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Sample records for radio-resistant bacteria prediction

  1. Minimal requirements in defined media for improved growth of some radio-resistant pink tetracocci.

    PubMed Central

    Shapiro, A; DiLello, D; Loudis, M C; Keller, D E; Hutner, S H

    1977-01-01

    Defined media permitting extensive growth of representative pink radio-resistant tetracocci (Micrococcus radiodurans, Micrococcus roseus, and Micrococcus radiophilus) and two controls (an ultraviolet-sensitive mutant of M. radiodurans and Micrococcus luteus) are described. Availability of Fe (especially Fe3+) proved essential for good growth, as evidenced by (i) favorable effects of hydroxamic acids, e.g., salicylhydroxamic acid, and (ii) the growth promotion by hemin when joined with elevated concentrations of Fe. Cobalamin (B12) and methionine were interchangeable as an absolute requirement for methionine not affected by B12. M. luteus required neither. Pink radio-resistant micrococci may form a coherent group. Some divergences among them might be attributable to the method for isolating them, which for ordinary bacteria would be mutagenic to the point of total lethality. The ecology of these tetracocci vis-à-vis other pink-red radio-resistant organisms is discussed in relation to a question: can these bacteria be isolated without dependence on radiation as the cardinal selective factor? PMID:879774

  2. The role of depressed metabolism in increased radio resistance

    NASA Technical Reports Server (NTRS)

    Musacchia, X. J.

    1972-01-01

    Studies are presented of the physiology of depressed metabolism, radio-resistance in depressed metabolic states, comparative aspects of depressed metabolism, and gastrointestinal responses to ionizing radiation. Specific data cover helium-cold induced hypothermia in white rats and hamsters, and radiation responses and intestinal absorption in the gerbil.

  3. Model to predict aerial dispersal of bacteria during environmental release.

    PubMed Central

    Knudsen, G R

    1989-01-01

    Risk assessment for genetically engineered bacteria sprayed onto crops includes determination of off-site dispersal and deposition. The ability to predict microbial dispersal patterns is essential to characterize the uncertainty (risk) associated with environmental release of recombinant organisms. Toward this end, a particle dispersal model was developed to predict recovery of bacteria on fallout plates at various distances and directions about a test site. The microcomputer simulation incorporates particle size distribution, wind speed and direction, turbulence, evaporation, sedimentation, and mortality, with a time step of 0.5 s. The model was tested against data reported from three field applications of nonrecombinant bacteria and two applications of recombinant bacteria. Simulated dispersal of 10(5) particles was compared with reported deposition measurements. The model may be useful in defining appropriate populations of organisms for release, methods of release or application, characteristics of a release site that influence containment or dispersal, and in developing an appropriate sampling methodology for monitoring the dispersal of organisms such as genetically engineered bacteria. PMID:2604402

  4. Validating regulatory predictions from diverse bacteria with mutant fitness data

    PubMed Central

    Sagawa, Shiori; Deutschbauer, Adam M.; Arkin, Adam P.

    2017-01-01

    Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium’s growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomics predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions. PMID:28542589

  5. Validating regulatory predictions from diverse bacteria with mutant fitness data

    DOE PAGES

    Sagawa, Shiori; Price, Morgan N.; Deutschbauer, Adam M.; ...

    2017-05-24

    Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium's growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomicsmore » predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions.« less

  6. Computational prediction of regulatory, premature transcription termination in bacteria

    PubMed Central

    Millman, Adi; Dar, Daniel; Shamir, Maya; Sorek, Rotem

    2017-01-01

    A common strategy for regulation of gene expression in bacteria is conditional transcription termination. This strategy is frequently employed by 5′UTR cis-acting RNA elements (riboregulators), including riboswitches and attenuators. Such riboregulators can assume two mutually exclusive RNA structures, one of which forms a transcriptional terminator and results in premature termination, and the other forms an antiterminator that allows read-through into the coding sequence to produce a full-length mRNA. We developed a machine-learning based approach, which, given a 5′UTR of a gene, predicts whether it can form the two alternative structures typical to riboregulators employing conditional termination. Using a large positive training set of riboregulators derived from 89 human microbiome bacteria, we show high specificity and sensitivity for our classifier. We further show that our approach allows the discovery of previously unidentified riboregulators, as exemplified by the detection of new LeuA leaders and T-boxes in Streptococci. Finally, we developed PASIFIC (www.weizmann.ac.il/molgen/Sorek/PASIFIC/), an online web-server that, given a user-provided 5′UTR sequence, predicts whether this sequence can adopt two alternative structures conforming with the conditional termination paradigm. This webserver is expected to assist in the identification of new riboswitches and attenuators in the bacterial pan-genome. PMID:27574119

  7. Prediction of molecular mimicry candidates in human pathogenic bacteria.

    PubMed

    Doxey, Andrew C; McConkey, Brendan J

    2013-08-15

    Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria.

  8. Prediction of molecular mimicry candidates in human pathogenic bacteria

    PubMed Central

    Doxey, Andrew C; McConkey, Brendan J

    2013-01-01

    Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria. PMID:23715053

  9. Isolation and analysis of UV and radio-resistant bacteria from Chernobyl.

    PubMed

    Zavilgelsky, G B; Abilev, S K; Sukhodolets, V V; Ahmad, S I

    1998-05-15

    The accident at the Chernobyl nuclear power station in 1986 led to the dispersal of large amounts of a variety of radioactive materials, most importantly uranium, plutonium, 137Cs, 131I and 90Sr, over very large distances estimated to reach as far as Sweden, Norway, Turkey and possibly the USA. As a consequence, the soil on which the radioactive materials fell was contaminated and the degree of contamination varied with distance from the station, the direction and strength of the wind and the amount of atmospheric scavenging by rainfall at that time. Some of the radioactive materials have left a significant impact on mankind in the form of chromosomal aberrations including trisomy, various forms of cancers and death, whilst others are still in the ground where they will remain for a prolonged period to continue to exert their effects. Likewise, microbes living in the soil and exposed to radioactive materials may have been affected in a number of ways; some perished, and others survived due to the acquisition of advantageous mutation. Six years after the accident, soil samples contaminated with different levels of radioactivity were obtained from five regions within a 30 km radius of the nuclear power plant. From these soil samples spore-forming bacilli were isolated, quantified, identified and tested for resistance to X-rays, UVC and 4-nitroquinoline 1-oxide (4NQO). As a control, spore-forming bacilli were obtained from 'Zeleny mys' (an area 50 km south-east of the power station and emitting basal levels of radioactivity). A mutant of Escherichia coli hyper-resistant to a variety of DNA-damaging agents and its parent strain were also included in the study. Analysis of results reveals that a proportion of isolates of the same species from near the power station and the E. coli mutant SA236 were more resistant to X-rays, UVC and 4NQO compared with isolates from the control site and the E. coli parent strain, KL14, respectively.

  10. Pivotal role for skin transendothelial radio-resistant anti-inflammatory macrophages in tissue repair

    PubMed Central

    Barreiro, Olga; Cibrian, Danay; Clemente, Cristina; Alvarez, David; Moreno, Vanessa; Valiente, Íñigo; Bernad, Antonio; Vestweber, Dietmar; Arroyo, Alicia G; Martín, Pilar; von Andrian, Ulrich H; Sánchez Madrid, Francisco

    2016-01-01

    Heterogeneity and functional specialization among skin-resident macrophages are incompletely understood. In this study, we describe a novel subset of murine dermal perivascular macrophages that extend protrusions across the endothelial junctions in steady-state and capture blood-borne macromolecules. Unlike other skin-resident macrophages that are reconstituted by bone marrow-derived progenitors after a genotoxic insult, these cells are replenished by an extramedullary radio-resistant and UV-sensitive Bmi1+ progenitor. Furthermore, they possess a distinctive anti-inflammatory transcriptional profile, which cannot be polarized under inflammatory conditions, and are involved in repair and remodeling functions for which other skin-resident macrophages appear dispensable. Based on all their properties, we define these macrophages as Skin Transendothelial Radio-resistant Anti-inflammatory Macrophages (STREAM) and postulate that their preservation is important for skin homeostasis. DOI: http://dx.doi.org/10.7554/eLife.15251.001 PMID:27304075

  11. Sensitization of radio-resistant prostate cancer cells with a unique cytolethal distending toxin

    PubMed Central

    Lai, Chih-Ho; Chang, Chia-Shuo; Liu, Hsin-Ho; Tsai, Yuh-Shyan; Hsu, Feng-Ming; Yu, Yung-Luen; Lai, Cheng-Kuo; Gandee, Leah; Pong, Rey-Chen; Hsu, Heng-Wei; Yu, Lan; Saha, Debabrata; Hsieh, Jer-Tsong

    2014-01-01

    Cytolethal distending toxin (CDT) produced by Campylobacter jejuni is a genotoxin that induces cell-cycle arrest and apoptosis in mammalian cells. Recent studies have demonstrated that prostate cancer (PCa) cells can acquire radio-resistance when DOC-2/DAB2 interactive protein (DAB2IP) is downregulated. In this study, we showed that CDT could induce cell death in DAB2IP-deficient PCa cells. A combination of CDT and radiotherapy significantly elicited cell death in DAB2IP-deficient PCa cells by inhibiting the repair of ionizing radiation (IR)-induced DNA double-strand break (DSB) during G2/M arrest, which is triggered by ataxia telangiectasia mutated (ATM)-dependent DNA damage checkpoint responses. We also found that CDT administration significantly increased the efficacy of radiotherapy in a xenograft mouse model. These results indicate that CDT can be a potent therapeutic agent for radio-resistant PCa. PMID:25015118

  12. Predicting Fecal Indicator Bacteria Concentrations in the South Fork Broad River Watershed Using Virtual Beach

    EPA Science Inventory

    Virtual Beach (VB) is a decision support tool that constructs site-specific statistical models to predict fecal indicator bacteria (FIB) at recreational beaches. Although primarily designed for making decisions regarding beach closures or issuance of swimming advisories based on...

  13. Predicting Fecal Indicator Bacteria Concentrations in the South Fork Broad River Watershed Using Virtual Beach

    EPA Science Inventory

    Virtual Beach (VB) is a decision support tool that constructs site-specific statistical models to predict fecal indicator bacteria (FIB) at recreational beaches. Although primarily designed for making decisions regarding beach closures or issuance of swimming advisories based on...

  14. Transient elevation of glycolysis confers radio-resistance by facilitating DNA repair in cells.

    PubMed

    Bhatt, Anant Narayan; Chauhan, Ankit; Khanna, Suchit; Rai, Yogesh; Singh, Saurabh; Soni, Ravi; Kalra, Namita; Dwarakanath, Bilikere S

    2015-05-01

    Cancer cells exhibit increased glycolysis for ATP production (the Warburg effect) and macromolecular biosynthesis; it is also linked with therapeutic resistance that is generally associated with compromised respiratory metabolism. Molecular mechanisms underlying radio-resistance linked to elevated glycolysis remain incompletely understood. We stimulated glycolysis using mitochondrial respiratory modifiers (MRMs viz. di-nitro phenol, DNP; Photosan-3, PS3; Methylene blue, MB) in established human cell lines (HEK293, BMG-1 and OCT-1). Glucose utilization and lactate production, levels of glucose transporters and glycolytic enzymes were investigated as indices of glycolysis. Clonogenic survival, DNA repair and cytogenetic damage were studied as parameters of radiation response. MRMs induced the glycolysis by enhancing the levels of two important regulators of glucose metabolism GLUT-1 and HK-II and resulted in 2 fold increase in glucose consumption and lactate production. This increase in glycolysis resulted in resistance against radiation-induced cell death (clonogenic survival) in different cell lines at an absorbed dose of 5 Gy. Inhibition of glucose uptake and glycolysis (using fasentin, 2-deoxy-D-glucose and 3-bromopyruvate) in DNP treated cells failed to increase the clonogenic survival of irradiated cells, suggesting that radio-resistance linked to inhibition of mitochondrial respiration is glycolysis dependent. Elevated glycolysis also facilitated rejoining of radiation-induced DNA strand breaks by activating both non-homologous end joining (NHEJ) and homologous recombination (HR) pathways of DNA double strand break repair leading to a reduction in radiation-induced cytogenetic damage (micronuclei formation) in these cells. These findings suggest that enhanced glycolysis generally observed in cancer cells may be responsible for the radio-resistance, partly by enhancing the repair of DNA damage.

  15. Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure

    PubMed Central

    Wallace, Amelia D.; Riley, Lee W.

    2016-01-01

    Social network structure is a fundamental determinant of human health, from infectious to chronic diseases. However, quantitative and unbiased approaches to measuring social network structure are lacking. We hypothesized that genetic relatedness of oral commensal bacteria could be used to infer social contact between humans, just as genetic relatedness of pathogens can be used to determine transmission chains of pathogens. We used a traditional, questionnaire survey-based method to characterize the contact network of the School of Public Health at a large research university. We then collected saliva from a subset of individuals to analyze their oral microflora using a modified deep sequencing multilocus sequence typing (MLST) procedure. We examined micro-evolutionary changes in the S. viridans group to uncover transmission patterns reflecting social network structure. We amplified seven housekeeping gene loci from the Streptococcus viridans group, a group of ubiquitous commensal bacteria, and sequenced the PCR products using next-generation sequencing. By comparing the generated S. viridans reads between pairs of individuals, we reconstructed the social network of the sampled individuals and compared it to the network derived from the questionnaire survey-based method. The genetic relatedness significantly (p-value < 0.001) correlated with social distance in the questionnaire-based network, and the reconstructed network closely matched the network derived from the questionnaire survey-based method. Oral commensal bacterial are thus likely transmitted through routine physical contact or shared environment. Their genetic relatedness can be used to represent a combination of social contact and shared physical space, therefore reconstructing networks of contact. This study provides the first step in developing a method to measure direct social contact based on commensal organism genotyping, potentially capable of unmasking hidden social networks that contribute to

  16. Reprogramming mediated radio-resistance of 3D-grown cancer cells

    PubMed Central

    Xue, Gang; Ren, Zhenxin; Grabham, Peter W.; Chen, Yaxiong; Zhu, Jiayun; Du, Yarong; Pan, Dong; Li, Xiaoman; Hu, Burong

    2015-01-01

    In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of β-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell–like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell–like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine. PMID:25883172

  17. Reprogramming mediated radio-resistance of 3D-grown cancer cells.

    PubMed

    Xue, Gang; Ren, Zhenxin; Grabham, Peter W; Chen, Yaxiong; Zhu, Jiayun; Du, Yarong; Pan, Dong; Li, Xiaoman; Hu, Burong

    2015-07-01

    In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of β-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell-like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell-like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine. © The Author 2015. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

  18. ERK/p38 MAPK inhibition reduces radio-resistance to a pulsed proton beam in breast cancer stem cells

    NASA Astrophysics Data System (ADS)

    Jung, Myung-Hwan; Park, Jeong Chan

    2015-10-01

    Recent studies have identified highly tumorigenic cells with stem cell-like characteristics, termed cancer stem cells (CSCs) in human cancers. CSCs are resistant to conventional radiotherapy and chemotherapy owing to their high DNA repair ability and oncogene overexpression. However, the mechanisms regulating CSC radio-resistance, particularly proton beam resistance, remain unclear. We isolated CSCs from the breast cancer cell lines MCF-7 and MDA-MB-231, which expressed the characteristic breast CSC membrane protein markers CD44+/CD24-/ low , and irradiated the CSCs with pulsed proton beams. We confirmed that CSCs were resistant to pulsed proton beams and showed that treatment with p38 and ERK inhibitors reduced CSC radio-resistance. Based on these results, BCSC radio-resistance can be reduced during proton beam therapy by co-treatment with ERK1/2 or p38 inhibitors, a novel approach to breast cancer therapy.

  19. Predicting Chemical Environments of Bacteria from Receptor Signaling

    PubMed Central

    Neumann, Silke; Sourjik, Victor; Endres, Robert G.

    2014-01-01

    Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber's law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine. PMID:25340783

  20. Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model.

    PubMed

    Aridhi, Sabeur; Sghaier, Haïtham; Zoghlami, Manel; Maddouri, Mondher; Nguifo, Engelbert Mephu

    2016-01-01

    Ionizing-radiation-resistant bacteria (IRRB) are important in biotechnology. In this context, in silico methods of phenotypic prediction and genotype-phenotype relationship discovery are limited. In this work, we analyzed basal DNA repair proteins of most known proteome sequences of IRRB and ionizing-radiation-sensitive bacteria (IRSB) in order to learn a classifier that correctly predicts this bacterial phenotype. We formulated the problem of predicting bacterial ionizing radiation resistance (IRR) as a multiple-instance learning (MIL) problem, and we proposed a novel approach for this purpose. We provide a MIL-based prediction system that classifies a bacterium to either IRRB or IRSB. The experimental results of the proposed system are satisfactory with 91.5% of successful predictions.

  1. Sensitivity and specificity of subgingival bacteria in predicting preterm birth- a pilot cohort study

    PubMed Central

    Hassan, Khalid S; El Tantawi, Maha M.; Alagl, Adel S; Alnimr, Amani M; Haseeb, Yasmeen A

    2016-01-01

    Objective Preterm birth (PTB) increases the risk of adverse outcomes for new born infants. Subgingival bacteria are implicated in causing PTB. The aim of the present study was to assess the accuracy of some subgingival gram positive and gram negative bacteria detected by routine lab procedures in predicting PTB. Methodology Pregnant Saudi women (n= 170) visiting King Fahad hospital, Dammam, Saudi Arabia, were included in a pilot cohort study. Plaque was collected in the 2nd trimester and screened for subgingival anaerobes using Vitek2. Pregnancy outcome (preterm/full term birth) was assessed at delivery. Sensitivity, specificity and positive and negative likelihood ratios were calculated for the identified bacteria to predict PTB. Results Data about time of delivery was available for 94 subjects and 22 (23.4%) had PTB. Three gram negative and 4 gram positive subgingival bacteria had sensitivity ≥ 95% with two of each having negative likelihood ratios ≤0.10. Three gram positive bacteria had specificity > 95% with only one having positive likelihood ratio >2. Conclusion Subgingival bacteria identified using readily available lab techniques in the plaque of pregnant Saudi women in their 2nd trimester have useful potential to rule out PTB. PMID:27833518

  2. Benefit of Carbon Ion Radiotherapy in the Treatment of Radio-resistant Tumors

    SciTech Connect

    Kamada, Tadashi; Tsujii, Hirohiko; Tsuji, Hiroshi; Yanagi, Tsuyoshi; Imai, Reiko; Mizoe, Jun-etsu; Miyamoto, Tadaaki; Kato, Hirotoshi; Yamada, Shigeru; Kato, Shingo; Yoshikawa, Kyousan; Kandatsu, Susumu

    2003-08-26

    The Heavy Ion Medical Accelerator in Chiba (HIMAC) is the world's first heavy ion accelerator complex dedicated to medical use in a hospital environment. Heavy ions have superior depth-dose distribution and greater cell-killing ability. In June 1994, clinical research for the treatment of cancer was begun using carbon ions generated by HIMAC. Until August 2002, a total of 1,297 patients were enrolled in clinical trials. Most of the patients had locally advanced and/or medically inoperable tumors. Tumors radio-resistant and/or located near critical organs were also included. The clinical trials revealed that carbon ion radiotherapy provided definite local control and offered a survival advantage without unacceptable morbidity in a variety of tumors that were hard to cure by other modalities.

  3. New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans.

    PubMed

    Farci, Domenica; Bowler, Matthew W; Kirkpatrick, Joanna; McSweeney, Sean; Tramontano, Enzo; Piano, Dario

    2014-07-01

    We have analyzed the cell wall of the radio-resistant bacterium Deinococcus radiodurans. Unexpectedly, the bacterial envelope appears to be organized in different complexes of high molecular weight. Each complex is composed of several proteins, most of which are coded by genes of unknown function and the majority are constituents of the inner/outer membrane system. One of the most abundant complexes is constituted by the gene DR_0774. This protein is a type of secretin which is a known subunit of the homo-oligomeric channel that represents the main bulk of the type IV piliation family. Finally, a minor component of the pink envelope consists of several inner-membrane proteins. The implications of these findings are discussed.

  4. Predicting Fecal Indicator Bacteria Fate and Removal in Urban Stormwater at the Watershed Scale

    NASA Astrophysics Data System (ADS)

    Wolfand, J.; Hogue, T. S.; Luthy, R. G.

    2016-12-01

    Urban stormwater is a major cause of water quality impairment, resulting in surface waters that fail to meet water quality standards and support their designated uses. Of the many stormwater pollutants, fecal indicator bacteria are particularly important to track because they are directly linked to pathogens which jeopardize public health; yet, their fate and transport in urban stormwater is poorly understood. Monitoring fecal bacteria in stormwater is possible, but due to the high variability of fecal indicators both spatially and temporally, single grab or composite samples do not fully capture fecal indicator loading. Models have been developed to predict fecal indicator bacteria at the watershed scale, but they are often limited to agricultural areas, or areas that receive frequent rainfall. Further, it is unclear whether best management practices (BMPs), such as bioretention or engineered wetlands, are able to reduce bacteria to meet water quality standards at watershed outlets. This research seeks to develop a model to predict fecal indicator bacteria in urban stormwater in a semi-arid climate at the watershed scale. Using the highly developed Ballona Creek watershed (89 mi2) located in Los Angeles County as a case study, several existing mechanistic models are coupled with a hydrologic model to predict fecal indicator concentrations (E. coli, enterococci, fecal coliform, and total coliform) at the outfall of Ballona Creek watershed, Santa Monica Bay. The hydrologic model was developed using InfoSWMM Sustain, calibrated for flow from WY 1998-2006 (NSE = 0.94; R2 = 0.95), and validated from WY 2007-2015 (NSE = 0.93; R2 = 0.95). The developed coupled model is being used to predict fecal indicator fate and transport and evaluate how BMPs can be optimized to reduce fecal indicator loading to surface waters and recreational beaches.

  5. A jungle in there: bacteria in belly buttons are highly diverse, but predictable.

    PubMed

    Hulcr, Jiri; Latimer, Andrew M; Henley, Jessica B; Rountree, Nina R; Fierer, Noah; Lucky, Andrea; Lowman, Margaret D; Dunn, Robert R

    2012-01-01

    The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (~1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that "oligarchs" dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons.

  6. A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

    PubMed Central

    Hulcr, Jiri; Latimer, Andrew M.; Henley, Jessica B.; Rountree, Nina R.; Fierer, Noah; Lucky, Andrea; Lowman, Margaret D.; Dunn, Robert R.

    2012-01-01

    The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (∼1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons. PMID:23144827

  7. Challenges in risk assessment and predictive microbiology of foodborne spore-forming bacteria.

    PubMed

    Augustin, Jean-Christophe

    2011-04-01

    Mathematical description of the behavior of bacterial foodborne pathogens and concepts of risk assessment were first applied to spore-forming bacteria and specially to Clostridium botulinum with numerous works dealing with spores heat destruction to ensure the safety of canned foods or with their germination and growth probability in foods. This paper discusses two aspects which appear specific to pathogenic sporeformers in comparison to vegetative microorganisms, that is, firstly, the extreme intra-species biodiversity of spore-forming bacteria and its consequences for risk assessment and, secondly, the modeling of spore germination and outgrowth processes. The intra-species biodiversity of spore-forming bacteria has a great impact on hazard identification, exposure assessment and hazard characterization leading thus to an extremely variable individual poisoning risk for consumers. The germination and outgrowth processes were shown independent at the single cell level and although numerous studies were performed to study the effect of spores treatments and growth conditions on these two events, the mathematical modeling and the prediction of these processes is still challenging today. The difficulties to accurately assess the biodiversity and the germination and outgrowth processes of spore-forming bacteria lead to a substantial uncertainty in risk estimates related to the exposure to these microorganisms. Nevertheless, significant progress have been made these last years improving the relevance of quantitative risk assessments for spore-forming bacteria and decreasing the risk uncertainty. Despite these difficulties, risk assessment still constitutes a valuable tool to justify the implementation of management options.

  8. Predicting relative toxicity of metal ions to bacteria (Microtox{reg_sign}) using ion characteristics

    SciTech Connect

    McCloskey, J.T.; Newman, M.C.; Clark, S.B.

    1995-12-31

    The use of predictive effects models with metals has received little attention in toxicology. The purpose of this study was to predict the relative toxicity of individual metal ions and metal mixtures using ion characteristics. The concentration of metal resulting in a 50% reduction in light output (EC50) in marine bacteria (Vibrio fischeri) was determined for several metals using the Microtox{reg_sign} Toxicity Analyzer. Trends in metal toxicity were predicted by combining metal speciation calculations with empirical models based on metal ion characteristics. These trends were consistent for nine divalent metals (Ca{prime} Cd, Cu, Hg, Mg, Mn, Ni, Pb and Zn) whether the media mimicked salt water (NaC, medium) or freshwater (NaNO{sub 3} medium). When expanding the study to include an additional 14 mono-, di-, and trivalent metal ions, ion characteristics were still useful for predicting the relative toxicity of metal ions to bacteria. The prediction of nonadditive toxic effects using metal mixtures was also possible based on ion characteristics. Overall, models based on ion characteristics show much promise for predicting the relative toxicity of metal ions using the Microtox{reg_sign} assay.

  9. MiR-20a-5p promotes radio-resistance by targeting Rab27B in nasopharyngeal cancer cells.

    PubMed

    Huang, Dabing; Bian, Geng; Pan, Yueyin; Han, Xinghua; Sun, Yubei; Wang, Yong; Shen, Guodong; Cheng, Min; Fang, Xiang; Hu, Shilian

    2017-01-01

    MicroRNAs (miRNAs) was reported to be involved in cancer radio-resistance, which remains a major obstacle for effective cancer therapy. The differently expressed miRNAs were detected by RNA-seq experiment in nasopharyngeal cancer (NPC) cells. MiR-20a-5p was selected as our target, which was subject to finding its target gene Rab27B via bioinformatics analysis. The qRT-PCR, western blot and the luciferase reporter assays were performed to confirm Rab27B as the target of miR-20a-5p. In addition, the roles of miR-20a-5p in NPC radio-resistance were detected by transfection of either miR-20a-5p-mimic or miR-20a-5p-antagomiR. The involvement of Rab27B with NPC radio-resistance was also detected by the experiments with siRNA-mediated repression of Rab27B or over-expression of GFP-Rab27B. Wound healing and invasion assays were performed to detect the roles of both miR-20a-5p and Rab27B. MiR-20a-5p promotes NPC radio-resistance. We identified that its target gene Rab27B negatively correlates with miR-20a-5p-mediated NPC radio-resistance by systematic studies of a radio-sensitive (CNE-2) and resistant (CNE-1) NPC cell lines. Repression of Rab27B by siRNA suppresses cell apoptosis and passivates CNE-2 cells, whereas over-expression of Rab27B triggered cell apoptosis and sensitizes CNE-1 cells. MiR-20a-5p and its target gene Rab27B might be involved in the NPC radio-resistance. Thus the key players and regulators involved in this pathway might be the potential targets for developing effective therapeutic strategies against NPC.

  10. Testing for aerobic heterotrophic bacteria allows no prediction of contamination with potentially pathogenic bacteria in the output water of dental chair units

    PubMed Central

    Bristela, Margit; Skolka, Astrid; Schmid-Schwap, Martina; Piehslinger, Eva; Indra, Alexander; Wewalka, Günther; Stauffer, Fritz

    2012-01-01

    Background: Currently, to our knowledge, quality of output water of dental chair units is not covered by specific regulations in the European Union, and national recommendations are heterogeneous. In Germany, water used in dental chair units must follow drinking water quality. In the United States of America, testing for aerobic heterotrophic bacteria is recommended. The present study was performed to evaluate whether the counts of aerobic heterotrophic bacteria correlate with the presence of potentially pathogenic bacteria such as Legionella spp. or Pseudomonas aeruginosa. Methods: 71 samples were collected from 26 dental chair units with integrated disinfection device and 31 samples from 15 outlets of the water distribution pipework within the department were examined. Samples were tested for aerobic heterotrophic bacteria at 35°C and 22°C using different culture media and for Legionella spp. and for Pseudomonas aeruginosa. Additionally, strains of Legionella pneumophila serogroup 1 were typed with monoclonal antibodies and representative samples of Legionella pneumophila serogroup 1 were typed by sequence based typing. Results: Our results showed a correlation between different agars for aerobic heterotrophic bacteria but no correlation for the count of aerobic heterotrophic bacteria and the presence of Legionella spp. or Pseudomonas aeruginosa. Conclusion: Testing for aerobic heterotrophic bacteria in output water or water distribution pipework within the departments alone is without any value for predicting whether the water is contaminated with potentially pathogenic bacteria like Legionella spp. or Pseudomonas aeruginosa. PMID:22558046

  11. Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses

    PubMed Central

    Serbus, Laura R.; Rodriguez, Brian Garcia; Sharmin, Zinat; Momtaz, A. J. M. Zehadee; Christensen, Steen

    2017-01-01

    The requirement of vitamins for core metabolic processes creates a unique set of pressures for arthropods subsisting on nutrient-limited diets. While endosymbiotic bacteria carried by arthropods have been widely implicated in vitamin provisioning, the underlying molecular mechanisms are not well understood. To address this issue, standardized predictive assessment of vitamin metabolism was performed in 50 endosymbionts of insects and arachnids. The results predicted that arthropod endosymbionts overall have little capacity for complete de novo biosynthesis of conventional or active vitamin forms. Partial biosynthesis pathways were commonly predicted, suggesting a substantial role in vitamin provisioning. Neither taxonomic relationships between host and symbiont, nor the mode of host-symbiont interaction were clear predictors of endosymbiont vitamin pathway capacity. Endosymbiont genome size and the synthetic capacity of nonsymbiont taxonomic relatives were more reliable predictors. We developed a new software application that also predicted that last-step conversion of intermediates into active vitamin forms may contribute further to vitamin biosynthesis by endosymbionts. Most instances of predicted vitamin conversion were paralleled by predictions of vitamin use. This is consistent with achievement of provisioning in some cases through upregulation of pathways that were retained for endosymbiont benefit. The predicted absence of other enzyme classes further suggests a baseline of vitamin requirement by the majority of endosymbionts, as well as some instances of putative mutualism. Adaptation of this workflow to analysis of other organisms and metabolic pathways will provide new routes for considering the molecular basis for symbiosis on a comprehensive scale. PMID:28455417

  12. Microbial radio-resistance of Salmonella Typhimurium in egg increases due to repetitive irradiation with electron beam

    NASA Astrophysics Data System (ADS)

    Tesfai, Adiam T.; Beamer, Sarah K.; Matak, Kristen E.; Jaczynski, Jacek

    2011-04-01

    Ionizing radiation improves food safety. However, foodborne pathogens develop increased resistance in response to sub-lethal stresses such as heat, pH, antibiotics, etc. Therefore, it is hypothesized that foodborne pathogens may develop increased radio-resistance to electron beam (e-beam) radiation. The objective was to determine if D10-value for Salmonella Typhimurium in de-shelled raw egg (egg white and yolk mixed together) increases due to repetitive processing with e-beam at sub-lethal doses. Survivors were enumerated on non-selective (TSA) and selective (XLD) media. Survivors from the highest dose were isolated and used in subsequent e-beam cycle. This process was repeated four times for a total of five e-beam cycles. D10-values for S. Typhimurium enumerated on TSA and XLD following each e-beam cycle were calculated as inverse reciprocal of the slope of survivor curves. D10-values for the ATCC strain were 0.59±0.031 and 0.46±0.022 kGy on TSA and XLD, respectively. However, following the fifth e-beam cycle, the respective D10-values increased (P<0.05) to 0.69±0.026 and 0.61±0.029 kGy, respectively. S. Typhimurium showed a trend (P>0.05) to develop radio-resistance faster on selective media, likely due to facilitated selection of radio-resistant cells within microbial population following each e-beam cycle. For all five e-beam cycles, S. Typhimurium had higher (P<0.05) D10-values on non-selective media, indicating that sub-lethal injury followed by cellular repair and recovery are important for radio-resistance and inactivation of this microorganism. This study demonstrated that e-beam efficiently inactivates S. Typhimurium in raw egg; however, similar to other inactivation techniques and factors affecting microbial growth, S. Typhimurium develops increased radio-resistance if repetitively processed with e-beam at sub-lethal doses.

  13. A critical role of toll-like receptor 4 (TLR4) and its' in vivo ligands in basal radio-resistance

    PubMed Central

    Liu, C; Zhang, C; Mitchel, R EJ; Cui, J; Lin, J; Yang, Y; Liu, X; Cai, J

    2013-01-01

    Toll-like receptor-4 (TLR4) plays a critical role in innate and acquired immunity, but its role in radio-resistance is unknown. We used TLR4 knockout (KO,−/−) mice and gut commensal depletion methods, to test the influence of TLR4 and its' in vivo agonist on basal radio-resistance. We found that mice deficient in TLR4 were more susceptible to IR-induced mortality and morbidity. Mortality of TLR4-deficient mice after IR was associated with a severe and persistent bone marrow cell loss. Injection of lipopolysaccharide into normal mice, which is known to activate TLR4 in vivo, induced radio-resistance. Moreover, TLR4 in vivo ligands are required for basal radio-resistance. We found that exposure to radiation leads to significant endotoxemia that also confers endogenous protection from irradiation. The circulating endotoxins appear to originate from the gut, as sterilization of the gut with antibiotics lead to increased mortality from radiation. Further data indicated that Myd88, but not TRIF, may be the critical adaptor in TLR4-induced radio-resistance. Taken together, these data strongly suggest that TLR4 plays a critical role in basal radio-resistance. Our data suggest, it is important not to give antibiotics that may sterilize the gut before the whole body irradiation. Further, these data also suggest that management of gut flora through antibiotic or possibly probiotic therapy may alter the innate response to the total body irradiation. PMID:23722538

  14. Modelling and predicting the simultaneous growth of Escherichia coli and lactic acid bacteria in milk.

    PubMed

    Ačai, P; Valík, L'; Medved'ová, A; Rosskopf, F

    2016-09-01

    Modelling and predicting the simultaneous competitive growth of Escherichia coli and starter culture of lactic acid bacteria (Fresco 1010, Chr. Hansen, Hørsholm, Denmark) was studied in milk at different temperatures and Fresco inoculum concentrations. The lactic acid bacteria (LAB) were able to induce an early stationary state in E. coli The developed model described and tested the growth inhibition of E. coli (with initial inoculum concentration 10(3) CFU/mL) when LAB have reached maximum density in different conditions of temperature (ranging from 12 ℃ to 30 ℃) and for various inoculum sizes of LAB (ranging from approximately 10(3) to 10(7) CFU/mL). The prediction ability of the microbial competition model (the Baranyi and Roberts model coupled with the Gimenez and Dalgaard model) was first performed only with parameters estimated from individual growth of E. coli and the LAB and then with the introduced competition coefficients evaluated from co-culture growth of E. coli and LAB in milk. Both the results and their statistical indices showed that the model with incorporated average values of competition coefficients improved the prediction of E. coli behaviour in co-culture with LAB.

  15. Predictive Factors of Spontaneous Bacterial Peritonitis Caused by Gram-Positive Bacteria in Patients With Cirrhosis.

    PubMed

    Kim, Jung Ho; Jeon, Yong Duk; Jung, In Young; Ahn, Mi Young; Ahn, Hea Won; Ahn, Jin Young; Ku, Nam Su; Han, Sang Hoon; Choi, Jun Yong; Ahn, Sang Hoon; Song, Young Goo; Han, Kwang Hyub; Kim, June Myung

    2016-04-01

    Spontaneous bacterial peritonitis (SBP) in patients with cirrhosis is typically caused by gram-negative bacteria. However, the number of SBP cases due to gram-positive bacteria is steadily increasing. To date, little is known about the predictive factors involved in SBP infections.We performed a retrospective cohort study of patients (>18 years) with SBP due to gram-positive and -negative bacteria who were enrolled from January 2006 to December 2013 at Severance Hospital in Seoul, Korea where the incidences of hepatitis B virus associated chronic liver disease, cirrhosis, and hepatocellular carcinoma are high. Only the 1st SBP episode for each patient within the study period was included in our analysis.We identified 77 patients with cirrhosis and SBP. Of these, 27 patients (35%) had gram-positive bacterial infections and 50 patients (65%) had gram-negative bacterial infections. Our univariate analysis revealed that an early stage of cirrhosis (P = 0.004), lower creatinine level (P = 0.011), lower Sequential Organ Failure Assessment (SOFA) score (P = 0.001), lower Model for End-Stage Liver Disease score (P = 0.005), and use of systemic antibiotics within 30 days before SBP diagnosis (P = 0.03) were significantly associated with gram-positive bacterial infections. Our multivariate analysis indicated that the use of systemic antibiotics within 30 days before SBP diagnosis (odds ratio, 3.94; 95% CI, 1.11-13.96; P = 0.033) and a lower SOFA score (odds ratio, 0.56; 95% CI, 0.37-0.86; P = 0.007) were independent predictive factors of SBP caused by gram-positive bacterial infections in patients with cirrhosis. However, we did not observe a statistically significant difference in the 28-day mortality between the gram-positive and -negative bacterial infection groups (40.7% vs 46.0%, respectively; P = 0.407).In this study, the incidence rate of SBP caused by gram-positive bacteria in patients with cirrhosis was similar to the rates reported

  16. Computational prediction of type III and IV secreted effectors in Gram-negative bacteria

    SciTech Connect

    McDermott, Jason E.; Corrigan, Abigail L.; Peterson, Elena S.; Oehmen, Christopher S.; Niemann, George; Cambronne, Eric; Sharp, Danna; Adkins, Joshua N.; Samudrala, Ram; Heffron, Fred

    2011-01-01

    In this review, we provide an overview of the methods employed by four recent papers that described novel methods for computational prediction of secreted effectors from type III and IV secretion systems in Gram-negative bacteria. The results of the studies in terms of performance at accurately predicting secreted effectors and similarities found between secretion signals that may reflect biologically relevant features for recognition. We discuss the web-based tools for secreted effector prediction described in these studies and announce the availability of our tool, the SIEVEserver (http://www.biopilot.org). Finally, we assess the accuracy of the three type III effector prediction methods on a small set of proteins not known prior to the development of these tools that we have recently discovered and validated using both experimental and computational approaches. Our comparison shows that all methods use similar approaches and, in general arrive at similar conclusions. We discuss the possibility of an order-dependent motif in the secretion signal, which was a point of disagreement in the studies. Our results show that there may be classes of effectors in which the signal has a loosely defined motif, and others in which secretion is dependent only on compositional biases. Computational prediction of secreted effectors from protein sequences represents an important step toward better understanding the interaction between pathogens and hosts.

  17. International Space Station Bacteria Filter Element Post-Flight Testing and Service Life Prediction

    NASA Technical Reports Server (NTRS)

    Perry, J. L.; von Jouanne, R. G.; Turner, E. H.

    2003-01-01

    The International Space Station uses high efficiency particulate air (HEPA) filters to remove particulate matter from the cabin atmosphere. Known as Bacteria Filter Elements (BFEs), there are 13 elements deployed on board the ISS's U.S. Segment. The pre-flight service life prediction of 1 year for the BFEs is based upon performance engineering analysis of data collected during developmental testing that used a synthetic dust challenge. While this challenge is considered reasonable and conservative from a design perspective, an understanding of the actual filter loading is required to best manage the critical ISS Program resources. Thus testing was conducted on BFEs returned from the ISS to refine the service life prediction. Results from this testing and implications to ISS resource management are discussed. Recommendations for realizing significant savings to the ISS Program are presented.

  18. International Space Station Bacteria Filter Element Post-Flight Testing and Service Life Prediction

    NASA Technical Reports Server (NTRS)

    Perry, J. L.; von Jouanne, R. G.; Turner, E. H.

    2003-01-01

    The International Space Station uses high efficiency particulate air (HEPA) filters to remove particulate matter from the cabin atmosphere. Known as Bacteria Filter Elements (BFEs), there are 13 elements deployed on board the ISS's U.S. Segment. The pre-flight service life prediction of 1 year for the BFEs is based upon performance engineering analysis of data collected during developmental testing that used a synthetic dust challenge. While this challenge is considered reasonable and conservative from a design perspective, an understanding of the actual filter loading is required to best manage the critical ISS Program resources. Thus testing was conducted on BFEs returned from the ISS to refine the service life prediction. Results from this testing and implications to ISS resource management are discussed. Recommendations for realizing significant savings to the ISS Program are presented.

  19. Use of predictive models and rapid methods to nowcast bacteria levels at coastal beaches

    USGS Publications Warehouse

    Francy, Donna S.

    2009-01-01

    The need for rapid assessments of recreational water quality to better protect public health is well accepted throughout the research and regulatory communities. Rapid analytical methods, such as quantitative polymerase chain reaction (qPCR) and immunomagnetic separation/adenosine triphosphate (ATP) analysis, are being tested but are not yet ready for widespread use.Another solution is the use of predictive models, wherein variable(s) that are easily and quickly measured are surrogates for concentrations of fecal-indicator bacteria. Rainfall-based alerts, the simplest type of model, have been used by several communities for a number of years. Deterministic models use mathematical representations of the processes that affect bacteria concentrations; this type of model is being used for beach-closure decisions at one location in the USA. Multivariable statistical models are being developed and tested in many areas of the USA; however, they are only used in three areas of the Great Lakes to aid in notifications of beach advisories or closings. These “operational” statistical models can result in more accurate assessments of recreational water quality than use of the previous day's Escherichia coli (E. coli)concentration as determined by traditional culture methods. The Ohio Nowcast, at Huntington Beach, Bay Village, Ohio, is described in this paper as an example of an operational statistical model. Because predictive modeling is a dynamic process, water-resource managers continue to collect additional data to improve the predictive ability of the nowcast and expand the nowcast to other Ohio beaches and a recreational river. Although predictive models have been shown to work well at some beaches and are becoming more widely accepted, implementation in many areas is limited by funding, lack of coordinated technical leadership, and lack of supporting epidemiological data.

  20. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria.

    PubMed

    Gardy, Jennifer L; Spencer, Cory; Wang, Ke; Ester, Martin; Tusnády, Gábor E; Simon, István; Hua, Sujun; deFays, Katalin; Lambert, Christophe; Nakai, Kenta; Brinkman, Fiona S L

    2003-07-01

    Automated prediction of bacterial protein subcellular localization is an important tool for genome annotation and drug discovery. PSORT has been one of the most widely used computational methods for such bacterial protein analysis; however, it has not been updated since it was introduced in 1991. In addition, neither PSORT nor any of the other computational methods available make predictions for all five of the localization sites characteristic of Gram-negative bacteria. Here we present PSORT-B, an updated version of PSORT for Gram-negative bacteria, which is available as a web-based application at http://www.psort.org. PSORT-B examines a given protein sequence for amino acid composition, similarity to proteins of known localization, presence of a signal peptide, transmembrane alpha-helices and motifs corresponding to specific localizations. A probabilistic method integrates these analyses, returning a list of five possible localization sites with associated probability scores. PSORT-B, designed to favor high precision (specificity) over high recall (sensitivity), attained an overall precision of 97% and recall of 75% in 5-fold cross-validation tests, using a dataset we developed of 1443 proteins of experimentally known localization. This dataset, the largest of its kind, is freely available, along with the PSORT-B source code (under GNU General Public License).

  1. ROS/Autophagy/Nrf2 Pathway Mediated Low-Dose Radiation Induced Radio-Resistance in Human Lung Adenocarcinoma A549 Cell.

    PubMed

    Chen, Ni; Wu, Lijun; Yuan, Hang; Wang, Jun

    2015-01-01

    Low-dose ionizing radiation (LDIR) can induce radio-resistance to following high dose radiation in various mammalian cells. The protective role of LDIR has been thought to be associated with the overall outcomes of cancer radiotherapy. NF-E2 related factor 2 (Nrf2) is a transcription factor that plays pivotal roles in maintaining cellular oxidative equilibrium. Since oxidative stress has been indicated to be a mediator of LDIR induced radio-resistance, the role of Nrf2 in this process was investigated in this research. Our results showed that in human lung adenocarcinoma A549 cell, 5cGy alpha particle induced radio-resistance to following 75cGy alpha particle radiation. The expression level of Nrf2 and its target Heme Oxygenase-1(HO-1) increased after 5cGy radiation. Both the shRNA of Nrf2 and the chemical inhibitor of HO-1 suppressed the induced radio-resistance, indicating the involvement of Nrf2 antioxidant pathway in this process. Further, we found 5cGy radiation stimulated autophagy process in A549. Inhibition of the autophagy process resulted in suppression of the radio-resistance and the induced expression of Nrf2 and HO-1. ROS scavenger N-acetyl-L-cysteine (NAC) blocked the autophagy process induced by 5cGy alpha particle, the upregulation of Nrf2 and HO-1, as well as the induced radio-resistance. In conclusion, ROS elevation caused by LDIR promoted Autophagy/Nrf2-HO-1 and conferred radio-resistance in A549.

  2. ROS/Autophagy/Nrf2 Pathway Mediated Low-Dose Radiation Induced Radio-Resistance in Human Lung Adenocarcinoma A549 Cell

    PubMed Central

    Chen, Ni; Wu, Lijun; Yuan, Hang; Wang, Jun

    2015-01-01

    Low-dose ionizing radiation (LDIR) can induce radio-resistance to following high dose radiation in various mammalian cells. The protective role of LDIR has been thought to be associated with the overall outcomes of cancer radiotherapy. NF-E2 related factor 2 (Nrf2) is a transcription factor that plays pivotal roles in maintaining cellular oxidative equilibrium. Since oxidative stress has been indicated to be a mediator of LDIR induced radio-resistance, the role of Nrf2 in this process was investigated in this research. Our results showed that in human lung adenocarcinoma A549 cell, 5cGy alpha particle induced radio-resistance to following 75cGy alpha particle radiation. The expression level of Nrf2 and its target Heme Oxygenase-1(HO-1) increased after 5cGy radiation. Both the shRNA of Nrf2 and the chemical inhibitor of HO-1 suppressed the induced radio-resistance, indicating the involvement of Nrf2 antioxidant pathway in this process. Further, we found 5cGy radiation stimulated autophagy process in A549. Inhibition of the autophagy process resulted in suppression of the radio-resistance and the induced expression of Nrf2 and HO-1. ROS scavenger N-acetyl-L-cysteine (NAC) blocked the autophagy process induced by 5cGy alpha particle, the upregulation of Nrf2 and HO-1, as well as the induced radio-resistance. In conclusion, ROS elevation caused by LDIR promoted Autophagy/Nrf2-HO-1 and conferred radio-resistance in A549. PMID:26078725

  3. Resource Islands Predict the Distribution of Heterotrophic Bacteria in Chihuahuan Desert Soils

    PubMed Central

    Herman, R. P.; Provencio, K. R.; Herrera-Matos, J.; Torrez, R. J.

    1995-01-01

    The resource island hypothesis predicts that soil resources such as nitrogen, phosphorus, and water will be distributed evenly in grasslands but have a patchy distribution focused around plants in shrublands. This hypothesis predicts that microorganism numbers will follow resources and be (i) evenly distributed in grasslands, (ii) concentrated around individual plants in shrublands, and (iii) higher where resources are higher when comparing the same vegetation type. This study enumerated total heterotrophic bacteria and a subset of these, the nitrogen-efficient guild (NEG), in three shrublands (playa fringe mesquite, tar bush, and creosote) and two grasslands (playa and bajada). Both heterotrophs and NEG members followed the distribution pattern predicted by the resource island hypothesis. There were no significant differences in heterotroph or NEG numbers comparing at-plant and interplant samples for both the playa and bajada grasslands. Furthermore, populations were generally higher in nutrient-rich playa grasslands than nutrient-poor bajada grasslands. In contrast, both heterotroph and NEG numbers were higher at shrubs than between shrubs in all three shrub sites. These results suggest that resource abundance in resource islands predicts the distribution of heterotrophic bacterial numbers in desert soils. PMID:16535022

  4. Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes.

    PubMed

    Cleary, Daniel F R; Becking, Leontine E; Polónia, Ana R M; Freitas, Rossana M; Gomes, Newton C M

    2015-03-01

    In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological

  5. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria.

    PubMed

    Barberán, Albert; Ramirez, Kelly S; Leff, Jonathan W; Bradford, Mark A; Wall, Diana H; Fierer, Noah

    2014-07-01

    Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non-existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km(2) area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait-based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait-based predictions of the biogeographical patterns exhibited by microbes.

  6. Prediction of acid lactic-bacteria growth in turkey ham processed by high hydrostatic pressure

    PubMed Central

    Mathias, S.P.; Rosenthal, A.; Gaspar, A.; Aragão, G.M.F.; Slongo-Marcusi, A.

    2013-01-01

    High hydrostatic pressure (HHP) has been investigated and industrially applied to extend shelf life of meat-based products. Traditional ham packaged under microaerophilic conditions may sometimes present high lactic acid bacteria population during refrigerated storage, which limits shelf life due to development of unpleasant odor and greenish and sticky appearance. This study aimed at evaluating the shelf life of turkey ham pressurized at 400 MPa for 15 min and stored at 4, 8 and 12 °C, in comparison to the non pressurized product. The lactic acid bacteria population up to 107 CFU/g of product was set as the criteria to determine the limiting shelf life According to such parameter the pressurized sample achieved a commercial viability within 75 days when stored at 4 °C while the control lasted only 45 days. Predictive microbiology using Gompertz and Baranyi and Roberts models fitted well both for the pressurized and control samples. The results indicated that the high hydrostatic pressure treatment greatly increased the turkey ham commercial viability in comparison to the usual length, by slowing down the growth of microorganisms in the product. PMID:24159279

  7. ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

    PubMed Central

    Paramasivam, Nagarajan; Linke, Dirk

    2011-01-01

    The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/ PMID:22073040

  8. Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions

    PubMed Central

    Vesselinova, Neda; Wall, Michael E.

    2016-01-01

    We present a dynamical model of drug accumulation in bacteria. The model captures key features in experimental time courses on ofloxacin accumulation: initial uptake; two-phase response; and long-term acclimation. In combination with experimental data, the model provides estimates of import and export rates in each phase, the time of entry into the second phase, and the decrease of internal drug during acclimation. Global sensitivity analysis, local sensitivity analysis, and Bayesian sensitivity analysis of the model provide information about the robustness of these estimates, and about the relative importance of different parameters in determining the features of the accumulation time courses in three different bacterial species: Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The results lead to experimentally testable predictions of the effects of membrane permeability, drug efflux and trapping (e.g., by DNA binding) on drug accumulation. A key prediction is that a sudden increase in ofloxacin accumulation in both E. coli and S. aureus is accompanied by a decrease in membrane permeability. PMID:27824914

  9. Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions

    DOE PAGES

    Vesselinova, Neda; Alexandrov, Boian; Wall, Michael E.

    2016-11-08

    We present a dynamical model of drug accumulation in bacteria. The model captures key features in experimental time courses on ofloxacin accumulation: initial uptake; two-phase response; and long-term acclimation. In combination with experimental data, the model provides estimates of import and export rates in each phase, the time of entry into the second phase, and the decrease of internal drug during acclimation. Global sensitivity analysis, local sensitivity analysis, and Bayesian sensitivity analysis of the model provide information about the robustness of these estimates, and about the relative importance of different parameters in determining the features of the accumulation time coursesmore » in three different bacterial species: Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The results lead to experimentally testable predictions of the effects of membrane permeability, drug efflux and trapping (e.g., by DNA binding) on drug accumulation. A key prediction is that a sudden increase in ofloxacin accumulation in both E. coli and S. aureus is accompanied by a decrease in membrane permeability.« less

  10. Including Sediment-Associated Bacteria Resuspension and Settling in SWAT Predictions of Microbial Water Quality

    USDA-ARS?s Scientific Manuscript database

    Streambed sediments have been shown to serve as environmental reservoirs for bacteria, including pathogenic strains. The Soil and Water Assessment Tool (SWAT) has been augmented with bacteria subroutine in 2005. Bacteria die-off is the only in-stream process considered in the current SWAT. The purpo...

  11. Predicting and Modelling the Growth of Potentially Pathogenic Bacteria in Coalho Cheese.

    PubMed

    de Araújo, Valdenice Gomes; de Oliveira Arruda, Maria Digian; Dantas Duarte, Francisca Nayara; de Sousa, Janaína Maria Batista; da Costa Lima, Maiara; da Conceição, Maria Lúcia; Schaffner, Donald W; de Souza, Evandro Leite

    2017-07-01

    Coalho is a semihard medium- to high-moisture cheese produced in various states in the northeastern region of Brazil. This study was conducted to predict the growth kinetics (maximum growth rate, Grmax) of Escherichia coli, Listeria monocytogenes, Salmonella, and Staphylococcus aureus using the ComBase predictor with various combinations of temperature, pH, and water activity (aw) in commercial Coalho cheese samples. The growth of two antibiotic-resistant derivative strains of L. monocytogenes (parental strains ATCC 19115 and ATCC 7644) and S. aureus (parental strains ATCC 13565 and ATCC 19095) was measured in commercial Coalho cheese samples during 14 days of storage as a function of the initial contamination level (3 and 5 log CFU/g) and storage temperature (7.5 and 12°C). The highest Grmax values predicted by ComBase under the various conditions of temperature, pH, and aw were for L. monocytogenes (0.006 to 0.065 log CFU/g/h) and S. aureus (0.003 to 0.048 log CFU/g/h). The Grmax values predicted by ComBase for E. coli and Salmonella were 0.007 to 0.026 and 0.008 to 0.041 log CFU/g/h, respectively. An experimental challenge in Coalho cheese revealed that the populations of all tested antibiotic-resistant derivative strains of L. monocytogenes and S. aureus increased (>0.5 log CFU/g) by day 14 of storage at 7.5 or 12°C. L. monocytogenes and S. aureus had higher Grmax values in cheese samples stored at 12°C than those stored at 7.5°C. The ComBase growth predictions under the temperature, pH, and aw conditions in commercial Coalho cheese samples were generally fail-safe for predicting the growth of L. monocytogenes and S. aureus in the actual product. These results indicate that Coalho cheese has pH and aw characteristics that allow the growth of E. coli, L. monocytogenes, Salmonella, and S. aureus. These cheeses are typically stored at temperatures that do not prevent the growth of these bacteria.

  12. Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.

    PubMed

    Bengtsson-Palme, Johan; Larsson, D G Joakim

    2016-01-01

    There are concerns that selection pressure from antibiotics in the environment may accelerate the evolution and dissemination of antibiotic-resistant pathogens. Nevertheless, there is currently no regulatory system that takes such risks into account. In part, this is due to limited knowledge of environmental concentrations that might exert selection for resistant bacteria. To experimentally determine minimal selective concentrations in complex microbial ecosystems for all antibiotics would involve considerable effort. In this work, our aim was to estimate upper boundaries for selective concentrations for all common antibiotics, based on the assumption that selective concentrations a priori need to be lower than those completely inhibiting growth. Data on Minimal Inhibitory Concentrations (MICs) were obtained for 111 antibiotics from the public EUCAST database. The 1% lowest observed MICs were identified, and to compensate for limited species coverage, predicted lowest MICs adjusted for the number of tested species were extrapolated through modeling. Predicted No Effect Concentrations (PNECs) for resistance selection were then assessed using an assessment factor of 10 to account for differences between MICs and minimal selective concentrations. The resulting PNECs ranged from 8 ng/L to 64 μg/L. Furthermore, the link between taxonomic similarity between species and lowest MIC was weak. This work provides estimated upper boundaries for selective concentrations (lowest MICs) and PNECs for resistance selection for all common antibiotics. In most cases, PNECs for selection of resistance were below available PNECs for ecotoxicological effects. The generated PNECs can guide implementation of compound-specific emission limits that take into account risks for resistance promotion. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions.

    PubMed

    Huete-Stauffer, Tamara Megan; Arandia-Gorostidi, Nestor; Díaz-Pérez, Laura; Morán, Xosé Anxelu G

    2015-10-01

    Using the metabolic theory of ecology (MTE) framework, we evaluated over a whole annual cycle the monthly responses to temperature of the growth rates (μ) and carrying capacities (K) of heterotrophic bacterioplankton at a temperate coastal site. We used experimental incubations spanning 6ºC with bacterial physiological groups identified by flow cytometry according to membrane integrity (live), nucleic acid content (HNA and LNA) and respiratory activity (CTC+). The temperature dependence of μ at the exponential phase of growth was summarized by the activation energy (E), which was variable (-0.52 to 0.72 eV) but followed a seasonal pattern, only reaching the hypothesized value for aerobic heterotrophs of 0.65 eV during the spring bloom for the most active bacterial groups (live, HNA, CTC+). K (i.e. maximum experimental abundance) peaked at 4 × 10(6) cells mL(-1) and generally covaried with μ but, contrary to MTE predictions, it did not decrease consistently with temperature. In the case of live cells, the responses of μ and K to temperature were positively correlated and related to seasonal changes in substrate availability, indicating that the responses of bacteria to warming are far from homogeneous and poorly explained by MTE at our site. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Phylogenomic Analysis and Predicted Physiological Role of the Proton-Translocating NADH:Quinone Oxidoreductase (Complex I) Across Bacteria

    PubMed Central

    Spero, Melanie A.; Aylward, Frank O.; Currie, Cameron R.

    2015-01-01

    ABSTRACT The proton-translocating NADH:quinone oxidoreductase (complex I) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. Although much research has focused on the enzyme’s central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. Here, we used a phylogenomic approach to better understand the distribution of complex I across bacteria, the evolution of this enzyme, and its potential roles in shaping the physiology of different bacterial groups. By surveying 970 representative bacterial genomes, we predict complex I to be present in ~50% of bacteria. While this includes bacteria with a wide range of energetic schemes, the presence of complex I is associated with specific lifestyles, including aerobic respiration and specific types of phototrophy (bacteria with only a type II reaction center). A phylogeny of bacterial complex I revealed five main clades of enzymes whose evolution is largely congruent with the evolution of the bacterial groups that encode complex I. A notable exception includes the gammaproteobacteria, whose members encode one of two distantly related complex I enzymes predicted to participate in different types of respiratory chains (aerobic versus anaerobic). Comparative genomic analyses suggest a broad role for complex I in reoxidizing NADH produced from various catabolic reactions, including the tricarboxylic acid (TCA) cycle and fatty acid beta-oxidation. Together, these findings suggest diverse roles for complex I across bacteria and highlight the importance of this enzyme in shaping diverse physiologies across the bacterial domain. PMID:25873378

  15. USING HYDROGRAPHIC DATA AND THE EPA VIRTUAL BEACH MODEL TO TEST PREDICTIONS OF BEACH BACTERIA CONCENTRATIONS

    EPA Science Inventory

    A modeling study of 2006 Huntington Beach (Lake Erie) beach bacteria concentrations indicates multi-variable linear regression (MLR) can effectively estimate bacteria concentrations compared to the persistence model. Our use of the Virtual Beach (VB) model affirms that fact. VB i...

  16. USING HYDROGRAPHIC DATA AND THE EPA VIRTUAL BEACH MODEL TO TEST PREDICTIONS OF BEACH BACTERIA CONCENTRATIONS

    EPA Science Inventory

    A modeling study of 2006 Huntington Beach (Lake Erie) beach bacteria concentrations indicates multi-variable linear regression (MLR) can effectively estimate bacteria concentrations compared to the persistence model. Our use of the Virtual Beach (VB) model affirms that fact. VB i...

  17. Maximum entropy principle for predicting response to multiple-drug exposure in bacteria and human cancer cells

    NASA Astrophysics Data System (ADS)

    Wood, Kevin; Nishida, Satoshi; Sontag, Eduardo; Cluzel, Philippe

    2012-02-01

    Drugs are commonly used in combinations larger than two for treating infectious disease. However, it is generally impossible to infer the net effect of a multi-drug combination on cell growth directly from the effects of individual drugs. We combined experiments with maximum entropy methods to develop a mechanism-independent framework for calculating the response of both bacteria and human cancer cells to a large variety of drug combinations comprised of anti-microbial or anti-cancer drugs. We experimentally show that the cellular responses to drug pairs are sufficient to infer the effects of larger drug combinations in gram negative bacteria, Escherichia coli, gram positive bacteria, Staphylococcus aureus, and also human breast cancer and melanoma cell lines. Remarkably, the accurate predictions of this framework suggest that the multi-drug response obeys statistical rather than chemical laws for combinations larger than two. Consequently, these findings offer a new strategy for the rational design of therapies using large drug combinations.

  18. Comparison of Clinical Prediction Models for Resistant Bacteria in Community-onset Pneumonia

    PubMed Central

    Self, Wesley H.; Wunderink, Richard G.; Williams, Derek J.; Barrett, Tyler W.; Baughman, Adrienne H.; Grijalva, Carlos G.

    2015-01-01

    Objectives Six recently published algorithms classify pneumonia patients presenting from the community into high- and low-risk groups for resistant bacteria. Our objective was to compare performance of these algorithms for identifying patients infected with bacteria resistant to traditional community-acquired pneumonia antibiotics. Methods This was a retrospective study of consecutive adult patients diagnosed with pneumonia in an emergency department and subsequently hospitalized. Each patient was classified as high- or low-risk for resistant bacteria according to the following algorithms: original health care-associated pneumonia (HCAP) criteria, Summit criteria, Brito and Niederman strategy, Shorr model, Aliberti model, and Shindo model. The reference for comparison was detection of resistant bacteria, defined as methicillin-resistant Staphylococcus aureus or gram-negative bacteria resistant to ceftriaxone or levofloxacin. Results Six hundred fourteen patients were studied, including 36 (5.9%) with resistant bacteria. The HCAP criteria classified 304 (49.5%) patients as high-risk, with an area under the receiver operating characteristic curve (AUC) of 0.63 (95% CI = 0.54 to 0.72), sensitivity of 0.69 (95% CI = 0.52 to 0.83), and specificity of 0.52 (95% CI = 0.48 to 0.56). None of the other algorithms improved both sensitivity and specificity, or significantly improved the AUC. Compared to the HCAP criteria, the Shorr and Aliberti models classified more patients as high-risk, resulting in higher sensitivity and lower specificity. The Shindo model classified fewer patients as high-risk, with lower sensitivity and higher specificity. Conclusions All algorithms for identification of resistant bacteria included in this study had suboptimal performance to guide antibiotic selection. New strategies for selecting empirical antibiotics for community-onset pneumonia are necessary. PMID:25996620

  19. Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri.

    PubMed

    Kulkarni, Prajna R; Cui, Xiaohui; Williams, Joshua W; Stevens, Ann M; Kulkarni, Rahul V

    2006-01-01

    The role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which control the activity of the global regulator CsrA. Given the critical role played by CsrA in several bacterial species, an important problem is the identification of CsrA-regulating small RNAs. In this paper, we develop a computer program (CSRNA_FIND) designed to locate potential CsrA-regulating small RNAs in bacteria. Using CSRNA_FIND to search the genomes of bacteria having homologs of CsrA, we identify all the experimentally known CsrA-regulating small RNAs and also make predictions for several novel small RNAs. We have verified experimentally our predictions for two CsrA-regulating small RNAs in Vibrio fischeri. As more genomes are sequenced, CSRNA_FIND can be used to locate the corresponding small RNAs that regulate CsrA homologs. This work thus opens up several avenues of research in understanding the mode of CsrA regulation through small RNAs in bacteria.

  20. INTRODUCTION TO A COMBINED MULTIPLE LINEAR REGRESSION AND ARMA MODELING APPROACH FOR BEACH BACTERIA PREDICTION

    EPA Science Inventory

    Due to the complexity of the processes contributing to beach bacteria concentrations, many researchers rely on statistical modeling, among which multiple linear regression (MLR) modeling is most widely used. Despite its ease of use and interpretation, there may be time dependence...

  1. INTRODUCTION TO A COMBINED MULTIPLE LINEAR REGRESSION AND ARMA MODELING APPROACH FOR BEACH BACTERIA PREDICTION

    EPA Science Inventory

    Due to the complexity of the processes contributing to beach bacteria concentrations, many researchers rely on statistical modeling, among which multiple linear regression (MLR) modeling is most widely used. Despite its ease of use and interpretation, there may be time dependence...

  2. miR-504 mediated down-regulation of nuclear respiratory factor 1 leads to radio-resistance in nasopharyngeal carcinoma

    PubMed Central

    Zhao, Luqing; Tang, Min; Hu, Zheyu; Yan, Bin; Pi, Weiwei; Li, Zhi; Zhang, Jing; Zhang, Liqin; Jiang, Wuzhong; Li, Guo; Qiu, Yuanzheng; Hu, Fang; Liu, Feng; Lu, Jingchen; Chen, Xue; Xiao, Lanbo; Xu, Zhijie; Tao, Yongguang; Yang, Lifang; Bode, Ann M.; Dong, Zigang; Zhou, Jian; Fan, Jia; Sun, Lunquan; Cao, Ya

    2015-01-01

    microRNAs (miRNAs) are involved in the various processes of DNA damage repair and play crucial roles in regulating response of tumors to radiation therapy. Here, we used nasopharyngeal carcinoma (NPC) radio-resistant cell lines as models and found that the expression of miR-504 was significantly up-regulated. In contrast, the expression of nuclear respiratory factor 1 (NRF1) and other mitochondrial metabolism factors, including mitochondrial transcription factor A (TFAM) and oxidative phosphorylation (OXPHOS) complex III were down-regulated in these cell lines. At the same time, the Seahorse cell mitochondrial stress test results indicated that the mitochondrial respiratory capacity was impaired in NPC radio-resistant cell lines and in a miR-504 over-expressing cell line. We also conducted dual luciferase reporter assays and verified that miR-504 could directly target NRF1. Additionally, miR-504 could down-regulate the expression of TFAM and OXPHOS complexes I, III, and IV and impaired the mitochondrial respiratory function of NPC cells. Furthermore, serum from NPC patients showed that miR-504 was up-regulated during different weeks of radiotherapy and correlated with tumor, lymph nodes and metastasis (TNM) stages and total tumor volume. The radio-therapeutic effect at three months after radiotherapy was evaluated. Results indicated that patients with high expression of miR-504 exhibited a relatively lower therapeutic effect ratio of complete response (CR), but a higher ratio of partial response (PR), compared to patients with low expression of miR-504. Taken together, these results demonstrated that miR-504 affected the radio-resistance of NPC by down-regulating the expression of NRF1 and disturbing mitochondrial respiratory function. Thus, miR-504 might become a promising biomarker of NPC radio-resistance and targeting miR-504 might improve tumor radiation response. PMID:26201446

  3. Prediction of periodontopathic bacteria in dental plaque of periodontal healthy subjects by measurement of volatile sulfur compounds in mouth air.

    PubMed

    Kishi, Mitsuo; Ohara-Nemoto, Yuko; Takahashi, Masahiro; Kishi, Kayo; Kimura, Shigenobu; Aizawa, Fumie; Yonemitsu, Masami

    2013-03-01

    The aim of this study was to determine whether measurements of volatile sulfur compounds (VSCs) are useful to predict colonization of periodontopathic bacteria. For this purpose, we assessed the relationships among distributions of 4 species of periodontopathic bacteria in tongue coating and dental plaque, oral conditions including VSC concentration in mouth air, and smoking habit of periodontal healthy young subjects. The subjects were 108 young adults (mean age, 23.5±2.56 years) without clinical periodontal pockets. Information regarding smoking habit was obtained by interview. After VSC concentration in mouth, air was measured with a portable sulfide monitor (Halimeter(®)), non-stimulated saliva flow and dental caries status were assessed, and tongue coating and dental plaque samples were collected from the subjects. The tongue coating samples were weighed to determine the amount. The colonization of Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, and Treponema denticola in both tongue coating and plaque samples was investigated using species-specific polymerase chain reaction assays. Significant relationships were observed between the colonization of periodontopathic bacteria in tongue coating and plaque samples, especially that of P. gingivalis. VSC concentration showed the most significant association with colonization of P. gingivalis in both tongue coating and dental plaque. Logistic regression analysis demonstrated that the adjusted partial correlation coefficient [Exp(B)] values for VSC concentration with the colonization of P. gingivalis, P. intermedia, and T. denticola in dental plaque were 135, 35.4 and 10.4, respectively. In addition, smoking habit was also shown to be a significant variable in regression models [Exp(B)=6.19, 8.92 and 2.53, respectively]. Therefore, receiver operating characteristic analysis was performed to predict the colonization of periodontal bacteria in dental plaque in the subjects divided by smoking

  4. Calculations of Light Scattering Measurements Predicting Sensitivity of Depolarization to Shape Changes of Spores and Bacteria

    DTIC Science & Technology

    2008-04-01

    either spores or bacteria. 44 LITERATURE CITED 1. Grund, C.J; Brilliant, N.; Bjork, C.; Craig, T. Eyesafe, Multi-function Coherent Doppler Lidar for...an aerosol containing biological particles. This is of interest both for lidar backscatter and for point measurements where samples of the aerosol are... laser light. Each of the added spheres was tangent to the center sphere but did not overlap it. The scattering calculated for the cluster of seven

  5. Caenorhabditis elegans Genomic Response to Soil Bacteria Predicts Environment-Specific Genetic Effects on Life History Traits

    PubMed Central

    Coolon, Joseph D.; Jones, Kenneth L.; Todd, Timothy C.; Carr, Bryanua C.; Herman, Michael A.

    2009-01-01

    With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential expression is predictive of functional importance has yet to be tested. Here we have addressed this expectation by employing Caenorhabditis elegans as a model for the interaction of native soil nematode taxa and soil bacteria. Using transcriptional profiling, we identified candidate genes regulated in response to different bacteria isolated in association with grassland nematodes or from grassland soils. Many of the regulated candidate genes are predicted to affect metabolism and innate immunity suggesting similar genes could influence nematode community dynamics in natural systems. Using mutations that inactivate 21 of the identified genes, we showed that most contribute to lifespan and/or fitness in a given bacterial environment. Although these bacteria may not be natural food sources for C. elegans, we show that changes in food source, as can occur in environmental disturbance, can have a large effect on gene expression, with important consequences for fitness. Moreover, we used regression analysis to demonstrate that for many genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life history traits in those environments. PMID:19503598

  6. Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus

    PubMed Central

    Becker, Matthew H.; Walke, Jenifer B.; Cikanek, Shawna; Savage, Anna E.; Mattheus, Nichole; Santiago, Celina N.; Minbiole, Kevin P. C.; Harris, Reid N.; Belden, Lisa K.; Gratwicke, Brian

    2015-01-01

    Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics. PMID:25788591

  7. Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus.

    PubMed

    Becker, Matthew H; Walke, Jenifer B; Cikanek, Shawna; Savage, Anna E; Mattheus, Nichole; Santiago, Celina N; Minbiole, Kevin P C; Harris, Reid N; Belden, Lisa K; Gratwicke, Brian

    2015-04-22

    Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  8. Predictable communities of soil bacteria in relation to nutrient concentration and successional stage in a laboratory culture experiment.

    PubMed

    Song, Woojin; Kim, Mincheol; Tripathi, Binu M; Kim, Hyoki; Adams, Jonathan M

    2016-06-01

    It is difficult to understand the processes that structure immensely complex bacterial communities in the soil environment, necessitating a simplifying experimental approach. Here, we set up a microcosm culturing experiment with soil bacteria, at a range of nutrient concentrations, and compared these over time to understand the relationship between soil bacterial community structure and time/nutrient concentration. DNA from each replicate was analysed using HiSeq2000 Illumina sequencing of the 16S rRNA gene. We found that each nutrient treatment, and each time point during the experiment, produces characteristic bacterial communities that occur predictably between replicates. It is clear that within the context of this experiment, many soil bacteria have distinct niches from one another, in terms of both nutrient concentration, and successional time point since a resource first became available. This fine niche differentiation may in part help to explain the coexistence of a diversity of bacteria in soils. In this experiment, we show that the unimodal relationship between nutrient concentration/time and species diversity often reported in communities of larger organisms is also evident in microbial communities.

  9. Genome-wide protein localization prediction strategies for gram negative bacteria

    SciTech Connect

    Romine, Margaret F.

    2011-06-15

    Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output. As part of an effort to manually curate the annotations of 19 strains of Shewanella, numerous insights were gained regarding the use of computational tools and proteomics data to predict protein localization. Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved accuracy. Comparisons of the computational predictions among orthologous proteins revealed inconsistencies in the computational outputs, which could often be resolved by adjusting the gene models or ortholog group memberships. While proteomic data was useful for verifying start site predictions and post-translational proteolytic cleavage, care was needed to distinguish cellular versus sample processing-mediated cleavage events. Searches for lipoprotein signal peptides revealed that neither TatP nor LipoP are designed for identification of lipoprotein substrates of the twin arginine translocation system and that the +2 rule for lipoprotein sorting does not apply to this Genus. Analysis of the relationships between domain occurrence and protein localization prediction enabled identification of numerous location-informative domains which could then be used to refine or increase confidence in location predictions. This collective knowledge was used to develop a general strategy for predicting protein localization that could be adapted to other organisms.

  10. Genome-wide protein localization prediction strategies for gram negative bacteria

    PubMed Central

    2011-01-01

    Background Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output. Results As part of an effort to manually curate the annotations of 19 strains of Shewanella, numerous insights were gained regarding the use of computational tools and proteomics data to predict protein localization. Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved accuracy. Comparisons of the computational predictions among orthologous proteins revealed inconsistencies in the computational outputs, which could often be resolved by adjusting the gene models or ortholog group memberships. While proteomic data was useful for verifying start site predictions and post-translational proteolytic cleavage, care was needed to distinguish cellular versus sample processing-mediated cleavage events. Searches for lipoprotein signal peptides revealed that neither TatP nor LipoP are designed for identification of lipoprotein substrates of the twin arginine translocation system and that the +2 rule for lipoprotein sorting does not apply to this Genus. Analysis of the relationships between domain occurrence and protein localization prediction enabled identification of numerous location-informative domains which could then be used to refine or increase confidence in location predictions. This collective knowledge was used to develop a general strategy for predicting protein localization that could be adapted to other organisms. Conclusion Improved localization prediction accuracy is not simply a matter of developing better computational algorithms. It

  11. Predictive Power of Clean Bed Filtration Theory for Fecal Indicator Bacteria Removal in Stormwater Biofilters.

    PubMed

    Parker, Emily A; Rippy, Megan A; Mehring, Andrew S; Winfrey, Brandon K; Ambrose, Richard F; Levin, Lisa A; Grant, Stanley B

    2017-05-16

    Green infrastructure (also referred to as low impact development, or LID) has the potential to transform urban stormwater runoff from an environmental threat to a valuable water resource. In this paper we focus on the removal of fecal indicator bacteria (FIB, a pollutant responsible for runoff-associated inland and coastal beach closures) in stormwater biofilters (a common type of green infrastructure). Drawing on a combination of previously published and new laboratory studies of FIB removal in biofilters, we find that 66% of the variance in FIB removal rates can be explained by clean bed filtration theory (CBFT, 31%), antecedent dry period (14%), study effect (8%), biofilter age (7%), and the presence or absence of shrubs (6%). Our analysis suggests that, with the exception of shrubs, plants affect FIB removal indirectly by changing the infiltration rate, not directly by changing the FIB removal mechanisms or altering filtration rates in ways not already accounted for by CBFT. The analysis presented here represents a significant step forward in our understanding of how physicochemical theories (such as CBFT) can be melded with hydrology, engineering design, and ecology to improve the water quality benefits of green infrastructure.

  12. Predicting conserved essential genes in bacteria: in silico identification of putative drug targets.

    PubMed

    Duffield, Melanie; Cooper, Ian; McAlister, Erin; Bayliss, Marc; Ford, Donna; Oyston, Petra

    2010-12-01

    Many genes have been listed as putatively essential for bacterial viability in the Database of Essential Genomes (DEG), although few have been experimentally validated. By prioritising targets according to the criteria suggested by the Research and Training in Tropical Diseases (TDR) Targets database, we have developed a modified down-selection tool to identify essential genes conserved across diverse genera. Using this approach we identified 52 proteins conserved to 7 or more of the 14 genomes in DEG. We confirmed the validity of the down-selection by attempting to make mutants of 8 of these targets in a model organism, Yersinia pseudotuberculosis, which is not closely related to any of the bacteria in DEG. Mutants were recovered for only one of the 8 targets, suggesting that the other 7 were essential in Y. pseudotuberculosis, an impressive success rate compared to other approaches of identification for such targets. Identification of essential proteins common in diverse bacterial genera can then be used to facilitate the selection of effective targets for novel broad-spectrum antibiotics.

  13. Comparisons of statistical models to predict fecal indicator bacteria concentrations enumerated by qPCR- and culture-based methods.

    PubMed

    Gonzalez, Raul A; Noble, Rachel T

    2014-01-01

    Recently, the United States Environmental Protection Agency (USEPA) revised their recreational water quality criteria, in which adjustments were made by approving enterococci (ENT) quantitative PCR (qPCR) as an alternative, rapid method and advocating the use of predictive models for water quality management. The implementation of qPCR-based methods and prediction models are meant to decrease the time between sample collection and public advisories and notifications. To date, few studies have compared qPCR-based models to culture-based prediction models and none of these studies have been conducted in coastal estuarine systems. In this study, we created prediction models using qPCR-based fecal indicator bacteria (FIB) data in dual-use recreational and shellfish harvesting waters and compared them to published ENT and Escherichia coli (EC) culture-based prediction models in eastern North Carolina estuaries. Furthermore, an empirical statistical model was created to predict qPCR inhibition levels so that proper remediation techniques can be applied when it is a problem. Predictor variable selection in both qPCR- and culture-based ENT models was very similar; both models included 14-day rain total, dissolved oxygen, and salinity/conductivity, with 89 and 90% of qPCR and culture data described, respectively. Using ENT management action thresholds, qPCR- and culture-based models showed high accuracy in management decisions. The qPCR model had 92 and 96% accuracy using the 110 and 1000 cell equivalents (CE)/100 ml thresholds, respectively, and the culture model had 90% accuracy in management decisions with the 110 MPN/100 ml threshold. EC models for qPCR- and culture-based concentrations used similar independent variables (14-day humidity, salinity/conductivity, a rain/storm variable, and a measure of air temperature), with each model explaining 26 and 55% of the data variation, respectively. When using different thresholds that were logs apart for management decisions

  14. Application of empirical predictive modeling using conventional and alternative fecal indicator bacteria in eastern North Carolina waters

    USGS Publications Warehouse

    Gonzalez, Raul; Conn, Kathleen E.; Crosswell, Joey; Noble, Rachel

    2012-01-01

    Coastal and estuarine waters are the site of intense anthropogenic influence with concomitant use for recreation and seafood harvesting. Therefore, coastal and estuarine water quality has a direct impact on human health. In eastern North Carolina (NC) there are over 240 recreational and 1025 shellfish harvesting water quality monitoring sites that are regularly assessed. Because of the large number of sites, sampling frequency is often only on a weekly basis. This frequency, along with an 18–24 h incubation time for fecal indicator bacteria (FIB) enumeration via culture-based methods, reduces the efficiency of the public notification process. In states like NC where beach monitoring resources are limited but historical data are plentiful, predictive models may offer an improvement for monitoring and notification by providing real-time FIB estimates. In this study, water samples were collected during 12 dry (n = 88) and 13 wet (n = 66) weather events at up to 10 sites. Statistical predictive models for Escherichiacoli (EC), enterococci (ENT), and members of the Bacteroidales group were created and subsequently validated. Our results showed that models for EC and ENT (adjusted R2 were 0.61 and 0.64, respectively) incorporated a range of antecedent rainfall, climate, and environmental variables. The most important variables for EC and ENT models were 5-day antecedent rainfall, dissolved oxygen, and salinity. These models successfully predicted FIB levels over a wide range of conditions with a 3% (EC model) and 9% (ENT model) overall error rate for recreational threshold values and a 0% (EC model) overall error rate for shellfish threshold values. Though modeling of members of the Bacteroidales group had less predictive ability (adjusted R2 were 0.56 and 0.53 for fecal Bacteroides spp. and human Bacteroides spp., respectively), the modeling approach and testing provided information on Bacteroidales ecology. This is the first example of a set of successful statistical

  15. Predicting and preventing antimicrobial resistance utilizing pharmacodynamics: Part I gram positive bacteria.

    PubMed

    Linder, Kristin E; Nicolau, David P; Nailor, Michael D

    2016-01-01

    Antimicrobial resistance is a potentially inevitable consequence of widespread use of antibiotics in the healthcare system. An enhanced understanding of pharmacodynamic (PD) targets that prevent antimicrobial resistance development will improve currently availably therapies and help to guide future drug development strategies. Current in vitro methods to predict bacterial resistance to antimicrobials consist of serial dilution experiments, determination of the mutant prevention concentration (MPC), mutant selection window (MSW), and human simulated pharmacodynamics studies. Clinical trial data and real -world surveillance studies can help validate or disprove in vitro modeling. This review will discuss methods of predicting development of resistance and how the use of pharmacodynamics can reduce or eliminate the emergence of resistance among Staphylococcus aureus, Streptococcus pneumoniae, and Enterococcus species. Pharmacodynamic targets can be used successfully to guide antimicrobial therapy to prevent resistance development. Currently, PD targets do not take into consideration horizontal resistance gene transfer and various factors may lead to different PD targets based on sites of infection. Further research is necessary to guide future drug development strategies and optimize new drug therapies.

  16. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

    PubMed Central

    Barroso-Batista, João; Demengeot, Jocelyne; Gordo, Isabel

    2015-01-01

    Co-evolution between the mammalian immune system and the gut microbiota is believed to have shaped the microbiota's astonishing diversity. Here we test the corollary hypothesis that the adaptive immune system, directly or indirectly, influences the evolution of commensal species. We compare the evolution of Escherichia coli upon colonization of the gut of wild-type and Rag2−/− mice, which lack lymphocytes. We show that bacterial adaptation is slower in immune-compromised animals, a phenomenon explained by differences in the action of natural selection within each host. Emerging mutations exhibit strong beneficial effects in healthy hosts but substantial antagonistic pleiotropy in immune-deficient mice. This feature is due to changes in the composition of the gut microbiota, which differs according to the immune status of the host. Our results indicate that the adaptive immune system influences the tempo and predictability of E. coli adaptation to the mouse gut. PMID:26615893

  17. Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates

    PubMed Central

    Lubner, Joshua M.; Church, George M.; Husson, Robert N.; Schwartz, Daniel

    2012-01-01

    The identification of protein kinase targets remains a significant bottleneck for our understanding of signal transduction in normal and diseased cellular states. Kinases recognize their substrates in part through sequence motifs on substrate proteins, which, to date, have most effectively been elucidated using combinatorial peptide library approaches. Here, we present and demonstrate the ProPeL method for easy and accurate discovery of kinase specificity motifs through the use of native bacterial proteomes that serve as in vivo libraries for thousands of simultaneous phosphorylation reactions. Using recombinant kinases expressed in E. coli followed by mass spectrometry, the approach accurately recapitulated the well-established motif preferences of human basophilic (Protein Kinase A) and acidophilic (Casein Kinase II) kinases. These motifs, derived for PKA and CK II using only bacterial sequence data, were then further validated by utilizing them in conjunction with the scan-x software program to computationally predict known human phosphorylation sites with high confidence. PMID:23300758

  18. Predictive model for the growth of spoilage bacteria on modified atmosphere packaged Atlantic salmon produced in Australia.

    PubMed

    Powell, S M; Ratkowsky, D A; Tamplin, M L

    2015-05-01

    Most existing models for the spoilage of modified atmosphere packed Atlantic salmon are based on the growth of the spoilage organism Photobacterium phosphoreum. However, there is evidence that this organism is not the specific spoilage organism on salmon produced and packaged in Australia. We developed a predictive model for the growth of bacteria in Australian-produced Atlantic salmon stored under modified atmosphere conditions (30-98% carbon dioxide in nitrogen) at refrigeration temperatures (0-10 °C). As expected, both higher levels of carbon dioxide and lower temperatures decreased the observed growth rates of the total population. A Bělehrádek-type model for growth rate fitted the data best with an acceptably low root mean square error. At low temperatures (∼0 °C) the growth rates in this study were similar to those predicted by other models but at higher temperatures (∼10 °C) the growth rates were significantly lower in the current study.

  19. Prediction of Fluoroquinolone Resistance in Gram-Negative Bacteria Causing Bloodstream Infections.

    PubMed

    Dan, Seejil; Shah, Ansal; Justo, Julie Ann; Bookstaver, P Brandon; Kohn, Joseph; Albrecht, Helmut; Al-Hasan, Majdi N

    2016-04-01

    Increasing rates of fluoroquinolone resistance (FQ-R) have limited empirical treatment options for Gram-negative infections, particularly in patients with severe beta-lactam allergy. This case-control study aims to develop a clinical risk score to predict the probability of FQ-R in Gram-negative bloodstream isolates. Adult patients with Gram-negative bloodstream infections (BSI) hospitalized at Palmetto Health System in Columbia, South Carolina, from 2010 to 2013 were identified. Multivariate logistic regression was used to identify independent risk factors for FQ-R. Point allocation in the fluoroquinolone resistance score (FQRS) was based on regression coefficients. Model discrimination was assessed by the area under receiver operating characteristic curve (AUC). Among 824 patients with Gram-negative BSI, 143 (17%) had BSI due to fluoroquinolone-nonsusceptible Gram-negative bacilli. Independent risk factors for FQ-R and point allocation in FQRS included male sex (adjusted odds ratio [aOR], 1.97; 95% confidence intervals [CI], 1.36 to 2.98; 1 point), diabetes mellitus (aOR, 1.54; 95% CI, 1.03 to 2.28; 1 point), residence at a skilled nursing facility (aOR, 2.28; 95% CI, 1.42 to 3.63; 2 points), outpatient procedure within 30 days (aOR, 3.68; 95% CI, 1.96 to 6.78; 3 points), prior fluoroquinolone use within 90 days (aOR, 7.87; 95% CI, 4.53 to 13.74; 5 points), or prior fluoroquinolone use within 91 to 180 days of BSI (aOR, 2.77; 95% CI, 1.17 to 6.16; 3 points). The AUC for both final logistic regression and FQRS models was 0.73. Patients with an FQRS of 0, 3, 5, or 8 had predicted probabilities of FQ-R of 6%, 22%, 39%, or 69%, respectively. The estimation of patient-specific risk of antimicrobial resistance using FQRS may improve empirical antimicrobial therapy and fluoroquinolone utilization in Gram-negative BSI. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Prediction of Fluoroquinolone Resistance in Gram-Negative Bacteria Causing Bloodstream Infections

    PubMed Central

    Dan, Seejil; Shah, Ansal; Justo, Julie Ann; Bookstaver, P. Brandon; Kohn, Joseph; Albrecht, Helmut

    2016-01-01

    Increasing rates of fluoroquinolone resistance (FQ-R) have limited empirical treatment options for Gram-negative infections, particularly in patients with severe beta-lactam allergy. This case-control study aims to develop a clinical risk score to predict the probability of FQ-R in Gram-negative bloodstream isolates. Adult patients with Gram-negative bloodstream infections (BSI) hospitalized at Palmetto Health System in Columbia, South Carolina, from 2010 to 2013 were identified. Multivariate logistic regression was used to identify independent risk factors for FQ-R. Point allocation in the fluoroquinolone resistance score (FQRS) was based on regression coefficients. Model discrimination was assessed by the area under receiver operating characteristic curve (AUC). Among 824 patients with Gram-negative BSI, 143 (17%) had BSI due to fluoroquinolone-nonsusceptible Gram-negative bacilli. Independent risk factors for FQ-R and point allocation in FQRS included male sex (adjusted odds ratio [aOR], 1.97; 95% confidence intervals [CI], 1.36 to 2.98; 1 point), diabetes mellitus (aOR, 1.54; 95% CI, 1.03 to 2.28; 1 point), residence at a skilled nursing facility (aOR, 2.28; 95% CI, 1.42 to 3.63; 2 points), outpatient procedure within 30 days (aOR, 3.68; 95% CI, 1.96 to 6.78; 3 points), prior fluoroquinolone use within 90 days (aOR, 7.87; 95% CI, 4.53 to 13.74; 5 points), or prior fluoroquinolone use within 91 to 180 days of BSI (aOR, 2.77; 95% CI, 1.17 to 6.16; 3 points). The AUC for both final logistic regression and FQRS models was 0.73. Patients with an FQRS of 0, 3, 5, or 8 had predicted probabilities of FQ-R of 6%, 22%, 39%, or 69%, respectively. The estimation of patient-specific risk of antimicrobial resistance using FQRS may improve empirical antimicrobial therapy and fluoroquinolone utilization in Gram-negative BSI. PMID:26833166

  1. Application of empirical predictive modeling using conventional and alternative fecal indicator bacteria in eastern North Carolina waters.

    PubMed

    Gonzalez, Raul A; Conn, Kathleen E; Crosswell, Joseph R; Noble, Rachel T

    2012-11-15

    Coastal and estuarine waters are the site of intense anthropogenic influence with concomitant use for recreation and seafood harvesting. Therefore, coastal and estuarine water quality has a direct impact on human health. In eastern North Carolina (NC) there are over 240 recreational and 1025 shellfish harvesting water quality monitoring sites that are regularly assessed. Because of the large number of sites, sampling frequency is often only on a weekly basis. This frequency, along with an 18-24 h incubation time for fecal indicator bacteria (FIB) enumeration via culture-based methods, reduces the efficiency of the public notification process. In states like NC where beach monitoring resources are limited but historical data are plentiful, predictive models may offer an improvement for monitoring and notification by providing real-time FIB estimates. In this study, water samples were collected during 12 dry (n = 88) and 13 wet (n = 66) weather events at up to 10 sites. Statistical predictive models for Escherichiacoli (EC), enterococci (ENT), and members of the Bacteroidales group were created and subsequently validated. Our results showed that models for EC and ENT (adjusted R(2) were 0.61 and 0.64, respectively) incorporated a range of antecedent rainfall, climate, and environmental variables. The most important variables for EC and ENT models were 5-day antecedent rainfall, dissolved oxygen, and salinity. These models successfully predicted FIB levels over a wide range of conditions with a 3% (EC model) and 9% (ENT model) overall error rate for recreational threshold values and a 0% (EC model) overall error rate for shellfish threshold values. Though modeling of members of the Bacteroidales group had less predictive ability (adjusted R(2) were 0.56 and 0.53 for fecal Bacteroides spp. and human Bacteroides spp., respectively), the modeling approach and testing provided information on Bacteroidales ecology. This is the first example of a set of successful

  2. Monitoring and predicting the fecal indicator bacteria concentrations from agricultural, mixed land use and urban stormwater runoff.

    PubMed

    Paule-Mercado, M A; Ventura, J S; Memon, S A; Jahng, D; Kang, J-H; Lee, C-H

    2016-04-15

    While the urban runoff are increasingly being studied as a source of fecal indicator bacteria (FIB), less is known about the occurrence of FIB in watershed with mixed land use and ongoing land use and land cover (LULC) change. In this study, Escherichia coli (EC) and fecal streptococcus (FS) were monitored from 2012 to 2013 in agricultural, mixed and urban LULC and analyzed according to the most probable number (MPN). Pearson correlation was used to determine the relationship between FIB and environmental parameters (physicochemical and hydrometeorological). Multiple linear regressions (MLR) were used to identify the significant parameters that affect the FIB concentrations and to predict the response of FIB in LULC change. Overall, the FIB concentrations were higher in urban LULC (EC=3.33-7.39; FS=3.30-7.36log10MPN/100mL) possibly because of runoff from commercial market and 100% impervious cover (IC). Also, during early-summer season; this reflects a greater persistence and growth rate of FIB in a warmer environment. During intra-event, however, the FIB concentrations varied according to site condition. Anthropogenic activities and IC influenced the correlation between the FIB concentrations and environmental parameters. Stormwater temperature (TEMP), turbidity, and TSS positively correlated with the FIB concentrations (p>0.01), since IC increased, implying an accumulation of bacterial sources in urban activities. TEMP, BOD5, turbidity, TSS, and antecedent dry days (ADD) were the most significant explanatory variables for FIB as determined in MLR, possibly because they promoted the FIB growth and survival. The model confirmed the FIB concentrations: EC (R(2)=0.71-0.85; NSE=0.72-0.86) and FS (R(2)=0.65-0.83; NSE=0.66-0.84) are predicted to increase due to urbanization. Therefore, these findings will help in stormwater monitoring strategies, designing the best management practice for FIB removal and as input data for stormwater models.

  3. Prediction of infection due to antibiotic-resistant bacteria by select risk factors for health care-associated pneumonia.

    PubMed

    Shorr, Andrew F; Zilberberg, Marya D; Micek, Scott T; Kollef, Marin H

    2008-11-10

    Pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa now cause pneumonia in patients presenting to the hospital. The concept of health care-associated pneumonia (HCAP) attempts to capture this, but its predictive value is unclear. We examined patients admitted with pneumonia; infection with a resistant pathogen served as the study end point. Health care-associated pneumonia was present if a patient met one of the following criteria: recent hospitalization, nursing home residence, long-term hemodialysis, or immunosuppression. We compared rates of resistant infection among patients meeting any criteria for HCAP with those who did not have HCAP and explored the individual components of the definition. Among the cohort (n = 639), resistant pathogens were recovered in 289 (45.2%). Although each component of HCAP occurred more frequently in persons with resistant infections, the broad definition had a specificity of only 48.6% and misclassified one-third of the subjects. Logistic regression showed 4 variables associated with resistant pneumonia: recent hospitalization, nursing home residence, hemodialysis, and intensive care unit admission. A scoring system assigning 4, 3, 2, and 1 points, respectively, for each variable had moderate predictive power for segregating those with and without resistant bacteria. Among patients with fewer than 3 points, the prevalence of resistant pathogens was less than 20% compared with 55% and more than 75% in persons with scores ranging from 3 to 5 and more than 5 points, respectively (P < .001). Although resistance is common in HCAP, not all component criteria for HCAP convey similar risk. Simple scoring tools may facilitate more accurate identification of persons with pneumonia caused by resistant pathogens.

  4. Activation of mitochondrial promoter P{sub H}-binding protein in a radio-resistant Chinese hamster cell strain associated with Bcl-2

    SciTech Connect

    Roychoudhury, Paromita; Ghosh, Utpal . E-mail: keyachaudhuri@yahoo.com

    2006-11-17

    The cellular response to ionizing radiation is mediated by a complex interaction of number of proteins involving different pathways. Previously, we have shown that up regulation of mitochondrial genes ND1, ND4, and COX1 transcribed from the heavy strand promoter (P{sub H}) has been increased in a radio-resistant cell strain designated as M5 in comparison with the parental Chinese hamster V79 cells. These genes are also up regulated in Chinese hamster V79 cells VB13 that express exogenous human Bcl2. In the present study, the expression of the gene ND6 that is expressed from the light strand promoter (P{sub L}) was found to be similar in both the cell lines, as determined by RT-PCR. To test the possibility that this differential expression of mitochondrial genes under these two promoters was mediated by differences in proteins' affinity to interact with these promoters, we have carried out electrophoretic mobility shift assay (EMSA) using mitochondrial cell extracts from these two cell lines. Our result of these experiments revealed that two different proteins formed complex with the synthetic promoters and higher amount of protein from M5 cell extracts interacted with the P{sub H} promoter in comparison to that observed with cell extracts from Chinese hamster V79 cells. The promoter-specific differential binding of proteins was also observed in VB13. These results showed that differential mitochondrial gene expression observed earlier in the radio-resistant M5 cells was due to enhanced interaction proteins with the promoters P{sub H} and mediated by the expression of Bcl2.

  5. HPV-E6 protein enriches the CD55(+) population in cervical cancer cells promoting radio-resistance and cancer aggressiveness.

    PubMed

    Leung, Thomas Ho-Yin; Tang, Hermit Wai-Man; Siu, Michelle Kwan-Yee; Chan, David Wai; Chan, Karen Kar-Loen; Cheung, Annie Nga-Yin; Ngan, Hextan Yuen-Sheung

    2017-09-25

    Accumulating evidence indicates that the human papilloma virus (HPV) E6 protein plays a crucial role in the development of cervical cancer. Sub-populations of cells that reside within tumors are responsible for tumor resistance to cancer therapy and recurrence. However, the identity of such cells residing in cervical cancer and their relationship with the HPV-E6 protein have not been identified. Here, we isolated sphere-forming cells, which exhibited self-renewal ability, from primary cervical tumors. Gene expression profiling revealed that CD55 was upregulated in primary cervical cancer sphere cells. Flow cytometric analysis detected abundant CD55(+) populations among a panel of HPV-positive cervical cancer cell lines, while only few CD55(+) cells were found in HPV-negative cervical cancer and normal cervical epithelial cell lines. The isolated CD55(+) sub-population from the C33A cell line exhibited significant sphere-forming ability and enhanced tumorigenicity, cell migration and radio-resistance. In contrast, the suppression of CD55 in HPV-positive CaSki cells inhibited tumorigenicity both in vitro and in vivo and sensitized cells to irradiation treatment. In addition, ectopic expression of HPV-E6 in HPV-negative cervical cancer cells dramatically enriched the CD55(+) sub-population. CRISPR/Cas9 knockout of the CD55 gene in an HPV-E6-overexpressing stable clone abolished the tumorigenic properties exerted by HPV-E6. Taken together, our data suggest that HPV-E6 protein expression enriches the CD55(+) population, which contributes to tumorigenicity and radio-resistance in cervical cancer cells. Targeting CD55 via CRISPR/Cas9 may represent a novel avenue for developing new strategies and effective therapies for the treatment of cervical cancer. This article is protected by copyright. All rights reserved.

  6. Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

    PubMed Central

    Martínez-del Campo, Ana; Bodea, Smaranda; Hamer, Hilary A.; Marks, Jonathan A.; Haiser, Henry J.; Turnbaugh, Peter J.

    2015-01-01

    ABSTRACT Elucidation of the molecular mechanisms underlying the human gut microbiota’s effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis and in vitro biochemical characterization of two cut gene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that the cut cluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessed cutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective. PMID:25873372

  7. Inter- and intra-cellular mechanism of NF-kB-dependent survival advantage and clonal expansion of radio-resistant cancer cells.

    PubMed

    Yu, Hui; Aravindan, Natarajan; Xu, Ji; Natarajan, Mohan

    2017-02-01

    Understanding the underlying mechanism by which cancer cells acquire resistance to radiation and favorably selected for its clonal expansion will provide molecular insight into tumor recurrence at the treatment site. In the present study, we investigated the molecular mechanisms prompted in MCF-7 breast cancer cells in response to clinical radiation and the associated coordination of intra- and inter-cellular signaling that orchestrate radio-resistance and tumor relapse/recurrence. Our findings showed that 2 or 10Gy of (137)Cs γ-rays at a dose rate of 1.03Gy/min trigger the activation of nuclear factor kappa B (NF-κB), its DNA-binding activity and recycles its own transcription. NF-κB DNA-binding kinetic analysis demonstrated both sustained and dual phase NF-κB activation with radiation. Gene manipulation approach revealed that radiation triggered NF-κB-mediated TNF-α transcriptional activity. TNF-α blocking approach confirmed that the de novo synthesis and secretion of TNF-α serves as a pre-requisite for the second phase of NF-κB activation and sustained maintenance. Radiation-associated NF-κB-dependent secretion of TNF-α from irradiated cells, in parallel, activates NF-κB in the non-targeted un-irradiated bystander cells. Together, these findings demonstrated that radiation-triggered NF-κB-dependent TNFα secretion is critical for self-sustenance of NF-κB (through autocrine positive feedback signaling) and for coordinating bystander response (through inter-cellular paracrine mechanism) after radiation exposure. Further, the data suggest that this self-sustained NF-κB in the irradiated cells determines radio-resistance, survival advantage and clonal expansion of the tumor cells at the treatment site. Parallel maintenance of NF-ΚB-TNF-α-NF-κB feedback-cycle in the un-irradiated non-targeted bystander cells initiates supportive mechanism for the promotion and progression of surviving tumor cells. Intervening this molecular pathway would help us to

  8. Predictive factors for the development of central line-associated bloodstream infection due to gram-negative bacteria in intensive care unit patients after surgery.

    PubMed

    Sreeramoju, Pranavi V; Tolentino, Jocelyn; Garcia-Houchins, Sylvia; Weber, Stephen G

    2008-01-01

    To examine the relative proportions of central line-associated bloodstream infection (BSI) due to gram-negative bacteria and due to gram-positive bacteria among patients who had undergone surgery and patients who had not. The study also evaluated clinical predictive factors and unadjusted outcomes associated with central line-associated BSI caused by gram-negative bacteria in the postoperative period. Observational, case-control study based on a retrospective review of medical records. University of Chicago Medical Center, a 500-bed tertiary care center located on Chicago's south side. Adult intensive care unit (ICU) patients who developed central line-associated BSI. There were a total of 142 adult patients who met the Centers for Disease Control and Prevention National Nosocomial Infection Surveillance System definition for central line-associated BSI. Of those, 66 patients (46.5%) had infections due to gram-positive bacteria, 49 patients (34.5%) had infections due to gram-negative bacteria, 23 patients (16.2%) had infections due to yeast, and 4 patients (2.8%) had mixed infections. Patients who underwent surgery were more likely to develop central line-associated BSI due to gram-negative bacteria within 28 days of the surgery, compared with patients who had not had surgery recently (57.6% vs 27.3%; P= .002). On multivariable logistic regression analysis, diabetes mellitus (adjusted odds ratio [OR], 4.6 [95% CI, 1.2-18.1]; P= .03) and the presence of hypotension at the time of the first blood culture positive for a pathogen (adjusted OR, 9.8 [95% CI, 2.5-39.1]; P= .001) were found to be independently predictive of central line-associated BSI caused by gram-negative bacteria. Unadjusted outcomes were not different in the group with BSI due to gram-negative pathogens, compared to the group with BSI due to gram-positive pathogens. Clinicians caring for critically ill patients after surgery should be especially concerned about the possibility of central line

  9. Anaerobic bacteria

    MedlinePlus

    Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Goldstein EJ. Diseases caused by non-spore forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman's Cecil ...

  10. Empirical prediction and validation of antibacterial inhibitory effects of various plant essential oils on common pathogenic bacteria.

    PubMed

    Akdemir Evrendilek, Gulsun

    2015-06-02

    In this study, fractional compound composition, antioxidant capacity, and phenolic substance content of 14 plant essential oils-anise (Pimpinella anisum), bay leaves (Laurus nobilis), cinnamon bark (Cinnamomum verum), clove (Eugenia caryophyllata), fennel (Foeniculum vulgare), hop (Humulus lupulus), Istanbul oregano (Origanum vulgare subsp. hirtum), Izmir oregano (Origanum onites), mint (Mentha piperita), myrtus (Myrtus communis), orange peel (Citrus sinensis), sage (Salvia officinalis), thyme (Thymbra spicata), and Turkish oregano (Origanum minutiflorum)--were related to inhibition of 10 bacteria through multiple linear or non-linear (M(N)LR) models-four Gram-positive bacteria of Listeria innocua, coagulase-negative staphylococci, Staphylococcus aureus, and Bacillus subtilis, and six Gram-negative bacteria of Yersinia enterocolitica, Salmonella Enteritidis, Salmonella Typhimurium, Proteus mirabilis, Escherichia coli O157:H7, and Klebsiella oxytoca. A total of 65 compounds with different antioxidant capacity, phenolic substance content and antibacterial properties were detected with 14 plant essential oils. The best-fit M(N)LR models indicated that relative to anise essential oil, the essential oils of oreganos, cinnamon, and thyme had consistently high inhibitory effects, while orange peel essential oil had consistently a low inhibitory effect. Regression analysis indicated that beta-bisabolene (Turkish and Istanbul oreganos), and terpinolene (thyme) were found to be the most inhibitory compounds regardless of the bacteria type tested. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

    PubMed Central

    Hapfelmeier, Siegfried; Freedrich, Susanne; Weber, Thomas C.; Kirundi, Jorum; Suar, Mrutyunjay; McCoy, Kathy D.; von Mering, Christian; Macpherson, Andrew J.; Hardt, Wolf-Dietrich

    2010-01-01

    The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCMcon21). 16S rRNA sequence analysis comparing LCM, LCMcon21 and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri RR strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut

  12. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.

    PubMed

    Stecher, Bärbel; Chaffron, Samuel; Käppeli, Rina; Hapfelmeier, Siegfried; Freedrich, Susanne; Weber, Thomas C; Kirundi, Jorum; Suar, Mrutyunjay; McCoy, Kathy D; von Mering, Christian; Macpherson, Andrew J; Hardt, Wolf-Dietrich

    2010-01-01

    The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCM(con21)). 16S rRNA sequence analysis comparing LCM, LCM(con21) and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri(RR) strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut

  13. AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria.

    PubMed

    Park, Sun-Yang; Lee, Sang Jun; Oh, Tae-Kwang; Oh, Jong-Won; Koo, Bon-Tag; Yum, Do-Young; Lee, Jung-Kee

    2003-06-01

    Quorum sensing is a signalling mechanism that controls diverse biological functions, including virulence, via N-acylhomoserine lactone (AHL) signal molecules in Gram-negative bacteria. With the aim of isolating strains or enzymes capable of blocking quorum sensing by inactivating AHL, bacteria were screened for AHL degradation by their ability to utilize N-3-oxohexanoyl-L-homoserine lactone (OHHL) as the sole carbon source. Among four isolates, strain IBN110, identified as Arthrobacter sp., was found to grow rapidly on OHHL, and to degrade various AHLs with different lengths and acyl side-chain substitutions. Co-culture of Arthrobacter sp. IBN110 and the plant pathogen Erwinia carotovora significantly reduced both the AHL amount and pectate lyase activity in co-culture medium, suggesting the possibility of applying Arthrobacter sp. IBN110 in the control of AHL-producing pathogenic bacteria. The ahlD gene from Arthrobacter sp. IBN110 encoding the enzyme catalysing AHL degradation was cloned, and found to encode a protein of 273 amino acids. A mass spectrometry analysis showed that AhlD probably hydrolyses the lactone ring of N-3-hexanoyl-L-homoserine lactone, indicating that AhlD is an N-acylhomoserine lactonase (AHLase). A comparison of AhlD with other known AHL-degrading enzymes, Bacillus sp. 240B1 AiiA, a Bacillus thuringiensis subsp. kyushuensis AiiA homologue and Agrobacterium tumefaciens AttM, revealed 25, 26 and 21 % overall identities, respectively, in the deduced amino acid sequences. Although these identities were relatively low, the HXDH approximately H approximately D motif was conserved in all the AHLases, suggesting that this motif is essential for AHLase activity. From a genome database search based on the conserved motif, putative AhlD-like lactonase genes were found in several other bacteria, and AHL-degrading activities were observed in Klebsiella pneumoniae and Bacillus stearothermophilus. Furthermore, it was verified that ahlK, an ahlD homologue

  14. A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

    PubMed Central

    Kulkarni, Prajna R.; Jia, Tao; Kuehne, Sarah A.; Kerkering, Thomas M.; Morris, Elizabeth R.; Searle, Mark S.; Heeb, Stephan; Rao, Jayasimha; Kulkarni, Rahul V.

    2014-01-01

    CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA_TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA. We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins. PMID:24782516

  15. A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa.

    PubMed

    Kulkarni, Prajna R; Jia, Tao; Kuehne, Sarah A; Kerkering, Thomas M; Morris, Elizabeth R; Searle, Mark S; Heeb, Stephan; Rao, Jayasimha; Kulkarni, Rahul V

    2014-06-01

    CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA_TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA. We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

    PubMed

    Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël; Willison, John C; Lenski, Richard E; Soyer, Orkun S; Schneider, Dominique

    2016-08-20

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.

  17. Predicting the concentration of verotoxin-producing Escherichia coli bacteria during processing and storage of fermented raw-meat sausages.

    PubMed

    Quinto, E J; Arinder, P; Axelsson, L; Heir, E; Holck, A; Lindqvist, R; Lindblad, M; Andreou, P; Lauzon, H L; Marteinsson, V Þ; Pin, C

    2014-05-01

    A model to predict the population density of verotoxigenic Escherichia coli (VTEC) throughout the elaboration and storage of fermented raw-meat sausages (FRMS) was developed. Probabilistic and kinetic measurement data sets collected from publicly available resources were completed with new measurements when required and used to quantify the dependence of VTEC growth and inactivation on the temperature, pH, water activity (aw), and concentration of lactic acid. Predictions were compared with observations in VTEC-contaminated FRMS manufactured in a pilot plant. Slight differences in the reduction of VTEC were predicted according to the fermentation temperature, 24 or 34°C, with greater inactivation at the highest temperature. The greatest reduction was observed during storage at high temperatures. A population decrease greater than 6 decimal logarithmic units was observed after 66 days of storage at 25°C, while a reduction of only ca. 1 logarithmic unit was detected at 12°C. The performance of our model and other modeling approaches was evaluated throughout the processing of dry and semidry FRMS. The greatest inactivation of VTEC was predicted in dry FRMS with long drying periods, while the smallest reduction was predicted in semidry FMRS with short drying periods. The model is implemented in a computing tool, E. coli SafeFerment (EcSF), freely available from http://www.ifr.ac.uk/safety/EcoliSafeFerment. EcSF integrates growth, probability of growth, and thermal and nonthermal inactivation models to predict the VTEC concentration throughout FRMS manufacturing and storage under constant or fluctuating environmental conditions.

  18. Predicting the Concentration of Verotoxin-Producing Escherichia coli Bacteria during Processing and Storage of Fermented Raw-Meat Sausages

    PubMed Central

    Quinto, E. J.; Arinder, P.; Axelsson, L.; Heir, E.; Holck, A.; Lindqvist, R.; Lindblad, M.; Andreou, P.; Lauzon, H. L.; Marteinsson, V. Þ.

    2014-01-01

    A model to predict the population density of verotoxigenic Escherichia coli (VTEC) throughout the elaboration and storage of fermented raw-meat sausages (FRMS) was developed. Probabilistic and kinetic measurement data sets collected from publicly available resources were completed with new measurements when required and used to quantify the dependence of VTEC growth and inactivation on the temperature, pH, water activity (aw), and concentration of lactic acid. Predictions were compared with observations in VTEC-contaminated FRMS manufactured in a pilot plant. Slight differences in the reduction of VTEC were predicted according to the fermentation temperature, 24 or 34°C, with greater inactivation at the highest temperature. The greatest reduction was observed during storage at high temperatures. A population decrease greater than 6 decimal logarithmic units was observed after 66 days of storage at 25°C, while a reduction of only ca. 1 logarithmic unit was detected at 12°C. The performance of our model and other modeling approaches was evaluated throughout the processing of dry and semidry FRMS. The greatest inactivation of VTEC was predicted in dry FRMS with long drying periods, while the smallest reduction was predicted in semidry FMRS with short drying periods. The model is implemented in a computing tool, E. coli SafeFerment (EcSF), freely available from http://www.ifr.ac.uk/safety/EcoliSafeFerment. EcSF integrates growth, probability of growth, and thermal and nonthermal inactivation models to predict the VTEC concentration throughout FRMS manufacturing and storage under constant or fluctuating environmental conditions. PMID:24561587

  19. Impact of TiO₂ and ZnO nanoparticles at predicted environmentally relevant concentrations on ammonia-oxidizing bacteria cultures under ammonia oxidation.

    PubMed

    Luo, Zhuanxi; Qiu, Zhaozheng; Chen, Zheng; Du Laing, Gijs; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Increased application of titanium dioxide and zinc oxide nanoparticles (nano-TiO2 and nano-ZnO) raises concerns related to their environmental impacts. The effects that such nanoparticles have on environmental processes and the bacteria that carry them out are largely unknown. In this study, ammonia-oxidizing bacteria (AOB) enrichment cultures, grown from surface sediments taken from an estuary wetland in Fujian Province, China, were spiked with nano-TiO2 and nano-ZnO (with an average size of 32 and 43 nm, respectively) at predicted environmentally relevant concentrations (≤2 mg L(-1)) to determine their impacts on ammonia oxidation and the mechanisms involved. Results showed that higher nano-TiO2 concentrations significantly inhibited ammonia oxidation in enrichment cultures. It is noteworthy that the average ammonia oxidation rate was significantly correlated to the Shannon index, the Simpson's index, and AOB abundance. This suggested that ammonia oxidation inhibition primarily resulted from a reduction of AOB biodiversity and abundance. However, AOB biodiversity and abundance as well as the average ammonia oxidation rate were not inhibited by nano-ZnO at predicted environmentally relevant concentrations. Accordingly, an insignificant correlation was established between biodiversity and abundance of the AOB amoA gene and the average ammonia oxidation rate under nano-ZnO treatments. AOB present in samples belonged to the β-Proteobacteria class with an affinity close to Nitrosospira and Nitrosomonas genera. This suggested that identified impacts of nano-TiO2 and nano-ZnO on ammonia oxidation processes can be extrapolated to some extent to natural aquatic environments. Complex impacts on AOB may result from different nanomaterials present in aquatic environments at various ambient conditions. Further investigation on how and to what extent different nanomaterials influence AOB diversity and abundance and their subsequent ammonia oxidation processes is therefore

  20. Predicting late-onset sepsis by routine neonatal screening for colonisation by gram-negative bacteria in neonates at intensive care units: a protocol for a systematic review

    PubMed Central

    Harder, Thomas; Seidel, Juliane; Eckmanns, Tim; Weiss, Bettina; Haller, Sebastian

    2017-01-01

    Introduction Hospitals conduct extensive screening procedures to assess colonisation of the body surface of neonates by gram-negative bacteria to avoid complications like late-onset sepsis. However, the benefits of these procedures are controversially discussed. Until now, no systematic review has investigated the value of routine screening for colonisation by gram-negative bacteria in neonates for late-onset sepsis prediction. Methods and analysis We will conduct a systematic review, considering studies of any design that include infants up to an age of 12 months. We will search MEDLINE and EMBASE (inception to 2016), reference lists and grey literature. Screening of titles, abstracts and full texts will be conducted by two independent reviewers. We will extract data on study characteristics and study results. Risk of bias will be assessed using Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) and Quality in Prognosis Studies (QUIPS) tools. Subgroup analyses are planned according to characteristics of studies, participants, index tests and outcome. For quantitative data synthesis on prognostic accuracy, sensitivity and specificity of screening to detect late-onset sepsis will be calculated. If sufficient data are available, we will calculate summary estimates using hierarchical summary receiver operating characteristics and bivariate models. Applying a risk factor approach, pooled summary estimates will be calculated as relative risk or OR, using fixed-effects and random-effects models. I-squared will be used to assess heterogeneity. All calculations will be performed in Stata V14.1 (College Station, Texas, USA). The results will be used to calculate positive and negative predictive value and number needed to be screened to prevent one case of sepsis. Grading of Recommendations Assessment, Development and Evaluation (GRADE) will be used to assess certainty in the evidence. The protocol follows the Preferred Reporting Items for Systematic Review and

  1. Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

    PubMed Central

    2012-01-01

    Background Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. Results To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be

  2. Antibiotic resistance in bacteria isolated from freshwater aquacultures and prediction of the persistence and toxicity of antimicrobials in the aquatic environment.

    PubMed

    Lim, Seung J; Jang, Eunhee; Lee, Sang-Hun; Yoo, Byeong-Hak; Kim, Sun-Kyoung; Kim, Tak-Hyun

    2013-01-01

    The occurrence of antibiotic-resistant bacteria isolated from freshwater aquaculture effluents was investigated. The bacterial strains were collected from four different freshwater aquaculture effluents (catfish, trout, eel, and loach). Based on sequence of 16S rRNA, a total of 20 bacterial strains was isolated and one half of the isolated bacteria were Aeromonas sp. The antimicrobial sensitivity test was performed using the disc diffusion method. Individual antibiotic-resistant bacteria to antimicrobials were 41.7% and multiple antibiotic resistant bacteria were 58.3%. The disinfection of antibiotic-resistant bacteria by electron beam (E-beam) irradiation was carried out using an electron accelerator. Antibiotic-resistant bacteria were effectively disinfected by E-beam irradiation. The isolated bacteria were completely disinfected at a dose of less than 2 kGy. The persistence and toxicity of each antimicrobial in the aquatic environment was estimated due to the human health and ecosystems. In order to estimate the persistence and toxicity of antimicrobials in the aquatic environment, two quantitative structure activity relationship (QSAR) models were used. The persistence and toxicity of each antimicrobial were influenced on its hydrophobicity. In addition, QSAR models showed that isoelectric point and hydrogen bonding acceptor are key parameters to estimate the persistence and toxicity of antimicrobials in the aquatic environment.

  3. Magnetic Bacteria.

    ERIC Educational Resources Information Center

    Nelson, Jane Bray; Nelson, Jim

    1992-01-01

    Describes the history of Richard Blakemore's discovery of magnetotaxic organisms. Discusses possible reasons why the magnetic response in bacteria developed. Proposes research experiments integrating biology and physics in which students investigate problems using cultures of magnetotaxic organisms. (MDH)

  4. Methanotrophic bacteria.

    PubMed Central

    Hanson, R S; Hanson, T E

    1996-01-01

    Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

  5. Bacteria Counter

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Science Applications, Inc.'s ATP Photometer makes a rapid and accurate count of the bacteria in a body fluid sample. Instrument provides information on the presence and quantity of bacteria by measuring the amount of light emitted by the reaction between two substances. Substances are ATP adenosine triphosphate and luciferase. The reactants are applied to a human body sample and the ATP Photometer observes the intensity of the light emitted displaying its findings in a numerical output. Total time lapse is usually less than 10 minutes, which represents a significant time savings in comparison of other techniques. Other applications are measuring organisms in fresh and ocean waters, determining bacterial contamination of foodstuffs, biological process control in the beverage industry, and in assay of activated sewage sludge.

  6. Nutritional Similarity between Leaf-Associated Nonpathogenic Bacteria and the Pathogen Is Not Predictive of Efficacy in Biological Control of Bacterial Spot of Tomato

    PubMed Central

    Dianese, Alexei C.; Ji, Pingsheng; Wilson, Mark

    2003-01-01

    It has been demonstrated that for a nonpathogenic, leaf-associated bacterium, effectiveness in the control of bacterial speck of tomato is correlated with the similarity in the nutritional needs of the nonpathogenic bacterium and the pathogen Pseudomonas syringae pv. tomato. This relationship was investigated further in this study by using the pathogen Xanthomonas campestris pv. vesicatoria, the causal agent of bacterial spot of tomato, and a collection of nonpathogenic bacteria isolated from tomato foliage. The effects of inoculation of tomato plants with one of 34 nonpathogenic bacteria prior to inoculation with the pathogen X. campestris pv. vesicatoria were quantified by determining (i) the reduction in disease severity (number of lesions per square centimeter) in greenhouse assays and (ii) the reduction in leaf surface pathogen population size (log10 of the number of CFU per leaflet) in growth chamber assays. Nutritional similarity between the nonpathogenic bacteria and X. campestris pv. vesicatoria was quantified by using either niche overlap indices (NOI) or relatedness in cluster analyses based upon in vitro utilization of carbon or nitrogen sources reported to be present in tomato tissues or in Biolog GN plates. In contrast to studies with P. syringae pv. tomato, nutritional similarity between the nonpathogenic bacteria and the pathogen X. campestris pv. vesicatoria was not correlated with reductions in disease severity. Nutritional similarity was also not correlated with reductions in pathogen population size. Further, the percentage of reduction in leaf surface pathogen population size was not correlated with the percentage of reduction in disease severity, suggesting that the epiphytic population size of X. campestris pv. vesicatoria is not related to disease severity and that X. campestris pv. vesicatoria exhibits behavior in the phyllosphere prior to lesion formation that is different from that of P. syringae pv. tomato. PMID:12788754

  7. Extensively drug-resistant bacteria are an independent predictive factor of mortality in 130 patients with spontaneous bacterial peritonitis or spontaneous bacteremia

    PubMed Central

    Alexopoulou, Alexandra; Vasilieva, Larisa; Agiasotelli, Danai; Siranidi, Kyriaki; Pouriki, Sophia; Tsiriga, Athanasia; Toutouza, Marina; Dourakis, Spyridon P

    2016-01-01

    AIM: To evaluate the epidemiology and outcomes of culture-positive spontaneous bacterial peritonitis (SBP) and spontaneous bacteremia (SB) in decompensated cirrhosis. METHODS: We prospectively collected clinical, laboratory characteristics, type of administered antibiotic, susceptibility and resistance of bacteria to antibiotics in one hundred thirty cases (68.5% males) with positive ascitic fluid and/or blood cultures during the period from January 1, 2012 to May 30, 2014. All patients with SBP had polymorphonuclear cell count in ascitic fluid > 250/mm3. In patients with SB a thorough study did not reveal any other cause of bacteremia. The patients were followed-up for a 30-d period following diagnosis of the infection. The final outcome of the patients was recorded in the end of follow-up and comparison among 3 groups of patients according to the pattern of drug resistance was performed. RESULTS: Gram-positive-cocci (GPC) were found in half of the cases. The most prevalent organisms in a descending order were Escherichia coli (33), Enterococcus spp (30), Streptococcus spp (25), Klebsiella pneumonia (16), S. aureus (8), Pseudomanas aeruginosa (5), other Gram-negative-bacteria (GNB) (11) and anaerobes (2). Overall, 20.8% of isolates were multidrug-resistant (MDR) and 10% extensively drug-resistant (XDR). Health-care-associated (HCA) and/or nosocomial infections were present in 100% of MDR/XDR and in 65.5% of non-DR cases. Meropenem was the empirically prescribed antibiotic in HCA/nosocomial infections showing a drug-resistance rate of 30.7% while third generation cephalosporins of 43.8%. Meropenem was ineffective on both XDR bacteria and Enterococcus faecium (E. faecium). All but one XDR were susceptible to colistin while all GPC (including E. faecium) and the 86% of GNB to tigecycline. Overall 30-d mortality was 37.7% (69.2% for XDR and 34.2% for the rest of the patients) (log rank, P = 0.015). In multivariate analysis, factors adversely affecting outcome included

  8. Classification of antibiotic resistance patterns of indicator bacteria by discriminant analysis: use in predicting the source of fecal contamination in subtropical waters.

    PubMed

    Harwood, V J; Whitlock, J; Withington, V

    2000-09-01

    The antibiotic resistance patterns of fecal streptococci and fecal coliforms isolated from domestic wastewater and animal feces were determined using a battery of antibiotics (amoxicillin, ampicillin, cephalothin, chlortetracycline, oxytetracycline, tetracycline, erythromycin, streptomycin, and vancomycin) at four concentrations each. The sources of animal feces included wild birds, cattle, chickens, dogs, pigs, and raccoons. Antibiotic resistance patterns of fecal streptococci and fecal coliforms from known sources were grouped into two separate databases, and discriminant analysis of these patterns was used to establish the relationship between the antibiotic resistance patterns and the bacterial source. The fecal streptococcus and fecal coliform databases classified isolates from known sources with similar accuracies. The average rate of correct classification for the fecal streptococcus database was 62.3%, and that for the fecal coliform database was 63.9%. The sources of fecal streptococci and fecal coliforms isolated from surface waters were identified by discriminant analysis of their antibiotic resistance patterns. Both databases identified the source of indicator bacteria isolated from surface waters directly impacted by septic tank discharges as human. At sample sites selected for relatively low anthropogenic impact, the dominant sources of indicator bacteria were identified as various animals. The antibiotic resistance analysis technique promises to be a useful tool in assessing sources of fecal contamination in subtropical waters, such as those in Florida.

  9. Classification of Antibiotic Resistance Patterns of Indicator Bacteria by Discriminant Analysis: Use in Predicting the Source of Fecal Contamination in Subtropical Waters

    PubMed Central

    Harwood, Valerie J.; Whitlock, John; Withington, Victoria

    2000-01-01

    The antibiotic resistance patterns of fecal streptococci and fecal coliforms isolated from domestic wastewater and animal feces were determined using a battery of antibiotics (amoxicillin, ampicillin, cephalothin, chlortetracycline, oxytetracycline, tetracycline, erythromycin, streptomycin, and vancomycin) at four concentrations each. The sources of animal feces included wild birds, cattle, chickens, dogs, pigs, and raccoons. Antibiotic resistance patterns of fecal streptococci and fecal coliforms from known sources were grouped into two separate databases, and discriminant analysis of these patterns was used to establish the relationship between the antibiotic resistance patterns and the bacterial source. The fecal streptococcus and fecal coliform databases classified isolates from known sources with similar accuracies. The average rate of correct classification for the fecal streptococcus database was 62.3%, and that for the fecal coliform database was 63.9%. The sources of fecal streptococci and fecal coliforms isolated from surface waters were identified by discriminant analysis of their antibiotic resistance patterns. Both databases identified the source of indicator bacteria isolated from surface waters directly impacted by septic tank discharges as human. At sample sites selected for relatively low anthropogenic impact, the dominant sources of indicator bacteria were identified as various animals. The antibiotic resistance analysis technique promises to be a useful tool in assessing sources of fecal contamination in subtropical waters, such as those in Florida. PMID:10966379

  10. Bacteria swimming in circles

    NASA Astrophysics Data System (ADS)

    Lauga, Eric; Diluzio, Willow; Garstecki, Piotr; Whitesides, George; Stone, Howard

    2004-11-01

    The bacteria E.coli, which lives in our stomach, swims in a viscous fluid by rotating its flagella together in a helical bundle. The rotation is due to the action of rotary motors embedded in the cell wall. Motivated by experimental observations (Frymier et al., 1995, PNAS vol. 92), as well as our own extensive experiments, that bacteria near solid surfaces do not swim in a straight line but swim in circles, we present a mechanical model for a swimming microorganism near a solid boundary. We show that the combination of a rotating helical bundle and a solid boundary leads to a circular motion to the right of the bacterium (as viewed from above), in accordance with experimental observations. Values of the radii of the circle and the rotation rate are predicted and compared with experimental data.

  11. Modelling and predicting the simultaneous growth of Listeria monocytogenes and psychrotolerant lactic acid bacteria in processed seafood and mayonnaise-based seafood salads.

    PubMed

    Mejlholm, Ole; Dalgaard, Paw

    2015-04-01

    A new combined model for Listeria monocytogenes and psychrotolerant Lactobacillus spp. was constructed and evaluated for processed seafood and mayonnaise-based seafood salads. The new model was constructed by combining existing cardinal parameter models for L. monocytogenes and Lactobacillus spp. using the classical Jameson effect to model microbial interaction. Maximum population density (MPD) values of L. monocytogenes were accurately predicted in processed seafood with a known initial cell concentration of Lactobacillus spp. For these experiments, average MPD values of 4.5 and 4.3 log (cfu/g) were observed and predicted, respectively for L. monocytogenes. In seafood salads, growth of L. monocytogenes continued at a reduced growth rate after Lactobacillus sakei had reached their MPD. This growth pattern was successfully described by an expanded version of the classical Jameson effect model, but only for products with pH of 6.0 or higher. For seafood salads with pH below 6.0 the performance of the new model was unacceptable, primarily due to prediction of no-growth by L. monocytogenes when growth was actually observed. Within its range of applicability the new model can be valuable for risk assessment and risk management of processed seafood as well as for evaluating the compliance of products with the EU regulation for ready-to-eat foods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Sampling bacteria with a laser

    NASA Astrophysics Data System (ADS)

    Schwarzwälder, Kordula; Rutschmann, Peter

    2014-05-01

    Water quality is a topic of high interest and it's getting more and more important due to climate change and the implementation of European Water Framework Directive (WFD). One point of interest here is the inflow of bacteria into a river caused by combined sewer overflows which lead untreated wastewater including bacteria directly into a river. These bacteria remain in the river for a certain time, they settle down and can be remobilised again. In our study we want to investigate these processes of sedimentation and resuspension and use the results for the development of a software module coupled with the software Flow3D. Thereby we should be able to simulate and therefore predict the water quality influenced by combined sewer overflows. Hence we need to get information about the bacteria transport and fate. We need to know about the size of the bacteria or of the bacteria clumps and the size of the particles the bacteria are attached to. The agglomerates lead to different characteristics and velocities of settlement. The timespan during this bacteria can be detected in the bulk phase depends on many factors like the intensity of UV light, turbidity of the water, the temperature of the water, if there are grazers and a lot more. The size, density and composition of the agglomerates is just a part of all these influencing factors, but it is extremely difficult to differ between the other effects if we have no information about the simple sedimentation in default of these basic information. However we have a big problem getting the data. The chaining between bacteria or bacteria and particles is not too strong, so filtering the water to get a sieving curve may destroy these connections. We did some experiments similar to PIV (particle image velocimetry) measurements and evaluated the pictures with a macro written for the software ImageJ. Doing so we were able to get the concentration of bacteria in the water and collect information about the size of the bacteria. We

  13. Back To Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1997-01-01

    Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

  14. Back To Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1997-01-01

    Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

  15. Pepsin homologues in bacteria

    PubMed Central

    Rawlings, Neil D; Bateman, Alex

    2009-01-01

    Background Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has arisen from an ancient duplication and fusion event. The only sequence similarity between the lobes is restricted to the motif around the active site aspartate and a hydrophobic-hydrophobic-Gly motif. Together, these contribute to an essential structural feature known as a psi-loop. There is one such psi-loop in each lobe, and so each lobe presents an active Asp. The human immunodeficiency virus peptidase, retropepsin, from peptidase family A2 also has a similar fold but consists of one lobe only and has to dimerize to be active. All known members of family A1 show the bilobed structure, but it is unclear if the ancestor of family A1 was similar to an A2 peptidase, or if the ancestral retropepsin was derived from a half-pepsin gene. The presence of a pepsin homologue in a prokaryote might give insights into the evolution of the pepsin family. Results Homologues of the aspartic peptidase pepsin have been found in the completed genomic sequences from seven species of bacteria. The bacterial homologues, unlike those from eukaryotes, do not possess signal peptides, and would therefore be intracellular acting at neutral pH. The bacterial homologues have Thr218 replaced by Asp, a change which in renin has been shown to confer activity at neutral pH. No pepsin homologues could be detected in any archaean genome. Conclusion The peptidase family A1 is found in some species of bacteria as well as eukaryotes. The bacterial homologues fall into two groups, one from oceanic bacteria and one from plant symbionts. The bacterial homologues are all predicted to be intracellular proteins, unlike the eukaryotic enzymes. The bacterial homologues are bilobed like pepsin, implying that if no horizontal gene transfer has occurred the duplication and fusion event might be

  16. Predictive models for the effect of storage temperature on Vibrio parahaemolyticus viability and counts of total viable bacteria in Pacific oysters (Crassostrea gigas).

    PubMed

    Fernandez-Piquer, Judith; Bowman, John P; Ross, Tom; Tamplin, Mark L

    2011-12-01

    Vibrio parahaemolyticus is an indigenous bacterium of marine environments. It accumulates in oysters and may reach levels that cause human illness when postharvest temperatures are not properly controlled and oysters are consumed raw or undercooked. Predictive models were produced by injecting Pacific oysters (Crassostrea gigas) with a cocktail of V. parahaemolyticus strains, measuring viability rates at storage temperatures from 3.6 to 30.4°C, and fitting the data to a model to obtain parameter estimates. The models were evaluated with Pacific and Sydney Rock oysters (Saccostrea glomerata) containing natural populations of V. parahaemolyticus. V. parahaemolyticus viability was measured by direct plating samples on thiosulfate-citrate-bile salts-sucrose (TCBS) agar for injected oysters and by most probable number (MPN)-PCR for oysters containing natural populations. In parallel, total viable bacterial counts (TVC) were measured by direct plating on marine agar. Growth/inactivation rates for V. parahaemolyticus were -0.006, -0.004, -0.005, -0.003, 0.030, 0.075, 0.095, and 0.282 log₁₀ CFU/h at 3.6, 6.2, 9.6, 12.6, 18.4, 20.0, 25.7, and 30.4°C, respectively. The growth rates for TVC were 0.015, 0.023, 0.016, 0.048, 0.055, 0.071, 0.133, and 0.135 log₁₀ CFU/h at 3.6, 6.2, 9.3, 14.9, 18.4, 20.0, 25.7, and 30.4°C, respectively. Square root and Arrhenius-type secondary models were generated for V. parahaemolyticus growth and inactivation kinetic data, respectively. A square root model was produced for TVC growth. Evaluation studies showed that predictive growth for V. parahaemolyticus and TVC were "fail safe." The models can assist oyster companies and regulators in implementing management strategies to minimize V. parahaemolyticus risk and enhancing product quality in supply chains.

  17. Cultivation of bacteria with ecological capsules in space

    NASA Astrophysics Data System (ADS)

    Sugiura, K.; Hashimoto, H.; Ishikawa, Y.; Kawasaki, Y.; Kobayashi, K.; Seki, K.; Koike, J.; Saito, T.

    1999-01-01

    A hermetically materially-closed aquatic microcosm containing bacteria, algae, and invertebrates was developed as a tool for determining the changes of ecological systems in space. The species composition was maintained for more than 365 days. The microcosm could be readily replicated. The results obtained from the simulation models indicated that there is a self-regulation homeostasis in coupling of production and consumption, which make the microcosm remarkably stable, and that the transfer of metabolites by diffusion is one of the important factors determining the behavior of the system. The microcosms were continuously irradiated using a 60 Co source. After 80 days, no elimination of organisms was found at any of the three irradiation levels (0.015, 0.55 and 3.0 mGy/day). The number of radio-resistance bacteria mutants was not increased in the microcosm at three irradiation levels. We proposed to research whether this microcosm is self-sustainable in space. When an aquatic ecosystem comes under stress due to the micro-gravity and enhanced radiation environment in space, whether the ecosystem is self-sustainable is not known. An aquatic ecosystem shows what happens as a result of the self-organizational processes of selection and adaptation. A microcosm is a useful tool for understanding such processes. We have proposed researching whether a microcosm is self-sustainable in space. The benefits of this project will be: (1) To acquire data for design of a Controlled Ecological Life Support System, (2) Possibility of microbial mutation in a space station. We report that a hermetically materially-closed microcosm, which could be a useful tool for determining changes of ecological processes in space, was developed, and that the effects of microgravity and enhanced radiation on the hermetically materially-closed microcosm were estimated through measurements on the Earth and simulation models.

  18. Bacteria isolated from amoebae/bacteria consortium

    DOEpatents

    Tyndall, R.L.

    1995-05-30

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  19. Bacteria isolated from amoebae/bacteria consortium

    DOEpatents

    Tyndall, Richard L.

    1995-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  20. Bacteria Inactivation During Lithotripsy

    NASA Astrophysics Data System (ADS)

    del Sol Quintero, María; Mora, Ulises; Gutiérrez, Jorge; Mues, Enrique; Castaño, Eduardo; Fernández, Francisco; Loske, Achim M.

    2006-09-01

    The influence of extracorporeal and intracorporeal lithotripsy on the viability of bacteria contained inside artificial kidney stones was investigated in vitro. Two different bacteria were exposed to the action of one extracorporeal shock wave generator and four intracorporeal lithotripters.

  1. Bleach vs. Bacteria

    MedlinePlus

    ... Articles | Inside Life Science Home Page Bleach vs. Bacteria By Sharon Reynolds Posted April 2, 2014 Your ... hypochlorous acid to help kill invading microbes, including bacteria. Researchers funded by the National Institutes of Health ...

  2. Phenotypic switching in bacteria

    NASA Astrophysics Data System (ADS)

    Merrin, Jack

    Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

  3. Light scattering by marine heterotrophic bacteria

    NASA Technical Reports Server (NTRS)

    Ulloa, Osvaldo; Sathyendranath, Shubha; Platt, Trevor; Quinones, Renato A.

    1992-01-01

    Mie theory is applied to estimate scattering by polydispersions of marine heterotrophic bacteria, and a simple expression is derived for the bacterial scattering coefficient. The error incurred in deriving bacterial optical properties by use of the van de Hulst approximations is computed. The scattering properties of natural bacterial assemblages in three marine environments, Georges Bank, Northeast Channel, and Sargasso Sea, are assessed by applying Mie theory to field data on bacterial size and abundance. Results are used to examine the potential contribution of bacteria to the scattering properties of seawater. The utility of using pigment data to predict the magnitude of scattering by bacteria is discussed.

  4. Light scattering by marine heterotrophic bacteria

    NASA Technical Reports Server (NTRS)

    Ulloa, Osvaldo; Sathyendranath, Shubha; Platt, Trevor; Quinones, Renato A.

    1992-01-01

    Mie theory is applied to estimate scattering by polydispersions of marine heterotrophic bacteria, and a simple expression is derived for the bacterial scattering coefficient. The error incurred in deriving bacterial optical properties by use of the van de Hulst approximations is computed. The scattering properties of natural bacterial assemblages in three marine environments, Georges Bank, Northeast Channel, and Sargasso Sea, are assessed by applying Mie theory to field data on bacterial size and abundance. Results are used to examine the potential contribution of bacteria to the scattering properties of seawater. The utility of using pigment data to predict the magnitude of scattering by bacteria is discussed.

  5. Pathogenic bacteria and timing of laying

    PubMed Central

    Møller, Anders Pape; Soler, Juan J; Nielsen, Jan Tøttrup; Galván, Ismael

    2015-01-01

    Pathogenic bacteria constitute a serious threat to viability of many organisms. Because growth of most bacteria is favored by humid and warm environmental conditions, earlier reproducers in seasonal environments should suffer less from the negative consequences of pathogenic bacteria. These relationships, and the effects on reproductive success, should be particularly prominent in predators because they are frequently exposed to pathogenic microorganisms from sick prey. Here, we presented and tested this hypothesis by sampling bacteria on adult and nestling goshawks Accipiter gentilis. We predicted that early breeders and their offspring should have fewer bacteria than those reproducing later during the breeding season. Adult goshawks with a high abundance of Staphylococcus on their beak and claws were easier to capture and their laying date was delayed. Moreover, goshawks that laid their eggs later had offspring with more Staphylococcus on their beaks and claws. The strength of the association between laying date and bacterial density of nestlings was stronger during the warm spring of 2013, when nestlings suffered from a higher abundance of pathogenic bacteria. Hatching failure and fledging failure were more common in nests with a higher abundance of Staphylococcus independently of the number of years occupied, laying date, and age of the female nest owner. These findings imply that timing of reproduction may be under the influence of pathogenic bacteria. Because early breeding goshawks produce more recruits than later breeders, our results suggest a role for pathogenic bacteria in the optimal timing of reproduction. PMID:25937910

  6. Genomics of Probiotic Bacteria

    NASA Astrophysics Data System (ADS)

    O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

    Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

  7. Bacteria turn tiny gears

    SciTech Connect

    2009-01-01

    Swarms of bacteria turn two 380-micron long gears, opening the possibility of building hybrid biological machines at the microscopic scale. Read more at Wired: http://www.wired.com/wiredscience/2009/12/bacterial-micro-machine/#more-15684 or Scientific American: http://www.scientificamerican.com/article.cfm?id=brownian-motion-bacteria

  8. Some bacteria are beneficial!

    USGS Publications Warehouse

    McMahon, Peter B.

    1995-01-01

    Most people would agree that bacteria usually spell trouble where the quality of drinking water is con cerned. However, recent studies conducted by the U.S. Geological Survey (USGS) under the National Water-Quality Assessment (NAWQA) program have shown that some bacteria can improve the quality of water.

  9. Some bacteria are beneficial!

    USGS Publications Warehouse

    McMahon, Peter B.

    1995-01-01

    Most people would agree that bacteria usually spell trouble where the quality of drinking water is con cerned. However, recent studies conducted by the U.S. Geological Survey (USGS) under the National Water-Quality Assessment (NAWQA) program have shown that some bacteria can improve the quality of water.

  10. Basis of predictive mycology.

    PubMed

    Dantigny, Philippe; Guilmart, Audrey; Bensoussan, Maurice

    2005-04-15

    For over 20 years, predictive microbiology focused on food-pathogenic bacteria. Few studies concerned modelling fungal development. On one hand, most of food mycologists are not familiar with modelling techniques; on the other hand, people involved in modelling are developing tools dedicated to bacteria. Therefore, there is a tendency to extend the use of models that were developed for bacteria to moulds. However, some mould specificities should be taken into account. The use of specific models for predicting germination and growth of fungi was advocated previously []. This paper provides a short review of fungal modelling studies.

  11. Modeling heterotrophic bacteria in plumbing system of drinking water.

    PubMed

    Chowdhury, Shakhawat; Al-Zahrani, Muhammad

    2014-06-01

    This study investigated occurrences of heterotrophic (HPC) bacteria and developed predictive models for HPC bacteria in plumbing pipes (PP) and hot water tanks (HWT) of two houses in Dhahran (Saudi Arabia). Heterotrophic bacteria in PP and HWT were observed to be 2.4 to 5.3 and 0.4 to 5.9 times the HPC bacteria in water distribution system (WDS), respectively. Three linear, one nonlinear, and one neural network models were investigated to predict HPC bacteria in PP and HWT. Significant factors for bacteria regrowth in PP and HWT were identified through numerical and graphical techniques. The R2 values of the models varied between 0.57 and 0.96, indicating moderate to excellent predictive ability for HPC bacteria in PP and HWT. The models were found to be statistically significant, which were also validated using additional data. These models can be used to predict HPC bacteria regrowth from WDS to PP and HWT, and could help to predict exposure and risks.

  12. Subcellular localization based comparative study on radioresistant bacteria: A novel approach to mine proteins involve in radioresistance.

    PubMed

    Vishambra, Divya; Srivastava, Malay; Dev, Kamal; Jaiswal, Varun

    2017-08-01

    Radioresistant bacteria (RRB) are among the most radioresistant organisms and has a unique role in evolution. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-aging and anti-cancer treatment. The study of radiation resistance in RRB was mainly focused on cytosolic mechanisms such as DNA repair mechanism, cell cleansing activity and high antioxidant activity. Although it was known that protein localized on outer areas of cell play role in resistance towards extreme condition but the mechanisms/proteins localized on the outer area of cells are not studied for radioresistance. Considering the fact that outer part of cell is more exposed to radiations and proteins present in outer area of the cell may have role in radioresistance. Localization based comparative study of proteome from RRB and non-radio resistant bacteria was carried out. In RRB 20 unique proteins have been identified. Further domain, structural, and pathway analysis of selected proteins were carried out. Out of 20 proteins, 8 proteins were direct involvement in radioresistance and literature study strengthens this, however, 1 proteins had assumed relation in radioresistance. Selected radioresistant proteins may be helpful for optimal use of RRB in industry and health care. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Quorum sensing in bacteria.

    PubMed

    Miller, M B; Bassler, B L

    2001-01-01

    Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. These processes include symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. In general, Gram-negative bacteria use acylated homoserine lactones as autoinducers, and Gram-positive bacteria use processed oligo-peptides to communicate. Recent advances in the field indicate that cell-cell communication via autoinducers occurs both within and between bacterial species. Furthermore, there is mounting data suggesting that bacterial autoinducers elicit specific responses from host organisms. Although the nature of the chemical signals, the signal relay mechanisms, and the target genes controlled by bacterial quorum sensing systems differ, in every case the ability to communicate with one another allows bacteria to coordinate the gene expression, and therefore the behavior, of the entire community. Presumably, this process bestows upon bacteria some of the qualities of higher organisms. The evolution of quorum sensing systems in bacteria could, therefore, have been one of the early steps in the development of multicellularity.

  14. Inactivation of biofilm bacteria.

    PubMed Central

    LeChevallier, M W; Cawthon, C D; Lee, R G

    1988-01-01

    The current project was developed to examine inactivation of biofilm bacteria and to characterize the interaction of biocides with pipe surfaces. Unattached bacteria were quite susceptible to the variety of disinfectants tested. Viable bacterial counts were reduced 99% by exposure to 0.08 mg of hypochlorous acid (pH 7.0) per liter (1 to 2 degrees C) for 1 min. For monochloramine, 94 mg/liter was required to kill 99% of the bacteria within 1 min. These results were consistent with those found by other investigators. Biofilm bacteria grown on the surfaces of granular activated carbon particles, metal coupons, or glass microscope slides were 150 to more than 3,000 times more resistant to hypochlorous acid (free chlorine, pH 7.0) than were unattached cells. In contrast, resistance of biofilm bacteria to monochloramine disinfection ranged from 2- to 100-fold more than that of unattached cells. The results suggested that, relative to inactivation of unattached bacteria, monochloramine was better able to penetrate and kill biofilm bacteria than free chlorine. For free chlorine, the data indicated that transport of the disinfectant into the biofilm was a major rate-limiting factor. Because of this phenomenon, increasing the level of free chlorine did not increase disinfection efficiency. Experiments where equal weights of disinfectants were used suggested that the greater penetrating power of monochloramine compensated for its limited disinfection activity. These studies showed that monochloramine was as effective as free chlorine for inactivation of biofilm bacteria. The research provides important insights into strategies for control of biofilm bacteria. Images PMID:2849380

  15. Antibiotics from predatory bacteria

    PubMed Central

    Korp, Juliane; Vela Gurovic, María S

    2016-01-01

    Summary Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism. PMID:27340451

  16. Antibiotics from predatory bacteria.

    PubMed

    Korp, Juliane; Vela Gurovic, María S; Nett, Markus

    2016-01-01

    Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism.

  17. Indicator For Pseudomonas Bacteria

    NASA Technical Reports Server (NTRS)

    Margalit, Ruth

    1990-01-01

    Characteristic protein extracted and detected. Natural protein marker found in Pseudomonas bacteria. Azurin, protein containing copper readily extracted, purified, and used to prepare antibodies. Possible to develop simple, fast, and accurate test for marker carried out in doctor's office.

  18. [Darwin and bacteria].

    PubMed

    Ledermann D, Walter

    2009-02-01

    As in 2009 the scientific world celebrates two hundreds years from the birthday of Charles Darwin and one hundred and fifty from the publication of The Origin of Species, an analysis of his complete work is performed, looking for any mention of bacteria. But it seems that the great naturahst never took knowledge about its existence, something rather improbable in a time when the discovery of bacteria shook the medical world, or he deliberately ignored them, not finding a place for such microscopic beings into his theory of evolution. But the bacteria badly affected his familiar life, killing scarlet fever one of his children and worsening to death the evolution of tuberculosis of his favourite Annie. Darwin himself could suffer the sickness of Chagas, whose etiological agent has a similar level to bacteria in the scale of evolution.

  19. Indicator For Pseudomonas Bacteria

    NASA Technical Reports Server (NTRS)

    Margalit, Ruth

    1990-01-01

    Characteristic protein extracted and detected. Natural protein marker found in Pseudomonas bacteria. Azurin, protein containing copper readily extracted, purified, and used to prepare antibodies. Possible to develop simple, fast, and accurate test for marker carried out in doctor's office.

  20. Gut bacteria and cancer

    PubMed Central

    Erdman, Susan E.; Poutahidis, Theofilos

    2015-01-01

    Microbiota on the mucosal surfaces of the gastrointestinal (GI) tract greatly outnumber the cells in the human body. Effects of antibiotics indicate that GI tract bacteria may be determining the fate of distal cancers. Recent data implicate dysregulated host responses to enteric bacteria leading to cancers in extra-intestinal sites. Together these findings point to novel anti-cancer strategies aimed at promoting GI tract homeostasis. PMID:26050963

  1. Lipopolysaccharides in diazotrophic bacteria.

    PubMed

    Serrato, Rodrigo V

    2014-01-01

    Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

  2. Aerobic Anoxygenic Phototrophic Bacteria

    PubMed Central

    Yurkov, Vladimir V.; Beatty, J. Thomas

    1998-01-01

    The aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. Although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthetically under anaerobic conditions. Aerobic anoxygenic phototrophic bacteria are classified in two marine (Erythrobacter and Roseobacter) and six freshwater (Acidiphilium, Erythromicrobium, Erythromonas, Porphyrobacter, Roseococcus, and Sandaracinobacter) genera, which phylogenetically belong to the α-1, α-3, and α-4 subclasses of the class Proteobacteria. Despite this phylogenetic information, the evolution and ancestry of their photosynthetic properties are unclear. We discuss several current proposals for the evolutionary origin of aerobic phototrophic bacteria. The closest phylogenetic relatives of aerobic phototrophic bacteria include facultatively anaerobic purple nonsulfur phototrophic bacteria. Since these two bacterial groups share many properties, yet have significant differences, we compare and contrast their physiology, with an emphasis on morphology and photosynthetic and other metabolic processes. PMID:9729607

  3. The fecal bacteria

    USGS Publications Warehouse

    Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

  4. MOTILE MARINE BACTERIA I.

    PubMed Central

    Leifson, Einar; Cosenza, B. J.; Murchelano, R.; Cleverdon, R. C.

    1964-01-01

    Leifson, Einar (Loyola University, Chicago, Ill.), B. J. Cosenza, R. Murchelano, and R. C. Cleverdon. Motile marine bacteria. I. Techniques, ecology, and general characteristics. J. Bacteriol. 87:652–666. 1964.—Aerobic, heterotrophic bacteria were isolated from the waters of the Long Island Sound, Narragansett Bay, Atlantic Ocean, and from the intestine of a variety of marine animals found along the shore of the Long Island Sound. A total of about 600 cultures of motile bacteria were studied morphologically and physiologically, with special emphasis on flagellar characteristics. The great majority of the bacteria isolated from the water were polar flagellate, nonfermentative, nonpigmented, and gramnegative. Most of these were straight, capsulated rods, but a considerable number were curved like vibrios. Yellow-pigmented isolates were often nonmotile, and the motile forms were most frequently subpolar flagellate. Several rosette-forming bacteria, including Caulobacter species, were isolated. Two typical spirilla and one flagellated coccus were found. Peritrichous flagellate bacteria, both gram-positive and gram-negative, were rare except in bottom mud. The normal intestinal flora of marine animals, such as fish and shellfish, consisted of polar flagellate, fermentative, non-pigmented, gram-negative, straight rods. Curved forms, like vibrios, were less common. Polar multitrichous flagellate forms were not uncommon and included all the luminescent types isolated. A considerable proportion of the polar monotrichous flagellate rods swarmed over the surface of agar media. When grown on solid media, all of these showed mixed polar and lateral flagellation; in liquid media, mainly polar flagellation was found. The ecology and general taxonomy of marine bacteria are discussed. Images PMID:14129669

  5. Ice-Nucleating Bacteria

    NASA Astrophysics Data System (ADS)

    Obata, Hitoshi

    Since the discovery of ice-nucleating bacteria in 1974 by Maki et al., a large number of studies on the biological characteristics, ice-nucleating substance, ice nucleation gene and frost damage etc. of the bacteria have been carried out. Ice-nucleating bacteria can cause the freezing of water at relatively warm temperature (-2.3°C). Tween 20 was good substrates for ice-nucleating activity of Pseudomonas fluorescens KUIN-1. Major fatty acids of Isolate (Pseudomonas fluorescens) W-11 grown at 30°C were palmitic, cis-9-hexadecenoic and cis-11-octadecenoic which amounted to 90% of the total fatty acids. Sequence analysis shows that an ice nucleation gene from Pseudomonas fluorescens is related to the gene of Pseudomonas syringae.

  6. The intrinsic resistance of bacteria.

    PubMed

    Gang, Zhang; Jie, Feng

    2016-10-20

    Antibiotic resistance is often considered to be a trait acquired by previously susceptible bacteria, on the basis of which can be attributed to the horizontal acquisition of new genes or the occurrence of spontaneous mutation. In addition to acquired resistance, bacteria have a trait of intrinsic resistance to different classes of antibiotics. An intrinsic resistance gene is involved in intrinsic resistance, and its presence in bacterial strains is independent of previous antibiotic exposure and is not caused by horizontal gene transfer. Recently, interest in intrinsic resistance genes has increased, because these gene products not only may provide attractive therapeutic targets for development of novel drugs that rejuvenate the activity of existing antibiotics, and but also might predict future emergence of resistant pathogens if they become mobilized. In the present review, we summarize the conventional examples of intrinsic resistance, including the impermeability of cellular envelopes, the activity of multidrug efflux pumps or lack of drug targets. We also demonstrate that transferases and enzymes involved in basic bacterial metabolic processes confer intrinsic resistance in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. We present as well information on the cryptic intrinsic resistance genes that do not confer resistance to their native hosts but are capable of conferring resistance when their expression levels are increased and the activation of the cryptic genes. Finally, we discuss that intrinsic genes could be the origin of acquired resistance, especially in the genus Acinetobacter.

  7. Pathogenesis of pigment gallstones in Western societies: the central role of bacteria.

    PubMed

    Stewart, Lygia; Oesterle, Adair L; Erdan, Ihsan; Griffiss, J MacLeod; Way, Lawrence W

    2002-01-01

    Bacteria are traditionally accorded a greater role in pigment gallstone formation in Eastern populations. Stone color is thought to predict the presence of bacteria; that is, black stones (Western predominant) are supposedly sterile and brown stones (Eastern predominant) contain bacteria. We previously reported that, regardless of appearance, most pigment gallstones contain bacteria. This study examined, in a large Western population (370 patients), the incidence, appearance, and chemical composition of pigment stones, and the characteristics of gallstone bacteria. One hundred eighty-six pigment stones were obtained aseptically. Bacteria were detected by means of scanning electron microscopy and gallstone culture. Chemical composition was determined by infrared spectroscopy. Bacteria were tested for slime and beta-glucuronidase production. Seventy-three percent of pigment stones contained bacteria. Choledocholithiasis was associated with gallstone bacteria. Ca-bilirubinate was present in all pigment stones. Ca-palmitate was characteristic of infected stones, and more than 75% Ca-carbonate was characteristic of sterile stones. Neither chemical composition nor stone appearance predicted the presence of bacteria. Ninety-five percent and 67% of infected pigment stones contained bacteria that produced slime and beta-glucuronidase, respectively. Most pigment stones contained bacteria that produced beta-glucuronidase, slime, and phospholipase, factors that facilitate stone formation. Thus bacteria have a major role in Western pigment gallstone formation. Furthermore, gallstone color did not predict composition or bacterial presence.

  8. Sterol Synthesis in Diverse Bacteria

    PubMed Central

    Wei, Jeremy H.; Yin, Xinchi; Welander, Paula V.

    2016-01-01

    Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria

  9. Bacteria dispersal by hitchhiking on zooplankton

    PubMed Central

    Grossart, Hans-Peter; Dziallas, Claudia; Leunert, Franziska; Tang, Kam W.

    2010-01-01

    Microorganisms and zooplankton are both important components of aquatic food webs. Although both inhabit the same environment, they are often regarded as separate functional units that are indirectly connected through nutrient cycling and trophic cascade. However, research on pathogenic and nonpathogenic bacteria has shown that direct association with zooplankton has significant influences on the bacteria's physiology and ecology. We used stratified migration columns to study vertical dispersal of hitchhiking bacteria through migrating zooplankton across a density gradient that was otherwise impenetrable for bacteria in both upward and downward directions (conveyor-belt hypothesis). The strength of our experiments is to permit quantitative estimation of transport and release of associated bacteria: vertical migration of Daphnia magna yielded an average dispersal rate of 1.3 × 105·cells·Daphnia−1·migration cycle−1 for the lake bacterium Brevundimonas sp. Bidirectional vertical dispersal by migrating D. magna was also shown for two other bacterial species, albeit at lower rates. The prediction that diurnally migrating zooplankton acquire different attached bacterial communities from hypolimnion and epilimnion between day and night was subsequently confirmed in our field study. In mesotrophic Lake Nehmitz, D. hyalina showed pronounced diel vertical migration along with significant diurnal changes in attached bacterial community composition. These results confirm that hitchhiking on migrating animals can be an important mechanism for rapidly relocating microorganisms, including pathogens, allowing them to access otherwise inaccessible resources. PMID:20547852

  10. Enteric bacteria mandibular osteomyelitis.

    PubMed

    Scolozzi, Paolo; Lombardi, Tommaso; Edney, Timothy; Jaques, Bertrand

    2005-06-01

    Osteomyelitis of the mandible is a relatively rare inflammatory disease that usually stems from the odontogenic polymicrobial flora of the oral cavity. We are reporting 2 unusual cases of mandibular osteomyelitis resulting from enteric bacteria infection. In one patient, abundant clinical evidence suggested a diagnosis of a chronic factitious disease, whereas in the second patient no obvious etiology was found.

  11. Antibiotic-Resistant Bacteria.

    ERIC Educational Resources Information Center

    Longenecker, Nevin E.; Oppenheimer, Dan

    1982-01-01

    A study conducted by high school advanced bacteriology students appears to confirm the hypothesis that the incremental administration of antibiotics on several species of bacteria (Escherichia coli, Staphylococcus epidermis, Bacillus sublitus, Bacillus megaterium) will allow for the development of antibiotic-resistant strains. (PEB)

  12. Monoclonal antibodies against bacteria.

    PubMed

    Macario, A J; Conway de Macario, E

    1988-01-01

    Highlights are presented of most recent work in which monoclonal antibodies have been instrumental in the study of bacteria and their products. Topics summarized pertain to human and veterinary medicines, dentistry, phytopathology, ichthyology, and bacterial ecophysiology, differentiation, evolution and methanogenic biotechnology.

  13. Bacteria-surface interactions.

    PubMed

    Tuson, Hannah H; Weibel, Douglas B

    2013-05-14

    The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field.

  14. PATHOGENICITY OF BIOFILM BACTERIA

    EPA Science Inventory

    There is a paucity of information concerning any link between the microorganisms commonly found in biofilms of drinking water systems and their impacts on human health. For bacteria, culture-based techniques detect only a limited number of the total microorganisms associated wit...

  15. Antibiotic-Resistant Bacteria.

    ERIC Educational Resources Information Center

    Longenecker, Nevin E.; Oppenheimer, Dan

    1982-01-01

    A study conducted by high school advanced bacteriology students appears to confirm the hypothesis that the incremental administration of antibiotics on several species of bacteria (Escherichia coli, Staphylococcus epidermis, Bacillus sublitus, Bacillus megaterium) will allow for the development of antibiotic-resistant strains. (PEB)

  16. Bacteria-surface interactions

    PubMed Central

    Tuson, Hannah H.; Weibel, Douglas B.

    2013-01-01

    The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field. PMID:23930134

  17. Modelling the fate and transport of faecal bacteria in estuarine and coastal waters.

    PubMed

    Gao, Guanghai; Falconer, Roger A; Lin, Binliang

    2015-11-15

    This paper details a numerical model developed to predict the fate and transport of faecal bacteria in receiving surface waters. The model was first validated by comparing model predicted faecal bacteria concentrations with available field measurements. The model simulations agreed well with the observation data. After calibration, the model was applied to investigate the effects of different parameters, including: tidal processes, river discharges from the upstream boundaries and bacteria inputs from the upstream boundaries, wastewater treatment works (WwTWs), rivers and combined sewer overflows (CSO), on the concentrations of faecal bacteria in the Ribble Estuary. The results revealed that the tide and upstream boundary bacteria inputs were the primary factors controlling the distribution of faecal bacteria. The bacteria inputs from the WwTWs in the model domain were generally found not to have a significant impact on distribution of faecal bacteria in the estuary. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Impedance Measurements Could Accelerate Phage-Based Identification of Bacillus anthracis and Other Bacteria

    DTIC Science & Technology

    2016-09-01

    Impedance Measurements Could Accelerate Phage-Based Identification of Bacillus anthracis And Other Bacteria Thomas Brown, Salwa Shan, Teresa...infection can be detected as early as one hour after exposing as few as 105 CFU bacteria to the stressor. We predicted that similar responses could be used... bacteria to form confluent growth and for phage-induced plaques to appear. Techniques that permit faster detection of species-specific bacteria /phage

  19. Flowthrough Bacteria-Detection System

    NASA Technical Reports Server (NTRS)

    Grana, D. C.; Wilkins, J. R.

    1983-01-01

    Online system allows repetitive cycling of sample intake, bacteria counting and sterilization. System measures bacteria count by using sample/incubate/ measure cycle. Steps in cycle are on/off operations to cycle automated easily.

  20. Manufacture of Probiotic Bacteria

    NASA Astrophysics Data System (ADS)

    Muller, J. A.; Ross, R. P.; Fitzgerald, G. F.; Stanton, C.

    Lactic acid bacteria (LAB) have been used for many years as natural biopreservatives in fermented foods. A small group of LAB are also believed to have beneficial health effects on the host, so called probiotic bacteria. Probiotics have emerged from the niche industry from Asia into European and American markets. Functional foods are one of the fastest growing markets today, with estimated growth to 20 billion dollars worldwide by 2010 (GIA, 2008). The increasing demand for probiotics and the new food markets where probiotics are introduced, challenges the industry to produce high quantities of probiotic cultures in a viable and stable form. Dried concentrated probiotic cultures are the most convenient form for incorporation into functional foods, given the ease of storage, handling and transport, especially for shelf-stable functional products. This chapter will discuss various aspects of the challenges associated with the manufacturing of probiotic cultures.

  1. Genomics of oral bacteria.

    PubMed

    Duncan, Margaret J

    2003-01-01

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

  2. Reanimation of Ancient Bacteria

    SciTech Connect

    Vreeland, Russell H.

    2009-01-09

    Recent highly publicized experiments conducted on salt crystals taken from the Permian Salado Formation in Southeastern New Mexico have shown that some ancient crystals contain viable microorganisms trapped within fluid inclusions. Stringent geological and microbiological selection criteria were used to select crystals and conduct all sampling. This talk will focus on how each of these lines of data support the conclusion that such isolated bacteria are as old as the rock in which they are trapped. In this case, the isolated microbes are salt tolerant bacilli that grow best in media containing 8% NaCl, and respond to concentrated brines by forming spores. One of the organisms is phylogenetically related to several bacilli, but does have several unique characteristics. This talk will trace the interdisciplinary data and procedures supporting these discoveries, and describe the various isolated bacteria.

  3. Reanimation of Ancient Bacteria

    SciTech Connect

    Vreeland, Russell H.

    2002-01-09

    Recent highly publicized experiments conducted on salt crystals taken from the Permian Salado Formation in Southeastern New Mexico have shown that some ancient crystals contain viable microorganisms trapped within fluid inclusions. Stringent geological and microbiological selection criteria were used to select crystals and conduct all sampling. This talk will focus on how each of these lines of data support the conclusion that such isolated bacteria are as old as the rock in which they are trapped. In this case, the isolated microbes are salt tolerant bacilli that grow best in media containing 8% NaCl, and respond to concentrated brines by forming spores. One of the organisms is phylogenetically related to several bacilli, but does have several unique characteristics. This talk will trace the interdisciplinary data and procedures supporting these discoveries, and describe the various isolated bacteria.

  4. Computation by Bacteria

    DTIC Science & Technology

    2011-01-03

    inversion symmetry and time reversal symmetry by dissipat - ing energy , and breaking both these symmetries allows ratcheting. The ability of...durations. All of these devices take advantage of the conversion of chemical energy into propulsion that occurs within bacteria. These devices break spatial...micromachines relying on energy that microorganisms would dissipate “anyway” even in the absence of ratchet structures suggests that researchers could

  5. How honey kills bacteria.

    PubMed

    Kwakman, Paulus H S; te Velde, Anje A; de Boer, Leonie; Speijer, Dave; Vandenbroucke-Grauls, Christina M J E; Zaat, Sebastian A J

    2010-07-01

    With the rise in prevalence of antibiotic-resistant bacteria, honey is increasingly valued for its antibacterial activity. To characterize all bactericidal factors in a medical-grade honey, we used a novel approach of successive neutralization of individual honey bactericidal factors. All bacteria tested, including Bacillus subtilis, methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase producing Escherichia coli, ciprofloxacin-resistant Pseudomonas aeruginosa, and vancomycin-resistant Enterococcus faecium, were killed by 10-20% (v/v) honey, whereas > or = 40% (v/v) of a honey-equivalent sugar solution was required for similar activity. Honey accumulated up to 5.62 +/- 0.54 mM H(2)O(2) and contained 0.25 +/- 0.01 mM methylglyoxal (MGO). After enzymatic neutralization of these two compounds, honey retained substantial activity. Using B. subtilis for activity-guided isolation of the additional antimicrobial factors, we discovered bee defensin-1 in honey. After combined neutralization of H(2)O(2), MGO, and bee defensin-1, 20% honey had only minimal activity left, and subsequent adjustment of the pH of this honey from 3.3 to 7.0 reduced the activity to that of sugar alone. Activity against all other bacteria tested depended on sugar, H(2)O(2), MGO, and bee defensin-1. Thus, we fully characterized the antibacterial activity of medical-grade honey.

  6. Growing Unculturable Bacteria

    PubMed Central

    2012-01-01

    The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field. PMID:22661685

  7. Growing unculturable bacteria.

    PubMed

    Stewart, Eric J

    2012-08-01

    The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.

  8. Biocide tolerance in bacteria.

    PubMed

    Ortega Morente, Elena; Fernández-Fuentes, Miguel Angel; Grande Burgos, Maria José; Abriouel, Hikmate; Pérez Pulido, Rubén; Gálvez, Antonio

    2013-03-01

    Biocides have been employed for centuries, so today a wide range of compounds showing different levels of antimicrobial activity have become available. At the present time, understanding the mechanisms of action of biocides has also become an important issue with the emergence of bacterial tolerance to biocides and the suggestion that biocide and antibiotic resistance in bacteria might be linked. While most of the mechanisms providing antibiotic resistance are agent specific, providing resistance to a single antimicrobial or class of antimicrobial, there are currently numerous examples of efflux systems that accommodate and, thus, provide tolerance to a broad range of structurally unrelated antimicrobials, both antibiotics and biocides. If biocide tolerance becomes increasingly common and it is linked to antibiotic resistance, not only resistant (even multi-resistant) bacteria could be passed along the food chain, but also there are resistance determinants that can spread and lead to the emergence of new resistant microorganisms, which can only be detected and monitored when the building blocks of resistance traits are understood on the molecular level. This review summarizes the main advances reached in understanding the mechanism of action of biocides, the mechanisms of bacterial resistance to both biocides and antibiotics, and the incidence of biocide tolerance in bacteria of concern to human health and the food industry.

  9. Denitrification by extremely halophilic bacteria

    NASA Technical Reports Server (NTRS)

    Hochstein, L. I.; Tomlinson, G. A.

    1985-01-01

    Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.

  10. Denitrification by extremely halophilic bacteria

    NASA Technical Reports Server (NTRS)

    Hochstein, L. I.; Tomlinson, G. A.

    1985-01-01

    Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.

  11. Living bacteria in silica gels

    NASA Astrophysics Data System (ADS)

    Nassif, Nadine; Bouvet, Odile; Noelle Rager, Marie; Roux, Cécile; Coradin, Thibaud; Livage, Jacques

    2002-09-01

    The encapsulation of enzymes within silica gels has been extensively studied during the past decade for the design of biosensors and bioreactors. Yeast spores and bacteria have also been recently immobilized within silica gels where they retain their enzymatic activity, but the problem of the long-term viability of whole cells in an inorganic matrix has never been fully addressed. It is a real challenge for the development of sol-gel processes. Generic tests have been performed to check the viability of Escherichia coli bacteria in silica gels. Surprisingly, more bacteria remain culturable in the gel than in an aqueous suspension. The metabolic activity of the bacteria towards glycolysis decreases slowly, but half of the bacteria are still viable after one month. When confined within a mineral environment, bacteria do not form colonies. The exchange of chemical signals between isolated bacteria rather than aggregates can then be studied, a point that could be very important for 'quorum sensing'.

  12. Bacteria counting method based on polyaniline/bacteria thin film.

    PubMed

    Zhihua, Li; Xuetao, Hu; Jiyong, Shi; Xiaobo, Zou; Xiaowei, Huang; Xucheng, Zhou; Tahir, Haroon Elrasheid; Holmes, Mel; Povey, Malcolm

    2016-07-15

    A simple and rapid bacteria counting method based on polyaniline (PANI)/bacteria thin film was proposed. Since the negative effects of immobilized bacteria on the deposition of PANI on glass carbon electrode (GCE), PANI/bacteria thin films containing decreased amount of PANI would be obtained when increasing the bacteria concentration. The prepared PANI/bacteria film was characterized with cyclic voltammetry (CV) technique to provide quantitative index for the determination of the bacteria count, and electrochemical impedance spectroscopy (EIS) was also performed to further investigate the difference in the PANI/bacteria films. Good linear relationship of the peak currents of the CVs and the log total count of bacteria (Bacillus subtilis) could be established using the equation Y=-30.413X+272.560 (R(2)=0.982) over the range of 5.3×10(4) to 5.3×10(8)CFUmL(-1), which also showed acceptable stability, reproducibility and switchable ability. The proposed method was feasible for simple and rapid counting of bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Films of bacteria at interfaces.

    PubMed

    Vaccari, Liana; Molaei, Mehdi; Niepa, Tagbo H R; Lee, Daeyeon; Leheny, Robert L; Stebe, Kathleen J

    2017-09-01

    Bacteria are often discussed as active colloids, self-propelled organisms whose collective motion can be studied in the context of non-equilibrium statistical mechanics. In such studies, the behavior of bacteria confined to interfaces or in the proximity of an interface plays an important role. For instance, many studies have probed collective behavior of bacteria in quasi two-dimensional systems such as soap films. Since fluid interfaces can adsorb surfactants and other materials, the stress and velocity boundary conditions at interfaces can alter bacteria motion; hydrodynamic studies of interfaces with differing boundary conditions are reviewed. Also, bacteria in bulk can become trapped at or near fluid interfaces, where they colonize and form structures comprising secretions like exopolysaccharides, surfactants, living and dead bacteria, thereby creating Films of Bacteria at Interfaces (FBI). The formation of FBI is discussed at air-water, oil-water, and water-water interfaces, with an emphasis on film mechanics, and with some allusion to genetic functions guiding bacteria to restructure fluid interfaces. At air-water interfaces, bacteria form pellicles or interfacial biofilms. Studies are reviewed that reveal that pellicle material properties differ for different strains of bacteria, and that pellicle physicochemistry can act as a feedback mechanism to regulate film formation. At oil-water interfaces, a range of FBI form, depending on bacteria strain. Some bacteria-laden interfaces age from an initial active film, with dynamics dominated by motile bacteria, through viscoelastic states, to form an elastic film. Others remain active with no evidence of elastic film formation even at significant interface ages. Finally, bacteria can adhere to and colonize ultra-low surface tension interfaces such as aqueous-aqueous systems common in food industries. Relevant literature is reviewed, and areas of interest for potential application are discussed, ranging from health

  14. Escherichia coli bacteria density in relation to turbidity, streamflow characteristics, and season in the Chattahoochee River near Atlanta, Georgia, October 2000 through September 2008—Description, statistical analysis, and predictive modeling

    USGS Publications Warehouse

    Lawrence, Stephen J.

    2012-01-01

    Regression analyses show that E. coli density in samples was strongly related to turbidity, streamflow characteristics, and season at both sites. The regression equation chosen for the Norcross data showed that 78 percent of the variability in E. coli density (in log base 10 units) was explained by the variability in turbidity values (in log base 10 units), streamflow event (dry-weather flow or stormflow), season (cool or warm), and an interaction term that is the cross product of streamflow event and turbidity. The regression equation chosen for the Atlanta data showed that 76 percent of the variability in E. coli density (in log base 10 units) was explained by the variability in turbidity values (in log base 10 units), water temperature, streamflow event, and an interaction term that is the cross product of streamflow event and turbidity. Residual analysis and model confirmation using new data indicated the regression equations selected at both sites predicted E. coli density within the 90 percent prediction intervals of the equations and could be used to predict E. coli density in real time at both sites.

  15. Bacteria in solitary confinement.

    PubMed

    Mullineaux, Conrad W

    2015-02-15

    Even in clonal bacterial cultures, individual bacteria can show substantial stochastic variation, leading to pitfalls in the interpretation of data derived from millions of cells in a culture. In this issue of the Journal of Bacteriology, as part of their study on osmoadaptation in a cyanobacterium, Nanatani et al. describe employing an ingenious microfluidic device that gently cages individual cells (J Bacteriol 197:676-687, 2015, http://dx.doi.org/10.1128/JB.02276-14). The device is a welcome addition to the toolkit available to probe the responses of individual cells to environmental cues.

  16. Surface layers of bacteria.

    PubMed Central

    Beveridge, T J; Graham, L L

    1991-01-01

    Since bacteria are so small, microscopy has traditionally been used to study them as individual cells. To this end, electron microscopy has been a most powerful tool for studying bacterial surfaces; the viewing of macromolecular arrangements of some surfaces is now possible. This review compares older conventional electron-microscopic methods with new cryotechniques currently available and the results each has produced. Emphasis is not placed on the methodology but, rather, on the importance of the results in terms of our perception of the makeup and function of bacterial surfaces and their interaction with the surrounding environment. Images PMID:1723487

  17. Phage-bacteria infection networks: From nestedness to modularity

    NASA Astrophysics Data System (ADS)

    Flores, Cesar O.; Valverde, Sergi; Weitz, Joshua S.

    2013-03-01

    Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we re-evaluated 38 prior studies and demonstrated that phage-bacteria infection networks tend to be statistically nested in small scale communities (Flores et al 2011). Nestedness is consistent with a hierarchy of infection and resistance within phages and bacteria, respectively. However, we predicted that at large scales, phage-bacteria infection networks should be typified by a modular structure. We evaluate and confirm this hypothesis using the most extensive study of phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-infections were evaluated between 215 marine phages and 286 marine bacteria. We develop a novel multi-scale network analysis and find that the Moebus and Nattkemper (1981) study, is highly modular (at the whole network scale), yet also exhibits nestedness and modularity at the within-module scale. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. CFG acknowledges the support of CONACyT Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and acknowledges the support of the James S. McDonnell Foundation

  18. In Vitro Resistance Studies with Bacteria That Exhibit Low Mutation Frequencies: Prediction of “Antimutant” Linezolid Concentrations Using a Mixed Inoculum Containing both Susceptible and Resistant Staphylococcus aureus

    PubMed Central

    Golikova, Maria V.; Strukova, Elena N.; Portnoy, Yury A.; Romanov, Andrey V.; Edelstein, Mikhail V.; Zinner, Stephen H.

    2014-01-01

    Bacterial resistance studies using in vitro dynamic models are highly dependent on the starting inoculum that might or might not contain spontaneously resistant mutants (RMs). To delineate concentration-resistance relationships with linezolid-exposed Staphylococcus aureus, a mixed inoculum containing both susceptible cells and RMs was used. An RM selected after the 9th passage of the parent strain (MIC, 2 μg/ml) on antibiotic-containing media (RM9; MIC, 8 μg/ml) was chosen for the pharmacodynamic studies, because the mutant prevention concentration (MPC) of linezolid against the parent strain in the presence of RM9 at 102 (but not at 104) CFU/ml did not differ from the MPC value determined in the absence of the RMs. Five-day treatments with twice-daily linezolid doses were simulated at concentrations either between the MIC and MPC or above the MPC. S. aureus RMs (resistant to 2× and 4× MIC but not 8× and 16× MIC) were enriched at ratios of the 24-h area under the concentration-time curve (AUC24) to the MIC that provide linezolid concentrations between the MIC and MPC for 100% (AUC24/MIC, 60 h) and 86% (AUC24/MIC, 120 h) of the dosing interval. No such enrichment occurred when linezolid concentrations were above the MIC and below the MPC for a shorter time (37% of the dosing interval; AUC24/MIC, 240 h) or when concentrations were consistently above the MPC (AUC24/MIC, 480 h). These findings obtained using linezolid-susceptible staphylococci supplemented with RMs support the mutant selection window hypothesis. This method provides an option to delineate antibiotic concentration-resistance relationships with bacteria that exhibit low mutation frequencies. PMID:25451050

  19. The role of depressed metabolism in increased radio-resistance

    NASA Technical Reports Server (NTRS)

    Musacchia, X. J.

    1975-01-01

    The results of experiments on hamsters and rats to determine physiological responses to various temperature conditions are presented. The experimental methods described are considered to be applicable to future mammalian experiments in space. Renal function was examined in the golden hamster as a function of body temperature. Hamsters were also acclimated to heat and metabolic rates, body temperature, skin temperature, cardiac distribution and whole body hematocrits were measured. In addition, the effects of heat stress on the intestinal transport of sugars in the hamster and rat were studied. The biological effects of prolonged space flight and methods of simulating weightlessness are also discussed.

  20. Molecular Determinants of Radio Resistance in Prostate Cancer

    DTIC Science & Technology

    2005-08-01

    34 Hypofractionated intensity modulated radiation therapy for prostate cancer". Presented at the 44th Meeting of the American Society of Therapeutic Radiation...Warde P, Crook J, McLean. " Hypofractionated Intensity Modulated Radiation Therapy (IMRT) for Localized Prostate Cancer". Presented at the 17th Meeting...Nonetheless, local moderate dose escalation with a hypofractionated reg- control, as assessed by prostatic biopsies 2-3 years imen. Recent analyses of

  1. Molecular Determinants of Radio Resistance in Prostate Cancer

    DTIC Science & Technology

    2004-08-01

    malignant prostate cell lines, the mRNA and protein levels of the HR-related Rad51, XRCC3 , Rad52, Rad54 genes were elevated -2-5 fold in comparison to normal...Antisense riboprobes (RAD50, MREll, RAD52, RAD54, RAD51, XRCC2, XRCC3 , RAD51B, RAD51C, RAD51D, L32 and GAPDH from DBSR1 set; ATM, NBS1, XRCC2, XRCC3 ...suggested by the supplier and included: Rad51, RPA, ot-tubulin (Oncogene Research Products, Inc.), Rad50, Nbsl(p95), XRCC3 , Rad5lC, Rad5lD (Novus

  2. Chemical communication in bacteria

    NASA Astrophysics Data System (ADS)

    Suravajhala, Srinivasa Sandeep; Saini, Deepak; Nott, Prabhu

    Luminescence in Vibrio fischeri is a model for quorum-sensing-gene-regulation in bacteria. We study luminescence response of V. fischeri to both internal and external cues at the single cell and population level. Experiments with ES114, a wild-type strain, and ainS mutant show that luminescence induction in cultures is not always proportional to cell-density and there is always a basal level of luminescence. At any given concentration of the exogenously added signals, C6-HSL and C8-HSL, luminescence per cell reaches a maximum during the exponential phase and decreases thereafter. We hypothesize that (1) C6-HSL production and LuxR activity are not proportional to cell-density, and (2) there is a shift in equilibrium from C6-HSL to C8-HSL during the later stages of growth of the culture. RT-PCR analysis of luxI and luxR shows that the expression of these genes is maximum corresponding to the highest level of luminescence. The shift in equilibrium is shown by studying competitive binding of C6-HSL and C8-HSL to LuxR. We argue that luminescence is a unicellular behaviour, and an intensive property like per cell luminescence is more important than gross luminescence of the population in understanding response of bacteria to chemical signalling. Funding from the Department of Science and Technology, India is acknowledged.

  3. Replication Restart in Bacteria.

    PubMed

    Michel, Bénédicte; Sandler, Steven J

    2017-07-01

    In bacteria, replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years, the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures. This work also revealed a close link between replication and homologous recombination, as replication restart from recombination intermediates is an essential step of DNA double-strand break repair in bacteria and, conversely, arrested replication forks can be acted upon by recombination proteins and converted into various recombination substrates. In this review, we summarize this intense period of research that led to the characterization of the ubiquitous replication restart protein PriA and its partners, to the definition of several replication restart pathways in vivo, and to the description of tight links between replication and homologous recombination, responsible for the importance of replication restart in the maintenance of genome stability. Copyright © 2017 American Society for Microbiology.

  4. Beneficial bacteria inhibit cachexia

    PubMed Central

    Varian, Bernard J.; Goureshetti, Sravya; Poutahidis, Theofilos; Lakritz, Jessica R.; Levkovich, Tatiana; Kwok, Caitlin; Teliousis, Konstantinos; Ibrahim, Yassin M.; Mirabal, Sheyla; Erdman, Susan E.

    2016-01-01

    Muscle wasting, known as cachexia, is a debilitating condition associated with chronic inflammation such as during cancer. Beneficial microbes have been shown to optimize systemic inflammatory tone during good health; however, interactions between microbes and host immunity in the context of cachexia are incompletely understood. Here we use mouse models to test roles for bacteria in muscle wasting syndromes. We find that feeding of a human commensal microbe, Lactobacillus reuteri, to mice is sufficient to lower systemic indices of inflammation and inhibit cachexia. Further, the microbial muscle-building phenomenon extends to normal aging as wild type animals exhibited increased growth hormone levels and up-regulation of transcription factor Forkhead Box N1 [FoxN1] associated with thymus gland retention and longevity. Interestingly, mice with a defective FoxN1 gene (athymic nude) fail to inhibit sarcopenia after L. reuteri therapy, indicating a FoxN1-mediated mechanism. In conclusion, symbiotic bacteria may serve to stimulate FoxN1 and thymic functions that regulate inflammation, offering possible alternatives for cachexia prevention and novel insights into roles for microbiota in mammalian ontogeny and phylogeny. PMID:26933816

  5. RNA localization in bacteria

    PubMed Central

    Buskila, Avi-ad Avraam; Kannaiah, Shanmugapriya; Amster-Choder, Orna

    2014-01-01

    One of the most important discoveries in the field of microbiology in the last two decades is that bacterial cells have intricate subcellular organization. This understanding has emerged mainly from the depiction of spatial and temporal organization of proteins in specific domains within bacterial cells, e.g., midcell, cell poles, membrane and periplasm. Because translation of bacterial RNA molecules was considered to be strictly coupled to their synthesis, they were not thought to specifically localize to regions outside the nucleoid. However, the increasing interest in RNAs, including non-coding RNAs, encouraged researchers to explore the spatial and temporal localization of RNAs in bacteria. The recent technological improvements in the field of fluorescence microscopy allowed subcellular imaging of RNAs even in the tiny bacterial cells. It has been reported by several groups, including ours that transcripts may specifically localize in such cells. Here we review what is known about localization of RNA and of the pathways that determine RNA fate in bacteria, and discuss the possible cues and mechanisms underlying these distribution patterns. PMID:25482897

  6. Functional amyloids in bacteria.

    PubMed

    Romero, Diego; Kolter, Roberto

    2014-06-01

    The term amyloidosis is used to refer to a family of pathologies altering the homeostasis of human organs. Despite having a name that alludes to starch content, the amyloid accumulations are made up of proteins that polymerize as long and rigid fibers. Amyloid proteins vary widely with respect to their amino acid sequences but they share similarities in their quaternary structure; the amyloid fibers are enriched in β-sheets arranged perpendicular to the axis of the fiber. This structural feature provides great robustness, remarkable stability, and insolubility. In addition, amyloid proteins specifically stain with certain dyes such as Congo red and thioflavin-T. The aggregation into amyloid fibers, however, it is not restricted to pathogenic processes, rather it seems to be widely distributed among proteins and polypeptides. Amyloid fibers are present in insects, fungi and bacteria, and they are important in maintaining the homeostasis of the organism. Such findings have motivated the use of the term "functional amyloid" to differentiate these amyloid proteins from their toxic siblings. This review focuses on systems that have evolved in bacteria that control the expression and assembly of amyloid proteins on cell surfaces, such that the robustness of amyloid proteins are used towards a beneficial end.

  7. Comparative genomics of green sulfur bacteria.

    PubMed

    Davenport, Colin; Ussery, David W; Tümmler, Burkhard

    2010-06-01

    Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO(2) fixation. Whole-genome gene family and single gene sequence comparisons yielded similar phylogenetic trees of the sequenced chromosomes indicating a concerted vertical evolution of large gene sets. Chromosomal synteny of genes is not preserved in the phylum Chlorobi. The accessory genome is characterized by anomalous oligonucleotide usage and endows the strains with individual features for transport, secretion, cell wall, extracellular constituents, and a few elements of the biosynthetic apparatus. Giant genes are a peculiar feature of the genera Chlorobium and Prosthecochloris. The predicted proteins have a huge molecular weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment.

  8. Methanogenic bacteria: presence in foodstuffs.

    PubMed

    Brusa, T; Ferrari, F; Canzi, E

    1998-01-01

    Methanogenic bacteria are anaerobic, oxygen-intolerant microorganisms, and it is only by studying the different habitats of such bacteria that fundamental information about their ecology becomes available. This research has evaluated methanogenic bacteria in apparently aerobic ecosystems, in foodstuffs not subjected to chemical-physical reclamation processes, where the presence of methanogenic bacteria has never been investigated. Methanogenic bacteria, ascribable to the Methanogenium, Methanobacterium and Methanosarcina genera, were found in vegetables, meat, fish and cheese but were generally absent in confectionery products and fruit. The microorganisms appear to be chance contaminants, usually being present in only very low numbers. It should be noted that none of the tested foods showed the presence of Methanobrevibacter smithii, M. oralis or Methanosphaera stadtmaneae, methanogenic bacteria sometimes present in the human digestive tract.

  9. Biotechnology of Anoxygenic Phototrophic Bacteria.

    PubMed

    Frigaard, Niels-Ulrik

    Anoxygenic phototrophic bacteria are a diverse collection of organisms that are defined by their ability to grow using energy from light without evolving oxygen. The dominant groups are purple sulfur bacteria, purple nonsulfur bacteria, green sulfur bacteria, and green and red filamentous anoxygenic phototrophic bacteria. They represent several bacterial phyla but they all have bacteriochlorophylls and carotenoids and photochemical reaction centers which generate ATP and cellular reductants used for CO2 fixation. They typically have an anaerobic lifestyle in the light, although some grow aerobically in the dark. Some of them oxidize inorganic sulfur compounds for light-dependent CO2 fixation; this ability can be exploited for photobiological removal of hydrogen sulfide from wastewater and biogas. The anoxygenic phototrophic bacteria also perform bioremediation of recalcitrant dyes, pesticides, and heavy metals under anaerobic conditions. Finally, these organisms may be useful for overexpression of membrane proteins and photobiological production of H2 and other valuable compounds.

  10. Kin Recognition in Bacteria.

    PubMed

    Wall, Daniel

    2016-09-08

    The ability of bacteria to recognize kin provides a means to form social groups. In turn these groups can lead to cooperative behaviors that surpass the ability of the individual. Kin recognition involves specific biochemical interactions between a receptor(s) and an identification molecule(s). Recognition specificity, ensuring that nonkin are excluded and kin are included, is critical and depends on the number of loci and polymorphisms involved. After recognition and biochemical perception, the common ensuing cooperative behaviors include biofilm formation, quorum responses, development, and swarming motility. Although kin recognition is a fundamental mechanism through which cells might interact, microbiologists are only beginning to explore the topic. This review considers both molecular and theoretical aspects of bacterial kin recognition. Consideration is also given to bacterial diversity, genetic relatedness, kin selection theory, and mechanisms of recognition.

  11. Phosphonate utilization by bacteria.

    PubMed Central

    Cook, A M; Daughton, C G; Alexander, M

    1978-01-01

    Bacteria able to use at least one of 13 ionic alkylphosphonates of O-alkyl or O,O-dialkyl alkylphosphonates as phosphorus sources were isolated from sewage and soil. Four of these isolates used 2-aminoethylphosphonic acid (AEP) as a sole carbon, nitrogen, and phosphorus source. None of the other phosphonates served as a carbon source for the organisms. One isolate, identified as Pseudomonas putida, grew with AEP as its sole carbon, nitrogen, and phosphorus source and released nearly all of the organic phosphorus as orthophosphate and 72% of the AEP nitrogen as ammonium. This is the first demonstration of utilization of a phosphonoalkyl moiety as a sole carbon source. Cell-free extracts of P. putida contained an inducible enzyme system that required pyruvate and pyridoxal phosphate to release orthophosphate from AEP; acetaldehyde was tentatively identified as a second product. Phosphite inhibited the enzyme system. PMID:618850

  12. Phages of dairy bacteria.

    PubMed

    Brussow, H

    2001-01-01

    Bacteriophages of lactic acid bacteria are a threat to industrial milk fermentation. Owing to their economical importance, dairy phages became the most thoroughly sequenced phage group in the database. Comparative genomics identified related cos-site and pac-site phages, respectively, in lactococci, lactic streptococci and lactobacilli. Each group was represented with closely related temperate and virulent phages. Over the structural genes their gene maps resembled that of lambdoid coliphages, suggesting distant evolutionary relationships. Despite a lack of sequence similarity, a number of biochemical characteristics of these dairy phages are lambda-like (genetic switch, DNA packaging, head and tail morphogenesis, and integration, but not excision). These dairy phages thus provide interesting variations to the phage lambda paradigm. The structural gene cluster of Lactococcus phage r1t resembled that of phages from mycobacteria. Virulent lactococcal phages with prolate heads (c2-like genus of Siphoviridae), in contrast, have no known counterparts in other bacterial genera.

  13. Acoustofluidic bacteria separation

    NASA Astrophysics Data System (ADS)

    Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E.; Zeng, Xiangqun; Huang, Tony Jun

    2017-01-01

    Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate Escherichia coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care sepsis diagnostic device.

  14. Topological Defects in a Living Nematic Ensnare Swimming Bacteria

    NASA Astrophysics Data System (ADS)

    Genkin, Mikhail M.; Sokolov, Andrey; Lavrentovich, Oleg D.; Aranson, Igor S.

    2017-01-01

    Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement with the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of +1 /2 topological defects and depletion of bacteria in the cores of -1 /2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.

  15. Characterization and Structure Prediction of Partial Length Protein Sequences of pcoA, pcoR and chrB Genes from Heavy Metal Resistant Bacteria from the Klip River, South Africa

    PubMed Central

    Chihomvu, Patience; Stegmann, Peter; Pillay, Michael

    2015-01-01

    The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. Copper and chromate resistance determinants were cloned and sequenced. Open reading frames (ORFs) related to the genes CopA and CopR were identified in E. coli KR29, PcoA in Lysinibacillus sp. KR25 and none related to chromate resistance were detected. The 3D-models predicted by I-TASSER disclose that the PcoA proteins consist of β-sheets, which form a part of the cupredoxin domain of the CopA copper resistance family of genes. The model for PcoR_29 revealed the presence of a helix turn helix; this forms part of a DNA binding protein, which is part of a heavy metal transcriptional regulator. The bacterial strains were cured using ethidium bromide. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E. coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element, which was not detected using gel electrophoresis. PMID:25837632

  16. Airborne bacteria in the atmosphere: Presence, purpose, and potential

    NASA Astrophysics Data System (ADS)

    Smets, Wenke; Moretti, Serena; Denys, Siegfried; Lebeer, Sarah

    2016-08-01

    Numerous recent studies have highlighted that the types of bacteria present in the atmosphere often show predictable patterns across space and time. These patterns can be driven by differences in bacterial sources of the atmosphere and a wide range of environmental factors, including UV intensity, precipitation events, and humidity. The abundance of certain bacterial taxa is of interest, not only for their ability to mediate a range of chemical and physical processes in the atmosphere, such as cloud formation and ice nucleation, but also for their implications -both beneficial and detrimental-for human health. Consequently, the widespread importance of airborne bacteria has stimulated the search for their applicability. Improving air quality, modelling the dispersal of airborne bacteria (e.g. pathogens) and biotechnological purposes are already being explored. Nevertheless, many technological challenges still need to be overcome to fully understand the roles of airborne bacteria in our health and global ecosystems.

  17. Vibrio bacteria in raw oysters: managing risks to human health.

    PubMed

    Froelich, Brett A; Noble, Rachel T

    2016-03-05

    The human-pathogenic marine bacteria Vibrio vulnificus and V. parahaemolyticus are strongly correlated with water temperature, with concentrations increasing as waters warm seasonally. Both of these bacteria can be concentrated in filter-feeding shellfish, especially oysters. Because oysters are often consumed raw, this exposes people to large doses of potentially harmful bacteria. Various models are used to predict the abundance of these bacteria in oysters, which guide shellfish harvest policy meant to reduce human health risk. Vibrio abundance and behaviour varies from site to site, suggesting that location-specific studies are needed to establish targeted risk reduction strategies. Moreover, virulence potential, rather than simple abundance, should be also be included in future modeling efforts.

  18. Vibrio bacteria in raw oysters: managing risks to human health

    PubMed Central

    Froelich, Brett A.; Noble, Rachel T.

    2016-01-01

    The human-pathogenic marine bacteria Vibrio vulnificus and V. parahaemolyticus are strongly correlated with water temperature, with concentrations increasing as waters warm seasonally. Both of these bacteria can be concentrated in filter-feeding shellfish, especially oysters. Because oysters are often consumed raw, this exposes people to large doses of potentially harmful bacteria. Various models are used to predict the abundance of these bacteria in oysters, which guide shellfish harvest policy meant to reduce human health risk. Vibrio abundance and behaviour varies from site to site, suggesting that location-specific studies are needed to establish targeted risk reduction strategies. Moreover, virulence potential, rather than simple abundance, should be also be included in future modeling efforts. PMID:26880841

  19. Swimming bacteria in liquid crystal

    NASA Astrophysics Data System (ADS)

    Sokolov, Andrey; Zhou, Shuang; Aranson, Igor; Lavrentovich, Oleg

    2014-03-01

    Dynamics of swimming bacteria can be very complex due to the interaction between the bacteria and the fluid, especially when the suspending fluid is non-Newtonian. Placement of swimming bacteria in lyotropic liquid crystal produces a new class of active materials by combining features of two seemingly incompatible constituents: self-propelled live bacteria and ordered liquid crystals. Here we present fundamentally new phenomena caused by the coupling between direction of bacterial swimming, bacteria-triggered flows and director orientations. Locomotion of bacteria may locally reduce the degree of order in liquid crystal or even trigger nematic-isotropic phase transition. Microscopic flows generated by bacterial flagella disturb director orientation. Emerged birefringence patterns allow direct optical observation and quantitative characterization of flagella dynamics. At high concentration of bacteria we observed the emergence of self-organized periodic texture caused by bacteria swimming. Our work sheds new light on self-organization in hybrid bio-mechanical systems and can lead to valuable biomedical applications. Was supported by the US DOE, Office of Basic Energy Sciences, Division of Materials Science and Engineering, under the Contract No. DE AC02-06CH11357.

  20. [Pseudomonas genus bacteria on weeds].

    PubMed

    Gvozdiak, R I; Iakovleva, L M; Pasichnik, L A; Shcherbina, T N; Ogorodnik, L E

    2005-01-01

    It has been shown in the work that the weeds (couch-grass and ryegrass) may be affected by bacterial diseases in natural conditions, Pseudomonas genus bacteria being their agents. The isolated bacteria are highly-aggressive in respect of the host-plant and a wide range of cultivated plants: wheat, rye, oats, barley, apple-tree and pear-tree. In contrast to highly aggressive bacteria isolated from the affected weeds, bacteria-epi phytes isolated from formally healthy plants (common amaranth, orache, flat-leaved spurge, field sow thistle, matricary, common coltsfoot, narrow-leaved vetch) and identified as P. syringae pv. coronafaciens, were characterized by weak aggression. A wide range of ecological niches of bacteria evidently promote their revival and distribution everywhere in nature.

  1. Pathways for phosphatidylcholine biosynthesis in bacteria.

    PubMed

    Martínez-Morales, Fernando; Schobert, Max; López-Lara, Isabel M; Geiger, Otto

    2003-12-01

    Phosphatidylcholine (PC) is the major membrane-forming phospholipid in eukaryotes with important structural and signalling functions. Although many prokaryotes lack PC, it can be found in significant amounts in membranes of rather diverse bacteria. Two pathways for PC biosynthesis are known in bacteria, the methylation pathway and the phosphatidylcholine synthase (PCS) pathway. In the methylation pathway, phosphatidylethanolamine is methylated three times to yield PC, in reactions catalysed by one or several phospholipid N-methyltransferases (PMTs). In the PCS pathway, choline is condensed directly with CDP-diacylglyceride to form PC in a reaction catalysed by PCS. Using cell-free extracts, it was demonstrated that Sinorhizobium meliloti, Agrobacterium tumefaciens, Rhizobium leguminosarum, Bradyrhizobium japonicum, Mesorhizobium loti and Legionella pneumophila have both PMT and PCS activities. In addition, Rhodobacter sphaeroides has PMT activity and Brucella melitensis, Pseudomonas aeruginosa and Borrelia burgdorferi have PCS activities. Genes from M. loti and L. pneumophila encoding a Pmt or a Pcs activity and the genes from P. aeruginosa and Borrelia burgdorferi responsible for Pcs activity have been identified. Based on these functional assignments and on genomic data, one might predict that if bacteria contain PC as a membrane lipid, they usually possess both bacterial pathways for PC biosynthesis. However, important pathogens such as Brucella melitensis, P. aeruginosa and Borrelia burgdorferi seem to be exceptional as they possess only the PCS pathway for PC formation.

  2. Dissemination of 6S RNA among Bacteria

    PubMed Central

    Wehner, Stefanie; Damm, Katrin; Hartmann, Roland K; Marz, Manja

    2014-01-01

    6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis. PMID:25483037

  3. Extracellular metalloproteases from bacteria.

    PubMed

    Wu, Ji-Wei; Chen, Xiu-Lan

    2011-10-01

    Bacterial extracellular metalloproteases (BEMPs) are a large group of metal-containing proteases secreted by heterotrophic bacteria. In this review, the diversity, structural characteristics, mechanisms of maturation, physiological roles, and applications of BEMPs are described. BEMPs are distributed among nine families of metalloproteases because of differences in primary sequences and structural characteristics. Until now, all of the BEMPs identified have been endoproteases harboring one catalytic Zn(2+) in the active centers. BEMPs are usually synthesized as inactive zymogens with a propeptide that is covalently linked to and inhibits the catalytic domain. The removal of the propeptides of BEMPs is dependent on other proteases or an autocleavage process. The main physiological function of BEMPs is to degrade environmental proteins and peptides for bacterial heterotrophic nutrition. As extracellular proteases, BEMPs vary greatly in enzymology properties to adapt to their respective environments. BEMPs have been widely used in the food and pharmaceutical industries. In order to broaden the application of BEMPs, it is essential to explore novel BEMPs and apply gene/protein engineering to improve the production and properties of promising BEMPs.

  4. Acoustofluidic bacteria separation.

    PubMed

    Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E; Zeng, Xiangqun; Huang, Tony Jun

    2017-01-01

    Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate E. coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells (RBCs) shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care (POC) sepsis diagnostic device.

  5. Tetrachloroethene-dehalogenating bacteria.

    PubMed

    Damborský, J

    1999-01-01

    Tetrachloroethene is a frequent groundwater contaminant often persisting in the subsurface environments. It is recalcitrant under aerobic conditions because it is in a highly oxidized state and is not readily susceptible to oxidation. Nevertheless, at least 15 organisms from different metabolic groups, viz. halorespirators (9), acetogens (2), methanogens (3) and facultative anaerobes (2), that are able to metabolize tetrachloroethene have been isolated as axenic cultures to-date. Some of these organisms couple dehalo-genation to energy conservation and utilize tetrachloroethene as the only source of energy while others dehalogenate tetrachloroethene fortuitously. Halorespiring organisms (halorespirators) utilize halogenated organic compounds as electron acceptors in an anaerobic respiratory process. Different organisms exhibit differences in the final products of tetrachloroethene dehalogenation, some strains convert tetrachloroethene to trichloroethene only, while others also carry out consecutive dehalogenation to dichloroethenes and vinyl chloride. Thus far, only a single organism, 'Dehalococcoides ethenogenes' strain 195, has been isolated which dechlorinates tetrachloroethene all the way down to ethylene. The majority of tetrachloroethene-dehalogenating organisms have been isolated only in the past few years and several of them, i.e., Dehalobacter restrictus, Desulfitobacterium dehalogenans, 'Dehalococcoides ethenogenes', 'Dehalospirillum multivorans', Desulfuromonas chloroethenica, and Desulfomonile tiedjei, are representatives of new taxonomic groups. This contribution summarizes the available information regarding the axenic cultures of the tetrachloroethene-dehalogenating bacteria. The present knowledge about the isolation of these organisms, their physiological characteristics, morphology, taxonomy and their ability to dechlorinate tetrachloroethene is presented to facilitate a comprehensive comparison.

  6. Sociomicrobiology and pathogenic bacteria

    PubMed Central

    Xavier, Joao B.

    2015-01-01

    The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action and potential drug targets, and much of medicine's success in the treatment of infectious disease comes from this approach. But many bacterial caused diseases cannot be explained by focusing on a single bacterium. Many aspects of bacterial pathogenesis will benefit from a more holistic approach that takes into account social interaction within bacteria of the same species and between different species in consortia such as the human microbiome. I discuss recent advances in the emerging discipline of sociomicrobiology and how it provides a framework to dissect microbial interactions in single and multispecies communities without compromising mechanistic detail. The study of bacterial pathogenesis can benefit greatly from incorporating concepts from other disciplines such as social evolution theory and microbial ecology where communities, their interactions with hosts and with the environment play key roles. PMID:27337482

  7. Marine bacteria exhibit a bipolar distribution.

    PubMed

    Sul, Woo Jun; Oliver, Thomas A; Ducklow, Hugh W; Amaral-Zettler, Linda A; Sogin, Mitchell L

    2013-02-05

    The microbial cosmopolitan dispersion hypothesis often invoked to explain distribution patterns driven by high connectivity of oceanographic water masses and widespread dispersal ability has never been rigorously tested. By using a global marine bacterial dataset and iterative matrix randomization simulation, we show that marine bacteria exhibit a significantly greater dispersal limitation than predicted by our null model using the "everything is everywhere" tenet with no dispersal limitation scenario. Specifically, marine bacteria displayed bipolar distributions (i.e., species occurring exclusively at both poles and nowhere else) significantly less often than in the null model. Furthermore, we observed fewer taxa present in both hemispheres but more taxa present only in a single hemisphere than expected under the null model. Each of these trends diverged further from the null expectation as the compared habitats became more geographically distant but more environmentally similar. Our meta-analysis supported a latitudinal gradient in bacterial diversity with higher richness at lower latitudes, but decreased richness toward the poles. Bacteria in the tropics also demonstrated narrower latitudinal ranges at lower latitudes and relatively larger ranges in higher latitudes, conforming to the controversial macroecological pattern of the "Rapoport rule." Collectively, our findings suggest that bacteria follow biogeographic patterns more typical of macroscopic organisms, and that dispersal limitation, not just environmental selection, likely plays an important role. Distributions of microbes that deliver critical ecosystem services, particularly those in polar regions, may be vulnerable to the same impacts that environmental stressors, climate warming, and degradation in habitat quality are having on biodiversity in animal and plant species.

  8. Multiphase Modelling of Bacteria Removal in a CSO Stream

    EPA Science Inventory

    Indicator bacteria are an important determinant of water quality in many water resources management situations. They are also one of the more complex phenomena to model and predict. Sources abound, the populations are dynamic and influenced by many factors, and mobility through...

  9. Multiphase Modelling of Bacteria Removal in a CSO Stream

    EPA Science Inventory

    Indicator bacteria are an important determinant of water quality in many water resources management situations. They are also one of the more complex phenomena to model and predict. Sources abound, the populations are dynamic and influenced by many factors, and mobility through...

  10. Watershed-Scale Fate and Transport of Bacteria

    USDA-ARS?s Scientific Manuscript database

    The added dimensionality provided by using multiple models to predict the fate and transport of bacteria at the watershed scale were investigated. Both HSPF and SWAT were applied to the 15.6 km2 catchment K of the Little River Experimental Watershed (LREW) in Georgia. Over the 7-year period from 19...

  11. Motility of Electric Cable Bacteria.

    PubMed

    Bjerg, Jesper Tataru; Damgaard, Lars Riis; Holm, Simon Agner; Schramm, Andreas; Nielsen, Lars Peter

    2016-07-01

    Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces with a highly variable speed of 0.5 ± 0.3 μm s(-1) (mean ± standard deviation) and time between reversals of 155 ± 108 s. They frequently moved forward in loops, and formation of twisted loops revealed helical rotation of the filaments. Cable bacteria responded to chemical gradients in their environment, and around the oxic-anoxic interface, they curled and piled up, with straight parts connecting back to the source of sulfide. Thus, it appears that motility serves the cable bacteria in establishing and keeping optimal connections between their distant electron donor and acceptors in a dynamic sediment environment. This study reports on the motility of cable bacteria, capable of transmitting electrons over centimeter distances. It gives us a new insight into their behavior in sediments and explains previously puzzling findings. Cable bacteria greatly influence their environment, and this article adds significantly to the body of knowledge about this organism. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Interactions between diatoms and bacteria.

    PubMed

    Amin, Shady A; Parker, Micaela S; Armbrust, E Virginia

    2012-09-01

    Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans.

  13. Bacteria detection by flow cytometry.

    PubMed

    Karo, Oliver; Wahl, Alexandra; Nicol, Sven-Boris; Brachert, Julia; Lambrecht, Bernd; Spengler, Hans-Peter; Nauwelaers, Frans; Schmidt, Michael; Schneider, Christian K; Müller, Thomas H; Montag, Thomas

    2008-01-01

    Since bacterial infection of the recipient has become the most frequent infection risk in transfusion medicine, suitable methods for bacteria detection in blood components are of great interest. Platelet concentrates are currently the focus of attention, as they are stored under temperature conditions, which enable the multiplication of most bacteria species contaminating blood donations. Rapid methods for bacteria detection allow testing immediately before transfusion in a bed-side like manner. This approach would overcome the sampling error observed in early sampling combined with culturing of bacteria and would, at least, prevent the transfusion of highly contaminated blood components leading to acute septic shock or even death of the patient. Flow cytometry has been demonstrated to be a rapid and feasible approach for detection of bacteria in platelet concentrates. The general aim of the current study was to develop protocols for the application of this technique under routine conditions. The effect of improved test reagents on practicability and sensitivity of the method is evaluated. Furthermore, the implementation of fluorescent absolute count beads as an internal standard is demonstrated. A simplified pre-incubation procedure has been undertaken to diminish the detection limit in a pragmatic manner. Additionally, the application of bacteria detection by flow cytometry as a culture method is shown, i.e., transfer of samples from platelet concentrates into a satellite bag, incubation of the latter at 37 degrees C, and measuring the contaminating bacteria in a flow cytometer.

  14. Commensal ocular bacteria degrade mucins.

    PubMed

    Berry, M; Harris, A; Lumb, R; Powell, K

    2002-12-01

    Antimicrobial activity in tears prevents infection while maintaining a commensal bacterial population. The relation between mucin and commensal bacteria was assessed to determine whether commensals possess mucinolytic activity, how degradation depends on mucin integrity, and whether mucins affect bacterial replication. Bacteria were sampled from healthy eyes and contact lenses from asymptomatic wearers. Intracellular mucins were extracted and purified from cadaver conjunctivas, and surface mucins from extended wear contact lenses. After exposure to bacteria, changes in mucin hydrodynamic volume (proteolytic cleavage) and subunit charge (oligosaccharide degradation) were assayed by size exclusion and ion exchange chromatography. The effect of mucin on bacterial replication was followed for up to 24 hours from the end of incubation with purified ocular mucins. Ocular bacteria decreased the hydrodynamic volume of intracellular and contact lens adherent mucins, irrespective of glycosylation density. A decrease in mucin sialylation was observed after exposure to commensal bacteria. Subunit charge distributions were generally shifted to lesser negative charge, consistent with loss of charged epitopes. Subunits with high negative charge, observed after digesting lightly adhering contact lens mucins with bacteria, suggest preferential cleavage sites in the mucin molecule. The presence of purified ocular mucin in the medium inhibited bacterial growth. Bacteria in the healthy ocular surface possess mucinolytic activity on both intact and surface processed mucins, targeted to discrete sites in the mucin molecule. Inhibition of bacterial growth by ocular mucins can be seen as part of the mucosal control of microbiota.

  15. Interactions between Diatoms and Bacteria

    PubMed Central

    Amin, Shady A.; Parker, Micaela S.

    2012-01-01

    Summary: Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans. PMID:22933565

  16. Motility of Electric Cable Bacteria

    PubMed Central

    Damgaard, Lars Riis; Holm, Simon Agner; Schramm, Andreas; Nielsen, Lars Peter

    2016-01-01

    ABSTRACT Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces with a highly variable speed of 0.5 ± 0.3 μm s−1 (mean ± standard deviation) and time between reversals of 155 ± 108 s. They frequently moved forward in loops, and formation of twisted loops revealed helical rotation of the filaments. Cable bacteria responded to chemical gradients in their environment, and around the oxic-anoxic interface, they curled and piled up, with straight parts connecting back to the source of sulfide. Thus, it appears that motility serves the cable bacteria in establishing and keeping optimal connections between their distant electron donor and acceptors in a dynamic sediment environment. IMPORTANCE This study reports on the motility of cable bacteria, capable of transmitting electrons over centimeter distances. It gives us a new insight into their behavior in sediments and explains previously puzzling findings. Cable bacteria greatly influence their environment, and this article adds significantly to the body of knowledge about this organism. PMID:27084019

  17. Surface Complexation Modelling in Metal-Mineral-Bacteria Systems

    NASA Astrophysics Data System (ADS)

    Johnson, K. J.; Fein, J. B.

    2002-12-01

    The reactive surfaces of bacteria and minerals can determine the fate, transport, and bioavailability of aqueous heavy metal cations. Geochemical models are instrumental in accurately accounting for the partitioning of the metals between mineral surfaces and bacteria cell walls. Previous research has shown that surface complexation modelling (SCM) is accurate in two-component systems (metal:mineral and metal:bacteria); however, the ability of SCMs to account for metal distribution in mixed metal-mineral-bacteria systems has not been tested. In this study, we measure aqueous Cd distributions in water-bacteria-mineral systems, and compare these observations with predicted distributions based on a surface complexation modelling approach. We measured Cd adsorption in 2- and 3-component batch adsorption experiments. In the 2-component experiments, we measured the extent of adsorption of 10 ppm aqueous Cd onto either a bacterial or hydrous ferric oxide sorbent. The metal:bacteria experiments contained 1 g/L (wet wt.) of B. subtilis, and were conducted as a function of pH; the metal:mineral experiments were conducted as a function of both pH and HFO content. Two types of 3-component Cd adsorption experiments were also conducted in which both mineral powder and bacteria were present as sorbents: 1) one in which the HFO was physically but not chemically isolated from the system using sealed dialysis tubing, and 2) others where the HFO, Cd and B. subtilis were all in physical contact. The dialysis tubing approach enabled the direct determination of the concentration of Cd on each sorbing surface, after separation and acidification of each sorbent. The experiments indicate that both bacteria and mineral surfaces can dominate adsorption in the system, depending on pH and bacteria:mineral ratio. The stability constants, determined using the data from the 2-component systems, along with those for other surface and aqueous species in the systems, were used with FITEQL to

  18. Mechanistic modeling of biocorrosion caused by biofilms of sulfate reducing bacteria and acid producing bacteria.

    PubMed

    Xu, Dake; Li, Yingchao; Gu, Tingyue

    2016-08-01

    Biocorrosion is also known as microbiologically influenced corrosion (MIC). Most anaerobic MIC cases can be classified into two major types. Type I MIC involves non-oxygen oxidants such as sulfate and nitrate that require biocatalysis for their reduction in the cytoplasm of microbes such as sulfate reducing bacteria (SRB) and nitrate reducing bacteria (NRB). This means that the extracellular electrons from the oxidation of metal such as iron must be transported across cell walls into the cytoplasm. Type II MIC involves oxidants such as protons that are secreted by microbes such as acid producing bacteria (APB). The biofilms in this case supply the locally high concentrations of oxidants that are corrosive without biocatalysis. This work describes a mechanistic model that is based on the biocatalytic cathodic sulfate reduction (BCSR) theory. The model utilizes charge transfer and mass transfer concepts to describe the SRB biocorrosion process. The model also includes a mechanism to describe APB attack based on the local acidic pH at a pit bottom. A pitting prediction software package has been created based on the mechanisms. It predicts long-term pitting rates and worst-case scenarios after calibration using SRB short-term pit depth data. Various parameters can be investigated through computer simulation. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Cytokinesis in Bacteria

    PubMed Central

    Errington, Jeffery; Daniel, Richard A.; Scheffers, Dirk-Jan

    2003-01-01

    Work on two diverse rod-shaped bacteria, Escherichia coli and Bacillus subtilis, has defined a set of about 10 conserved proteins that are important for cell division in a wide range of eubacteria. These proteins are directed to the division site by the combination of two negative regulatory systems. Nucleoid occlusion is a poorly understood mechanism whereby the nucleoid prevents division in the cylindrical part of the cell, until chromosome segregation has occurred near midcell. The Min proteins prevent division in the nucleoid-free spaces near the cell poles in a manner that is beginning to be understood in cytological and biochemical terms. The hierarchy whereby the essential division proteins assemble at the midcell division site has been worked out for both E. coli and B. subtilis. They can be divided into essentially three classes depending on their position in the hierarchy and, to a certain extent, their subcellular localization. FtsZ is a cytosolic tubulin-like protein that polymerizes into an oligomeric structure that forms the initial ring at midcell. FtsA is another cytosolic protein that is related to actin, but its precise function is unclear. The cytoplasmic proteins are linked to the membrane by putative membrane anchor proteins, such as ZipA of E. coli and possibly EzrA of B. subtilis, which have a single membrane span but a cytoplasmic C-terminal domain. The remaining proteins are either integral membrane proteins or transmembrane proteins with their major domains outside the cell. The functions of most of these proteins are unclear with the exception of at least one penicillin-binding protein, which catalyzes a key step in cell wall synthesis in the division septum. PMID:12626683

  20. Motility enhancement of bacteria actuated microstructures using selective bacteria adhesion.

    PubMed

    Park, Sung Jun; Bae, Hyeoni; Kim, Joonhwuy; Lim, Byungjik; Park, Jongoh; Park, Sukho

    2010-07-07

    Microrobots developed by the technological advances are useful for application in various fields. Nevertheless, they have limitations with respect to their actuator and motility. Our experiments aim to determine whether a bioactuator using the flagellated bacteria Serratia marcescens would enhance the motility of microrobots. In this study, we investigate that the flagellated bacteria Serratia marcescens could be utilized as actuators for SU-8 microstructures by bovine serum albumin-selective patterning. Firstly, we analyze the adherence of the bacteria to the SU-8 micro cube by selective patterning using 5% BSA. The results show that number of attached-bacteria in the uncoated side of the selectively- coated micro cube with BSA increased by 200% compared with that in all sides of the non treated micro cube. Secondly, the selectively BSA coated micro cube had 210% higher motility than the uncoated micro cube. The results revealed that the bacteria patterned to a specific site using 5% BSA significantly increase the motility of the bacteria actuated microstructure.

  1. Environmental sources of fecal bacteria

    USGS Publications Warehouse

    Byappanahalli, Muruleedhara N.; Ishii, Satoshi; Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    This chapter provides a review of the research on environmental occurrences of faecal indicator bacteria in a variety of terrestrial and aquatic habitats under different geographic and climatic conditions, and discusses how these external sources may affect surface water quality.

  2. Biopreservation by lactic acid bacteria.

    PubMed

    Stiles, M E

    1996-10-01

    Biopreservation refers to extended storage life and enhanced safety of foods using the natural microflora and (or) their antibacterial products. Lactic acid bacteria have a major potential for use in biopreservation because they are safe to consume and during storage they naturally dominate the microflora of many foods. In milk, brined vegetables, many cereal products and meats with added carbohydrate, the growth of lactic acid bacteria produces a new food product. In raw meats and fish that are chill stored under vacuum or in an environment with elevated carbon dioxide concentration, the lactic acid bacteria become the dominant population and preserve the meat with a "hidden' fermentation. The same applies to processed meats provided that the lactic acid bacteria survive the heat treatment or they are inoculated onto the product after heat treatment. This paper reviews the current status and potential for controlled biopreservation of foods.

  3. Clinical microbiology of coryneform bacteria.

    PubMed Central

    Funke, G; von Graevenitz, A; Clarridge, J E; Bernard, K A

    1997-01-01

    Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed. PMID:8993861

  4. [Nosocomial bacteria: profiles of resistance].

    PubMed

    Sow, A I

    2005-01-01

    Nosocomial infections may be parasitic, mycosal or viral, but bacterial infections are more frequent. They are transmitted by hands or by oral route. This paper describes the main bacteria responsive of nosocomial infections, dominated by Staphylococcus, enterobacteria and Pseudomonas aeruginosa. The author relates natural and savage profiles of these bacterias, characterized by multiresistance due to large use of antibiotics. Knowledge of natural resistance and verification of aquired resistance permit to well lead probabilist antibiotherapy.

  5. The Mechanical World of Bacteria

    PubMed Central

    Persat, Alexandre; Nadell, Carey D.; Kim, Minyoung Kevin; Ingremeau, Francois; Siryaporn, Albert; Drescher, Knut; Wingreen, Ned S.; Bassler, Bonnie L.; Gitai, Zemer; Stone, Howard A.

    2015-01-01

    Summary In the wild, bacteria are predominantly associated with surfaces as opposed to existing as free-swimming, isolated organisms. They are thus subject to surface-specific mechanics including hydrodynamic forces, adhesive forces, the rheology of their surroundings and transport rules that define their encounters with nutrients and signaling molecules. Here, we highlight the effects of mechanics on bacterial behaviors on surfaces at multiple length scales, from single bacteria to the development of multicellular bacterial communities such as biofilms. PMID:26000479

  6. Caenorhabditis elegans responses to bacteria from its natural habitats

    PubMed Central

    Rowedder, Holli; Braendle, Christian; Félix, Marie-Anne; Ruvkun, Gary

    2016-01-01

    Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology. PMID:27317746

  7. Cable Bacteria in Freshwater Sediments.

    PubMed

    Risgaard-Petersen, Nils; Kristiansen, Michael; Frederiksen, Rasmus B; Dittmer, Anders Lindequist; Bjerg, Jesper Tataru; Trojan, Daniela; Schreiber, Lars; Damgaard, Lars Riis; Schramm, Andreas; Nielsen, Lars Peter

    2015-09-01

    In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. Bioreporter bacteria for landmine detection

    SciTech Connect

    Burlage, R.S.; Youngblood, T.; Lamothe, D.

    1998-04-01

    Landmines (and other UXO) gradually leak explosive chemicals into the soil at significant concentrations. Bacteria, which have adapted to scavenge low concentrations of nutrients, can detect these explosive chemicals. Uptake of these chemicals results in the triggering of specific bacterial genes. The authors have created genetically recombinant bioreporter bacteria that detect small concentrations of energetic chemicals. These bacteria are genetically engineered to produce a bioluminescent signal when they contact specific explosives. A gene for a brightly fluorescent compound can be substituted for increased sensitivity. By finding the fluorescent bacteria, you find the landmine. Detection might be accomplished using stand-off illumination of the minefield and GPS technology, which would result in greatly reduced risk to the deminers. Bioreporter technology has been proven at the laboratory scale, and will be tested under field conditions in the near future. They have created a bacterial strain that detects sub-micromolar concentrations of o- and p-nitrotoluene. Related bacterial strains were produced using standard laboratory protocols, and bioreporters of dinitrotoluene and trinitrotoluene were produced, screening for activity with the explosive compounds. Response time is dependent on the growth rate of the bacteria. Although frill signal production may require several hours, the bacteria can be applied over vast areas and scanned quickly, producing an equivalent detection speed that is very fast. This technology may be applicable to other needs, such as locating buried explosives at military and ordnance/explosive manufacturing facilities.

  9. Cable Bacteria in Freshwater Sediments

    PubMed Central

    Kristiansen, Michael; Frederiksen, Rasmus B.; Dittmer, Anders Lindequist; Bjerg, Jesper Tataru; Trojan, Daniela; Schreiber, Lars; Damgaard, Lars Riis; Schramm, Andreas; Nielsen, Lars Peter

    2015-01-01

    In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage. PMID:26116678

  10. Filtrating forms of soil bacteria

    NASA Astrophysics Data System (ADS)

    Van'kova, A. A.; Ivanov, P. I.; Emtsev, V. T.

    2013-03-01

    Filtrating (ultramicroscopic) forms (FF) of bacteria were studied in a soddy-podzolic soil and the root zone of alfalfa plants as part of populations of the most widespread physiological groups of soil bacteria. FF were obtained by filtering soil solutions through membrane filters with a pore diameter of 0.22 μm. It was established that the greater part of the bacteria in the soil and in the root zone of the plants has an ultramicroscopic size: the average diameter of the cells is 0.3 μm, and their length is 0.6 μm, which is significantly less than the cell size of banal bacteria. The number of FF varies within a wide range depending on the physicochemical conditions of the habitat. The FF number's dynamics in the soil is of a seasonal nature; i.e., the number of bacteria found increases in the summer and fall and decreases in the winter-spring period. In the rhizosphere of the alfalfa, over the vegetation period, the number of FF and their fraction in the total mass of the bacteria increase. A reverse tendency is observed in the rhizoplane. The morphological particularities (identified by an electron microscopy) and the nature of the FF indicate their physiological activity.

  11. SOME STATISTICAL ISSUES RELATED TO MULTIPLE LINEAR REGRESSION MODELING OF BEACH BACTERIA CONCENTRATIONS

    EPA Science Inventory

    As a fast and effective technique, the multiple linear regression (MLR) method has been widely used in modeling and prediction of beach bacteria concentrations. Among previous works on this subject, however, several issues were insufficiently or inconsistently addressed. Those is...

  12. SOME STATISTICAL ISSUES RELATED TO MULTIPLE LINEAR REGRESSION MODELING OF BEACH BACTERIA CONCENTRATIONS

    EPA Science Inventory

    As a fast and effective technique, the multiple linear regression (MLR) method has been widely used in modeling and prediction of beach bacteria concentrations. Among previous works on this subject, however, several issues were insufficiently or inconsistently addressed. Those is...

  13. Isolation and Identification of Concrete Environment Bacteria

    NASA Astrophysics Data System (ADS)

    Irwan, J. M.; Anneza, L. H.; Othman, N.; Husnul, T.; Alshalif, A. F.

    2016-07-01

    This paper presents the isolation and molecular method for bacteria identification through PCR and DNA sequencing. Identification of the bacteria species is required in order to fully utilize the bacterium capability for precipitation of calcium carbonate in concrete. This process is to enable the addition of suitable catalyst according to the bacterium enzymatic pathway that is known through the bacteria species used. The objective of this study is to isolate, enriched and identify the bacteria species. The bacteria in this study was isolated from fresh urine and acid mine drainage water, Kota Tinggi, Johor. Enrichment of the isolated bacteria was conducted to ensure the bacteria survivability in concrete. The identification of bacteria species was done through polymerase chain reaction (PCR) and rRDNA sequencing. The isolation and enrichment of the bacteria was done successfully. Whereas, the results for bacteria identification showed that the isolated bacteria strains are Bacillus sp and Enterococus faecalis.

  14. Protein Complexes in Bacteria

    PubMed Central

    Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter

    2015-01-01

    Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

  15. DLVO, hydrophobic, capillary and hydrodynamic forces acting on bacteria at solid-air-water interfaces: Their relative impact on bacteria deposition mechanisms in unsaturated porous media.

    PubMed

    Bai, Hongjuan; Cochet, Nelly; Pauss, André; Lamy, Edvina

    2017-02-01

    Experimental and modeling studies were performed to investigate bacteria deposition behavior in unsaturated porous media. The coupled effect of different forces, acting on bacteria at solid-air-water interfaces and their relative importance on bacteria deposition mechanisms was explored by calculating Derjaguin-Landau-Verwey-Overbeek (DLVO) and non-DLVO interactions such as hydrophobic, capillary and hydrodynamic forces. Negatively charged non-motile bacteria and quartz sands were used in packed column experiments. The breakthrough curves and retention profiles of bacteria were simulated using the modified Mobile-IMmobile (MIM) model, to identify physico-chemical attachment or physical straining mechanisms involved in bacteria retention. These results indicated that both mechanisms might occur in both sand. However, the attachment was found to be a reversible process, because attachment coefficients were similar to those of detachment. DLVO calculations supported these results: the primary minimum did not exist, suggesting no permanent retention of bacteria to solid-water and air-water interfaces. Calculated hydrodynamic and resisting torques predicted that bacteria detachment in the secondary minimum might occur. The capillary potential energy was greater than DLVO, hydrophobic and hydrodynamic potential energies, suggesting that film straining by capillary forces might largely govern bacteria deposition under unsaturated conditions.

  16. Microgravity effects on magnetotactic bacteria

    NASA Astrophysics Data System (ADS)

    Urban, James E.

    1998-01-01

    An unusual group of iron bacteria has recently been discovered which form inclusion bodies containing a form of iron oxide known as magnetite (ferrosoferric oxide, Fe3O4.) The inclusions are of a nano-particle size, are encased within a protein envelope, and are called magnetosomes. Magnetosomes are arranged adjacent to one another and parallel to the long axis of the cell such that cells appear to contain an electron-dense string of beads. The bacteria containing magnetosomes exhibit metal reductase activity, an activity critical to element recycling in nature, and the inclusions are a means for the organism to sequester reduced iron atoms and thereby keep iron reduction stoichiometry favorable. The magnetosomes also allow the bacteria to display magnetotaxis, which is movement in response to a magnetic field, such as the north or south magnetic poles. It is presumed that the bacteria use the alignment to the earth's magnetic field to orient themselves downward towards sediments where the habitat is favorable to their growth and metabolism. The comparatively few species of these bacteria isolated in the northern and southern hemispheres respond to magnetic north and south respectively, or alternatively respond only to the magnetic pole of the hemisphere from which they were isolated. This apparent dichotomy in response to magnetism could mean that the organisms are not responding to magnetism, per se, but instead are using the magnetosomes to respond to gravity. To resolve if magnetosomes respond to gravity in addition to magnetism we have used Magnetospirillum magnetotacticum, a well-studied magnetotactic bacterium isolated in the northern hemisphere, to examine magnetotactic behavior in the absence of gravity. Experiments to compare the orientation of Magnetospirillum magnetotacticum to north- or south-pole magnets were conducted in normal gravity and in the microgravity environments aboard the Space Shuttle and Space Station MIR. In each of the microgravity

  17. Periodontitis, periodontopathic bacteria and lactoferrin.

    PubMed

    Wakabayashi, Hiroyuki; Kondo, Ichiro; Kobayashi, Tetsuo; Yamauchi, Koji; Toida, Tomohiro; Iwatsuki, Keiji; Yoshie, Hiromasa

    2010-06-01

    Lactoferrin (LF) is a component of saliva and is suspected to be a defense factor against oral pathogens including Streptococcus mutans and Candida albicans. Periodontitis is a very common oral disease caused by periodontopathic bacteria. Antimicrobial activities and other biological effects of LF against representative periodontopathic bacteria, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia, have been widely studied. Association of polymorphisms in LF with incidence of aggressive periodontitis and the role of LF in the gingival crevicular fluid as a marker of periodontitis severity have also been reported. Periodontopathic bacteria reside as a biofilm in supragingival and subgingival plaque. Our recent study indicated that LF exhibits antibacterial activity against planktonic forms of P. gingivalis and P. intermedia at higher concentrations, and furthermore, LF effectively inhibits biofilm formation and reduces the established biofilm of these bacteria at physiological concentrations. A small-scale clinical study indicated that oral administration of bovine LF reduces P. gingivalis and P. intermedia in the subgingival plaque of chronic periodontitis patients. LF seems to be a biofilm inhibitor of periodontopathic bacteria in vitro and in vivo.

  18. Human body may produce bacteria.

    PubMed

    Salerian, Alen J

    2017-06-01

    "Human body may produce bacteria" proposes that human body may produce bacteria and represent an independent source of infections contrary to the current paradigm of infectious disorders proposed by Louis Pasteur in 1880. The following observations are consistent with this hypothesis: A. Bidirectional transformations of both living and nonliving things have been commonly observed in nature. B. Complex multicellular organisms harbor the necessary properties to produce bacteria (water, nitrogen and oxygen). C. Physical laws suggest any previously observed phenomenon or action will occur again (life began on earth; a non living thing). D. Animal muscle cells may generate energy (fermentation). E. Sterilized food products (i.e. boiled eggs), may produce bacteria and fungus under special conditions and without any exposure to foreign living cells. "Human body may produce bacteria" may challenge the current medical paradigm that views human infectious disorders as the exclusive causative byproducts of invading foreign cells. It may also introduce new avenues to treat infectious disorders. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Biosynthesis of phosphatidylcholine in bacteria.

    PubMed

    Sohlenkamp, Christian; López-Lara, Isabel M; Geiger, Otto

    2003-03-01

    Phosphatidylcholine (PC) is the major membrane-forming phospholipid in eukaryotes and can be synthesized by either of two pathways, the methylation pathway or the CDP-choline pathway. Many prokaryotes lack PC, but it can be found in significant amounts in membranes of rather diverse bacteria and based on genomic data, we estimate that more than 10% of all bacteria possess PC. Enzymatic methylation of phosphatidylethanolamine via the methylation pathway was thought to be the only biosynthetic pathway to yield PC in bacteria. However, a choline-dependent pathway for PC biosynthesis has been discovered in Sinorhizobium meliloti. In this pathway, PC synthase, condenses choline directly with CDP-diacylglyceride to form PC in one step. A number of symbiotic (Rhizobium leguminosarum, Mesorhizobium loti) and pathogenic (Agrobacterium tumefaciens, Brucella melitensis, Pseudomonas aeruginosa, Borrelia burgdorferi and Legionella pneumophila) bacteria seem to possess the PC synthase pathway and we suggest that the respective eukaryotic host functions as the provider of choline for this pathway. Pathogens entering their hosts through epithelia (Streptococcus pneumoniae, Haemophilus influenzae) require phosphocholine substitutions on their cell surface components that are biosynthetically also derived from choline supplied by the host. However, the incorporation of choline in these latter cases proceeds via choline phosphate and CDP-choline as intermediates. The occurrence of two intermediates in prokaryotes usually found as intermediates in the eukaryotic CDP-choline pathway for PC biosynthesis raises the question whether some bacteria might form PC via a CDP-choline pathway.

  20. Bacteria foraging in turbulent waters

    NASA Astrophysics Data System (ADS)

    Taylor, John; Tang, Wenbo; Stocker, Roman

    2009-11-01

    Marine bacteria are the Ocean's recyclers, contributing to as much as 50% of the productivity of the marine food web. Bacteria forage on patches of dissolved nutrients using chemotaxis, the ability to swim up chemical gradients. As turbulence is ubiquitous in the Ocean, it is important to understand how turbulent flow conditions affect bacterial foraging. We used three-dimensional, isotropic direct numerical simulations coupled with a bacterial transport equation to address this problem. After the flow is continuously forced until it reaches a steady state, microscale nutrient patches are injected into the turbulent flow, and stirring produces thin nutrient filaments. Two populations of bacteria compete against each other: one population is motile and chemotactic (`active'), the other is non-motile (`passive'). The distribution of both populations is initially uniform. Chemotaxis allows active bacteria to cluster near the center of the nutrient filaments, increasing their nutrient uptake relative to passive bacteria. Increasing the turbulence intensity increases the short-term chemotactic advantage by quickly producing large gradients in the nutrient concentration, but also leads to rapid mixing of the nutrient field, which makes the chemotactic advantage short-lived. The results suggest that the evolutionary advantage of chemotaxis, based on the increase in nutrient uptake relative to the energetic cost of swimming, strongly depends on the turbulence level.

  1. Quantification of Spore-forming Bacteria Carried by Dust Particles

    NASA Technical Reports Server (NTRS)

    Lin, Ying; Cholakian, Tanya; Gao, Wenming; Osman, Shariff; Barengoltz, Jack

    2006-01-01

    In order to establish a biological contamination transport model for predicting the cross contamination risk during spacecraft assembly and upon landing on Mars, it is important to understand the relationship between spore-forming bacteria and their carrier particles. We conducted air and surface sampling in indoor, outdoor, and cleanroom environments to determine the ratio of spore forming bacteria to their dust particle carriers of different sizes. The number of spore forming bacteria was determined from various size groups of particles in a given environment. Our data also confirms the existence of multiple spores on a single particle and spore clumps. This study will help in developing a better bio-contamination transport model, which in turn will help in determining forward contamination risks for future missions.

  2. Quantification of Spore-forming Bacteria Carried by Dust Particles

    NASA Technical Reports Server (NTRS)

    Lin, Ying; Cholakian, Tanya; Gao, Wenming; Osman, Shariff; Barengoltz, Jack

    2006-01-01

    In order to establish a biological contamination transport model for predicting the cross contamination risk during spacecraft assembly and upon landing on Mars, it is important to understand the relationship between spore-forming bacteria and their carrier particles. We conducted air and surface sampling in indoor, outdoor, and cleanroom environments to determine the ratio of spore forming bacteria to their dust particle carriers of different sizes. The number of spore forming bacteria was determined from various size groups of particles in a given environment. Our data also confirms the existence of multiple spores on a single particle and spore clumps. This study will help in developing a better bio-contamination transport model, which in turn will help in determining forward contamination risks for future missions.

  3. Commensal bacteria and cutaneous immunity.

    PubMed

    Nakamizo, Satoshi; Egawa, Gyohei; Honda, Tetsuya; Nakajima, Saeko; Belkaid, Yasmine; Kabashima, Kenji

    2015-01-01

    The skin is the human body's largest organ and is home to a diverse and complex variety of innate and adaptive immune functions that protect against pathogenic invasion. Recent studies have demonstrated that cutaneous commensal bacteria modulated the host immune system. For example, Staphylococcus epidermidis, a skin commensal bacterium, has been demonstrated to induce cutaneous interferon (IFN)-γ- and interleukin (IL)-17A-producing T cells. In addition, cutaneous microbiota changes occur in the chronic inflammatory skin disorders, such as atopic dermatitis, and may influence the activity of skin diseases. In this article, we will review the recent findings related to the interactions of the commensal bacteria with skin homeostasis and discuss the role of the dysbiosis of these bacteria in the pathogenesis of skin diseases.

  4. Methylotrophic bacteria in sustainable agriculture.

    PubMed

    Kumar, Manish; Tomar, Rajesh Singh; Lade, Harshad; Paul, Diby

    2016-07-01

    Excessive use of chemical fertilizers to increase production from available land has resulted in deterioration of soil quality. To prevent further soil deterioration, the use of methylotrophic bacteria that have the ability to colonize different habitats, including soil, sediment, water, and both epiphytes and endophytes as host plants, has been suggested for sustainable agriculture. Methylotrophic bacteria are known to play a significant role in the biogeochemical cycle in soil ecosystems, ultimately fortifying plants and sustaining agriculture. Methylotrophs also improve air quality by using volatile organic compounds such as dichloromethane, formaldehyde, methanol, and formic acid. Additionally, methylotrophs are involved in phosphorous, nitrogen, and carbon cycling and can help reduce global warming. In this review, different aspects of the interaction between methylotrophs and host plants are discussed, including the role of methylotrophs in phosphorus acquisition, nitrogen fixation, phytohormone production, iron chelation, and plant growth promotion, and co-inoculation of these bacteria as biofertilizers for viable agriculture practices.

  5. Genetic transfer in acidophilic bacteria

    SciTech Connect

    Roberto, F.F.; Glenn, A.W.; Bulmer, D.; Ward, T.E.

    1990-01-01

    There is increasing interest in the use of microorganisms to recover metals from ores, as well as to remove sulfur from coal. These so-called bioleaching processes are mediated by a number of bacteria. The best-studied of these organisms are acidophiles including Thiobacillus and Acidiphilium species. Our laboratory has focused on developing genetic strategies to allow the manipulation of acidophilic bacteria to improve and augment their utility in large scale operations. We have recently been successful in employing conjugation for interbacterial transfer of genetic information, as well as in directly transforming Acidiphilium by use of electroporation. We are now testing the properties of IncPl, IncW and IncQ plasmid vectors in Acidiphilium to determine their relative usefulness in routine manipulation of acidophiles and transfer between organisms. This study also allows us to determine the natural ability of these bacteria to transfer genetic material amongst themselves in their particular environment. 21 refs., 3 figs., 2 tabs.

  6. Chemical signature of magnetotactic bacteria.

    PubMed

    Amor, Matthieu; Busigny, Vincent; Durand-Dubief, Mickaël; Tharaud, Mickaël; Ona-Nguema, Georges; Gélabert, Alexandre; Alphandéry, Edouard; Menguy, Nicolas; Benedetti, Marc F; Chebbi, Imène; Guyot, François

    2015-02-10

    There are longstanding and ongoing controversies about the abiotic or biological origin of nanocrystals of magnetite. On Earth, magnetotactic bacteria perform biomineralization of intracellular magnetite nanoparticles under a controlled pathway. These bacteria are ubiquitous in modern natural environments. However, their identification in ancient geological material remains challenging. Together with physical and mineralogical properties, the chemical composition of magnetite was proposed as a promising tracer for bacterial magnetofossil identification, but this had never been explored quantitatively and systematically for many trace elements. Here, we determine the incorporation of 34 trace elements in magnetite in both cases of abiotic aqueous precipitation and of production by the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1. We show that, in biomagnetite, most elements are at least 100 times less concentrated than in abiotic magnetite and we provide a quantitative pattern of this depletion. Furthermore, we propose a previously unidentified method based on strontium and calcium incorporation to identify magnetite produced by magnetotactic bacteria in the geological record.

  7. The Role of Bacteria in Iron Biomineralization

    NASA Astrophysics Data System (ADS)

    Konhauser, K. O.

    2012-04-01

    Bacteria contribute significantly to the development of extremely fine-grained iron mineral precipitates, including oxyhydroxides, carbonates, silicates, phosphates, and sulphides. They influence biomineralization in two significant ways. First, bacteria possess a negative surface charge at pH values characteristic of most natural environments, and in doing so, will become reactive towards metal cations. Once bound, those cations react with more ions, potentially leading to mineral precipitation if a state of supersaturation is achieved. Second, during metabolism, the bacterium affects the redox and saturation states of the fluids around the living cells. In this regard, the microenvironment surrounding each cell can be quite different from the bulk aqueous environment, and as a result, mineral phases form that would not normally be predicted from the geochemistry of the bulk fluid. The impact that iron biomineralization has on elemental cycling in aqueous and sedimentary environments cannot be overstated because many major elemental cycles are strongly linked to iron biomineralizing processes. Although individual 'biomineral' grains are micrometer in scale, if one adds the total amount of biomineralizing biomass, it is not difficult to imagine how they can be significant in partitioning metals from the hydrosphere into the sedimentary system. Indeed, the extensive record of banded iron formation (BIF), from 3.8 to 0.5 billion years ago, testifies to the enormous magnitude of ferric iron sequestration into the sediments throughout much of Earth's history.

  8. Rapid Enrichment of Dehalococcoides-Like Bacteria by Partial Hydrophobic Separation

    PubMed Central

    Temme, Hanna R.; Sande, Kipp; Yan, Tao

    2017-01-01

    limit their predictable use for the bioremediation of contaminated sites. This paper describes a method to quickly separate Dehalococcoides-like bacteria, a group of organisms containing organohalide-respiring bacteria, from other bacteria in a mixed community. From this work, Dehalococcoides-like bacteria appear to have a hydrophobic cell surface, facilitating a rapid (20 min) partial separation from a mixed culture at the surface of a hydrophobic liquid. This method was verified in a polychlorinated biphenyl-enriched sediment-free culture, an anaerobic digester sludge, and uncontaminated sediment. The method described can drastically reduce the amount of time required to partially separate Dehalococcoides-like bacteria from a complex mixed culture, improving researchers' ability to study these important bacteria. PMID:28087526

  9. Periodic reversals allow bacteria to swarm

    NASA Astrophysics Data System (ADS)

    Wu, Yilin; Kaiser, Dale; Jiang, Yi; Alber, Mark

    2009-03-01

    Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm track their neighbors while interfering minimally with the motion of others'. We choose myxobacteria as our model system. Individual myxobacteria cells regularly reverse their gliding directions. With a cell- and behavior-based computational model, we show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal myxobacteria cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Our work suggests a crucial componentin the general behavioral algorithm governing bacterial swarming.

  10. Structure Formation by Self Attracting Bacteria

    NASA Astrophysics Data System (ADS)

    Betterton, Meredith; Brenner, Michael

    1998-11-01

    Consider a box of material (initially of constant density) which both attracts itself and has some dispersive character. Eventually the material will clump into high density regions. The question addressed in this talk is: what are the number and sizes of the clumps that are formed? We address this in the context of chemotactic collapse of e. Coli. Experiments have given a detailed picture of the collapse process, showing that the bacteria initially form cylindrical structures which then destabilize into spherical clumps. On the other hand, linear stability analysis predicts that the system should form spherical aggregates directly. Our theory for the structure formation develops a generalization of an idea of Zeldovich (invented for a problem in cosmology). We present various calculations and numerical simulations to explain the patterns observed in experiments.

  11. Evolution of filamentous bacteria during urban wastewater treatment by MBR.

    PubMed

    Parada-Albarracín, J A; Marin, E; Pérez, J I; Moreno, B; Gómez, M A

    2012-01-01

    Evolution of filamentous bacteria in two full-scale experimental MBR systems (microfiltration and ultrafiltration) was studied during two years. Sludge Retention Time (SRT) and Hydraulic Retention Time (HRT) were modified and acted as variables, together with temperature and variation in loading. With SRT values between 20 and 35 d and HRT between 31 and 40 h, both MBR systems presented a high density of filamentous bacteria, according to the Filamentous Index (FI) and Simplified Technique of Filamentous Count (STFC). Highest density was achieved when contaminant loads were high and temperature was low. However, the elevated presence of filamentous bacteria did not affect the quality of effluent or the permeability of the membranes. Nocardioform bacteria showed a high degree of adaptation to the characteristics of the system. Predominance of Nocardioforms gave rise to isolated episodes of massive growth at temperatures between 15 and 20°C, which in turn caused episodes of intense foaming whose most significant consequence was a loss in biomass, leading to a slight increase in transmembrane pressure. In the light of these results, FI and STFC should not be considered as suitable tools for predicting operational problems deriving from filamentous bacteria in MBR systems, which could be prevented through identification.

  12. Characterization of Bioluminescent Derivatives of Assimilable Organic Carbon Test Bacteria

    PubMed Central

    Haddix, Pryce L.; Shaw, Nancy J.; LeChevallier, Mark W.

    2004-01-01

    The assimilable organic carbon (AOC) test is a standardized measure of the bacterial growth potential of treated water. We describe the design and initial development of an AOC assay that uses bioluminescent derivatives of AOC test bacteria. Our assay is based on the observation that bioluminescence peaks at full cell yield just prior to the onset of the stationary phase during growth in a water sample. Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX bacteria were mutagenized with luxCDABE operon fusion and inducible transposons and were selected on minimal medium. Independent mutants were screened for high luminescence activity and predicted AOC assay sensitivity. All mutants tested were able to grow in tap water under AOC assay conditions. Strains P-17 I5 (with p-aminosalicylate inducer) and NOX I3 were chosen for use in the bioluminescence AOC test. Peak bioluminescence and plate count AOC were linearly related for both test bacteria, though data suggest that the P-17 bioluminescence assay requires more consistent luminescence monitoring. Bioluminescence results were obtained 2 or 3 days postinoculation, compared with 5 days for the ATP luminescence AOC assay and 8 days for the plate count assay. Plate count AOC assay results for nonmutant and bioluminescent bacteria from 36 water samples showed insignificant differences, indicating that the luminescent bacteria retained a full range of AOC measurement capability. This bioluminescence method is amenable to automation with a microplate format with programmable reagent injection. PMID:14766564

  13. Characterization of bioluminescent derivatives of assimilable organic carbon test bacteria.

    PubMed

    Haddix, Pryce L; Shaw, Nancy J; LeChevallier, Mark W

    2004-02-01

    The assimilable organic carbon (AOC) test is a standardized measure of the bacterial growth potential of treated water. We describe the design and initial development of an AOC assay that uses bioluminescent derivatives of AOC test bacteria. Our assay is based on the observation that bioluminescence peaks at full cell yield just prior to the onset of the stationary phase during growth in a water sample. Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX bacteria were mutagenized with luxCDABE operon fusion and inducible transposons and were selected on minimal medium. Independent mutants were screened for high luminescence activity and predicted AOC assay sensitivity. All mutants tested were able to grow in tap water under AOC assay conditions. Strains P-17 I5 (with p-aminosalicylate inducer) and NOX I3 were chosen for use in the bioluminescence AOC test. Peak bioluminescence and plate count AOC were linearly related for both test bacteria, though data suggest that the P-17 bioluminescence assay requires more consistent luminescence monitoring. Bioluminescence results were obtained 2 or 3 days postinoculation, compared with 5 days for the ATP luminescence AOC assay and 8 days for the plate count assay. Plate count AOC assay results for nonmutant and bioluminescent bacteria from 36 water samples showed insignificant differences, indicating that the luminescent bacteria retained a full range of AOC measurement capability. This bioluminescence method is amenable to automation with a microplate format with programmable reagent injection.

  14. Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria.

    PubMed

    Smriga, Steven; Fernandez, Vicente I; Mitchell, James G; Stocker, Roman

    2016-02-09

    The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These "phycospheres" may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean.

  15. Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

    PubMed Central

    Smriga, Steven; Fernandez, Vicente I.; Mitchell, James G.; Stocker, Roman

    2016-01-01

    The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These “phycospheres” may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean. PMID:26802122

  16. Hydrodynamic entrapment of bacteria swimming near a solid surface

    NASA Astrophysics Data System (ADS)

    Giacché, Davide; Ishikawa, Takuji; Yamaguchi, Takami

    2010-11-01

    The near-surface motility of bacteria is important in the initial formation of biofilms and in many biomedical applications. The swimming motion of Escherichia coli near a solid surface is investigated both numerically and experimentally. A boundary element method is used to predict the hydrodynamic entrapment of E. coli bacteria, their trajectories, and the minimum separation of the cell from the surface. The numerical results show the existence of a stable swimming distance from the boundary that depends only on the shape of the cell body and the flagellum. The experimental validation of the numerical approach allows one to use the numerical method as a predictive tool to estimate with reasonable accuracy the near-wall motility of swimming bacteria of known geometry. The analysis of the numerical database demonstrated the existence of a correlation between the radius of curvature of the near-wall circular trajectory and the separation gap. Such correlation allows an indirect estimation of either of the two quantities by a direct measure of the other without prior knowledge of the cell geometry. This result may prove extremely important in those biomedical and technical applications in which the near-wall behavior of bacteria is of fundamental importance.

  17. Antibacterial susceptibility of plaque bacteria.

    PubMed

    Newman, M G; Hulem, C; Colgate, J; Anselmo, C

    1979-07-01

    Selected anaerobic, capnophilic and facultative bacteria isolated from patients with various forms of periodontal health and disease were tested for their susceptibility to antibiotics and antimicrobial agents. Specific bactericidal and minimum inhibitory concentrations were compared to disc zone diameters, thereby generating new standards for the potential selection of antimicrobial agents.

  18. Manipulating Genetic Material in Bacteria

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Lisa Crawford, a graduate research assistant from the University of Toledo, works with Laurel Karr of Marshall Space Flight Center (MSFC) in the molecular biology laboratory. They are donducting genetic manipulation of bacteria and yeast for the production of large amount of desired protein. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  19. Role of Bacteria in Oncogenesis

    PubMed Central

    Chang, Alicia H.; Parsonnet, Julie

    2010-01-01

    Summary: Although scientific knowledge in viral oncology has exploded in the 20th century, the role of bacteria as mediators of oncogenesis has been less well elucidated. Understanding bacterial carcinogenesis has become increasingly important as a possible means of cancer prevention. This review summarizes clinical, epidemiological, and experimental evidence as well as possible mechanisms of bacterial induction of or protection from malignancy. PMID:20930075

  20. Bacteria, it's what's for dinner.

    PubMed

    Cadwell, Ken

    2013-06-12

    While intestinal epithelial cells are known for secreting antimicrobial molecules, cell intrinsic defense mechanisms are less characterized. In this issue, Benjamin et al. (2013) demonstrate that MyD88 and autophagy within the intestinal epithelium detect invasive bacteria and prevent dissemination. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Manipulating Genetic Material in Bacteria

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Lisa Crawford, a graduate research assistant from the University of Toledo, works with Laurel Karr of Marshall Space Flight Center (MSFC) in the molecular biology laboratory. They are donducting genetic manipulation of bacteria and yeast for the production of large amount of desired protein. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  2. Hydrocarbon degradation by antarctic bacteria

    SciTech Connect

    Cavanagh, J.A.E.; Nichols, P.D.; McMeekin, T.A.; Franzmann, P.D.

    1996-12-31

    Bacterial cultures obtained from sediment samples collected during a trial oil spill experiment conducted at Airport beach, Eastern Antarctica were selectively enriched for n-alkane-degrading and phenanthrenedegrading bacteria. Samples were collected from a control site and sites treated with different hydrocarbon mixtures - Special Antarctic blend (SAB), BP-Visco and orange roughy oils. One set of replicate sites was also treated with water from Organic Lake which had previously been shown to contain hydrocarbon-degrading bacteria. No viable bacteria were obtained from samples collected from sites treated with orange roughy oil. Extensive degradation of n-alkanes by enrichment cultures obtained from sites treated with SAB and BP-Visco occurred at both 25{degrees}C and 10{degrees}C. Extensive degradation of phenanthrene also occurred in enrichment cultures from these sites grown at 25{degrees}C. Concurrent increases of polar lipid in these cultures were also observed. The presence of 1,4-naphthaquinone and 1-naphthol during the growth of the cultures on phenanthrene is unusual and warrants further investigation of the mechanism of phenanthrene-degradation by these Antarctic bacteria.

  3. Raman spectroscopy of oral bacteria

    NASA Astrophysics Data System (ADS)

    Berger, Andrew J.; Zhu, Qingyuan; Quivey, Robert G.

    2003-10-01

    Raman spectroscopy has been employed to measure the varying concentrations of two oral bacteria in simple mixtures. Evaporated droplets of centrifuged mixtures of Streptococcus sanguis and Streptococcus mutans were analyzed via Raman microspectroscopy. The concentration of s. sanguis was determined based upon the measured Raman spectrum, using partial least squares cross-validation, with an r2 value of 0.98.

  4. Optical properties of marine bacteria

    NASA Astrophysics Data System (ADS)

    Stramski, Dariusz; Kiefer, Dale A.

    1990-09-01

    Optical properties of naturally derived bacterioplankton grown in unenriched seawater are described. The beam attenuation coefficient, absorption coefficient and size distribution of cells suspension of bacteria were measured in order to determine their optical efficiency factors. In addition, the bulk refractive index as well as the angular pattern of light scattering were obtained from Mie theory. The cellular scatering efficiency increases with decreasing light wavelength as A , the backscattering efficiency is almost spectrally neutral, and the absorption efficiency exhibits features associated with respiratory cytochromes. Except for backscattering, the efficiences are significantly lower than those for larger biological inicroparticles. We suggest that baceria are a xrtajor source of light scattering in oligotrophic waters, where their contribution to the scattering coefficient may far exceed 50%. This large contribution is caused by the fact that total geometric cross sectional area for the bacteria compensates for their lower scattering efficiency. The contribution by bacteria to particle absorption, although less certain, appears also to be important in oligotrophic waters, and it may even predominate a non-'phytoplankton component. The effects of changes in size and refractive index on optical efficiencies of bacteria are also discussed in terms of a recent hypothesis concerning the regulation of cellular water content.

  5. Functional genomics of intracellular bacteria.

    PubMed

    de Barsy, Marie; Greub, Gilbert

    2013-07-01

    During the genomic era, a large amount of whole-genome sequences accumulated, which identified many hypothetical proteins of unknown function. Rapidly, functional genomics, which is the research domain that assign a function to a given gene product, has thus been developed. Functional genomics of intracellular pathogenic bacteria exhibit specific peculiarities due to the fastidious growth of most of these intracellular micro-organisms, due to the close interaction with the host cell, due to the risk of contamination of experiments with host cell proteins and, for some strict intracellular bacteria such as Chlamydia, due to the absence of simple genetic system to manipulate the bacterial genome. To identify virulence factors of intracellular pathogenic bacteria, functional genomics often rely on bioinformatic analyses compared with model organisms such as Escherichia coli and Bacillus subtilis. The use of heterologous expression is another common approach. Given the intracellular lifestyle and the many effectors that are used by the intracellular bacteria to corrupt host cell functions, functional genomics is also often targeting the identification of new effectors such as those of the T4SS of Brucella and Legionella.

  6. Are extreme halophiles actually "bacteria"?

    PubMed

    Magrum, L J; Luehrsen, K R; Woese, C R

    1978-05-12

    Comparative cataloging of the 16SrRNA of Halobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather, H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.

  7. Are extreme halophiles actually 'bacteria'

    NASA Technical Reports Server (NTRS)

    Magrum, L. J.; Luehrsen, K. R.; Woese, C. R.

    1978-01-01

    Comparative cataloging of the 16S rRNA of Halobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather, H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.

  8. Killer Pigments in Bacteria: An Ecological Nightmare.

    ERIC Educational Resources Information Center

    Benathen, Isaiah A.; Saccardi, Marion

    2000-01-01

    Describes an alternative to teaching ecology by using bacteria to test competitor survival. Students observe a time-dependent selective killing of other unrelated bacteria by Pseudomonas aeruginosa. (SAH)

  9. Certain Bacteria May Affect Preterm Birth Risk

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_163401.html Certain Bacteria May Affect Preterm Birth Risk Bad 'bugs' tied ... Feb. 3, 2017 (HealthDay News) -- Certain types of bacteria in a pregnant woman's cervix and vagina can ...

  10. Killer Pigments in Bacteria: An Ecological Nightmare.

    ERIC Educational Resources Information Center

    Benathen, Isaiah A.; Saccardi, Marion

    2000-01-01

    Describes an alternative to teaching ecology by using bacteria to test competitor survival. Students observe a time-dependent selective killing of other unrelated bacteria by Pseudomonas aeruginosa. (SAH)

  11. Swimming bacteria power microscopic gears

    PubMed Central

    Sokolov, Andrey; Apodaca, Mario M.; Grzybowski, Bartosz A.; Aranson, Igor S.

    2010-01-01

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be “rectified” under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears’ angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms. PMID:20080560

  12. Genetics of Lactic Acid Bacteria

    NASA Astrophysics Data System (ADS)

    Zagorec, Monique; Anba-Mondoloni, Jamila; Coq, Anne-Marie Crutz-Le; Champomier-Vergès, Marie-Christine

    Many meat (or fish) products, obtained by the fermentation of meat originating from various animals by the flora that naturally contaminates it, are part of the human diet since millenaries. Historically, the use of bacteria as starters for the fermentation of meat, to produce dry sausages, was thus performed empirically through the endogenous micro-biota, then, by a volunteer addition of starters, often performed by back-slopping, without knowing precisely the microbial species involved. It is only since about 50 years that well defined bacterial cultures have been used as starters for the fermentation of dry sausages. Nowadays, the indigenous micro-biota of fermented meat products is well identified, and the literature is rich of reports on the identification of lactic acid bacteria (LAB) present in many traditional fermented products from various geographical origin, obtained without the addition of commercial starters (See Talon, Leroy, & Lebert, 2007, and references therein).

  13. Dissipative shocks behind bacteria gliding.

    PubMed

    Virga, Epifanio G

    2014-11-28

    Gliding is a means of locomotion on rigid substrates used by a number of bacteria, including myxobacteria and cyanobacteria. One of the hypotheses advanced to explain this motility mechanism hinges on the role played by the slime filaments continuously extruded from gliding bacteria. This paper solves, in full, a non-linear mechanical theory that treats as dissipative shocks both the point where the extruded slime filament comes into contact with the substrate, called the filament's foot, and the pore on the bacterium outer surface from where the filament is ejected. I prove that kinematic compatibility for shock propagation requires that the bacterium uniform gliding velocity (relative to the substrate) and the slime ejecting velocity (relative to the bacterium) must be equal, a coincidence that seems to have already been observed. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  14. Swimming bacteria power microscopic gears.

    SciTech Connect

    Sokolov, A.; Apodaca, M. M.; Grzybowski, B. A.; Aranson, I. S.; Materials Science Division; Princeton Univ.; Northwestern Univ.

    2010-01-19

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be 'rectified' under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.

  15. Swimming bacteria power microscopic gears.

    PubMed

    Sokolov, Andrey; Apodaca, Mario M; Grzybowski, Bartosz A; Aranson, Igor S

    2010-01-19

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be "rectified" under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears' angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.

  16. Volatilization of Mercury By Bacteria

    PubMed Central

    Magos, L.; Tuffery, A. A.; Clarkson, T. W.

    1964-01-01

    Volatilization of mercury has been observed from various biological media (tissue homogenates, infusion broth, plasma, urine) containing mercuric chloride. That micro-organisms were responsible was indicated by the finding that the rates of volatilization were highly variable, that a latent period often preceded volatilization, that toluene inhibited the process, and that the capacity to volatilize mercury could be transferred from one biological medium to another. Two species of bacteria when isolated and cultured from these homogenates were able to volatilize mercury. Two other bacteria, one of which was isolated from the local water supply, were also highly active. The volatile mercury was identified as mercury vapour. The importance of these findings in relation to the storage of urine samples prior to mercury analysis is discussed. PMID:14249899

  17. Envisaging bacteria as phage targets

    PubMed Central

    Abedon, Stephen T.

    2011-01-01

    It can be difficult to appreciate just how small bacteria and phages are or how large, in comparison, the volumes that they occupy. A single milliliter, for example, can represent to a phage what would be, with proper scaling, an “ocean” to you and me. Here I illustrate, using more easily visualized macroscopic examples, the difficulties that a phage, as a randomly diffusing particle, can have in locating bacteria to infect. I conclude by restating the truism that the rate of phage adsorption to a given target bacterium is a function of phage density, that is, titer, in combination with the degree of bacterial susceptibility to adsorption by an encountering phage. PMID:23616932

  18. Swimming bacteria power microscopic gears

    SciTech Connect

    Sokolov, Andrey; Apodaca, Mario M.; Grzybowski, Bartosz A.; Aranson, Igor S.

    2010-01-19

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be “rectified” under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears’ angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.

  19. Re-engineering bacteria for ethanol production

    SciTech Connect

    Yomano, Lorraine P; York, Sean W; Zhou, Shengde; Shanmugam, Keelnatham; Ingram, Lonnie O

    2014-05-06

    The invention provides recombinant bacteria, which comprise a full complement of heterologous ethanol production genes. Expression of the full complement of heterologous ethanol production genes causes the recombinant bacteria to produce ethanol as the primary fermentation product when grown in mineral salts medium, without the addition of complex nutrients. Methods for producing the recombinant bacteria and methods for producing ethanol using the recombinant bacteria are also disclosed.

  20. Bacteria turn a tiny gear

    SciTech Connect

    2009-01-01

    Thousands of tiny Bacillus subtillis bacteria turn a single gear, just 380 microns across. (A human hair is about 100 microns across.) The method could be used to create micro-machines. Argonne National Laboratory scientist Igor Aronson pioneered this technique. Read more at the New York Times: http://ow.ly/ODfI or at Argonne: http://ow.ly/ODfa Video courtesy Igor Aronson.

  1. Bacteria, fungi and protozoa paper

    EPA Pesticide Factsheets

    Bacteria and fungi in source and treated drinking waterThis dataset is associated with the following publication:King , D., S. Pfaller , M. Donohue , S. Vesper , E. Villegas , M. Ware , S. Glassmeyer , M. Vogal, E. Furlong, and D. Kolpin. Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 562: 987–995, (2016).

  2. Endocytosis of Viruses and Bacteria

    PubMed Central

    Cossart, Pascale; Helenius, Ari

    2014-01-01

    Of the many pathogens that infect humans and animals, a large number use cells of the host organism as protected sites for replication. To reach the relevant intracellular compartments, they take advantage of the endocytosis machinery and exploit the network of endocytic organelles for penetration into the cytosol or as sites of replication. In this review, we discuss the endocytic entry processes used by viruses and bacteria and compare the strategies used by these dissimilar classes of pathogens. PMID:25085912

  3. Anaerobic bacteria from hypersaline environments.

    PubMed Central

    Ollivier, B; Caumette, P; Garcia, J L; Mah, R A

    1994-01-01

    Strictly anaerobic halophiles, namely fermentative, sulfate-reducing, homoacetogenic, phototrophic, and methanogenic bacteria are involved in the oxidation of organic carbon in hypersaline environments. To date, six anaerobic fermentative genera, containing nine species, have been described. Two of them are homoacetogens. Six species belong to the family Haloanaerobiaceae, as indicated by their unique 16S rRNA oligonucleotide sequences. Desulfohalobium retbaense and Desulfovibrio halophilus represent the only two moderately halophilic sulfate reducers so far reported. Among anoxygenic phototrophic anaerobes, a few purple bacteria with optimal growth at salinities between 6 and 11% NaCl have been isolated from hypersaline habitats. They belong to the genera Rhodospirillum, Chromatium, Thiocapsa, and Ectothiorhodospira. The commonest organisms isolated so far are Chromatium salexigens, Thiocapsa halophila, and Rhodospirillum salinarum. Extremely halophilic purple bacteria have most commonly been isolated from alkaline brines and require about 20 to 25% NaCl for optimal growth. They belong to the family Ectothiorodhospiraceae. Their osmoregulation involves synthesis or uptake of compatible solutes such as glycine-betaine that accumulate in their cytoplasm. The existence of methanogens in hypersaline environments is related to the presence of noncompetitive substrates such as methylamines, which originate mainly from the breakdown of osmoregulatory amines. Methanogenesis probably does not contribute to the mineralization of carbohydrates at NaCl concentrations higher than 15%. Above this concentration, sulfate reduction is probably the main way to oxidize H2 (although at rates too low to use up all the H2 formed) and occupies a terminal function kn the degradation of carbohydrates. Three genera and five species of halophilic methylotrophic methanogens have been reported. A bloom of phototrophic bacteria in the marine salterns of Salins-de-Giraud, located on the

  4. Anaerobic bacteria from hypersaline environments.

    PubMed

    Ollivier, B; Caumette, P; Garcia, J L; Mah, R A

    1994-03-01

    Strictly anaerobic halophiles, namely fermentative, sulfate-reducing, homoacetogenic, phototrophic, and methanogenic bacteria are involved in the oxidation of organic carbon in hypersaline environments. To date, six anaerobic fermentative genera, containing nine species, have been described. Two of them are homoacetogens. Six species belong to the family Haloanaerobiaceae, as indicated by their unique 16S rRNA oligonucleotide sequences. Desulfohalobium retbaense and Desulfovibrio halophilus represent the only two moderately halophilic sulfate reducers so far reported. Among anoxygenic phototrophic anaerobes, a few purple bacteria with optimal growth at salinities between 6 and 11% NaCl have been isolated from hypersaline habitats. They belong to the genera Rhodospirillum, Chromatium, Thiocapsa, and Ectothiorhodospira. The commonest organisms isolated so far are Chromatium salexigens, Thiocapsa halophila, and Rhodospirillum salinarum. Extremely halophilic purple bacteria have most commonly been isolated from alkaline brines and require about 20 to 25% NaCl for optimal growth. They belong to the family Ectothiorodhospiraceae. Their osmoregulation involves synthesis or uptake of compatible solutes such as glycine-betaine that accumulate in their cytoplasm. The existence of methanogens in hypersaline environments is related to the presence of noncompetitive substrates such as methylamines, which originate mainly from the breakdown of osmoregulatory amines. Methanogenesis probably does not contribute to the mineralization of carbohydrates at NaCl concentrations higher than 15%. Above this concentration, sulfate reduction is probably the main way to oxidize H2 (although at rates too low to use up all the H2 formed) and occupies a terminal function kn the degradation of carbohydrates. Three genera and five species of halophilic methylotrophic methanogens have been reported. A bloom of phototrophic bacteria in the marine salterns of Salins-de-Giraud, located on the

  5. Bacteria under simulated Martian conditions.

    PubMed

    Young, R S; Deal, P H; Bell, J; Allen, J L

    1964-01-01

    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.

  6. Chemical signature of magnetotactic bacteria

    PubMed Central

    Amor, Matthieu; Busigny, Vincent; Durand-Dubief, Mickaël; Tharaud, Mickaël; Ona-Nguema, Georges; Gélabert, Alexandre; Alphandéry, Edouard; Menguy, Nicolas; Benedetti, Marc F.; Chebbi, Imène; Guyot, François

    2015-01-01

    There are longstanding and ongoing controversies about the abiotic or biological origin of nanocrystals of magnetite. On Earth, magnetotactic bacteria perform biomineralization of intracellular magnetite nanoparticles under a controlled pathway. These bacteria are ubiquitous in modern natural environments. However, their identification in ancient geological material remains challenging. Together with physical and mineralogical properties, the chemical composition of magnetite was proposed as a promising tracer for bacterial magnetofossil identification, but this had never been explored quantitatively and systematically for many trace elements. Here, we determine the incorporation of 34 trace elements in magnetite in both cases of abiotic aqueous precipitation and of production by the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1. We show that, in biomagnetite, most elements are at least 100 times less concentrated than in abiotic magnetite and we provide a quantitative pattern of this depletion. Furthermore, we propose a previously unidentified method based on strontium and calcium incorporation to identify magnetite produced by magnetotactic bacteria in the geological record. PMID:25624469

  7. Differential staining of bacteria: acid fast stain.

    PubMed

    Reynolds, Jackie; Moyes, Rita B; Breakwell, Donald P

    2009-11-01

    Acid-fastness is an uncommon characteristic shared by the genera Mycobacterium (Section 10A) and Nocardia. Because of this feature, this stain is extremely helpful in identification of these bacteria. Although Gram positive, acid-fast bacteria do not take the crystal violet into the wall well, appearing very light purple rather than the deep purple of normal Gram-positive bacteria.

  8. Laser-Based Identification of Pathogenic Bacteria

    ERIC Educational Resources Information Center

    Rehse, Steven J.

    2009-01-01

    Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the…

  9. Simple chamber facilitates chemiluminescent detection of bacteria

    NASA Technical Reports Server (NTRS)

    Marts, E. C.; Wilkins, J. R.

    1970-01-01

    Test chamber enables rapid estimation of bacteria in a test sample through the reaction of luminol and an oxidant with the cytochrome C portion of certain species of bacteria. Intensity of the light emitted in the reaction is a function of the specific bacteria in the test sample.

  10. Laser-Based Identification of Pathogenic Bacteria

    ERIC Educational Resources Information Center

    Rehse, Steven J.

    2009-01-01

    Bacteria are ubiquitous in our world. From our homes, to our work environment, to our own bodies, bacteria are the omnipresent although often unobserved companions to human life. Physicists are typically untroubled professionally by the presence of these bacteria, as their study usually falls safely outside the realm of our typical domain. In the…

  11. Growth of bacteria in 3-d colonies

    PubMed Central

    Mugler, Andrew; Kim, Justin

    2017-01-01

    The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in physically structured habitats as colonies, within which individual cells vary in their access to nutrients. The dynamics of bacterial growth in such conditions is poorly understood, and, unlike that for liquid culture, there is not a standard broadly used mathematical model for bacterial populations growing in colonies in three dimensions (3-d). By extending the classic Monod model of resource-limited population growth to allow for spatial heterogeneity in the bacterial access to nutrients, we develop a 3-d model of colonies, in which bacteria consume diffusing nutrients in their vicinity. By following the changes in density of E. coli in liquid and embedded in glucose-limited soft agar, we evaluate the fit of this model to experimental data. The model accounts for the experimentally observed presence of a sub-exponential, diffusion-limited growth regime in colonies, which is absent in liquid cultures. The model predicts and our experiments confirm that, as a consequence of inter-colony competition for the diffusing nutrients and of cell death, there is a non-monotonic relationship between total number of colonies within the habitat and the total number of individual cells in all of these colonies. This combined theoretical-experimental study reveals that, within 3-d colonies, E. coli cells are loosely packed, and colonies produce about 2.5 times as many cells as the liquid culture from the same amount of nutrients. We verify that this is because cells in liquid culture are larger than in colonies. Our model provides a baseline description of bacterial growth in 3-d, deviations from which can be used to identify phenotypic heterogeneities and inter-cellular interactions that further contribute to the structure of bacterial

  12. Predicting reaerosolization

    SciTech Connect

    Daniel, William Brent; Omberg, Kristin M

    2010-11-29

    Outdoor studies of the environmental persistence of bacteria have led to many interesting results. It turns out that the initial deposition of bacteria is not the end of the story. We examined both the ongoing daily deposition and aerosolization of bacteria for two weeks following an initial deposition event. Differences between samples collected in a clearing and those collected beneath a forest canopy were also examined. There were two important results: first, bacteria were still moving about in significant quantities after two weeks, though the local environment where they were most prevalent appeared to shift over time; second, we were able to develop a simple mathematical model that could fairly accurately estimate the average daily airborne concentration of bacteria over the duration of the experiment using readily available environmental information. The implication is that deposition patterns are very likely to shift over an extended period of time following a release, possibly quite significantly, but there is hope that we may be able to estimate these changes fairly accurately.

  13. Predator vs aliens: bacteria interactions with Acanthamoeba.

    PubMed

    Khan, Naveed Ahmed; Siddiqui, Ruqaiyyah

    2014-06-01

    By interactions with other microbes, free-living amoebae play a significant role in microbiology, environmental biology, physiology, cellular interactions, ecology and evolution. Here, we discuss astonishing interactions of bacteria and amoebae, in the light of evolution and functional aspects impacting human health. In favourable environmental conditions, the interaction of Acanthamoeba with non-virulent bacteria results in lysis of the bacteria. However, the interaction with weak-virulent bacteria results in a symbiotic relationship or amoebal lysis may occur. The microbial survival of amoebae in harsh environments, ability to interact with bacteria, and their ability to aid transmission to susceptible hosts is of great concern to human, animal and ecosystem health.

  14. In vitro fermentation of lactulose by human gut bacteria.

    PubMed

    Mao, Bingyong; Li, Dongyao; Zhao, Jianxin; Liu, Xiaoming; Gu, Zhennan; Chen, Yong Q; Zhang, Hao; Chen, Wei

    2014-11-12

    Lactulose has been known as a prebiotic that can selectively stimulate the growth of beneficial bifidobacteria and lactobacilli. Recent studies have indicated that Streptococcus mutans, Clostridium perfringens, and Faecalibacterium prausnitzii are also able to utilize lactulose. However, the previous studies mainly focused on the utilization of lactulose by individual strains, and few studies were designed to identify the species that could utilize lactulose among gut microbiota. This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in silico and traditional culture methods. The prediction results suggested that genes for the transporters and glycosidases of lactulose are well distributed in the genomes of 222 of 453 strains of gastrointestinal-tract bacteria. The screening assays identified 35 species with the ability to utilize lactulose, of which Cronobacter sakazakii, Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas putida were reported for the first time to be capable of utilizing lactulose. In addition, significant correlations between lactulose and galactooligosaccharide metabolism were found. Thus, more attention should be paid to bacteria besides bifidobacteria and lactobacilli to further investigate the relationship between functional oligosaccharides and gut bacteria.

  15. [Bacteria ecology in planting-culturing system].

    PubMed

    Huang, Fenglian; Xia, Beicheng; Dai, Xin; Chen, Guizhu

    2004-06-01

    Planting-culturing system in inter-tidal zone is a new type eco-culturing model. The survey on bacteria biomass and water quality in the designed planting-culturing system in inter-tidal zone showed that the mangrove planted in the system improved water quality and made water quality to II-III type, better than the IV and V type in the control pond. Designed ponds made heterotrophic bacteria, vibrio, phosphorus bacteria and enzyme-producing bacteria populations 1-2 order lower than the control pond without mongrove planting. Correlation analyses with CORREL software showed that the biomass of these bacteria was positively related with the nitrogen and phosphorus contents in water of the system, and the correlation coefficient for heterogeneous bacteria and vibrio was up to 0.9205. Heterotrophic bacteria and vibrio could be used as the water-quality monitoring organisms.

  16. Chromosome dynamics in multichromosome bacteria.

    PubMed

    Jha, Jyoti K; Baek, Jong Hwan; Venkova-Canova, Tatiana; Chattoraj, Dhruba K

    2012-07-01

    On the basis of limited information, bacteria were once assumed to have no more than one chromosome. In the era of genomics, it has become clear that some, like eukaryotes, have more than one chromosome. Multichromosome bacteria provide opportunities to investigate how split genomes emerged, whether the individual chromosomes communicate to coordinate their replication and segregation, and what selective advantages split genomes might provide. Our current knowledge of these topics comes mostly from studies in Vibrio cholerae, which has two chromosomes, chr1 and chr2. Chr1 carries out most of the house-keeping functions and is considered the main chromosome, whereas chr2 appears to have originated from a plasmid and has acquired genes of mostly unknown origin and function. Nevertheless, unlike plasmids, chr2 replicates once and only once per cell cycle, like a bona fide chromosome. The two chromosomes replicate and segregate using separate programs, unlike eukaryotic chromosomes. They terminate replication synchronously, suggesting that there might be communication between them. Replication of the chromosomes is affected by segregation genes but in a chromosome specific fashion, a new development in the field of DNA replication control. The split genome allows genome duplication to complete in less time and with fewer replication forks, which could be beneficial for genome maintenance during rapid growth, which is the norm for V. cholerae in broth cultures and in the human host. In the latter, the expression of chr2 genes increases preferentially. Studies of chromosome maintenance in multichromosomal bacteria, although in their infancy, are already broadening our view of chromosome biology. This article is part of a Special Issue entitled: Chromatin in time and space. Published by Elsevier B.V.

  17. Endocarditis caused by anaerobic bacteria.

    PubMed

    Kestler, M; Muñoz, P; Marín, M; Goenaga, M A; Idígoras Viedma, P; de Alarcón, A; Lepe, J A; Sousa Regueiro, D; Bravo-Ferrer, J M; Pajarón, M; Costas, C; García-López, M V; Hidalgo-Tenorio, C; Moreno, M; Bouza, E

    2017-04-05

    Infective endocarditis (IE) caused by anaerobic bacteria is a rare and poorly characterized disease. Most data reported in the literature are from case reports [1-3]. Therefore, we assessed the situation of anaerobic IE (AIE) in Spain using the database of the Spanish Collaboration on Endocarditis (GAMES). We performed a prospective study from 2008 to 2016 in 26 Spanish centers. We included 2491 consecutive cases of definite IE (Duke criteria). Anaerobic bacteria caused 22 cases (0.9%) of definite IE. Median age was 66 years (IQR, 56-73), and 19 (86.4%) patients were men. Most patients (14 [63.6%]) had prosthetic valve IE and all episodes were left-sided: aortic valves, 12 (54.5%); and mitral valves, 8 (36.4%). The most common pathogens were Propionibacterium acnes (14 [63.6%]), Lactobacillus spp (3 [13.63%]), and Clostridium spp. (2 [9.0%]), and the infection was mainly odontogenic. Fifteen of the 22 patients (68.2%) underwent cardiac surgery. Mortality was 18.2% during admission and 5.5% after 1 year of follow-up. When patients with AIE were compared with the rest of the cohort, we found that although those with AIE had a similar age and Charlson comorbidity index, they were more likely to have community-acquired IE (86.4% vs. 60.9%, p = 0.01), have undergone cardiac surgery (68.2% vs 48.7% p = 0.06), and have had lower mortality rates during admission (18.2% vs. 27.3%). IE due to anaerobic bacteria is an uncommon disease that affects mainly prosthetic valves and frequently requires surgery. Otherwise, there are no major differences between AIE and IE caused by other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. [Pathogenic bacteria in cystic fibrosis].

    PubMed

    Mariani-Kurkdjian, P; Bingen, E

    2003-09-01

    Since the CF gene identification in 1989 and despite the improvement of our knowledge in the physiopathology of the disease, bronchopulmonary infection determines the vital prognosis. Following Staphylococcus aureus infection, patients are colonized or colonized by Pseudomonas aeruginosa, greatly involved in the pulmonary deterioration. Other bacteria may be involved Burkholderia cepacia, Stenotrophomonas maltophilia, Alcaligenes sp. Intensive antibiotic treatment of primocolonisation helps to prevent or delay chronic colonisation. Chronic colonization needs a rational long term antibiotic strategy to prevent the occurrence of multiresistant germs; antibiotic cures are performed every 3 or 4 months before pulmonary exacerbation symptoms.

  19. Bacteria detection instrument and method

    NASA Technical Reports Server (NTRS)

    Renner, W.; Fealey, R. D. (Inventor)

    1972-01-01

    A method and apparatus for screening a sample fluid for bacterial presence are disclosed wherein the fluid sample is mixed with culture media of sufficient quantity to permit bacterial growth in order to obtain a test solution. The concentration of oxygen dissolved in the test solution is then monitored using the potential difference between a reference electrode and a noble metal electrode which are in contact with the test solution. The change in oxygen concentration which occurs during a period of time as indicated by the electrode potential difference is compared with a detection criterion which exceeds the change which would occur absent bacteria.

  20. Bacteria and vampirism in cinema.

    PubMed

    Castel, O; Bourry, A; Thévenot, S; Burucoa, C

    2013-09-01

    A vampire is a non-dead and non-alive chimerical creature, which, according to various folklores and popular superstitions, feeds on blood of the living to draw vital force. Vampires do not reproduce by copulation, but by bite. Vampirism is thus similar to a contagious disease contracted by intravascular inoculation with a suspected microbial origin. In several vampire films, two real bacteria were staged, better integrated than others in popular imagination: Yersinia pestis and Treponema pallidum. Bacillus vampiris was created for science-fiction. These films are attempts to better define humans through one of their greatest fears: infectious disease.

  1. Climate prediction and predictability

    NASA Astrophysics Data System (ADS)

    Allen, Myles

    2010-05-01

    Climate prediction is generally accepted to be one of the grand challenges of the Geophysical Sciences. What is less widely acknowledged is that fundamental issues have yet to be resolved concerning the nature of the challenge, even after decades of research in this area. How do we verify or falsify a probabilistic forecast of a singular event such as anthropogenic warming over the 21st century? How do we determine the information content of a climate forecast? What does it mean for a modelling system to be "good enough" to forecast a particular variable? How will we know when models and forecasting systems are "good enough" to provide detailed forecasts of weather at specific locations or, for example, the risks associated with global geo-engineering schemes. This talk will provide an overview of these questions in the light of recent developments in multi-decade climate forecasting, drawing on concepts from information theory, machine learning and statistics. I will draw extensively but not exclusively from the experience of the climateprediction.net project, running multiple versions of climate models on personal computers.

  2. The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility.

    PubMed

    Wei, Yan; Wang, Xiaolin; Liu, Jingfang; Nememan, Ilya; Singh, Amoolya H; Weiss, Howie; Levin, Bruce R

    2011-03-08

    Why is motility so common in bacteria? An obvious answer to this ecological and evolutionary question is that in almost all habitats, bacteria need to go someplace and particularly in the direction of food. Although the machinery required for motility and chemotaxis (acquiring and processing the information needed to direct movement toward nutrients) are functionally coupled in contemporary bacteria, they are coded for by different sets of genes. Moreover, information that resources are more abundant elsewhere in a habitat would be of no value to a bacterium unless it already had the means to get there. Thus, motility must have evolved before chemotaxis, and bacteria with flagella and other machinery for propulsion in random directions must have an advantage over bacteria relegated to moving at the whim of external forces alone. However, what are the selection pressures responsible for the evolution and maintenance of undirected motility in bacteria? Here we use a combination of mathematical modeling and experiments with Escherichia coli to generate and test a parsimonious and ecologically general hypothesis for the existence of undirected motility in bacteria: it enables bacteria to move away from each other and thereby obtain greater individual shares of resources in physically structured environments. The results of our experiments not only support this hypothesis, but are quantitatively and qualitatively consistent with the predictions of our model.

  3. Effect of predatory bacteria on the gut bacterial microbiota in rats.

    PubMed

    Shatzkes, Kenneth; Tang, Chi; Singleton, Eric; Shukla, Sean; Zuena, Michael; Gupta, Shilpi; Dharani, Sonal; Rinaggio, Joseph; Connell, Nancy D; Kadouri, Daniel E

    2017-03-06

    Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative proteobacteria that are obligate predators of other Gram-negative bacteria and are considered potential alternatives to antibiotics. Most studies focusing on predatory bacteria have been performed in vitro, thus the effect of predatory bacteria on a live host, including the impact on the ecology of the native microbiota, has yet to be fully examined. In this study, intrarectal inoculations of Sprague-Dawley rats with predatory bacteria were performed. Additionally, feces were collected for seven days post-inoculation to determine the effect on gut bacterial diversity. Rat colonic tissue exhibited no abnormal histopathological effects due to predatory bacteria. A modest increase in pro-inflammatory cytokines was measured in the colons of rats inoculated with predatory bacteria by 24 and 48 hours, with all but IL-13 returning to baseline by seven days. V4 16S rRNA gene sequencing of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory bacteria. Changes in bacterial populations due to exposure to B. bacteriovorus are predicted to contribute to health, however, an overgrowth of Prevotella was observed due to exposure to M. aeruginosavorus. This study further addresses safety concerns associated with the potential use of predatory bacteria to treat infections.

  4. Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest.

    PubMed

    Kivlin, Stephanie N; Hawkes, Christine V

    2016-01-01

    The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.

  5. Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

    PubMed Central

    Kivlin, Stephanie N; Hawkes, Christine V

    2016-01-01

    The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change. PMID:27391450

  6. Coliform bacteria and nitrate contamination of wells in major soils of Frederick, Maryland

    SciTech Connect

    Tuthill, A.; Meikle, D.B.; Alavanja, M.C.R.

    1998-04-01

    An investigation was conducted on the hypothesis that inadequate septic system construction or placement may cause contamination of wells with coliform bacteria and/or nitrates. Specifically, two predictions were tested: (1) A negative correlation between lot size and coliform bacteria and nitrate contamination will exist in unsewered areas. (2) Coliform bacteria and nitrate contamination will decrease with increasing casing length. The relationship of coliform bacteria and nitrate levels to lot size and casing length was tested for all wells in unsewered areas (n = 832) and for wells in 10 soil groups in Frederick County, Maryland, to determine if septic system construction or placement contributed to well contamination. Coliform bacteria and nitrate contamination were negatively correlated with lot size. In addition, coliform bacteria levels were negatively correlated with casing length, and there was a trend toward nitrate levels being associated with casing length. The results suggest that septic systems may be a source of coliform bacteria and nitrate contamination of wells. The casing length required in well construction should be increased in areas where wells may be prone to coliform bacteria contamination if the minimum amount of casing is used.

  7. Effect of predatory bacteria on the gut bacterial microbiota in rats

    PubMed Central

    Shatzkes, Kenneth; Tang, Chi; Singleton, Eric; Shukla, Sean; Zuena, Michael; Gupta, Shilpi; Dharani, Sonal; Rinaggio, Joseph; Connell, Nancy D.; Kadouri, Daniel E.

    2017-01-01

    Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative proteobacteria that are obligate predators of other Gram-negative bacteria and are considered potential alternatives to antibiotics. Most studies focusing on predatory bacteria have been performed in vitro, thus the effect of predatory bacteria on a live host, including the impact on the ecology of the native microbiota, has yet to be fully examined. In this study, intrarectal inoculations of Sprague-Dawley rats with predatory bacteria were performed. Additionally, feces were collected for seven days post-inoculation to determine the effect on gut bacterial diversity. Rat colonic tissue exhibited no abnormal histopathological effects due to predatory bacteria. A modest increase in pro-inflammatory cytokines was measured in the colons of rats inoculated with predatory bacteria by 24 and 48 hours, with all but IL-13 returning to baseline by seven days. V4 16S rRNA gene sequencing of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory bacteria. Changes in bacterial populations due to exposure to B. bacteriovorus are predicted to contribute to health, however, an overgrowth of Prevotella was observed due to exposure to M. aeruginosavorus. This study further addresses safety concerns associated with the potential use of predatory bacteria to treat infections. PMID:28262674

  8. Money and transmission of bacteria

    PubMed Central

    2013-01-01

    Money is one of the most frequently passed items in the world. The aim of this study was to ascertain the survival status of bacteria including Staphylococcus aureus, Escherichia coli, and Vancomycin- Resistant Enterococci (VRE) on banknotes from different countries and the transmission of bacteria to people who come in contact with the banknotes. The survival rate was highest for the Romanian Leu yielding all three microorganisms used after both three and six hours of drying. Furthermore, the Leu was the only banknote to yield VRE after one day of drying. Other currencies either enabled the survival of Extended-Spectrum Beta-Lactamases (ESBL) and VRE (e.g. Euro), but not of MRSA, or the other way round (e.g. US Dollar). While a variety of factors such as community hygiene levels, people’s behaviour, and antimicrobial resistance rates at community level obviously have influence on the transmission of resistant microorganisms, the type of banknote-paper may be an additional variable to consider. PMID:23985137

  9. Genetic manipulation of acidophilic bacteria

    SciTech Connect

    Ward, T.E.; Rowland, M.L.; Glenn, A.W.; Watkins, C.S.; Bruhn, D.F.; Bulmer, D.; Roberto, F.F.

    1989-01-01

    Thiobacillus ferrooxidans is important in leaching of metals from mineral ores and in the removal of pyritic sulfur from coal. It is also intimately involved in production of acid mine drainage. Other acidophilic bacteria, including members of the genus Acidiphilium, are usually present in the same environments as T. ferrooxidans, and there is evidence to suggest that these acidophilic heterotrophs may increase the rate of T. ferrooxidans' attack on inorganic sulfides. Our laboratory is studying the genetic characteristics of these acidophilic bacteria and developing techniques for introducing desirable genes into them. Several endogenous plasmids from Acidiphilium strains have been cloned into E. coli vectors. Some of the resulting plasmids are able to confer antibiotic resistance to Acidiphilium after transformation by electroporation. In addition, a broad-host range plasmid conferring resistance to tetracycline has been introduced into Acidiphilium strains by electroporation. This same plasmid, has also been transferred to Acidiphilium from E. coli directly by conjugation. A temperate bacteriophage which infects a number of Acidiphilium isolates has been discovered and partially characterized. It has a lambdoid morphology and a genome of approximately 97 kb, comprised of double-stranded DNA which is probably modified. 16 refs., 2 figs., 4 tabs.

  10. Mitochondria are not captive bacteria.

    PubMed

    Harish, Ajith; Kurland, Charles G

    2017-12-07

    Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic). Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. DMTB: the magnetotactic bacteria database

    NASA Astrophysics Data System (ADS)

    Pan, Y.; Lin, W.

    2012-12-01

    Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

  12. Bromate Reduction by Denitrifying Bacteria

    PubMed Central

    Hijnen, W.; Voogt, R.; Veenendaal, H. R.; van der Jagt, H.; van der Kooij, D.

    1995-01-01

    In the presence of bromide, ozonation as applied in water treatment results in the formation of bromate, an ion with carcinogenic properties. The reduction of bromate by mixed bacterial populations as well as pure cultures was studied under laboratory conditions. Bromate was reduced to bromide by a mixed bacterial population with and without a preceding nitrate reduction step in an anaerobically incubated medium with ethanol as the energy and carbon source at 20 and 25 deg C. The predominating bacteria isolated from the batches showing bromate reduction were identified as Pseudomonas spp. Strains of Pseudomonas fluorescens reduced BrO(inf3)(sup-) to Br(sup-) but at a much lower rate than the mixed bacterial population did. Nitrate is a preferred electron acceptor for the bromate-reducing bacteria. Bromate reduction did not occur in the presence of NO(inf3)(sup-), and the rate of bromate reduction was at least 100 times lower than the rate of nitrate reduction. Bromate was completely converted to Br(sup-), indicating that intermediates, e.g., BrO(inf2)(sup-), did not accumulate during bromate reduction. PMID:16534907

  13. Growth mechanics of bacterial cell wall and morphology of bacteria

    NASA Astrophysics Data System (ADS)

    Jiang, Hongyuan; Sun, Sean

    2010-03-01

    The peptidoglycan cell wall of bacteria is responsible for maintaining the cell shape and integrity. During the bacterial life cycle, the growth of the cell wall is affected by mechanical stress and osmotic pressure internal to the cell. We develop a theory to describe cell shape changes under the influence of mechanical forces. We find that the theory predicts a steady state size and shape for bacterial cells ranging from cocci to spirillum. Moreover, the theory suggest a mechanism by which bacterial cytoskeletal proteins such as MreB and crescentin can maintain the shape of the cell. The theory can also explain the several recent experiments on growing bacteria in micro-environments.

  14. Computational modeling of the quorum-sensing network in bacteria

    NASA Astrophysics Data System (ADS)

    Fenley, Andrew; Banik, Suman; Kulkarni, Rahul

    2007-03-01

    Certain species of bacteria are able produce and sense the concentration of small molecules called autodinducers in order to coordinate gene regulation in response to population density, a process known as ``quorum-sensing''. The resulting regulation of gene expression involves both transcriptional and post-transcriptional regulators. In particular, the species of bacteria in the Vibrio genus use small RNAs to regulate the master protein controlling the quorum-sensing response (luminescence, biofilm formation, virulence...). We model the network of interactions using a modular approach which provides a quantitative understanding of how signal transduction occurs. The parameters of the input-module are fit to current experimental results allowing for testable predictions to be made for future experiments. The results of our analysis offer a revised perspective on quorum-sensing based regulation.

  15. Characterization of cells and bacteria by photophoretic velocimetry

    NASA Astrophysics Data System (ADS)

    Helmbrecht, Clemens; Niessner, Reinhard; Haisch, Christoph

    2008-02-01

    The migration induced by intensive light is termed photophoresis. We could show that the evaluation of light-induced velocities of microparticles, bacteria and cells suspended in water is valuable for the prediction of their intrinsic properties. Two different laser setups were evaluated for photophoretic migration, a He-Ne laser (P = 45 mW, λ = 633 nm) and a diode-pumped cw-Nd:YAG (P = 1.1 W, λ = 532 nm). When analyzing the migration behavior of particles, we find significant differences depending on both, geometrical size and refractive index. We describe migration of PS particles of different size as well as with different refractive index but same diameter, SiO II and melamine resin. The potential for the separation of biological matter is shown as velocity distributions of heat killed bacteria of Escherichia coli, Salmonella enteritidis, and baker's yeast is reported.

  16. Source specific fecal bacteria modeling using soil and water assessment tool model.

    PubMed

    Parajuli, Prem B; Mankin, Kyle R; Barnes, Philip L

    2009-01-01

    Fecal bacteria can contaminate water and result in illness or death. It is often difficult to accurately determine sources of fecal bacteria contamination, but bacteria source tracking can help identify non-point sources of fecal bacteria such as livestock, humans and wildlife. The Soil and Water Assessment Tool (SWAT) microbial sub-model 2005 was used to evaluate source-specific fecal bacteria using three years (2004-2006) of observed modified deterministic probability of bacteria source tracking data, as well as measure hydrologic and water quality data. This study modeled source-specific bacteria using a model previously calibrated for flow, sediment and total fecal coliform bacteria (FCB) concentration. The SWAT model was calibrated at the Rock Creek sub-watershed, validated at the Deer Creek sub-watershed, and verified at the Auburn sub-watershed and then at the entire Upper Wakarusa watershed for predicting daily flow, sediment, nutrients, total fecal bacteria, and source-specific fecal bacteria. Watershed characteristics for livestock, humans, and wildlife fecal bacterial sources were first modeled together then with three separate sources and combinations of source-specific FCB concentration: livestock and human, livestock and wildlife and human and wildlife. Model results indicated both coefficient of determination (R(2)) and Nash-Sutcliffe Efficiency Index (E) parameters ranging from 0.52 to 0.84 for daily flow and 0.50-0.87 for sediment (good to very good agreement); 0.14-0.85 for total phosphorus (poor to very good agreement); -3.55 to 0.79 for total nitrogen (unsatisfactory to very good agreement) and -2.2 to 0.52 for total fecal bacteria (unsatisfactory to good agreement). Model results generally determined decreased agreement for each single source of bacteria (R(2) and E range from -5.03 to 0.39), potentially due to bacteria source tracking (BST) uncertainty and spatial variability. This study contributes to new knowledge in bacteria modeling and

  17. Diversity, distribution and sources of bacteria in residential kitchens

    PubMed Central

    Flores, Gilberto E.; Bates, Scott T.; Caporaso, J. Gregory; Lauber, Christian L.; Leff, Jonathan W.; Knight, Rob; Fierer, Noah

    2016-01-01

    Summary Bacteria readily colonize kitchen surfaces, and the exchange of microbes between humans and the kitchen environment can impact human health. However, we have a limited understanding of the overall diversity of these communities, how they differ across surfaces, and sources of bacteria to kitchen surfaces. Here we used high-throughput sequencing of the 16S rRNA gene to explore biogeographical patterns of bacteria across >80 surfaces within the kitchens of each of four households. In total, 34 bacterial and two archaeal phyla were identified, with most sequences belonging to the Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. Genera known to contain common food-borne pathogens were low in abundance but broadly distributed throughout the kitchens, with different taxa exhibiting distinct distribution patterns. The most diverse communities were associated with infrequently cleaned surfaces such as fans above stoves, refrigerator/freezer door seals, and floors. In contrast, the least diverse communities were observed in and around sinks, which were dominated by biofilm-forming gram-negative lineages. Community composition was influenced by conditions on individual surfaces, usage patterns, and dispersal from source environments. Human skin was the primary source of bacteria across all kitchen surfaces, with contributions from food and faucet water dominating in a few specific locations. This study demonstrates that diverse bacterial communities are widely distributed in residential kitchens and that the composition of these communities is often predictable. These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces. PMID:23171378

  18. Diet-dependent effects of gut bacteria on their insect host: the symbiosis of Erwinia sp. and western flower thrips.

    PubMed Central

    de Vries, Egbert J.; Jacobs, Gerrit; Sabelis, Maurice W.; Menken, Steph B. J.; Breeuwer, Johannes A. J.

    2004-01-01

    Studies on bacteria in the gut of insect species are numerous, but their focus is hardly ever on the impact on host performance. We showed earlier that Erwinia bacteria occur in the gut of western flower thrips, most probably acquired during feeding. Here, we investigate whether thrips gain a net benefit or pay a net cost because of these gut bacteria. On a diet of cucumber leaves, the time to maturity is shorter and the oviposition rate is higher in thrips with bacteria than in thrips without (aposymbionts). When fed on cucumber leaves and pollen, aposymbionts develop faster and lay more eggs. So Erwinia bacteria benefit or parasitize their thrips hosts depending on the diet, which is in accordance with theoretical predictions for fitness of organisms engaged in symbiotic interactions. Possibly, the transmission of gut bacteria has not become strictly vertical because of this diet-dependent fitness variability. PMID:15475338

  19. Calcium Carbonate Precipitation by Ureolytic Subsurface Bacteria

    SciTech Connect

    Fujita, Y.; Colwell, Frederick Scott; Smith, Robert William; Ferris, F. G.; Lawson, R. L.

    2000-10-01

    Coprecipitation in carbonate minerals offers a means of slowing the transport of divalent radionuclides and contaminant metals (e.g.,90Sr2+, UO2+, Co2+) in the subsurface. It may be possible to accelerate this process by stimulating the native microbial community to generate chemical conditions favoring carbonate precipitation. In a preliminary evaluation of this approach, we investigated the ability of ureolytic subsurface bacteria to produce alkaline conditions conducive to calcium carbonate precipitation. Groundwater samples from the Eastern Snake River Plain (ESRP) aquifer in Idaho were screened for urea-hydrolyzing microorganisms; three isolates were selected for further evaluation. Analysis of 16S rRNA gene sequences indicated that two of the ESRP isolates were of the genus Pseudomonas , and the other was a Variovorax sp. The specific urease activities of the ESRP isolates appeared to be similar to each other but less than that of Bacillus pasteurii , a known urease-positive organism. However, calcium carbonate was rapidly precipitated in all cultures that were supplied with urea and calcium, and X-ray diffraction analyses indicated that calcite was always the predominant carbonate polymorph produced. The correspondence between measured calcium concentrations and equilibrium predictions suggested that the rate of calcite precipitation was directly linked to the rate of urea hydrolysis. These results are promising with respect to the potential utility of this approach for in situ remediation and indicate that further evaluation of this approach under conditions more closely simulating environmental conditions is warranted.

  20. Characterizing relationships among fecal indicator bacteria ...

    EPA Pesticide Factsheets

    Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

  1. Characterizing relationships among fecal indicator bacteria ...

    EPA Pesticide Factsheets

    Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

  2. Bacteria as trigger for chronic gastrointestinal disorders.

    PubMed

    Marteau, Philippe; Chaput, Ulriikka

    2011-01-01

    Apart from acute infections, microorganisms may also induce or perpetuate chronic inflammatory diseases and reversible or irreversible proliferation of various cells in the gastrointestinal tract (the extreme being adenocarcinoma and lymphoma). Helicobacter pylori is not only involved in the pathogenesis of lymphoma and gastric adenocarcinoma. The steps and mechanisms of the carcinogenic process involve host predisposition, environmental factors, and strain virulence. The steps of lymphoma genesis include chronic inflammation, acquisition of mucosa-associated lymphoid tissue in the stomach, proliferation of the B lymphocytes in an inflammatory context, acquisition of genetic anomalies and dysregulation of the NF-κB pathway. The role of Campylobacter jejuni in immunoproliferative small bowel disease has also been shown and eradication of this bacterium can cure the lymphoma at its early stage. The evidence for the role of some bacteria in colon cancer development is discussed. Opportunistic pathogens are detected in the stools or mucosa of a proportion of subjects with Crohn's disease. They include Mycobacterium avium paratuberculosis, adherent invasive Escherichia coli, and Clostridium difficile. A dysbiosis has been repeatedly observed in patients with inflammatory bowel disease. Instability of the dominant microbiota and decreased biodiversity (especially in the firmicutes phylum) are major characteristics. The decrease of Faecalibacterium prausnitzii seems to have a prognostic value to predict relapse of Crohn's disease after surgery. Finally, important perspectives are opened by new tools such as metagenomics and metabolomics of the gastrointestinal ecosystems. Major tracks concern irritable bowel syndrome, colon cancer and obesity. Copyright © 2011 S. Karger AG, Basel.

  3. Therapeutic potential of bacteria against solid tumors.

    PubMed

    Hatzikirou, Haralampos; Lopez Alfonso, Juan Carlos; Leschner, Sara; Weiss, Siegfried; Meyer-Hermann, Michael

    2017-02-15

    Intentional bacterial infections can produce efficacious anti-tumor responses in mice, rats, dogs and humans. However, low overall success rates and intense side-effects prevent such approaches from being employed clinically. In this work, we titered bacteria and/or the pro-inflammatory cytokine TNF-α in a set of established murine models of cancer. To interpret the experiments conducted, we considered and calibrated a tumor-effector cell recruitment model under the influence of functional tumor-associated vasculature. In this model, bacterial infections and TNF-α enhanced immune activity and altered vascularization in the tumor bed. Information to predict bacterial therapy outcomes was provided by pre-treatment tumor size and the underlying immune recruitment dynamics. Notably, increasing bacterial loads did not necessarily produce better long-term tumor control, suggesting that tumor sizes affected optimal bacterial loads. Short-term treatment responses were favored by high concentrations of effector cells post-injection, such as induced by higher bacterial loads, but in the longer term did not correlate with an effective restoration of immune surveillance. Overall, our findings suggested that a combination of intermediate bacterial loads with low levels TNF-α administration could enable more favorable outcomes elicited by bacterial infections in tumor-bearing subjects.

  4. Sporulation in Bacteria: Beyond the Standard Model.

    PubMed

    Hutchison, Elizabeth A; Miller, David A; Angert, Esther R

    2014-10-01

    Endospore formation follows a complex, highly regulated developmental pathway that occurs in a broad range of Firmicutes. Although Bacillus subtilis has served as a powerful model system to study the morphological, biochemical, and genetic determinants of sporulation, fundamental aspects of the program remain mysterious for other genera. For example, it is entirely unknown how most lineages within the Firmicutes regulate entry into sporulation. Additionally, little is known about how the sporulation pathway has evolved novel spore forms and reproductive schemes. Here, we describe endospore and internal offspring development in diverse Firmicutes and outline progress in characterizing these programs. Moreover, comparative genomics studies are identifying highly conserved sporulation genes, and predictions of sporulation potential in new isolates and uncultured bacteria can be made from these data. One surprising outcome of these comparative studies is that core regulatory and some structural aspects of the program appear to be universally conserved. This suggests that a robust and sophisticated developmental framework was already in place in the last common ancestor of all extant Firmicutes that produce internal offspring or endospores. The study of sporulation in model systems beyond B. subtilis will continue to provide key information on the flexibility of the program and provide insights into how changes in this developmental course may confer advantages to cells in diverse environments.

  5. Serological studies on chloridazon-degrading bacteria.

    PubMed

    Layh, G; Böhm, R; Eberspächer, J; Lingens, F

    1983-01-01

    Agglutination tests and immunofluorescence tests with antisera against four strains of chloridazon-degrading bacteria revealed the serological uniformity of a group of 22 chloridazon-degrading bacterial strains. No serological relationship could be found between chloridazon-degrading bacteria and representatives of other Gram-negative bacteria. This was demonstrated by agglutination tests, including testing of the antiserum against Acinetobacter calcoaceticus, and by immunofluorescence tests, including testing of the sera against Pseudomonas and Acinetobacter strains. The tests were performed with 31 representatives of different Gram-negative bacteria, and with 22 strains of chloridazon-degrading bacteria as antigens. Differences in the extent of agglutination reactions and antibody titres among chloridazon-degrading bacterial strains together with cross-adsorption xperiments, suggest a rough classification of chloridazon-degrading bacteria into two subgroups. On the basis of immunofluorescence data, a linkage-map was worked out to represent serological relationships in the group of chloridazon-degrading strains.

  6. Using soil bacteria to facilitate phytoremediation.

    PubMed

    Glick, Bernard R

    2010-01-01

    In the past twenty years or so, researchers have endeavored to utilize plants to facilitate the removal of both organic and inorganic contaminants from the environment, especially from soil. These phytoremediation approaches have come a long way in a short time. However, the majority of this work has been done under more controlled laboratory conditions and not in the field. As an adjunct to various phytoremediation strategies and as part of an effort to make this technology more efficacious, a number of scientists have begun to explore the possibility of using various soil bacteria together with plants. These bacteria include biodegradative bacteria, plant growth-promoting bacteria and bacteria that facilitate phytoremediation by other means. An overview of bacterially assisted phytoremediation is provided here for both organic and metallic contaminants, with the intent of providing some insight into how these bacteria aid phytoremediation so that future field studies might be facilitated. (c) 2010 Elsevier Inc. All rights reserved.

  7. Commensal bacteria mediated defenses against pathogens

    PubMed Central

    Abt, Michael C.; Pamer, Eric G.

    2014-01-01

    Commensal bacterial communities residing within the intestinal lumen of mammals have evolved to flourish in this microenvironment. To preserve this niche, commensal bacteria act with the host to prevent colonization by invasive pathogens that induce inflammation and disrupt the intestinal niche commensal bacteria rely upon. Thus, it is mutually beneficial to the host and commensal bacteria to inhibit a pathogen's ability to establish an infection. Commensal bacteria express factors that support colonization, maximize nutrient uptake, and produce metabolites that confer a survival advantage over pathogens. Further, commensal bacteria stimulate the host's immune defenses and drive tonic expression of anti-microbial factors. In combination, these mechanisms preserve the niche for commensal bacteria and assist the host in preventing infection. PMID:24727150

  8. Lactic acid bacteria as probiotics.

    PubMed

    Ljungh, Asa; Wadström, Torkel

    2006-09-01

    A number of Lactobacillus species, Bifidobacterium sp, Saccharomyces boulardii, and some other microbes have been proposed as and are used as probiotic strains, i.e. live microorganisms as food supplement in order to benefit health. The health claims range from rather vague as regulation of bowel activity and increasing of well-being to more specific, such as exerting antagonistic effect on the gastroenteric pathogens Clostridium difficile, Campylobacter jejuni, Helicobacter pylori and rotavirus, neutralising food mutagens produced in colon, shifting the immune response towards a Th2 response, and thereby alleviating allergic reactions, and lowering serum cholesterol (Tannock, 2002). Unfortunately, most publications are case reports, uncontrolled studies in humans, or reports of animal or in vitro studies. Whether or not the probiotic strains employed shall be of human origin is a matter of debate but this is not a matter of concern, as long as the strains can be shown to survive the transport in the human gastrointestinal (GI) tract and to colonise the human large intestine. This includes survival in the stressful environment of the stomach - acidic pH and bile - with induction of new genes encoding a number of stress proteins. Since the availability of antioxidants decreases rostrally in the GI tract production of antioxidants by colonic bacteria provides a beneficial effect in scavenging free radicals. LAB strains commonly produce antimicrobial substance(s) with activity against the homologous strain, but LAB strains also often produce microbicidal substances with effect against gastric and intestinal pathogens and other microbes, or compete for cell surface and mucin binding sites. This could be the mechanism behind reports that some probiotic strains inhibit or decrease translocation of bacteria from the gut to the liver. A protective effect against cancer development can be ascribed to binding of mutagens by intestinal bacteria, reduction of the enzymes beta

  9. Earthquake prediction

    NASA Technical Reports Server (NTRS)

    Turcotte, Donald L.

    1991-01-01

    The state of the art in earthquake prediction is discussed. Short-term prediction based on seismic precursors, changes in the ratio of compressional velocity to shear velocity, tilt and strain precursors, electromagnetic precursors, hydrologic phenomena, chemical monitors, and animal behavior is examined. Seismic hazard assessment is addressed, and the applications of dynamical systems to earthquake prediction are discussed.

  10. Earthquake prediction

    NASA Technical Reports Server (NTRS)

    Turcotte, Donald L.

    1991-01-01

    The state of the art in earthquake prediction is discussed. Short-term prediction based on seismic precursors, changes in the ratio of compressional velocity to shear velocity, tilt and strain precursors, electromagnetic precursors, hydrologic phenomena, chemical monitors, and animal behavior is examined. Seismic hazard assessment is addressed, and the applications of dynamical systems to earthquake prediction are discussed.

  11. Time to recognise that mitochondria are bacteria?

    PubMed

    Pallen, Mark J

    2011-02-01

    The scientific community is comfortable with recognising mitochondria as organelles that happen to be descendants of bacteria. Here, I playfully explore the arguments for and against a phylogenetic fundamentalism that states that mitochondria are bacteria and should be given their own taxonomic family, the Mitochondriaceae. I also explore the consequences of recognizing mitochondria as bacteria for our understanding of the systemic response to trauma and for the prospects of creating transgenic mitochondria.

  12. Transformation of gram positive bacteria by sonoporation

    DOEpatents

    Yang, Yunfeng; Li, Yongchao

    2014-03-11

    The present invention provides a sonoporation-based method that can be universally applied for delivery of compounds into Gram positive bacteria. Gram positive bacteria which can be transformed by sonoporation include, for example, Bacillus, Streptococcus, Acetobacterium, and Clostridium. Compounds which can be delivered into Gram positive bacteria via sonoporation include nucleic acids (DNA or RNA), proteins, lipids, carbohydrates, viruses, small organic and inorganic molecules, and nano-particles.

  13. Evaluation of bacteria-facilitated cadmium transport in gravel columns using the HYDRUS colloid-facilitated solute transport model

    NASA Astrophysics Data System (ADS)

    Pang, Liping; Å Imå¯Nek, Jirka

    2006-12-01

    The colloid-facilitated solute transport model, based on HYDRUS-1D, was evaluated using the column experimental data of Pang et al. (2005) for cadmium (Cd) transport facilitated by B. subtilis spores or E. coli in saturated coarse alluvial gravels. We simulated Cd transport involving convection, dispersion, kinetic adsorption/desorption to/from the aquifer media and to/from mobile/immobile bacteria, and kinetic attachment/detachment of the bacteria to/from the aquifer media. To reduce the number of parameters to be optimized, we independently estimated Cd sorption/desorption rates to mobile bacteria from a batch study. The model described the collected experimental data reasonably well. Extensive sensitivity analysis to various reaction parameters was carried out to obtain an understanding of the relative importance of individual model parameters on model predictions. Our modeling results suggest that the rates of Cd sorption or desorption differ not only between different bacterial species but also between unattached and deposited bacteria. The results of the sensitivity analysis indicated that the Cd sorption rate to unattached bacteria had a significantly greater impact on the model results than its sorption rate to deposited bacteria. For the experimental system investigated here, model results were most sensitive to parameters describing interactions between Cd-aquifer media, bacteria-aquifer media, and Cd-mobile bacteria, and they were less sensitive to interactions between Cd-immobile bacteria and desorption rate from mobile bacteria.

  14. Bioenergetics of photoheterotrophic bacteria in the oceans.

    PubMed

    Kirchman, David L; Hanson, Thomas E

    2013-04-01

    Photoheterotrophic microbes, such as proteorhodopsin (PR)-based phototrophic (PRP) and aerobic anoxygenic phototrophic (AAP) bacteria, are well known to be abundant in the oceans, potentially playing unique roles in biogeochemical cycles. However, the contribution of phototrophy to the energy requirements of these bacteria has not been quantitatively examined to date. To better understand the implications of photoheterophy in the oceans, we calculated energy benefits and costs of phototrophy and compared net benefits with maintenance costs. Benefits depend on the number of photosynthetic units (PSUs), absorption cross-section area of each PSU as function of wavelength, the in situ light quality, and the energy yield per absorbed photon. For costs we considered the energy required for the synthesis of pigments, amino acids and proteins in each PSU. Our calculations indicate that AAP bacteria harvest more light energy than do PRP bacteria, but the costs of phototrophy are much higher for AAP bacteria. Still, the net energy gained by AAP bacteria is often sufficient to meet maintenance costs, while that is not the case for PRP bacteria except with high light intensities and large numbers of proteorhodopsin molecules per cell. The low costs and simplicity of PR-based phototrophy explain the high abundance of proteorhodopsin genes in the oceans. However, even for AAP bacteria, the net energy yield of phototrophy is apparently too low to influence the distribution of photoheterotrophic bacteria among various marine systems.

  15. Survival of soil bacteria during prolonged desiccation.

    NASA Technical Reports Server (NTRS)

    Chen, M.; Alexander, M.

    1973-01-01

    A determination was made of the kinds and numbers of bacteria surviving when two soils were maintained in the laboratory under dry conditions for more than half a year. Certain non-spore-forming bacteria were found to survive in the dry condition for long periods. A higher percentage of drought-tolerant than drought-sensitive bacteria was able to grow at low water activities. When they were grown in media with high salt concentrations, bacteria generally became more tolerant of prolonged drought and they persisted longer. The percent of cells in a bacterial population that remained viable when exposed to drought stress varied with the stage of growth.

  16. Survival of soil bacteria during prolonged desiccation.

    NASA Technical Reports Server (NTRS)

    Chen, M.; Alexander, M.

    1973-01-01

    A determination was made of the kinds and numbers of bacteria surviving when two soils were maintained in the laboratory under dry conditions for more than half a year. Certain non-spore-forming bacteria were found to survive in the dry condition for long periods. A higher percentage of drought-tolerant than drought-sensitive bacteria was able to grow at low water activities. When they were grown in media with high salt concentrations, bacteria generally became more tolerant of prolonged drought and they persisted longer. The percent of cells in a bacterial population that remained viable when exposed to drought stress varied with the stage of growth.

  17. Spectroscopic diagnostics for bacteria in biologic sample

    DOEpatents

    El-Sayed, Mostafa A.; El-Sayed, Ivan H.

    2002-01-01

    A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

  18. Isolation of bacteria envelope proteins.

    PubMed

    Quan, Shu; Hiniker, Annie; Collet, Jean-François; Bardwell, James C A

    2013-01-01

    Proteomic analysis on cell envelope proteins from Gram-negative bacteria requires specific isolation techniques. We found that conventional extraction methods such as osmotic shock cause extracts to be heavily contaminated with soluble cytoplasmic proteins. These cytoplasmic protein contaminants constitute the major signal in proteomic analysis and can overwhelm the signals coming from genuine envelope components. After extensive testing of various protocols for the preparation of envelope contents, we found that a modified version of the method of Oliver and Beckwith consistently produces the cleanest extract of periplasmic and outer membrane proteins.We have designated this very simple method TSE extraction because it uses a Tris-sucrose solution supplemented with EDTA.Cytoplasmic and inner membrane protein contaminants are not evident on 1D SDS polyacrylamide gels and contribute to less than 6% of total signal in very sensitive mass spectrometry analysis. This straightforward method is therefore ideal for -analyzing specific proteomic changes in the cell envelope.

  19. Single Bacteria as Turing Machines

    NASA Astrophysics Data System (ADS)

    Bos, Julia; Zang, Qiucen; Vyawahare, Saurabh; Austin, Robert

    2014-03-01

    In Allan Turing's famous 1950 paper on Computing Machinery and Intelligence, he started with the provocative statement: ``I propose to consider the question, `Can machines think?' This should begin with definitions of the meaning of the terms `machine' and `think'.'' In our own work on exploring the way that organisms respond to stress and evolve, it seems at times as if they come to remarkably fast solutions to problems, indicating some sort of very clever computational machinery. I'll discuss how it would appear that bacteria can indeed create a form of a Turing Machine, the first example of a computer, and how they might use this algorithm to do rapid evolution to solve a genomics problem.

  20. Regulated Proteolysis in Bacteria: Caulobacter.

    PubMed

    Joshi, Kamal Kishore; Chien, Peter

    2016-11-23

    Protein degradation is essential for all living things. Bacteria use energy-dependent proteases to control protein destruction in a highly specific manner. Recognition of substrates is determined by the inherent specificity of the proteases and through adaptor proteins that alter the spectrum of substrates. In the α-proteobacterium Caulobacter crescentus, regulated protein degradation is required for stress responses, developmental transitions, and cell cycle progression. In this review, we describe recent progress in our understanding of the regulated and stress-responsive protein degradation pathways in Caulobacter. We discuss how organization of highly specific adaptors into functional hierarchies drives destruction of proteins during the bacterial cell cycle. Because all cells must balance the need for degradation of many true substrates with the toxic consequences of nonspecific protein destruction, principles found in one system likely generalize to others.

  1. Cell Size Regulation in Bacteria

    NASA Astrophysics Data System (ADS)

    Amir, Ariel

    2014-05-01

    Various bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant, but is typically distributed over a narrow range. Here, we propose an analytically tractable model for cell size control, and calculate the cell size and interdivision time distributions, as well as the correlations between these variables. We suggest ways of extracting the model parameters from experimental data, and show that existing data for E. coli supports partial size control, and a particular explanation: a cell attempts to add a constant volume from the time of initiation of DNA replication to the next initiation event. This hypothesis accounts for the experimentally observed correlations between mother and daughter cells as well as the exponential dependence of size on growth rate.

  2. Modeling Political Populations with Bacteria

    NASA Astrophysics Data System (ADS)

    Cleveland, Chris; Liao, David

    2011-03-01

    Results from lattice-based simulations of micro-environments with heterogeneous nutrient resources reveal that competition between wild-type and GASP rpoS819 strains of E. Coli offers mutual benefit, particularly in nutrient deprived regions. Our computational model spatially maps bacteria populations and energy sources onto a set of 3D lattices that collectively resemble the topology of North America. By implementing Wright-Fishcer re- production into a probabilistic leap-frog scheme, we observe populations of wild-type and GASP rpoS819 cells compete for resources and, yet, aid each other's long term survival. The connection to how spatial political ideologies map in a similar way is discussed.

  3. Phosphatidic Acid Synthesis in Bacteria

    PubMed Central

    Yao, Jiangwei; Rock, Charles O.

    2012-01-01

    Membrane phospholipid synthesis is a vital facet of bacterial physiology. Although the spectrum of phospholipid headgroup structures produced by bacteria is large, the key precursor to all of these molecules is phosphatidic acid (PtdOH). Glycerol-3-phosphate derived from the glycolysis via glycerol-phosphate synthase is the universal source for the glycerol backbone of PtdOH. There are two distinct families of enzymes responsible for the acylation of the 1-position of glycerol-3-phosphate. The PlsB acyltransferase was discovered in Escherichia coli, and homologs are present in many eukaryotes. This protein family primarily uses acyl-acyl carrier protein (ACP) endproducts of fatty acid synthesis as acyl donors, but may also use acyl-CoA derived from exogenous fatty acids. The second protein family, PlsY, is more widely distributed in bacteria and utilizes the unique acyl donor, acyl-phosphate, which is produced from acyl-ACP by the enzyme PlsX. The acylation of the 2-position is carried out by members of the PlsC protein family. All PlsCs use acyl-ACP as the acyl donor, although the PlsCs of the γ-proteobacteria also may use acyl-CoA. Phospholipid headgroups are precursors in the biosynthesis of other membrane-associated molecules and the diacylglycerol product of these reactions is converted to PtdOH by one of two distinct families of lipid kinases. The central importance of the de novo and recycling pathways to PtdOH in cell physiology suggest these enzymes are suitable targets for the development of antibacterial therapeutics in Gram-positive pathogens. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism. PMID:22981714

  4. Mitochondria: a target for bacteria.

    PubMed

    Lobet, Elodie; Letesson, Jean-Jacques; Arnould, Thierry

    2015-04-01

    Eukaryotic cells developed strategies to detect and eradicate infections. The innate immune system, which is the first line of defence against invading pathogens, relies on the recognition of molecular patterns conserved among pathogens. Pathogen associated molecular pattern binding to pattern recognition receptor triggers the activation of several signalling pathways leading to the establishment of a pro-inflammatory state required to control the infection. In addition, pathogens evolved to subvert those responses (with passive and active strategies) allowing their entry and persistence in the host cells and tissues. Indeed, several bacteria actively manipulate immune system or interfere with the cell fate for their own benefit. One can imagine that bacterial effectors can potentially manipulate every single organelle in the cell. However, the multiple functions fulfilled by mitochondria especially their involvement in the regulation of innate immune response, make mitochondria a target of choice for bacterial pathogens as they are not only a key component of the central metabolism through ATP production and synthesis of various biomolecules but they also take part to cell signalling through ROS production and control of calcium homeostasis as well as the control of cell survival/programmed cell death. Furthermore, considering that mitochondria derived from an ancestral bacterial endosymbiosis, it is not surprising that a special connection does exist between this organelle and bacteria. In this review, we will discuss different mitochondrial functions that are affected during bacterial infection as well as different strategies developed by bacterial pathogens to subvert functions related to calcium homeostasis, maintenance of redox status and mitochondrial morphology.

  5. Sputum colour and bacteria in chronic bronchitis exacerbations: a pooled analysis.

    PubMed

    Miravitlles, Marc; Kruesmann, Frank; Haverstock, Daniel; Perroncel, Renee; Choudhri, Shurjeel H; Arvis, Pierre

    2012-06-01

    We examined the correlation between sputum colour and the presence of potentially pathogenic bacteria in acute exacerbations of chronic bronchitis (AECBs). Data were pooled from six multicentre studies comparing moxifloxacin with other antimicrobials in patients with an AECB. Sputum was collected before antimicrobial therapy, and bacteria were identified by culture and Gram staining. Association between sputum colour and bacteria was determined using logistic regression. Of 4,089 sputum samples, a colour was reported in 4,003; 1,898 (46.4%) were culture-positive. Green or yellow sputum samples were most likely to yield bacteria (58.9% and 45.5% of samples, respectively), compared with 18% of clear and 39% of rust-coloured samples positive for potentially pathogenic microorganisms. Factors predicting a positive culture were sputum colour (the strongest predictor), sputum purulence, increased dyspnoea, male sex and absence of fever. Green or yellow versus white sputum colour was associated with a sensitivity of 94.7% and a specificity of 15% for the presence of bacteria. Sputum colour, particularly green and yellow, was a stronger predictor of potentially pathogenic bacteria than sputum purulence and increased dyspnoea in AECB patients. However, it does not necessarily predict the need for antibiotic treatment in all patients with AECB.

  6. Coliform bacteria, fabrics, and the environment.

    PubMed

    Colclasure, Victoria J; Soderquist, Thomas J; Lynch, Thomas; Schubert, Nina; McCormick, Deirdre S; Urrutia, Erika; Knickerbocker, Corey; McCord, Devon; Kavouras, Jerry H

    2015-02-01

    People come into contact with coliform bacteria at recreational sites. Previous research on bacteria adhering to fabrics and surfaces focused on the viability of clinically significant microbes, but did not examine the quantity of bacteria. This study examined the viability and quantity of coliform bacteria adhered to common fabrics. The fabrics of 100% cotton, blended cotton, and silk were exposed to a mixture of environmental coliform isolates. Fabrics were incubated in the dark at 25°C or 37°C or in direct sunlight at room temperature for 30, 60, 90, and 120 days. The quantity and viability of the bacteria were determined by the Most Probable Number technique using Colilert reagent (IDEXX Laboratories, Westbrook, ME) and eosin methylene blue agar, respectively. The highest numbers of bacteria were detected for each type of fabric when stored in the dark at 25°C, whereas the lowest numbers of bacteria were detected when fabrics were stored in the dark at 37°C. Low numbers of bacteria were detected on silk and blended cotton exposed to sunlight at room temperature, but not 100% cotton. It appears that coliform bacteria can survive on fabrics longer than previous studies have reported. Coliform bacteria survive better in the dark, at lower temperatures, and on fabrics that can retain moisture. These findings can be applied directly to the viability of bacteria on clothing and potential human exposure to fecal pathogens. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  7. Reduced efficiency of magnetotaxis in magnetotactic coccoid bacteria in higher than geomagnetic fields.

    PubMed

    Pan, Yongxin; Lin, Wei; Li, Jinhua; Wu, Wenfang; Tian, Lanxiang; Deng, Chenglong; Liu, Qingsong; Zhu, Rixiang; Winklhofer, Michael; Petersen, Nikolai

    2009-08-19

    Magnetotactic bacteria are microorganisms that orient and migrate along magnetic field lines. The classical model of polar magnetotaxis predicts that the field-parallel migration velocity of magnetotactic bacteria increases monotonically with the strength of an applied magnetic field. We here test this model experimentally on magnetotactic coccoid bacteria that swim along helical trajectories. It turns out that the contribution of the field-parallel migration velocity decreases with increasing field strength from 0.1 to 1.5 mT. This unexpected observation can be explained and reproduced in a mathematical model under the assumption that the magnetosome chain is inclined with respect to the flagellar propulsion axis. The magnetic disadvantage, however, becomes apparent only in stronger than geomagnetic fields, which suggests that magnetotaxis is optimized under geomagnetic field conditions. It is therefore not beneficial for these bacteria to increase their intracellular magnetic dipole moment beyond the value needed to overcome Brownian motion in geomagnetic field conditions.

  8. Method of dispersing a hydrocarbon using bacteria

    DOEpatents

    Tyndall, Richard L.

    1996-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  9. Medical Textiles For Uniform Bacteria Mitigation

    DTIC Science & Technology

    2004-12-01

    antimicrobial, on the other hand, remains affixed to the textile, and, on a molecular scale, physically penetrates the bacteria membrane and...washing at Natick Soldier Center, followed by microbial assay testing using both gram-positive and gram-negative bacteria . The research addresses the

  10. Symbiosis: Gut Bacteria Manipulate Host Behaviour.

    PubMed

    Yuval, Boaz

    2017-08-07

    Bacteria resident in the gut of Drosophila modify the fly's innate chemosensory responses to nutritional stimuli. In effect, the gut microbiome compels the host to forage on food patches that favour particular assemblages of bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Analyzing arthropods for the presence of bacteria.

    PubMed

    Andrews, Elizabeth S

    2013-02-01

    Bacteria within arthropods can be identified using culture-independent methods. This unit describes protocols for surface sterilization of arthropods, DNA extraction of whole bodies and tissues, touchdown PCR amplification using 16S rDNA general bacteria primers, and profiling the bacterial community using denaturing gradient gel electrophoresis. © 2013 by John Wiley & Sons, Inc.

  12. Problems in the cultivation of cervical bacteria.

    PubMed

    Brown, E R; Keith, L G; Rosen, G F

    1985-03-01

    Multiple variations in the types, species and prevalence of cervical bacteria are described in the literature. A review of the literature was undertaken to determine the effect of delay on the ability to identify bacteria. Experiments were initiated to elaborate on those observations. The rate of organism isolation was related to the delay in transport to the laboratory.

  13. Method of dispersing a hydrocarbon using bacteria

    DOEpatents

    Tyndall, R.L.

    1996-09-24

    A new protozoan derived microbial consortia and method for their isolation are provided. The isolated consortia and bacteria are useful for treating wastes such as trichloroethylene and trinitrotoluene. The isolated consortia, bacteria, and dispersants are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  14. Rock-degrading endophytic bacteria in cacti

    Treesearch

    M. Esther Puente; Ching Y. Li; Yoav Bashan

    2009-01-01

    A plant-bacterium association of the cardon cactus (Pachycereus pringlei) and endophytic bacteria promotes establishment of seedlings and growth on igneous rocks without soil. These bacteria weather several rock types and minerals, unbind significant amounts of useful minerals for plants from the rocks, fix in vitro N2. produce...

  15. Encapsulation of lactic acid bacteria in colloidosomes.

    PubMed

    Keen, Polly H R; Slater, Nigel K H; Routh, Alexander F

    2012-11-20

    Polymeric colloidosomes encapsulating viable lactic acid bacteria were prepared. An aqueous suspension of 153 nm poly(methyl methacrylate-co-butyl acrylate) latex particles plus Lactobacillus crispatus was emulsified in a continuous phase of sunflower oil. By adding a small amount of ethanol and salt to the oil phase, the latex particles at the surface of the emulsion droplets aggregate to form the colloidosome shells. The colloidosomes have been examined using optical, confocal, and scanning electron microscopies. The viability of the bacteria was tested using fluorescent molecular probes. The encapsulated lactic acid bacteria were able to metabolize glucose from solution and produce acid albeit at a slower rate compared to unencapsulated microbes. This demonstrates transport limitation through the colloidosome shell and restriction of the cellular metabolism due to encapsulation. Protection of the bacteria by encapsulation in colloidosomes was also demonstrated; a significantly larger number of encapsulated bacteria maintained viability in simulated stomach conditions compared to unencapsulated microbes.

  16. Chemotactic selection of pollutant degrading soil bacteria

    DOEpatents

    Hazen, T.C.

    1991-03-04

    A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  17. HYDROCARBON-DEGRADING BACTERIA AND SURFACTANT ACTIVITY

    SciTech Connect

    Brigmon, R; Topher Berry, T; Grazyna A. Plaza, G; jacek Wypych, j

    2006-08-15

    Fate of benzene ethylbenzene toluene xylenes (BTEX) compounds through biodegradation was investigated using two different bacteria, Ralstonia picketti (BP-20) and Alcaligenes piechaudii (CZOR L-1B). These bacteria were isolated from extremely polluted petroleum hydrocarbon contaminated soils. PCR and Fatty Acid Methyl Ester (FAME) were used to identify the isolates. Biodegradation was measured using each organism individually and in combination. Both bacteria were shown to degrade each of the BTEX compounds. Alcaligenes piechaudii biodegraded BTEXs more efficiently while mixed with BP-20 and individually. Biosurfactant production was observed by culture techniques. In addition 3-hydroxy fatty acids, important in biosurfactant production, was observed by FAME analysis. In the all experiments toluene and m+p- xylenes were better growth substrates for both bacteria than the other BTEX compounds. In addition, the test results indicate that the bacteria could contribute to bioremediation of aromatic hydrocarbons (BTEX) pollution increase biodegradation through the action by biosurfactants.

  18. The genomic basis of trophic strategy in marine bacteria.

    PubMed

    Lauro, Federico M; McDougald, Diane; Thomas, Torsten; Williams, Timothy J; Egan, Suhelen; Rice, Scott; DeMaere, Matthew Z; Ting, Lily; Ertan, Haluk; Johnson, Justin; Ferriera, Steven; Lapidus, Alla; Anderson, Iain; Kyrpides, Nikos; Munk, A Christine; Detter, Chris; Han, Cliff S; Brown, Mark V; Robb, Frank T; Kjelleberg, Staffan; Cavicchioli, Ricardo

    2009-09-15

    Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.

  19. Growth of saprotrophic fungi and bacteria in soil.

    PubMed

    Rousk, Johannes; Bååth, Erland

    2011-10-01

    Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed.

  20. Revisiting the cape cod bacteria injection experiment using a stochastic modeling approach

    USGS Publications Warehouse

    Maxwell, R.M.; Welty, C.; Harvey, R.W.

    2007-01-01

    Bromide and resting-cell bacteria tracer tests conducted in a sandy aquifer at the U.S. Geological Survey Cape Cod site in 1987 were reinterpreted using a three-dimensional stochastic approach. Bacteria transport was coupled to colloid filtration theory through functional dependence of local-scale colloid transport parameters upon hydraulic conductivity and seepage velocity in a stochastic advection - dispersion/attachment - detachment model. Geostatistical information on the hydraulic conductivity (K) field that was unavailable at the time of the original test was utilized as input. Using geostatistical parameters, a groundwater flow and particle-tracking model of conservative solute transport was calibrated to the bromide-tracer breakthrough data. An optimization routine was employed over 100 realizations to adjust the mean and variance ofthe natural-logarithm of hydraulic conductivity (InK) field to achieve best fit of a simulated, average bromide breakthrough curve. A stochastic particle-tracking model for the bacteria was run without adjustments to the local-scale colloid transport parameters. Good predictions of mean bacteria breakthrough were achieved using several approaches for modeling components of the system. Simulations incorporating the recent Tufenkji and Elimelech (Environ. Sci. Technol. 2004, 38, 529-536) correlation equation for estimating single collector efficiency were compared to those using the older Rajagopalan and Tien (AIChE J. 1976, 22, 523-533) model. Both appeared to work equally well at predicting mean bacteria breakthrough using a constant mean bacteria diameter for this set of field conditions. Simulations using a distribution of bacterial cell diameters available from original field notes yielded a slight improvement in the model and data agreement compared to simulations using an average bacterial diameter. The stochastic approach based on estimates of local-scale parameters for the bacteria-transport process reasonably captured

  1. Antibiotic resistance in probiotic bacteria

    PubMed Central

    Gueimonde, Miguel; Sánchez, Borja; G. de los Reyes-Gavilán, Clara; Margolles, Abelardo

    2013-01-01

    Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. The main probiotic bacteria are strains belonging to the genera Lactobacillus and Bifidobacterium, although other representatives, such as Bacillus or Escherichia coli strains, have also been used. Lactobacillus and Bifidobacterium are two common inhabitants of the human intestinal microbiota. Also, some species are used in food fermentation processes as starters, or as adjunct cultures in the food industry. With some exceptions, antibiotic resistance in these beneficial microbes does not constitute a safety concern in itself, when mutations or intrinsic resistance mechanisms are responsible for the resistance phenotype. In fact, some probiotic strains with intrinsic antibiotic resistance could be useful for restoring the gut microbiota after antibiotic treatment. However, specific antibiotic resistance determinants carried on mobile genetic elements, such as tetracycline resistance genes, are often detected in the typical probiotic genera, and constitute a reservoir of resistance for potential food or gut pathogens, thus representing a serious safety issue. PMID:23882264

  2. Mycelial bacteria of saline soils

    NASA Astrophysics Data System (ADS)

    Zvyagintsev, D. G.; Zenova, G. M.; Oborotov, G. V.

    2008-10-01

    The actinomycetal complexes of saline soils comprise the representatives of the Streptomyces and Micromonospora genera, the number of which are hundreds and thousands of CFU/g soil. Complexes of mycelial bacteria in saline soils are poorer in terms of number (by 1-3 orders of magnitude) and taxonomic composition than the complexes of the zonal soil types. A specific feature of the actinomycetal complexes of saline soils is the predominance of halophilic, alkaliphilic, and haloalkaliphilic streptomycetes that well grow at pH 8-9 and concentrations of NaCl close to 5%. Actinomycetes in saline soils grow actively, and the length of their mycelium reaches 140 m in 1 gram of soil. The haloalkaliphilic streptomycetes grow fast and inhibit the formation of spores at pH 9 and high concentrations of salts (Na2SO4 and MgCl2, 5%) as compared to their behavior on a neutral medium with a salt concentration of 0.02%. They are characterized by the maximal radial growth rate of colonies on an alkaline medium with 5% NaCl.

  3. Cell Size Control in Bacteria

    PubMed Central

    Chien, An-Chun; Hill, Norbert S.; Levin, Petra Anne

    2012-01-01

    Like eukaryotes, bacteria must coordinate division with growth to ensure cells are the appropriate size for a given environmental condition or developmental fate. As single-celled organisms, nutrient availability is one of the strongest influences on bacterial cell size. Classic physiological experiments conducted over four decades ago first demonstrated that cell size is directly correlated with nutrient source and growth rate in the Gram-negative bacterium Salmonella typhimurium. This observation subsequently served as the basis for studies revealing a role for cell size in cell cycle progression in a closely related organism, Escherichia coli. More recently, the development of powerful genetic, molecular, and imaging tools has allowed us to identify and characterize the nutrient-dependent pathway responsible for coordinating cell division and cell size with growth rate in the Gram-positive model organism B. subtilis. Here, we discuss the role of cell size in bacterial growth and development and propose a broadly applicable model for cell size control in this important and highly divergent domain of life. PMID:22575476

  4. Tape Cassette Bacteria Detection System

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The design, fabrication, and testing of an automatic bacteria detection system with a zero-g capability and based on the filter-capsule approach is described. This system is intended for monitoring the sterility of regenerated water in a spacecraft. The principle of detection is based on measuring the increase in chemiluminescence produced by the action of bacterial porphyrins (i.e., catalase, cytochromes, etc.) on a luminol-hydrogen peroxide mixture. Since viable as well as nonviable organisms initiate this luminescence, viable organisms are detected by comparing the signal of an incubated water sample with an unincubated control. Higher signals for the former indicate the presence of viable organisms. System features include disposable sealed sterile capsules, each containing a filter membrane, for processing discrete water samples and a tape transport for moving these capsules through a processing sequence which involves sample concentration, nutrient addition, incubation, a 4 Molar Urea wash and reaction with luminol-hydrogen peroxide in front of a photomultiplier tube. Liquids are introduced by means of a syringe needle which pierces a rubber septum contained in the wall of the capsule. Detection thresholds obtained with this unit towards E. coli and S. marcescens assuming a 400 ml water sample are indicated.

  5. [Geographical distribution of magnetotactic bacteria].

    PubMed

    Zhang, Wen-yan; Zhang, Sheng-da; Xiao, Tian; Pan, Yong-xin; Wu, Long-fei

    2010-02-01

    Magnetotactic bacteria (MTB) are widely distributed in aquatic environments. To assess the correlation between their evolutionary relatedness and geographic distribution, we analyzed 239 16S rDNA sequences available in the Genbank, and constructed phylogenetic trees based on the sequences. After elimination of redundant sequences by grouping those with identity > 97% into a single one, we analyzed in detail total 139 16S rDNA sequences, including 55 from marine MTB and 82 from freshwater sequences, and belonging to Proteobacteria and Nitrospirae. Phylogeny analysis based on those sequences suggests that the geographical distribution of MTB has certain regional distribution character: marine MTB is distinct from freshwater MTB, and off coast MTB are remotely related with ocean MTB. In contrast, the MTB from similar habitats, such as offshore in Brazil and the United States or freshwater lakes in Germany and China, are closely related. It is found that similar species have a large geographic distribution and tend to adopt the similar habitats, morphotypes of MTB and their living environment conditions have a significant relevance. This observation suggests that MTB may have multiple evolutionary origins. And also, it suggests the environmental conditions, as an important evolutionary pressure, play an important role in the long-term evolution of MTB.

  6. Comparative cytotoxicity of periodontal bacteria

    SciTech Connect

    Stevens, R.H.; Hammond, B.F.

    1988-11-01

    The direct cytotoxicity of sonic extracts (SE) from nine periodontal bacteria for human gingival fibroblasts (HGF) was compared. Equivalent dosages (in terms of protein concentration) of SE were used to challenge HGF cultures. The cytotoxic potential of each SE was assessed by its ability to (1) inhibit HGF proliferation, as measured by direct cell counts; (2) inhibit 3H-thymidine incorporation in HGF cultures; or (3) cause morphological alterations of the cells in challenged cultures. The highest concentration (500 micrograms SE protein/ml) of any of the SEs used to challenge the cells was found to be markedly inhibitory to the HGFs by all three of the criteria of cytotoxicity. At the lowest dosage tested (50 micrograms SE protein/ml); only SE from Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, and Fusobacterium nucleatum caused a significant effect (greater than 90% inhibition or overt morphological abnormalities) in the HGFs as determined by any of the criteria employed. SE from Capnocytophaga sputigena, Eikenella corrodens, or Wolinella recta also inhibited cell proliferation and thymidine incorporation at this dosage; however, the degree of inhibition (5-50%) was consistently, clearly less than that of the first group of three organisms named above. The SE of the three other organisms tested (Actinomyces odontolyticus, Bacteroides intermedius, and Streptococcus sanguis) had little or no effect (0-10% inhibition) at this concentration. The data suggest that the outcome of the interaction between bacterial components and normal resident cells of the periodontium is, at least in part, a function of the bacterial species.

  7. Are Uncultivated Bacteria Really Uncultivable?

    PubMed Central

    Puspita, Indun Dewi; Kamagata, Yoichi; Tanaka, Michiko; Asano, Kozo; Nakatsu, Cindy H.

    2012-01-01

    Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency. PMID:23059723

  8. Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria

    PubMed Central

    Veith, Nadine; Feldman-Salit, Anna; Cojocaru, Vlad; Henrich, Stefan; Kummer, Ursula; Wade, Rebecca C.

    2013-01-01

    Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may

  9. Potential role of bacteria packaging by protozoa in the persistence and transmission of pathogenic bacteria

    PubMed Central

    Denoncourt, Alix M.; Paquet, Valérie E.; Charette, Steve J.

    2014-01-01

    Many pathogenic bacteria live in close association with protozoa. These unicellular eukaryotic microorganisms are ubiquitous in various environments. A number of protozoa such as amoebae and ciliates ingest pathogenic bacteria, package them usually in membrane structures, and then release them into the environment. Packaged bacteria are more resistant to various stresses and are more apt to survive than free bacteria. New evidence indicates that protozoa and not bacteria control the packaging process. It is possible that packaging is more common than suspected and may play a major role in the persistence and transmission of pathogenic bacteria. To confirm the role of packaging in the propagation of infections, it is vital that the molecular mechanisms governing the packaging of bacteria by protozoa be identified as well as elements related to the ecology of this process in order to determine whether packaging acts as a Trojan Horse. PMID:24904553

  10. Potential role of bacteria packaging by protozoa in the persistence and transmission of pathogenic bacteria.

    PubMed

    Denoncourt, Alix M; Paquet, Valérie E; Charette, Steve J

    2014-01-01

    Many pathogenic bacteria live in close association with protozoa. These unicellular eukaryotic microorganisms are ubiquitous in various environments. A number of protozoa such as amoebae and ciliates ingest pathogenic bacteria, package them usually in membrane structures, and then release them into the environment. Packaged bacteria are more resistant to various stresses and are more apt to survive than free bacteria. New evidence indicates that protozoa and not bacteria control the packaging process. It is possible that packaging is more common than suspected and may play a major role in the persistence and transmission of pathogenic bacteria. To confirm the role of packaging in the propagation of infections, it is vital that the molecular mechanisms governing the packaging of bacteria by protozoa be identified as well as elements related to the ecology of this process in order to determine whether packaging acts as a Trojan Horse.

  11. Global phenotypic characterization of bacteria

    PubMed Central

    Bochner, Barry R

    2009-01-01

    The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described. PMID:19054113

  12. Predictive Evaluation

    ERIC Educational Resources Information Center

    Scriven, Michael

    2007-01-01

    Noting that there has been extensive discussion of the relation of evaluation to: (1) research; (2) explanations (a.k.a. theory-driven, logic model, or realistic evaluation); and (3) recommendations, the author introduces: (4) prediction. He advocates that unlike the first three concepts, prediction is necessarily part of most kinds of evaluation,…

  13. Graphing Predictions

    ERIC Educational Resources Information Center

    Connery, Keely Flynn

    2007-01-01

    Graphing predictions is especially important in classes where relationships between variables need to be explored and derived. In this article, the author describes how his students sketch the graphs of their predictions before they begin their investigations on two laboratory activities: Distance Versus Time Cart Race Lab and Resistance; and…

  14. Graphing Predictions

    ERIC Educational Resources Information Center

    Connery, Keely Flynn

    2007-01-01

    Graphing predictions is especially important in classes where relationships between variables need to be explored and derived. In this article, the author describes how his students sketch the graphs of their predictions before they begin their investigations on two laboratory activities: Distance Versus Time Cart Race Lab and Resistance; and…

  15. Using Liquid Crystals to Reveal How Mechanical Anisotropy Changes Interfacial Behaviors of Motile Bacteria

    PubMed Central

    Mushenheim, Peter C.; Trivedi, Rishi R.; Weibel, Douglas B.; Abbott, Nicholas L.

    2014-01-01

    Bacteria often inhabit and exhibit distinct dynamical behaviors at interfaces, but the physical mechanisms by which interfaces cue bacteria are still poorly understood. In this work, we use interfaces formed between coexisting isotropic and liquid crystal (LC) phases to provide insight into how mechanical anisotropy and defects in LC ordering influence fundamental bacterial behaviors. Specifically, we measure the anisotropic elasticity of the LC to change fundamental behaviors of motile, rod-shaped Proteus mirabilis cells (3 μm in length) adsorbed to the LC interface, including the orientation, speed, and direction of motion of the cells (the cells follow the director of the LC at the interface), transient multicellular self-association, and dynamical escape from the interface. In this latter context, we measure motile bacteria to escape from the interfaces preferentially into the isotropic phase, consistent with the predicted effects of an elastic penalty associated with strain of the LC about the bacteria when escape occurs into the nematic phase. We also observe boojums (surface topological defects) present at the interfaces of droplets of nematic LC (tactoids) to play a central role in mediating the escape of motile bacteria from the LC interface. Whereas the bacteria escape the interface of nematic droplets via a mechanism that involved nematic director-guided motion through one of the two boojums, for isotropic droplets in a continuous nematic phase, the elasticity of the LC generally prevented single bacteria from escaping. Instead, assemblies of bacteria piled up at boojums and escape occurred through a cooperative, multicellular phenomenon. Overall, our studies show that the dynamical behaviors of motile bacteria at anisotropic LC interfaces can be understood within a conceptual framework that reflects the interplay of LC elasticity, surface-induced order, and topological defects. PMID:24988359

  16. Quantification of spatial distribution and spread of bacteria in soil at microscale

    NASA Astrophysics Data System (ADS)

    Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Baveye, Philippe; Otten, Wilfred

    2015-04-01

    Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. Soil is a complex heterogeneous environment comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota including bacteria and fungi. Bacteria occupy a very small portion of available pore space in soil which demonstrates that their spatial arrangement in soil has a huge impact on the contact to their target and on the way they interact to carry out their functions. Due to limitation of techniques, there is scant information on spatial distribution of indigenous or introduced bacteria at microhabitat scale. There is a need to understand the interaction between soil structure and microorganisms including fungi for ecosystem-level processes such as carbon sequestration and improving the predictive models for soil management. In this work, a combination of techniques was used including X-ray CT to characterize the soil structure and in-situ detection via fluorescence microscopy to visualize and quantify bacteria in soil thin sections. Pseudomonas fluorescens bacteria were introduced in sterilized soil of aggregate size 1-2 mm and packed at bulk-densities 1.3 g cm-3 and 1.5 g cm-3. A subset of samples was fixed with paraformaldehyde and subsequently impregnated with resin. DAPI and fluorescence in situ hybridization (FISH) were used to visualize bacteria in thin sections of soil cores by epifluorescence microscopy to enumerate spatial distribution of bacteria in soil. The pore geometry of soil was quantified after X-ray microtomography scanning. The distribution of bacteria introduced locally reduced significantly (P

  17. Responses, applications, and analysis of microgravity effects on bacteria

    NASA Astrophysics Data System (ADS)

    Benoit, Michael Robert

    ) to evaluate changes in extracellular fluid density on convective mass transport. From the theoretical analysis results, I predicted convective and diffusive transport regimes for bacteria grown under microgravity, 1 g, and hyper-gravity conditions. Finally, using a numerical model, I successfully simulated an experimentally observed phenomenon of buoyancy-driven convection created by cellular metabolism.

  18. Terpene synthases are widely distributed in bacteria

    PubMed Central

    Yamada, Yuuki; Kuzuyama, Tomohisa; Komatsu, Mamoru; Shin-ya, Kazuo; Omura, Satoshi; Cane, David E.; Ikeda, Haruo

    2015-01-01

    Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes. PMID:25535391

  19. Genetics of lipopolysaccharide biosynthesis in enteric bacteria.

    PubMed Central

    Schnaitman, C A; Klena, J D

    1993-01-01

    From a historical perspective, the study of both the biochemistry and the genetics of lipopolysaccharide (LPS) synthesis began with the enteric bacteria. These organisms have again come to the forefront as the blocks of genes involved in LPS synthesis have been sequenced and analyzed. A number of new and unanticipated genes were found in these clusters, indicating a complexity of the biochemical pathways which was not predicted from the older studies. One of the most dramatic areas of LPS research has been the elucidation of the lipid A biosynthetic pathway. Four of the genes in this pathway have now been identified and sequenced, and three of them are located in a complex operon which also contains genes involved in DNA and phospholipid synthesis. The rfa gene cluster, which contains many of the genes for LPS core synthesis, includes at least 17 genes. One of the remarkable findings in this cluster is a group of several genes which appear to be involved in the synthesis of alternate rough core species which are modified so that they cannot be acceptors for O-specific polysaccharides. The rfb gene clusters which encode O-antigen synthesis have been sequenced from a number of serotypes and exhibit the genetic polymorphism anticipated on the basis of the chemical complexity of the O antigens. These clusters appear to have originated by the exchange of blocks of genes among ancestral organisms. Among the large number of LPS genes which have now been sequenced from these rfa and rfb clusters, there are none which encode proteins that appear to be secreted across the cytoplasmic membrane and surprisingly few which encode integral membrane proteins or proteins with extensive hydrophobic domains. These data, together with sequence comparison and complementation experiments across strain and species lines, suggest that the LPS biosynthetic enzymes may be organized into clusters on the inner surface of the cytoplasmic membrane which are organized around a few key membrane

  20. Hypothesis: Bacteria Control Host Appetites

    PubMed Central

    Molina, Franck; Gewirtz, Andrew T.

    2013-01-01

    To help investigate the relationship between inflammatory and other diseases and the composition of the gut microbiota, we propose that a positive-feedback loop exists between the preferences of the host for a particular dietary regimen, the composition of the gut microbiota that depends on this regimen, and the preferences of the host as influenced by the gut microbiota. We cite evidence in support of this hypothesis and make testable predictions. PMID:23144247

  1. Temporal Synchronization Analysis for Improving Regression Modeling of Fecal Indicator Bacteria Levels

    EPA Science Inventory

    Multiple linear regression models are often used to predict levels of fecal indicator bacteria (FIB) in recreational swimming waters based on independent variables (IVs) such as meteorologic, hydrodynamic, and water-quality measures. The IVs used for these analyses are traditiona...

  2. Temporal Synchronization Analysis for Improving Regression Modeling of Fecal Indicator Bacteria Levels

    EPA Science Inventory

    Multiple linear regression models are often used to predict levels of fecal indicator bacteria (FIB) in recreational swimming waters based on independent variables (IVs) such as meteorologic, hydrodynamic, and water-quality measures. The IVs used for these analyses are traditiona...

  3. International Space Station Bacteria Filter Element Service Life Evaluation

    NASA Technical Reports Server (NTRS)

    Perry, J. L.

    2005-01-01

    The International Space Station (ISS) uses high-efficiency particulate air filters to remove particulate matter from the cabin atmosphere. Known as bacteria filter elements (BFEs), there are 13 elements deployed on board the ISS's U.S. segment in the flight 4R assembly level. The preflight service life prediction of 1 yr for the BFEs is based upon engineering analysis of data collected during developmental testing that used a synthetic dust challenge. While this challenge is considered reasonable and conservative from a design perspective, an understanding of the actual filter loading is required to best manage the critical ISS program resources. Testing was conducted on BFEs returned from the ISS to refine the service life prediction. Results from this testing and implications to ISS resource management are provided.

  4. Decreased bacteria density on nanostructured polyurethane.

    PubMed

    Yao, Chang; Webster, Thomas J; Hedrick, Matthew

    2014-06-01

    As is well known, medical device infections are a growing clinical problem with no clear solution due to previous failed attempts of using antibiotics to decrease bacteria functions for which bacteria quickly develop a resistance toward. Because of their altered surface energetics, the objective of the present in vitro study was to create nanoscale surface features on polyurethane (PU) by soaking PU films in HNO3 and to determine bacteria (specifically, S. epidermidis, E. coli, and P. mirabilis) colony forming units after 1 h. Such bacteria frequently infect numerous medical devices. Results provided the first evidence that without using antibiotics, S. epidermidis density decreased by 5 and 13 times, E. coli density decreased by 6 and 20 times, and P. mirabilis density decreased by 8 and 35 times compared to conventional PU and a tissue engineering control small intestine submucosa (SIS), respectively. Material characterization studies revealed significantly greater nanoscale roughness and hydrophobicity for the HNO3-treated nanostructured PU compared to conventional PU (albeit, still hydrophilic) which may provide a rationale for the observed decreased bacteria responses. In addition, significantly greater amounts of fibronectin adsorption from serum were measured on nanorough compared conventional PU which may explain the decreased bacteria growth. In summary, this study provides significant promise for the use of nanostructured PU to decrease bacteria functions without the use of antibiotics, clearly addressing the wide spread problem of increased medical device infections observed today.

  5. In Vivo Bioluminescence Imaging of Intratumoral Bacteria.

    PubMed

    Cronin, Michelle; Akin, Ali R; Francis, Kevin P; Tangney, Mark

    2016-01-01

    This chapter describes the use of whole-body bioluminescent imaging (BLI) for the study of bacterial trafficking in live mice, with an emphasis on the use of bacteria in therapy of cancer. Bacteria present an attractive class of vector for cancer therapy, possessing a natural ability to grow preferentially within tumors following systemic administration. Bacteria engineered to express the lux gene cassette permit BLI detection of the bacteria and tumor sites concurrently. The location and levels of bacteria within tumors over time can be readily examined, visualized in two or three dimensions. The method is applicable to a wide range of bacterial species and tumor xenograft types. This article describes the protocol for analysis of bioluminescent bacteria within subcutaneous tumor-bearing mice. This powerful, and inexpensive, real-time imaging strategy represents an ideal method for the study of bacteria in vivo in the context of cancer research. This protocol outlines the procedure for studying lux-tagged Escherichia coli and Bifidobacterium breve in mice, demonstrating the spatial and temporal readout from 2D and 3D BLI achievable with whole-body in vivo luminescence imaging.

  6. Coryneform bacteria associated with canine otitis externa.

    PubMed

    Aalbæk, Bent; Bemis, David A; Schjærff, Mette; Kania, Stephen A; Frank, Linda A; Guardabassi, Luca

    2010-10-26

    This study aims to investigate the occurrence of coryneform bacteria in canine otitis externa. A combined case series and case-control study was carried out to improve the current knowledge on frequency and clinical significance of coryneform bacteria in samples from canine otitis externa. A total of 16 cases of otitis externa with involvement of coryneform bacteria were recorded at two referral veterinary hospitals in Denmark and the US, respectively. Coryneform bacteria were identified by partial 16S rRNA gene sequencing. Corynebacterium auriscanis was the most common coryneform species (10 cases). Small colony variants of this species were also observed. Other coryneform isolates were identified as Corynebacterium amycolatum (3 cases), Corynebacterium freneyi (2 cases) and an Arcanobacterium-like species (1 case). The coryneform bacteria were in all cases isolated together with other bacteria, mainly Staphylococcus pseudintermedius alone (n=5) or in combination with Malassezia pachydermatis (n=5). Some coryneform isolates displayed resistance to fusidic acid or enrofloxacin, two antimicrobial agents commonly used for the treatment of otitis externa in dogs. The frequency of isolation of coryneform bacteria was 16% among 55 cases of canine otitis externa examined at the Danish hospital during 2007. In contrast, detectable levels of coryneform bacteria were not demonstrated in samples from the acustic meatus of 35 dogs with apparently healthy ears, attending the hospital during the same year. On basis of the current knowledge, these coryneform bacteria should be regarded as potential secondary pathogens able to proliferate in the environment of an inflamed ear canal. Copyright © 2010 Elsevier B.V. All rights reserved.

  7. Magnetotactic Bacteria from Extreme Environments

    NASA Astrophysics Data System (ADS)

    Bazylinski, Dennis A.; Lefère, Christopher T.

    2013-03-01

    Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells to align along the Earth's geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic-anoxic interface (OAI) in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0.

  8. R-body-producing bacteria.

    PubMed Central

    Pond, F R; Gibson, I; Lalucat, J; Quackenbush, R L

    1989-01-01

    Until 10 years ago, R bodies were known only as diagnostic features by which endosymbionts of paramecia were identified as kappa particles. They were thought to be limited to the cytoplasm of two species in the Paramecium aurelia species complex. Now, R bodies have been found in free-living bacteria and other Paramecium species. The organisms now known to form R bodies include the cytoplasmic kappa endosymbionts of P. biaurelia and P. tetraurelia, the macronuclear kappa endosymbionts of P. caudatum, Pseudomonas avenae (a free-living plant pathogen), Pseudomonas taeniospiralis (a hydrogen-oxidizing soil microorganism), Rhodospirillum centenum (a photosynthetic bacterium), and a soil bacterium, EPS-5028, which is probably a pseudomonad. R bodies themselves fall into five distinct groups, distinguished by size, the morphology of the R-body ribbons, and the unrolling behavior of wound R bodies. In recent years, the inherent difficulties in studying the organization and assembly of R bodies by the obligate endosymbiont kappa, have been alleviated by cloning and expressing genetic determinants for these R bodies (type 51) in Escherichia coli. Type 51 R-body synthesis requires three low-molecular-mass polypeptides. One of these is modified posttranslationally, giving rise to 12 polypeptide species, which are the major structural subunits of the R body. R bodies are encoded in kappa species by extrachromosomal elements. Type 51 R bodies, produced in Caedibacter taeniospiralis, are encoded by a plasmid, whereas bacteriophage genomes probably control R-body synthesis in other kappa species. However, there is no evidence that either bacteriophages or plasmids are present in P. avenae or P. taeniospiralis. No sequence homology was detected between type 51 R-body-encoding DNA and DNA from any R-body-producing species, except C. varicaedens 1038. The evolutionary relatedness of different types of R bodies remains unknown. Images PMID:2651865

  9. Magnetotactic Bacteria from Extreme Environments

    PubMed Central

    Bazylinski, Dennis A.; Lefèvre, Christopher T.

    2013-01-01

    Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI) in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0. PMID:25369742

  10. Bacteria Interactions with Dying Diatoms

    NASA Astrophysics Data System (ADS)

    Smriga, S.; Juarez, G.; Fernandez, V.; Stocker, R.

    2016-02-01

    Dying phytoplankton are surrounded by microscale gradients of dissolved organic matter (DOM) that can attract bacteria. These 'phycospheres' may impact the trophic transfer of DOM in the marine microbial food web and enable the growth of bacterial populations, yet these effects remain poorly quantified particularly in relation to the physiological state of the phytoplankton. We dissected phycosphere interactions at unprecedented spatial and temporal resolution using the model diatom Thalassiosira weissflogii and the bacterium Marinobacter adhaerans. Diatom stress was stimulated by addition of polyunsaturated aldehyde (PUA) and both diatom and bacterial responses were captured via time-lapse fluorescence microscopy. We found that stressed diatoms underwent lysis 10-15 h after PUA treatment. Coordinated with the timing of this transition into phytodetritus, wild-type Marinobacter accumulated via chemotaxis near the diatoms immediately following lysis. In contrast, at lysis there was no accumulation of either a non-chemotactic or a non-motile mutant of Marinobacter, pointing to behavioral rather than demographic responses as drivers for the accumulation. Despite the lack of response, non-chemotactic as well as non-swimming bacterial cells that by chance attached to or were located near (<30 µm) stressed diatoms experienced more growth than cells further afield. Growth within the phycosphere was even greater after diatom lysis. Through quantification at the microscale, these results reveal that chemotaxis may precede rapid bacterial attachment to stressed and dying diatoms and may be integral to the microbial colonization of new phytodetritus during phytoplankton blooms and bloom collapses in coastal ecosystems. Even while chemotactic cells retain a growth advantage given their ability to sense and respond to lysis events, phycosphere DOM provides growth benefits to both motile and non-motile taxa that become attached to or happen to be co-located with new

  11. Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

    PubMed Central

    van den Berg, Eveline M.; Elisário, Marina P.; Kuenen, J. Gijs; Kleerebezem, Robbert; van Loosdrecht, Mark C. M.

    2017-01-01

    study clearly show that not only the ratio of available substrates, but also the nature of the electron donor influences the outcome of competition between DNRA and denitrification. Apparently, fermentative bacteria are competitive for the electron donor and thereby alter the ratio of available substrates for nitrate reduction. PMID:28928722

  12. Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria.

    PubMed

    van den Berg, Eveline M; Elisário, Marina P; Kuenen, J Gijs; Kleerebezem, Robbert; van Loosdrecht, Mark C M

    2017-01-01

    study clearly show that not only the ratio of available substrates, but also the nature of the electron donor influences the outcome of competition between DNRA and denitrification. Apparently, fermentative bacteria are competitive for the electron donor and thereby alter the ratio of available substrates for nitrate reduction.

  13. Transport capabilities of eleven gram-positive bacteria: comparative genomic analyses.

    PubMed

    Lorca, Graciela L; Barabote, Ravi D; Zlotopolski, Vladimir; Tran, Can; Winnen, Brit; Hvorup, Rikki N; Stonestrom, Aaron J; Nguyen, Elizabeth; Huang, Li-Wen; Kim, David S; Saier, Milton H

    2007-06-01

    The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G+C lactic acid bacteria and two high G+C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to 18% of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes. Our studies

  14. Transport Capabilities of Eleven Gram-positive Bacteria: Comparative Genomic Analyses

    PubMed Central

    Lorca, Graciela L.; Barabote, Ravi D.; Zlotopolski, Vladimir; Tran, Can; Winnen, Brit; Hvorup, Rikki N.; Stonestrom, Aaron J.; Nguyen, Elizabeth; Huang, Li-Wen; Kim, David S.; Saier, Milton H.

    2007-01-01

    The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G+C lactic acid bacteria and two high G+C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to eighteen percent of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes

  15. The passage of bacteria through surgical drapes.

    PubMed Central

    Blom, A.; Estela, C.; Bowker, K.; MacGowan, A.; Hardy, J. R.

    2000-01-01

    The passage of bacteria through surgical drapes is a potential cause of wound infection. Previous studies have shown that liquids and human albumin penetrate certain types of drapes. We studied the passage of bacteria through seven different types of surgical drape and an operating tray. Bacteria easily penetrated all the woven re-usable fabrics within 30 min. The disposable non-woven drapes proved to be impermeable, as did the operating tray. We recommend the use of non-woven disposable drapes or woven drapes with an impermeable operating tray in all surgical cases. PMID:11103158

  16. Survival of Bacteria in Respiratory Protective Filters.

    PubMed

    Miaśkiewicz-Pęska, Ewa B; Słomczyński, Tomasz

    2017-01-02

    The aim of this study was to estimate the susceptibility of Staphylococcus hominis bacteria to the bacteriostatic agent in respiratory protective filters. Four types of filter media of different characteristics were tested. The number of bacteria was estimated by a culture-based method. It was proved that in treated filters the number of S. hominis was significantly reduced, even below the detection limit, while in untreated material bacteria were able to grow and multiply up to 100-fold within 8 hours. There was no correlation between filter structure and changes in the number of bacterial cells.

  17. Do symbiotic bacteria subvert host immunity?

    PubMed

    Hooper, Lora V

    2009-05-01

    The mammalian intestine is home to dense and complex indigenous bacterial communities. Most of these bacteria establish beneficial symbiotic relationships with their hosts, making important contributions to host metabolism and digestive efficiency. The vast numbers of intestinal bacteria and their proximity to host tissues raise the question of how symbiotic host-bacterial relationships are established without eliciting potentially harmful immune responses. In light of the varied ways in which pathogenic bacteria manipulate host immunity, this Opinion article explores the role of immune suppression, subversion and evasion in the establishment of symbiotic host-bacterial associations.

  18. Suppression of resistance to flow in suspensions of bacteria

    NASA Astrophysics Data System (ADS)

    Lopez, Hector; Gachelin, Jérémie; Douarche, Carine; Clément, Eric; Auradou, Harold

    2014-11-01

    It is usually believed that the influence of small amounts of bacteria on the rheological properties of a fluid is negligible. However, recent theoretical studies predict that the activity results in a decrease of the viscosity at values lower than the suspending fluid viscosity. We present experimental measurements of the viscosity of suspensions of Escherichia coli (volume fractions ϕ<1%) in a simple Couette flow over a broad range of shear rates. For shear rates larger than 1.5 s-1, the viscosity is constant and slightly above the viscosity of the suspending fluid. This behavior is similar to the one expected for non-active particles. For lower shear rates the fluid exhibits a non-Newtonian behavior: the viscosity decreases and finally reaches a second Newtonian plateau for shear rates below 0.1 s-1. For ϕ <0.6%, the decrease is proportional to the bacteria concentration, as predicted by the theories, suggesting that it is a result of the energy input of each individual microswimmer. For ϕ >0.6%, we evidence for the first time the existence of a super-lubrication regime where the viscous resistance to shear vanishes. We will demonstrate that this regime holds up over a large window of concentration.

  19. Statistical Signatures of a Targeted Search by Bacteria.

    PubMed

    Jashnsaz, Hossein; Anderson, Gregory G; Pressé, Steve

    2017-08-15

    Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena -- such as the volcano effect or banding -- have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium's diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy. © 2017 IOP Publishing Ltd.

  20. Viewing marine bacteria, their activity and response to environmental drivers from orbit: satellite remote sensing of bacteria.

    PubMed

    Grimes, D Jay; Ford, Tim E; Colwell, Rita R; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G

    2014-04-01

    Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.

  1. Substratum interfacial energetic effects on the attachment of marine bacteria

    NASA Astrophysics Data System (ADS)

    Ista, Linnea Kathryn

    attachment of bacteria to a substratum. We use VCG to model DeltaGadh and interfacial tensions as they relate to model bacterial attachment on SAMs that accumulate cells to different degrees. Even with the more complex interactions measured by VCG, surface energy of the attachment substratum alone was insufficient to predict attachment. VCG was then employed to model attachment of C. marina to a series of SAMs varying systematically in the number of ethylene glycol residues present in the molecule; an identical series has been previously shown to vary dramatically in the number of cells attached as a function of ethylene glycols present. Our results indicate that while VCG adequately models the interfacial tension between water and ethylene glycol SAMs in a manner that predicts bacterial attachment, DeltaGadh as calculated by VCG neither qualitatively nor quantitatively reflects the attachment data. The VCG model, thus, fails to capture specific information regarding the interactions between the attaching bacteria, water, and the SAM. We show that while hydrogen-bond accepting interactions are very well captured by this model, the ability for SAMs and bacteria to donate hydrogen bonds is not adequately described as the VCG model is currently applied. We also describe ways in which VCG fails to capture two specific biological aspects that may be important in bacterial attachment to surfaces:1.) specific interactions between molecules on the surface and bacteria and 2.) bacterial cell surface heterogeneities that may be important in differential attachment to different substrata.

  2. Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China.

    PubMed

    Tang, Jing Yan; Ma, Jing; Li, Xue Dong; Li, Yan Hong

    2016-11-16

    with the ten liverworts. The result of further analysis of the bacterial community in different bryophytes revealed that the phylogeny of hosts might portray a strong influence on the associated bacterial community and that niche also played important roles when the hosts were phylogenetically more similar. Further studies are needed to confirm the role of phylogeny on bacterial communities and determine the level of influence on predicting which bacteria is associated with the host.

  3. Comparative genomics of the lactic acid bacteria

    SciTech Connect

    Makarova, K.; Slesarev, A.; Wolf, Y.; Sorokin, A.; Mirkin, B.; Koonin, E.; Pavlov, A.; Pavlova, N.; Karamychev, V.; Polouchine, N.; Shakhova, V.; Grigoriev, I.; Lou, Y.; Rokhsar, D.; Lucas, S.; Huang, K.; Goodstein, D. M.; Hawkins, T.; Plengvidhya, V.; Welker, D.; Hughes, J.; Goh, Y.; Benson, A.; Baldwin, K.; Lee, J. -H.; Diaz-Muniz, I.; Dosti, B.; Smeianov, V; Wechter, W.; Barabote, R.; Lorca, G.; Altermann, E.; Barrangou, R.; Ganesan, B.; Xie, Y.; Rawsthorne, H.; Tamir, D.; Parker, C.; Breidt, F.; Broadbent, J.; Hutkins, R.; O'Sullivan, D.; Steele, J.; Unlu, G.; Saier, M.; Klaenhammer, T.; Richardson, P.; Kozyavkin, S.; Weimer, B.; Mills, D.

    2006-06-01

    Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

  4. Ecology: Electrical Cable Bacteria Save Marine Life.

    PubMed

    Nielsen, Lars Peter

    2016-01-11

    Animals at the bottom of the sea survive oxygen depletion surprisingly often, and a new study identifies cable bacteria in the sediment as the saviors. The bacterial electrical activity creates an iron 'carpet', trapping toxic hydrogen sulfide.

  5. Physiological assessment of bacteria using fluorochromes

    NASA Technical Reports Server (NTRS)

    McFeters, G. A.; Yu, F. P.; Pyle, B. H.; Stewart, P. S.

    1995-01-01

    This minireview focuses on the application of fluorogenic compounds in the detection of bacteria with particular emphasis on the assessment of physiological activity using epifluorescence microscopy. Microbiological applications of several related methods will also be reviewed.

  6. Protection of probiotic bacteria in synbiotic matrices

    USDA-ARS?s Scientific Manuscript database

    Probiotics, like Lactobacillus acidophilus, Lactobacillus reuteri, Bifidobacterium breve, Bifidobacterium longum, when encapsulated with prebiotic fibers such as fructo-oligosaccharides (FOS), inulin (I) and pectic-oligosaccharides (POS), formed a synbiotic matrix system that protected the bacteria ...

  7. Isolation and characterization of fenamiphos degrading bacteria.

    PubMed

    Cabrera, J Alfonso; Kurtz, Andreas; Sikora, Richard A; Schouten, Alexander

    2010-11-01

    The biological factors responsible for the microbial breakdown of the organophosphorus nematicide fenamiphos were investigated. Microorganisms responsible for the enhanced degradation of fenamiphos were isolated from soil that had a long application history of this nematicide. Bacteria proved to be the most important group of microbes responsible for the fenamiphos biodegradation process. Seventeen bacterial isolates utilized the pure active ingredient fenamiphos as a carbon source. Sixteen isolates rapidly degraded the active ingredient in Nemacur 5GR. Most of the fenamiphos degrading bacteria were Microbacterium species, although Sinorhizobium, Brevundimonas, Ralstonia and Cupriavidus were also identified. This array of gram positive and gram negative fenamiphos degrading bacteria appeared to be pesticide-specific, since cross-degradation toward fosthiazate, another organophosphorus pesticide used for nematode control, did not occur. It was established that the phylogenetical relationship among nematicide degrading bacteria is closer than that to non-degrading isolates.

  8. Physiological assessment of bacteria using fluorochromes

    NASA Technical Reports Server (NTRS)

    McFeters, G. A.; Yu, F. P.; Pyle, B. H.; Stewart, P. S.

    1995-01-01

    This minireview focuses on the application of fluorogenic compounds in the detection of bacteria with particular emphasis on the assessment of physiological activity using epifluorescence microscopy. Microbiological applications of several related methods will also be reviewed.

  9. Acetamide Agar for Differentiation of Nonfermentative Bacteria

    PubMed Central

    Oberhofer, Thomas R.; Rowen, Joyce W.

    1974-01-01

    An acetamide agar medium is described for use in the differentiation of nonfermentative gram-negative bacteria. With few exceptions, indicator reactions were rapid, intense, and clear-cut. PMID:4417708

  10. Preparation of genomic DNA from bacteria.

    PubMed

    Andreou, Lefkothea-Vasiliki

    2013-01-01

    The purpose of this protocol is the isolation of bulk cellular DNA from bacteria (alternatively see Preparation of genomic DNA from Saccharomyces cerevisiae or Isolation of Genomic DNA from Mammalian Cells protocols). Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall

    PubMed Central

    Seigle-Murandi, F.; Guiraud, P.; Croize, J.; Falsen, E.; Eriksson, K. L.

    1996-01-01

    Bacteria have been isolated from 10 different strains of Phanerochaete chrysosporium, a white rot fungus which degrades lignocellulosic materials. The investigations showed that one or more bacterial species were always associated with the fungus. Various attempts to eliminate the bacteria on the fungus were unsuccessful. Three different bacterial species were isolated and identified. One of these was Agrobacterium radiobacter, while another may represent a new taxon close to the genus Burkholderia. A third strain remains unidentified but is most probably a member of rRNA superfamily IV or the Woese (alpha) group. Besides P. chrysosporium, 23 other white rot fungi and 9 brown rot fungi were also investigated. None of these was associated with bacteria. The physiological significance of the association between the fungus and the bacteria remains to be elucidated. PMID:16535357

  12. Distribution of phytopathogenic bacteria in infested seeds

    USDA-ARS?s Scientific Manuscript database

    Populations of phytopathogenic bacteria representing five host-pathogen combinations were assessed to determine if there was a mathematical relationship common across seedborne bacterial diseases. Bacterial populations were estimated from naturally-infested seeds of cowpea (Vigna unguiculata), peppe...

  13. Preliminary staining of bacteria: simple stains.

    PubMed

    Moyes, Rita B; Reynolds, Jackie; Breakwell, Donald P

    2009-11-01

    Simple staining involves directly staining the bacterial cell with a positively charged dye in order to see bacterial detail, in contrast to negative staining where the bacteria remain unstained against a dark background. (c) 2009 by John Wiley & Sons, Inc.

  14. Methods for dispersing hydrocarbons using autoclaved bacteria

    DOEpatents

    Tyndall, R.L.

    1996-11-26

    A method of dispersing a hydrocarbon includes the following steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; autoclaving the bacterium to derive a dispersant solution; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; and autoclaving the bacterium to derive a dispersant solution.

  15. Methods for dispersing hydrocarbons using autoclaved bacteria

    DOEpatents

    Tyndall, Richard L.

    1996-01-01

    A method of dispersing a hydrocarbon includes the steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; autoclaving the bacterium to derive a dispersant solution therefrom; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures thereof; and autoclaving the bacterium to derive a dispersant solution therefrom.

  16. [Significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection].

    PubMed

    Zou, X H; Zhu, Y P; Ren, G Q; Li, G C; Zhang, J; Zou, L J; Feng, Z B; Li, B H

    2017-02-20

    Objective: To evaluate the significance of bacteria detection with filter paper method on diagnosis of diabetic foot wound infection. Methods: Eighteen patients with diabetic foot ulcer conforming to the study criteria were hospitalized in Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology from July 2014 to July 2015. Diabetic foot ulcer wounds were classified according to the University of Texas diabetic foot classification (hereinafter referred to as Texas grade) system, and general condition of patients with wounds in different Texas grade was compared. Exudate and tissue of wounds were obtained, and filter paper method and biopsy method were adopted to detect the bacteria of wounds of patients respectively. Filter paper method was regarded as the evaluation method, and biopsy method was regarded as the control method. The relevance, difference, and consistency of the detection results of two methods were tested. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of filter paper method in bacteria detection were calculated. Receiver operating characteristic (ROC) curve was drawn based on the specificity and sensitivity of filter paper method in bacteria detection of 18 patients to predict the detection effect of the method. Data were processed with one-way analysis of variance and Fisher's exact test. In patients tested positive for bacteria by biopsy method, the correlation between bacteria number detected by biopsy method and that by filter paper method was analyzed with Pearson correlation analysis. Results: (1) There were no statistically significant differences among patients with wounds in Texas grade 1, 2, and 3 in age, duration of diabetes, duration of wound, wound area, ankle brachial index, glycosylated hemoglobin, fasting blood sugar, blood platelet count, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, serum creatinine, and

  17. Antimicrobial drug resistance: "Prediction is very difficult, especially about the future".

    PubMed

    Courvalin, Patrice

    2005-10-01

    Evolution of bacteria towards resistance to antimicrobial drugs, including multidrug resistance, is unavoidable because it represents a particular aspect of the general evolution of bacteria that is unstoppable. Therefore, the only means of dealing with this situation is to delay the emergence and subsequent dissemination of resistant bacteria or resistance genes. Resistance to antimicrobial drugs in bacteria can result from mutations in housekeeping structural or regulatory genes. Alternatively, resistance can result from the horizontal acquisition of foreign genetic information. The 2 phenomena are not mutually exclusive and can be associated in the emergence and more efficient spread of resistance. This review discusses the predictable future of the relationship between antimicrobial drugs and bacteria.

  18. Bacteria Aggregation in a Steady Vortical Flow

    NASA Astrophysics Data System (ADS)

    Yazdi, Shahrzad; Li, Sixing; Huang, Tony Jun; Ardekani, Arezoo

    2011-11-01

    The interaction between microorganisms and flow field is an important, yet complicated topic that affects the design of biological reactors, marine ecological processes, and biofilm formation in porous media. Vortical structures and secondary flows are inherently present in porous media despite small Reynolds numbers. Our experimental results show that bacteria in a steady vortical flow aggregate and subsequently form biofilm streamers in a microfluidic system. The combined effects of shape, motility and the vortical background flow contribute to this fast bacteria aggregation.

  19. [Teichoic acids from lactic acid bacteria].

    PubMed

    Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

    2012-01-01

    The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

  20. Response surface method optimization of ectoine fermentation medium with moderate halophilic bacteria Halomonas sp. H02

    NASA Astrophysics Data System (ADS)

    Li, T. T.; Qu, A.; Yuan, X. N.; Tan, F. X.; Li, X. W.; Wang, T.; Zhang, L. H.

    2017-07-01

    Moderate halophilic bacteria are of halophilic bacteria whose suitable growth of NaCl is 5-10%. When the moderate halophilic bacteria response to high osmotic stress, the intracellular will synthesize small organic molecule compatible solutes. Ectoine, which is the major synthetic osmotic compatible solutes for moderate halophilic bacteria, can help microbial enzymes, nucleic acids and the whole cell resist to hypertonic, high temperature, freezing and other inverse environment. In order to increase the Ectoine production of Moderate halophilic bacteria Halomonas sp. H02, the Ectoine fermentation medium component was optimized by Plackett-Burman (PB) and Response Surface Methodology (RSM) based on the principle of non-complete equilibrium The results of PB experiments showed that the three main influencing factors of Moderate halophilic bacteria Halomonas sp. H02 synthesis Ectoine culture medium were C5H8NNaO4 concentration, NaCl concentration and initial pH. According to the center point of the steepest climbing experiment, the central combination design experiment was used to show that the model is consistent with the actual situation. The optimum combination of three influencing factors were C5H8NNaO4 41 g/L, NaCl 87.2 g/L and initial pH 5.9, and the predicted amount of Ectoine was 1835.8 mg/L, increased by 41.6%.

  1. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria.

    PubMed

    Salman, Verena; Amann, Rudolf; Girnth, Anne-Christin; Polerecky, Lubos; Bailey, Jake V; Høgslund, Signe; Jessen, Gerdhard; Pantoja, Silvio; Schulz-Vogt, Heide N

    2011-06-01

    The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.

  2. Microalgae-bacteria models evolution: From microalgae steady-state to integrated microalgae-bacteria wastewater treatment models - A comparative review.

    PubMed

    Solimeno, Alessandro; García, Joan

    2017-12-31

    The search for environmentally neutral alternative fuels had revived the interest for microalgae-bacteria wastewater treatment systems. The potential achieving of bioproducts from microalgae biomass has also greatly contributed. The reactions that occur in these systems are complex, and the degree of scientific knowledge is still scarce compared to that of conventional bacteria wastewater treatments. Mathematical models offer a great opportunity to study the simultaneous effect of the multiple factors affecting microalgae and bacteria, thus allowing for the prediction of final biomass production, and contributing to the system design optimization in terms of operation and control. During the last decades, numerous models describing microalgae growth have been proposed. However, a lower number of integral models considering microalgae as well as bacteria is available. In this paper, the evolution of microalgae models from simple steady-state models (usually dependent on one factor) to more complex dynamic models (with two or more factors) has been revised. A summary of integrated microalgae-bacteria models has been reviewed, outlining their main features and presenting their processes and value parameters. Eventually, a critical discussion on integrated models has been put forward. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Fuel from Bacteria: Bioconversion of Carbon Dioxide to Biofuels by Facultatively Autotrophic Hydrogen Bacteria

    SciTech Connect

    2010-07-01

    Electrofuels Project: Ohio State is genetically modifying bacteria to efficiently convert carbon dioxide directly into butanol, an alcohol that can be used directly as a fuel blend or converted to a hydrocarbon, which closely resembles a gasoline. Bacteria are typically capable of producing a certain amount of butanol before it becomes too toxic for the bacteria to survive. Ohio State is engineering a new strain of the bacteria that could produce up to 50% more butanol before it becomes too toxic for the bacteria to survive. Finding a way to produce more butanol more efficiently would significantly cut down on biofuel production costs and help make butanol cost competitive with gasoline. Ohio State is also engineering large tanks, or bioreactors, to grow the biofuel-producing bacteria in, and they are developing ways to efficiently recover biofuel from the tanks.

  4. Adhesion and biofilm formation on polystyrene by drinking water-isolated bacteria.

    PubMed

    Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

    2010-10-01

    This study was performed in order to characterize the relationship between adhesion and biofilm formation abilities of drinking water-isolated bacteria (Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp.). Adhesion was assessed by two distinct methods: thermodynamic prediction of adhesion potential by quantifying hydrophobicity and the free energy of adhesion; and by microtiter plate assays. Biofilms were developed in microtiter plates for 24, 48 and 72 h. Polystyrene (PS) was used as adhesion substratum. The tested bacteria had negative surface charge and were hydrophilic. PS had negative surface charge and was hydrophobic. The free energy of adhesion between the bacteria and PS was > 0 mJ/m(2) (thermodynamic unfavorable adhesion). The thermodynamic approach was inappropriate for modelling adhesion of the tested drinking water bacteria, underestimating adhesion to PS. Only three (B. cepacia, Sph. capsulata and Staphylococcus sp.) of the six bacteria were non-adherent to PS. A. calcoaceticus, Methylobacterium sp. and M. mucogenicum were weakly adherent. This adhesion ability was correlated with the biofilm formation ability when comparing with the results of 24 h aged biofilms. Methylobacterium sp. and M. mucogenicum formed large biofilm amounts, regardless the biofilm age. Given time, all the bacteria formed biofilms; even those non-adherents produced large amounts of matured (72 h aged) biofilms. The overall results indicate that initial adhesion did not predict the ability of the tested drinking water-isolated bacteria to form a mature biofilm, suggesting that other events such as phenotypic and genetic switching during biofilm development and the production of extracellular polymeric substances (EPS), may play a significant role on biofilm formation and differentiation. This understanding of the relationship between adhesion and biofilm formation is important for

  5. Peptide conversations in Gram-positive bacteria.

    PubMed

    Monnet, Véronique; Juillard, Vincent; Gardan, Rozenn

    2016-05-01

    Within Gram-positive bacteria, the expression of target genes is controlled at the population level via signaling peptides, also known as pheromones. Pheromones control a wide range of functions, including competence, virulence, and others that remain unknown. Until now, their role in bacterial gene regulation has probably been underestimated; indeed, bacteria are able to produce, by ribosomal synthesis or surface protein degradation, an extraordinary variety of peptides which are released outside bacteria and among which, some are pheromones that mediate cell-to-cell communication. The review aims at giving an updated overview of these peptide-dependant communication pathways. More specifically, it follows the whole peptide circuit from the peptide production and secretion in the extracellular medium to its interaction with sensors at bacterial surface or re-import into the bacteria where it plays its regulation role. In recent years, as we have accumulated more knowledge about these systems, it has become apparent that they are more complex than they first appeared. For this reason, more research on peptide-dependant pathways is needed to develop new strategies for controlling functions of interest in Gram-positive bacteria. In particular, such research could lead to alternatives to the use of antibiotics against pathogenic bacteria. In perspective, the review identifies new research questions that emerge in this field and that have to be addressed.

  6. Tyramine and phenylethylamine biosynthesis by food bacteria.

    PubMed

    Marcobal, Angela; De las Rivas, Blanca; Landete, José María; Tabera, Laura; Muñoz, Rosario

    2012-01-01

    Tyramine poisoning is caused by the ingestion of food containing high levels of tyramine, a biogenic amine. Any foods containing free tyrosine are subject to tyramine formation if poor sanitation and low quality foods are used or if the food is subject to temperature abuse or extended storage time. Tyramine is generated by decarboxylation of the tyrosine through tyrosine decarboxylase (TDC) enzymes derived from the bacteria present in the food. Bacterial TDC have been only unequivocally identified and characterized in Gram-positive bacteria, especially in lactic acid bacteria. Pyridoxal phosphate (PLP)-dependent TDC encoding genes (tyrDC) appeared flanked by a similar genetic organization in several species of lactic acid bacteria, suggesting a common origin by a single mobile genetic element. Bacterial TDC are also able to decarboxylate phenylalanine to produce phenylethylamine (PEA), another biogenic amine. The molecular knowledge of the genes involved in tyramine production has led to the development of molecular methods for the detection of bacteria able to produce tyramine and PEA. These rapid and simple methods could be used for the analysis of the ability to form tyramine by bacteria in order to evaluate the potential risk of tyramine biosynthesis in food products.

  7. The association between bacteria and urinary stones

    PubMed Central

    Wolfe, Alan J.

    2017-01-01

    Urinary stone disease (USD) is an increasing clinical problem in both children and adults. One in ten individuals will experience a urinary stone, yet the mechanisms responsible for urinary stones remain largely unknown. Bacteria have long been recognized to contribute to struvite urinary stones; however, the role of bacteria in the development of the more common calcium oxalate (CaOx) and calcium phosphate (CaPhos) stones has not been extensively investigated. However, several findings do indicate a possible association between urinary stones and bacteria, including the high rate of urinary tract infections (UTI) in urinary stone patients and multiple case series of culture-positive urinary stones, including stones composed of CaOx or CaPhos. New technology, such as next generation sequencing, may be used to lend additional insight regarding the association between urinary stones and bacteria. In 2015, we published the initial bacterial sequencing results from five urinary stones, from which we sequenced multiple types of bacterial DNA. Whether these bacteria are causal, disease modifying or passively present remains to be determined. However, initial exploration of underlying mechanisms for this association indicate that bacteria aggregate selectively to crystals, that their presence is associated with increased clumping of crystals, and that they stimulate incorporation of proteins into the stone matrix. PMID:28217697

  8. Molecular probe technology detects bacteria without culture

    PubMed Central

    2012-01-01

    Background Our ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require growth of the bacteria in culture. Rather, the molecular probe technology requires only a sequence of forty sequential bases unique to the genome of the bacterium of interest. In this communication, we report the first results of employing our molecular probes to detect bacteria in clinical samples. Results While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the bacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To multiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing Sequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each clinical sample, we combine the samples after processing, but before sequencing, and sequence them together. Conclusions Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in twenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the Sequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent. PMID:22404909

  9. How methylglyoxal kills bacteria: An ultrastructural study.

    PubMed

    Rabie, Erika; Serem, June Cheptoo; Oberholzer, Hester Magdalena; Gaspar, Anabella Regina Marques; Bester, Megan Jean

    2016-01-01

    Antibacterial activity of honey is due to the presence of methylglyoxal (MGO), H2O2, bee defensin as well as polyphenols. High MGO levels in manuka honey are the main source of antibacterial activity. Manuka honey has been reported to reduce the swarming and swimming motility of Pseudomonas aeruginosa due to de-flagellation. Due to the complexity of honey it is unknown if this effect is directly due to MGO. In this ultrastructural investigation the effects of MGO on the morphology of bacteria and specifically the structure of fimbriae and flagella were investigated. MGO effectively inhibited Gram positive (Bacillus subtilis; MIC 0.8 mM and Staphylococcus aureus; MIC 1.2 mM) and Gram negative (P. aeruginosa; MIC 1.0 mM and Escherichia coli; MIC 1.2 mM) bacteria growth. The ultrastructural effects of 0.5, 1.0 and 2 mM MGO on B. substilis and E. coli morphology was then evaluated. At 0.5 mM MGO, bacteria structure was unaltered. For both bacteria at 1 mM MGO fewer fimbriae were present and the flagella were less or absent. Identified structures appeared stunted and fragile. At 2 mM MGO fimbriae and flagella were absent while the bacteria were rounded with shrinkage and loss of membrane integrity. Antibacterial MGO causes alterations in the structure of bacterial fimbriae and flagella which would limit bacteria adherence and motility.

  10. Patterned and Specific Attachment of Bacteria on Biohybrid Bacteria-Driven Microswimmers.

    PubMed

    Singh, Ajay Vikram; Sitti, Metin

    2016-09-01

    A surface patterning technique and a specific and strong biotin-streptavidin bonding of bacteria on patterned surfaces are proposed to fabricate Janus particles that are propelled by the attached bacteria. Bacteria-driven Janus microswimmers with diameters larger than 3 μm show enhanced mean propulsion speed. Such microswimmers could be used for future applications such as targeted drug delivery and environmental remediation.

  11. PREDICTIVE MODELS

    SciTech Connect

    Ray, R.M. )

    1986-12-01

    PREDICTIVE MODELS is a collection of five models - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1) chemical flooding, where soap-like surfactants are injected into the reservoir to wash out the oil; 2) carbon dioxide miscible flooding, where carbon dioxide mixes with the lighter hydrocarbons making the oil easier to displace; 3) in-situ combustion, which uses the heat from burning some of the underground oil to thin the product; 4) polymer flooding, where thick, cohesive material is pumped into a reservoir to push the oil through the underground rock; and 5) steamflood, where pressurized steam is injected underground to thin the oil. CFPM, the Chemical Flood Predictive Model, models micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive Model, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive Model, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive Model, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive Model, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes.

  12. Bacteria associated with deep, alkaline, anaerobic groundwaters in Southeast Washington.

    PubMed

    Stevens, T O; McKinley, J P; Fredrickson, J K

    1993-01-01

    The microbial diversity in two deep, confined aquifers, the Grande Ronde (1270 m) and the Priest Rapids (316 m), Hanford Reservation, Washington, USA, was investigated by sampling from artesian wells. These basaltic aquifers were alkaline (pH 8.5 to 10.5) and anaerobic (Eh -200 to -450 mV). The wells were allowed to free-flow until pH and Eh stabilized, then the microflora was sampled with water filtration and flow-through sandtrap methods. Direct microscopic counts showed 7.6 × 10(5) and 3.6 × 10(3) bacteria ml(-1) in water from the Grande Ronde and Priest Rapids aquifers, respectively. The sand filter method yielded 5.7 × 10(8) and 1.1 × 10(5) cells g(-1) wet weight of sand. The numbers of bacteria did not decrease as increasing volumes of water were flushed out. The heterotrophic diversity of these bacterial populations was assessed using enrichments for 20 functional groups. These groups were defined by their ability to grow in a matrix of five different electron acceptors (O2, Fe(III), NO3 (-), SO4 (2-), HCO3 (-)) and four groups of electron donors (fermentation products, monomers, polymers, aromatics) in a mineral salts medium at pH 9.5. Growth was assessed by protein production. Culture media were subsequently analyzed to determine substrate utilization patterns. Substrate utilization patterns proved to be more reliable indicators of the presence of a particular physiological group than was protein production. The sand-trap method obtained a greater diversity of bacteria than did water filtration, presumably by enriching the proportion of normally sessile bacteria relative to planktonic bacteria. Substrate utilization patterns were different for microflora from the two aquifers and corresponded to their different geochemistries. Activities in the filtered water enrichments more closely matched those predicted by aquifer geochemistry than did the sand-trap enrichments. The greatest activities were found in Fe(III)-reducing enrichments from both wells, SO4

  13. Discovery of a new family of relaxases in Firmicutes bacteria

    PubMed Central

    Singh, Praveen K.; Hao, Jian An; Luque-Ortega, Juan Roman; Wu, Ling J.; Boer, D. Roeland

    2017-01-01

    Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research. PMID:28207825

  14. Bugbuster: Survivability of Living Bacteria Upon Shock Compression

    NASA Astrophysics Data System (ADS)

    Willis, M. J.; Ahrens, T. J.; Bertani, L. E.; Nash, C. Z.

    2003-12-01

    Survivability of bacteria during impact events has implications both for the transport of life between planets and development of organisms on Hadean Earth and other planets during the period of heavy bombardment which ended 3.5 Gyr before the present [1]. We envision that life existed within internal rock surfaces immersed in the early ocean. We performed shock recovery experiments on live E. coli bacteria to determine survival rate vs. shock pressure. Samples of 2x107 cells were suspended in ˜10-5 l of a buffer solution (TE: a 10:1 solution of Tris and EDTA), sealed into stainless steel chambers that are impacted by 1.5 mm thick flyer plates at 670-760 m s-1 using a 20 mm gun. Recovered liquid was mixed with a nutrient broth (LB: growth medium containing tryptone, yeast extract and NaCl) and spread on a Petrie dish containing agar (a polysaccharide growth medium extracted from marine algae Rhodophyceae). Recovered samples were cultured for ˜16 hours at 37° C. In addition, sample bacteria studied under an optical microscope with DAPI fluorescent stain to verify presence of bacteria in shock recovered samples. Initial and reverberated shock pressures in H2O varied from 0.2 to 2.0 and 2.4 to 14.9 GPa respectively. We modeled the bacteria cell walls with stilbene, ρ 0=1.16 g cm-3, US=2.866+1.588uP and the cell interiors as water. Upon initial loading the net strain imposed on E. coli that just caused non-survival for 10-6 s duration stress was 2.8. If this strain is characteristic of that tolerable by E. coli, we predict that shock stresses of 25 MPa, 25 kPa and 25 Pa are sustainable upon shock loading by 0.1 ms, 0.1 s and 100 s shock duration pulses. Such shock durations are induced by 2.5 m, 2.5 km and 2,500 km diameter silicate impactors. References: [1] Maher K.A. & Stevenson D.J., Nature, 331, pp.612-614, 1988

  15. Dynamical predictors of an imminent phenotypic switch in bacteria

    NASA Astrophysics Data System (ADS)

    Wang, Huijing; Ray, J. Christian J.

    2017-08-01

    Single cells can stochastically switch across thresholds imposed by regulatory networks. Such thresholds can act as a tipping point, drastically changing global phenotypic states. In ecology and economics, imminent transitions across such tipping points can be predicted using dynamical early warning indicators. A typical example is ‘flickering’ of a fast variable, predicting a longer-lasting switch from a low to a high state or vice versa. Considering the different timescales between metabolite and protein fluctuations in bacteria, we hypothesized that metabolic early warning indicators predict imminent transitions across a network threshold caused by enzyme saturation. We used stochastic simulations to determine if flickering predicts phenotypic transitions, accounting for a variety of molecular physiological parameters, including enzyme affinity, burstiness of enzyme gene expression, homeostatic feedback, and rates of metabolic precursor influx. In most cases, we found that metabolic flickering rates are robustly peaked near the enzyme saturation threshold. The degree of fluctuation was amplified by product inhibition of the enzyme. We conclude that sensitivity to flickering in fast variables may be a possible natural or synthetic strategy to prepare physiological states for an imminent transition.

  16. The first demonstration of the existence of reverse transcriptases in bacteria.

    PubMed

    Inouye, Masayori

    2017-01-15

    It has been long thought that reverse transcriptases are unique to the eukaryotes. However, through our research on a peculiar single stranded DNA called msDNA in Myxococcus xanthus, it was predicted that its synthesis requires reverse transcriptases. Subsequently, Lim and Maas as well as our group demonstrated the existence of reverse transcriptases for the production of msDNA. In this review, I describe how the discovery of msDNA led to the discovery of reverse transcriptases in bacteria and discuss the evolutionary significance of the discovery of revise transcriptases in bacteria.

  17. Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers.

    PubMed

    Suzuki, Katsunori; Moriguchi, Kazuki; Yamamoto, Shinji

    2015-12-01

    Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.

  18. [Spectrum and susceptibility of preoperative conjunctival bacteria].

    PubMed

    Fernández-Rubio, M E; Cuesta-Rodríguez, T; Urcelay-Segura, J L; Cortés-Valdés, C

    2013-12-01

    To describe the conjunctival bacterial spectrum of our patients undergoing intraocular surgery and their antibiotic sensitivity during the study period. A retrospective study of preoperative conjunctival culture of patients consecutively scheduled for intraocular surgery from 21 February 2011 to 1 April 2013. Specimens were directly seeded onto blood-agar and MacConkey-agar (aerobiosis incubation, 2 days), and on chocolate-agar (6% CO2 incubation, 7 days). The identified bacteria were divided into 3 groups according to their origin; the bacteria susceptibility tests were performed on those more pathogenic and on some of the less pathogenic when more than 5 colonies were isolated. The sensitivity of the exigent growing bacteria was obtained with disk diffusion technique, and for of the non-exigent bacteria by determining their minimum inhibitory concentration. The Epidat 3.1 program was used for statistical calculations. A total of 13,203 bacteria were identified in 6,051 cultures, with 88.7% being typical colonizers of conjunctiva (group 1), 8.8% typical of airways (group 2), and the remaining 2.5% of undetermined origin (group 3). 530 cultures (8.8%) were sterile. The sensitivity of group 1 was: 99% vancomycin, 95% rifampicin, 87% chloramphenicol, 76% tetracycline. Levels of co-trimoxazole, aminoglycosides, quinolones, β-lactams and macrolides decreased since 2007. The group 2 was very sensitive to chloramphenicol, cefuroxime, rifampicin, ciprofloxacin and amoxicillin/clavulanate. In group 3, to levofloxacin 93%, ciprofloxacin 89%, tobramycin 76%, but ceftazidime 53% and cefuroxime 29% decreased. None of the tested antibiotics could eradicate all possible conjunctival bacteria. Bacteria living permanently on the conjunctiva (group 1) have achieved higher resistance than the eventual colonizers. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

  19. Reliability Prediction

    NASA Technical Reports Server (NTRS)

    1993-01-01

    RELAV, a NASA-developed computer program, enables Systems Control Technology, Inc. (SCT) to predict performance of aircraft subsystems. RELAV provides a system level evaluation of a technology. Systems, the mechanism of a landing gear for example, are first described as a set of components performing a specific function. RELAV analyzes the total system and the individual subsystem probabilities to predict success probability, and reliability. This information is then translated into operational support and maintenance requirements. SCT provides research and development services in support of government contracts.

  20. Successful Predictions

    NASA Astrophysics Data System (ADS)

    Pierrehumbert, R.

    2012-12-01

    In an observational science, it is not possible to test hypotheses through controlled laboratory experiments. One can test parts of the system in the lab (as is done routinely with infrared spectroscopy of greenhouse gases), but the collective behavior cannot be tested experimentally because a star or planet cannot be brought into the lab; it must, instead, itself be the lab. In the case of anthropogenic global warming, this is all too literally true, and the experiment would be quite exciting if it weren't for the unsettling fact that we and all our descendents for the forseeable future will have to continue making our home in the lab. There are nonetheless many routes though which the validity of a theory of the collective behavior can be determined. A convincing explanation must not be a"just-so" story, but must make additional predictions that can be verified against observations that were not originally used in formulating the theory. The field of Earth and planetary climate has racked up an impressive number of such predictions. I will also admit as "predictions" statements about things that happened in the past, provided that observations or proxies pinning down the past climate state were not available at the time the prediction was made. The basic prediction that burning of fossil fuels would lead to an increase of atmospheric CO2, and that this would in turn alter the Earth's energy balance so as to cause tropospheric warming, is one of the great successes of climate science. It began in the lineage of Fourier, Tyndall and Arrhenius, and was largely complete with the the radiative-convective modeling work of Manabe in the 1960's -- all well before the expected warming had progressed far enough to be observable. Similarly, long before the increase in atmospheric CO2 could be detected, Bolin formulated a carbon cycle model and used it to predict atmospheric CO2 out to the year 2000; the actual values come in at the high end of his predicted range, for

  1. ENSO predictability

    NASA Astrophysics Data System (ADS)

    Larson, Sarah Michelle

    The overarching goal of this work is to explore seasonal El Nino -- Southern Oscillation (ENSO) predictability. More specifically, this work investigates how intrinsic variability affects ENSO predictability using a state-of-the-art climate model. Topics related to the effects of systematic model errors and external forcing are not included in this study. Intrinsic variability encompasses a hierarchy of temporal and spatial scales, from high frequency small-scale noise-driven processes including coupled instabilities to low frequency large-scale deterministic climate modes. The former exemplifies what can be considered intrinsic "noise" in the climate system that hinders predictability by promoting rapid error growth whereas the latter often provides the slow thermal ocean inertia that supplies the coupled ENSO system with predictability. These two ends of the spectrum essentially provide the lower and upper bounds of ENSO predictability that can be attributed to internal variability. The effects of noise-driven coupled instabilities on sea surface temperature (SST) predictability in the ENSO region is quantified by utilizing a novel coupled model methodology paired with an ensemble approach. The experimental design allows for rapid growth of intrinsic perturbations that are not prescribed. Several cases exhibit sufficiently rapid growth to produce ENSO-like final states that do not require a previous ENSO event, large-scale wind trigger, or subsurface heat content precursor. Results challenge conventional ENSO theory that considers the subsurface precursor as a necessary condition for ENSO. Noise-driven SST error growth exhibits strong seasonality and dependence on the initialization month. A dynamical analysis reveals that much of the error growth behavior is linked to the seasonal strength of the Bjerknes feedback in the model, indicating that the noise-induced perturbations grow via an ENSO-like mechanism. The daily error fields reveal that persistent

  2. Dropout Prediction.

    ERIC Educational Resources Information Center

    Curtis, Jonathan; And Others

    Secondary school students who drop out of school are put at great social and economic disadvantage. If potential dropouts can be identified early, prevention may be possible. To construct a prediction model which, through readily available school information, will aid in the identification of students likely to drop out, schools in the Austin,…

  3. Surface plasmon resonance immunosensor for bacteria detection.

    PubMed

    Baccar, H; Mejri, M B; Hafaiedh, I; Ktari, T; Aouni, M; Abdelghani, A

    2010-07-15

    This work describes an approach for the development of two bacteria biosensors based on surface plasmon resonance (SPR) technique. The first biosensor was based on functionalized gold substrate and the second one on immobilized gold nanoparticles. For the first biosensor, the gold substrate was functionalized with acid-thiol using the self-assembled monolayer technique, while the second one was functionalized with gold nanoparticles immobilized on modified gold substrate. A polyclonal anti-Escherichia coli antibody was immobilized for specific (E. coli) and non-specific (Lactobacillus) bacteria detection. Detection limit with a good reproducibility of 10(4) and 10(3) cfu mL(-1) of E. coli bacteria has been obtained for the first biosensor and for the second one respectively. A refractive index variation below 5x10(-3) due to bacteria adsorption is able to be detected. The refractive index of the multilayer structure and of the E. coli bacteria layer was estimated with a modeling software.

  4. Modulation of immune homeostasis by commensal bacteria.

    PubMed

    Ivanov, Ivaylo I; Littman, Dan R

    2011-02-01

    Intestinal bacteria form a resident community that has co-evolved with the mammalian host. In addition to playing important roles in digestion and harvesting energy, commensal bacteria are crucial for the proper functioning of mucosal immune defenses. Most of these functions have been attributed to the presence of large numbers of 'innocuous' resident bacteria that dilute or occupy niches for intestinal pathogens or induce innate immune responses that sequester bacteria in the lumen, thus quenching excessive activation of the mucosal immune system. However it has recently become obvious that commensal bacteria are not simply beneficial bystanders, but are important modulators of intestinal immune homeostasis and that the composition of the microbiota is a major factor in pre-determining the type and robustness of mucosal immune responses. Here we review specific examples of individual members of the microbiota that modify innate and adaptive immune responses, and we focus on potential mechanisms by which such species-specific signals are generated and transmitted to the host immune system.

  5. Role of rhomboid proteases in bacteria.

    PubMed

    Rather, Philip

    2013-12-01

    The first member of the rhomboid family of intramembrane serine proteases in bacteria was discovered almost 20years ago. It is now known that rhomboid proteins are widely distributed in bacteria, with some bacteria containing multiple rhomboids. At the present time, only a single rhomboid-dependent function in bacteria has been identified, which is the cleavage of TatA in Providencia stuartii. Mutational analysis has shown that loss of the GlpG rhomboid in Escherichia coli alters cefotaxime resistance, loss of the YqgP (GluP) rhomboid in Bacillus subtilis alters cell division and glucose uptake, and loss of the MSMEG_5036 and MSMEG_4904 genes in Mycobacterium smegmatis results in altered colony morphology, biofilm formation and antibiotic susceptibilities. However, the cellular substrates for these proteins have not been identified. In addition, analysis of the rhombosortases, together with their possible Gly-Gly CTERM substrates, may shed new light on the role of these proteases in bacteria. This article is part of a Special Issue entitled: Intramembrane Proteases.

  6. Single bacteria identification by Raman spectroscopy.

    PubMed

    Strola, Samy Andrea; Baritaux, Jean-Charles; Schultz, Emmanuelle; Simon, Anne Catherine; Allier, Cédric; Espagnon, Isabelle; Jary, Dorothée; Dinten, Jean-Marc

    2014-01-01

    We report on rapid identification of single bacteria using a low-cost, compact, Raman spectroscope. We demonstrate that a 60-s procedure is sufficient to acquire a comprehensive Raman spectrum in the range of 600 to 3300 cm⁻¹. This time includes localization of small bacteria aggregates, alignment on a single individual, and spontaneous Raman scattering signal collection. Fast localization of small bacteria aggregates, typically composed of less than a dozen individuals, is achieved by lensfree imaging over a large field of view of 24 mm². The lensfree image also allows precise alignment of a single bacteria with the probing beam without the need for a standard microscope. Raman scattered light from a 34-mW continuous laser at 532 nm was fed to a customized spectrometer (prototype Tornado Spectral Systems). Owing to the high light throughput of this spectrometer, integration times as low as 10 s were found acceptable. We have recorded a total of 1200 spectra over seven bacterial species. Using this database and an optimized preprocessing, classification rates of ~90% were obtained. The speed and sensitivity of our Raman spectrometer pave the way for high-throughput and nondestructive real-time bacteria identification assays. This compact and low-cost technology can benefit biomedical, clinical diagnostic, and environmental applications.

  7. Single bacteria identification by Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Strola, Samy Andrea; Baritaux, Jean-Charles; Schultz, Emmanuelle; Simon, Anne Catherine; Allier, Cédric; Espagnon, Isabelle; Jary, Dorothée; Dinten, Jean-Marc

    2014-11-01

    We report on rapid identification of single bacteria using a low-cost, compact, Raman spectroscope. We demonstrate that a 60-s procedure is sufficient to acquire a comprehensive Raman spectrum in the range of 600 to 3300. This time includes localization of small bacteria aggregates, alignment on a single individual, and spontaneous Raman scattering signal collection. Fast localization of small bacteria aggregates, typically composed of less than a dozen individuals, is achieved by lensfree imaging over a large field of view of 24. The lensfree image also allows precise alignment of a single bacteria with the probing beam without the need for a standard microscope. Raman scattered light from a 34-mW continuous laser at 532 nm was fed to a customized spectrometer (prototype Tornado Spectral Systems). Owing to the high light throughput of this spectrometer, integration times as low as 10 s were found acceptable. We have recorded a total of 1200 spectra over seven bacterial species. Using this database and an optimized preprocessing, classification rates of ˜90% were obtained. The speed and sensitivity of our Raman spectrometer pave the way for high-throughput and nondestructive real-time bacteria identification assays. This compact and low-cost technology can benefit biomedical, clinical diagnostic, and environmental applications.

  8. Chemotactic selection of pollutant degrading soil bacteria

    DOEpatents

    Hazen, Terry C.

    1994-01-01

    A method for identifying soil microbial strains which may be bacterial degraders of pollutants comprising the steps of placing a concentration of a pollutant in a substantially closed container, placing the container in a sample of soil for a period of time ranging from one minute to several hours, retrieving the container, collecting the contents of the container, and microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to inoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  9. Bacteria-induced hatching of Trichuris muris eggs occurs without direct contact between eggs and bacteria.

    PubMed

    Koyama, Koichi

    2016-01-01

    Using three isolates of the murine parasitic nematode Trichuris muris, E, E/J (the E isolate maintained in Japan), and S, I have previously demonstrated that when the embryonated eggs of the E/J and E isolates are incubated with the intestinal bacteria Escherichia coli and Staphylococcus aureus, they are induced to hatch in vitro. However, the eggs of the S isolate are unresponsive to these bacteria. In the present study, I investigated whether direct contact between the embryonated eggs of the E/J and E isolates and bacteria is required to induce their hatching. To do so, a new co-culture system for eggs and bacteria (E. coli or S. aureus) was developed to block any direct contact between the eggs and the bacteria. In the hatching experiment using the new system, when direct contact between the eggs and bacteria was completely prevented, the eggs still hatched. However, the peak levels of hatching without direct contact were about 20 % lower than those with direct contact, and peak hatching occurred later without direct contact. This evidence suggests that hatching occurs without direct contact between the eggs and bacteria, and that unidentified material derived from active bacteria induces the hatching of embryonated eggs of the E/J and E isolates of T. muris in vitro.

  10. Method of Detecting Coliform Bacteria and Escherichia Coli Bacteria from Reflected Light

    NASA Technical Reports Server (NTRS)

    Vincent, Robert (Inventor)

    2013-01-01

    The present invention relates to a method of detecting coliform bacteria in water from reflected light and a method of detecting Eschericha Coli bacteria in water from reflected light, and also includes devices for the measurement, calculation and transmission of data relating to that method.

  11. [Role of lactic acid bacteria in the spread of antibiotic resistant bacteria among healthy persons].

    PubMed

    Zigangirova, N A; Tokarskaia, E A; Narodnitskiĭ, B S; Gintsburg, A L; Tugel'ian, V A

    2006-01-01

    The wide use of antibiotics in livestock raising has contributed to the selection and accumulation of representatives of commensal microflora, as well as pathogenic bacteria, colonizing livestock and poultry. For this reason the problem of the possible transfer of antibiotic-resistance genes along the chain from bacteria, autochthonous for agricultural animals, to bacteria used for the production of foodstuffs, which are incorporated into normal microflora and may thus participate in the exchange of these genes with bacteria, enteropathogenic for humans, is a highly important task of medical microbiology. The article deals with the review of experimental data, indicative the possibility of the appearance of antibiotic-resistant pathogenic bacteria due to the transfer of antibiotic-resistance genes via alimentary chains.

  12. Studies on ultrasmall bacteria in relation to the presence of bacteria in the stratosphere

    NASA Astrophysics Data System (ADS)

    Alshammari, Fawaz; Wainwright, Milton; Alabri, Khalid; Alharbi, Sulamain A.

    2011-04-01

    Recent studies confirm that bacteria exist in the stratosphere. It is generally assumed that these bacteria are exiting from Earth, although it is possible that some are incoming from space. Most stratospheric bacterial isolates belong to the spore-forming genus Bacillus, although non-spore formers have also been isolated. Theoretically, the smaller a bacterium is, the more likely it is to be carried from Earth to the stratosphere. Ultrasmall bacteria have been frequently isolated from Earth environments, but not yet from the stratosphere. This is an anomalous situation, since we would expect such small bacteria to be over represented in the stratosphere-microflora. Here, we show that ultrasmall bacteria are present in the environment on Earth (i.e. in seawater and rainwater) and discuss the paradox of why they have not been isolated from the stratosphere.

  13. Noncontact Cohesive Swimming of Bacteria in Two-Dimensional Liquid Films

    NASA Astrophysics Data System (ADS)

    Li, Ye; Zhai, He; Sanchez, Sandra; Kearns, Daniel B.; Wu, Yilin

    2017-07-01

    Bacterial swimming in confined two-dimensional environments is ubiquitous in nature and in clinical settings. Characterizing individual interactions between swimming bacteria in 2D confinement will help to understand diverse microbial processes, such as bacterial swarming and biofilm formation. Here we report a novel motion pattern displayed by flagellated bacteria in 2D confinement: When two nearby cells align their moving directions, they tend to engage in cohesive swimming without direct cell body contact, as a result of hydrodynamic interaction but not flagellar intertwining. We further found that cells in cohesive swimming move with higher directional persistence, which can increase the effective diffusivity of cells by ˜3 times as predicted by computational modeling. As a conserved behavior for peritrichously flagellated bacteria, cohesive swimming in 2D confinement may be key to collective motion and self-organization in bacterial swarms; it may also promote bacterial dispersal in unsaturated soils and in interstitial space during infections.

  14. Computational and experimental study of chemotaxis of an ensemble of bacteria attached to a microbead.

    PubMed

    Traoré, Mahama A; Sahari, Ali; Behkam, Bahareh

    2011-12-01

    Micro-objects propelled by whole cell actuators, such as flagellated bacteria, are being increasingly studied and considered for a wide variety of applications. In this work we present theoretical and experimental investigations of chemotactic motility of a 10 μm diameter microbead propelled by an ensemble of attached flagellated bacteria. The stochastic model presented here encompasses the behavior of each individual bacterium attached to the microbead in a spatiotemporally varying chemoattractant field. The computational model shows that in a chemotactic environment, the ensemble of bacteria, although constrained, propel the bead in a chemotactic manner with a 67% enhancement in displacement to distance ratio (defined as directionality) compared to nonchemotactic propulsion. The simulation results are validated experimentally. Close agreement between theory and experiments demonstrates the possibility of using the presented model as a predictive tool for other similar biohybrid systems.

  15. Bacteria-Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality.

    PubMed

    Scanlan, Pauline D

    2017-08-01

    Antagonistic coevolution (AC) between bacteria and bacteriophages plays a key role in driving and maintaining microbial diversity. Consequently, AC is predicted to affect all levels of biological organisation, from the individual to ecosystem scales. Nonetheless, we know nothing about bacteria-bacteriophage AC in perhaps the most important and clinically relevant microbial ecosystem known to humankind - the human gut microbiome. In this opinion piece I review current research on bacteria-phage AC in in vitro and natural populations of microbes. I then examine the evidence and discuss the potential role of AC in driving observed patterns of intra- and interindividual variation in the gut microbiome together with detailing the potential functional consequences of such AC-driven microbial variation for human health and disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Mortality of fecal bacteria in seawater

    SciTech Connect

    Garcia-Lara, J.; Menon, P.; Servais, P.; Billen, G. )

    1991-03-01

    The authors propose a method for determining the mortality rate for allochthonous bacteria released in aquatic environments without interference due to the loss of culturability in specific culture media. This method consists of following the disappearance of radioactivity from the trichloracetic acid-insoluble fraction in water samples to which ({sup 3}H)thymidine-prelabeled allochthonous bacteria have been added. In coastal seawater, they found that the actual rate of disappearance of fecal bacteria was 1 order of magnitude lower than the rate of loss of culturability on specific media. Minor adaptation of the procedure may facilitate assessment of the effect of protozoan grazing and bacteriophage lysis on the overall bacterial mortality rate.

  17. ["Quorum sensing" or social behavior of bacteria].

    PubMed

    Gintsburg, A L; Il'ina, T S; Romanova, Iu M

    2003-01-01

    The review deals with the data of literature on the role of the "quorum sensing" (QS) system ensuring the social behavior of bacteria in the regulation of virulence genes. The mechanisms of the action of these systems in Gram-negative and Gram-positive bacteria, as well as the influence of acyl-homoserine lactones, one of the components of the QS system, on the immune response of the infected host are discussed. In addition, in this review the data of literature on the existence of bacteria in the form of biofilms are presented. The methods of the identification of biofilms, the methods of their experimental preparation and the role of the QS system in the process of their formation are considered.

  18. Encapsulation of probiotic bacteria in biopolymeric system.

    PubMed

    Huq, Tanzina; Khan, Avik; Khan, Ruhul A; Riedl, Bernard; Lacroix, Monique

    2013-01-01

    Encapsulation of probiotic bacteria is generally used to enhance the viability during processing, and also for the target delivery in gastrointestinal tract. Probiotics are used with the fermented dairy products, pharmaceutical products, and health supplements. They play a great role in maintaining human health. The survival of these bacteria in the human gastrointestinal system is questionable. In order to protect the viability of the probiotic bacteria, several types of biopolymers such as alginate, chitosan, gelatin, whey protein isolate, cellulose derivatives are used for encapsulation and several methods of encapsulation such as spray drying, extrusion, emulsion have been reported. This review focuses on the method of encapsulation and the use of different biopolymeric system for encapsulation of probiotics.

  19. Threats and opportunities of plant pathogenic bacteria.

    PubMed

    Tarkowski, Petr; Vereecke, Danny

    2014-01-01

    Plant pathogenic bacteria can have devastating effects on plant productivity and yield. Nevertheless, because these often soil-dwelling bacteria have evolved to interact with eukaryotes, they generally exhibit a strong adaptivity, a versatile metabolism, and ingenious mechanisms tailored to modify the development of their hosts. Consequently, besides being a threat for agricultural practices, phytopathogens may also represent opportunities for plant production or be useful for specific biotechnological applications. Here, we illustrate this idea by reviewing the pathogenic strategies and the (potential) uses of five very different (hemi)biotrophic plant pathogenic bacteria: Agrobacterium tumefaciens, A. rhizogenes, Rhodococcus fascians, scab-inducing Streptomyces spp., and Pseudomonas syringae. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Copper tolerance and virulence in bacteria

    PubMed Central

    Ladomersky, Erik; Petris, Michael J.

    2015-01-01

    Copper (Cu) is an essential trace element for all aerobic organisms. It functions as a cofactor in enzymes that catalyze a wide variety of redox reactions due to its ability to cycle between two oxidation states, Cu(I) and Cu(II). This same redox property of copper has the potential to cause toxicity if copper homeostasis is not maintained. Studies suggest that the toxic properties of copper are harnessed by the innate immune system of the host to kill bacteria. To counter such defenses, bacteria rely on copper tolerance genes for virulence within the host. These discoveries suggest bacterial copper intoxication is a component of host nutritional immunity, thus expanding our knowledge of the roles of copper in biology. This review summarizes our current understanding of copper tolerance in bacteria, and the extent to which these pathways contribute to bacterial virulence within the host. PMID:25652326

  1. Whole genome plasticity in pathogenic bacteria.

    PubMed

    Dobrindt, U; Hacker, J

    2001-10-01

    The exploitation of bacterial genome sequences has so far provided a wealth of new general information about the genetic diversity of bacteria, such as that of many pathogens. Comparative genomics uncovered many genome variations in closely related bacteria and revealed basic principles involved in bacterial diversification, improving our knowledge of the evolution of bacterial pathogens. A correlation between metabolic versatility and genome size has become evident. The degenerated life styles of obligate intracellular pathogens correlate with significantly reduced genome sizes, a phenomenon that has been termed "evolution by reduction". These mechanisms can permanently alter bacterial genotypes and result in adaptation to their environment by genome optimization. In this review, we summarize the recent results of genome-wide approaches to studying the genetic diversity of pathogenic bacteria that indicate that the acquisition of DNA and the loss of genetic information are two important mechanisms that contribute to strain-specific differences in genome content.

  2. Transition Metals and Virulence in Bacteria.

    PubMed

    Palmer, Lauren D; Skaar, Eric P

    2016-11-23

    Transition metals are required trace elements for all forms of life. Due to their unique inorganic and redox properties, transition metals serve as cofactors for enzymes and other proteins. In bacterial pathogenesis, the vertebrate host represents a rich source of nutrient metals, and bacteria have evolved diverse metal acquisition strategies. Host metal homeostasis changes dramatically in response to bacterial infections, including production of metal sequestering proteins and the bombardment of bacteria with toxic levels of metals. In response, bacteria have evolved systems to subvert metal sequestration and toxicity. The coevolution of hosts and their bacterial pathogens in the battle for metals has uncovered emerging paradigms in social microbiology, rapid evolution, host specificity, and metal homeostasis across domains. This review focuses on recent advances and open questions in our understanding of the complex role of transition metals at the host-pathogen interface.

  3. Molecular Evolution of Threonine Dehydratase in Bacteria

    PubMed Central

    Yu, Xuefei; Li, Ye; Wang, Xiaoyuan

    2013-01-01

    Threonine dehydratase converts L-threonine to 2-ketobutyrate. Several threonine dehydratases exist in bacteria, but their origins and evolutionary pathway are unknown. Here we analyzed all the available threonine dehydratases in bacteria and proposed an evolutionary pathway leading to the genes encoding three different threonine dehydratases CTD, BTD1 and BTD2. The ancestral threonine dehydratase might contain only a catalytic domain, but one or two ACT-like subdomains were fused during the evolution, resulting BTD1 and BTD2, respectively. Horizontal gene transfer, gene fusion, gene duplication, and gene deletion may occur during the evolution of this enzyme. The results are important for understanding the functions of various threonine dehydratases found in bacteria. PMID:24324624

  4. [Bacteriocins produced by lactic acid bacteria].

    PubMed

    Bilková, Andrea; Sepova, Hana Kinová; Bilka, Frantisek; Balázová, Andrea

    2011-04-01

    Lactic acid bacteria comprise several genera of gram-positive bacteria that are known for the production of structurally different antimicrobial substances. Among them, bacteriocins are nowadays in the centre of scientific interest. Bacteriocins, proteinaceous antimicrobial substances, are produced ribosomally and have usually a narrow spectrum of bacterial growth inhibition. According to their structure and the target of their activity, they are divided into four classes, although there are some suggestions for a renewed classification. The most interesting and usable class are lantibiotics. They comprise the most widely commercially used and well examined bacteriocin, nisin. The non-pathogenic character of lactic acid bacteria is advantageous for using their bacteriocins in food preservation as well as in feed supplements or in veterinary medicine.

  5. Inorganic nanoparticles engineered to attack bacteria.

    PubMed

    Miller, Kristen P; Wang, Lei; Benicewicz, Brian C; Decho, Alan W

    2015-11-07

    Antibiotics were once the golden bullet to constrain infectious bacteria. However, the rapid and continuing emergence of antibiotic resistance (AR) among infectious microbial pathogens has questioned the future utility of antibiotics. This dilemma has recently fueled the marriage of the disparate fields of nanochemistry and antibiotics. Nanoparticles and other types of nanomaterials have been extensively developed for drug delivery to eukaryotic cells. However, bacteria have very different cellular architectures than eukaryotic cells. This review addresses the chemistry of nanoparticle-based antibiotic carriers, and how their technical capabilities are now being re-engineered to attack, kill, but also non-lethally manipulate the physiologies of bacteria. This review also discusses the surface functionalization of inorganic nanoparticles with small ligand molecules, polymers, and charged moieties to achieve drug loading and controllable release.

  6. Transition Metals and Virulence in Bacteria

    PubMed Central

    Palmer, Lauren D.; Skaar, Eric P.

    2016-01-01

    Transition metals are required trace elements for all forms of life. Due to their unique inorganic and redox properties, transition metals serve as cofactors for enzymes and other proteins. In bacterial pathogenesis, the vertebrate host represents a rich source of nutrient metals, and bacteria have evolved diverse metal acquisition strategies. Host metal homeostasis changes dramatically in response to bacterial infections, including production of metal sequestering proteins and the bombardment of bacteria with toxic levels of metals. Presumably, in response, bacteria have evolved systems to subvert metal sequestration and toxicity. The coevolution of hosts and their bacterial pathogens in the battle for metals has uncovered emerging paradigms in social microbiology, rapid evolution, host specificity, and metal homeostasis across domains. This review focuses on recent advances and open questions in our understanding of the complex role of transition metals at the host-pathogen interface. PMID:27617971

  7. Interactions among sulfide-oxidizing bacteria

    NASA Technical Reports Server (NTRS)

    Poplawski, R.

    1985-01-01

    The responses of different phototrophic bacteria in a competitive experimental system are studied, one in which primary factors such as H2S or light limited photometabolism. Two different types of bacteria shared one limited source of sulfide under specific conditions of light. The selection of a purple and a green sulfur bacteria and the cyanobacterium was based on their physiological similarity and also on the fact that they occur together in microbial mats. They all share anoxygenic photosynthesis, and are thus probably part of an evolutionary continuum of phototrophic organisms that runs from, strictly anaerobic physiology to the ability of some cyanobacteria to shift between anoxygenic bacterial style photosynthesis and the oxygenic kind typical of eukaryotes.

  8. THE FLOCCULATION OF BACTERIA BY PROTEINS

    PubMed Central

    Eggerth, Arnold H.; Bellows, Margaret

    1922-01-01

    1. The effect of adding pure proteins to bacterial suspensions at different H ion concentrations has been studied. 2. The zone of flocculation of protein-treated bacteria bears a significant relationship to the isoelectric point of the protein used. With the higher concentration of protein, agglutination occurs at or near the isoelectric point of that protein; at reactions acid to this, the bacteria carry a positive charge and are not agglutinated. With diminishing concentration of protein, the zone of flocculation shifts toward and goes beyond that characteristic of the untreated bacteria. This occurs both in the presence and absence of salts. 3. A diversity of other suspensions, such as sols of gold, mastic, cellulose nitrate, cellulose acetate, Fe(OH)3, oil emulsions, and erythrocytes, have been found by ourselves and others to exhibit a similar altered stability when treated with proteins in the same way. PMID:19871966

  9. Study examines sulfate-reducing bacteria activity

    SciTech Connect

    McElhiney, J.E.; Hardy, J.A.; Rizk, T.Y.; Stott, J.F.D.; Eden, R.D.

    1996-12-09

    Low-sulfate seawater injection can reduce the potential of an oil reservoir turning sour because of sulfate-reducing bacteria. Sulfate-reducing bacteria (SRB) convert sulfate ions in seawater used in waterflooding into sulfide with the concomitant oxidation of a carbon source. A recent study at Capcis investigated the efficiency of SRB under various conditions of sulfate limitation. This study was conducted in a flowing bioreactor at 2,000 psia with different temperature zones (mesophilic 35 C and thermophilic 60--80 C). The study mixed microfloral populations derived from real North Sea-produced fluids, and included an active population of marine methanogenic bacteria present to provide competition for the available carbon sources. In general, results showed that SRB continue to convert sulfate to sulfide in stoichiometric quantities without regard to absolute concentrations. The paper discusses the results and recommends nanofiltration of seawater for ``sweet`` reservoirs.

  10. High Life Expectancy of Bacteria on Lichens.

    PubMed

    Cernava, Tomislav; Berg, Gabriele; Grube, Martin

    2016-10-01

    Self-sustaining lichen symbioses potentially can become very old, sometimes even thousands of years in nature. In the joint structures, algal partners are sheltered between fungal structures that are externally colonized by bacterial communities. With this arrangement lichens survive long periods of drought, and lichen thalli can be revitalized even after decades of dry storage in a herbarium. To study the effects of long-term ex situ storage on viability of indigenous bacterial communities we comparatively studied herbarium-stored material of the lung lichen, Lobaria pulmonaria. We discovered that a significant fraction of the lichen-associated bacterial community survives herbarium storage of nearly 80 years, and living bacteria can still be found in even older material. As the bacteria reside in the upper surface layers of the lichen material, we argue that the extracellular polysaccharides of lichens contribute to superior life expectancy of bacteria. Deeper understanding of underlying mechanisms could provide novel possibilities for biotechnological applications.

  11. Quorum sensing in plant-associated bacteria.

    PubMed

    Loh, John; Pierson, Elizabeth A; Pierson, Leland S; Stacey, Gary; Chatterjee, Arun

    2002-08-01

    N-acyl homoserine lactone (AHL)-mediated quorum sensing by bacteria regulates traits that are involved in symbiotic, pathogenic and surface-associated relationships between microbial populations and their plant hosts. Recent advances demonstrate deviations from the classic LuxR/LuxI paradigm, which was first developed in Vibrio. For example, LuxR homologs can repress as well as activate gene expression, and non-AHL signals and signal mimics can affect the expression of genes that are controlled by quorum sensing. Many bacteria utilize multiple quorum-sensing systems, and these may be modulated via post-transcriptional and other global regulatory mechanisms. Microbes inhabiting plant surfaces also produce and respond to a diverse mixture of AHL signals. The production of AHL mimics by plants and the identification of AHL degradative pathways suggest that bacteria and plants utilize this method of bacterial communication as a key control point for influencing the outcome of their interactions.

  12. Copper tolerance and virulence in bacteria.

    PubMed

    Ladomersky, Erik; Petris, Michael J

    2015-06-01

    Copper (Cu) is an essential trace element for all aerobic organisms. It functions as a cofactor in enzymes that catalyze a wide variety of redox reactions due to its ability to cycle between two oxidation states, Cu(I) and Cu(II). This same redox property of copper has the potential to cause toxicity if copper homeostasis is not maintained. Studies suggest that the toxic properties of copper are harnessed by the innate immune system of the host to kill bacteria. To counter such defenses, bacteria rely on copper tolerance genes for virulence within the host. These discoveries suggest bacterial copper intoxication is a component of host nutritional immunity, thus expanding our knowledge of the roles of copper in biology. This review summarizes our current understanding of copper tolerance in bacteria, and the extent to which these pathways contribute to bacterial virulence within the host.

  13. Monitoring of environmental pollutants by bioluminescent bacteria.

    PubMed

    Girotti, Stefano; Ferri, Elida Nora; Fumo, Maria Grazia; Maiolini, Elisabetta

    2008-02-04

    This review deals with the applications of bioluminescent bacteria to the environmental analyses, published during the years 2000-2007. The ecotoxicological assessment, by bioassays, of the environmental risks and the luminescent approaches are reported. The review includes a brief introduction to the characteristics and applications of bioassays, a description of the characteristics and applications of natural bioluminescent bacteria (BLB), and a collection of the main applications to organic and inorganic pollutants. The light-emitting genetically modified bacteria applications, as well as the bioluminescent immobilized systems and biosensors are outlined. Considerations about commercially available BLB and BLB catalogues are also reported. Most of the environmental applications, here mentioned, of luminescent organisms are on wastewater, seawater, surface and ground water, tap water, soil and sediments, air. Comparison to other bioindicators and bioassay has been also made. Various tables have been inserted, to make easier to take a rapid glance at all possible references concerning the topic of specific interest.

  14. Bacteria-phage interactions in natural environments.

    PubMed

    Díaz-Muñoz, Samuel L; Koskella, Britt

    2014-01-01

    Phages are considered the most abundant and diverse biological entities on Earth and are notable not only for their sheer abundance, but also for their influence on bacterial hosts. In nature, bacteria-phage relationships are complex and have far-reaching consequences beyond particular pairwise interactions, influencing everything from bacterial virulence to eukaryotic fitness to the carbon cycle. In this review, we examine bacteria and phage distributions in nature first by highlighting biogeographic patterns and nonhost environmental influences on phage distribution, then by considering the ways in which phages and bacteria interact, emphasizing phage life cycles, bacterial responses to phage infection, and the complex patterns of phage host specificity. Finally, we discuss phage impacts on bacterial abundance, genetics, and physiology, and further aim to clarify distinctions between current theoretical models and point out areas in need of future research.

  15. Using Fluorescent Viruses for Detecting Bacteria in Water

    NASA Technical Reports Server (NTRS)

    Tabacco, Mary Beth; Qian, Xiaohua; Russo, Jaimie A.

    2009-01-01

    A method of detecting water-borne pathogenic bacteria is based partly on established molecular-recognition and fluorescent-labeling concepts, according to which bacteria of a species of interest are labeled with fluorescent reporter molecules and the bacteria can then be detected by fluorescence spectroscopy. The novelty of the present method lies in the use of bacteriophages (viruses that infect bacteria) to deliver the fluorescent reporter molecules to the bacteria of the species of interest.

  16. Biogeography and habitat modelling of high-alpine bacteria.

    PubMed

    King, Andrew J; Freeman, Kristen R; McCormick, Katherine F; Lynch, Ryan C; Lozupone, Catherine; Knight, Rob; Schmidt, Steven K

    2010-08-10

    Soil microorganisms dominate terrestrial biogeochemical cycles; however, we know very little about their spatial distribution and how changes in the distributions of specific groups of microbes translate into landscape and global patterns of biogeochemical processes. In this paper, we use a nested sampling scheme at scales ranging from 2 to 2,000 m to show that bacteria have significant spatial autocorrelation in community composition up to a distance of 240 m, and that this pattern is driven by changes in the relative abundance of specific bacterial clades across the landscape. Analysis of clade habitat distribution models and spatial co-correlation maps identified soil pH, plant abundance and snow depth as major variables structuring bacterial communities across this landscape, and revealed an unexpected and important oligotrophic niche for the Rhodospirillales in soil. Furthermore, our global analysis of high-elevation soils from the Andes, Rockies, Himalayas and Alaskan range shows that habitat distribution models for bacteria have a strong predictive power across the entire globe.

  17. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

    PubMed Central

    Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D.; Pati, Amrita; Lykidis, Athanasios; Spring, Stefan; Anderson, Iain J.; D’haeseleer, Patrik; Zemla, Adam; Singer, Mitchell; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Han, Cliff; Chen, Feng; Cheng, Jan-Fang; Lucas, Susan; Kerfeld, Cheryl; Lang, Elke; Gronow, Sabine; Chain, Patrick; Bruce, David; Rubin, Edward M.; Kyrpides, Nikos C.; Klenk, Hans-Peter; Eisen, Jonathan A.

    2011-01-01

    Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms1. There are now nearly 1,000 completed bacterial and archaeal genomes available2, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution3–5. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. PMID:20033048

  18. Bacteria in Ostreococcus tauri cultures – friends, foes or hitchhikers?

    PubMed Central

    Abby, Sophie S.; Touchon, Marie; De Jode, Aurelien; Grimsley, Nigel; Piganeau, Gwenael

    2014-01-01

    Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri. PMID:25426102

  19. Iterative Polyketide Biosynthesis by Modular Polyketide Synthases in Bacteria

    PubMed Central

    Chen, Haotong; Du, Liangcheng

    2015-01-01

    Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is “non-iterative” in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the “canonical rules”, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively-used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides. PMID:26549236

  20. Equilibrium temperature in a clump of bacteria heated in fluid.

    PubMed Central

    Davey, K R

    1990-01-01

    A theoretical model was developed and used to estimate quantitatively the "worst case", i.e., the longest, time to reach equilibrium temperature in the center of a clump of bacteria heated in fluid. For clumps with 10 to 10(6) cells heated in vapor, such as dry and moist air, and liquid fluids such as purees and juices, predictions show that temperature equilibrium will occur with sterilization temperatures up to 130 degrees C in under 0.02 s. Model development highlighted that the controlling influence on time for heating up the clump is the surface convection thermal resistance and that the internal conduction resistance of the clump mass is negligible by comparison. The time for a clump to reach equilibrium sterilization temperature was therefore decreased with relative turbulence (velocity) of the heating fluid, such as occurs in many process operations. These results confirm widely held suppositions that the heat-up time of bacteria in vapor or liquid is not significant with usual sterilization times. PMID:2306095

  1. Machine Reading for Extraction of Bacteria and Habitat Taxonomies

    PubMed Central

    Kordjamshidi, Parisa; Massa, Wouter; Provoost, Thomas; Moens, Marie-Francine

    2015-01-01

    There is a vast amount of scientific literature available from various resources such as the internet. Automating the extraction of knowledge from these resources is very helpful for biologists to easily access this information. This paper presents a system to extract the bacteria and their habitats, as well as the relations between them. We investigate to what extent current techniques are suited for this task and test a variety of models in this regard. We detect entities in a biological text and map the habitats into a given taxonomy. Our model uses a linear chain Conditional Random Field (CRF). For the prediction of relations between the entities, a model based on logistic regression is built. Designing a system upon these techniques, we explore several improvements for both the generation and selection of good candidates. One contribution to this lies in the extended exibility of our ontology mapper that uses an advanced boundary detection and assigns the taxonomy elements to the detected habitats. Furthermore, we discover value in the combination of several distinct candidate generation rules. Using these techniques, we show results that are significantly improving upon the state of art for the BioNLP Bacteria Biotopes task. PMID:27077141

  2. Theory of periodic swarming of bacteria: Application to Proteus mirabilis

    NASA Astrophysics Data System (ADS)

    Czirók, A.; Matsushita, M.; Vicsek, T.

    2001-03-01

    The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth), a series of concentric rings are developed as the bacteria multiply and swarm following a scenario that periodically repeats itself. We have developed a theoretical description for this process in order to obtain a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. Our approach is based on simple assumptions directly related to the latest experimental observations on colony formation under various conditions. The corresponding one-dimensional model consists of two coupled differential equations investigated here both by numerical integrations and by analyzing the various expressions obtained from these equations using a few natural assumptions about the parameters of the model. We determine the phase diagram corresponding to systems exhibiting periodic swarming, and discuss in detail how the various stages of the colony development can be interpreted in our framework. We point out that all of our theoretical results are in excellent agreement with the complete set of available observations. Thus the present study represents one of the few examples where self-organized biological pattern formation is understood within a relatively simple theoretical approach, leading to results and predictions fully compatible with experiments.

  3. Modulating immune responses with probiotic bacteria.

    PubMed

    Matsuzaki, T; Chin, J

    2000-02-01

    For many years, probiotic bacteria have been known to confer health benefits to the consumer. One possible mechanism for this may be the ability of probiotic bacteria to modulate immune responses. Oral administration of Lactobacillus casei strain Shirota (LcS) has been found to enhance innate immunity by stimulating the activity of splenic NK cells. Oral feeding with killed LcS was able to stimulate the production of Th1 cytokines, resulting in repressed production of IgE antibodies against Ovalbumin in experimental mice. The ability to switch mucosal immune responses towards Th1 with probiotic bacteria provides a strategy for treatment of allergic disorders. Growth of Meth A tumour cells in the lungs was also inhibited by intrapleural injection of LcS. Oral administration of other probiotic bacteria, such as Streptococcus thermophilus (St), Lactobacillus fermentum (Lf) and yeast (Y), elicited different immune responses. Mice that were prefed yeast or Lf followed by feeding with ovalbumin (OVA) responded better to vaccination with OVA than mice not given either probiotic or OVA or mice that had been prefed only OVA. However, antibody responses were significantly suppressed in response to vaccination with OVA in mice that had been prefed yeast followed by yeast and OVA as well as mice prefed Lf followed by Lf and OVA. Prefeeding St followed by OVA feeding enhanced cellular immune responses against ovalbumin. In contrast, mice prefed St followed by St + OVA were hyporesponsive against OVA. While antigen feeding alone appears to prime for an immune response, cofeeding antigen with probiotic bacteria can suppress both antibody and cellular immune responses and may provide an efficacious protocol to attenuate autoimmune diseases, such as experimental allergic encephalomyelitis, by jointly dosing with myelin basic protein and probiotic bacteria.

  4. Modeling Facilitated Contaminant Transport by Mobile Bacteria

    NASA Astrophysics Data System (ADS)

    Corapcioglu, M. Yavuz; Kim, Seunghyun

    1995-01-01

    Introduction of exogenous biocolloids such as genetically engineered bacteria in a bioremediation operation can enhance the transport of contaminants in groundwater by reducing the retardation effects. Because of their colloidal size and favorable surface conditions, bacteria are efficient contaminant carriers. In cases where contaminants have a low mobility in porous media because of their high partition with solid matrix, facilitated contaminant transport by mobile bacteria can create high contaminant fluxes. When metabolically active mobile bacteria are present in a subsurface environment, the system can be treated as consisting of three phases: water phase, bacterial phase, and stationary solid matrix phase. In this work a mathematical model based on mass balance equations is developed to describe the facilitated transport and fate of a contaminant and bacteria in a porous medium. Bacterial partition between the bulk solution and the stationary solid matrix and contaminant partition among three phases are represented by expressions in terms of measurable quantities. Solutions were obtained to provide estimates of contaminant and bacterial concentrations. A dimensional analysis of the transport model was utilized to estimate model parameters from the experimental data and to assess the effect of several parameters on model behavior. The model results matched favorably with experimental data of Jenkins and Lion (1993). The presence of mobile bacteria enhances the contaminant transport. However, bacterial consumption of the contaminant, which serves as a bacterial nutrient, can attenuate the contaminant mobility. The work presented in this paper is the first three-phase model to include the effects of substrate metabolism on the fate of groundwater contaminants.

  5. Gastric spiral bacteria in small felids.

    PubMed

    Kinsel, M J; Kovarik, P; Murnane, R D

    1998-06-01

    Nine small cats, including one bobcat (Felis rufus), one Pallas cat (F. manul), one Canada lynx (F. lynx canadensis), two fishing cats (F. viverrina), two margays (F. wiedii), and two sand cats (F. margarita), necropsied between June 1995 and March 1997 had large numbers of gastric spiral bacteria, whereas five large cats, including one African lion (Panthera leo), two snow leopards (P. uncia), one Siberian tiger (P. tigris altaica), and one jaguar (P. onca), necropsied during the same period had none. All of the spiral organisms from the nine small cats were histologically and ultrastructurally similar. Histologically, the spiral bacteria were 5-14 microm long with five to nine coils per organism and were located both extracellularly within gastric glands and surface mucus, and intracellularly in parietal cells. Spiral bacteria in gastric mucosal scrapings from the Canada lynx, one fishing cat, and the two sand cats were gram negative and had corkscrewlike to tumbling motility when viewed with phase contrast microscopy. The bacteria were 0.5-0.7 microm wide, with a periodicity of 0.65-1.1 microm in all cats. Bipolar sheathed flagella were occasionally observed, and no periplasmic fibrils were seen. The bacteria were extracellular in parietal cell canaliculi and intracellular within parietal cells. Culture of mucosal scrapings from the Canada lynx and sand cats was unsuccessful. Based on morphology, motility, and cellular tropism, the bacteria were probably Helicobacter-like organisms. Although the two margays had moderate lymphoplasmacytic gastritis, the other cats lacked or had only mild gastric lymphoid infiltrates, suggesting that these organisms are either commensals or opportunistic pathogens.

  6. Quorum sensing and swarming migration in bacteria.

    PubMed

    Daniels, Ruth; Vanderleyden, Jos; Michiels, Jan

    2004-06-01

    Bacterial cells can produce and sense signal molecules, allowing the whole population to initiate a concerted action once a critical concentration (corresponding to a particular population density) of the signal has been reached, a phenomenon known as quorum sensing. One of the possible quorum sensing-regulated phenotypes is swarming, a flagella-driven movement of differentiated swarmer cells (hyperflagellated, elongated, multinucleated) by which bacteria can spread as a biofilm over a surface. The glycolipid or lipopeptide biosurfactants thereby produced function as wetting agent by reducing the surface tension. Quorum sensing systems are almost always integrated into other regulatory circuits. This effectively expands the range of environmental signals that influence target gene expression beyond population density. In this review, we first discuss the regulation of AHL-mediated surface migration and the involvement of other low-molecular-mass signal molecules (such as the furanosyl borate diester AI-2) in biosurfactant production of different bacteria. In addition, population density-dependent regulation of swarmer cell differentiation is reviewed. Also, several examples of interspecies signalling are reported. Different signal molecules either produced by bacteria (such as other AHLs and diketopiperazines) or excreted by plants (such as furanones, plant signal mimics) might influence the quorum sensing-regulated swarming behaviour in bacteria different from the producer. On the other hand, specific bacteria can reduce the local available concentration of signal molecules produced by others. In the last part, the role and regulation of a surface-associated movement in biofilm formation is discussed. Here we also describe how quorum sensing may disperse existing biofilms and control the interaction between bacteria and higher organisms (such as the Rhizobium-bean symbiosis).

  7. Exogenous fatty acid metabolism in bacteria.

    PubMed

    Yao, Jiangwei; Rock, Charles O

    2017-10-01

    Bacterial type II fatty acid synthesis (FASII) is a target for novel antibiotic development. All bacteria encode for mechanisms to incorporate exogenous fatty acids, and some bacteria can use exogenous fatty acids to bypass FASII inhibition. Bacteria encode three different mechanisms for activating exogenous fatty acids for incorporation into phospholipid synthesis. Exogenous fatty acids are converted into acyl-CoA in Gammaproteobacteria such as E. coli. Acyl-CoA molecules constitute a separate pool from endogenously synthesized acyl-ACP. Acyl-CoA can be used for phospholipid synthesis or broken down by β-oxidation, but cannot be used for lipopolysaccharide synthesis. Exogenous fatty acids are converted into acyl-ACP in some Gram-negative bacteria. The resulting acyl-ACP undergoes the same fates as endogenously synthesized acyl-ACP. Exogenous fatty acids are converted into acyl-phosphates in Gram-positive bacteria, and can be used for phospholipid synthesis or become acyl-ACP. Only the order Lactobacillales can use exogenous fatty acids to bypass FASII inhibition. FASII shuts down completely in presence of exogenous fatty acids in Lactobacillales, allowing Lactobacillales to synthesize phospholipids entirely from exogenous fatty acids. Inhibition of FASII cannot be bypassed in other bacteria because FASII is only partially down-regulated in presence of exogenous fatty acid or FASII is required to synthesize essential metabolites such as β-hydroxyacyl-ACP. Certain selective pressures such as FASII inhibition or growth in biofilms can select for naturally occurring one step mutations that attenuate endogenous fatty acid synthesis. Although attempts have been made to estimate the natural prevalence of these mutants, culture-independent metagenomic methods would provide a better estimate. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  8. Sulfur metabolism in phototrophic sulfur bacteria.

    PubMed

    Frigaard, Niels-Ulrik; Dahl, Christiane

    2009-01-01

    Phototrophic sulfur bacteria are characterized by oxidizing various inorganic sulfur compounds for use as electron donors in carbon dioxide fixation during anoxygenic photosynthetic growth. These bacteria are divided into the purple sulfur bacteria (PSB) and the green sulfur bacteria (GSB). They utilize various combinations of sulfide, elemental sulfur, and thiosulfate and sometimes also ferrous iron and hydrogen as electron donors. This review focuses on the dissimilatory and assimilatory metabolism of inorganic sulfur compounds in these bacteria and also briefly discusses these metabolisms in other types of anoxygenic phototrophic bacteria. The biochemistry and genetics of sulfur compound oxidation in PSB and GSB are described in detail. A variety of enzymes catalyzing sulfur oxidation reactions have been isolated from GSB and PSB (especially Allochromatium vinosum, a representative of the Chromatiaceae), and many are well characterized also on a molecular genetic level. Complete genome sequence data are currently available for 10 strains of GSB and for one strain of PSB. We present here a genome-based survey of the distribution and phylogenies of genes involved in oxidation of sulfur compounds in these strains. It is evident from biochemical and genetic analyses that the dissimilatory sulfur metabolism of these organisms is very complex and incompletely understood. This metabolism is modular in the sense that individual steps in the metabolism may be performed by different enzymes in different organisms. Despite the distant evolutionary relationship between GSB and PSB, their photosynthetic nature and their dependency on oxidation of sulfur compounds resulted in similar ecological roles in the sulfur cycle as important anaerobic oxidizers of sulfur compounds.

  9. Revisiting the Cape Cod Bacteria Injection Experiment Using a Stochastic Modeling Approach

    SciTech Connect

    Maxwell, R M; Welty, C; Harvey, R W

    2006-11-22

    Bromide and resting-cell bacteria tracer tests carried out in a sand and gravel aquifer at the USGS Cape Cod site in 1987 were reinterpreted using a three-dimensional stochastic approach and Lagrangian particle tracking numerical methods. Bacteria transport was strongly coupled to colloid filtration through functional dependence of local-scale colloid transport parameters on hydraulic conductivity and seepage velocity in a stochastic advection-dispersion/attachment-detachment model. Information on geostatistical characterization of the hydraulic conductivity (K) field from a nearby plot was utilized as input that was unavailable when the original analysis was carried out. A finite difference model for groundwater flow and a particle-tracking model of conservative solute transport was calibrated to the bromide-tracer breakthrough data using the aforementioned geostatistical parameters. An optimization routine was utilized to adjust the mean and variance of the lnK field over 100 realizations such that a best fit of a simulated, average bromide breakthrough curve is achieved. Once the optimal bromide fit was accomplished (based on adjusting the lnK statistical parameters in unconditional simulations), a stochastic particle-tracking model for the bacteria was run without adjustments to the local-scale colloid transport parameters. Good predictions of the mean bacteria breakthrough data were achieved using several approaches for modeling components of the system. Simulations incorporating the recent Tufenkji and Elimelech [1] equation for estimating single collector efficiency were compared to those using the Rajagopalan and Tien [2] model. Both appeared to work equally well at predicting mean bacteria breakthrough using a constant mean bacteria diameter for this set of field conditions, with the Rajagopalan and Tien model yielding approximately a 30% lower peak concentration and less tailing than the Tufenkji and Elimelech formulation. Simulations using a distribution

  10. Windshear Prediction

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Windshear microbursts and extreme air turbulence caused by sudden intense changes in wind direction or speed are difficult to detect and thus dangerous to air traffic. They have been positively identified as the cause of 28 aviation accidents that claimed 491 lives. Many groups are investigating ways to detect and predict windshear. The Federal Aviation Consulting Services, Ltd. (FACS) is applying artificial intelligence to windshear prediction. FACS' artificial intelligence based airline dispatcher program is intended as a backup not a replacement for human dispatcher. It would incorporate the same data that a human would request to make a decision and then draw a conclusion using the same rules of logic as the human expert.

  11. RNA-Mediated Regulation in Pathogenic Bacteria

    PubMed Central

    Caldelari, Isabelle; Chao, Yanjie; Romby, Pascale; Vogel, Jörg

    2013-01-01

    Pathogenic bacteria possess intricate regulatory networks that temporally control the production of virulence factors, and enable the bacteria to survive and proliferate after host infection. Regulatory RNAs are now recognized as important components of these networks, and their study may not only identify new approaches to combat infectious diseases but also reveal new general control mechanisms involved in bacterial gene expression. In this review, we illustrate the diversity of regulatory RNAs in bacterial pathogens, their mechanism of action, and how they can be integrated into the regulatory circuits that govern virulence-factor production. PMID:24003243

  12. Bacteriophage biosensors for antibiotic-resistant bacteria.

    PubMed

    Sorokulova, Irina; Olsen, Eric; Vodyanoy, Vitaly

    2014-03-01

    An increasing number of disease-causing bacteria are resistant to one or more anti-bacterial drugs utilized for therapy. Early and speedy detection of these pathogens is therefore very important. Traditional pathogen detection techniques, that include microbiological and biochemical assays are long and labor-intensive, while antibody or DNA-based methods require substantial sample preparation and purification. Biosensors based on bacteriophages have demonstrated remarkable potential to surmount these restrictions and to offer rapid, efficient and sensitive detection technique for antibiotic-resistant bacteria.

  13. Differential staining of bacteria: gram stain.

    PubMed

    Moyes, Rita B; Reynolds, Jackie; Breakwell, Donald P

    2009-11-01

    In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram-positive cocci, Gram-negative cocci, Gram-positive rods, and Gram-negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures.

  14. Bacteria Provide Cleanup of Oil Spills, Wastewater

    NASA Technical Reports Server (NTRS)

    2010-01-01

    Through Small Business Innovation Research (SBIR) contracts with Marshall Space Flight Center, Micro-Bac International Inc., of Round Rock, Texas, developed a phototrophic cell for water purification in space. Inside the cell: millions of photosynthetic bacteria. Micro-Bac proceeded to commercialize the bacterial formulation it developed for the SBIR project. The formulation is now used for the remediation of wastewater systems and waste from livestock farms and food manufacturers. Strains of the SBIR-derived bacteria also feature in microbial solutions that treat environmentally damaging oil spills, such as that resulting from the catastrophic 2010 Deepwater Horizon oil rig explosion in the Gulf of Mexico.

  15. Functional Encyclopedia of Bacteria and Archaea

    SciTech Connect

    Blow, M. J.; Deutschbauer, A. M.; Hoover, C. A.; Lamson, J.; Lamson, J.; Price, M. N.; Waters, J.; Wetmore, K. M.; Bristow, J.; Arkin, A. P.

    2013-03-20

    Bacteria and Archaea exhibit a huge diversity of metabolic capabilities with fundamental importance in the environment, and potential applications in biotechnology. However, the genetic bases of these capabilities remain unclear due largely to an absence of technologies that link DNA sequence to molecular function. To address this challenge, we are developing a pipeline for high throughput annotation of gene function using mutagenesis, growth assays and DNA sequencing. By applying this pipeline to annotate gene function in 50 diverse microbes we hope to discover thousands of new gene functions and produce a proof of principle `Functional Encyclopedia of Bacteria and Archaea?.

  16. Fatty acid composition of selected prosthecate bacteria.

    PubMed

    Carter, R N; Schmidt, J M

    1976-10-11

    The cellular fatty acid composition of 14 strains of Caulobacter speices and types, two species of Prosthecomicrobium, and two species of Asticcacaulis was determined by gas-liquid chromatography. In most of these bacteria, the major fatty acids were octadecenoic acid (C18:1), hexadecenoic acid (C16:1) and hexadecanoic acid (C16:0). Some cyclopropane and branched chain fatty acids were detected in addition to the straight chained acids. Hydroxytetradecanoic acid was an important component of P.enhydrum but significant amounts of hydroxy acids were not detected in other prosthecate bacteria examined.

  17. Dynamic Clustering in Suspension of Motile Bacteria

    NASA Astrophysics Data System (ADS)

    Zhang, Hepeng; Chen, Xiao; Yang, Xiang; Yang, Mingcheng

    2015-03-01

    Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we investigate dynamic clusters of motile bacteria near an air-liquid interface. Cell in a cluster orient its flagella perpendicular to the interface and generate attractive radial fluid flow that leads to cluster formation. Rotating cell also creates tangential forces on neighbors that sets clusters into counter-clockwise rotation. We construct a numerical model of self-propelled particles that interact via pair-wise forces extracted from hydrodynamic calculations; such a model reproduces many properties of observed cluster dynamics.

  18. Protein glycosylation in bacteria: sweeter than ever.

    PubMed

    Nothaft, Harald; Szymanski, Christine M

    2010-11-01

    Investigations into bacterial protein glycosylation continue to progress rapidly. It is now established that bacteria possess both N-linked and O-linked glycosylation pathways that display many commonalities with their eukaryotic and archaeal counterparts as well as some unexpected variations. In bacteria, protein glycosylation is not restricted to pathogens but also exists in commensal organisms such as certain Bacteroides species, and both the N-linked and O-linked glycosylation pathways can modify multiple proteins. Improving our understanding of the intricacies of bacterial protein glycosylation systems should lead to new opportunities to manipulate these pathways in order to engineer glycoproteins with potential value as novel vaccines.

  19. Understanding protein glycosylation pathways in bacteria.

    PubMed

    Li, Hong; Debowski, Aleksandra W; Liao, Tingting; Tang, Hong; Nilsson, Hans-Olof; Marshall, Barry J; Stubbs, Keith A; Benghezal, Mohammed

    2017-01-01

    Through advances in analytical methods to detect glycoproteins and to determine glycan structures, there have been increasing reports of protein glycosylation in bacteria. In this review, we summarize the known pathways for bacterial protein glycosylation: lipid carrier-mediated 'en bloc' glycosylation; and cytoplasmic stepwise protein glycosylation. The exploitation of bacterial protein glycosylation systems, especially the 'mix and match' of three independent but similar pathways (oligosaccharyltransferase-mediated protein glycosylation, lipopolysaccharide and peptidoglycan biosynthesis) in Gram-negative bacteria for glycoengineering recombinant glycoproteins is also discussed.

  20. Tooth brushing inhibits oral bacteria in dogs.

    PubMed

    Watanabe, Kazuhiro; Hayashi, Kotaro; Kijima, Saku; Nonaka, Chie; Yamazoe, Kazuaki

    2015-10-01

    In this study, scaling, polishing and daily tooth brushing were performed in 20 beagle dogs, and the number of oral bacteria was determined using a bacterial counter. The dogs were randomized into the scaling (S), scaling + polishing (SP), scaling + tooth daily brushing (SB) and scaling + polishing + tooth daily brushing (SPB) groups. Samples were collected from the buccal surface of the maxillary fourth premolars of the dogs immediately after scaling and every week thereafter from weeks 1 to 8. Throughout the study, the number of bacteria was significantly lower in the SB and SPB groups compared with the S group. The findings suggest that daily tooth brushing inhibited oral bacterial growth in the dogs.