; Mutations in the DNA mismatch repair system increase mutation and recombination . They may thereby promote the genetic divergence that underlies speciation, after which the reacquisition of a functional repair system may sustain that divergence by creating a barrier to recombination . We tested several lines of Escherichia coli, derived from a common ancestor and evolved for 20,000 generations, for their recombination ability . Some lines, but not others, had become mismatch repair-defective mutators during experimental evolution, providing different opportunities for DNA sequence divergence . We knocked out the repair system in lines that had retained this function, and we restored function to those lines that had become defective . We then estimated recombination rates in various crosses between these repair-deficient and -proficient strains . The effect of the mismatch repair system on recombination was greatest in those lines that had evolved nonfunctional repair, indicating they had undergone more sequence divergence and, consequently, were more sensitive to the recombination-inhibiting effect of a functional repair system . These results demonstrate the establishment of an incipient genetic barrier between formerly identical lines, and they support a model in which the mismatch repair system can influence speciation dynamics through its simultaneous effects on mutation and recombination. Parassitologia, 1998 Sep, 40(3), 247 - 9 Preliminary results on the effect of tetracycline on the embryogenesis and symbiotic bacteria (Wolbachia) of Dirofilaria immitis . An update and discussion; Genchi C et al.; The distribution and phylogeny of Wolbachia in filarial species suggests that these endosymbiotic bacteria may be important in the biology of their filarial hosts . An experiment to falsify this hypothesis would be to treat filarial worms with antibiotics which are active against intracellular bacteria . Indeed, it has already been shown that tetracycline treatment inhibits development in a model filarial species (Brugia pahangi) at different stages of the life cycle, in both mosquito and mammalian hosts . Here we discuss these previous data and present new results on the effect of tetracycline on the embryogenesis of the canine filaria Dirofilaria immitis. Mar Biotechnol (NY), 1999 Jan, 1(1), 107 - 111 Requisite Morphologic Interaction for Attachment between Ulva pertusa (Chlorophyta) and Symbiotic Bacteria; Nakanishi K et al.; : In order to understand the morphogenesis-inducing mechanism of Ulva pertusa by symbiotic bacteria, we observed the requisite conditions of bacteria for attachment to U . pertusa for algal morphogenesis . Non-morphogenesis-inducing bacterial mutants derived by ultraviolet irradiation did not attach onto the surface of this alga . Scanning electron microscopic observation during the process of morphogenesis in U . pertusa revealed a network-like structure formed on the algal surface within 1 week after application of bacteria . The bacteria attached onto the alga after 2 weeks of incubation . After this attachment process the morphologic change was observed in U . pertusa. Virology, 1999 Jun 20, 259(1), 176 - 89 Catalytic features of the recombinant reverse transcriptase of bovine leukemia virus expressed in bacteria; Perach M et al.; We have expressed the recombinant reverse transcriptase (RT) of bovine leukemia virus (BLV) in bacteria . The gene encoding the RT was designed to start at its 5' end next to the last codon of the mature viral protease, namely the amino terminus of the RT matches the last 26 codons of the pro gene and is coded for by the pro reading frame . The RT sequence extends into the pol gene, utilizing the pol reading frame after overcoming the stop codon by adding an extra nucleotide (thus imitating the naturally occurring frameshift event) . Hence we have generated a transframe polypeptide that is a 584-residues-long protein (see Rice, Stephens, Burny, and Gilden (1985) Virology 142, 357-377) . This protein was partially purified after adding a six-histidine tag and studied biochemically testing a variety of parameters . The enzyme exhibits all activities typical of RTs, i.e., both RNA- and DNA-dependent DNA polymerase as well as a ribonuclease H (RNase H) activity . Unlike most RTs, the BLV RT is enzymatically active as a monomer even after binding a DNA substrate . The enzyme shows a preference for Mg2+ over Mn2+ in both its DNA polymerase and RNase H activities . BLV RT is relatively resistant to nucleoside triphosphate analogues, which are known to be potent inhibitors of other RTs such as that of HIV . J Hosp Infect, 1999 May, 42(1), 61 - 8 Correlation between surface and air counts of particles carrying aerobic bacteria in operating rooms with turbulent ventilation: an experimental study; Friberg B et al.; Airborne contamination with bacteria-carrying particles (cfu/m3) and their sedimentation rate (cfu/m2/h) was compared in an operating room (OR) equipped with two turbulent ventilation systems . One was a thermally based system with inlet of cool clean air at the floor level and evacuation of the air at the ceiling by convection (17 air changes/h) . The other was a conventional plenum pressure system with air supply at the ceiling and evacuation at the floor level (16 air changes/h) . The study was made during rigidly standardised sham operations (N = 20) performed in the same OR by the same six member team wearing non-woven disposable or cotton clothing . Airborne contamination in the wound and instrument areas was related to the surface contamination rate in the same areas and in addition, on the patient chest and in the periphery of the OR . With the exception of the periphery of the OR, the surface and air contamination rates were highly correlated in both ventilation systems (P = 0.02-0.0006, r2 = 0.52-0.79) . This was also true particularly when disposable clothing was used while the correlation was weaker in cotton clothing experiments . An equation describing the relation between surface and air counts is given . Typically, the surface counts were numerically 16-fold the air counts, i.e., the number of colonies sedimenting on four 14 cm-diameter agar plates during 1 h will almost equal the number of airborne cfu per m3 . We propose, that sedimentation plates represent not only a technically easier method than air sampling but when correctly used, are also the most realistic indicator of airborne bacterial OR contamination in areas critical for surgery. Biochem Biophys Res Commun, 1999 Jun 7, 259(2), 271 - 82 Mass spectrometric determination of a novel modification of the N-terminus of histidine-tagged proteins expressed in bacteria; Yan Z et al.; Two proteins, FKBP, and Spo0F, were expressed in bacteria as histidine-tagged fusion proteins and isolated under native conditions . MALDI-TOF-MS analysis revealed that each protein preparation contained two components, neither of which corresponded to the molecular weights predicted from DNA sequences . The difference in molecular weight between the two FKBP components and two Spo0F components was approximately 178 +/- 14 Da . Site-specific proteolytic cleavage resulted in the release of histidine-tagged peptide from the recombinant proteins . MALDI mass spectra of the cleaved proteins showed a single molecular ion peak for each species with the predicted molecular weights . The histidine-tagged peptide released from both fusion proteins displayed two distinct peaks by MALDI-FT-MS corresponding to monoisotopic molecular weights of 2269 . 027 Da and 2447.087 Da, respectively, which were both inconsistent with the predicted peptide sequence M-G-H-H-H-H-H-H-H-H-H-H-S-S-G-H-I-E-G-R of 2400.055 Da . The peptide at 2269.027 Da was sequenced by ESI-MS-MS and found to be a truncated histidine tag resulting from an initiator methionine deletion . ESI-MS-MS analysis of the peptide at 2447.087 Da indicated a moiety of 178.0 Da attached to the second residue glycine of the histidine tag . This alteration of the N-terminus does not fit any known modifications . A synthetic peptide with the identical sequence of the isolated his-tag M-G-H-H-H-H-H-H-H-H-H-H remained unmodified during the protein purification process, suggesting that modification of the initiator methionine was carried out in vivo, rather than the result of a chemical reaction from the isolation procedure . Med Hypotheses, 1999 Mar, 52(3), 209 - 12 Mouth bacteria as the cause of Paget's disease of bone; Dickinson CJ; The many viruses associated with Pagetic osteoclasts could be opportunistic rather than causative . Some mouth bacteria can lyse bone . One (Actinobacillus actinomycetemcomitans) can grow and even multiply inside human cell lines in culture, producing osteolytic materials -- one 62 kDa protein having a potency in the picomolar range . A small focus of this, or of one of the other periodontitis-causing bacteria, in a bone might gradually spread its influence to activate osteoclasts -- the first stage in Paget's disease . The focus in each bone might be small and easily overlooked, as other intracellular bacteria have been in the past. Anal Chem, 1999 May 15, 71(10), 1990 - 6 Monitoring the growth of a bacteria culture by MALDI-MS of whole cells; Arnold RJ et al.; We have probed the time evolution of a growing bacteria culture by extracting samples periodically and performing matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) on whole cells . The mass spectra generated by this method contain tens of peaks in the 3-11-kDa mass range . Cultures of E . coli strain K-12 were grown in two types of containers and at two nutrient concentrations and sampled periodically from 6 to 84 h after inoculation . The relative intensities of several of the stronger peaks vary quite dramatically as a function of time . These temporal characteristics must be taken into account when MALDI-MS is applied to identify bacteria . The results also suggest that MALDI-MS can be used to follow the aging of a bacteria culture. Genetics, 1999 Jun, 152(2), 485 - 93 Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria; Tenaillon O et al.; Selection of mutator alleles, increasing the mutation rate up to 10, 000-fold, has been observed during in vitro experimental evolution . This spread is ascribed to the hitchhiking of mutator alleles with favorable mutations, as demonstrated by a theoretical model using selective parameters corresponding to such experiments . Observations of unexpectedly high frequencies of mutators in natural isolates suggest that the same phenomenon could occur in the wild . But it remains questionable whether realistic in natura parameter values could also result in selection of mutators . In particular, the main parameters of adaptation, the size of the adapting population and the height and steepness of the adaptive peak characterizing adaptation, are very variable in nature . By simulation approach, we studied the effect of these parameters on the selection of mutators in asexual populations, assuming additive fitness . We show that the larger the population size, the more likely the fixation of mutator alleles . At a large population size, at least four adaptive mutations are needed for mutator fixation; moreover, under stronger selection stronger mutators are selected . We propose a model based on multiple mutations to illustrate how second-order selection can optimize population fitness when few favorable mutations are required for adaptation. Biochemistry, 1999 Jun 1, 38(22), 7159 - 67 ENDOR and special TRIPLE resonance spectroscopy of photoaccumulated semiquinone electron acceptors in the reaction centers of green sulfur bacteria and heliobacteria; Muhiuddin IP et al.; Photoaccumulation at 205 K in the presence of dithionite produces EPR signals in anaerobically prepared membranes from Chlorobium limicola and Heliobacterium chlorum that resemble the EPR spectrum of phyllosemiquinone (A1*-) photoaccumulated in photosystem I . We have used ENDOR and special TRIPLE resonance spectroscopy to demonstrate conclusively that these signals arise from menasemiquinone electron acceptors reduced by photoaccumulation . Hyperfine couplings to two protons H-bonded to the semiquinone oxygens have been identified by exchange of H . chlorum into D2O, and hyperfine couplings to the methyl group, and the methylene group of the phytyl side chain, of the semiquinone have also been assigned . The electronic structure of these menasemiquinones in these reaction centers is very similar to that of phyllosemiquinone in PSI, and shows a distorted electron spin density distribution relative to that of phyllosemiquinone in vitro . Special TRIPLE resonance spectrometry has been used to investigate the effect of detergents and oxygen on membranes of C . limicola . Triton X-100 and oxygen affect the menaquinone binding site, but n-dodecyl beta-D-maltoside preparations exhibit a relatively unaltered special TRIPLE spectrum for the photoaccumulated menasemiquinone. J Microbiol Methods, 1999 May, 36(1-2), 29 - 33 Community level physiological profile of soil bacteria unaffected by extraction method; Mayr C et al.; Extraction and purification of bacteria from soil by the Nycodenz gradient centrifugation procedure described by Bakken and Lindahl (1995; Recovery of bacterial cells from soil . In: van Elsas, J.D., Trevors, J.T . (Eds.), Nucleic Acids in the Environment: Methods and Applications . Springer Verlag, Berlin, pp . 9-27) were compared to soil slurry extractions . Bacterial communities from four different soils were described by the bacterial abundance, CTC-reducing capacity, culturability and the community level physiological profiles (CLPP) in BIOLOG GN plates . A significant loss of both total and culturable number of bacteria g(-1) soil dry weight were found after extraction and purification of cells . The origin of soil influenced the yield of cells and a difference between the four soils and an interaction between the soils and extraction procedure were found . The culturability and the CLPP were different between the four soils but were unaffected by the extraction procedure . The bacterial community obtained after extraction and purification thus represented the same fraction of the indigenous bacterial community. J Microbiol Methods, 1999 May, 36(1-2), 3 - 10 Study of the interaction of sulphate-reducing bacteria exopolymers with iron using X-ray photoelectron spectroscopy and time-of-flight secondary ionisation mass spectrometry; Beech IB et al.; Time-of-flight secondary ionisation mass spectrometry and X-ray photoelectron spectroscopy were employed to determine the interaction of crude extracellular polymeric substances recovered from static batch cultures of two isolates of marine sulphate-reducing bacteria of the genus Desulfovibrio, grown in the presence of and without mild steel surfaces, with Fe ions released from steel . The results demonstrated that exopolymers synthesised by different strains of sulphate-reducers varied in their ability to bind iron originating from steel . Based on the X-ray photoelectron spectroscopy analysis it is proposed that Fe released from steel was associated with bacterial exopolymers such as Fe(III) ion . The application of surface science techniques to study exopolymer/metal interaction allowed quantitative evaluation of Fe binding using small sample size. FASEB J, 1999, 13 Suppl, S55 - 61 Mechanosensitive channels in bacteria as membrane tension reporters; Sukharev S; The purpose of this short review is to discuss recent data on the molecular structure and mechanism of gating of MscL, a mechanosensitive channel of large conductance from Escherichia coli . MscL is the first isolated molecule shown to convert mechanical stress of the membrane into a simple response, the opening of a large aqueous pore . The functional complex appears to be a stable homo-pentamer of 15-kDa subunits, the gating transitions in which are driven by stretch forces conveyed through the lipid bilayer . We have measured the open probability of MscL and the kinetics of transitions as a function of membrane tension . The parameters extracted from the single-channel current recordings and dose-response curves such as the energy difference between the closed, open, and intermediate conducting states, and the transition-related changes in protein dimensions suggest a large conformational rearrangement of the channel complex . The estimations show that in native conditions MscL openings could be driven primarily by forces of osmotic nature . The thermodynamic and spatial parameters reasonably correlate with the available data on the structure of a single MscL subunit and multimeric organization of the complex . Combined with the functional analysis of mutations, these data give grounds to hypotheses on the nature of the channel mechanosensitivity. Appl Environ Microbiol, 1999 Jun, 65(6), 2758 - 61 Iron-oxidizing bacteria are associated with ferric hydroxide precipitates (Fe-plaque) on the roots of wetland plants Emerson D, Weiss JV, Megonigal JP. The presence of Fe-oxidizing bacteria in the rhizosphere of four different species of wetland plants was investigated in a diverse wetland environment that had Fe(II) concentrations ranging from tens to hundreds of micromoles per liter and a pH range of 3.5 to 6.8 . Enrichments for neutrophilic, putatively lithotrophic Fe-oxidizing bacteria were successful on roots from all four species; acidophilic Fe-oxidizing bacteria were enriched only on roots from plants whose root systems were exposed to soil solutions with a pH of <4 . In Sagittaria australis there was a positive correlation (P < 0.01) between cell numbers and the total amount of Fe present; the same correlation was not found for Leersia oryzoides . These results present the first evidence for culturable Fe-oxidizing bacteria associated with Fe-plaque in the rhizosphere. Can J Microbiol, 1998 Dec, 44(12), 1177 - 82 Interactions between gut-associated lymphoid tissue and colonization levels of indigenous, segmented, filamentous bacteria in the small intestine of mice; Snel J et al.; Unlike most other indigenous bacteria, segmented filamentous bacteria (SFB) are potent activators of the mucosal immune system . SFB are strongly anchored to the epithelial cells of the small intestine where they have a preference for mucosal lymphoid epithelium . Since SFB are only present in high numbers shortly after weaning, it was investigated whether an SFB-induced immune reaction results in the removal of these bacteria from the small intestine . A correlation was found between age and colonization levels in the small intestines of SFB monoassociated Swiss mice . Five-week-old athymic BALB/c (nu/nu) mice showed lower colonization levels than their heterozygous littermates, but the opposite was found at the age of 12 weeks . However, SFB inoculation of germfree Swiss mice resulted in higher colonization levels in 5-week-old mice when compared with 4-month-old mice . We conclude that SFB colonization levels in the small intestine are likely influenced by the activity of the mucosal immune system . However, an additional age-dependent factor that modulates SFB colonization levels cannot be excluded. Appl Environ Microbiol, 1999 Jun, 65(6), 2565 - 9 Cellobiose transport by mixed ruminal bacteria from a Cow; Kajikawa H et al.; The transport of cellobiose in mixed ruminal bacteria harvested from a holstein cow fed an Italian ryegrass hay was determined in the presence of nojirimycin-1-sulfate, which almost inhibited cellobiase activity . The kinetic parameters of cellobiose uptake were 14 microM for the Km and 10 nmol/min/mg of protein for the Vmax . Extracellular and cell-associated cellobiases were detected in the rumen, with both showing higher Vmax values and lower affinities than those determined for cellobiose transport . The proportion of cellobiose that was directly transported before it was extracellularly degraded into glucose increased as the cellobiose concentration decreased, reaching more than 20% at the actually observed levels of cellobiose in the rumen, which were less than 0.02 mM . The inhibitor experiment showed that cellobiose was incorporated into the cells mainly by the phosphoenolpyruvate phosphotransferase system and partially by an ATP-dependent and proton-motive-force-independent active transport system . This finding was also supported by determinations of phosphoenolpyruvate phosphotransferase-dependent NADH oxidation with cellobiose and the effects of artificial potentials on cellobiose transport . Cellobiose uptake was sensitive to a decrease in pH (especially below 6.0), and it was weakly but significantly inhibited in the presence of glucose. Appl Environ Microbiol, 1999 Jun, 65(6), 2300 - 6 Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp . nov . and Acetobacterium psammolithicum sp . nov., and their ecological roles; Krumholz LR et al.; We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem . Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract . Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated . Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp . nov . and Acetobacterium psammolithicum sp . nov . The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined . In an experiment in which direct competition for H2 between D . hypogeium and A . psammolithicum was examined, sulfate reduction was the dominant process. Biochemistry, 1999 May 25, 38(21), 6817 - 25 Separate oligosaccharide determinants mediate interactions of the low-molecular-weight salivary mucin with neutrophils and bacteria; Prakobphol A et al.; The low-molecular-weight human salivary mucin (MG2) coats oral surfaces, where it is in a prime location for governing cell adhesion . Since oligosaccharides form many of the interactive facets on mucin molecules, we examined MG2 glycosylation as it relates to the molecule's adhesive functions . Our previous study of MG2 oligosaccharide structures showed that the termini predominantly carry T, sialyl-T, Lewisx (Lex), sialyl Lex (sLex), lactosamine, and sialyl lactosamine determinants {Prakobphol, A., et al . (1998) Biochemistry 37, 4916-4927} . In addition, we showed that sLex determinants confer L-selectin ligand activity to this molecule . Here we studied adhesive interactions between MG2 and cells that traffic in the oral cavity: neutrophils and bacteria . Under flow conditions, neutrophils tethered to MG2-coated surfaces at forces between 1.25 and 2 dyn/cm2, i.e., comparable to the shear stress generated at the tooth surface by salivary flow ( approximately 0.8 dyn/cm2) . MG2 was also found in association with neutrophils isolated from the oral cavity, evidence that the cells interact with this mucin in vivo . Since MG2 serves as an adhesion receptor for bacteria, the MG2 saccharides that serve this function were also identified . Seven of 18 oral bacteria strains that were tested adhered to MG2 . Importantly, six of these seven strains adhered via T antigen, sialyl-T antigen, and/or lactosamine sequences . No adherence to Lex and sLex epitopes was detected in all the strains that were tested . Together, these results suggest that distinct subsets of MG2 saccharides function as ligands for neutrophil L-selectin and receptors for bacterial adhesion, a finding with interesting implications for both oral health and mucin function. Arch Microbiol, 1999 Mar, 171(4), 265 - 72 Specific detection of green sulfur bacteria by in situ hybridization with a fluorescently labeled oligonucleotide probe; Tuschak C et al.; An oligodeoxynucleotide probe (GSB-532) specific for green sulfur bacteria was developed . Highly stringent hybridization conditions were established using whole cells of Chlorobium limicola DSM249 immobilized on glass slides . At a formamide concentration of 10%, the optimum specificity was reached at 47 degrees C . When a conventional fixation procedure was used, a conspicuous autofluorescence developed within the cells . This autofluorescence was due to the liberation of bacteriochlorophyll by the detergent Triton X-100 and a subsequent conversion to bacteriophenophytin and related compounds . The signal-to-noise ratio could be increased by a final dehydration of the samples with methanol . Finally, the method was adapted to the hybridization of natural samples collected on polycarbonate membrane filters . In situ hybridization of pure cultures, various enrichments, and natural samples from the chemocline of a freshwater lake confirmed that probe GSB-532 hybridized exclusively to cells of green sulfur bacteria . Our protocol allows the highly specific detection of green sulfur bacteria in water samples and a rapid screening of natural bacterial communities . Employing probe GSB-532, the phylogenetic affiliation of the epibionts in "Chlorochromatium aggregatum" and "Pelochromatium roseum" could be demonstrated for the first time. J Basic Microbiol, 1999, 39(2), 137 - 40 Effect of thioredoxin on the sensitivity of bacteria to chemical damage; Musrati RA et al.; The ability of thioredoxin (Trx) to protect cells from chemical damage was determined by comparing the growth of a control strain of Escherichia coli JM101 and isogenic strain transformed with the plasmid pKKTS1 containing the Streptomyces aureofaciens thioredoxin gene, in the presence of the nucleoside analogs arabinosylcytosine, 5-fluorouridine, ftorafur and carcinogen beta-naftylamine . Arabinosylcytosine showed no effect on the growth of either of the two strains . 5-fluorouridine, ftorafur {1-((R,S)-tetrahydrofuran-2-yl)-5-fluorouracil} and beta-naftylamine demonstrated lower inhibitory effects on the growth of the thioredoxin overproducing strain than on the growth of the control strain . These results suggested that Trx could protect the cells from chemical damage under certain metabolic conditions. Curr Opin Microbiol, 1999 Apr, 2(2), 195 - 201 Carbon catabolite repression in bacteria; Stulke J et al.; Carbon catabolite repression (CCR) is a regulatory mechanism by which the expression of genes required for the utilization of secondary sources of carbon is prevented by the presence of a preferred substrate . This enables bacteria to increase their fitness by optimizing growth rates in natural environments providing complex mixtures of nutrients . In most bacteria, the enzymes involved in sugar transport and phosphorylation play an essential role in signal generation leading through different transduction mechanisms to catabolite repression . The actual mechanisms of regulation are substantially different in various bacteria . The mechanism of lactose-glucose diauxie in Escherichia coli has been reinvestigated and was found to be caused mainly by inducer exclusion . In addition, the gene encoding HPr kinase, a key component of CCR in many bacteria, was discovered recently. Genes Cells, 1999 Mar, 4(3), 135 - 43 Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival; Ishihama A; Upon sensing an impending saturation level of their population density, Escherichia coli cells enter into the stationary phase . We have identified structural and functional modulations of the nucleoid, the transcription apparatus and the translation machinery occurring during the transition from exponential growth to stationary phase . The major DNA-binding proteins, Fis, HU and Hfq, in the exponential-phase nucleoid are replaced by a single stationary-phase protein Dps, thereby compacting the nucleoid and ultimately leading to silencing of the DNA functions . The transcription apparatus is modified by replacing the major promoter recognition subunit, sigma70, with sigmaS . A stationary-phase protein, Rsd (Regulator of Sigma D), with the binding activity of sigma70 is involved in the efficient replacement of sigma and/or the storage of unused sigma70 . Changes in cytoplasmic composition also differentially influence the activity of Esigma70 and EsigmaS holoenzymes . Together, these effects may result in the preferential transcription of stationary-phase specific genes . The translation machinery is also modulated in stationary phase, by the formation of translationally incompetent 100S ribosomes . A small stationary-phase protein, RMF (Ribosome Modulation Factor), is involved in the dimerization of 70S ribosome monomers. Int J Syst Bacteriol, 1999 Apr, 49 Pt 2, 729 - 35 Rhodovulum iodosum sp . nov . and Rhodovulum robiginosum sp . nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria; Straub KL et al.; Two new strains of marine purple bacteria, N1T and N2T, were isolated from coastal sediment of the North Sea (Germany) with ferrous iron as the only electron donor for anoxygenic photosynthesis . The isolates are the first salt-dependent, ferrous-iron-oxidizing purple bacteria characterized so far . Analysis of 16S rRNA gene sequences revealed an affiliation with the genus Rhodovulum, which until now comprises only marine species . The sequence similarity of both strains was 95.2%, and their closest relative was Rhodovulum adriaticum . Like all known Rhodovulum species, the new strains had ovoid to rod-shaped cells, contained bacteriochlorophyll a and carotenoids of the spheroidene series, and were able to oxidize sulfide and thiosulfate . Like Rhodovulum adriaticum, both strains were unable to assimilate sulfate; for growth they needed a reduced sulfur source, e.g . thiosulfate . In contrast to the new strains, none of the known Rhodovulum species tested was able to oxidize ferrous iron or iron sulfide . In growth experiments, strains N1T and N2T oxidized 65 and 95%, respectively, of the ferrous iron supplied . Electron diffraction analysis revealed ferrihydrite as the main product of ferrous iron oxidation . In addition, traces of magnetite were formed . Strains N1T (= DSM 12328T) and N2T (= DSM 12329T) are described as Rhodovulum iodosum sp . nov . and Rhodovulum robiginosum sp . nov., respectively. Mikrobiologiia, 1998 Nov-Dec, 67(6), 815 - 20 {Immunochemical analysis of O-specific polysaccharides from the soil nitrogen-fixing bacteria Azospirillum brasilense}; Matora LIu et al.; Immunochemical reactivity of O-specific polysaccharide and the monosaccharide composition of O-antigenic determinants of the lipopolysaccharide isolated from the type strain Sp7 of Azospirillum brasilense were studied . An original modification of the method of spectroturbidimetry for disperse biological systems and a nonstandard procedure for the preparation of monospecific antibodies against cell surface antigens were used . The polysaccharide fraction, which contained residues of galactose, rhamnose, and galacturonic acid, was able to bind about 50% of the antibodies raised against whole bacterial cells . Twelve immunodeterminant groups were shown to be present in its molecule . Galactose and, less effectively, rhamnose but not galacturonic acid inhibited the antigen-antibody reactions . It is concluded that the serotype of the strain studied is determined by galactose residues. Biol Blood Marrow Transplant, 1999, 5(1), 46 - 50 Defective anticarbohydrate antibody responses to naturally occurring bacteria following bone marrow transplantation; Kapoor N et al.; The long-term recipients of allogeneic bone marrow transplantation (BMT) are at an increased risk of death due to bacterial infections . We evaluated the anticarbohydrate antibody responses of BMT recipients to a naturally occurring bacterial carbohydrate, polyribose phosphate (PRP) . The recipients of autologous BMT achieved protective anti-PRP levels (>100 ng/mL) by 3 years after transplantation, with a pattern consistent with a recapitulation of the ontogeny of anticarbohydrate antibody responses . None of the six recipients of unrelated BMT who were off immunosuppressive therapy had protective anti-PRP levels, though their response to a protein antigen (tetanus toxoid) was normal . Of 48 recipients of histocompatible BMT, 22 (46%) had protective anti-PRP antibody levels, whereas 13 (27%) recipients who were >3 years post-BMT did not have protective levels . Therefore, all unrelated recipients and a significant proportion of histocompatible recipients without clinical graft-vs.-host disease had persistent and prolonged defects in their capacity to produce antibodies to naturally occurring bacterial carbohydrate antigens . These results suggest that allogeneic BMT recipients should be longitudinally evaluated for their anticarbohydrate antibody responses and that patients with defective antibody responses should receive prophylactic antibiotics or replacement immunoglobulin therapy or both to reduce their risk of late bacterial infections. Immunotechnology, 1999 Mar, 4(3-4), 189 - 201 Functional expression in bacteria and plants of an scFv antibody fragment against tospoviruses; Franconi R et al.; BACKGROUND: Recombinant antibodies expressed in plants ('plantibodies'), directed against crucial antigens and addressed to the right cell compartment, may be able to protect against viral diseases . Moreover, antibody fragments produced in bacteria or plants may provide low cost reagents for immunodiagnosis . OBJECTIVES: In an attempt to develop genetic immunisation against tomato spotted wilt tospovirus (TSWV), we engineered an scFv fragment starting from a monoclonal antibody (mAb) able to recognise an epitope of the glycoprotein G1 conserved among a large number of tospoviruses . After establishing functional expression in bacteria, we aimed to drive expression of this molecule in the secretory pathway of plants . STUDY DESIGN: An antibody phage display expression system was used to isolate the correct VH and VL binding regions from the hybridoma secreting the original mAb . To assess functional expression in plant, we first used an epichromosomal expression vector derived from potato virus X (PVX) . In this vector the scFv gene was cloned to produce a cytosolic or a secretory protein . For secretion, the signal sequence derived from the polygalacturonase-inhibiting protein (PGIP) of Phaseolus vulgaris was used . Subsequently, the gene encoding the secretory scFv, was used to transform Nicotiana benthamiana plants . RESULTS: High expression levels of fully active molecule were obtained in Escherichia coli . The engineered molecule retained the binding specificity and dissociation rate constant (k(off)) of the cognate monoclonal antibody . Both PVX-infected and transformed plants expressed fully functional scFv molecules in the secretory pathway . CONCLUSION: This engineered scFv may be valuable for inexpensive diagnosis, for studying the role of the glycoproteins in virus transmission and, possibly, for a 'plantibody'-mediated resistance to tospoviruses. Arch Environ Contam Toxicol, 1999 May, 36(4), 477 - 84 Reducing dust, lead, dust mites, bacteria, and fungi in carpets by vacuuming Roberts JW, Clifford WS, Glass G, Hummer PG. Old carpets may be reservoirs of dust, lead (Pb), and dust mite allergen . The purpose of this study was to determine if the dust, Pb, dust mite allergen, bacteria, and fungi on the surface of carpets could be reduced by 90% in 1 week with the use of a Hoover Self Propelled Vacuum with Embedded Dirt Finder (HSPF) . A high-volume surface sampler (HVS3) was used to measure surface dust and pollutants before and after the use of the HSPF to remove deep dust in carpets 12 to 20 years old in nine middle-class homes and two small offices . The minimum, median, and maximum surface loading for the first and final samples are as follows: first fine dust loading: min 0.32 g/m2, max 14.4 g/m2, median 1.30 g/m2; final fine dust loading: min 0.019 g/m2, max 0.289 g/m2, median 0.102 g/m2; first Pb loading: min 38 &mgr;g/m2, max 3,871 &mgr;g/m2, median 471 &mgr;g/m2; final Pb loading: min 13 &mgr;g/m2, max 2,023 &mgr;g/m2, median 86 &mgr;g/m2; first mite loading: min 0.11 &mgr;g/m2, max 12 . 88 &mgr;g/m2, median 2.82 &mgr;g/m2; final mite loading: min 0.06 &mgr;g/m2, max 3.67 &mgr;g/m2, median 0.28 &mgr;g/m2 . Data were insufficient to determine if the loadings of bacteria and fungi were reduced a similar amount . Six to 45 min/m2 of vacuuming with the HSPF removed deep dust from these carpets . The median surface loadings of fine dust, Pb, and dust mite allergen in these 11 carpets were reduced by 91, 82, and 94%, respectively, in 1 to 15 h of vacuuming . The loading of the deep dust collected with the HSPF ranged from 8 to 171 g/m2 with a median of 66 g/m2. FEMS Microbiol Lett, 1999 Apr 15, 173(2), 365 - 72 Isolation of poly(beta-L-malic acid)-degrading bacteria and purification and characterization of the PMA hydrolase from Comamonas acidovorans strain 7789; Godde C et al.; Several bacteria were isolated which were able to utilize poly(beta-L-malic acid) as sole carbon source for growth . The poly(beta-L-malic acid) hydrolyzing enzyme of Comamonas acidovorans strain 7789 was detected in the membrane fraction . The enzyme was purified by isolation of crude cell membranes by ultracentrifugation of disrupted cells, solubilization of the membrane fraction with octylglucoside, selective precipitation with 50% saturated ammonium sulfate and preparative isolectric focusing . SDS-PAGE analysis revealed a M(r) of 43,000 . The pH optimum was 8.1 and the Km was 0.13 microM (in terms of monomeric units) and 0.0021 microM poly(beta-L-malic acid) at pH 8.1 (100 mM glycylglycine buffer) . Addition of NaCl, KCl, CaCl2 or MgCl2 (from 25 to 100 mM) decreased the hydrolase activity, whereas EDTA or polymethane sulfonic acid fluoride had no influence on the enzyme . The depolymerization of poly(beta-L-malic acid) proceeded from the ends of the polyester resulting in the formation of L-malate . Esterase activity was not detectable with p-nitrophenyl acetate or p-nitrophenyl butyrate, which is used to determine for example poly(3-hydroxybutyric acid) depolymerase activity. Mutat Res, 1999 Apr 26, 441(1), 21 - 7 Genotoxic effects in bacteria of the light emitted by halogen tungsten lamps having treated quartz bulbs; Camoirano A et al.; Traditional halogen tungsten lamps, which are extensively used worldwide for the illumination of indoor environments, have a quartz bulb which transmits not only visible light but also ultraviolet (UV) light . Due to the output of far-UV wavelengths, halogen lamps were found in previous studies to be potently genotoxic in bacteria, clastogenic in cultured human cells, and carcinogenic in hairless mice . This discovery prompted the launching of new halogen lamps, known as UV-Stop, UV-Block, or similar trade names, which have the quartz glass treated in such a way to reduce its permeability to UV radiation . Surprisingly, these lamps are advertised for attenuating discolouration of UV-sensitive materials, such as fabrics, paintings, works of art and furniture, whereas protection of the human skin from potential carcinogenic risks is overlooked . We tested forty-seven 12 V-powered lamps with treated quartz bulb, which were made available by five producers as blind-coded samples . After exposure to either 1000 lx for 30 min or 2500 lx for 60 min, the 50 W lamps from two producers were borderline mutagenic in strains TA100 and TA104 of S . typhimurium, and induced an evident and dose-related DNA damage in the E . coli strain CM871 (uvrA- recA- lexA-), as compared to its isogenic, DNA repair-proficient counterpart WP2 . The 50 W lamps supplied by the other three producers also induced a significant genotoxic damage, but only after exposure for 60 min at illuminance levels of 2500 lx or higher . In calibration experiments, one of these three lamp brands was found to induce in 60 min a genotoxic damage which was equivalent to the one induced in just 55 s by a traditional halogen lamp . Therefore, the new types of lamps with treated quartz bulbs provide an appreciable step forward in the safety of halogen lamps, but some output of genotoxic UV radiations does still occur . Moreover, the lamps manufactured by different producers are not equally effective to this respect . By comparison, the simple application of a glass cover to a traditional halogen lamp completely prevented genotoxic effects, even after 60 min of exposure at an illuminance of 10,000 lx . Suitable regulations are urgently needed for controlling the biological safety or artificial illumination systems . Shock, 1999 Apr, 11(4), 276 - 82 Nitric oxide promotes the internalization and passage of viable bacteria through cultured Caco-2 intestinal epithelial cells; Inaba T et al.; Nitric oxide (NO) may play an important role in the pathophysiology of intestinal barrier disruption . Our purpose was to investigate the effects of NO donors on the internalization and passage of bacteria through cultured intestinal epithelial cells . Human intestinal epithelial cell line Caco-2 cells were grown on microtiter plastic plates . The cells were incubated with Escherichia coli and sodium nitroprusside (SNP) or S-nitroso-N-acetyl-penicillamine (SNAP), as NO donors, at several concentrations . The numbers of viable bacteria internalized into the epithelial cells were measured . Caco-2 cells were also grown to confluency on membranes of bicameral systems . The cells were incubated with E . coli and SNP . The numbers of viable bacteria passed through the epithelial layer were determined . Viability of the bacteria and the intestinal epithelial cells after culture with SNP or SNAP were also determined . Both SNP and SNAP at .1 or 1 mmol/L increased the number of viable bacteria internalized into the enterocytes . Both 1 or 10 mmol/L SNP promoted bacterial passage through the intestinal epithelial layer . However, 10 mmol/L SNP decreased the number of viable Caco-2 cells and failed to increase the bacterial internalization into Caco-2 cells . Incubation of E . coli with SNAP at 10 mmol/L slightly decreased the number of viable bacteria and failed to increase the bacterial internalization into Caco-2 cells . We conclude that NO donors promote both the viable bacterial uptake and passage through the intestinal epithelial layer. FEMS Immunol Med Microbiol, 1999 Mar, 23(3), 253 - 7 13C-urea breath test results in pigs challenged with Helicobacter pylori or other urease producing bacteria; Enroth H et al.; The gastric bacterial flora and its influence on the 13C-urea breath test (UBT) for detection of Helicobacter pylori infection was studied in a pig model . Seven SPF minipigs were used . H . pylori or a mix of other urease positive bacteria were administered orally . UBT, serum and biopsies for histology and culture were collected . Our results show that UBT is not specific for H . pylori in pigs as the gastric bacterial flora is responsible for the high UBT values observed . Furthermore, the Ellegaard Gottingen SPF minipigs are not useful in an animal model for H . pylori studies. Eur J Clin Microbiol Infect Dis, 1999 Feb, 18(2), 133 - 6 Association between institutionalization and carriage of multiresistant bacteria in the elderly at the time of admission to a general hospital; Eveillard M et al.; The impact of institutionalization on the carriage of multiresistant bacteria among the elderly was assessed prospectively by comparing the carriage rate in institutionalized patients over 70 years of age to the carriage rate in patients over 70 living at home (58 patients/group) . Nares, skin, and rectal swabs were obtained within 24 h of admission to the hospital . Among the 20 carriers identified, 75% came from institutions . Significantly, institutionalized patients were incontinent (P < 0.001), less autonomous than those living at home (P < 10(-6)), and had taken antibiotics recently (P < 0.02) . The primary characteristics associated with bacterial colonization were institutional living (P < 0.02), having at least one underlying disease (P < 0.001), dependence (Karnofsky index < or = 50; P < 0.02), recent treatment with antibiotics (P < 0.02), and the presence of skin lesions (P < 0.02) . Among the risk factors identified, institutionalization can be readily determined upon admission; systematic communication of carrier status of transfer patients would improve overall patient care. Mol Microbiol, 1999 Apr, 32(1), 11 - 6 Universal replication biases in bacteria; Rocha EP et al.; Analysis of 15 complete bacterial chromosomes revealed important biases in gene organization . Strong compositional asymmetries between the genes lying on the leading versus lagging strands were observed at the level of nucleotides, codons and, surprisingly, amino acids . For some species, the bias is so high that the sole knowledge of a protein sequence allows one to predict with almost no errors whether the gene is transcribed from one strand or the other . Furthermore, we show that these biases are not species specific but appear to be universal . These findings may have important consequences in our understanding of fundamental biological processes in bacteria, such as replication fidelity, codon usage in genes and even amino acid usage in proteins. Biochimie, 1999 Jan-Feb, 81(1-2), 147 - 53 Repair and mutagenesis survey of 8-hydroxyguanine in bacteria and human cells; Le Page F et al.; 8-Hydroxyguanine is one of the major products formed by the reactive oxygen species which are generated in living cells as a consequence of either the normal metabolic pathways or an exogeneous chemical or physical stress . The production of the oxidative damage is described and the different repair pathways of the oxidative lesions are analyzed from bacteria to human cells . Analysis of repair in human cells harboring different deficiencies in the nucleotide excision repair mechanism such as xeroderma pigmentosum cells from different complementation groups and cells from Cockayne's syndrome patients allows us to emphasize the possibility of the intervention of this repair mechanism on the elimination of oxidative damages . Finally, a repair model of oxidative lesions is proposed. Trends Microbiol, 1999 Mar, 7(3), 124 - 8 Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria; Dorman CJ et al.; The bacterial nucleoid-associated proteins H-NS and StpA can form homomeric or heteromeric complexes, a parallel with protein HU . Thus, functional modulation of H-NS and StpA by one another and by other proteins with appropriate interaction domains is possible . This has implications for bacterial pathogenesis and adaptation to environmental stress. Novartis Found Symp, 1999, 221, 218 - 29; discussion 229-34 Proton ATPases in bacteria: comparison to Escherichia coli F1F0 as the prototype; Fillingame RH et al.; The F1F0 ATP synthase complex of Escherichia coli functions reversibly in coupling proton translocation to ATP synthesis or hydrolysis . The structural organization and subunit composition corresponds to that seen in many other bacteria, i.e . a membrane extrinsic F1 sector with five subunits in an alpha 3 beta 3 gamma delta epsilon stoichiometry, and a membrane-traversing F0 sector with three subunits in an a1b2c12 stoichiometry . The structure of much of the F1 sector is known from a X-ray diffraction model . During function, The gamma subunit is known to rotate within a hexameric ring of alternating alpha and beta subunits to promote sequential substrate binding and product release from catalytic sites on the three beta subunits . Proton transport through F0 must be coupled to this rotation . Subunit c folds in the membrane as a hairpin to two alpha helices to generate the proton-binding site in F0 . Its structure was determined by NMR, and the structure of the c oligomer was deduced by cross-linking experiments and molecular mechanics calculations . The implications of the oligomeric structure of subunit c will be considered and related to the H+/ATP pumping ratio, P/O ratios and the cation-binding site in other types of F0 . The possible limits of the structure in changing the ion-binding specificity, stoichiometry and routes of proton entrance/exit to the binding site will be considered. Novartis Found Symp, 1999, 221, 19 - 28; discussions 28-37 The regulation of intracellular pH in bacteria; Booth IR; The regulation of intracellular pH (pHi) in bacterial cells is achieved through control over cation (and anion) permeability . In addition to the active components of homeostasis there are contributions from essentially passive elements, such as the lipid composition of the membrane and the buffering capacity of the cytoplasm . Active homeostasis involves control over the movement of K+, Na+ and H+ . Alterations in the membrane permeability for any of these cations may cause perturbation of homeostasis . In Escherichia coli this is exemplified by the controlled activation of K+ efflux systems by glutathione adducts leading to temporary acidification of the cytoplasm . This is achieved by sophisticated control over the KefB and KefC systems, and is tightly integrated with glutathione-dependent detoxification mechanisms . Such control over pHi facilitates survival of the cell following exposure to toxic electrophiles . The components of pH homeostasis will be reviewed and the molecular mechanisms, and role of, the KefB and KefC systems will be discussed. J Periodontal Res, 1999 Feb, 34(2), 105 - 12 Induction of anti-thymocyte/T lymphocyte antibodies in mice injected with lipopolysaccharides from periodontopathic bacteria; Kaneko T et al.; We examined the levels of anti-thymocyte/T lymphocyte autoantibody (ATA) in the serum of mice injected intraperitoneally with lipopolysaccharides (LPS) from periodontopathic bacteria; Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Capnocytophaga ochracea, and non-oral Escherichia coli . All of the LPS induced IgM-ATA . Among these, LPS from C . ochracea induced the highest level of IgM-ATA, whereas that of P . gingivalis induced the lowest . The peritoneal T lymphocytes of mice injected with LPS were bound by IgM-ATA . Peritoneal B-1 (CD5+B) cells stimulated by each LPS produced much more IgM-ATA than splenic B-2 (CD5-B) cells, suggesting that B-1 cells might be responsible for the production of these antibodies . Serum of mice injected with C . ochracea and F . nucleatum LPS showed cytotoxicity against thymocytes in the presence of rabbit complements . Binding and cytotoxicity were confirmed by IgM purified from serum of the mice injected with C . ochracea LPS . Furthermore, serum of mice treated with C . ochracea, F . nucleatum or A . actinomycetemcomitans LPS inhibited the proliferation of thymocytes . However, purified IgM from the serum of mice treated with C . ochracea LPS failed to produce the same inhibition . Our results suggest that LPS from certain species of periodontopathic bacteria can induce IgM-ATA in the serum and these antibodies may modulate the local immune network in periodontal tissues. J Appl Microbiol, 1999 Mar, 86(3), 496 - 504 Rapid enumeration of physiologically active bacteria in purified water used in the pharmaceutical manufacturing process; Kawai M et al.; Physiologically active bacteria in purified water used in the manufacturing process of pharmaceutical products were enumerated in situ . Bacteria with growth potential were enumerated using the micro-colony technique and direct viable counting (DVC), followed by 24 h of incubation in 100-fold diluted SCDB (Soybean Casein Digest Broth) at 30 degrees C . Respiring and esterase-active bacteria were detected by fluorescent staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) and 6-carboxyfluorescein diacetate (6CFDA), respectively . A large number of bacteria in purified water retained physiological activity, while most could not form colonies on conventional media . The techniques applied in this study enabled bacteria to be counted within 24 h so results could be available within one working day . These rapid and convenient techniques should be useful for the systematic monitoring of bacteria in water used for pharmaceutical manufacturing. Appl Environ Microbiol, 1999 Apr, 65(4), 1753 - 61 Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe; Christensen H et al.; A fluorescence in situ hybridization (FISH) technique based on binding of a rhodamine-labelled oligonucleotide probe to 16S rRNA was used to estimate the numbers of ribosome-rich bacteria in soil samples . Such bacteria, which have high cellular rRNA contents, were assumed to be active (and growing) in the soil . Hybridization to an rRNA probe, EUB338, for the domain Bacteria was performed with a soil slurry, and this was followed by collection of the bacteria by membrane filtration (pore size, 0.2 micrometer) . A nonsense probe, NONEUB338 (which has a nucleotide sequence complementary to the nucleotide sequence of probe EUB338), was used as a control for nonspecific staining . Counting and size classification into groups of small, medium, and large bacteria were performed by fluorescence microscopy . To compensate for a difference in the relative staining intensities of the probes and for binding by the rhodamine part of the probe, control experiments in which excess unlabelled probe was added were performed . This resulted in lower counts with EUB338 but not with NONEUB338, indicating that nonspecific staining was due to binding of rhodamine to the bacteria . A value of 4.8 x 10(8) active bacteria per g of dry soil was obtained for bulk soil incubated for 2 days with 0.3% glucose . In comparison, a value of 3.8 x 10(8) active bacteria per g of dry soil was obtained for soil which had been air dried and subsequently rewetted . In both soils, the majority (68 to 77%) of actively growing bacteria were members of the smallest size class (cell width, 0.25 to 0.5 micrometer), but the active (and growing) bacteria still represented only approximately 5% of the total bacterial population determined by DAPI (4', 6-diamidino-2-phenylindole) staining . The FISH technique in which slurry hybridization is used holds great promise for use with phylogenetic probes and for automatic counting of soil bacteria. Biotechnol Bioeng, 1998 Mar 20, 57(6), 676 - 85 Long-term competition between sulfate reducing and methanogenic bacteria in UASB reactors treating volatile fatty acids; Omil F et al.; The competition between acetate utilizing methane-producing bacteria (MB) and sulfate-reducing bacteria (SRB) was studied in mesophilic (30 degrees C) upflow anaerobic sludge bed (UASB) reactors (upward velocity 1 m h-1; pH 8) treating volatile fatty acids and sulfate . The UASB reactors treated a VFA mixture (with an acetate:propionate:butyrate ratio of 5:3:2 on COD basis) or acetate as the sole substrate at different COD:sulfate ratios . The outcome of the competition was evaluated in terms of conversion rates and specific methanogenic and sulfidogenic activities . The COD:sulfate ratio was a key factor in the partitioning of acetate utilization between MB and SRB . In excess of sulfate (COD:sulfate ratio lower than 0.67), SRB became predominant over MB after prolonged reactor operation: 250 and 400 days were required to increase the amount of acetate used by SRB from 50 to 90% in the reactor treating, respectively, the VFA mixture or acetate as the sole substrate . The competition for acetate was further studied by dynamic simulations using a mathematical model based on the Monod kinetic parameters of acetate utilizing SRB and MB . The simulations confirmed the long term nature of the competition between these acetotrophs . A high reactor pH (+/-8), a short solid retention time (<150 days), and the presence of a substantial SRB population in the inoculum may considerably reduce the time required for acetate-utilising SRB to outcompete MB . Proc Natl Acad Sci U S A, 1999 Mar 30, 96(7), 3807 - 12 Genomic evolution during a 10,000-generation experiment with bacteria; Papadopoulos D et al.; Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species . However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms . To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations . We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations . The evolving genomes became increasingly different from their ancestor over time . Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations . As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population . Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find . More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief. J Virol Methods, 1999 Feb, 77(2), 125 - 9 Generation of infectious genome of bovine adenovirus type 3 by homologous recombination in bacteria; van Olphen AL et al.; The widely used technique of generating adenovirus vectors by homologous recombination in mammalian cells is usually not very efficient . This communication describes a simple method of generating a plasmid containing the full-length genome of an adenovirus by homologous recombination in bacteria . Following transfection of a suitable mammalian cell line with the full-length adenovirus genome, infectious virus progeny could easily be generated . Using this technique the generation of adenovirus recombinants would be efficient and straightforward. Blood, 1999 Apr 1, 93(7), 2395 - 403 Influenza A virus accelerates neutrophil apoptosis and markedly potentiates apoptotic effects of bacteria; Colamussi ML et al.; Neutrophils are recruited into the airway in the early phase of uncomplicated influenza A virus (IAV) infection and during the bacterial superinfections that are a significant cause of morbidity and mortality in IAV-infected subjects . In this report, we show that IAV accelerates neutrophil apoptosis . Unopsonized Escherichia coli had similar effects, although apoptotic effects of opsonized E coli were greater . When neutrophils were treated with both IAV and unopsonized E coli, a marked enhancement of the rate and extent of neutrophil apoptosis occurred as compared with that caused by either pathogen alone . Treatment of neutrophils with IAV markedly increased phagocytosis of E coli . Simultaneous treatment of neutrophils with IAV and E coli also elicited greater hydrogen peroxide production than did either pathogen alone . IAV increased neutrophil expression of Fas antigen and Fas ligand, and it also increased release of Fas ligand into the cell supernatant . These findings may have relevance to the understanding of inflammatory responses to IAV in vivo and of bacterial superinfection of IAV-infected subjects. Glycobiology, 1999 Apr, 9(4), 323 - 34 Divergent evolution of fucosyltransferase genes from vertebrates, invertebrates, and bacteria; Oriol R et al.; On the basis of function and sequence similarities, the vertebrate fucosyltransferases can be classified into three groups: alpha-2-, alpha-3-, and alpha-6-fucosyltransferases . Thirty new putative fucosyltransferase genes from invertebrates and bacteria and six conserved peptide motifs have been identified in DNA and protein databanks . Two of these motifs are specific of alpha-3-fucosyltransferases, one is specific of alpha-2-fucosyltransferases, another is specific of alpha-6-fucosyltransferases, and two are shared by both alpha-2- and alpha-6-fucosyltranserases . Based on these data, literature data, and the phylogenetic analysis of the conserved peptide motifs, a model for the evolution offucosyltransferase genes by successive duplications, followed by divergent evolution is proposed, with either two different ancestors, one for the alpha-2/6-fucosyltransferases and one for the alpha-3-fucosyltransferases or a single common ancestor for the two families . The expected properties of such an hypothetical ancestor suggest that the plant or insect alpha-3-fucosyltransferases using chitobiose as acceptor might be the present forms of this ancestor, since fucosyltransferases using chitobiose as acceptor are expected to be of earlier appearance in evolution than enzymes using N -acetyllactosamine . However, an example of convergent evolution of fucosyltransferase genes is suggested for the appearance of the Leaepitopes found in plants and primates. Virology, 1999 Mar 30, 256(1), 75 - 84 A GroEL homologue from endosymbiotic bacteria of the whitefly Bemisia tabaci is implicated in the circulative transmission of tomato yellow leaf curl virus; Morin S et al.; Evidence for the involvement of a Bemisia tabaci GroEL homologue in the transmission of tomato yellow leaf curl geminivirus (TYLCV) is presented . A approximately 63-kDa protein was identified in B . tabaci whole-body extracts using an antiserum raised against aphid Buchnera GroEL . The GroEL homologue was immunolocalized to a coccoid-shaped whitefly endosymbiont . The 30 N-terminal amino acids of the whitefly GroEL homologue showed 80% homology with that from different aphid species and GroEL from Escherichia coli . Purified GroEL from B . tabaci exhibited ultrastructural similarities to that of the endosymbiont from aphids and E . coli . In vitro ligand assays showed that tomato yellow leaf curl virus (TYLCV) particles displayed a specific affinity for the B . tabaci 63-kDa GroEL homologue . Feeding whiteflies anti-Buchnera GroEL antiserum before the acquisition of virions reduced TYLCV transmission to tomato test plants by >80% . In the haemolymph of these whiteflies, TYLCV DNA was reduced to amounts below the threshold of detection by Southern blot hybridization . Active antibodies were recovered from the insect haemolymph suggesting that by complexing the GoEL homologue, the antibody disturbed interaction with TYLCV, leading to degradation of the virus . We propose that GroEL of B . tabaci protects the virus from destruction during its passage through the haemolymph . Antonie Van Leeuwenhoek, 1998 Nov, 74(4), 211 - 27 Current topics in signal transduction in bacteria; Hellingwerf KJ et al.; Among the signal transfer systems in bacteria two types predominate: two-component regulatory systems and quorum sensing systems . Both types of system can mediate signal transfer across the bacterial cell envelope; however, the signalling molecule typically is not taken up into the cells in the former type of system, whereas it usually is in the latter . The Two-component systems include the recently described (eukaryotic) phosphorelay systems; quorum sensing systems can be based upon autoinducers of the N-acylated homoserine lactones, and on autoinducers of a peptidic nature . A single bacterial cell contains many signalling modules that primarily operate in parallel . This may give rise to neural-network behaviour . Recently, however, for both types of basic signal transfer modules, it has been demonstrated that they also can be organised in series (i.e . in a hierarchical order) . Besides their hierarchical position in the signal transduction network of the cell, the spatial distribution of individual signalling modules may also be an important factor in their efficiency in signal transfer . Many challenges lie hidden in future work to understand these signal transfer processes in more detail . These are discussed here, with emphasis on the mutual interactions between different signal transfer processes . Successful contributions to this work will require rigorous mathematical modelling of the performance of signal transduction components, and -networks, as well as studies on light-sensing signal transduction systems, because of the unsurpassed time resolution obtainable in those latter systems, the opportunity to apply repeated reproducible stimuli, etc . The increased understanding of bacterial behaviour that already has resulted--and may further result--from these studies, can be used to fine-tune the beneficial activities of bacteria and/or more efficiently inhibit their deleterious ones. Biochem Biophys Res Commun, 1999 Mar 24, 256(3), 474 - 9 The IalA invasion gene of Bartonella bacilliformis encodes a (de)nucleoside polyphosphate hydrolase of the MutT motif family and has homologs in other invasive bacteria; Cartwright JL et al.; The product of the ialA invasion gene of Bartonella bacilliformis has been expressed as a thioredoxin fusion protein . It is a (di)nucleoside polyphosphate hydrolase of the MutT motif protein family with strong sequence similarity to plant diadenosine tetraphosphate hydrolases . It hydrolyses nucleoside and dinucleoside polyphosphates with four or more phosphate groups, always producing an NTP as one product . Diadenosine tetraphosphate (Ap4A) is the preferred substrate with a Km of 10 microM and a kcat of 3.0 s-1 . It is inhibited by Ca2+ and F- (Ki = 30 microM) . Hydrolysis of Ap4A in H218O yielded {18O}AMP as the only labelled product . In terms of sequence, reaction mechanism and properties, IalA is very similar to eukaryotic Ap4A hydrolases and unlike previously described bacterial Ap4A hydrolases . Homologs are present in the genomes of other invasive pathogens . They may function to reduce stress-induced dinucleotide levels during invasion and so enhance pathogen survival . Chest Surg Clin N Am, 1999 Feb, 9(1), 167 - 92, ix-x Opportunistic thoracic infections . Bacteria, viruses, and protozoa; Talbot EA et al.; The range of potential bacterial, viral, and protozoan pathogens that can cause pulmonary infections in immunocompromised patients is extensive . An aggressive diagnostic approach is essential to maximizing chances for a successful outcome . This article discusses the general diagnostic approach and provides a discussion of the most important bacterial, viral, and protozoan chest infections occurring in this setting. Biofizika, 1998 Nov-Dec, 43(6), 1026 - 9 {Effect of temperature on H+-K+ exchange in Escherichia coli bacteria during their anaerobic growth}; Vardanian V et al.; The H(+)-K(+)-exchange in E.coli grown under anaerobic conditions at temperatures from 17 to 37 degrees C was studied . The Arrhenius plots for both the N,N'-dicyclohexylcarbodiimide-sensitive release of H+ and K+ uptake by cells transferred into a fresh medium containing a carbon source (glucose) are nonlinear . The activation energy values for the transport of these cations at different temperatures significantly differ . It is shown that as the temperature decreases, the accumulation of K+ by cells is reduced . In this process, the initial rate of K+ absorption through the TrkA system, the time of accumulation of these cations by cells and the osmosensitivity of K+ uptake substantially decrease . At temperatures below 20 degrees C, the absorption becomes insensitive to the secondary osmoshock . However, the stoichiometry of N,N'-dicyclohexylcar-bodiimide-sensitive cation fluxes remains unchanged and is equal to 2H+:K+ . It is assumed that the H(+)-K(+)-exchange proceeds by the operation of an ensemble of oligomers, formed from the protomers of F0F1 and TrkA, which rearrange by the action of temperature, whereas F0F1 and TrkA in each protomer do not change. Artif Organs, 1992 Apr, 16(2), 141 - 5 Bacteria and endotoxin removal from bicarbonate dialysis fluids for use in conventional, high-efficiency, and high-flux hemodialysis; Oliver JC et al.; The use of bicarbonate-based dialysis fluids in hemodialysis centers in the United States has increased with the advent of high-efficiency and high-flux hemodialysis . However, bicarbonate dialysis fluids can support rapid bacterial growth and high endotoxin concentrations . This study determined the efficacy of an ultrafiltration device in reducing the bacterial and endotoxin concentrations in bicarbonate dialysis fluids . A polysulfone hollow fiber dialyzer was used to ultrafilter bicarbonate concentrate before entering the central proportioner and bicarbonate dialysate after exiting the proportioner in single patient dialysis machines . Pre- and post-ultrafilter samples were collected for bacterial and endotoxin assays over 10 months . Ultrafiltration of bicarbonate concentrate reduced bacterial and endotoxin concentrations from 288,330 colony forming units (CFU)/ml and 42,804 pg/ml to 0.47 CFU/ml and 109 pg/ml, respectively . Ultrafiltration of the dialysate in single patient systems decreased bacterial and endotoxin concentrations from 15,889 CFU/ml and 1,746 pg/ml to 0.003 CFU/ml and 0.109 pg/ml, respectively . These results demonstrate that ultrafiltration of bicarbonate dialysis fluids is effective in reducing bacterial and endotoxin contamination inherently associated with the use of bicarbonate-based dialysates. Arch Pharm Res, 1999 Feb, 22(1), 30 - 4 Metabolism of liriodendrin and syringin by human intestinal bacteria and their relation to in vitro cytotoxicity; Kim DH et al.; When liriodendrin or syringin was incubated for 24 h with human intestinal bacteria, two metabolites, (+)-syringaresinol-beta-D-glucopyranoside and (+)-syringaresinol, from liriodendrin and one metabolite, synapyl alcohol, from syringin were produced . The metabolic time course of liriodendrin was as follows: at early time, liriodendrin was converted to (+)-syringaresinol-beta-D-glucopyranoside, and then (+)-syringaresinol . The in vitro cytotoxicities of these metabolites, (+)-syringaresinol and synapyl alcohol, were superior to those of liriodendrin and syringin. Curr Opin Microbiol, 1998 Oct, 1(5), 580 - 3 Rates and patterns of chromosome evolution in enteric bacteria; Ochman H et al.; Although several types of large-scale alterations potentially affect the structure and organization of bacterial genomes, recent analyses of physical maps and complete genomic sequences reveal that chromosome heterogeneity in enteric bacteria has resulted from the acquisition and deletion of large segments of DNA . These acquired sequences can provide novel functions immediately upon their introduction and play a significant role in the diversification of bacterial species. Microbiol Mol Biol Rev, 1999 Mar, 63(1), 230 - 62 Osmosensing by bacteria: signals and membrane-based sensors; Wood JM; Bacteria can survive dramatic osmotic shifts . Osmoregulatory responses mitigate the passive adjustments in cell structure and the growth inhibition that may ensue . The levels of certain cytoplasmic solutes rise and fall in response to increases and decreases, respectively, in extracellular osmolality . Certain organic compounds are favored over ions as osmoregulatory solutes, although K+ fluxes are intrinsic to the osmoregulatory response for at least some organisms . Osmosensors must undergo transitions between "off" and "on" conformations in response to changes in extracellular water activity (direct osmosensing) or resulting changes in cell structure (indirect osmosensing) . Those located in the cytoplasmic membranes and nucleoids of bacteria are positioned for indirect osmosensing . Cytoplasmic membrane-based osmosensors may detect changes in the periplasmic and/or cytoplasmic solvent by experiencing changes in preferential interactions with particular solvent constituents, cosolvent-induced hydration changes, and/or macromolecular crowding . Alternatively, the membrane may act as an antenna and osmosensors may detect changes in membrane structure . Cosolvents may modulate intrinsic biomembrane strain and/or topologically closed membrane systems may experience changes in mechanical strain in response to imposed osmotic shifts . The osmosensory mechanisms controlling membrane-based K+ transporters, transcriptional regulators, osmoprotectant transporters, and mechanosensitive channels intrinsic to the cytoplasmic membrane of Escherichia coli are under intensive investigation . The osmoprotectant transporter ProP and channel MscL act as osmosensors after purification and reconstitution in proteoliposomes . Evidence that sensor kinase KdpD receives multiple sensory inputs is consistent with the effects of K+ fluxes on nucleoid structure, cellular energetics, cytoplasmic ionic strength, and ion composition as well as on cytoplasmic osmolality . Thus, osmoregulatory responses accommodate and exploit the effects of individual cosolvents on cell structure and function as well as the collective contribution of cosolvents to intracellular osmolality. Curr Opin Microbiol, 1998 Jun, 1(3), 303 - 10 Expression systems and physiological control of promoter activity in bacteria; Cases I et al.; Promoter activity in vivo is not just dependent on the performance of the regulator/promoter pair which may predominantly control transcription initiation in response to a given signal, it also relies on overimposed mechanisms that connect the activity of individual promoters to the metabolic and energetic status of the bacterial cells . Such mechanisms - which frequently become limiting for biotechnological applications involving regulated promoters - include classic (i.e . cAMP/CRP-mediated) or alternative catabolite control checks, recruitment of protein intermediates of the phosphotransferase sugar transport system, coregulation through protein-induced DNA bending and the interplay of sigma factors during various growth stages. Curr Opin Microbiol, 1998 Apr, 1(2), 160 - 9 Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling; Goudreau PN et al.; In bacteria, adaptive responses to changing environmental conditions are mediated by signal transduction systems that involve modular protein domains . Despite great diversity in the integration of domains into different systems, studies of individual components have revealed molecular strategies that are widely applicable . Studies of receptors have advanced our understanding of how information is transmitted across membranes, the determination of three-dimensional structures of domains of histidine protein kinase domains and response regulator proteins has begun to reveal the molecular basis of signaling via two-component phosphoryltransfer pathways, and the description of 'eukaryotic-like' protein domains involved in bacterial signaling has emphasized the universality of intracellular signaling mechanisms. Curr Opin Microbiol, 1998 Feb, 1(1), 43 - 8 How bacteria initiate inflammation: aspects of the emerging story; Hersh D et al.; Recent studies have shown that bacteria possess an array of proinflammatory molecules in addition to the extensively studied lipopolysaccharide and superantigens . These bacterial molecules include soluble and membrane-associated inducers of cytokine release, inducers of host cell apoptosis, and immunostimulatory DNA . There is therefore much greater diversity in the class of molecules and mechanisms by which bacteria engage the host immune system than previously appreciated. Appl Environ Microbiol, 1999 Mar, 65(3), 1325 - 30 In situ analysis of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland); Tonolla M et al.; Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) revealed the presence of a diverse number of phototrophic sulfur bacteria . Sequences resembled those of rRNA of type strains Chromatium okenii DSM169 and Amoebobacter purp