J Endod, 2002 Apr, 28(4), 272 - 5 Evaluation of leakage of bacteria and endotoxins in teeth treated endodontically by two different techniques; Carratu P et al.; Root canal recontamination occurs after contact between oral-bacterial flora and the coronal extremity of the root canal . The aim of this study was to evaluate the time required for endotoxins and bacteria to penetrate through root-canal obturations performed with vertical and lateral gutta-percha condensation techniques . Specimens prepared by the two alternative methods were exposed to contaminated saliva, and leakage into the root was evaluated over time . None of the obturated roots was infiltrated by endotoxins after 31 days . On the contrary, between day 13 and day 37 bacteria had infiltrated all specimens. DNA Cell Biol, 2002 Apr, 21(4), 281 - 95 Processing of heme and heme-containing proteins by bacteria; Stojiljkovic I et al.; An extensive amount of new knowledge on bacterial systems involved in heme processing has been accumulated in the last 10 years . We discuss common themes in heme transport across bacterial outer and inner membranes, emphasizing proteins and mechanisms involved . The processing of heme in the bacterial cytoplasm is extensively covered, and a new hypothesis about the fate of heme in the bacterial cell is presented . Auxiliary genes involved in heme utilization, i.e., TonB, proteases, proteins involved in heme storage and pigmentation, as well as genes involved in regulation of heme assimilation are reviewed. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 2001, 33(5), 573 - 576 The Ultrafast Energy Transfer Process in Purple Bacteria Photosynthetic Reaction Center; Guo LJ et al.; The ultrafast energy transfer process, which takes place in femtosecond time range, in bacterial photosynthetic reaction center RS601 was investigated using femtosecond pump-probe technique with selective excitation . Upon 755 nmexcitation, the excited state of bacteriopheophytin H decayed to bacteriochlorophyll B with a time constant of about 130 fs, while the excited state of B transported the energy to its energy acceptor, the dimeric bacteriochlorophyll P, in about 240 fs with the 800 nm excitation . The internal conversion process between the upper and lower exciton levels of special pair P might exist upon the excitation of 850 nm pulses . In addition, from the results obtained in our experiments, the charge separation and electron transfer from P to the acceptor H was also observed via the real intermediate B within a few picoseconds. Microb Ecol, 2000 Apr, 39(3), 222 - 235 Surface Attachment of Ammonia-Oxidizing Bacteria in Soil; Aakra A et al.; A BSTRACTIndigenous ammonia-oxidizing bacteria (AOB) in a clay loam soil were extremely difficult to release from soil particles compared to most heterotrophic bacteria; less than 1% of indigenous AOB (estimated as potential ammonia oxidation rate) were extractable by the dispersion-density-gradient centrifugation technique . This is at least 10-fold less than the extractability of heterotrophic bacteria . Urea applications to the same soil induced a 5-fold increase in the potential ammonia oxidation rate, and this resulted in a much higher percentage (8%) extractability of AOB . Thus, the newly grown AOB in the urea-treated soil were less strongly attached to the soil particles . The contrast suggests that the strong attachment of indigenous AOB is a gradual process taking place due to a long residence time (infrequent/slow cell division) compared to heterotrophic organisms . However, the contrast could also reflect differences in species composition of the original AOB community and those growing in response to urea inputs . Specific detection of AOB in extinction dilution cultures was done by PCR and sequencing of the products . Considerable diversity was found within the genus Nitrosospira, but severe problems with the specificity of the primers were observed . Two allegedly AOB specific PCR primers pairs were used: one specific for Nitrosospira (SPIRA) and one which should encompass all AOB within the beta- Proteobacteria (GAOB) . Only 33% of the cultures that gave PCR products with GAOB also gave products with the SPIRA primer pair, suggesting the presence of AOB other than Nitrosospira . However, the phylogeny based on the sequencing placed all the cultures in various clusters of the Nitrosospira clade, suggesting that the SPIRA primers do not match all members of the Nitrosospira genus . The cultures obtained from the urea-treated soil were different from the others in giving PCR products only with the SPIRA primers and not with the GAOB . Since sequencing also here confirmed the presence of Nitrosospira, these observations suggest that the GAOB primers do not match all AOB species. Microb Ecol, 2001 Feb, 41(2), 97 - 105 Role of Predatory Bacteria in the Termination of a Cyanobacterial Bloom; Rashidan KK et al.; Changes in cyanobacterial abundance and in the occurrence of bacteria capable of lysing cyanobacteria were monitored over a period of 6 months (May to October 1998) in eutrophic Brome Lake (Quebec, Canada), in which dense cyanobacterial blooms recur regularly . By screening lake water, we isolated two strains of lytic bacteria from the family Cytophagaceae . When tested on 12 cyanobacteria and 6 heterotrophic bacteria, strain 1 lysed only Anabaena flos-aquae and strain 2 lysed only Synechococcus cedorum, Synechococcus leopoliensis, Synechococcus elongatus, and Anacystis nidulans: both liquid and agar-grown cultures of these cyanobacteria were lysed . The number of plaque-forming units of bacteria increased dramatically during the decline of the bloom . The results are consistent with an important role for these host-specific lytic bacteria in control and elimination of cyanobacterial blooms in this lake. Arch Microbiol, 2002 Jun, 177(6), 475 - 85 Epub 2002 Apr 13. Novel bacteriochlorophyll e structures and species-specific variability of pigment composition in green sulfur bacteria; Glaeser J et al.; The relative composition of bacteriochlorophyll (BChl) homologs in five different strains of brown-colored green sulfur bacteria was investigated by HPLC-MS/MS and NMR analyses . In addition, the effect of incubation light intensities on homolog distribution was studied in one of the strains (strain Dagow III) . A total of 23 different BChl e structures were detected and comprise four homologous porphyrin ring systems and eight different esterifying alcohols . Several BChl e structures are novel . These include a C-8 ethyl, C-12 methyl {E, M} BChl e(F) homolog which was identified by (1)H-NMR analyses of the isolated, main farnesyl homologs (BChl e(F)) . In addition, five previously unknown homolog series with dodecanol, pentadecenol, tetradecanol, hexadecenol and phytol as the esterifying alcohols were detected . The composition of BChl e homologs from the five strains of green sulfur bacteria differed with respect to the relative abundance of the homologs (BChl e(F) : 25.6-67.0% of total BChl e content in stationary cultures) . In strain Dagow III, the abundance of BChl e(F) homologs decreased upon entry into the stationary phase . In all free-living strains, the abundance of BChl e(F) was increased when the relative carotenoid content was low . The present results provide a detailed picture of pigment composition in chlorosomes and thus will help to elucidate their structure and function . Furthermore, the newly discovered BChl e molecules are valuable biomarkers for the study of the occurrence and metabolism of green sulfur bacteria in past and present ecosystems. Proc R Soc Lond B Biol Sci, 2002 May 7, 269(1494), 937 - 42 Modelling the survival of bacteria in drylands: the advantage of being dormant; Bar M et al.; We introduce a simple mathematical model for the description of 'dormancy', a survival strategy used by some bacterial populations that are intermittently exposed to external stress . We focus on the case of the cyanobacterial crust in drylands, exposed to severe water shortage, and compare the fate of ideal populations that are, respectively, capable or incapable of becoming dormant . The results of the simple model introduced here indicate that under a constant, even though low, supply of water the dormant strategy does not provide any benefit and it can, instead, decrease the chances of survival of the population . The situation is reversed for highly intermittent external stress, due to the presence of prolonged periods of dry conditions intermingled with short periods of intense precipitation . In this case, dormancy allows for the survival of the population during the dry periods . In contrast, bacteria that are incapable of turning into a dormant state cannot overcome the difficult times . The model also rationalizes why dormant bacteria, such as those composing the cyanobacterial crust in the desert, are extremely sensitive to other disturbances, such as trampling cattle. J Nutr Sci Vitaminol (Tokyo), 2002 Feb, 48(1), 24 - 9 Intestinal urea metabolism: could the bacteria involved in nitrogen cycle lead to reutilization of intestinal urea nitrogen in uremic rabbits? Kavukcu S, Turkmen M, Soylu A, Bora S, Yurt P, Unak P. We aimed to evaluate the effect of bacteria involved in the nitrogen cycle on the reutilization of intestinal urea nitrogen in uremic rabbits . New Zealand white rabbits were made uremic via bilateral nephrectomy . Study and control rabbits were given live and heat-inactivated bacteria through their jejunostomies . After they were injected with 99mTc biurea intravenously, serial serum and stool levels of labeled nitrogen were assessed by instant thin-layer chromatography, and the change in the labeled-nitrogen level was determined . The serum labeled-nitrogen level increased significantly in the study group (r=0.990); however, this level decreased in the control group (r=0.662) . Furthermore, the labeled-nitrogen level in the stool samples increased throughout the study in the control rabbits, but it decreased after the 6th hour in the study group . In conclusion, the results of this study suggest that when the bacterial flora of the intestinal system is changed to include bacteria involved in the nitrogen cycle in uremic rabbits, the intraintestinal and systemic nitrogen metabolisms could both be altered in favor of positive nitrogen balance. Mikrobiologiia, 2002 Mar-Apr, 71(2), 187 - 93 {Effect of the medium composition and cultivation conditions on sporulation in chemolithotrophic bacteria}; Bogdanova TI et al.; The possibility of controlling endospore formation by changing cultivation conditions was for the first time shown in acidophilic chemolithotrophic bacteria Sulfobacillus thermosulfidooxidans type strain 1269 and the thermotolerant strain K1 formerly described as "S . thermosulfidooxidans subsp . thermotolerans" . Suppression of sporulation occurred when these strains were cultured in Manning's liquid medium with yeast extract . This medium was optimized by gradually reducing the concentrations of ferrous iron salts (the source of energy), phosphorous, nitrogen, and yeast extract and simultaneously increasing the concentrations of calcium, magnesium, and manganese (the elements important for sporogenesis) to attain higher yields of endospores by strains 1269 and K1 . As a result, a new medium A was proposed, in which the life cycle of the strains studied culminated in sporulation at a level of 45 and 60%, respectively, of the total cell number . In a series of additional tests, the growth temperature and medium pH were adjusted to obtain the maximum yield of endospores . The optimal ranges found were 40-50 degrees C and pH 1.8-2.2 for strain 1269 and 35-40 degrees C and pH 2.5-2.7 for strain K1 . An even higher yield of endospores, amounting to 55 and 75% for strains 1269 and K1, respectively, was obtained when the above growth conditions were combined (growth on medium A at optimal temperatures and pH) . Our results suggest a new approach to optimizing sporulation by acidophilic chemolithotrophs, which consists in limiting the energy and nutrient sources and using temperature and pH values within the tolerance bounds of these cultures but outside their growth of optimum ranges. Microb Ecol, 2001 Oct, 42(3), 474 - 481 Naked Amoebas and Bacteria in an Oil-Impacted Salt Marsh Community; Anderson OR et al.; Populations of soil amoebas were monitored in two salt marshes in Staten Island, NY for 2 years . One site, Gulfport Reach on the Arthur Kill, has been highly impacted by numerous oil spills . In particular, in 1990 a massive no . 2 fuel oil spill from a ruptured pipe flooded the area; its sediments had total petroleum hydrocarbon (TPH) concentrations in the range 800-46,000 ppm . A reference site 11 km away, on the Atlantic coast, had low TPH levels . Amoeba population densities were in general higher in the impacted sediments . In laboratory microcosm experiments, sediment samples from unimpacted sites were treated with added fresh (unweathered) hydrocarbons (no . 2 fuel oil) and cultured; these also yielded higher amoeba numbers than untreated controls . Four distinct amoeba morphotypes were monitored . Changes in population levels of total amoebas were correlated in the two sites, particularly for morphotype 2 (r = 0.83) . The ratios of total amoebas to total bacterial numbers were also correlated (r = 0.85) between the sites . This suggests the amoebas may function as generalists, and that their trophic relation to bacterial prey is not much affected by the presence of petroleum hydrocarbons, but rather may reflect regional parameters such as ambient temperature or other physical factors. FEBS Lett, 2002 May 22, 519(1-3), 164 - 8 N-terminal methylation of the core light-harvesting complex in purple photosynthetic bacteria; Wang ZY et al.; Several core light-harvesting complexes from both sulfur and non-sulfur purple photosynthetic bacteria have been identified to be methylated at the N-terminal alpha-amino group of beta-polypeptides by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nuclear magnetic resonance . Monomethylation has been confirmed for the N-terminal alanine residues of the beta-polypeptides from Rhodospirillum rubrum, Thermochromatium tepidum and Chromatium vinosum, but not for the beta-polypeptide from Rhodobacter sphaeroides . The modification appears to be related with the amino acid sequence and charge distribution in the N-terminal end . Some common features and possible functions are discussed. Microb Ecol, 2002 Jul, 44(1), 19 - 29 Epub 2002 May 20. Water discharge-regulated bacteria/heterotrophic nanoflagellate (HNF) interactions in the water column of the river Rhine; Weitere M et al.; Heterotrophic nanoflagellates (HNF) make up a large fraction of the zooplankton biomass of rivers . Their abundance can be strongly affected by water discharge, but the consequences of this highly dynamic factor for their main prey, the bacteria, is still unknown . The focus of this study was on bacterial/HNF interactions in the Lower River Rhine (Germany) with respect to the discharge-dependent dynamics . The bacterial and HNF abundances and biomasses were determined over the course of 17 months . The potential consumption of bacteria by HNF was calculated based on the biomass data and on data on the HNF production . The mean bacterial abundance in the Rhine at Cologne ranged from 0.3 x 10(6) to 3.5 x 10(6) cells mL(-1), with lowest abundances in winter and highest in late spring . No significant changes in abundance during the downstream passage were found . Neither could a significant correlation be found between bacterial and HNF abundance . The ratio of bacterial to HNF abundance showed high variations which lay between 166 and 19,055 and was negatively dependent on water discharge . Monthly routine calculations on the potential bacterial consumption by HNF revealed a clearance of between 2 and 82% of the bacterial standing stock d(-1) . The values increased greatly with water discharge and could exceed 100% d(-1) at times of high water flow . The presented data suggests a change in the top-down control of the planktonic bacteria due to the water discharge: The importance of benthic predation at low water flow (high contact probability to benthic predators) gives way to an increased importance in predation by planktonic HNF at high water flow. J Biol Chem, 2002 Aug 16, 277(33), 29825 - 31 Epub 2002 May 20. Genetic analysis of the twin arginine translocator secretion pathway in bacteria; DeLisa MP et al.; The twin arginine translocation (Tat) pathway of bacteria and plant chloroplasts mediates translocation of essentially folded proteins across the cytoplasmic membrane . The detailed understanding of the mechanism of protein targeting to the Tat pathway has been hampered by the lack of screening or selection systems suitable for genetic analysis . We report here the development of a highly quantitative protein reporter for genetic analysis of Tat-specific export . Specifically, export via the Tat pathway rescues green fluorescent protein (GFP) fused to an SsrA peptide from degradation by the cytoplasmic proteolytic ClpXP machinery . As a result, cellular fluorescence is determined by the amount of GFP in the periplasmic space . We used the GFP-SsrA reporter to isolate gain-of-function mutants of a Tat-specific leader peptide and for the genetic analysis of the "invariant" signature RR dipeptide motif . Flow cytometric screening of trimethylamine N-oxide reductase (TorA) leader peptide libraries resulted in isolation of six gain-of function mutants that conferred significantly higher steady-state levels of export relative to the wild-type TorA leader . All the gain-of-function mutations occurred within or near the (S/T)RRXFLK consensus motif, highlighting the significance of this region in interactions with the Tat export machinery . Randomization of the consensus RR dipeptide in the TorA leader revealed that a basic side chain (R/K) is required at the first position whereas the second position can also accept Gln and Asn in addition to basic amino acids . This result indicates that twin arginine translocation does not require the presence of an arginine dipeptide within the conserved sequence motif. Nature . 2002 May 16;417(6886):244. Phylogeny: a non-hyperthermophilic ancestor for bacteria; Brochier C et al.; The first phyla that emerge in the tree of life based on ribosomal RNA (rRNA) sequences are hyperthermophilic, which led to the hypothesis that the universal ancestor, and possibly the original living organism, was hyperthermophilic . Here we reanalyse the bacterial phylogeny based on rRNA using a more reliable approach, and find that hyperthermophilic bacteria (such as Aquificales and Thermotogales) do not emerge first, suggesting that the Bacteria had a non-hyperthermophilic ancestor . It seems that Planctomycetales, a phylum with numerous peculiarities, could be the first emerging bacterial group. Sci STKE . 2002 May 14;2002(132):PE24. Amplification of signaling events in bacteria; Dahlquist FW; Bacteria respond to extremely shallow chemical gradients by modifying their motility in a process called chemotaxis . This chemotactic response is characterized by high sensitivity to small concentration differences, which extends over a large range of concentrations . This combination of high signal gain and large dynamic range results from both a memory of past events and the ability to amplify small differences in signal between the memory and the current environment . Dahlquist describes the signaling mechanism used by bacteria to regulate the flagellar motor and the places in this pathway where signal amplification may occur. Infect Immun, 2002 Jun, 70(6), 3277 - 80 Segmented filamentous bacteria interact with intraepithelial mononuclear cells; Meyerholz DK et al.; Segmented filamentous bacteria (SFB) are found in multiple species and play an important role in the development of mucosal immunity . The mechanism by which the bacteria interact with the immune system has not been well defined . We provide morphologic evidence of direct interaction between SFB and intraepithelial mononuclear cells. Infect Immun, 2002 Jun, 70(6), 3143 - 8 Bacteria induce osteoclastogenesis via an osteoblast-independent pathway; Jiang Y et al.; Bacteria or their products may cause chronic inflammation and subsequent bone loss . This inflammation and bone loss may be associated with significant morbidity in chronic otitis media, periodontitis, endodontic lesions, and loosening of orthopedic implants caused by lipopolysaccharide (LPS)-contaminated implant particles . Currently, it is not clear how bacteria or endotoxin-induced bone resorption occurs and what cell types are involved . Here we report that Porphyromonas gingivalis, a periodontal pathogen, and Escherichia coli LPS induce osteoclastic cell formation from murine leukocytes in the absence of osteoblasts . In contrast, stimulation with parathyroid hormone had no effect . These multinucleated, tartrate-resistant acid phosphatase-positive cells were positive for receptor activator of NF-kappaB (RANK), the receptor for osteoprotegerin ligand (OPGL), also known as RANK ligand (RANKL) . Blocking antibodies demonstrated that their formation was dependent upon expression of OPGL and, to a lesser extent, on tumor necrosis factor alpha . Mononuclear cells represented a significant source of OPGL production . In vivo, P . gingivalis injection stimulated OPGL expression in both mononuclear leukocytes and osteoblastic cells . Thus, these findings describe a pathway by which bacteria could enhance osteolysis independently of osteoblasts and suggest that the mix of cells that participate in inflammatory and physiologic bone resorption may be different . This may give insight into new targets of therapeutic intervention. Cell, 2002 Apr 19, 109(2), 141 - 4 Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes; Wassarman KM; Bacterial small, untranslated RNAs are important regulators that often act to transmit environmental signals when cells encounter suboptimal or stressful growth conditions . These RNAs help modulate changes in cellular metabolism to optimize utilization of available nutrients and improve the probability for survival. Ann Occup Hyg, 2002 Jan, 46(1), 113 - 8 Effect of sampling time on the culturability of airborne fungi and bacteria sampled by filtration; Durand KT et al.; Air sampling of bioaerosols by filtration may be preferable for many epidemiological studies because the methods can be used to collect personal samples for a full work-shift . There is some concern, however, that the viability of fungal spores and bacterial cells might be compromised by sampling for as long as a full shift . This study was designed to determine the effect of sampling up to 6 h on the viability (measured by culture) of airborne fungi and bacteria at composting facilities . Six side-by-side samples were collected in two locations at each of three composting facilities for 1 h at 2 l/m on polycarbonate filters . Two samples in each set were then capped while clean, HEPA-filtered air was drawn across two others for an additional 2 h and across the last two for an additional 5 h . Filters were washed and the samples were analyzed for culturable bacteria and fungi, and for total bacteria and fungi by microscopic counting . Concentrations ranged from 1.7 x 10(3) to 6.2 x 10(7) c.f.u./m3 of culturable fungi and 1.17 x 10(4) to 1.0 x 10(6) c.f.u./m3 of culturable bacteria . In linear models that included duration of sampling, location, and the interaction of location and sample duration, neither sample duration nor the interaction term were significant predictors of the logs of the concentrations of culturable fungi or bacteria or of the ratio of the logs of the culturable concentrations to total concentrations for fungi or bacteria . This suggests that increased sampling time does not affect the viability of the organisms commonly found in the air at composting facilities. Radiats Biol Radioecol, 2002 Mar-Apr, 42(2), 159 - 63 {Influence of ionizing radiation of low intensity on the processes of reproduction, aging and dying off of Escherichia coli bacteria}; Morozov II et al.; The influence of 60Co gamma-ray irradiation of low intensity (0.1-0.4, 0.76 x 10(3) microGy/h) on the processes of reproduction, aging and dying off of E . coli B/r and E . coli BS-1 bacteria have been investigated . It was shown that the reproduction of this bacteria strains was not dependent on the dose rate in the range 0.1-0.4 microGy/h . It was shown in comparison with the irradiated E . coli B/r cells dynamics of the aging and dying off of the irradiated E . coli BS-1 is decreased in the process of prolonged (about 190 days) irradiation with a dose rate of 0.76 x 10(3) microGy/h . It is proposed the relationship between the revealed phenomenon of the decrease in the intensity of the irradiated E . coli BS-1 cell aging and dying and the Vavilov-Cerenkov emission. Nature, 2002 May 9, 417(6885), 202 - 5 Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria; Giraud E et al.; Plants use a set of light sensors to control their growth and development in response to changes in ambient light . In particular, phytochromes exert their regulatory activity by switching between a biologically inactive red-light-absorbing form (Pr) and an active far-red-light absorbing form (Pfr) . Recently, biochemical and genetic studies have demonstrated the occurrence of phytochrome-like proteins in photosynthetic and non-photosynthetic bacteria--but little is known about their functions . Here we report the discovery of a bacteriophytochrome located downstream from the photosynthesis gene cluster in a Bradyrhizobium strain symbiont of Aeschynomene . The synthesis of the complete photosynthetic apparatus is totally under the control of this bacteriophytochrome . A similar behaviour is observed for the closely related species Rhodopseudomonas palustris, but not for the more distant anoxygenic photosynthetic bacteria of the genus Rhodobacter, Rubrivivax or Rhodospirillum . Unlike other (bacterio)phytochromes, the carboxy-terminal domain of this bacteriophytochrome contains no histidine kinase features . This suggests a light signalling pathway involving direct protein-protein interaction with no phosphorelay cascade . This specific mechanism of regulation may represent an important ecological adaptation to optimize the plant-bacteria interaction. Environ Microbiol, 2002 Mar, 4(3), 148 - 57 Population dynamics of type I and II methanotrophic bacteria in rice soils; Macalady JL et al.; Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere . Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots . Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season . The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth . Both type I and type II methanotrophs were abundant throughout the year . However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth. Environ Sci Technol, 2002 Apr 1, 36(7), 1497 - 504 Effects of different quinoid redox mediators on the anaerobic reduction of azo dyes by bacteria; Rau J et al.; The addition of quinoid redox mediators to anaerobically incubated cultures of various taxonomically different bacterial species resulted in significantly increased reduction rates for the azo dye amaranth . From different quinones tested, generally anthraquinone-2-sulfonate (AQS) and lawsone (2-hydroxy-1,4-naphthoquinone) caused the highest increase in the azoreductase activities . The effects of AQS and lawsone were studied in greater detail with Sphingomonas xenophaga BN6 and Escherichia coli K12 . Both strains reduced the quinones under anaerobic conditions with significantly different relative activities . The chemically reduced forms of AQS, lawsone, and different other quinones were assayed for their ability to decolorize amaranth, and a good correlation between the redox potentials of the quinones and the reduction rates of the azo dyes was observed . The addition of AQS or lawsone also increased the ability of unacclimated sewage sludge to reduce azo dyes . Chemically pure lawsone could be replaced by the powdered leaves of the henna plant which contain significant amounts of lawsone. J Microbiol Methods, 2002 Jul, 50(2), 141 - 53 Second derivative UV absorbance analysis to monitor nitrate-reduction by bacteria in most probable number determinations; Eckford RE et al.; Heterotrophic and autotrophic nitrate-reducing bacteria (NRB) play important roles in many environments . These bacteria are often enumerated by most probable number (MPN) methods . Measuring NO(3)(-) depletion in the MPN cultures is the definitive way to determine the presence of NRB . Media used for MPN determinations of NRB in oil field waters usually contain high Cl(-) concentrations, matching those in the water samples . Many methods for measuring NO(3)(-) concentrations, such as ion chromatography (IC), cadmium reduction and ion electrode methods, are adversely affected by high concentrations of Cl(-) and organic compounds . A second derivative UV absorbance method proved to be a fast and reliable means for measuring NO(3)(-) depletion in MPN media used for enumerating autotrophic and heterotrophic NRB, without interferences from Cl(-) or the organic components in the latter medium . The MPN results for heterotrophic NRB determined by the second derivative UV absorbance agreed well with those determined by the production of nitrous oxide, and were often higher than those determined by measuring nitrate depletion by the diphenylamine spot test. Environ Sci Technol, 2002 Apr 15, 36(8), 1720 - 7 Anaerobic electrochemical corrosion of mild steel in the presence of extracellular polymeric substances produced by a culture enriched in sulfate-reducing bacteria; Chan KY et al.; The corrosion of mild steel in a seawater medium containing extracellular polymeric substances (EPS) produced by sulfate-reducing bacteria (SRB) was studied by electrochemical experiments and atomic force microscopy (AFM) . Under anaerobic conditions, the corrosion of mild steel increased up to 5-fold in the presence of a 1% (w/w) EPS solution but in the absence of SRB . The enhanced corrosion is mainly due to the oxidizing power of EPS with a reduction potential of E1/2 at -0.54 V (saturated calomel electrode), which is 0.4 V above that of hydrogen reduction . The electrochemical reduction of EPS provides a couple to iron oxidation, as demonstrated by H-shaped cell experiments in which the steel sample and EPS are not in physical contact but are ionically connected via the solution and electronically connected through an external wire . Fourier transformation infrared spectroscopy and X-ray photoelectron spectroscopy showed that EPS derived from SRB are comprised of 60% proteins, 37% polysaccharides, and 3% hydrocarbons . The XPS results showed that, upon corrosion, polysaccharide components were mostly converted to hydrocarbons. J Plant Growth Regul, 2001 Dec, 20(4), 387 - 442 Occurrence of Gibberellins in Vascular Plants, Fungi, and Bacteria; MacMillan J; The occurrence of GA1 to GA126 in vascular plants, fungi, and bacteria is listed . The data are discussed with reference to criteria for identification and to the frequency of occurrence of GAs in vascular plants. Transfus Med, 2002 Apr, 12(2), 115 - 23 Electrochemiluminescent detection of bacteria in blood components; Rider J et al.; Transfusion-transmitted bacterial infections cause significant patient morbidity and mortality . This study aimed to improve the sensitivity of a nucleic acid-based electrochemiluminescence (ECL) assay for pretransfusion bacterial testing of cellular blood components . The approach is dependent on the detection of bacterial 16S ribosomal RNA (rRNA) . The modifications studied included the use of a chaotrope-based lysis buffer with high-energy mechanical cell disruption by RiboLysis, increased ruthenium (Ru2+) labelling per 16S rRNA molecule and concomitant use of fluorescent nucleic acid dyes (CyQUANT, Syto 17 red and Syto 61 red) . The methodological changes made did lead to more effective bacterial cell disruption and enhanced ECL signal generation . Nevertheless, assay sensitivity was only slightly improved at approximately 10(4)-10(5) colony forming units per mL (CFU mL(-1)) and the results were highly inconsistent . The method is still not sensitive to the required 10(2) CFU mL(-1) and remains impractical for routine use in blood centres. Eur J Immunol, 2002 May, 32(5), 1309 - 18 Block of Stat-1 activation in macrophages phagocytosing bacteria causes reduced transcription of CIITA and consequent impaired antigen presentation; Barbaro Ade L et al.; The IFN-gamma-induced HLA class II expression in human macrophages was drastically reduced after phagocytosis of Escherichia coli . HLA class II down-modulation depended on phagocytosis of bacteria and could not be reproduced by phagocytosis of inert particles or by treatment with lipopolysaccharide . Study of the kinetics and molecular analysis showed that class II molecules and corresponding mRNA were up-regulated at 6 h after phagocytosis of bacteria . Subsequently, a progressive reduction of mRNA occurred, and, at 72 h, as little as 25% of the class II mRNA level of IFN-gamma-treated control cells was found . This was due to reduced transcription of the class II transcriptional activator CIITA, as a consequence of reduced immediate-early inducible factor (IRF-1) and particularly of reduced phosphorylated Stat-1 homodimers, nuclear factors both necessary for optimal triggering of the CIITA promoter . Failure to sustain IFN-gamma-induced CIITA up-modulation during phagocytosis of bacteria had functional implications, as human macrophages could not adequately process and present antigenic peptides to HLA-DR-restricted antigen-specific T cells . This is the first evidence that phagocytosis of bacteria can down-modulate HLA class II expression in normal human macrophages by acting at the level of expression of CIITA. Semin Immunol, 2002 Apr, 14(2), 123 - 32 Molecular mechanisms of neutrophil recruitment elicited by bacteria in the lungs; Mizgerd JP; The recruitment of leukocytes to an extravascular destination requires intercellular communication between tissue cells and leukocytes . The molecules mediating this intercellular communication play differing roles in recruiting different types of leukocytes, in response to different stimuli, in different tissues, and in different hosts . The present communication reviews the adhesion molecules, chemokines, other cytokines, and NF- kappa B proteins which regulate the recruitment of neutrophils elicited by bacteria in the lungs . Biofizika, 2002 Mar-Apr, 47(2), 283 - 94 {Modeling of energy migration and trapping in purple bacteria . Analysis of extreme formulae}; Borisov AIu et al.; Homogeneous pigment ensembles similar to those of purple bacteria Rhodospirillum rubrum were studied . Two formulae were advanced for the limiting values of excitation lifetime and quantum yield of excitation trapping in these ensembles, provided all reaction centers are in an active state . It was demonstrated by mathematical modeling that these limiting values strictly depend on three parameters of molecular ensembles: the numbers of core-bacteriochlorophyll molecules per reaction center, the values of rate constants for excitation trapping in reaction centers, and excitation wasteful deactivation in all molecules . The excitation lifetime and quantum yield were proved to approach their limiting values as the rate constants of excitation intermolecular migration increase . The closeness of experimental values for two above mentioned functions to their calculated limiting values proves the migration-limited type of the photosynthetic unit investigated and a high efficiency of excitation trapping in its reaction centers. Curr Opin Infect Dis, 2000 Oct, 13(5), 503 - 509 Bacteria and inflammatory bowel disease; Martin HM et al.; The cause of inflammatory bowel disease is unknown, but both environmental and genetic factors are implicated . This review presents evidence from recent studies involving both animal models and inflammatory bowel disease patients, which supports a role for bacteria in the aetiology and pathogenesis of Crohn's disease and ulcerative colitis. Ying Yong Sheng Tai Xue Bao, 2002 Jan, 13(1), 95 - 100 {Main factors influencing the growth of planktonic bacteria in fish pond ecosystem}; Tan H et al.; Focused on the main factors influencing the growth of bacteria in fish pond ecosystem, the variation of abundance in bacterial culture, the effects of substrate on bacterial growth, nutrient uptake and mineralization, the effects of bacterivorous predator and water temperature on bacterial growth were investigated in this paper . The results showed that the growth of bacteria and its uptake of C and N were enhanced by application of inorganic phosphorus into the water, but not by application of organic carbon and nitrogen, and that the N mineralization was increased by adding organic nitrogen, indicating that the bacterial growth was limited by inorganic P in the substrate, not by organic C and N . Among the five test groups, predator bacteria had the slowest growth rate, being lower than the control by 6.26-15.4% . The abundance of bacteria, its number increment and growth rate in the fish pond were found to be positively correlated with water temperature in different seasons . In addition, at higher temperature, the positive effects of nutrient application on bacterial growth were enhanced, while the negative effects of predator bacteria on bacterial growth were weakened. Appl Microbiol Biotechnol, 2002 Apr, 58(5), 675 - 8 Epub 2002 Feb 14. Autotrophic synthesis of polyhydroxyalkanoates by the bacteria Ralstonia eutropha in the presence of carbon monoxide; Volova TG et al.; It has been found that the carbon monoxide (CO)-resistant strain of the hydrogen bacteria Ralstonia eutropha B5786 is able to synthesise polyhydroxyalkanoates (PHAs) in the presence of CO under autotrophic conditions . This strain, grown on model gas mixtures containing 5-25% CO (v/v), accumulates up to 70-75% (of absolutely dry matter) PHA, without significant variation in the yield coefficient on hydrogen . No suppression of the activities of the key enzymes of PHA synthesis ( beta-ketothiolase, acetoacetyl-CoA-reductase, butyrate dehydrogenase and poly-3-hydroxybutyrate synthase) was recorded . The PHA synthesised is a co-polymer containing mostly beta-hydroxybutyrate (more than 99 mol%) with trace amounts of beta-hydroxyvalerate . The investigated properties of the polymer (molecular weight, crystallinity, temperature characteristics) do not differ from those of the polymer synthesised on electrolytic hydrogen. Hunan Yi Ke Da Xue Xue Bao, 1999, 24(2), 183 - 5 {Urotoxic effect to intestinal bacteria in patients with chronic renal failure}; Chen L et al.; To analyse the differences of intestinal bacterial quality and quantity, the feces taken from chronic renal failure(CRF) and healthy subject were cultured aerobicly . Then the isolated E . coli from CRF patients and healthy subjects was inoculated respectively into cultural medium with CRF serum and incubated whose concentration of UN, Cr and UA in medium before and after incubation was measured to observe the bacteria degrade of the above-mentioned urotoxin . RESULT: The intestinal E . coli can apparently degrade UN, Cr and UA in CRF patients which suggests that urotoxin may induce E . coli variation. Curr Opin Microbiol, 2002 Apr, 5(2), 202 - 5 Phospholipid modifications in bacteria; Cronan JE Jr; Many bacteria alter the acyl chains of their membrane phospholipids in response to changing environmental conditions . Two of these modifications are reviewed: cis-->trans isomerization and cyclopropanation of double bonds . The isomerization reaction is now known to be catalyzed by a periplasmic protein that contains a covalently bound heme . Cyclopropanation has been shown to play a role in Mycobacterium tuberculosis pathogenesis and, in Escherichia coli, plays an important role in resistance to acidic conditions. Cytometry, 2002 Apr 1, 47(4), 243 - 7 Simultaneous detection of bacteria expressing GFP and DsRed genes with a flow cytometer; Maksimow M et al.; BACKGROUND: In this study, Escherichia coli cells producing red fluorescent protein of Discosoma sp . (drFP583 DsRed) were investigated with flow cytometry by using 488 nm excitation . We also studied whether green fluorescent protein (GFP) and drFP583 could be detected simultaneously from a single bacterial cell . METHODS: Plasmids pDsRed and pEGFP were used for the production of drFP583 and enhanced GFP, respectively, in E . coli MC1061 cells . To produce enhanced GFP and drFP583 simultaneously, plasmids pG9R and pG19R were constructed . These encode tandem fusions of enhanced GFP and drFP583 to ensure similar production levels for both proteins . RESULTS: Bacteria producing enhanced GFP and drFP583 were found to be brightly green and red fluorescent, respectively . Production of enhanced GFP and drFP583 fusion proteins resulted in bacteria that emitted both green and red fluorescence, which was detected easily by a flow cytometer using single laser excitation . Previously reported tetramerization of drFP583 did not restrict its use as a reporter gene, although it maturated significantly slower than enhanced GFP . CONCLUSIONS: The results show that enhanced GFP and drFP583 proteins can be detected simultaneously from single bacteria with a standard flow cytometer with simple optical configuration . J Med Entomol, 2002 Jan, 39(1), 130 - 4 Responses of fertile and sterile screwworm (Diptera: Calliphoridae) flies to bovine blood inoculated with bacteria originating from screwworm-infested animal wounds; Chaudhury MF et al.; ABSTRACT A simple bioassay system was developed to study locomotory and ovipositional responses of screwworm, Cochliomyia hominivorax (Coquerel), flies to bovine blood inoculated with eight species of coliform bacteria that were isolated from screwworm-infested animal wounds . When exposed to odors from bacteria-inoculated blood which was incubated for 72 h at 37 degrees C, approximately 50% of 7- and 10-d-old gravid females landed on the blood by the end of 15 min test exposure . Only 17% of 7-d-old reproductively sterile females (from irradiated pupae) with previtellogenic ovaries and 2% of 4-d-old vitellogenic females responded to the same treatment . Females generally reacted in greatest numbers to bacteria-inoculated blood incubated for 72 h, followed by 48 h, then 24 and 96 h . Males of all ages tested were unresponsive . Although oviposition occurred in tests with gravid females lasting for 1 h, with both inoculated blood and an uninoculated control, the inoculated sample was significantly better than the control at 48, 72, and 96 h incubation duration . Our results are consistent with the conclusion that the inoculated blood, when incubated for 48-72 h, gives off volatile chemicals which attract gravid females and contains an oviposition stimulant that acts following contact and feeding . The volatiles, once isolated and identified, may be useful for sampling gravid females in the field as well as improving the oviposition system in the mass-production facility of the screwworm eradication program. Adv Genet, 2002, 46, 361 - 98 Antisense RNAs in bacteria and their genetic elements; Wagner EG et al.; Antisense RNA-mediated regulation is widespread in bacteria . Most antisense RNA control systems have been found in plasmids, phages, and transposons . Fewer examples were identified in bacterial chromosomes . This chapter summarizes our current knowledge about antisense RNAs with respect to their occurrence, their biological roles, and their diverse mechanisms of action . Examples of cis- or trans-encoded antisense RNAs are discussed, and their properties compared . Most antisense RNAs are posttranscriptionally acting inhibitors of target genes, but a few examples of activator antisense RNAs are known . The implications of RNA structure on topologically and kinetically favored binding pathways are addressed, and solutions that have evolved to permit productive interactions between intricately folded RNAs are discussed . Finally, we describe how particular properties of individual antisense/target RNA systems match their respective biological roles. Zhonghua Kou Qiang Yi Xue Za Zhi, 2001 Nov, 36(6), 431 - 3 {The influence of surface roughness on bacteria adhesion on titanium}; Li M et al.; OBJECTIVE: To investigate the correlation between surface roughness and bacteria adhesion . METHODS: Surface roughness of four abutments were determined by Talysurf/6p-120 topographer . Ra, Rz, Rp, Rv, Ry and Sm values were gathered . Commercial pure titanium and titanium alloy discs, S . mutans and A . viscosus were used in adhesion experiment . RESULTS: Ra values (in microns) of the tested abutments were: 0.1556, 0.2073, 0.6976, and 0.3811 . No statistical difference was observed in bacterial quantity when Ra < 0.4528 microns and Rz < 3.3882 microns in adhesion experiment . CONCLUSIONS: The surface roughness of Ra < 0.4 micron and Rz < 3.4 microns is recommended for implant abutment. Chemosphere, 2002 Feb, 46(6), 859 - 70 Mercury removal, methylmercury formation, and sulfate-reducing bacteria profiles in wetland mesocosms; King JK et al.; A pilot-scale model was constructed to determine if a wetland treatment system (WTS) could effectively remove low-level mercury from an outfall located at the Department of Energy's Savannah River Site . Site-specific hydrosoil was planted with giant bulrush, Scirpus californicus, and surface amended with gypsum (CaSO4) prior to investigating the biogeochemical dynamics of sediment-based sulfur and mercury speciation . On average, the pilot WTS decreased total mercury concentrations in the outfall stream by 50% . Transformation of mercury to a more "bioavailable" species, methylmercury, was also observed in the wetland treatment system . Methylmercury formation in the wetland was ascertained with respect to sediment biogeochemistry and S . californicus influences . Differences in sulfate-reduction rates (SRRs) were observed between mesocosms that received additional decomposing Scirpus matter and mesocosms that were permitted growth of the submerged macrophyte, Potamogeton pusillus . Relative abundance measurements of sulfate-reducing bacteria (SRB) as characterized using oligonucleotide probes were also noticeably different between the two mesocosms . A positive correlation between increased sulfide, dissolved total mercury, and dissolved methylmercury concentrations was also observed in porewater . The data suggest that soluble mercury-sulfide complexes were formed and contributed, in part, to a slight increase in mercury solubility . Observed increases in methylmercury concentration also suggest that soluble mercury-sulfide complexes represent a significant source of mercury that is "available" for methylation . Finally, a volunteer macrophyte, Potamogeton pusillus, is implicated as having contributed additional suspended particulate matter in surface water that subsequently reduced the pool of dissolved mercury while also providing an environment suitable for demethylation. Ned Tijdschr Tandheelkd, 1996 Apr, 103(4), 127 - 31 {Typing and transmission of periodontal bacteria}; van Steenbergen TJ et al.; An overview is given of typing methods for bacteria that are associated with periodontitis . Special attention is paid to new molecular biological techniques, based on the characterization of protein and DNA . Bacteria that are associated with periodontitis have a population structure similar to that of opportunistic bacteria . Typing methods are used to study transmission of bacteria . P . gingivalis can be transmitted between spouses, but transmission from parent to child seems to be uncommon . A . actinomycetemcomitans transmission between adults does not occur frequently, while transmission from parent to child can occur in a low frequency. Br J Community Nurs, 2001 Mar, 6(3), 126 - 34 The effect of bacteria on leg ulcer healing; Harker J; It is a common belief that bacterial infection will delay the healing of leg ulcers, or lead to a deterioration in the wound bed or surrounding skin . Despite many years of research however, there is still no agreement on whether this is in fact the case . This article reviews a selection of the available literature regarding the effects of bacteria on leg ulcer healing . Attempts have been made to distinguish differing levels of bacterial presence (e.g . contamination, colonization, infection), but these terms are still loosely applied and consequently ill-defined . Furthermore, the variety of treatment and assessment methods used in the various studies hampers their comparison . The article concludes that future studies should adhere to a uniform methodology in order to provide clear evidence on which to base practice. Biophys J, 2002 Apr, 82(4), 2184 - 97 Absorption and CD spectroscopy and modeling of various LH2 complexes from purple bacteria; Georgakopoulou S et al.; The absorption (OD) and circular dichroism (CD) spectra of LH2 complexes from various purple bacteria have been measured and modeled . Based on the lineshapes of the spectra we can sort the LH2 complexes into two distinguishable groups: "acidophila"-like (type 1) and "molischianum"-like (type 2) . Starting from the known geometric structures of Rhodopseudomonas (Rps.) acidophila and Rhodospirillum (Rsp.) molischianum we can model the OD and CD spectra of all species by just slightly varying some key parameters: the interaction strength, the energy difference of alpha- and beta-bound B850 bacteriochlorophylls (BChls), the orientation of the B800 and B850 BChls, and the (in)homogeneous broadening . Although the ring size can vary, the data are consistent with all the LH2 complexes having basically very similar structures. Bull Tokyo Dent Coll, 2001 Nov, 42(4), 243 - 9 Comparison of the activity of four chitosan derivatives in reducing initial adherence of oral bacteria onto tooth surfaces; Sano H et al.; We examined the effects of four kinds of chitosan derivatives on initial adherence of oral bacteria onto human anterior teeth surfaces . The buccal surfaces of anterior teeth were used as the experimental surfaces . They were divided into five rectangle areas with outer dimensions of about 2 mm x 4 mm . After applying two ml of a sample solution onto the tooth surfaces, an examiner wiped each rectangle area with a sterilized plastic swab one, three and six hours later . Then we measured bacterial counts in sterilized swabs with mitis salivarius agar . We found that the order of magnitude of the inhibitory effect on the adherence of oral bacteria was low molecular chitosan > phosphorylated chitosan > amorphous chitosan > carboxymethyl chitosan . The solution containing 0.5% low molecular chitosan depressed the bacterial adherence to the same extent as a 50 ppm chlorhexidine digluconate solution for three hours, and 0.1% phosphorylated chitosan also exhibited an inhibitory effect in bacterial adherence for one hour . Amorphous chitosan had a moderate inhibitory effect, but no clear inhibitory activity was found with 0.1% carboxymethyl chitosan . These results suggest that low molecular chitosan and phosphorylated chitosan have the potential to effectively inhibit the initial adherence of oral bacteria onto human tooth surfaces. Arch Environ Contam Toxicol, 2002 Apr, 42(3), 263 - 71 Toxicity of tetracyclines and tetracycline degradation products to environmentally relevant bacteria, including selected tetracycline-resistant bacteria; Halling-Sorensen B et al.; Tetracyclines used in veterinary therapy invariably will find their way as parent compound and degradation products to the agricultural field . Major degradation products formed due to the limited stability of parent tetracyclines (tetracycline, chlortetracycline, and oxytetracycline) in aqueous solution were theoretically identified at various environmental conditions, such as pH, presence of chelating metals, and light . Their potency was assessed on sludge bacteria, tetracycline-sensitive soil bacteria, and tetracycline-resistant strains . Several of the degradation products had potency at the same concentration level as tetracycline, chlortetracycline, and oxytetracycline on both the sludge and the tetracycline-sensitive soil bacteria . Further, both 5a,6-anhydrotetracycline and 5a,6-anhydrochlortetracycline had potency on tetracycline-resistant bacteria supporting a mode of action different from that of the parent compounds. Genetics, 2002 Mar, 160(3), 1075 - 86 History of infection with different male-killing bacteria in the two-spot ladybird beetle Adalia bipunctata revealed through mitochondrial DNA sequence analysis; v d Schulenburg JH et al.; The two-spot ladybird beetle Adalia bipunctata (Coleoptera: Coccinellidae) is host to four different intracellular maternally inherited bacteria that kill male hosts during embryogenesis: one each of the genus Rickettsia (alpha-Proteobacteria) and Spiroplasma (Mollicutes) and two distinct strains of Wolbachia (alpha-Proteobacteria) . The history of infection with these male-killers was explored using host mitochondrial DNA, which is linked with the bacteria due to joint maternal inheritance . Two variable regions, 610 bp of cytochrome oxidase subunit I and 563 bp of NADH dehydrogenase subunit 5, were isolated from 52 A . bipunctata with known infection status and different geographic origin from across Eurasia . Two outgroup taxa were also considered . DNA sequence analysis revealed that the distribution of mitochondrial haplotypes is not associated with geography . Rather, it correlates with infection status, confirming linkage disequilibrium between mitochondria and bacteria . The data strongly suggest that the Rickettsia male-killer invaded the host earlier than the other taxa . Further, the male-killing Spiroplasma is indicated to have undergone a recent and extensive spread through host populations . In general, male-killing in A . bipunctata seems to represent a highly dynamic system, which should prove useful in future studies on the evolutionary dynamics of this peculiar type of symbiont-host association. EMBO Rep, 2002 Apr, 3(4), 373 - 7 Epub 2002 Mar 15. Release factor 2 frameshifting sites in different bacteria; Baranov PV et al.; The mRNA encoding Escherichia coli polypeptide chain release factor 2 (RF2) has two partially overlapping reading frames . Synthesis of RF2 involves ribosomes shifting to the +1 reading frame at the end of the first open reading frame (ORF) . Frameshifting serves an autoregulatory function . The RF2 gene sequences from the 86 additional bacterial species now available have been analyzed . Thirty percent of them have a single ORF and their expression does not require frameshifting . In the approximately 70% that utilize frameshifting, the sequence cassette responsible for frameshifting is highly conserved . In the E . coli RF2 gene, an internal Shine-Dalgarno (SD) sequence just before the shift site was shown earlier to be important for frameshifting . Mutagenic data presented here show that the spacer region between the SD sequence and the shift site influences frameshifting, and possible mechanisms are discussed . Internal translation initiation occurs at the shift site, but any functional role is obscure. EMBO J, 1983, 2(1), 27 - 32 Binding between the par region of plasmids R1 and pSC101 and the outer membrane fraction of the host bacteria; Gustafsson P et al.; The binding between par+ and par plasmid DNA to different membrane fractions of Escherichia coli was investigated . Membrane material from cells carrying different Par+ and Par- derivatives of plasmids R1 and pSC101 was isolated and fractionated into an outer and a cytoplasmic membrane fraction . The presence of plasmid DNA in the two membrane fractions was measured either by nick-translation of the membrane-bound DNA, followed by filter-hybridization to homologous DNA, or by filter-hybridization of the membrane-bound DNA to nick-translated homologous purified plasmid DNA . The DNA of par derivatives of plasmids R1 and pSC101 could be detected only in the cytoplasmic membrane fraction, whereas the corresponding par+ plasmid DNA also appeared in the outer membrane material, indicating a specific binding between the R1 and pSC101 partition loci and the bacterial outer membrane . The experiment was then modified by fractionation of the membrane material from cells carrying hybrids between the vector pSF2124 and the par region or the basic replicon region of plasmid R1 . The DNA of the membrane fractions were filter-hybridized to nick-translated probes . Again, the par+ region caused hybridization to the outer membrane material . Therefore, we may conclude that controlled partitioning involves binding of DNA to membrane material that has the same density as the outer membrane of the host bacteria . This finding offers a biochemical 'assay' for studies of the molecular biology of plasmid partitioning. Biosens Bioelectron, 2002 May, 17(5), 433 - 40 A portable toxicity biosensor using freeze-dried recombinant bioluminescent bacteria; Choi SH et al.; A portable biosensor has been developed to meet the demands of field toxicity analysis . This biosensor consists of three parts, a freeze-dried biosensing strain within a vial, a small light-proof test chamber, and an optic-fiber connected between the sample chamber and a luminometer . Various genetically engineered bioluminescent bacteria were freeze-dried to measure different types of toxicity based upon their modes of action . GC2 (lac::luxCDABE), a constitutively bioluminescent strain, was used to monitor the general toxicity of samples through a decrease in its bioluminescence, while specific toxicity was detected through the use of strains such as DPD2540 (fabA::luxCDABE), TV1061 (grpE::luxCDABE), DPD2794 (recA::luxCDABE), and DPD2511 (katG::luxCDABE) . These inducible strains show an increase in bioluminescence under specific stressful conditions, i.e . membrane-, protein-, DNA-, and oxidative-stress, respectively . The toxicity of a sample could be detected by measuring the bioluminescence 30 min after addition to the freeze-dried strains . In an attempt to enhance the sensitivity of the freeze-dried cells, glucose and Tween 80 were tested as additives . It was found that the addition of glucose had a negative effect on the viability of the freeze-dried cells, while samples having Tween 80 showed an increase in their viability . On the other hand, the addition of either Tween 80 or glucose decreased the final bioluminescent response of DPD2540 in response to 4-chlorophenol . Using these strains, many different chemicals were tested and characterized . This portable biosensor, with a very simple protocol, can be used for field sample analysis and the monitoring of various water systems on-site. Ann Periodontol, 2001 Dec, 6(1), 41 - 7 Role for periodontal bacteria in cardiovascular diseases; Kuramitsu HK et al.; BACKGROUND: Several epidemiological studies as well as a recent animal model approach have suggested a role for periodontal diseases in the development of cardiovascular disease (CVD) . This relationship could be mediated by inflammatory responses induced by periodontal pathogens as well as direct interaction of these organisms with cardiac tissue . METHODS: In order to explore these possibilities, the effects of the periodontal pathogen Porphyromonas gingivalis on cellular events proposed to play a role in CVD were investigated . RESULTS: P . gingivalis, as well as its outer membrane vesicles (OMV), was able to induce foam cell formation (an important characteristic of CVD) in the murine macrophage cell line J774 A.1 . This property appears to be mediated by the lipopolysaccharide (LPS) fraction of the cells . Several other oral bacteria were also able to induce foam cell formation . Furthermore, since the rupture of the fibrous cap of plaque appears to be an important factor in acute coronary syndrome, it was demonstrated that P . gingivalis 381 degraded fibrous caps isolated from autopsy samples . In addition, it was observed that strain 381 strongly induced matrix metalloproteinase (MMP)-9 protease activity, implicated in plaque rupture, from the J774 A.1 macrophages . Finally, strain 381 was able to enhance monocyte chemoattractant protein-1 (MCP-1) and NADH oxidase expression from endothelial cells . CONCLUSIONS: Therefore, P . gingivalis exhibits several properties which could play a role in CVD as mediators of LDL oxidation, foam cell formation, and rupture of atherosclerotic plaque. Science, 2002 Mar 8, 295(5561), 1892 - 5 The role of endosymbiotic Wolbachia bacteria in the pathogenesis of river blindness; Saint Andre A et al.; Parasitic filarial nematodes infect more than 200 million individuals worldwide, causing debilitating inflammatory diseases such as river blindness and lymphatic filariasis . Using a murine model for river blindness in which soluble extracts of filarial nematodes were injected into the corneal stroma, we demonstrated that the predominant inflammatory response in the cornea was due to species of endosymbiotic Wolbachia bacteria . In addition, the inflammatory response induced by these bacteria was dependent on expression of functional Toll-like receptor 4 (TLR4) on host cells. Am J Reprod Immunol, 2002 Jan, 47(1), 57 - 63 Modulation of the uterine response to infectious bacteria in postpartum ewes; Seals RC et al.; PROBLEM: Exogenous progesterone and prostaglandin E2 (PGE2) can downregulate uterine immune functions and render the uterus susceptible to bacterial infection . METHOD OF STUDY: Ewes were sham-ovariectomized (SHAM) or ovariectomized (OVEX) 9 days after parturition (day 0), and their uteri were inoculated with Arcanobacterium pyogenes and Escherichia coli on day 15 . Vena caval blood was collected on day 14 and days 16-19, and uteri were collected on day 20 . Ewes began receiving either canola oil (OIL) or progesterone in oil (PROG) on day 10 . Lymphocytes from each blood sample were assigned to a 2 x 2 factorial array of in vitro treatments; 10(-7) M PGE2 and 10(-7) M indomethacin (INDO) were main effects . {3H}Thymidine incorporation (expressed in picomoles) was used to quantify proliferation . RESULTS: Progesterone was greater (P = 0.001) in PROG than in OIL ewes (3.6 versus 0.7 ng/mL), and only PROG ewes developed infections . Lymphocyte proliferation was least (P = 0.02) in PROG-OVEX ewes (4.1 versus 5.4, 5.7, and 5.8 pmol for OIL-SHAM, PROG-SHAM, and OIL-OVEX, respectively) . Concanavalin A (Con-A)-stimulated proliferation was less (P < 0.01) for PGE2- and PGE2 + INDO-treated lymphocytes (7.5 and 8.3 pmol, respectively) than for control or INDO-treated cells (12.9 and 14.7 pmol, respectively) . CONCLUSIONS: Progesterone treatment of postpartum ewes suppressed uterine immunity . In vitro PGE, treatment suppressed lymphocyte proliferation, regardless of PROG, and highlights a progesterone-independent level of regulation of uterine immune function. Life Sci Space Res, 1964, 2, 105 - 11 Bacteria under simulated Martian conditions; Young RS et al.; The behavior of organisms in simulated Martian conditions is of great importance to exobiology for two reasons: (1) Because of the extreme environment of Mars, the likelihood of contamination of the planet by earth organisms is considered slight by some scientists . To date, there has been little evidence to contradict this supposition . Such evidence is presented . (2) The selection and adaptation of earth bacteria to Martian conditions is potentially significant in understanding Martian life, if it exists, and may be helpful in designing life-detection techniques and devices . Of course, simulation attempts, based on current knowledge of the Mars environment, may be far from the actual conditions, and extrapolations made from such situations of no real significance . However, generalizations can be made and cautious interpretation of the results of those experiments seems well worth reporting . A new technique for simulation of known parameters of the Martian environment is discussed along with possible biological implications . The response of bacteria to such simulation is demonstrated in terms of survival and growth, showing that certain bacteria will not only survive, but grow during simulated Martian freeze-thaw cycling if water is present . Ways are demonstrated in which water can be present on Mars although not detectable with current technology . Plans for future experimentation are discussed. Proc Natl Acad Sci U S A, 2002 Mar 5, 99(5), 2654 - 9 Proteome-scale purification of human proteins from bacteria; Braun P et al.; The completion of the human genome project and the development of high-throughput approaches herald a dramatic acceleration in the pace of biological research . One of the most compelling next steps will be learning the functional roles of all proteins . Achievement of this goal depends in part on the rapid expression and isolation of proteins at large scale . We exploited recombinational cloning to facilitate the development of methods for the high-throughput purification of human proteins . cDNAs were introduced into a master vector from which they could be rapidly transferred into a variety of protein expression vectors for further analysis . A test set of 32 sequence-verified human cDNAs of various sizes and activities was moved into four different expression vectors encoding different affinity-purification tags . By means of an automatable 2-hr protein purification procedure, all 128 proteins were purified and subsequently characterized for yield, purity, and steps at which losses occurred . Under denaturing conditions when the His6 tag was used, 84% of samples were purified . Under nondenaturing conditions, both the glutathione S-transferase and maltose-binding protein tags were successful in 81% of samples . The developed methods were applied to a larger set of 336 randomly selected cDNAs . Sixty percent of these proteins were successfully purified under denaturing conditions and 82% of these under nondenaturing conditions . A relational database, FLEXProt, was built to compare properties of proteins that were successfully purified and proteins that were not . We observed that some domains in the Pfam database were found almost exclusively in proteins that were successfully purified and thus may have predictive character. Appl Environ Microbiol, 2002 Mar, 68(3), 1478 - 84 Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria; Hollibaugh JT et al.; We analyzed the phylogenetic compositions of ammonia-oxidizing bacteria of the beta subclass of Proteobacteria from 42 Southern Ocean samples . We found a Nitrosospira-like 16S rRNA gene sequence in all 20 samples that yielded PCR products (8 of 30 samples from the Ross Sea and 12 of 12 samples from the Palmer Peninsula) . We also found this sequence in Arctic Ocean samples, indicating a transpolar, if not global, distribution; however, slight differences between Arctic and Antarctic sequences may be evidence of polar endemism. J Appl Microbiol, 2002, 92(3), 443 - 50 Bacteria in heart and lungs of young chicks; Tankson JD et al.; AIMS: The purpose of these experiments was to determine whether the heart and lungs of young chicks harboured bacteria . METHODS AND RESULTS: Samples of the heart and lungs were aseptically removed from chicks on scheduled sampling days . Experiment 1 showed that of the 360 birds evaluated during the late embryonic and early post-hatching periods, only 10.8% harboured bacteria in the heart, lungs, and heart and lungs simultaneously . Experiment 2 suggested that bacteria in these organs were transient . Twenty-three bacterial species were found in the hearts whereas 30 were found in the lungs . Experiment 3 showed that only 1.4% of embryos harboured bacteria in the yolk, albumen, heart and lungs whereas 12.9% of the embryos had bacteria in the air cell . CONCLUSIONS: During the post-hatching period, there was a higher incidence of bacterial isolation in the heart and lungs, whilst during the embryonic development period, there was a lower incidence of bacterial isolation from these two organs . Results suggested that the heart and lungs do not have a residual bacterial flora; rather, opportunistic bacteria occasionally pass through these tissues . SIGNIFICANCE AND IMPACT OF THE STUDY: These experiments proved that bacteria could be isolated in the heart and lungs of healthy chicks reared from E17 to 3 weeks of age. Genet Res, 2001 Dec, 78(3), 303 - 16 Statistical power of QTL mapping methods applied to bacteria counts; Tilquin P et al.; Most QTL mapping methods assume that phenotypes follow a normal distribution, but many phenotypes of interest are not normally distributed, e.g . bacteria counts (or colony-forming units, CFU) . Such data are extremely skewed to the right and can present a high amount of zero values, which are ties from a statistical point of view . Our objective is therefore to assess the efficiency of four QTL mapping methods applied to bacteria counts: (1) least-squares (LS) analysis, (2) maximum-likelihood (ML) analysis, (3) non-parametric (NP) mapping and (4) nested ANOVA (AN) . A transformation based on quantiles is used to mimic observed distributions of bacteria counts . Single positions (1 marker, 1 QTL) as well as chromosome scans (11 markers, 1 QTL) are simulated . When compared with the analysis of a normally distributed phenotype, the analysis of raw bacteria counts leads to a strong decrease in power for parametric methods, but no decrease is observed for NP . However, when a mathematical transformation (MT) is applied to bacteria counts prior to analysis, parametric methods have the same power as NP . Furthermore, parametric methods, when coupled with MT, outperform NP when bacteria counts have a very high proportion of zeros (70.8%) . Our results show that the loss of power is mainly explained by the asymmetry of the phenotypic distribution, for parametric methods, and by the existence of ties, for the non-parametric method . Therefore, mapping of QTL for bacterial diseases, as well as for other diseases assessed by a counting process, should focus on the occurrence of ties in phenotypes before choosing the appropriate QTL mapping method. Vojnosanit Pregl, 2001 Nov-Dec, 58(6), 615 - 20 {Reliability of plasmid profile analysis in the identification of epidemic strains of bacteria causing an outbreak of intestinal infections}; Suljagic V et al.; The aim of the study was to determine the plasmid profile of isolates originated from the outbreaks of gastrointestinal tract infection in the attempt to identify the outbreak strains . Plasmid profile analysis was performed on 163 isolates; 82 isolates originated from foodborne outbreakes and 81 isolates originated from waterborne outbreakes or outbreakes spread by contact . Outbreak strain was identified in 1 (10%) of 10 foodborne outbreakes and in 7 (70%) of 10 waterborne outbreakes or outbreakes spread by contact . According to the obtained results, the method of plasmid profile analysis was more reliable in the investigation of outbreaks of gastrointestinal tract infection spread by water or contact compared to the outbreakes spread by food. Biotechnol Bioeng, 2002 Apr 5, 78(1), 24 - 30 Kinetic studies on elemental sulfur oxidation by Acidithiobacillus ferrooxidans: sulfur limitation and activity of free and adsorbed bacteria; Ceskova P et al.; The kinetics of sulfur oxidation by Acidithiobacillus ferrooxidans in shaking flasks and a 10-L reactor was studied . The observed linearity of growth and sulfur oxidation was explained by sulfur limitation . Total cell yield was not significantly different for exponential growth as compared to growth during the sulfur-limiting phase . Kinetic studies of sulfur oxidation by growing and nongrowing bacteria indicated that both free and adsorbed bacteria oxidize sulfur . Changes in the number of free bacteria rather than cells adsorbed on sulfur were better predictors of the kinetics of sulfur oxidation, indicating that the free bacteria were performing sulfur oxidation . The active growth phase always followed adsorption of bacteria on sulfur; however, the special metabolic role of adsorbed bacteria was unclear . Their activity in sulfur solubilization was considered . Kidney Int, 2002 Feb, 61(2), 444 - 55 Human renal epithelial cells express iNOS in response to cytokines but not bacteria; Poljakovic M et al.; BACKGROUND: Epithelial cells form the mucosal barriers that prevent the entry of mucosal pathogens, and respond to bacterial infections by producing various host defense molecules . In this study, we examined the inducible nitric oxide synthase (iNOS) response of primary human renal tubular epithelial cells (HRTEC) following infection with uropathogenic Escherichia coli Hu734, or stimulation with lipopolysaccharide (LPS) or cytokines . METHODS: Induction of iNOS was examined by RT-PCR, Western blot, immunohistochemistry and nitrite measurements . The effects of endogenously produced nitric oxide (NO), and exogenously applied DETA/NO, SIN-1 and H2O2 on cell viability were analyzed using a respiration assay . RESULTS: HRTEC did not produce NO following infection with E . coli Hu734, LPS alone, or in combination with interferon-gamma (IFN-gamma), even though these agents caused a marked increase in iNOS expression by RAW 264.7, a macrophage cell line . In contrast, iNOS protein and mRNA expression by HRTEC increased after exposure to a cytokine mixture consisting of interleukin (IL)-1beta, tumor necrosis factor-alpha (TNF-alpha) and IFN-gamma . This was due to the combination of IL-1beta and IFN-gamma, but the individual cytokines had no effect . Inducible NOS-expressing cell cultures showed reduced viability, and this effect was inhibited with the NOS inhibitor L-NMMA in RAW 264.7 cells, but not in HRTEC . HRTEC were more sensitive to oxidative stress induced by H2O2 than to nitrogen stress induced by DETA/NO . CONCLUSIONS: We conclude that uropathogenic E . coli that attach to HRTEC fail to directly activate iNOS expression, and that iNOS expression during bacterial infection is more likely to result from stimulation by local cytokines such as IL-1beta and IFN-gamma. Water Res, 2002 Feb, 36(4), 1076 - 83 Effects of high salinity and constituent organic compounds on treatment of photo-processing waste by a sulfur-oxidizing bacteria/granular activated carbon sludge system; Lin BL et al.; To achieve practical treatment of photo-processing waste (PW) using our previously proposed sulfur-oxidizing bacteria (SOB)/granular activated carbon (GAC) sludge system, this paper elucidates why 3- to 5-X dilution of PW was required . That is, a series of experiments were carried out to show the effects of high salinity and constituent organic compounds in PW, respectively . Both an inorganic salts system and calcination PW system showed that SOB completely oxidizes S2O(3)2- -S to SO(4)2- -S even at 12.3 or 13.6% salinity, respectively; hence the dilution requirement is not attributable to high salinity . In experiments employing SOB and SOB/GAC systems to investigate the effects of 23 constituent compounds in PW, compounds were classified into Groups I, II, IIIa, and IIIb . Even with 10 g/l GAC, the nine compounds in Group IIIb still exhibited a toxic effect on SOB activity at 1- and 3-X dilutions; thus it is these compounds that are responsible for requiring dilution of PW . Accordingly, a reduction in their use within the photodeveloping and fix-stabilizing industry, and/or use of > 10g/l GAC, are new considerations for establishing a more practical PW treatment process. Chem Pharm Bull (Tokyo), 2002 Feb, 50(2), 160 - 4 Biotransformation of phorbol by human intestinal bacteria; Abdel-Hafez AA et al.; Anaerobic incubation of phorbol (1) from Croton tiglium with human intestinal bacteria afforded five metabolites: isophorbol (2), deoxyphorbol (3), 4beta,9alpha,20-trihydroxy-13,15-seco-1,6,15-tigliatriene-3,13-dione (4), 4beta,9alpha,20-trihydroxy-15,16,17-trinor-1,6-tigliadiene-3,13-dione (5) and 4beta,9a,20-trihydroxy-14(13-->12)-abeo-12alphaH-1,6-tigliadiene-3,13-dione (6) . All these metabolites (2-6) were identified and characterized by spectroscopic means, including two-dimensional (2D)-NMR . Nine defined strains from the human intestine showed an ability to transform 1 to these metabolites. Hum Antibodies, 2001, 10(3-4), 149 - 54 A novel expression vector for production of epitope-tagged recombinant Fab fragments in bacteria; Burioni R et al.; Labeling of recombinant Fab molecules is an important yet cumbersome and time-consuming procedure that is needed in many immunological experimental designs . This work describes the development of a novel expression vector fusing to the carboxyterminal of the Fab heavy chain fragments a tag peptide (FLAG) that is consistently recognized by a mouse monoclonal antibody . The presence of the FLAG peptide does not alter the binding characteristics of the unmodified Fab molecule, as demonstrated by relative affinity determinations and competition experiments . This new method is suitable for extensive utilization in immunological experimental work using recombinant Fabs. Environ Microbiol, 2001 Dec, 3(12), 743 - 54 Osmoadaptation in bacteria and archaea: common principles and differences; Roesser M et al.; The availability of water is the most important prerequisite for life of any living cell, and exposure of cells to hypersaline conditions always threatens the cells with a drastic loss of water . To re-establish the essential turgor pressure, cells increase the water activity of their cytoplasm by accumulation of compatible solutes, either by synthesis or by uptake . The ability to respond to increasing osmolality is well conserved in all three lines of descent and, here, we compare the osmoadaptive strategies of Bacteria and Archaea . The temporal sequence of events after an osmotic upshock will be discussed, with a focus on the most rapid response, notably the mechanisms of transport activation at the protein level, and different signals for osmolality will be compared . The spectrum of compatible solutes used by different organisms is rather diverse and a comparison of 'bacterial' and 'archaeal' compatible solutes will be given. Mass Spectrom Rev, 2001 Jul-Aug, 20(4), 172 - 94 MALDI-TOF mass spectrometry of bacteria; Lay JO Jr; The development of MALDI-TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed . The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins . More surprising was the observation that MALDI-TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification . Versatility and the rapidity of analysis led to the rapid development of a number of MALDI-TOF methods involving bacteria . Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level . The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI-TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real-time methods for the characterization of bacteria . Biotechnol Bioeng, 2002 Mar 30, 77(7), 734 - 51 Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria; Klamt S et al.; Metabolite balancing has turned out to be a powerful computational tool in metabolic engineering . However, the linear equation systems occurring in this analysis are often underdetermined . If it is difficult or impossible to find the missing constraints, it is nevertheless feasible in some cases to determine the values of a subset of the unknown rates . Here, a procedure for finding out which reaction rates can be uniquely calculated in underdetermined metabolic networks and computing these rates is given . The method is based on the null space to the stoichiometry matrix corresponding to the reactions with unknown rates . It is shown that this method is considerably easier to handle than an algorithm given previously (Van der Heijden et al., 1994a) . Furthermore, a useful elementary representation of the null space is presented which is closely related with the elementary flux modes . This unique representation is central to a more general approach to observability/calculability analysis . In particular, it allows one to find, in an easy way, those sets of measurable rates that enable a calculation of a certain unknown rate . Besides, rates which are never calculable by metabolite balancing may be easily detected by this method . The applicability of these methods is illustrated by a model of the central metabolism in purple nonsulfur bacteria . The photoheterotrophic growth of these representatives of anoxygenic photosynthetic bacteria is stoichiometrically analyzed . Interesting metabolic constraints caused by the necessary balancing of NADPH can be detected in a highly underdetermined system . This is, to our knowledge, the first application of stoichiometric analysis to the metabolic network in this bacteria group using metabolite balancing techniques . A new software tool, the FluxAnalyzer, is introduced . It allows quantitative and structural analysis of metabolic networks in a graphical user interface . Nature, 2002 Feb 7, 415(6872), 644 - 6 Genome shuffling leads to rapid phenotypic improvement in bacteria; Zhang YX et al.; For millennia, selective breeding, on the basis of biparental mating, has led to the successful improvement of plants and animals to meet societal needs . At a molecular level, DNA shuffling mimics, yet accelerates, evolutionary processes, and allows the breeding and improvement of individual genes and subgenomic DNA fragments . We describe here whole-genome shuffling; a process that combines the advantage of multi-parental crossing allowed by DNA shuffling with the recombination of entire genomes normally associated with conventional breeding . We show that recursive genomic recombination within a population of bacteria can efficiently generate combinatorial libraries of new strains . When applied to a population of phenotypically selected bacteria, many of these new strains show marked improvements in the selected phenotype . We demonstrate the use of this approach through the rapid improvement of tylosin production from Streptomyces fradiae . This approach has the potential to facilitate cell and metabolic engineering and provide a non-recombinant alternative to the rapid production of improved organisms. Microbiology, 2002 Feb, 148(Pt 2), 519 - 28 Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets; Skuce RA et al.; The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis . With the recent availability of genome sequences for strains of the M . tuberculosis complex, novel PCR-based M . tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs) . This paper describes the identification of seven VNTR loci in M . tuberculosis H37Rv, the copy number of which varies in other strains of the M . tuberculosis complex . Six of these VNTRs were applied to a panel of 100 different M . bovis isolates, and their discrimination and correlation with spoligotyping and an established set of ETRs were assessed . The number of alleles varied from three to seven at the novel VNTR loci, which differed markedly in their discrimination index . There was positive correlation between spoligotyping, ETR- and VNTR-typing . VNTR-PCR discriminates well between M . bovis strains . Thirty-three allele profiles were identified by the novel VNTRs, 22 for the ETRs and 29 for spoligotyping . When VNTR- and ETR-typing results were combined, a total of 51 different profiles were identified . Digital nomenclature and databasing were intuitive . VNTRs were located both in intergenic regions and annotated ORFs, including PPE (novel glycine-asparigine-rich) proteins, a proposed source of antigenic variation, where VNTRs potentially code repeating amino acid motifs . VNTR-PCR is a valuable tool for strain typing and for the study of the global molecular epidemiology of the M . tuberculosis complex . The novel VNTR targets identified in this study should additionally increase the power of this approach. Microbiology, 2002 Feb, 148(Pt 2), 413 - 20 Kinetics of binding, uptake and degradation of live fluorescent (DsRed) bacteria by Dictyostelium discoideum; Maselli A et al.; The kinetics of binding, uptake and degradation of bacteria by vegetative Dictyostelium amoeba using Escherichia coli expressing the recombinant fluorescent protein DsRed have been characterized . There are significant advantages to using DsRed-expressing bacteria for phagocytosis assays . Stable expression of the fluorescent protein, DsRed, provides living bacteria with a bright internal fluorescent signal that is degradable in the phagolysosomal pathway . Unlike assays with chemically labelled bacteria or latex beads, the bacteria are alive and possess a natural, unaltered external surface for receptor interaction . Dictyostelium cells rapidly bind and phagocytose DsRed bacteria . Pulse-chase experiments show that the signal derived from DsRed is degraded with a half-life of approximately 45 min . To distinguish internalized bacteria from those bound to the surface, an assay was developed in which sodium azide was used to release surface-bound particles . Surprisingly, surface particle release appears to be independent of myosin II function . Using this assay it was shown that the uptake of bacteria into cells is extremely rapid . After 1 min incubation, 20% of the signal is derived from internalized bacteria . The proportion of the signal from internalized bacteria increases gradually and reaches 50% at steady state . This assay will be useful in investigations of the molecular machinery of phagocytosis and post-internalization vesicle trafficking. Proc Natl Acad Sci U S A, 2002 Feb 19, 99(4), 1853 - 8 Epub 2002 Feb 05. A poxvirus-like type IB topoisomerase family in bacteria; Krogh BO et al.; We report that diverse species of bacteria encode a type IB DNA topoisomerase that resembles vaccinia virus topoisomerase . Deinococcus radiodurans topoisomerase IB (DraTopIB), an exemplary member of this family, relaxes supercoiled DNA in the absence of a divalent cation or ATP . DraTopIB has a compact size (346 aa) and is a monomer in solution . Mutational analysis shows that the active site of DraTopIB is composed of the same constellation of catalytic side chains as the vaccinia enzyme . Sequence comparisons and limited proteolysis suggest that their folds are conserved . These findings imply an intimate evolutionary relationship between the poxvirus and bacterial type IB enzymes, and they engender a scheme for the evolution of topoisomerase IB and tyrosine recombinases from a common ancestral strand transferase in the bacterial domain . Remarkably, bacteria that possess topoisomerase IB appear to lack DNA topoisomerase III. Trends Microbiol, 2001 Nov, 9(11), 518 - 21 Tricorn-like proteases in bacteria; Pallen MJ et al.; The tricorn protease is an archaeal protease that forms massive proteasome-like capsids with a hollow chamber . beta-Propeller and PDZ domains are thought to play a role in substrate selection . By analysis of predicted proteins from novel bacterial genome sequences, we have identified four new bacterial tricorn-like proteases, complete with similar beta-propeller, PDZ and catalytic domains . We propose various hypotheses as to the function of these domains that can now be tested in the laboratory. Math Biosci, 2002 Feb, 175(2), 117 - 31 On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment; Carletti M; In this paper we extend the deterministic model for the epidemics induced by virulent phages on bacteria in marine environment introduced by Beretta and Kuang {Math . Biosci . 149 (1998) 57}, allowing random fluctuations around the positive equilibrium . The stochastic stability properties of the model are investigated both analytically and numerically suggesting that the deterministic model is robust with respect to stochastic perturbations. Can J Microbiol, 2001 Dec, 47(12), 1132 - 6 Elemental analysis of uncultured magnetotactic bacteria exposed to heavy metals; Keim CN et al.; Natural enrichments of magnetotactic bacteria were used to study the sites where heavy metals accumulate in uncultured bacteria . Most bacteria obtained by magnetic concentration from these enrichments contained, in addition to the magnetosomes, large phosphorus-rich granules in the cytoplasm . Metal (Zn, Mn, Sr, Cd, Al, Cr, and Pb) chlorides were added independently to the enrichments, and after 24 h, the elemental composition of the phosphorus-rich granules, magnetosomes, and "soft parts" (cytoplasm plus cell envelope) of whole bacteria was analyzed by energy-dispersive X-ray analysis on a transmission electron microscope . All bacteria contained Mn and Sr in the phosphorus-rich granules; some of them presented Mn peaks also in the soft parts . Zinc accumulation was variable and was found mainly in the phosphorus-rich granules, but also in the soft part of some bacteria . Some analyzed bacteria presented Zn peaks only in the soft parts, and some of them did not present Zn in any structure . Cadmium and Al were found only in the granules of some bacteria . Chromium was found in the soft parts of some bacteria . Lead was not detected in any bacteria . We concluded that the phosphorus-rich granules are major sites for metal accumulation by these bacteria . No conclusive results for magnetosomes were obtained because of the limitations of the analytical techniques particularly when used for whole cell analysis. Toxicon, 2002 May, 40(5), 543 - 9 mRNA secondary structure can greatly affect production of recombinant phospholipase A(2) toxins in bacteria; Ivanovski G et al.; The neurotoxic activity of ammodytoxin A (AtxA), a phospholipase A(2) from Vipera ammodytes ammodytes venom, has been investigated by protein engineering . With the aim of obtaining AtxA as a non-fused protein in the bacterial cytoplasm and avoiding problems with incomplete cleavage in vivo of the initial Met preceding the first residue (Ser1), a double mutant (S1A/E4Q) was prepared and expressed in Escherichia coli . Immunoblotting of the bacterial lysate showed that the mutant was synthesized at a low level not exceeding 0.5% of total cell protein . Analysis of the potential secondary structure of the mutant mRNA in the translation initiation region suggested that the Ala1 (GCC) and Leu2 (CUG) codons used are likely to be involved in a hairpin structure with the Thr13 (ACG) and Gly14 (GGG) codons, hindering effective translation at the ribosome . To weaken this structure (by DeltaG of about 20 kJ/mol) the same double mutant was prepared using another mutagenic oligonucleotide with silent mutations in the Ala1 (GCU) and Leu2 (UUG) codons . The mutant was successfully produced at a level of approximately 15% of total protein, with the initial Met completely removed in the bacterial cell . Such an approach could be important in solving similar problems in bacterial production of other toxic proteins. Biochem Biophys Res Commun, 2002 Feb 8, 290(5), 1462 - 9 Arginine residues in domain V have a central role for bacteria-binding activity of macrophage scavenger receptor MARCO; Brannstrom A et al.; MARCO is a bacteria-binding macrophage-specific scavenger receptor that plays a role in innate immune response . MARCO has short intracellular and transmembrane domains, as well as a large extracellular domain composed of a spacer domain, a long collagenous domain, and a C-terminal scavenger receptor cysteine-rich domain (SRCR), domain V . As yet, no specific function has been assigned to the SRCR domain of scavenger receptors . In the present study, we generated several human and mouse MARCO variants with deletions or single amino acid substitutions and localized the primary bacteria-binding region to domain V . Furthermore, analysis of the MARCO variants containing only portions of domain V demonstrated a crucial role for an arginine-rich segment for this function . More precisely, the motif RXR was identified as an essential element for high-affinity bacterial binding . The results indicate that the binding properties of MARCO differ from those of the other class A scavenger receptors, SR-A and SRCL, whose ligand-binding function has been localized to the collagenous domain . (c)2002 Elsevier Science (USA). Int Microbiol, 2001 Sep, 4(3), 143 - 50 Intracellular bacteria in ciliates; Gortz HD; Ciliates are frequently colonized by other micro-organisms . The large size of ciliate cells offers habitats for hundreds to thousands of bacteria in different compartments, such as cytoplasm, nuclei and even perinuclear spaces . Size, phagocytic feeding habit and other features appear to be favorable pre-adaptations of ciliates for symbiosis with bacteria . Certain intracellular bacteria are permanent symbionts that are not infectious, whereas others are highly infectious . Both types show specific adaptations . With their wide spectrum of phylogenetic positions, intracellular bacteria in ciliates show relationships to different taxa of free-living bacteria and even archaea . Certain symbionts may be deleterious for their host ciliates, whereas others may provide a selective advantage under appropriate conditions or even be essential for the host cells . Depending on the nature of a symbiont, its prevalence in a host population may be low or high . Symbionts that express a killer toxin affecting non-infected ciliates achieve high infection rates in a host population . whereas certain infectious bacteria may only show a low prevalence. IMA J Math Appl Med Biol, 2001 Sep, 18(3), 263 - 92 Mathematical modelling of quorum sensing in bacteria; Ward JP et al.; The regulation of density-dependent behaviour by means of quorum sensing is widespread in bacteria, the relevant phenomena including bioluminescence and population expansion by swarming, as well as virulence . The process of quorum sensing is regulated by the production and monitoring of certain molecules (referred to as QSMs); on reaching an apparent threshold concentration of QSMs (reflecting high bacterial density) the bacterial colony in concert 'switches on' the density-dependent trait . In this paper a mathematical model which describes bacterial population growth and quorum sensing in a well mixed system is proposed and studied . We view the population of bacteria as consisting of down-regulated and up-regulated sub-populations, with QSMs being produced at a much faster rate by the up-regulated cells . Using curve fitting techniques for parameter estimation, solutions of the resulting system of ordinary differential equations are shown to agree well with experimental data . Asymptotic analysis in a biologically relevant limit is used to investigate the timescales for up-regulation of an exponentially growing population of bacteria, revealing the existence of bifurcation between limited and near-total up-regulation . For a fixed population of cells steady-state analysis reveals that in general one physical steady-state solution exists and is linearly stable; we believe this solution to be a global attractor . A bifurcation between limited and near-total up-regulation is also discussed in the steady-state limit. Arch Immunol Ther Exp (Warsz), 2001, 49(6), 431 - 8 Lactoferrin stimulates killing and clearance of bacteria but does not prevent mortality of diabetic mice; Zagulski T et al.; We have previously shown that bovine lactoferrin (BLF) given intravenously (i.v.) protected mice against a lethal dose of Escherichia coli and strongly stimulated both the clearing and killing activities in liver, lungs, spleen and kidney . Since some studies indicated a reduction of the manifestation of experimental pancreatitis with lactoferrin (LF), we decided to examine the protective activity of BLF against lethal E . coli infection in animals with alloxan (Alx)-induced diabetes . It appeared that 48 h diabetes substantially lowered the killing activity in all four organs as well as the clearing rate of E . coli from the circulation . BLF given i.v . reduced this undesirable effect of diabetes . However, in 10- and 20-day diabetic animals, the diabetes alone stimulated the killing activity in the organs investigated, and upregulated the clearing rate of E . coli from the circulation . Lactoferrin significantly increased both the killing and the clearing activity in these long-term diabetic animals . In some cases the stimulating effect of BLF was very high, suggesting a concerted action of BLF and diabetes in that category of mice . Despite these beneficial effects of BLF and diabetes on the killing process in the investigated organs, the survival time of animals from all the diabetic groups (48 h, 10 and 20 days) was not prolonged by BLF . The protective properties of BLF did not depend on the blood glucose levels in the diabetic animals . BLF partly delayed the development of experimental Alx-induced diabetes, measured by the glucose level, but only if administered shortly after Alx injection . In conclusion, we demonstrated that the state of diabetes alone could increase killing of bacteria in the investigated organs and LF enhanced this process . However, LF had no protective effect against the mortality of diabetic mice infected with a lethal dose of E . coli. J Infect Chemother, 2000 Jun, 6(2), 121 - 5 Viable but nonculturable bacteria: a survival strategy; Colwell RR; When bacteria are introduced into a new environment, environmental changes with which they are confronted may include temperature, nutrient concentration, salinity, osmotic pressure, and pH . Bacterial cells dynamically adapt to these shifts in their environment, employing a variety of genetic mechanisms . Bacteria, with the ability to utilize constitutive and inducible enzyme synthesis, can accommodate to growth-limiting nutrients and adjust or reroute metabolic pathways to avoid metabolic and/or structural disruption caused by specific nutrient limitations . Furthermore, they are able to coordinate their rates of synthesis to maintain their cellular structure and function . These adaptive capabilities provide bacterial cells with an extraordinary set of mechanisms by which they are able to respond to their surrounding environment and survive. Am J Phys Med Rehabil, 2002 Jan, 81(1), 40 - 6 Inhibiting bacteria and skin pH in hemiplegia: effects of washing hands with acidic mineral water; Kurabayashi H et al.; OBJECTIVE: To evaluate bacterial flora in hemiplegic hands as a possible pathogen of endogenous infection in a rehabilitation unit and to examine the effect of cleansing hands with acidic mineral water on the flora . DESIGN: Case-control study in a university affiliated hospital . Seventy-two patients with hemiplegia caused by cerebrovascular diseases were included in this study . Bacterial flora by the swab method, bacterial frequency on the palm by the stamp method, and skin surface pH were examined before and after single cleansing by immersion in plain or acidic mineral water . RESULTS: The bacterial frequencies of patients with hemiplegia and diabetes were higher than those of normal healthy subjects . After cleansing with acidic mineral water, skin surface pH was decreased and bacterial frequency was markedly decreased . A prolonged decrease in skin surface pH was observed in patients with hemiplegia in contrast to normal healthy subjects who presented a short-term decrease . CONCLUSION: Increased bacterial frequencies were associated with a high skin surface pH caused by disordered skin systems in patients with hemiplegia . Acidic mineral water may be useful for inhibiting bacterial growth in patients with hemiplegia. Mech Dev, 2002 Feb, 111(1-2), 3 - 15 The distribution and proliferation of the intracellular bacteria Wolbachia during spermatogenesis in Drosophila; Clark ME et al.; Wolbachia is a cytoplasmically inherited alpha-proteobacterium found in a wide range of host arthropod and nematode taxa . Wolbachia infection in Drosophila is closely associated with the expression of a unique form of post-fertilization lethality termed cytoplasmic incompatibility (CI) . This form of incompatibility is only expressed by infected males suggesting that Wolbachia exerts its effect during spermatogenesis . The growth and distribution of Wolbachia throughout sperm development in individual spermatocysts and elongating sperm bundles is described . Wolbachia growth within a developing cyst seems to begin during the pre-meiotic spermatocyte growth phase with the majority of bacteria accumulating during cyst elongation . Wolbachia are predominantly localized in the proximal end of the immature cyst, opposite the spermatid nuclei, and throughout development there appears little movement of Wolbachia between spermatids via the connecting cytoplasmic bridges . The overall number of new cysts infected as well as the number of spermatids/cysts infected seems to decrease with age and corresponds to the previously documented drop in CI with age . In contrast, in one CI expressing line of Drosophila melanogaster, fewer cysts are infected and a much greater degree of variation in numbers is observed between spermatids . Furthermore, the initiation and extent of the fastest period of Wolbachia growth in the D . melanogaster strain lags behind that of Drosophila simulans . The possible implications on the as yet unexplained mechanism of CI are discussed. Sheng Wu Gong Cheng Xue Bao, 2001 Sep, 17(5), 539 - 42 {Expression of C3 epitope of poliovirus and a ten-peptides epitope of C-myc on the surface of recombinant bacteria}; Gao RK et al.; To confirm the possibility of pCSB136 and pCSX72 as vectors for displaying heterologous epitopes, the gene fragments coding for C3 epitope of poliovirus and a ten-peptides epitope of C-myc were synthesized and inserted into pCSB136 and pCSX72 respectively . The recombinants were screened by whole-strain PCR . The expression of recombinant proteins were detected by whole-cell ELISA and electronic microscopy . The results indicated the recombinant proteins were expressed as hybrid fimbriae, and the antigenicity of both CS3 and inserted epitopes kept . All results above showed vectors pCSB136 and pCSX72 could be used to display the foreign epitopes. Arch Microbiol, 2001 Dec, 177(1), 1 - 10 Epub 2001 Oct 12. Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes; Gich F et al.; The phylogenetic diversity of green nonsulfur bacteria in nine stratified freshwater lakes was investigated . A set of oligonucleotide primers was developed that permitted the selective amplification of 16S rRNA gene sequences of this group . Subsequently, amplification products were separated by denaturing gradient gel electrophoresis (DGGE) and sequenced, which yielded a total of 19 novel sequence types . Ten of the sequences were related to those of different cultivated members of the C hloroflexus assemblage, whereas nine fell into the T78 group of environmental clones . For the latter subgroup of the green nonsulfur bacteria, no molecular isolate from freshwater plankton has been reported so far . Several of the sequence types occurred in more than one lake, indicating that not only relatives of the C hloroflexus assemblage, but also bacteria of the clone T78 group represent indigenous bacteria of nonthermal stratified freshwater ecosystems . Our results indicate that the natural diversity in the phylum of the green nonsulfur bacteria has been significantly underestimated in the past. Biosci Biotechnol Biochem, 2001 Nov, 65(11), 2448 - 55 Intestinal absorbability of wheat allergens, subunits of a wheat alpha-amylase inhibitor, expressed by bacteria; Kusaba-Nakayama M et al.; Wheat CM2, CM3 and CM16 proteins are known as subunits of the tetrameric alpha-amylase inhibitor as well as major allergens to baker's asthma . The purpose of this study is to produce these CM proteins by bacteria in a quantity adequate for studying the penetration characteristics of the CM proteins through intestinal mucosa in rats and Caco-2 cells . cDNAs encoding the mature proteins were expressed in Escherichia coli and purified by an Ni2+-chelating column . The recombinant proteins were radioiodinated and admministered orally to rats or applied to the apical site of the Caco-2 cell monolayer . The radioactivity in the trichloroacetic acid-insoluble fraction, which was mainly composed of peptides with molecular mass less than that of the intact CM proteins, in the serum and the basolateral medium was highest in recombinant CM3 . Accordingly, the intestinal absorption of these three proteins in the form present in wheat should be evaluated. Int Dent J, 2001 Dec, 51(6), 413 - 6 The usefulness of the modified extra-oral vacuum aspirator (EOVA) from household vacuum cleaner in reducing bacteria in dental aerosols; Teanpaisan R et al.; AIMS AND OBJECTIVES: Currently, as a preventive measure against air contamination caused by dental procedures, dust-collecting aspirators such as an extra-oral vacuum aspirator (EOVA) are coming into general use . In this study, we tested the ability of a modified EOVA that uses a household vacuum m