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Sample records for radio-resistant bacteria prediction

  1. 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.

  2. 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.

  3. 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. PMID:9679315

  4. 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.

  5. 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

  6. 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

  7. Quantitative prediction of genome-wide resource allocation in bacteria.

    PubMed

    Goelzer, Anne; Muntel, Jan; Chubukov, Victor; Jules, Matthieu; Prestel, Eric; Nölker, Rolf; Mariadassou, Mahendra; Aymerich, Stéphane; Hecker, Michael; Noirot, Philippe; Becher, Dörte; Fromion, Vincent

    2015-11-01

    Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications.

  8. 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.

  9. A critical role of toll-like receptor 2 (TLR2) and its' in vivo ligands in radio-resistance.

    PubMed

    Gao, Fu; Zhang, Chaoxiong; Zhou, Chuanfeng; Sun, Weimin; Liu, Xin; Zhang, Pei; Han, Jiaqi; Xian, Linfeng; Bai, Dongchen; Liu, Hu; Cheng, Ying; Li, Bailong; Cui, Jianguo; Cai, Jianming; Liu, Cong

    2015-08-13

    The role of Toll-like receptor-2 (TLR2) in radio-resistance remained largely unknown. TLR2 knockout (TLR2(-/-)) mice received radiation of 6.5 Gy, and then were studied. We found that radiation resulted in more severe mortality and morbidity rates in TLR2(-/-) mice. The cause of death in TLR2(-/-) mice may be severe and persistent bone marrow cell loss. Injection of the TLR2 agonist Pam3CSK4 into wild type (WT) mice induced radio-resistance. Myd88(-/-) mice were more susceptible to radiation. In conclusion, our data indicate that, similar to TLR4, TLR2 plays a critical role in radio-resistance.

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

    NASA Astrophysics Data System (ADS)

    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

    2003-08-01

    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.

  11. 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.

  12. 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.

  13. A physical descriptive model for predicting bacteria level variation at a dynamic beach.

    PubMed

    He, Cheng; Post, Yvonne; Dony, John; Edge, Tom; Patel, Mahesh; Rochfort, Quintin

    2016-08-01

    A rational-based physical descriptive model (PDM) has been developed to predict the levels of Escherichia coli in water at a beach with dynamic conditions in the Greater Toronto Area (GTA), Ontario, Canada. Bacteria loadings in the water were affected not only by multiple physical factors (precipitation, discharge, wind, etc.), but also by cumulative effects, intensity, duration and timing of storm events. These may not be linearly related to the observed variations in bacteria levels, and are unlikely to be properly represented by a widely used multiple linear regression model. In order to account for these complex relationships, the amounts of precipitation and nearby creek discharge, the impact of various time-related factors, lag time between events and sample collection, and threshold for different parameters were used in determining bacteria levels. This new comprehensive PDM approach improved the accuracy of the E. coli level predictions in the studied beach water compared to the previously developed statistical predictive and presently used geometric mean models. In spite of the complexity and dynamic conditions at the studied beach, the PDM achieved 75% accuracy overall for the five case years examined. PMID:27441857

  14. Bacteria-polymeric membrane interactions: atomic force microscopy and XDLVO predictions.

    PubMed

    Thwala, Justice M; Li, Minghua; Wong, Mavis C Y; Kang, Seoktae; Hoek, Eric M V; Mamba, Bhekie B

    2013-11-12

    Atomic force microscopy (AFM) in conjunction with a bioprobe developed using a polydopamine wet adhesive was used to directly measure the adhesive force between bacteria and different polymeric membrane surfaces. Bacterial cells of Pseudomonas putida and Bacillus subtilis were immobilized onto the tip of a standard AFM cantilever, and force measurements made using the modified cantilever on various membranes. Interaction forces measured with the bacterial probe were compared, qualitatively, to predictions by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory with steric interactions included. The XDLVO theory predicted attractive interactions between low energy hydrophobic membranes with high energy hydrophilic bacterium (P. putida). It also predicted a shallow primary maximum with the most hydrophilic bacterium, B. subtilis . Discrepancies between predictions using the XDLVO theory and theory require involvement of factors such as bridging effects. Differences in interaction between P. putida and B. subtilis are attributed to acid-base interactions and steric interactions. P. putida is Gram negative with lipopolysaccharides present in the outer cell membrane. A variation in forces of adhesion for bacteria on polymeric membranes studied was interpreted in terms of hydrophilicity and interfacial surface potential calculated from physicochemical properties.

  15. 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. PMID:26683482

  16. 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

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

    PubMed Central

    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

    2016-01-01

    Abstract 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

  18. RNA binding protein RBM14 promotes radio-resistance in glioblastoma by regulating DNA repair and cell differentiation

    PubMed Central

    Yuan, Ming; Eberhart, Charles G.; Kai, Mihoko

    2014-01-01

    Glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor. Standard treatment for GBM patients is surgery followed by radiotherapy and/or chemotherapy, but tumors always recur. Traditional therapies seem to fail because they eliminate only the bulk of the tumors and spare a population of stem-like cells termed tumor-initiating cells. The stem-like state and preferential activation of DNA damage response in the GBM tumor-initiating cells contribute to their radio-resistance and recurrence. The molecular mechanisms underlying this efficient activation of damage response and maintenance of stem-like state remain elusive. Here we show that RBM14 controls DNA repair pathways and also prevents cell differentiation in GBM spheres, causing radio-resistance. Knockdown of RBM14 affects GBM sphere maintenance and sensitizes radio-resistant GBM cells at the cellular level. We demonstrate that RBM14 knockdown blocks GBM regrowth after irradiation in vivo. In addition, RBM14 stimulates DNA repair by controlling the DNA-PK-dependent non-homologous end-joining (NHEJ) pathway. These results reveal unexpected functions of the RNA-binding protein RBM14 in control of DNA repair and maintenance of tumor-initiating cells. Targeting the RBM14-dependent pathway may prevent recurrence of tumors and eradicate the deadly disease completely. PMID:24811242

  19. In vitro stemness characterization of radio-resistant clones isolated from a medulloblastoma cell line ONS-76

    PubMed Central

    Sun, Lue; Moritake, Takashi; Zheng, Yun-Wen; Suzuki, Kenshi; Gerelchuluun, Ariungerel; Hong, Zhengshan; Zenkoh, Junko; Taniguchi, Hideki; Tsuboi, Koji

    2013-01-01

    One-third of patients with medulloblastoma die due to recurrence after various treatments including radiotherapy. Although it has been postulated that cancer stem-like cells are radio-resistant and play an important role in tumor recurrence, the “stemness” of medulloblastoma cells surviving irradiation has not yet been elucidated. Using a medulloblastoma cell line ONS-76, cells that survived gamma irradiation were investigated on their “stemness” in vitro. From 10 500 cells, 20 radio-resistant clones were selected after gamma ray irradiation (5 Gy × two fractions) using the replica micro-well technique. These 20 resistant clones were screened for CD133 positivity by flow cytometry followed by side population assay, tumor sphere formation assay and clonogenic survival assay. Results revealed CD133 fractions were significantly elevated in three clones, which also exhibited significantly increased levels of tumor sphere formation ability and side population fraction. Clonogenic survival assay demonstrated that their radio-resistance was significantly higher than the parental ONS-76. This may support the hypothesis that a small number of cancer stem-like cells (CSCs) are the main culprits in local recurrence after radiotherapy, and disruption of the resistance mechanism of these CSCs is a critical future issue in improving the outcome of patients with medulloblastoma. PMID:22951319

  20. 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.

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

    USGS Publications Warehouse

    Francy, D.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. ?? 2009 AEHMS.

  2. 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.

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

    PubMed

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

    2013-05-30

    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.

  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. 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

  6. Hydrometeorological variables predict fecal indicator bacteria densities in freshwater: data-driven methods for variable selection.

    PubMed

    Jones, Rachael M; Liu, Li; Dorevitch, Samuel

    2013-03-01

    Statistical models of microbial water quality inform risk management for water recreation. Current research focuses on resource-intensive, location-specific data collection and water quality modeling, but this approach may be cost-prohibitive for risk managers responsible for numerous recreation sites. As an alternative, we tested the ability of two data-driven models, tree regression and random forests with conditional inference trees, to select readily available hydrometeorological variables for use in linear mixed effects (LME) models predicting bacterial density. The study included the Chicago Area Waterway System (CAWS) and Lake Michigan beaches and harbors in Chicago, Illinois, at which Escherichia coli and enterococci were measured seasonally in 2007-2009. Tree regression node variables reduced data dimensionality by >50 %. Variable importance ranks from random forests were used in a forward-step selection based on R (2) and root mean squared prediction error (RMSPE). We found two to three variables explained bacteria densities well relative to random forests with all variables. LME models with tree- or forest-selected variables performed reasonably well (0.335 < R (2) < 0.658). LME models for Lake Michigan had good prediction accuracy with respect to the single sample maximum standard (72-77 %), but limited sensitivity (23-62 %). Results suggest that our alternative approach is feasible and performs similarly to more resource-intensive approaches.

  7. Predicting metal effects and interactions on light output in bacteria (Photobacterium phosphoreum) using coordination chemistry data

    SciTech Connect

    McCloskey, J.T.; Newman, M.C.

    1994-12-31

    Previous studies have shown correlations between Log of the negative solubility product for the metal hydroxide (Log -KsoMOH) and bioaccumulation of metals. The concentration of metal at which light output was reduced 50% (EC-50) in a marine bacteria (Photobacterium phosphoreum) was determined for several metals using Microtox{reg_sign}. Median affect concentrations were corrected for the amount of free ion using MINTEQ and graphed against Log -KsoMOH. A negative relationship was found between 15 minute EC50`s for all metals tested and Log -KsoMOH. The interaction between metal pairs were then determined to see if the interaction between metals could be predicted from Log -KsoMOH. In general, metals with similar values of Log KsoMOH interacted more strongly than metals with very different values. The authors conclude that metal effects (EC-50) could be predicted based on the Log -KsoMOH and that for metals with similar mechanisms of toxicity, the interaction between metals was also predictable based on Log -KsoMOH.

  8. 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.

  9. 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.

  10. 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. PMID:26362925

  11. 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

  12. 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...

  13. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.

    PubMed

    Barinov, Aleksandr; Loux, Valentin; Hammani, Amal; Nicolas, Pierre; Langella, Philippe; Ehrlich, Dusko; Maguin, Emmanuelle; van de Guchte, Maarten

    2009-01-01

    The in silico prediction of bacterial surface exposed proteins is of growing interest for the rational development of vaccines and in the study of bacteria-host relationships, whether pathogenic or host beneficial. This interest is driven by the increase in the use of DNA sequencing as a major tool in the early characterization of pathogenic bacteria and, more recently, even of complex ecosystems at the host-environment interface in metagenomics approaches. Current protein localization protocols are not suited to this prediction task as they ignore the potential surface exposition of many membrane-associated proteins. Therefore, we developed a new flow scheme, SurfG+, for the processing of protein sequence data with the particular aim of identification of potentially surface exposed (PSE) proteins from Gram-positive bacteria, which was validated for Streptococcus pyogenes. The results of an exploratory case study on closely related lactobacilli of the acidophilus group suggest that the yogurt bacterium Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) dedicates a relatively important fraction of its coding capacity to secreted proteins, while the probiotic gastrointestinal (GI) tract bacteria L. johnsonii and L. gasseri appear to encode a larger variety of PSE proteins, that may play a role in the interaction with the host.

  14. 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

  15. 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...

  16. The prediction of bacteria type and culture growth phase by an electronic nose with a multi-layer perceptron network

    NASA Astrophysics Data System (ADS)

    Gardner, J. W.; Craven, M.; Dow, C.; Hines, E. L.

    1998-01-01

    An investigation into the use of an electronic nose to predict the class and growth phase of two potentially pathogenic micro-organisms, Eschericha coli ( E. coli) and Staphylococcus aureus ( S. aureus), has been performed. In order to do this we have developed an automated system to sample, with a high degree of reproducibility, the head space of bacterial cultures grown in a standard nutrient medium. Head spaces have been examined by using an array of six different metal oxide semiconducting gas sensors and classified by a multi-layer perceptron (MLP) with a back-propagation (BP) learning algorithm. The performance of 36 different pre-processing algorithms has been studied on the basis of nine different sensor parameters and four different normalization techniques. The best MLP was found to classify successfully 100% of the unknown S. aureus samples and 92% of the unknown E. coli samples, on the basis of a set of 360 training vectors and 360 test vectors taken from the lag, log and stationary growth phases. The real growth phase of the bacteria was determined from optical cell counts and was predicted from the head space samples with an accuracy of 81%. We conclude that these results show considerable promise in that the correct prediction of the type and growth phase of pathogenic bacteria may help both in the more rapid treatment of bacterial infections and in the more efficient testing of new anti-biotic drugs.

  17. 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.

  18. 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. PMID:25788591

  19. 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

  20. Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits.

    PubMed

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

    2009-06-01

    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.

  1. 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.

  2. Neuropilin 1 expression correlates with the Radio-resistance of human non-small-cell lung cancer cells.

    PubMed

    Dong, Juan Cong; Gao, Hui; Zuo, Si Yao; Zhang, Hai Qin; Zhao, Gang; Sun, Shi Long; Han, Hai Ling; Jin, Lin Lin; Shao, Li Hong; Wei, Wei; Jin, Shun Zi

    2015-09-01

    The purpose of this study was to determine the correlation between over-expression of the neuropilin 1 (NRP1) gene and growth, survival, and radio-sensitivity of non-small cell lung carcinoma (NSCLC) cells. 3-[4,5-dimethylthylthiazol-2-yl]-2,5 diphenyltetrazolium broide (MTT) and colony assays were then performed to determine the effect of NRP1 inhibition on the in vitro growth of NSCLC cells. The Annexin V-Fluorescein Isothiocyanate (FITC) apoptosis detection assay was performed to analyse the effect of NRP1 enhancement on apoptosis of NSCLC cells. Transwell invasion and migration assays were employed to examine the metastatic ability of A549 cells post X-ray irradiation. In addition, Western blot assays were carried out to detect the protein level of VEGFR2, PI3K and NF-κB. Finally, to examine the effect of shNRP1 on proliferation and radio-sensitivity in vivo, a subcutaneous tumour formation assay in nude mice was performed. Microvessel density in tumour tissues was assessed by immunohistochemistry. The stable transfected cell line (shNRP1-A549) showed a significant reduction in colony-forming ability and proliferation not only in vitro, but also in vivo. Moreover, shRNA-mediated NRP1 inhibition also significantly enhanced the radio-sensitivity of NSCLC cells both in vitro and in vivo. The over-expression of NRP1 was correlated with growth, survival and radio-resistance of NSCLC cells via the VEGF-PI3K- NF-κB pathway, and NRP1 may be a molecular therapeutic target for gene therapy or radio-sensitization of NSCLC.

  3. 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

  4. Population similarity analysis of indicator bacteria for source prediction of faecal pollution in a coastal lake.

    PubMed

    Ahmed, W; Hargreaves, M; Goonetilleke, A; Katouli, M

    2008-08-01

    Biochemical fingerprinting (BF) databases of 524 enterococci and 571 Escherichia coli isolates and an antibiotic resistance analysis (ARA) database comprising of 380 E. coli isolates from four suspected sources (i.e. dogs, chickens, waterfowls, and human sewage) were developed to predict the sources of faecal pollution in a recreational coastal lake. Twenty water samples representing four sampling episodes were collected from five sites and the enterococci and E. coli population from each site were compared with those of the databases. The degree of similarity between bacterial populations was measured as population similarity (Sp) coefficient. Using the BF-database, bacterial populations of waterfowls showed the highest similarity with the water samples followed by a sewage treatment plant (STP). Higher population similarities were found between samples from STP and water samples especially at two sites (T2 and T3) which were located near the sewerage pipes collecting wastewater from the study area. When using the ARA-database, the highest similarity was found between E. coli populations from STP and water samples at sites T2 and T4. Both faecal indicators and as well as methods predicted human faecal pollution, possibly through leakage from submerged sewerage pipes. The results indicated that the Sp-analysis of faecal indicator bacterial populations from suspected sources and water samples can be used as a simple tool to predict the source(s) of faecal pollution in surface waters.

  5. 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

  6. Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria.

    PubMed

    Zheng, Amy; Panja, Subrata; Woodson, Sarah A

    2016-06-01

    The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram-negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram-positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis, and Staphylococcus aureus were compared using minimal RNAs and fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms. PMID:27049793

  7. Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria.

    PubMed

    Zheng, Amy; Panja, Subrata; Woodson, Sarah A

    2016-06-01

    The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram-negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram-positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis, and Staphylococcus aureus were compared using minimal RNAs and fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms.

  8. Using SWAT, Bacteroidales microbial source tracking markers, and fecal indicator bacteria to predict waterborne pathogen occurrence in an agricultural watershed.

    PubMed

    Frey, Steven K; Topp, Edward; Edge, Thomas; Fall, Claudia; Gannon, Victor; Jokinen, Cassandra; Marti, Romain; Neumann, Norman; Ruecker, Norma; Wilkes, Graham; Lapen, David R

    2013-10-15

    Developing the capability to predict pathogens in surface water is important for reducing the risk that such organisms pose to human health. In this study, three primary data source scenarios (measured stream flow and water quality, modelled stream flow and water quality, and host-associated Bacteroidales) are investigated within a Classification and Regression Tree Analysis (CART) framework for classifying pathogen (Escherichia coli 0157:H7, Salmonella, Campylobacter, Cryptosporidium, and Giardia) presence and absence (P/A) for a 178 km(2) agricultural watershed. To provide modelled data, a Soil Water Assessment Tool (SWAT) model was developed to predict stream flow, total suspended solids (TSS), total N and total P, and fecal indicator bacteria loads; however, the model was only successful for flow and total N and total P simulations, and did not accurately simulate TSS and indicator bacteria transport. Also, the SWAT model was not sensitive to an observed reduction in the cattle population within the watershed that may have resulted in significant reduction in E. coli concentrations and Salmonella detections. Results show that when combined with air temperature and precipitation, SWAT modelled stream flow and total P concentrations were useful for classifying pathogen P/A using CART methodology. From a suite of host-associated Bacteroidales markers used as independent variables in CART analysis, the ruminant marker was found to be the best initial classifier of pathogen P/A. Of the measured sources of independent variables, air temperature, precipitation, stream flow, and total P were found to be the most important variables for classifying pathogen P/A. Results indicate a close relationship between cattle pollution and pathogen occurrence in this watershed, and an especially strong link between the cattle population and Salmonella detections. PMID:24079968

  9. 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

  10. 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.

  11. 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. PMID:26895037

  12. 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

  13. 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.

  14. Sorafenib induces preferential apoptotic killing of a drug- and radio-resistant Hep G2 cells through a mitochondria-dependent oxidative stress mechanism.

    PubMed

    Chiou, Jeng-Fong; Tai, Cheng-Jeng; Wang, Yu-Huei; Liu, Tsan-Zon; Jen, Yee-Min; Shiau, Chia-Yang

    2009-10-01

    Sorafenib (Nexavar, BAY43-9006), a bi-arylurea, is a newly established anti-cancer drug and its functional attribute of cytotoxicity is based on the multi-kinase inhibitory action. Here, we report yet another novel pathway in which sorafenib can induce apoptotic cell death preferentially and efficaciously on an experimentally proven drug- and radio-resistant human Hep G2 cells via a mitochondria-dependent oxidative stress mechanism. A real time confocal imaging assay revealed that sorafenib could rapidly provoke the production of ROS plethorically, mainly concentrating in the mitochondria, albeit substantial amounts of ROS could also be detected in cytosol and nucleus. The rapid production of ROS could simultaneously induce intracellular glutathione (iGSH) depletion. A nearly 90% of iGSH was found to be depleted in 1h period after the cells received the drug treatment. Besides mitochondria, iGSH depletion could also be detected in other cellular compartment including cytoplasm and nucleus. Interestingly, we also demonstrated that sorafenib could trigger mitochondrial Ca(2+) overload. All these events compoundedly serve as the final arbitrator to initiate lethal apoptotic process through the release of cytochrome c and caspase 3/7 activation. Collectively, we provide first evidence here that sorafenib can provoke an alternative pathway for apoptosis induction of Hep G2 cells through a mitochondria-dependent oxidative stress mechanism which is independent of original kinase inhibitory attribute of the drug action. Most importantly, we also demonstrate that sorafenib can effectively eradicate a highly drug- and radio-resistant HCC cells. Thus, our data can provide the basis for a potential applicability of sorafenib in a combined treatment modality.

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

    PubMed

    Akdemir Evrendilek, Gulsun

    2015-06-01

    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. PMID:25764982

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

    PubMed

    Akdemir Evrendilek, Gulsun

    2015-06-01

    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.

  17. 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

  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. 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.

  20. Anaerobic bacteria

    MedlinePlus

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

  1. Spatio-temporal changes in glutathione and thioredoxin redox couples during ionizing radiation-induced oxidative stress regulate tumor radio-resistance.

    PubMed

    Patwardhan, R S; Sharma, D; Checker, R; Thoh, M; Sandur, S K

    2015-10-01

    Ionizing radiation (IR)-induced oxidative stress in tumor cells is effectively managed by constitutive and inducible antioxidant defense systems. This study was initiated to understand the relative contribution of different redox regulatory systems in determining the tumor radio-resistance. In this study, human T-cell lymphoma (Jurkat) cells were exposed to IR (4 Gy) and monitored for the spatio-temporal changes in cellular redox regulatory parameters. We monitored the changes in the levels of reactive oxygen species (ROS) (total, mitochondrial, primary, and secondary), thiols (total, surface, and intracellular), GSH/GSSG ratio, antioxidant enzyme activity viz. thioredoxin (Trx), Trx reductase (TrxR), glutathione peroxidase, and glutathione reductase with respect to time. We have also measured protein glutathionylation. We observed that tumor cells mount a biphasic response after IR exposure which can be divided into early (0-6 h) and late (16-48 h) responses in terms of changes in cellular redox parameters. During early response, constitutively active GSH and Trx systems respond to restore cellular redox balance to pre-exposure levels and help in activation of redox-sensitive transcription factor Nrf-2. During late response, increase in the levels of antioxidants GSH and Trx rescue cells against IR-mediated damage. We observed that disruption of either glutathione or thioredoxin metabolism led to partial impairment of ability of cells to survive against IR-induced damage. But simultaneous disruption of both the pathways significantly increased radio sensitivity of Jurkat cells. This highlighted the importance of these two antioxidant pathways in regulating redox homeostasis under conditions of IR-induced oxidative stress. PMID:26021764

  2. Spatio-temporal changes in glutathione and thioredoxin redox couples during ionizing radiation-induced oxidative stress regulate tumor radio-resistance.

    PubMed

    Patwardhan, R S; Sharma, D; Checker, R; Thoh, M; Sandur, S K

    2015-10-01

    Ionizing radiation (IR)-induced oxidative stress in tumor cells is effectively managed by constitutive and inducible antioxidant defense systems. This study was initiated to understand the relative contribution of different redox regulatory systems in determining the tumor radio-resistance. In this study, human T-cell lymphoma (Jurkat) cells were exposed to IR (4 Gy) and monitored for the spatio-temporal changes in cellular redox regulatory parameters. We monitored the changes in the levels of reactive oxygen species (ROS) (total, mitochondrial, primary, and secondary), thiols (total, surface, and intracellular), GSH/GSSG ratio, antioxidant enzyme activity viz. thioredoxin (Trx), Trx reductase (TrxR), glutathione peroxidase, and glutathione reductase with respect to time. We have also measured protein glutathionylation. We observed that tumor cells mount a biphasic response after IR exposure which can be divided into early (0-6 h) and late (16-48 h) responses in terms of changes in cellular redox parameters. During early response, constitutively active GSH and Trx systems respond to restore cellular redox balance to pre-exposure levels and help in activation of redox-sensitive transcription factor Nrf-2. During late response, increase in the levels of antioxidants GSH and Trx rescue cells against IR-mediated damage. We observed that disruption of either glutathione or thioredoxin metabolism led to partial impairment of ability of cells to survive against IR-induced damage. But simultaneous disruption of both the pathways significantly increased radio sensitivity of Jurkat cells. This highlighted the importance of these two antioxidant pathways in regulating redox homeostasis under conditions of IR-induced oxidative stress.

  3. Multi-Target QSAR Approaches for Modeling Protein Inhibitors. Simultaneous Prediction of Activities Against Biomacromolecules Present in Gram-Negative Bacteria.

    PubMed

    Speck-Planche, Alejandro; Cordeiro, M N D S

    2015-01-01

    Drug discovery is aimed at finding therapeutic agents for the treatment of many diverse diseases and infections. However, this is a very slow an expensive process, and for this reason, in silico approaches are needed to rationalize the search for new molecular entities with desired biological profiles. Models focused on quantitative structure-activity relationships (QSAR) have constituted useful complementary tools in medicinal chemistry, allowing the virtual predictions of dissimilar pharmacological activities of compounds. In the last 10 years, multi-target (mt) QSAR models have been reported, representing great advances with respect to those models generated from classical approaches. Thus, mt- QSAR models can simultaneously predict activities against different biological targets (proteins, microorganisms, cell lines, etc.) by using large and heterogeneous datasets of chemicals. The present review is devoted to discuss the most promising mt-QSAR models, particularly those developed for the prediction of protein inhibitors. We also report the first multi-tasking QSAR (mtk-QSAR) model for simultaneous prediction of inhibitors against biomacromolecules (specifically proteins) present in Gram-negative bacteria. This model allowed us to consider both different proteins and multiple experimental conditions under which the inhibitory activities of the chemicals were determined. The mtk-QSAR model exhibited accuracies higher than 98% in both training and prediction sets, also displaying a very good performance in the classification of active and inactive cases that depended on the specific elements of the experimental conditions. The physicochemical interpretations of the molecular descriptors were also analyzed, providing important insights regarding the molecular patterns associated with the appearance/enhancement of the inhibitory potency. PMID:25961517

  4. 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

  5. Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation.

    PubMed

    Beaume, Nicolas; Pathak, Rajiv; Yadav, Vinod Kumar; Kota, Swathi; Misra, Hari S; Gautam, Hemant K; Chowdhury, Shantanu

    2013-01-01

    A remarkable number of guanine-rich sequences with potential to adopt non-canonical secondary structures called G-quadruplexes (or G4 DNA) are found within gene promoters. Despite growing interest, regulatory role of quadruplex DNA motifs in intrinsic cellular function remains poorly understood. Herein, we asked whether occurrence of potential G4 (PG4) DNA in promoters is associated with specific function(s) in bacteria. Using a normalized promoter-PG4-content (PG4(P)) index we analysed >60,000 promoters in 19 well-annotated species for (a) function class(es) and (b) gene(s) with enriched PG4(P). Unexpectedly, PG4-associated functional classes were organism specific, suggesting that PG4 motifs may impart specific function to organisms. As a case study, we analysed radioresistance. Interestingly, unsupervised clustering using PG4(P) of 21 genes, crucial for radioresistance, grouped three radioresistant microorganisms including Deinococcus radiodurans. Based on these predictions we tested and found that in presence of nanomolar amounts of the intracellular quadruplex-binding ligand N-methyl mesoporphyrin (NMM), radioresistance of D. radiodurans was attenuated by ~60%. In addition, important components of the RecF recombinational repair pathway recA, recF, recO, recR and recQ genes were found to harbour promoter-PG4 motifs and were also down-regulated in presence of NMM. Together these results provide first evidence that radioresistance may involve G4 DNA-mediated regulation and support the rationale that promoter-PG4s influence selective functions. PMID:23161683

  6. 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.

  7. 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)

  8. 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

  9. 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

  10. 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.

  11. The Value of Combining Blood Culture and SeptiFast Data for Predicting Complicated Bloodstream Infections Caused by Gram-Positive Bacteria or Candida Species

    PubMed Central

    Marín, Mercedes; Kestler, Martha; Alcalá, Luis; Rodriguez-Créixems, Marta; Bouza, Emilio

    2013-01-01

    Management of complicated bloodstream infections requires more aggressive treatment than uncomplicated bloodstream infections. We assessed the value of follow-up blood culture in bloodstream infections caused by Staphylococcus aureus, Enterococcus spp., Streptococcus spp., and Candida spp. and studied the value of persistence of DNA in blood (using SeptiFast) for predicting complicated bloodstream infections. Patients with bloodstream infections caused by these microorganisms were enrolled prospectively. After the first positive blood culture, samples were obtained every third day to perform blood culture and SeptiFast analyses simultaneously. Patients were followed to detect complicated bloodstream infection. The study sample comprised 119 patients. One-third of the patients developed complicated bloodstream infections. The values of persistently positive tests to predict complicated bloodstream infections were as follows: SeptiFast positive samples (sensitivity, 56%; specificity, 79.5%; positive predictive value, 54%; negative predictive value, 80.5%; accuracy, 72.3%) and positive blood cultures (sensitivity, 30.5%; specificity, 92.8%; positive predictive value, 64%; negative predictive value, 75.5%; accuracy, 73.9%). Multivariate analysis showed that patients with a positive SeptiFast result between days 3 and 7 had an almost 8-fold-higher risk of developing a complicated bloodstream infection. In S. aureus, the combination of both techniques to exclude endovascular complications was significantly better than the use of blood culture alone. We obtained a score with variables selected by the multivariate model. With a cutoff of 7, the negative predictive value for complicated bloodstream infection was 96.6%. Patients with a positive SeptiFast result between days 3 and 7 after a positive blood culture have an almost 8-fold-higher risk of developing complicated bloodstream infections. A score combining clinical data with the SeptiFast result may improve the

  12. Lipoprotein sorting in bacteria.

    PubMed

    Okuda, Suguru; Tokuda, Hajime

    2011-01-01

    Bacterial lipoproteins are synthesized as precursors in the cytoplasm and processed into mature forms on the cytoplasmic membrane. A lipid moiety attached to the N terminus anchors these proteins to the membrane surface. Many bacteria are predicted to express more than 100 lipoproteins, which play diverse functions on the cell surface. The Lol system, composed of five proteins, catalyzes the localization of Escherichia coli lipoproteins to the outer membrane. Some lipoproteins play vital roles in the sorting of other lipoproteins, lipopolysaccharides, and β-barrel proteins to the outer membrane. On the basis of results from biochemical, genetic, and structural studies, we discuss the biogenesis of lipoproteins in bacteria, their importance in cellular functions, and the molecular mechanisms underlying efficient sorting of hydrophobic lipoproteins to the outer membrane through the hydrophilic periplasm. PMID:21663440

  13. Oxasetin from Lophiostoma sp. of the Baltic Sea: identification, in silico binding mode prediction and antibacterial evaluation against fish pathogenic bacteria.

    PubMed

    Shushni, Muftah Ali M; Azam, Faizul; Lindequist, Ulrike

    2013-09-01

    Because of the evolving resistance of microorganisms against existing antibiotics, there is an increasing need for new ones, not only in human, but also in veterinary medicine. The dichloromethane extract of a fungal strain of the genus Lophiostoma, isolated from driftwood collected from the coast of the Baltic Sea, displayed antibacterial activity against some fish pathogenic bacteria. Ergosterol epoxide (1), cerebroside C (2) and oxasetin (3) were isolated from the extract and structurally elucidated on the basis of spectroscopic data and chemical evidence. Compound 3 exhibited in vitro activity against Vibrio anguillarum, Flexibacter maritimus and Pseudomonas anguilliseptica with minimal inhibitory concentrations of 12.5, 12.5 and 6.25 microg/mL, respectively. Molecular docking studies were performed to understand the interaction of compound 3 with different macromolecular targets. Analysis of in silico results, together with experimental findings, validates the antimicrobial activity associated with compound 3. These results may be exploited in lead optimization and development of potent antibacterial agents. PMID:24273851

  14. 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

  15. Magnetic bacteria against MIC

    SciTech Connect

    Javaherdashti, R.

    1997-12-01

    In this article, it is suggested to use the sensitivity of magnetotactic bacteria to changes of magnetic field direction and the natural ability of this bacteria in rapid growth during relatively short time intervals against corrosion-enhancing bacteria and especially sulfate-reducing bacteria. If colonies of sulfate-reducing bacteria could be packed among magnetotactic bacteria, then, by applying sufficiently powerful magnetic field (about 0.5 gauss), all of these bacteria (magnetic and non-magnetic) will be oriented towards an Anti-bacteria agent (oxygen or biocide). So, Microbiologically-Influenced Corrosion in the system would be controlled to a large extent.

  16. 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)

  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. Intracellular Bacteria in Protozoa

    NASA Astrophysics Data System (ADS)

    Görtz, Hans-Dieter; Brigge, Theo

    Intracellular bacteria in humans are typically detrimental, and such infections are regarded by the patients as accidental and abnormal. In protozoa it seems obvious that many bacteria have coevolved with their hosts and are well adapted to the intracellular way of life. Manifold interactions between hosts and intracellular bacteria are found, and examples of antibacterial resistance of unknown mechanisms are observed. The wide diversity of intracellular bacteria in protozoa has become particularly obvious since they have begun to be classified by molecular techniques. Some of the bacteria are closely related to pathogens; others are responsible for the production of toxins.

  1. 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.

  2. 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

  3. 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.

  4. 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. PMID:25109196

  5. Bleach vs. Bacteria

    MedlinePlus

    ... Inside Life Science > Bleach vs. Bacteria Inside Life Science View All Articles | Inside Life Science Home Page Bleach vs. Bacteria By Sharon Reynolds ... For Proteins, Form Shapes Function This Inside Life Science article also appears on LiveScience . Learn about related ...

  6. 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

  7. 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.

  8. 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

  9. 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. PMID:27340451

  10. [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. PMID:19350162

  11. Bacteria subsisting on antibiotics.

    PubMed

    Dantas, Gautam; Sommer, Morten O A; Oluwasegun, Rantimi D; Church, George M

    2008-04-01

    Antibiotics are a crucial line of defense against bacterial infections. Nevertheless, several antibiotics are natural products of microorganisms that have as yet poorly appreciated ecological roles in the wider environment. We isolated hundreds of soil bacteria with the capacity to grow on antibiotics as a sole carbon source. Of 18 antibiotics tested, representing eight major classes of natural and synthetic origin, 13 to 17 supported the growth of clonal bacteria from each of 11 diverse soils. Bacteria subsisting on antibiotics are surprisingly phylogenetically diverse, and many are closely related to human pathogens. Furthermore, each antibiotic-consuming isolate was resistant to multiple antibiotics at clinically relevant concentrations. This phenomenon suggests that this unappreciated reservoir of antibiotic-resistance determinants can contribute to the increasing levels of multiple antibiotic resistance in pathogenic bacteria. PMID:18388292

  12. 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.

  13. [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.

  14. 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

  15. 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.

  16. Anaerobic bacteria in otitis media.

    PubMed

    Fulghum, R S; Daniel, H J; Yarborough, J G

    1977-01-01

    Anaerobic bacteria, Peptostrepotococcus intermedius and Propionibacterium acnes, were found in mixed culture specimens from four to ten tested cases of chronic secretory otitis media. These anaerobic bacteria were in a mixed infection flora with aerobic bacteria most often Staphylococcus epidermidis and Cornybacterium sp. which do not fit any established species. The findings of anaerobic bacteria in otitis media is consistent with the sporadic report of the involvement of anaerobic bacteria in otitis media in the literature since 1898.

  17. 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.

  18. 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

  19. 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

  20. Sterol Synthesis in Diverse Bacteria.

    PubMed

    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

  1. Sterol Synthesis in Diverse Bacteria.

    PubMed

    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

  2. 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.

  3. 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. PMID:26384864

  4. 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

  5. Communication among Oral Bacteria

    PubMed Central

    Kolenbrander, Paul E.; Andersen, Roxanna N.; Blehert, David S.; Egland, Paul G.; Foster, Jamie S.; Palmer, Robert J.

    2002-01-01

    Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities. PMID:12209001

  6. 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...

  7. 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)

  8. 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.

  9. 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.

  10. 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.

  11. Bacteria, food, and cancer

    PubMed Central

    Rooks, Michelle G.

    2011-01-01

    Gut microbes are essential components of the human organism—helping us metabolize food into energy, produce micronutrients, and shape our immune systems. Having a particular pattern of gut microbes is also increasingly being linked to medical conditions including obesity, inflammatory bowel disease, and diabetes. Recent studies now indicate that our resident intestinal bacteria may also play a critical role in determining one's risk of developing cancer, ranging from protection against cancer to promoting its initiation and progression. Gut bacteria are greatly influenced by diet and in this review we explore evidence that they may be the missing piece that explains how dietary intake influences cancer risk, and discuss possible prevention and treatment strategies. PMID:21876723

  12. 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.

  13. Stress responses of bacteria.

    PubMed

    Marles-Wright, Jon; Lewis, Richard J

    2007-12-01

    Bacteria, irrespective of natural habitat, are exposed to constant fluctuations in their growth conditions. Consequently they have developed sophisticated responses, modulated by the re-modelling of protein complexes and by phosphorylation-dependent signal transduction systems, to adapt to and to survive a variety of insults. Ultimately these signalling systems affect transcriptional regulons either by activating an alternative sigma factor subunit of RNA polymerase, for example, sigma E (sigma(E)) of Escherichia coli and sigma B (sigma(B)) and sigma F (sigma(F)) in Bacillus subtilis or by activating DNA-binding two-component response regulators. Recent structure determinations, and systems biology analysis of key regulators in well-characterised stress-responsive pathways, illustrate conserved and novel mechanisms in these representative model bacteria.

  14. Bacteria in Confined Spaces

    NASA Astrophysics Data System (ADS)

    Wilking, Connie; Weitz, David

    2010-03-01

    Bacterial cells can display differentiation between several developmental pathways, from planktonic to matrix-producing, depending upon the colony conditions. We study the confinement of bacteria in hydrogels as well as in liquid-liquid double emulsion droplets and observe the growth and morphology of these colonies as a function of time and environment. Our results can give insight into the behavior of bacterial colonies in confined spaces that can have applications in the areas of food science, cosmetics, and medicine.

  15. 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

  16. 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.

  17. 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. PMID:26921555

  18. 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

  19. Dynamics of swimming bacteria at complex interfaces

    NASA Astrophysics Data System (ADS)

    Lopez, Diego; Lauga, Eric

    2014-07-01

    Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and counter-clockwise (CCW) below a free surface. Recent experimental investigations showed that complex physicochemical processes at the nearby surface could lead to a change in the direction of rotation, both at solid surfaces absorbing slip-inducing polymers and interfaces covered with surfactants. Motivated by these results, we use a far-field hydrodynamic model to predict the kinematics of swimming near three types of interfaces: clean fluid-fluid interface, slipping rigid wall, and a fluid interface covered by incompressible surfactants. Representing the helical swimmer by a superposition of hydrodynamic singularities, we first show that in all cases the surfaces reorient the swimmer parallel to the surface and attract it, both of which are a consequence of the Stokes dipole component of the swimmer flow field. We then show that circular motion is induced by a higher-order singularity, namely, a rotlet dipole, and that its rotation direction (CW vs. CCW) is strongly affected by the boundary conditions at the interface and the bacteria shape. Our results suggest thus that the hydrodynamics of complex interfaces provide a mechanism to selectively stir bacteria.

  20. 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

  1. Nitrogen control in bacteria.

    PubMed

    Merrick, M J; Edwards, R A

    1995-12-01

    Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn. PMID:8531888

  2. Beneficial bacteria inhibit cachexia.

    PubMed

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

    2016-03-15

    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

  3. 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.

  4. Nitrogen control in bacteria.

    PubMed Central

    Merrick, M J; Edwards, R A

    1995-01-01

    Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn. PMID:8531888

  5. 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

    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

  6. 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

  7. 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.

  8. Programmed Death in Bacteria

    PubMed Central

    Lewis, Kim

    2000-01-01

    Programmed cell death (PCD) in bacteria plays an important role in developmental processes, such as lysis of the mother cell during sporulation of Bacillus subtilis and lysis of vegetative cells in fruiting body formation of Myxococcus xanthus. The signal transduction pathway leading to autolysis of the mother cell includes the terminal sporulation sigma factor EςK, which induces the synthesis of autolysins CwlC and CwlH. An activator of autolysin in this and other PCD processes is yet to be identified. Autolysis plays a role in genetic exchange in Streptococcus pneumoniae, and the gene for the major autolysin, lytA, is located in the same operon with recA. DNA from lysed cells is picked up by their neighbors and recombined into the chromosome by RecA. LytA requires an unknown activator controlled by a sensory kinase, VncS. Deletion of vncS inhibits autolysis and also decreases killing by unrelated antibiotics. This observation suggests that PCD in bacteria serves to eliminate damaged cells, similar to apoptosis of defective cells in metazoa. The presence of genes affecting survival without changing growth sensitivity to antibiotics (vncS, lytA, hipAB, sulA, and mar) indicates that bacteria are able to control their fate. Elimination of defective cells could limit the spread of a viral infection and donate nutrients to healthy kin cells. An altruistic suicide would be challenged by the appearance of asocial mutants without PCD and by the possibility of maladaptive total suicide in response to a uniformly present lethal factor or nutrient depletion. It is proposed that a low rate of mutation serves to decrease the probability that asocial mutants without PCD will take over the population. It is suggested that PCD is disabled in persistors, rare cells that are resistant to killing, to ensure population survival. It is suggested that lack of nutrients leads to the stringent response that suppresses PCD, producing a state of tolerance to antibiotics, allowing cells to

  9. Trail following by gliding bacteria.

    PubMed Central

    Burchard, R P

    1982-01-01

    Slime trails, which are deposited on surfaces by gliding bacteria and which serve as preferential pathways for gliding motility, were tested for the species specificity of their support of movement. Among the pairs of bacteria tested, a variety of gliding bacteria and a flagellated bacterium moved along trails of unrelated species. Thus, the trails did not serve as pheromones. Rather, they may have guided gliding elasticotactically. Some biological implications of this finding are considered. Images PMID:6811562

  10. Bacteriophages of methanotrophic bacteria

    SciTech Connect

    Tyutikow, F.M.; Bespalova, I.A.; Rebentish, B.A.; Aleksandrushkina, N.N.; Krivisky, A.S.

    1980-10-01

    Bacteriophages of methanotrophic bacteria have been found in 16 out of 88 studied samples (underground waters, pond water, soil, gas and oil installation waters, fermentor cultural fluids, bacterial paste, and rumen of cattle) taken in different geographic zones of the Soviet Union. Altogether, 23 phage strains were isolated. By fine structure, the phages were divided into two types (with very short or long noncontractile tails); by host range and serological properties, they fell into three types. All phages had guanine- and cytosine-rich double-stranded deoxyribonucleic acid consisting of common nitrogen bases. By all of the above-mentioned properties, all phages within each of the groups were completely identical to one another, but differed from phages of other groups.

  11. Kin Recognition in Bacteria.

    PubMed

    Wall, Daniel

    2016-09-01

    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. PMID:27359217

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

    PubMed

    Froelich, Brett A; Noble, Rachel T

    2016-03-01

    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

  13. 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.

  14. 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.

  15. Multilocus sequence typing of bacteria.

    PubMed

    Maiden, Martin C J

    2006-01-01

    Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.

  16. Metabolic engineering of bacteria.

    PubMed

    Kumar, Ravi R; Prasad, Satish

    2011-07-01

    Yield and productivity are critical for the economics and viability of a bioprocess. In metabolic engineering the main objective is the increase of a target metabolite production through genetic engineering. Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the production of a certain substance. In the last years, the development of recombinant DNA technology and other related technologies has provided new tools for approaching yields improvement by means of genetic manipulation of biosynthetic pathway. Industrial microorganisms like Escherichia coli, Actinomycetes, etc. have been developed as biocatalysts to provide new or to optimize existing processes for the biotechnological production of chemicals from renewable plant biomass. The factors like oxygenation, temperature and pH have been traditionally controlled and optimized in industrial fermentation in order to enhance metabolite production. Metabolic engineering of bacteria shows a great scope in industrial application as well as such technique may also have good potential to solve certain metabolic disease and environmental problems in near future. PMID:22754024

  17. 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

  18. Marine bacteria exhibit a bipolar distribution.

    PubMed

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

    2013-02-01

    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.

  19. 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...

  20. 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.

  1. Bacteria-mediated disease therapy.

    PubMed

    Yu, Hao

    2011-12-01

    Laboratory bacteria have been model systems for studying gene function or developing molecular biotechnologies; industrial bacteria have been used to produce drugs, foods, fuel etc.; while pathogenic bacteria have been the subject of infectious diseases studies with aim of controlling them. Recently, with our increasing knowledge in molecular biology, bacterial genetics, and immunology, bacteria have gained increased interest in therapeutic applications. This review will summarize recent advances toward applying bacteria in treatment of diseases, such as inflammatory disease, cancer, and virus infection. Probiotics have long been appreciated for their immunomodulatory effect, which are discussed in the anti-inflammatory section. Anaerobic bacteria have been applied for destructing tumor cells or used as a magic bullet to specifically deliver therapeutic agents to tumor tissue. Examples and strategies of applying those tumor-targeting bacteria are discussed in the antitumor section. Finally, the pioneer study of applying Salmonella in delivering RNase P that was specifically engineered to target essential mRNAs of virus is summarized.

  2. 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

  3. Caenorhabditis elegans responses to bacteria from its natural habitats.

    PubMed

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

    2016-07-01

    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

  4. 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

  5. Intermittent filtration of bacteria and colloids in porous media

    NASA Astrophysics Data System (ADS)

    Auset, Maria; Keller, Arturo A.; Brissaud, FrançOis; Lazarova, Valentina

    2005-09-01

    Intermittent filtration through porous media used for water and wastewater treatment can achieve high pathogen and colloid removal efficiencies. To predict the removal of bacteria, the effects of cyclic infiltration and draining events (transient unsaturated flow) were investigated. Using physical micromodels, we visualized the intermittent transport of bacteria and other colloids in unsaturated porous media. Column experiments provided quantitative measurements of the phenomena observed at the pore scale. Tagged Escherichia coli and a conservative tracer (NaI) were introduced in an initial pulse into a 1.5 m sand column. Subsequent hydraulic flushes without tagged bacteria or tracer were repeated every 4 hours for the next 4 days, during which outflow concentrations were monitored. Breakthrough behavior between colloids and dissolved tracer differed significantly, reflecting the differences in transport processes. Advancement of the wetting front remobilized bacteria which were held in thin water films, attached to the air-water interface (AWI), or entrapped in stagnant pore water between gas bubbles. In contrast, the tracer was only remobilized by diffusion from immobile to mobile water. Remobilization led to successive concentration peaks of bacteria and tracer in the effluent but with significant temporal differences. Observations at the pore-scale indicated that the colloids were essentially irreversibly attached to the solid-water interface, which explained to some extent the high removal efficiency of microbes in the porous media. Straining, cluster filtration, cell lysis, protozoa grazing, and bacteriophage parasitism could also contribute to the removal efficiency of bacteria.

  6. 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...

  7. 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.

  8. Magnetosome biogenesis in magnetotactic bacteria.

    PubMed

    Uebe, René; Schüler, Dirk

    2016-09-13

    Magnetotactic bacteria derive their magnetic orientation from magnetosomes, which are unique organelles that contain nanometre-sized crystals of magnetic iron minerals. Although these organelles have evident potential for exciting biotechnological applications, a lack of genetically tractable magnetotactic bacteria had hampered the development of such tools; however, in the past decade, genetic studies using two model Magnetospirillum species have revealed much about the mechanisms of magnetosome biogenesis. In this Review, we highlight these new insights and place the molecular mechanisms of magnetosome biogenesis in the context of the complex cell biology of Magnetospirillum spp. Furthermore, we discuss the diverse properties of magnetosome biogenesis in other species of magnetotactic bacteria and consider the value of genetically 'magnetizing' non-magnetotactic bacteria. Finally, we discuss future prospects for this highly interdisciplinary and rapidly advancing field. PMID:27620945

  9. 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. PMID:8879414

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. [Genetic resources of nodule bacteria].

    PubMed

    Rumiantseva, M L

    2009-09-01

    Nodule bacteria (rhizobia) form highly specific symbiosis with leguminous plants. The efficiency of accumulation of biological nitrogen depends on molecular-genetic interaction between the host plant and rhizobia. Genetic characteristics of microsymbiotic strains are crucial in developing highly productive and stress-resistant symbiotic pairs: rhizobium strain-host plant cultivar (species). The present review considers the issue of studying genetic resources of nodule bacteria to identify genes and their blocks, responsible for the ability of rhizobia to form highly effective symbiosis in various agroecological conditions. The main approaches to investigation of intraspecific and interspecific genetic and genomic diversity of nodule bacteria are considered, from MLEE analysis to the recent methods of genomic DNA analysis using biochips. The data are presented showing that gene centers of host plants are centers of genetic diversification of nodule bacteria, because the intraspecific polymorphism of genetic markers of the core and the accessory rhizobial genomes is extremely high in them. Genotypic features of trapped and nodule subpopulations of alfalfa nodule bacteria are discussed. A survey of literature showed that the genomes of natural strains in alfalfa gene centers exhibit significant differences in genes involved in control of metabolism, replication, recombination, and the formation of defense response (hsd genes). Natural populations of rhizobia are regarded as a huge gene pool serving as a source of evolutionary innovations.

  20. 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.

  1. 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.

  2. Kinetics of Thermal Death of Bacteria

    PubMed Central

    Moats, William A.

    1971-01-01

    Experimental observations on thermal injury and death of bacteria in the stationary phase can be explained by assuming that death results from inactivation of (XL) of N critical sites. It is assumed: (i) that inactivation of individual sites occurs at random and follows first-order kinetics, (ii) that the critical sites are identical and of equal heat resistance, and (iii) the bacterial population is homogeneous in heat resistance. A method is described for calculating k (the rate constant for inactivation of individual sites), N (sites per cell), and XL (the number which must be inactivated to cause death under the experimental conditions used) from experimental data. Theoretical curves calculated by using this model are identical with experimental curves, providing support for the assumptions used. Calculated values of N and XL were 130 and 21.7 for Pseudomonas viscosa and 175 and 2.7 for Salmonella anatum. There is considerable uncertainty in the absolute values of N, but they are probably > 100. It is predicted that XL will vary depending on the recovery medium used after heating. This theory is consistent with all experimental observations on thermal injury and death of bacteria. PMID:4925119

  3. 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.

  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. Radioresistant Bacteria Came From Mars?

    NASA Astrophysics Data System (ADS)

    Pavlov, A.; Kalinin, V.; Konstantinov, A.; Shelegedin, V.

    We propose that the radioresistant bacteria (i.e. Deinococcus radiodurans) has been originated on Mars. This bacteria possesses an ability which should have been ab- solutely "unnecessary" in the Earth environment. It can survive very high doses of the ionizing radiation. Our experiments demonstrate that different kinds of non- radioresistant bacteria are able to develop very high radioresistance ability also. To develop radioresistance we exposed different bacterial cultures to several dozens of cycles of high irradiation. Therefore, radioresistance is not a result of some early spontaneous bacterial mutation but rather a consequence of the very specific plane- tary environment. Polar regions of Mars are the most probable (if not the only) place in the Solar System for such a periodical high-dosage irradiation process. We pro- pose a plausible scenario of where and when such an adaptation process could have taken place and also discuss indirect arguments of the Martian origin of Deinococcus Radiodurans based on their specific genetic structure.

  8. 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. PMID:27263015

  9. Adaptation, Bacteria and Maxwell's Demons

    NASA Astrophysics Data System (ADS)

    Galajda, Peter; Keymer, Juan E.; Austin, Robert H.

    2007-03-01

    We propose a method to study the adaptation of bacterial populations with an asymmetric wall of Maxwell Demon openings. A Maxwell Demon opening is a funnel which is easier to enter than to leave. The interaction of swimming cells with such a Maxwell Demon Wall results in a population density separation, in apparent (but not real) violation of the Second Law of Thermodynamics, as we will show. Bacteria can be exposed to spatial challenges in order to move to e. g. higher food levels. The question we address in these experiments is: do the bacteria adapt and overcome the Maxwell Demon Wall?

  10. Molecular adaptations in Antarctic fish and bacteria

    NASA Astrophysics Data System (ADS)

    Russo, Roberta; Riccio, Alessia; di Prisco, Guido; Verde, Cinzia; Giordano, Daniela

    2010-08-01

    Marine organisms, living in the cold waters of the Southern Ocean, are exposed to high oxygen concentrations. Cold-adapted organisms have developed networks of defence mechanisms to protect themselves against oxidative stress. The dominant suborder Notothenioidei of the Southern Ocean is one of the most interesting models, within vertebrates, to study the evolutionary biological responses to extreme environment. Within bacteria, the psychrophilic Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 gives the opportunity to explore the cellular strategies adopted in vivo by cold-adapted microorganisms to cope with cold and high oxygen concentration. Understanding the molecular mechanisms underlying how a range of Antarctic organisms have responded to climate change in the past will enable predictions as to how they and other species will adapt to global climate change, in terms of physiological function, distribution patterns and ecosystem balance.

  11. 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.

  12. 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. PMID:22423993

  13. 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

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

    PubMed

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

    2016-02-01

    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.

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

    PubMed

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

    2016-02-01

    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. 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)

  17. 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

  18. 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.

  19. Heteropolysaccharides from lactic acid bacteria.

    PubMed

    De Vuyst, L; Degeest, B

    1999-04-01

    Microbial exopolysaccharides are biothickeners that can be added to a wide variety of food products, where they serve as viscosifying, stabilizing, emulsifying or gelling agents. Numerous exopolysaccharides with different composition, size and structure are synthesized by lactic acid bacteria. The heteropolysaccharides from both mesophilic and thermophilic lactic acid bacteria have received renewed interest recently. Structural analysis combined with rheological studies revealed that there is considerable variation among the different exopolysaccharides; some of them exhibit remarkable thickening and shear-thinning properties and display high intrinsic viscosities. Hence, several slime-producing lactic acid bacterium strains and their biopolymers have interesting functional and technological properties, which may be exploited towards different products, in particular, natural fermented milks. However, information on the biosynthesis, molecular organization and fermentation conditions is rather scarce, and the kinetics of exopolysaccharide formation are poorly described. Moreover, the production of exopolysaccharides is low and often unstable, and their downstream processing is difficult. This review particularly deals with microbiological, biochemical and technological aspects of heteropolysaccharides from, and their production by, lactic acid bacteria. The chemical composition and structure, the biosynthesis, genetics and molecular organization, the nutritional and physiological aspects, the process technology, and both food additive and in situ applications (in particular in yogurt) of heterotype exopolysaccharides from lactic acid bacteria are described. Where appropriate, suggestions are made for strain improvement, enhanced productivities and advanced modification and production processes (involving enzyme and/or fermentation technology) that may contribute to the economic soundness of applications with this promising group of biomolecules.

  20. 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. PMID:286720

  1. Photosynthetic reaction centers in bacteria

    SciTech Connect

    Norris, J.R. Univ. of Chicago, IL ); Schiffer, M. )

    1990-07-30

    The photochemistry of photosynthesis begins in complexes called reaction centers. These have become model systems to study the fundamental process by which plants and bacteria convert and store solar energy as chemical free energy. In green plants, photosynthesis occurs in two systems, each of which contains a different reaction center, working in series. In one, known as photosystem 1, oxidized nicotinamide adenine dinucleotide phosphate (NADP[sup +]) is reduced to NADPH for use in a series of dark reactions called the Calvin cycle, named for Nobel Laureate Melvin Calvin, by which carbon dioxide is converted into useful fuels such as carbohydrates and sugars. In the other half of the photosynthetic machinery of green plants, called photosystem 2, water is oxidized to produce molecular oxygen. A different form of photosynthesis occurs in photosynthetic bacteria, which typically live at the bottom of ponds and feed on organic debris. Two main types of photosynthetic bacteria exist: purple and green. Neither type liberates oxygen from water. Instead, the bacteria feed on organic media or inorganic materials, such as sulfides, which are easier to reduce or oxidize than carbon dioxide or water. Perhaps in consequence, their photosynthetic machinery is simpler than that of green, oxygen-evolving plants and their primary photochemistry is better understood.

  2. 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.

  3. Marine bacteria which produce tetrodotoxin.

    PubMed Central

    Simidu, U; Noguchi, T; Hwang, D F; Shida, Y; Hashimoto, K

    1987-01-01

    A number of type strains of marine bacteria, including members of the family Vibrionaceae, were cultured and examined for tetrodotoxin productivity by high-performance liquid chromatography and gas chromatography-mass spectrometry. Most of the Vibrionaceae strains produced tetrodotoxin, anhydrotetrodotoxin, or both. PMID:3310884

  4. 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.

  5. 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)

  6. Survival of bacteria in carcasses.

    PubMed

    Gill, C O; Penney, N

    1979-04-01

    Bacteria injected into the bloodstream of guinea pigs shortly before death decreased in number in carcass tissues for about 1 h after death. If initial bacterial numbers were sufficiently low, all bacteria were eliminated, and carcass tissues were sterile 24 h after death. Carcass tissue sterility was maintained with an initial density of Clostridium perfringens or Salmonella typhimurium of 20 cells per g or with an initial density of the other species examined of several hundred cells per gram. With larger numbers of strict and facultative anaerobes, growth commenced after 3 h in carcasses incubated at 30 degrees C. Spores of C. perfringens were killed over the same period as vegetative cells, but growth did not commence until 8 h after death. Bactericidal activity in carcass tissues must therefore be taken into account in evaluating the significance of reports of deep-tissue contamination of carcasses from meat animals.

  7. 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).

  8. Viability of bacteria in peatlands

    NASA Astrophysics Data System (ADS)

    Bogdanova, O. Yu.; Golovchenko, A. V.; Lysak, L. V.; Glukhova, T. V.; Zvyagintsev, D. G.

    2014-04-01

    The viability of bacteria in oligotrofic bogs and fens was determined by the luminescent microscopy method with the help of a two-component fluorescent dye (L7012 LIVE/DEAD). Living bacterial cells were found in the entire peat profiles. Their portion was maximal (up to 60%) in the upper layers and did not exceed 25% in the lower layers. The portion of dead bacterial cells varied from 3 to 19%, and dormant cells constituted 25 to 95% of the total number of bacterial cells. The numbers of dormant cells increased down the profiles irrespectively of the peat type. The portion of nanoforms did not exceed 5% of the total. The cells of the nanoforms, unlike the bacteria of typical sizes, were characterized by their high viability (93-98%).

  9. 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.

  10. 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.

  11. 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.

  12. Sand Beach Bacteria: Enumeration and Characterization

    PubMed Central

    Khiyama, H. M.; Makemson, J. C.

    1973-01-01

    Bacteria in the water-saturated sand of a relatively unpolluted sand beach were enumerated by direct microscope and viable counting. The number of interstitial bacteria was estimated to be a significant fraction of the total number of bacteria present. Three hundred sixty-two strains were isolated and submitted to cultural and biochemical tests. Fermentational abilities and the production of indole suggested that a significant number of these bacteria were symbiotically associated with resident metazoans. PMID:4356458

  13. 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.

  14. 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

  15. Enteric bacteria: friend or foe?

    PubMed

    Batt, R M; Rutgers, H C; Sancak, A A

    1996-06-01

    The normal gastrointestinal tract contains an enormous number of aerobic and anaerobic bacteria which normally enjoy a symbiotic relationship with the host but can have adverse effects with local and systemic consequences. The small intestine constitutes a zone of transition between the sparsely populated stomach and the luxuriant bacterial flora of the colon. Regulation of the intestinal flora depends on complex interactions between many factors including secretion of gastric acid, intestinal motility, biliary and pancreatic secretions, local immunity, the surface glycocalyx and mucus layer, and diet. Microbial interactions are also important, and can involve alterations in redox potential, substrate depletion and production of substances such as bacteriocins that inhibit bacterial growth. The beneficial effect of the normal enteric flora include the competitive exclusion of potentially pathogenic organisms, and the production of nutrients such as short-chain fatty acids (which represent an important energy source for the colonic mucosa) and vitamins. Detrimental effects of the enteric flora include competition for calories and essential nutrients, particularly by bacteria located in the small intestine, and a capacity to damage the mucosa, in some circumstances causing or contributing to inflammatory bowel disease. These problems can be accentuated by interference with the physiological regulation of intraluminal bacteria allowing overgrowth by a normal resident, or colonisation by transient pathogens. The pathophysiological consequences may involve direct damage to the intestinal mucosa, and bacterial metabolism of intraluminal constituents, for example forming deconjugated bile acids and hydroxylated fatty acids which stimulate fluid secretion. Additional problems arise if there is interference with the mucosal barrier since this can result in increased passage of bacteria and bacterial products stimulating mucosal inflammation, while bacterial translocation

  16. Compartmentalization of bacteria in microcapsules.

    PubMed

    van Wijk, Judith; Heunis, Tiaan; Harmzen, Elrika; Dicks, Leon M T; Meuldijk, Jan; Klumperman, Bert

    2014-12-18

    Lactobacillus plantarum strain 423 was encapsulated in hollow poly(organosiloxane) microcapsules by templating water-in-oil Pickering emulsion droplets via the interfacial reaction of alkylchlorosilanes. The bacteria were suspended in growth medium or buffer to protect the cells against pH changes during the interfacial reactions with alkylchlorosilanes. The results of this work open up novel avenues for the encapsulation of microbial cells.

  17. 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

  18. 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.

  19. The sulphate-reducing bacteria

    SciTech Connect

    Postgate, J.R.

    1984-01-01

    This monograph surveys knowledge about an unusual and little-studied group of microbes, bringing together information that has hitherto been widely scattered throughout the scientific literature. The sulphate-reducing bacteria cannot grow in air; they respire sulphates instead of oxygen and are difficult to isolate and study. Nevertheless, much progress has been made in recent years and has revealed novelties of biochemistry and physiology. Sulphate-reducing bacteria affect man in a variety of subtle and occasionally blatant ways although, unlike many bacteria, they cause no disease. Among harmful attributes are being agents of pollution, corrosion and spoilage of food and materials. Their beneficial attributes include the generation of most of the world's sulphur supplies and several other mineral resources, as well as contributing to the oil reserves of this planet. They grow in oil wells, sulphur springs, natural gas stores, sewage sludge and comparable habitats. They are not only of great academic interest but also of increasing practical importance in oil, gas, mineral and corrosion technology.

  20. 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.

  1. 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.

  2. 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…

  3. Resistance in antimicrobial photodynamic inactivation of bacteria.

    PubMed

    Maisch, Tim

    2015-08-01

    Antibiotics have increasingly lost their impact to kill bacteria efficiently during the last 10 years. The emergence and dissemination of superbugs with resistance to multiple antibiotic classes have occurred among Gram-positive and Gram-negative strains including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter strains. These six superbugs can "escape" more or less any single kind of antibiotic treatment. That means bacteria are very good at developing resistance against antibiotics in a short time. One new approach is called photodynamic antimicrobial chemotherapy (PACT) which already has demonstrated an efficient antimicrobial efficacy among multi-resistant bacteria. Until now it has been questionable if bacteria can develop resistance against PACT. This perspective summarises the current knowledge about the susceptibility of bacteria towards oxidative stress and sheds some light on possible strategies of the development of photodynamic inactivation of bacteria (PACT)-induced oxidative stress resistance by bacteria.

  4. 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

  5. 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. 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. 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…

  8. 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. PMID:23916557

  9. Genetics of acidophilic, heterotrophic bacteria

    SciTech Connect

    Ward, T.E.; Bruhn, D.F.; Watkins, C.S.; Rowland, M.L.; Bulmer, D.K.; Winston, V.

    1988-01-01

    The genetic characteristics of members of the genus Acidiphilium are poorly understood. As part of our study of the genetics of these bacteria, a search was made for an inducible, lysogenic bacteriophage. Such a bacteriophage has been discovered. Several properties of the phage have been investigated. The phage has a lambdoid morphology and is somewhat larger than lambda. A variety of factors which affect phage stability have been investigated. The bacteriophage infects several of the strains that have been tested. Study of this bacteriophage should greatly increase our understanding of genetic mechanisms in Acidiphilium. 23 refs., 3 figs., 1 tab.

  10. 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.

  11. 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.

  12. Turning Bacteria Suspensions into Superfluids.

    PubMed

    López, Héctor Matías; Gachelin, Jérémie; Douarche, Carine; Auradou, Harold; Clément, Eric

    2015-07-10

    The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidence for a low-shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semidilute regime, for particularly active bacteria, the suspension displays a "superfluidlike" transition where the viscous resistance to shear vanishes, thus showing that, macroscopically, the activity of pusher swimmers organized by shear is able to fully overcome the dissipative effects due to viscous loss.

  13. Theory of hydrokinetic clearance of bacteria from the urinary bladder. I. Effect of variations in bacterial growth rate.

    PubMed

    Mackintosh, I P; Hammond, B J; Watson, B W; O'Grady, F

    1975-05-01

    If the bladder is regularly emptied in appropriate circumstances the concentration of bacteria in successively voided samples progressively falls. By making a number of assumptions about conditions of bacterial growth in the bladder the way in which this washout of bacteria will occur can be predicted. Such predictions give a form of washout curve which differs significantly from that commonly encountered in patients. The shape of the predicted washout curve is affected by the form of the bacterial growth curve but this influence is not sufficient to account for the observed difference between patients and predictions.

  14. Theory of hydrokinetic clearance of bacteria from the urinary bladder. I. Effect of variations in bacterial growth rate.

    PubMed

    Mackintosh, I P; Hammond, B J; Watson, B W; O'Grady, F

    1975-05-01

    If the bladder is regularly emptied in appropriate circumstances the concentration of bacteria in successively voided samples progressively falls. By making a number of assumptions about conditions of bacterial growth in the bladder the way in which this washout of bacteria will occur can be predicted. Such predictions give a form of washout curve which differs significantly from that commonly encountered in patients. The shape of the predicted washout curve is affected by the form of the bacterial growth curve but this influence is not sufficient to account for the observed difference between patients and predictions. PMID:1120639

  15. 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.

  16. 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.

  17. 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.

  18. Medicinal smoke reduces airborne bacteria.

    PubMed

    Nautiyal, Chandra Shekhar; Chauhan, Puneet Singh; Nene, Yeshwant Laxman

    2007-12-01

    This study represents a comprehensive analysis and scientific validation of our ancient knowledge about the effect of ethnopharmacological aspects of natural products' smoke for therapy and health care on airborne bacterial composition and dynamics, using the Biolog microplate panels and Microlog database. We have observed that 1h treatment of medicinal smoke emanated by burning wood and a mixture of odoriferous and medicinal herbs (havan sámagri=material used in oblation to fire all over India), on aerial bacterial population caused over 94% reduction of bacterial counts by 60 min and the ability of the smoke to purify or disinfect the air and to make the environment cleaner was maintained up to 24h in the closed room. Absence of pathogenic bacteria Corynebacterium urealyticum, Curtobacterium flaccumfaciens, Enterobacter aerogenes (Klebsiella mobilis), Kocuria rosea, Pseudomonas syringae pv. persicae, Staphylococcus lentus, and Xanthomonas campestris pv. tardicrescens in the open room even after 30 days is indicative of the bactericidal potential of the medicinal smoke treatment. We have demonstrated that using medicinal smoke it is possible to completely eliminate diverse plant and human pathogenic bacteria of the air within confined space. PMID:17913417

  19. 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

  20. 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. PMID:21734380

  1. Gene transfer in bacteria: speciation without species?

    PubMed

    Lawrence, Jeffrey G

    2002-06-01

    Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages. Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome. First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration). As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events. Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination. Gene exchange by this route serves to distribute genes throughout distantly related clades and therefore may confer complex abilities--not otherwise found among closely related lineages--onto the recipient organisms. These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages. Although the delineation of microbial "species" then becomes difficult--if not impossible--to achieve, a cogent process of speciation can be predicted.

  2. Endophytic bacteria in Coffea arabica L.

    PubMed

    Vega, Fernando E; Pava-Ripoll, Monica; Posada, Francisco; Buyer, Jeffrey S

    2005-01-01

    Eighty-seven culturable endophytic bacterial isolates in 19 genera were obtained from coffee plants collected in Colombia (n = 67), Hawaii (n = 17), and Mexico (n = 3). Both Gram positive and Gram negative bacteria were isolated, with a greater percentage (68%) being Gram negative. Tissues yielding bacterial endophytes included adult plant leaves, various parts of the berry (e.g., crown, pulp, peduncle and seed), and leaves, stems, and roots of seedlings. Some of the bacteria also occurred as epiphytes. The highest number of bacteria among the berry tissues sampled was isolated from the seed, and includes Bacillus , Burkholderia , Clavibacter , Curtobacterium , Escherichia , Micrococcus , Pantoea , Pseudomonas , Serratia , and Stenotrophomonas . This is the first survey of the endophytic bacteria diversity in various coffee tissues, and the first study reporting endophytic bacteria in coffee seeds. The possible role for these bacteria in the biology of the coffee plant remains unknown.

  3. 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

  4. 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.

  5. Repulsion of bacteria from marine surfaces.

    PubMed Central

    Chet, I; Asketh, P; Mitchell, R

    1975-01-01

    Organic compounds are capable of repelling motile bacteria from marine surfaces. The most effective compounds were acrylamide and benzoic and tannic acids. These were active at concentrations that were not toxic to the bacteria. Repellents were incorporated in nontoxic paints and applied to metal panels. Treated panels immersed in seawater developed a bacterial film of only 10(6) bacteria per cm6 after 12 days compared with untreated panels, which had 5 times 10(12) bacteria per cm2 after the same period. Field studies confirmed the effectiveness of these repellents. The use of biological repellents provides a new approach to the control of marine fouling. PMID:1211933

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Toward an ecological classification of soil bacteria.

    PubMed

    Fierer, Noah; Bradford, Mark A; Jackson, Robert B

    2007-06-01

    Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere

  14. 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.

  15. 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

  16. Research Advances in Bacteria-based Microrobot.

    PubMed

    Liang, Yao-Jie; Sun, Jun-Zhong

    2016-08-01

    The concept of bacteria-based microrobot has been well recognized. It has shown great advantages and potentials for the early diagnosis and early treatment of malignant tumor and in reducing chemotherapy toxicities. In this article we review the concept,structure,and potential clinical applications of bacteria-based microrobot. PMID:27594160

  17. 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.

  18. 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.

  19. 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.

  20. Hydrogen metabolism of photosynthetic bacteria and algae

    SciTech Connect

    Kumazawa, S.; Mitsui, A.

    1982-01-01

    The metabolism, metabolic pathways and biochemistry of hydrogen in photosynthetic bacteria and algae are reviewed. Detailed information on the occurrence and measurement of hydrogenase activity is presented. Hydrogen production rates for different species of algae and bacteria are presented. 173 references, 1 figure, 7 tables.

  1. 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

  2. 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.

  3. Filamentous bacteria existence in aerobic granular reactors.

    PubMed

    Figueroa, M; Val del Río, A; Campos, J L; Méndez, R; Mosquera-Corral, A

    2015-05-01

    Filamentous bacteria are associated to biomass settling problems in wastewater treatment plants. In systems based on aerobic granular biomass they have been proposed to contribute to the initial biomass aggregation process. However, their development on mature aerobic granular systems has not been sufficiently studied. In the present research work, filamentous bacteria were studied for the first time after long-term operation (up to 300 days) of aerobic granular systems. Chloroflexi and Sphaerotilus natans have been observed in a reactor fed with synthetic wastewater. These filamentous bacteria could only come from the inoculated sludge. Thiothrix and Chloroflexi bacteria were observed in aerobic granular biomass treating wastewater from a fish canning industry. Meganema perideroedes was detected in a reactor treating wastewater from a plant processing marine products. As a conclusion, the source of filamentous bacteria in these mature aerobic granular systems fed with industrial effluents was the incoming wastewater.

  4. 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.

  5. PCR detection of uncultured rumen bacteria.

    PubMed

    Rosero, Jaime A; Strosová, Lenka; Mrázek, Jakub; Fliegerová, Kateřina; Kopečný, Jan

    2012-07-01

    16S rRNA sequences of ruminal uncultured bacterial clones from public databases were phylogenetically examined. The sequences were found to form two unique clusters not affiliated with any known bacterial species: cluster of unidentified sequences of free floating rumen fluid uncultured bacteria (FUB) and cluster of unidentified sequences of bacteria associated with rumen epithelium (AUB). A set of PCR primers targeting 16S rRNA of ruminal free uncultured bacteria and rumen epithelium adhering uncultured bacteria was designed based on these sequences. FUB primers were used for relative quantification of uncultured bacteria in ovine rumen samples. The effort to increase the population size of FUB group has been successful in sulfate reducing broth and culture media supplied with cellulose.

  6. Chemotaxis by Naegleria fowleri for bacteria.

    PubMed

    Marciano-Cabral, F; Cline, M

    1987-05-01

    Naegleria fowleri amebae demonstrated a chemotactic and chemokinetic response toward live cells and extracts of Escherichia coli and other bacterial species when experiments were performed using a blind-well chemotaxis chamber. The peptide N-formyl-methionyl-leucyl-phenylalanine acted as a chemokinetic rather than a chemotactic factor for N. fowleri amebae. Competition experiments in which nerve cell extracts or bacteria were placed on either side of the filter in chemotaxis chambers resulted in increased movement towards bacteria. A scanning electron microscopy study of the interaction of N. fowleri with different bacterial species confirmed that when the amebae were near ingestible bacteria they moved toward the bacteria by pseudopod formation. Naegleria fowleri appeared to respond to bacteria by three interrelated but distinct processes: chemokinesis, chemotaxis, and formation of food cups.

  7. 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

  8. Prediction techniques

    NASA Astrophysics Data System (ADS)

    1981-12-01

    Prediction methods and related propagation results for the evaluation of Earth-space communication paths operating above 10 GHz are presented. Gaseous attenuation, rain, cloud, fog, sand, and dust attenuation, path diversity, signal fluctuations and low angle fading, depolarization effects, bandwidth coherence, and sky noise are considered.

  9. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.

    PubMed

    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

  10. Competition between phytoplankton and bacteria: exclusion and coexistence.

    PubMed

    Grognard, Frédéric; Masci, Pierre; Benoît, Eric; Bernard, Olivier

    2015-04-01

    Resource-based competition between microorganisms species in continuous culture has been studied extensively both experimentally and theoretically, mostly for bacteria through Monod and Contois "constant yield" models, or for phytoplankton through the Droop "variable yield" models. For homogeneous populations of N bacterial species (Monod) or N phytoplanktonic species (Droop), with one limiting substrate and under constant controls, the theoretical studies indicated that competitive exclusion occurs: only one species wins the competition and displaces all the others (Armstrong and McGehee in Am Nat 115:151, 1980; Hsu and Hsu in SIAM J Appl Math 68:1600-1617, 2008). The winning species expected from theory is the one with the lowest "substrate subsistence concentration" s([star]), such that its corresponding equilibrium growth rate is equal to the dilution rate D. This theoretical result was validated experimentally with phytoplankton (Tilman and Sterner in Oecologia 61(2):197-200, 1984) and bacteria (Hansen and Hubell in Science 207(4438):1491-1493, 1980), and observed in a lake with microalgae (Tilman in Ecology 58(22):338-348, 1977). On the contrary for aggregating bacterial species described by a Contois model, theory predicts coexistence between several species (Grognard et al. in Discrete Contin Dyn Syst Ser B 8(1):73-93, 2007). In this paper we present a generalization of these results by studying a competition between three different types of microorganisms: planktonic (or free) bacteria (represented by a generalized Monod model), aggregating bacteria (represented by a Contois model) and free phytoplankton (represented by a Droop model). We prove that the outcome of the competition is a coexistence between several aggregating bacterial species with a free species of bacteria or phytoplankton, all the other free species being washed out. This demonstration is based mainly on the study of the substrate concentration's evolution caused by competition; it

  11. 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.

  12. Multiscale Model of Swarming Bacteria

    NASA Astrophysics Data System (ADS)

    Alber, Mark

    2011-03-01

    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. In the beginning of the talk, swarms of the M. xanthus will be described in detail. Individual M. xanthus cells are elongated; they always move in the direction of their long axis; and they are in constant motion, repeatedly touching each other. As a cell glides, the slime capsule of a cell interacts with the bare agar surface, non-oriented slime which arises from the surface contact with the slime capsule, or oriented slime trails. Remarkably, cells regularly reverse their gliding directions. In this talk a detailed cell- and behavior-based computational model of M. xanthus swarming will be used to demonstrate that reversals of gliding direction and cell bending are essential for swarming and that specific reversal frequencies result in optimal swarming rate of the whole population. This suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming.

  13. 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.

  14. Cell size control in bacteria.

    PubMed

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

    2012-05-01

    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 Bacillus 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.

  15. 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.

  16. Recombinant bacteria for mosquito control.

    PubMed

    Federici, B A; Park, H-W; Bideshi, D K; Wirth, M C; Johnson, J J

    2003-11-01

    Bacterial insecticides have been used for the control of nuisance and vector mosquitoes for more than two decades. Nevertheless, due primarily to their high cost and often only moderate efficacy, these insecticides remain of limited use in tropical countries where mosquito-borne diseases are prevalent. Recently, however, recombinant DNA techniques have been used to improve bacterial insecticide efficacy by markedly increasing the synthesis of mosquitocidal proteins and by enabling new endotoxin combinations from different bacteria to be produced within single strains. These new strains combine mosquitocidal Cry and Cyt proteins of Bacillus thuringiensis with the binary toxin of Bacillus sphaericus, improving efficacy against Culex species by 10-fold and greatly reducing the potential for resistance through the presence of Cyt1A. Moreover, although intensive use of B. sphaericus against Culex populations in the field can result in high levels of resistance, most of this can be suppressed by combining this bacterial species with Cyt1A; the latter enables the binary toxin of this species to enter midgut epithelial cells via the microvillar membrane in the absence of a midgut receptor. The availability of these novel strains and newly discovered mosquitocidal proteins, such as the Mtx toxins of B. sphaericus, offers the potential for constructing a range of recombinant bacterial insecticides for more effective control of the mosquito vectors of filariasis, Dengue fever and malaria. PMID:14506223

  17. 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

  18. Synthetic biology in Streptomyces bacteria.

    PubMed

    Medema, Marnix H; Breitling, Rainer; Takano, Eriko

    2011-01-01

    Actinomycete bacteria of the genus Streptomyces are major producers of bioactive compounds for the biotechnology industry. They are the source of most clinically used antibiotics, as well as of several widely used drugs against common diseases, including cancer . Genome sequencing has revealed that the potential of Streptomyces species for the production of valuable secondary metabolites is even larger than previously realized. Accessing this rich genomic resource to discover new compounds by activating "cryptic" pathways is an interesting challenge for synthetic biology. This approach is facilitated by the inherent natural modularity of secondary metabolite biosynthetic pathways, at the level of individual enzymes (such as modular polyketide synthases), but also of gene cassettes/operons and entire biosynthetic gene clusters. It also benefits from a long tradition of molecular biology in Streptomyces, which provides a number of specific tools, ranging from cloning vectors to inducible promoters and translational control elements. In this chapter, we first provide an overview of the synthetic biology challenges in Streptomyces and then present the existing toolbox of molecular methods that can be employed in this organism. PMID:21601100

  19. 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

  20. 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

  1. 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.

  2. 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. PMID:24904553

  3. 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

  4. 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

  5. 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

  6. 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...

  7. 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.

  8. 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

  9. Evolutionary tradeoffs in cellular composition across diverse bacteria

    PubMed Central

    Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

    2016-01-01

    One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

  10. Evolutionary tradeoffs in cellular composition across diverse bacteria.

    PubMed

    Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

    2016-09-01

    One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content-the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

  11. Francois N. Frenkiel Award Talk: Swimming bacteria at complex interfaces

    NASA Astrophysics Data System (ADS)

    Lopez, Diego; Lauga, Eric

    2015-11-01

    Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Past fluid dynamic studies predict this circular motion to be clockwise above a rigid surface (when viewed from inside the fluid) and counter- clockwise below a free surface. Recent experimental investigations showed that complex physicochemical processes at the nearby surface could lead to a change in the direction of rotation, both at solid surfaces absorbing slip-inducing polymers and interfaces covered with surfactants. Motivated by these results, we use a far-field hydrodynamic model to predict the kinematics of swimming near three types of interfaces: clean fluid-fluid interface, slipping rigid wall, and a fluid interface covered by incompressible surfactants. Representing the helical swimmer by a superposition of hydrodynamic singularities, we first show that in all cases the surfaces reorient the swimmer parallel to the surface and attract it, both of which are a consequence of the Stokes dipole component of the swimmer flow field. We then show that circular motion is induced by a higher-order singularity, namely, a rotlet dipole, and that its rotation direction is strongly affected by the boundary conditions at the interface and the bacteria shape. In collaboration with Eric Lauga, DAMTP, University of Cambridge.

  12. Antibacterial activity of aquatic gliding bacteria.

    PubMed

    Sangnoi, Yutthapong; Anantapong, Theerasak; Kanjana-Opas, Akkharawit

    2016-01-01

    The study aimed to screen and isolate strains of freshwater aquatic gliding bacteria, and to investigate their antibacterial activity against seven common pathogenic bacteria. Submerged specimens were collected and isolated for aquatic gliding bacteria using four different isolation media (DW, MA, SAP2, and Vy/2). Gliding bacteria identification was performed by 16S rRNA gene sequencing and phylogenetic analysis. Crude extracts were obtained by methanol extraction. Antibacterial activity against seven pathogenic bacteria was examined by agar-well diffusion assay. Five strains of aquatic gliding bacteria including RPD001, RPD008, RPD018, RPD027 and RPD049 were isolated. Each submerged biofilm and plastic specimen provided two isolates of gliding bacteria, whereas plant debris gave only one isolate. Two strains of gliding bacteria were obtained from each DW and Vy/2 isolation medium, while one strain was obtained from the SAP2 medium. Gliding bacteria strains RPD001, RPD008 and RPD018 were identified as Flavobacterium anhuiense with 96, 82 and 96 % similarity, respectively. Strains RPD049 and RPD027 were identified as F. johnsoniae and Lysobacter brunescens, respectively, with similarity equal to 96 %. Only crude extract obtained from RPD001 inhibited growth of Listeria monocytogenes (MIC 150 µg/ml), Staphylococcus aureus (MIC 75 µg/ml) and Vibrio cholerae (MIC 300 µg/ml), but showed weak inhibitory effect on Salmonella typhimurium (MIC > 300 µg/ml). Gliding bacterium strain RPD008 should be considered to a novel genus separate from Flavobacterium due to its low similarity value. Crude extract produced by RPD001 showed potential for development as a broad antibiotic agent. PMID:26885469

  13. 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.

  14. Analysis of polysomes from bacteria.

    PubMed

    Qin, Daoming; Fredrick, Kurt

    2013-01-01

    In actively growing cells, the rate of translation initiation is relatively rapid. As a result, multiple ribosomes simultaneously engaged in translation become spaced along single mRNA molecules. These structures, termed polysomes, can be separated from ribosomal subunits and single ribosomes because they migrate faster through sucrose gradients (Noll, 2008). In fact, polysomes containing various numbers of ribosomes can be resolved from one another since each ribosome adds substantial mass. It is straightforward to prepare bacterial lysates and resolve all the ribosomal fractions using sucrose gradient sedimentation. The resulting polysome 'profile' can provide a sort of snapshot of the translation activity in the cell. Polysome analysis has been used to study the effects of mutations and/or growth conditions on translation and to address whether particular cellular components are associated with the translational machinery (Powers and Noller, 1990; Gregory et al., 1994; Moine and Dahlberg, 1994; Firpo et al., 1996; Fredrick et al., 2000; Ataide et al., 2009; Melamed et al., 2009; Saini et al., 2009). In combination with other techniques, polysome analysis has been used to deduce rate constants for certain phases of translation (e.g., initiation, elongation, termination) (Arava et al., 2003; 2005). Finally, use of purified polysomes in biochemical experiments has been instrumental for the isolation and characterization of translation factors such as ribosome recycling factor (RRF) (Hirashima and Kaji, 1972; Fujiwara et al., 2001; Hirokawa et al., 2002; Ito et al., 2002). Here, we describe a simple and convenient method of preparing and analyzing polysomes from Escherichia coli, which should be generally applicable to many bacteria. We also discuss parameters that influence the ribosome density on mRNA, which should be kept in mind when polysome profiles are being interpreted.

  15. R-body-producing bacteria.

    PubMed

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

    1989-03-01

    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. PMID:2651865

  16. 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

  17. Folate production by probiotic bacteria.

    PubMed

    Rossi, Maddalena; Amaretti, Alberto; Raimondi, Stefano

    2011-01-01

    Probiotic bacteria, mostly belonging to the genera Lactobacillus and Bifidobacterium, confer a number of health benefits to the host, including vitamin production. With the aim to produce folate-enriched fermented products and/or develop probiotic supplements that accomplish folate biosynthesis in vivo within the colon, bifidobacteria and lactobacilli have been extensively studied for their capability to produce this vitamin. On the basis of physiological studies and genome analysis, wild-type lactobacilli cannot synthesize folate, generally require it for growth, and provide a negative contribution to folate levels in fermented dairy products. Lactobacillus plantarum constitutes an exception among lactobacilli, since it is capable of folate production in presence of para-aminobenzoic acid (pABA) and deserves to be used in animal trials to validate its ability to produce the vitamin in vivo. On the other hand, several folate-producing strains have been selected within the genus Bifidobacterium, with a great variability in the extent of vitamin released in the medium. Most of them belong to the species B. adolescentis and B. pseudocatenulatum, but few folate producing strains are found in the other species as well. Rats fed a probiotic formulation of folate-producing bifidobacteria exhibited increased plasma folate level, confirming that the vitamin is produced in vivo and absorbed. In a human trial, the same supplement raised folate concentration in feces. The use of folate-producing probiotic strains can be regarded as a new perspective in the specific use of probiotics. They could more efficiently confer protection against inflammation and cancer, both exerting the beneficial effects of probiotics and preventing the folate deficiency that is associated with premalignant changes in the colonic epithelia. PMID:22254078

  18. 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.

  19. Stop the Spread of Superbugs: Help Fight Drug Resistant Bacteria

    MedlinePlus

    ... the Spread of Superbugs Help Fight Drug-Resistant Bacteria For nearly a century, bacteria-fighting drugs known as antibiotics have helped to control and destroy many of the harmful bacteria that can make us sick. But in recent ...

  20. Genetic parts to program bacteria.

    PubMed

    Voigt, Christopher A

    2006-10-01

    Genetic engineering is entering a new era, where microorganisms can be programmed using synthetic constructs of DNA encoding logic and operational commands. A toolbox of modular genetic parts is being developed, comprised of cell-based environmental sensors and genetic circuits. Systems have already been designed to be interconnected with each other and interfaced with the control of cellular processes. Engineering theory will provide a predictive framework to design operational multicomponent systems. On the basis of these developments, increasingly complex cellular machines are being constructed to build specialty chemicals, weave biomaterials, and to deliver therapeutics.

  1. Trap and track: designing self-reporting porous Si photonic crystals for rapid bacteria detection.

    PubMed

    Massad-Ivanir, Naama; Mirsky, Yossi; Nahor, Amit; Edrei, Eitan; Bonanno-Young, Lisa M; Ben Dov, Nadav; Sa'ar, Amir; Segal, Ester

    2014-08-21

    The task of rapid detection and identification of bacteria remains a major challenge in both medicine and industry. This work introduces a new concept for the design of self-reporting optical structures that can detect and quantify bacteria in real-time. The sensor is based on a two-dimensional periodic structure of porous Si photonic crystals in which the pore size is adjusted to fit the target bacteria cells (Escherichia coli). Spontaneous bacteria capture within the pores induces measurable changes in the zero-order reflectivity spectrum collected from the periodic structure. Confocal laser microscopy and electron microscopy confirm that the Escherichia coli cells are individually imprisoned within the porous array. A simple model is suggested to correlate the optical readout and the bacteria concentration and its predictions are found to be in good agreement with experimental results. In addition, we demonstrate that sensing scheme can be easily modified to potentially allow monitoring of concentration, growth and physiological state of bacteria cells. This generic platform can be tailored to target different microorganisms by tuning the array periodicity and its surface chemistry for rapid and label-free detection outside the laboratory environment.

  2. Relationship of selected bacterial vaginosis-associated bacteria to Nugent score bacterial vaginosis among urban women early in pregnancy.

    PubMed

    Nelson, Deborah B; Komaroff, Eugene; Nachamkin, Irving; Haggerty, Catherine L; Dibble, LaVette; Mastrogiannis, Dimitrios; Liu, Congzhou; Fredricks, David N; David, Fredricks N

    2013-09-01

    Among urban, primarily African American pregnant women, 74% were identified with Nugent score bacterial vaginosis (BV). All BV-associated bacteria were more prevalent among women with Nugent score BV. Bacterial vaginosis-associated bacteria 3 (BVAB3) had the highest positive predictive value, whereas Gardnerella vaginalis and Atopobium spp. had the highest sensitivity. Atopobium spp. levels had the most significant area under the curve.

  3. GIPSy: Genomic island prediction software.

    PubMed

    Soares, Siomar C; Geyik, Hakan; Ramos, Rommel T J; de Sá, Pablo H C G; Barbosa, Eudes G V; Baumbach, Jan; Figueiredo, Henrique C P; Miyoshi, Anderson; Tauch, Andreas; Silva, Artur; Azevedo, Vasco

    2016-08-20

    Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits. PMID:26376473

  4. GIPSy: Genomic island prediction software.

    PubMed

    Soares, Siomar C; Geyik, Hakan; Ramos, Rommel T J; de Sá, Pablo H C G; Barbosa, Eudes G V; Baumbach, Jan; Figueiredo, Henrique C P; Miyoshi, Anderson; Tauch, Andreas; Silva, Artur; Azevedo, Vasco

    2016-08-20

    Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits.

  5. Acidophilic, heterotrophic bacteria of acidic mine waters

    SciTech Connect

    Wichlacz, P.L.; Unz, R.F.

    1981-05-01

    Obligately acidophilic, heterotrophic bacteria were isolated both from enrichment cultures developed with acidic mine water and from natural mine drainage. The bacteria were grouped by the ability to utilize a number of organic acids as sole carbon sources. None of the strains were capable of chemolithotrophic growth on inorganic reduced iron and sulfur compounds. All bacteria were rod shaped, gram negative, nonencapsulated, motile, capable of growth at pH 2.6 but not at pH 6.0, catalase and oxidase positive, strictly aerobic, and capable of growth on citric acid. The bacteria were cultivatable on solid nutrient media only if agarose was employed as the hardening agent. Bacterial densities in natural mine waters ranged from approximately 20 to 250 cells per ml, depending upon source and culture medium.

  6. Protection of probiotic bacteria in synbiotic matrices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. 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.

  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. 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.

  10. 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.

  11. Smokeless Tobacco May Contain Potentially Harmful Bacteria

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_160769.html Smokeless Tobacco May Contain Potentially Harmful Bacteria Infections, diarrhea and ... HealthDay News) -- There's a new concern about smokeless tobacco -- those products can harbor several species of potentially ...

  12. Distribution of phytopathogenic bacteria in infested seeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. 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.

  14. 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

  15. Bacteria make gasohol from corn stalk wastes

    SciTech Connect

    Not Available

    1980-11-03

    Scientists at MIT have developed two strains of bacteria that convert corn stalks into ethanol. The bacteria, isolated from the first compartment of the cows rumen, were chemically treated to cause genetic mutations that could tolerate higher concentrations of alcohol and produce little lactic acid. The bacterial methods end product is a fuel that consists of 4% ethanol and 96% water, and by the fermentation of cellulose, rather than starch, the hydrolyzation step is eliminated.

  16. Corrosion inhibition of steel by bacteria

    SciTech Connect

    Hernandez, G.; Kucera, V.; Thierry, D.; Pedersen, A. ); Hermansson, M. . Dept. of General and Marine Microbiology)

    1994-08-01

    Mild steel was exposed to Pseudomonas sp. S9 or Serratia marcescens in synthetic seawater. An increase in corrosion resistance over that i natural seawater was monitored by electrochemical techniques. Biological analyses were performed to characterize the system. The inhibition effect also was observed when mild steel was coated with bacteria and then immersed in synthetic seawater. When specimens coated with bacteria were transferred to a natural seawater flow system, the inhibition effect disappeared during the first 2 weeks.

  17. Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

    PubMed

    Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

    1982-11-01

    Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

  18. 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.

  19. Bacteria under stress by complement and coagulation.

    PubMed

    Berends, Evelien T M; Kuipers, Annemarie; Ravesloot, Marietta M; Urbanus, Rolf T; Rooijakkers, Suzan H M

    2014-11-01

    The complement and coagulation systems are two related protein cascades in plasma that serve important roles in host defense and hemostasis, respectively. Complement activation on bacteria supports cellular immune responses and leads to direct killing of bacteria via assembly of the Membrane Attack Complex (MAC). Recent studies have indicated that the coagulation system also contributes to mammalian innate defense since coagulation factors can entrap bacteria inside clots and generate small antibacterial peptides. In this review, we will provide detailed insights into the molecular interplay between these protein cascades and bacteria. We take a closer look at how these pathways are activated on bacterial surfaces and discuss the mechanisms by which they directly cause stress to bacterial cells. The poorly understood mechanism for bacterial killing by the MAC will be reevaluated in light of recent structural insights. Finally, we highlight the strategies used by pathogenic bacteria to modulate these protein networks. Overall, these insights will contribute to a better understanding of the host defense roles of complement and coagulation against bacteria.

  20. 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. PMID:26986806

  1. 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

  2. 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

  3. Swimming of bacteria under dielectrophoresis

    NASA Astrophysics Data System (ADS)

    Tran, Ngoc Phu; Marcos, Marcos

    In this work, we present a model to predict the response of a swimming helically flagellated bacterium to a unidirectional dielectrophoretic (DEP) force with its strength varying linearly in space. We employ resistive force theory to compute the hydrodynamic force on the flagellar bundle, and the effects of DEP force and rotational diffusion are examined using the Fokker-Planck equation. The DEP force greatly contributes to the reorientation of the bacterium such that the bacterium's primary axis is aligned with the direction of the force. Interestingly, when the DEP strength varies perpendicularly to the direction of the force, the bacterium's primary axis is no longer aligned with the DEP force, which results in a translation of the bacterium perpendicular to its primary axis. Finally, we show the feasibility to utilize this phenomenon to achieve bacterial focusing. The full name of the second author is MARCOS.

  4. The flexibility of UV-inducible mutation in Deinococcus ficus as evidenced by the existence of the imuB-dnaE2 gene cassette and generation of superior feather degrading bacteria.

    PubMed

    Zeng, You-Hong; Shen, Fo-Ting; Tan, Chen-Chung; Huang, Chieh-Chen; Young, Chiu-Chung

    2011-12-20

    The lexA-imuB-dnaE2 gene cassette contributing to the TLS (translesion synthesis) polymerase activity and can easily cause mutation after DNA damage in many bacteria. But it was previously thought that TLS polymerase activity was unlikely to exist in the radio-resistant genus Deinococcus. In our preliminary studies, the lexA-imuB-dnaE2 gene cassette was found in a newly isolated feather-degrading Deinococcus ficus. Here we have attempted to determine the imuB gene sequence from another Deinococcus species namely D. grandis, by using the newly designed primers. The destroying of either imuB or dnaE2 gene in D. ficus leads to the increase in UV sensitivity and decrease in UV-induced mutations, which demonstrated the existence of TLS polymerase activity in D. ficus. In the presence of lexA-imuB-dnaE2, it is possible to obtain mutants with various keratinolytic activities after UV exposure. The keratinolytic activity of mutant strain CC-ZG207 increased by approximately twofold during growth in liquid feather medium. In contrast, the mutant strain CC-ZG227 showed only half of the keratinolytic activity compared with the wild type strain. By utilizing SDS-PAGE and zymogram profile analysis, the change in the protease activity was observed. We have proposed that the superior mutants of D. ficus can be created under UV stress, which is mediated by the lexA-imuB-dnaE2 gene cassette.

  5. 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.

  6. Visualizing bacteria in nematodes using fluorescent microscopy.

    PubMed

    Murfin, Kristen E; Chaston, John; Goodrich-Blair, Heidi

    2012-10-19

    Symbioses, the living together of two or more organisms, are widespread throughout all kingdoms of life. As two of the most ubiquitous organisms on earth, nematodes and bacteria form a wide array of symbiotic associations that range from beneficial to pathogenic (1-3). One such association is the mutually beneficial relationship between Xenorhabdus bacteria and Steinernema nematodes, which has emerged as a model system of symbiosis (4). Steinernema nematodes are entomopathogenic, using their bacterial symbiont to kill insects (5). For transmission between insect hosts, the bacteria colonize the intestine of the nematode's infective juvenile stage (6-8). Recently, several other nematode species have been shown to utilize bacteria to kill insects (9-13), and investigations have begun examining the interactions between the nematodes and bacteria in these systems (9). We describe a method for visualization of a bacterial symbiont within or on a nematode host, taking advantage of the optical transparency of nematodes when viewed by microscopy. The bacteria are engineered to express a fluorescent protein, allowing their visualization by fluorescence microscopy. Many plasmids are available that carry genes encoding proteins that fluoresce at different wavelengths (i.e. green or red), and conjugation of plasmids from a donor Escherichia coli strain into a recipient bacterial symbiont is successful for a broad range of bacteria. The methods described were developed to investigate the association between Steinernema carpocapsae and Xenorhabdus nematophila (14). Similar methods have been used to investigate other nematode-bacterium associations (9) (,) (15-18)and the approach therefore is generally applicable. The method allows characterization of bacterial presence and localization within nematodes at different stages of development, providing insights into the nature of the association and the process of colonization (14) (,) (16) (,) (19). Microscopic analysis reveals both

  7. [Immobilization of introduced bacteria and degradation of pyrene and benzo(alpha) pyrene in soil by immobilized bacteria].

    PubMed

    Wang, Xin; Li, Peijun; Song, Shouzhi; Zhong, Yong; Zhang, Hui; Verkhozina, E V

    2006-11-01

    In this study, introduced bacteria were applied in the bioremediation of pyrene and benzo (alpha) pyrene in organic pollutants-contaminated soils, aimed to test whether it was feasible to introduce bacteria to environmental engineering. Three introduced bacteria were immobilized separately or together to degrade the pyrene and benzo (alpha) pyrene in soil, taking dissociated bacteria as the control, and comparing with three indigenous bacteria. The results showed that immobilized introduced bacteria, either single or mixed, had higher degradation efficiency than dissociated bacteria. Compared with indigenous bacteria, some introduced bacteria had predominance to some degree. The introduced bacteria-mixture had better degradation efficiency after being immobilized. The degradation rate of pyrene and benzo(alpha) pyrene after treated with immobilized bacteria-( B61-B67)-mixture for 96 hours was 43.49% and 38.55%, respectively.

  8. Platelets and infections - complex interactions with bacteria.

    PubMed

    Hamzeh-Cognasse, Hind; Damien, Pauline; Chabert, Adrien; Pozzetto, Bruno; Cognasse, Fabrice; Garraud, Olivier

    2015-01-01

    Platelets can be considered sentinels of vascular system due to their high number in the circulation and to the range of functional immunoreceptors they express. Platelets express a wide range of potential bacterial receptors, including complement receptors, FcγRII, Toll-like receptors but also integrins conventionally described in the hemostatic response, such as GPIIb-IIIa or GPIb. Bacteria bind these receptors either directly, or indirectly via fibrinogen, fibronectin, the first complement C1q, the von Willebrand Factor, etc. The fate of platelet-bound bacteria is questioned. Several studies reported the ability of activated platelets to internalize bacteria such as Staphylococcus aureus or Porphyromonas gingivalis, though there is no clue on what happens thereafter. Are they sheltered from the immune system in the cytoplasm of platelets or are they lysed? Indeed, while the presence of phagolysosome has not been demonstrated in platelets, they contain antimicrobial peptides that were shown to be efficient on S. aureus. Besides, the fact that bacteria can bind to platelets via receptors involved in hemostasis suggests that they may induce aggregation; this has indeed been described for Streptococcus sanguinis, S. epidermidis, or C. pneumoniae. On the other hand, platelets are able to display an inflammatory response to an infectious triggering. We, and others, have shown that platelet release soluble immunomodulatory factors upon stimulation by bacterial components. Moreover, interactions between bacteria and platelets are not limited to only these two partners. Indeed, platelets are also essential for the formation of neutrophil extracellular traps by neutrophils, resulting in bacterial clearance by trapping bacteria and concentrating antibacterial factors but in enhancing thrombosis. In conclusion, the platelet-bacteria interplay is a complex game; its fine analysis is complicated by the fact that the inflammatory component adds to the aggregation response

  9. Flagellated ectosymbiotic bacteria propel a eucaryotic cell.

    PubMed

    Tamm, S L

    1982-09-01

    A devescovinid flagellate from termites exhibits rapid gliding movements only when in close contact with other cells or with a substrate. Locomotion is powered not by the cell's own flagella nor by its remarkable rotary axostyle, but by the flagella of thousands of rod bacteria which live on its surface. That the ectosymbiotic bacteria actually propel the protozoan was shown by the following: (a) the bacteria, which lie in specialized pockets of the host membrane, bear typical procaryotic flagella on their exposed surface; (b) gliding continues when the devescovinid's own flagella and rotary axostyle are inactivated; (c) agents which inhibit bacterial flagellar motility, but not the protozoan's motile systems, stop gliding movements; (d) isolated vesicles derived from the surface of the devescovinid rotate at speeds dependent on the number of rod bacteria still attached; (e) individual rod bacteria can move independently over the surface of compressed cells; and (f) wave propagation by the flagellar bundles of the ectosymbiotic bacteria is visualized directly by video-enhanced polarization microscopy. Proximity to solid boundaries may be required to align the flagellar bundles of adjacent bacteria in the same direction, and/or to increase their propulsive efficiency (wall effect). This motility-linked symbiosis resembles the association of locomotory spirochetes with the Australian termite flagellate Mixotricha (Cleveland, L. R., and A. V. Grimstone, 1964, Proc. R. Soc. Lond. B Biol. Sci., 159:668-686), except that in our case propulsion is provided by bacterial flagella themselves. Since bacterial flagella rotate, an additional novelty of this system is that the surface bearing the procaryotic rotary motors is turned by the eucaryotic rotary motor within.

  10. Infections caused by halophilic marine Vibrio bacteria.

    PubMed Central

    Howard, R J; Bennett, N T

    1993-01-01

    OBJECTIVE: The authors reviewed patients who developed sepsis or soft tissue infections caused by marine Vibrio bacteria in Florida. SUMMARY BACKGROUND DATA: Marine Vibrio bacteria are the most common bacteria found in seawater. They are concentrated in marine animals that feed by filtration such as oysters and clams. These bacteria can cause gastroenteritis, sepsis, cellulitis leading to necrotizing soft tissue infection after exposure to seawater or consumption of raw seafood. METHODS: The authors received 182 systemic infections that occurred in Florida between January 1, 1979, and December 31, 1991, which were treated by the authors or were reported to the Florida Department of Health and Rehabilitative Services. Patients were divided into two groups depending on whether they presented with primary bacteremia or soft tissue infection. RESULTS: Seventy-one patients had been exposed to these bacteria by eating raw seafood, 94 had direct exposure to seawater, and exposure was uncertain in 27 patients. Vibrio species were cultured from the blood of 103 patients and from wounds or soft tissues of 113. An additional 5 patients had cellulitis but bacteria were not cultured from these sites. In patients in whom it could be determined, 93 had primary soft tissue infections and 82 had primary bacteremia. Twenty-four patients had necrotizing soft tissue infections and required surgical debridement. Three of these 24 patients required amputation. Thirty-seven (20.3%) patients died. Severe liver disease occurred in 54 patients and 25 of these patients died. CONCLUSIONS: Marine Vibrio bacteria can cause sepsis and soft tissue infections, especially in individuals with severe liver disease and other chronic illnesses such as diabetes mellitus. The authors believe all individuals, especially those with systemic illness, should be warned against eating raw seafood. Images Figure 1. PMID:8489315

  11. 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. PMID:25028774

  12. Morphological plasticity of bacteria-Open questions.

    PubMed

    Shen, Jie-Pan; Chou, Chia-Fu

    2016-05-01

    Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular mechanisms remain largely unknown. Physical and chemical factors causing morphological changes in bacteria have been investigated and mostly associated with potential pathways linked to the cell wall synthetic machinery. These include starvation, oxidative stresses, predation effectors, antimicrobial agents, temperature stresses, osmotic shock, and mechanical constraints. In an extreme scenario of morphological plasticity, bacteria can be induced to be shapeshifters when the cell walls are defective or deficient. They follow distinct developmental pathways and transform into assorted morphological variants, and most of them would eventually revert to typical cell morphology. It is suggested that phenotypic heterogeneity might play a functional role in the development of morphological diversity and/or plasticity within an isogenic population. Accordingly, phenotypic heterogeneity and inherited morphological plasticity are found to be survival strategies adopted by bacteria in response to environmental stresses. Here, microfluidic and nanofabrication technology is considered to provide versatile solutions to induce morphological plasticity, sort and isolate morphological variants, and perform single-cell analysis including transcriptional and epigenetic profiling. Questions such as how morphogenesis network is modulated or rewired (if epigenetic controls of cell morphogenesis apply) to induce bacterial morphological plasticity could be resolved with the aid of micro-nanofluidic platforms and optimization algorithms, such as feedback system control. PMID:27375812

  13. Bacteria-induced sexual isolation in Drosophila.

    PubMed

    Ringo, John; Sharon, Gil; Segal, Daniel

    2011-01-01

    Commensal bacteria can induce sexual isolation between populations of Drosophila. This phenomenon has implications for speciation, and raises questions about its behavioral and developmental mechanisms, which are not yet known. In this Extra View, we discuss related work by others, bearing directly on these issues, and we speculate about how bacteria might influence fly behavior. There are many reports of interaction between Drosophila and their microbiota that significantly impacts mating preferences. Sexual isolation can be enhanced or reduced by altering the culture media, or the microbiota inhabiting those media. More dramatically, the endoparasite Wolbachia has induced strong mate preferences in some instances. While a sudden, ecologically induced shift in mating preferences falls far short of the changes required for speciation, it might be a first step in that direction. We hypothesize that bacteria-induced sexual isolation is caused by chemosensory cues. In our experiments, bacteria altered the profile of cuticular hydrocarbons, which function as sex pheromones. Commensal bacteria may act directly on these hydrocarbons, or they may affect their synthesis. Alternatively, bacterial metabolites might perfume the flies in ways that affect mate choice. In that event, habituation or conditioning likely plays a role.

  14. 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.

  15. 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. PMID:20602974

  16. Airborne Bacteria in an Urban Environment

    PubMed Central

    Mancinelli, Rocco L.; Shulls, Wells A.

    1978-01-01

    Samples were taken at random intervals over a 2-year period from urban air and tested for viable bacteria. The number of bacteria in each sample was determined, and each organism isolated was identified by its morphological and biochemical characteristics. The number of bacteria found ranged from 0.013 to 1.88 organisms per liter of air sampled. Representatives of 19 different genera were found in 21 samples. The most frequently isolated organisms and their percent of occurence were Micrococcus (41%), Staphylococcus (11%), and Aerococcus (8%). The bacteria isolated were correlated with various weather and air pollution parameters using the Pearson product-moment correlation coefficient method. Statistically significant correlations were found between the number of viable bacteria isolated and the concentrations of nitric oxide (−0.45), nitrogen dioxide (+0.43), and suspended particulate pollutants (+0.56). Calculated individually, the total number of Micrococcus, Aerococcus, and Staphylococcus, number of rods, and number of cocci isolated showed negative correlations with nitric oxide and positive correlations with nitrogen dioxide and particulates. Statistically significant positive correlations were found between the total number of rods isolated and the concentration of nitrogen dioxide (+0.54) and the percent relative humidity (+0.43). The other parameters tested, sulfur dioxide, hydrocarbons, and temperature, showed no significant correlations. Images PMID:677875

  17. 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.

  18. Dynamics of planktonic bacteria and heterotrophic microflagellates in the Parker Estuary, northern Massachusetts

    NASA Astrophysics Data System (ADS)

    Wright, Richard T.; Coffin, Richard B.; Lebo, Martin E.

    1987-11-01

    The temporal and spatial abundance and activities of members of the planktonic microbial food web in a salt marsh estuary were analysed over the course of a year. Analysis of the data was focused on the factors that control the density and productivity of the heterotrophic bacteria. Temperature exercises a long-term influence on substrate sources, but short-term control is a function of the interaction of grazing and substrate supply. A model has been developed to give a framework for understanding how the microbial food web may work under steady-state assumptions. The model assumptions and predictions appear to be supported by the field data. Equations were generated for estimating substrate flux through the bacteria and estimating bacterial density as a result of grazing and substrate input. The results give some insights into the question of whether the heterotrophic bacteria function as a link to higher organisms or as an energy sink.

  19. New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria.

    PubMed

    Gutierrez-Preciado, A; Jensen, R A; Yanofsky, C; Merino, E

    2005-08-01

    The tryptophan operon of Bacillus subtilis serves as an excellent model for investigating transcription regulation in Gram-positive bacteria. In this article, we extend this knowledge by analyzing the predicted regulatory regions in the trp operons of other fully sequenced Gram-positive bacteria. Interestingly, it appears that in eight of the organisms examined, transcription of the trp operon appears to be regulated by tandem T-box elements. These regulatory elements have recently been described in the trp operons of two bacterial species. Single T-box elements are commonly found in Gram-positive bacteria in operons encoding aminoacyl tRNA synthetases and proteins performing other functions. Different regulatory mechanisms appear to be associated with variations of trp gene organization within the trp operon. PMID:15953653

  20. Computational and experimental study of chemotaxis of an ensemble of bacteria attached to a microbead

    NASA Astrophysics Data System (ADS)

    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.

  1. [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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Growth Kinetics of Attached Iron-Oxidizing Bacteria

    PubMed Central

    Wichlacz, Paul L.; Unz, Richard F.

    1985-01-01

    A model of growth and substrate utilization for ferrous-iron-oxidizing bacteria attached to the disks of a rotating biological contactor was developed and tested. The model describes attached bacterial growth as a saturation function in which the rate of substrate utilization is determined by a maximum substrate oxidation rate constant (P), a half-saturation constant (Ks), and the concentration of substrate within the rotating biological contactor (S1). The maximum oxidation rate constant was proportional to flow rate, and the substrate concentration in the reactor varied with influent substrate concentration (S0). The model allowed the prediction of metabolic constants and included terms for both constant and growth-rate-dependent maintenance energies. Estimates for metabolic constants of the attached population of acidophilic, chemolithotrophic, iron-oxidizing bacteria limited by ferrous iron were: maximum specific growth rate (μmax), 1.14 h−1; half-saturation constant (Ks) for ferrous iron, 54.9 mg/liter; constant maintenance energy coefficient (m1), 0.154 h−1; growth-rate-dependent maintenance energy coefficient (m′), 0.07 h−1; maximum yield (Yg), 0.063 mg of organic nitrogen per mg of Fe(II) oxidized. PMID:16346863

  7. 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.

  8. Strategies of isoprenoids production in engineered bacteria.

    PubMed

    Li, Y; Wang, G

    2016-10-01

    Isoprenoids are the largest family of natural products, over 40 000 compounds have been described, which have been widely used in various fields. Currently, the isoprenoid products are mainly produced by natural extraction or chemical synthesis, however, limited yield and high cost is far behind the increasing need. Most bacteria synthesize the precursors of isoprenoids through the methylerythritol 4-phosphate pathway, microbial synthesis of isoprenoids by fermentation becomes more attractive mainly in terms of environmental concern and renewable resources. In this review, the strategies of isoprenoid production in bacteria by synthetic biology are discussed. Introducing foreign genes associated with desired products made it possible to produce isoprenoids in bacteria. Furthermore, the yield of isoprenoids is increased by the strategies of overexpression of native or foreign genes, introducing heterologous mevalonate pathway, balancing of the precursors and inactivating the competing pathway, these methods were used separately or simultaneously. PMID:27428054

  9. Lethal photosensitization of biofilm-grown bacteria

    NASA Astrophysics Data System (ADS)

    Wilson, Michael

    1997-12-01

    Antibacterial agents are increasingly being used for the prophylaxis and treatment of oral diseases. As these agents can be rendered ineffective by resistance development in the target organisms there is a need to develop alternative antimicrobial approaches. Light-activated antimicrobial agents release singlet oxygen and free radicals which can kill adjacent bacteria and a wide range of cariogenic and periodontopathogenic bacteria has been shown to be susceptible to such agents. In the oral cavity these organisms are present as biofilms (dental plaques) which are less susceptible to traditional antimicrobial agents than bacterial suspensions. The results of these studies have shown that biofilm-grown oral bacteria are also susceptible to lethal photosensitization although the light energy doses required are grater than those needed to kill the organisms when they are grown as aqueous suspensions.

  10. 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.

  11. 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. PMID:25131402

  12. 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.

  13. 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.

  14. Inorganic nanoparticles engineered to attack bacteria.

    PubMed

    Miller, Kristen P; Wang, Lei; Benicewicz, Brian C; Decho, Alan W

    2015-11-01

    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.

  15. 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

  16. Detection of cytosolic bacteria by inflammatory caspases.

    PubMed

    Hagar, Jon A; Miao, Edward A

    2014-02-01

    The sanctity of the cytosolic compartment is rigorously maintained by a number of innate immune mechanisms. Inflammasomes detect signatures of microbial infection and trigger caspase-1 or caspase-11 activation, culminating in cytokine secretion and obliteration of the replicative niche via pyroptosis. Recent studies have examined inflammatory caspase responses to cytosolic bacteria, including Burkholderia, Shigella, Listeria, Francisella, and Mycobacterium species. For example, caspase-11 responds to LPS introduced into the cytosol after Gram-negative bacteria escape the vacuole. Not surprisingly, bacteria antagonize these responses; for example, Shigella delivers OspC3 to inhibit caspase-4, a potential human homolog of murine caspase-11. These findings underscore bacterial coevolution with the innate immune system, which has resulted in few, but highly specialized cytosolic pathogens.

  17. Detection of cytosolic bacteria by inflammatory caspases

    PubMed Central

    Hagar, Jon A.; Miao, Edward A.

    2014-01-01

    The sanctity of the cytosolic compartment is rigorously maintained by a number of innate immune mechanisms. Inflammasomes detect signatures of microbial infection and trigger caspase-1 or caspase-11 activation, culminating in cytokine secretion and obliteration of the replicative niche via pyroptosis. Recent studies have examined inflammatory caspase responses to cytosolic bacteria, including Burkholderia, Shigella, Listeria, Francisella, and Mycobacterium species. For example, caspase-11 responds to LPS introduced into the cytosol after Gram-negative bacteria escape the vacuole. Not surprisingly, bacteria antagonize these responses; for example, Shigella delivers OspC3 to inhibit caspase-4. These findings underscore bacterial coevolution with the innate immune system, which has resulted in few, but highly specialized cytosolic pathogens. PMID:24581694

  18. 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. PMID:9732040

  19. 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?.

  20. 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.

  1. 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.

  2. Pervasive transcription: detecting functional RNAs in bacteria.

    PubMed

    Lybecker, Meghan; Bilusic, Ivana; Raghavan, Rahul

    2014-01-01

    Pervasive, or genome-wide, transcription has been reported in all domains of life. In bacteria, most pervasive transcription occurs antisense to protein-coding transcripts, although recently a new class of pervasive RNAs was identified that originates from within annotated genes. Initially considered to be non-functional transcriptional noise, pervasive transcription is increasingly being recognized as important in regulating gene expression. The function of pervasive transcription is an extensively debated question in the field of transcriptomics and regulatory RNA biology. Here, we highlight the most recent contributions addressing the purpose of pervasive transcription in bacteria and discuss their implications.

  3. Formation of magnetosomes in magnetotactic bacteria.

    PubMed

    Schüler, D

    1999-08-01

    The ability of magnetotactic bacteria to orient and migrate along geomagnetic field lines is based on intracellular magnetic structures, the magnetosomes, which comprise nano-sized, membrane bound crystals of magnetic iron minerals. The formation of magnetosomes is achieved by a biological mechanism that controls the accumulation of iron and the biomineralization of magnetic crystals with a characteristic size and morphology within membrane vesicles. This paper focuses on the current knowledge about magnetotactic bacteria and will outline aspects of the physiology and molecular biology of magnetosome formation. The biotechnological potential of the biomineralization process is discussed.

  4. 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.

  5. Degradation of monomethylhydrazine by two soil bacteria

    SciTech Connect

    Ou, L.T.

    1988-12-01

    It has been reported that three heterotrophic soil bacteria had the capacity to degrade hydrazine. One of these organisms, Achromobacter sp., degraded hydrazine to N/sub 2/ gas. Furthermore, it was reported that monomethylhydrazine (MMH) in Arredondo fine sand was mineralized to CO/sub 2/, and that such degradation is microbial. However, microorganisms that degrade MMH have not been reported. MMH and hydrazine are chemically similar to one another. Therefore, this study was initiated to test the capacity of the two hydrazine-degrading bacteria, Achromobacter sp. and Pseudomonas sp., to degrade MMH.

  6. Anammox bacteria: from discovery to application.

    PubMed

    Kuenen, J Gijs

    2008-04-01

    Anaerobic ammonium oxidation (anammox) bacteria, which were discovered in waste-water sludge in the early 1990s, have the unique metabolic ability to combine ammonium and nitrite or nitrate to form nitrogen gas. This discovery led to the realization that a substantial part of the enormous nitrogen losses that are observed in the marine environment--up to 50% of the total nitrogen turnover--were due to the activity of these bacteria. In this Timeline, Gijs Kuenen recalls the discovery of these unique microorganisms and describes the continuing elucidation of their roles in environmental and industrial microbiology.

  7. [Quorum sensing in bacteria and yeast].

    PubMed

    March Rosselló, Gabriel Alberto; Eiros Bouza, José María

    2013-10-19

    Bacterial sets are complex dynamic systems, which interact with each other and through the interaction, bacteria coexist, collaborate, compete and share information in a coordinated manner. A way of bacterial communication is quorum sensing. Through this mechanism the bacteria can recognize its concentration in a given environment and they can decide the time at which the expression of a particular set of genes should be started for developing a specific and simultaneous response. The result of these interconnections raises properties that cannot be explained from a single isolated bacterial cell.

  8. 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.

  9. 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

  10. 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.

  11. Cadmium uptake and resistance among selected bacteria

    SciTech Connect

    Burke, B.E.

    1987-01-01

    The purpose of this research was to determine the relationship between Cd resistance and Cd uptake by lake sediment bacteria. For the Gram positive and gram negative sediment bacteria that were tested, the relationship between resistance and Cd uptake varied and was dependent on the isolate under consideration. Results of this study indicated that bacterial communities in lake sediments may influence the concentration and availability of Cd in sediments and the water column. In addition, results of this study did not support the theory that the genes encoding for Cd resistance are usually carried on antibiotic resistance plasmids.

  12. Flavones with antibacterial activity against cariogenic bacteria.

    PubMed

    Sato, M; Fujiwara, S; Tsuchiya, H; Fujii, T; Iinuma, M; Tosa, H; Ohkawa, Y

    1996-11-01

    Methanolic extracts obtained from 13 plants were studied for their antibacterial activity against cariogenic bacteria. Among them, the extract from Artocarpus heterophyllus showed the most intensive activity. Serial chromatographic purifications offered two active compounds which were identified as 6-(3-methyl-1-butenyl)-5,2',4'-trihydroxy-3-isoprenyl-7-methoxy flavone and 5,7,2',4'-tetrahydroxy-6-isoprenylflavone. Both isolates completely inhibited the growth of primary cariogenic bacteria at 3.13-12.5 micrograms/ml. They also exhibited the growth inhibitory effects on plaque-forming streptococci. These phytochemical isoprenylflavones would be potent compounds for the prevention of dental caries.

  13. Basic Laboratory Culture Methods for Anaerobic Bacteria

    NASA Astrophysics Data System (ADS)

    Strobel, Herbert J.

    Oxygen is either limiting or absent in many ecosystems. Anaerobic bacteria are often key players in such environments and these organisms have important roles in geo-elemental cycling, agriculture, and medicine. The metabolic versatility of anaerobes is exploited in a variety of industrial processes including fermented food production, biochemical synthesis, and bioremediation. There has been recent considerable interest in developing and enhancing technologies that employ anaerobes as biocatalysts. The study of anaerobic bacteria requires specialized techniques, and specific methods are described for the culture and manipulation of these microbes.

  14. Life with compass: diversity and biogeography of magnetotactic bacteria.

    PubMed

    Lin, Wei; Bazylinski, Dennis A; Xiao, Tian; Wu, Long-Fei; Pan, Yongxin

    2014-09-01

    Magnetotactic bacteria (MTB) are unique in their ability to synthesize intracellular nano-sized minerals of magnetite and/or greigite magnetosomes for magnetic orientation. Thus, they provide an excellent model system to investigate mechanisms of biomineralization. MTB play important roles in bulk sedimentary magnetism and have numerous versatile applications in paleoenvironmental reconstructions, and biotechnological and biomedical fields. Significant progress has been made in recent years in describing the composition of MTB communities and distribution through innovative cultivation-dependent and -independent techniques. In this review, the most recent contributions to the field of diversity and biogeography of MTB are summarized and reviewed. Emphasis is on the novel insights into various factors/processes potentially affecting MTB community distribution. An understanding of the present-day biogeography of MTB, and the ruling parameters of their spatial distribution, will eventually help us predict MTB community shifts with environmental changes and assess their roles in global iron cycling. PMID:24148107

  15. Growth Yields of Bacteria on Selected Organic Compounds

    PubMed Central

    Mayberry, W. R.; Prochazka, G. J.; Payne, W. J.

    1967-01-01

    Cell yields were determined for two bacterial soil isolants grown aerobically in minimal media on a variety of synthetic organic compounds. 1-Dodecanol, benzoic acid, phenylacetic acid, phenylglyoxylic acid, and diethylene, triethylene, and tetraethylene glycols were tested. Two “biochemicals,” succinate and acetate, were also tested for comparison. Yields were calculated on the basis of grams of cells obtained per mole of substrate utilized, gram atom of carbon utilized, mole of oxygen consumed, and equivalent of “available electrons” in the substrates. This latter value appears to be nearly constant at 3 g of cells per equivalent of “available electrons.” Yields predicted on this basis for other bacteria and for yeasts on other substrates are in fair agreement with reported values. PMID:16349741

  16. Modelling strategies for the industrial exploitation of lactic acid bacteria.

    PubMed

    Teusink, Bas; Smid, Eddy J

    2006-01-01

    Lactic acid bacteria (LAB) have a long tradition of use in the food industry, and the number and diversity of their applications has increased considerably over the years. Traditionally, process optimization for these applications involved both strain selection and trial and error. More recently, metabolic engineering has emerged as a discipline that focuses on the rational improvement of industrially useful strains. In the post-genomic era, metabolic engineering increasingly benefits from systems biology, an approach that combines mathematical modelling techniques with functional-genomics data to build models for biological interpretation and--ultimately--prediction. In this review, the industrial applications of LAB are mapped onto available global, genome-scale metabolic modelling techniques to evaluate the extent to which functional genomics and systems biology can live up to their industrial promise.

  17. Life with compass: diversity and biogeography of magnetotactic bacteria

    SciTech Connect

    Lin, Wei; Bazylinski, Dennis A; Xiao, Tian; Wu, Long-Fei; Pan, Yongxin

    2013-11-12

    Magnetotactic bacteria (MTB) are unique in their ability to synthesize intracellular nano-sized minerals of magnetite and/or greigite magnetosomes for magnetic orientation. Thus, they provide an excellent model system to investigate mechanisms of biomineralization. MTB play important roles in bulk sedimentary magnetism and have numerous versatile applications in paleoenvironmental reconstructions, and biotechnological and biomedical fields. Significant progress has been made in recent years in describing the composition of MTB communities and distribution through innovative cultivation-dependent and -independent techniques. In this review, the most recent contributions to the field of diversity and biogeography of MTB are summarized and reviewed. Emphasis is on the novel insights into various factors/processes potentially affecting MTB community distribution. An understanding of the present-day biogeography of MTB, and the ruling parameters of their spatial distribution, will eventually help us predict MTB community shifts with environmental changes and assess their roles in global iron cycling.

  18. Climate change alters ecological strategies of soil bacteria.

    PubMed

    Evans, Sarah E; Wallenstein, Matthew D

    2014-02-01

    The timing and magnitude of rainfall events are expected to change in future decades, resulting in longer drought periods and larger rainfall events. Although microbial community composition and function are both sensitive to changes in rainfall, it is unclear whether this is because taxa adopt strategies that maximise fitness under new regimes. We assessed whether bacteria exhibited phylogenetically conserved ecological strategies in response to drying-rewetting, and whether these strategies were altered by historical exposure to experimentally intensified rainfall patterns. By clustering relative abundance patterns, we identified three discrete ecological strategies and found that tolerance to drying-rewetting increased with exposure to intensified rainfall patterns. Changes in strategy were primarily due to changes in community composition, but also to strategy shifts within taxa. These moisture regime-selected ecological strategies may be predictable from disturbance history, and are likely to be linked to traits that influence the functional potential of microbial communities.

  19. By their genes ye shall know them: genomic signatures of predatory bacteria

    PubMed Central

    Pasternak, Zohar; Pietrokovski, Shmuel; Rotem, Or; Gophna, Uri; Lurie-Weinberger, Mor N; Jurkevitch, Edouard

    2013-01-01

    Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria. PMID:23190728

  20. Oxidative Stress Parameters in Saliva and Its Association with Periodontal Disease and Types of Bacteria

    PubMed Central

    Almerich-Silla, Jose Manuel; Montiel-Company, Jose María; Pastor, Sara; Serrano, Felipe; Puig-Silla, Miriam; Dasí, Francisco

    2015-01-01

    Objective. To determine the association between oxidative stress parameters with periodontal disease, bleeding, and the presence of different periodontal bacteria. Methods. A cross-sectional study in a sample of eighty-six patients, divided into three groups depending on their periodontal status. Thirty-three with chronic periodontitis, sixteen with gingivitis, and thirty-seven with periodontal healthy as control. Oxidative stress biomarkers (8-OHdG and MDA), total antioxidant capacity (TAOC), and the activity of two antioxidant enzymes (GPx and SOD) were determined in saliva. Subgingival plaque samples were obtained from the deepest periodontal pocket and PCR was used to determine the presence of the 6 fimA genotypes of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, and Treponema denticola. Results. Periodontal disease was found to be associated with increased oxidative stress parameter levels. These levels rose according to the number and type of different periodontal bacteria found in the periodontal pockets. The presence of different types of periodontal bacteria is predictive independent variables in linear regresion models of oxidative stress parameters as dependent variable, above all 8-OHdG. Conclusions. Oxidative stress parameter levels are correlated with the presence of different types of bacteria. Determination of these levels and periodontal bacteria could be a potent tool for controlling periodontal disease development. PMID:26494938

  1. Modelling the effect of lactic acid bacteria from starter- and aroma culture on growth of Listeria monocytogenes in cottage cheese.

    PubMed

    Østergaard, Nina Bjerre; Eklöw, Annelie; Dalgaard, Paw

    2014-10-01

    Four mathematical models were developed and validated for simultaneous growth of mesophilic lactic acid bacteria from added cultures and Listeria monocytogenes, during chilled storage of cottage cheese with fresh- or cultured cream dressing. The mathematical models include the effect of temperature, pH, NaCl, lactic- and sorbic acid and the interaction between these environmental factors. Growth models were developed by combining new and existing cardinal parameter values. Subsequently, the reference growth rate parameters (μref at 25°C) were fitted to a total of 52 growth rates from cottage cheese to improve model performance. The inhibiting effect of mesophilic lactic acid bacteria from added cultures on growth of L. monocytogenes was efficiently modelled using the Jameson approach. The new models appropriately predicted the maximum population density of L. monocytogenes in cottage cheese. The developed models were successfully validated by using 25 growth rates for L. monocytogenes, 17 growth rates for lactic acid bacteria and a total of 26 growth curves for simultaneous growth of L. monocytogenes and lactic acid bacteria in cottage cheese. These data were used in combination with bias- and accuracy factors and with the concept of acceptable simulation zone. Evaluation of predicted growth rates of L. monocytogenes in cottage cheese with fresh- or cultured cream dressing resulted in bias-factors (Bf) of 1.07-1.10 with corresponding accuracy factor (Af) values of 1.11 to 1.22. Lactic acid bacteria from added starter culture were on average predicted to grow 16% faster than observed (Bf of 1.16 and Af of 1.32) and growth of the diacetyl producing aroma culture was on average predicted 9% slower than observed (Bf of 0.91 and Af of 1.17). The acceptable simulation zone method showed the new models to successfully predict maximum population density of L. monocytogenes when growing together with lactic acid bacteria in cottage cheese. 11 of 13 simulations of L

  2. Modelling the effect of lactic acid bacteria from starter- and aroma culture on growth of Listeria monocytogenes in cottage cheese.

    PubMed

    Østergaard, Nina Bjerre; Eklöw, Annelie; Dalgaard, Paw

    2014-10-01

    Four mathematical models were developed and validated for simultaneous growth of mesophilic lactic acid bacteria from added cultures and Listeria monocytogenes, during chilled storage of cottage cheese with fresh- or cultured cream dressing. The mathematical models include the effect of temperature, pH, NaCl, lactic- and sorbic acid and the interaction between these environmental factors. Growth models were developed by combining new and existing cardinal parameter values. Subsequently, the reference growth rate parameters (μref at 25°C) were fitted to a total of 52 growth rates from cottage cheese to improve model performance. The inhibiting effect of mesophilic lactic acid bacteria from added cultures on growth of L. monocytogenes was efficiently modelled using the Jameson approach. The new models appropriately predicted the maximum population density of L. monocytogenes in cottage cheese. The developed models were successfully validated by using 25 growth rates for L. monocytogenes, 17 growth rates for lactic acid bacteria and a total of 26 growth curves for simultaneous growth of L. monocytogenes and lactic acid bacteria in cottage cheese. These data were used in combination with bias- and accuracy factors and with the concept of acceptable simulation zone. Evaluation of predicted growth rates of L. monocytogenes in cottage cheese with fresh- or cultured cream dressing resulted in bias-factors (Bf) of 1.07-1.10 with corresponding accuracy factor (Af) values of 1.11 to 1.22. Lactic acid bacteria from added starter culture were on average predicted to grow 16% faster than observed (Bf of 1.16 and Af of 1.32) and growth of the diacetyl producing aroma culture was on average predicted 9% slower than observed (Bf of 0.91 and Af of 1.17). The acceptable simulation zone method showed the new models to successfully predict maximum population density of L. monocytogenes when growing together with lactic acid bacteria in cottage cheese. 11 of 13 simulations of L

  3. Influence of the Biliary System on Biliary Bacteria Revealed by Bacterial Communities of the Human Biliary and Upper Digestive Tracts.

    PubMed

    Ye, Fuqiang; Shen, Hongzhang; Li, Zhen; Meng, Fei; Li, Lei; Yang, Jianfeng; Chen, Ying; Bo, Xiaochen; Zhang, Xiaofeng; Ni, Ming

    2016-01-01

    Biliary bacteria have been implicated in gallstone pathogenesis, though a clear understanding of their composition and source is lacking. Moreover, the effects of the biliary environment, which is known to be generally hostile to most bacteria, on biliary bacteria are unclear. Here, we investigated the bacterial communities of the biliary tract, duodenum, stomach, and oral cavity from six gallstone patients by using 16S rRNA amplicon sequencing. We found that all observed biliary bacteria were detectable in the upper digestive tract. The biliary microbiota had a comparatively higher similarity with the duodenal microbiota, versus those of the other regions, but with a reduced diversity. Although the majority of identified bacteria were greatly diminished in bile samples, three Enterobacteriaceae genera (Escherichia, Klebsiella, and an unclassified genus) and Pyramidobacter were abundant in bile. Predictive functional analysis indicated enhanced abilities of environmental information processing and cell motility of biliary bacteria. Our study provides evidence for the potential source of biliary bacteria, and illustrates the influence of the biliary system on biliary bacterial communities.

  4. Influence of the Biliary System on Biliary Bacteria Revealed by Bacterial Communities of the Human Biliary and Upper Digestive Tracts

    PubMed Central

    Ye, Fuqiang; Shen, Hongzhang; Li, Zhen; Meng, Fei; Li, Lei; Yang, Jianfeng; Chen, Ying; Bo, Xiaochen; Zhang, Xiaofeng; Ni, Ming

    2016-01-01

    Biliary bacteria have been implicated in gallstone pathogenesis, though a clear understanding of their composition and source is lacking. Moreover, the effects of the biliary environment, which is known to be generally hostile to most bacteria, on biliary bacteria are unclear. Here, we investigated the bacterial communities of the biliary tract, duodenum, stomach, and oral cavity from six gallstone patients by using 16S rRNA amplicon sequencing. We found that all observed biliary bacteria were detectable in the upper digestive tract. The biliary microbiota had a comparatively higher similarity with the duodenal microbiota, versus those of the other regions, but with a reduced diversity. Although the majority of identified bacteria were greatly diminished in bile samples, three Enterobacteriaceae genera (Escherichia, Klebsiella, and an unclassified genus) and Pyramidobacter were abundant in bile. Predictive functional analysis indicated enhanced abilities of environmental information processing and cell motility of biliary bacteria. Our study provides evidence for the potential source of biliary bacteria, and illustrates the influence of the biliary system on biliary bacterial communities. PMID:26930491

  5. Bacteria in Crude Oil Survived Autoclaving and Stimulated Differentially by Exogenous Bacteria

    PubMed Central

    Guo, Peng; Chi, Chang-Qiao; Chen, Jian; Wang, Xing-Biao; Tang, Yue-Qin; Wu, Xiao-Lei; Liu, Chun-Zhong

    2012-01-01

    Autoclaving of crude oil is often used to evaluate the hydrocarbon-degrading abilities of bacteria. This may be potentially useful for bioaugmentation and microbial enhanced oil recovery (MEOR). However, it is not entirely clear if “endogenous” bacteria (e.g., spores) in/on crude oil survive the autoclaving process, or influence subsequent evaluation of the hydrocarbon-degradation abilities of the “exogenous” bacterial strains. To test this, we inoculated autoclaved crude oil medium with six exogenous bacterial strains (three Dietzia strains, two Acinetobacter strains, and one Pseudomonas strain). The survival of the spore-forming Bacillus and Paenibacillus and the non-spore-forming mesophilic Pseudomonas, Dietzia, Alcaligenes, and Microbacterium was detected using a 16S rRNA gene clone library and terminal restriction fragment length polymorphism (T-RFLP) analysis. However, neither bacteria nor bacterial activity was detected in three controls consisting of non-inoculated autoclaved crude oil medium. These results suggest that detection of endogenous bacteria was stimulated by the six inoculated strains. In addition, inoculation with Acinetobacter spp. stimulated detection of Bacillus, while inoculation with Dietzia spp. and Pseudomonas sp. stimulated the detection of more Pseudomonas. In contrast, similar exogenous bacteria stimulated similar endogenous bacteria at the genus level. Based on these results, special emphasis should be applied to evaluate the influence of bacteria capable of surviving autoclaving on the hydrocarbon-degrading abilities of exogenous bacteria, in particular, with regard to bioaugmentation and MEOR. Bioaugmentation and MEOR technologies could then be developed to more accurately direct the growth of specific endogenous bacteria that may then improve the efficiency of treatment or recovery of crude oil. PMID:23028421

  6. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

    NASA Astrophysics Data System (ADS)

    Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

    2013-04-01

    Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

  7. Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System

    PubMed Central

    Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

    2013-01-01

    Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population. PMID:23492852

  8. Heterotrophic bacteria in drinking water distribution system: a review.

    PubMed

    Chowdhury, Shakhawat

    2012-10-01

    The microbiological quality of drinking water in municipal water distribution systems (WDS) depends on several factors. Free residual chlorine and/or chloramines are typically used to minimize bacterial recontamination and/or regrowth in WDS. Despite such preventive measures, regrowth of heterotrophic (HPC) and opportunistic bacteria in bulk water and biofilms has yet to be controlled completely. No approach has shown complete success in eliminating biofilms or HPC bacteria from bulk water and pipe surfaces. Biofilms can provide shelter for pathogenic bacteria and protect these bacteria from disinfectants. Some HPC bacteria may be associated with aesthetic and non-life threatening diseases. Research to date has achieved important success in understanding occurrence and regrowth of bacteria in bulk water and biofilms in WDS. To achieve comprehensive understanding and to provide efficient control against bacteria regrowth, future research on bacteria regrowth dynamics and their implications is warranted. In this study, a review was performed on the literature published in this area. The findings and limitations of these papers are summarized. Occurrences of bacteria in WDS, factors affecting bacteria regrowth in bulk water and biofilms, bacteria control strategies, sources of nutrients, human health risks from bacterial exposure, modelling of bacteria regrowth and methods of bacteria sampling and detection and quantification are investigated. Advances to date are noted, and future research needs are identified. Finally, research directions are proposed to effectively control HPC and opportunistic bacteria in bulk water and biofilms in WDS.

  9. Transport of free and particulate-associated bacteria in karst

    USGS Publications Warehouse

    Mahler, B.J.; Personne, J.-C.; Lods, G.F.; Drogue, C.

    2000-01-01

    high bacterial concentrations found in both wells, despite the difference in hydraulic conductivity, demonstrates the difficulty of predicting vulnerability of individual wells to bacterial contamination in karst. The extreme temporal variability in bacterial concentrations underscores the importance of event-based monitoring of the bacterial quality of public water supplies in karst. (C) 2000 Elsevier Science B.V.Karst aquifers, because of their unique hydrogeologic characteristics, are extremely susceptible to contamination by pathogens. Here we present the results of an investigation of contamination of a karst aquifer by fecal indicator bacteria. Two wells intercepting zones with contrasting effective hydraulic conductivities, as determined by pump test, were monitored both during the dry season and in response to a rain event. Samples were also collected from the adjacent ephemeral surface stream, which is known to be impacted by an upstream wastewater treatment plant after rainfall. Whole water and suspended sediment samples were analyzed for fecal coliforms and enterococci. During the dry season, pumping over a 2-day period resulted in increases in concentrations of fecal coliforms to greater than 10,000 CFU/100 ml in the high-conductivity well; enterococci and total suspended solids also increased, to a lesser degree. Toward the end of the pumping period, as much as 50% of the fecal coliforms were associated with suspended sediment. Irrigation of an up-gradient pine plantation with primary-treated wastewater is the probable source of the bacterial contamination. Sampling after a rain event revealed the strong influence of water quality of the adjacent Terrieu Creek on the ground water. Bacterial concentrations in the wells showed a rapid response to increased concentrations in the surface water, with fecal coliform concentrations in ground water ultimately reaching 60,000 CFU/100 ml. Up to 100% of the bacteria in the ground water was associated with suspended

  10. Measurement of hydrocarbon transport in bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to the hydrophobic, volatility, and relatively low aqueous solubility of aliphatic and aromatic hydrocarbons, transport of these chemicals by bacteria has not been extensively studied. These issues make transport assays difficult to carry out, and as a result, strong evidence for the active tran...

  11. Measurement of Hydrocarbon Transport in Bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hydrocarbon uptake by bacteria has not been extensively studied, and strong evidence for active transport of hydrocarbons is lacking. The volatile nature of hydrocarbons, their hydrophobicity, and their relatively low aqueous solubilities can complicate transport assays. Here we present a detailed...

  12. Jumping Genes: The Transposable DNAs of Bacteria.

    ERIC Educational Resources Information Center

    Berg, Claire M.; Berg, Douglas E.

    1984-01-01

    Transposons are transposable elements that carry genes for antibiotic resistance. Provides background information on the structure and organization of these "jumping genes" in bacteria. Also describes the use of transposons in tagging genes and lists pertinent references and resource materials. (DH)

  13. ACETOGENIC BACTERIA ASSOCIATED WITH SEAGRASS ROOTS

    EPA Science Inventory

    Seagrasses are adapted to being rooted in reduced, anoxic sediments with high rates of sulfate reduction. During the day, an oxygen gradient is generated around the roots, becoming anoxic at night. Thus, obligate anaerobic bacteria in the rhizosphere have to tolerate elevated oxy...

  14. Platinum electrodes for electrochemical detection of bacteria

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R.

    1979-01-01

    Bacteria is detected electro-chemically by measuring evolution of hydrogen in test system with platinum and reference electrode. Using system, electrodes of platinum are used to detect and enumerate varieties of gram-positive and gram-negative organisms compared in different media.

  15. [Transport of subsurface bacteria in porous media

    SciTech Connect

    Not Available

    1992-08-01

    This report describes studies undertaken to better understand basic microbiology of deep underground regions with special reference to Savannah River Plant. The studies related herein describe studies to enhance sampling methods of deep aquifers and soil columns, to develop equipment to better understand the migration of bacteria in deep soils, and to improve methods to culturing and maintaining deep isolates.

  16. (Transport of subsurface bacteria in porous media)

    SciTech Connect

    Not Available

    1992-01-01

    This report describes studies undertaken to better understand basic microbiology of deep underground regions with special reference to Savannah River Plant. The studies related herein describe studies to enhance sampling methods of deep aquifers and soil columns, to develop equipment to better understand the migration of bacteria in deep soils, and to improve methods to culturing and maintaining deep isolates.

  17. Transport of bacteria in unsaturated porous media

    NASA Astrophysics Data System (ADS)

    Schäfer, Anke; Ustohal, Petr; Harms, Hauke; Stauffer, Fritz; Dracos, Themistocles; Zehnder, Alexander J. B.

    1998-09-01

    Bacterial mobility in unsaturated soils plays an important role in bioremediation, biofacilitated transport of pollutants, and dispersal of pathogenic microorganisms. A sand column equipped with ports for measuring water pressure and water saturation has been used to study bacterial transport under well-defined unsaturated flow conditions. Bacterial breakthrough curves at various water saturations were obtained for two soil bacteria. Retention of hydrophobic Rhodococcus sp. C125 and mesohydrophilic Pseudomonas putida mt2 was markedly increased at lower water saturation. A mechanistic model for bacterial transport under unsaturated conditions is proposed. The model attributes stronger bacterial retention under unsaturated conditions to the accumulation of bacteria at the air-water interface. Moreover, the model takes into account changes in the available surface areas of both the solid surface and the air-water interface due to coverage by bacteria and changes in the water flow. Application of the model to our own data and data from the literature showed that short-term breakthrough experiments can be simulated, but that the model deviates from experimental observation in long-term experiments. Reasons for this deviation are discussed, and suggestions for a further model extension are made. All investigated colloidal particles had a higher affinity to the air-water interface than to the solid surface. Therefore, trapping of bacteria by air-water interfaces is an important process possibly controlling bacterial transport in unsaturated soils.

  18. Freeze-drying of lactic acid bacteria.

    PubMed

    Fonseca, Fernanda; Cenard, Stéphanie; Passot, Stéphanie

    2015-01-01

    Lactic acid bacteria are of great importance for the food and biotechnology industry. They are widely used as starters for manufacturing food (e.g., yogurt, cheese, fermented meats, and vegetables) and probiotic products, as well as for green chemistry applications. Freeze-drying or lyophilization is a convenient method for preservation of bacteria. By reducing water activity to values below 0.2, it allows long-term storage and low-cost distribution at suprazero temperatures, while minimizing losses in viability and functionality. Stabilization of bacteria via freeze-drying starts with the addition of a protectant solution to the bacterial suspension. Freeze-drying includes three steps, namely, (1) freezing of the concentrated and protected cell suspension, (2) primary drying to remove ice by sublimation, and (3) secondary drying to remove unfrozen water by desorption. In this chapter we describe a method for freeze-drying of lactic acid bacteria at a pilot scale, thus allowing control of the process parameters for maximal survival and functionality recovery.

  19. INTERACTIONS OF INTRODUCED BACTERIA AND AQUATIC INVERTEBRATES

    EPA Science Inventory

    Bacteria enter into stream environments from a variety of sources and interact in varying ways with other biota. There were three basic objectives for this project: 1) to examine the effect of different types of macroinvertebrates on bacterial survival and distribution, 2) to com...

  20. Automated detection of bacteria in urine

    NASA Technical Reports Server (NTRS)

    Fleig, A. J.; Picciolo, G. L.; Chappelle, E. W.; Kelbaugh, B. N.

    1972-01-01

    A method for detecting the presence of bacteria in urine was developed which utilizes the bioluminescent reaction of adenosine triphosphate with luciferin and luciferase derived from the tails of fireflies. The method was derived from work on extraterrestrial life detection. A device was developed which completely automates the assay process.

  1. Metabolic engineering of bacteria for ethanol production

    SciTech Connect

    Ingram, L.O.; Gomez, P.F.; Lai, X.; Moniruzzaman, M.; Wood, B.E.; Yomano, L.P.; York, S.W.

    1998-04-20

    Technologies are available which will allow the conversion of lignocellulose into fuel ethanol using genetically engineered bacteria. Assembling these into a cost-effective process remains a challenge. The authors` work has focused primarily on the genetic engineering of enteric bacteria using a portable ethanol production pathway. Genes encoding Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase have been integrated into the chromosome of Escherichia coli B to produce strain KO11 for the fermentation of hemicellulose-derived syrups. This organism can efficiently ferment all hexose and pentose sugars present in the polymers of hemicellulose. Klebsiella oxytoca M5A1 has been genetically engineered in a similar manner to produce strain P2 for ethanol production from cellulose. This organism has the native ability to ferment cellobiose and cellotriose, eliminating the need for one class of cellulase enzymes. The optimal pH for cellulose fermentation with this organism is near that of fungal cellulases. The general approach for the genetic engineering of new biocatalysts has been most successful with enteric bacteria thus far. However, this approach may also prove useful with gram-positive bacteria which have other important traits for lignocellulose conversion. Many opportunities remain for further improvements in the biomass to ethanol processes.

  2. Antibiotic-Resistant Bacteria: There is Hope.

    ERIC Educational Resources Information Center

    Offner, Susan

    1998-01-01

    Argues that reduction in the use of antibiotics would enable antibiotic-sensitive bacteria to flourish. Presents an activity designed to show students how a small, seemingly unimportant difference in doubling time can, over a period of time, make an enormous difference in population size. (DDR)

  3. Trans unsaturated fatty acids in bacteria.

    PubMed

    Keweloh, H; Heipieper, H J

    1996-02-01

    The occurrence of trans unsaturated fatty acids as by-products of fatty acid transformations carried out by the obligate anaerobic ruminal microflora has been well known for a long time. In recent years, fatty acids with trans configurations also have been detected in the membrane lipids of various aerobic bacteria. Besides several psychrophilic organisms, bacteria-degrading pollutants, such as Pseudomonas putida, are able to synthesize these compounds de novo. In contrast to the trans fatty acids formed by rumen bacteria, the membrane constituents of aerobic bacteria are synthesized by a direct isomerization of the complementary cis configuration of the double bond without a shift of the position. This system of isomerization is located in the cytoplasmic membrane. The conversion of cis unsaturated fatty acids to trans changes the membrane fluidity in response to environmental stimuli, particularly where growth is inhibited due to the presence of high concentrations of toxic substances. Under these conditions, lipid synthesis also stops so that the cells are not able to modify their membrane fluidity by any other mechanism.

  4. Regulating alternative lifestyles in entomopathogenic bacteria.

    PubMed

    Crawford, Jason M; Kontnik, Renee; Clardy, Jon

    2010-01-12

    Bacteria belonging to the genera Photorhabdus and Xenorhabdus participate in a trilateral symbiosis in which they enable their nematode hosts to parasitize insect larvae. The bacteria switch from persisting peacefully in a nematode's digestive tract to a lifestyle in which pathways to produce insecticidal toxins, degrading enzymes to digest the insect for consumption, and antibiotics to ward off bacterial and fungal competitors are activated. This study addresses three questions: (1) What molecular signal triggers antibiotic production in the bacteria? (2) What small molecules are regulated by the signal? And (3), how do the bacteria recognize the signal? Differential metabolomic profiling in Photorhabdus luminescens TT01 and Xenorhabdus nematophila revealed that L-proline in the insect's hemolymph initiates a metabolic shift. Small molecules known to be crucial for virulence and antibiosis in addition to previously unknown metabolites are dramatically upregulated by L-proline, linking the recognition of host environment to bacterial metabolic regulation. To identify the L-proline-induced signaling pathway, we deleted the proline transporters putP and proU in P. luminescens TT01. Studies of these strains support a model in which acquisition of L-proline both regulates the metabolic shift and maintains the bacterial proton motive force that ultimately regulates the downstream bacterial pathways affecting virulence and antibiotic production. PMID:20022247

  5. Endocarditis Due to Rare and Fastidious Bacteria

    PubMed Central

    Brouqui, P.; Raoult, D.

    2001-01-01

    The etiologic diagnosis of infective endocarditis is easily made in the presence of continuous bacteremia with gram-positive cocci. However, the blood culture may contain a bacterium rarely associated with endocarditis, such as Lactobacillus spp., Klebsiella spp., or nontoxigenic Corynebacterium, Salmonella, Gemella, Campylobacter, Aeromonas, Yersinia, Nocardia, Pasteurella, Listeria, or Erysipelothrix spp., that requires further investigation to establish the relationship with endocarditis, or the blood culture may be uninformative despite a supportive clinical evaluation. In the latter case, the etiologic agents are either fastidious extracellular or intracellular bacteria. Fastidious extracellular bacteria such as Abiotrophia, HACEK group bacteria, Clostridium, Brucella, Legionella, Mycobacterium, and Bartonella spp. need supplemented media, prolonged incubation time, and special culture conditions. Intracellular bacteria such as Coxiella burnetii cannot be isolated routinely. The two most prevalent etiologic agents of culture-negative endocarditis are C. burnetti and Bartonella spp. Their diagnosis is usually carried out serologically. A systemic pathologic examination of excised heart valves including periodic acid-Schiff (PAS) staining and molecular methods has allowed the identification of Whipple's bacillus endocarditis. Pathologic examination of the valve using special staining, such as Warthin-Starry, Gimenez, and PAS, and broad-spectrum PCR should be performed systematically when no etiologic diagnosis is evident through routine laboratory evaluation. PMID:11148009

  6. Bacteria-mediated bisphenol A degradation.

    PubMed

    Zhang, Weiwei; Yin, Kun; Chen, Lingxin

    2013-07-01

    Bisphenol A (BPA) is an important monomer in the manufacture of polycarbonate plastics, food cans, and other daily used chemicals. Daily and worldwide usage of BPA and BPA-contained products led to its ubiquitous distribution in water, sediment/soil, and atmosphere. Moreover, BPA has been identified as an environmental endocrine disruptor for its estrogenic and genotoxic activity. Thus, BPA contamination in the environment is an increasingly worldwide concern, and methods to efficiently remove BPA from the environment are urgently recommended. Although many factors affect the fate of BPA in the environment, BPA degradation is mainly depended on the metabolism of bacteria. Many BPA-degrading bacteria have been identified from water, sediment/soil, and wastewater treatment plants. Metabolic pathways of BPA degradation in specific bacterial strains were proposed, based on the metabolic intermediates detected during the degradation process. In this review, the BPA-degrading bacteria were summarized, and the (proposed) BPA degradation pathway mediated by bacteria were referred. PMID:23681588

  7. Network models of phage-bacteria coevolution

    NASA Astrophysics Data System (ADS)

    Rosvall, Martin; Dodd, Ian B.; Krishna, Sandeep; Sneppen, Kim

    2006-12-01

    Bacteria and their bacteriophages are the most abundant, widespread, and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages, and temperate phages might affect the diversity of these groups, we developed a stochastic network model for examining the coevolution of these ecologies. In our approach, nodes represent whole species or strains of bacteria or phages, rather than individuals, with “speciation” and extinction modeled by duplication and removal of nodes. Phage-bacteria links represent host-parasite relationships and temperate-virulent phage links denote prophage-encoded resistance. The effect of horizontal transfer of genetic information between strains was also included in the dynamical rules. The observed networks evolved in a highly dynamic fashion but the ecosystems were prone to collapse (one or more entire groups going extinct). Diversity could be stably maintained in the model only if the probability of speciation was independent of the diversity. Such an effect could be achieved in real ecosystems if the speciation rate is primarily set by the availability of ecological niches.

  8. Automatic bio-sample bacteria detection system

    NASA Technical Reports Server (NTRS)

    Chappelle, E. W.; Colburn, M.; Kelbaugh, B. N.; Picciolo, G. L.

    1971-01-01

    Electromechanical device analyzes urine specimens in 15 minutes and processes one sample per minute. Instrument utilizes bioluminescent reaction between luciferase-luciferin mixture and adenosine triphosphate (ATP) to determine number of bacteria present in the sample. Device has potential application to analysis of other body fluids.

  9. NSAID enteropathy and bacteria: a complicated relationship.

    PubMed

    Syer, Stephanie D; Blackler, Rory W; Martin, Rebeca; de Palma, Giada; Rossi, Laura; Verdu, Elena; Bercik, Premek; Surette, Michael G; Aucouturier, Anne; Langella, Philippe; Wallace, John L

    2015-04-01

    The clinical significance of small intestinal damage caused by nonsteroidal anti-inflammatory drugs (NSAIDs) remains under-appreciated. It occurs with greater frequency than the damage caused by these drugs in the upper gastrointestinal tract, but is much more difficult to diagnose and treat. Although the pathogenesis of NSAID enteropathy remains incompletely understood, it is clear that bacteria, bile, and the enterohepatic circulation of NSAIDs are all important factors. However, they are also interrelated with one another. Bacterial enzymes can affect the cytotoxicity of bile and are essential for enterohepatic circulation of NSAIDs. Gram-negative bacteria appear to be particularly important in the pathogenesis of NSAID enteropathy, possibly through release of endotoxin. Inhibitors of gastric acid secretion significantly aggravate NSAID enteropathy, and this effect is due to significant changes in the intestinal microbiome. Treatment with antibiotics can, in some circumstances, reduce the severity of NSAID enteropathy, but published results are inconsistent. Specific antibiotic-induced changes in the microbiota have not been causally linked to prevention of intestinal damage. Treatment with probiotics, particularly Bifidobacterium, Lactobacillus, and Faecalibacteriaum prausnitzii, has shown promising effects in animal models. Our studies suggest that these beneficial effects are due to colonization by the bacteria, rather than to products released by the bacteria.

  10. [Innovative treatments for multidrug-resistant bacteria].

    PubMed

    Pierre, Tattevin; Aurélien, Lorleac'h; Matthieu, Revest

    2014-03-01

    The spread of multidrug-resistant bacteria has accelerated sharply in the last decade. According to the World Health Organization they are responsible for an estimated 25 000 deaths in Europe each year. In addition, few new antibiotics are under development, raising the spectrum of a return to the "pre-antibiotic era". Non antibiotic antibacterial agents have recently attracted renewed interest. The most promising candidates are: i) phages (bacteria-infecting viruses) have been widely used in Eastern European countries since the 1930s but come up against logistic and regulatory obstacles due to the evolutionary nature of these biologic agents, while convincing clinical data are lacking; ii) bacteriocines are smallantibacterialpeptidesproducedby numerous bacteria; some have a rapid bactericidal effect, good tolerability, and a limited impact on the commensal flora; however, clinical use of bacteriocines is complicated by their fragility, poor penetration, and substantial risk of resistance selection ; iii) antisense oligonucleo tides act by inactivating genes through specific interaction with a complementary DNA or RNA fragment, potentially allowing specific inhibition of selected bacterial virulence factors. However, this therapeutic class may be more suitable for viral or genetic diseases than for multidrug-resistant bacterial infections, owing to the difficulty of delivering them inside bacteria. PMID:26427289

  11. Invasion of dentinal tubules by oral bacteria.

    PubMed

    Love, R M; Jenkinson, H F

    2002-01-01

    Bacterial invasion of dentinal tubules commonly occurs when dentin is exposed following a breach in the integrity of the overlying enamel or cementum. Bacterial products diffuse through the dentinal tubule toward the pulp and evoke inflammatory changes in the pulpo-dentin complex. These may eliminate the bacterial insult and block the route of infection. Unchecked, invasion results in pulpitis and pulp necrosis, infection of the root canal system, and periapical disease. While several hundred bacterial species are known to inhabit the oral cavity, a relatively small and select group of bacteria is involved in the invasion of dentinal tubules and subsequent infection of the root canal space. Gram-positive organisms dominate the tubule microflora in both carious and non-carious dentin. The relatively high numbers of obligate anaerobes present-such as Eubacterium spp., Propionibacterium spp., Bifidobacterium spp., Peptostreptococcus micros, and Veillonella spp.-suggest that the environment favors growth of these bacteria. Gram-negative obligate anaerobic rods, e.g., Porphyromonas spp., are less frequently recovered. Streptococci are among the most commonly identified bacteria that invade dentin. Recent evidence suggests that streptococci may recognize components present within dentinal tubules, such as collagen type I, which stimulate bacterial adhesion and intra-tubular growth. Specific interactions of other oral bacteria with invading streptococci may then facilitate the invasion of dentin by select bacterial groupings. An understanding the mechanisms involved in dentinal tubule invasion by bacteria should allow for the development of new control strategies, such as inhibitory compounds incorporated into oral health care products or dental materials, which would assist in the practice of endodontics. PMID:12097359

  12. Nutrient transport by ruminal bacteria: a review.

    PubMed

    Martin, S A

    1994-11-01

    Fermentation pathways have been elucidated for predominant ruminal bacteria, but information is limited concerning the specific transport mechanisms used by these microorganisms for C, energy, and N sources. In addition, it is possible that changes in ruminal environmental conditions could affect transport activity. Five carrier-mediated soluble nutrient transport mechanisms have been identified in bacteria: 1) facilitated diffusion, 2) shock sensitive systems, 3) proton symport, 4) Na+ symport, and the 5) phosphoenolpyruvate phosphotransferase system (PEP-PTS). Several regulatory mechanisms are also involved at the cell membrane to coordinate utilization of different sugars. Recent research has shown that predominant ruminal bacteria are capable of transporting soluble nutrients by several of the mechanisms outlined above. Megasphaera elsdenii, Selenomonas ruminantium, and Streptococcus bovis transport glucose by the PEP-PTS, and S. ruminantium and S. bovis also possess PEP-PTS activity for disaccharides. Glucose PTS activity in S. bovis was highest at a growth pH of 5.0, low glucose concentrations, and a dilution rate of .10 h-1. The cellulolytic ruminal bacterium Fibrobacter succinogenes uses a Na+ symport mechanism for glucose transport that is sensitive to low extracellular pH and ionophores. Sodium also stimulated cellobiose transport by F. succinogenes, and there is evidence for a proton symport in the transport of both arabinose and xylose by S. ruminantium. A chemical gradient of Na+ seems to play an important role in AA transport in several ruminal bacteria. Studying nutrient transport mechanisms in ruminal bacteria will lead to a better understanding of the ruminal fermentation.

  13. [Methanotrophic bacteria of acid sphagnum bogs].

    PubMed

    Dedysh, S N

    2002-01-01

    Acid sphagnum bogs cover a considerable part of the territory of Russia and are an important natural source of biogenic methane, which is formed in their anaerobic layers. A considerable portion of this methane is consumed in the aerobic part of the bog profile by acidophilic methanotrophic bacteria, which comprise the methane filter of sphagnum bogs and decrease CH4 emission to the atmosphere. For a long time, these bacteria escaped isolation, which became possible only after the elucidation of the optimal conditions of their functioning in situ: pH 4.5 to 5.5; temperature, from 15 to 20 degrees C; and low salt concentration in the solution. Reproduction of these conditions and rejection of earlier used media with a high content of biogenic elements allowed methanotrophic bacteria of two new genera and species--Methylocella palustris and Methylocapsa acidophila--to be isolated from the peat of sphagnum bogs of the northern part of European Russia and West Siberia. These bacteria are well adapted to the conditions in cold, acid, oligotrophic sphagnum bogs. They grow in a pH range of 4.2-7.5 with an optimum at 5.0-5.5, prefer moderate temperatures (15-25 degrees C) and media with a low content of mineral salts (200-500 mg/l), and are capable of active nitrogen fixation. Design of fluorescently labeled 16S rRNA-targeted oligonucleotide probes for the detection of Methylocella palustris and Methylocapsa acidophila and their application to the analysis of sphagnum peat samples showed that these bacteria represent dominant populations of methanotrophs with a density of 10(5)-10(6) cells/g peat. In addition to Methylocella and Methylocapsa populations, one more abundant population of methanotrophs was revealed (10(6) cells/g peat), which were phylogenetically close to the genus Methylocystis. PMID:12526194

  14. Coupling of heterotrophic bacteria to phytoplankton bloom development at different pCO2 levels: a mesocosm study

    NASA Astrophysics Data System (ADS)

    Allgaier, M.; Riebesell, U.; Vogt, M.; Thyrhaug, R.; Grossart, H.-P.

    2008-07-01

    The predicted rise in anthropogenic CO2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics) affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO2 (pCO2): 350 μatm (1×CO2), 700 μatm (2×CO2) and 1050 μatm (3×CO2). The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP) of free-living and attached bacteria as well as cell-specific BPP (csBPP) of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed with pCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes in pCO2, although reflected by changes in community structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly correlated to phytoplankton development and, hence, may also potentially depend on changes in pCO2.

  15. Coupling of heterotrophic bacteria to phytoplankton bloom development at different pCO2 levels: a mesocosm study

    NASA Astrophysics Data System (ADS)

    Allgaier, M.; Riebesell, U.; Vogt, M.; Thyrhaug, R.; Grossart, H.-P.

    2008-01-01

    The predicted rise in anthropogenic CO2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics) affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO2 (pCO2): 350 µatm (1×CO2), 700 µatm (2×CO2) and 1050 µatm (3×CO2). The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP) of free-living and attached bacteria as well as cell-specific BPP (csBPP) of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed with pCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes in pCO2, although reflected by changes in community structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly linked to phytoplankton development and, hence, may also potentially depend on changes in pCO2.

  16. Antibacterial activity of silver-killed bacteria: the "zombies" effect

    NASA Astrophysics Data System (ADS)

    Wakshlak, Racheli Ben-Knaz; Pedahzur, Rami; Avnir, David

    2015-04-01

    We report a previously unrecognized mechanism for the prolonged action of biocidal agents, which we denote as the zombies effect: biocidally-killed bacteria are capable of killing living bacteria. The concept is demonstrated by first killing Pseudomonas aeruginosa PAO1 with silver nitrate and then challenging, with the dead bacteria, a viable culture of the same bacterium: Efficient antibacterial activity of the killed bacteria is observed. A mechanism is suggested in terms of the action of the dead bacteria as a reservoir of silver, which, due to Le-Chatelier's principle, is re-targeted to the living bacteria. Langmuirian behavior, as well as deviations from it, support the proposed mechanism.

  17. Antibacterial activity of silver-killed bacteria: the "zombies" effect.

    PubMed

    Wakshlak, Racheli Ben-Knaz; Pedahzur, Rami; Avnir, David

    2015-04-23

    We report a previously unrecognized mechanism for the prolonged action of biocidal agents, which we denote as the zombies effect: biocidally-killed bacteria are capable of killing living bacteria. The concept is demonstrated by first killing Pseudomonas aeruginosa PAO1 with silver nitrate and then challenging, with the dead bacteria, a viable culture of the same bacterium: Efficient antibacterial activity of the killed bacteria is observed. A mechanism is suggested in terms of the action of the dead bacteria as a reservoir of silver, which, due to Le-Chatelier's principle, is re-targeted to the living bacteria. Langmuirian behavior, as well as deviations from it, support the proposed mechanism.

  18. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

    PubMed Central

    2013-01-01

    Background In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels. An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. Results A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. Conclusions The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and

  19. Observation of polyphosphate granules in cable bacteria

    NASA Astrophysics Data System (ADS)

    Yang, T.; Nielsen, L. P.; Risgaard-Petersen, N.

    2015-12-01

    Cable bacteria are long filamentous bacteria that capable for long distance electron transport: transporting electrons derived from oxidizing sulfide in anoxic layers, to oxygen at the sediment surface, over a distance of centimeters. Cable bacteria are found in many types of freshwater and marine sediment all over the world, with density of approximately thousands of kilometers per square meter. These long filaments are composed by individual cells closely related to Desulfobulbaceae, connected with a shared outer membrane inside which the strings structure are presumed to be highly conductive. The observed doubling time of cells within the filament is about 20 min, which is among the shortest compare to other bacteria. In these cable cells, we constantly observed polyphosphate granules (poly-P), regardless of cell dimension and shape. This is very interesting since it has long been recognized that the microbial polyP content is low during rapid growth and increases under unfavorable conditions, for example, increasing sulfide concentration and anoxia resulted in a decomposition of poly-P in Beggiatoa. Here, we investigated marine cable bacteria from Netherland and Aarhus Bay, focusing on the poly-P dynamics under various redox conditions. In poly-P stained cells, typically there are two big poly-P granules locate at each polar. In dividing cells, however, the morphology of poly-P changed to six small granules precisely arranged to two row. Moreover, the cells seem be able to continuously divide more than one time without elongation step. These varied poly-P morphologies demonstrate that poly-P is closely related to the cell growth and cell division, by an unknown mechanism. Individual cable filaments were picked up and were exposed to different redox conditions; our primary data indicated the cable cells could suffer anoxic condition better than oxic condition. We also detected decomposition of poly-P under anoxia. These results call for an in-depth examination

  20. Comparison of the multiple-sample means with composite sample results for fecal indicator bacteria by quantitative PCR and culture.

    PubMed

    Converse, Reagan R; Wymer, Larry J; Dufour, Alfred P; Wade, Timothy J

    2012-10-01

    Few studies have addressed the efficacy of composite sampling for measuring indicator bacteria by quantitative PCR (qPCR). We compared results from composited samples with multiple-sample means for culture- and qPCR-based water quality monitoring. Results from composited samples for both methods were similarly correlated to multiple-sample means and predicted criteria exceedances equally.

  1. PSORTdb: a protein subcellular localization database for bacteria

    PubMed Central

    Rey, Sébastien; Acab, Michael; Gardy, Jennifer L.; Laird, Matthew R.; deFays, Katalin; Lambert, Christophe; Brinkman, Fiona S. L.

    2005-01-01

    Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets. PSORTdb (http://db.psort.org/) is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (∼2000 proteins) was manually curated by us and represents the largest dataset of its kind. Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins. Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats. Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources. PSORTdb is freely available under GNU General Public License. PMID:15608169

  2. Programming stress-induced altruistic death in engineered bacteria

    PubMed Central

    Tanouchi, Yu; Pai, Anand; Buchler, Nicolas E; You, Lingchong

    2012-01-01

    Programmed death is often associated with a bacterial stress response. This behavior appears paradoxical, as it offers no benefit to the individual. This paradox can be explained if the death is ‘altruistic': the killing of some cells can benefit the survivors through release of ‘public goods'. However, the conditions where bacterial programmed death becomes advantageous have not been unambiguously demonstrated experimentally. Here, we determined such conditions by engineering tunable, stress-induced altruistic death in the bacterium Escherichia coli. Using a mathematical model, we predicted the existence of an optimal programmed death rate that maximizes population growth under stress. We further predicted that altruistic death could generate the ‘Eagle effect', a counter-intuitive phenomenon where bacteria appear to grow better when treated with higher antibiotic concentrations. In support of these modeling insights, we experimentally demonstrated both the optimality in programmed death rate and the Eagle effect using our engineered system. Our findings fill a critical conceptual gap in the analysis of the evolution of bacterial programmed death, and have implications for a design of antibiotic treatment. PMID:23169002

  3. MICROBIOLOGICAL CHARACTERIZATION OF BACTERIA INHABITING A WATER DISTRIBUTION SYSTEM SIMULATOR

    EPA Science Inventory

    The impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia oxidizing bacteria (AOB) inhabiting a water distribution system simulator was investigated. Notable changes in bacterial densities were observed during this monitoring study. For e...

  4. Gut Bacteria May Hold Clues to Chronic Fatigue Syndrome

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_159905.html Gut Bacteria May Hold Clues to Chronic Fatigue Syndrome Intestinal ... doctors -- may be influenced by a person's intestinal bacteria -- sometimes called gut microbiome, new research finds. "Patients with chronic fatigue ...

  5. Molecular clue links bacteria to the origin of animals.

    PubMed

    Hadfield, Michael G

    2012-10-15

    Bacteria have a role in the formation of colonies by a species of single-celled organisms whose ancestors gave rise to the animals, which suggests that bacteria might also have influenced the origin of multicellularity in animals.

  6. Rapid detection of bacteria in foods and biological fluids

    NASA Technical Reports Server (NTRS)

    Fealey, R. D.; Renner, W.

    1973-01-01

    Simple and inexpensive apparatus, called "redox monitoring cell," rapidly detects presence of bacteria. Bacteria is detected by measuring drop in oxygen content in test solution. Apparatus consists of vial with two specially designed electrodes connected to sensitive voltmeter.

  7. Bioconjugated magnetic nanoparticles for the detection of bacteria.

    PubMed

    Chu, Yu W; Engebretson, David A; Carey, James R

    2013-12-01

    Blood culture is traditionally a time-consuming method and has not changed significantly in several decades. Using nanotechnology, such as the use of magnetic nanoparticles (MNPs), the blood culture process may be streamlined. An important advantage of using MNPs to capture bacteria is the simple separation of bacteria from biological samples using magnets. Indeed, high bacteria capture efficiencies have been realized using MNPs. The binding events between MNPs and bacteria can be tightly controlled through carefully selected biorecognition events, using molecules such as vancomycin, daptomycin, antibodies, and others. These biomolecules can be readily conjugated onto MNPs followed by tethering to bacteria, thus enabling detection using the beacon produced by the bacteria conjugated MNPs. Methods to prepare bioconjugated MNPs and their performance with bacteria are reviewed. Finally, future directions on bacteria detection using giant magnetoresistance (GMR) biosensors are discussed.

  8. OCCURRENCE OF HETEROTROPHIC BACTERIA WITH VIRULENCE CHARACTERISTICS IN POTABLE WATER

    EPA Science Inventory

    Treated potable water contains a variety of heterotrophic bacteria that survive current treatment processes. There is evidence that these bacteria are not hazardous to the healthy population, however, the possibility exists that some of them may be opportunistic pathogens capabl...

  9. THE ECOLOGY OF BACTERIA IN THE ALFRESCO ATMOSPHERE

    EPA Science Inventory

    This MiniReview is concerned with the sources,flux and the spacial and temporal distributions of culturable airborne bacteria; how meteorological conditions modulate these distributions; and how death, culture media, and experimental devices relate to measuring airborne bacteria....

  10. Overcoming chemo/radio-resistance of pancreatic cancer by inhibiting STAT3 signaling

    PubMed Central

    Wu, Xiaoqing; Tang, Wenhua; Marquez, Rebecca T.; Li, Ke; Highfill, Chad A.; He, Fengtian; Lian, Jiqin; Lin, Jiayuh; Fuchs, James R.; Ji, Min; Li, Ling; Xu, Liang

    2016-01-01

    Chemo/radio-therapy resistance to the deadly pancreatic cancer is mainly due to the failure to kill pancreatic cancer stem cells (CSCs). Signal transducer and activator of transcription 3 (STAT3) is activated in pancreatic CSCs and, therefore, may be a valid target for overcoming therapeutic resistance. Here we investigated the potential of STAT3 inhibition in sensitizing pancreatic cancer to chemo/radio-therapy. We found that the levels of nuclear pSTAT3 in pancreatic cancer correlated with advanced tumor grade and poor patient outcome. Liposomal delivery of a STAT3 inhibitor FLLL32 (Lip-FLLL32) inhibited STAT3 phosphorylation and STAT3 target genes in pancreatic cancer cells and tumors. Consequently, Lip-FLLL32 suppressed pancreatic cancer cell growth, and exhibited synergetic effects with gemcitabine and radiation treatment in vitro and in vivo. Furthermore, Lip-FLLL32 reduced ALDH1-positive CSC population and modulated several potential stem cell markers. These results demonstrate that Lip-FLLL32 suppresses pancreatic tumor growth and sensitizes pancreatic cancer cells to radiotherapy through inhibition of CSCs in a STAT3-dependent manner. By targeting pancreatic CSCs, Lip-FLLL32 provides a novel strategy for pancreatic cancer therapy via overcoming radioresistance. PMID:26887043

  11. Partial least squares for efficient models of fecal indicator bacteria on Great Lakes beaches

    USGS Publications Warehouse

    Brooks, Wesley R.; Fienen, Michael N.; Corsi, Steven R.

    2013-01-01

    At public beaches, it is now common to mitigate the impact of water-borne pathogens by posting a swimmer's advisory when the concentration of fecal indicator bacteria (FIB) exceeds an action threshold. Since culturing the bacteria delays public notification when dangerous conditions exist, regression models are sometimes used to predict the FIB concentration based on readily-available environmental measurements. It is hard to know which environmental parameters are relevant to predicting FIB concentration, and the parameters are usually correlated, which can hurt the predictive power of a regression model. Here the method of partial least squares (PLS) is introduced to automate the regression modeling process. Model selection is reduced to the process of setting a tuning parameter to control the decision threshold that separates predicted exceedances of the standard from predicted non-exceedances. The method is validated by application to four Great Lakes beaches during the summer of 2010. Performance of the PLS models compares favorably to that of the existing state-of-the-art regression models at these four sites.

  12. Physics of Intracellular Organization in Bacteria.

    PubMed

    Wingreen, Ned S; Huang, Kerwyn Casey

    2015-01-01

    With the realization that bacteria achieve exquisite levels of spatiotemporal organization has come the challenge of discovering the underlying mechanisms. In this review, we describe three classes of such mechanisms, each of which has physical origins: the use of landmarks, the creation of higher-order structures that enable geometric sensing, and the emergence of length scales from systems of chemical reactions coupled to diffusion. We then examine the diversity of geometric cues that exist even in cells with relatively simple geometries, and end by discussing both new technologies that could drive further discovery and the implications of our current knowledge for the behavior, fitness, and evolution of bacteria. The organizational strategies described here are employed in a wide variety of systems and in species across all kingdoms of life; in many ways they provide a general blueprint for organizing the building blocks of life.

  13. Evolution of Drug Resistance in Bacteria.

    PubMed

    Waclaw, B

    2016-01-01

    Resistance to antibiotics is an important and timely problem of contemporary medicine. Rapid evolution of resistant bacteria calls for new preventive measures to slow down this process, and a longer-term progress cannot be achieved without a good understanding of the mechanisms through which drug resistance is acquired and spreads in microbial populations. Here, we discuss recent experimental and theoretical advances in our knowledge how the dynamics of microbial populations affects the evolution of antibiotic resistance . We focus on the role of spatial and temporal drug gradients and show that in certain situations bacteria can evolve de novo resistance within hours. We identify factors that lead to such rapid onset of resistance and discuss their relevance for bacterial infections. PMID:27193537

  14. Have sex or not? Lessons from bacteria.

    PubMed

    Lodé, T

    2012-01-01

    Sex is one of the greatest puzzles in evolutionary biology. A true meiotic process occurs only in eukaryotes, while in bacteria, gene transcription is fragmentary, so asexual reproduction in this case really means clonal reproduction. Sex could stem from a signal that leads to increased reproductive output of all interacting individuals and could be understood as a secondary consequence of primitive metabolic reactions. Meiotic sex evolved in proto-eukaryotes to solve a problem that bacteria did not have, namely a large amount of DNA material, occurring in an archaic step of proto-cell formation and genetic exchanges. Rather than providing selective advantages through reproduction, sex could be thought of as a series of separate events which combines step-by-step some very weak benefits of recombination, meiosis, gametogenesis and syngamy.

  15. Sulfate-reducing bacteria: Microbiology and physiology

    NASA Technical Reports Server (NTRS)

    Peck, H. D.

    1985-01-01

    The sulfate reducing bacteria, the first nonphotosynthetic anaerobic bacteria demonstrated to contain c type cytochromes, perform electron transfer coupled to phosphorylation. A new bioenergetic scheme for the formation of a proton gradient for growth of Desulfovibrio on organic substrates and sulfate involving vectors electron transfer and consistent with the cellular localization of enzymes and electron transfer components was proposed. Hydrogen is produced in the cytoplasm from organic substrates and, as a permease molecule diffuses rapidly across the cytoplasmic membrane, it is oxidized to protons and electrons by the periplasmic hydrogenase. The electrons only are transferred across the cytoplasmic membrane to the cytoplasm where they are used to reduce sulfate to sulfide. The protons are used for transport or to drive a reversible ATPOSE. The net effect is the transfer of protons across the cytoplasmic membrane with the intervention of a proton pump. This type of H2 cycling is relevant to the bioenergetics of other types of anaerobic microorganisms.

  16. Evolution of Drug Resistance in Bacteria.

    PubMed

    Waclaw, B

    2016-01-01

    Resistance to antibiotics is an important and timely problem of contemporary medicine. Rapid evolution of resistant bacteria calls for new preventive measures to slow down this process, and a longer-term progress cannot be achieved without a good understanding of the mechanisms through which drug resistance is acquired and spreads in microbial populations. Here, we discuss recent experimental and theoretical advances in our knowledge how the dynamics of microbial populations affects the evolution of antibiotic resistance . We focus on the role of spatial and temporal drug gradients and show that in certain situations bacteria can evolve de novo resistance within hours. We identify factors that lead to such rapid onset of resistance and discuss their relevance for bacterial infections.

  17. In situ soil remediation: Bacteria or fungi?

    SciTech Connect

    Cutright, T.J.; Lee, S.

    1995-07-01

    Contamination of the environment is not a new problem. For most of recorded history, the unwanted byproducts of industrial and residential processes have been dumped into unlined pits or nearby streams. Although disposal techniques have greatly improved, significant quantities of hazardous materials are still being released to the environment via accidental spills and leaking underground storage tanks. One particular group of contaminants of critical environmental concern is polycyclic aromatic hydrocarbons (PAHs). PAH-contaminated sites typically cover large areas; therefore, the development of in situ remediation techniques such as bioremediation is strongly emphasized. In situations when inherent microorganisms are not capable of degrading the contaminants, foreign strains must be used. Bioremediation experiments were conducted to compare the remediation efficiencies of a bacteria and a fungus for an industrially PAH contaminated soil. Specifically, the use of three supplemental nutrient solutions were investigated in conjunction with the bacteria Achromobacter sp. and fungus Cunninghamella echinulata var. elegans.

  18. Molecular Determinants in Phagocyte-Bacteria Interactions.

    PubMed

    Kaufmann, Stefan H E; Dorhoi, Anca

    2016-03-15

    Phagocytes are crucial for host defense against bacterial pathogens. As first demonstrated by Metchnikoff, neutrophils and mononuclear phagocytes share the capacity to engulf, kill, and digest microbial invaders. Generally, neutrophils focus on extracellular, and mononuclear phagocytes on intracellular, pathogens. Reciprocally, extracellular pathogens often capitalize on hindering phagocytosis and killing of phagocytes, whereas intracellular bacteria frequently allow their engulfment and then block intracellular killing. As foreseen by Metchnikoff, phagocytes become highly versatile by acquiring diverse phenotypes, but still retaining some plasticity. Further, phagocytes engage in active crosstalk with parenchymal and immune cells to promote adjunctive reactions, including inflammation, tissue healing, and remodeling. This dynamic network allows the host to cope with different types of microbial invaders. Here we present an update of molecular and cellular mechanisms underlying phagocyte functions in antibacterial defense. We focus on four exemplary bacteria ranging from an opportunistic extracellular to a persistent intracellular pathogen. PMID:26982355

  19. Sulfur-oxidizing bacteria in environmental technology.

    PubMed

    Pokorna, Dana; Zabranska, Jana

    2015-11-01

    Hydrogen sulfide is widely known as the most undesirable component of biogas that caused not only serious sensoric and toxic problems, but also corrosion of concrete and steel structures. Many agricultural and industrial waste used in biogas production, may contain a large amount of substances that serve as direct precursors to the formation of sulfide sulfur-sources of hydrogen sulfide in the biogas. Biological desulfurization methods are currently promoted to abiotic methods because they are less expensive and do not produce undesirable materials which must be disposed of. The final products of oxidation of sulfides are no longer hazardous. Biological removal of sulfide from a liquid or gaseous phase is based on the activity of sulfur-oxidizing bacteria. They need an oxidizing agent such as an acceptor of electrons released during the oxidation of sulfides-atmospheric oxygen or oxidized forms of nitrogen. Different genera of sulfur-oxidizing bacteria and their technological application are discussed. PMID:25701621

  20. Sulfur-oxidizing bacteria in environmental technology.

    PubMed

    Pokorna, Dana; Zabranska, Jana

    2015-11-01

    Hydrogen sulfide is widely known as the most undesirable component of biogas that caused not only serious sensoric and toxic problems, but also corrosion of concrete and steel structures. Many agricultural and industrial waste used in biogas production, may contain a large amount of substances that serve as direct precursors to the formation of sulfide sulfur-sources of hydrogen sulfide in the biogas. Biological desulfurization methods are currently promoted to abiotic methods because they are less expensive and do not produce undesirable materials which must be disposed of. The final products of oxidation of sulfides are no longer hazardous. Biological removal of sulfide from a liquid or gaseous phase is based on the activity of sulfur-oxidizing bacteria. They need an oxidizing agent such as an acceptor of electrons released during the oxidation of sulfides-atmospheric oxygen or oxidized forms of nitrogen. Different genera of sulfur-oxidizing bacteria and their technological application are discussed.

  1. Biotechnological potential of Clostridium butyricum bacteria

    PubMed Central

    Szymanowska-Powałowska, Daria; Orczyk, Dorota; Leja, Katarzyna

    2014-01-01

    In response to demand from industry for microorganisms with auspicious biotechnological potential, a worldwide interest has developed in bacteria and fungi isolation. Microorganisms of interesting metabolic properties include non-pathogenic bacteria of the genus Clostridium, particularly C. acetobutylicum, C. butyricum and C. pasteurianum. A well-known property of C. butyricum is their ability to produce butyric acid, as well as effectively convert glycerol to 1,3-propanediol (38.2 g/L). A conversion rate of 0.66 mol 1,3-propanediol/mol of glycerol has been obtained. Results of the studies described in the present paper broaden our knowledge of characteristic features of C. butyricum specific isolates in terms of their phylogenetic affiliation, fermentation capacity and antibacterial properties. PMID:25477923

  2. Effect of Essential Oils on Pathogenic Bacteria

    PubMed Central

    Nazzaro, Filomena; Fratianni, Florinda; De Martino, Laura; Coppola, Raffaele; De Feo, Vincenzo

    2013-01-01

    The increasing resistance of microorganisms to conventional chemicals and drugs is a serious and evident worldwide problem that has prompted research into the identification of new biocides with broad activity. Plants and their derivatives, such as essential oils, are often used in folk medicine. In nature, essential oils play an important role in the protection of plants. Essential oils contain a wide variety of secondary metabolites that are capable of inhibiting or slowing the growth of bacteria, yeasts and moulds. Essential oils and their components have activity against a variety of targets, particularly the membrane and cytoplasm, and in some cases, they completely change the morphology of the cells. This brief review describes the activity of essential oils against pathogenic bacteria. PMID:24287491

  3. Mechanism of Transcriptional Bursting in Bacteria

    PubMed Central

    Chong, Shasha; Chen, Chongyi; Ge, Hao; Xie, X. Sunney

    2014-01-01

    SUMMARY Transcription of highly expressed genes has been shown to occur in stochastic bursts. But the origin of such ubiquitous phenomenon has not been understood. Here we present the mechanism in bacteria. We developed a high-throughput in vitro single-molecule assay to follow transcription on individual DNA templates in real time. We showed that positive supercoiling buildup on a DNA segment by transcription slows down transcription elongation and eventually stops transcription initiation. Transcription can be resumed upon gyrase binding to the DNA segment. Furthermore, using single-cell mRNA counting fluorescence in situ hybridization (FISH), we found the extent of transcriptional bursting depends on the intracellular gyrase concentration. Together, these findings prove that transcriptional bursting of highly expressed genes in bacteria is primarily caused by reversible gyrase dissociation from and rebinding to a DNA segment, changing the supercoiling level of the segment. PMID:25036631

  4. Gene Flow and Molecular Innovation in Bacteria.

    PubMed

    Ruzzini, Antonio C; Clardy, Jon

    2016-09-26

    The small molecules produced by environmental bacteria have been mainstays of both chemical and biological research for decades, and some have led to important therapeutic interventions. These small molecules have been shaped by natural selection as they evolved to fulfill changing functional roles in their native environments. This minireview describes some recent systematic studies providing illustrative examples that involve the acquisition and alteration of genetic information for molecular innovation by bacteria in well-defined environments. Two different bacterial genera are featured, Pseudonocardia and Salinispora, and, although the small-molecule repertoires of both have benefited from horizontal gene transfer, Pseudonocardia spp. have relied on plasmid-based tactics while Salinispora spp. have relied on chromosomally integrated genomic islands. PMID:27676308

  5. Elimination of bacteria from dogs with antibiotics*

    PubMed Central

    Hayes, Norman R.; van der Waaij, D.; Cohen, Bennett J.

    1974-01-01

    The effect of oral administration of neomycin cephalothin or kanamycin cephalothin on the aerobic intestinal bacterial flora, was studied in dogs maintained under isolation conditions in a conventional animal room. The dogs were successfully freed of aerobic bacteria with both combinations within two to seven days after the start of antibiotic treatment, and were maintained bacteria free for up to 21 days. Decontamination was attained more rapidly in dogs that were bathed in hexachlorophene surgical soap before and during the first and third days of antibiotic treatment. There was no evidence of toxicity from either of the antibiotic combinations. These results indicate that, as with mice and monkeys, decontamination of dogs with oral antibiotics is feasible. The technique is of potential value in preventing endogenous bacterial infections in canine experimental studies involving use of immunosuppressive agents. PMID:4529233

  6. Manipulating bacteria with opto-electrokinetic methods

    NASA Astrophysics Data System (ADS)

    Wereley, Steve; Kwon, Jae-Sung; Ravindranath, Sandeep; Irudayaraj, Joseph

    2010-11-01

    Recently we developed an opto-electrokinetic method for manipulating particles and cells called Rapid Electrokinetic Patterning (REP). REP is a very fast method for manipulating thousands of particles simultaneously and controllably owing to the creation of an electrothermal vortex that transports particles rapidly and in parallel to a site determined by the focal point of a laser beam. Whether particles are trapped at the center of the vortex or not is determined by their electrical properties (conductivity and permittivity). In this talk we demonstrate that REP can be used to manipulate the bacterium Shewanella oneidensis MR-1. The bacteria are assembled into large planar arrays of organisms. The dependence of this assembly process on voltage and frequency is quantified. REP can even be used to selectively manipulate and collect live or dead bacteria.

  7. Evaluation of chitoligosaccharides effect upon probiotic bacteria.

    PubMed

    Fernandes, João C; Eaton, Peter; Franco, Isabel; Ramos, Oscar S; Sousa, Sérgio; Nascimento, Henrique; Gomes, Ana; Santos-Silva, Alice; Malcata, F Xavier; Pintado, Manuela E

    2012-01-01

    The main objective of the present study was to evaluate the antibacterial effect - through the determination of minimum inhibitory (and lethal) concentrations, as well as the possible prebiotic potential of chitooligosaccharides (COS) - through the determination of growth curves, on Bifidobacterium animalis Bb12, Bifidobacterium animalis Bo and Lactobacillus acidophilus Ki. Atomic force microscopy was further used to obtain high resolution images of COS effects upon the cell morphology. Our results demonstrate that COS do not stimulate the growth of those strains, neither the strains are capable of using COS as a primary source of carbon. Analysis of morphology when exposed to inhibitory/bactericidal concentrations, suggested that COS do not exert any direct damage upon the bacteria structure, instead the bacteria are apparently covered by COS, which likely prevent nutrient uptake. PMID:22024313

  8. Physiological adaptations of key oral bacteria.

    PubMed

    Douglas, C W Ian; Naylor, Kathryn; Phansopa, Chatchawal; Frey, Andrew M; Farmilo, Thomas; Stafford, Graham P

    2014-01-01

    Oral colonising bacteria are highly adapted to the various environmental niches harboured within the mouth, whether that means while contributing to one of the major oral diseases of caries, pulp infections, or gingival/periodontal disease or as part of a commensal lifestyle. Key to these infections is the ability to adhere to surfaces via a range of specialised adhesins targeted at both salivary and epithelial proteins, their glycans and to form biofilm. They must also resist the various physical stressors they are subjected to, including pH and oxidative stress. Possibly most strikingly, they have developed the ability to harvest both nutrient sources provided by the diet and those derived from the host, such as protein and surface glycans. We have attempted to review recent developments that have revealed much about the molecular mechanisms at work in shaping the physiology of oral bacteria and how we might use this information to design and implement new treatment strategies.

  9. Probiotic bacteria induce a 'glow of health'.

    PubMed

    Levkovich, Tatiana; Poutahidis, Theofilos; Smillie, Christopher; Varian, Bernard J; Ibrahim, Yassin M; Lakritz, Jessica R; Alm, Eric J; Erdman, Susan E

    2013-01-01

    Radiant skin and hair are universally recognized as indications of good health. However, this 'glow of health' display remains poorly understood. We found that feeding of probiotic bacteria to aged mice induced integumentary changes mimicking peak health and reproductive fitness characteristic of much younger animals. Eating probiotic yogurt triggered epithelial follicular anagen-phase shift with sebocytogenesis resulting in thick lustrous fur due to a bacteria-triggered interleukin-10-dependent mechanism. Aged male animals eating probiotics exhibited increased subcuticular folliculogenesis, when compared with matched controls, yielding luxuriant fur only in probiotic-fed subjects. Female animals displayed probiotic-induced hyperacidity coinciding with shinier hair, a feature that also aligns with fertility in human females. Together these data provide insights into mammalian evolution and novel strategies for integumentary health. PMID:23342023

  10. RNA-Seq for Plant Pathogenic Bacteria

    PubMed Central

    Kimbrel, Jeffrey A.; Di, Yanming; Cumbie, Jason S.; Chang, Jeff H.

    2011-01-01

    The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions. PMID:24710287

  11. Satellite Water Impurity Marker (SWIM) for predicting seasonal cholera outbreaks

    NASA Astrophysics Data System (ADS)

    Jutla, A. S.; Akanda, A. S.; Islam, S.

    2011-12-01

    Prediction of outbreaks of cholera, a deadly water related disease, remains elusive. Since coastal brackish water provides a natural ecological niche for cholera bacteria and because a powerful evidence of new biotypes is emerging, it is highly unlikely that cholera will be fully eradicated. Therefore, it is necessary to develop cholera prediction model with several months' of lead time. Satellite based estimates of chlorophyll, a surrogate for phytoplankton abundance, has been associated with proliferation of cholera bacteria. However, survival of cholera bacteria in a variety of coastal ecological environment put constraints on predictive abilities of chlorophyll algorithm since it only measures greenness in coastal waters. Here, we propose a new remote sensing reflectance based statistical index: Satellite Water Impurity Marker, or SWIM. This statistical index estimates impurity levels in the coastal waters and is based on the variability observed in the difference between the blue (412nm) and green (555nm) wavelengths in coastal waters. The developed index is bounded between clear and impure water and shows the ability to predict cholera outbreaks in the Bengal Delta with a predicted r2 of 78% with two months lead time. We anticipate that a predictive system based on SWIM will provide essential lead time allowing effective intervention and mitigation strategies to be developed for other cholera endemic regions of the world.

  12. Bacteria fate and transport in a river - simulating the processes in a flume

    NASA Astrophysics Data System (ADS)

    Schwarzwälder, Kordula; Walters, Eve; Rutschmann, Peter

    2014-05-01

    The water quality in rivers is influenced inter alia by the inlet of untreated wastewater due to combined sewer overflows. Such processes of water quality degradation are a problem even in Europe and even nowadays. This wastewater is a mixture of organic and inorganic material e.g. bacteria which can be found as freely suspended or agglomerated to sediment in the water phase of a river. To make a prediction of water quality we have to know details about the transport of these bacteria in this bulk phase, about the sorption and desorption rates, the sedimentation and the remobilization of the bacteria. We investigated the sedimentation and remobilisation processes of E. coli and Enterococci in a flume mimicking an oligotrophic river. The flume is a large-scale flume in the outside area of our lab (Oskar von Miller Institute) to make sure that the influence of different important factors for inactivation e.g. UV-light or grazers can be taken into account. In addition there we are able to use a flume, which is not downscaled but simulates a slice of a river. So we can minimize some scaling problems, which could occur combining a scaled flume and the bacteria which can't be scaled. We also use natural water coming directly from a natural river. We also had natural soil so realistic grain size. Hence it is possible to simulate realistic effects of the turbidity on inactivation and the sedimentation due to the higher probability of the bacteria to get attached to inorganic material of suspended bed load. It is also possible to get realistic biofilm on the stones, which influences the remobilisation processes and rates of settled bacteria back into the bulk phase. The results of our experiments are now used for a module in the 3D software Flow3D to simulate the effects of a point source inlet of raw wastewater on the water quality.

  13. The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR–Mediated Immunity

    PubMed Central

    Levin, Bruce R.; Moineau, Sylvain; Bushman, Mary; Barrangou, Rodolphe

    2013-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with associated genes (cas), form the CRISPR–cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host–phage interactions in a model CRISPR–cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs) and CRISPR–escape mutant phage (CEMs) obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10−6), our population studies indicate that there is more to the dynamics of phage–host interactions and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity. Among the unanticipated observations are: (i) the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers, (ii) the survival of sensitive bacteria despite the presence of high densities of phage, and (iii) the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i) to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii) and (iii) can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of

  14. Antimicrobial action of natural substances on oral bacteria.

    PubMed

    Saeki, Y; Ito, Y; Shibata, M; Sato, Y; Okuda, K; Takazoe, I

    1989-08-01

    The antimicrobial action of natural substances was investigated in vitro against oral bacteria including Streptococcus sp., Actinomyces sp., Actinobacillus sp., Bacteroides sp., Capnocytophaga sp., Eikenella sp., Fusobacterium sp. and Propionibacterium sp. Among the natural substances tested, hinokitiol was the most inhibitory to oral bacteria. Cinnamon bark oil, papua-mace extracts, and clove bud oil in spice extracts were also inhibitory against many oral bacteria. Egg white lysozyme exhibited antimicrobial action against the periodontitis associated bacteria. PMID:2637783

  15. [Genetic virulence markers of opportunistic bacteria].

    PubMed

    Bondarenko, V M

    2011-01-01

    The analysis of opportunistic bacteria phenotypic and genetic virulence markers indicates that pathogenicity formation is based on a structural modification of bacterial DNA which is linked with migration of interbacterial pathogenicity "islands" genetic determinants. Structural organization features of these mobile genetic elements determine high expression probability, and PCR detection of pathogenicity "islands" determinants that control adhesins, invasins, cytotoxic and cytolitic toxines synthesis may indicate etiopathogenetic significance of clinical isolates.

  16. Differentiation of genera of the coryneform bacteria.

    PubMed

    Golovlev, E L; Baryshnikova, L M

    1979-01-01

    A scheme of the generic structure of the group of coryneform bacteria, including the genera Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium, and Rhodococcus, is suggested. Morphological, chemotaxonomic (presence and stereochemical form of diaminopimelic acid, lipid A, and L-arabinose), and physiological features were used as diagnostic criteria. The position of Microbacterum and Mycococcus and of coryneforms with a nocardial wall but giving a positive Hugh-Leifson anaerobic test, and also of Arthrobacter pascens, which may be identical with Mycoplana sp., remains uncertain.

  17. Understanding the Collective Nose of Bacteria.

    PubMed

    Meijler, Michael M

    2016-03-17

    Bacteria use a rich chemical vocabulary to "smell out" environmental conditions and communicate with each other about what is going on. This helps them optimize their virulence and attack differently, depending on whether they are, for example, in the lungs or the gut. In this issue of Cell Chemical Biology, Welsh and Blackwell (2016) start to unravel this complexity using chemical probes and offer insights into how we might start targeting these processes in a new way. PMID:26991099

  18. Nitrate reduction in sulfate-reducing bacteria.

    PubMed

    Marietou, Angeliki

    2016-08-01

    Sulfate-reducing bacteria (SRBs) gain their energy by coupling the oxidation of organic substrate to the reduction of sulfate to sulfide. Several SRBs are able to use alternative terminal electron acceptors to sulfate such as nitrate. Nitrate-reducing SRBs have been isolated from a diverse range of environments. In order to be able to understand the significance of nitrate reduction in SRBs, we need to examine the ecology and physiology of the nitrate-reducing SRB isolates.

  19. Macrophage defense mechanisms against intracellular bacteria

    PubMed Central

    Weiss, Günter; Schaible, Ulrich E

    2015-01-01

    Macrophages and neutrophils play a decisive role in host responses to intracellular bacteria including the agent of tuberculosis (TB), Mycobacterium tuberculosis as they represent the forefront of innate immune defense against bacterial invaders. At the same time, these phagocytes are also primary targets of intracellular bacteria to be abused as host cells. Their efficacy to contain and eliminate intracellular M. tuberculosis decides whether a patient initially becomes infected or not. However, when the infection becomes chronic or even latent (as in the case of TB) despite development of specific immune activation, phagocytes have also important effector functions. Macrophages have evolved a myriad of defense strategies to combat infection with intracellular bacteria such as M. tuberculosis. These include induction of toxic anti-microbial effectors such as nitric oxide and reactive oxygen intermediates, the stimulation of microbe intoxication mechanisms via acidification or metal accumulation in the phagolysosome, the restriction of the microbe's access to essential nutrients such as iron, fatty acids, or amino acids, the production of anti-microbial peptides and cytokines, along with induction of autophagy and efferocytosis to eliminate the pathogen. On the other hand, M. tuberculosis, as a prime example of a well-adapted facultative intracellular bacterium, has learned during evolution to counter-balance the host's immune defense strategies to secure survival or multiplication within this otherwise hostile environment. This review provides an overview of innate immune defense of macrophages directed against intracellular bacteria with a focus on M. tuberculosis. Gaining more insights and knowledge into this complex network of host-pathogen interaction will identify novel target sites of intervention to successfully clear infection at a time of rapidly emerging multi-resistance of M. tuberculosis against conventional antibiotics. PMID:25703560

  20. Method of detecting and counting bacteria

    NASA Technical Reports Server (NTRS)

    Picciolo, G. L.; Chappelle, E. W. (Inventor)

    1976-01-01

    An improved method is provided for determining bacterial levels, especially in samples of aqueous physiological fluids. The method depends on the quantitative determination of bacterial adenosine triphosphate (ATP) in the presence of nonbacterial ATP. The bacterial ATP is released by cell rupture and is measured by an enzymatic bioluminescent assay. A concentration technique is included to make the method more sensitive. It is particularly useful where the fluid to be measured contains an unknown or low bacteria count.

  1. Bacteria that glide with helical tracks

    PubMed Central

    Nan, Beiyan; McBride, Mark J.; Chen, Jing; Zusman, David R.; Oster, George

    2014-01-01

    Many bacteria glide smoothly on surfaces, but with no discernable propulsive organelles on their surface. Recent experiments with Myxococcus xanthus and Flavobacterium johnsoniae show that both distantly related bacterial species glide utilizing proteins that move in helical tracks, albeit with significantly different motility mechanisms. Both species utilize proton motive force for movement. However, the motors that power gliding in M. xanthus have been identified, while the F. johnsoniae motors remain to be discovered. PMID:24556443

  2. Evidence for metabolic activity of airborne bacteria

    NASA Technical Reports Server (NTRS)

    Chatigny, M. A.; Wolochow, H.

    1974-01-01

    Aerosols of the bacterium Serratia marcescens, and of uniformly labeled C-14 glucose were produced simultaneously and mixed in tubing leading to an aerosol chamber. During a subsequent period of about 5 hrs, carbon dioxide was produced metabolically within the chamber, and labeled material incorporated within the suspended particles first increased then decreased. This constitutes the first direct evidence of microbial metabolism of bacteria suspended in the air.

  3. New fluorescein precursors for live bacteria detection.

    PubMed

    Guilini, Celia; Baehr, Corinne; Schaeffer, Etienne; Gizzi, Patrick; Rufi, Frédéric; Haiech, Jacques; Weiss, Etienne; Bonnet, Dominique; Galzi, Jean-Luc

    2015-09-01

    Swiftness, reliability, and sensitivity of live bacteria detection in drinking water are key issues for human safety. The most widespread used indicator of live bacteria is a caged form of carboxyfluorescein in which 3' and 6' hydroxyl groups are masked as acetate esters (CFDA). This derivatization altogether abolishes fluorescein fluorescence and renders the molecule prone to passive diffusion through bacterial membranes. Once in the cytoplasm, acetate groups from CFDA are removed by bacterial hydrolases and fluorescence develops, rendering live but not dead cells detectable. Yet the reagent, carboxyfluorescein diacetate, still possesses a free carboxyl group whose ionization constant is such that the majority of the probe is charged at physiological pH. This unfavors probe permeation through membranes. Here, we prepare several chemical modifications of the carboxyl moiety of CFDA, in order to neutralize its charge and improve its passive diffusion through membranes. We show that the ethylamido derivative of the 5-carboxyl group from 5-carboxy-fluorescein diacetate or from Oregon green diacetate or from Oregon green diacetoxymethylester are stable molecules in biological media, penetrate into bacterial cells and are metabolized into fluorescent species. Only live bacteria are revealed since bleached samples are not labeled. Other derivatives with modification of the 5-carboxyl group with an ester group or with a thiourea-based moiety were almost inefficient probes. The most interesting probe, triembarine (5-ethylaminocarboxy-oregon green, 3',6'diacetoxymethyl ester) leads to 6-10 times more sensitive detection of bacteria as compared to CFDA. Addition of contrast agents (trypan blue or brilliant blue R) improve the signal-to-noise ratio by quenching extracellular fluorescence while bromophenol blue quenches both intracellular and extracellular fluorescence, allowing standardization of detections.

  4. Macrophage defense mechanisms against intracellular bacteria.

    PubMed

    Weiss, Günter; Schaible, Ulrich E

    2015-03-01

    Macrophages and neutrophils play a decisive role in host responses to intracellular bacteria including the agent of tuberculosis (TB), Mycobacterium tuberculosis as they represent the forefront of innate immune defense against bacterial invaders. At the same time, these phagocytes are also primary targets of intracellular bacteria to be abused as host cells. Their efficacy to contain and eliminate intracellular M. tuberculosis decides whether a patient initially becomes infected or not. However, when the infection becomes chronic or even latent (as in the case of TB) despite development of specific immune activation, phagocytes have also important effector functions. Macrophages have evolved a myriad of defense strategies to combat infection with intracellular bacteria such as M. tuberculosis. These include induction of toxic anti-microbial effectors such as nitric oxide and reactive oxygen intermediates, the stimulation of microbe intoxication mechanisms via acidification or metal accumulation in the phagolysosome, the restriction of the microbe's access to essential nutrients such as iron, fatty acids, or amino acids, the production of anti-microbial peptides and cytokines, along with induction of autophagy and efferocytosis to eliminate the pathogen. On the other hand, M. tuberculosis, as a prime example of a well-adapted facultative intracellular bacterium, has learned during evolution to counter-balance the host's immune defense strategies to secure survival or multiplication within this otherwise hostile environment. This review provides an overview of innate immune defense of macrophages directed against intracellular bacteria with a focus on M. tuberculosis. Gaining more insights and knowledge into this complex network of host-pathogen interaction will identify novel target sites of intervention to successfully clear infection at a time of rapidly emerging multi-resistance of M. tuberculosis against conventional antibiotics. PMID:25703560

  5. Predominant bacteria diversity in Chinese traditional sourdough.

    PubMed

    Zhang, Guohua; He, Guoqing

    2013-08-01

    The purpose of this study was to identify the major bacteria in Chinese traditional sourdough (CTS). Five CTS samples (Hn-87, Sx-91, Gs-107, Hf-112, and Hr-122) were collected from different Chinese steamed breads shops or private households. The total bacterial DNA was extracted from sourdough samples and sequenced using Illumina Hiseq 2000 system. Illumina tags were assigned to BLASTN server based on 16S rRNA libraries to reveal a genetic profile. Phylogenetic analysis revealed that the bacteria in traditional sourdough samples were dominated by the genera Leuconostoc and Lactobacillus. Beta diversity analysis, principal component analysis, and cluster analysis compared the bacterial differences in traditional sourdough samples. The results showed that Leuconostoc, Lactobacillus, and Weissella were the predominant genera among the 5 samples. This differentiated the sourdoughs into 3 typologies, namely, 1) Gs-107 and Sx-91, 2) Hr-122 and Hn-87, and 3) Hf-112. This study identified 3 unique major bacteria genus in CTS bread ecosystems.

  6. Multitasking SecB chaperones in bacteria.

    PubMed

    Sala, Ambre; Bordes, Patricia; Genevaux, Pierre

    2014-01-01

    Protein export in bacteria is facilitated by the canonical SecB chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor SecA to ensure their proper targeting to the Sec translocon at the cytoplasmic membrane. Besides its key contribution to the Sec pathway, SecB chaperone tasking is critical for the secretion of the Sec-independent heme-binding protein HasA and actively contributes to the cellular network of chaperones that control general proteostasis in Escherichia coli, as judged by the significant interplay found between SecB and the trigger factor, DnaK and GroEL chaperones. Although SecB is mainly a proteobacterial chaperone associated with the presence of an outer membrane and outer membrane proteins, secB-like genes are also found in Gram-positive bacteria as well as in certain phages and plasmids, thus suggesting alternative functions. In addition, a SecB-like protein is also present in the major human pathogen Mycobacterium tuberculosis where it specifically controls a stress-responsive toxin-antitoxin system. This review focuses on such very diverse chaperone functions of SecB, both in E. coli and in other unrelated bacteria.

  7. Selenium uptake by sulfur-accumulating bacteria

    NASA Astrophysics Data System (ADS)

    Nelson, Douglas C.; Casey, William H.; Sison, Jennette D.; Mack, E. Erin; Ahmad, Azeem; Pollack, Jeffrey S.

    1996-09-01

    Selenium is a trace metal in many rock-forming minerals but is a major environmental contaminant worldwide. Uptake of selenium by S-accumulating bacteria was examined in both pure cultures of Chromatium vinosum and in co-culture with Desulfovibrio desulfuricans. We used dual cultures including these bacteria to concentrate selenium into intracellular globules. The bacterium D. desulfuricans reduces sulfate [SO 42- (aq)] to sulfide [H 2S(aq)] and also reduces selenate [SeO 42- (aq)] to selenide [H 2Se (aq)]. Once reduced, sulfide is enzymatically oxidized and formed into intracellular globules by C. vinosum. We found that the selenium also forms an intercellular solid but the reaction is thermodynamically driven and proceeds by reducing S° (s) with H 2Se(aq). Relative to the initial molar ratio of selenate and sulfate in the medium, selenium is concentrated 4.5 to 32-fold in the globules. Because solid selenium is so much more stable than sulfur at growth conditions, other S-depositing bacteria, such as Beggiatoa and Chlorobium, should also concentrate selenium via this reaction, providing a strategy for eliminating contamination or for concentrating low natural levels into a usable form.

  8. High efficiency recombineering in lactic acid bacteria

    PubMed Central

    van Pijkeren, Jan-Peter; Britton, Robert A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria. Mutations were incorporated in the chromosome of Lactobacillus reuteri and Lactococcus lactis without selection at frequencies ranging between 0.4% and 19%. Whole genome sequence analysis showed that ssDNA recombineering is specific and not hypermutagenic. To highlight the utility of ssDNA recombineering we reduced the intrinsic vancomymycin resistance of L. reuteri >100-fold. By creating a single amino acid change in the d-Ala-d-Ala ligase enzyme we reduced the minimum inhibitory concentration for vancomycin from >256 to 1.5 µg/ml, well below the clinically relevant minimum inhibitory concentration. Recombineering thus allows high efficiency mutagenesis in lactobacilli and lactococci, and may be used to further enhance beneficial properties and safety of strains used in medicine and industry. We expect that this work will serve as a blueprint for the adaptation of ssDNA recombineering to other Gram-positive bacteria. PMID:22328729

  9. Induction of Type I Interferons by Bacteria

    PubMed Central

    Monroe, Kathryn M.; McWhirter, Sarah M.; Vance, Russell E.

    2010-01-01

    SUMMARY Type I interferons (IFNs) are secreted cytokines that orchestrate diverse immune responses to infection. Although typically considered to be most important in the response to viruses, type I IFNs are also induced by most, if not all, bacterial pathogens. Although diverse mechanisms have been described, bacterial induction of type I IFNs occurs upon stimulation of two main pathways: (1) Toll-like receptor (TLR) recognition of bacterial molecules such as lipopolysaccharide (LPS); (2) TLR-independent recognition of molecules delivered to the host cell cytosol. Cytosolic responses can be activated by two general mechanisms. First, viable bacteria can secrete stimulatory ligands into the cytosol via specialized bacterial secretion systems. Second, ligands can be released from bacteria that lyse or are degraded. The bacterial ligands that induce the cytosolic pathways remains uncertain in many cases, but appear to include various nucleic acids. In this review, we discuss recent advances in our understanding of how bacteria induce type I interferons and the roles type I IFNs play in host immunity. PMID:20482555

  10. Rotating bacteria aggregate into active crystals

    NASA Astrophysics Data System (ADS)

    Petroff, Alexander; Wu, Xiao-Lun; Libchaber, Albert

    2014-11-01

    The dynamics of many microbial ecosystems are determined not only by the response of individual bacteria to their chemical and physical environments but also the dynamics that emerge from interactions between cells. Here we investigate the collective dynamics displayed by communities of Thiovulum majus, one of the fastest known bacteria. We observe that when these bacteria swim close to a microscope cover slip, the cells spontaneously aggregate into a visually-striking two-dimensional hexagonal lattice of rotating cells. Each cell in an aggregate rotates its flagella, exerting a force that pushes the cell into the cover slip and a torque that causes the cell to rotate. As cells rotate against their neighbors, they exert forces and torques on the aggregate that cause the crystal to move and cells to hop to new positions in the lattice. We show how these dynamics arises from hydrodynamic and surface forces between cells. We derive the equations of motion for an aggregate, show that this model reproduces many aspects of the observed dynamics, and discuss the stability of these and similar active crystals. Finally, we discuss the ecological significance of this behavior to understand how the ability to aggregate into these communities may have evolved.

  11. Rotating Bacteria Aggregate into Active Crystals

    NASA Astrophysics Data System (ADS)

    Petroff, A. P.; Wu, X. L.; Libchaber, A.

    2014-12-01

    The dynamics of many microbial ecosystems are determined not only by the response of individual bacteria to their chemical and physical environments but also the dynamics that emerge from interactions between cells. Here we investigate collective dynamics displayed by communities of Thiovulum majus, one of the fastest known bacteria. We observe that when these bacteria swim close to a microscope cover slip, the cells spontaneously aggregate into a visually-striking, two-dimensional hexagonal lattice of rotating cells. Each cell in an aggregate rotates its flagella, exerting a force that pushes the cell into the cover slip and a torque that causes the cell to rotate. As cells rotate against their neighbors, they exert forces and torques on the aggregate that cause the crystal to move and cells to hop to new positions in the lattice. We show how these dynamics arise from hydrodynamic and surface forces between cells. We derive the equations of motion for an aggregate, show that this model reproduces many aspects of the observed dynamics, and discuss the stability of these and similar active crystals. Finally, we discuss the ecological significance of this behavior to understand how the ability to aggregate into these communities may have evolved.

  12. Transfer of DNA from Bacteria to Eukaryotes.

    PubMed

    Lacroix, Benoît; Citovsky, Vitaly

    2016-01-01

    Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen), Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium), or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs), the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer. PMID:27406565

  13. Antimicrobial Peptides Targeting Gram-Positive Bacteria.

    PubMed

    Malanovic, Nermina; Lohner, Karl

    2016-01-01

    Antimicrobial peptides (AMPs) have remarkably different structures as well as biological activity profiles, whereupon most of these peptides are supposed to kill bacteria via membrane damage. In order to understand their molecular mechanism and target cell specificity for Gram-positive bacteria, it is essential to consider the architecture of their cell envelopes. Before AMPs can interact with the cytoplasmic membrane of Gram-positive bacteria, they have to traverse the cell wall composed of wall- and lipoteichoic acids and peptidoglycan. While interaction of AMPs with peptidoglycan might rather facilitate penetration, interaction with anionic teichoic acids may act as either a trap for AMPs or a ladder for a route to the cytoplasmic membrane. Interaction with the cytoplasmic membrane frequently leads to lipid segregation affecting membrane domain organization, which affects membrane permeability, inhibits cell division processes or leads to delocalization of essential peripheral membrane proteins. Further, precursors of cell wall components, especially the highly conserved lipid II, are directly targeted by AMPs. Thereby, the peptides do not inhibit peptidoglycan synthesis via binding to proteins like common antibiotics, but form a complex with the precursor molecule, which in addition can promote pore formation and membrane disruption. Thus, the multifaceted mode of actions will make AMPs superior to antibiotics that act only on one specific target. PMID:27657092

  14. Degradation of 2-Methylisoborneol by Aquatic Bacteria

    PubMed Central

    Izaguirre, George; Wolfe, Roy L.; Means, Edward G.

    1988-01-01

    2-Methylisoborneol (MIB) is a musty- or muddy-smelling compound which occurs in some natural waters and which is difficult to remove by conventional water treatment methods. Bacterial degradation of MIB was examined in batch culture experiments. Cultures able to metabolize MIB were enriched in a mineral salts medium supplemented with milligram-per-liter levels of the compound and were inoculated with water and sediment samples from reservoirs where MIB is seasonally produced. Bacteria from degrading cultures were isolated on R2A agar and identified as predominantly Pseudomonas spp. Degradation occurred only in cultures consisting of three or more different bacteria. MIB supported growth as the sole added carbon source at 1 to 6.7 mg/liter. MIB was also degraded at microgram-per-liter levels in sterile filtered lake water inoculated with washed bacteria and in synthetic medium supplemented with various sugars or acetate. Complete degradation of MIB took from 5 days to more than 2 weeks. Enrichment with isoborneol, a structural analog of MIB, failed as a preenrichment for MIB degraders. Isoborneol at 20 to 40 mg/liter readily supported bacterial growth, whereas MIB at 12 to 20 mg/liter took months to degrade. The relative recalcitrance of MIB compared with isoborneol may be a result of the additional methyl group in MIB. PMID:16347753

  15. Antimicrobial Peptides Targeting Gram-Positive Bacteria

    PubMed Central

    Malanovic, Nermina; Lohner, Karl

    2016-01-01

    Antimicrobial peptides (AMPs) have remarkably different structures as well as biological activity profiles, whereupon most of these peptides are supposed to kill bacteria via membrane damage. In order to understand their molecular mechanism and target cell specificity for Gram-positive bacteria, it is essential to consider the architecture of their cell envelopes. Before AMPs can interact with the cytoplasmic membrane of Gram-positive bacteria, they have to traverse the cell wall composed of wall- and lipoteichoic acids and peptidoglycan. While interaction of AMPs with peptidoglycan might rather facilitate penetration, interaction with anionic teichoic acids may act as either a trap for AMPs or a ladder for a route to the cytoplasmic membrane. Interaction with the cytoplasmic membrane frequently leads to lipid segregation affecting membrane domain organization, which affects membrane permeability, inhibits cell division processes or leads to delocalization of essential peripheral membrane proteins. Further, precursors of cell wall components, especially the highly conserved lipid II, are directly targeted by AMPs. Thereby, the peptides do not inhibit peptidoglycan synthesis via binding to proteins like common antibiotics, but form a complex with the precursor molecule, which in addition can promote pore formation and membrane disruption. Thus, the multifaceted mode of actions will make AMPs superior to antibiotics that act only on one specific target. PMID:27657092

  16. Magnesium and Manganese Content of Halophilic Bacteria

    PubMed Central

    Médicis, Eveline De; Paquette, Jean; Gauthier, Jean-Jacques; Shapcott, Dennis

    1986-01-01

    Magnesium and manganese contents were measured by atomic absorption spectrophotometry in bacteria of several halophilic levels, in Vibrio costicola, a moderately halophilic eubacterium growing in 1 M NaCl, Halobacterium volcanii, a halophilic archaebacterium growing in 2.5 M NaCl, Halobacterium cutirubrum, an extremely halophilic archaebacterium growing in 4 M NaCl, and Escherichia coli, a nonhalophilic eubacterium growing in 0.17 M NaCl. Magnesium and manganese contents varied with the growth phase, being maximal at the early log phase. Magnesium and manganese molalities in cell water were shown to increase with the halophilic character of the logarithmically growing bacteria, from 30 mmol of Mg per kg of cell water and 0.37 mmol of Mn per kg of cell water for E. coli to 102 mmol of Mg per kg of cell water and 1.6 mmol of Mn per kg of cell water for H. cutirubrum. The intracellular concentrations of manganese were determined independently by a radioactive tracer technique in V. costicola and H. volcanii. The values obtained by 54Mn loading represented about 70% of the values obtained by atomic absorption. The increase of magnesium and manganese contents associated with the halophilic character of the bacteria suggests that manganese and magnesium play a role in haloadaptation. Images PMID:16347151

  17. Bacteria-powered battery on paper.

    PubMed

    Fraiwan, Arwa; Choi, Seokheun

    2014-12-21

    Paper-based devices have recently emerged as simple and low-cost paradigms for fluid manipulation and analytical/clinical testing. However, there are significant challenges in developing paper-based devices at the system level, which contain integrated paper-based power sources. Here, we report a microfabricated paper-based bacteria-powered battery that is capable of generating power from microbial metabolism. The battery on paper showed a very short start-up time relative to conventional microbial fuel cells (MFCs); paper substrates eliminated the time traditional MFCs required to accumulate and acclimate bacteria on the anode. Only four batteries connected in series provided desired values of current and potential to power an LED for more than 30 minutes. The battery featured (i) a low-cost paper-based proton exchange membrane directly patterned on commercially available parchment paper and (ii) paper reservoirs for holding the anolyte and the catholyte for an extended period of time. Based on this concept, we also demonstrate the use of paper-based test platforms for the rapid characterization of electricity-generating bacteria. This paper-based microbial screening tool does not require external pumps/tubings and represents the most rapid test platform (<50 min) compared with the time needed by using traditional screening tools (up to 103 days) and even recently proposed MEMS arrays (< 2 days).

  18. Engineering Hybrid Chemotaxis Receptors in Bacteria.

    PubMed

    Bi, Shuangyu; Pollard, Abiola M; Yang, Yiling; Jin, Fan; Sourjik, Victor

    2016-09-16

    Most bacteria use transmembrane sensors to detect a wide range of environmental stimuli. A large class of such sensors are the chemotaxis receptors used by motile bacteria to follow environmental chemical gradients. In Escherichia coli, chemotaxis receptors are known to mediate highly sensitive responses to ligands, making them potentially useful for biosensory applications. However, with only four ligand-binding chemotaxis receptors, the natural ligand spectrum of E. coli is limited. The design of novel chemoreceptors to extend the sensing capabilities of E. coli is therefore a critical aspect of chemotaxis-based biosensor development. One path for novel sensor design is to harvest the large natural diversity of chemosensory functions found in bacteria by creating hybrids that have the signaling domain from E. coli chemotaxis receptors and sensory domains from other species. In this work, we demonstrate that the E. coli receptor Tar can be successfully combined with most typical sensory domains found in chemotaxis receptors and in evolutionary-related two-component histidine kinases. We show that such functional hybrids can be generated using several different fusion points. Our work further illustrates how hybrid receptors could be used to quantitatively characterize ligand specificity of chemotaxis receptors and histidine kinases using standardized assays in E. coli.

  19. Transfer of DNA from Bacteria to Eukaryotes

    PubMed Central

    2016-01-01

    ABSTRACT Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen), Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium), or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs), the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer. PMID:27406565

  20. Lineage-dependent ecological coherence in bacteria.

    PubMed

    Koeppel, Alexander F; Wu, Martin

    2012-09-01

    Bacteria comprise an essential element of all ecosystems, including those present on and within the human body. Understanding bacterial diversity therefore offers enormous scientific and medical benefit, but significant questions remain regarding how best to characterize that diversity and organize it into biologically meaningful units. Bacterial communities are routinely characterized based on the relative abundances of taxa at the genus or even the phylum level, but the ecological coherence of these high-level taxonomic units is uncertain. Using human microbiota from the skin and gut as our model systems, we tested the ecological coherence of bacteria by investigating the habitat associations of bacteria at all levels of the taxonomic hierarchy. We observed four distinct taxonomic patterns of habitat association, reflecting different levels of ecological coherence among taxa. Our results support the hypothesis that deep-branch bacterial clades could be ecologically coherent and suggest that the phylogenetic depth of ecological coherence varies among the bacterial lineages and is an important factor to consider in studies of human microbiome associations.

  1. Precision genome engineering in lactic acid bacteria

    PubMed Central

    2014-01-01

    Innovative new genome engineering technologies for manipulating chromosomes have appeared in the last decade. One of these technologies, recombination mediated genetic engineering (recombineering) allows for precision DNA engineering of chromosomes and plasmids in Escherichia coli. Single-stranded DNA recombineering (SSDR) allows for the generation of subtle mutations without the need for selection and without leaving behind any foreign DNA. In this review we discuss the application of SSDR technology in lactic acid bacteria, with an emphasis on key factors that were critical to move this technology from E. coli into Lactobacillus reuteri and Lactococcus lactis. We also provide a blueprint for how to proceed if one is attempting to establish SSDR technology in a lactic acid bacterium. The emergence of CRISPR-Cas technology in genome engineering and its potential application to enhancing SSDR in lactic acid bacteria is discussed. The ability to perform precision genome engineering in medically and industrially important lactic acid bacteria will allow for the genetic improvement of strains without compromising safety. PMID:25185700

  2. Stress-Induced Mutagenesis in Bacteria

    PubMed Central

    Foster, Patricia L.

    2009-01-01

    Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution. PMID:17917873

  3. Safety of industrial lactic acid bacteria.

    PubMed

    Adams, M R

    1999-02-19

    Lactic acid bacteria (LAB) are ubiquitous in fermented and non-fermented foods and are common components of the human commensal microflora. This long history of human exposure and consumption has led to the reasonable conclusion that they are generally safe. Recent attention has also focused on their possible role as probiotic bacteria, promoting beneficial health effects. There have, however, been a number of reports of human infections caused by LAB and these are reviewed. In most cases, the source of the infection was the commensal LAB flora rather than ingested bacteria and the patient had some underlying disease or predisposing condition. Even as opportunistic pathogens, the LAB, with the notable exception of the enterococci, are much less successful than a number of other members of the commensal microflora. The use of new strains for probiotic use is likely to require more detailed evidence for their safety, particularly if the strains have been genetically modified or have been derived from animals. Procedures that have been proposed for assessing the safety of new strains are described.

  4. Bacteria associated with Amblyomma cajennense tick eggs

    PubMed Central

    Machado-Ferreira, Erik; Vizzoni, Vinicius Figueiredo; Piesman, Joseph; Gazeta, Gilberto Salles; Soares, Carlos Augusto Gomes

    2015-01-01

    Abstract Ticks represent a large group of pathogen vectors that blood feed on a diversity of hosts. In the Americas, the Ixodidae ticks Amblyomma cajennense are responsible for severe impact on livestock and public health. In the present work, we present the isolation and molecular identification of a group of culturable bacteria associated with A. cajennense eggs from females sampled in distinct geographical sites in southeastern Brazil. Additional comparative analysis of the culturable bacteria from Anocentor nitens, Rhipicephalus sanguineus and Ixodes scapularis tick eggs were also performed. 16S rRNA gene sequence analyses identified 17 different bacterial types identified as Serratia marcescens, Stenotrophomonas maltophilia, Pseudomonas fluorescens, Enterobacter spp., Micrococcus luteus, Ochrobactrum anthropi, Bacillus cereus and Staphylococcus spp., distributed in 12 phylogroups. Staphylococcus spp., especially S. sciuri, was the most prevalent bacteria associated with A. cajennense eggs, occurring in 65% of the samples and also frequently observed infecting A. nitens eggs. S. maltophilia, S. marcescens and B. cereus occurred infecting eggs derived from specific sampling sites, but in all cases rising almost as pure cultures from infected A. cajennense eggs. The potential role of these bacterial associations is discussed and they possibly represent new targets for biological control strategies of ticks and tick borne diseases. PMID:26537602

  5. Predicting community composition from pairwise interactions

    NASA Astrophysics Data System (ADS)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

  6. Mutations and Misconceptions: The Isolation and Study of Mutant Bacteria.

    ERIC Educational Resources Information Center

    Corner, Thomas R.

    1992-01-01

    Describes simple, inexpensive activities for teaching students about mutants and mutations in bacteria. Explains how to isolate bacteria from soil and leaves and how to grow bacteria on agar or in broth. Describes how to construct a gradient plate for finding the minimum inhibitory concentration of a substance and how to use this set up to find…

  7. Antibiotics and gene transfer in swine gut bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mammalian gastrointestinal (GI) tract hosts a diverse collection bacteria, most of which are beneficial for host health. This bacterial community also supports a community of viruses that infect bacteria (called bacteriophages or phages). Phages transfer genes between bacteria, and phage-media...

  8. Hydrodynamic tracer diffusion in suspensions of swimming bacteria

    NASA Astrophysics Data System (ADS)

    Kasyap, T. V.; Koch, Donald L.; Wu, Mingming

    2014-08-01

    We present theoretical predictions, simulations, and experimental measurements of the diffusion of passive, Brownian tracer particles in the bulk of three-dimensional suspensions of swimming bacteria performing run-tumble random walks. In the theory, we derive an explicit expression for the "hydrodynamic" tracer diffusivity that results from the fluid disturbances created by a slender-body model of bacteria by ensemble averaging the mass conservation equation of the tracer over the space of tracer-bacterium interactions which are assumed to be binary. The theory assumes that the orientations of the bacterium before and after a tumble are uncorrelated and the fluid velocity disturbance created by the bacterium is small compared to its swimming speed. The dependence of the non-dimensional hydrodynamic diffusivity widetilde{D_h} obtained by scaling the dimensional hydrodynamic diffusivity by nL3UsL on the persistence in bacterial swimming and the Brownian diffusivity of the tracer are studied in detail through two nondimensional parameters—a Peclet number Pe = UsL/D which is the ratio of the time scale of bacterial swimming to the tracer diffusion time scale and a non-dimensional persistence time τ* = Usτ/L obtained by scaling the dimensional bacterial persistence time by the time that a bacterium takes to swim over a distance equal to its length. Here, n, Us, τ, and L are the concentration, swimming speed, tumbling time, and the overall length of the bacteria, respectively, and D is the Brownian diffusivity of the tracer. widetilde{D_h} is found to be a monotonically increasing function of τ* and a non-monotonic function of Pe with a Pe1/2 scaling in the Pe ≪ 1 limit, an intermediate peak and a constant value in the Pe ≫ 1 limit for the typical case of wild-type bacteria with τ* = O(1). In the simulation study we compute the bacterial contribution to the tracer diffusivity from explicit numerical simulations of binary tracer-bacterium interactions to

  9. Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

    USGS Publications Warehouse

    Hyer, Kenneth; Moyer, Douglas

    2003-01-01

    (maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

  10. Effect of conventional dental restorative treatment on bacteria in saliva.

    PubMed

    Wright, J T; Cutter, G R; Dasanayake, A P; Stiles, H M; Caufield, P W

    1992-06-01

    Dental caries results from the dissolution of mineralized dental tissues by the metabolic by-products of oral bacteria colonizing the surface of teeth. The principal modality for dealing with this infectious process is through restorative treatment which removes the pathologic tissue and replaces it with a variety of inert materials. The purpose of this study was to evaluate the effect of traditional restorative treatment on select oral bacterial populations. Fifty-two females demonstrating high levels of mutans streptococci (greater than or equal to 2.5 x 10(4) colony forming units (cfu) per ml saliva) with no more than four missing posterior teeth were recruited for this study. Salivary levels of mutans streptococci, lactobacilli, total streptococci, and total cultivable bacteria were evaluated before, during, and after restorative treatment. Initial DMFS scores were established by two standardized examiners using bitewing radiographs and clinical examination, which was conducted under optimal conditions. All restorative treatment was completed by faculty members of the University of Alabama School of Dentistry using treatment plans developed by the DMFS examiners. The participants received a mean of 16.4 restored surfaces, which resulted in significant reductions of all the bacterial populations tested. All microbial populations monitored were predicted to return to their baseline levels within 151 days after restorative treatment in 50% of the participants. This study shows that conventional restorative treatment results in a significant reduction of bacterial populations including those associated with the dental caries process, i.e., mutans streptococci and lactobacilli.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Bacteria-Targeting Nanoparticles for Managing Infections

    NASA Astrophysics Data System (ADS)

    Radovic-Moreno, Aleksandar Filip

    Bacterial infections continue to be a significant concern particularly in healthcare settings and in the developing world. Current challenges include the increasing spread of drug resistant (DR) organisms, the side effects of antibiotic therapy, the negative consequences of clearing the commensal bacterial flora, and difficulties in developing prophylactic vaccines. This thesis was an investigation of the potential of a class of polymeric nanoparticles (NP) to contribute to the management of bacterial infections. More specifically, steps were taken towards using these NPs (1) to achieve greater spatiotemporal control over drug therapy by more targeted antibiotic delivery to bacteria, and (2) to develop a prophylactic vaccine formulation against the common bacterial sexually transmitted disease (STD) caused by Chlamydia trachomatis. In the first part, we synthesized polymeric NPs containing poly(lactic-co-glycolic acid)-block-poly(L-histidine)-block-poly(ethylene glycol) (PLGA-PLH-PEG). We show that these NPs are able to bind to bacteria under model acidic infection conditions and are able to encapsulate and deliver vancomycin to inhibit the growth of Staphylococcus aureus bacteria in vitro. Further work showed that the PLGA-PLH-PEG-based NPs demonstrated the potential for competition for binding bacteria at a site of infection from soluble protein and model phagocytic and tissue-resident cells in a NP composition dependent manner. The NPs demonstrated low toxicity in vitro, were well tolerated by mice in vivo, and circulated in the blood on timescales comparable to control PLGA-PEG NPs. In the second part, we used PLGA-PLH-PEG-based NPs to design a prophylactic vaccine against the obligate intracellular bacterium Chlamydia trachomatis, the most common cause of bacterial STD in the world. Currently, no vaccines against this pathogen are approved for use in humans. We first formulated NPs encapsulating the TLR7 agonist R848 conjugated to poly(lactic acid) (R848-PLA

  12. Enumeration of indicator bacteria exposed to chlorine.

    PubMed

    McFeters, G A; Camper, A K

    1983-01-01

    Stress resulting from a variety of chemical and physical environments has been recognized in indicator bacteria. A review by Busta (1976) summarizes the extensive work that has been carried out to describe indicator microorganisms sublethally impaired due to a variety of causes associated with foods. Workers in the area of water microbiology are also gaining an appreciation of the importance of these stressed cells in the assessment of water quality using bacterial indicators. Chemical agents, including chlorine, that are employed in water disinfection processes are important causes of bacterial stress injury. As a result, a significant portion of the total population of indicator bacteria in water might not be enumerated (using the selective procedures that are currently employed) and inaccurate water quality determinations could result. Alternative water disinfection agents that are being suggested, such as ozone, chlorine dioxide, and ultraviolet irradiation, will also probably lead to the same result. In addition, heat from thermal pollution and interactions with other microorganisms or chemicals (including disinfectants and metals) also exert stress that could further debilitate indicator bacteria in various waters and effluents. A need for improved enumeration procedures has accompanied the recognition of injured indicator bacteria in chlorinated waters and wastewaters. This movement has also stimulated interest in the underlying mechanism of cellular damage that is responsible for the submaximal recovery of coliforms from disinfected waters. Various groups have reported that a number of biochemical, genetic, and physiological processes are impaired by chlorine exposure under differing conditions. Evidence from our laboratory and elsewhere implicates functions associated with the cell envelope, i.e., the uptake of extracellular organic substrates, as the primary cellular target of chlorine under conditions that are similar to those in the field. Additional

  13. Absence of association between total heterotrophic and total coliform bacteria from a public water supply.

    PubMed Central

    Edberg, S; Smith, D B

    1989-01-01

    Heterotrophic plate counts (HPC) and total coliforms (TC) are two major microbial indicators that are used to monitor the potability of water. Although the presence of heterotrophs has been hypothesized to predict the presence of TC, there have been few documented reports. Intensive sampling of raw, treated effluent and distribution water from a public water supply serving 400,000 people provided an opportunity to study the relationship between these two indicator groups of bacteria. A total of 26,158 samples were analyzed, including 12,970 from 1986 and 13,188 from 1985. There were 13,429 samples from the distribution system, 5,524 from treatment effluents, and 7,205 from raw water. The associations between HPC and TC were made on both a hits-and-misses and numerical comparison (CFU per milliliter) basis. The periodicity of the two indicators was also analyzed to determine whether the presence of one group could predict the presence of the other. Atypical bacteria were also related to the presence of these two indicator bacteria. Venn diagrams and nonparametric statistics revealed the following correlation coefficients for HPC and TC for 1985 and 1986 combined: raw water r = 0.45, treated effluent r = 0.06, and distribution system r = 0.10. Atypical bacteria showed a similar relationship with HPC. There was no predictive periodicity for HPC and TC within +/- 10 days of isolation of each other. Therefore, in a 2-year survey of a public water supply, the presence of HPC had a low correlation coefficient with TC, as determined by hits-and-misses and numerical comparisons. The enumeration of one group was found to be independent of the other. PMID:2719479

  14. Making detailed predictions makes (some) predictions worse

    NASA Astrophysics Data System (ADS)

    Kelly, Theresa F.

    In this paper, we investigate whether making detailed predictions about an event makes other predictions worse. Across 19 experiments, 10,895 participants, and 415,960 predictions about 724 professional sports games, we find that people who made detailed predictions about sporting events (e.g., how many hits each baseball team would get) made worse predictions about more general outcomes (e.g., which team would win). We rule out that this effect is caused by inattention or fatigue, thinking too hard, or a differential reliance on holistic information about the teams. Instead, we find that thinking about game-relevant details before predicting winning teams causes people to give less weight to predictive information, presumably because predicting details makes information that is relatively useless for predicting the winning team more readily accessible in memory and therefore incorporated into forecasts. Furthermore, we show that this differential use of information can be used to predict what kinds of games will and will not be susceptible to the negative effect of making detailed predictions.

  15. Interaction of ambient conditions and fecal coliform bacteria in southern Lake Michigan beach waters: Monitoring program implications

    USGS Publications Warehouse

    Whitman, Richard L.; Nevers, Meredith Becker; Gerovac, Paul J.

    1999-01-01

    Excessive fecal coliform bacteria in public swimming waters can potentially threaten visitor health. Fecal coliform bacteria (1984-1989) and Escherichia coli (1990-1995) density were monitored weekly at the Indiana Dunes National Lakeshore beaches for 12 summers, and park officials closed swimming areas when fecal coliform density exceeded the state water quality criteria (400 CFU fecal coliforms/ 100 ml; 235 CFU E. coli/100 ml water). Due to a 24-hour incubation in the fecal coliform and E. coli assays, beaches were closed the day after collection of high fecal coliform. Our analysis suggests that it is not possible to predict one day's fecal coliform count based on the previous day's results in waters taken from southern Lake Michigan beaches. Dispersal and deposition of bacteria were not uniform among sites or across time apparently due to interactions among environmental variables including rainfall, wind direction, water temperature, and bacteria source. Rainfall combined with northwest winds increased bacteria concentrations. Escherichia coli followed a seasonal trend with similar fluctuations in density among beaches. We suggest that the current beach monitoring protocol is inadequate for predicting fecal coliform density at the time of beach closure, and, subsequently, its use for ensuring visitor safety remains questionable.

  16. Bacteria-Mineral Interactions on the Surfaces of Metal-Resistant Bacteria

    SciTech Connect

    Malkin, A J

    2010-03-24

    The extraordinary ability of indigenous microorganisms, like metal-resistant bacteria, for biotransformation of toxic compounds is of considerable interest for the emerging area of environmental bioremediation. However, the underlying mechanisms by which metal-resistant bacteria transform toxic compounds are currently unknown and await elucidation. The project's objective was to study stress-induced responses of metal-resistant bacteria to environmental changes and chemical stimulants. This project involved a multi-institutional collaboration of our LLNL group with the group of Dr. H.-Y. Holman (Lawrence Berkeley National Laboratory). In this project, we have utilized metal-resistant bacteria Arthrobacter oxydans as a model bacterial system. We have utilized atomic force microscopy (AFM) to visualize for the first time at the nanometer scale formation of stress-induced structures on bacterial surfaces in response to Cr (VI) exposure. We have demonstrated that structure, assembly, and composition of these stress-induced structures are dependent on Cr (VI) concentrations. Our AFM observations of the appearance and development of stress-induced layers on the surfaces of Arthrobacter oxydans bacteria exposed to Cr (VI) were confirmed by Dr. Holman's biochemical, electron microscopy, and synchrotron infrared spectromicroscopy studies. In general, in vitro imaging of live microbial and cellular systems represents one of the most challenging issues in application of AFM. Various approaches for immobilization of bacteria on the substrate for in vitro imaging were tested in this project. Imaging of live bacteria was achieved, however further optimization of experimental methods are needed for high-resolution visualization of the cellular environmental structural dynamics by AFM. This project enhanced the current insight into molecular architecture, structural and environmental variability of bacterial systems. The project partially funded research for two book chapters (1

  17. A study to estimate the fate and transport of bacteria in river water from birds nesting under a bridge.

    PubMed

    Nayamatullah, M M M; Bin-Shafique, S; Sharif, H O

    2013-01-01

    To investigate the effect of input parameters, such as the number of bridge-dwelling birds, decay rate of the bacteria, flow at the river, water temperature, and settling velocity, a parametric study was conducted using a water quality model developed with QUAL2Kw. The reach of the bacterial-impaired section from the direct droppings of bridge-nesting birds at the Guadalupe River near Kerrville, Texas was estimated using the model. The concentration of Escherichia coli bacteria were measured upstream, below the bridge, and downstream of the river for one-and-a-half years. The decay rate of the indicator bacteria in the river water was estimated from the model using measured data, and was found to be 6.5/day. The study suggests that the number of bridge-dwelling birds, the decay rate, and flow at the river have the highest impact on the fate and transport of bacteria. The water temperature moderately affects the fate and transport of bacteria, whereas, the settling velocity of bacteria did not show any significant effect. Once the decay rates are estimated, the reach of the impaired section was predicted from the model using the average flow of the channel. Since the decay rate does not vary significantly in the ambient environment at this location, the length of the impaired section primarily depends on flow.

  18. Interactions between amino-acid-degrading bacteria and methanogenic bacteria in anaerobic digestion

    SciTech Connect

    Nagase, M.; Matsuo, T.

    1982-10-01

    The degradation of amino acids in anaerobic digestion was examined in terms of the interactions between amino-acid-degrading bacteria and methanogenic bacteria. Certain amino acids were degraded oxidatively by dehydrogenation, with methanogenic bacteria acting as H/sub 2/ acceptors. The inhibition of methanogenesis by chloroform also inhibited the degradation of these amino acids and/or caused variations in the composition of volatile acids produced from them. The presence of glycine reduced the inhibitory effect caused by chloroform, probably because glycine acted as an H/sub 2/ acceptor in place of methanogenic bacteria. This fact suggested that the coupled oxidation-reduction reactions between two amino acids - one acting as the H/sub 2/ donor and the other acting as the H/sub 2/ acceptor - may occur in the anaerobic digestion of proteins or amino-acid mixtures. The conversion of some proteins to volatile acids was not affected when methanogensis was inhibited by chloroform. This suggested that the component amino acids of proteins may be degraded by the coupled oxidation-reduction reactions and that the degradation of proteins may not be dependent on the activity of methanogenic bacteria as H/sub 2/ acceptors.

  19. Isolation of fucosyltransferase-producing bacteria from marine environments.

    PubMed

    Kajiwara, Hitomi; Toda, Munetoyo; Mine, Toshiki; Nakada, Hiroshi; Yamamoto, Takeshi

    2012-01-01

    Fucose-containing oligosaccharides on the cell surface of some pathogenic bacteria are thought to be important for host-microbe interactions and to play a major role in the pathogenicity of bacterial pathogens. Here, we screened marine bacteria for glycosyltransferases using two methods: a one-pot glycosyltransferase assay method and a lectin-staining method. Using this approach, we isolated marine bacteria with fucosyltransferase activity. There have been no previous reports of marine bacteria producing fucosyltransferase. This paper thus represents the first report of fucosyltransferase-producing marine bacteria.

  20. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

    PubMed

    O'Connor, Roberta M; Fung, Jennifer M; Sharp, Koty H; Benner, Jack S; McClung, Colleen; Cushing, Shelley; Lamkin, Elizabeth R; Fomenkov, Alexey I; Henrissat, Bernard; Londer, Yuri Y; Scholz, Matthew B; Posfai, Janos; Malfatti, Stephanie; Tringe, Susannah G; Woyke, Tanja; Malmstrom, Rex R; Coleman-Derr, Devin; Altamia, Marvin A; Dedrick, Sandra; Kaluziak, Stefan T; Haygood, Margo G; Distel, Daniel L

    2014-11-25

    Bacteria play many important roles in animal digestive systems, including the provision of enzymes critical to digestion. Typically, complex communities of bacteria reside in the gut lumen in direct contact with the ingested materials they help to digest. Here, we demonstrate a previously undescribed digestive strategy in the wood-eating marine bivalve Bankia setacea, wherein digestive bacteria are housed in a location remote from the gut. These bivalves, commonly known as shipworms, lack a resident microbiota in the gut compartment where wood is digested but harbor endosymbiotic bacteria within specialized cells in their gills. We show that this comparatively simple bacterial community produces wood-degrading enzymes that are selectively translocated from gill to gut. These enzymes, which include just a small subset of the predicted wood-degrading enzymes encoded in the endosymbiont genomes, accumulate in the gut to the near exclusion of other endosymbiont-made proteins. This strategy of remote enzyme production provides the shipworm with a mechanism to capture liberated sugars from wood without competition from an endogenous gut microbiota. Because only those proteins required for wood digestion are translocated to the gut, this newly described system reveals which of many possible enzymes and enzyme combinations are minimally required for wood degradation. Thus, although it has historically had negative impacts on human welfare, the shipworm digestive process now has the potential to have a positive impact on industries that convert wood and other plant biomass to renewable fuels, fine chemicals, food, feeds, textiles, and paper products.

  1. Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria.

    PubMed

    Hwang, In Young; Koh, Elvin; Kim, Hye Rim; Yew, Wen Shan; Chang, Matthew Wook

    2016-07-01

    The discovery of antimicrobial drugs and their subsequent use has offered an effective treatment option for bacterial infections, reducing morbidity and mortality over the past 60 years. However, the indiscriminate use of antimicrobials in the clinical, community and agricultural settings has resulted in selection for multidrug-resistant bacteria, which has led to the prediction of possible re-entrance to the pre-antibiotic era. The situation is further exacerbated by significantly reduced antimicrobial drug discovery efforts by large pharmaceutical companies, resulting in a steady decline in the number of new antimicrobial agents brought to the market in the past several decades. Consequently, there is a pressing need for new antimicrobial therapies that can be readily designed and implemented. Recently, it has become clear that the administration of broad-spectrum antibiotics can lead to collateral damage to the human commensal microbiota, which plays several key roles in host health. Advances in genetic engineering have opened the possibility of reprogramming commensal bacteria that are in symbiotic existence throughout the human body to implement antimicrobial drugs with high versatility and efficacy against pathogenic bacteria. In this review, we discuss recent advances and potentialities of engineered bacteria in providing a novel antimicrobial strategy against antibiotic resistance. PMID:27449598

  2. Cell wall reactivity of acidophilic and alkaliphilic bacteria determined by potentiometric titrations and Cd adsorption experiments.

    PubMed

    Kenney, Janice P L; Fein, Jeremy B

    2011-05-15

    In this study, we used potentiometric titrations and Cd adsorption experiments to determine the binding capacities of two acidophilic (A. cryptum and A. acidophilum) and two alkaliphilic (B. pseudofirmus and B. circulans) bacterial species in order to determine if any consistent trends could be observed relating bacterial growth environment to proton and Cd binding properties and to compare those binding behaviors to those of neutrophilic bacteria. All of the bacterial species studied exhibited significant proton buffering over the pH range in this study, with the alkaliphiles exhibiting significantly higher acidity constants than the acidophiles as well as the neutrophilic bacterial consortia. The calculated average site concentrations for each of the bacteria in this study are within 2σ experimental error of each other, with the exception of A. cryptum, which has a significantly higher Site 2 concentration than the other species. Despite differing acidity constants between the acidophiles and alkaliphiles, all bacteria except A. cryptum exhibited remarkably similar Cd adsorption behavior to each other, and the observed extent of adsorption was also similar to that predicted from a generalized model derived using neutrophilic bacterial consortia. This study demonstrates that bacteria that grow under extreme conditions exhibit similar proton and metal adsorption behavior to that of previously studied neutrophilic species and that a single set of proton and metal binding constants can be used to model the behavior of bacterial adsorption under a wide range of environmental conditions.

  3. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk

    PubMed Central

    O’Connor, Roberta M.; Fung, Jennifer M.; Sharp, Koty H.; Benner, Jack S.; McClung, Colleen; Cushing, Shelley; Lamkin, Elizabeth R.; Fomenkov, Alexey I.; Henrissat, Bernard; Londer, Yuri Y.; Scholz, Matthew B.; Posfai, Janos; Malfatti, Stephanie; Tringe, Susannah G.; Woyke, Tanja; Malmstrom, Rex R.; Coleman-Derr, Devin; Altamia, Marvin A.; Dedrick, Sandra; Kaluziak, Stefan T.; Haygood, Margo G.; Distel, Daniel L.

    2014-01-01

    Bacteria play many important roles in animal digestive systems, including the provision of enzymes critical to digestion. Typically, complex communities of bacteria reside in the gut lumen in direct contact with the ingested materials they help to digest. Here, we demonstrate a previously undescribed digestive strategy in the wood-eating marine bivalve Bankia setacea, wherein digestive bacteria are housed in a location remote from the gut. These bivalves, commonly known as shipworms, lack a resident microbiota in the gut compartment where wood is digested but harbor endosymbiotic bacteria within specialized cells in their gills. We show that this comparatively simple bacterial community produces wood-degrading enzymes that are selectively translocated from gill to gut. These enzymes, which include just a small subset of the predicted wood-degrading enzymes encoded in the endosymbiont genomes, accumulate in the gut to the near exclusion of other endosymbiont-made proteins. This strategy of remote enzyme production provides the shipworm with a mechanism to capture liberated sugars from wood without competition from an endogenous gut microbiota. Because only those proteins required for wood digestion are translocated to the gut, this newly described system reveals which of many possible enzymes and enzyme combinations are minimally required for wood degradation. Thus, although it has historically had negative impacts on human welfare, the shipworm digestive process now has the potential to have a positive impact on industries that convert wood and other plant biomass to renewable fuels, fine chemicals, food, feeds, textiles, and paper products. PMID:25385629

  4. Method efficiency and signal quantification of bacteria for a groundwater transport experiment

    SciTech Connect

    Burlage, R.S.; Palumbo, A.V.; McCarthy, J.

    1995-04-01

    Bacterial transport is a key process in delivery of microbes to contaminated sites for bioremediation of chemicals. However, relatively little is known about the geochemical and hydrologic factors controlling the mobility of bacteria and viruses within subsurface systems. Laboratory-scale column studies have provided useful information (Harvey et al, 1989, 1993). However, successful application to in situ remediation will require that one identify and understand properties relevant to transport in aquifers. Only through field experiments can one evaluate the scales of physical and chemical heterogeneity in natural aquifers that affect the transport of microbiota in ways not predicted from experiments conducted at the laboratory-scale. Bacterial transport field experiments cannot be replicated as can column experiments. Rigorous testing of experimental hypotheses will require comparisons of the mobility of multiple strains with contrasting transport properties under identical field conditions. Consequently, a technique is needed to permit the transport of multiple strains of bacteria to be monitored simultaneously in a single field experiment. Molecular techniques can also detect very low levels of injected bacteria. Polymerase chain reaction (PCR) has been used successfully for the detection of microorganisms. This paper explores the use of PCR for identifying and enumerating the arrival of several individual strains of bacteria at monitoring wells downgradient of an experimental tracer injection well.

  5. Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria.

    PubMed

    Zimmerman, Amy E; Allison, Steven D; Martiny, Adam C

    2014-05-01

    The objective of this study was to evaluate the contribution of evolutionary history to variation in the biomass stoichiometry and underlying biochemical allocation patterns of heterotrophic marine bacteria. We hypothesized that phylogeny significantly constrains biochemical allocation strategy and elemental composition among taxa of heterotrophic marine bacteria. Using a 'common-garden' experimental design, we detected significant interspecific variation in stoichiometry, macromolecule allocation and growth rate among 13 strains of marine Proteobacteria. However, this variation was not well explained by 16S rRNA phylogenetic relationships or differences in growth rate. Heterotrophic bacteria likely experience C-limitation when consuming resources in Redfield proportions, which consequently decouples growth rate from allocation to rRNA and biomass P content. Accordingly, overall bacterial C : nutrient ratios (C : P = 77, C : N = 4.9) were lower than Redfield proportions, whereas the average N : P ratio of 17 was consistent with the Redfield ratio. Our results suggest that strain-level diversity is an important driver of variation in the C : N : P ratios of heterotrophic bacterial biomass and that the potential importance of non-nucleic acid pools of P warrants further investigation. Continued work clarifying the range and controls on the stoichiometry of heterotrophic marine bacteria will help improve understanding and predictions of global ocean C, N and P dynamics.

  6. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

    PubMed

    O'Connor, Roberta M; Fung, Jennifer M; Sharp, Koty H; Benner, Jack S; McClung, Colleen; Cushing, Shelley; Lamkin, Elizabeth R; Fomenkov, Alexey I; Henrissat, Bernard; Londer, Yuri Y; Scholz, Matthew B; Posfai, Janos; Malfatti, Stephanie; Tringe, Susannah G; Woyke, Tanja; Malmstrom, Rex R; Coleman-Derr, Devin; Altamia, Marvin A; Dedrick, Sandra; Kaluziak, Stefan T; Haygood, Margo G; Distel, Daniel L

    2014-11-25

    Bacteria play many important roles in animal digestive systems, including the provision of enzymes critical to digestion. Typically, complex communities of bacteria reside in the gut lumen in direct contact with the ingested materials they help to digest. Here, we demonstrate a previously undescribed digestive strategy in the wood-eating marine bivalve Bankia setacea, wherein digestive bacteria are housed in a location remote from the gut. These bivalves, commonly known as shipworms, lack a resident microbiota in the gut compartment where wood is digested but harbor endosymbiotic bacteria within specialized cells in their gills. We show that this comparatively simple bacterial community produces wood-degrading enzymes that are selectively translocated from gill to gut. These enzymes, which include just a small subset of the predicted wood-degrading enzymes encoded in the endosymbiont genomes, accumulate in the gut to the near exclusion of other endosymbiont-made proteins. This strategy of remote enzyme production provides the shipworm with a mechanism to capture liberated sugars from wood without competition from an endogenous gut microbiota. Because only those proteins required for wood digestion are translocated to the gut, this newly described system reveals which of many possible enzymes and enzyme combinations are minimally required for wood degradation. Thus, although it has historically had negative impacts on human welfare, the shipworm digestive process now has the potential to have a positive impact on industries that convert wood and other plant biomass to renewable fuels, fine chemicals, food, feeds, textiles, and paper products. PMID:25385629

  7. Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States ▿ †

    PubMed Central

    Bowers, Robert M.; Sullivan, Amy P.; Costello, Elizabeth K.; Collett, Jeff L.; Knight, Rob; Fierer, Noah

    2011-01-01

    Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere. PMID:21803902

  8. Sources of bacteria in outdoor air across cities in the midwestern United States.

    PubMed

    Bowers, Robert M; Sullivan, Amy P; Costello, Elizabeth K; Collett, Jeff L; Knight, Rob; Fierer, Noah

    2011-09-01

    Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere.

  9. Population of Nitrifying Bacteria and Nitrification in Ammonium Saturated Clinoptilolite

    NASA Technical Reports Server (NTRS)

    McGilloway, R. L.; Weaver, R. W.; Ming, Douglas W.; Gruener, J.

    1999-01-01

    As humans begin to spend longer periods of time in space, plants will be incorporated into life support systems. Ammonium saturated clinoptilolite is one plant growth substrate but a balance between ammonium and nitrate is needed. A laboratory study was conducted to determine effects of nitrifying bacteria on ammonium concentrations and kinetics of nitrification. Columns containing clinoptilolite substrate amended with nitrifying bacteria obtained from soil enrichment were analyzed weekly for a 90 day period. The enrichment culture initially contained 1 x 10(exp 5) ammonium oxidizing bacteria and 1 x 10(exp 2) nitrite oxidizing bacteria per gram of substrate. Populations of ammonium oxidizing bacteria increased to 1 x 10(exp 6) and nitrite oxidizing bacteria increased to 1 x 10(exp 3) per gram of substrate. The nitrification rate was approximately 0.25mg NO3(-)-N/kg.hr. Experiments were also conducted to enumerate nitrifying bacteria in a clinoptilolite substrate used to grow wheat (Triticum aestivum L.). Seventy days following the initial inoculation with an unknown number of commercial nitrifying bacteria, 1 x 10(exp 5) ammonium oxidizing bacteria per gram of substrate were present. The number of nitrite oxidizing bacteria was between 1 x 10(exp 3) to 10(exp 4) per gram of substrate as measured by the most probable number method. Nitrification rates were approximately 0.20mg NO3(-)-N/kg.hr. Clinoptilolite readily exchanged sufficient concentrations of ammonium to support nitrifying bacteria and they survived well in this medium.

  10. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.

    PubMed

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L; McDermott, Timothy R; Macur, Richard E; Inskeep, William P; Nealson, Kenneth H

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

  11. Distribution of bacteria in inhalable particles and its implications for health risks in kindergarten children in Hong Kong

    NASA Astrophysics Data System (ADS)

    Deng, Wenjing; Chai, Yemao; Lin, Huiying; So, Winnie W. M.; Ho, K. W. K.; Tsui, A. K. Y.; Wong, R. K. S.

    2016-03-01

    Health risks in children caused by bacteria in indoor environments have attracted much attention in recent years. There are many harmful bacteria, and children have greater health risks than adults in the same environment. To investigate the association between children's health risks and the distribution and concentration of bacteria in particulate matter smaller than 2.5 μm in indoor and outdoor air at three kindergartens in Hong Kong, quantitative polymerase chain reaction was used to determine the concentration of bacteria, and the terminal restriction fragment length polymorphism method targeting 16S ribosomal RNA genes was used to predict the phylogenetic airborne bacterial community structures. The bacterial concentrations indoors were higher than those outdoors in the three kindergartens, but no obvious differences were found (P > 0.05). Statistical analysis showed that the different schools had significantly different concentrations (P < 0.05). The abundance of bacteria in schools downtown (in Kowloon) was the greatest, reaching 3.3 × 103 to 4.95 × 104 cells per m3. However, the results showed no significant differences between the microbial populations obtained indoors and those obtained outdoors. The dominant genera were very similar among the six samples. Our results suggest that the majority of the inhalable bacteria were harmless to humans. Only a small fraction of microbial pathogens were identified, and their relative abundance appeared to increase as the concentration of particulate matter pollution increased. Analysis of these bacteria can give important clues regarding the exposure of kindergarten children to bacteria in indoor and outdoor air.

  12. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.

    PubMed

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L; McDermott, Timothy R; Macur, Richard E; Inskeep, William P; Nealson, Kenneth H

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur. PMID:26973602

  13. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

    PubMed Central

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L.; McDermott, Timothy R.; Macur, Richard E.; Inskeep, William P.; Nealson, Kenneth H.

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur. PMID:26973602

  14. Draft genome sequence and annotation of Lactobacillus acetotolerans BM-LA14527, a beer-spoilage bacteria.

    PubMed

    Liu, Junyan; Li, Lin; Peters, Brian M; Li, Bing; Deng, Yang; Xu, Zhenbo; Shirtliff, Mark E

    2016-09-01

    Lactobacillus acetotolerans is a hard-to-culture beer-spoilage bacterium capable of entering into the viable putative nonculturable (VPNC) state. As part of an initial strategy to investigate the phenotypic behavior of L. acetotolerans, draft genome sequencing was performed. Results demonstrated a total of 1824 predicted annotated genes, with several potential VPNC- and beer-spoilage-associated genes identified. Importantly, this is the first genome sequence of L. acetotolerans as beer-spoilage bacteria and it may aid in further analysis of L. acetotolerans and other beer-spoilage bacteria, with direct implications for food safety control in the beer brewing industry.

  15. Evaluation of the Rapidec Carba NP Test Kit for Detection of Carbapenemase-Producing Gram-Negative Bacteria.

    PubMed

    Garg, Atul; Garg, Jaya; Upadhyay, G C; Agarwal, Anurag; Bhattacharjee, Amitabha

    2015-12-01

    Recently, bioMérieux, France, introduced the Rapidec Carba NP test kit for rapid detection of carbapenemase-producing Gram-negative bacteria. This kit was evaluated in this study, and we report sensitivity, specificity, and positive and negative predictive values of 92.6%, 96.2%, 95.83%, and 92.6%, respectively. The test was easy to perform and interpret and relatively inexpensive ($5/Rs 300 per test) and provides a practical solution for early detection of carbapenemase-producing, multidrug-resistant Gram-negative bacteria.

  16. Draft genome sequence and annotation of Lactobacillus acetotolerans BM-LA14527, a beer-spoilage bacteria.

    PubMed

    Liu, Junyan; Li, Lin; Peters, Brian M; Li, Bing; Deng, Yang; Xu, Zhenbo; Shirtliff, Mark E

    2016-09-01

    Lactobacillus acetotolerans is a hard-to-culture beer-spoilage bacterium capable of entering into the viable putative nonculturable (VPNC) state. As part of an initial strategy to investigate the phenotypic behavior of L. acetotolerans, draft genome sequencing was performed. Results demonstrated a total of 1824 predicted annotated genes, with several potential VPNC- and beer-spoilage-associated genes identified. Importantly, this is the first genome sequence of L. acetotolerans as beer-spoilage bacteria and it may aid in further analysis of L. acetotolerans and other beer-spoilage bacteria, with direct implications for food safety control in the beer brewing industry. PMID:27559043

  17. Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater.

    PubMed

    Ferguson, Andrew S; Layton, Alice C; Mailloux, Brian J; Culligan, Patricia J; Williams, Daniel E; Smartt, Abby E; Sayler, Gary S; Feighery, John; McKay, Larry D; Knappett, Peter S K; Alexandrova, Ekaterina; Arbit, Talia; Emch, Michael; Escamilla, Veronica; Ahmed, Kazi Matin; Alam, Md Jahangir; Streatfield, P Kim; Yunus, Mohammad; van Geen, Alexander

    2012-08-01

    Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.

  18. Archaeal-like chaperonins in bacteria

    PubMed Central

    Techtmann, Stephen M.; Robb, Frank T.

    2010-01-01

    Chaperonins (CPN) are ubiquitous oligomeric protein machines that mediate the ATP-dependent folding of polypeptide chains. These chaperones have not only been assigned stress response and normal housekeeping functions but also have a role in certain human disease states. A longstanding convention divides CPNs into two groups that share many conserved sequence motifs but differ in both structure and distribution. Group I complexes are the well known GroEL/ES heat-shock proteins in bacteria, that also occur in some species of mesophilic archaea and in the endosymbiotic organelles of eukaryotes. Group II CPNs are found only in the cytosol of archaea and eukaryotes. Here we report a third, divergent group of CPNs found in several species of bacteria. We propose to name these Group III CPNs because of their distant relatedness to both Group I and II CPNs as well as their unique genomic context, within the hsp70 operon. The prototype Group III CPN, Carboxydothermus hydrogenoformans chaperonin (Ch-CPN), is able to refold denatured proteins in an ATP-dependent manner and is structurally similar to the Group II CPNs, forming a 16-mer with each subunit contributing to a flexible lid domain. The Group III CPN represent a divergent group of bacterial CPNs distinct from the GroEL/ES CPN found in all bacteria. The Group III lineage may represent an ancient horizontal gene transfer from an archaeon into an early Firmicute lineage. An analysis of their functional and structural characteristics may provide important insights into the early history of this ubiquitous family of proteins. PMID:21057109

  19. Potent antibacterial nanoparticles for pathogenic bacteria.

    PubMed

    Lai, Hong-Zheng; Chen, Wei-Yu; Wu, Ching-Yi; Chen, Yu-Chie

    2015-01-28

    Antibiotic-resistant bacteria have emerged because of the prevalent use of antibacterial agents. Thus, new antibacterial agents and therapeutics that can treat bacterial infections are necessary. Vancomycin is a potent antibiotic. Unfortunately, some bacterial strains have developed their resistance toward vancomycin. Nevertheless, it has been demonstrated that vancomycin-immobilized nanoparticles (NPs) are capable to be used in inhibition of the cell growth of vancomycin-resistant bacterial strains through multivalent interactions. However, multistep syntheses are usually necessary to generate vancomycin-immobilized NPs. Thus, maintaining the antibiotic activity of vancomycin when the drug is immobilized on the surface of NPs is challenging. In this study, a facile approach to generate vancomycin immobilized gold (Van-Au) NPs through one-pot stirring of vancomycin with aqueous tetrachloroauric acid at pH 12 and 25 °C for 24 h was demonstrated. Van-Au NPs (8.4 ± 1.3 nm in size) were readily generated. The generated Van-Au NPs maintained their antibiotic activities and inhibited the cell growth of pathogens, which included Gram-positive and Gram-negative bacteria as well as antibiotic-resistant bacterial strains. Furthermore, the minimum inhibitory concentration of the Van-Au NPs against bacteria was lower than that of free-form vancomycin. Staphylococcus aureus-infected macrophages were used as the model samples to examine the antibacterial activity of the Van-Au NPs. Macrophages have the tendency to engulf Van-Au NPs through endocytosis. The results showed that the cell growth of S. aureus in the macrophages was effectively inhibited, suggesting the potential of using the generated Van-Au NPs as antibacterial agents for bacterial infectious diseases.

  20. Close Encounters of Lymphoid Cells and Bacteria

    PubMed Central

    Cruz-Adalia, Aranzazu; Veiga, Esteban

    2016-01-01

    During infections, the first reaction of the host against microbial pathogens is carried out by innate immune cells, which recognize conserved structures on pathogens, called pathogen-associated molecular patterns. Afterward, some of these innate cells can phagocytose and destroy the pathogens, secreting cytokines that would modulate the immune response to the challenge. This rapid response is normally followed by the adaptive immunity, more specific and essential for a complete pathogen clearance in many cases. Some innate immune cells, usually named antigen-presenting cells, such as macrophages or dendritic cells, are able to process internalized invaders and present their antigens to lymphocytes, triggering the adaptive immune response. Nevertheless, the traditional boundary of separated roles between innate and adaptive immunity has been blurred by several studies, showing that very specialized populations of lymphocytes (cells of the adaptive immunity) behave similarly to cells of the innate immunity. These “innate-like” lymphocytes include γδ T cells, invariant NKT cells, B-1 cells, mucosal-associated invariant T cells, marginal zone B cells, and innate response activator cells, and together with the newly described innate lymphoid cells are able to rapidly respond to bacterial infections. Strikingly, our recent data suggest that conventional CD4+ T cells, the paradigm of cells of the adaptive immunity, also present innate-like behavior, capturing bacteria in a process called transinfection. Transinfected CD4+ T cells digest internalized bacteria like professional phagocytes and secrete large amounts of proinflammatory cytokines, protecting for further bacterial challenges. In the present review, we will focus on the data showing such innate-like behavior of lymphocytes following bacteria encounter. PMID:27774092