Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi.

PubMed

Löffler, Frank E; Yan, Jun; Ritalahti, Kirsti M; Adrian, Lorenz; Edwards, Elizabeth A; Konstantinidis, Konstantinos T; Müller, Jochen A; Fullerton, Heather; Zinder, Stephen H; Spormann, Alfred M

2013-02-01

Six obligately anaerobic bacterial isolates (195(T), CBDB1, BAV1, VS, FL2 and GT) with strictly organohalide-respiring metabolisms were obtained from chlorinated solvent-contaminated aquifers, contaminated and uncontaminated river sediments or anoxic digester sludge. Cells were non-motile with a disc-shaped morphology, 0.3-1 µm in diameter and 0.1-0.2 µm thick, and characteristic indentations on opposite flat sides of the cell. Growth occurred in completely synthetic, reduced medium amended with a haloorganic electron acceptor (mostly chlorinated but also some brominated compounds), hydrogen as electron donor, acetate as carbon source, and vitamins. No other growth-supporting redox couples were identified. Aqueous hydrogen consumption threshold concentrations were <1 nM. Growth ceased when vitamin B(12) was omitted from the medium. Addition of sterile cell-free supernatant of Dehalococcoides-containing enrichment cultures enhanced dechlorination and growth of strains 195 and FL2, suggesting the existence of so-far unidentified stimulants. Dechlorination occurred between pH 6.5 and 8.0 and over a temperature range of 15-35 °C, with an optimum growth temperature between 25 and 30 °C. The major phospholipid fatty acids were 14 : 0 (15.7 mol%), br15 : 0 (6.2 mol%), 16 : 0 (22.7 mol%), 10-methyl 16 : 0 (25.8 mol%) and 18 : 0 (16.6 mol%). Unusual furan fatty acids including 9-(5-pentyl-2-furyl)-nonanoate and 8-(5-hexyl-2-furyl)-octanoate were detected in strains FL2, BAV1 and GT, but not in strains 195(T) and CBDB1. The 16S rRNA gene sequences of the six isolates shared more than 98 % identity, and phylogenetic analysis revealed an affiliation with the phylum Chloroflexi and more than 10 % sequence divergence from other described isolates. The genome sizes and G+C contents ranged from 1.34 to 1.47 Mbp and 47 to 48.9 mol% G+C, respectively. Based on 16S rRNA gene sequence comparisons, genome-wide average nucleotide identity and phenotypic characteristics, the organohalide-respiring isolates represent a new genus and species, for which the name Dehalococcoides mccartyi gen. nov., sp. nov. is proposed. Isolates BAV1 ( = ATCC BAA-2100  = JCM 16839  = KCTC 5957), FL2 ( = ATCC BAA-2098  = DSM 23585  = JCM 16840  = KCTC 5959), GT ( = ATCC BAA-2099  = JCM 16841  = KCTC 5958), CBDB1, 195(T) ( = ATCC BAA-2266(T)  = KCTC 15142(T)) and VS are considered strains of Dehalococcoides mccartyi, with strain 195(T) as the type strain. The new class Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov. are described to accommodate the new taxon.

Interaction Mode and Regioselectivity in Vitamin B12-Dependent Dehalogenation of Aryl Halides by Dehalococcoides mccartyi Strain CBDB1.

PubMed

Zhang, Shangwei; Adrian, Lorenz; Schüürmann, Gerrit

2018-02-20

The bacterium Dehalococcoides, strain CBDB1, transforms aromatic halides through reductive dehalogenation. So far, however, the structures of its vitamin B 12 -containing dehalogenases are unknown, hampering clarification of the catalytic mechanism and substrate specificity as basis for targeted remediation strategies. This study employs a quantum chemical donor-acceptor approach for the Co(I)-substrate electron transfer. Computational characterization of the substrate electron affinity at carbon-halogen bonds enables discriminating aromatic halides ready for dehalogenation by strain CBDB1 (active substrates) from nondehalogenated (inactive) counterparts with 92% accuracy, covering 86 of 93 bromobenzenes, chlorobenzenes, chlorophenols, chloroanilines, polychlorinated biphenyls, and dibenzo-p-dioxins. Moreover, experimental regioselectivity is predicted with 78% accuracy by a site-specific parameter encoding the overlap potential between the Co(I) HOMO (highest occupied molecular orbital) and the lowest-energy unoccupied sigma-symmetry substrate MO (σ*), and the observed dehalogenation pathways are rationalized with a success rate of 81%. Molecular orbital analysis reveals that the most reactive unoccupied sigma-symmetry orbital of carbon-attached halogen X (σ C-X * ) mediates its reductive cleavage. The discussion includes predictions for untested substrates, thus providing opportunities for targeted experimental investigations. Overall, the presently introduced orbital interaction model supports the view that with bacterial strain CBDB1, an inner-sphere electron transfer from the supernucleophile B 12 Co(I) to the halogen substituent of the aromatic halide is likely to represent the rate-determining step of the reductive dehalogenation.

Acetylene fuels TCE reductive dechlorination by defined Dehalococcoides/Pelobacter consortia

USGS Publications Warehouse

Mao, Xinwei; Oremland, Ronald S.; Liu, Tong; Landers, Abigail A; Baesman, Shaun; Alvarez-Cohen, Lisa

2017-01-01

Acetylene (C2H2) can be generated in contaminated groundwater sites as a consequence of chemical degradation of trichloroethene (TCE) by in situ minerals, and C2H2 is known to inhibit bacterial dechlorination. In this study, we show that while high C2H2 (1.3 mM) concentrations reversibly inhibit reductive dechlorination of TCE by Dehalococcoides mccartyi isolates as well as enrichment cultures containing D. mccartyi sp., low C2H2 (0.4 mM) concentrations do not inhibit growth or metabolism of D. mccartyi. Cocultures of Pelobacter SFB93, a C2H2-fermenting bacterium, with D. mccartyi strain 195 or with D. mccartyi strain BAV1 were actively sustained by providing acetylene as the electron donor and carbon source while TCE or cis-DCE served as the electron acceptor. Inhibition by acetylene of reductive dechlorination and methanogenesis in the enrichment culture ANAS was observed, and the inhibition was removed by adding Pelobacter SFB93 into the consortium. Transcriptomic analysis of D. mccartyi strain 195 showed genes encoding for reductive dehalogenases (e.g., tceA) were not affected during the C2H2-inhibition, while genes encoding for ATP synthase, biosynthesis, and Hym hydrogenase were down-regulated during C2H2 inhibition, consistent with the physiological observation of lower cell yields and reduced dechlorination rates in strain 195. These results will help facilitate the optimization of TCE-bioremediation at contaminated sites containing both TCE and C2H2.

Acetylene Fuels TCE Reductive Dechlorination by Defined Dehalococcoides/Pelobacter Consortia.

PubMed

Mao, Xinwei; Oremland, Ronald S; Liu, Tong; Gushgari, Sara; Landers, Abigail A; Baesman, Shaun M; Alvarez-Cohen, Lisa

2017-02-21

Acetylene (C 2 H 2 ) can be generated in contaminated groundwater sites as a consequence of chemical degradation of trichloroethene (TCE) by in situ minerals, and C 2 H 2 is known to inhibit bacterial dechlorination. In this study, we show that while high C 2 H 2 (1.3 mM) concentrations reversibly inhibit reductive dechlorination of TCE by Dehalococcoides mccartyi isolates as well as enrichment cultures containing D. mccartyi sp., low C 2 H 2 (0.4 mM) concentrations do not inhibit growth or metabolism of D. mccartyi. Cocultures of Pelobacter SFB93, a C 2 H 2 -fermenting bacterium, with D. mccartyi strain 195 or with D. mccartyi strain BAV1 were actively sustained by providing acetylene as the electron donor and carbon source while TCE or cis-DCE served as the electron acceptor. Inhibition by acetylene of reductive dechlorination and methanogenesis in the enrichment culture ANAS was observed, and the inhibition was removed by adding Pelobacter SFB93 into the consortium. Transcriptomic analysis of D. mccartyi strain 195 showed genes encoding for reductive dehalogenases (e.g., tceA) were not affected during the C 2 H 2 -inhibition, while genes encoding for ATP synthase, biosynthesis, and Hym hydrogenase were down-regulated during C 2 H 2 inhibition, consistent with the physiological observation of lower cell yields and reduced dechlorination rates in strain 195. These results will help facilitate the optimization of TCE-bioremediation at contaminated sites containing both TCE and C 2 H 2 .

Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure.

PubMed

Zhang, Shangwei; Wondrousch, Dominik; Cooper, Myriel; Zinder, Stephen H; Schüürmann, Gerrit; Adrian, Lorenz

2017-04-04

Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH 2 , whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.

Triple-element compound-specific stable isotope analysis of 1,2-dichloroethane for characterization of the underlying dehalogenation reaction in two Dehalococcoides mccartyi strains.

PubMed

Franke, Steffi; Lihl, Christina; Renpenning, Julian; Elsner, Martin; Nijenhuis, Ivonne

2017-12-01

Chlorinated ethanes belong to the most common groundwater and soil contaminants. Of these, 1,2-dichloroethane (1,2-DCA) is a man-made, persistent and toxic contaminant, released due to improper waste treatment at versatile production sites. This study investigated the anaerobic transformation of 1,2-DCA by Dehalococcoides mccartyi strain 195 and strain BTF08 using triple-element compound-specific stable isotope analysis of carbon, chlorine and hydrogen for the first time. Isotope fractionation patterns for carbon (εCBTF08 = -28.4 ± 3.7‰; εC195 = -30.9 ± 3.6‰) and chlorine (εClBTF08 = -4.6 ± 0.7‰; εCl195 = -4.2 ± 0.5‰) within both investigated D. mccartyi strains, as well as the dual-element analysis (ΛBTF08 = 6.9 ± 1.2; Λ195 = 7.1 ± 0.2), supported identical reaction mechanisms for dehalogenation of 1,2-DCA. Hydrogen isotope fractionation analysis revealed dihaloelimination as prevalent reaction mechanism. Vinyl chloride as major intermediate could be excluded by performing the experiment in deuterated aqueous media. Furthermore, evaluation of the derived apparent kinetic isotope effects (AKIECBTF08 = 1.029/AKIEC195 = 1.031; AKIEClBTF08 = 1.005/AKIECl195 = 1.004) pointed towards simultaneous abstraction of both involved chlorine-substituents in a concerted matter. It was shown that D. mccartyi strain BTF08 and strain 195 are capable of complete, direct dihaloelimination of 1,2-DCA to ethene. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23

PubMed Central

Rupakula, Aamani; Lu, Yue; Kruse, Thomas; Boeren, Sjef; Holliger, Christof; Smidt, Hauke; Maillard, Julien

2015-01-01

De novo corrinoid biosynthesis represents one of the most complicated metabolic pathways in nature. Organohalide-respiring bacteria (OHRB) have developed different strategies to deal with their need of corrinoid, as it is an essential cofactor of reductive dehalogenases, the key enzymes in OHR metabolism. In contrast to Dehalococcoides mccartyi, the genome of Dehalobacter restrictus strain PER-K23 contains a complete set of corrinoid biosynthetic genes, of which cbiH appears to be truncated and therefore non-functional, possibly explaining the corrinoid auxotrophy of this obligate OHRB. Comparative genomics within Dehalobacter spp. revealed that one (operon-2) of the five distinct corrinoid biosynthesis associated operons present in the genome of D. restrictus appeared to be present only in that particular strain, which encodes multiple members of corrinoid transporters and salvaging enzymes. Operon-2 was highly up-regulated upon corrinoid starvation both at the transcriptional (346-fold) and proteomic level (46-fold on average), in line with the presence of an upstream cobalamin riboswitch. Together, these data highlight the importance of this operon in corrinoid homeostasis in D. restrictus and the augmented salvaging strategy this bacterium adopted to cope with the need for this essential cofactor. PMID:25610435

Incomplete Wood–Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi

PubMed Central

Zhuang, Wei-Qin; Yi, Shan; Bill, Markus; Brisson, Vanessa L.; Feng, Xueyang; Men, Yujie; Conrad, Mark E.; Tang, Yinjie J.; Alvarez-Cohen, Lisa

2014-01-01

The acetyl-CoA “Wood–Ljungdahl” pathway couples the folate-mediated one-carbon (C1) metabolism to either CO2 reduction or acetate oxidation via acetyl-CoA. This pathway is distributed in diverse anaerobes and is used for both energy conservation and assimilation of C1 compounds. Genome annotations for all sequenced strains of Dehalococcoides mccartyi, an important bacterium involved in the bioremediation of chlorinated solvents, reveal homologous genes encoding an incomplete Wood–Ljungdahl pathway. Because this pathway lacks key enzymes for both C1 metabolism and CO2 reduction, its cellular functions remain elusive. Here we used D. mccartyi strain 195 as a model organism to investigate the metabolic function of this pathway and its impacts on the growth of strain 195. Surprisingly, this pathway cleaves acetyl-CoA to donate a methyl group for production of methyl-tetrahydrofolate (CH3-THF) for methionine biosynthesis, representing an unconventional strategy for generating CH3-THF in organisms without methylene-tetrahydrofolate reductase. Carbon monoxide (CO) was found to accumulate as an obligate by-product from the acetyl-CoA cleavage because of the lack of a CO dehydrogenase in strain 195. CO accumulation inhibits the sustainable growth and dechlorination of strain 195 maintained in pure cultures, but can be prevented by CO-metabolizing anaerobes that coexist with D. mccartyi, resulting in an unusual syntrophic association. We also found that this pathway incorporates exogenous formate to support serine biosynthesis. This study of the incomplete Wood–Ljungdahl pathway in D. mccartyi indicates a unique bacterial C1 metabolism that is critical for D. mccartyi growth and interactions in dechlorinating communities and may play a role in other anaerobic communities. PMID:24733917

Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration.

PubMed

Werner, Jeffrey J; Ptak, A Celeste; Rahm, Brian G; Zhang, Sheng; Richardson, Ruth E

2009-10-01

The quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp. when reducing carbon atoms in the common pollutants trichloroethene (TCE) and tetrachloroethene (PCE). From complex whole-sample digests of two different dechlorinating mixed communities, we monitored the chromatographic peaks of selected tryptic peptides chosen to represent 19 specific Dehalococcoides proteins. This was accomplished using multiple-reaction monitoring (MRM) assays using nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), which provided the selectivity, sensitivity and reproducibility required to quantify Dehalococcoides proteins in complex samples. We observed reproducible peak areas (average CV = 0.14 over 4 days, n = 3) and linear responses in standard curves (n = 5, R(2) > 0.98) using synthetic peptide standards spiked into a background matrix of sediment peptides. We detected and quantified TCE reductive dehalogenase (TceA) at 7.6 +/- 1.7 x 10(3) proteins cell(-1) in the KB1 bioaugmentation culture, previously thought to be lacking TceA. Fragmentation data from MS/MS shotgun proteomics experiments were helpful in developing the MRM targets. Similar shotgun proteomics data are emerging in labs around the world for many environmentally relevant microbial proteins, and these data are a valuable resource for the future development of MRM assays. We expect targeted peptide quantification in environmental samples to be a useful tool in environmental monitoring.

Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.

PubMed

Yohda, Masafumi; Yagi, Osami; Takechi, Ayane; Kitajima, Mizuki; Matsuda, Hisashi; Miyamura, Naoaki; Aizawa, Tomoko; Nakajima, Mutsuyasu; Sunairi, Michio; Daiba, Akito; Miyajima, Takashi; Teruya, Morimi; Teruya, Kuniko; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Nakano, Kazuma; Aoyama, Misako; Terabayashi, Yasunobu; Satou, Kazuhito; Hirano, Takashi

2015-07-01

A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Insights Gained from the Dehalococcoides ethenogenes Strain 195’s Transcriptome Responding to a Wide Range of Respiration Rates and Substrate Types

DTIC Science & Technology

2012-04-01

fermented yeast , pure hydrogen, or endogenous biomass decay). When similarly respiring (~120 ?eeq PCE/(L-hr)) batch and PSS cultures were contrasted, the...electron equivalence (eeq) basis), and electron donor type (butyrate, lactate, yeast extract, fermented yeast , pure hydrogen, or endogenous biomass...acceptor ratios (0.7 to 17 on an electron equivalence (eeq) basis), and 12 electron donor type (butyrate, lactate, yeast extract, fermented yeast , pure

Identification of a multi-protein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement.

PubMed

Kublik, Anja; Deobald, Darja; Hartwig, Stefanie; Schiffmann, Christian L; Andrades, Adarelys; von Bergen, Martin; Sawers, R Gary; Adrian, Lorenz

2016-09-01

Dehalococcoides mccartyi strain CBDB1 is an obligate organohalide-respiring bacterium using only hydrogen as electron donor and halogenated organics as electron acceptor. Here, we studied proteins involved in the respiratory chain under non-denaturing conditions. Using blue native gel electrophoresis (BN-PAGE), gel filtration and ultrafiltration an active dehalogenating protein complex with a molecular mass of 250-270 kDa was identified. The active subunit of reductive dehalogenase (RdhA) colocalised with a complex iron-sulfur molybdoenzyme (CISM) subunit (CbdbA195) and an iron-sulfur cluster containing subunit (CbdbA131) of the hydrogen uptake hydrogenase (Hup). No colocalisation between the catalytically active subunits of hydrogenase and reductive dehalogenase was found. By two-dimensional BN/SDS-PAGE the stability of the complex towards detergents was assessed, demonstrating stepwise disintegration with increasing detergent concentrations. Chemical cross-linking confirmed the presence of a higher molecular mass reductive dehalogenase protein complex composed of RdhA, CISM I and Hup hydrogenase and proved to be a potential tool for stabilising protein-protein interactions of the dehalogenating complex prior to membrane solubilisation. Taken together, the identification of the respiratory dehalogenase protein complex and the absence of indications for quinone participation in the respiration suggest a quinone-independent protein-based respiratory electron transfer chain in D. mccartyi. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

RELATIONSHIP BETWEEN DEHALOCOCCOIDES DNA AND GEOCHEMICAL PARAMETERS IN CHLOROETHYLENE-CONTAMINATED AQUIFERS

EPA Science Inventory

Dehalococcoides organisms are very attractive for application in natural or engineered bioremediation of chloroethylene-contaminated sites because they are the only organisms known to date that can completely dechlorinate chloroethylenes to harmless ethylene. The use of genetic a...

RELATIONSHIP BETWEEN DEHALOCOCCOIDES DNA AND GEOCHEMICAL PARAMETERS IN CHLOROETHYLENE-CONTAMINATED AQUIFERS

EPA Science Inventory

Dehalococcoides organisms are very attractive for application in natural or engineered bioremediation of chloroethylene-contaminated sites because they are the only organisms known to date that can completely dechlorinate chloroethylenes to harmless ethylene. The use of genetic ...

RELATIONSHIP BETWEEN DEHALOCOCCOIDES DNA AND DECHLORINATION RATES AT FIELD SITES

EPA Science Inventory

Chlorinated ethenes are common contaminants in groundwater. To date, Dehalococcoides species are the only known organisms capable of completely dechlorinating all chlorinated ethenes to non-toxic ethene. Studies in the laboratory have shown a good correlation between Dehalococco...

Interlaboratory Comparison of Quantitative PCR Test Results for Dehalococcoides

EPA Science Inventory

Quantitative PCR (qPCR) techniques have been widely used to measure Dehalococcoides (Dhc) DNA in the groundwater at field sites for several years. Interpretation of these data may be complicated when different laboratories using alternate methods conduct the analysis. An...

RELATIONSHIP BETWEEN DEHALOCOCCOIDES DNA IN GROUND WATER AND NATURAL ATTENUATION OF CHLORINATED SOLVENTS

EPA Science Inventory

Biological reductive dechlorination is the primary mechanism for natural attenuation of chlorinated solvents in ground water. The only organisms that are known to completely dechlorinate cis-DCE past vinyl chloride to ethylene or ethane are members of the Dehalococcoides group. ...

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to Dehalococcoides strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siddaramappa, Shivakumara; Delano, Susana; Green, Lance D.

2012-01-01

Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore forming, Gram negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) its unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) its phylogenetic position distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9{sup T} contains 1,720 predicted proteinmore » coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus.« less

Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors.

PubMed

Freeborn, Ryan A; West, Kimberlee A; Bhupathiraju, Vishvesh K; Chauhan, Sadhana; Rahm, Brian G; Richardson, Ruth E; Alvarez-Cohen, Lisa

2005-11-01

Two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate TCE to ethene. Each electron donor enrichment subculture demonstrated the ability to dechlorinate TCE to ethene through several serial transfers. Microbial community analyses based upon 16S rDNA, including terminal restriction fragment length polymorphism (T-RFLP) and clone library/sequencing, were performed to assess major changes in microbial community structure associated with electron donors capable of stimulating reductive dechlorination. Results demonstrated that five phylogenic subgroups or genera of bacteria were present in all consortia, including Dehalococcoides sp., low G+C Gram-positives (mostly Clostridium and Eubacterium sp.), Bacteroides sp., Citrobacter sp., and delta Proteobacteria (mostly Desulfovibrio sp.). Phylogenetic association indicates that only minor shifts in the microbial community structure occurred between the four alternate electron donor enrichments and the parent consortium. Inconsistent detection of Dehalococcoides spp. in clone libraries and T-RFLP of enrichment subcultures was resolved using quantitative polymerase chain reaction (Q-PCR). Q-PCR with primers specific to Dehalococcoides 16S rDNA resulted in positive detection of this species in all enrichments. Our results suggest that TCE-dechlorinating consortia can be stably maintained on a variety of electron donors and that quantities of Dehalococcoides cells detected with Dehalococcoides specific 16S rDNA primer/probe sets do not necessarily correlate well with solvent degradation rates.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

PubMed Central

Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa

2017-01-01

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions. PMID:28188205

Comparison of an Assay for Dehalococcoides DNA and a Microcosm Study in Predicting Reductive Dechlorination of Chlorinated Ethenes in the field

EPA Science Inventory

The study aims to compare the detection of 16S rRNA gene of Dehalococcoides species and the microcosm study for biotransformation in predicting reductive dechlorination of chlorinated ethylenes in ground water at hazardous waste sites. A total of 72 ground water samples were coll...

Chemostat Studies of TCE-Dehalogenating Anaerobic Consortia under Excess and Limited Electron Donor Addition

NASA Astrophysics Data System (ADS)

Semprini, L.; Azizian, M.; Green, J.; Mayer-Blackwell, K.; Spormann, A. M.

2015-12-01

Two cultures - the Victoria Strain (VS) and the Evanite Strain (EV), enriched with the organohalide respiring bacteria Dehalococcoides mccartyi - were grown in chemostats for more than 4 years at a mean cell residence time of 50 days. The slow doubling rate represents growth likely experienced in the subsurface. The chemostats were fed formate as an electron donor and trichloroethene (TCE) as the terminal electron acceptor. Under excess formate conditions, stable operation was observed with respect to TCE transformation, steady-state hydrogen (H2) concentrations (40 nM), and the structure of the dehalogenating community. Both cultures completely transformed TCE to ethene, with minor amounts of vinyl chloride (VC) observed, along with acetate formation. When formate was limited, TCE was transformed incompletely to ethene (40-60%) and VC (60- 40%), and H2 concentrations ranged from 1 to 3 nM. The acetate concentration dropped below detection. Batch kinetic studies of TCE transformation with chemostat harvested cells found transformation rates of c-DCE and VC were greatly reduced when the cells were grown with limited formate. Upon increasing formate addition to the chemostats, from limited to excess, essentially complete transformation of TCE to ethene was achieved. The increase in formate was associated with an increase in H2 concentration and the production of acetate. Results of batch kinetic tests showed increases in transformation rates for TCE and c-DCE by factors of 3.5 and 2.5, respectively, while VC rates increased by factors of 33 to 500, over a six month period. Molecular analysis of chemostat samples is being performed to quantify the changes in copy numbers of reductase genes and to determine whether shifts in the strains of Dehalococcoides mccartyi where responsible for the observed rate increases. The results demonstrate the importance of electron donor supply for successful in-situ remediation.

Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia.

PubMed

Men, Yujie; Seth, Erica C; Yi, Shan; Allen, Robert H; Taga, Michiko E; Alvarez-Cohen, Lisa

2014-04-01

Corrinoids are essential cofactors of reductive dehalogenases in Dehalococcoides mccartyi, an important bacterium in bioremediation, yet sequenced D. mccartyi strains do not possess the complete pathway for de novo corrinoid biosynthesis. Pelosinus sp. and Desulfovibrio sp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growing D. mccartyi strain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)- and lactate-amended medium in cocultures with Desulfovibrio vulgaris Hildenborough (DvH) or Pelosinus fermentans R7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.

PCE dechlorination by non-Dehalococcoides in a microbial electrochemical system.

PubMed

Yu, Jaecheul; Park, Younghyun; Nguyen, Van Khanh; Lee, Taeho

2016-08-01

The bioremediation of tetrachloroethene (perchloroethene; PCE) contaminated sites generally requires a supply of some fermentable organic substrates as an electron donor. On the other hand, organic substrates can induce the massive growth of microorganisms around the injection wells, which can foul the contaminated subsurface environment. In this study, PCE dechlorination to ethene was performed in a microbial electrochemical system (MES) using the electrode (a cathode polarized at -500 mV vs. standard hydrogen electrode) as the electron donor. Denaturing gel gradient electrophoresis and pyrosequencing revealed a variety of non-Dehalococcoides bacteria dominant in MES, such as Acinetobacter sp. (25.7 % for AS1 in suspension of M3), Rhodopseudomonas sp. (10.5 % for AE1 and 10.1 % for AE2 in anodic biofilm of M3), Pseudomonas aeruginosa (22.4 % for BS1 in suspension of M4), and Enterobacter sp. (21.7 % for BE1 in anodic biofilm of M4) which are capable of electron transfer, hydrogen production and dechlorination. The Dehalococcoides group, however, was not detected in this system. Therefore, these results suggest that a range of bacterial species outside the Dehalococcoides can play an important role in the microbial electrochemical dechlorination process, which may lead to innovative bioremediation technology.

Acetylene fuels reductive dechlorination of TCE by Dehalococcoides/Pelobacter-containing microbial consortia

NASA Astrophysics Data System (ADS)

Oremland, R. S.; Mao, X.; Mahandra, C.; Baesman, S. M.; Gushgari, S.; Alvarez-Cohen, L.; Liu, T.

2015-12-01

Groundwater contamination by trichloroethene (TCE) poses a threat to health and leads to the generation of vinyl chloride (VC), a carcinogen. Dehalococcoides mccartyi is the only bacterium that can completely dechlorinate TCE to ethene (C2H4). Acetylene (C2H2) occurs in TCE-contaminated sites as a consequence of chemical degradation of TCE. Yet acetylene inhibits a variety of microbial processes including methanogesis and reductive dechlorination. Pelobacter acetylenicus and related species can metabolize acetylene via acetylene hydratase and acetaldehyde dismutatse thereby generating acetate and H2 as endproducts, which could serve as electron donor and carbon source for growth of D. mccartyi. We found that 1mM acetylene (aqueous) inhibits growth of D. mccartyi strain 195 on 0.3 mM TCE, but that the inhibition was removed after 12 days with the addition of an acetylene-utilizing isolate from San Francisco Bay, Pelobacter strain SFB93. TCE did not inhibit the growth of this Pelobacter at the concentrations tested (0.1-0.5 mM) and TCE was not consumed by strain SFB93. Co-cultures of strain 195 with strain SFB93 at 5% inoculation were established in 120 mL serum bottles containing 40 mL defined medium. TCE was supplied at a liquid concentration of 0.1 mM, with 0.1 mM acetylene and N2/CO2 (90:10 v/v) headspace at 34 °C. Co-cultures were subsequently transferred (5% vol/vol inoculation) to generate subcultures after 20 μmol TCE was reduced to VC and 36 μmol acetylene was depleted. Aqueous H2 ranged from 114 to 217 nM during TCE-dechlorination, and the cell yield of strain 195 was 3.7 ±0.3 × 107 cells μmol-1 Cl- released. In a D. mccartyi-containing enrichment culture (ANAS) under the same conditions as above, it was found that inhibition of dechlorination by acetylene was reversed after 19 days by adding SFB93. Thus we showed that a co-culture of Pelobacter SFB93 and D. mccartyi 195 could be maintained with C2H2 as the electron donor and carbon source while TCE served as the electron acceptor. Inhibition by C2H2 of reductive dechlorination in both the D. mccartyi isolate and the enrichment culture ANAS were observed, but the inhibition was eliminated by adding Pelobacter SFB93 to the cultures. These results will help facilitate the optimization of TCE-bioremediation at contaminated sites containing both TCE and C2H2.

Integrated Anaerobic-Aerobic Biodegradation of Multiple Contaminants Including Chlorinated Ethylenes, Benzene, Toluene, and Dichloromethane.

PubMed

Yoshikawa, Miho; Zhang, Ming; Toyota, Koki

2017-01-01

Complete bioremediation of soils containing multiple volatile organic compounds (VOCs) remains a challenge. To explore the possibility of complete bioremediation through integrated anaerobic-aerobic biodegradation, laboratory feasibility tests followed by alternate anaerobic-aerobic and aerobic-anaerobic biodegradation tests were performed. Chlorinated ethylenes, including tetrachloroethylene (PCE), trichloroethylene (TCE), cis -dichloroethylene ( cis -DCE), and vinyl chloride (VC), and dichloromethane (DCM) were used for anaerobic biodegradation, whereas benzene, toluene, and DCM were used for aerobic biodegradation tests. Microbial communities involved in the biodegradation tests were analyzed to characterize the major bacteria that may contribute to biodegradation. The results demonstrated that integrated anaerobic-aerobic biodegradation was capable of completely degrading the seven VOCs with initial concentration of each VOC less than 30 mg/L. Benzene and toluene were degraded within 8 days, and DCM was degraded within 20 to 27 days under aerobic conditions when initial oxygen concentrations in the headspaces of test bottles were set to 5.3% and 21.0%. Dehalococcoides sp., generally considered sensitive to oxygen, survived aerobic conditions for 28 days and was activated during the subsequent anaerobic biodegradation. However, degradation of cis -DCE was suppressed after oxygen exposure for more than 201 days, suggesting the loss of viability of Dehalococcoides sp., as they are the only known anaerobic bacteria that can completely biodegrade chlorinated ethylenes to ethylene. Anaerobic degradation of DCM following previous aerobic degradation was complete, and yet-unknown microbes may be involved in the process. The findings may provide a scientific and practical basis for the complete bioremediation of multiple contaminants in situ and a subject for further exploration.

Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Chen, Mingjie; Abriola, Linda M.; Amos, Benjamin K.; Suchomel, Eric J.; Pennell, Kurt D.; Löffler, Frank E.; Christ, John A.

2013-08-01

Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time), strongly influenced the extent of reductive dechlorination. When cis-DCE inhibition was neglected, the model over-predicted ethene production ten-fold, while reductions in residence time (i.e., a two-fold decrease in column length or two-fold increase in flow rate) resulted in a more than 70% decline in ethene production. These results suggest that spatial and temporal variations in microbial community composition and activity must be understood to model, predict, and manage bioenhanced NAPL dissolution.

Dehalogenation of chlorobenzenes, dichlorotoluenes, and tetrachloroethene by three Dehalobacter spp.

PubMed

Nelson, Jennifer L; Jiang, Jiandong; Zinder, Stephen H

2014-04-01

Three enrichment cultures containing Dehalobacter spp. were developed that dehalogenate each of the dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and the strains using 1,2-DCB (12DCB1) or 1,3-DCB (13DCB1) are now considered isolated, whereas the strain using 1,4-DCB (14DCB1) is considered highly enriched. In this study, we examined the dehalogenation capability of each strain to use chlorobenzenes with three or more chlorines, tetrachloroethene (PCE), or dichlorotoluene (DCT) isomers. Strain 12DCB1 preferentially dehalogenated singly flanked chlorines, but not doubly flanked or unflanked chlorines. It dehalogenated pentachlorobenzene to MCB with little buildup of intermediates. Strain 13DCB1, which could use either 1,3-DCB or 1,2-DCB, demonstrated the widest dehalogenation spectrum of electron acceptors tested, and dehalogenated every chlorobenzene isomer except 1,4-DCB. Notably, strain 13DCB1 dehalogenated the recalcitrant 1,3,5-trichlorobenzene isomer to MCB, and qPCR of 16S rRNA genes indicated that strain 13DCB1 grew. Strain 14DCB1 exhibited the narrowest range of substrate utilization, but was the only strain to dehalogenate para-substituted chlorines. Strains 12DCB1 and 13DCB1 dehalogenated PCE to cis-dichloroethene, and all strains dehalogenated 3,4-DCT to monochlorotoluene. These findings show that Dehalobacter spp., like Dehalococcoides spp., are versatile dehalogenators and should be considered when determining the fate of chlorinated organics at contaminated sites.

Discovery of a trans-Dichloroethene-Respiring Dehalogenimonas Species in the 1,1,2,2-Tetrachloroethane-Dechlorinating WBC-2 Consortium

PubMed Central

Manchester, Marie J.; Hug, Laura A.; Zarek, Matt; Zila, Anna

2012-01-01

The WBC-2 consortium is an organohalide-respiring anaerobic microbial enrichment culture capable of dechlorinating 1,1,2,2-tetrachloroethane (TeCA) to ethene. In the WBC-2 culture, TeCA is first transformed to trans-dichloroethene (tDCE) by dichloroelimination; tDCE is subsequently transformed to vinyl chloride (VC) and then to ethene by hydrogenolysis. Analysis of 16S rRNA gene clone libraries from culture DNA revealed sequences from three putative dechlorinating organisms belonging to Dehalococcoides, Dehalobacter, and Dehalogenimonas genera. Quantitative PCR primers were designed for each of these sequences, and their abundance was quantified in enrichment cultures over time. These data revealed that complete dechlorination of TeCA to ethene involves all three organisms. Dehalobacter spp. grew during the dihaloelimination of TeCA to tDCE, while Dehalococcoides and Dehalogenimonas spp. grew during hydrogenolysis of tDCE to ethene. This is the first time a genus other than Dehalococcoides has been implicated in dechlorination of tDCE to VC. PMID:22635995

Identification and environmental distribution of dcpA encoding the 1,2-dichloropropane-to-propene reductive dehalogenase in organohalide-respiring Chloroflexi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Padilla-Crespo, Elizabeth; Yan, Jun; Swift, Cynthia M

2014-01-01

Dehalococcoides mccartyi (Dhc) strains KS and RC grow with 1,2-dichloropropane (1,2-D) as an electron acceptor in enrichment cultures derived from hydrocarbon-contaminated and pristine river sediments, respectively. Transcription, expression, enzymatic and PCR analyses implicated the reductive dehalogenase gene dcpA in 1,2-D dichloroelimination to propene and inorganic chloride. Quantitative real-time PCR (qPCR) analyses demonstrated Dhc cell increase during growth with 1,2-D and suggested that both Dhc strains carried a single dcpA gene copy per genome. Dhc strain RC and strain KS produced 1.8 0.1 x 107 and 1.4 0.5 x 107 cells per mole of propene formed, respectively. The dcpA gene wasmore » identified in 1,2-D-to-propene-dechlorinating microcosms established with sediment samples collected from different geographical locations in Europe and North and South America. Clone library analysis revealed two distinct dcpA phylogenetic clusters, both of which the dcpA gene-targeted qPCR assay captured, suggesting the qPCR assay is useful for site assessment and bioremediation monitoring at 1,2-D-contaminated sites.« less

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Men, Yujie; Feil, Helene; Verberkmoes, Nathan C

2012-01-01

Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0 0.01 lmol per day for the co-culture and 10.1 0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8 0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0 0.5107 cells permore » lmol Cl released, compared with 6.8 0.9107 cells per lmol Cl released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3 1.8107 cells per lmol Cl released). The transcriptome of DE195 grown in the co-culture was analyzed using a wholegenome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.« less

Triclosan enriches for Dehalococcoides-like Chloroflexi in anaerobic soil at environmentally relevant concentrations.

PubMed

McNamara, Patrick J; Krzmarzick, Mark J

2013-07-01

Triclosan is an antimicrobial agent that is discharged to soils with land-applied wastewater biosolids, is persistent under anaerobic conditions, and yet its impact on anaerobic microbial communities in soils is largely unknown. We hypothesized that triclosan enriches for Dehalococcoides-like Chloroflexi because these bacteria respire organochlorides and are likely less sensitive, relative to other bacteria, to the antimicrobial effects of triclosan. Triplicate anaerobic soil microcosms were seeded with agricultural soil, which was not previously exposed to triclosan, and were amended with 1 mg kg(-1) of triclosan. Triplicate control microcosms did not receive triclosan, and the experiment was run for 618 days. The overall bacterial community (assessed by automated ribosomal intergenic spacer analysis and denaturing gradient gel electrophoresis) was not impacted by triclosan; however, the abundance of Dehalococcoides-like Chloroflexi 16S rRNA genes (determined by qPCR) increased 20-fold with triclosan amendment compared with a fivefold increase without triclosan. This work demonstrates that triclosan impacts anaerobic soil communities at environmentally relevant levels. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Anaerobic microbial dehalogenation of organohalides-state of the art and remediation strategies.

PubMed

Nijenhuis, Ivonne; Kuntze, Kevin

2016-04-01

Contamination and remediation of groundwater with halogenated organics and understanding of involved microbial reactions still poses a challenge. Over the last years, research in anaerobic microbial dehalogenation has advanced in many aspects providing information about the reaction, physiology of microorganisms as well as approaches to investigate the activity of microorganisms in situ. Recently published crystal structures of reductive dehalogenases (Rdh), heterologous expression systems and advanced analytical, proteomic and stable isotope approaches allow addressing the overall reaction and specific enzymes as well as co-factors involved during anaerobic microbial dehalogenation. In addition to Dehalococcoides spp., Dehalobacter and Dehalogenimonas strains have been recognized as important and versatile organohalide respirers. Together, these provide perspectives for integrated concepts allowing to improve and monitor in situ biodegradation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection.

PubMed

Kocur, Chris M D; Lomheim, Line; Molenda, Olivia; Weber, Kela P; Austrins, Leanne M; Sleep, Brent E; Boparai, Hardiljeet K; Edwards, Elizabeth A; O'Carroll, Denis M

2016-07-19

Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.

Chloroethene degradation and expression of Dehalococcoides dehalogenase genes in cultures originating from Yangtze sediments.

PubMed

Kranzioch, Irene; Ganz, Selina; Tiehm, Andreas

2015-02-01

The anaerobic Dehalococcoides spp. is the only microorganism known to completely dechlorinate the hazardous compounds tetrachloroethene (PCE) or trichloroethene (TCE) via dichloroethene (DCE) and vinyl chloride (VC) to the terminal product, ethene. In this study, growth of Dehalococcoides spp. (DHC) and the expression of DHC dehalogenase genes were demonstrated for Yangtze enrichment cultures. Reductive dechlorination of chloroethenes occurred in Yangtze sediment without the addition of any external auxiliary substrates. All Yangtze enrichment cultures completely dechlorinated PCE and cis-DCE to ethene. To investigate expression of the dehalogenase genes pceA, tceA, vcrA, and bvcA, a protocol for messenger RNA (mRNA) extraction followed by reverse transcription and quantitative PCR analysis was established. During dechlorination, an increase in gene copy numbers of pceA, tceA, and vcrA was observed. However, temporary formation of mRNA was only measured in the case of the dehalogenase genes tceA and vcrA. Comparison of DHC dehalogenase patterns indicated that the Yangtze DHC community does not match any of the previously published enrichment cultures that were obtained from contaminated areas in the USA or Europe.

Resilience and recovery of Dehalococcoides mccartyi following low pH exposure.

PubMed

Yang, Yi; Cápiro, Natalie L; Yan, Jun; Marcet, Tyler F; Pennell, Kurt D; Löffler, Frank E

2017-12-01

Bioremediation treatment (e.g. biostimulation) can decrease groundwater pH with consequences for Dehalococcoides mccartyi (Dhc) reductive dechlorination activity. To explore the pH resilience of Dhc, the Dhc-containing consortium BDI was exposed to pH 5.5 for up to 40 days. Following 8- and 16-day exposure periods to pH 5.5, dechlorination activity and growth recovered when returned to pH 7.2; however, the ability of the culture to dechlorinate vinyl chloride (VC) to ethene was impaired (i.e. decreased rate of VC transformation). Dhc cells exposed to pH 5.5 for 40 days did not recover the ethene-producing phenotype upon transfer to pH 7.2 even after 200 days of incubation. When returned to pH 7.2 conditions after an 8-, a 16- and a 40-day low pH exposure, tceA and vcrA genes showed distinct fold increases, suggesting Dhc strain-specific responses to low pH exposure. Furthermore, a survey of Dhc biomarker genes in groundwater samples revealed the average abundances of Dhc 16S rRNA, tceA and vcrA genes in pH 4.5-6 groundwater were significantly lower (P-value < 0.05) than in pH 6-8.3 groundwater. Overall, the results of the laboratory study and the assessment of field data demonstrate that sustained Dhc activity should not be expected in low pH groundwater, and the duration of low pH exposure affects the ability of Dhc to recover activity at circumneutral pH. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

PubMed Central

Praveckova, Martina; Brennerova, Maria V.; Holliger, Christof; De Alencastro, Felippe; Rossi, Pierre

2016-01-01

Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating taxa. PMID:27379063

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms.

PubMed

Praveckova, Martina; Brennerova, Maria V; Holliger, Christof; De Alencastro, Felippe; Rossi, Pierre

2016-01-01

Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating taxa.

Isolation of novel bacteria within the Chloroflexi capable of reductive dechlorination of 1,2,3-trichloropropane.

PubMed

Yan, J; Rash, B A; Rainey, F A; Moe, W M

2009-04-01

Two strictly anaerobic bacterial strains were isolated from contaminated groundwater at a Superfund site located near Baton Rouge, LA, USA. These strains represent the first isolates reported to reductively dehalogenate 1,2,3-trichloropropane. Allyl chloride (3-chloro-1-propene), which is chemically unstable, was produced from 1,2,3-trichloropropane, and it was hydrolysed abiotically to allyl alcohol and also reacted with the sulfide- and cysteine-reducing agents in the medium to form various allyl sulfides. Both isolates also dehalogenated a variety of other vicinally chlorinated alkanes (1,2-dichloropropane, 1,2-dichloroethane, 1,1,2-trichloroethane, 1,1,2,2- tetrachloroethane) via dichloroelimination reactions. A quantitative real-time PCR (qPCR) approach targeting 16S rRNA genes indicated that both strains couple reductive dechlorination to cell growth. Growth was not observed in the absence of hydrogen (H2) as an electron donor and a polychlorinated alkane as an electron acceptor. Alkanes containing only a single chlorine substituent (1-chloropropane, 2-chloropropane), chlorinated alkenes (tetrachlorothene, trichlorothene, cisdichloroethene, trans-dichloroethene, vinyl chloride) and chlorinated benzenes (1-chlorobenzene and 1,2- dichlorobenzene) were not dechlorinated. Phylogenetic analysis based on 16S rRNA gene sequence data showed these isolates to represent a new lineage within the Chloroflexi. Their closest previously cultured relatives are 'Dehalococcoides' strains, with 16S rRNA gene sequence similarities of only 90%.

Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

PubMed Central

Kanitkar, Yogendra H.; Stedtfeld, Robert D.; Steffan, Robert J.; Hashsham, Syed A.

2016-01-01

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures. PMID:26746711

Advances in Biodegradation of Multiple Volatile Organic Compounds

NASA Astrophysics Data System (ADS)

Zhang, M.; Yoshikawa, M.

2017-12-01

Bioremediation of soil and groundwater containing multiple contaminants remains a challenge in environmental science and engineering because complete biodegradation of all components is necessary but very difficult to accomplish in practice. This presentation provides a brief overview on advances in biodegradation of multiple volatile organic compounds (VOCs) including chlorinated ethylenes, benzene, toluene and dichloromethane (DCM). Case studies on aerobic biodegradation of benzene, toluene and DCM, and integrated anaerobic-aerobic biodegradation of 7 contaminants, specifically, tetrachloroethylene (PCE), trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), vinyl chloride (VC), DCM, benzene and toluene will be provided. Recent findings based on systematic laboratory experiments indicated that aerobic toluene degradation can be enhanced by co-existence of benzene. Propioniferax, not a known benzene, toluene and DCM degrader can be a key microorganism that involves in biodegradation when the three contaminants co-exist. Integrated anaerobic-aerobic biodegradation is capable of completely degrading the seven VOCs with initial concentrations less than 30 mg/L. Dehalococcoides sp., generally considered sensitive to oxygen, can survive aerobic conditions for at least 28 days, and can be activated during the subsequent anaerobic biodegradation. This presentation may provide a systematic information about biodegradation of multiple VOCs, and a scientific basis for the complete bioremediation of multiple contaminants in situ.

Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques.

PubMed

Richardson, Ruth E; Bhupathiraju, Vishvesh K; Song, Donald L; Goulet, Tanuja A; Alvarez-Cohen, Lisa

2002-06-15

An anaerobic microbial consortium (referred to as ANAS) that reductively dechlorinates trichloroethene (TCE) completely to ethene with the transient production of cisdichloroethene (cDCE) and vinyl chloride was enriched from contaminated soil obtained from Alameda Naval Air Station. ANAS uses lactate as its electron donor and has been functionally stable for over 2 years. Following a brief exposure to oxygen, a subculture (designated VCC) derived from ANAS could dechlorinate TCE only to vinyl chloride with lactate as its electron donor. Three molecular methods were used concurrently to characterize the community structure of ANAS and VCC: clone library construction/clone sequencing, terminal restriction fragment length polymorphism (T-RFLP) analysis, and fluorescent in situ hybridization (FISH) with rRNA probes. The community structure of ANAS did not change significantly over the course of a single feeding/dechlorination cycle, and only minor fluctuations occurred over many feeding cycles spanning the course of 1 year. Clone libraries and T-RFLP analyses suggested that ANAS was dominated by populations belonging to three phylogenetic groups: Dehalococcoides species, Desulfovibrio species, and members of the Clostridiaceae (within the low G + C Gram-positives). FISH results suggest that members of the Cytophaga/Flavobacterium/Bacteroides (CFB) cluster and high G + C Gram-positives (HGCs) were numerically important in ANAS despite their under-representation in the clone libraries. Parallel analyses of VCC samples suggested that Dehalococcoides species and Clostridiaceae were only minor populations in this community. Instead, VCC had increased populations of organisms in the beta and gamma subclasses of the Proteobacteria as well as significant populations of organisms in the CFB cluster. It is possible that symbiotic interactions are occurring between some of ANAS's phylogenetic groups under the enrichment conditions, including interspecies hydrogen transfer from Desulfovibrio species to Dehalococcoides species. However, the nucleic acid-based analyses performed here would need to be supplemented with chemical species data in order to test any hypotheses about functional roles of various community members. Additionally, these results suggest that an organism outside the Dehalococcoides genus may be capable of dechlorinating cDCE to vinyl chloride.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

DOE PAGES

Men, Yujie; Yu, Ke; Bælum, Jacob; ...

2017-02-10

The aim of this paper is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expressionmore » when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.« less

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Men, Yujie; Yu, Ke; Bælum, Jacob

The aim of this paper is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expressionmore » when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.« less

Degradation of perchloroethene by combined application of microorganisms and zero valent iron particles

NASA Astrophysics Data System (ADS)

Schöftner, Philipp; Summer, Dorothea; Wimmer, Bernhard; Reichenauer, Thomas

2017-04-01

Chlorinated hydrocarbons (CHCs) are especially toxic pollutants which are frequently found at contaminated sites in urban areas which are densely covered with buildings. In specific in such areas, in-situ technologies are favourable since conventional remediation technologies as excavation are often not applicable. This project examines a combination of two in-situ remediation methods, in which the biotic degradation via bacteria (dehalococcoides) is combined with abiotic degradation by zero-valent iron particles (ZVI). ZVI particles are injected into the aquifer where CHC-molecules are reductively dechlorinated. However Fe(0) is also oxidized by reaction with water leading to generation of H2 without any CHC degradation. To achieve biotic degradation often strictly anaerobic strains of the bacteria Dehalococcoides are used. These bacteria can dechlorinate CHC by utilizing H2. By combining these processes the H2, produced during the anaerobic corrosion of Fe(0), could be used by bacteria for further CHC degradation. Different Fe(0) particles (nano- and micro-scale) were combined with microbial dehalogenation for dehalogenation of perchloroethene (PCE) in batch experiments. PCE degradation rates and H2 production rates of the different particles and cultures were determined. Additionally an artificial aquifer (approximately 1.0 x 0.5 x 0.5 metres) was established. This aquifer was spiked with PCE and subsequently treated with Fe(0) particles and microbial. Molasses was added to facilitate microbial dehalogenation. Preliminary results showed that all H2 evolved during oxidation of Fe(0) were used by the associated microbial community. Nevertheless the overall dehalogenation of chlorinated compounds as well as the production of methane was hardly influenced by the addition of Fe(0), at least not over the experimental period of 28 days. Independent if Fe(0) was added or not all chlorinated compounds were dehalogenated whereby ethene and ethane were the only end products.

Successful operation of continuous reactors at short retention times results in high-density, fast-rate Dehalococcoides dechlorinating cultures.

PubMed

Delgado, Anca G; Fajardo-Williams, Devyn; Popat, Sudeep C; Torres, César I; Krajmalnik-Brown, Rosa

2014-03-01

The discovery of Dehalococcoides mccartyi reducing perchloroethene and trichloroethene (TCE) to ethene was a key landmark for bioremediation applications at contaminated sites. D. mccartyi-containing cultures are typically grown in batch-fed reactors. On the other hand, continuous cultivation of these microorganisms has been described only at long hydraulic retention times (HRTs). We report the cultivation of a representative D. mccartyi-containing culture in continuous stirred-tank reactors (CSTRs) at a short, 3-d HRT, using TCE as the electron acceptor. We successfully operated 3-d HRT CSTRs for up to 120 days and observed sustained dechlorination of TCE at influent concentrations of 1 and 2 mM TCE to ≥ 97 % ethene, coupled to the production of 10(12) D. mccartyi cells Lculture (-1). These outcomes were possible in part by using a medium with low bicarbonate concentrations (5 mM) to minimize the excessive proliferation of microorganisms that use bicarbonate as an electron acceptor and compete with D. mccartyi for H2. The maximum conversion rates for the CSTR-produced culture were 0.13 ± 0.016, 0.06 ± 0.018, and 0.02 ± 0.007 mmol Cl(-) Lculture (-1) h(-1), respectively, for TCE, cis-dichloroethene, and vinyl chloride. The CSTR operation described here provides the fastest laboratory cultivation rate of high-cell density Dehalococcoides cultures reported in the literature to date. This cultivation method provides a fundamental scientific platform for potential future operations of such a system at larger scales.

Standardized Procedures for Use of Nucleic Acid-Based Tools

EPA Science Inventory

Groundwater and soil samples are frequently analyzed using molecular biological tools (MBTs) to detect unique genetic biomarkers associated with Dehalococcoides (Dhc) and other environmentally relevant microorganisms. The results of these analyses are increasingly used b...

Numerical Modeling Analysis of Hydrodynamic and Microbial Controls on DNAPL Pool Dissolution and Detoxification: Dehalorespirers in Co-culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wesseldyke, Eric S.; Becker, Jennifer G.; Seagren, Eric A.

Dissolution of dense non-aqueous phase liquid (DNAPL) contaminants like tetrachloroethene (PCE) can be “bioenhanced” via biodegradation, which increases the concentration gradient at the DNAPL–water interface. Model simulations were used to evaluate the impact of ecological interactions between different dehalorespiring strains and hydrodynamics on the bioenhancement effect and the extent of PCE dechlorination. Simulations were performed using a two-dimensional coupled flow-transport model, with a DNAPL pool source and two microbial species, Dehalococcoides mccartyi 195 and Desulfuromonas michiganensis, which compete for electron acceptors (e.g., PCE), but not for their electron donors. Under biostimulation, low vx conditions, D. michiganensis alone significantly enhanced dissolutionmore » by rapidly utilizing aqueous-phase PCE. In co-culture under these conditions, D. mccartyi 195 increased this bioenhancement modestly and greatly increased the extent of PCE transformation. Although D. michiganensis was the dominant population under low velocity conditions, D. mccartyi 195 dominated under high velocity conditions due to bioclogging effects.« less

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Shuiquan; Wang, Po Hsiang; Higgins, Steven A.

Here we report that the genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 andmore » Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. Ultimately, this analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.« less

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

DOE PAGES

Tang, Shuiquan; Wang, Po Hsiang; Higgins, Steven A.; ...

2016-02-12

Here we report that the genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 andmore » Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. Ultimately, this analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.« less

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes.

PubMed

Sewell, Holly L; Kaster, Anne-Kristin; Spormann, Alfred M

2017-12-19

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi IMPORTANCE The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides . Copyright © 2017 Sewell et al.

EVALUATION OF THE ROLE OF DEHALOCOCCOIDES ORGANISMS IN THE NATURAL ATTENUATION OF CHLORINATED ETHYLENES IN GROUNDWATER

EPA Science Inventory

At most hazardous waste sites where monitored natural attenuation (MNA) of chlorinated solvents in ground water is successful as a remedy, the chlorinated solvents are biologically degraded to harmless end products such as ethylene or ethane. Many organisms can degrade chlorinat...

Electrokinetic-enhanced bioaugmentation for remediation of chlorinated solvents contaminated clay

PubMed Central

Mao, Xuhui; Wang, James; Ciblak, Ali; Cox, Evan E.; Riis, Charlotte; Terkelsen, Mads; Gent, David B.; Alshawabkeh, Akram N.

2012-01-01

Successful bioremediation of contaminated soils is controlled by the ability to deliver bioremediation additives, such as bacteria and/or nutrients, to the contaminated zone. Because hydraulic advection is not practical for delivery in clays, electrokinetic (EK) injection is an alternative for efficient and uniform delivery of bioremediation additive into low-permeability soil and heterogeneous deposits. EK–enhanced bioaugmentation for remediation of clays contaminated with chlorinated solvents is evaluated. Dehalococcoides (Dhc) bacterial strain and lactate ions are uniformly injected in contaminated clay and complete dechlorination of chlorinated ethene is observed in laboratory experiments. The injected bacteria can survive, grow, and promote effective dechlorination under EK conditions and after EK application. The distribution of Dhc within the clay suggests that electrokinetic transport of Dhc is primarily driven by electroosmosis. In addition to biodegradation due to bioaugmentation of Dhc, an EK-driven transport of chlorinated ethenes is observed in the clay, which accelerates cleanup of chlorinated ethenes from the anode side. Compared with conventional advection-based delivery, EK injection is significantly more effective forestablis hingmicrobial reductive dechlorination capacity in low-permeability soils. PMID:22365139

GROWTH OF A DEHALOCOCCOIDES-LIKE MICROORGANISM ON VINYL CHLORIDE AND CIS-DICHLOROETHENE AS ELECTRON ACCEPTORS AS DETERMINED BY COMPETITIVE PCR. (R828772)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Integrating Stable Isotope - Reactive Transport Model Approach for Assessment of Chlorinated Solvent Degradation

DTIC Science & Technology

2016-06-01

Dehalococcoides species require molecular hydrogen as the immediate electron donor. In the microcosm, H2 was produced by fermentation of lactate. It was...superimposed depletion upon H2/H2O equilibrium rather than being tied to the H isotope composition of the fermentation substrate (see Kuder et al., 2013 for more

Assessment of chloroethene biodegradation in the subsurface by microbiological, molecular and isotopic tools

NASA Astrophysics Data System (ADS)

Schmidt, K. R.; Kranzioch, I.; Heidinger, M.; Ertl, S.; Tiehm, A.

2012-04-01

A multiple lines of evidence approach to assess the biodegradation potential of contaminated sites includes - site investigation analysing pollutant distribution (compounds, concentrations, isotopic composition) and hydrochemical conditions (redox conditions) - determination of the presence of pollutant degrading bacteria in the field by microbiological (most probable number, MPN) and molecular (polymerase chain reaction, PCR) methods - analysis of degradation processes in the laboratory by microcosms with determination of site specific isotopic enrichment factors enabling the quantification of biodegradation processes in the field. Results will be shown of the application of such a multiple lines of evidence approach at a chloroethene-contaminated site in Frankenthal, Germany. In anaerobic groundwater microcosms, reductive transformation of perchloroethene (PCE) and trichloroethene (TCE) was observed to mainly proceed to cis-1,2-dichloroethene (cDCE). 16S-PCR analysis showed a wide distribution of halorespiring bacteria capable of PCE degradation to cDCE, whereas Dehalococcoides - the only organisms described so far being able of complete reductive dechlorination down to ethene - was only found in one groundwater sample. Aerobic microcosms showed metabolic degradation of the lower chlorinated compounds cDCE and vinyl chloride (VC). Co-metabolic degradation of cDCE with VC as auxiliary substrate occurred, too. Significant stable carbon isotope fractionation was observed during anaerobic degradation of PCE and TCE as well as during aerobic degradation of cDCE and VC. Compiling the results of the different assessment methods, sequential dechlorination - PCE/TCE to cDCE anaerobically and cDCE to CO2 aerobically - was demonstrated to occur at the Frankenthal site. The extent of biodegradation in the field was calculated based on the enrichment factors determined in microcosms and the 13C-isotopic composition of the contaminants on site. The application of molecular methods is continuously increasing. For example, microbiological and molecular tools showed the presence and activity of halorespiring bacteria in sediment samples of the Yangtze river, China. PCR-detection demonstrated the presence of five different halorespiring bacterial groups as well as of four different dechlorinating enzymes of Dehalococcoides. In conclusion, our study demonstrates that (i) multiple lines of evidence approaches result in a profound understanding of the biodegradation processes occurring in the field, (ii) stable isotope fractionation is suitable for assessing and quantifying anaerobic and aerobic chloroethene degradation and (iii) detection and quantification of dechlorinating bacteria and enzymes by PCR methods provide more insight into biodegradation processes. Acknowledgement The authors gratefully acknowledge financial support by the German Ministry of Education and Research (BMBF, grant no 02WN0446, 02WN0447 and 02WT1130), the German Ministry of Economics and Technology (BMWi, grant no KF2265705AK9 and KF2285302AK9) and the federal state of Rhineland-Palatinate. We thank all project partners for fruitful cooperation.

Vertical distribution of dehalogenating bacteria in mangrove sediment and their potential to remove polybrominated diphenyl ether contamination.

PubMed

Pan, Ying; Chen, Juan; Zhou, Haichao; Farzana, Shazia; Tam, Nora F Y

2017-11-30

The removal and degradation of polybrominated diphenyl ethers (PBDEs) in sediments are not clear. The vertical distribution of total and dehalogenating bacteria in sediment cores collected from a typical mangrove swamp in South China and their intrinsic degradation potential were investigated. These bacterial groups had the highest abundances in surface sediments (0-5cm). A 5-months microcosm experiment also showed that surface sediments had the highest rate to remove BDE-47 than deeper sediments (5-30cm) under anaerobic condition. The deeper sediments, being more anaerobic, had lower population of dehalogenating bacteria leading to a weaker BDE-47 removal potential than surface sediments. Stepwise multiple regression analysis indicated that Dehalococcoides spp. were the most important dehalogenating bacteria affecting the anaerobic removal of BDE-47 in mangrove sediments. This is the first study reporting that mangrove sediments harbored diverse groups of dehalogenating bacteria and had intrinsic potential to remove PBDE contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial based chlorinated ethene destruction

DOEpatents

Bagwell, Christopher E [Aiken, SC; Freedman, David L [Clemson, SC; Brigmon, Robin L [North Augusta, SC; Bratt, William B [Atlanta, GA; Wood, Elizabeth A [Marietta, GA

2009-11-10

A mixed culture of Dehalococcoides species is provided that has an ability to catalyze the complete dechlorination of polychlorinated ethenes such as PCE, TCE, cDCE, 1,1-DCE and vinyl chloride as well as halogenated ethanes such as 1,2-DCA and EDB. The mixed culture demonstrates the ability to achieve dechlorination even in the presence of high source concentrations of chlorinated ethenes.

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

PubMed Central

Sewell, Holly L.; Kaster, Anne-Kristin

2017-01-01

ABSTRACT The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi. PMID:29259088

A Continuous Flow Column Study of Anaerobic PCE Transformation With the Evanite Culture and Hanford Aquifer Solids

NASA Astrophysics Data System (ADS)

Semprini, L.; Behrens, S.; Azizian, M.; Sabalowsky, A.; Dolan, M.; Ruiz-Hass, P.; Ingle, J.; Spormann, A.

2005-12-01

Anaerobic reductive dehalogenation of tetrachloroethene (PCE) and trichoroethene (TCE) is a promising technology for the in situ treatment of high concentration source zones in contaminated aquifers. Continuous flow column studies were performed where a mixed dehalogenating culture (Evanite culture) that contains Dehalococcides-like microorganisms was bioaugmented into aquifer solids from the Hanford DOE site. Studies conducted prior to bioaugmentation showed PCE transport was retarded due to sorption onto the aquifer solids. Upon bioaugmentation and with continuous lactate addition, PCE (10 mg/L) was transformed to cis-dichloroethene ( cis-DCE), and enhanced transformation of sorbed PCE was observed. Prolonged production of cis-DCE was associated with iron reducing conditions, while eventual vinyl chloride (VC) reduction to ethene was associated with sulfate reducing conditions. Microbial processes included lactate fermentation to acetate and propionate, iron reduction, sulfate reduction, and reductive dehalogenation, with reductive dehalogenation utilizing 2 to 3% of the electron donor addition. PCE was completely transformed to ethene within a hydraulic residence time of one day. Upon competition of the column tests spatial samples of aquifer solids were analyzed using molecular methods and solids were used in batch microcosm activity tests. Dehalococcoides sp. 16S rRNA gene copy numbers dropped from ~ 74% of total Eubacterial 16S rRNA genes in the original inoculum, to about 0.5 to 4% through out the column, consistent with the estimates of electron donor utilization for dehalogenation reactions. Microcosm tests showed most of PCE transformation activity at the entrance of the column, consistent with the Dehalococcoides sp. 16S rRNA gene copy numbers being highest in that area. Roughly 20% of the Dehalococcoides sp. population in the column possessed a vcrA gene for the respiration of VC to ethene. The vcrA-positive subpopulation decreases to about 5% towards the column outflow, while VC microcosm activity tests show fairly constant rates of VC transformation across the column. The column studies demonstrated that complete transformation of PCE to ethene can be obtained over short spatial and temporal scales.

Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater.

PubMed

Kanitkar, Yogendra H; Stedtfeld, Robert D; Hatzinger, Paul B; Hashsham, Syed A; Cupples, Alison M

2017-06-01

TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 10 5  gene copies per L for vcrA and 1.3 × 10 5  gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.

Effects of Aqueous Film-Forming Foams (AFFFs) on Trichloroethene (TCE) Dechlorination by a Dehalococcoides mccartyi-Containing Microbial Community.

PubMed

Harding-Marjanovic, Katie C; Yi, Shan; Weathers, Tess S; Sharp, Jonathan O; Sedlak, David L; Alvarez-Cohen, Lisa

2016-04-05

The application of aqueous film-forming foams (AFFFs) to extinguish chlorinated solvent-fueled fires has led to the co-contamination of poly- and perfluoroalkyl substances (PFASs) and trichloroethene (TCE) in groundwater and soil. Although reductive dechlorination of TCE by Dehalococcoides mccartyi is a frequently used remediation strategy, the effects of AFFF and PFASs on TCE dechlorination are not well-understood. Various AFFF formulations, PFASs, and ethylene glycols were amended to the growth medium of a D. mccartyi-containing enrichment culture to determine the impact on dechlorination, fermentation, and methanogenesis. The community was capable of fermenting organics (e.g., diethylene glycol butyl ether) in all AFFF formulations to hydrogen and acetate, but the product concentrations varied significantly according to formulation. TCE was dechlorinated in the presence of an AFFF formulation manufactured by 3M but was not dechlorinated in the presence of formulations from two other manufacturers. Experiments amended with AFFF-derived PFASs and perfluoroalkyl acids (PFAAs) indicated that dechlorination could be inhibited by PFASs but that the inhibition depends on surfactant concentration and structure. This study revealed that the fermentable components of AFFF can stimulate TCE dechlorination, while some of the fluorinated compounds in certain AFFF formulations can inhibit dechlorination.

Monitoring Anaerobic TCE Degradation by Evanite Cultre in Column Packed with TCE-Contaminated Soil

NASA Astrophysics Data System (ADS)

Ko, J.; Han, K.; Ahn, G.; Park, S.; Kim, N.; Ahn, H.; Kim, Y.

2011-12-01

Trichloroethylene (TCE) is a long-term common groundwater pollutant because the compound with high density is slowly released into groundwater. Physical and chemical remediation processes have been used to clean-up the contaminant, but novel remediation technology is required to overcome a low efficiency of the traditional treatment process. Many researchers focused on biological process using an anaerobic TCE degrading culture, dehalococcoides spp., but it still needs to evaluate whether the process can be applied into field scale under aerobic condition. Therefore, in this work we examined two different types (i.e., Natural attenuation and bioaugmentation) of biological remediation process in anaerobic column packed with TCE-contaminated soil. A TCE degradation by indigenous microorganisms was confirmed by monitoring TCE and the metabolites (c-DCE, VC, ETH). However, TCE was transformed and stoichiometry amount of c-DCE was produced, and VC and ETH was not detected. To test bioaugmentation of Evanite culture containing dehalococcoides spp., Evanite culture was injected into the column and TCE degradation to c-DCE, VC, ETH was monitored. We are evaluating the transport of the Evanite culture in the column by measuring TCE and VC reductases. In the result, the TCE was completely degraded to ETH using hydrogen as electron donor generate by hydrogen-production fermentation from formate.

Sustainable remediation: electrochemically assisted microbial dechlorination of tetrachloroethene-contaminated groundwater.

PubMed

Patil, Sayali S; Adetutu, Eric M; Rochow, Jacqueline; Mitchell, James G; Ball, Andrew S

2014-01-01

Microbial electric systems (MESs) hold significant promise for the sustainable remediation of chlorinated solvents such as tetrachlorethene (perchloroethylene, PCE). Although the bio-electrochemical potential of some specific bacterial species such as Dehalcoccoides and Geobacteraceae have been exploited, this ability in other undefined microorganisms has not been extensively assessed. Hence, the focus of this study was to investigate indigenous and potentially bio-electrochemically active microorganisms in PCE-contaminated groundwater. Lab-scale MESs were fed with acetate and carbon electrode/PCE as electron donors and acceptors, respectively, under biostimulation (BS) and BS-bioaugmentation (BS-BA) regimes. Molecular analysis of the indigenous groundwater community identified mainly Spirochaetes, Firmicutes, Bacteroidetes, and γ and δ-Proteobacteria. Environmental scanning electron photomicrographs of the anode surfaces showed extensive indigenous microbial colonization under both regimes. This colonization and BS resulted in 100% dechlorination in both treatments with complete dechlorination occurring 4 weeks earlier in BS-BA samples and up to 11.5 μA of current being generated. The indigenous non-Dehalococcoides community was found to contribute significantly to electron transfer with ∼61% of the current generated due to their activities. This study therefore shows the potential of the indigenous non-Dehalococcoides bacterial community in bio-electrochemically reducing PCE that could prove to be a cost-effective and sustainable bioremediation practice. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Coupling Bioflocculation of Dehalococcoides mccartyi to High-Rate Reductive Dehalogenation of Chlorinated Ethenes.

PubMed

Delgado, Anca G; Fajardo-Williams, Devyn; Bondank, Emily; Esquivel-Elizondo, Sofia; Krajmalnik-Brown, Rosa

2017-10-03

Continuous bioreactors operated at low hydraulic retention times have rarely been explored for reductive dehalogenation of chlorinated ethenes. The inability to consistently develop such bioreactors affects the way growth approaches for Dehalococcoides mccartyi bioaugmentation cultures are envisioned. It also affects interpretation of results from in situ continuous treatment processes. We report bioreactor performance and dehalogenation kinetics of a D. mccartyi-containing consortium in an upflow bioreactor. When fed synthetic groundwater at 11-3.6 h HRT, the upflow bioreactor removed >99.7% of the influent trichloroethene (1.5-2.8 mM) and produced ethene as the main product. A trichloroethene removal rate of 98.51 ± 0.05 me - equiv L -1 d -1 was achieved at 3.6 h HRT. D. mccartyi cell densities were 10 13 and 10 12 16S rRNA gene copies L -1 in the bioflocs and planktonic culture, respectively. When challenged with a feed of natural groundwater containing various competing electron acceptors and 0.3-0.4 mM trichloroethene, trichloroethene removal was sustained at >99.6%. Electron micrographs revealed that D. mccartyi were abundant within the bioflocs, not only in multispecies structures, but also as self-aggregated microcolonies. This study provides fundamental evidence toward the feasibility of upflow bioreactors containing D. mccartyi as high-density culture production tools or as a high-rate, real-time remediation biotechnology.

Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons.

PubMed

Hamonts, Kelly; Ryngaert, Annemie; Smidt, Hauke; Springael, Dirk; Dejonghe, Winnie

2014-03-01

Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic, CAH-polluted sediments of the Zenne River. Based on PCR-DGGE analysis, a high diversity of Bacteria, sulfate-reducing bacteria, Geobacteraceae, methanogenic archaea, and CAH-respiring Dehalococcoides was found. Depth in the riverbed, organic carbon content, CAH content and texture of the sediment, pore water temperature and conductivity, and concentrations of toluene and methane significantly contributed to the variance in the microbial community structure. On a meter scale, CAH concentrations alone explained only 6% of the variance in the Dehalococcoides and sulfate-reducing communities. On a cm-scale, however, CAHs explained 14.5-35% of the variation in DGGE profiles of Geobacteraceae, methanogens, sulfate-reducing bacteria, and Bacteria, while organic carbon content explained 2-14%. Neither the presence of the CAH reductive dehalogenase genes tceA, bvcA, and vcrA, nor the community structure of the targeted groups significantly differed between riverbed locations showing either no attenuation or reductive dechlorination, indicating that the microbial community composition was not a limiting factor for biotransformation in the Zenne sediments. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Distribution of Dechlorinating Bacteria between the Aqueous and Solid Phases

NASA Astrophysics Data System (ADS)

Cápiro, N. L.; Hatt, J. K.; Wang, Y.; Loeffler, F. E.; Pennell, K. D.

2010-12-01

Microbial monitoring of aquifers relies on nucleic acid biomarker analysis, which is typically performed with biomass recovered from groundwater samples; however, it is unclear what fraction of the target population(s) is associated with groundwater (i.e., planktonic cells) or is attached to solid phases (i.e., biofilms). Understanding how the titer of target organism(s) in groundwater correlates with the true cell titers of the target organism in the aquifer (i.e., planktonic plus attached cells) is critical for a meaningful interpretation of the data, the prediction of bioremediation performance, and the implementation of site management strategies. To evaluate the distribution of active cells between resident solid phase and the aqueous phase, one-dimensional columns were packed under water-saturated conditions with Bio-Dechlor INOCULUM, a PCE-to ethene-dechlorinating bacterial consortium containing both multiple Dehalococcoides (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ). The columns were packed with two distinct solid matrices: a low organic content sandy Federal Fine Ottawa soil or Appling soil with higher organic matter content. Influent reduced mineral salts medium supplied at a groundwater pore-water velocity of 0.3 m/day contained both 10 mM lactate as electron donor and 0.33 mM PCE as electron acceptor. Routine collection of biomass from column side ports and effluent samples measured the titers of target cells in the aqueous phase and determined when steady state conditions had been reached. A second set of column experiments evaluated delivery and filtration effects by the solid matrix (i.e., Federal Fine Ottawa sand versus Appling soil) under the same conditions except that electron donor or acceptor were omitted (no growth conditions). Quantitative real-time PCR (qPCR) analysis using Dhc and GeoSZ 16S rRNA gene-targeted primer and probe sets determined the planktonic cell counts, and destructive sampling of the columns allowed measurement of the total cell titer (i.e., attached plus planktonic cells). The results indicate that within the higher organic matter Appling soil, the fraction of target cells associated with the solid phase was nearly 2-orders of magnitude higher compared to the fraction attached to the aqueous phase. In the sandy soil, differences were approximately 1-order of magnitude. Ongoing efforts use dynamic light scattering and electrophoretic mobility measurements over a range of ionic strengths and pH values to shed light on the parameters that control microbial attachment behavior. Knowledge of factors that affect microbial distribution between aqueous and solid phases is essential for interpreting qPCR data obtained from site groundwater where biological remedies are implemented.

Impact of estuarine gradients on reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin in river sediment enrichment cultures.

PubMed

Dam, Hang T; Häggblom, Max M

2017-02-01

Polychlorinated dibenzo-p-dioxins (PCDDs) are among the most persistent organic pollutants. Although the total input of PCDDs into the environment has decreased substantially over the past four decades, their input via non-point sources is still increasing, especially in estuarine metropolitan areas. Here we report on the microbially mediated reductive dechlorination of PCDDs in anaerobic enrichment cultures established from sediments collected from five locations along the Hackensack River, NJ and investigate the impacts of sediment physicochemical characteristics on dechlorination activity. Dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) and abundance of Dehalococcoides spp. negatively correlated with salinity and sulfate concentration in sediments used to establish the cultures. 1,2,3,4-TeCDD was dechlorinated to a lesser extent in cultures established from sediments from the tidally influenced estuarine mouth of the river. In cultures established from low salinity sediments, 1,2,3,4-TeCDD was reductively dechlorinated with the accumulation of 2-monochlorodibenzo-p-dioxin as the major product. Sulfate concentrations above 2 mM inhibited 1,2,3,4-TecDD dechlorination activity. Consecutive lateral- and peri- dechlorination took place in enrichment cultures with a minimal accumulation of 2,3-dichlorodibenzo-p-dioxin in active cultures. A Dehalococcoides spp. community was enriched and accounted for up to 64% of Chloroflexi detected in these sediment cultures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater.

PubMed

Munro, Jacob E; Kimyon, Önder; Rich, Deborah J; Koenig, Joanna; Tang, Sihui; Low, Adrian; Lee, Matthew; Manefield, Mike; Coleman, Nicholas V

2017-11-01

1,2-Dichloroethane (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA-degrading bacteria are not well understood, which has hampered their application for bioremediation. Here, we used quantitative PCR to investigate the distribution of putative DCA-dehalogenating bacteria at a DCA-impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were detected in all groundwater samples (n = 15), while vcrA was found in 11/15 samples. The 16S rRNA gene sequences specific to the dehalogenating genera Dehalobacter, Desulfitobacterium and Dehalogenimonas were detected in 15/15, 13/15 and 13/15 samples, respectively, while Dehalococcoides sequences were found in 9/15 samples. The tceA, bvcA and vcrA genes occurred in the same samples as Dehalococcoides and Dehalobacter. Microcosm experiments confirmed the presence of bacteria capable of dechlorination under anoxic conditions. The abundance of the dhlA gene, which is found in hydrolytic DCA degraders, was positively correlated to the DCA concentration, and was unexpectedly most abundant in samples with low oxygen conditions. A dhlA-containing bacterium isolated from the site (Xanthobacter EL8) was capable of anaerobic growth on DCA under denitrifying conditions. The presence of diverse DCA-dehalogenating bacteria at this site indicates that natural attenuation or biostimulation could be valid approaches for site cleanup. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Dehalococcoides abundance and alternate electron acceptor effects on large, flow-through trichloroethene dechlorinating columns.

PubMed

Mirza, Babur S; Sorensen, Darwin L; Dupont, R Ryan; McLean, Joan E

2016-03-01

Trichloroethene (TCE) in groundwater is a major health concern and biostimulation/bioaugmentation-based strategies have been evaluated to achieve complete reductive dechlorination with varying success. Different carbon sources were hypothesized to stimulate different extents of TCE reductive dechlorination. Ecological conditions that developed different dechlorination stages were investigated by quantitating Dehalococcoides 16S rRNA (Dhc) and reductive dehalogenase gene abundance, and by describing biogeochemical properties of laboratory columns in response to this biostimulation. Eight large columns (183 cm × 15.2 cm), packed with aquifer material from Hill AFB, Utah, that were continuously fed TCE for 7.5 years. Duplicate columns were biostimulated with whey or one of two different Newman Zone® emulsified oil formulations containing either nonionic surfactant (EOLN) or standard surfactant (EOL). Two columns were non-stimulated controls. Complete (whey amended), partial (EOLN amended), limited (EOL), and non-TCE dehalogenating systems (controls) developed over the course of the study. Bioaugmentation of half of the columns with Bachman Road culture 3 years prior to dismantling did not influence the extent of TCE dehalogenation. Multivariate analysis clustered samples by biostimulation treatments and extent of TCE dehalogenation. Dhc, tceA, and bvcA gene concentrations did not show a consistent relationship with TCE dehalogenation but the vcrA gene was more abundant in completely dehalogenating, whey-treated columns. The whey columns developed strongly reducing conditions producing Fe(II), sulfide, and methane. Biostimulation with different carbon and energy sources can support high concentrations of diverse Dhc, but carbon addition has a major influence on biogeochemical processes effecting the extent of TCE dehalogenation.

Impact of the morphology and reactivity of nanoscale zero-valent iron (NZVI) on dechlorinating bacteria.

PubMed

Rónavári, Andrea; Balázs, Margit; Tolmacsov, Péter; Molnár, Csaba; Kiss, István; Kukovecz, Ákos; Kónya, Zoltán

2016-05-15

Nanoscale zero-valent iron (NZVI) is increasingly used for reducing chlorinated organic contaminants in soil or groundwater. However, little is known about what impact the particles will have on the biochemical processes and the indigenous microbial communities. Nanoiron reactivity is affected by the structure and morphology of nanoparticles that complicates the applicability in bioremediation. In this study, the effect of precursors (ferrous sulfate and ferric chloride) and reducing agents (sodium dithionite and sodium borohydride) on the morphology and the reactivity of NZVIs was investigated. We also studied the impact of differently synthesized NZVIs on microbial community, which take part in reductive dechlorination. We demonstrated that both the applied iron precursor and the reducing agent had influence on the structure of the nanoparticles. Spherical nanoparticles with higher Fe(0) content (>90%) was observed by using sodium borohydride as reducing agent, while application of sodium dithionite as reducing agent resulted nanostructures with lower Fe(0) content (between 68,7 and 85,5%). To determine the influence of differently synthesized NZVIs on cell viability anaerobic enriched microcosm were used. NVZI was used in 0.1 g/L concentration in all batch experiments. Relative amount of Dehalococcoides, sulfate reducers (SRBs) and methanogens were measured by quantitative PCR. We found that the relative amount of Dehalococcoides slowly decreased in all experiments independently from the precursor and reducing agent, whereas the total amount of microbes increased. The only clear distinction was in relative amount of sulfate reducers which were higher in the presence of NZVIs synthesized from sodium dithionite. Copyright © 2016 Elsevier Ltd. All rights reserved.

Distinct Dual C-Cl Isotope Fractionation Patterns during Anaerobic Biodegradation of 1,2-Dichloroethane: Potential To Characterize Microbial Degradation in the Field.

PubMed

Palau, J; Yu, R; Hatijah Mortan, S; Shouakar-Stash, O; Rosell, M; Freedman, D L; Sbarbati, C; Fiorenza, S; Aravena, R; Marco-Urrea, E; Elsner, M; Soler, A; Hunkeler, D

2017-03-07

This study investigates, for the first time, dual C-Cl isotope fractionation during anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via dihaloelimination by Dehalococcoides and Dehalogenimonas-containing enrichment cultures. Isotopic fractionation of 1,2-DCA (ε bulk C and ε bulk Cl ) for Dehalococcoides (-33.0 ± 0.4‰ and -5.1 ± 0.1‰) and Dehalogenimonas-containing microcosms (-23 ± 2‰ and -12.0 ± 0.8‰) resulted in distinctly different dual element C-Cl isotope correlations (Λ = Δδ 13 C/Δδ 37 Cl ≈ ε bulk C /ε bulk Cl ), 6.8 ± 0.2 and 1.89 ± 0.02, respectively. Determined isotope effects and detected products suggest that the difference on the obtained Λ values for biodihaloelimination could be associated with a different mode of concerted bond cleavage rather than two different reaction pathways (i.e., stepwise vs concerted). Λ values of 1,2-DCA were, for the first time, determined in two field sites under reducing conditions (2.1 ± 0.1 and 2.2 ± 2.9). They were similar to the one obtained for the Dehalogenimonas-containing microcosms (1.89 ± 0.02) and very different from those reported for aerobic degradation pathways in a previous laboratory study (7.6 ± 0.1 and 0.78 ± 0.03). Thus, this study illustrates the potential of a dual isotope analysis to differentiate between aerobic and anaerobic biodegradation pathways of 1,2-DCA in the field and suggests that this approach might also be used to characterize dihaloelimination of 1,2-DCA by different bacteria, which needs to be confirmed in future studies.

Nature's Helpers: Using Microorganisms to Remove Trichloroethene (TCE) from Groundwater

NASA Astrophysics Data System (ADS)

Delgado, A. G.; Krajmlanik-Brown, R.; Fajardo-Williams, D.; Halloum, I.

2015-12-01

Organic chlorinated solvents, such as perchloroethene (PCE) and trichloroethene (TCE), are toxic pollutants threatening ground water quality worldwide and present at many superfund sites. Bioremediation using microorganisms is a promising, green, efficient, and sustainable approach to remove PCE and TCE contamination from soil and groundwater. Under anaerobic conditions, specialized microorganisms (dechlorinators) can reduce these chlorinated ethenes to ethene, an innocuous product, and gain energy for growth by a process known as reductive dechlorination. Dechlorinators are most often present in the environment and in dechlorinating cultures alongside other microbes such as fermenters, methanogens, and acetogens. Fermenters, methanogens, and acetogens syntrophically provide essential nutrients and growth factors to dechlorinators, most specifically to the only members able to reduce TCE all the way to ethene: Dehalococcoides; unfortunately, they also compete with dechlorinators for electron donors. My laboratory devises reductive chlorination platforms to study competition and syntrophy among Dehalococcoides, and other microbes to optimize remediation reactions and transport in the subsurface. We look at competing processes present as part of the natural soil chemistry and microbiology and address these challenges through a combination of enrichment techniques, molecular microbial ecology (deep sequencing), water chemistry, and electron balances. We have applied knowledge gathered in my laboratory to: 1) enrich microbial dechlorinating cultures capable of some of the fastest rates of TCE to ethene dechlorination ever reported, and 2) successfully design and operate three different continuous dechlorinating reactor types. We attribute our successful reactor operations to our multidisciplinary approach which links microbiology and engineering. Our reactors produce robust dechlorinating cultures used for in-situ bioaugmentation of PCE and TCE at contaminated sites. The results gathered to date provide a fundamental understanding of the role of homoacetogens and methanogens in electron and carbon flow in dechlorinating consortia.

Organohalide Respiration with Chlorinated Ethenes under Low pH Conditions

DOE PAGES

Yang, Yi; Cápiro, Natalie L.; Marcet, Tyler F.; ...

2017-06-30

Bioremediation at chlorinated solvent sites often leads to groundwater acidification due to electron donor fermentation and enhanced dechlorination activity. The microbial reductive dechlorination process is robust at circumneutral pH, but activity declines at groundwater pH values below 6.0. Consistent with this observation, the activity of tetrachloroethene (PCE) dechlorinating cultures declined at pH 6.0 and was not sustained in pH 5.5 medium, with one notable exception. Sulf urospirillum multivorans dechlorinated PCE to cis-1,2-dichloroethene (cDCE) in pH 5.5 medium and maintained this activity upon repeated transfers. Microcosms established with soil and aquifer materials from five distinct locations dechlorinated PCE-to-ethene at pH 5.5more » and pH 7.2. Dechlorination to ethene was maintained following repeated transfers at pH 7.2, but no ethene was produced at pH 5.5, and only the transfer cultures derived from the Axton Cross Superfund (ACS) microcosms sustained PCE dechlorination to cDCE as a final product. 16S rRNA gene amplicon sequencing of pH 7.2 and pH 5.5 ACS enrichments revealed distinct microbial communities, with the dominant dechlorinator being Dehalococcoides in pH 7.2 and Sulf urospirillum in pH 5.5 cultures. PCE-to-trichloroethene- (TCE-) and PCE-to-cDCEdechlorinating isolates obtained from the ACS pH 5.5 enrichment shared 98.6%, and 98.5% 16S rRNA gene sequence similarities to Sulf urospirillum multivorans. Lastly, these findings imply that sustained Dehalococcoides activity cannot be expected in low pH (i.e., ≤ 5.5) groundwater, and organohalide-respiring Sulf urospirillum spp. are key contributors to in situ PCE reductive dechlorination under low pH conditions.« less

Organohalide Respiration with Chlorinated Ethenes under Low pH Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yi; Cápiro, Natalie L.; Marcet, Tyler F.

Bioremediation at chlorinated solvent sites often leads to groundwater acidification due to electron donor fermentation and enhanced dechlorination activity. The microbial reductive dechlorination process is robust at circumneutral pH, but activity declines at groundwater pH values below 6.0. Consistent with this observation, the activity of tetrachloroethene (PCE) dechlorinating cultures declined at pH 6.0 and was not sustained in pH 5.5 medium, with one notable exception. Sulf urospirillum multivorans dechlorinated PCE to cis-1,2-dichloroethene (cDCE) in pH 5.5 medium and maintained this activity upon repeated transfers. Microcosms established with soil and aquifer materials from five distinct locations dechlorinated PCE-to-ethene at pH 5.5more » and pH 7.2. Dechlorination to ethene was maintained following repeated transfers at pH 7.2, but no ethene was produced at pH 5.5, and only the transfer cultures derived from the Axton Cross Superfund (ACS) microcosms sustained PCE dechlorination to cDCE as a final product. 16S rRNA gene amplicon sequencing of pH 7.2 and pH 5.5 ACS enrichments revealed distinct microbial communities, with the dominant dechlorinator being Dehalococcoides in pH 7.2 and Sulf urospirillum in pH 5.5 cultures. PCE-to-trichloroethene- (TCE-) and PCE-to-cDCEdechlorinating isolates obtained from the ACS pH 5.5 enrichment shared 98.6%, and 98.5% 16S rRNA gene sequence similarities to Sulf urospirillum multivorans. Lastly, these findings imply that sustained Dehalococcoides activity cannot be expected in low pH (i.e., ≤ 5.5) groundwater, and organohalide-respiring Sulf urospirillum spp. are key contributors to in situ PCE reductive dechlorination under low pH conditions.« less

SYNTHETIC BIOLOGY. Emergent genetic oscillations in a synthetic microbial consortium.

PubMed

Chen, Ye; Kim, Jae Kyoung; Hirning, Andrew J; Josić, Krešimir; Bennett, Matthew R

2015-08-28

A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a synthetic microbial consortium consisting of two distinct cell types—an "activator" strain and a "repressor" strain. These strains produced two orthogonal cell-signaling molecules that regulate gene expression within a synthetic circuit spanning both strains. The two strains generated emergent, population-level oscillations only when cultured together. Certain network topologies of the two-strain circuit were better at maintaining robust oscillations than others. The ability to program population-level dynamics through the genetic engineering of multiple cooperative strains points the way toward engineering complex synthetic tissues and organs with multiple cell types. Copyright © 2015, American Association for the Advancement of Science.

In vitro transfer of multiple resistance observed in vivo during a Salmonella london epidemic.

PubMed

Lantos, J; Marjai, E

1980-01-01

Between 1976 and 1978, waves of Salmonella london infections conveyed by raw meat and meat products were observed. The strains isolated during the epidemic were first susceptible then developed multiple antibiotic resistance. The identical antibiotic resistance patterns of the strain and their more frequent occurrence in hospital environments indicated plasmid-mediated resistance. R-plasmid transfer, minimum inhibition concentration and resistance elimination were studied in representative strains. The resistant S. london strain and transconjugants of Escherichia coli rendered resistant were compared. The results proved that multiple resistance was plasmid-mediated.

Compartmentalization and Transmission of Multiple Epstein-Barr Virus Strains in Asymptomatic Carriers

PubMed Central

Sitki-Green, Diane; Covington, Mary; Raab-Traub, Nancy

2003-01-01

Infection with the Epstein-Barr virus (EBV) is often subclinical in the presence of a healthy immune response; thus, asymptomatic infection is largely uncharacterized. This study analyzed the nature of EBV infection in 20 asymptomatic immunocompetent hosts over time through the identification of EBV strain variants in the peripheral blood and oral cavity. A heteroduplex tracking assay specific for the EBV gene LMP1 precisely identified the presence of multiple EBV strains in each subject. The strains present in the peripheral blood and oral cavity were often completely discordant, indicating the existence of distinct infections, and the strains present and their relative abundance changed considerably between time points. The possible transmission of strains between the oral cavity and peripheral blood compartments could be tracked within subjects, suggesting that reactivation in the oral cavity and subsequent reinfection of B lymphocytes that reenter the periphery contribute to the maintenance of persistence. In addition, distinct virus strains persisted in the oral cavity over many time points, suggesting an important role for epithelial cells in the maintenance of persistence. Asymptomatic individuals without tonsillar tissue, which is believed to be an important source of virus for the oral cavity, also exhibited multiple strains and a cyclic pattern of transmission between compartments. This study revealed that the majority of patients with infectious mononucleosis were infected with multiple strains of EBV that were also compartmentalized, suggesting that primary infection involves the transmission of multiple strains. Both the primary and carrier states of infection with EBV are more complex than previously thought. PMID:12525618

Compartmentalization and transmission of multiple epstein-barr virus strains in asymptomatic carriers.

PubMed

Sitki-Green, Diane; Covington, Mary; Raab-Traub, Nancy

2003-02-01

Infection with the Epstein-Barr virus (EBV) is often subclinical in the presence of a healthy immune response; thus, asymptomatic infection is largely uncharacterized. This study analyzed the nature of EBV infection in 20 asymptomatic immunocompetent hosts over time through the identification of EBV strain variants in the peripheral blood and oral cavity. A heteroduplex tracking assay specific for the EBV gene LMP1 precisely identified the presence of multiple EBV strains in each subject. The strains present in the peripheral blood and oral cavity were often completely discordant, indicating the existence of distinct infections, and the strains present and their relative abundance changed considerably between time points. The possible transmission of strains between the oral cavity and peripheral blood compartments could be tracked within subjects, suggesting that reactivation in the oral cavity and subsequent reinfection of B lymphocytes that reenter the periphery contribute to the maintenance of persistence. In addition, distinct virus strains persisted in the oral cavity over many time points, suggesting an important role for epithelial cells in the maintenance of persistence. Asymptomatic individuals without tonsillar tissue, which is believed to be an important source of virus for the oral cavity, also exhibited multiple strains and a cyclic pattern of transmission between compartments. This study revealed that the majority of patients with infectious mononucleosis were infected with multiple strains of EBV that were also compartmentalized, suggesting that primary infection involves the transmission of multiple strains. Both the primary and carrier states of infection with EBV are more complex than previously thought.

Risk factors for fecal colonization with multiple distinct strains of Escherichia coli among long-term care facility residents.

PubMed

Lautenbach, Ebbing; Tolomeo, Pam; Black, Nicole; Maslow, Joel N

2009-05-01

Of 49 long-term care facility residents, 21 (43%) were colonized with 2 or more distinct strains of Escherichia coli. There were no significant risk factors for colonization with multiple strains of E. coli. These results suggest that future efforts to efficiently identify the diversity of colonizing strains will be challenging.

Risk Factors for Fecal Colonization with Multiple Distinct Strains of Escherichia coli Among Long-Term Care Facility Residents

PubMed Central

Lautenbach, Ebbing; Tolomeo, Pam; Black, Nicole; Maslow, Joel N.

2009-01-01

Of 49 long-term care facility residents, 21 (43%) were colonized with two or more distinct strains of Escherichia coli. There were no significant risk factors for colonization with multiple strains of E. coli. These results suggest future efforts to efficiently identify diversity of colonizing strains will be challenging. PMID:19292660

Diversity of Staphylococcus pseudintermedius in carriage sites and skin lesions of dogs with superficial bacterial folliculitis: potential implications for diagnostic testing and therapy.

PubMed

Larsen, Rikke Friis; Boysen, Lene; Jessen, Lisbeth Rem; Guardabassi, Luca; Damborg, Peter

2018-05-21

Staphylococcus pseudintermedius is genotypically diverse within the canine population and multiple strains may colonize individual dogs at any given time. If multiple strains with distinct antimicrobial resistance profiles are present in superficial bacterial folliculitis (SBF), sampling a single skin lesion for culture and antimicrobial susceptibility testing (AST) might be inadequate to select effective therapy. To investigate S. pseudintermedius diversity in carriage sites and lesions of dogs with SBF. Fourteen dogs with SBF. Staphylococcus pseudintermedius isolates obtained from perineum, gingiva and four to six skin lesions per dog were subjected to pulsed-field gel electrophoresis (PFGE) and AST to assess diversity between lesions. For two dogs, 14-16 isolates per lesion were included in the analysis to assess diversity within lesions. Analysis of one isolate per lesion revealed one to four strains displaying unique PFGE profiles, and up to three unique antimicrobial resistance (AMR) profiles for each dog. Multiple pustules from the same dog always harboured the same strain, whereas papules, crusts and collarettes did not. Up to four strains with distinct AMR profiles were isolated from the same lesion in two dogs. In 12 dogs, at least one carriage site strain also was represented in lesions. Lesions of SBF may harbour multiple S. pseudintermedius strains with distinct antimicrobial resistance profiles. Pustules are the best target for bacterial culture. It remains unclear whether isolation of different strains from other lesion types is a consequence of contamination or co-infection by multiple strains. © 2018 ESVD and ACVD.

Assessment of In-Situ Reductive Dechlorination Using Compound-Specific Stable Isotopes, Functional-Gene Pcr, and Geochemical Data

PubMed Central

Carreón-Diazconti, Concepción; Santamaría, Johanna; Berkompas, Justin; Field, James A.; Brusseau, Mark L.

2010-01-01

Isotopic analysis and molecular-based bioassay methods were used in conjunction with geochemical data to assess intrinsic reductive dechlorination processes for a chlorinated-solvent contaminated site in Tucson, Arizona. Groundwater samples were obtained from monitoring wells within a contaminant plume comprising tetrachloroethene and its metabolites trichloroethene, cis-1,2-dichloroethene, vinyl chloride, and ethene, as well as compounds associated with free-phase diesel present at the site. Compound specific isotope (CSI) analysis was performed to characterize biotransformation processes influencing the transport and fate of the chlorinated contaminants. PCR analysis was used to assess the presence of indigenous reductive dechlorinators. The target regions employed were the 16s rRNA gene sequences of Dehalococcoides sp. and Desulfuromonas sp., and DNA sequences of genes pceA, tceA, bvcA, and vcrA, which encode reductive dehalogenases. The results of the analyses indicate that relevant microbial populations are present and that reductive dechlorination is presently occurring at the site. The results further show that potential degrader populations as well as biotransformation activity is non-uniformly distributed within the site. The results of laboratory microcosm studies conducted using groundwater collected from the field site confirmed the reductive dechlorination of tetrachloroethene to dichloroethene. This study illustrates the use of an integrated, multiple-method approach for assessing natural attenuation at a complex chlorinated-solvent contaminated site. PMID:19603638

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

DOE PAGES

Şimşir, Burcu; Yan, Jun; Im, Jeongdae; ...

2017-03-22

Contaminant discharge from fractured bedrock formations remains a remediation challenge. Here, we applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C 1-C 3 chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of knownmore » dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinatedC 1-C 3 alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 10 5 and 5.4 ± 0.9 × 10 6 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.« less

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Şimşir, Burcu; Yan, Jun; Im, Jeongdae

Contaminant discharge from fractured bedrock formations remains a remediation challenge. Here, we applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C 1-C 3 chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of knownmore » dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinatedC 1-C 3 alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 10 5 and 5.4 ± 0.9 × 10 6 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.« less

Strain preservation of experimental animals: vitrification of two-cell stage embryos for multiple mouse strains.

PubMed

Eto, Tomoo; Takahashi, Riichi; Kamisako, Tsutomu

2015-04-01

Strain preservation of experimental animals is crucial for experimental reproducibility. Maintaining complete animal strains, however, is costly and there is a risk for genetic mutations as well as complete loss due to disasters or illness. Therefore, the development of effective vitrification techniques for cryopreservation of multiple experimental animal strains is important. We examined whether a vitrification method using cryoprotectant solutions, P10 and PEPeS, is suitable for preservation of multiple inbred and outbred mouse strains. First, we investigated whether our vitrification method using cryoprotectant solutions was suitable for two-cell stage mouse embryos. In vitro development of embryos exposed to the cryoprotectant solutions was similar to that of fresh controls. Further, the survival rate of the vitrified embryos was extremely high (98.1%). Next, we collected and vitrified two-cell stage embryos of 14 mouse strains. The average number of embryos obtained from one female was 7.3-33.3. The survival rate of vitrified embryos ranged from 92.8% to 99.1%, with no significant differences among mouse strains. In vivo development did not differ significantly between fresh controls and vitrified embryos of each strain. For strain preservation using cryopreserved embryos, two offspring for inbred lines and one offspring for outbred lines must be produced from two-cell stage embryos collected from one female. The expected number of surviving fetuses obtained from embryos collected from one female of either the inbred or outbred strains ranged from 2.9 to 19.5. The findings of the present study indicated that this vitrification method is suitable for strain preservation of multiple mouse strains. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Inflatable device for installing strain gage bridges

NASA Technical Reports Server (NTRS)

Cook, C. E.; Smith, G. E.; Monaghan, R. C. (Inventor)

1983-01-01

Methods and devices for installing in a tubular shaft multiple strain gages are disclosed with focus on a method and a device for pneumatically forcing strain gages into seated engagement with the internal surfaces of a tubular shaft in an installation of multiple strain gages in a tubular shaft. The strain gages or other electron devices are seated in a template-like component which is wrapped about a pneumatically expansible body. The component is inserted into a shaft and the body is pneumatically expanded after a suitable adhesive was applied to the surfaces.

Estimate the contribution of incubation parameters influence egg hatchability using multiple linear regression analysis

PubMed Central

Khalil, Mohamed H.; Shebl, Mostafa K.; Kosba, Mohamed A.; El-Sabrout, Karim; Zaki, Nesma

2016-01-01

Aim: This research was conducted to determine the most affecting parameters on hatchability of indigenous and improved local chickens’ eggs. Materials and Methods: Five parameters were studied (fertility, early and late embryonic mortalities, shape index, egg weight, and egg weight loss) on four strains, namely Fayoumi, Alexandria, Matrouh, and Montazah. Multiple linear regression was performed on the studied parameters to determine the most influencing one on hatchability. Results: The results showed significant differences in commercial and scientific hatchability among strains. Alexandria strain has the highest significant commercial hatchability (80.70%). Regarding the studied strains, highly significant differences in hatching chick weight among strains were observed. Using multiple linear regression analysis, fertility made the greatest percent contribution (71.31%) to hatchability, and the lowest percent contributions were made by shape index and egg weight loss. Conclusion: A prediction of hatchability using multiple regression analysis could be a good tool to improve hatchability percentage in chickens. PMID:27651666

Spatial and temporal dynamics of organohalide-respiring bacteria in a heterogeneous PCE-DNAPL source zone

NASA Astrophysics Data System (ADS)

Cápiro, Natalie L.; Löffler, Frank E.; Pennell, Kurt D.

2015-11-01

Effective treatment of sites contaminated with dense non-aqueous phase liquids (DNAPLs) requires detailed understanding of the microbial community responses to changes in source zone strength and architecture. Changes in the spatial and temporal distributions of the organohalide-respiring Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ) were examined in a heterogeneous tetrachloroethene- (PCE-) DNAPL source zone within a two-dimensional laboratory-scale aquifer flow cell. As part of a combined remedy approach, flushing with 2.3 pore volumes (PVs) of 4% (w/w) solution of the nonionic, biodegradable surfactant Tween® 80 removed 55% of the initial contaminant mass, and resulted in a PCE-DNAPL distribution that contained 51% discrete ganglia and 49% pools (ganglia-to-pool ratio of 1.06). Subsequent bioaugmentation with the PCE-to-ethene-dechlorinating consortium BDI-SZ resulted in cis-1,2-dichloroethene (cis-DCE) formation after 1 PV (ca. 7 days), while vinyl chloride (VC) and ethene were detected 10 PVs after bioaugmentation. Maximum ethene yields (ca. 90 μM) within DNAPL pool and ganglia regions coincided with the detection of the vcrA reductive dehalogenase (RDase) gene that exceeded the Dhc 16S rRNA genes by 2.0 ± 1.3 and 4.0 ± 1.7 fold in the pool and ganglia regions, respectively. Dhc and GeoSZ cell abundance increased by up to 4 orders-of-magnitude after 28 PVs of steady-state operation, with 1 to 2 orders-of-magnitude increases observed in close proximity to residual PCE-DNAPL. These observations suggest the involvement of these dechlorinators the in observed PCE dissolution enhancements of up to 2.3 and 6.0-fold within pool and ganglia regions, respectively. Analysis of the solid and aqueous samples at the conclusion of the experiment revealed that the highest VC (≥ 155 μM) and ethene (≥ 65 μM) concentrations were measured in zones where Dhc and GeoSZ were predominately attached to the solids. These findings demonstrate dynamic responses of organohalide-respiring bacteria in a heterogeneous DNAPL source zone, and emphasize the influence of source zone architecture on bioremediation performance.

Seroprevalence, isolation, and co-infection of multiple Toxoplasma gondii strains in individual bobcats (Lynx rufus) from Mississippi, USA

USDA-ARS?s Scientific Manuscript database

Toxoplasma gondii causes lifelong chronic infection in both feline definitive hosts and intermediate hosts. Multiple exposures of the parasite are likely to occur in nature because of high environmental contamination. Here, we present data of high seroprevalence and multiple T. gondii strain co-infe...

Feeling stretched or compressed? The multiple mechanosensitive responses of wood formation to bending.

PubMed

Roignant, Jeanne; Badel, Éric; Leblanc-Fournier, Nathalie; Brunel-Michac, Nicole; Ruelle, Julien; Moulia, Bruno; Decourteix, Mélanie

2018-05-11

Trees constantly experience wind, perceive resulting mechanical cues, and modify their growth and development accordingly. Previous studies have demonstrated that multiple bending treatments trigger ovalization of the stem and the formation of flexure wood in gymnosperms, but ovalization and flexure wood have rarely been studied in angiosperms, and none of the experiments conducted so far has used multidirectional bending treatments at controlled intensities. Assuming that bending involves tensile and compressive strain, we hypothesized that different local strains may generate specific growth and wood differentiation responses. Basal parts of young poplar stems were subjected to multiple transient controlled unidirectional bending treatments during 8 weeks, which enabled a distinction to be made between the wood formed under tensile or compressive flexural strains. This set-up enabled a local analysis of poplar stem responses to multiple stem bending treatments at growth, anatomical, biochemical and molecular levels. In response to multiple unidirectional bending treatments, poplar stems developed significant cross-sectional ovalization. At the tissue level, some aspects of wood differentiation were similarly modulated in the compressed and stretched zones (vessel frequency and diameter of fibres without a G-layer), whereas other anatomical traits (vessel diameter, G-layer formation, diameter of fibres with a G-layer and microfibril angle) and the expression of fasciclin-encoding genes were differentially modulated in the two zones. This work leads us to propose new terminologies to distinguish the 'flexure wood' produced in response to multiple bidirectional bending treatments from wood produced under transient tensile strain (tensile flexure wood; TFW) or under transient compressive strain (compressive flexure wood; CFW). By highlighting similarities and differences between tension wood and TFW and by demonstrating that plants could have the ability to discriminate positive strains from negative strains, this work provides new insight into the mechanisms of mechanosensitivity in plants.

Safety Evaluation of Enterocin Producer Enterococcus sp. Strains Isolated from Traditional Turkish Cheeses.

PubMed

Avcı, Mine; Özden Tuncer, Banu

2017-07-06

The purpose of this study was to determine the antimicrobial activity and occurrence of bacteriocin structural genes in Enterococcus spp. isolated from different cheeses and also investigate some of their virulence factors. Enterococcus strains were isolated from 33 different cheeses. Enterococcus faecium (6 strains) and Enterococcus faecalis (5 strains) enterocin-producing strains were identified by 16S rDNA analyses. Structural genes entA, entB, entP and entX were detected in some isolates. Multiple enterocin structural genes were found in 7 strains. None of the tested enterococci demonstrated anyβ-haemolytic activity and only one strain had gelatinase activity. Six strains showed multiple antibiotic resistance patterns and in addition, vanA and several virulence genes were detected in many strains. Only E. faecalis MBE1-9 showed tyrosine decarboxylase activity and tdc gene was detected only in this strain.

Biology of Epstein-Barr virus during infectious mononucleosis.

PubMed

Sitki-Green, Diane L; Edwards, Rachel Hood; Covington, Mary M; Raab-Traub, Nancy

2004-02-01

Infectious mononucleosis is the clinical manifestation of primary infection with Epstein-Barr virus (EBV). We monitored primary infection during convalescence and during the establishment of persistent infection. The profiles of EBV strains in the oral cavity and in peripheral blood were determined by use of a heteroduplex tracking assay specific for the EBV gene encoding latent membrane protein 1. Multiple EBV strains were detected in most patients and persisted in and were possibly transmitted among 3 distinct compartments of infection, including the oral cavity, peripheral blood lymphocytes, and the cell-free fraction of the blood plasma. We also tracked transmission of multiple strains from an asymptomatic carrier to a patient diagnosed with primary EBV infection. These data reveal that primary EBV infection is complex, with transmission of multiple strains and clear differences in relative abundance of strains in distinct compartments.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Men, Yujie; Yu, Ke; Bælum, Jacob

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin wasmore » not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCEThe key chloroethene-dechlorinating bacteriumDehalococcoides mccartyiis a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions betweenDehalococcoidesand the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles ofVeillonellaceaespecies in the communities compared to other coexisting community members in producing and providing corrinoids forDehalococcoidesspecies under cobalamin-limited conditions.« less

Pinellas County, Florida Site Environmental Restoration Project Semiannual Progress Report for the 4.5 Acre Site June through November 2016 January 2017

DOE Office of Scientific and Technical Information (OSTI.GOV)

Survochak, Scott; Daniel, Joe

This Pinellas County, Florida, Site Environmental Restoration Project Semiannual Progress Report for the 4.5 Acre Site describes environmental restoration activities for the 4.5 Acre Site located in Pinellas County, Largo, Florida (Figure 1). The former U.S. Department of Energy (DOE) Pinellas Plant facility consisted of the 4.5 Acre Site and what is now the STAR Center (Young - Rainey Science, Technology, and Research Center). Both the 4.5 Acre Site and the STAR Center are part of the overall Pinellas County, Florida, Site (Figure 2). The 4.5 Acre Site is located immediately northwest of the STAR Center, in the northeast quartermore » of Section 13, Township 30 South, Range 15 East. DOE owned this parcel from 1957 to 1972, at which time it was sold to a private landowner. During the period of DOE ownership, the property was used for the disposal of drums of waste resins and solvents. As a result of this practice, the surficial aquifer was impacted by volatile organic compounds (VOCs)—trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), trans-1,2-dichloroethene (tDCE), vinyl chloride (VC), and benzene. Detailed background information for the site is contained in the Long-Term Surveillance and Maintenance Plan for the Pinellas Site (DOE 2016). That document and other site-related documents can be accessed at this website: http://www.lm.doe.gov/Pinellas/Sites.aspx. Recent remediation activities consist of the injection of emulsified soybean oil and the microorganism Dehalococcoides mccartyi (formerly known as Dehalococcoides ethenogenes) into the subsurface in February 2010 and again in July 2013 to enhance contaminant biodegradation (hereafter described as bioinjection). Monitoring the performance of these actions, in the form of monitoring well sampling, is ongoing.« less

Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods

NASA Astrophysics Data System (ADS)

Abe, Yumiko; Aravena, Ramon; Zopfi, Jakob; Parker, Beth; Hunkeler, Daniel

2009-06-01

The occurrence of chlorinated ethene transformation in a streambed was investigated using concentration and carbon isotope data from water samples taken at different locations and depths within a 15 × 25 m study area across which a tetrachloroethene (PCE) plume discharges. Furthermore, it was evaluated how the degree of transformation is related to groundwater discharge rates, redox conditions, solid organic matter content (SOM) and microbial factors. Groundwater discharge rates were quantified based on streambed temperatures, and redox conditions using concentrations of dissolved redox-sensitive species. The degree of chlorinated ethene transformation was highly variable in space from no transformation to transformation beyond ethene. Complete reductive dechlorination to ethane and ethene occurred at locations with at least sulfate-reducing conditions and with a residence time in the samples streambed zone (80 cm depth) of at least 10 days. Among these locations, Dehalococcoides was detected using a PCR method where SOM contents were > 2% w/w and where transformation proceeded beyond ethene. However, it was not detected at locations with low SOM, which may cause an insufficient H 2 supply to sustain a detectably dense Dehalococcoides population. Additionally, it is possible that other organisms are responsible for the biodegradation. A microcosm study with streambed sediments demonstrated the potential of VC oxidation throughout the site even at locations without a pre-exposure to VC, consistent with the detection of the epoxyalkane:coenzyme M transferase (EaCoMT) gene involved in the degradation of chlorinated ethenes via epoxidation. In contrast, no aerobic transformation of cDCE in microcosms over a period of 1.5 years was observed. In summary, the study demonstrated that carbon isotope analysis is a sensitive tool to identify the degree of chlorinated ethene transformation even in hydrologically and geochemically complex streambed systems. In addition, it was observed that the degree of transformation is related to redox conditions, which in turn depend on groundwater discharge rates.

Temporal variations in patterns of Escherichia coli strain diversity and antimicrobial resistance in the migrant Egyptian vulture

PubMed Central

Maherchandani, Sunil; Shringi, B. N.; Kashyap, Sudhir Kumar

2018-01-01

ABSTRACT Aims: Multiple antimicrobial resistance in Escherichia coli of wild vertebrates is a global concern with scarce assessments on the subject from developing countries that have high human-wild species interactions. We studied the ecology of E. coli in a wintering population of Egyptian Vultures in India to understand temporal changes in both E. coli strains and patterns of antimicrobial resistance. Methods and Results: We ribotyped E. coli strains and assessed antimicrobial resistance from wintering vultures at a highly synanthropic carcass dump in north-west India. Both E. coli occurence (90.32%) and resistance to multiple antimicrobials (71.43%) were very high. Clear temporal patterns were apparent. Diversity of strains changed and homogenized at the end of the Vultures’ wintering period, while the resistance pattern showed significantly difference inter-annually, as well as between arrival and departing individuals within a wintering cycle. Significance of study: The carcass dump environment altered both E. coli strains and multiple antimicrobial resistance in migratory Egyptian Vultures within a season. Long-distance migratory species could therefore disseminate resistant E. coli strains across broad geographical scales rendering regional mitigation strategies to control multiple antimicrobial resistance in bacteria ineffective. PMID:29755700

Quantitative assessment of viable cells of Lactobacillus plantarum strains in single, dual and multi-strain biofilms.

PubMed

Fernández Ramírez, Mónica D; Kostopoulos, Ioannis; Smid, Eddy J; Nierop Groot, Masja N; Abee, Tjakko

2017-03-06

Biofilms of Lactobacillus plantarum are a potential source for contamination and recontamination of food products. Although biofilms have been mostly studied using single species or even single strains, it is conceivable that in a range of environmental settings including food processing areas, biofilms are composed of multiple species with each species represented by multiple strains. In this study six spoilage related L. plantarum strains FBR1-FBR6 and the model strain L. plantarum WCFS1 were characterised in single, dual and multiple strain competition models. A quantitative PCR approach was used with added propidium monoazide (PMA) enabling quantification of intact cells in the biofilm, representing the viable cell fraction that determines the food spoilage risk. Our results show that the performance of individual strains in multi-strain cultures generally correlates with their performance in pure culture, and relative strain abundance in multi-strain biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The total biofilm quantified by CV staining of the dual and multi-strain biofilms formed was mainly correlated to CV values of the dominant strain obtained in single strain studies. However, the combination of strain FBR5 and strain WCFS1 showed significantly higher CV values compared to the individual performances of both strains indicating that total biofilm formation was higher in this specific condition. Notably, L. plantarum FBR5 was able to outgrow all other strains and showed the highest relative abundance in dual and multi-strain biofilms. All the dual and multi-strain biofilms contained a considerable number of viable cells, representing a potential source of contamination. Copyright © 2016 Elsevier B.V. All rights reserved.

Cellular mechanisms contributing to multiple stress tolerance in Saccharomyces cerevisiae strains with potential use in high-temperature ethanol fermentation.

PubMed

Kitichantaropas, Yasin; Boonchird, Chuenchit; Sugiyama, Minetaka; Kaneko, Yoshinobu; Harashima, Satoshi; Auesukaree, Choowong

2016-12-01

High-temperature ethanol fermentation has several benefits including a reduction in cooling cost, minimizing risk of bacterial contamination, and enabling simultaneous saccharification and fermentation. To achieve the efficient ethanol fermentation at high temperature, yeast strain that tolerates to not only high temperature but also the other stresses present during fermentation, e.g., ethanol, osmotic, and oxidative stresses, is indispensable. The C3253, C3751, and C4377 Saccharomyces cerevisiae strains, which have been previously isolated as thermotolerant yeasts, were found to be multiple stress-tolerant. In these strains, continuous expression of heat shock protein genes and intracellular trehalose accumulation were induced in response to stresses causing protein denaturation. Compared to the control strains, these multiple stress-tolerant strains displayed low intracellular reactive oxygen species levels and effective cell wall remodeling upon exposures to almost all stresses tested. In response to simultaneous multi-stress mimicking fermentation stress, cell wall remodeling and redox homeostasis seem to be the primary mechanisms required for protection against cell damage. Moreover, these strains showed better performances of ethanol production than the control strains at both optimal and high temperatures, suggesting their potential use in high-temperature ethanol fermentation.

[Molecular-genetic characteristics of Mycobacterium tuberculosis strains isolated from patients with tuberculous spondylitis].

PubMed

Viazovaia, A A; Solov'eva, N S; Zhuravlev, V Iu; Mokrousov, I V; Manicheva, O A; Vishnevskiĭ, B I; Narvskaia, O V

2013-01-01

Molecular-genetic characteristic of M. tuberculosis strains isolated from operation material of patients with tuberculous spondylitis. 107 strains of M. tuberculosis isolated in 2007 - 2011 from patients with spine tuberculosis were studied by methods of spoligotyping and MIRU-VNTR by 12 and 24 loci. Strains of genetic family Beijing dominated (n = 80), 78% of those had multiple drug resistance (MDR). Strains of genetic families T, H3 (Ural), LAM, Manu, H4 and S were also detected. Differentiating of 80 strains of Beijing genotype by MIRU-VNTR method by 24 loci revealed 24 variants (HGI = 0.83) including 7 clusters, the largest of those (100-32) included 23 strains (87% MDR). The leading role of Beijing genotype M. tuberculosis strains in development of tuberculous spondylitis with multiple drug resistance of the causative agent is shown.

Statistical Physics of Vaccine Design

NASA Astrophysics Data System (ADS)

Deem, Michael

2009-03-01

I will define a new parameter to quantify the antigenic distance between two H3N2 influenza strains. I will use this parameter to measure antigenic distance between circulating H3N2 strains and the closest vaccine component of the influenza vaccine. For the data between 1971 and 2004, the measure of antigenic distance correlates better with efficacy in humans of the H3N2 influenza A annual vaccine than do current state of the art measures of antigenic distance such as phylogenetic sequence analysis or ferret antisera inhibition assays. I suggest that this measure of antigenic distance can be used to guide the design of the annual flu vaccine. I will describe combining this measure of antigenic distance with a multiple-strain avian influenza transmission model to study the threat of simultaneous introduction of multiple avian influenza strains. For H3N2 influenza, the model is validated against observed viral fixation rates and epidemic progression rates from the World Health Organization FluNet - Global Influenza Surveillance Network. I find that a multiple-component avian influenza vaccine is helpful to control a simultaneous multiple introduction of bird-flu strains. I introduce Population at Risk (PaR) to quantify the risk of a flu pandemic, and calculate by this metric the improvement that a multiple vaccine offers.

Survival of Serratia marcescens in benzalkonium chloride and in multiple-dose medication vials: relationship to epidemic septic arthritis.

PubMed Central

Nakashima, A K; Highsmith, A K; Martone, W J

1987-01-01

In an epidemic of septic arthritis due to Serratia marcescens, the intra-articular injection of contaminated methylprednisolone may have played a key role. The epidemic strain was found in used multiple-dose vials of methylprednisolone and in a canister of cotton balls soaked in benzalkonium chloride. The cotton balls had been used for antisepsis and disinfection. Growth characteristics of the epidemic strain of S. marcescens were compared with those of control strains of S. marcescens which had been obtained from unrelated nosocomial outbreaks. The epidemic strain was able to survive in 1:100 dilutions of benzalkonium chloride and was able to grow to greater than 10(5) CFU/ml in multiple-dose vials of methylprednisoline; control strains could not be recovered after 24 h in the same solutions. The preservative in methylprednisolone is gamma-myristyl picolinium chloride, a compound chemically related to benzalkonium chloride. We speculate that the epidemic strain of S. marcescens, which was resistant to benzalkonium chloride, had cross-resistance to gamma-myristyl picolinium chloride. If the cotton balls were used to disinfect the tops of the multiple-dose vials of methylprednisolone, small numbers of organisms subsequently introduced into the solution could have grown to high concentrations. PMID:3298309

Normalized Rotational Multiple Yield Surface Framework (NRMYSF) stress-strain curve prediction method based on small strain triaxial test data on undisturbed Auckland residual clay soils

NASA Astrophysics Data System (ADS)

Noor, M. J. Md; Ibrahim, A.; Rahman, A. S. A.

2018-04-01

Small strain triaxial test measurement is considered to be significantly accurate compared to the external strain measurement using conventional method due to systematic errors normally associated with the test. Three submersible miniature linear variable differential transducer (LVDT) mounted on yokes which clamped directly onto the soil sample at equally 120° from the others. The device setup using 0.4 N resolution load cell and 16 bit AD converter was capable of consistently resolving displacement of less than 1µm and measuring axial strains ranging from less than 0.001% to 2.5%. Further analysis of small strain local measurement data was performed using new Normalized Multiple Yield Surface Framework (NRMYSF) method and compared with existing Rotational Multiple Yield Surface Framework (RMYSF) prediction method. The prediction of shear strength based on combined intrinsic curvilinear shear strength envelope using small strain triaxial test data confirmed the significant improvement and reliability of the measurement and analysis methods. Moreover, the NRMYSF method shows an excellent data prediction and significant improvement toward more reliable prediction of soil strength that can reduce the cost and time of experimental laboratory test.

Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

PubMed Central

Schouls, Leo M.; van der Heide, Han G. J.; Vauterin, Luc; Vauterin, Paul; Mooi, Frits R.

2004-01-01

Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected. PMID:15292152

CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains.

PubMed

Woźniak, Michał; Wong, Limsoon; Tiuryn, Jerzy

2011-12-01

A number of inconsistencies in genome annotations are documented among bacterial strains. Visualization of the differences may help biologists to make correct decisions in spurious cases. We have developed a visualization tool, CAMBerVis, to support comparative analysis of multiple bacterial strains. The software manages simultaneous visualization of multiple bacterial genomes, enabling visual analysis focused on genome structure annotations. The CAMBerVis software is freely available at the project website: http://bioputer.mimuw.edu.pl/camber. Input datasets for Mycobacterium tuberculosis and Staphylocacus aureus are integrated with the software as examples. m.wozniak@mimuw.edu.pl Supplementary data are available at Bioinformatics online.

Multiple strains probiotics appear to be the most effective probiotics in the prevention of necrotizing enterocolitis and mortality: An updated meta-analysis.

PubMed

Chang, Hung-Yang; Chen, Jin-Hua; Chang, Jui-Hsing; Lin, Hung-Chih; Lin, Chien-Yu; Peng, Chun-Chih

2017-01-01

Some oral probiotics have been shown to prevent necrotizing enterocolitis (NEC) and decrease mortality effectively in preterm very low birth weight (PVLBW) infants. However, it is unclear whether a single probiotic or a mixture of probiotics is most effective for the prevention of NEC. A meta-analysis was conducted by reviewing the most up to date literature to investigate whether multiple strains probiotics are more effective than a single strain in reducing NEC and death in PVLBW infants. Relevant studies were identified by searches of the MEDLINE, EMBASE, and Cochrane CENTRAL databases, from 2001 to 2016. The inclusion criteria were randomized controlled trials of any enteral probiotic supplementation that was initiated within the first 7 days and continued for at least 14 days in preterm infants (≤ 34 weeks' gestation) and/or those of a birth weight ≤1500 g. A total of 25 trials (n = 7345 infants) were eligible for inclusion in the meta-analysis using a fixed-effects model. Multiple strains probiotics were associated with a marked reduction in the incidence of NEC, with a pooled OR of 0.36 (95% CI, 0.24-0.53; P < .00001). Single strain probiotic using Lactobacillus species had a borderline effect in reducing NEC (OR of 0.60; 95% CI 0.36-1.0; P = .05), but not mortality. Multiple strains probiotics had a greater effectiveness in reducing mortality and were associated with a pooled OR of 0.58 (95% CI, 0.43-0.79; P = .0006). Trials using single strain of Bifidobacterium species and Saccharomyces boulardii did not reveal any beneficial effects in terms of reducing NEC or mortality. This updated report found that multiple strains probiotics appear to be the most feasible and effective strategy for the prevention of NEC and reduction of mortality in PVLBW neonates. Further clinical trials should focus on which probiotic combinations are most effective.

The combination of energy-dependent internal adaptation mechanisms and external factors enables Listeria monocytogenes to express a strong starvation survival response during multiple-nutrient starvation.

PubMed

Lungu, Bwalya; Saldivar, Joshua C; Story, Robert; Ricke, Steven C; Johnson, Michael G

2010-05-01

The goal of this study was to characterize the starvation survival response (SSR) of a wild-type Listeria monocytogenes 10403S and an isogenic DeltasigB mutant strain during multiple-nutrient starvation conditions over 28 days. This study examined the effects of inhibitors of protein synthesis, the proton motive force, substrate level phosphorylation, and oxidative phosphorylation on the SSR of L. monocytogenes 10403S and a DeltasigB mutant during multiple-nutrient starvation. The effects of starvation buffer changes on viability were also examined. During multiple-nutrient starvation, both strains expressed a strong SSR, suggesting that L. monocytogenes possesses SigB-independent mechanism(s) for survival during multiple-nutrient starvation. Neither strain was able to express an SSR following starvation buffer changes, indicating that the nutrients/factors present in the starvation buffer could be a source of energy for cell maintenance and survival. Neither the wild-type nor the DeltasigB mutant strain was able to elicit an SSR when exposed to the protein synthesis inhibitor chloramphenicol within the first 4 h of starvation. However, both strains expressed an SSR when exposed to chloramphenicol after 6 h or more of starvation, suggesting that the majority of proteins required to elicit an effective SSR in L. monocytogenes are likely produced somewhere between 4 and 6 h of starvation. The varying SSRs of both strains to the different metabolic inhibitors under aerobic or anaerobic conditions suggested that (1) energy derived from the proton motive force is important for an effective SSR, (2) L. monocytogenes utilizes an anaerobic electron transport during multiple-nutrient starvation conditions, and (3) the glycolytic pathway is an important energy source during multiple-nutrient starvation when oxygen is available, and less important under anaerobic conditions. Collectively, the data suggest that the combination of energy-dependent internal adaptation mechanisms of cells and external nutrients/factors enables L. monocytogenes to express a strong SSR.

A Modified Double Multiple Nonlinear Regression Constitutive Equation for Modeling and Prediction of High Temperature Flow Behavior of BFe10-1-2 Alloy

NASA Astrophysics Data System (ADS)

Cai, Jun; Wang, Kuaishe; Shi, Jiamin; Wang, Wen; Liu, Yingying

2018-01-01

Constitutive analysis for hot working of BFe10-1-2 alloy was carried out by using experimental stress-strain data from isothermal hot compression tests, in a wide range of temperature of 1,023 1,273 K, and strain rate range of 0.001 10 s-1. A constitutive equation based on modified double multiple nonlinear regression was proposed considering the independent effects of strain, strain rate, temperature and their interrelation. The predicted flow stress data calculated from the developed equation was compared with the experimental data. Correlation coefficient (R), average absolute relative error (AARE) and relative errors were introduced to verify the validity of the developed constitutive equation. Subsequently, a comparative study was made on the capability of strain-compensated Arrhenius-type constitutive model. The results showed that the developed constitutive equation based on modified double multiple nonlinear regression could predict flow stress of BFe10-1-2 alloy with good correlation and generalization.

Theory of multiple quantum dot formation in strained-layer heteroepitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu

2016-07-11

We develop a theory for the experimentally observed formation of multiple quantum dots (QDs) in strained-layer heteroepitaxy based on surface morphological stability analysis of a coherently strained epitaxial thin film on a crystalline substrate. Using a fully nonlinear model of surface morphological evolution that accounts for a wetting potential contribution to the epitaxial film's free energy as well as surface diffusional anisotropy, we demonstrate the formation of multiple QD patterns in self-consistent dynamical simulations of the evolution of the epitaxial film surface perturbed from its planar state. The simulation predictions are supported by weakly nonlinear analysis of the epitaxial filmmore » surface morphological stability. We find that, in addition to the Stranski-Krastanow instability, long-wavelength perturbations from the planar film surface morphology can trigger a nonlinear instability, resulting in the splitting of a single QD into multiple QDs of smaller sizes, and predict the critical wavelength of the film surface perturbation for the onset of the nonlinear tip-splitting instability. The theory provides a fundamental interpretation for the observations of “QD pairs” or “double QDs” and other multiple QDs reported in experimental studies of epitaxial growth of semiconductor strained layers and sets the stage for precise engineering of tunable-size nanoscale surface features in strained-layer heteroepitaxy by exploiting film surface nonlinear, pattern forming phenomena.« less

Multistrain Infections with Lyme Borreliosis Pathogens in the Tick Vector.

PubMed

Durand, Jonas; Herrmann, Coralie; Genné, Dolores; Sarr, Anouk; Gern, Lise; Voordouw, Maarten J

2017-02-01

Mixed or multiple-strain infections are common in vector-borne diseases and have important implications for the epidemiology of these pathogens. Previous studies have mainly focused on interactions between pathogen strains in the vertebrate host, but little is known about what happens in the arthropod vector. Borrelia afzelii and Borrelia garinii are two species of spirochete bacteria that cause Lyme borreliosis in Europe and that share a tick vector, Ixodes ricinus Each of these two tick-borne pathogens consists of multiple strains that are often differentiated using the highly polymorphic ospC gene. For each Borrelia species, we studied the frequencies and abundances of the ospC strains in a wild population of I. ricinus ticks that had been sampled from the same field site over a period of 3 years. We used quantitative PCR (qPCR) and 454 sequencing to estimate the spirochete load and the strain diversity within each tick. For B. afzelii, there was a negative relationship between the two most common ospC strains, suggesting the presence of competitive interactions in the vertebrate host and possibly the tick vector. The flat relationship between total spirochete abundance and strain richness in the nymphal tick indicates that the mean abundance per strain decreases as the number of strains in the tick increases. Strains with the highest spirochete load in the nymphal tick were the most common strains in the tick population. The spirochete abundance in the nymphal tick appears to be an important life history trait that explains why some strains are more common than others in nature. Lyme borreliosis is the most common vector-borne disease in the Northern Hemisphere and is caused by spirochete bacteria that belong to the Borrelia burgdorferi sensu lato species complex. These tick-borne pathogens are transmitted among vertebrate hosts by hard ticks of the genus Ixodes Each Borrelia species can be further subdivided into genetically distinct strains. Multiple-strain infections are common in both the vertebrate host and the tick vector and can result in competitive interactions. To date, few studies on multiple-strain vector-borne pathogens have investigated patterns of cooccurrence and abundance in the arthropod vector. We demonstrate that the abundance of a given strain in the tick vector is negatively affected by the presence of coinfecting strains. In addition, our study suggests that the spirochete abundance in the tick is an important life history trait that can explain why some strains are more common in nature than others. Copyright © 2017 American Society for Microbiology.

Genomic sequence analysis of the Illinois strain of the Agrotis ipsilon multiple nucleopolyhedrovirus

USDA-ARS?s Scientific Manuscript database

The Agrotis ipsilon multiple nucleopolyhedrovirus (AgipMNPV) is a group II nucleopolyhedrovirus (NPV) from the black cutworm, A. ipsilon, with potential as a biopesticide to control infestations of cutworm larvae. The genome of the Illinois strain of AgipMNPV was completely sequenced. The AgipMNPV...

Geographic isolates of Lymantria dispar multiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains

USDA-ARS?s Scientific Manuscript database

Geographic isolates of Lymantria dispar multiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains. To evaluate the genetic diversity of Lymantria dispar nucleopolyhedrovirus (LdMNPV) at the genomic level, the genomes of three isolates of...

Multiple metal resistance in the cyanobacterium Nostoc muscorum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verma, S.K.; Singh, S.P.

1995-04-01

Metal tolerant strains of microbes are likely to originate in habitats having elevated metal levels. This aspect has been reviewed quite extensively by Silvers and Misra and the suggested mechanism of metal tolerance are: (a) cellular exclusion of metals; (b) extrusion of metals; and (c) intracellular immobilization. Similar studies on cyanobacterial strains appear to have been initiated by Shehata and Whitton who isolated a Zn-tolerant strain of Anacystis nidulans displaying a Zn uptake comparable to the Zn-sensitive wild type. The metal tolerance in the above strain was attributed to the intracellular detoxification mechanisms as suggested for Plectonema boryanum and Nostocmore » calcicola. The Cd-resistant strain of A. nidulans showed a protection of Cd-induced growth inhibition due to reduce uptake of metal. Recently we reported an energy- and dilution-dependent efflux of copper as the mechanism of Cu tolerance in a copper-resistant strain of Nostoc calcicola. The above studies were concerned mainly with single-metal resistance in cyanobacteria. Since natural habitats are generally characterized by the coexistence of a large number of toxic and nontoxic cations, it is necessary to study multiple-metal response on the physiology and biochemistry of microorganisms. In the presence study, therefore, we describe a multiple metal resistant strain of the cyanobacterium Nostoc muscorum. 15 refs., 1 fig., 1 tab.« less

Combinatorial Strategies for Improving Multiple-Stress Resistance in Industrially Relevant Escherichia coli Strains

PubMed Central

Herrgård, Markus J.

2014-01-01

High-cell-density fermentation for industrial production of chemicals can impose numerous stresses on cells due to high substrate, product, and by-product concentrations; high osmolarity; reactive oxygen species; and elevated temperatures. There is a need to develop platform strains of industrial microorganisms that are more tolerant toward these typical processing conditions. In this study, the growth of six industrially relevant strains of Escherichia coli was characterized under eight stress conditions representative of fed-batch fermentation, and strains W and BL21(DE3) were selected as platforms for transposon (Tn) mutagenesis due to favorable resistance characteristics. Selection experiments, followed by either targeted or genome-wide next-generation-sequencing-based Tn insertion site determination, were performed to identify mutants with improved growth properties under a subset of three stress conditions and two combinations of individual stresses. A subset of the identified loss-of-function mutants were selected for a combinatorial approach, where strains with combinations of two and three gene deletions were systematically constructed and tested for single and multistress resistance. These approaches allowed identification of (i) strain-background-specific stress resistance phenotypes, (ii) novel gene deletion mutants in E. coli that confer single and multistress resistance in a strain-background-dependent manner, and (iii) synergistic effects of multiple gene deletions that confer improved resistance over single deletions. The results of this study underscore the suboptimality and strain-specific variability of the genetic network regulating growth under stressful conditions and suggest that further exploration of the combinatorial gene deletion space in multiple strain backgrounds is needed for optimizing strains for microbial bioprocessing applications. PMID:25085490

Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.

PubMed

Beres, Stephen B; Richter, Ellen W; Nagiec, Michal J; Sumby, Paul; Porcella, Stephen F; DeLeo, Frank R; Musser, James M

2006-05-02

In recent years we have studied the relationship between strain genotypes and patient phenotypes in group A Streptococcus (GAS), a model human bacterial pathogen that causes extensive morbidity and mortality worldwide. We have concentrated our efforts on serotype M3 organisms because these strains are common causes of pharyngeal and invasive infections, produce unusually severe invasive infections, and can exhibit epidemic behavior. Our studies have been hindered by the lack of genome-scale phylogenies of multiple GAS strains and whole-genome sequences of multiple serotype M3 strains recovered from individuals with defined clinical phenotypes. To remove some of these impediments, we sequenced to closure the genome of four additional GAS strains and conducted comparative genomic resequencing of 12 contemporary serotype M3 strains representing distinct genotypes and phenotypes. Serotype M3 strains are a single phylogenetic lineage. Strains from asymptomatic throat carriers were significantly less virulent for mice than sterile-site isolates and evolved to a less virulent phenotype by multiple genetic pathways. Strain persistence or extinction between epidemics was strongly associated with presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone significantly underrepresented among necrotizing fasciitis cases has a unique frameshift mutation that truncates MtsR, a transcriptional regulator controlling expression of genes encoding iron-acquisition proteins. Expression microarray analysis of this clone confirmed significant alteration in expression of genes encoding iron metabolism proteins. Our analysis provided unprecedented detail about the molecular anatomy of bacterial strain genotype-patient phenotype relationships.

[Development of poliovirus infection in laboratory animals of different species].

PubMed

Koroleva, G A; Lashkevich, V A; Voroshilova, M K

1975-01-01

The capacity of vaccine and virulent strains of poliomyelitis virus to multiply in laboratory animals of different species was studied. Virus reproduction was judged by formation of photoresistant virus progeny in response to inoculation of the animals with photosensitized virus. Multiplication of virulent poliomyelitis virus strains observed in the majority of animal species examined (monkeys, newborn and adult cotton rats, newborn and adult white mice, chickens, chick embryos) resulted in active formation of photoresistant virus population and in some cases was accompanied by clinical symptoms of the disease. Multiplication of vaccine strains was observed in a smaller number of animal species and was limited, as a rule. Among non-primate animals, newborn cotton rats were most susceptible to poliovirus infection. Newborn guinea pigs were the only species of laboratory animals in which no multiplication of any of the six strains under study could be detected.

PULMONARY AND SYSTEMIC EFFECTS OF ZINC-CONTAINING EMISSION PARTICLES IN THREE RAT STRAINS: MULTIPLE EXPOSURE SCENARIOS

EPA Science Inventory

Abstract
Pulmonary and Systemic Effects of Zinc-Containing Emission Particles in Three Rat Strains: Multiple Exposure Scenarios. Kodavanti, U. P., Schladweiler, M. C. J., Ledbetter, A. D., Hauser, R.*, Christiani, D. C.*, McGee, J., Richards, J. R., and Costa, D. L. (2002)....

Evaluation of prestress cable strain in multiple beam configurations.

DOT National Transportation Integrated Search

1996-08-01

A system to measure prestress cable strain was fabricated, software written, and the unit calibrated. Strain measurements were made by attaching four Linear Variable Differential Transformers (LVDT) to prestress cable before they were stressed.

A multiple antibiotic and serum resistant oligotrophic strain, Klebsiella pneumoniae MB45 having novel dfrA30, is sensitive to ZnO QDs

PubMed Central

2011-01-01

Background The aim of this study was to describe a novel trimethoprim resistance gene cassette, designated dfrA30, within a class 1 integron in a facultatively oligotrophic, multiple antibiotic and human serum resistant test strain, MB45, in a population of oligotrophic bacteria isolated from the river Mahananda; and to test the efficiency of surface bound acetate on zinc oxide quantum dots (ZnO QDs) as bactericidal agent on MB45. Methods Diluted Luria broth/Agar (10-3) media was used to cultivate the oligotrophic bacteria from water sample. Multiple antibiotic resistant bacteria were selected by employing replica plate method. A rapid assay was performed to determine the sensitivity/resistance of the test strain to human serum. Variable region of class 1 integron was cloned, sequenced and the expression of gene coding for antibiotic resistance was done in Escherichia coli JM 109. Identity of culture was determined by biochemical phenotyping and 16S rRNA gene sequence analyses. A phylogenetic tree was constructed based on representative trimethoprim resistance-mediating DfrA proteins retrieved from GenBank. Growth kinetic studies for the strain MB45 were performed in presence of varied concentrations of ZnO QDs. Results and conclusions The facultatively oligotrophic strain, MB45, resistant to human serum and ten antibiotics trimethoprim, cotrimoxazole, ampicillin, gentamycin, netilmicin, tobramycin, chloramphenicol, cefotaxime, kanamycin and streptomycin, has been identified as a new strain of Klebsiella pneumoniae. A novel dfr gene, designated as dfrA30, found integrated in class 1 integron was responsible for resistance to trimethoprim in Klebsiella pneumoniae strain MB45. The growth of wild strain MB45 was 100% arrested at 500 mg/L concentration of ZnO QDs. To our knowledge this is the first report on application of ZnO quantum dots to kill multiple antibiotics and serum resistant K. pneumoniae strain. PMID:21595893

Spread of Botrytis cinerea Strains with Multiple Fungicide Resistance in German Horticulture

PubMed Central

Rupp, Sabrina; Weber, Roland W. S.; Rieger, Daniel; Detzel, Peter; Hahn, Matthias

2017-01-01

Botrytis cinerea is a major plant pathogen, causing gray mold rot in a variety of cultures. Repeated fungicide applications are common but have resulted in the development of fungal populations with resistance to one or more fungicides. In this study, we have monitored fungicide resistance frequencies and the occurrence of multiple resistance in Botrytis isolates from raspberries, strawberries, grapes, stone fruits and ornamental flowers in Germany in 2010 to 2015. High frequencies of resistance to all classes of botryticides was common in all cultures, and isolates with multiple fungicide resistance represented a major part of the populations. A monitoring in a raspberry field over six seasons revealed a continuous increase in resistance frequencies and the emergence of multiresistant Botrytis strains. In a cherry orchard and a vineyard, evidence of the immigration of multiresistant strains from the outside was obtained. Inoculation experiments with fungicide-treated leaves in the laboratory and with strawberry plants cultivated in the greenhouse or outdoors revealed a nearly complete loss of fungicide efficacy against multiresistant strains. B. cinerea field strains carrying multiple resistance mutations against all classes of site-specific fungicides were found to show similar fitness as sensitive field strains under laboratory conditions, based on their vegetative growth, reproduction, stress resistance, virulence and competitiveness in mixed infection experiments. Our data indicate an alarming increase in the occurrence of multiresistance in B. cinerea populations from different cultures, which presents a major threat to the chemical control of gray mold. PMID:28096799

Spread of Botrytis cinerea Strains with Multiple Fungicide Resistance in German Horticulture.

PubMed

Rupp, Sabrina; Weber, Roland W S; Rieger, Daniel; Detzel, Peter; Hahn, Matthias

2016-01-01

Botrytis cinerea is a major plant pathogen, causing gray mold rot in a variety of cultures. Repeated fungicide applications are common but have resulted in the development of fungal populations with resistance to one or more fungicides. In this study, we have monitored fungicide resistance frequencies and the occurrence of multiple resistance in Botrytis isolates from raspberries, strawberries, grapes, stone fruits and ornamental flowers in Germany in 2010 to 2015. High frequencies of resistance to all classes of botryticides was common in all cultures, and isolates with multiple fungicide resistance represented a major part of the populations. A monitoring in a raspberry field over six seasons revealed a continuous increase in resistance frequencies and the emergence of multiresistant Botrytis strains. In a cherry orchard and a vineyard, evidence of the immigration of multiresistant strains from the outside was obtained. Inoculation experiments with fungicide-treated leaves in the laboratory and with strawberry plants cultivated in the greenhouse or outdoors revealed a nearly complete loss of fungicide efficacy against multiresistant strains. B. cinerea field strains carrying multiple resistance mutations against all classes of site-specific fungicides were found to show similar fitness as sensitive field strains under laboratory conditions, based on their vegetative growth, reproduction, stress resistance, virulence and competitiveness in mixed infection experiments. Our data indicate an alarming increase in the occurrence of multiresistance in B. cinerea populations from different cultures, which presents a major threat to the chemical control of gray mold.

Algal bioremediation of waste waters from land-based aquaculture using ulva: selecting target species and strains.

PubMed

Lawton, Rebecca J; Mata, Leonardo; de Nys, Rocky; Paul, Nicholas A

2013-01-01

The optimised reduction of dissolved nutrient loads in aquaculture effluents through bioremediation requires selection of appropriate algal species and strains. The objective of the current study was to identify target species and strains from the macroalgal genus Ulva for bioremediation of land-based aquaculture facilities in Eastern Australia. We surveyed land-based aquaculture facilities and natural coastal environments across three geographic locations in Eastern Australia to determine which species of Ulva occur naturally in this region and conducted growth trials at three temperature treatments on a subset of samples from each location to determine whether local strains had superior performance under local environmental conditions. DNA barcoding using the markers ITS and tufA identified six species of Ulva, with U. ohnoi being the most common blade species and U. sp. 3 the most common filamentous species. Both species occurred at multiple land-based aquaculture facilities in Townsville and Brisbane and multiple strains of each species grew well in culture. Specific growth rates of U. ohnoi and U. sp. 3 were high (over 9% and 15% day(-1) respectively) across temperature treatments. Within species, strains of U. ohnoi had higher growth in temperatures corresponding to local conditions, suggesting that strains may be locally adapted. However, across all temperature treatments Townsville strains had the highest growth rates (11.2-20.4% day(-1)) and Sydney strains had the lowest growth rates (2.5-8.3% day(-1)). We also found significant differences in growth between strains of U. ohnoi collected from the same geographic location, highlighting the potential to isolate and cultivate fast growing strains. In contrast, there was no clearly identifiable competitive strain of filamentous Ulva, with multiple species and strains having variable performance. The fast growth rates and broad geographical distribution of U. ohnoi make this an ideal species to target for bioremediation activities at land-based aquaculture facilities in Eastern Australia.

Multiple strains probiotics appear to be the most effective probiotics in the prevention of necrotizing enterocolitis and mortality: An updated meta-analysis

PubMed Central

Chang, Hung-Yang; Chen, Jin-Hua; Chang, Jui-Hsing; Lin, Hung-Chih; Lin, Chien-Yu; Peng, Chun-Chih

2017-01-01

Background Some oral probiotics have been shown to prevent necrotizing enterocolitis (NEC) and decrease mortality effectively in preterm very low birth weight (PVLBW) infants. However, it is unclear whether a single probiotic or a mixture of probiotics is most effective for the prevention of NEC. Objective A meta-analysis was conducted by reviewing the most up to date literature to investigate whether multiple strains probiotics are more effective than a single strain in reducing NEC and death in PVLBW infants. Data sources Relevant studies were identified by searches of the MEDLINE, EMBASE, and Cochrane CENTRAL databases, from 2001 to 2016. Data extraction and synthesis The inclusion criteria were randomized controlled trials of any enteral probiotic supplementation that was initiated within the first 7 days and continued for at least 14 days in preterm infants (≤ 34 weeks’ gestation) and/or those of a birth weight ≤1500 g. Results A total of 25 trials (n = 7345 infants) were eligible for inclusion in the meta-analysis using a fixed-effects model. Multiple strains probiotics were associated with a marked reduction in the incidence of NEC, with a pooled OR of 0.36 (95% CI, 0.24–0.53; P < .00001). Single strain probiotic using Lactobacillus species had a borderline effect in reducing NEC (OR of 0.60; 95% CI 0.36–1.0; P = .05), but not mortality. Multiple strains probiotics had a greater effectiveness in reducing mortality and were associated with a pooled OR of 0.58 (95% CI, 0.43–0.79; P = .0006). Trials using single strain of Bifidobacterium species and Saccharomyces boulardii did not reveal any beneficial effects in terms of reducing NEC or mortality. Conclusion This updated report found that multiple strains probiotics appear to be the most feasible and effective strategy for the prevention of NEC and reduction of mortality in PVLBW neonates. Further clinical trials should focus on which probiotic combinations are most effective. PMID:28182644

A Facile and General Approach to Recoverable High-Strain Multishape Shape Memory Polymers.

PubMed

Li, Xingjian; Pan, Yi; Zheng, Zhaohui; Ding, Xiaobin

2018-03-01

Fabricating a single polymer network with no need to design complex structures to achieve an ideal combination of tunable high-strain multiple-shape memory effects and highly recoverable shape memory property is a great challenge for the real applications of advanced shape memory devices. Here, a facile and general approach to recoverable high-strain multishape shape memory polymers is presented via a random copolymerization of acrylate monomers and a chain-extended multiblock copolymer crosslinker. As-prepared shape memory networks show a large width at the half-peak height of the glass transition, far wider than current classical multishape shape memory polymers. A combination of tunable high-strain multishape memory effect and as high as 1000% recoverable strain in a single chemical-crosslinking network can be obtained. To the best of our knowledge, this is the first thermosetting material with a combination of highly recoverable strain and tunable high-strain multiple-shape memory effects. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities

PubMed Central

Fajardo-Williams, Devyn; Kegerreis, Kylie L.; Parameswaran, Prathap

2016-01-01

ABSTRACT Syntrophic interactions between organohalide-respiring and fermentative microorganisms are critical for effective bioremediation of halogenated compounds. This work investigated the effect of ammonium concentration (up to 4 g liter−1 NH4+-N) on trichloroethene-reducing Dehalococcoides mccartyi and Geobacteraceae in microbial communities fed lactate and methanol. We found that production of ethene by D. mccartyi occurred in mineral medium containing ≤2 g liter−1 NH4+-N and in landfill leachate. For the partial reduction of trichloroethene (TCE) to cis-dichloroethene (cis-DCE) at ≥1 g liter−1 NH4+-N, organohalide-respiring dynamics shifted from D. mccartyi and Geobacteraceae to mainly D. mccartyi. An increasing concentration of ammonium was coupled to lower metabolic rates, longer lag times, and lower gene abundances for all microbial processes studied. The methanol fermentation pathway to acetate and H2 was conserved, regardless of the ammonium concentration provided. However, lactate fermentation shifted from propionic to acetogenic at concentrations of ≥2 g liter−1 NH4+-N. Our study findings strongly support a tolerance of D. mccartyi to high ammonium concentrations, highlighting the feasibility of organohalide respiration in ammonium-contaminated subsurface environments. IMPORTANCE Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium. PMID:27303735

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron.

PubMed

Srinivasa Varadhan, A; Khodadoust, Amid P; Brenner, Richard C

2011-10-01

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2-8.6) and an average hydrogen concentration of 0.75% (range of 0.3-1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.

Characterization of a Defined 2,3,5,6-Tetrachlorobiphenyl-ortho-Dechlorinating Microbial Community by Comparative Sequence Analysis of Genes Coding for 16S rRNA

PubMed Central

Pulliam Holoman, Tracey R.; Elberson, Margaret A.; Cutter, Leah A.; May, Harold D.; Sowers, Kevin R.

1998-01-01

Defined microbial communities were developed by combining selective enrichment with molecular monitoring of total community genes coding for 16S rRNAs (16S rDNAs) to identify potential polychlorinated biphenyl (PCB)-dechlorinating anaerobes that ortho dechlorinate 2,3,5,6-tetrachlorobiphenyl. In enrichment cultures that contained a defined estuarine medium, three fatty acids, and sterile sediment, a Clostridium sp. was predominant in the absence of added PCB, but undescribed species in the δ subgroup of the class Proteobacteria, the low-G+C gram-positive subgroup, the Thermotogales subgroup, and a single species with sequence similarity to the deeply branching species Dehalococcoides ethenogenes were more predominant during active dechlorination of the PCB. Species with high sequence similarities to Methanomicrobiales and Methanosarcinales archaeal subgroups were predominant in both dechlorinating and nondechlorinating enrichment cultures. Deletion of sediment from PCB-dechlorinating enrichment cultures reduced the rate of dechlorination and the diversity of the community. Substitution of sodium acetate for the mixture of three fatty acids increased the rate of dechlorination, further reduced the community diversity, and caused a shift in the predominant species that included restriction fragment length polymorphism patterns not previously detected. Although PCB-dechlorinating cultures were methanogenic, inhibition of methanogenesis and elimination of the archaeal community by addition of bromoethanesulfonic acid only slightly inhibited dechlorination, indicating that the archaea were not required for ortho dechlorination of the congener. Deletion of Clostridium spp. from the community profile by addition of vancomycin only slightly reduced dechlorination. However, addition of sodium molybdate, an inhibitor of sulfate reduction, inhibited dechlorination and deleted selected species from the community profiles of the class Bacteria. With the exception of one 16S rDNA sequence that had the highest sequence similarity to the obligate perchloroethylene-dechlorinating Dehalococcoides, the 16S rDNA sequences associated with PCB ortho dechlorination had high sequence similarities to the δ, low-G+C gram-positive, and Thermotogales subgroups, which all include sulfur-, sulfate-, and/or iron(III)-respiring bacterial species. PMID:9726883

Spatial and temporal dynamics of organohalide-respiring bacteria in a heterogeneous PCE-DNAPL source zone.

PubMed

Cápiro, Natalie L; Löffler, Frank E; Pennell, Kurt D

2015-11-01

Effective treatment of sites contaminated with dense non-aqueous phase liquids (DNAPLs) requires detailed understanding of the microbial community responses to changes in source zone strength and architecture. Changes in the spatial and temporal distributions of the organohalide-respiring Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ) were examined in a heterogeneous tetrachloroethene- (PCE-) DNAPL source zone within a two-dimensional laboratory-scale aquifer flow cell. As part of a combined remedy approach, flushing with 2.3 pore volumes (PVs) of 4% (w/w) solution of the nonionic, biodegradable surfactant Tween® 80 removed 55% of the initial contaminant mass, and resulted in a PCE-DNAPL distribution that contained 51% discrete ganglia and 49% pools (ganglia-to-pool ratio of 1.06). Subsequent bioaugmentation with the PCE-to-ethene-dechlorinating consortium BDI-SZ resulted in cis-1,2-dichloroethene (cis-DCE) formation after 1 PV (ca. 7 days), while vinyl chloride (VC) and ethene were detected 10 PVs after bioaugmentation. Maximum ethene yields (ca. 90 μM) within DNAPL pool and ganglia regions coincided with the detection of the vcrA reductive dehalogenase (RDase) gene that exceeded the Dhc 16S rRNA genes by 2.0±1.3 and 4.0±1.7 fold in the pool and ganglia regions, respectively. Dhc and GeoSZ cell abundance increased by up to 4 orders-of-magnitude after 28 PVs of steady-state operation, with 1 to 2 orders-of-magnitude increases observed in close proximity to residual PCE-DNAPL. These observations suggest the involvement of these dechlorinators the in observed PCE dissolution enhancements of up to 2.3 and 6.0-fold within pool and ganglia regions, respectively. Analysis of the solid and aqueous samples at the conclusion of the experiment revealed that the highest VC (≥155 μM) and ethene (≥65 μM) concentrations were measured in zones where Dhc and GeoSZ were predominately attached to the solids. These findings demonstrate dynamic responses of organohalide-respiring bacteria in a heterogeneous DNAPL source zone, and emphasize the influence of source zone architecture on bioremediation performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiple Epstein-Barr virus strains in patients with infectious mononucleosis: comparison of ex vivo samples with in vitro isolates by use of heteroduplex tracking assays.

PubMed

Tierney, Rosemary J; Edwards, Rachel Hood; Sitki-Green, Diane; Croom-Carter, Deborah; Roy, Sushmita; Yao, Qing-Yun; Raab-Traub, Nancy; Rickinson, Alan B

2006-01-15

Recent work using a heteroduplex tracking assay (HTA) to identify resident viral sequences has suggested that patients with infectious mononucleosis (IM) who are undergoing primary Epstein-Barr virus (EBV) infection frequently harbor different EBV strains. Here, we examine samples from patients with IM by use of a new Epstein-Barr nuclear antigen 2 HTA alongside the established latent membrane protein 1 HTA. Coresident allelic sequences were detected in ex vivo blood and throat wash samples from 13 of 14 patients with IM; most patients carried 2 or more type 1 strains, 1 patient carried 2 type 2 strains, and 1 patient carried both virus types. In contrast, coresident strains were detected in only 2 of 14 patients by in vitro B cell transformation, despite screening >20 isolates/patient. We infer that coacquisition of multiple strains is common in patients with IM, although only 1 strain tends to be rescued in vitro; whether nonrescued strains are present in low abundance or are transformation defective remains to be determined.

Optical Fibers Would Sense Local Strains

NASA Technical Reports Server (NTRS)

Egalon, Claudio O.; Rogowski, Robert S.

1994-01-01

Proposed fiber-optic transducers measure local strains. Includes lead-in and lead-out lengths producing no changes in phase shifts, plus short sensing length in which phase shift is sensitive to strain. Phase shifts in single-mode fibers vary with strains. In alternative version, multiple portions of optical fiber sensitive to strains characteristic of specific vibrational mode of object. Same principle also used with two-mode fiber.

A comparison of the adaptations of strains of Lymantria dispar multiple nucleopolyhedrovirus to hosts from spatially isolated populations

Treesearch

V.V. Martemyanov; J.D. Podgwaite; I.A. Belousova; S.V. Pavlushin; J.M. Slavicek; O.A. Baturina; M.R. Kabilov; A.V. Ilyinykh

2017-01-01

The adaptation of pathogens to either their hosts or to environmental conditions is the focus of many current ecological studies. In this work we compared the ability of six spatially-distant Lymantria dispar (gypsy moth) multiple nucleopolyhedrovirus (LdMNPV) strains (three from eastern North America and three from central Asia) to induce acute...

A prospective follow-up of Epstein-Barr virus LMP1 genotypes in saliva and blood during infectious mononucleosis.

PubMed

Fafi-Kremer, Samira; Morand, Patrice; Germi, Raphaele; Ballout, Mirvat; Brion, Jean-Paul; Genoulaz, Odile; Nicod, Sandrine; Stahl, Jean-Paul; Ruigrok, Rob W H; Seigneurin, Jean-Marie

2005-12-15

To monitor multiple Epstein-Barr virus (EBV) infections during the early and convalescent stages of infectious mononucleosis (IM), a cloning and sequencing study of the LMP1 gene was conducted in saliva and peripheral blood mononuclear cells (PBMCs) from 23 patients with IM at day 0 (D0) and day 180 (D180) after the onset of the disease. Multiple EBV strains were detected in 9 (39%) of the patients during follow-up, with 7 of 9 cases detected as early as D0. Six of the nine patients harbored the same dominant strain in saliva and PBMCs during follow-up, with a trend toward a restriction of the number of EBV strains in saliva but not in PBMCs at D180. Furthermore, transmission of a minor strain was observed between partners in a heterosexual couple. There was no correlation between multiple infections and EBV DNA load in either compartment.

Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis

PubMed Central

Igawa, Takeshi; Watanabe, Ai; Suzuki, Atsushi; Kashiwagi, Akihiko; Kashiwagi, Keiko; Noble, Anna; Guille, Matt; Simpson, David E.; Horb, Marko E.; Fujii, Tamotsu; Sumida, Masayuki

2015-01-01

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts. PMID:26222540

Clinical and Molecular Characteristics of Human Rotavirus G8P[8] Outbreak Strain, Japan, 2014.

PubMed

Kondo, Kenji; Tsugawa, Takeshi; Ono, Mayumi; Ohara, Toshio; Fujibayashi, Shinsuke; Tahara, Yasuo; Kubo, Noriaki; Nakata, Shuji; Higashidate, Yoshihito; Fujii, Yoshiki; Katayama, Kazuhiko; Yoto, Yuko; Tsutsumi, Hiroyuki

2017-06-01

During March-July 2014, rotavirus G8P[8] emerged as the predominant cause of rotavirus gastroenteritis among children in Hokkaido Prefecture, Japan. Clinical characteristics were similar for infections caused by G8 and non-G8 strains. Sequence and phylogenetic analyses suggest the strains were generated by multiple reassortment events between DS-1-like P[8] strains and bovine strains from Asia.

Comparison of the Live Attenuated Yellow Fever Vaccine 17D-204 Strain to Its Virulent Parental Strain Asibi by Deep Sequencing

PubMed Central

Beck, Andrew; Tesh, Robert B.; Wood, Thomas G.; Widen, Steven G.; Ryman, Kate D.; Barrett, Alan D. T.

2014-01-01

Background. The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. Methods. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Results. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Conclusions. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence. PMID:24141982

Improved Displacement Transfer Functions for Structure Deformed Shape Predictions Using Discretely Distributed Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2012-01-01

In the formulations of earlier Displacement Transfer Functions for structure shape predictions, the surface strain distributions, along a strain-sensing line, were represented with piecewise linear functions. To improve the shape-prediction accuracies, Improved Displacement Transfer Functions were formulated using piecewise nonlinear strain representations. Through discretization of an embedded beam (depth-wise cross section of a structure along a strain-sensing line) into multiple small domains, piecewise nonlinear functions were used to describe the surface strain distributions along the discretized embedded beam. Such piecewise approach enabled the piecewise integrations of the embedded beam curvature equations to yield slope and deflection equations in recursive forms. The resulting Improved Displacement Transfer Functions, written in summation forms, were expressed in terms of beam geometrical parameters and surface strains along the strain-sensing line. By feeding the surface strains into the Improved Displacement Transfer Functions, structural deflections could be calculated at multiple points for mapping out the overall structural deformed shapes for visual display. The shape-prediction accuracies of the Improved Displacement Transfer Functions were then examined in view of finite-element-calculated deflections using different tapered cantilever tubular beams. It was found that by using the piecewise nonlinear strain representations, the shape-prediction accuracies could be greatly improved, especially for highly-tapered cantilever tubular beams.

Comparison of the live attenuated yellow fever vaccine 17D-204 strain to its virulent parental strain Asibi by deep sequencing.

PubMed

Beck, Andrew; Tesh, Robert B; Wood, Thomas G; Widen, Steven G; Ryman, Kate D; Barrett, Alan D T

2014-02-01

The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence.

Interfacial relaxation analysis of InGaAs/GaAsP strain-compensated multiple quantum wells and its optical property

NASA Astrophysics Data System (ADS)

Dong, Hailiang; Sun, Jing; Ma, Shufang; Liang, Jian; Jia, Zhigang; Liu, Xuguang; Xu, Bingshe

2018-02-01

InGaAs/GaAsP strain-compensated multiple quantum wells were prepared by metal organic chemical vapor deposition on GaAs (100) substrates with misorientation of 15° toward [111]. In order to obtain better strain-compensated abrupt heterojunction interfaces, the compressive strain and relaxation of different quantum well and the total accumulated strain were investigated by adjusting In composition and the thickness of InxGa1-xAs well and GaAs1-yPy barrier keep constant. High resolution X-ray diffraction results indicate the crystal and interfacial structures of In0.18Ga0.82As (7 nm)/GaAs1-yPy with the least relaxation and total strain mismatch are better than others. From in-situ surface reflectivity curves, we observed the slope of reflectivity curve of multiple quantum wells increases with increasing lattice relaxation. Atomic force microscopic results show surface morphologies of three samples are Volmer-Weber mode. Indium segregation at heterointerface between well and barrier were investigated by secondary ion mass spectrometry which indicate indium diffusion width increase with the increasing total strain mismatch. Finally, a shoulder peak was observed from Gaussian fitting of photoluminescence, stemming from the lattice relaxation. These results demonstrate that the relaxation process is introduced and indium segregation length widens as the relaxation increases. The experimental results will be favorable for optimizing the epitaxial growth of InGaAs/GaAsP strain-compensated quantum wells in order to obtain high quality smooth heterointerface.

Metabolomic analysis reveals key metabolites related to the rapid adaptation of Saccharomyce cerevisiae to multiple inhibitors of furfural, acetic acid, and phenol.

PubMed

Wang, Xin; Li, Bing-Zhi; Ding, Ming-Zhu; Zhang, Wei-Wen; Yuan, Ying-Jin

2013-03-01

During hydrolysis of lignocellulosic biomass, a broad range of inhibitors are generated, which interfere with yeast growth and bioethanol production. In order to improve the strain tolerance to multiple inhibitors--acetic acid, furfural, and phenol (three representative lignocellulose-derived inhibitors) and uncover the underlying tolerant mechanism, an adaptation experiment was performed in which the industrial Saccharomyces cerevisiae was cultivated repeatedly in a medium containing multiple inhibitors. The adaptation occurred quickly, accompanied with distinct increase in growth rate, glucose utilization rate, furfural metabolism rate, and ethanol yield, only after the first transfer. A similar rapid adaptation was also observed for the lab strains of BY4742 and BY4743. The metabolomic analysis was employed to investigate the responses of the industrial S. cereviaise to three inhibitors during the adaptation. The results showed that higher levels of 2-furoic acid, 2, 3-butanediol, intermediates in glycolytic pathway, and amino acids derived from glycolysis, were discovered in the adapted strains, suggesting that enhanced metabolic activity in these pathways may relate to resistance against inhibitors. Additionally, through single-gene knockouts, several genes related to alanine metabolism, GABA shunt, and glycerol metabolism were verified to be crucial for the resistance to multiple inhibitors. This study provides new insights into the tolerance mechanism against multiple inhibitors, and guides for the improvement of tolerant ethanologenic yeast strains for lignocellulose-bioethanol fermentation.

Mathematical analysis of a multiple strain, multi-locus-allele system for antigenically variable infectious diseases revisited.

PubMed

Cherif, Alhaji

2015-09-01

Many important pathogens such as HIV/AIDS, influenza, malaria, dengue and meningitis generally exist in phenotypically distinct serotypes that compete for hosts. Models used to study these diseases appear as meta-population systems. Herein, we revisit one of the multiple strain models that have been used to investigate the dynamics of infectious diseases with co-circulating serotypes or strains, and provide analytical results underlying the numerical investigations. In particular, we establish the necessary conditions for the local asymptotic stability of the steady states and for the existence of oscillatory behaviors via Hopf bifurcation. In addition, we show that the existence of discrete antigenic forms among pathogens can either fully or partially self-organize, where (i) strains exhibit no strain structures and coexist or (ii) antigenic variants sort into non-overlapping or minimally overlapping clusters that either undergo the principle of competitive exclusion exhibiting discrete strain structures, or co-exist cyclically. Copyright © 2015. Published by Elsevier Inc.

Amplification of a Gene Related to Mammalian mdr Genes in Drug-Resistant Plasmodium falciparum

NASA Astrophysics Data System (ADS)

Wilson, Craig M.; Serrano, Adelfa E.; Wasley, Annemarie; Bogenschutz, Michael P.; Shankar, Anuraj H.; Wirth, Dyann F.

1989-06-01

The malaria parasite Plasmodium falciparum contains at least two genes related to the mammalian multiple drug resistance genes, and at least one of the P. falciparum genes is expressed at a higher level and is present in higher copy number in a strain that is resistant to multiple drugs than in a strain that is sensitive to the drugs.

Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium

PubMed Central

Lee, Gun Woong; Lee, Kui-Jae

2012-01-01

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and plant growth promotion. PMID:22815460

Potato virus Y transmission efficiency from different potato cultivars infected with single or multiple virus strains

USDA-ARS?s Scientific Manuscript database

There has been a shift in the prevalence of Potato virus Y (PVY) strains affecting the U.S. potato crop in recent years. The incidence of the ordinary strain, PVYO, is now significantly less than the emerging recombinant strains, e.g. PVYNTN, PVYN:O/NWi. It is not uncommon to find several PVY strai...

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.

PubMed

Herath, Damayanthi; Tang, Sen-Lin; Tandon, Kshitij; Ackland, David; Halgamuge, Saman Kumara

2017-12-28

In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains. Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome. The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.

Clinical and Molecular Characteristics of Human Rotavirus G8P[8] Outbreak Strain, Japan, 2014

PubMed Central

Kondo, Kenji; Ono, Mayumi; Ohara, Toshio; Fujibayashi, Shinsuke; Tahara, Yasuo; Kubo, Noriaki; Nakata, Shuji; Higashidate, Yoshihito; Fujii, Yoshiki; Katayama, Kazuhiko; Yoto, Yuko; Tsutsumi, Hiroyuki

2017-01-01

During March–July 2014, rotavirus G8P[8] emerged as the predominant cause of rotavirus gastroenteritis among children in Hokkaido Prefecture, Japan. Clinical characteristics were similar for infections caused by G8 and non-G8 strains. Sequence and phylogenetic analyses suggest the strains were generated by multiple reassortment events between DS-1–like P[8] strains and bovine strains from Asia. PMID:28518031

Metastable coexistence of multiple genotypes in a constant environment with a single resource through fixed settings of a multiplication-survival trade-off.

PubMed

Maharjan, Ram; Ferenci, Thomas

2016-04-01

The biological complexity of trade-offs has been a major obstacle in understanding bacterial diversity and coexistence. Here we reduce the biological complexity by using isogenic Escherichia coli strains differing only in a multiplication-survival trade-off regulated by RpoS. The contribution of trade-off characteristics to fitness in different environments was determined. We then designed an environment with intermediate-stress levels that elicits an equivalent fitness. We found metastable coexistence of three strains in steady-state chemostats until mutations changed the relative fitness of competing strains. Our results help explain the rich intra- and inter-species diversity of bacteria through alternative settings of relatively few trade-offs. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Anaplasma marginale superinfection attributable to pathogen strains with distinct genomic backgrounds.

USDA-ARS?s Scientific Manuscript database

Microbial strain structure is dynamic over space and time; shifts in pathogen strain structure result in changing patterns of disease. The scale of change in space and time differs markedly among pathogens depending on multiple factors including pathogen-specific mechanisms of genetic change and the...

Moire strain analysis of paper

Treesearch

R. E. Rowlands; P. K. Beasley; D. E. Gunderson

1983-01-01

Efficient use of paper products involves using modern aspects of materials science and engineering mechanics. This implies the ability to determine simultaneously different components of strain at multiple locations and under static or dynamic conditions. Although measuring strains in paper has been a topic of interest for over 40 years, present capability remains...

Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species.

PubMed

de Barros Lopes, Miguel; Bellon, Jennifer R; Shirley, Neil J; Ganter, Philip F

2002-01-01

Fluorescent amplified fragment length polymorphism analysis demonstrates a high level of gene exchange between Saccharomyces sensu stricto species, with some strains having undergone multiple interspecific hybridization events with subsequent changes in genome complexity. Two lager strains were shown to be hybrids between Saccharomyces cerevisiae and the alloploid species Saccharomyces pastorianus. The genome structure of CBS 380(T), the type strain of Saccharomyces bayanus, is also consistent with S. pastorianus gene transfer. The results indicate that the cider yeast, CID1, possesses nuclear DNA from three separate species. Mating experiments show that there are no barriers to interspecific conjugation of haploid cells. Furthermore, the allopolyploid strains were able to undergo further hybridizations with other Saccharomyces sensu stricto yeasts. These results demonstrate that introgression between the Saccharomyces sensu stricto species is likely.

Survival and multiplication of Vibrio cholerae in the upper bowel of infant mice.

PubMed

Baselski, V S; Medina, R A; Parker, C D

1978-11-01

The survival and multiplication of Vibrio cholerae strains of varying virulence in the upper bowel of orally challenged infant mice early in infection has been examined. Analysis of changes in the apparent specific activity (counts per minute per colony-forming unit) of the cell population after 4 h compared with the inoculum indicated that strain CA401 established a viable, multiplying cell population, whereas strains VB12 (a rough variant) and 569B were subject to host bactericidal and bacteriolytic mechanisms. An analysis of parameters which may affect the specific activity is included. We have defined the infective potential of the strains in terms of the changes in specific activity. The relative infective potentials are CA401 greater than 569B greater than VB12.

Survival and multiplication of Vibrio cholerae in the upper bowel of infant mice.

PubMed Central

Baselski, V S; Medina, R A; Parker, C D

1978-01-01

The survival and multiplication of Vibrio cholerae strains of varying virulence in the upper bowel of orally challenged infant mice early in infection has been examined. Analysis of changes in the apparent specific activity (counts per minute per colony-forming unit) of the cell population after 4 h compared with the inoculum indicated that strain CA401 established a viable, multiplying cell population, whereas strains VB12 (a rough variant) and 569B were subject to host bactericidal and bacteriolytic mechanisms. An analysis of parameters which may affect the specific activity is included. We have defined the infective potential of the strains in terms of the changes in specific activity. The relative infective potentials are CA401 greater than 569B greater than VB12. PMID:730364

Isolation and genotyping of Toxoplasma gondii from Ugandan chickens reveals frequent multiple infections.

PubMed

Lindström, I; Sundar, N; Lindh, J; Kironde, F; Kabasa, J D; Kwok, O C H; Dubey, J P; Smith, J E

2008-01-01

The genetic make-up of an infecting Toxoplasma gondii strain may be important for the outcome of infection and the risk of reactivation of chronic disease. In order to survey the distribution of different genotypes within an area, free-range chickens act as a good model species. In this study 85 chickens were used to investigate the prevalence, genotype and mouse virulence of T. gondii in Kampala, Uganda. Antibodies were detected in 40 chickens, of which 20 had MAT-titres of 1:20 or higher and were also positive by PCR. Genotyping of 5 loci (SAG1, SAG2, SAG3, BTUB and GRA6) showed that 6 strains belonged to genotype I, 8 to Type II and 1 to Type III. Five chickens had multiple infections; 3 individuals with Type I plus Type II and a further 2 harbouring Types I, II and III. Isolates were obtained from 9 chickens via bioassay in mice, 6 were Type II strains and 3 were from animals with mixed infection. This is the first set of African T. gondii strains to be genotyped at multiple loci and in addition to the 3 predominant lineages we found a small number of new polymorphisms and a high frequency of multiple infections.

Molecular characterization of enterohemorrhagic Escherichia coli O157:H7 isolates dispersed across Japan by pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analysis.

PubMed

Pei, Yingxin; Terajima, Jun; Saito, Yasunori; Suzuki, Reiko; Takai, Nobuko; Izumiya, Hidemasa; Morita-Ishihara, Tomoko; Ohnishi, Makoto; Miura, Masashi; Iyoda, Sunao; Mitobe, Jiro; Wang, Binyou; Watanabe, Haruo

2008-01-01

We identified seven distinct subtypes of enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates that were derived from sporadic cases and outbreaks from multiple prefectures in Japan in 2005. A surveillance system utilizing pulsed-field gel electrophoresis (PFGE), PulseNet Japan, was used. Some strains showed indistinguishable PFGE patterns using another restriction enzyme (BlnI or SpeI) in each subtype of EHEC O157:H7 isolates that were routinely subtyped by the XbaI PFGE pattern. In order to examine the genotypic relatedness of these strains, we carried out a multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). By using the MLVA system, we found that three of seven subtypes of EHEC O157:H7 strains that were isolated from sporadic cases dispersed across multiple prefectures within a few months showed indistinguishable PFGE patterns and identical MLVA types. Strains belonging to the other four subtypes of EHEC O157:H7 in the PFGE analysis were further classified into different clusters of EHEC O157:H7. Therefore, compared to PFGE, MLVA showed greater discriminatory power with respect to analysis of the isolates in this study.

Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome reassortment events between human, bovine, caprine and porcine strains.

PubMed

Bwogi, Josephine; Jere, Khuzwayo C; Karamagi, Charles; Byarugaba, Denis K; Namuwulya, Prossy; Baliraine, Frederick N; Desselberger, Ulrich; Iturriza-Gomara, Miren

2017-01-01

Rotaviruses of species A (RVA) are a common cause of diarrhoea in children and the young of various other mammals and birds worldwide. To investigate possible interspecies transmission of RVAs, whole genomes of 18 human and 6 domestic animal RVA strains identified in Uganda between 2012 and 2014 were sequenced using the Illumina HiSeq platform. The backbone of the human RVA strains had either a Wa- or a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin. All eleven genes of one bovine RVA strain were closely related to those of human RVAs. One caprine strain had a mixed genotype backbone, suggesting that it emerged from multiple reassortment events involving different host species. The porcine RVA strains had mixed genotype backbones with possible multiple reassortant events with strains of human and bovine origin.Overall, whole genome characterisation of rotaviruses found in domestic animals in Uganda strongly suggested the presence of human-to animal RVA transmission, with concomitant circulation of multi-reassortant strains potentially derived from complex interspecies transmission events. However, whole genome data from the human RVA strains causing moderate and severe diarrhoea in under-fives in Uganda indicated that they were primarily transmitted from person-to-person.

Core neuropathological abnormalities in progranulin-deficient mice are penetrant on multiple genetic backgrounds.

PubMed

Petkau, T L; Hill, A; Leavitt, B R

2016-02-19

Loss-of-function mutations in the progranulin gene (GRN) are a common cause of familial frontotemporal lobar degeneration (FTLD). A high degree of heterogeneity in the age-of-onset, duration of disease, and clinical presentation of FTLD, even among families carrying the same GRN mutation, suggests that additional modifying genes may be important to pathogenesis. Progranulin-knockout mice display subtle behavioral abnormalities and progressive neuropathological changes, as well as altered dendritic morphology and synaptic deficits in the hippocampus. In this study we evaluated multiple neuropathological endpoints in aged progranulin knockout mice and their wild-type littermates on two different genetic backgrounds: C57Bl/6 and 129/SvImJ. We find that in most brain regions, both strains are susceptible to progranulin-mediated neuropathological phenotypes, including astrogliosis, microgliosis, and highly accelerated deposition of the aging pigment lipofuscin. Neuroinflammation due to progranulin deficiency is exaggerated in the B6 strain and present, but less pronounced, in the 129 strain. Differences between the strains in hippocampal neuron counts and neuronal morphology suggest a complex role for progranulin in the hippocampus. We conclude that core progranulin-mediated neurodegenerative phenotypes are penetrant on multiple inbred mouse strains, but that genetic background modulates progranulin's role in neuroinflammation and hippocampal biology. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

Molecular Characterization of a Dechlorinating Community Resulting from In Situ Biostimulation in a Trichloroethene-Contaminated Deep, Fractured Basalt Aquifer and Comparison to a Derivative Laboratory Culture

PubMed Central

Macbeth, Tamzen W.; Cummings, David E.; Spring, Stefan; Petzke, Lynn M.; Sorenson, Kent S.

2004-01-01

Sodium lactate additions to a trichloroethene (TCE) residual source area in deep, fractured basalt at a U.S. Department of Energy site have resulted in the enrichment of the indigenous microbial community, the complete dechlorination of nearly all aqueous-phase TCE to ethene, and the continued depletion of the residual source since 1999. The bacterial and archaeal consortia in groundwater obtained from the residual source were assessed by using PCR-amplified 16S rRNA genes. A clone library of bacterial amplicons was predominated by those from members of the class Clostridia (57 of 93 clones), of which a phylotype most similar to that of the homoacetogen Acetobacterium sp. strain HAAP-1 was most abundant (32 of 93 clones). The remaining Bacteria consisted of phylotypes affiliated with Sphingobacteria, Bacteroides, Spirochaetes, Mollicutes, and Proteobacteria and candidate divisions OP11 and OP3. The two proteobacterial phylotypes were most similar to those of the known dechlorinators Trichlorobacter thiogenes and Sulfurospirillum multivorans. Although not represented by the bacterial clones generated with broad-specificity bacterial primers, a Dehalococcoides-like phylotype was identified with genus-specific primers. Only four distinct phylotypes were detected in the groundwater archaeal library, including predominantly a clone affiliated with the strictly acetoclastic methanogen Methanosaeta concilii (24 of 43 clones). A mixed culture that completely dechlorinates TCE to ethene was enriched from this groundwater, and both communities were characterized by terminal restriction fragment length polymorphism (T-RFLP). According to T-RFLP, the laboratory enrichment community was less diverse overall than the groundwater community, with 22 unique phylotypes as opposed to 43 and a higher percentage of Clostridia, including the Acetobacterium population. Bioreactor archaeal structure was very similar to that of the groundwater community, suggesting that methane is generated primarily via the acetoclastic pathway, using acetate generated by lactate fermentation and acetogenesis in both systems. PMID:15574933

Transcriptome profiles of chicken intestinal intraepithelial lymphocytes altered by the intake of a multi-strain direct-fed microbials

USDA-ARS?s Scientific Manuscript database

The current study was conducted to investigate the effects of the direct-fed microbials (DFM) including three Bacillus subtilis strains on the modulation of transcriptional profile in chicken intestinal intraepithelial lymphocytes (IEL). The multiple-strain DFM product modified 453 probes from 1,98...

Differences in multiplication of virulent and vaccine strains of poliovirus type I, II, and III in laboratory animals.

PubMed

Koroleva, G A; Lashkevich, V A; Voroshilova, M K

1977-01-01

Multiplication of virulent and vaccine strains of poliovirus type I, II and III in laboratory animals of different species was studied comparatively. The main criterion of virus reproduction was the production of the photoresistant virus progeny after inoculation of the animals with proflavin-photosensitized virus strains. On the whole, virulent poliovirus strains were characterized by replication in a wide range of hosts (monkeys, cotton rats, white mice, guinea pigs, rabbits, chickens, chick embryos), a low infective dose, production of the photoresistant progeny to a high titre, clinically overt disease in some animal species. The vaccine strains multiplied in a norrower range of hosts, had a high infective dose, a low titre of virus progeny, and caused no clinical symptoms of infection. These differences may serve as a marker for differentiation between virulent and attenuated strains in vivo. Administration of guanidine before inoculation of newborn cotton rats completely prevented or delayed by several days the production of photoresistant virus progeny. This fact confirms the stability of the proflavin-poliovirus complex under conditions ruling out virus replication.

A Single Streptomyces Symbiont Makes Multiple Antifungals to Support the Fungus Farming Ant Acromyrmex octospinosus

PubMed Central

Seipke, Ryan F.; Barke, Jörg; Brearley, Charles; Hill, Lionel; Yu, Douglas W.; Goss, Rebecca J. M.; Hutchings, Matthew I.

2011-01-01

Attine ants are dependent on a cultivated fungus for food and use antibiotics produced by symbiotic Actinobacteria as weedkillers in their fungus gardens. Actinobacterial species belonging to the genera Pseudonocardia, Streptomyces and Amycolatopsis have been isolated from attine ant nests and shown to confer protection against a range of microfungal weeds. In previous work on the higher attine Acromyrmex octospinosus we isolated a Streptomyces strain that produces candicidin, consistent with another report that attine ants use Streptomyces-produced candicidin in their fungiculture. Here we report the genome analysis of this Streptomyces strain and identify multiple antibiotic biosynthetic pathways. We demonstrate, using gene disruptions and mass spectrometry, that this single strain has the capacity to make candicidin and multiple antimycin compounds. Although antimycins have been known for >60 years we report the sequence of the biosynthetic gene cluster for the first time. Crucially, disrupting the candicidin and antimycin gene clusters in the same strain had no effect on bioactivity against a co-evolved nest pathogen called Escovopsis that has been identified in ∼30% of attine ant nests. Since the Streptomyces strain has strong bioactivity against Escovopsis we conclude that it must make additional antifungal(s) to inhibit Escovopsis. However, candicidin and antimycins likely offer protection against other microfungal weeds that infect the attine fungal gardens. Thus, we propose that the selection of this biosynthetically prolific strain from the natural environment provides A. octospinosus with broad spectrum activity against Escovopsis and other microfungal weeds. PMID:21857911

Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli.

PubMed

Iguchi, Atsushi; Shirai, Hiroki; Seto, Kazuko; Ooka, Tadasuke; Ogura, Yoshitoshi; Hayashi, Tetsuya; Osawa, Kayo; Osawa, Ro

2011-01-01

Most Escherichia coli O157-serogroup strains are classified as enterohemorrhagic E. coli (EHEC), which is known as an important food-borne pathogen for humans. They usually produce Shiga toxin (Stx) 1 and/or Stx2, and express H7-flagella antigen (or nonmotile). However, O157 strains that do not produce Stxs and express H antigens different from H7 are sometimes isolated from clinical and other sources. Multilocus sequence analysis revealed that these 21 O157:non-H7 strains tested in this study belong to multiple evolutionary lineages different from that of EHEC O157:H7 strains, suggesting a wide distribution of the gene set encoding the O157-antigen biosynthesis in multiple lineages. To gain insight into the gene organization and the sequence similarity of the O157-antigen biosynthesis gene clusters, we conducted genomic comparisons of the chromosomal regions (about 59 kb in each strain) covering the O-antigen gene cluster and its flanking regions between six O157:H7/non-H7 strains. Gene organization of the O157-antigen gene cluster was identical among O157:H7/non-H7 strains, but was divided into two distinct types at the nucleotide sequence level. Interestingly, distribution of the two types did not clearly follow the evolutionary lineages of the strains, suggesting that horizontal gene transfer of both types of O157-antigen gene clusters has occurred independently among E. coli strains. Additionally, detailed sequence comparison revealed that some positions of the repetitive extragenic palindromic (REP) sequences in the regions flanking the O-antigen gene clusters were coincident with possible recombination points. From these results, we conclude that the horizontal transfer of the O157-antigen gene clusters induced the emergence of multiple O157 lineages within E. coli and speculate that REP sequences may involve one of the driving forces for exchange and evolution of O-antigen loci.

Genetic Analysis of Hepatitis A Virus Strains That Induced Epidemics in Korea during 2007–2009

PubMed Central

Lee, Hyeokjin; Jeong, Hyesook; Yun, Heasun; Kim, Kisang; Kim, Jong-Hyun; Yang, Jai Myung

2012-01-01

Hepatitis A virus is one of the most prominent causes of fecally transmitted acute hepatitis worldwide. In order to characterize the viral agents causing an outbreak in Korea (comprising North and South Korea) from June 2007 to May 2009, we collected specimens and performed genotyping of the VP1/P2A and VP3/VP1 regions of hepatitis A virus. We then used a multiple-alignment algorithm to compare the nucleotide sequences of the 2 regions with those of reference strains. Hepatitis A virus antibodies were detected in 64 patients from 5 reported outbreaks (North Korea, June 2007 [n = 11]; Jeonnam, April 2008 [n = 15]; Daegu, May 2008 [n = 13]; Seoul, May 2009 [n = 22]; and Incheon, May 2009 [n = 3]). We found 100% homology between strains isolated from the Kaesong Industrial Region and Jeonnam. While those strains were classified as genotype IA strains, strains from Seoul and Incheon were identified as genotype IIIA strains and showed 98.9 to 100% homology. Genotype IIIA was also dominant in Daegu, where strains were 95.7 to 100% homologous. All hepatitis A virus strains isolated from the Kaesong Industrial Region, Jeonnam, Seoul, and Incheon belonged to a single cluster. However, strains from Daegu could be classified into 2 clusters, suggesting that the outbreak had multiple sources. This study indicates that hepatitis A virus strains of 2 different genotypes are currently cocirculating in Korea. Moreover, it documents an increasing prevalence of genotype IIIA strains in the country. PMID:22238447

Directed evolution of Oenococcus oeni strains for more efficient malolactic fermentation in a multi-stressor wine environment.

PubMed

Jiang, Jiao; Sumby, Krista M; Sundstrom, Joanna F; Grbin, Paul R; Jiranek, Vladimir

2018-08-01

High concentrations of ethanol, low pH, the presence of sulfur dioxide and some polyphenols have been reported to inhibit Oenococcus oeni growth, thereby negatively affecting malolactic fermentation (MLF) of wine. In order to generate superior O. oeni strains that can conduct more efficient MLF, despite these multiple stressors, a continuous culture approach was designed to directly evolve an existing ethanol tolerant O. oeni strain, A90. The strain was grown for ∼350 generations in a red wine-like environment with increasing levels of stressors. Three strains were selected from screening experiments based on their completion of fermentation in a synthetic wine/wine blend with 15.1% (v/v) ethanol, 26 mg/L SO 2 at pH 3.35 within 160 h, while the parent strain fermented no more than two thirds of l-malic acid in this medium. These superior strains also fermented faster and/or had a larger population in four different wines. A reduced or equivalent amount of the undesirable volatile, acetic acid, was produced by the optimised strains compared to a commercial strain in Mouvedre and Merlot wines. These findings demonstrate the feasibility of using directed evolution as a tool to generate more efficient MLF starters tailored for wines with multiple stressors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Global Existence Results for Viscoplasticity at Finite Strain

NASA Astrophysics Data System (ADS)

Mielke, Alexander; Rossi, Riccarda; Savaré, Giuseppe

2018-01-01

We study a model for rate-dependent gradient plasticity at finite strain based on the multiplicative decomposition of the strain tensor, and investigate the existence of global-in-time solutions to the related PDE system. We reveal its underlying structure as a generalized gradient system, where the driving energy functional is highly nonconvex and features the geometric nonlinearities related to finite-strain elasticity as well as the multiplicative decomposition of finite-strain plasticity. Moreover, the dissipation potential depends on the left-invariant plastic rate, and thus depends on the plastic state variable. The existence theory is developed for a class of abstract, nonsmooth, and nonconvex gradient systems, for which we introduce suitable notions of solutions, namely energy-dissipation-balance and energy-dissipation-inequality solutions. Hence, we resort to the toolbox of the direct method of the calculus of variations to check that the specific energy and dissipation functionals for our viscoplastic models comply with the conditions of the general theory.

The roles of inoculants' carbon source use in the biocontrol of potato scab disease.

PubMed

Sun, Pingping; Zhao, Xinbei; Shangguan, Nini; Chang, Dongwei; Ma, Qing

2015-04-01

Despite the application of multiple strains in the biocontrol of plant diseases, multistrain inoculation is still constrained by its inconsistency in the field. Nutrients, especially carbons, play an important role in the biocontrol processes. However, little work has been done on the systematic estimation of inoculants' carbon source use on biocontrol efficacies in vivo. In the present study, 7 nonpathogenic Streptomyces strains alone and in different combinations were inoculated as biocontrol agents against the potato scab disease, under field conditions and greenhouse treatments. The influence of the inoculants' carbon source use properties on biocontrol efficacies was investigated. The results showed that increasing the number of inoculated strains did not necessarily result in greater biocontrol efficacy in vivo. However, single strains with higher growth rates or multiple strains with less carbon source competition had positive effects on the biocontrol efficacies. These findings may shed light on optimizing the consistent biocontrol of plant disease with the consideration of inoculants' carbon source use properties.

Local Plasticity of Al Thin Films as Revealed by X-Ray Microdiffraction

NASA Astrophysics Data System (ADS)

Spolenak, R.; Brown, W. L.; Tamura, N.; MacDowell, A. A.; Celestre, R. S.; Padmore, H. A.; Valek, B.; Bravman, J. C.; Marieb, T.; Fujimoto, H.; Batterman, B. W.; Patel, J. R.

2003-03-01

Grain-to-grain interactions dominate the plasticity of Al thin films and establish effective length scales smaller than the grain size. We have measured large strain distributions and their changes under plastic strain in 1.5-μm-thick Al0.5%Cu films using a 0.8-μm-diameter white x-ray probe at the Advanced Light Source. Strain distributions arise not only from the distribution of grain sizes and orientation, but also from the differences in grain shape and from stress environment. Multiple active glide plane domains have been found within single grains. Large grains behave like multiple smaller grains even before a dislocation substructure can evolve.

First report of a resistance-breaking strain of Raspberry bushy dwarf virus in red raspberry (Rubus idaeus) in North America

USDA-ARS?s Scientific Manuscript database

Raspberry bushy dwarf virus (RBDV) is pollen-transmitted and the most important virus of Rubus worldwide. Infection of RBDV is associated with drupelet abortion, resulting in crumbly fruit. Multiple RBDV strains have been reported, with the Scottish-type (D200) strains being the most prevalent, and...

Comparative genome analysis of multiple vancomycin-resistant Enterococcus faecium isolated from two fatal cases.

PubMed

Lim, Shu Yong; Yap, Kien-Pong; Teh, Cindy Shuan Ju; Jabar, Kartini Abdul; Thong, Kwai Lin

2017-04-01

Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VRE fm ) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17. This is the first report on the emergence of ST80 strains in Malaysia. Three of the studied strains (VREr5, VREr6, VREr7) were each isolated from different body sites of a single patient (patient Y) and had different PFGE patterns. While VREr6 and VREr7 were phenotypically and genotypically similar, the initial isolate, VREr5, was found to be more similar to VRE2 isolated from another patient (patient X), in terms of the genome contents, sequence types and phylogenomic relationship. Both the clinical records and genome sequence data suggested that patient Y was infected by multiple strains from different clones and the strain that infected patient Y could have derived from the same clone from patient X. These multidrug resistant strains harbored a number of virulence genes such as the epa locus and pilus-associated genes which could enhance their persistence. Apart from that, a homolog of E. faecalis bee locus was identified in VREr5 which might be involved in biofilm formation. Overall, our comparative genomic analyses had provided insight into the genetic relatedness, as well as the virulence potential, of the four clinical strains. Copyright © 2016 Elsevier B.V. All rights reserved.

Multiple-Strain Approach and Probabilistic Modeling of Consumer Habits in Quantitative Microbial Risk Assessment: A Quantitative Assessment of Exposure to Staphylococcal Enterotoxin A in Raw Milk.

PubMed

Crotta, Matteo; Rizzi, Rita; Varisco, Giorgio; Daminelli, Paolo; Cunico, Elena Cosciani; Luini, Mario; Graber, Hans Ulrich; Paterlini, Franco; Guitian, Javier

2016-03-01

Quantitative microbial risk assessment (QMRA) models are extensively applied to inform management of a broad range of food safety risks. Inevitably, QMRA modeling involves an element of simplification of the biological process of interest. Two features that are frequently simplified or disregarded are the pathogenicity of multiple strains of a single pathogen and consumer behavior at the household level. In this study, we developed a QMRA model with a multiple-strain approach and a consumer phase module (CPM) based on uncertainty distributions fitted from field data. We modeled exposure to staphylococcal enterotoxin A in raw milk in Lombardy; a specific enterotoxin production module was thus included. The model is adaptable and could be used to assess the risk related to other pathogens in raw milk as well as other staphylococcal enterotoxins. The multiplestrain approach, implemented as a multinomial process, allowed the inclusion of variability and uncertainty with regard to pathogenicity at the bacterial level. Data from 301 questionnaires submitted to raw milk consumers were used to obtain uncertainty distributions for the CPM. The distributions were modeled to be easily updatable with further data or evidence. The sources of uncertainty due to the multiple-strain approach and the CPM were identified, and their impact on the output was assessed by comparing specific scenarios to the baseline. When the distributions reflecting the uncertainty in consumer behavior were fixed to the 95th percentile, the risk of exposure increased up to 160 times. This reflects the importance of taking into consideration the diversity of consumers' habits at the household level and the impact that the lack of knowledge about variables in the CPM can have on the final QMRA estimates. The multiple-strain approach lends itself to use in other food matrices besides raw milk and allows the model to better capture the complexity of the real world and to be capable of geographical specificity.

High levels of multiple infections, recombination and horizontal transmission of Wolbachia in the Andricus mukaigawae (Hymenoptera; Cynipidae) communities.

PubMed

Yang, Xiao-Hui; Zhu, Dao-Hong; Liu, Zhiwei; Zhao, Ling; Su, Cheng-Yuan

2013-01-01

Wolbachia are maternally inherited endosymbiotic bacteria of arthropods and nematodes. In arthropods, they manipulate the reproduction of their hosts to facilitate their own spread in host populations, causing cytoplasmic incompatibility, parthenogenesis induction, feminization of genetic males and male-killing. In this study, we investigated Wolbachia infection and studied wsp (Wolbachia surface protein) sequences in three wasp species associated with the unisexual galls of A. mukaigawae with the aim of determining the transmission mode and the reason for multiple infections of Wolbachia. Frequency of Wolbachia infected populations for A. mukaigawae, Synergus japonicus (inquiline), and Torymus sp. (parasitoid) was 75%, 100%, and 100%, respectively. Multiple Wolbachia infections were detected in A. mukaigawae and S. japonicus, with 5 and 8 Wolbachia strains, respectively. The two host species shared 5 Wolbachia strains and were infected by identical strains in several locations, indicating horizontal transmission of Wolbachia. The transmission potentially takes place through gall tissues, which the larvae of both wasps feed on. Furthermore, three recombination events of Wolbachia were observed: the strains W8, W2 and W6 apparently have derived from W3 and W5a, W6 and W7, W4 and W9, respectively. W8 and W2 and their respective parental strains were detected in S. japonicus. W6 was detected with only one parent (W4) in S. japonicus; W9 was detected in Torymus sp., suggesting horizontal transmission between hosts and parasitoids. In conclusion, our research supports earlier studies that horizontal transmission of Wolbachia, a symbiont of the Rickettsiales order, may be plant-mediated or take place between hosts and parasitoids. Our research provides novel molecular evidence for multiple recombination events of Wolbachia in gall wasp communities. We suggest that genomic recombination and potential plant-mediated horizontal transmission may be attributable to the high levels of multiple Wolbachia infections observed in A. mukaigawae and S. japonicus.

Material mechanical characterization method for multiple strains and strain rates

DOEpatents

Erdmand, III, Donald L.; Kunc, Vlastimil; Simunovic, Srdjan; Wang, Yanli

2016-01-19

A specimen for measuring a material under multiple strains and strain rates. The specimen including a body having first and second ends and a gage region disposed between the first and second ends, wherein the body has a central, longitudinal axis passing through the first and second ends. The gage region includes a first gage section and a second gage section, wherein the first gage section defines a first cross-sectional area that is defined by a first plane that extends through the first gage section and is perpendicular to the central, longitudinal axis. The second gage section defines a second cross-sectional area that is defined by a second plane that extends through the second gage section and is perpendicular to the central, longitudinal axis and wherein the first cross-sectional area is different in size than the second cross-sectional area.

Strain diversity and host specificity in a specialized gut symbiont of honeybees and bumblebees.

PubMed

Powell, Elijah; Ratnayeke, Nalin; Moran, Nancy A

2016-09-01

Host-restricted lineages of gut bacteria often include many closely related strains, but this fine-scale diversity is rarely investigated. The specialized gut symbiont Snodgrassella alvi has codiversified with honeybees (Apis mellifera) and bumblebees (Bombus) for millions of years. Snodgrassella alvi strains are nearly identical for 16S rRNA gene sequences but have distinct gene repertoires potentially affecting host biology and community interactions. We examined S. alvi strain diversity within and between hosts using deep sequencing both of a single-copy coding gene (minD) and of the V4 region of the 16S rRNA gene. We sampled workers from domestic and feral A. mellifera colonies and wild-caught Bombus representing 14 species. Conventional analyses of community profiles, based on the V4 region of the 16S rRNA gene, failed to expose most strain variation. In contrast, the minD analysis revealed extensive strain variation within and between host species and individuals. Snodgrassella alvi strain diversity is significantly higher in A. mellifera than in Bombus, supporting the hypothesis that colony founding by swarms of workers enables retention of more diversity than colony founding by a single queen. Most Bombus individuals (72%) are dominated by a single S. alvi strain, whereas most A. mellifera (86%) possess multiple strains. No S. alvi strains are shared between A. mellifera and Bombus, indicating some host specificity. Among Bombus-restricted strains, some are restricted to a single host species or subgenus, while others occur in multiple subgenera. Findings demonstrate that strains diversify both within and between host species and can be highly specific or relatively generalized in their host associations. © 2016 John Wiley & Sons Ltd.

Job strain in nursing homes-Exploring the impact of leadership.

PubMed

Backman, Annica; Sjögren, Karin; Lövheim, Hugo; Edvardsson, David

2018-04-01

To explore the association between nursing home managers' leadership, job strain and social support as perceived by direct care staff in nursing homes. It is well known that aged care staff experience high levels of job strain, and that aged care staff experiencing job strain are exposed to increased risk for adverse health effects. Leadership styles have been associated with job strain in the literature; however, the impact of perceived leadership on staff job strain and social support has not been clarified within nursing home contexts. This study had a cross-sectional design. Participating staff (n = 3,605) completed surveys which included questions about staff characteristics, valid and reliable measures of nursing home managers' leadership, perceived job strain and social support. Statistical analyses of correlations and multiple regression analysis with interaction terms were conducted. Nursing home managers' leadership were significantly associated with lower level of job strain and higher level of social support among direct care staff. A multiple regression analysis including an interaction term indicated individual and joint effects of nursing home managers' leadership and social support on job strain. Nursing home managers' leadership and social support were both individually and in combination associated with staff perception of lesser job strain. Thus, nursing home managers' leadership are beneficial for the working situation and strain of staff. Promoting a supporting work environment through leadership is an important implication for nursing home managers as it can influence staff perception of job strain and social support within the unit. By providing leadership, offering support and strategies towards a healthy work environment, nursing home managers can buffer adverse health effects among staff. © 2017 John Wiley & Sons Ltd.

Comparative analysis of the Rotarix™ vaccine strain and G1P[8] rotaviruses detected before and after vaccine introduction in Belgium.

PubMed

Zeller, Mark; Heylen, Elisabeth; Tamim, Sana; McAllen, John K; Kirkness, Ewen F; Akopov, Asmik; De Coster, Sarah; Van Ranst, Marc; Matthijnssens, Jelle

2017-01-01

G1P[8] rotaviruses are responsible for the majority of human rotavirus infections worldwide. The effect of universal mass vaccination with rotavirus vaccines on circulating G1P[8] rotaviruses is still poorly understood. Therefore we analyzed the complete genomes of the Rotarix™ vaccine strain, and 70 G1P[8] rotaviruses, detected between 1999 and 2010 in Belgium (36 before and 34 after vaccine introduction) to investigate the impact of rotavirus vaccine introduction on circulating G1P[8] strains. All rotaviruses possessed a complete Wa-like genotype constellation, but frequent intra-genogroup reassortments were observed as well as multiple different cluster constellations circulating in a single season. In addition, identical cluster constellations were found to circulate persistently over multiple seasons. The Rotarix™ vaccine strain possessed a unique cluster constellation that was not present in currently circulating G1P[8] strains. At the nucleotide level, the VP6, VP2 and NSP2 gene segments of Rotarix™ were relatively distantly related to any Belgian G1P[8] strain, but other gene segments of Rotarix™ were found in clusters also containing circulating Belgian strains. At the amino acid level, the genetic distance between Rotarix™ and circulating Belgian strains was considerably lower, except for NSP1. When we compared the Belgian G1P[8] strains collected before and after vaccine introduction a reduction in the proportion of strains that were found in the same cluster as the Rotarix™ vaccine strain was observed for most gene segments. The reduction in the proportion of strains belonging to the same cluster may be the result of the vaccine introduction, although natural fluctuations cannot be ruled out.

Determining heterogeneous slip activity on multiple slip systems from single crystal orientation pole figures

DOE PAGES

Pagan, Darren C.; Miller, Matthew P.

2016-09-01

A new experimental method to determine heterogeneity of shear strains associated with crystallographic slip in the bulk of ductile, crystalline materials is outlined. The method quantifies the time resolved evolution of misorientation within plastically deforming crystals using single crystal orientation pole figures (SCPFs) measured in-situ with X-ray diffraction. A multiplicative decomposition of the crystal kinematics is used to interpret the distributions of lattice plane orientation observed on the SCPFs in terms of heterogeneous slip activity (shear strains) on multiple slip systems. Here, to show the method’s utility, the evolution of heterogeneous slip is quantified in a silicon single crystal plasticallymore » deformed at high temperature at multiple load steps, with slip activity in sub-volumes of the crystal analyzed simultaneously.« less

All-optical, Three-axis Fiber Laser Magnetometer

DTIC Science & Technology

2012-04-16

into each core using an ultraviolet laser. Measurements of the differences in induced strain between the FBGs enables bending in two dimensions to...housing. This is repeated for multiple inclinations. The difference in strain between two FBGs as a function of rotation for three inclination...angles of 9°, 45°, and 81° is shown in Fig. 10(a). The FBG strain is measured using an interferometric method, and as such, the difference in strain is

Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles▿†

PubMed Central

Kumar, Vinod; Sun, Peng; Vamathevan, Jessica; Li, Yong; Ingraham, Karen; Palmer, Leslie; Huang, Jianzhong; Brown, James R.

2011-01-01

There is a global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology of K. pneumoniae strains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes of K. pneumoniae are available. To better understand the multidrug resistance factors in K. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other published K. pneumoniae genomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to other K. pneumoniae strains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data on K. pneumoniae strains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates. PMID:21746949

Occurrence of Propionibacterium freudenreichii bacteriophages in swiss cheese.

PubMed Central

Gautier, M; Rouault, A; Sommer, P; Briandet, R

1995-01-01

We isolated bacteriophages active against Propionibacterium freudenreichii from 16 of 32 swiss cheese samples. Bacteriophage concentrations ranged from 14 to 7 x 10(5) PFU/g, depending on the sample and the sensitive strain used for detection. Only a few strains, 8 of the 44 strains of P. freudenreichii in our collection, were sensitive. We observed that multiplication of bacteriophages occurred in the cheese loaf during multiplication of propionibacteria in a warm curing room, but it seems that these bacteriophages have no adverse effect on the development of the propionic flora. We also found that sensitive cells, originating from either the starter or the cheese-making milk, were present at a high level (10(9) CFU/g) in the cheese. PMID:7618869

Resequencing Pathogen Microarray (RPM) for prospective detection and identification of emergent pathogen strains and variants

NASA Astrophysics Data System (ADS)

Tibbetts, Clark; Lichanska, Agnieszka M.; Borsuk, Lisa A.; Weslowski, Brian; Morris, Leah M.; Lorence, Matthew C.; Schafer, Klaus O.; Campos, Joseph; Sene, Mohamadou; Myers, Christopher A.; Faix, Dennis; Blair, Patrick J.; Brown, Jason; Metzgar, David

2010-04-01

High-density resequencing microarrays support simultaneous detection and identification of multiple viral and bacterial pathogens. Because detection and identification using RPM is based upon multiple specimen-specific target pathogen gene sequences generated in the individual test, the test results enable both a differential diagnostic analysis and epidemiological tracking of detected pathogen strains and variants from one specimen to the next. The RPM assay enables detection and identification of pathogen sequences that share as little as 80% sequence similarity to prototype target gene sequences represented as detector tiles on the array. This capability enables the RPM to detect and identify previously unknown strains and variants of a detected pathogen, as in sentinel cases associated with an infectious disease outbreak. We illustrate this capability using assay results from testing influenza A virus vaccines configured with strains that were first defined years after the design of the RPM microarray. Results are also presented from RPM-Flu testing of three specimens independently confirmed to the positive for the 2009 Novel H1N1 outbreak strain of influenza virus.

Hepatitis A virus strains circulating during 1997-2015 in Campania, a Southern Italy region with periodic outbreaks.

PubMed

Costantino, Angela; Coppola, Nicola; Spada, Enea; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Marcantonio, Cinzia; Sagnelli, Caterina; Dell'Isola, Chiara; Tosone, Grazia; Mascolo, Silvia; Sagnelli, Evangelista; Ciccaglione, Anna Rita

2017-11-01

In Italy, the incidence of hepatitis A has progressively declined over the last 30 years, though not homogeneously throughout the country. In Campania, Southern Italy, high annual incidence rates have been reported and several periodic outbreaks have occurred. To investigate the phylogenetic and epidemiologic relationships among HAV strains circulating in Campania over the period 1997-2015, 87 hepatitis A cases were investigated. The most frequent risk factor was the consumption of raw/undercooked shellfish (75/87, 86.2%). During 1997-2002 most viral strains were subtype IA (16/23, 70%); the phylogenetic pattern suggests that the incidence peaks observed in 2000-2001 had likely been caused by multiple strains. During a large 2004 outbreak, almost all viral variants were subtype IB (38/41, 93%); most of them (22/38, 58%) were recognized to be one of two main strains (differing for just a single nucleotide), the remaining sequences were strictly related variants. In 2014/2015, only IA strains were observed; two phylogenetically related but distinct strains were responsible, respectively, for a small cluster in 2014 and an outbreak in 2015. In each outbreak, several strains unrelated to those responsible for most cases were detected in a minority of patients, documenting a background of sporadic cases occurring even in the course of outbreaks; some of them proved to be identical to strains detected 11-14 years previously. Overall, the data suggest that several related and unrelated HAV strains have endemically circulated over the last 15 years in Campania, with some strains gaining epidemic transmission likely because of a local combination of multiple factors, including inadequate waste water purification and dietary habits. © 2017 Wiley Periodicals, Inc.

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

PubMed Central

Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon; Firek, Brian; Baker, Robyn; Burstein, David; Soenjoyo, Karina; Thomas, Brian C.; Morowitz, Michael; Banfield, Jillian F.

2017-01-01

The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity. PMID:28073918

Assessment of the Toxicity of CuO Nanoparticles by Using Saccharomyces cerevisiae Mutants with Multiple Genes Deleted

PubMed Central

Bao, Shaopan; Lu, Qicong; Dai, Heping; Zhang, Chao

2015-01-01

To develop applicable and susceptible models to evaluate the toxicity of nanoparticles, the antimicrobial effects of CuO nanoparticles (CuO-NPs) on various Saccharomyces cerevisiae (S. cerevisiae) strains (wild type, single-gene-deleted mutants, and multiple-gene-deleted mutants) were determined and compared. Further experiments were also conducted to analyze the mechanisms associated with toxicity using copper salt, bulk CuO (bCuO), carbon-shelled copper nanoparticles (C/Cu-NPs), and carbon nanoparticles (C-NPs) for comparisons. The results indicated that the growth inhibition rates of CuO-NPs for the wild-type and the single-gene-deleted strains were comparable, while for the multiple-gene deletion mutant, significantly higher toxicity was observed (P < 0.05). When the toxicity of the CuO-NPs to yeast cells was compared with the toxicities of copper salt and bCuO, we concluded that the toxicity of CuO-NPs should be attributed to soluble copper rather than to the nanoparticles. The striking difference in adverse effects of C-NPs and C/Cu-NPs with equivalent surface areas also proved this. A toxicity assay revealed that the multiple-gene-deleted mutant was significantly more sensitive to CuO-NPs than the wild type. Specifically, compared with the wild-type strain, copper was readily taken up by mutant strains when cell permeability genes were knocked out, and the mutants with deletions of genes regulated under oxidative stress (OS) were likely producing more reactive oxygen species (ROS). Hence, as mechanism-based gene inactivation could increase the susceptibility of yeast, the multiple-gene-deleted mutants should be improved model organisms to investigate the toxicity of nanoparticles. PMID:26386067

Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes In Vitro.

PubMed

Tran, Thao D; Huynh, Steven; Parker, Craig T; Hnasko, Robert; Gorski, Lisa; McGarvey, Jeffery A

2018-06-21

Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains isolated from alfalfa, almond drupes, and grapes that inhibited the growth of Listeria monocytogenes strain 2011L-2857 in vitro We also report multiple gene clusters encoding secondary metabolites that may be responsible for the growth inhibition of L. monocytogenes . Copyright © 2018 Tran et al.

Serological and genetic examination of some nontypical Streptococcus mutans strains.

PubMed

Coykendall, A L; Bratthall, D; O'Connor, K; Dvarskas, R A

1976-09-01

Thirty-four strains of Streptococcus mutans whose antigenic or genetic positions were unclear or unknown with respect to the serological scheme of Bratthall (1970) and Perch et al. (1974), or the genetic (deoxyribonucleic acid base sequence homology) scheme of Coykendall were analyzed to clarify their relationship to previously well-characterized strains. Strain OMZ175 of the "new" serotype f was genetically homologous with strains of S. mutans subsp. mutans. Strains of the "new" serotype g were homologous with serotype d strains (S. mutans subsp. sobrinus). Strains isolated from wild rats constituted a new genetic group but carried the c antigen. Thus, strains within a "genospecies" (subspecies) of S. mutans may not always carry a unique or characteristic antigen. We suggest that the existence of multiple serotypes within subspecies represents antigenic variation and adaptations to hosts.

Emergence of pathogenic and multiple-antibiotic-resistant Macrococcus caseolyticus in commercial broiler chickens.

PubMed

Li, Gen; Du, Xusheng; Zhou, Defang; Li, Chengui; Huang, Libo; Zheng, Qiankun; Cheng, Ziqiang

2018-05-25

Macrococcus caseolyticus is generally considered to be a non-pathogenic bacterium that does not cause human or animal diseases. However, recently, a strain of M. caseolyticus (SDLY strain) that causes high mortality rates was isolated from commercial broiler chickens in China. The main pathological changes caused by SDLY included caseous exudation in cranial cavities, inflammatory infiltration, haemorrhages and multifocal necrosis in various organs. The whole genome of the SDLY strain was sequenced and was compared with that of the non-pathogenic JCSC5402 strain of M. caseolyticus. The results showed that the SDLY strain harboured a large quantity of mutations, antibiotic resistance genes and numerous insertions and deletions of virulence genes. In particular, among the inserted genes, there is a cluster of eight connected genes associated with the synthesis of capsular polysaccharide. This cluster encodes a transferase and capsular polysaccharide synthase, promotes the formation of capsules and causes changes in pathogenicity. Electron microscopy revealed a distinct capsule surrounding the SDLY strain. The pathogenicity test showed that the SDLY strain could cause significant clinical symptoms and pathological changes in both SPF chickens and mice. In addition, these clinical symptoms and pathological changes were the same as those observed in field cases. Furthermore, the anti-microbial susceptibility test demonstrated that the SDLY strain exhibits multiple-antibiotic resistance. The emergence of pathogenic M. caseolyticus indicates that more attention should be paid to the effects of this micro-organism on both poultry and public health. © 2018 Blackwell Verlag GmbH.

The influence of H-2 genetic factors on the development of benign monoclonal gammopathy in ageing H-2 congenic C57BL and BALB mice.

PubMed Central

van den Akker, T W; Tio-Gillen, A P; Benner, R; Zurcher, C; Radl, J

1987-01-01

The role of H-2 genetic factors in the development of benign monoclonal gammopathy (BMG) was investigated in six H-2 congenic C57BL and BALB strains (C57BL/10.ScSn and BALB.B: H-2b; B10.D2 and BALB/c: H-2d; B10.BR and BALB.K: H-2k) during ageing. The frequencies of homogeneous immunoglobulins (H-Ig), both single and multiple, in the three C57BL strains were higher than those in the corresponding three BALB strains. No relationship was found with a particular H-2 haplotype. The most frequent H-Ig isotype within the C57BL strains was IgG2a, within BALB.B and BALB.K mice IgG3 and in BALB/c mice IgG1. Categorization of the monoclonal gammopathies (MG) on the basis of their origin showed a single transient monoclonal B-cell proliferation in 2-5% and 3-9% of the C57BL and BALB mice positive for H-Ig, respectively. Multiple myeloma or B-cell lymphoma were found to be responsible for about 1% of the paraproteinaemias in all strains. Persistent, non-progressive MG, most likely BMG, was detected in 70-81% and 39-46% of the C57BL and BALB mice positive for H-Ig, respectively. The remaining 14-24% and 50-58% of the, respectively, C57BL and BALB mice positive for H-Ig could not be evaluated in time. The H-2 haplotypes under investigation were not associated with the onset, occurrence, multiplicity, persistence or isotype of the MG developing in these H-2 congenic C57BL and BALB strains during ageing. PMID:3443448

Preliminary Investigation on Multiple-Locus Variable Number Tandem Repeat Analysis Profiles of Listeria Monocytogenes Isolates from Pork Meat Tested from Packaging to Fork

PubMed Central

Parisi, Antonio; Caruso, Marta; Pasquali, Frédérique; Manfreda, Gerardo

2014-01-01

Listeria monocytogenes is recognised as a public health issue and a serious challenge for the food industry. L. monocytogenes strain characterisation on the basis of serotyping and molecular typing methods is used for surveillance, epidemiological tracking and outbreak investigation purposes. Genetic variants of L. monocytogenes have diversified into four major phylogenetic lineages, with lineages 1 and 2 each containing multiple clonal groups of public health importance. Standardised tools for easy identification of clonal groups are needed to trace such groups and determine their presence in a large variety of sources. Given the current limitations of available methods for L. monocytogenes strain typing, a potentially useful approach is multiple locus variable number of tandem repeats (VNTR) analysis (MLVA). In this study, MLVA has been applied to a random group of 82 L. monocytogenes strains isolated from 8 different batches of loin chops obtained from the same facility and tested between packaging and consumption time. The strains typed were classified into 10 MLVA profiles containing a number of isolates ranging between 1 to 20. According to the identified MLVA profiles, 75.6% of the pork isolates belonged to the phylogenetic lineage 2 and serotype 1/2c, frequently associated to food isolates. However, 3 pork strains belonged to the phylogenetic lineage 1 and serotype 4b. Moreover, 17 isolates were classified in the phylogenetic lineages 2 and serotype 1/2a. Both serotypes 4b and 1/2a are frequently associated to human isolates of L. monocytogenes. These preliminary results show how the MLVA profiles can support the assessment of the risk profile of food products based on the contaminating L. monocytogenes strain types. PMID:27800312

Characterization of plant growth-promoting traits of free-living diazotrophic bacteria and their inoculation effects on growth and nitrogen uptake of crop plants.

PubMed

Islam, Md Rashedul; Madhaiyan, M; Deka Boruah, Hari P; Yim, Woojong; Lee, Gillseung; Saravanan, V S; Fu, Qingling; Hu, Hongqing; Sa, Tongmin

2009-10-01

The search for diverse plant growth-promoting (PGP) diazotrophic bacteria is gaining momentum as efforts are made to exploit them as biofertilizers for various economically important crops. In the present study, 17 diazotrophic strains belonging to eight different genera isolated from rice paddy fields were screened for multiple PGP traits and evaluated for their inoculation effects on canola and rice plants. All of the strains tested positive for 1- aminocyclopropane-1-carboxylate (ACC) deaminase activity and production of indole 3-acetic acid (IAA) and ammonia (NH3). Additionally, four of the strains were able to solubilize phosphorus (P), five tested positive for zinc (Zn) solubilization and sulfur (S) oxidation, and eight strains produced siderophores. Based on the presence of multiple PGP traits, 10 strains were selected for inoculation studies. Treatment with Herbaspirillum sp. RFNB26 resulted in maximum root length (54.3%), seedling vigor, and dry biomass in canola, whereas Paenibacillus sp. RFNB4 exhibited the lowest activity under gnotobiotic conditions. However, under pot culture conditions, Paenibacillus sp. RFNB4 significantly increased plant height and dry biomass production by 42.3% and 29.5%, respectively. Canola plants and rhizosphere soils inoculated with Bacillus sp. RFNB6 exhibited significantly higher nitrogenase activity. In greenhouse experiments, Serratia sp. RFNB18 increased rice plant height by 35.1%, Xanthomonas sp. RFNB24 enhanced biomass production by 84.6%, and rice rhizosphere soils inoculated with Herbaspirillum sp. RFNB26 exhibited the highest nitrogenase activity. Our findings indicate that most of the selected strains possess multiple PGP properties that significantly improve the growth parameters of the two plants when tested under controlled conditions.

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

PubMed Central

Gan, Mingyu; Liu, Qingyun; Yang, Chongguang; Gao, Qian; Luo, Tao

2016-01-01

Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates. PMID:27391214

Multiple Crimean-Congo Hemorrhagic Fever Virus Strains Are Associated with Disease Outbreaks in Sudan, 2008–2009

PubMed Central

Aradaib, Imadeldin E.; Erickson, Bobbie R.; Karsany, Mubarak S.; Khristova, Marina L.; Elageb, Rehab M.; Mohamed, Mohamed E. H.; Nichol, Stuart T.

2011-01-01

Background Crimean-Congo hemorrhagic fever (CCHF) activity has recently been detected in the Kordufan region of Sudan. Since 2008, several sporadic cases and nosocomial outbreaks associated with high case-fatality have been reported in villages and rural hospitals in the region. Principal Findings In the present study, we describe a cluster of cases occurring in June 2009 in Dunkop village, Abyei District, South Kordufan, Sudan. Seven CCHF cases were involved in the outbreak; however, clinical specimens could be collected from only two patients, both of whom were confirmed as acute CCHF cases using CCHF-specific reverse transcriptase polymerase chain reaction (RT-PCR). Phylogenetic analysis of the complete S, M, and L segment sequences places the Abyei strain of CCHF virus in Group III, a virus group containing strains from various countries across Africa, including Sudan, South Africa, Mauritania, and Nigeria. The Abyei strain detected in 2009 is genetically distinct from the recently described 2008 Sudanese CCHF virus strains (Al-fulah 3 and 4), and the Abyei strain S and L segments closely match those of CCHF virus strain ArD39554 from Mauritania. Conclusions The present investigation illustrates that multiple CCHF virus lineages are circulating in the Kordufan region of Sudan and are associated with recent outbreaks of the disease occurring during 2008–2009. PMID:21655310

[Attenuated rabies virus, ERA strain, in cattle and dogs vaccinated with multiple doses].

PubMed

Titoli, F; Pestalozza, S; Irsara, A; Palliola, E; Frescura, T; Civardi, A

1982-01-01

Investigation on the vaccination of 18 cattle and 5 dogs against rabies is reported. Each animal received multiple doses of ERA strain vaccine intramuscularly in the gluteal or masseter region. The saliva, the brain and salivary glands of the vaccinated animals were examined to detect the presence of ERA virus using immunofluorescent test and mouse inoculation. The virus was never found in the saliva and organs of treated animals. Circulating antibodies against ERA rabies virus were detected in all vaccinated cattle and dogs.

Prevalence and Diversity of Bartonella spp. in Bats in Peru

PubMed Central

Bai, Ying; Recuenco, Sergio; Gilbert, Amy Turmelle; Osikowicz, Lynn M.; Gómez, Jorge; Rupprecht, Charles; Kosoy, Michael Y.

2012-01-01

Bartonella infections were investigated in bats in the Amazon part of Peru. A total of 112 bats belonging to 19 species were surveyed. Bartonella bacteria were cultured from 24.1% of the bats (27/112). Infection rates ranged from 0% to 100% per bat species. Phylogenetic analyses of gltA of the Bartonella isolates revealed 21 genetic variants clustering into 13 divergent phylogroups. Some Bartonella strains were shared by bats of multiple species, and bats of some species were infected with multiple Bartonella strains, showing no evident specific Bartonella sp.–bat relationships. Rarely found in other bat species, the Bartonella strains of phylogroups I and III discovered from the common vampire bats (Desmodus rotundus) were more specific to the host bat species, suggesting some level of host specificity. PMID:22826480

Five-Factor Personality Traits and Subjective Health Among Caregivers: The Role of Caregiver Strain and Self-Efficacy

PubMed Central

Löckenhoff, Corinna E.; Duberstein, Paul R.; Friedman, Bruce; Costa, Paul T.

2011-01-01

This study examined the association among caregivers’ five-factor personality traits and subjective health with particular emphasis on the role of two theoretically implicated mediators: multi-domain self-efficacy and caregiver strain. The sample comprised 536 informal caregivers (mean age = 62.9 years, SD = 19.9, 72% female, 98% White) of community-dwelling older adults with multiple functional impairments. Both physical health and mental health were negatively associated with neuroticism and positively associated with extraversion and conscientiousness. Agreeableness and openness were associated with better subjective mental health and physical health, respectively. Multiple mediation analyses indicated that self-efficacy mediated all observed associations between personality and subjective health, whereas caregiver strain selectively mediated the associations of neuroticism and agreeableness with mental health. PMID:21417534

Nanoscale strain mapping in battery nanostructures

NASA Astrophysics Data System (ADS)

Ulvestad, A.; Cho, H. M.; Harder, R.; Kim, J. W.; Dietze, S. H.; Fohtung, E.; Meng, Y. S.; Shpyrko, O. G.

2014-02-01

Coherent x-ray diffraction imaging is used to map the local three dimensional strain inhomogeneity and electron density distribution of two individual LiNi0.5Mn1.5O4-δ cathode nanoparticles in both ex-situ and in-situ environments. Our reconstructed images revealed a maximum strain of 0.4%. We observed different variations in strain inhomogeneity due to multiple competing effects. The compressive/tensile component of the strain is connected to the local lithium content and, on the surface, interpreted in terms of a local Jahn-Teller distortion of Mn3+. Finally, the measured strain distributions are discussed in terms of their impact on competing theoretical models of the lithiation process.

Screening of the Enterocin-Encoding Genes and Antimicrobial Activity in Enterococcus Species.

PubMed

Ogaki, Mayara Baptistucci; Rocha, Katia Real; Terra, MÁrcia Regina; Furlaneto, MÁrcia Cristina; Maia, Luciana Furlaneto

2016-06-28

In the current study, a total of 135 enterococci strains from different sources were screened for the presence of the enterocin-encoding genes entA, entP, entB, entL50A, and entL50B. The enterocin genes were present at different frequencies, with entA occurring the most frequently, followed by entP and entB; entL50A and L50B were not detected. The occurrence of single enterocin genes was higher than the occurrence of multiple enterocin gene combinations. The 80 isolates that harbor at least one enterocin-encoding gene (denoted "Gene(+) strains") were screened for antimicrobial activity. A total of 82.5% of the Gene(+) strains inhibited at least one of the indicator strains, and the isolates harboring multiple enterocin-encoding genes inhibited a larger number of indicator strains than isolates harboring a single gene. The indicator strains that exhibited growth inhibition included Listeria innocua strain CLIP 12612 (ATCC BAA-680), Listeria monocytogenes strain CDC 4555, Enterococcus faecalis ATCC 29212, Staphylococcus aureus ATCC 25923, S. aureus ATCC 29213, S. aureus ATCC 6538, Salmonella enteritidis ATCC 13076, Salmonella typhimurium strain UK-1 (ATCC 68169), and Escherichia coli BAC 49LT ETEC. Inhibition due to either bacteriophage lysis or cytolysin activity was excluded. The growth inhibition of antilisterial Gene+ strains was further tested under different culture conditions. Among the culture media formulations, the MRS agar medium supplemented with 2% (w/v) yeast extract was the best solidified medium for enterocin production. Our findings extend the current knowledge of enterocin-producing enterococci, which may have potential applications as biopreservatives in the food industry due to their capability of controlling food spoilage pathogens.

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khodayari, Ali; Maranas, Costas D.

Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions. Parameterization is carried out using a genetic algorithm by simultaneously imposing all available fluxomic data (about 30 measured fluxes per mutant). Furthermore, the Pearson correlation coefficient between experimentalmore » data and predicted product yields for 320 engineered strains spanning 24 product metabolites is 0.84. This is substantially higher than that using flux balance analysis, minimization of metabolic adjustment or maximization of product yield exhibiting systematic errors with correlation coefficients of, respectively, 0.18, 0.37 and 0.47.« less

Identification of prostate cancer modifier pathways using parental strain expression mapping

PubMed Central

Xu, Qing; Majumder, Pradip K.; Ross, Kenneth; Shim, Yeonju; Golub, Todd R.; Loda, Massimo; Sellers, William R.

2007-01-01

Inherited genetic risk factors play an important role in cancer. However, other than the Mendelian fashion cancer susceptibility genes found in familial cancer syndromes, little is known about risk modifiers that control individual susceptibility. Here we developed a strategy, parental strain expression mapping, that utilizes the homogeneity of inbred mice and genome-wide mRNA expression analyses to directly identify candidate germ-line modifier genes and pathways underlying phenotypic differences among murine strains exposed to transgenic activation of AKT1. We identified multiple candidate modifier pathways and, specifically, the glycolysis pathway as a candidate negative modulator of AKT1-induced proliferation. In keeping with the findings in the murine models, in multiple human prostate expression data set, we found that enrichment of glycolysis pathways in normal tissues was associated with decreased rates of cancer recurrence after prostatectomy. Together, these data suggest that parental strain expression mapping can directly identify germ-line modifier pathways of relevance to human disease. PMID:17978178

Drug Resistance in Newly Presenting and Previously Treated Tuberculosis Patients in Guangxi Province, People's Republic of China.

PubMed

Luo, Dan; Zhao, Jinming; Lin, Mei; Liu, Feiying; Huang, Shuhai; Zhang, Yingkun; Huang, Minying; Li, Juan; Zhou, Yang; Lan, Rushu; Zhao, Yanlin

2017-05-01

Drug-resistant Mycobacterium tuberculosis strains are a major threat to the control of tuberculosis (TB), but the prevalence of drug-resistant TB is still unknown in the southern ethnic region of China. A cluster-randomized sampling method was used to include the study population. Isolates were tested for resistance to 6 antituberculosis drugs, and genotyped to identify Beijing strains. Overall, 11.3% (139/1229) of new cases and 33.0% (126/382) of retreated cases had drug-resistant tuberculosis. Multiple previous TB treatment episodes and multiple treatment interruptions were risk factors for both drug-resistant and multidrug-resistant TB among retreated cases. A total of 53.2% of the patients were infected with a Beijing strain of M tuberculosis. Infection with a Beijing strain was significantly associated with drug resistance among new cases (odds ratio, 1.44; 95% CI, 1.01-2.07). Novel strategies to rapid diagnosis and effective treatment are urgently needed to prevent the development of drug resistance.

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

DOE PAGES

Khodayari, Ali; Maranas, Costas D.

2016-12-20

Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions. Parameterization is carried out using a genetic algorithm by simultaneously imposing all available fluxomic data (about 30 measured fluxes per mutant). Furthermore, the Pearson correlation coefficient between experimentalmore » data and predicted product yields for 320 engineered strains spanning 24 product metabolites is 0.84. This is substantially higher than that using flux balance analysis, minimization of metabolic adjustment or maximization of product yield exhibiting systematic errors with correlation coefficients of, respectively, 0.18, 0.37 and 0.47.« less

Laboratory and wild-derived mice with multiple loci for production of xenotropic murine leukemia virus.

PubMed

Kozak, C A; Hartley, J W; Morse, H C

1984-07-01

Mendelian segregation analysis was used to define genetic loci for the induction of infectious xenotropic murine leukemia virus in several laboratory and wild-derived mice. MA/My mice contain two loci for xenotropic virus inducibility, one of which, Bxv -1, is the only induction locus carried by five other inbred strains. The second, novel MA/My locus, designated Mxv -1, is unlinked to Bxv -1 and shows a lower efficiency of virus induction. The NZB mouse carries two induction loci; both are distinct from Bxv -1 since neither is linked to the Pep-3 locus on chromosome 1. Finally, one partially inbred strain derived from the wild Japanese mouse, Mus musculus molossinus, carries multiple (at least three) unlinked loci for induction of xenotropic virus. Although it is probable that inbred strains inherited xenotropic virus inducibility from Japanese mice, our data suggest that none of the induction loci carried by this particular M. m. molossinus strain are allelic with Bxv -1.

Laboratory and wild-derived mice with multiple loci for production of xenotropic murine leukemia virus.

PubMed Central

Kozak, C A; Hartley, J W; Morse, H C

1984-01-01

Mendelian segregation analysis was used to define genetic loci for the induction of infectious xenotropic murine leukemia virus in several laboratory and wild-derived mice. MA/My mice contain two loci for xenotropic virus inducibility, one of which, Bxv -1, is the only induction locus carried by five other inbred strains. The second, novel MA/My locus, designated Mxv -1, is unlinked to Bxv -1 and shows a lower efficiency of virus induction. The NZB mouse carries two induction loci; both are distinct from Bxv -1 since neither is linked to the Pep-3 locus on chromosome 1. Finally, one partially inbred strain derived from the wild Japanese mouse, Mus musculus molossinus, carries multiple (at least three) unlinked loci for induction of xenotropic virus. Although it is probable that inbred strains inherited xenotropic virus inducibility from Japanese mice, our data suggest that none of the induction loci carried by this particular M. m. molossinus strain are allelic with Bxv -1. PMID:6328046

Strained layer InP/InGaAs quantum well laser

NASA Technical Reports Server (NTRS)

Forouhar, Siamak (Inventor); Larsson, Anders G. (Inventor); Ksendzov, Alexander (Inventor); Lang, Robert J. (Inventor)

1993-01-01

Strained layer single or multiple quantum well lasers include an InP substrate, a pair of lattice-matched InGaAsP quarternary layers epitaxially grown on the substrate surrounding a pair of lattice matched In.sub.0.53 Ga.sub.0.47 As ternary layers surrounding one or more strained active layers of epitaxially grown, lattice-mismatched In.sub.0.75 Ga.sub.0.25 As. The level of strain is selected to control the bandgap energy to produce laser output having a wavelength in the range of 1.6 to 2.5 .mu.m. The multiple quantum well structure uses between each active layer. Diethyl zinc is used for p-type dopant in an InP cladding layer at a concentration level in the range of about 5.times.10.sup.17 /cm.sup.3 to about 2.times.10.sup.18 /cm.sup.3. Hydrogen sulfide is used for n-type dopant in the substrate.

Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus

PubMed Central

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor

2012-01-01

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified. PMID:22740681

Draft genome sequence of Serratia sp. strain M24T3, isolated from pinewood disease nematode Bursaphelenchus xylophilus.

PubMed

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-07-01

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified.

Competitive effect of commensal faecal bacteria from growing swine fed chlortetracycline-supplemented feed on beta-haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids

USDA-ARS?s Scientific Manuscript database

Multidrug-resistant (MDR) bacteria are an increasing threat to human and animal health. The objectives of the present study were to determine: (1) the effect of Aureomycin® on MDR E. coli field strains in growing swine fecal fluid; (2) the competitive fitness of each of these strains in long-term c...

Bromate Reduction by Rhodococcus sp. Br-6 in the Presence of Multiple Redox Mediators.

PubMed

Tamai, Naoko; Ishii, Takahiro; Sato, Yusuke; Fujiya, Hiroko; Muramatsu, Yasuyuki; Okabe, Nobuaki; Amachi, Seigo

2016-10-04

A bromate (BrO 3 - )-reducing bacterium, designated Rhodococcus sp. strain Br-6, was isolated from soil. The strain reduced 250 μM bromate completely within 4 days under growth conditions transitioning from aerobic to anaerobic conditions, while no reduction was observed under aerobic and anaerobic growth conditions. Bromate was reduced to bromide (Br - ) stoichiometrically, and acetate was required as an electron donor. Interestingly, bromate reduction by strain Br-6 was significantly dependent on both ferric iron and a redox dye 2,6-dichloroindophenol (DCIP). Cell free extract of strain Br-6 showed a dicumarol-sensitive diaphorase activity, which catalyzes the reduction of DCIP in the presence of NADH. Following abiotic experiments showed that the reduced form of DCIP was reoxidized by ferric iron, and that the resulting ferrous iron reduced bromate abiotically. Furthermore, activity staining of the cell free extract revealed that one of diaphorase isoforms possessed a bromate-reducing activity. Our results demonstrate that strain Br-6 utilizes multiple redox mediators, that is, DCIP and ferric iron, for bromate reduction. Since the apparent rate of bromate reduction by this strain (60 μM day -1 ) was 3 orders of magnitude higher than that of known bromate-reducing bacteria, it could be applicable to removal of this probable human carcinogen from drinking water.

[The combination effects of antibacterial agents against clinical isolated multiple-drug resistant Pseudomonas aeruginosa].

PubMed

Maesaki, Shigefumi; Yamaguchi, Toshiyuki; Sasaki, Kazumasa; Hashikita, Giichi; Shibuya, Shunsuke; Watanabe, Masaharu; Takayama, Sadao; Kawakami, Sayoko; Nagasawa, Mitsuaki; Suzuki, Noriyasu; Uchida, Takashi; Okabe, Tadashi; Kobayashi, Sugako

2006-02-01

The effectiveness of antibacterial agents against 70 strains of clinically isolated multiple-drug resistant Pseudomonas aeruginosa (MDRP) was measured by the micro dilution method. Fifty of all strains (71%) produced metallo-beta-lactamase and the IMP-1 gene was detected by polymerase chain reaction (PCR). The MIC90 (the minimum inhibitory concentration of an antibiotic necessary to inhibit the growth of 90% of bacterial strains) values of biapenem (BIPM), meropenem (MEPM), tazobactam/piperacillin (TAZ/PIPC), sulbactam/ cefoperazone (SBT/CPZ), cefepime (CFPM), ciprofloxacin (CPFX), pazufloxacin (PZFX), amikacin (AMK) and aztreonam (AZT) were found to be 265, 512, 256, 512, 512, 64, 128, 128 and 128 microg/mL, respectively. The in vitro combination effects of antibacterial agents were examined against 62 strains of MDRP and the synergy or additive effects were evaluated by fractional inhibitory concentration (FIC) index calculated by the checkerboard method. The combination of AMK and AZT showed synergy effects on 15/59 (25.4%) strains of MDRP. The synergy and additive effects on the MDRP strains were also found by the other antibacterial agents combination such as TAZ/PIPC and AMK, CFPM and AMK, and SBT/CPZ and AZT. These results suggested the necessity of further investigation of clinical usefulness.

Evidence of Brucella strain ST27 in bottlenose dolphin (Tursiops truncatus) in Europe.

PubMed

Cvetnić, Željko; Duvnjak, Sanja; Đuras, Martina; Gomerčić, Tomislav; Reil, Irena; Zdelar-Tuk, Maja; Špičić, Silvio

2016-11-30

Marine mammal brucellosis has been known for more than 20 years, but recent work suggests it is more widespread than originally thought. Brucella (B.) pinnipedialis has been isolated from pinnipeds, while B. ceti strains have been associated with cetaceans. Here we report a Brucella strain isolated from multiple lymph nodes of one bottlenose dolphin (Tursiops truncatus) during routine examination of dolphin carcasses found in the Croatian part of the northern Adriatic Sea during the summer of 2015. Classical bacteriological biotyping, PCR-based techniques (single, multiplex, PCR-RFLP) and 16S rRNA DNA sequencing were used to identify Brucella spp. Multiple-locus variable number tandem repeat analysis of 16 loci and multilocus sequence typing of 9 loci were used for genotyping and species determination. The combination of bacteriological, molecular and genotyping techniques identified our strain as ST27, previously identified as a human pathogen. This report provides, to our knowledge, the first evidence of ST27 in the Adriatic Sea in particular and in European waters in general. The zoonotic nature of the strain and its presence in the Adriatic, which is inhabited by bottlenose dolphins, suggest that the strain may pose a significant threat to human health. Copyright © 2016 Elsevier B.V. All rights reserved.

Curved Displacement Transfer Functions for Geometric Nonlinear Large Deformation Structure Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran; Lung, Shun-Fat

2017-01-01

For shape predictions of structures under large geometrically nonlinear deformations, Curved Displacement Transfer Functions were formulated based on a curved displacement, traced by a material point from the undeformed position to deformed position. The embedded beam (depth-wise cross section of a structure along a surface strain-sensing line) was discretized into multiple small domains, with domain junctures matching the strain-sensing stations. Thus, the surface strain distribution could be described with a piecewise linear or a piecewise nonlinear function. The discretization approach enabled piecewise integrations of the embedded-beam curvature equations to yield the Curved Displacement Transfer Functions, expressed in terms of embedded beam geometrical parameters and surface strains. By entering the surface strain data into the Displacement Transfer Functions, deflections along each embedded beam can be calculated at multiple points for mapping the overall structural deformed shapes. Finite-element linear and nonlinear analyses of a tapered cantilever tubular beam were performed to generate linear and nonlinear surface strains and the associated deflections to be used for validation. The shape prediction accuracies were then determined by comparing the theoretical deflections with the finiteelement- generated deflections. The results show that the newly developed Curved Displacement Transfer Functions are very accurate for shape predictions of structures under large geometrically nonlinear deformations.

Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China.

PubMed

Sun, Mingjun; Jing, Zhigang; Di, Dongdong; Yan, Hao; Zhang, Zhicheng; Xu, Quangang; Zhang, Xiyue; Wang, Xun; Ni, Bo; Sun, Xiangxiang; Yan, Chengxu; Yang, Zhen; Tian, Lili; Li, Jinping; Fan, Weixing

2017-01-01

Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2) was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2) and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs) were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS)-single-nucleotide polymorphism (SNP)-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.

Engineering Strain for Improved III-Nitride Optoelectronic Device Performance

NASA Astrophysics Data System (ADS)

Van Den Broeck, Dennis Marnix

Due to growing environmental and economic concerns, renewable energy generation and high-efficiency lighting are becoming even more important in the scientific community. III-Nitride devices have been essential in production of high-brightness light-emitting diodes (LEDs) and are now entering the photovoltaic (PV) realm as the technology advances. InGaN/GaN multiple quantum well LEDs emitting in the blue/green region have emerged as promising candidates for next-generation lighting technologies. Due to the large lattice mismatch between InN and GaN, large electric fields exist within the quantum well layers and result in low rates of radiative recombination, especially for the green spectral region. This is commonly referred to as the "green gap" and results in poor external quantum efficiencies for light-emitting diodes and laser diodes. In order to mitigate the compressive stress of InGaN QWs, a novel growth technique is developed in order to grown thick, strain-relaxed In yGa1-yN templates for 0.08 < y < 0.11. By inserting 2 nm GaN interlayers into the growing InyGa1-yN film, and subsequently annealing the structure, "semibulk" InGaN templates were achieved with vastly superior crystal and optical properties than bulk InGaN films. These semibulk InGaN templates were then utilized as new templates for multiple quantum well active layers, effectively reducing the compressive strain in the InGaN wells due to the larger lattice constant of the InGaN template with respect to a GaN template. A zero-stress balance method was used in order to realize a strain-balanced multiple quantum well structure, which again showed improved optical characteristics when compared to fully-strain active regions. The semibulk InGaN template was then implemented into "strain-compensated" LED structures, where light emission was achieved with very little leakage current. Discussion of these strain-compensated devices compared to conventional LEDs is detailed.

The Asd(+)-DadB(+) dual-plasmid system offers a novel means to deliver multiple protective antigens by a recombinant attenuated Salmonella vaccine.

PubMed

Xin, Wei; Wanda, Soo-Young; Zhang, Xiangmin; Santander, Javier; Scarpellini, Giorgio; Ellis, Karen; Alamuri, Praveen; Curtiss, Roy

2012-10-01

We developed means to deliver multiple heterologous antigens on dual plasmids with non-antibiotic-resistance markers in a single recombinant attenuated vaccine strain of Salmonella enterica serotype Typhimurium. The first component of this delivery system is a strain of S. Typhimurium carrying genomic deletions in alr, dadB, and asd, resulting in obligate requirements for diaminopimelic acid (DAP) and d-alanine for growth. The second component is the Asd(+)-DadB(+) plasmid pair carrying wild-type copies of asdA and dadB, respectively, to complement the mutations. To evaluate the protection efficacy of the dual-plasmid vaccine, S. Typhimurium strain χ9760 (a strain with multiple attenuating mutations: Δasd Δalr ΔdadB ΔrecF) was transformed with Asd(+) and DadB(+) plasmids specifying pneumococcal antigens PspA and PspC, respectively. Both plasmids were stable in χ9760 for 50 generations when grown in nonselective medium. This was significantly (P < 0.05) greater than the stability seen in its recF(+) counterpart χ9590 and could be attributed to reduced interplasmid recombination in χ9760. Oral immunization of BALB/c mice with 1 × 10(9) CFU of χ9760 (carrying Asd(+)-PspA and DadB(+)-PspC plasmids) elicited a dominant Th1-type serum IgG response against both antigens and protected mice against intraperitoneal challenge with 200 50% lethal doses (LD(50)s) of virulent Streptococcus pneumoniae strain WU2 or intravenous challenge with 100 LD(50)s of virulent S. pneumoniae strain L81905 or intranasal challenge with a lethal dose of S. pneumoniae A66.1 in a pneumonia model. Protection offered by χ9760 was superior to that offered by the mixture of two strains, χ9828 (Asd(+)-PspA) and χ11026 (DadB(+)-PspC). This novel dual-plasmid system marks a remarkable improvement in the development of live bacterial vaccines.

The Asd+-DadB+ Dual-Plasmid System Offers a Novel Means To Deliver Multiple Protective Antigens by a Recombinant Attenuated Salmonella Vaccine

PubMed Central

Xin, Wei; Wanda, Soo-Young; Zhang, Xiangmin; Santander, Javier; Scarpellini, Giorgio; Ellis, Karen; Alamuri, Praveen

2012-01-01

We developed means to deliver multiple heterologous antigens on dual plasmids with non-antibiotic-resistance markers in a single recombinant attenuated vaccine strain of Salmonella enterica serotype Typhimurium. The first component of this delivery system is a strain of S. Typhimurium carrying genomic deletions in alr, dadB, and asd, resulting in obligate requirements for diaminopimelic acid (DAP) and d-alanine for growth. The second component is the Asd+-DadB+ plasmid pair carrying wild-type copies of asdA and dadB, respectively, to complement the mutations. To evaluate the protection efficacy of the dual-plasmid vaccine, S. Typhimurium strain χ9760 (a strain with multiple attenuating mutations: Δasd Δalr ΔdadB ΔrecF) was transformed with Asd+ and DadB+ plasmids specifying pneumococcal antigens PspA and PspC, respectively. Both plasmids were stable in χ9760 for 50 generations when grown in nonselective medium. This was significantly (P < 0.05) greater than the stability seen in its recF+ counterpart χ9590 and could be attributed to reduced interplasmid recombination in χ9760. Oral immunization of BALB/c mice with 1 × 109 CFU of χ9760 (carrying Asd+-PspA and DadB+-PspC plasmids) elicited a dominant Th1-type serum IgG response against both antigens and protected mice against intraperitoneal challenge with 200 50% lethal doses (LD50s) of virulent Streptococcus pneumoniae strain WU2 or intravenous challenge with 100 LD50s of virulent S. pneumoniae strain L81905 or intranasal challenge with a lethal dose of S. pneumoniae A66.1 in a pneumonia model. Protection offered by χ9760 was superior to that offered by the mixture of two strains, χ9828 (Asd+-PspA) and χ11026 (DadB+-PspC). This novel dual-plasmid system marks a remarkable improvement in the development of live bacterial vaccines. PMID:22868499

High spatial resolution distributed optical fiber dynamic strain sensor with enhanced frequency and strain resolution.

PubMed

Masoudi, Ali; Newson, Trevor P

2017-01-15

A distributed optical fiber dynamic strain sensor with high spatial and frequency resolution is demonstrated. The sensor, which uses the ϕ-OTDR interrogation technique, exhibited a higher sensitivity thanks to an improved optical arrangement and a new signal processing procedure. The proposed sensing system is capable of fully quantifying multiple dynamic perturbations along a 5 km long sensing fiber with a frequency and spatial resolution of 5 Hz and 50 cm, respectively. The strain resolution of the sensor was measured to be 40 nε.

Quantification of carotid artery plaque stability with multiple region of interest based ultrasound strain indices and relationship with cognition

NASA Astrophysics Data System (ADS)

Meshram, N. H.; Varghese, T.; Mitchell, C. C.; Jackson, D. C.; Wilbrand, S. M.; Hermann, B. P.; Dempsey, R. J.

2017-08-01

Vulnerability and instability in carotid artery plaque has been assessed based on strain variations using noninvasive ultrasound imaging. We previously demonstrated that carotid plaques with higher strain indices in a region of interest (ROI) correlated to patients with lower cognition, probably due to cerebrovascular emboli arising from these unstable plaques. This work attempts to characterize the strain distribution throughout the entire plaque region instead of being restricted to a single localized ROI. Multiple ROIs are selected within the entire plaque region, based on thresholds determined by the maximum and average strains in the entire plaque, enabling generation of additional relevant strain indices. Ultrasound strain imaging of carotid plaques, was performed on 60 human patients using an 18L6 transducer coupled to a Siemens Acuson S2000 system to acquire radiofrequency data over several cardiac cycles. Patients also underwent a battery of neuropsychological tests under a protocol based on National Institute of Neurological Disorders and Stroke and Canadian Stroke Network guidelines. Correlation of strain indices with composite cognitive index of executive function revealed a negative association relating high strain to poor cognition. Patients grouped into high and low cognition groups were then classified using these additional strain indices. One of our newer indices, namely the average L  -  1 norm with plaque (AL1NWP) presented with significantly improved correlation with executive function when compared to our previously reported maximum accumulated strain indices. An optimal combination of three of the new indices generated classifiers of patient cognition with an area under the curve (AUC) of 0.880, 0.921 and 0.905 for all (n  =  60), symptomatic (n  =  33) and asymptomatic patients (n  =  27) whereas classifiers using maximum accumulated strain indices alone provided AUC values of 0.817, 0.815 and 0.813 respectively.

[Use of multiple locus variable number tandem repeats analysis for the Brucella systematization].

PubMed

Kulakov, Iu K; Kovalev, D A; Misetova, E N; Golovneva, S I; Liapustina, L V; Zheludkov, M M

2012-01-01

The methods of molecular-genetic differentiation to strain level acquire increasing significance in the current system of struggle with brucellosis. MLVA (multiple locus variable number tandem repeats analysis) was selected for molecular-genetic differentiation to strain level and simultaneous establishment of the genetic relationship of investigated Brucella strains. The goal of this work was MLVA typing of three pathogenic Brucella species strains with the analysis of stability of chosen loci, discrimination power and concordance to conventional phenotypic methods of the Brucella differentiation for use in systematization of brucellosis causing agents. Twenty six Brucella strains representing reference (n = 15), vaccine (n = 2) and field strains of three pathogenic Brucella species were tested: B. melitensis (n = 3), B. abortus (n = 2), B. suis (n = 2), and isolates (n = 2) with unidentified taxonomic position using MLVA with 9 pairs primers on known variable loci of Brucella genome. The analysis of the stability of chosen loci, discrimination power on Hunter-Gaston discrimination index (HGDI) and consistency to phenotypic methods of identification was performed. MLVA was confirmed for the results of phenotypic methods of identification, stability of the chosen loci in majority reference, and vaccine strains with a high index of variability HGDI 0.9969 for all loci. A dendrogram was plotted on the basis of MLVA data on distributed Brucella strains in related clusters according to its taxonomic species and biovar positions and construction of 25 genotypes. B. melitensis strains formed cluster related to the reference strain of B. melitensis 63/9 biovar 2. Australian isolates of Brucella 83-4 and Brucella 83-6 isolated from rodents formed a cluster distant from other strains of Brucella. MLVA is a promising method for differentiation of Brucella strains with known and unresolved taxonomic status for their systematization and creation of MLVA genotype catalogue that will promote qualitative improvement of brucellosis surveillance system in Russia.

Quantification of carotid artery plaque stability with multiple region of interest based ultrasound strain indices and relationship with cognition.

PubMed

Meshram, N H; Varghese, T; Mitchell, C C; Jackson, D C; Wilbrand, S M; Hermann, B P; Dempsey, R J

2017-07-17

Vulnerability and instability in carotid artery plaque has been assessed based on strain variations using noninvasive ultrasound imaging. We previously demonstrated that carotid plaques with higher strain indices in a region of interest (ROI) correlated to patients with lower cognition, probably due to cerebrovascular emboli arising from these unstable plaques. This work attempts to characterize the strain distribution throughout the entire plaque region instead of being restricted to a single localized ROI. Multiple ROIs are selected within the entire plaque region, based on thresholds determined by the maximum and average strains in the entire plaque, enabling generation of additional relevant strain indices. Ultrasound strain imaging of carotid plaques, was performed on 60 human patients using an 18L6 transducer coupled to a Siemens Acuson S2000 system to acquire radiofrequency data over several cardiac cycles. Patients also underwent a battery of neuropsychological tests under a protocol based on National Institute of Neurological Disorders and Stroke and Canadian Stroke Network guidelines. Correlation of strain indices with composite cognitive index of executive function revealed a negative association relating high strain to poor cognition. Patients grouped into high and low cognition groups were then classified using these additional strain indices. One of our newer indices, namely the average L  -  1 norm with plaque (AL1NWP) presented with significantly improved correlation with executive function when compared to our previously reported maximum accumulated strain indices. An optimal combination of three of the new indices generated classifiers of patient cognition with an area under the curve (AUC) of 0.880, 0.921 and 0.905 for all (n  =  60), symptomatic (n  =  33) and asymptomatic patients (n  =  27) whereas classifiers using maximum accumulated strain indices alone provided AUC values of 0.817, 0.815 and 0.813 respectively.

Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation

PubMed Central

Dafopoulou, Konstantina; Xavier, Basil Britto; Hotterbeekx, An; Janssens, Lore; Lammens, Christine; Dé, Emmanuelle; Goossens, Herman; Tsakris, Athanasios; Malhotra-Kumar, Surbhi

2015-01-01

In two pairs of clinical colistin-susceptible/colistin-resistant (Csts/Cstr) Acinetobacter baumannii strains, the Cstr strains showed significantly decreased biofilm formation in static and dynamic assays (P < 0.001) and lower relative fitness (P < 0.05) compared with those of the Csts counterparts. The whole-genome sequencing comparison of strain pairs identified a mutation converting a stop codon to lysine (*241K) in LpsB (involved in lipopolysaccharide [LPS] synthesis) in one Cstr strain and a frameshift mutation in CarO and the loss of a 47,969-bp element containing multiple genes associated with biofilm production in the other. PMID:26666921

Bioelectrochemically-assisted reductive dechlorination of 1,2-dichloroethane by a Dehalococcoides-enriched microbial culture.

PubMed

Leitão, Patrícia; Rossetti, Simona; Nouws, Henri P A; Danko, Anthony S; Majone, Mauro; Aulenta, Federico

2015-11-01

The aim of this study was to verify the possibility to use a polarized graphite electrode as an electron donor for the reductive dechlorination of 1,2-dichloroethane, an ubiquitous groundwater contaminant. The rate of 1,2-DCA dechlorination almost linearly increased by decreasing the set cathode potential over a broad range of set cathode potentials (i.e., from -300 mV to -900 mV vs. the standard hydrogen electrode). This process was primarily dependent on electrolytic H2 generation. On the other hand, reductive dechlorination proceeded (although quite slowly) with a very high Coulombic efficiency (near 70%) at a set cathode potential of -300 mV, where no H2 production occurred. Under this condition, reductive dechlorination was likely driven by direct electron uptake from the surface of the polarized electrode. Taken as a whole, this study further extends the range of chlorinated contaminants which can be treated with bioelectrochemical systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite.

PubMed

Nijenhuis, Ivonne; Stollberg, Reiner; Lechner, Ute

2018-04-01

The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.

Contributions of Abiotic and Biotic Dechlorination Following Carboxymethyl Cellulose Stabilized Nanoscale Zero Valent Iron Injection.

PubMed

Kocur, Chris M D; Lomheim, Line; Boparai, Hardiljeet K; Chowdhury, Ahmed I A; Weber, Kela P; Austrins, Leanne M; Edwards, Elizabeth A; Sleep, Brent E; O'Carroll, Denis M

2015-07-21

A pilot scale injection of nanoscale zerovalent iron (nZVI) stabilized with carboxymethyl cellulose (CMC) was performed at an active field site contaminated with a range of chlorinated volatile organic compounds (cVOC). The cVOC concentrations and microbial populations were monitored at the site before and after nZVI injection. The remedial injection successfully reduced parent compound concentrations on site. A period of abiotic degradation was followed by a period of enhanced biotic degradation. Results suggest that the nZVI/CMC injection created conditions that stimulated the native populations of organohalide-respiring microorganisms. The abundance of Dehalococcoides spp. immediately following the nZVI/CMC injection increased by 1 order of magnitude throughout the nZVI/CMC affected area relative to preinjection abundance. Distinctly higher cVOC degradation occurred as a result of the nZVI/CMC injection over a 3 week evaluation period when compared to control wells. This suggests that both abiotic and biotic degradation occurred following injection.

Effects of different electron donor feeding patterns on TCE reductive dechlorination performance.

PubMed

Panagiotakis, I; Antoniou, K; Mamais, D; Pantazidou, M

2015-03-01

This study investigates how the feeding pattern of e(-) donors might affect the efficiency of enhanced in situ bioremediation in TCE-contaminated aquifers. A series of lab-scale batch experiments were conducted using butyrate or hydrogen gas (H2) as e(-) donor and a TCE-dechlorinating microbial consortium dominated by Dehalococcoides spp. The results of these experiments demonstrate that butyrate is similarly efficient for TCE dechlorination whether it is injected once or in doses. Moreover, the present work indicates that the addition of butyrate in great excess cannot be avoided, since it most likely provide, even indirectly, significant part of the H2 required. Furthermore, methanogenesis appears to be the major ultimate e(-) accepting process in all experiments, regardless the e(-) donor used and the feeding pattern. Finally, the timing of injection of H2 seems to significantly affect dechlorination performance, since the injection during the early stages improves VC-to-ETH dechlorination and reduce methanogenic activity.

Genetic Heterogeneity in Mycobacterium tuberculosis Isolates Reflected in IS6110 Restriction Fragment Length Polymorphism Patterns as Low-Intensity Bands

PubMed Central

de Boer, Annette S.; Kremer, Kristin; Borgdorff, Martien W.; de Haas, Petra E. W.; Heersma, Herre F.; van Soolingen, Dick

2000-01-01

Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to originate from the same ancestral strain and thus to reflect ongoing transmission. In this study, we investigated 1,277 IS6110 RFLP patterns for the presence of multiple low-intensity bands (LIBs), which may indicate infections with multiple M. tuberculosis strains. We did not find any multiple LIBs, suggesting that multiple infections are rare in the Netherlands. However, we did observe a few LIBs in 94 patterns (7.4%) and examined the nature of this phenomenon. With single-colony cultures it was found that LIBs mostly represent mixed bacterial populations with slightly different RFLP patterns. Mixtures were expressed in RFLP patterns as LIBs when 10 to 30% of the DNA analyzed originated from a bacterial population with another RFLP pattern. Presumably, a part of the LIBs did not represent mixed bacterial populations, as in some clusters all strains exhibited LIBs in their RFLP patterns. The occurrence of LIBs was associated with increased age in patients. This may reflect either a gradual change of the bacterial population in the human body over time or IS6110-mediated genetic adaptation of M. tuberculosis to changes in the environmental conditions during the dormant state or reactivation thereafter. PMID:11101583

[Multiplication of Brucella abortus and production of nitric oxide in two macrophage cell lines of different origin].

PubMed

Serafino, J; Conde, S; Zabal, O; Samartino, L

2007-01-01

Brucella abortus is a bacterium which causes abortions and infertility in cattle and undulant fever in humans. It multiplies intracellularly, evading the mechanisms of cellular death. Nitric oxide (NO) is important in the regulation of the immune response. In the present work, we studied the ability of three B. abortus strains to survive intracellularly in two macrophage cell lines. The bacterial multiplication in both cell lines was determined at two different times in UFC/ ml units. Moreover the inoculated cells were also observed under light-field and fluorescence microscopy stained with Giemsa and acridine orange, respectively. The stain of both cellular lines showed similar results with respect to the UFC/ml determination. The presence of B. abortus was confirmed by electronic microscopy. In both macrophage cell lines inoculated with the rough strain RB51, the multiplication diminished and the level of NO was higher, compared with cells inoculated with smooth strains (S19 and 2308). These results suggest that the absence of O-chain of LPS probably affects the intracellular growth of B. abortus.

An Experimental Study of Large Compressive Loads Upon Residual Strain Fields and the Interaction Between Surface Strain Fields Created by Coldworking Fastener Holes.

DTIC Science & Technology

1981-02-01

Strains" (J. of Basic Eng., Vol. 82, Series D, June 1960), pp, 426-434. 10. Morse, S., A.J. Durelli, and C.A. Sciammarella , "Geo- metry of Moire...grid Method, a Practical Moire Stress-analysis Tool" (Exp. Mech., Vol. 7, July 1967), pp. 19A-22A. 20. Sciammarella , C., "Moire-fringe Multiplication

Effects of feedstock and co-culture of Lactobacillus fermentum and wild Saccharomyces cerevisiae strain during fuel ethanol fermentation by the industrial yeast strain PE-2.

PubMed

Reis, Vanda R; Bassi, Ana Paula G; Cerri, Bianca C; Almeida, Amanda R; Carvalho, Isis G B; Bastos, Reinaldo G; Ceccato-Antonini, Sandra R

2018-02-16

Even though contamination by bacteria and wild yeasts are frequently observed during fuel ethanol fermentation, our knowledge regarding the effects of both contaminants together is very limited, especially considering that the must composition can vary from exclusively sugarcane juice to a mixture of molasses and juice, affecting the microbial development. Here we studied the effects of the feedstock (sugarcane juice and molasses) and the co-culture of Lactobacillus fermentum and a wild Saccharomyces cerevisiae strain (rough colony and pseudohyphae) in single and multiple-batch fermentation trials with an industrial strain of S. cerevisiae (PE-2) as starter yeast. The results indicate that in multiple-cycle batch system, the feedstock had a minor impact on the fermentation than in single-cycle batch system, however the rough yeast contamination was more harmful than the bacterial contamination in multiple-cycle batch fermentation. The inoculation of both contaminants did not potentiate the detrimental effect in any substrate. The residual sugar concentration in the fermented broth had a higher concentration of fructose than glucose for all fermentations, but in the presence of the rough yeast, the discrepancy between fructose and glucose concentrations were markedly higher, especially in molasses. The biggest problem associated with incomplete fermentation seemed to be the lower consumption rate of sugar and the reduced fructose preference of the rough yeast rather than the lower invertase activity. Lower ethanol production, acetate production and higher residual sugar concentration are characteristics strongly associated with the rough yeast strain and they were not potentiated with the inoculation of L. fermentum.

Natural Hot Spots for Gain of Multiple Resistances: Arsenic and Antibiotic Resistances in Heterotrophic, Aerobic Bacteria from Marine Hydrothermal Vent Fields

PubMed Central

Farias, Pedro; Espírito Santo, Christophe; Branco, Rita; Francisco, Romeu; Santos, Susana; Hansen, Lars; Sorensen, Soren

2015-01-01

Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and arsB genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the “Rapid Annotation using the Subsystems Technology” server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population. PMID:25636836

[The characteristics of Vibrio cholerae isolated in Dagestan in 1994].

PubMed

Podosinnikova, L S; Mazrukho, B L; Lomov, Iu M; Khanum'ian, T A; Voronezhskaia, L G; Kudriakova, T A; Makedonova, L D; Mironova, A V

1995-01-01

A high degree of resistance to cholera diagnostic phages and carriership of prophages characteristic of V. cholerae eltor strains vct+ were shown to be the specific features V. cholerae isolated in Daghestan during the period of June-October 1994. Among the strains under study, isolated respectively in 12 and 18 out of 19 regions of Daghestan, a high proportion was found to have resistance to tetracycline (65%) and chloramphenicol (28.6%). Moreover, some strains were found to be resistant to furagin and erythromycin. Out of 242 strains resistant to antibacterial preparations, 163 strains were found to have multiple resistance. Gentamicin, cipropfloxacin and doxicycline were shown to have high in vitro activity with respect to the strains under study.

ISOLATION OF THE GENOME SEQUENCE STRAIN MYCOBACTERIUM AVIUM 104 FROM MULTIPLE PATIENTS OVER A 17-YEAR PERIOD

EPA Science Inventory

The genome sequence strain 104 of the opportunistic pathogen Mycobacterium avium was isolated form an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosis M. avium from 207 other patients in Southern California and elsewhere were examined for genoty...

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

PubMed Central

Borneman, Anthony R.; Desany, Brian A.; Riches, David; Affourtit, Jason P.; Forgan, Angus H.; Pretorius, Isak S.; Egholm, Michael; Chambers, Paul J.

2011-01-01

Human intervention has subjected the yeast Saccharomyces cerevisiae to multiple rounds of independent domestication and thousands of generations of artificial selection. As a result, this species comprises a genetically diverse collection of natural isolates as well as domesticated strains that are used in specific industrial applications. However the scope of genetic diversity that was captured during the domesticated evolution of the industrial representatives of this important organism remains to be determined. To begin to address this, we have produced whole-genome assemblies of six commercial strains of S. cerevisiae (four wine and two brewing strains). These represent the first genome assemblies produced from S. cerevisiae strains in their industrially-used forms and the first high-quality assemblies for S. cerevisiae strains used in brewing. By comparing these sequences to six existing high-coverage S. cerevisiae genome assemblies, clear signatures were found that defined each industrial class of yeast. This genetic variation was comprised of both single nucleotide polymorphisms and large-scale insertions and deletions, with the latter often being associated with ORF heterogeneity between strains. This included the discovery of more than twenty probable genes that had not been identified previously in the S. cerevisiae genome. Comparison of this large number of S. cerevisiae strains also enabled the characterization of a cluster of five ORFs that have integrated into the genomes of the wine and bioethanol strains on multiple occasions and at diverse genomic locations via what appears to involve the resolution of a circular DNA intermediate. This work suggests that, despite the scrutiny that has been directed at the yeast genome, there remains a significant reservoir of ORFs and novel modes of genetic transmission that may have significant phenotypic impact in this important model and industrial species. PMID:21304888

Growth dynamics of Salmonella enterica strains on alfalfa sprouts and in waste seed irrigation water.

PubMed

Howard, Michael B; Hutcheson, Steven W

2003-01-01

Alfalfa sprouts and other seed sprouts have been implicated in numerous outbreaks of salmonellosis. The source of these epidemics appears to have been low-level contamination of seeds by Salmonella bacteria that developed into clinically significant populations during the seed germination process. To test the possibility that Salmonella enterica strains carry host range determinants that allow them to grow on alfalfa, strains isolated from alfalfa or other sources were surveyed for their ability to grow on germinating alfalfa seeds. An S. enterica serovar Cubana strain originally isolated from contaminated alfalfa sprouts multiplied most rapidly during the initial 24 h of the seed germination process. Germinating alfalfa seeds supported the multiplication of S. enterica cells prior to the emergence of the root radicle at 72 h. Thereafter, much lower rates of multiplication were apparent. The ability of S. enterica to grow on germinating alfalfa seeds was independent of the serovar, isolation source, or virulence of the strain. Isolates obtained from alfalfa attained population levels similar to those observed for strains isolated from contaminated meat products or stools. Each of the strains could be detected in the waste irrigation water, with populations being strongly correlated with those detected on the germinating alfalfa seeds. The S. enterica strains were capable of utilizing the waste irrigation water as a sole carbon and nitrogen source. S. enterica strains thus appear to grow saprophytically on soluble organics released from seeds during early phases of germination. The ability to detect S. enterica in the waste irrigation water early in the germination process indicates that this method may be used as a simple way to monitor the contamination of sprouts during commercial operations.

Arthritis symptoms, the work environment, and the future: measuring perceived job strain among employed persons with arthritis.

PubMed

Gignac, Monique A M; Sutton, Deborah; Badley, Elizabeth M

2007-06-15

To develop a measure of job strain related to differing aspects of working with arthritis and to examine the demographic, illness, work context, and psychosocial variables associated with it. Study participants were 292 employed individuals with osteoarthritis or inflammatory arthritis. Participants were from wave 3 of a 4-wave longitudinal study examining coping and adaptation efforts used to remain employed. Participants completed an interview-administered structured questionnaire, including a Chronic Illness Job Strain Scale (CIJSS) and questions on demographic (e.g., age, sex), illness and disability (e.g., disease type, pain, activity limitations), work context (e.g., job type, job control), and psychosocial variables (e.g., arthritis-work spillover, coworker/managerial support, job perceptions). Principal component analysis and multiple linear regression were used to analyze the data. A single factor solution emerged for the CIJSS. The scale had an internal reliability of 0.95. Greater job strain was reported for future uncertainty, balancing multiple roles, and difficulties accepting the disease than for current workplace conditions. Participants with inflammatory arthritis, more frequent severe pain, greater workplace activity limitations, fewer hours of work, less coworker support, and greater arthritis-work spillover reported greater job strain. The findings underscore the diverse areas that contribute to perceptions of job strain and suggest that existing models of job strain do not adequately capture the stress experienced by individuals working with chronic illnesses or the factors associated with job strain. Measures similar to the CIJSS can enhance the tools researchers and clinicians have available to examine the impact of arthritis in individuals' lives.

Financial strain and cancer risk behaviors among African Americans.

PubMed

Advani, Pragati S; Reitzel, Lorraine R; Nguyen, Nga T; Fisher, Felicia D; Savoy, Elaine J; Cuevas, Adolfo G; Wetter, David W; McNeill, Lorna H

2014-06-01

African Americans suffer disproportionately from the adverse consequences of behavioral risk factors for cancer relative to other ethnic groups. Recent studies have assessed how financial strain might uniquely contribute to engagement in modifiable behavioral risk factors for cancer, but not among African Americans. The current study examined associations between financial strain and modifiable cancer risk factors (smoking, at-risk alcohol use, overweight/obesity, insufficient physical activity, inadequate fruit and vegetable intake, and multiple risk factors) among 1,278 African American adults (age, 46.5 ± 12.6 years; 77% female) and explored potential mediators (stress and depressive symptoms) of those associations. Logistic regression models were used to examine associations between financial strain and cancer risk factors. Analyses were adjusted for age, sex, partner status, income, educational level, and employment status. Analyses involving overweight/obesity status additionally controlled for fruit and vegetable intake and physical activity. Nonparametric bootstrapping procedures were used to assess mediation. Greater financial strain was associated with greater odds of insufficient physical activity (P < 0.003) and smoking (P = 0.005) and was positively associated with the total number of cancer risk factors (P < 0.0001). There was a significant indirect effect of both stress and depressive symptoms on the relations of financial strain with physical inactivity and multiple risk factors, respectively. Future interventions aimed at reducing cancer disparities should focus on African Americans experiencing higher financial strain while addressing their stress and depressive symptoms. Longitudinal studies are needed to assess the temporal and causal relations between financial strain and modifiable behavioral cancer risk factors among African Americans. ©2014 American Association for Cancer Research.

Competition between two virulent Marek's disease virus strains in vivo.

PubMed

Dunn, John R; Silva, Robert F; Lee, Lucy F; Witter, Richard L

2012-01-01

Previous studies have demonstrated the presence of multiple strains of Marek's disease virus simultaneously circulating within poultry flocks, leading to the assumption that individual birds are repeatedly exposed to a variety of virus strains in their lifetime. Virus competition within individual birds may be an important factor that influences the outcome of co-infection under field conditions, including the potential outcome of emergence or evolution of more virulent strains. A series of experiments was designed to evaluate virus competition within chickens following simultaneous challenge with two virulent serotype 1 Marek's disease virus strains, using either pathogenically similar (rMd5 and rMd5/pp38CVI) or dissimilar (JM/102W and rMd5/pp38CVI) virus pairs. Bursa of Fabricius, feather follicle epithelium, spleen, and tumour samples were collected at multiple time points to determine the frequency and distribution of each virus present using pyrosequencing, immunohistochemistry and virus isolation. In the similar pair, rMd5 appeared to have a competitive advantage over rMd5/pp38CVI, which in turn had a competitive advantage over the less virulent JM/102W in the dissimilar virus pair. Dominance of one strain over the other was not absolute for either virus pair, as the subordinate virus was rarely eliminated. Interestingly, competition between two viruses with either pair rarely ended in a draw. Further work is needed to identify factors that influence virus-specific dominance to better understand what characteristics favour emergence of one strain in chicken populations at the expense of other strains.

Screening of freshwater fungi for decolorizing multiple synthetic dyes.

PubMed

Yang, Panpan; Shi, Wenxiao; Wang, Hongkai; Liu, Hongmei

The biodegradation of synthetic dyes by fungi is emerging as an effective and promising approach. In the present study, freshwater fungal strains isolated from submerged woods were screened for the decolorization of 7 synthetic dyes. Subsequently, 13 isolates with high decolorization capability were assessed in a liquid system; they belonged to 9 different fungal species. Several strains exhibited a highly effective decolorization of multiple types of dyes. New absorbance peaks appeared after the treatment with 3 fungal strains, which suggests that a biotransformation process occurred through fungal biodegradation. These results showed the unexploited and valuable capability of freshwater fungi for the treatment of dye-containing effluents. The ability of certain fungi to decolorize dyes is reported here for the first time. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Listeria monocytogenes Strains Underrepresented during Selective Enrichment with an ISO Method Might Dominate during Passage through Simulated Gastric Fluid and In Vitro Infection of Caco-2 Cells

PubMed Central

Zilelidou, Evangelia; Karmiri, Christina-Vasiliki; Zoumpopoulou, Georgia; Mavrogonatou, Eleni; Kletsas, Dimitris; Tsakalidou, Effie; Papadimitriou, Konstantinos; Drosinos, Eleftherios

2016-01-01

ABSTRACT Various Listeria monocytogenes strains may contaminate a single food product, potentially resulting in simultaneous exposure of consumers to multiple strains. However, due to bias in strain recovery, L. monocytogenes strains isolated from foods by selective enrichment (SE) might not always represent those that can better survive the immune system of a patient. We investigated the effect of cocultivation in tryptic soy broth with 0.6% yeast extract (TSB-Y) at 10°C for 8 days on (i) the detection of L. monocytogenes strains during SE with the ISO 11290-1:1996/Amd 1:2004 protocol and (ii) the in vitro virulence of strains toward the Caco-2 human colon epithelial cancer cell line following exposure to simulated gastric fluid (SGF; pH 2.0)-HCl (37°C). We determined whether the strains which were favored by SE would be effective competitors under the conditions of challenges related to gastrointestinal passage of the pathogen. Interstrain competition of L. monocytogenes in TSB-Y determined the relative population of each strain at the beginning of SE. This in turn impacted the outcome of SE (i.e., favoring survival of competitors with better fitness) and the levels exposed subsequently to SGF. However, strong growth competitors could be outcompeted after SGF exposure and infection of Caco-2 cells by strains outgrown in TSB-Y and underdetected (or even missed) during enrichment. Our data demonstrate a preferential selection of certain L. monocytogenes strains during enrichments, often not reflecting a selective advantage of strains during infection. These findings highlight a noteworthy scenario associated with the difficulty of matching the source of infection (food) with the L. monocytogenes isolate appearing to be the causative agent during listeriosis outbreak investigations. IMPORTANCE This report is relevant to understanding the processes involved in selection and prevalence of certain L. monocytogenes strains in different environments (i.e., foods or sites of humans exposed to the pathogen). It highlights the occurrence of multiple strains in the same food as an important aspect contributing to mismatches between clinical isolates and infection sources during listeriosis outbreak investigations. PMID:27637880

Dislocation Multiplication by Single Cross Slip for FCC at Submicron Scales

NASA Astrophysics Data System (ADS)

Cui, Yi-Nan; Liu, Zhan-Li; Zhuang, Zhuo

2013-04-01

The operation mechanism of single cross slip multiplication (SCSM) is investigated by studying the response of one dislocation loop expanding in face-centered-cubic (FCC) single crystal using three-dimensional discrete dislocation dynamic (3D-DDD) simulation. The results show that SCSM can trigger highly correlated dislocation generation in a short time, which may shed some light on understanding the large strain burst observed experimentally. Furthermore, we find that there is a critical stress and material size for the operation of SCSM, which agrees with that required to trigger large strain burst in the compression tests of FCC micropillars.

Distributed Sensing of Carbon-Epoxy Composites and Filament Wound Pressure Vessels Using Fiber-Bragg Gratings

NASA Technical Reports Server (NTRS)

Grant, J.; Kaul, R.; Taylor, S.; Myer, G.; Jackson, K.; Osei, A.; Sharma, A.

2003-01-01

Multiple Fiber Bragg-gratings are embedded in carbon-epoxy laminates as well as in composite wound pressure vessel. Structural properties of such composites are investigated. The measurements include stress-strain relation in laminates and Poisson's ratio in several specimens with varying orientation of the optical fiber Bragg-sensor with respect to the carbon fiber in an epoxy matrix. Additionally, fiber Bragg gratings are bonded on the surface of these laminates and cylinders fabricated out of carbon-epoxy composites and multiple points are monitored and compared for strain measurements at several locations.

Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes.

PubMed

Ziemons, Sandra; Koutsantas, Katerina; Becker, Kordula; Dahlmann, Tim; Kück, Ulrich

2017-02-16

Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.

Sequence analysis of human rhinovirus aspirated from the nasopharynx of patients with relapsing-remitting MS.

PubMed

Kneider, M; Bergström, T; Gustafsson, C; Nenonen, N; Ahlgren, C; Nilsson, S; Andersen, O

2009-04-01

Upper respiratory infections were reported to trigger multiple sclerosis relapses. A relationship between picornavirus infections and MS relapses was recently reported. To evaluate whether human rhinovirus is associated with multiple sclerosis relapses and whether any particular strain is predominant. Nasopharyngeal fluid was aspirated from 36 multiple sclerosis patients at pre-defined critical time points. Reverse-transcriptase-PCR was performed to detect human rhinovirus-RNA. Positive amplicons were sequenced. We found that rhinovirus RNA was present in 17/40 (43%) of specimens obtained at the onset of a URTI in 19 patients, in 1/21 specimens during convalescence after URTI in 14 patients, in 0/6 specimens obtained in 5 patients on average a week after the onset of an "at risk" relapse, occurring within a window in time from one week before to three weeks after an infection, and in 0/17 specimens obtained after the onset of a "not at risk" relapse not associated with any infection in 12 patients. Fifteen specimens from healthy control persons not associated with URTI were negative. The frequency of HRV presence in URTI was similar to that reported for community infections. Eight amplicons from patients represented 5 different HRV strains. We were unable to reproduce previous findings of association between HRV infections and multiple sclerosis relapses. HRV was not present in nasopharyngeal aspirates obtained during "at risk" or "not at risk" relapses. Sequencing of HRV obtained from patients during URTI did not reveal any strain with predominance in multiple sclerosis.

Induction of Broad-Spectrum Protective Immunity against Disparate Cryptococcus Serotypes

PubMed Central

Van Dyke, Marley C. Caballero; Chaturvedi, Ashok K.; Hardison, Sarah E.; Leopold Wager, Chrissy M.; Castro-Lopez, Natalia; Hole, Camaron R.; Wozniak, Karen L.; Wormley, Floyd L.

2017-01-01

Cryptococcosis is a fungal disease caused by multiple Cryptococcus serotypes; particularly C. neoformans (serotypes A and D) and C. gattii (serotypes B and C). To date, there is no clinically available vaccine to prevent cryptococcosis. Mice given an experimental pulmonary vaccination with a C. neoformans serotype A strain engineered to produce interferon-γ, denoted H99γ, are protected against a subsequent otherwise lethal experimental infection with C. neoformans serotype A. Thus, we determined the efficacy of immunization with C. neoformans strain H99γ to elicit broad-spectrum protection in BALB/c mice against multiple disparate Cryptococcus serotypes. We observed significantly increased survival rates and significantly decreased pulmonary fungal burden in H99γ immunized mice challenged with Cryptococcus serotypes A, B, or D compared to heat-killed H99γ (HKH99γ) immunized mice. Results indicated that prolonged protection against Cryptococcus serotypes B or D in H99γ immunized mice was CD4+ T cell dependent and associated with the induction of predominantly Th1-type cytokine responses. Interestingly, immunization with H99γ did not elicit greater protection against challenge with the Cryptococcus serotype C tested either due to low overall virulence of this strain or enhanced capacity of this strain to evade host immunity. Altogether, these studies provide “proof-of-concept” for the development of a cryptococcal vaccine that provides cross-protection against multiple disparate serotypes of Cryptococcus. PMID:29163469

Nitrogen-fixing bacteria with multiple plant growth-promoting activities enhance growth of tomato and red pepper.

PubMed

Islam, Md Rashedul; Sultana, Tahera; Joe, M Melvin; Yim, Woojong; Cho, Jang-Cheon; Sa, Tongmin

2013-12-01

As a suitable alternative to chemical fertilizers, the application of plant growth-promoting rhizobacteria has been increasing in recent years due to their potential to be used as biofertilizers. In the present work, 13 nitrogen-fixing bacterial strains belonging to 11 different genera were tested for their PGP attributes. All of the strains were positive for 1-aminocyclopropane-1-carboxylate deaminase (ACCD), indole-3-acetic acid (IAA), salicylic acid, and ammonia production while negative for cellulase, pectinase, and hydrocyanic acid production. The strains Pseudomonas sp. RFNB3 and Serratia sp. RFNB14 were the most effective in solubilizing both tri-calcium phosphate and zinc oxide. In addition, all strains except Pseudomonas sp. RFNB3 were able to oxidize sulfur, and six strains were positive for siderophore synthesis. Each strain tested in this study possesses at least four PGP properties in addition to nitrogen fixation. Nine strains were selected based on their multiple PGP potential, particularly ACCD and IAA production, and evaluated for their effects on early growth of tomato and red pepper under gnotobiotic conditions. Bacterial inoculation considerably influenced root and shoot length, seedling vigor, and dry biomass of the two crop plants. Three strains that demonstrated substantial effects on plant performance were further selected for greenhouse trials with red pepper, and among them Pseudomonas sp. RFNB3 resulted in significantly higher plant height (26%) and dry biomass (28%) compared to control. The highest rate of nitrogen fixation, as determined by acetylene reduction assay, occurred in Novosphingobium sp. RFNB21 inoculated red pepper root (49.6 nM of ethylene/h/g of dry root) and rhizosphere soil (41.3 nM of ethylene/h/g of dry soil). Inoculation with nitrogen-fixing bacteria significantly increased chlorophyll content, and the uptake of different macro- and micro-nutrient contents enhancing also in red pepper shoots, in comparison with uninoculated controls. The population estimation studies showed that nitrogen-fixing as well as total heterotrophic bacteria were also noticeably increased in soil and plant samples. The findings of this study suggest that certain nitrogen-fixing strains possessing multiple PGP traits could be applied in the development of biofertilizers. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical properties of a-plane (Al, Ga)N/GaN multiple quantum wells grown on strain engineered Zn1-xMgxO layers by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Xia, Y.; Brault, J.; Nemoz, M.; Teisseire, M.; Vinter, B.; Leroux, M.; Chauveau, J.-M.

2011-12-01

Nonpolar (112¯0) Al0.2Ga0.8N/GaN multiple quantum wells (MQWs) have been grown by molecular beam epitaxy on (112¯0) Zn0.74Mg0.26O templates on r-plane sapphire substrates. The quantum wells exhibit well-resolved photoluminescence peaks in the ultra-violet region, and no sign of quantum confined Stark effect is observed in the complete multiple quantum well series. The results agree well with flat band quantum well calculations. Furthermore, we show that the MQW structures are strongly polarized along the [0001] direction. The origin of the polarization is discussed in terms of the strain anisotropy dependence of the exciton optical oscillator strengths.

Micro/Nano-scale Strain Distribution Measurement from Sampling Moiré Fringes.

PubMed

Wang, Qinghua; Ri, Shien; Tsuda, Hiroshi

2017-05-23

This work describes the measurement procedure and principles of a sampling moiré technique for full-field micro/nano-scale deformation measurements. The developed technique can be performed in two ways: using the reconstructed multiplication moiré method or the spatial phase-shifting sampling moiré method. When the specimen grid pitch is around 2 pixels, 2-pixel sampling moiré fringes are generated to reconstruct a multiplication moiré pattern for a deformation measurement. Both the displacement and strain sensitivities are twice as high as in the traditional scanning moiré method in the same wide field of view. When the specimen grid pitch is around or greater than 3 pixels, multi-pixel sampling moiré fringes are generated, and a spatial phase-shifting technique is combined for a full-field deformation measurement. The strain measurement accuracy is significantly improved, and automatic batch measurement is easily achievable. Both methods can measure the two-dimensional (2D) strain distributions from a single-shot grid image without rotating the specimen or scanning lines, as in traditional moiré techniques. As examples, the 2D displacement and strain distributions, including the shear strains of two carbon fiber-reinforced plastic specimens, were measured in three-point bending tests. The proposed technique is expected to play an important role in the non-destructive quantitative evaluations of mechanical properties, crack occurrences, and residual stresses of a variety of materials.

Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions.

PubMed

Troyer, Jennifer L; Pecon-Slattery, Jill; Roelke, Melody E; Black, Lori; Packer, Craig; O'Brien, Stephen J

2004-04-01

Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS-like immunodeficiency disease in domestic cats. Free-ranging lions, Panthera leo, carry a chronic species-specific strain of FIV, FIV-Ple, which so far has not been convincingly connected with immune pathology or mortality. FIV-Ple, harboring the three distinct strains A, B, and C defined by pol gene sequence divergences, is endemic in the large outbred population of lions in the Serengeti ecosystem in Tanzania. Here we describe the pattern of variation in the three FIV genes gag, pol-RT, and pol-RNase among lions within 13 prides to assess the occurrence of FIV infection and coinfection. Genome diversity within and among FIV-Ple strains is shown to be large, with strain divergence for each gene approaching genetic distances observed for FIV between different species of cats. Multiple in fections with two or three strains were found in 43% of the FIV-positive individuals based on pol-RT sequence analysis, which may suggest that antiviral immunity or interference evoked by one strain is not consistently protective against infection by a second. This comprehensive study of FIV-Ple in a free-ranging population of lions reveals a dynamic transmission of virus in a social species that has historically adapted to render the virus benign.

Patterns of Feline Immunodeficiency Virus Multiple Infection and Genome Divergence in a Free-Ranging Population of African Lions

PubMed Central

Troyer, Jennifer L.; Pecon-Slattery, Jill; Roelke, Melody E.; Black, Lori; Packer, Craig; O'Brien, Stephen J.

2004-01-01

Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS-like immunodeficiency disease in domestic cats. Free-ranging lions, Panthera leo, carry a chronic species-specific strain of FIV, FIV-Ple, which so far has not been convincingly connected with immune pathology or mortality. FIV-Ple, harboring the three distinct strains A, B, and C defined by pol gene sequence divergences, is endemic in the large outbred population of lions in the Serengeti ecosystem in Tanzania. Here we describe the pattern of variation in the three FIV genes gag, pol-RT, and pol-RNase among lions within 13 prides to assess the occurrence of FIV infection and coinfection. Genome diversity within and among FIV-Ple strains is shown to be large, with strain divergence for each gene approaching genetic distances observed for FIV between different species of cats. Multiple in fections with two or three strains were found in 43% of the FIV-positive individuals based on pol-RT sequence analysis, which may suggest that antiviral immunity or interference evoked by one strain is not consistently protective against infection by a second. This comprehensive study of FIV-Ple in a free-ranging population of lions reveals a dynamic transmission of virus in a social species that has historically adapted to render the virus benign. PMID:15016897

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak

PubMed Central

Saelens, Joseph W.; Lau-Bonilla, Dalia; Moller, Anneliese; Medina, Narda; Guzmán, Brenda; Calderón, Maylena; Herrera, Raúl; Sisk, Dana M.; Xet-Mull, Ana M.; Stout, Jason E.; Arathoon, Eduardo; Samayoa, Blanca; Tobin, David M.

2015-01-01

Summary Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City. PMID:26542222

Hamp1 mRNA and plasma hepcidin levels are influenced by sex and strain but do not predict tissue iron levels in inbred mice.

PubMed

McLachlan, Stela; Page, Kathryn E; Lee, Seung-Min; Loguinov, Alex; Valore, Erika; Hui, Simon T; Jung, Grace; Zhou, Jie; Lusis, Aldons J; Fuqua, Brie; Ganz, Tomas; Nemeth, Elizabeta; Vulpe, Chris D

2017-11-01

Iron homeostasis is tightly regulated, and the peptide hormone hepcidin is considered to be a principal regulator of iron metabolism. Previous studies in a limited number of mouse strains found equivocal sex- and strain-dependent differences in mRNA and serum levels of hepcidin and reported conflicting data on the relationship between hepcidin ( Hamp1 ) mRNA levels and iron status. Our aim was to clarify the relationships between strain, sex, and hepcidin expression by examining multiple tissues and the effects of different dietary conditions in multiple inbred strains. Two studies were done: first, Hamp1 mRNA, liver iron, and plasma diferric transferrin levels were measured in 14 inbred strains on a control diet; and second, Hamp1 mRNA and plasma hepcidin levels in both sexes and iron levels in the heart, kidneys, liver, pancreas, and spleen in males were measured in nine inbred/recombinant inbred strains raised on an iron-sufficient or high-iron diet. Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). However, liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice fed iron-sufficient or high-iron diets, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least in males. We also measured plasma erythroferrone, performed RNA-sequencing analysis of liver samples from six inbred strains fed the iron-sufficient, low-iron, or high-iron diets, and explored differences in gene expression between the strains with the highest and lowest hepcidin levels. NEW & NOTEWORTHY Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). Liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least in males. Copyright © 2017 the American Physiological Society.

Relationships between Child Emotional and Behavioral Symptoms and Caregiver Strain and Parenting Stress

ERIC Educational Resources Information Center

Vaughan, Ellen L.; Feinn, Richard; Bernard, Stanley; Brereton, Maria; Kaufman, Joy S.

2013-01-01

Children with emotional and behavioral disturbance often have difficulties in multiple symptom domains. This study investigates the relationships between child symptoms and caregiver strain and parenting stress among 177 youth and their caregivers participating in a school-based system of care. Youth were grouped by symptom domain and included…

Microgravity Foam Structure and Rheology

NASA Technical Reports Server (NTRS)

Durian, Douglas J.

1997-01-01

To exploit rheological and multiple-light scattering techniques, and ultimately microgravity conditions, in order to quantify and elucidate the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Special interest is in determining how this elastic character vanishes, i.e. how the foam melts into a simple viscous liquid, as a function of both increasing liquid content and shear strain rate. The unusual elastic character of foams will be quantified macroscopically by measurement of the shear stress as a function of static shear strain, shear strain rate, and time following a step strain; such data will be analyzed in terms of a yield stress, a static shear modulus, and dynamical time scales. Microscopic information about bubble packing and rearrangement dynamics, from which these macroscopic non-Newtonian properties presumably arise, will be obtained non-invasively by novel multiple-light scattering diagnostics such as Diffusing-Wave Spectroscopy (DWS). Quantitative trends with materials parameters, such as average bubble size, and liquid content, will be sought in order to elucidate the fundamental connection between the microscopic structure and dynamics and the macroscopic rheology.

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile

PubMed Central

Boudry, Pierre; Semenova, Ekaterina; Monot, Marc; Datsenko, Kirill A.; Lopatina, Anna; Sekulovic, Ognjen; Ospina-Bedoya, Maicol; Fortier, Louis-Charles; Severinov, Konstantin; Dupuy, Bruno

2015-01-01

ABSTRACT Clostridium difficile is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen, C. difficile must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in C. difficile reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic C. difficile strain. Through genome sequencing and host range analysis of several new C. difficile phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both C. difficile strains. We further demonstrate that C. difficile Cas proteins are capable of interference in a heterologous host, Escherichia coli. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites. PMID:26330515

MULTIPLE-LOCUS VARIABLE-NUMBER TANDEM REPEAT ANALYSIS OF BRUCELLA ISOLATES FROM THAILAND.

PubMed

Kumkrong, Khurawan; Chankate, Phanita; Tonyoung, Wittawat; Intarapuk, Apiradee; Kerdsin, Anusak; Kalambaheti, Thareerat

2017-01-01

Brucellosis-induced abortion can result in significant economic loss to farm animals. Brucellosis can be transmitted to humans during slaughter of infected animals or via consumption of contaminated food products. Strain identification of Brucella isolates can reveal the route of transmission. Brucella strains were isolated from vaginal swabs of farm animal, cow milk and from human blood cultures. Multiplex PCR was used to identify Brucella species, and owing to high DNA homology among Brucella isolates, multiple-locus variable-number tandem repeat analysis (MLVA) based on the number of tandem repeats at 16 different genomic loci was used for strain identification. Multiplex PCR categorized the isolates into B. abortus (n = 7), B. melitensis (n = 37), B. suis (n = 3), and 5 of unknown Brucella spp. MLVA-16 clustering analysis differentiated the strains into various genotypes, with Brucella isolates from the same geographic region being closely related, and revealed that the Thai isolates were phylogenetically distinct from those in other countries, including within the Southeast Asian region. Thus, MLVA-16 typing has utility in epidemiological studies.

Strain and deformations engineered germanene bilayer double gate-field effect transistor by first principles

NASA Astrophysics Data System (ADS)

Meher Abhinav, E.; Chandrasekaran, Gopalakrishnan; Kasmir Raja, S. V.

2017-10-01

Germanene, silicene, stanene, phosphorene and graphene are some of single atomic materials with novel properties. In this paper, we explored bilayer germanene-based Double Gate-Field Effect Transistor (DG-FET) with various strains and deformations using Density Functional Theory (DFT) and Green's approach by first-principle calculations. The DG-FET of 1.6 nm width, 6 nm channel length (Lch) and HfO2 as gate dielectric has been modeled. For intrinsic deformation of germanene bilayer, we have enforced minute mechanical deformation of wrap and twist (5°) and ripple (0.5 Å) on germanene bilayer channel material. By using NEGF formalism, I-V Characteristics of various strains and deformation tailored DG-FET was calculated. Our results show that rough edge and single vacancy (5-9) in bilayer germanene diminishes the current around 47% and 58% respectively as compared with pristine bilayer germanene. In case of strain tailored bilayer DG-FET, multiple NDR regions were observed which can be utilized in building stable multiple logic states in digital circuits and high frequency oscillators using negative resistive techniques.

Characterization of measles virus strains circulating in Southern Italy (Palermo area, Sicily) between 2010 and 2011.

PubMed

Urone, Noemi; Colomba, Claudia; Ferraro, Donatella

2016-03-01

Measles virus (MV) was classified in 24 genotypes that show a distinct geographic distribution. Genotypes contain multiple distinct lineages. In 2011 large outbreaks of measles occurred in Italy and in many European countries. Aims of this study are to analyze the intra-genotype variability and to follow the importation and the spread of new MV strains in Sicily. A fragment of 450 bps of MV C-terminal nucleoprotein was sequenced from sera of 73 Sicilian patients with symptomatic measles infections, occurred between 2010 and 2011. Five MV strains were D4 genotype and 68 were D8 genotype. The MV/D4 sequences were related to MV/D4-Enfield variant. Two lineages of MV/D8 genotypes, related to MV/D8-Villupuram variant and to a strain found in Birmingham in 2006 respectively, were identified. This is the first study that reports the co-circulation of different MV genotypes and lineages in Sicily suggesting multiple origins of the outbreak that occurred during 2010 and 2011 years. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Characteristics of Mycobacterium tuberculosis Strains Isolated from Cutaneous Tuberculosis Patients in China.

PubMed

Jiang, Haiqin; Jin, Yali; Vissa, Varalakshmi; Zhang, Liangfen; Liu, Weijun; Qin, Lianhua; Wan, Kanglin; Wu, Xiaocui; Wang, Hongsheng; Liu, Weida; Wang, Baoxi

2017-04-06

Cutaneous tuberculosis (CTB) is probably underreported due to difficulties in detection and diagnosis. To address this issue, genotypes of Mycobacterium tuberculosis strains isolated from 30 patients with CTB were mapped at multiple loci, namely, RD105 deletions, spacer oligonucleotides, and Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTRs). Fifty-eight strains of pulmonary tuberculosis (PTB) were mapped as experimental controls. Drug resistance-associated gene mutations were determined by amplicon sequencing of target regions within 7 genes. Beijing family isolates were the most prevalent strains in CTB and PTB. MIRU-VNTR typing separated the Beijing strains from the non-Beijing strains, and the majority of CTB could be separated from PTB counterparts. Drug resistance determining regions showed only one CTB strain expressing isomazid resistance. Thus, while the CTB strains belonged to the same phylogenetic lineages and sub-lineages as the PTB strains, they differed at the level of several MIRU-VNTRs and in the proportion of drug resistance.

Identification of Chromium Resistant Bacteria from Dry Fly Ash Sample of Mejia MTPS Thermal Power Plant, West Bengal, India.

PubMed

Roychowdhury, Roopali; Mukherjee, Pritam; Roy, Madhumita

2016-02-01

Eight chromium resistant bacteria were isolated from a dry fly ash sample of DVC-MTPS thermal power plant located in Bankura, West Bengal, India. These isolates displayed different degrees of chromate reduction under aerobic conditions. According to 16S rDNA gene analysis, five of them were Staphylococcus, two were Bacillus and one was Micrococcus. The minimum inhibitory concentration towards chromium and the ability to reduce hexavalent chromium to trivalent chromium was highest in Staphylococcus haemolyticus strain HMR17. All the strains were resistant to multiple heavy metals (As, Cu, Cd, Co, Zn, Mn, Pb and Fe) and reduced toxic hexavalent chromium to relatively non toxic trivalent chromium even in the presence of these multiple heavy metals. All of them showed resistance to different antibiotics. In a soil microcosm study, S. haemolyticus strain HMR17 completely reduced 4 mM hexavalent chromium within 7 days of incubation.

Overexpression of Multiple Detoxification Genes in Deltamethrin Resistant Laodelphax striatellus (Hemiptera: Delphacidae) in China

PubMed Central

Xu, Lu; Wu, Min; Han, Zhaojun

2013-01-01

Background The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is one of the major rice pests in Asia and has developed resistance to multiple classes of insecticides. Understanding resistance mechanisms is essential to the management of this pest. Biochemical and molecular assays were performed in this study to systematically characterize deltamethrin resistance mechanisms with laboratory-selected resistant and susceptible strains of SBPH. Methodology/Principal Findings Deltamethrin resistant strains of SBPH (JH-del) were derived from a field population by continuously selections (up to 30 generations) in the laboratory, while a susceptible strain (JHS) was obtained from the same population by removing insecticide pressure for 30 generations. The role of detoxification enzymes in the resistance was investigated using synergism and enzyme activity assays with strains of different resistant levels. Furthermore, 71 cytochrome P450, 93 esterases and 12 glutathione-S-transferases cDNAs were cloned based on transcriptome data of a field collected population. Semi-quantitative RT-PCR screening analysis of 176 identified detoxification genes demonstrated that multiple P450 and esterase genes were overexpressed (>2-fold) in JH-del strains (G4 and G30) when compared to that in JHS, and the results of quantitative PCR coincided with the semi-quantitative RT-PCR results. Target mutation at IIS3–IIS6 regions encoded by the voltage-gated sodium channel gene was ruled out for conferring the observed resistance. Conclusion/Significance As the first attempt to discover genes potentially involved in SBPH pyrethroid resistance, this study putatively identified several candidate genes of detoxification enzymes that were significantly overexpressed in the resistant strain, which matched the synergism and enzyme activity testing. The biochemical and molecular evidences suggest that the high level pyrethroid resistance in L. striatellus could be due to enhanced detoxification rather than target insensitivity. The findings lay a solid ground for further resistance mechanism elucidation studies. PMID:24324548

Infection by Rhodococcus fascians maintains cotyledons as a sink tissue for the pathogen

PubMed Central

Dhandapani, Pragatheswari; Song, Jiancheng; Novak, Ondrej

2017-01-01

Background and Aims Pisum sativum L. (pea) seed is a source of carbohydrate and protein for the developing plant. By studying pea seeds inoculated by the cytokinin-producing bacterium, Rhodococcus fascians, we sought to determine the impact of both an epiphytic (avirulent) strain and a pathogenic strain on source–sink activity within the cotyledons during and following germination. Methods Bacterial spread was monitored microscopically, and real-time reverse transcription–quantitative PCR was used to determine the expression of cytokinin biosynthesis, degradation and response regulator gene family members, along with expression of family members of SWEET, SUT, CWINV and AAP genes – gene families identified initially in pea by transcriptomic analysis. The endogenous cytokinin content was also determined. Key Results The cotyledons infected by the virulent strain remained intact and turned green, while multiple shoots were formed and root growth was reduced. The epiphytic strain had no such marked impact. Isopentenyl adenine was elevated in the cotyledons infected by the virulent strain. Strong expression of RfIPT, RfLOG and RfCKX was detected in the cotyledons infected by the virulent strain throughout the experiment, with elevated expression also observed for PsSWEET, PsSUT and PsINV gene family members. The epiphytic strain had some impact on the expression of these genes, especially at the later stages of reserve mobilization from the cotyledons. Conclusions The pathogenic strain retained the cotyledons as a sink tissue for the pathogen rather than the cotyledon converting completely to a source tissue for the germinating plant. We suggest that the interaction of cytokinins, CWINVs and SWEETs may lead to the loss of apical dominance and the appearance of multiple shoots. PMID:27864224

Rapid and Sensitive Detection of Shigella spp. and Salmonella spp. by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique

PubMed Central

Wang, Yi; Wang, Yan; Luo, Lijuan; Liu, Dongxin; Luo, Xia; Xu, Yanmei; Hu, Shoukui; Niu, Lina; Xu, Jianguo; Ye, Changyun

2015-01-01

Shigella and Salmonella are frequently isolated from various food samples and can cause human gastroenteritis. Here, a novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully established and validated for simultaneous detection of Shigella strains and Salmonella strains in only a single reaction. Two sets of MERT-LAMP primers for 2 kinds of pathogens were designed from ipaH gene of Shigella spp. and invA gene of Salmonella spp., respectively. Under the constant condition at 63°C, the positive results were yielded in as short as 12 min with the genomic DNA extracted from the 19 Shigella strains and 14 Salmonella strains, and the target pathogens present in a sample could be simultaneously identified based on distinct fluorescence curves in real-time format. Accordingly, the multiplex detection assay significantly reduced effort, materials and reagents used, and amplification and differentiation were conducted at the same time, obviating the use of postdetection procedures. The analytical sensitivity of MERT-LAMP was found to be 62.5 and 125 fg DNA/reaction with genomic templates of Shigella strains and Salmonella strains, which was consist with normal LAMP assay, and at least 10- and 100-fold more sensitive than that of qPCR and conventional PCR approaches. The limit of detection of MERT-LAMP for Shigella strains and Salmonella strains detection in artificially contaminated milk samples was 5.8 and 6.4 CFU per vessel. In conclusion, the MERT-LAMP methodology described here demonstrated a potential and valuable means for simultaneous screening of Shigella and Salmonella in a wide variety of samples. PMID:26697000

Co-Infection Dynamics of a Major Food-Borne Zoonotic Pathogen in Chicken

PubMed Central

Skånseng, Beate; Trosvik, Pål; Zimonja, Monika; Johnsen, Gro; Bjerrum, Lotte; Pedersen, Karl; Wallin, Nina; Rudi, Knut

2007-01-01

A major bottleneck in understanding zoonotic pathogens has been the analysis of pathogen co-infection dynamics. We have addressed this challenge using a novel direct sequencing approach for pathogen quantification in mixed infections. The major zoonotic food-borne pathogen Campylobacter jejuni, with an important reservoir in the gastrointestinal (GI) tract of chickens, was used as a model. We investigated the co-colonisation dynamics of seven C. jejuni strains in a chicken GI infection trial. The seven strains were isolated from an epidemiological study showing multiple strain infections at the farm level. We analysed time-series data, following the Campylobacter colonisation, as well as the dominant background flora of chickens. Data were collected from the infection at day 16 until the last sampling point at day 36. Chickens with two different background floras were studied, mature (treated with Broilact, which is a product consisting of bacteria from the intestinal flora of healthy hens) and spontaneous. The two treatments resulted in completely different background floras, yet similar Campylobacter colonisation patterns were detected in both groups. This suggests that it is the chicken host and not the background flora that is important in determining the Campylobacter colonisation pattern. Our results showed that mainly two of the seven C. jejuni strains dominated the Campylobacter flora in the chickens, with a shift of the dominating strain during the infection period. We propose a model in which multiple C. jejuni strains can colonise a single host, with the dominant strains being replaced as a consequence of strain-specific immune responses. This model represents a new understanding of C. jejuni epidemiology, with future implications for the development of novel intervention strategies. PMID:18020703

Effects of space environment on T-7 bacteriophage and spores of Bacillus subtilis 168

NASA Technical Reports Server (NTRS)

Spizizen, J.; Isherwood, J. E.

1973-01-01

Two strains of Bacillus subtilis were exposed to components of the ultraviolet spectrum in space. Both strains possess multiple genetic markers, and one of the strains is defective in the ability to repair ultraviolet damage. The T-7 bacteriophage of Escherichia coli was also exposed to selected wavelengths and energy levels of ultraviolet light in space. Preliminary findings do not reveal anomalies in survival rates. Data are not yet available on detailed genetic analyses.

Multiple Functional Domains of Enterococcus faecalis Aggregation Substance Asc10 Contribute to Endocarditis Virulence ▿ †

PubMed Central

Chuang, Olivia N.; Schlievert, Patrick M.; Wells, Carol L.; Manias, Dawn A.; Tripp, Timothy J.; Dunny, Gary M.

2009-01-01

Aggregation substance proteins encoded by sex pheromone plasmids increase the virulence of Enterococcus faecalis in experimental pathogenesis models, including infectious endocarditis models. These large surface proteins may contain multiple functional domains involved in various interactions with other bacterial cells and with the mammalian host. Aggregation substance Asc10, encoded by plasmid pCF10, is induced during growth in the mammalian bloodstream, and pCF10 carriage gives E. faecalis a significant selective advantage in this environment. We employed a rabbit model to investigate the role of various functional domains of Asc10 in endocarditis. The data suggested that the bacterial load of the infected tissue was the best indicator of virulence. Isogenic strains carrying either no plasmid, wild-type pCF10, a pCF10 derivative with an in-frame deletion of the prgB gene encoding Asc10, or pCF10 derivatives expressing other alleles of prgB were examined in this model. Previously identified aggregation domains contributed to the virulence associated with the wild-type protein, and a strain expressing an Asc10 derivative in which glycine residues in two RGD motifs were changed to alanine residues showed the greatest reduction in virulence. Remarkably, this strain and the strain carrying the pCF10 derivative with the in-frame deletion of prgB were both significantly less virulent than an isogenic plasmid-free strain. The data demonstrate that multiple functional domains are important in Asc10-mediated interactions with the host during the course of experimental endocarditis and that in the absence of a functional prgB gene, pCF10 carriage is actually disadvantageous in vivo. PMID:18955479

Evidence of multiple/cross resistance to Bt and organophosphate insecticides in Puerto Rico population of the fall armyworm, Spodoptera frugiperda.

PubMed

Zhu, Yu Cheng; Blanco, Carlos A; Portilla, Maribel; Adamczyk, John; Luttrell, Randall; Huang, Fangneng

2015-07-01

Fall armyworm (FAW) is a damaging pest of many economic crops. Long-term use of chemical control prompted resistance development to many insecticide classes. Many populations were found to be significantly less susceptible to major Bt toxins expressed in transgenic crops. In this study, a FAW strain collected from Puerto Rico (PR) with 7717-fold Cry1F-resistance was examined to determine if it had also developed multiple/cross resistance to non-Bt insecticides. Dose response assays showed that the PR strain developed 19-fold resistance to acephate. Besides having a slightly smaller larval body weight and length, PR also evolved a deep (2.8%) molecular divergence in mitochondrial oxidase subunit II. Further examination of enzyme activities in the midgut of PR larvae exhibited substantial decreases of alkaline phosphatase (ALP), aminopeptidase (APN), 1-NA- and 2-NA-specific esterase, trypsin, and chymotrypsin activities, and significant increases of PNPA-specific esterase and glutathione S-transferase (GST) activities. When enzyme preparations from the whole larval body were examined, all three esterase, GST, trypsin, and chymotrypsin activities were significantly elevated in the PR strain, while ALP and APN activities were not significantly different from those of susceptible strain. Data indicated that multiple/cross resistances may have developed in the PR strain to both Bt toxins and conventional insecticides. Consistently reduced ALP provided evidence to support an ALP-mediated Bt resistance mechanism. Esterases and GSTs may be associated with acephate resistance through elevated metabolic detoxification. Further studies are needed to clarify whether and how esterases, GSTs, and other enzymes (such as P450s) are involved in cross resistance development to Bt and other insecticide classes. Published by Elsevier Inc.

Synergistic degradation of chlorinated hydrocarbons with microorganisms and zero valent iron

NASA Astrophysics Data System (ADS)

Schöftner, Philipp; Summer, Dorothea; Leitner, Simon; Watzinger, Andrea; Wimmer, Bernhard; Reichenauer, Thomas

2016-04-01

Sites contaminated with chlorinated hydrocarbons (CHC) are located mainly within build-up regions. Therefore in most cases only in-situ technologies without excavation of soil material can be used for remediation. This project examines a novel in-situ remediation method, in which the biotic degradation via bacteria is combined with abiotic degradation via zero-valent iron particles (ZVI). ZVI particles are injected into the aquifer where CHC-molecules are reductively dechlorinated. However Fe0 is also oxidized by reaction with water leading to generation of H2 without any CHC degradation. To achieve biotic degradation often strictly anaerobic strains of the bacteria Dehalococcoides are used. These bacteria can dechlorinate CHC by utilizing H2. By combining these processes the H2, produced during the anaerobic corrosion of Fe0, could be used by bacteria for further CHC degradation. Therefore the amount of used Fe0 and as a consequence also remediation costs could be reduced. Additionally the continuous supply of H2 could make the bacterial degradation more controllable. Different Fe0 particles (nano- and micro-scale) were tested for their perchloroethene (PCE) degradation rate and H2 production rate in microcosms. PCE-degradation rate by different bacterial cultures was investigated in the same microcosm system. In course of these experiments the 13C enrichment factors of the PCE degradation of the different particles and cultures were determined to enable the differentiation of biotic and abiotic degradation. Preliminary results showed, that the nano-scale particles reacted faster with PCE and water than their micro-scaled counterparts. The PCE degradation via micro-scaled particles lead to 13C enrichment factors in the range of -3,6 ‰ ± 0,6 to -9,5 ‰ ± 0,2. With one of the examined bacterial cultures a fast reduction of PCE to ethene was observed. Although PCE and TCE were completely degraded by this culture the metabolites DCE and VC could still be detected. Further microcosm experiments will be implemented by the time of the EGU General Assembly 2016. In the framework of these experiments other bacterial cultures and ZVI particles as well as the combination of biotic and abiotic dehalogenation will be investigated.

Host–parasite genotypic interactions in the honey bee: the dynamics of diversity

PubMed Central

Evison, Sophie E F; Fazio, Geraldine; Chappell, Paula; Foley, Kirsten; Jensen, Annette B; Hughes, William O H

2013-01-01

Parasites are thought to be a major driving force shaping genetic variation in their host, and are suggested to be a significant reason for the maintenance of sexual reproduction. A leading hypothesis for the occurrence of multiple mating (polyandry) in social insects is that the genetic diversity generated within-colonies through this behavior promotes disease resistance. This benefit is likely to be particularly significant when colonies are exposed to multiple species and strains of parasites, but host–parasite genotypic interactions in social insects are little known. We investigated this using honey bees, which are naturally polyandrous and consequently produce genetically diverse colonies containing multiple genotypes (patrilines), and which are also known to host multiple strains of various parasite species. We found that host genotypes differed significantly in their resistance to different strains of the obligate fungal parasite that causes chalkbrood disease, while genotypic variation in resistance to the facultative fungal parasite that causes stonebrood disease was less pronounced. Our results show that genetic variation in disease resistance depends in part on the parasite genotype, as well as species, with the latter most likely relating to differences in parasite life history and host–parasite coevolution. Our results suggest that the selection pressure from genetically diverse parasites might be an important driving force in the evolution of polyandry, a mechanism that generates significant genetic diversity in social insects. PMID:23919163

Host-parasite genotypic interactions in the honey bee: the dynamics of diversity.

PubMed

Evison, Sophie E F; Fazio, Geraldine; Chappell, Paula; Foley, Kirsten; Jensen, Annette B; Hughes, William O H

2013-07-01

Parasites are thought to be a major driving force shaping genetic variation in their host, and are suggested to be a significant reason for the maintenance of sexual reproduction. A leading hypothesis for the occurrence of multiple mating (polyandry) in social insects is that the genetic diversity generated within-colonies through this behavior promotes disease resistance. This benefit is likely to be particularly significant when colonies are exposed to multiple species and strains of parasites, but host-parasite genotypic interactions in social insects are little known. We investigated this using honey bees, which are naturally polyandrous and consequently produce genetically diverse colonies containing multiple genotypes (patrilines), and which are also known to host multiple strains of various parasite species. We found that host genotypes differed significantly in their resistance to different strains of the obligate fungal parasite that causes chalkbrood disease, while genotypic variation in resistance to the facultative fungal parasite that causes stonebrood disease was less pronounced. Our results show that genetic variation in disease resistance depends in part on the parasite genotype, as well as species, with the latter most likely relating to differences in parasite life history and host-parasite coevolution. Our results suggest that the selection pressure from genetically diverse parasites might be an important driving force in the evolution of polyandry, a mechanism that generates significant genetic diversity in social insects.

Isolation of Escherichia coli 0157:H7 Strain from Fecal Samples of Zoo Animal

PubMed Central

Mohammed Hamzah, Aseel; Mohammed Hussein, Aseel; Mahmoud Khalef, Jenan

2013-01-01

The isolation and characterization of Escherichia coli O157:H7 strains from 22 out of 174 fecal samples from petting zoo animals representing twenty-two different species (camel, lion, goats, zebra, bear, baboon monkey, Siberian monkey, deer, elk, llama, pony, horses, fox, kangaroo, wolf, porcupine, chickens, tiger, ostrich, hyena, dogs, and wildcats) were investigated. One petting Al-Zawraa zoological society of Baghdad was investigated for E. coli O157:H7 over a 16-month period that spanned two summer and two autumn seasons. Variation in the occurrence of E. coli O157:H7-positive petting zoo animals was observed, with animals being culture positive only in the summer months but not in the spring, autumn, or winter. E. coli O157:H7 isolates were distinguished by agglutination with E. coli O157:H7 latex reagent (Oxoid), identified among the isolates, which showed that multiple E. coli strains were isolated from one petting zoo animal, in which a single animal simultaneously shed multiple E. coli strains; E. coli O157:H7 was isolated only by selective enrichment culture of 2 g of petting zoo animal feces. In contrast, strains other than O157:H7 were cultured from feces of petting zoo animals without enrichment. PMID:24489514

Multiple introductions and onward transmission of non-pandemic HIV-1 subtype B strains in North America and Europe.

PubMed Central

Cabello, Marina; Romero, Hector; Bello, Gonzalo

2016-01-01

Most HIV-1 subtype B infections in North America and Europe seem to have resulted from the expansion of a single pandemic lineage (BPANDEMIC) disseminated from the United States (US). Some non-pandemic subtype B strains of Caribbean origin (BCAR) may have also reached North America and Europe, but their epidemiological relevance in those regions remains largely unknown. Here we analyze a total of 20,045 HIV-1 subtype B pol sequences from the US, Canada, and Europe, to estimate the prevalence and to reconstruct the spatiotemporal dynamics of dissemination of HIV-1 BCAR strains in those regions. We find that BCAR strains were probably disseminated from the Caribbean into North America and Europe at multiple times since the early 1970s onwards. The BCAR strains reached the US, Canada and at least 16 different European countries, where they account for a very low fraction (<5%) of subtype B infections, with exception of the Czech Republic (7.7%). We also find evidence of the onward transmission of BCAR clades in the US, Canada, the Czech Republic, Germany, Italy, Spain and the UK, as well as short-distance spreading of BCAR lineages between neighboring European countries from Central and Western Europe, and long-distance dissemination between the US and Europe. PMID:27653834

Isolation of Escherichia coli 0157:H7 strain from fecal samples of zoo animal.

PubMed

Mohammed Hamzah, Aseel; Mohammed Hussein, Aseel; Mahmoud Khalef, Jenan

2013-01-01

The isolation and characterization of Escherichia coli O157:H7 strains from 22 out of 174 fecal samples from petting zoo animals representing twenty-two different species (camel, lion, goats, zebra, bear, baboon monkey, Siberian monkey, deer, elk, llama, pony, horses, fox, kangaroo, wolf, porcupine, chickens, tiger, ostrich, hyena, dogs, and wildcats) were investigated. One petting Al-Zawraa zoological society of Baghdad was investigated for E. coli O157:H7 over a 16-month period that spanned two summer and two autumn seasons. Variation in the occurrence of E. coli O157:H7-positive petting zoo animals was observed, with animals being culture positive only in the summer months but not in the spring, autumn, or winter. E. coli O157:H7 isolates were distinguished by agglutination with E. coli O157:H7 latex reagent (Oxoid), identified among the isolates, which showed that multiple E. coli strains were isolated from one petting zoo animal, in which a single animal simultaneously shed multiple E. coli strains; E. coli O157:H7 was isolated only by selective enrichment culture of 2 g of petting zoo animal feces. In contrast, strains other than O157:H7 were cultured from feces of petting zoo animals without enrichment.

Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae.

PubMed

Ishii, Jun; Kondo, Takashi; Makino, Harumi; Ogura, Akira; Matsuda, Fumio; Kondo, Akihiko

2014-05-01

Yeast has the potential to be used in bulk-scale fermentative production of fuels and chemicals due to its tolerance for low pH and robustness for autolysis. However, expression of multiple external genes in one host yeast strain is considerably labor-intensive due to the lack of polycistronic transcription. To promote the metabolic engineering of yeast, we generated systematic and convenient genetic engineering tools to express multiple genes in Saccharomyces cerevisiae. We constructed a series of multi-copy and integration vector sets for concurrently expressing two or three genes in S. cerevisiae by embedding three classical promoters. The comparative expression capabilities of the constructed vectors were monitored with green fluorescent protein, and the concurrent expression of genes was monitored with three different fluorescent proteins. Our multiple gene expression tool will be helpful to the advanced construction of genetically engineered yeast strains in a variety of research fields other than metabolic engineering. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Streptococcus mitis Strains Causing Severe Clinical Disease in Cancer Patients

PubMed Central

Sahasrabhojane, Pranoti; Saldana, Miguel; Yao, Hui; Su, Xiaoping; Horstmann, Nicola; Thompson, Erika; Flores, Anthony R.

2014-01-01

The genetically diverse viridans group streptococci (VGS) are increasingly recognized as the cause of a variety of human diseases. We used a recently developed multilocus sequence analysis scheme to define the species of 118 unique VGS strains causing bacteremia in patients with cancer; Streptococcus mitis (68 patients) and S. oralis (22 patients) were the most frequently identified strains. Compared with patients infected with non–S. mitis strains, patients infected with S. mitis strains were more likely to have moderate or severe clinical disease (e.g., VGS shock syndrome). Combined with the sequence data, whole-genome analyses showed that S. mitis strains may more precisely be considered as >2 species. Furthermore, we found that multiple S. mitis strains induced disease in neutropenic mice in a dose-dependent fashion. Our data define the prominent clinical effect of the group of organisms currently classified as S. mitis and lay the groundwork for increased understanding of this understudied pathogen. PMID:24750901

Hot Deformation and Dynamic Recrystallization Behavior of the Cu-Cr-Zr-Y Alloy

NASA Astrophysics Data System (ADS)

Zhang, Yi; Huili, Sun; Volinsky, Alex A.; Tian, Baohong; Chai, Zhe; Liu, Ping; Liu, Yong

2016-03-01

To study the workability and to optimize the hot deformation processing parameters of the Cu-Cr-Zr-Y alloy, the strain hardening effect and dynamic softening behavior of the Cu-Cr-Zr-Y alloy were investigated. The flow stress increases with the strain rate and stress decreases with deformation temperature. The critical conditions, including the critical strain and stress for the occurrence of dynamic recrystallization, were determined based on the alloy strain hardening rate. The critical stress related to the onset of dynamic recrystallization decreases with temperature. The evolution of DRX microstructure strongly depends on the deformation temperature and the strain rate. Dynamic recrystallization appears at high temperatures and low strain rates. The addition of Y can refine the grain and effectively accelerate dynamic recrystallization. Dislocation generation and multiplication are the main hot deformation mechanisms for the alloy. The deformation temperature increase and the strain rate decrease can promote dynamic recrystallization of the alloy.

The Association Between Depression, Suicidal Ideation and Psychological Strains in College Students: A Cross-National Study.

PubMed

Zhao, Sibo; Zhang, Jie

2018-06-19

This study examined the differences of psychological strains between Chinese and American college students and discussed how strains may influence individuals' suicidal ideation and depression. A total of 539 college students (298 from China and 241 from the U.S.) were recruited in March 2016 to complete the survey study. Multiple linear regressions were used in data analysis. Students in America had higher scores on depression and stress than students in China, while students in China rated higher on suicidal ideation than students in America. In contrast of students in America facing more coping strains, students in China were confronting more value strains in their life. The cross-cultural variations in the effect of psychological strains have been substantiated in current study, indicating that understanding the psychological strains in different cultural contexts is necessary for the early intervention and prevention in college aged populations.

Characterization of Francisella species isolated from the cooling water of an air conditioning system.

PubMed

Gu, Quan; Li, Xunde; Qu, Pinghua; Hou, Shuiping; Li, Juntao; Atwill, Edward R; Chen, Shouyi

2015-01-01

Strains of Francisella spp. were isolated from cooling water from an air conditioning system in Guangzhou, China. These strains are Gram negative, coccobacilli, non-motile, oxidase negative, catalase negative, esterase and lipid esterase positive. In addition, these bacteria grow on cysteine-supplemented media at 20 °C to 40 °C with an optimal growth temperature of 30 °C. Analysis of 16S rRNA gene sequences revealed that these strains belong to the genus Francisella. Biochemical tests and phylogenetic and BLAST analyses of 16S rRNA, rpoB and sdhA genes indicated that one strain was very similar to Francisella philomiragia and that the other strains were identical or highly similar to the Francisella guangzhouensis sp. nov. strain 08HL01032 we previously described. Biochemical and molecular characteristics of these strains demonstrated that multiple Francisella species exist in air conditioning systems.

Financial strain, social relations, and psychological distress among older people: a cross-cultural analysis.

PubMed

Ferraro, K F; Su, Y

1999-01-01

This article examines how financial strain and social relations may independently and jointly influence psychological distress among older people in four nations. Data from four Western Pacific nations (N = 3,277) are used to test additive and multiplicative models of the relationships between financial strain, social relations, and psychological distress. Financial strain is associated with higher levels of psychological distress in three of the four nations. Interactive models of the effects of financial strain and social relations on distress were uncovered in three of the four nations, but the type of social relation influencing the strain-distress relationship varied. Subjective-health and IADLs were significant predictors of psychological distress in all four nations. Findings suggest that although financial strain is quite likely to lead to psychological distress among elders, this can be mitigated, at least in part, by social relationships. Modernization was not associated with higher psychological distress.

A Novel Sensor System for Measuring Wheel Loads of Vehicles on Highways

PubMed Central

Zhang, Wenbin; Suo, Chunguang; Wang, Qi

2008-01-01

With the development of the highway transportation and business trade, vehicle Weigh-In-Motion (WIM) technology has become a key technology for measuring traffic loads. In this paper a novel WIM system based on monitoring of pavement strain responses in rigid pavement was investigated. In this WIM system multiple low cost, light weight, small volume and high accuracy embedded concrete strain sensors were used as WIM sensors to measure rigid pavement strain responses. In order to verify the feasibility of the method, a system prototype based on multiple sensors was designed and deployed on a relatively busy freeway. Field calibration and tests were performed with known two-axle truck wheel loads and the measurement errors were calculated based on the static weights measured with a static weighbridge. This enables the weights of other vehicles to be calculated from the calibration constant. Calibration and test results for individual sensors or three-sensor fusions are both provided. Repeatability, sources of error, and weight accuracy are discussed. Successful results showed that the proposed method was feasible and proven to have a high accuracy. Furthermore, a sample mean approach using multiple fused individual sensors could provide better performance compared to individual sensors. PMID:27873952

Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

PubMed Central

2013-01-01

Background Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI)). This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA) haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep). Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina fuscipes fuscipes, but it is not limited to a single host haplotype, suggesting that CI did not impact its population structure. However, host population genetic differentiation could have been generated if multiple Wolbachia strains interacted in some populations. Here, we investigated Wolbachia genetic variation in G. f. fuscipes populations of known host genetic composition in Uganda. We tested for the presence of multiple Wolbachia strains using Multi-Locus Sequence Typing (MLST) and for an association between geographic region and host mtDNA haplotype using Wolbachia DNA sequence from a variable locus, groEL (heat shock protein 60). Results MLST demonstrated that some G. f. fuscipes carry Wolbachia strains from two lineages. GroEL revealed high levels of sequence diversity within and between individuals (Haplotype diversity = 0.945). We found Wolbachia associated with 26 host mtDNA haplotypes, an unprecedented result. We observed a geographical association of one Wolbachia lineage with southern host mtDNA haplotypes, but it was non-significant (p = 0.16). Though most Wolbachia-infected host haplotypes were those found in the contact region between host mtDNA groups, this association was non-significant (p = 0.17). Conclusions High Wolbachia sequence diversity and the association of Wolbachia with multiple host haplotypes suggest that different Wolbachia strains infected G. f. fuscipes multiple times independently. We suggest that these observations reflect a transient phase in Wolbachia evolution that is influenced by the long gestation and low reproductive output of tsetse. Although G. f. fuscipes is superinfected with Wolbachia, our data does not support that bidirectional CI has influenced host genetic diversity in Uganda. PMID:23384159

Multiple Serotypes of the Moderate Thermophile Thiobacillus caldus, a Limitation of Immunological Assays for Biomining Microorganisms.

PubMed

Hallberg, K B; Lindstrom, E B

1996-11-01

Phylogenetic and phenotypic analysis indicates that a moderately thermophilic isolate, C-SH12, from Australia belongs to the species Thiobacillus caldus. Antiserum generated against whole cells of T. caldus KU recognized protein antigens common to cell lysates of the three T. caldus strains KU, BC13, and C-SH12 but did not recognize whole cells of isolate C-SH12. Differences in the lipopolysaccharide (LPS) of strain C-SH12 and those of the other two T. caldus strains were found, and the anti-KU antiserum did not recognize the LPS from strain C-SH12. These data indicate that this T. caldus isolate belongs to a serotype different from that of strains KU and BC13.

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.

PubMed

Saelens, Joseph W; Lau-Bonilla, Dalia; Moller, Anneliese; Medina, Narda; Guzmán, Brenda; Calderón, Maylena; Herrera, Raúl; Sisk, Dana M; Xet-Mull, Ana M; Stout, Jason E; Arathoon, Eduardo; Samayoa, Blanca; Tobin, David M

2015-12-01

Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microevolution of the Direct Repeat Locus of Mycobacterium tuberculosis in a Strain Prevalent in San Francisco

PubMed Central

Aga, Roxanne S.; Fair, Elizabeth; Abernethy, Neil F.; DeRiemer, Kathryn; Paz, E. Antonio; Kawamura, L. Masae; Small, Peter M.; Kato-Maeda, Midori

2006-01-01

We describe a microevolutionary event of a prevalent strain of Mycobacterium tuberculosis that caused two outbreaks in San Francisco. During the second outbreak, a direct variable repeat was lost. We discuss the mechanisms of this change and the implications of analyzing multiple genetic loci in this context. PMID:16597893

Cultivar-Dependent Transcript Accumulation in Wheat Roots Colonized by Pseudomonas fluorescens Q8r1-96 Wild Type and Mutant Strains

USDA-ARS?s Scientific Manuscript database

In Triticum aestivum L. (wheat), the root-colonizing bacterium Pseudomonas fluorescens strain Q8r1-96 produces the antifungal metabolite 2,4-diacetylphloroglucinol (DAPG), suppresses damage caused by soilborne root pathogens, and modulates multiple stress or defense pathways in wheat roots. To test...

Single Parents and the Work Setting: The Impact of Multiple Job and Homelife Responsibilities.

ERIC Educational Resources Information Center

Burden, Dianne S.

1986-01-01

Examines the impact of combined work/family responsibilities on single-parent employees. Results indicated that parent employees, but particularly single female parents, were at risk for high job-family role strain and reduced levels of well-being. In spite of increased strain, however, single parents exhibited high levels of job satisfaction and…

Multiple mechanisms responsible for strong Congo red-binding variants of Escherichia coli O157:H7 strains

USDA-ARS?s Scientific Manuscript database

High variability in the expression of csgD-dependent, biofilm-forming and adhesive properties is common among Shiga toxin-producing Escherichia coli (STEC). Although many strains of serotype O157:H7 form little biofilm, conversion to stronger biofilm phenotypes has been observed. In this study we sc...

Large-Deformation Displacement Transfer Functions for Shape Predictions of Highly Flexible Slender Aerospace Structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2013-01-01

Large deformation displacement transfer functions were formulated for deformed shape predictions of highly flexible slender structures like aircraft wings. In the formulation, the embedded beam (depth wise cross section of structure along the surface strain sensing line) was first evenly discretized into multiple small domains, with surface strain sensing stations located at the domain junctures. Thus, the surface strain (bending strains) variation within each domain could be expressed with linear of nonlinear function. Such piecewise approach enabled piecewise integrations of the embedded beam curvature equations [classical (Eulerian), physical (Lagrangian), and shifted curvature equations] to yield closed form slope and deflection equations in recursive forms.

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

NASA Astrophysics Data System (ADS)

Vatanparast, Maryam; Vullum, Per Erik; Nord, Magnus; Zuo, Jian-Min; Reenaas, Turid W.; Holmestad, Randi

2017-09-01

Geometric phase analysis (GPA), a fast and simple Fourier space method for strain analysis, can give useful information on accumulated strain and defect propagation in multiple layers of semiconductors, including quantum dot materials. In this work, GPA has been applied to high resolution Z-contrast scanning transmission electron microscopy (STEM) images. Strain maps determined from different g vectors of these images are compared to each other, in order to analyze and assess the GPA technique in terms of accuracy. The SmartAlign tool has been used to improve the STEM image quality getting more reliable results. Strain maps from template matching as a real space approach are compared with strain maps from GPA, and it is discussed that a real space analysis is a better approach than GPA for aberration corrected STEM images.

Improved Polysaccharide Production by Homologous Co-overexpression of Phosphoglucomutase and UDP Glucose Pyrophosphorylase Genes in the Mushroom Coprinopsis cinerea.

PubMed

Zhou, Jiangsheng; Bai, Yang; Dai, Rujuan; Guo, Xiaoli; Liu, Zhong-Hua; Yuan, Sheng

2018-05-09

Coprinopsis polysaccharides exhibit hypoglycemic and antioxidant activities. In this report, increases in polysaccharide production by homologous co-overexpression or individual homologous overexpression of phosphoglucomutase and UDP glucose pyrophosphorylase gene in Coprinopsis cinerea, which participate in polysaccharide biosynthesis. The transcription levels of the target genes were upregulated significantly in the oePGM-UGP strain when compared with the oePGM or oeUGP strain. The maximum intracellular polysaccharide content obtained in the oePGM-UGP strain was 1.49-fold higher than that of the WT strain, whereas a slight improvement in polysaccharide production was obtained in the oePGM and oeUGP strains. Extracellular polysaccharide production was enhanced by 75% in the oePGM-UGP strain when compared with that of the WT strain, whereas improvements of 30% and 16% were observed for the oePGM and oeUGP strains, respectively. These results show that multiple interventions in polysaccharide biosynthesis pathways of Basidiomycetes might improve polysaccharide yields when compared with that of single interventions.

Brewing characteristics of haploid strains isolated from sake yeast Kyokai No. 7.

PubMed

Katou, Taku; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi

2008-11-01

Sake yeast exhibit various characteristics that make them more suitable for sake brewing compared to other yeast strains. Since sake yeast strains are Saccharomyces cerevisiae heterothallic diploid strains, it is likely that they have heterozygous alleles on homologous chromosomes (heterozygosity) due to spontaneous mutations. If this is the case, segregation of phenotypic traits in haploid strains after sporulation and concomitant meiosis of sake yeast strains would be expected to occur. To examine this hypothesis, we isolated 100 haploid strains from Kyokai No. 7 (K7), a typical sake yeast strain in Japan, and compared their brewing characteristics in small-scale sake-brewing tests. Analyses of the resultant sake samples showed a smooth and continuous distribution of analytical values for brewing characteristics, suggesting that K7 has multiple heterozygosities that affect brewing characteristics and that these heterozygous alleles do segregate after sporulation. Correlation and principal component analyses suggested that the analytical parameters could be classified into two groups, indicating fermentation ability and sake flavour. (c) 2008 John Wiley & Sons, Ltd.

Biological Chlorine Cycling in Arctic Peat Soils

NASA Astrophysics Data System (ADS)

Zlamal, J. E.; Raab, T. K.; Lipson, D.

2014-12-01

Soils of the Arctic tundra near Barrow, Alaska are waterlogged and anoxic throughout most of the profile due to underlying permafrost. Microbial communities in these soils are adapted for the dominant anaerobic conditions and are capable of a surprising diversity of metabolic pathways. Anaerobic respiration in this environment warrants further study, particularly in the realm of electron cycling involving chlorine, which preliminary data suggest may play an important role in arctic anaerobic soil respiration. For decades, Cl was rarely studied outside of the context of solvent-contaminated sites due to the widely held belief that it is an inert element. However, Cl has increasingly become recognized as a metabolic player in microbial communities and soil cycling processes. Organic chlorinated compounds (Clorg) can be made by various organisms and used metabolically by others, such as serving as electron acceptors for microbes performing organohalide respiration. Sequencing our arctic soil samples has uncovered multiple genera of microorganisms capable of participating in many Cl-cycling processes including organohalide respiration, chlorinated hydrocarbon degradation, and perchlorate reduction. Metagenomic analysis of these soils has revealed genes for key enzymes of Cl-related metabolic processes such as dehalogenases and haloperoxidases, and close matches to genomes of known organohalide respiring microorganisms from the Dehalococcoides, Dechloromonas, Carboxydothermus, and Anaeromyxobacter genera. A TOX-100 Chlorine Analyzer was used to quantify total Cl in arctic soils, and these data were examined further to separate levels of inorganic Cl compounds and Clorg. Levels of Clorg increased with soil organic matter content, although total Cl levels lack this trend. X-ray Absorption Near Edge Structure (XANES) was used to provide information on the structure of Clorg in arctic soils, showing great diversity with Cl bound to both aromatic and alkyl groups. Incubations were conducted in the laboratory providing arctic soils with Clorg, and measurements taken to assess rates of organohalide respiration show an increase in chloride production due to microbial activity. Investigating these soils with diverse techniques affirms the importance of Cl-cycling in a pristine arctic tundra ecosystem.

Over-expression of multiple cytochrome P450 genes in fenvalerate-resistant field strains of Helicoverpa armigera from north of China.

PubMed

Xu, Li; Li, Dongzhi; Qin, Jianying; Zhao, Weisong; Qiu, Lihong

2016-09-01

Pyrethroid resistance was one of the main reasons for control failure of cotton bollworm Helicoverpa armigera (Hübner) in China. The promotion of Bt crops decreased the application of chemical insecticides in controlling H.armigera. However, the cotton bollworm still kept high levels of resistance to fenvalerate. In this study, the resistance levels of 8 field-collected strains of H. armigera from north of China to 4 insecticides, as well as the expression levels of related P450 genes were investigated. The results of bioassay indicated that the resistance levels to fenvalerate in the field strains varied from 5.4- to 114.7-fold, while the resistance levels to lambda-cyhalothrin, phoxim and methomyl were low, which were ranged from 1.5- to 5.2-, 0.2- to 1.6-, and 2.9- to 8.3- fold, respectively, compared to a susceptible strain. Synergistic experiment showed that PBO was the most effective synergist in increasing the sensitivity of H. armigera to fenvalerate, suggesting that P450 enzymes were involved in the pyrethroid resistance in the field strains. The results of quantitative RT-PCR indicated that eight P450 genes (CYP332A1, CYP4L11, CYP4L5, CYP4M6, CYP4M7, CYP6B7, CYP9A12, CYP9A14) were all significantly overexpressed in Hejian1 and Xiajin1 strains of H. armigera collected in 2013, and CYP4L5 was significantly overexpressed in all the 6 field strains collected in 2014. CYP332A1, CYP6B7 and CYP9A12 had very high overexpression levels in all the field strains, indicating their important roles in fenvalerate resistance. The results suggested that multiple P450 genes were involved in the high-level fenvalerate-resistance in different field strains of H. armigera collected from north of China. Copyright © 2016 Elsevier B.V. All rights reserved.

Calving laws and strain rates: a comparison between modelled relationships and observations from InSAR velocity maps from across Greenland.

NASA Astrophysics Data System (ADS)

Lea, James; Nick, Faezeh; Benn, Douglas; Kirchner, Nina

2017-04-01

Calving is a major mechanism of cryospheric ice mass loss and a significant contributor to global sea level change, though it is currently poorly understood as a process. Longitudinal strain rate is often cited as a first order control on calving, however multiple different calving laws (not always including the strain rate) have been used to represent this in numerical models of ice sheets. This study seeks to investigate how (1) different calving laws within a 1D flowline model predict strain rate will evolve within increasing terminus thickness for steady state and transient simulations, and (2) how these relationships compare with observed strains (derived from MEaSUREs Greenland InSAR velocity maps; Joughin et al., 2010 [updated 2016]) and depths (from BedMachine v.2 subglacial topography data; Morlighem et al., 2014). We identify that systematic relationships with terminus thickness exist for height above buoyancy, waterline and full-depth crevasse calving laws amongst others for both steady state and transient simulations. However, analysis of observed near-terminus strain rates for multiple Greenlandic glaciers using a variety of metrics (with a range of bed depths predicted by BedMachine) does not reproduce the shape or magnitude of any of these modelled relationships. Relationships between strain rate and depth derived from simple 1D model simulations therefore cannot be realistically compared to current real-world observations. This suggests that the magnitude of observed strain rates at an individual point, or area-averaged conditions near a real-world terminus are not meaningful in determining the potential for calving when taken in isolation. To improve understanding of first/second order calving processes, future modelling work should therefore look to analyse how/if the distribution of strain across the terminus region impacts calving as part of 2D-planform/3D models.

Characterisation of a rare, reassortant human G10P[14] rotavirus strain detected in Honduras

PubMed Central

Quaye, Osbourne; Roy, Sunando; Rungsrisuriyachai, Kunchala; Esona, Mathew D; Xu, Ziqian; Tam, Ka Ian; Banegas, Dina J Castro; Rey-Benito, Gloria; Bowen, Michael D

2018-01-01

BACKGROUND Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in humans resulted from interspecies transmission and reassortment between human and bovine rotavirus strains. OBJECTIVES In this study, a G10P[14] rotavirus genotype detected in a human stool sample in Honduras during the 2010-2011 rotavirus season, from an unvaccinated 30-month old boy who reported at the hospital with severe diarrhea and vomiting, was characterised to determine the possible evolutionary origin of the rare strain. METHODS For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were constructed using PhyML version 3.0. FINDINGS The next generation sequencing and phylogenetic analyses of the 11-segmented genome of the G10P[14] strain allowed classification as G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Six of the genes (VP1, VP2, VP3, VP6, NSP2 and NSP4) were DS-1-like. NSP1 and NSP5 were AU-1-like and NSP3 was T6, which suggests that multiple reassortment events occurred in the evolution of the strain. The phylogenetic analyses and genetic distance calculations showed that the VP7, VP4, VP6, VP1, VP3, NSP1, NSP3 and NSP4 genes clustered predominantly with bovine strains. NSP2 and VP2 genes were most closely related to simian and human strains, respectively, and NSP5 was most closely related to a rhesus strain. MAIN CONCLUSIONS The genetic characterisation of the G10P[14] strain from Honduras suggests that its genome resulted from multiple reassortment events which were possibly mediated through interspecies transmissions. PMID:29211103

Chimeric GII.4 norovirus virus-like-particle-based vaccines induce broadly blocking immune responses.

PubMed

Debbink, Kari; Lindesmith, Lisa C; Donaldson, Eric F; Swanstrom, Jesica; Baric, Ralph S

2014-07-01

There is currently no licensed vaccine for noroviruses, and development is hindered, in part, by an incomplete understanding of the host adaptive immune response to these highly heterogeneous viruses and rapid GII.4 norovirus molecular evolution. Emergence of a new predominant GII.4 norovirus strain occurs every 2 to 4 years. To address the problem of GII.4 antigenic variation, we tested the hypothesis that chimeric virus-like particle (VLP)-based vaccine platforms, which incorporate antigenic determinants from multiple strains into a single genetic background, will elicit a broader immune response against contemporary and emergent strains. Here, we compare the immune response generated by chimeric VLPs to that of parental strains and a multivalent VLP cocktail. Results demonstrate that chimeric VLPs induce a more broadly cross-blocking immune response than single parental VLPs and a similar response to a multivalent GII.4 VLP cocktail. Furthermore, we show that incorporating epitope site A alone from one strain into the background of another is sufficient to induce a blockade response against the strain donating epitope site A. This suggests a mechanism by which population-wide surveillance of mutations in a single epitope could be used to evaluate antigenic changes in order to identify potential emergent strains and quickly reformulate vaccines against future epidemic strains as they emerge in human populations. Noroviruses are gastrointestinal pathogens that infect an estimated 21 million people per year in the United States alone. GII.4 noroviruses account for >70% of all outbreaks, making them the most clinically important genotype. GII.4 noroviruses undergo a pattern of epochal evolution, resulting in the emergence of new strains with altered antigenicity over time, complicating vaccine design. This work is relevant to norovirus vaccine design as it demonstrates the potential for development of a chimeric VLP-based vaccine platform that may broaden the protective response against multiple GII.4 strains and proposes a potential reformulation strategy to control newly emergent strains in the human population. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Characterisation of a rare, reassortant human G10P[14] rotavirus strain detected in Honduras.

PubMed

Quaye, Osbourne; Roy, Sunando; Rungsrisuriyachai, Kunchala; Esona, Mathew D; Xu, Ziqian; Tam, Ka Ian; Banegas, Dina J Castro; Rey-Benito, Gloria; Bowen, Michael D

2018-01-01

Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in humans resulted from interspecies transmission and reassortment between human and bovine rotavirus strains. In this study, a G10P[14] rotavirus genotype detected in a human stool sample in Honduras during the 2010-2011 rotavirus season, from an unvaccinated 30-month old boy who reported at the hospital with severe diarrhea and vomiting, was characterised to determine the possible evolutionary origin of the rare strain. For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were constructed using PhyML version 3.0. The next generation sequencing and phylogenetic analyses of the 11-segmented genome of the G10P[14] strain allowed classification as G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Six of the genes (VP1, VP2, VP3, VP6, NSP2 and NSP4) were DS-1-like. NSP1 and NSP5 were AU-1-like and NSP3 was T6, which suggests that multiple reassortment events occurred in the evolution of the strain. The phylogenetic analyses and genetic distance calculations showed that the VP7, VP4, VP6, VP1, VP3, NSP1, NSP3 and NSP4 genes clustered predominantly with bovine strains. NSP2 and VP2 genes were most closely related to simian and human strains, respectively, and NSP5 was most closely related to a rhesus strain. The genetic characterisation of the G10P[14] strain from Honduras suggests that its genome resulted from multiple reassortment events which were possibly mediated through interspecies transmissions.

Assuming Multiple Roles: The Time Crunch.

ERIC Educational Resources Information Center

McKitric, Eloise J.

Women's increased labor force participation and continued responsibility for most household work and child care have resulted in "time crunch." This strain results from assuming multiple roles within a fixed time period. The existence of an egalitarian family has been assumed by family researchers and writers but has never been verified. Time…

Mothers of Young Adults with Intellectual Disability: Multiple Roles, Ethnicity and Well-Being

ERIC Educational Resources Information Center

Eisenhower, A.; Blacher, J.

2006-01-01

Background: Two opposing perspectives--role strain and role enhancement--were considered as predictive of women's psychological and physical health. The authors examined the relation between multiple role occupancy (parenting, employment, marriage) and well-being (depression and health) among mothers of young adults with intellectual disability…

Continuing multiplication of Salmonella Enteritidis strains in egg yolk during refrigeration at 7.2° C

USDA-ARS?s Scientific Manuscript database

The continuing attribution of human illness caused by Salmonella Enteritidis (SE) to the consumption of contaminated eggs has led to widespread implementation of risk reduction programs for commercial egg production. Prompt refrigeration of eggs to prevent bacterial multiplication to dangerously hig...

Multiple-Locus VNTR Analysis (MLVA) for Bacterial Strain Identification - Quarterly Progress Report for the period 7/1/00 to 10/30/00

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Paul Keim

2000-11-07

Multiple locus VNTR analysis (MLVA) systems are being developed for B. anthracis, Y. pestis and F. tularensis. These are high resolution DNA fingerprinting systems that will allow for molecular epidemiology and forensic analysis of these pathogens.

Multiple-Locus VNTR Analysis (MLVA) for Bacterial Strain Identification - Quarterly Progress Report for the Period 4/1/00 to 6/30/00

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Paul Keim

2000-11-07

Multiple locus VNTR analysis (MLVA) systems are being developed for B. anthracis, Y. pestis and F. tularensis. These are high resolution DNA fingerprinting systems that will allow for molecular epidemiology and forensic analysis of these pathogens.

Computing Fault Displacements from Surface Deformations

NASA Technical Reports Server (NTRS)

Lyzenga, Gregory; Parker, Jay; Donnellan, Andrea; Panero, Wendy

2006-01-01

Simplex is a computer program that calculates locations and displacements of subterranean faults from data on Earth-surface deformations. The calculation involves inversion of a forward model (given a point source representing a fault, a forward model calculates the surface deformations) for displacements, and strains caused by a fault located in isotropic, elastic half-space. The inversion involves the use of nonlinear, multiparameter estimation techniques. The input surface-deformation data can be in multiple formats, with absolute or differential positioning. The input data can be derived from multiple sources, including interferometric synthetic-aperture radar, the Global Positioning System, and strain meters. Parameters can be constrained or free. Estimates can be calculated for single or multiple faults. Estimates of parameters are accompanied by reports of their covariances and uncertainties. Simplex has been tested extensively against forward models and against other means of inverting geodetic data and seismic observations. This work

Theoretical study of polarization insensitivity of carrier-induced refractive index change of multiple quantum well.

PubMed

Miao, Qingyuan; Zhou, Qunjie; Cui, Jun; He, Ping-An; Huang, Dexiu

2014-12-29

Characteristics of polarization insensitivity of carrier-induced refractive index change of 1.55 μm tensile-strained multiple quantum well (MQW) are theoretically investigated. A comprehensive MQW model is proposed to effectively extend the application range of previous models. The model considers the temperature variation as well as the nonuniform distribution of injected carrier in MQW. Tensile-strained MQW is expected to achieve polarization insensitivity of carrier-induced refractive index change over a wide wavelength range as temperature varies from 0°C to 40°C, while the magnitude of refractive index change keeps a large value (more than 3 × 10^-3). And that the polarization insensitivity of refractive index change can maintain for a wide range of carrier concentration. Multiple quantum well with different material and structure parameters is anticipated to have the similar polarization insensitivity of refractive index change, which shows the design flexibility.

Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

PubMed Central

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship. PMID:25815838

Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

PubMed

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

PubMed Central

Doddapaneni, Harshavardhan; Yao, Jiqiang; Lin, Hong; Walker, M Andrew; Civerolo, Edwin L

2006-01-01

Background The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. Results There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. Conclusion INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the X. fastidiosa. Results of this analysis are publicly available in the form of a web database. PMID:16948851

Lactose-fermenting, multiple drug-resistant Salmonella typhi strains isolated from a patient with postoperative typhoid fever.

PubMed Central

Kohbata, S; Takahashi, M; Yabuuchi, E

1983-01-01

Two lactose-fermenting Salmonella typhi strains were isolated from bile and blood specimens of a typhoid fever patient who underwent a cholecystectomy due to cholelithiasis. One lactose-fermenting S. typhi strain was also isolated from a pus specimen which was obtained at the tip of the T-shaped tube withdrawn from the operative wound of the common bile duct of the patient. These three lactose-fermenting isolates: GIFU 11924 from bile, GIFU 11926 from pus, and GIFU 11927 from blood, were phenotypically identical to the type strain (GIFU 11801 = ATCC 19430 = NCTC 8385) of S. typhi, except that the three strains fermented lactose and failed to blacken the butt of Kligler iron agar or triple sugar iron agar medium. All three lactose-fermenting strains were resistant to chloramphenicol, ampicillin, sulfomethoxazole, trimethoprim, gentamicin, cephaloridine, and four other antimicrobial agents. The type strain was uniformly susceptible to these 10 drugs. The strain GIFU 11925, a lactose-negative dissociant from strain GIFU 11926, was also susceptible to these drugs, with the sole exception of chloramphenicol (minimal inhibitory concentration, 100 micrograms/ml). PMID:6630471

Genome sequence of a novel multiple antibiotic resistant member of Erysipelotrichaceae family isolated from a swine manure storage pit

USDA-ARS?s Scientific Manuscript database

The swine gastro intestinal (GI) tract and stored manure may serve as reservoirs of antibiotic resistance genes as well as sources of novel bacteria. We report the draft genome sequence of “Cottaibacterium suis” strain MTC7, a novel antibiotic resistant bacterium. The strain was isolated from a swin...

Identification of an atypical strain of Toxoplasma gondii as the cause of a waterborne outbreak of toxoplasmosis in Santa IsabeldoIvai, Brazil

USDA-ARS?s Scientific Manuscript database

We have identified an atypical strain of Toxoplasmagondii as the causative agent of the 2001 outbreak of toxoplasmosis in Santa Isabel do Ivai, Brazil, which resulted in approximately 426 human infections. The epidemic clone was isolated from multiple water filters collected from a cistern linked ep...

A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms

PubMed Central

Marenda, Marc; Barbe, Valérie; Gourgues, Géraldine; Mangenot, Sophie; Sagne, Evelyne; Citti, Christine

2006-01-01

An integrative conjugative element, ICEA, was characterized in Mycoplasma agalactiae strain 5632, in which it occurs as multiple chromosomal copies and as a free circular form. The distribution of ICEA sequences in M. agalactiae strains and their occurrence in Mycoplasma bovis suggest the spreading of the element within or between species. PMID:16707706

Selective sweep analysis in the genomes of the 91-R and 91-C Drosophila melanogaster strains reveals few of the ‘usual suspects’ in Dichlorodiphenyltrichloroethane (DDT) resistance

USDA-ARS?s Scientific Manuscript database

Adaptation of insect phenotypes for survival after exposure to xenobiotics can result from selection at multiple loci with additive genetic effects. A high level dichlorodiphenyltrichloroethane (DDT) resistance phenotype in the Drosophila melanogaster strain 91-R has resulted due to continuous labo...

Enhancement of the proline and nitric oxide synthetic pathway improves fermentation ability under multiple baking-associated stress conditions in industrial baker's yeast

PubMed Central

2012-01-01

Background During the bread-making process, industrial baker's yeast, mostly Saccharomyces cerevisiae, is exposed to baking-associated stresses, such as air-drying and freeze-thaw stress. These baking-associated stresses exert severe injury to yeast cells, mainly due to the generation of reactive oxygen species (ROS), leading to cell death and reduced fermentation ability. Thus, there is a great need for a baker's yeast strain with higher tolerance to baking-associated stresses. Recently, we revealed a novel antioxidative mechanism in a laboratory yeast strain that is involved in stress-induced nitric oxide (NO) synthesis from proline via proline oxidase Put1 and N-acetyltransferase Mpr1. We also found that expression of the proline-feedback inhibition-less sensitive mutant γ-glutamyl kinase (Pro1-I150T) and the thermostable mutant Mpr1-F65L resulted in an enhanced fermentation ability of baker's yeast in bread dough after freeze-thaw stress and air-drying stress, respectively. However, baker's yeast strains with high fermentation ability under multiple baking-associated stresses have not yet been developed. Results We constructed a self-cloned diploid baker's yeast strain with enhanced proline and NO synthesis by expressing Pro1-I150T and Mpr1-F65L in the presence of functional Put1. The engineered strain increased the intracellular NO level in response to air-drying stress, and the strain was tolerant not only to oxidative stress but also to both air-drying and freeze-thaw stresses probably due to the reduced intracellular ROS level. We also showed that the resultant strain retained higher leavening activity in bread dough after air-drying and freeze-thaw stress than that of the wild-type strain. On the other hand, enhanced stress tolerance and fermentation ability did not occur in the put1-deficient strain. This result suggests that NO is synthesized in baker's yeast from proline in response to oxidative stresses that induce ROS generation and that increased NO plays an important role in baking-associated stress tolerance. Conclusions In this work, we clarified the importance of Put1- and Mpr1-mediated NO generation from proline to the baking-associated stress tolerance in industrial baker's yeast. We also demonstrated that baker's yeast that enhances the proline and NO synthetic pathway by expressing the Pro1-I150T and Mpr1-F65L variants showed improved fermentation ability under multiple baking-associated stress conditions. From a biotechnological perspective, the enhancement of proline and NO synthesis could be promising for breeding novel baker's yeast strains. PMID:22462683

Enhancement of the proline and nitric oxide synthetic pathway improves fermentation ability under multiple baking-associated stress conditions in industrial baker's yeast.

PubMed

Sasano, Yu; Haitani, Yutaka; Hashida, Keisuke; Ohtsu, Iwao; Shima, Jun; Takagi, Hiroshi

2012-04-01

During the bread-making process, industrial baker's yeast, mostly Saccharomyces cerevisiae, is exposed to baking-associated stresses, such as air-drying and freeze-thaw stress. These baking-associated stresses exert severe injury to yeast cells, mainly due to the generation of reactive oxygen species (ROS), leading to cell death and reduced fermentation ability. Thus, there is a great need for a baker's yeast strain with higher tolerance to baking-associated stresses. Recently, we revealed a novel antioxidative mechanism in a laboratory yeast strain that is involved in stress-induced nitric oxide (NO) synthesis from proline via proline oxidase Put1 and N-acetyltransferase Mpr1. We also found that expression of the proline-feedback inhibition-less sensitive mutant γ-glutamyl kinase (Pro1-I150T) and the thermostable mutant Mpr1-F65L resulted in an enhanced fermentation ability of baker's yeast in bread dough after freeze-thaw stress and air-drying stress, respectively. However, baker's yeast strains with high fermentation ability under multiple baking-associated stresses have not yet been developed. We constructed a self-cloned diploid baker's yeast strain with enhanced proline and NO synthesis by expressing Pro1-I150T and Mpr1-F65L in the presence of functional Put1. The engineered strain increased the intracellular NO level in response to air-drying stress, and the strain was tolerant not only to oxidative stress but also to both air-drying and freeze-thaw stresses probably due to the reduced intracellular ROS level. We also showed that the resultant strain retained higher leavening activity in bread dough after air-drying and freeze-thaw stress than that of the wild-type strain. On the other hand, enhanced stress tolerance and fermentation ability did not occur in the put1-deficient strain. This result suggests that NO is synthesized in baker's yeast from proline in response to oxidative stresses that induce ROS generation and that increased NO plays an important role in baking-associated stress tolerance. In this work, we clarified the importance of Put1- and Mpr1-mediated NO generation from proline to the baking-associated stress tolerance in industrial baker's yeast. We also demonstrated that baker's yeast that enhances the proline and NO synthetic pathway by expressing the Pro1-I150T and Mpr1-F65L variants showed improved fermentation ability under multiple baking-associated stress conditions. From a biotechnological perspective, the enhancement of proline and NO synthesis could be promising for breeding novel baker's yeast strains.

Structural and functional characterization of two alpha-synuclein strains

NASA Astrophysics Data System (ADS)

Bousset, Luc; Pieri, Laura; Ruiz-Arlandis, Gemma; Gath, Julia; Jensen, Poul Henning; Habenstein, Birgit; Madiona, Karine; Olieric, Vincent; Böckmann, Anja; Meier, Beat H.; Melki, Ronald

2013-10-01

α-synuclein aggregation is implicated in a variety of diseases including Parkinson’s disease, dementia with Lewy bodies, pure autonomic failure and multiple system atrophy. The association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. Here we structurally and functionally characterize two polymorphs of α-synuclein. We present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. Specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. Such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies.

Hospital strain colonization by Staphylococcus epidermidis.

PubMed

Blum-Menezes, D; Bratfich, O J; Padoveze, M C; Moretti, M L

2009-03-01

The skin and mucous membranes of healthy subjects are colonized by strains of Staphylococcus epidermidis showing a high diversity of genomic DNA polymorphisms. Prolonged hospitalization and the use of invasive procedures promote changes in the microbiota with subsequent colonization by hospital strains. We report here a patient with prolonged hospitalization due to chronic pancreatitis who was treated with multiple antibiotics, invasive procedures and abdominal surgery. We studied the dynamics of skin colonization by S. epidermidis leading to the development of catheter-related infections and compared the genotypic profile of clinical and microbiota strains by pulsed field gel electrophoresis. During hospitalization, the normal S. epidermidis skin microbiota exhibiting a polymorphic genomic DNA profile was replaced with a hospital-acquired biofilm-producer S. epidermidis strain that subsequently caused repetitive catheter-related infections.

Systematic characterization of Bacillus Genetic Stock Center Bacillus thuringiensis strains using Multi-Locus Sequence Typing.

PubMed

Wang, Kui; Shu, Changlong; Soberón, Mario; Bravo, Alejandra; Zhang, Jie

2018-04-30

The goal of this work was to perform a systematic characterization of Bacillus thuringiensis (Bt) strains from the Bacillus Genetic Stock Center (BGSC) collection using Multi-Locus Sequence Typing (MLST). Different genetic markers of 158 Bacillus thuringiensis (Bt) strains from 73 different serovars stored in the BGSC, that represented 92% of the different Bt serovars of the BGSC were analyzed, the 8% that were not analyzed were not available. In addition, we analyzed 72 Bt strains from 18 serovars available at the pubMLST bcereus database, and Bt strains G03, HBF18 and Bt185, with no H serovars provided by our laboratory. We performed a systematic MLST analysis using seven housekeeping genes (glpF, gmK, ilvD, pta, pur, pycA and tpi) and analyzed correlation of the results of this analysis with strain serovars. The 233 Bt strains analyzed were assigned to 119 STs from which 19 STs were new. Genetic relationships were established by phylogenetic analysis and showed that STs could be grouped in two major Clusters containing 21 sub-groups. We found that a significant number of STs (101 in total) correlated with specific serovars, such as ST13 that corresponded to nine Bt isolates from B. thuringiensis serovar kenyae. However, other serovars showed high genetic variability and correlated with multiple STs; for example, B. thuringiensis serovar morrisoni correlated with 11 different STs. In addition, we found that 16 different STs correlated with multiple serovars (2-4 different serovars); for example, ST12 correlated with B. thuringiensis serovar alesti, dakota, palmanyolensis and sotto/dendrolimus. These data indicated that only partial correspondence between MLST and serotyping can be established. Copyright © 2018 Elsevier Inc. All rights reserved.

Examining the Link between Biofilm Formation and the Ability of Pathogenic Salmonella Strains to Colonize Multiple Host Species

PubMed Central

MacKenzie, Keith D.; Palmer, Melissa B.; Köster, Wolfgang L.; White, Aaron P.

2017-01-01

Salmonella are important pathogens worldwide and a predominant number of human infections are zoonotic in nature. The ability of strains to form biofilms, which is a multicellular behavior characterized by the aggregation of cells, is predicted to be a conserved strategy for increased persistence and survival. It may also contribute to the increasing number of infections caused by ingestion of contaminated fruits and vegetables. There is a correlation between biofilm formation and the ability of strains to colonize and replicate within the intestines of multiple host species. These strains predominantly cause localized gastroenteritis infections in humans. In contrast, there are salmonellae that cause systemic, disseminated infections in a select few host species; these “invasive” strains have a narrowed host range, and most are unable to form biofilms. This includes host-restricted Salmonella serovar Typhi, which are only able to infect humans, and atypical gastroenteritis strains associated with the opportunistic infection of immunocompromised patients. From the perspective of transmission, biofilm formation is advantageous for ensuring pathogen survival in the environment. However, from an infection point of view, biofilm formation may be an anti-virulence trait. We do not know if the capacity to form biofilms prevents a strain from accessing the systemic compartments within the host or if loss of the biofilm phenotype reflects a change in a strain’s interaction with the host. In this review, we examine the connections between biofilm formation, Salmonella disease states, degrees of host adaptation, and how this might relate to different transmission patterns. A better understanding of the dynamic lifecycle of Salmonella will allow us to reduce the burden of livestock and human infections caused by these important pathogens. PMID:29159172

Prevalence of Avian-Pathogenic Escherichia coli Strain O1 Genomic Islands among Extraintestinal and Commensal E. coli Isolates

PubMed Central

Johnson, Timothy J.; Wannemuehler, Yvonne; Kariyawasam, Subhashinie; Johnson, James R.; Logue, Catherine M.

2012-01-01

Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include pathogens of humans and animals. Previously, the genome of avian-pathogenic E. coli (APEC) O1:K1:H7 strain O1, from ST95, was sequenced and compared to those of several other E. coli strains, identifying 43 genomic islands. Here, the genomic islands of APEC O1 were compared to those of other sequenced E. coli strains, and the distribution of 81 genes belonging to 12 APEC O1 genomic islands among 828 human and avian ExPEC and commensal E. coli isolates was determined. Multiple islands were highly prevalent among isolates belonging to the O1 and O18 serogroups within phylogenetic group B2, which are implicated in human neonatal meningitis. Because of the extensive genomic similarities between APEC O1 and other human ExPEC strains belonging to the ST95 phylogenetic lineage, its ability to cause disease in a rat model of sepsis and meningitis was assessed. Unlike other ST95 lineage strains, APEC O1 was unable to cause bacteremia or meningitis in the neonatal rat model and was significantly less virulent than uropathogenic E. coli (UPEC) CFT073 in a mouse sepsis model, despite carrying multiple neonatal meningitis E. coli (NMEC) virulence factors and belonging to the ST95 phylogenetic lineage. These results suggest that host adaptation or genome modifications have occurred either in APEC O1 or in highly virulent ExPEC isolates, resulting in differences in pathogenicity. Overall, the genomic islands examined provide targets for further discrimination of the different ExPEC subpathotypes, serogroups, phylogenetic types, and sequence types. PMID:22467781

Prevalence of avian-pathogenic Escherichia coli strain O1 genomic islands among extraintestinal and commensal E. coli isolates.

PubMed

Johnson, Timothy J; Wannemuehler, Yvonne; Kariyawasam, Subhashinie; Johnson, James R; Logue, Catherine M; Nolan, Lisa K

2012-06-01

Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include pathogens of humans and animals. Previously, the genome of avian-pathogenic E. coli (APEC) O1:K1:H7 strain O1, from ST95, was sequenced and compared to those of several other E. coli strains, identifying 43 genomic islands. Here, the genomic islands of APEC O1 were compared to those of other sequenced E. coli strains, and the distribution of 81 genes belonging to 12 APEC O1 genomic islands among 828 human and avian ExPEC and commensal E. coli isolates was determined. Multiple islands were highly prevalent among isolates belonging to the O1 and O18 serogroups within phylogenetic group B2, which are implicated in human neonatal meningitis. Because of the extensive genomic similarities between APEC O1 and other human ExPEC strains belonging to the ST95 phylogenetic lineage, its ability to cause disease in a rat model of sepsis and meningitis was assessed. Unlike other ST95 lineage strains, APEC O1 was unable to cause bacteremia or meningitis in the neonatal rat model and was significantly less virulent than uropathogenic E. coli (UPEC) CFT073 in a mouse sepsis model, despite carrying multiple neonatal meningitis E. coli (NMEC) virulence factors and belonging to the ST95 phylogenetic lineage. These results suggest that host adaptation or genome modifications have occurred either in APEC O1 or in highly virulent ExPEC isolates, resulting in differences in pathogenicity. Overall, the genomic islands examined provide targets for further discrimination of the different ExPEC subpathotypes, serogroups, phylogenetic types, and sequence types.

Development of a Markerless Genetic Exchange System in Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keller, Kimberly L.; Bender, Kelly S.; Wall, Judy D.

2009-07-21

In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been developed. The counterselectable marker that makes this deletion system possible is the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded by upp. In wild-type D. vulgaris, growth was shown to bemore » inhibited by the toxic pyrimidine analog 5-fluorouracil (5-FU); whereas, a mutant bearing a deletion of the upp gene was resistant to 5-FU. When a plasmid containing the wild-type upp gene expressed constitutively from the aph(3')-II promoter (promoter for the kanamycin resistance gene in Tn5) was introduced into the upp deletion strain, sensitivity to 5-FU was restored. This observation allowed us to develop a two-step integration and excision strategy for the deletion of genes of interest. Since this inframe deletion strategy does not retain an antibiotic cassette, multiple deletions can be generated in a single strain without the accumulation of genes conferring antibiotic resistances. We used this strategy to generate a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I restriction-modification system, that we designated JW7035. The transformation efficiency of the JW7035 strain was found to be 100 to 1000 times greater than that of the wild-type strain when stable plasmids were introduced via electroporation.« less

Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

PubMed

Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

2016-04-15

Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecological Success of a Group of Saccharomyces cerevisiae/Saccharomyces kudriavzevii Hybrids in the Northern European Wine-Making Environment

PubMed Central

Erny, C.; Raoult, P.; Alais, A.; Butterlin, G.; Delobel, P.; Matei-Radoi, F.; Casaregola, S.

2012-01-01

The hybrid nature of lager-brewing yeast strains has been known for 25 years; however, yeast hybrids have only recently been described in cider and wine fermentations. In this study, we characterized the hybrid genomes and the relatedness of the Eg8 industrial yeast strain and of 24 Saccharomyces cerevisiae/Saccharomyces kudriavzevii hybrid yeast strains used for wine making in France (Alsace), Germany, Hungary, and the United States. An array-based comparative genome hybridization (aCGH) profile of the Eg8 genome revealed a typical chimeric profile. Measurement of hybrids DNA content per cell by flow cytometry revealed multiple ploidy levels (2n, 3n, or 4n), and restriction fragment length polymorphism analysis of 22 genes indicated variable amounts of S. kudriavzevii genetic content in three representative strains. We developed microsatellite markers for S. kudriavzevii and used them to analyze the diversity of a population isolated from oaks in Ardèche (France). This analysis revealed new insights into the diversity of this species. We then analyzed the diversity of the wine hybrids for 12 S. cerevisiae and 7 S. kudriavzevii microsatellite loci and found that these strains are the products of multiple hybridization events between several S. cerevisiae wine yeast isolates and various S. kudriavzevii strains. The Eg8 lineage appeared remarkable, since it harbors strains found over a wide geographic area, and the interstrain divergence measured with a (δμ)2 genetic distance indicates an ancient origin. These findings reflect the specific adaptations made by S. cerevisiae/S. kudriavzevii cryophilic hybrids to winery environments in cool climates. PMID:22344648

Brachiaria Grasses (Brachiaria spp.) harbor a diverse bacterial community with multiple attributes beneficial to plant growth and development.

PubMed

Mutai, Collins; Njuguna, Joyce; Ghimire, Sita

2017-10-01

Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA-based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth-promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils. © 2017 International Livestock Research Institute. MicrobiologyOpen published by John Wiley & Sons Ltd.

The distribution of a phage-related insertion sequence element in the cyanobacterium, Microcystis aeruginosa.

PubMed

Kuno, Sotaro; Yoshida, Takashi; Kamikawa, Ryoma; Hosoda, Naohiko; Sako, Yoshihiko

2010-01-01

The cyanophage Ma-LMM01, specifically-infecting Microcystis aeruginosa, has an insertion sequence (IS) element that we named IS607-cp showing high nucleotide similarity to a counterpart in the genome of the cyanobacterium Cyanothece sp. We tested 21 strains of M. aeruginosa for the presence of IS607-cp using PCR and detected the element in strains NIES90, NIES112, NIES604, and RM6. Thermal asymmetric interlaced PCR (TAIL-PCR) revealed each of these strains has multiple copies of IS607-cp. Some of the ISs were classified into three types based on their inserted positions; IS607-cp-1 is common in strains NIES90, NIES112 and NIES604, whereas IS607-cp-2 and IS607-cp-3 are specific to strains NIES90 and RM6, respectively. This multiplicity may reflect the replicative transposition of IS607-cp. The sequence of IS607-cp in Ma-LMM01 showed robust affinity to those found in M. aeruginosa and Cyanothece spp. in a phylogenetic tree inferred from counterparts of various bacteria. This suggests the transfer of IS607-cp between the cyanobacterium and its cyanophage. We discuss the potential role of Ma-LMM01-related phages as donors of IS elements that may mediate the transfer of IS607-cp; and thereby partially contribute to the genome plasticity of M. aeruginosa.

Characterization of Escherichia coli O157:H7 strains from contaminated raw beef trim during "high event periods".

PubMed

Arthur, Terrance M; Bono, James L; Kalchayanand, Norasak

2014-01-01

The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by Escherichia coli O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple E. coli O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as "high event periods" (HEP) of contamination. The results reported here detail the characterization of E. coli O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of E. coli O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.

Highly tensile-strained Ge/InAlAs nanocomposites

NASA Astrophysics Data System (ADS)

Jung, Daehwan; Faucher, Joseph; Mukherjee, Samik; Akey, Austin; Ironside, Daniel J.; Cabral, Matthew; Sang, Xiahan; Lebeau, James; Bank, Seth R.; Buonassisi, Tonio; Moutanabbir, Oussama; Lee, Minjoo Larry

2017-01-01

Self-assembled nanocomposites have been extensively investigated due to the novel properties that can emerge when multiple material phases are combined. Growth of epitaxial nanocomposites using lattice-mismatched constituents also enables strain-engineering, which can be used to further enhance material properties. Here, we report self-assembled growth of highly tensile-strained Ge/In0.52Al0.48As (InAlAs) nanocomposites by using spontaneous phase separation. Transmission electron microscopy shows a high density of single-crystalline germanium nanostructures coherently embedded in InAlAs without extended defects, and Raman spectroscopy reveals a 3.8% biaxial tensile strain in the germanium nanostructures. We also show that the strain in the germanium nanostructures can be tuned to 5.3% by altering the lattice constant of the matrix material, illustrating the versatility of epitaxial nanocomposites for strain engineering. Photoluminescence and electroluminescence results are then discussed to illustrate the potential for realizing devices based on this nanocomposite material.

Effects of value strains on psychopathology of Chinese rural youths.

PubMed

Zhang, Jie; Zhao, Sibo

2013-12-01

The Strain Theory of Suicide postulates that psychological strains usually precede mental disorders including suicidal behavior. This paper focuses on the effect of conflicting social value strains on the individual's psychopathology. We analyzed the data of 2031 respondents who were proxy informants for suicides and community living controls in a large scale psychological autopsy study in rural China, with the CES-D depression measure for the psychopathology. Individuals having experienced value conflicts between Confucian gender role and gender equalitarianism in modern society scored on depression significantly higher than the individuals who do not experience the value conflict, and it is also true when several other relevant variables were held constant in the multiple regression model. This study supports the hypotheses that people who confront value conflicts are likely to experience psychopathological strain, and the higher the level of strain, the stronger the depression. Copyright © 2013 Elsevier B.V. All rights reserved.

Association of arginase I or nitric oxide-related factors with job strain in healthy workers

PubMed Central

Eguchi, Eri; Nagaoka, Kenjiro

2017-01-01

This study evaluated the associations between job strain and arginase I in 378 healthy Japanese factory workers by a cross-sectional study measuring nitric oxide (NO)-related parameters (arginase I, L-arginine, exhaled nitric oxide (FeNO), and NOx), clinical parameters, and job strain using a Japanese version of the Job Content Questionnaire by Karasek. Arginase I and FEV1% were negatively correlated with job strain and positively correlated with job control and social support. FeNO and hs-CRP were negatively correlated with job strain. Multiple regression analysis showed negative association of arginase I with job strain and positive association with job control and social support in females. It is concluded that serum levels of arginase I may be useful biomarkers for the diagnosis of job stress in healthy female workers, although many factors can be influencing the data. PMID:28403218

Effects of Value Strains on Psychopathology of Chinese Rural Youths

PubMed Central

Zhang, Jie; Zhao, Sibo

2013-01-01

The Strain Theory of Suicide postulates that psychological strains usually precede mental disorders including suicidal behavior. This paper focuses on the effect of conflicting social value strains on the individual’s psychopathology. We analyzed the data of 2,031 respondents who were proxy informants for suicides and community living controls in a large scale psychological autopsy study in rural China, with the CES-D depression measure for the psychopathology. Individuals having experienced value conflicts between Confucian gender role and gender equalitarianism in modern society scored on depression significantly higher than the individuals who do not experience the value conflict, and it is also true when several other relevant variables were held constant in the multiple regression model. This study supports the hypotheses that people who confront value conflicts is likely to lead to psychopathological strain, and the higher the level of strain, the stronger the depression. PMID:24309863

Highly tensile-strained Ge/InAlAs nanocomposites

PubMed Central

Jung, Daehwan; Faucher, Joseph; Mukherjee, Samik; Akey, Austin; Ironside, Daniel J.; Cabral, Matthew; Sang, Xiahan; Lebeau, James; Bank, Seth R.; Buonassisi, Tonio; Moutanabbir, Oussama; Lee, Minjoo Larry

2017-01-01

Self-assembled nanocomposites have been extensively investigated due to the novel properties that can emerge when multiple material phases are combined. Growth of epitaxial nanocomposites using lattice-mismatched constituents also enables strain-engineering, which can be used to further enhance material properties. Here, we report self-assembled growth of highly tensile-strained Ge/In0.52Al0.48As (InAlAs) nanocomposites by using spontaneous phase separation. Transmission electron microscopy shows a high density of single-crystalline germanium nanostructures coherently embedded in InAlAs without extended defects, and Raman spectroscopy reveals a 3.8% biaxial tensile strain in the germanium nanostructures. We also show that the strain in the germanium nanostructures can be tuned to 5.3% by altering the lattice constant of the matrix material, illustrating the versatility of epitaxial nanocomposites for strain engineering. Photoluminescence and electroluminescence results are then discussed to illustrate the potential for realizing devices based on this nanocomposite material. PMID:28128282

QTL mapping of sake brewing characteristics of yeast.

PubMed

Katou, Taku; Namise, Masahiro; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi

2009-04-01

A haploid sake yeast strain derived from the commercial diploid sake yeast strain Kyokai no. 7 showed better characteristics for sake brewing compared to the haploid laboratory yeast strain X2180-1B, including higher production of ethanol and aromatic components. A hybrid of these two strains showed intermediate characteristics in most cases. After sporulation of the hybrid strain, we obtained 100 haploid segregants of the hybrid. Small-scale sake brewing tests of these segregants showed a smooth continuous distribution of the sake brewing characteristics, suggesting that these traits are determined by multiple quantitative trait loci (QTLs). To examine these sake brewing characteristics at the genomic level, we performed QTL analysis of sake brewing characteristics using 142 DNA markers that showed heterogeneity between the two parental strains. As a result, we identified 25 significant QTLs involved in the specification of sake brewing characteristics such as ethanol fermentation and the production of aromatic components.

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd.

PubMed

Upadhyay, Anamika; Kochar, Mandira; Rajam, Manchikatla V; Srivastava, Sheela

2017-01-01

Fluorescent Pseudomonas strain Psd is a soil isolate, possessing multiple plant growth promoting (PGP) properties and biocontrol potential. In addition, the strain also possesses high Zn 2+ biosorption capability. In this study, we have investigated the role exopolysaccharides (EPS) play in Zn 2+ biosorption. We have identified that alginates are the prime components contributing to Zn 2+ biosorption. Deletion of the alg8 gene, which codes for a sub-unit of alginate polymerase, led to a significant reduction in EPS production by the organism. We have also demonstrated that the increased alginate production in response to Zn 2+ exposure leads to improved biofilm formation by the strain. In the alg8 deletion mutant, however, biofilm formation was severely compromised. Further, we have studied the functional implications of Zn 2+ biosorption by Pseudomonas strain Psd by demonstrating the effect on the PGP and biocontrol potential of the strain.

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd

PubMed Central

Upadhyay, Anamika; Kochar, Mandira; Rajam, Manchikatla V.; Srivastava, Sheela

2017-01-01

Fluorescent Pseudomonas strain Psd is a soil isolate, possessing multiple plant growth promoting (PGP) properties and biocontrol potential. In addition, the strain also possesses high Zn2+ biosorption capability. In this study, we have investigated the role exopolysaccharides (EPS) play in Zn2+ biosorption. We have identified that alginates are the prime components contributing to Zn2+ biosorption. Deletion of the alg8 gene, which codes for a sub-unit of alginate polymerase, led to a significant reduction in EPS production by the organism. We have also demonstrated that the increased alginate production in response to Zn2+ exposure leads to improved biofilm formation by the strain. In the alg8 deletion mutant, however, biofilm formation was severely compromised. Further, we have studied the functional implications of Zn2+ biosorption by Pseudomonas strain Psd by demonstrating the effect on the PGP and biocontrol potential of the strain. PMID:28286498

A novel and rapid method for obtaining high titre intact prion strains from mammalian brain.

PubMed

Wenborn, Adam; Terry, Cassandra; Gros, Nathalie; Joiner, Susan; D'Castro, Laura; Panico, Silvia; Sells, Jessica; Cronier, Sabrina; Linehan, Jacqueline M; Brandner, Sebastian; Saibil, Helen R; Collinge, John; Wadsworth, Jonathan D F

2015-05-07

Mammalian prions exist as multiple strains which produce characteristic and highly reproducible phenotypes in defined hosts. How this strain diversity is encoded by a protein-only agent remains one of the most interesting and challenging questions in biology with wide relevance to understanding other diseases involving the aggregation or polymerisation of misfolded host proteins. Progress in understanding mammalian prion strains has however been severely limited by the complexity and variability of the methods used for their isolation from infected tissue and no high resolution structures have yet been reported. Using high-throughput cell-based prion bioassay to re-examine prion purification from first principles we now report the isolation of prion strains to exceptional levels of purity from small quantities of infected brain and demonstrate faithful retention of biological and biochemical strain properties. The method's effectiveness and simplicity should facilitate its wide application and expedite structural studies of prions.

A novel and rapid method for obtaining high titre intact prion strains from mammalian brain

PubMed Central

Wenborn, Adam; Terry, Cassandra; Gros, Nathalie; Joiner, Susan; D’Castro, Laura; Panico, Silvia; Sells, Jessica; Cronier, Sabrina; Linehan, Jacqueline M.; Brandner, Sebastian; Saibil, Helen R.; Collinge, John; Wadsworth, Jonathan D. F.

2015-01-01

Mammalian prions exist as multiple strains which produce characteristic and highly reproducible phenotypes in defined hosts. How this strain diversity is encoded by a protein-only agent remains one of the most interesting and challenging questions in biology with wide relevance to understanding other diseases involving the aggregation or polymerisation of misfolded host proteins. Progress in understanding mammalian prion strains has however been severely limited by the complexity and variability of the methods used for their isolation from infected tissue and no high resolution structures have yet been reported. Using high-throughput cell-based prion bioassay to re-examine prion purification from first principles we now report the isolation of prion strains to exceptional levels of purity from small quantities of infected brain and demonstrate faithful retention of biological and biochemical strain properties. The method’s effectiveness and simplicity should facilitate its wide application and expedite structural studies of prions. PMID:25950908

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

PubMed Central

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.; Walko, Donald A.; Landahl, Eric C.

2016-01-01

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acoustic oscillations at frequencies of several GHz. PMID:26751616

Linking strain anisotropy and plasticity in copper metallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murray, Conal E., E-mail: conal@us.ibm.com; Jordan-Sweet, Jean; Priyadarshini, Deepika

2015-05-04

The elastic anisotropy of copper leads to significant variation in the x-ray elastic constants (XEC), which link diffraction-based strain measurements to stress. An accurate depiction of the mechanical response in copper thin films requires a determination of an appropriate grain interaction model that lies between Voigt and Reuss limits. It is shown that the associated XEC weighting fraction, x*, between these limits provides a metric by which strain anisotropy can be quantified. Experimental values of x*, as determined by a linear regression scheme of diffraction data collected from multiple reflections, reveal the degree of strain anisotropy and its dependence onmore » plastic deformation induced during in-situ and ex-situ thermal treatments.« less

Temperature effects on the fractionation of multiple sulfur isotopes by Thermodesulfobacterium and Desulfovibrio strains

NASA Astrophysics Data System (ADS)

Wang, P.; Sun, C.; Ono, S.; Lin, L.

2012-12-01

Microbial dissimilatory sulfate reduction is one of the major mechanisms driving anaerobic mineralization of organic matter in global ocean. While sulfate-reducing prokaryotes are well known to fractionate sulfur isotopes during dissimilatory sulfate reduction, unraveling the isotopic compositions of sulfur-bearing minerals preserved in sedimentary records could provide invaluable constraints on the evolution of seawater chemistry and metabolic pathways. Variations in the sulfur isotope fractionations are partly due to inherent differences among species and also affected by environmental conditions. The isotope fractionations caused by microbial sulfate reduction have been interpreted to be a sequence of enzyme-catalyzed isotope fractionation steps. Therefore, the fractionation factor depends on (1) the sulfate flux into and out of the cell, and (2) the flux of sulfur transformation between the internal pools. Whether the multiple sulfur isotope effect could be quantitatively predicted using such a metabolic flux model would provide insights into the cellular machinery catalyzing with sulfate reduction. This study examined the multiple sulfur isotope fractionation patterns associated with a thermophilic Thermodesulfobacterium-related strain and a mesophilic Desulfovibrio gigas over a wide temperature range. The Thermodesulfobacterium-related strain grew between 34 and 79°C with an optimal temperature at 72°C and the highest cell-specific sulfate reduction rate at 77°C. The 34ɛ values ranged between 8.2 and 31.6‰ with a maximum at 68°C. The D. gigas grew between 10 and 45 °C with an optimal temperature at 30°C and the highest cell-specific sulfate reduction rate at 41°C. The 34ɛ values ranged between 10.3 and 29.7‰ with higher magnitude at both lower and higher temperatures. The results of multiple sulfur isotope measurements expand the previously reported range and cannot be described by a solution field of the metabolic flux model, which calculates the Δ33S and 34ɛ values assuming equilibrium fractionation among internal steps. Either larger isotope effects or kinetic fractionation has to be considered in the metabolic flux model to explain the multiple sulfur isotope effect produced by these two strains. Overall, the metabolic flux model warrants further revision and further studies regarding physiological responses to growth conditions may probably offer a linkage between multiple sulfur isotope effects and environmental factors for microbial dissimilatory sulfate reduction.

Risk factors for development of multiple-class resistance to Streptococcus pneumoniae Strains in Belgium over a 10-year period: antimicrobial consumption, population density, and geographic location.

PubMed

Van Eldere, Johan; Mera, Robertino M; Miller, Linda A; Poupard, James A; Amrine-Madsen, Heather

2007-10-01

We investigated the impact of the usage of antibiotics in ambulatory patients in Belgium in 147 defined geographical circumscriptions and at the individual isolate level. The study included 14,448 Streptococcus pneumoniae strains collected by the Belgium national reference lab from 1994 to 2004. Additional risk factors for resistance, such as population density/structure and day care attendance, were investigated for the same time-space window. A statistical model that included resistance to two or more antimicrobial classes offered the best fit for measuring the changes in nonsusceptibility to penicillin, macrolides, and tetracycline over time and place in Belgium. Analysis at the geographic level identified antimicrobial consumption with a 1-year lag (0.5% increase per additional defined daily dose) and population density as independent predictors of multiple resistance. Independent risk factors at the isolate level were age (odds ratio [OR], 1.55 for children aged <5 years), population density (7% increase in multiple resistance per 100 inhabitants/km(2)), conjugate 7-valent vaccine serotype (OR, 14.3), location (OR, 1.55 for regions bordering high-resistance France), and isolate source (OR, 1.54 for ear isolates). The expansion of multiple-resistant strains explains most of the overall twofold increase and subsequent decrease in single antimicrobial resistance between 1994 and 2004. We conclude that factors in addition to antibiotic use, such as high population density and proximity to high-resistance regions, favor multiple resistance. Regional resistance rates are not linearly related to actual antibiotic use but are linked to past antibiotic use plus a combination of demographic and geographic factors.

Improved robustness of an ethanologenic yeast strain through adaptive evolution in acetic acid is associated with its enzymatic antioxidant ability.

PubMed

Gurdo, N; Novelli Poisson, G F; Juárez, Á B; Ríos de Molina, M C; Galvagno, M A

2018-05-16

To investigate multiple tolerance of Saccharomyces cerevisiae obtained through a laboratory strategy of adaptive evolution in acetic acid, its relation with enzymatic ROS detoxification and bioethanol 2G production. After adaptive evolution in acetic acid, a clone (Y8A) was selected for its tolerance to high acetic acid concentrations (13 g l -1 ) in batch cultures. Y8A was resistant to multiple stresses: osmotic, thermic, oxidative, saline, ethanol, organic acid, phenolic compounds and slow freeze-thawing cycles. Also, Y8A was able to maintain redox homeostasis under oxidative stress, whereas the isogenic parental strain (Y8) could not, indicating higher basal activity levels of antioxidative enzyme Catalase (CAT) and Gluthatione-S-Transferase (GST) in Y8A. Y8A reached higher bioethanol levels in a fermentation medium containing up to 8 g l -1 of acetic acid when compared to parental strain Y8. A multiple-stress-tolerant clone was obtained using adaptive evolution in acetic acid. Stress cross-tolerance could be explained by its enzymatic antioxidative capacity, namely CAT and GST. We demonstrate that adaptive evolution used in S. cerevisiae was a useful strategy to obtain a yeast clone tolerant to multiple stresses. At the same time, our findings support the idea that tolerance to oxidative stress is the common basis for stress co-tolerance, which is related to an increase in the specific enzymes CAT and GST but not in Superoxide dismutase (SOD), emphasizing the fact that detoxification of H 2 O 2 and not O 2 . is a key condition for multiple stress tolerance in S. cerevisiae. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Enrichment of hexachlorobenzene and 1,3,5-trichlorobenzene transforming bacteria from sediments in Germany and Vietnam.

PubMed

Duan, Tran Hoa; Adrian, Lorenz

2013-07-01

Bacterial cultures were enriched from sediments in Germany and Vietnam reductively dechlorinating hexachlorobenzene and the highly persistent 1,3,5-trichlorobenzene to monochlorobenzene. The main products of the reductive dechlorination of hexachlorobenzene were monochlorobenzene and dichlorobenzenes (1,2-; 1,3- and 1,4-dichlorobenzene) while no trichlorobenzenes accumulated. For the reductive dechlorination of 1,3,5-trichlorobenzene with the mixed culture from Vietnam sediment, 1,3- dichlorobenzene and monochlorobenzene were produced as intermediate and final end-product, respectively. The pattern of dechlorination did not change when the cultures were repeatedly exposed to oxygen over seven transfers demonstrating oxygen tolerance of the dechlorinating bacteria. However, reductive dechlorination of 1,3,5-trichlorobenzene was inhibited by vancomycin at a concentration of 5 mg L(-1). Vancomycin delayed reductive dechlorination of hexachlorobenzene in mixed cultures by about 6 months. When repeatedly applied, vancomycin completely abolished the ability of the mixed culture to transform hexachlorobenzene. Sensitivity to vancomycin and insensitivity to brief exposure of oxygen indicates that the dechlorinating bacteria in the mixed cultures did not belong to the genus Dehalococcoides.

Retention and transport of an anaerobic trichloroethene dechlorinating microbial culture in anaerobic porous media.

PubMed

Zhang, Huixin; Ulrich, Ania C; Liu, Yang

2015-06-01

The influence of solution chemistry on microbial transport was examined using the strictly anaerobic trichloroethene (TCE) bioaugmentation culture KB-1(®). A column was employed to determine transport behaviors and deposition kinetics of three distinct functional species in KB-1(®), Dehalococcoides, Geobacter, and Methanomethylovorans, over a range of ionic strengths under a well-controlled anaerobic condition. A quantitative polymerase chain reaction (qPCR) was utilized to enumerate cell concentration and complementary techniques were implemented to evaluate cell surface electrokinetic potentials. Solution chemistry was found to positively affect the deposition rates, which was consistent with calculated Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies. Retained microbial profiles showed spatially constant colloid deposition rate coefficients, in agreement with classical colloid filtration theory (CFT). It was interesting to note that the three KB-1(®) species displayed similar transport and retention behaviors under the defined experimental conditions despite their different cell electrokinetic properties. A deeper analysis of cell characteristics showed that factors, such as cell size and shape, concentration, and motility were involved in determining adhesion behavior. Copyright © 2015 Elsevier B.V. All rights reserved.

Electron transport chains in organohalide-respiring bacteria and bioremediation implications.

PubMed

Wang, Shanquan; Qiu, Lan; Liu, Xiaowei; Xu, Guofang; Siegert, Michael; Lu, Qihong; Juneau, Philippe; Yu, Ling; Liang, Dawei; He, Zhili; Qiu, Rongliang

In situ remediation employing organohalide-respiring bacteria represents a promising solution for cleanup of persistent organohalide pollutants. The organohalide-respiring bacteria conserve energy by utilizing H 2 or organic compounds as electron donors and organohalides as electron acceptors. Reductive dehalogenase (RDase), a terminal reductase of the electron transport chain in organohalide-respiring bacteria, is the key enzyme that catalyzes halogen removal. Accumulating experimental evidence thus far suggests that there are distinct models for respiratory electron transfer in organohalide-respirers of different lineages, e.g., Dehalococcoides, Dehalobacter, Desulfitobacterium and Sulfurospirillum. In this review, to connect the knowledge in organohalide-respiratory electron transport chains to bioremediation applications, we first comprehensively review molecular components and their organization, together with energetics of the organohalide-respiratory electron transport chains, as well as recent elucidation of intramolecular electron shuttling and halogen elimination mechanisms of RDases. We then highlight the implications of organohalide-respiratory electron transport chains in stimulated bioremediation. In addition, major challenges and further developments toward understanding the organohalide-respiratory electron transport chains and their bioremediation applications are identified and discussed. Copyright © 2018 Elsevier Inc. All rights reserved.

FIV diversity: FIVPle subtype composition may influence disease outcome in African lions

PubMed Central

Troyer, Jennifer L.; Roelke, Melody E.; Jespersen, Jillian M.; Baggett, Natalie; Buckley-Beason, Valerie; MacNulty, Dan; Craft, Meggan; Packer, Craig; Pecon-Slattery, Jill; O’Brien, Stephen J.

2011-01-01

Feline immunodeficiency virus (FIV) infects domestic cats and at least 20 additional species of non-domestic felids throughout the world. Strains specific to domestic cat (FIVFca) produce AIDS-like disease progression, sequelae and pathology providing an informative model for HIV infection in humans. Less is known about the immunological and pathological influence of FIV in other felid species although multiple distinct strains of FIV circulate in natural populations. As in HIV-1 and HIV-2, multiple diverse cross-species infections may have occurred. In the Serengeti National Park, Tanzania, three divergent subtypes of lion FIV (FIVPle) are endemic, whereby 100% of adult lions are infected with one or more of these strains. Herein, the relative distribution of these subtypes in the population are surveyed and, combined with observed differences in lion mortality due to secondary infections based on FIVPle subtypes, the data suggest that FIVPle subtypes may have different patterns of pathogenicity and transmissibility among wild lion populations. PMID:21723622

High frequency, spontaneous motA mutations in Campylobacter jejuni strain 81-176.

PubMed

Mohawk, Krystle L; Poly, Frédéric; Sahl, Jason W; Rasko, David A; Guerry, Patricia

2014-01-01

Campylobacter jejuni is an important cause of bacterial diarrhea worldwide. The pathogenesis of C. jejuni is poorly understood and complicated by phase variation of multiple surface structures including lipooligosaccharide, capsule, and flagellum. When C. jejuni strain 81-176 was plated on blood agar for single colonies, the presence of translucent, non-motile colonial variants was noted among the majority of opaque, motile colonies. High-throughput genomic sequencing of two flagellated translucent and two opaque variants as well as the parent strain revealed multiple genetic changes compared to the published genome. However, the only mutated open reading frame common between the two translucent variants and absent from the opaque variants and the parent was motA, encoding a flagellar motor protein. A total of 18 spontaneous motA mutations were found that mapped to four distinct sites in the gene, with only one class of mutation present in a phase variable region. This study exemplifies the mutative/adaptive properties of C. jejuni and demonstrates additional variability in C. jejuni beyond phase variation.

Multiple-locus variable number of tandem repeat analysis (MLVA) of Irish verocytotoxigenic Escherichia coli O157 from feedlot cattle: uncovering strain dissemination routes.

PubMed

Murphy, Mary; Minihan, Donal; Buckley, James F; O'Mahony, Micheál; Whyte, Paul; Fanning, Séamus

2008-01-24

The identification of the routes of dissemination of Escherichia coli (E. coli) O157 through a cohort of cattle is a critical step to control this pathogen at farm level. The aim of this study was to identify potential routes of dissemination of E. coli O157 using Multiple-Locus Variable number of tandem repeat Analysis (MLVA). Thirty-eight environmental and sixteen cattle faecal isolates, which were detected in four adjacent pens over a four-month period were sub-typed. MLVA could separate these isolates into broadly defined clusters consisting of twelve MLVA types. Strain diversity was observed within pens, individual cattle and the environment. Application of MLVA is a broadly useful and convenient tool when applied to uncover the dissemination of E. coli O157 in the environment and in supporting improved on-farm management of this important pathogen. These data identified diverse strain types based on amplification of VNTR markers in each case.

Job strain associated with increases in ambulatory blood and pulse pressure during and after work hours among female hotel room cleaners.

PubMed

Feaster, Matt; Krause, Niklas

2018-06-01

Previously documented elevated hypertension rates among Las Vegas hotel room cleaners are hypothesized to be associated with job strain. Job strain was assessed by questionnaire. Ambulatory blood pressure (ABP) was recorded among 419 female cleaners from five hotels during 18 waking hours. Multiple linear regression models assessed associations of job strain with ABP and pulse pressure for 18-h, work hours, and after work hours. Higher job strain was associated with increased 18-h systolic ABP, after work hours systolic ABP, and ambulatory pulse pressure. Dependents at home but not social support at work attenuated effects. Among hypertensive workers, job strain effects were partially buffered by anti-hypertensive medication. High job strain is positively associated with blood pressure among female hotel workers suggesting potential for primary prevention at work. Work organizational changes, stress management, and active ABP surveillance and hypertension management should be considered for integrated intervention programs. © 2018 Wiley Periodicals, Inc.

Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress

PubMed Central

Jensen, Sheila I.; Lennen, Rebecca M.; Herrgård, Markus J.; Nielsen, Alex T.

2015-01-01

Generation of multiple genomic alterations is currently a time consuming process. Here, a method was established that enables highly efficient and simultaneous deletion of multiple genes in Escherichia coli. A temperature sensitive plasmid containing arabinose inducible lambda Red recombineering genes and a rhamnose inducible flippase recombinase was constructed to facilitate fast marker-free deletions. To further speed up the procedure, we integrated the arabinose inducible lambda Red recombineering genes and the rhamnose inducible FLP into the genome of E. coli K-12 MG1655. This system enables growth at 37 °C, thereby facilitating removal of integrated antibiotic cassettes and deletion of additional genes in the same day. Phosphorothioated primers were demonstrated to enable simultaneous deletions during one round of electroporation. Utilizing these methods, we constructed strains in which four to seven genes were deleted in E. coli W and E. coli K-12. The growth rate of an E. coli K-12 quintuple deletion strain was significantly improved in the presence of high concentrations of acetate and NaCl. In conclusion, we have generated a method that enables efficient and simultaneous deletion of multiple genes in several E. coli variants. The method enables deletion of up to seven genes in as little as seven days. PMID:26643270

Mouse androgenetic embryonic stem cells differentiated to multiple cell lineages in three embryonic germ layers in vitro.

PubMed

Teramura, Takeshi; Onodera, Yuta; Murakami, Hideki; Ito, Syunsuke; Mihara, Toshihiro; Takehara, Toshiyuki; Kato, Hiromi; Mitani, Tasuku; Anzai, Masayuki; Matsumoto, Kazuya; Saeki, Kazuhiro; Fukuda, Kanji; Sagawa, Norimasa; Osoi, Yoshihiko

2009-06-01

The embryos of some rodents and primates can precede early development without the process of fertilization; however, they cease to develop after implantation because of restricted expressions of imprinting genes. Asexually developed embryos are classified into parthenote/gynogenote and androgenote by their genomic origins. Embryonic stem cells (ESCs) derived from asexual origins have also been reported. To date, ESCs derived from parthenogenetic embryos (PgESCs) have been established in some species, including humans, and the possibility to be alternative sources for autologous cell transplantation in regenerative medicine has been proposed. However, some developmental characteristics, which might be important for therapeutic applications, such as multiple differentiation capacity and transplantability of the ESCs of androgenetic origin (AgESCs) are uncertain. Here, we induced differentiation of mouse AgESCs and observed derivation of neural cells, cardiomyocytes and hepatocytes in vitro. Following differentiated embryoid body (EB) transplantation in various mouse strains including the strain of origin, we found that the EBs could engraft in theoretically MHC-matched strains. Our results indicate that AgESCs possess at least two important characteristics, multiple differentiation properties in vitro and transplantability after differentiation, and suggest that they can also serve as a source of histocompatible tissues for transplantation.

Multifocal laser surgery: cutting enhancement by hydrodynamic interactions between cavitation bubbles.

PubMed

Toytman, I; Silbergleit, A; Simanovski, D; Palanker, D

2010-10-01

Transparent biological tissues can be precisely dissected with ultrafast lasers using optical breakdown in the tight focal zone. Typically, tissues are cut by sequential application of pulses, each of which produces a single cavitation bubble. We investigate the hydrodynamic interactions between simultaneous cavitation bubbles originating from multiple laser foci. Simultaneous expansion and collapse of cavitation bubbles can enhance the cutting efficiency, by increasing the resulting deformations in tissue, and the associated rupture zone. An analytical model of the flow induced by the bubbles is presented and experimentally verified. The threshold strain of the material rupture is measured in a model tissue. Using the computational model and the experimental value of the threshold strain one can compute the shape of the rupture zone in tissue resulting from application of multiple bubbles. With the threshold strain of 0.7 two simultaneous bubbles produce a continuous cut when applied at the distance 1.35 times greater than that required in sequential approach. Simultaneous focusing of the laser in multiple spots along the line of intended cut can extend this ratio to 1.7. Counterpropagating jets forming during collapse of two bubbles in materials with low viscosity can further extend the cutting zone-up to approximately a factor of 1.5.

Uncovering Wolbachia Diversity upon Artificial Host Transfer

PubMed Central

Schneider, Daniela I.; Riegler, Markus; Arthofer, Wolfgang; Merçot, Hervé; Stauffer, Christian; Miller, Wolfgang J.

2013-01-01

The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system. PMID:24376534

Uncovering Wolbachia diversity upon artificial host transfer.

PubMed

Schneider, Daniela I; Riegler, Markus; Arthofer, Wolfgang; Merçot, Hervé; Stauffer, Christian; Miller, Wolfgang J

2013-01-01

The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.

Resistance of the Extreme Halophile Halobacterium sp. NRC-1 to Multiple Stresses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gygli, Patrick E.; Prajapati, Surendra; DeVeaux, Linda C.

2009-03-10

The model Archaeon Halobacterium sp. NRC-1 is an extreme halophile known for its resistance to multiple stressors, including electron-beam and ultraviolet radiation. It is a well-developed system with a completely sequenced genome and extensive post-genomic tools for the study of a variety of biological processes. To further understand the mechanisms of Halobacterium's, radiation resistance, we previously reported the selection for multiple independent highly resistant mutants using repeated exposure to high doses of 18-20 MeV electrons using a medical S-band Linac. Molecular analysis of the transcriptional profile of several of these mutants revealed a single common change: upregulation of the rfa3more » operon. These genes encode proteins homologous to the subunits of eukaryotic Replication Protein A (RPA), a DNA binding protein with major roles in DNA replication, recombination, and repair. This operon has also been implicated in a somewhat lesser role in resistance of wild type Halobacterium to ultraviolet radiation, suggesting common mechanisms for resistance. To further understand the mechanism of radiation resistance in the mutant strains, we measured the survival after exposure to both electron-beam and ultraviolet radiation, UV-A, B, and C All mutant strains showed increased resistance to electrons when compared with the parent. However, the mutant strains do not display increased UV resistance, and in one case is more sensitive than the parent strain. Thus, the protective role of increased RPA expression within a cell may be specific to the DNA damage caused by the different physical effects induced by high energy electron-beam radiation.« less

Static versus dynamic fracturing in shallow carbonate fault zones

NASA Astrophysics Data System (ADS)

Fondriest, M.; Doan, M. L.; Aben, F. M.; Fusseis, F.; Mitchell, T. M.; Di Toro, G.

2015-12-01

Moderate to large earthquakes often nucleate within and propagate through carbonates in the shallow crust, therefore several field and experimental studies were recently aimed to constrain earthquake-related deformation processes within carbonate fault rocks. In particular, the occurrence of thick belts (10-100s m) of low-strain fault-related breccias (average size of rock fragments >1 cm), which is relatively common within carbonate damage zones, was generally interpreted as resulting from the quasi-static growth of fault zones rather than from the cumulative effect of multiple earthquake ruptures. Here we report the occurrence of up to hundreds of meters thick belts of intensely fragmented dolostones along the major transpressive Foiana Fault Zone (Italian Southern Alps) which was exhumed from < 2 km depth. Such dolostones are reduced into fragments ranging from few centimeters down to few millimeters in size with ultrafine-grained layers in proximity to the principal slip zones. Preservation of the original bedding indicates a lack of significant shear strain in the fragmented dolostones which seem to have been shattered in situ. To investigate the origin of the in-situ shattered rocks, the host dolostones were deformed in uniaxial compression both under quasi-static loading (strain rate ~10-3 s-1) and dynamic loading (strain rate >50 s-1). Dolostones deformed up to failure under low-strain rate were affected by single to multiple discrete (i.e. not interconnected) extensional fractures sub-parallel to the loading direction. Dolostones deformed under high-strain rate were shattered above a strain rate threshold of ~200 s-1(strain >1.2%) while they were split in few fragments or were macroscopically intact for lower strain rates. Experimentally shattered dolostones were reduced into a non-cohesive material with most rock fragments a few millimeters in size and elongated parallel to the loading direction. Fracture networks were investigated by X-ray microtomography showing that low- and high-strain rate damage patterns are different with the latter being similar to that of natural in-situ shattered dolostones. In-situ shattered dolostones are thus interpreted as the product of off-fault dynamic stress wave loading and can potentially be used to constrain coseismic energy release in fault zones.

MULTIPLE ENZYME RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS FOR HIGH RESOLUTION DISTINCTION OF PSEUDOMONAS (SENSU STRICTO) 16S RRNA GENES

EPA Science Inventory

Pseudomonas specific 16S rDNA PCR amplification and multiple enzyme restriction fragment length polymorphism (MERFLP) analysis using a single digestion mixture of Alu I, Hinf I, Rsa I, and Tru 9I distinguished 150 published sequences and reference strains of authentic Pseudomonas...

Mapping the future: U.S. exposure to multiple landscape stressors

Treesearch

Marie Oliver; Becky Kerns; John Kim; Jeff Kline

2017-01-01

Landscape exposure to multiple stressors can pose risks to human health, biodiversity, and ecosystem services. Attempts to study, control, or mitigate these stressors can strain public and private budgets. An interdisciplinary team of Pacific Northwest Research Station and Oregon State University scientists created maps of the conterminous United States that indicate...

Aminoglycoside-Resistant Aeromonas hydrophila as Part of a Polymicrobial Infection following a Traumatic Fall into Freshwater▿

PubMed Central

Shak, Joshua R.; Whitaker, Jennifer A.; Ribner, Bruce S.; Burd, Eileen M.

2011-01-01

Amikacin is a first-line treatment for Aeromonas infection due to high efficacy. There are few reports of aminoglycoside-resistant Aeromonas spp. We report a soft tissue infection containing multiple pathogens, including a strain of Aeromonas hydrophila resistant to amikacin, tobramycin, and multiple cephalosporins. PMID:21209173

Aminoglycoside-resistant Aeromonas hydrophila as part of a polymicrobial infection following a traumatic fall into freshwater.

PubMed

Shak, Joshua R; Whitaker, Jennifer A; Ribner, Bruce S; Burd, Eileen M

2011-03-01

Amikacin is a first-line treatment for Aeromonas infection due to high efficacy. There are few reports of aminoglycoside-resistant Aeromonas spp. We report a soft tissue infection containing multiple pathogens, including a strain of Aeromonas hydrophila resistant to amikacin, tobramycin, and multiple cephalosporins.

Multiplication in egg yolk and survival in egg albumen of genetically and phenotypically characterized Salmonella Enteritidis strains

USDA-ARS?s Scientific Manuscript database

Prompt refrigeration of eggs to prevent the multiplication of Salmonella Enteritidis to high levels during storage is an important practice for reducing the risk of egg-transmitted human illness. The efficacy of egg refrigeration for achieving this goal depends on the location of contamination, the ...

Multiple Cross Displacement Amplification Coupled With Nanoparticles-Based Lateral Flow Biosensor for Detection of Staphylococcus aureus and Identification of Methicillin-Resistant S. aureus.

PubMed

Wang, Yi; Yan, Weiqiang; Fu, Shanshan; Hu, Shoukui; Wang, Yan; Xu, Jianguo; Ye, Changyun

2018-01-01

Staphylococcus aureus ( S. aureus ), including methicillin-resistant S. aureus (MRSA), is one of the most important human pathogens, which is responsible for bacteremia, soft-tissue infections, and food poisoning. Hence, multiple cross displacement amplification (MCDA) is employed to detect all S. aureus strains, and differentiates MRSA from methicillin-sensitive S. aureus . Multiplex MCDA (m-MCDA), which targets the nuc gene ( S. aureus -specific gene) and mecA gene (encoding penicillin-binding protein-2'), could detect S. aureus strains and identify MRSA within 85 min. Detection of the m-MCDA products is achieved using disposable lateral flow biosensors. A total of 58 strains, including various species of Gram-positive and Gram-negative strains, are used for evaluating and optimizing m-MCDA assays. The optimal amplification condition is found to be 63°C for 40 min, with detection limits at 100 fg DNA/reaction for nuc and mecA genes in the pure cultures, and 10 CFU/tube for nuc and mecA genes in the blood samples. The analytical specificity of m-MCDA assay is of 100%, and no cross-reactions to non- S. aureus strains are produced according to the specificity testing. Particularly, two additional components, including AUDG enzyme and dUTP, are added into the m-MCDA amplification mixtures, which are used for eliminating the unwanted results arising from carryover contamination. Thus, the m-MCDA technique appears to be a simple, rapid, sensitive, and reliable assay to detect all S. aureus strains, and identify MRSA infection for appropriate antibiotic therapy.

Comparative study of all Salmonella enterica serovar Enteritidis strains isolated from food and food animals in Greece from 2008 to 2010 with clinical isolates.

PubMed

Papadopoulos, T; Petridou, E; Zdragas, A; Mandilara, G; Nair, S; Peters, T; Chattaway, M; de Pinna, E; Passiotou, M; Vatopoulos, A

2016-05-01

The aim of the present work was to study the epidemiology of Salmonella enterica serovar Enteritidis (S. Enteritidis) in Greece, comparing all the food and food animal isolates during a 3-year period with clinical isolates. Submission of the generated data to the PulseNet Europe database was carried out in order to study the population structure of this particular serovar and indicate possible connections with European strains. One hundred and sixty-eight (168) S. Enteritidis strains of human, animal, and food origin, isolated during the period 2008-2010 in Greece, were studied. Strains were characterized by phenotypic (antibiotic resistance) and molecular [pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)] methods. PFGE revealed 39 XbaI, 48 BlnI, and 80 XbaI-BlnI distinct pulsotypes, suggesting several clones circulating through the food chain and multiple sources of transmission. Submission to the PulseNet Europe database indicated that PFGE profile SENTXB.0001, the most common PFGE profile in Europe, was also predominant in Greece (33.3 %). MLST showed that all the strains studied shared the same sequence type (ST11), representing the most common ST in Europe. High rates of resistance to nalidixic acid were observed among human and poultry isolates (~25 %), indicating the potential fluoroquinolone treatment failure. Our data suggest that strains originating from multiple reservoirs circulated in Greece through the food chain during the study period. Predominant profiles in Greece were common to PulseNet Europe profiles, indicating similarities between the S. Enteritidis populations in Greece and Europe.

Identification of Bacterial Plant Pathogens Using Multilocus Polymerase Chain Reaction/Electrospray Ionization-Mass Spectrometry

DTIC Science & Technology

2008-01-01

sandii FK-53; OLF#1 Oleander; USA 1 Xylophilus ampelinus FB-1178 Grape; S. Africa 1 Xylophilus ampelinus FJ-3; 60002 Grape; S. Africa 1 1160...campestris Xanthomonas campestris Xylella fastidiosa (6 strains) Xylella fastidiosa Xylophilus ampelinus (2 strains) Xylophilus ampelinus ...Rathayibacter iranicus Rathayibacter iranicus Xylophilus ampelinus Xylophilus ampelinus a Purified DNAs from multiple bacteria were mixed at equal

Notice of Release of FC1018, FC1019, FC1020 and FC1022 Multigerm Sugarbeet Germplasms with Multiple Disease Resistance

USDA-ARS?s Scientific Manuscript database

FC1018 (PI 658059) has excellent resistance to root-rotting strains (AG-2-2) of Rhizoctonia solani Kühn and carries the Rz1 gene, which confers resistance to some strains of Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. FC1018 has shown a moderate tolerance to cercospora ...

Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna.

PubMed

Burguener, Germán F; Maldonado, Marcos J; Revale, Santiago; Fernández Do Porto, Darío; Rascován, Nicolás; Vázquez, Martín; Farías, María Eugenia; Marti, Marcelo A; Turjanski, Adrián Gustavo

2014-02-06

Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from Laguna Antofalla in the Argentinian Puna. The draft genome sequence suggests the presence of potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

Acceleration of the formation of biofilms on contact lens surfaces in the presence of neutrophil-derived cellular debris is conserved across multiple genera

PubMed Central

Patel, Naiya B.; Hinojosa, Jorge A.; Zhu, Meifang

2018-01-01

Purpose We have previously shown that invasive strains of Pseudomonas aeruginosa exploit the robust neutrophil response to form biofilms on contact lens surfaces and invade the corneal epithelium. The present study investigated the ability of multiple bacterial genera, all commonly recovered during contact lens–related infectious events, to adhere to and form biofilms on contact lens surfaces in the presence of neutrophils. Methods Five reference strains from the American Type Culture Collection were used: P. aeruginosa, Serratia marcescens, Stenotrophomonas maltophilia, Staphylococcus aureus, and Staphylococcus epidermidis. Each bacterial strain was incubated overnight with or without stimulated human neutrophils in the presence of an unworn contact lens. Standard colony counts and laser scanning confocal microscopy of BacLight-stained contact lenses were used to assess bacterial viability. Three-dimensional modeling of lens-associated biofilms with Imaris software was used to determine the biofilm volume. Lenses were further examined using scanning electron microscopy. Results Less than 1% of the starting inoculum adhered to the contact lens surface incubated with bacteria alone. There were no differences in adhesion rates to contact lens surfaces between bacteria in the absence of neutrophils for either the Gram-negative or Gram-positive test strains. Bacterial adhesion to contact lens surfaces was accelerated in the presence of human neutrophils for all test strains. This effect was least evident with S. epidermidis. There was also an increase in the number of viable bacteria recovered from contact lens surfaces (p<0.001 for the Gram-negative and Gram-positive test strains, respectively) and in biofilm volume (p<0.001 for the Gram-negative test strains, p = 0.005 for S. aureus). Conclusions These results show that in addition to P. aeruginosa, other bacteria commonly encountered during contact lens wear possess the capacity to utilize neutrophil-derived cellular debris to facilitate colonization of the lens surface. These data suggest that this phenomenon is conserved among multiple genera. Thus, during contact lens wear, the presence of inflammation and the accumulation of neutrophil debris under the posterior lens surface likely contribute to colonization of the lens. Further studies are needed to correlate these findings with risk for infection in an animal model. PMID:29422767

Molecular epidemiology and evolutionary genetics of Mycobacterium tuberculosis in Taipei.

PubMed

Dou, Horng-Yunn; Tseng, Fan-Chen; Lin, Chih-Wei; Chang, Jia-Ru; Sun, Jun-Ren; Tsai, Wen-Shing; Lee, Shi-Yi; Su, Ih-Jen; Lu, Jang-Jih

2008-12-22

The control of tuberculosis in densely populated cities is complicated by close human-to-human contacts and potential transmission of pathogens from multiple sources. We conducted a molecular epidemiologic analysis of 356 Mycobacterium tuberculosis (MTB) isolates from patients presenting pulmonary tuberculosis in metropolitan Taipei. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture. A total of 356 isolates were genotyped by standard spoligotyping and the strains were compared with in the international spoligotyping database (SpolDB4). All isolates were also categorized using the 15 loci MIRU-VNTR typing method and combin with NTF locus and RD deletion analyses. Of 356 isolates spoligotyped, 290 (81.4%) displayed known spoligotypes and 66 were not identified in the database. Major spoligotypes found were Beijing lineages (52.5%), followed by Haarlem lineages (13.5%) and EAI plus EAI-like lineages (11%). When MIRU-VNTR was employed, 140 patterns were identified, including 36 clusters by 252 isolates and 104 unique patterns, and the largest cluster comprised 95 isolates from the Beijing family. The combination of spoligotyping and MIRU-VNTR revealed that 236 (67%) of the 356 isolates were clustered in 43 genotypes. Strains of the Beijing family was more likely to be of modern strain and a higher percentage of multiple drug resistance than other families combined (P = 0.08). Patients infected with Beijing strains were younger than those with other strains (mean 58.7 vs. 64.2, p = 0.02). Moreover, 85.3% of infected persons younger than 25 years had Beijing modern strain, suggesting a possible recent spread in the young population by this family of TB strain in Taipei. Our data on MTB genotype in Taipei suggest that MTB infection has not been optimally controlled. Control efforts should be reinforced in view of the high prevalence of the Beijing strain in young population and association with drug resistance.

Molecular epidemiology and evolutionary genetics of Mycobacterium tuberculosis in Taipei

PubMed Central

Dou, Horng-Yunn; Tseng, Fan-Chen; Lin, Chih-Wei; Chang, Jia-Ru; Sun, Jun-Ren; Tsai, Wen-Shing; Lee, Shi-Yi; Su, Ih-Jen; Lu, Jang-Jih

2008-01-01

Background The control of tuberculosis in densely populated cities is complicated by close human-to-human contacts and potential transmission of pathogens from multiple sources. We conducted a molecular epidemiologic analysis of 356 Mycobacterium tuberculosis (MTB) isolates from patients presenting pulmonary tuberculosis in metropolitan Taipei. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture. Methods A total of 356 isolates were genotyped by standard spoligotyping and the strains were compared with in the international spoligotyping database (SpolDB4). All isolates were also categorized using the 15 loci MIRU-VNTR typing method and combin with NTF locus and RD deletion analyses. Results Of 356 isolates spoligotyped, 290 (81.4%) displayed known spoligotypes and 66 were not identified in the database. Major spoligotypes found were Beijing lineages (52.5%), followed by Haarlem lineages (13.5%) and EAI plus EAI-like lineages (11%). When MIRU-VNTR was employed, 140 patterns were identified, including 36 clusters by 252 isolates and 104 unique patterns, and the largest cluster comprised 95 isolates from the Beijing family. The combination of spoligotyping and MIRU-VNTR revealed that 236 (67%) of the 356 isolates were clustered in 43 genotypes. Strains of the Beijing family was more likely to be of modern strain and a higher percentage of multiple drug resistance than other families combined (P = 0.08). Patients infected with Beijing strains were younger than those with other strains (mean 58.7 vs. 64.2, p = 0.02). Moreover, 85.3% of infected persons younger than 25 years had Beijing modern strain, suggesting a possible recent spread in the young population by this family of TB strain in Taipei. Conclusion Our data on MTB genotype in Taipei suggest that MTB infection has not been optimally controlled. Control efforts should be reinforced in view of the high prevalence of the Beijing strain in young population and association with drug resistance. PMID:19102768

Clonal Relatedness of Enterotoxigenic Escherichia coli (ETEC) Strains Expressing LT and CS17 Isolated from Children with Diarrhoea in La Paz, Bolivia

PubMed Central

Rodas, Claudia; Klena, John D.; Nicklasson, Matilda; Iniguez, Volga; Sjöling, Åsa

2011-01-01

Background Enterotoxigenic Escherichia coli (ETEC) is a major cause of traveller's and infantile diarrhoea in the developing world. ETEC produces two toxins, a heat-stable toxin (known as ST) and a heat-labile toxin (LT) and colonization factors that help the bacteria to attach to epithelial cells. Methodology/Principal Findings In this study, we characterized a subset of ETEC clinical isolates recovered from Bolivian children under 5 years of age using a combination of multilocus sequence typing (MLST) analysis, virulence typing, serotyping and antimicrobial resistance test patterns in order to determine the genetic background of ETEC strains circulating in Bolivia. We found that strains expressing the heat-labile (LT) enterotoxin and colonization factor CS17 were common and belonged to several MLST sequence types but mainly to sequence type-423 and sequence type-443 (Achtman scheme). To further study the LT/CS17 strains we analysed the nucleotide sequence of the CS17 operon and compared the structure to LT/CS17 ETEC isolates from Bangladesh. Sequence analysis confirmed that all sequence type-423 strains from Bolivia had a single nucleotide polymorphism; SNPbol in the CS17 operon that was also found in some other MLST sequence types from Bolivia but not in strains recovered from Bangladeshi children. The dominant ETEC clone in Bolivia (sequence type-423/SNPbol) was found to persist over multiple years and was associated with severe diarrhoea but these strains were variable with respect to antimicrobial resistance patterns. Conclusion/Significance The results showed that although the LT/CS17 phenotype is common among ETEC strains in Bolivia, multiple clones, as determined by unique MLST sequence types, populate this phenotype. Our data also appear to suggest that acquisition and loss of antimicrobial resistance in LT-expressing CS17 ETEC clones is more dynamic than acquisition or loss of virulence factors. PMID:22140423

Algorithms for Determining Physical Responses of Structures Under Load

NASA Technical Reports Server (NTRS)

Richards, W. Lance; Ko, William L.

2012-01-01

Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

Clonal relatedness of enterotoxigenic Escherichia coli (ETEC) strains expressing LT and CS17 isolated from children with diarrhoea in La Paz, Bolivia.

PubMed

Rodas, Claudia; Klena, John D; Nicklasson, Matilda; Iniguez, Volga; Sjöling, Asa

2011-01-01

Enterotoxigenic Escherichia coli (ETEC) is a major cause of traveller's and infantile diarrhoea in the developing world. ETEC produces two toxins, a heat-stable toxin (known as ST) and a heat-labile toxin (LT) and colonization factors that help the bacteria to attach to epithelial cells. In this study, we characterized a subset of ETEC clinical isolates recovered from Bolivian children under 5 years of age using a combination of multilocus sequence typing (MLST) analysis, virulence typing, serotyping and antimicrobial resistance test patterns in order to determine the genetic background of ETEC strains circulating in Bolivia. We found that strains expressing the heat-labile (LT) enterotoxin and colonization factor CS17 were common and belonged to several MLST sequence types but mainly to sequence type-423 and sequence type-443 (Achtman scheme). To further study the LT/CS17 strains we analysed the nucleotide sequence of the CS17 operon and compared the structure to LT/CS17 ETEC isolates from Bangladesh. Sequence analysis confirmed that all sequence type-423 strains from Bolivia had a single nucleotide polymorphism; SNP(bol) in the CS17 operon that was also found in some other MLST sequence types from Bolivia but not in strains recovered from Bangladeshi children. The dominant ETEC clone in Bolivia (sequence type-423/SNP(bol)) was found to persist over multiple years and was associated with severe diarrhoea but these strains were variable with respect to antimicrobial resistance patterns. The results showed that although the LT/CS17 phenotype is common among ETEC strains in Bolivia, multiple clones, as determined by unique MLST sequence types, populate this phenotype. Our data also appear to suggest that acquisition and loss of antimicrobial resistance in LT-expressing CS17 ETEC clones is more dynamic than acquisition or loss of virulence factors.

Constitutive relations for determining the critical conditions for dynamic recrystallization behavior

NASA Astrophysics Data System (ADS)

Choe, J. I.

2016-04-01

A series mathematical model has been developed for the prediction of flow stress and microstructure evolution during the hot deformation of metals such as copper or austenitic steels with low stacking fault energies, involving features of both diffusional flow and dislocation motion. As the strain rate increases, multiple peaks on the stress-strain curve decrease. At a high strain rate, the stress rises to a single peak, while dynamic recrystallization causes an oscillatory behavior. At a low strain rate (when there is sufficient time for the recrystallizing grains to grow before they become saturated with high dislocation density with an increase in strain rate), the difference in stored stress between recrystallizing and old grains diminishes, resulting in reduced driving force for grain growth and rendering smaller grains in the alloy. The final average grain size at the steady stage (large strain) increases with a decrease in the strain rate. During large strain deformation, grain size reduction accompanying dislocation creep might be balanced by the grain growth at the border delimiting the ranges of realization (field boundary) of the dislocation-creep and diffusion-creep mechanisms.

Structural and functional characterization of two alpha-synuclein strains

PubMed Central

Bousset, Luc; Pieri, Laura; Ruiz-Arlandis, Gemma; Gath, Julia; Jensen, Poul Henning; Habenstein, Birgit; Madiona, Karine; Olieric, Vincent; Böckmann, Anja; Meier, Beat H.; Melki, Ronald

2013-01-01

α-synuclein aggregation is implicated in a variety of diseases including Parkinson’s disease, dementia with Lewy bodies, pure autonomic failure and multiple system atrophy. The association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. Here we structurally and functionally characterize two polymorphs of α-synuclein. We present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. Specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. Such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies. PMID:24108358

Local and transient nanoscale strain mapping during in situ deformation

DOE PAGES

Gammer, C.; Kacher, J.; Czarnik, C.; ...

2016-08-26

The mobility of defects such as dislocations controls the mechanical properties of metals. This mobility is determined both by the characteristics of the defect and the material, as well as the local stress and strain applied to the defect. Therefore, the knowledge of the stress and strain during deformation at the scale of defects is important for understanding fundamental deformation mechanisms. In this paper, we demonstrate a method of measuring local stresses and strains during continuous in situ deformation with a resolution of a few nanometers using nanodiffraction strain mapping. Finally, our results demonstrate how large multidimensional data sets capturedmore » with high speed electron detectors can be analyzed in multiple ways after an in situ TEM experiment, opening the door for true multimodal analysis from a single electron scattering experiment.« less

Analysis and experimental study on the strain transfer mechanism of an embedded basalt fiber-encapsulated fiber Bragg grating sensor

NASA Astrophysics Data System (ADS)

Zhang, Zhenglin; Wang, Yuan; Sun, Yangyang; Zhang, Qinghua; You, Zewei; Huang, Xiaodi

2017-01-01

The precision of the encapsulated fiber optic sensor embedded into a host suffers from the influences of encapsulating materials. Furthermore, an interface transfer effect of strain sensing exists. This study uses an embedded basalt fiber-encapsulated fiber Bragg grating (FBG) sensor as the research object to derive an expression in a multilayer interface strain transfer coefficient by considering the mechanical properties of the host material. The direct impact of the host material on the strain transfer at an embedded multipoint continuous FBG (i.e., multiple gratings written on a single optical fiber) monitoring strain sensor, which was self-developed and encapsulated with basalt fiber, is studied to present the strain transfer coefficients corresponding to the positions of various gratings. The strain transfer coefficients of the sensor are analyzed based on the experiments designed for this study. The error of the experimental results is ˜2 μɛ when the strain is at 60 μɛ and below. Moreover, the measured curves almost completely coincide with the theoretical curves. The changes in the internal strain field inside the embedded structure of the basalt fiber-encapsulated FBG strain sensor could be easily monitored. Hence, important references are provided to measure the internal stress strain of the sensor.

Technical note: development of a quantitative PCR method for monitoring strain dynamics during yogurt manufacture.

PubMed

Miller, D M; Dudley, E G; Roberts, R F

2012-09-01

Yogurt starter cultures may consist of multiple strains of Lactobacillus delbrueckii ssp. bulgaricus (LB) and Streptococcus thermophilus (ST). Conventional plating methods for monitoring LB and ST levels during yogurt manufacture do not allow for quantification of individual strains. The objective of the present work was to develop a quantitative PCR method for quantification of individual strains in a commercial yogurt starter culture. Strain-specific primers were designed for 2 ST strains (ST DGCC7796 and ST DGCC7710), 1 LB strain (DGCC4078), and 1 Lactobacillus delbrueckii ssp. lactis strain (LL; DGCC4550). Primers for the individual ST and LB strains were designed to target unique DNA sequences in clustered regularly interspersed short palindromic repeats. Primers for LL were designed to target a putative mannitol-specific IIbC component of the phosphotransferase system. Following evaluation of primer specificity, standard curves relating cell number to cycle threshold were prepared for each strain individually and in combination in yogurt mix, and no significant differences in the slopes were observed. Strain balance data was collected for yogurt prepared at 41 and 43°C to demonstrate the potential application of this method. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Bioinjection Performance Review for the Building 100 Area and 4.5 Acre Site at the Pinellas County, Florida, Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Survochak, Scott; Daniel, Joe

This document provides a summary of a review of the performance of bioinjection activities at the Building 100 Area and the 4.5 Acre Site at the Pinellas County, Florida, Site since 2010, determines how best to optimize future injection events, and identifies the approach for the bioinjection event in 2016 at (1) the 4.5 Acre Site and (2) the Essentra property at the Building 100 Area. Because this document describes the next bioinjection event at the 4.5 Acre Site, it also serves as an addendum to the Interim Remedial Action Plan for Emulsified Edible Oil Injection at the 4.5 Acremore » Site (DOE 2013). In addition, this document revises the injection layout and injection intervals for the Essentra property that were originally described in the Interim Corrective Measure Work Plan for Source and Plume Treatment at the Building 100 Area (DOE 2014), and is a de facto update of that document. Bioinjection consists of injection of emulsified vegetable oil (EVO) and the microorganism Dehalococcoides mccartyi (DHM; formerly known as Dehalococcoides ethenogenes) into the subsurface to enhance biodegradation of trichloroethene (TCE), dichloroethene (DCE), and vinyl chloride (VC). VC is the only contaminant that exceeds its maximum contaminant level (10 micrograms per liter onsite and 1 microgram per liter onsite) on the 4.5 Acre Site and the Essentra property. Bioinjection was conducted at the 4.5 Acre Site in 2010 and 2013. Approximately 49,900 gallons of EVO and DHM were injected at 95 injection points in February 2010, and approximately 22,900 gallons of EVO and DHM were injected at 46 injection points in July 2013. The injection locations are shown on Figure 1. The goal of bioinjection at the 4.5 Acre Site is to decrease contaminant concentrations to maximum contaminant levels along the west and southwest property boundaries (to meet risk–based corrective action requirements) and to minimize the extent of the contaminant plume in the interior of the site. Bioinjection was conducted at the Building 100 Area in 3 phases from October 2014 through November 2015 (Figures 2–4). Approximately 32,850 gallons of EVO and DHM were injected using 62 temporary injection points in the onsite plumes in October and November 2014, 16,500 gallons were injected using 33 temporary injection points in the offsite plumes in February 2015, and 51,000 gallons were injected beneath the building using 8 horizontal wells in November 2015. The goal of bioinjection at the Building 100 Area is to enhance contaminant biodegradation to stabilize or shrink the contaminant plumes.« less

Distributed optical fiber dynamic magnetic field sensor based on magnetostriction.

PubMed

Masoudi, Ali; Newson, Trevor P

2014-05-01

A distributed optical fiber sensor is introduced which is capable of quantifying multiple magnetic fields along a 1 km sensing fiber with a spatial resolution of 1 m. The operation of the proposed sensor is based on measuring the magnetorestrictive induced strain of a nickel wire attached to an optical fiber. The strain coupled to the optical fiber was detected by measuring the strain-induced phase variation between the backscattered Rayleigh light from two segments of the sensing fiber. A magnetic field intensity resolution of 0.3 G over a bandwidth of 50-5000 Hz was demonstrated.

Multiplex engineering of industrial yeast genomes using CRISPRm.

PubMed

Ryan, Owen W; Cate, Jamie H D

2014-01-01

Global demand has driven the use of industrial strains of the yeast Saccharomyces cerevisiae for large-scale production of biofuels and renewable chemicals. However, the genetic basis of desired domestication traits is poorly understood because robust genetic tools do not exist for industrial hosts. We present an efficient, marker-free, high-throughput, and multiplexed genome editing platform for industrial strains of S. cerevisiae that uses plasmid-based expression of the CRISPR/Cas9 endonuclease and multiple ribozyme-protected single guide RNAs. With this multiplex CRISPR (CRISPRm) system, it is possible to integrate DNA libraries into the chromosome for evolution experiments, and to engineer multiple loci simultaneously. The CRISPRm tools should therefore find use in many higher-order synthetic biology applications to accelerate improvements in industrial microorganisms.

An optically detectable CO2 sensor utilizing polyethylenimine and starch functionalized InGaN/GaN multiple quantum wells

NASA Astrophysics Data System (ADS)

Chen, Y. C.; Shih, H. Y.; Chen, J. Y.; Tan, W. J.; Chen, Y. F.

2013-07-01

An optically detectable gas sensor based on the high surface sensitivity of functionalized polyethylenimine/starch In0.15Ga0.85N/GaN strained semiconductor multiple quantum wells (MQWs) has been developed. Due to the excellent piezoelectricity of the MQWs, the change of surface charges caused by chemical interaction can introduce a strain and induce an internal field. In turn, it tilts the energy levels of the MQWs and modifies the optical properties. Through the measurement of the changes in photoluminescence as well as Raman scattering spectra under different concentrations of carbon dioxide gas, we demonstrate the feasibility and high sensitivity of the sensors derived from our methodology.

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Finally, using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acousticmore » oscillations at frequencies of several GHz.« less

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

DOE PAGES

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.; ...

2016-01-11

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Finally, using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acousticmore » oscillations at frequencies of several GHz.« less

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

PubMed Central

Youssef, Noha H.; Couger, M. B.; Struchtemeyer, Christopher G.; Liggenstoffer, Audra S.; Prade, Rolf A.; Najar, Fares Z.; Atiyeh, Hasan K.; Wilkins, Mark R.

2013-01-01

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production. PMID:23709508

The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.

PubMed

Youssef, Noha H; Couger, M B; Struchtemeyer, Christopher G; Liggenstoffer, Audra S; Prade, Rolf A; Najar, Fares Z; Atiyeh, Hasan K; Wilkins, Mark R; Elshahed, Mostafa S

2013-08-01

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.

Comparative performance evaluation of multi-metal resistant fungal strains for simultaneous removal of multiple hazardous metals.

PubMed

Dey, Priyadarshini; Gola, Deepak; Mishra, Abhishek; Malik, Anushree; Kumar, Peeyush; Singh, Dileep Kumar; Patel, Neelam; von Bergen, Martin; Jehmlich, Nico

2016-11-15

In the present study, five fungal strains viz., Aspergillus terreus AML02, Paecilomyces fumosoroseus 4099, Beauveria bassiana 4580, Aspergillus terreus PD-17, Aspergillus fumigatus PD-18, were screened for simultaneous multimetal removal. Highest metal tolerance index for each individual metal viz., Cd, Cr, Cu, Ni, Pb and Zn (500mg/L) was recorded for A. fumigatus for the metals (Cd, 0.72; Cu, 0.72; Pb, 1.02; Zn, 0.94) followed by B. bassiana for the metals (Cd, 0.56; Cu, 0.14; Ni, 0.29; Zn, 0.85). Next, the strains were exposed to multiple metal mixture (Cd, Cr, Cu, Ni, Pb and Zn) of various concentrations (6, 12, 18, 30mg/L). Compared to other strains, B. bassiana and A. fumigatus had higher cube root growth (k) constants indicating their better adaptability to multi metal stress. After 72h, multimetal accumulation potential of B. bassiana (26.94±0.07mg/L) and A. fumigatus (27.59±0.09mg/L) were higher than the other strains at initial multimetal concentration of 30mg/L. However, considering the post treatment concentrations of individual metals in multimetal mixture (at all the tested concentrations), A. fumigatus demonstrated exceptional performance and could bring down the concentrations of Cd, Cu, Ni, Pb and Zn below the threshold level for irrigation prescribed by Food and Agriculture Organization (FAO). Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic and phenotypic intra-species variation in Candida albicans

PubMed Central

Hirakawa, Matthew P.; Martinez, Diego A.; Sakthikumar, Sharadha; Anderson, Matthew Z.; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M.; Greenberg, Joshua M.; Berman, Judith

2015-01-01

Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity. PMID:25504520

Stable Isotope-Assisted Metabolic Profiling Reveals Growth Mode Dependent Differential Metabolism and Multiple Catabolic Pathways of l-Phenylalanine in Rubrivivax benzoatilyticus JA2.

PubMed

Mekala, Lakshmi Prasuna; Mohammed, Mujahid; Chintalapati, Sasikala; Chintalapati, Venkata Ramana

2018-01-05

Anoxygenic phototrophic bacteria are metabolically versatile and survive under different growth modes using diverse organic compounds, yet their metabolic diversity is largely unexplored. In the present study, we employed stable-isotope-assisted metabolic profiling to unravel the l-phenylalanine catabolism in Rubrivivax benzoatilyticus JA2 under varying growth modes. Strain JA2 grows under anaerobic and aerobic conditions by utilizing l-phenylalanine as a nitrogen source. Furthermore, ring-labeled 13 C 6 -phenylalanine feeding followed by liquid chromatography-mass spectrometry exometabolite profiling revealed 60 labeled metabolic features (M + 6, M + 12, and M + 18) derived solely from l-phenylalanine, of which 11 were identified, 7 putatively identified, and 42 unidentified under anaerobic and aerobic conditions. However, labeled metabolites were significantly higher in aerobic compared to anaerobic conditions. Furthermore, detected metabolites and enzyme activities indicated multiple l-phenylalanine catabolic routes mainly Ehrlich, homogentisate-dependent melanin, benzenoid, and unidentified pathways operating under anaerobic and aerobic conditions in strain JA2. Interestingly, the study indicated l-phenylalanine-dependent and independent benzenoid biosynthesis in strain JA2 and a differential flux of l-phenylalanine to Ehrlich and benzenoid pathways under anaerobic and aerobic conditions. Additionally, unidentified labeled metabolites strongly suggest the presence of unknown phenylalanine catabolic routes in strain JA2. Overall, the study uncovered the l-phenylalanine catabolic diversity in strain JA2 and demonstrated the potential of stable isotope-assisted metabolomics in unraveling the hidden metabolic repertoire.

Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

PubMed

Blakely, Collin M; Stoddard, Alexander J; Belka, George K; Dugan, Katherine D; Notarfrancesco, Kathleen L; Moody, Susan E; D'Cruz, Celina M; Chodosh, Lewis A

2006-06-15

Women who have their first child early in life have a substantially lower lifetime risk of breast cancer. The mechanism for this is unknown. Similar to humans, rats exhibit parity-induced protection against mammary tumorigenesis. To explore the basis for this phenomenon, we identified persistent pregnancy-induced changes in mammary gene expression that are tightly associated with protection against tumorigenesis in multiple inbred rat strains. Four inbred rat strains that exhibit marked differences in their intrinsic susceptibilities to carcinogen-induced mammary tumorigenesis were each shown to display significant protection against methylnitrosourea-induced mammary tumorigenesis following treatment with pregnancy levels of estradiol and progesterone. Microarray expression profiling of parous and nulliparous mammary tissue from these four strains yielded a common 70-gene signature. Examination of the genes constituting this signature implicated alterations in transforming growth factor-beta signaling, the extracellular matrix, amphiregulin expression, and the growth hormone/insulin-like growth factor I axis in pregnancy-induced alterations in breast cancer risk. Notably, related molecular changes have been associated with decreased mammographic density, which itself is strongly associated with decreased breast cancer risk. Our findings show that hormone-induced protection against mammary tumorigenesis is widely conserved among divergent rat strains and define a gene expression signature that is tightly correlated with reduced mammary tumor susceptibility as a consequence of a normal developmental event. Given the conservation of this signature, these pathways may contribute to pregnancy-induced protection against breast cancer.

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

PubMed Central

Laukkanen-Ninios, R.; Ortiz Martínez, P.; Siitonen, A.; Fredriksson-Ahomaa, M.; Korkeala, H.

2013-01-01

Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared. PMID:23637293

Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna.

PubMed

Ordoñez, Omar F; Lanzarotti, Esteban; Kurth, Daniel; Gorriti, Marta F; Revale, Santiago; Cortez, Néstor; Vazquez, Martin P; Farías, María E; Turjanski, Adrian G

2013-07-25

Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

Dynamic Failure of Materials. Volume 1 - Experiments and Analyses

DTIC Science & Technology

1998-11-01

initial increments of voids do not lead to substantial relaxation of stress. In this case, the condition (8.1) gives Vv = Ao- aVv * ß=— (8.10) pc...enough strain steps to define the process accurately. At each strain step, a combined Newton-Raphson and regulafalsi solution technique (multiple trials ...laser surgery. Clinical studies have demonstrated that, for some applications, surgical lasers are superior to conventional surgical procedures

Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation

PubMed Central

Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G.

2015-01-01

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. PMID:26067950

Strain mapping in TEM using precession electron diffraction

DOEpatents

Taheri, Mitra Lenore; Leff, Asher Calvin

2017-02-14

A sample material is scanned with a transmission electron microscope (TEM) over multiple steps having a predetermined size at a predetermined angle. Each scan at a predetermined step and angle is compared to a template, wherein the template is generated from parameters of the material and the scanning. The data is then analyzed using local mis-orientation mapping and/or Nye's tensor analysis to provide information about local strain states.

Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna

PubMed Central

Burguener, Germán F.; Maldonado, Marcos J.; Revale, Santiago; Fernández Do Porto, Darío; Rascován, Nicolás; Vázquez, Martín; Farías, María Eugenia; Marti, Marcelo A.

2014-01-01

Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from Laguna Antofalla in the Argentinian Puna. The draft genome sequence suggests the presence of potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high UV radiation, elevated salinity, and the presence of critical arsenic concentrations. PMID:24503991

Wolbachia endosymbionts in haplodiploid and diploid scolytine beetles (Coleoptera: Curculionidae: Scolytinae).

PubMed

Kawasaki, Yuuki; Schuler, Hannes; Stauffer, Christian; Lakatos, Ferenc; Kajimura, Hisashi

2016-05-19

Haplodiploidy is a sex determination system in which fertilized diploid eggs develop into females and unfertilized haploid eggs develop into males. The evolutionary explanations for this phenomenon include the possibility that haplodiploidy can be reinforced by infection with endosymbiotic bacteria, such as Wolbachia. The subfamily Scolytinae contains species with haplodiploid and diploid sex determination systems. Thus, we studied the association with Wolbachia in 12 diploid and 11 haplodiploid scolytine beetles by analyzing wsp and multilocus sequence typing (MLST) of five loci in this endosymbiont. Wolbachia genotypes were compared with mitochondrial (COI) and nuclear (EF) genotypes in the scolytines. Eight of the 23 scolytine species were infected with Wolbachia, with haplodiploids at significantly higher rates than diploid species. Cloning and sequencing detected multiple infections with up to six Wolbachia strains in individual species. Phylogenetic analyses of wsp and five MLST genes revealed different Wolbachia strains in scolytines. Comparisons between the beetle and Wolbachia phylogenies revealed that closely related beetles were infected with genetically different Wolbachia strains. These results suggest the horizontal transmission of multiple Wolbachia strains between scolytines. We discuss these results in terms of the evolution of different sex determination systems in scolytine beetles. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

A rapid method of accurate detection and differentiation of Newcastle disease virus pathotypes by demonstrating multiple bands in degenerate primer based nested RT-PCR.

PubMed

Desingu, P A; Singh, S D; Dhama, K; Kumar, O R Vinodh; Singh, R; Singh, R K

2015-02-01

A rapid and accurate method of detection and differentiation of virulent and avirulent Newcastle disease virus (NDV) pathotypes was developed. The NDV detection was carried out for different domestic avian field isolates and pigeon paramyxo virus-1 (25 field isolates and 9 vaccine strains) by using APMV-I "fusion" (F) gene Class II specific external primer A and B (535bp), internal primer C and D (238bp) based reverses transcriptase PCR (RT-PCR). The internal degenerative reverse primer D is specific for F gene cleavage position of virulent strain of NDV. The nested RT-PCR products of avirulent strains showed two bands (535bp and 424bp) while virulent strains showed four bands (535bp, 424bp, 349bp and 238bp) on agar gel electrophoresis. This is the first report regarding development and use of degenerate primer based nested RT-PCR for accurate detection and differentiation of NDV pathotypes by demonstrating multiple PCR band patterns. Being a rapid, simple, and economical test, the developed method could serve as a valuable alternate diagnostic tool for characterizing NDV isolates and carrying out molecular epidemiological surveillance studies for this important pathogen of poultry. Copyright © 2014 Elsevier B.V. All rights reserved.

Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain.

PubMed

Zago, Miriam; Orrù, Luigi; Rossetti, Lia; Lamontanara, Antonella; Fornasari, Maria Emanuela; Bonvini, Barbara; Meucci, Aurora; Carminati, Domenico; Cattivelli, Luigi; Giraffa, Giorgio

2017-09-01

In this study the presence and functionality of phage defence mechanisms in Lactobacillus helveticus ATCC 10386, a strain of dairy origin which is sensitive to ΦLh56, were investigated. After exposure of ATCC 10386 to ΦLh56, the whole-genome sequences of ATCC 10386 and of a phage-resistant derivative (LhM3) were compared. LhM3 showed deletions in the S-layer protein and a higher expression of the genes involved in the restriction/modification (R/M) system. Genetic data were substantiated by measurements of bacteriophage adsorption rates, efficiency of plaquing, cell wall protein size and by gene expression analysis. In LhM3 two phage resistance mechanisms, the inhibition of phage adsorption and the upregulation of Type I R/M genes, take place and explain its resistance to ΦLh56. Although present in both ATCC 10386 and LhM3 genomes, the CRISPR machinery did not seem to play a role in the phage resistance of LhM3. Overall, the natural selection of phage resistant strains resulted successful in detecting variants carrying multiple phage defence mechanisms in L. helveticus. The concurrent presence of multiple phage-resistance systems should provide starter strains with increased fitness and robustness in dairy ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Flow behaviour and constitutive modelling of a ferritic stainless steel at elevated temperatures

NASA Astrophysics Data System (ADS)

Zhao, Jingwei; Jiang, Zhengyi; Zu, Guoqing; Du, Wei; Zhang, Xin; Jiang, Laizhu

2016-05-01

The flow behaviour of a ferritic stainless steel (FSS) was investigated by a Gleeble 3500 thermal-mechanical test simulator over the temperature range of 900-1100 °C and strain rate range of 1-50 s-1. Empirical and phenomenological constitutive models were established, and a comparative study was made on the predictability of them. The results indicate that the flow stress decreases with increasing the temperature and decreasing the strain rate. High strain rate may cause a drop in flow stress after a peak value due to the adiabatic heating. The Zener-Hollomon parameter depends linearly on the flow stress, and decreases with raising the temperature and reducing the strain rate. Significant deviations occur in the prediction of flow stress by the Johnson-Cook (JC) model, indicating that the JC model cannot accurately track the flow behaviour of the FSS during hot deformation. Both the multiple-linear and the Arrhenius-type models can track the flow behaviour very well under the whole hot working conditions, and have much higher accuracy in predicting the flow behaviour than that of the JC model. The multiple-linear model is recommended in the current work due to its simpler structure and less time needed for solving the equations relative to the Arrhenius-type model.

Growth advantage of Escherichia coli O104:H4 strains on 5-N-acetyl-9-O-acetyl neuraminic acid as a carbon source is dependent on heterogeneous phage-Borne nanS-p esterases.

PubMed

Saile, Nadja; Schwarz, Lisa; Eißenberger, Kristina; Klumpp, Jochen; Fricke, Florian W; Schmidt, Herbert

2018-06-01

Enterohemorrhagic E. coli (EHEC) are serious bacterial pathogens which are able to cause a hemorrhagic colitis or the life-threatening hemolytic-uremic syndrome (HUS) in humans. EHEC strains can carry different numbers of phage-borne nanS-p alleles that are responsible for acetic acid release from mucin from bovine submaxillary gland and 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac 2 ), a carbohydrate present in mucin. Thus, Neu5,9Ac 2 can be transformed to 5-N-acetyl neuraminic acid, an energy source used by E. coli strains. We hypothesize that these NanS-p proteins are involved in competitive growth of EHEC in the gastrointestinal tract of humans and animals. The aim of the current study was to demonstrate and characterize the nanS-p alleles of the 2011 E. coli O104:H4 outbreak strain LB226692 and analyze whether the presence of multiple nanS-p alleles in the LB226692 genome causes a competitive growth advantage over a commensal E. coli strain. We detected and characterized five heterogeneous phage-borne nanS-p alleles in the genome of E. coli O104:H4 outbreak strain LB226692 by in silico analysis of its genome. Furthermore, successive deletion of all nanS-p alleles, subsequent complementation with recombinant NanS-p13-His, and in vitro co-culturing experiments with the commensal E. coli strain AMC 198 were conducted. We could show that nanS-p genes of E. coli O104:H4 are responsible for growth inhibition of strain AMC 198, when Neu5,9Ac 2 was used as sole carbon source in co-culture. The results of this study let us suggest that multiple nanS-p alleles may confer a growth advantage by outcompeting other E. coli strains in Neu5,9Ac 2 rich environments, such as mucus in animal and human gut. Copyright © 2018 Elsevier GmbH. All rights reserved.

Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis.

PubMed

Christensen, Gitte J M; Scholz, Christian F P; Enghild, Jan; Rohde, Holger; Kilian, Mogens; Thürmer, Andrea; Brzuszkiewicz, Elzbieta; Lomholt, Hans B; Brüggemann, Holger

2016-02-29

Propionibacterium acnes and Staphylococcus epidermidis live in close proximity on human skin, and both bacterial species can be isolated from normal and acne vulgaris-affected skin sites. The antagonistic interactions between the two species are poorly understood, as well as the potential significance of bacterial interferences for the skin microbiota. Here, we performed simultaneous antagonism assays to detect inhibitory activities between multiple isolates of the two species. Selected strains were sequenced to identify the genomic basis of their antimicrobial phenotypes. First, we screened 77 P. acnes strains isolated from healthy and acne-affected skin, and representing all known phylogenetic clades (I, II, and III), for their antimicrobial activities against 12 S. epidermidis isolates. One particular phylogroup (I-2) exhibited a higher antimicrobial activity than other P. acnes phylogroups. All genomes of type I-2 strains carry an island encoding the biosynthesis of a thiopeptide with possible antimicrobial activity against S. epidermidis. Second, 20 S. epidermidis isolates were examined for inhibitory activity against 25 P. acnes strains. The majority of S. epidermidis strains were able to inhibit P. acnes. Genomes of S. epidermidis strains with strong, medium and no inhibitory activities against P. acnes were sequenced. Genome comparison underlined the diversity of S. epidermidis and detected multiple clade- or strain-specific mobile genetic elements encoding a variety of functions important in antibiotic and stress resistance, biofilm formation and interbacterial competition, including bacteriocins such as epidermin. One isolate with an extraordinary antimicrobial activity against P. acnes harbors a functional ESAT-6 secretion system that might be involved in the antimicrobial activity against P. acnes via the secretion of polymorphic toxins. Taken together, our study suggests that interspecies interactions could potentially jeopardize balances in the skin microbiota. In particular, S. epidermidis strains possess an arsenal of different mechanisms to inhibit P. acnes. However, if such interactions are relevant in skin disorders such as acne vulgaris remains questionable, since no difference in the antimicrobial activity against, or the sensitivity towards S. epidermidis could be detected between health- and acne-associated strains of P. acnes.

Characterization and probiotic potential of Lactobacillus plantarum strains isolated from cheeses.

PubMed

Zago, Miriam; Fornasari, Maria Emanuela; Carminati, Domenico; Burns, Patricia; Suàrez, Viviana; Vinderola, Gabriel; Reinheimer, Jorge; Giraffa, Giorgio

2011-08-01

Ninety-eight Lactobacillus plantarum strains isolated from Italian and Argentinean cheeses were evaluated for probiotic potential. After a preliminary subtractive screening based on the presence of msa and bsh genes, 27 strains were characterized. In general, the selected strains showed high resistance to lysozyme, good adaptation to simulated gastric juice, and a moderate to low bile tolerance. The capacity to agglutinate yeast cells in a mannose-specific manner, as well as the cell surface hydrophobicity was found to be variable among strains. Very high β-galactosidase activity was shown by a considerable number of the tested strains, whereas variable prebiotic utilization ability was observed. Only tetracycline resistance was observed in two highly resistant strains which harbored the tetM gene, whereas none of the strains showed β-glucuronidase activity or was capable of inhibiting pathogens. Three strains (Lp790, Lp813, and Lp998) were tested by in vivo trials. A considerable heterogeneity was found among a number of L. plantarum strains screened in this study, leading to the design of multiple cultures to cooperatively link strains showing the widest range of useful traits. Among the selected strains, Lp790, Lp813, and Lp998 showed the best probiotic potential and would be promising candidates for inclusion as starter cultures for the manufacture of probiotic fermented foods. Copyright © 2011 Elsevier Ltd. All rights reserved.

Phenotypic evaluation and characterization of 21 industrial Saccharomyces cerevisiae yeast strains.

PubMed

Kong, In Iok; Turner, Timothy Lee; Kim, Heejin; Kim, Soo Rin; Jin, Yong-Su

2018-02-01

Microorganisms have been studied and used extensively to produce value-added fuels and chemicals. Yeasts, specifically Saccharomyces cerevisiae, receive industrial attention because of their well-known ability to ferment glucose and produce ethanol. Thousands of natural or genetically modified S. cerevisiae have been found in industrial environments for various purposes. These industrial strains are isolated from industrial fermentation sites, and they are considered as potential host strains for superior fermentation processes. In many cases, industrial yeast strains have higher thermotolerance, increased resistances towards fermentation inhibitors and increased glucose fermentation rates under anaerobic conditions when compared with laboratory yeast strains. Despite the advantages of industrial strains, they are often not well characterized. Through screening and phenotypic characterization of commercially available industrial yeast strains, industrial fermentation processes requiring specific environmental conditions may be able to select an ideal starting yeast strain to be further engineered. Here, we have characterized and compared 21 industrial S. cerevisiae strains under multiple conditions, including their tolerance to varying pH conditions, resistance to fermentation inhibitors, sporulation efficiency and ability to ferment lignocellulosic sugars. These data may be useful for the selection of a parental strain for specific biotechnological applications of engineered yeast. © FEMS 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni

PubMed Central

Parker, Craig T; Miller, William G; Horn, Sharon T; Lastovica, Albert J

2007-01-01

Background Campylobacter jejuni has been divided into two subspecies: C. jejuni subsp. jejuni (Cjj) and C. jejuni subsp. doylei (Cjd). Nearly all of the C. jejuni strains isolated are Cjj; nevertheless, although Cjd strains are isolated infrequently, they differ from Cjj in two key aspects: they are obtained primarily from human clinical samples and are associated often with bacteremia, in addition to gastroenteritis. In this study, we utilized multilocus sequence typing (MLST) and a DNA microarray-based comparative genomic indexing (CGI) approach to examine the genomic diversity and gene content of Cjd strains. Results A geographically diverse collection of eight Cjd strains was examined by MLST and determined to be phylogenetically distinct from Cjj strains. Microarray-based CGI approach also supported this. We were able to demonstrate that Cjd strains exhibited divergence from Cjj strains NCTC 11168 and RM1221 in many of the intraspecies hypervariable regions. Moreover, multiple metabolic, transport and virulence functions (e.g. cytolethal distending toxin) were shown to be absent in the Cjd strains examined. Conclusion Our data demonstrate that Cjd are phylogenetically distinct from Cjj strains. Using the CGI approach, we identified subsets of absent genes from amongst the C. jejuni genes that provide clues as to the potential evolutionary origin and unusual pathogenicity of Cjd. PMID:17535437

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks.

PubMed

Muramoto, Nobuhiko; Oda, Arisa; Tanaka, Hidenori; Nakamura, Takahiro; Kugou, Kazuto; Suda, Kazuki; Kobayashi, Aki; Yoneda, Shiori; Ikeuchi, Akinori; Sugimoto, Hiroki; Kondo, Satoshi; Ohto, Chikara; Shibata, Takehiko; Mitsukawa, Norihiro; Ohta, Kunihiro

2018-05-18

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.

High resolution skin-like sensor capable of sensing and visualizing various sensations and three dimensional shape.

PubMed

Xu, Tianbai; Wang, Wenbo; Bian, Xiaolei; Wang, Xiaoxue; Wang, Xiaozhi; Luo, J K; Dong, Shurong

2015-08-13

Human skin contains multiple receptors, and is able to sense various stimuli such as temperature, pressure, force, corrosion etc, and to feel pains and the shape of objects. The development of skin-like sensors capable of sensing these stimuli is of great importance for various applications such as robots, touch detection, temperature monitoring, strain gauges etc. Great efforts have been made to develop high performance skin-like sensors, but they are far from perfect and much inferior to human skin as most of them can only sense one stimulus with focus on pressure (strain) or temperature, and are unable to visualize sensations and shape of objects. Here we report a skin-like sensor which imitates real skin with multiple receptors, and a new concept of pain sensation. The sensor with very high resolution not only has multiple sensations for touch, pressure, temperature, but also is able to sense various pains and reproduce the three dimensional shape of an object in contact.

The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Shihui; Pelletier, Dale A; Lu, Tse-Yuan

Zymomonas mobilis produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed Z. mobilis ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions. We have shown the utility of the pKNOCK suicide plasmid for mutant construction in Z. mobilis, and constructed a Gateway compatible expressionmore » plasmid for use in Z. mobilis for the first time. We have also used genetics to show Z. mobilis Hfq and S. cerevisiae Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.« less

Characterization of esculin-positive Pseudomonas fluorescens strains isolated from an underground brook.

PubMed

Svec, P; Stegnerová, H; Durnová, E; Sedlácek, I

2004-01-01

A group of sixteen esculin-positive fluorescent pseudomonads isolated from an underground brook flowing through a cave complex was characterized by biotyping, multiple enzyme restriction fragment length polymorphism analysis of 16S rDNA (MERFLP), ribotyping and whole-cell fatty-acid methyl-esters analysis (FAME). All strains were phenotypically close to Pseudomonas fluorescens, but they revealed high biochemical variability as well as some reactions atypical for P. fluorescens species. Because identification of pseudomonads by of biochemical testing is often unclear, further techniques were employed. Fingerprints obtained by MERFLP clearly showed that all strains represent P. fluorescens species. Ribotyping separated the strains analyzed into four groups corresponding almost completely (with the exception of one strain) to the clustering based on biochemical profiles. FAME analysis grouped all the strains into one cluster together with the P. putida (biotype A, B), P. chlororaphis and P. fluorescens biotype F representatives, but differentiated them from other FAME profiles of all pseudomonads included in the standard library TSBA 40 provided by MIDI, Inc.

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

PubMed

Müller, Romy; Roberts, Charlotte A; Brown, Terence A

2014-04-22

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

Correlated terahertz acoustic and electromagnetic emission in dynamically screened InGaN/GaN quantum wells

NASA Astrophysics Data System (ADS)

van Capel, P. J. S.; Turchinovich, D.; Porte, H. P.; Lahmann, S.; Rossow, U.; Hangleiter, A.; Dijkhuis, J. I.

2011-08-01

We investigate acoustic and electromagnetic emission from optically excited strained piezoelectric In0.2Ga0.8N/GaN multiple quantum wells (MQWs), using optical pump-probe spectroscopy, time-resolved Brillouin scattering, and THz emission spectroscopy. A direct comparison of detected acoustic signals and THz electromagnetic radiation signals demonstrates that transient strain generation in InGaN/GaN MQWs is correlated with electromagnetic THz generation, and both types of emission find their origin in ultrafast dynamical screening of the built-in piezoelectric field in the MQWs. The measured spectral intensity of the detected Brillouin signal corresponds to a maximum strain amplitude of generated acoustic pulses of 2%. This value coincides with the static lattice-mismatch-induced strain in In0.2Ga0.8N/GaN, demonstrating the total release of static strain in MQWs via impulsive THz acoustic emission. This confirms the ultrafast dynamical screening mechanism in MQWs as a highly efficient method for impulsive strain generation.

Divergent prion strain evolution driven by PrPC expression level in transgenic mice

PubMed Central

Le Dur, Annick; Laï, Thanh Lan; Stinnakre, Marie-George; Laisné, Aude; Chenais, Nathalie; Rakotobe, Sabine; Passet, Bruno; Reine, Fabienne; Soulier, Solange; Herzog, Laetitia; Tilly, Gaëlle; Rézaei, Human; Béringue, Vincent; Vilotte, Jean-Luc; Laude, Hubert

2017-01-01

Prions induce a fatal neurodegenerative disease in infected host brain based on the refolding and aggregation of the host-encoded prion protein PrPC into PrPSc. Structurally distinct PrPSc conformers can give rise to multiple prion strains. Constrained interactions between PrPC and different PrPSc strains can in turn lead to certain PrPSc (sub)populations being selected for cross-species transmission, or even produce mutation-like events. By contrast, prion strains are generally conserved when transmitted within the same species, or to transgenic mice expressing homologous PrPC. Here, we compare the strain properties of a representative sheep scrapie isolate transmitted to a panel of transgenic mouse lines expressing varying levels of homologous PrPC. While breeding true in mice expressing PrPC at near physiological levels, scrapie prions evolve consistently towards different strain components in mice beyond a certain threshold of PrPC overexpression. Our results support the view that PrPC gene dosage can influence prion evolution on homotypic transmission. PMID:28112164

Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

PubMed Central

Li, Jia; Liu, Fei; Wang, Qi; Ge, Pupu; Woo, Patrick C. Y.; Yan, Jinghua; Zhao, Yanlin; Gao, George F.; Liu, Cui Hua; Liu, Changting

2014-01-01

The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens. PMID:25163721

Job strain among rubber-glove-factory workers in central Thailand.

PubMed

Sein, Muang Muang; Howteerakul, Nopporn; Suwannapong, Nawarat; Jirachewee, Jirachai

2010-01-01

Job strain has become a major concern because of its potential impacts on worker well-being and performance. This cross-sectional study aimed to assess the prevalence of, and examine factors associated with, job strain among workers in a rubber-glove factory, in a central province of Thailand. A total of 200 workers aged 18-55 yr, who had worked at the factory for at least 6 months, completed the Job Content Questionnaire (JCQ) (Thai Version). Two of 5 scales in the JCQ were used to measure job strain, i.e.; job control and psychological job demand. The prevalence of job strain was 27.5%. Multiple logistic regression analysis indicated two variables significantly associated with job strain: low supervisor social support (adjusted OR=3.08; 95%CI: 1.38-6.91) and high job insecurity (adjusted OR=2.25; 95%CI: 1.04-4.88). Effective training for supervisors, to create good relationships among workers and supervisors, and ensuring steady and secure jobs for good employees, are necessary.

Low cycle fatigue behavior of a ferritic reactor pressure vessel steel

NASA Astrophysics Data System (ADS)

Sarkar, Apu; Kumawat, Bhupendra K.; Chakravartty, J. K.

2015-07-01

The cyclic stress-strain response and the low cycle fatigue (LCF) behavior of 20MnMoNi55 pressure vessel steel were studied. Tensile strength and LCF properties were examined at room temperature (RT) using specimens cut from rolling direction of a rolled block. The fully reversed strain-controlled LCF tests were conducted at a constant total strain rate with different axial strain amplitude levels. The cyclic strain-stress relationships and the strain-life relationships were obtained through the test results, and related LCF parameters of the steel were calculated. The studied steel exhibits cyclic softening behavior. Furthermore, analysis of stabilized hysteresis loops showed that the steel exhibits non-Masing behavior. Complementary scanning electron microscopy examinations were also carried out on fracture surfaces to reveal dominant damage mechanisms during crack initiation, propagation and fracture. Multiple crack initiation sites were observed on the fracture surface. The investigated LCF behavior can provide reference for pressure vessel life assessment and fracture mechanisms analysis.

Extremely Elastic Wearable Carbon Nanotube Fiber Strain Sensor for Monitoring of Human Motion.

PubMed

Ryu, Seongwoo; Lee, Phillip; Chou, Jeffrey B; Xu, Ruize; Zhao, Rong; Hart, Anastasios John; Kim, Sang-Gook

2015-06-23

The increasing demand for wearable electronic devices has made the development of highly elastic strain sensors that can monitor various physical parameters an essential factor for realizing next generation electronics. Here, we report an ultrahigh stretchable and wearable device fabricated from dry-spun carbon nanotube (CNT) fibers. Stretching the highly oriented CNT fibers grown on a flexible substrate (Ecoflex) induces a constant decrease in the conductive pathways and contact areas between nanotubes depending on the stretching distance; this enables CNT fibers to behave as highly sensitive strain sensors. Owing to its unique structure and mechanism, this device can be stretched by over 900% while retaining high sensitivity, responsiveness, and durability. Furthermore, the device with biaxially oriented CNT fiber arrays shows independent cross-sensitivity, which facilitates simultaneous measurement of strains along multiple axes. We demonstrated potential applications of the proposed device, such as strain gauge, single and multiaxial detecting motion sensors. These devices can be incorporated into various motion detecting systems where their applications are limited to their strain.

Genotypic diversity of merozoite surface antigen 1 of Babesia bovis within an endemic population.

PubMed

Lau, Audrey O T; Cereceres, Karla; Palmer, Guy H; Fretwell, Debbie L; Pedroni, Monica J; Mosqueda, Juan; McElwain, Terry F

2010-08-01

Multiple genetically distinct strains of a pathogen circulate and compete for dominance within populations of animal reservoir hosts. Understanding the basis for genotypic strain structure is critical for predicting how pathogens respond to selective pressures and how shifts in pathogen population structure can lead to disease outbreaks. Evidence from related Apicomplexans such as Plasmodium, Toxoplasma, Cryptosporidium and Theileria suggests that various patterns of population dynamics exist, including but not limited to clonal, oligoclonal, panmictic and epidemic genotypic strain structures. In Babesia bovis, genetic diversity of variable merozoite surface antigen (VMSA) genes has been associated with disease outbreaks, including in previously vaccinated animals. However, the extent of VMSA diversity within a defined population in an endemic area has not been examined. We analyzed genotypic diversity and temporal change of MSA-1, a member of the VMSA family, in individual infected animals within a reservoir host population. Twenty-eight distinct MSA-1 genotypes were identified within the herd. All genotypically distinct MSA-1 sequences clustered into three groups based on sequence similarity. Two thirds of the animals tested changed their dominant MSA-1 genotypes during a 6-month period. Five animals within the population contained multiple genotypes. Interestingly, the predominant genotypes within those five animals also changed over the 6-month sampling period, suggesting ongoing transmission or emergence of variant MSA-1 genotypes within the herd. This study demonstrated an unexpected level of diversity for a single copy gene in a haploid genome, and illustrates the dynamic genotype structure of B. bovis within an individual animal in an endemic region. Co-infection with multiple diverse MSA-1 genotypes provides a basis for more extensive genotypic shifts that characterizes outbreak strains.

Identification of five novel modifier loci of ApcMin harbored in the BXH14 recombinant inbred strain

PubMed Central

Siracusa, Linda D.

2012-01-01

Every year thousands of people in the USA are diagnosed with small intestine and colorectal cancers (CRC). Although environmental factors affect disease etiology, uncovering underlying genetic factors is imperative for risk assessment and developing preventative therapies. Familial adenomatous polyposis is a heritable genetic disorder in which individuals carry germ-line mutations in the adenomatous polyposis coli (APC) gene that predisposes them to CRC. The Apc Min mouse model carries a point mutation in the Apc gene and develops polyps along the intestinal tract. Inbred strain background influences polyp phenotypes in Apc Min mice. Several Modifier of Min (Mom) loci that alter tumor phenotypes associated with the Apc Min mutation have been identified to date. We screened BXH recombinant inbred (RI) strains by crossing BXH RI females with C57BL/6J (B6) Apc Min males and quantitating tumor phenotypes in backcross progeny. We found that the BXH14 RI strain harbors five modifier loci that decrease polyp multiplicity. Furthermore, we show that resistance is determined by varying combinations of these modifier loci. Gene interaction network analysis shows that there are multiple networks with proven gene–gene interactions, which contain genes from all five modifier loci. We discuss the implications of this result for studies that define susceptibility loci, namely that multiple networks may be acting concurrently to alter tumor phenotypes. Thus, the significance of this work resides not only with the modifier loci we identified but also with the combinations of loci needed to get maximal protection against polyposis and the impact of this finding on human disease studies. Abbreviations:APCadenomatous polyposis coliGWASgenome-wide association studiesQTLquantitative trait lociSNPsingle-nucleotide polymorphism. PMID:22637734

Influence of long-term equine herpesvirus type 1 (EHV-1) infection on primary murine neurons-the possible effects of the multiple passages of EHV-1 on its neurovirulence.

PubMed

Cymerys, Joanna; Słońska, A; Tucholska, A; Golke, A; Chmielewska, A; Bańbura, M W

2018-01-01

Equine herpesvirus 1 (EHV-1), like other members of the Alphaherpesvirinae subfamily, is a neurotropic virus causing latent infections in the nervous system of the natural host. In the present study, we have investigated EHV-1 replication (wild-type Jan-E strain and Rac-H laboratory strain) during long-term infection and during the passages of the virus in cultured neurons. The studies were performed on primary murine neurons, which are an excellent in vitro model for studying neurotropism and neurovirulence of EHV-1. Using real-time cell growth analysis, we have demonstrated for the first time that primary murine neurons are able to survive long-term EHV-1 infection. Positive results of real-time PCR test indicated a high level of virus DNA in cultured neurons, and during long-term infection, these neurons were still able to transmit the virus to the other cells. We also compared the neurovirulence of Rac-H and Jan-E EHV-1 strains after multiple passages of these strains in neuron cell culture. The results showed that multiple passages of EHV-1 in neurons lead to the inhibition of viral replication as early as in the third passage. Interestingly, the inhibition of the EHV-1 replication occurred exclusively in neurons, because the equine dermal (ED) cells co-cultivated with neuroculture medium from the third passage showed the presence of large amount of viral DNA. In conclusion, our results showed that certain balance between EHV-1 and neurons has been established during in vitro infection allowing neurons to survive long-term infection.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

PubMed

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

PubMed Central

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S. K.; Mammel, Mark K.; Tarr, Phillip I.; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies. PMID:27446025

Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli.

PubMed

Timmons, Chris; Trees, Eija; Ribot, Efrain M; Gerner-Smidt, Peter; LaFon, Patti; Im, Sung; Ma, Li Maria

2016-06-01

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of growing concern worldwide that have been associated with several recent multistate and multinational outbreaks of foodborne illness. Rapid and sensitive molecular-based bacterial strain discrimination methods are critical for timely outbreak identification and contaminated food source traceback. One such method, multiple-locus variable-number tandem repeat analysis (MLVA), is being used with increasing frequency in foodborne illness outbreak investigations to augment the current gold standard bacterial subtyping technique, pulsed-field gel electrophoresis (PFGE). The objective of this study was to develop a MLVA assay for intra- and inter-serogroup discrimination of six major non-O157 STEC serogroups-O26, O111, O103, O121, O45, and O145-and perform a preliminary internal validation of the method on a limited number of clinical isolates. The resultant MLVA scheme consists of ten variable number tandem repeat (VNTR) loci amplified in three multiplex PCR reactions. Sixty-five unique MLVA types were obtained among 84 clinical non-O157 STEC strains comprised of geographically diverse sporadic and outbreak related isolates. Compared to PFGE, the developed MLVA scheme allowed similar discrimination among serogroups O26, O111, O103, and O121 but not among O145 and O45. To more fully compare the discriminatory power of this preliminary MLVA method to PFGE and to determine its epidemiological congruence, a thorough internal and external validation needs to be performed on a carefully selected large panel of strains, including multiple isolates from single outbreaks. Copyright © 2016. Published by Elsevier B.V.

Co-feeding transmission facilitates strain coexistence in Borrelia burgdorferi, the Lyme disease agent.

PubMed

States, S L; Huang, C I; Davis, S; Tufts, D M; Diuk-Wasser, M A

2017-06-01

Coexistence of multiple tick-borne pathogens or strains is common in natural hosts and can be facilitated by resource partitioning of the host species, within-host localization, or by different transmission pathways. Most vector-borne pathogens are transmitted horizontally via systemic host infection, but transmission may occur in the absence of systemic infection between two vectors feeding in close proximity, enabling pathogens to minimize competition and escape the host immune response. In a laboratory study, we demonstrated that co-feeding transmission can occur for a rapidly-cleared strain of Borrelia burgdorferi, the Lyme disease agent, between two stages of the tick vector Ixodes scapularis while feeding on their dominant host, Peromyscus leucopus. In contrast, infections rapidly became systemic for the persistently infecting strain. In a field study, we assessed opportunities for co-feeding transmission by measuring co-occurrence of two tick stages on ears of small mammals over two years at multiple sites. Finally, in a modeling study, we assessed the importance of co-feeding on R 0 , the basic reproductive number. The model indicated that co-feeding increases the fitness of rapidly-cleared strains in regions with synchronous immature tick feeding. Our results are consistent with increased diversity of B. burgdorferi in areas of higher synchrony in immature feeding - such as the midwestern United States. A higher relative proportion of rapidly-cleared strains, which are less human pathogenic, would also explain lower Lyme disease incidence in this region. Finally, if co-feeding transmission also occurs on refractory hosts, it may facilitate the emergence and persistence of new pathogens with a more limited host range. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Toward Non-Invasive and Automatic Intravenous Infiltration Detection: Evaluation of Bioimpedance and Skin Strain in a Pig Model.

PubMed

Bicen, A Ozan; West, Leanne L; Cesar, Liliana; Inan, Omer T

2018-01-01

Intravenous (IV) therapy is prevalent in hospital settings, where fluids are typically delivered with an IV into a peripheral vein of the patient. IV infiltration is the inadvertent delivery of fluids into the extravascular space rather than into the vein (and requires urgent treatment to avoid scarring and severe tissue damage), for which medical staff currently needs to check patients periodically. In this paper, the performance of two non-invasive sensing modalities, electrical bioimpedance (EBI), and skin strain sensing, for the automatic detection of IV infiltration was investigated in an animal model. Infiltrations were physically simulated on the hind limb of anesthetized pigs, where the sensors for EBI and skin strain sensing were co-located. The obtained data were used to examine the ability to distinguish between infusion into the vein and an infiltration event using bioresistance and bioreactance (derived from EBI), as well as skin strain. Skin strain and bioresistance sensing could achieve detection rates greater than 0.9 for infiltration fluid volumes of 2 and 10 mL, respectively, for a given false positive, i.e., false alarm rate of 0.05. Furthermore, the fusion of multiple sensing modalities could achieve a detection rate of 0.97 with a false alarm rate of 0.096 for 5mL fluid volume of infiltration. EBI and skin strain sensing can enable non-invasive and real-time IV infiltration detection systems. Fusion of multiple sensing modalities can help to detect expanded range of leaking fluid volumes. The provided performance results and comparisons in this paper are an important step towards clinical translation of sensing technologies for detecting IV infiltration.

Toward Non-Invasive and Automatic Intravenous Infiltration Detection: Evaluation of Bioimpedance and Skin Strain in a Pig Model

PubMed Central

Bicen, A. Ozan; West, Leanne L.; Cesar, Liliana

2018-01-01

Intravenous (IV) therapy is prevalent in hospital settings, where fluids are typically delivered with an IV into a peripheral vein of the patient. IV infiltration is the inadvertent delivery of fluids into the extravascular space rather than into the vein (and requires urgent treatment to avoid scarring and severe tissue damage), for which medical staff currently needs to check patients periodically. In this paper, the performance of two non-invasive sensing modalities, electrical bioimpedance (EBI), and skin strain sensing, for the automatic detection of IV infiltration was investigated in an animal model. Infiltrations were physically simulated on the hind limb of anesthetized pigs, where the sensors for EBI and skin strain sensing were co-located. The obtained data were used to examine the ability to distinguish between infusion into the vein and an infiltration event using bioresistance and bioreactance (derived from EBI), as well as skin strain. Skin strain and bioresistance sensing could achieve detection rates greater than 0.9 for infiltration fluid volumes of 2 and 10 mL, respectively, for a given false positive, i.e., false alarm rate of 0.05. Furthermore, the fusion of multiple sensing modalities could achieve a detection rate of 0.97 with a false alarm rate of 0.096 for 5mL fluid volume of infiltration. EBI and skin strain sensing can enable non-invasive and real-time IV infiltration detection systems. Fusion of multiple sensing modalities can help to detect expanded range of leaking fluid volumes. The provided performance results and comparisons in this paper are an important step towards clinical translation of sensing technologies for detecting IV infiltration. PMID:29692956

Impact of strain on electronic and transport properties of 6 nm hydrogenated germanane nano-ribbon channel double gate field effect transistor

NASA Astrophysics Data System (ADS)

Meher Abhinav, E.; Sundararaj, Anuraj; Gopalakrishnan, Chandrasekaran; Kasmir Raja, S. V.; Chokhra, Saurabh

2017-11-01

In this work, chair like fully hydrogenated germanane (CGeH) nano-ribbon 6 nm short channel double gate field effect transistor (DG-FET) has been modeled and the impact of strain on the I-V characteristics of CGeH channel has been examined. The bond lengths, binding and formation energies of various hydrogenated geometries of buckled germanane channel were calculated using local density approximation (LDA) with Perdew-Zunger (PZ) and generalized gradient approximation (GGA) with Perdew Burke Ernzerhof (PBE) parameterization. From four various geometries, chair like structure is found to be more stable compared to boat like obtuse, stiruup structure and table like structure. The bandgap versus width, bandgap versus strain characteristics and I-V characteristics had been analyzed at room temperature using density functional theory (DFT). Using self consistent calculation it was observed that the electronic properties of nano-ribbon is independent of length and band structure, but dependent on edge type, strain [Uni-axial (ɛ xx ), bi-axial (ɛ xx   =  ɛ yy )] and width of the ribbon. The strain engineered hydrogenated germanane (GeH) showed wide direct bandgap (2.3 eV) which could help to build low noise electronic devices that operates at high frequencies. The observed bi-axial compression has high impact on the device transport characteristics with peak to valley ratio (PVR) of 2.14 and 380% increase in peak current compared to pristine CGeH device. The observed strain in CGeH DG-FET could facilitate in designing novel multiple-logic memory devices due to multiple negative differential resistance (NDR) regions.

As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.

PubMed

Hargreaves, Katherine R; Otieno, James R; Thanki, Anisha; Blades, Matthew J; Millard, Andrew D; Browne, Hilary P; Lawley, Trevor D; Clokie, Martha R J

2015-05-27

The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile "mobilome," which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile

PubMed Central

Hargreaves, Katherine R.; Otieno, James R.; Thanki, Anisha; Blades, Matthew J.; Millard, Andrew D.; Browne, Hilary P.; Lawley, Trevor D.; Clokie, Martha R.J.

2015-01-01

The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile “mobilome,” which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics. PMID:26019165

Highly Invasive Listeria monocytogenes Strains Have Growth and Invasion Advantages in Strain Competition

PubMed Central

Manthou, Evanthia; Ciolacu, Luminita; Wagner, Martin; Skandamis, Panagiotis N.

2015-01-01

Multiple Listeria monocytogenes strains can be present in the same food sample; moreover, infection with more than one L. monocytogenes strain can also occur. In this study we investigated the impact of strain competition on the growth and in vitro virulence potential of L. monocytogenes. We identified two strong competitor strains, whose growth was not (or only slightly) influenced by the presence of other strains and two weak competitor strains, which were outcompeted by other strains. Cell contact was essential for growth inhibition. In vitro virulence assays using human intestinal epithelial Caco2 cells showed a correlation between the invasion efficiency and growth inhibition: the strong growth competitor strains showed high invasiveness. Moreover, invasion efficiency of the highly invasive strain was further increased in certain combinations by the presence of a low invasive strain. In all tested combinations, the less invasive strain was outcompeted by the higher invasive strain. Studying the effect of cell contact on in vitro virulence competition revealed a complex pattern in which the observed effects depended only partially on cell-contact suggesting that competition occurs at two different levels: i) during co-cultivation prior to infection, which might influence the expression of virulence factors, and ii) during infection, when bacterial cells compete for the host cell. In conclusion, we show that growth of L. monocytogenes can be inhibited by strains of the same species leading potentially to biased recovery during enrichment procedures. Furthermore, the presence of more than one L. monocytogenes strain in food can lead to increased infection rates due to synergistic effects on the virulence potential. PMID:26529510

Strain dependence of perfluorinated polymer optical fiber Bragg grating measured at different wavelengths

NASA Astrophysics Data System (ADS)

Ishikawa, Ryo; Lee, Heeyoung; Lacraz, Amédée; Theodosiou, Antreas; Kalli, Kyriacos; Mizuno, Yosuke; Nakamura, Kentaro

2018-03-01

We measure the strain dependence of multiple Bragg wavelengths (corresponding to different diffraction orders) of a fiber Bragg grating (FBG) inscribed in a perfluorinated graded-index polymer optical fiber (PFGI-POF) in the wavelength range up to 1550 nm. On the basis of this result, we show that the fractional sensitivity, which has been conventionally used as a wavelength-independent index for fair comparison of the FBG performance measured at different wavelengths, is dependent on wavelength in this range. The reason for this behavior seems to originate from the non-negligible wavelength dependence of refractive index and its strain-dependence coefficient. Using the wavelength dependence of the refractive index already reported for bulk, we deduce the wavelength dependence of the strain coefficient of the refractive index. This information will be a useful archive in implementing PFGI-POF-based strain sensors based on not only FBGs but also Brillouin scattering in the future.

Predicting employees' well-being using work-family conflict and job strain models.

PubMed

Karimi, Leila; Karimi, Hamidreza; Nouri, Aboulghassem

2011-04-01

The present study examined the effects of two models of work–family conflict (WFC) and job-strain on the job-related and context-free well-being of employees. The participants of the study consisted of Iranian employees from a variety of organizations. The effects of three dimensions of the job-strain model and six forms of WFC on affective well-being were assessed. The results of hierarchical multiple regression analysis revealed that the number of working hours, strain-based work interfering with family life (WIF) along with job characteristic variables (i.e. supervisory support, job demands and job control) all make a significant contribution to the prediction of job-related well-being. On the other hand, strain-based WIF and family interfering with work (FIW) significantly predicted context-free well-being. Implications are drawn and recommendations made regarding future research and interventions in the workplace.

Effect of polysaccharide admixtures on expression of multiple polysaccharide-degrading enzymes in Microbulbifer strain CMC-5.

PubMed

Jonnadula, RaviChand; Imran, Md; Poduval, Preethi B; Ghadi, Sanjeev C

2018-03-01

Microbulbifer strain CMC-5 produces agarase, alginate lyase, xylanase, carboxymethyl cellulase and carrageenase. The extracellular production of the above carbohydrases was investigated by growing Microbulbifer strain CMC-5 in a sea water based medium containing homologous/heterologous polysaccharides as a single substrate or as a combination of mixed assorted substrate. Presence of singular homologous polysaccharides in the growth medium induces respective carbohydrase at high levels. Any two polysaccharides in various combinations produced high level of homologous carbohydrase and low level of other heterologous carbohydrase. All five carbohydrases were consistently produced by strain CMC-5, when carboxymethyl cellulose was included as one of the substrate in dual substrate combination, or in presence of mix blends of all five polysaccharides. Interestingly, thalli of Gracilaria sp. that contain agar and cellulose predominantly in their cell wall induces only agarase expression in strain CMC-5.

A method of batch-purifying microalgae with multiple antibiotics at extremely high concentrations

NASA Astrophysics Data System (ADS)

Han, Jichang; Wang, Song; Zhang, Lin; Yang, Guanpin; Zhao, Lu; Pan, Kehou

2016-01-01

Axenic microalgal strains are highly valued in diverse microalgal studies and applications. Antibiotics, alone or in combination, are often used to avoid bacterial contamination during microalgal isolation and culture. In our preliminary trials, we found that many microalgae ceased growing in antibiotics at extremely high concentrations but could resume growth quickly when returned to an antibiotics-free liquid medium and formed colonies when spread on a solid medium. We developed a simple and highly efficient method of obtaining axenic microalgal cultures based on this observation. First, microalgal strains of different species or strains were treated with a mixture of ampicillin, gentamycin sulfate, kanamycin, neomycin and streptomycin (each at a concentration of 600 mg/L) for 3 days; they were then transferred to antibiotics-free medium for 5 days; and finally they were spread on solid f/2 media to allow algal colonies to form. With this method, five strains of Nannochloropsis sp. (Eustigmatophyceae), two strains of Cylindrotheca sp. (Bacillariophyceae), two strains of Tetraselmis sp. (Chlorodendrophyceae) and one strain of Amphikrikos sp. (Trebouxiophyceae) were purified successfully. The method shows promise for batch-purifying microalgal cultures.

Resistance to drugs and heavy metals, colicin production, and biochemical characteristics of selected bovine and porcine Escherichia coli strains.

PubMed Central

Harnett, N M; Gyles, C L

1984-01-01

A study was made of resistance to heavy metals and antibiotics, biochemical characteristics, and colicinogeny in selected strains of Escherichia coli of O serogroups 8, 9, 20, 64, 101, and X46. Of 42 strains that were investigated, 26 were porcine enterotoxigenic E. coli (ETEC), 8 were porcine non-enterotoxigenic E. coli (NETEC), and 8 were bovine ETEC. Multiple resistance to antimicrobial agents was common among the strains, and resistance to chloramphenicol and kanamycin was less common than resistance to other drugs, possibly reflecting the lower frequency of use of these agents in pigs and calves. Colicin production was a more common property of porcine ETEC (80.8%) than of porcine NETEC (25%), and all porcine ETEC of O serogroups 101 and 64 were colicinogenic. Equal numbers of bovine ETEC strains were colicinogenic as were non-colicinogenic. Resistance of bovine and porcine strains to sodium arsenate, mercury, and tellerium was 90, 16, and 5%, respectively. There was a close relationship between serogroup and biochemical reactions among the E. coli strains tested. PMID:6391383

Genomic changes in an attenuated genotype I Japanese encephalitis virus and comparison with virulent parental strain.

PubMed

Zhou, Yuyong; Wu, Rui; Feng, Yao; Zhao, Qin; Wen, Xintian; Huang, Xiaobo; Wen, Yiping; Yan, Qigui; Huang, Yong; Ma, Xiaoping; Han, Xinfeng; Cao, Sanjie

2018-06-01

Genotype I Japanese encephalitis virus (JEV) strain SCYA201201 was previously isolated from brain tissues of aborted piglets. In this study, we obtained an attenuated SCYA201201-0901 strain by serial passage of strain SCYA201201-1 in Syrian baby hamster kidney cells, combined with multiple plaque purifications and selection for virulence in mice. We investigated the genetic changes associated with attenuation by comparing the entire genomes of SCYA201201-0901 and SCYA201201-1. Sequence comparisons identified 14 common amino acid substitutions in the coding region, with two nucleotide point mutations in the 5'-untranslated region (UTR) and another three in the 3'-UTR, which differed between the attenuated and virulent strains. In addition, a total of 13 silent nucleotide mutations were found after attenuation. These substitutions, alone or in combination, may be responsible for the attenuated phenotype of the SCYA201201-0901 strain in mice. This information will contribute to our understanding of attenuation and of the molecular basis of virulence in genotype I strains such as SCYA201201-0901, as well as aiding the development of safer JEV vaccines.

Review of current methods for characterizing virulence and pathogenicity potential of industrial Saccharomyces cerevisiae strains towards humans.

PubMed

Anoop, Valar; Rotaru, Sever; Shwed, Philip S; Tayabali, Azam F; Arvanitakis, George

2015-09-01

Most industrial Saccharomyces cerevisiae strains used in food or biotechnology processes are benign. However, reports of S. cerevisiae infections have emerged and novel strains continue to be developed. In order to develop recommendations for the human health risk assessment of S. cerevisiae strains, we conducted a literature review of current methods used to characterize their pathogenic potential and evaluated their relevance towards risk assessment. These studies revealed that expression of virulence traits in S. cerevisiae is complex and depends on many factors. Given the opportunistic nature of this organism, an approach using multiple lines of evidence is likely necessary for the reasonable prediction of the pathogenic potential of a particular strain. Risk assessment of S. cerevisiae strains would benefit from more research towards the comparison of virulent and non-virulent strains in order to better understand those genotypic and phenotypic traits most likely to be associated with pathogenicity. © Her Majesty the Queen in Right of Canada 2015. Reproduced with the permission of the Minister of Health.

Applications of Ko Displacement Theory to the Deformed Shape Predictions of the Doubly-Tapered Ikhana Wing

NASA Technical Reports Server (NTRS)

Ko, William L.; Richards, W. Lance; Fleischer, Van Tran

2009-01-01

The Ko displacement theory, formulated for weak nonuniform (slowly changing cross sections) cantilever beams, was applied to the deformed shape analysis of the doubly-tapered wings of the Ikhana unmanned aircraft. The two-line strain-sensing system (along the wingspan) was used for sensing the bending strains needed for the wing-deformed shapes (deflections and cross-sectional twist) analysis. The deflection equation for each strain-sensing line was expressed in terms of the bending strains evaluated at multiple numbers of strain-sensing stations equally spaced along the strain-sensing line. For the preflight shape analysis of the Ikhana wing, the strain data needed for input to the displacement equations for the shape analysis were obtained from the nodal-stress output of the finite-element analysis. The wing deflections and cross-sectional twist angles calculated from the displacement equations were then compared with those computed from the finite-element computer program. The Ko displacement theory formulated for weak nonlinear cantilever beams was found to be highly accurate in the deformed shape predictions of the doubly-tapered Ikhana wing.

Ectopic Integration of Transforming DNA Is Rare among Neurospora Transformants Selected for Gene Replacement

PubMed Central

Miao, VPW.; Rountree, M. R.; Selker, E. U.

1995-01-01

In a variety of organisms, DNA-mediated transformation experiments commonly produce transformants with multiple copies of the transforming DNA, including both selected and unselected molecules. Such ``cotransformants'' are much more common than expected from the individual transformation frequencies, suggesting that subpopulations of cells, or nuclei, are particularly competent for transformation. We found that Neurospora crassa transformants selected for gene replacement at the am gene had not efficiently incorporated additional DNA, suggesting that nuclei that undergo transformation by homologous recombination are not highly competent at integration of DNA by illegitimate recombination. Spheroplasts were treated with DNA fragments homologous to am and with an Escherichia coli hph plasmid. Transformants were initially selected for hph (hygromycin(R)), allowed to conidiate to generate homokaryons and then selected for either Am(-) (gene replacements) or hph. Surprisingly, most am replacement strains were hygromycin(S) (124/140) and carried no extraneous DNA (116/140). Most transformants selected for hph also had ectopic copies of am DNA and/or multiple copies of hph sequences (32/35), generally at multiple sites, confirming that efficient cotransformation could occur. To test the implication that cotransformation involving gene replacement and ectopic integration is rare, we compared the yields of am replacement strains with or without prior selection for hph. The initial selection did not appreciably help (or hinder) recovery of strains with replacements. PMID:7789758

Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries.

PubMed

Ruppé, Etienne; Barbier, François; Mesli, Yasmine; Maiga, Aminata; Cojocaru, Radu; Benkhalfat, Mokhtar; Benchouk, Samia; Hassaine, Hafida; Maiga, Ibrahim; Diallo, Amadou; Koumaré, Abdel Karim; Ouattara, Kalilou; Soumaré, Sambou; Dufourcq, Jean-Baptiste; Nareth, Chhor; Sarthou, Jean-Louis; Andremont, Antoine; Ruimy, Raymond

2009-02-01

In staphylococci, methicillin (meticillin) resistance (MR) is mediated by the acquisition of the mecA gene, which is carried on the size and composition variable staphylococcal cassette chromosome mec (SCCmec). MR has been extensively studied in Staphylococcus aureus, but little is known about MR coagulase-negative staphylococci (MR-CoNS). Here, we describe the diversity of SCCmec structures in MR-CoNS from outpatients living in countries with contrasting environments: Algeria, Mali, Moldova, and Cambodia. Their MR-CoNS nasal carriage rates were 29, 17, 11, and 31%, respectively. Ninety-six MR-CoNS strains, comprising 75 (78%) Staphylococcus epidermidis strains, 19 (20%) Staphylococcus haemolyticus strains, 1 (1%) Staphylococcus hominis strain, and 1 (1%) Staphylococcus cohnii strain, were analyzed. Eighteen different SCCmec types were observed, with 28 identified as type IV (29%), 25 as type V (26%), and 1 as type III (1%). Fifteen strains (44%) were untypeable for their SCCmec. Thirty-four percent of MR-CoNS strains contained multiple ccr copies. Type IV and V SCCmec were preferentially associated with S. epidermidis and S. haemolyticus, respectively. MR-CoNS constitute a widespread and highly diversified MR reservoir in the community.

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

PubMed Central

Borneman, Anthony R.; Forgan, Angus H.; Kolouchova, Radka; Fraser, James A.; Schmidt, Simon A.

2016-01-01

Humans have been consuming wines for more than 7000 yr . For most of this time, fermentations were presumably performed by strains of Saccharomyces cerevisiae that naturally found their way into the fermenting must . In contrast, most commercial wines are now produced by inoculation with pure yeast monocultures, ensuring consistent, reliable and reproducible fermentations, and there are now hundreds of these yeast starter cultures commercially available. In order to thoroughly investigate the genetic diversity that has been captured by over 50 yr of commercial wine yeast development and domestication, whole genome sequencing has been performed on 212 strains of S. cerevisiae, including 119 commercial wine and brewing starter strains, and wine isolates from across seven decades. Comparative genomic analysis indicates that, despite their large numbers, commercial strains, and wine strains in general, are extremely similar genetically, possessing all of the hallmarks of a population bottle-neck, and high levels of inbreeding. In addition, many commercial strains from multiple suppliers are nearly genetically identical, suggesting that the limits of effective genetic variation within this genetically narrow group may be approaching saturation. PMID:26869621

Ductility of Advanced High-Strength Steel in the Presence of a Sheared Edge

NASA Astrophysics Data System (ADS)

Ruggles, Tim; Cluff, Stephen; Miles, Michael; Fullwood, David; Daniels, Craig; Avila, Alex; Chen, Ming

2016-07-01

The ductility of dual-phase (DP) 980 and transformation-induced plasticity (TRIP) assisted bainitic ferritic (TBF) 980 steels was studied in the presence of a sheared edge. Specimens were tested in uniaxial tension in a standard test frame as well as in situ in the scanning electron microscope (SEM). Incremental tensile straining was done in the SEM with images taken at each strain increment. Then digital image correlation (DIC) was used to compute the effective strain at the level of the individual phases in the microstructure. Shear banding across multiple phases was seen in strained TBF specimens, while the DP specimens exhibited more of a patchwork strain pattern, with high strains concentrated in ferrite and low strains observed in the martensite. Two-point statistics were applied to the strain data from the DIC work and the corresponding microstructure images to evaluate the effect of phase hardness on localization and fracture. It was observed that the DP 980 material had a greater tendency for localization around hard phases compared to the TBF 980. This at least partially explains the greater ductility of the TBF material, especially in specimens where a sheared edge was present.

Proteins involved in difference of sorbitol fermentation rates of the toxigenic and nontoxigenic Vibrio cholerae El Tor strains revealed by comparative proteome analysis

PubMed Central

2009-01-01

Background The nontoxigenic V. cholerae El Tor strains ferment sorbitol faster than the toxigenic strains, hence fast-fermenting and slow-fermenting strains are defined by sorbitol fermentation test. This test has been used for more than 40 years in cholera surveillance and strain analysis in China. Understanding of the mechanisms of sorbitol metabolism of the toxigenic and nontoxigenic strains may help to explore the genome and metabolism divergence in these strains. Here we used comparative proteomic analysis to find the proteins which may be involved in such metabolic difference. Results We found the production of formate and lactic acid in the sorbitol fermentation medium of the nontoxigenic strain was earlier than of the toxigenic strain. We compared the protein expression profiles of the toxigenic strain N16961 and nontoxigenic strain JS32 cultured in sorbitol fermentation medium, by using fructose fermentation medium as the control. Seventy-three differential protein spots were found and further identified by MALDI-MS. The difference of product of fructose-specific IIA/FPR component gene and mannitol-1-P dehydrogenase, may be involved in the difference of sorbitol transportation and dehydrogenation in the sorbitol fast- and slow-fermenting strains. The difference of the relative transcription levels of pyruvate formate-lyase to pyruvate dehydrogenase between the toxigenic and nontoxigenic strains may be also responsible for the time and ability difference of formate production between these strains. Conclusion Multiple factors involved in different metabolism steps may affect the sorbitol fermentation in the toxigenic and nontoxigenic strains of V. cholerae El Tor. PMID:19589152

Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives

NASA Astrophysics Data System (ADS)

War, Javeed Ahmad; Srivastava, Santosh Kumar; Srivastava, Savitri Devi

2017-02-01

The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues.

Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives.

PubMed

War, Javeed Ahmad; Srivastava, Santosh Kumar; Srivastava, Savitri Devi

2017-02-15

The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues. Copyright © 2016 Elsevier B.V. All rights reserved.

FIV diversity: FIV Ple subtype composition may influence disease outcome in African lions.

PubMed

Troyer, Jennifer L; Roelke, Melody E; Jespersen, Jillian M; Baggett, Natalie; Buckley-Beason, Valerie; MacNulty, Dan; Craft, Meggan; Packer, Craig; Pecon-Slattery, Jill; O'Brien, Stephen J

2011-10-15

Feline immunodeficiency virus (FIV) infects domestic cats and at least 20 additional species of non-domestic felids throughout the world. Strains specific to domestic cat (FIV(Fca)) produce AIDS-like disease progression, sequelae and pathology providing an informative model for HIV infection in humans. Less is known about the immunological and pathological influence of FIV in other felid species although multiple distinct strains of FIV circulate in natural populations. As in HIV-1 and HIV-2, multiple diverse cross-species infections may have occurred. In the Serengeti National Park, Tanzania, three divergent subtypes of lion FIV (FIV(Ple)) are endemic, whereby 100% of adult lions are infected with one or more of these strains. Herein, the relative distribution of these subtypes in the population are surveyed and, combined with observed differences in lion mortality due to secondary infections based on FIV(Ple) subtypes, the data suggest that FIV(Ple) subtypes may have different patterns of pathogenicity and transmissibility among wild lion populations. Copyright © 2011 Elsevier B.V. All rights reserved.

The Part-Time Student Role: Implications for the Emotional Experience of Managing Multiple Roles amongst Hong Kong Public Health Nurses.

ERIC Educational Resources Information Center

Shiu, Ann Tak-Ying

1999-01-01

Nine public-health nurses studying part time and 11 other nurses sampled their mood states randomly over seven days. The part-time student role created additional strain for nurses with children. The stress of managing multiple roles was greatest when both work and nonwork role responsibilities were heavy. (SK)

Geographic isolates of Lymantria dispar multiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains

Treesearch

Harrison Robert L.; Daniel L. Rowley; Melody A. Keena

2016-01-01

Isolates of the baculovirus species Lymantria dispar multiple nucleopolyhedrovirus have been formulated and applied to suppress outbreaks of the gypsy moth, L. dispar. To evaluate the genetic diversity in this species at the genomic level, the genomes of three isolates from Massachusetts, USA (LdMNPV-Aba624), Spain (LdMNPV-3054...

Delayed efficacy of Beauveria bassiana foliar spray applications against Colorado potato beetle: impacts of number and timing of applications on larval and next-generation adult populations

USDA-ARS?s Scientific Manuscript database

Spray programs comprising multiple or single foliar applications of the fungal pathogen Beauveria bassiana strain GHA (Bb) made during morning (AM) vs. evening (PM) hours were tested against Colorado potato beetle Leptinotarsa decemlineata (CPB) in small research plots of potatoes over multiple fiel...

A simple cage-autonomous method for the maintenance of the barrier status of germ-free mice during experimentation.

PubMed

Hecht, G; Bar-Nathan, C; Milite, G; Alon, I; Moshe, Y; Greenfeld, L; Dotsenko, N; Suez, J; Levy, M; Thaiss, C A; Dafni, H; Elinav, E; Harmelin, A

2014-10-01

The use of germ-free (GF) isolators for microbiome-related research is exponentially increasing, yet limited by its cost, isolator size and potential for trans-contamination. As such, current isolator technology is highly limiting to researchers engaged in short period experiments involving multiple mouse strains and employing a variety of mono-inoculated microorganisms. In this study, we evaluate the use of positive pressure Isocages as a solution for short period studies (days to 2-3 weeks) of experimentation with GF mice at multiple simultaneous conditions. We demonstrate that this new Isocage technology is cost-effective and room-sparing, and enables maintenance of multiple simultaneous groups of GF mice. Using this technology, transferring GF mice from isolators to Isocage racks for experimentation, where they are kept under fully germ-free conditions, enables parallel inoculation with different bacterial strains and simultaneous experimentation with multiple research conditions. Altogether, the new GF Isocage technology enables the expansion of GF capabilities in a safe and cost-effective manner that can facilitate the growth, elaboration and flexibility of microbiome research. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Multiple-Locus Variable-Number Tandem-Repeats Analysis of Escherichia coli O157 using PCR multiplexing and multi-colored capillary electrophoresis.

PubMed

Lindstedt, Bjørn-Arne; Vardund, Traute; Kapperud, Georg

2004-08-01

The Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA) method is currently being used as the primary typing tool for Shiga-toxin-producing Escherichia coli (STEC) O157 isolates in our laboratory. The initial assay was performed using a single fluorescent dye and the different patterns were assigned using a gel image. Here, we present a significantly improved assay using multiple dye colors and enhanced PCR multiplexing to increase speed, and ease the interpretation of the results. The different MLVA patterns are now based on allele sizes entered as character values, thus removing the uncertainties introduced when analyzing band patterns from the gel image. We additionally propose an easy numbering scheme for the identification of separate isolates that will facilitate exchange of typing data. Seventy-two human and animal strains of Shiga-toxin-producing E. coli O157 were used for the development of the improved MLVA assay. The method is based on capillary separation of multiplexed PCR products of VNTR loci in the E. coli O157 genome labeled with multiple fluorescent dyes. The different alleles at each locus were then assigned to allele numbers, which were used for strain comparison.

Tradespace Assessment: Thermal Strain Modeling Comparison Of Multiple Clothing Configurations Based On Different Environmental Conditions

DTIC Science & Technology

2017-02-01

risks, by modeling thermal strain. Twenty clothing ensembles were tested for thermal and evaporative resistances according to American Society of...e.g., football, hockey, etc.) or during military, law enforcement, or first responder operations (e.g., body armor, flame resistant clothing, etc...Each clothing configuration was tested to American Society of Testing and Materials (ASTM) standards for “dry” thermal resistance (Rct) (ASTM F1291

Genome Sequences for Multiple Clavibacter Strains from Different Subspecies

PubMed Central

Yuan, Xiaoli (Kat)

2017-01-01

ABSTRACT The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a variety of agricultural crops, such as potato, tomato, corn, barley, etc. Here, we report five new genome sequences, those of strains CFIA-Cs3N, CFIA-CsR14, LMG 3663T, LMG 7333T, and ATCC 33566T, from different subspecies of Clavibacter michiganensis. All these genomic data will be used for reclassification and niche-adapted feature comparisons. PMID:28935724

Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.

PubMed

Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G; Madamwar, Datta

2015-06-11

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. Copyright © 2015 Shah et al.

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan

PubMed Central

Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan. PMID:27907105

Epidemiology of Brucellosis and Genetic Diversity of Brucella abortus in Kazakhstan.

PubMed

Shevtsova, Elena; Shevtsov, Alexandr; Mukanov, Kasim; Filipenko, Maxim; Kamalova, Dinara; Sytnik, Igor; Syzdykov, Marat; Kuznetsov, Andrey; Akhmetova, Assel; Zharova, Mira; Karibaev, Talgat; Tarlykov, Pavel; Ramanculov, Erlan

2016-01-01

Brucellosis is a major zoonotic infection in Kazakhstan. However, there is limited data on its incidence in humans and animals, and the genetic diversity of prevalent strains is virtually unstudied. Additionally, there is no detailed overview of Kazakhstan brucellosis control and eradication programs. Here, we analyzed brucellosis epidemiological data, and assessed the effectiveness of eradication strategies employed over the past 70 years to counteract this infection. We also conducted multiple loci variable-number tandem repeat analysis (MLVA) of Brucella abortus strains found in Kazakhstan. We analyzed official data on the incidence of animal brucellosis in Kazakhstan. The records span more than 70 years of anti-brucellosis campaigns, and contain a brief description of the applied control strategies, their effectiveness, and their impact on the incidence in humans. The MLVA-16 method was used to type 94 strains of B. abortus and serial passages of B. abortus 82, a strain used in vaccines. MLVA-8 and MLVA-11 analyses clustered strains into a total of four and seven genotypes, respectively; it is the first time that four of these genotypes have been described. MLVA-16 analysis divided strains into 28 distinct genotypes having genetic similarity coefficient that varies from 60 to100% and a Hunter & Gaston diversity index of 0.871. MST analysis reconstruction revealed clustering into "Kazakhstani-Chinese (Central Asian)", "European" and "American" lines. Detection of multiple genotypes in a single outbreak confirms that poorly controlled trade of livestock plays a crucial role in the spread of infection. Notably, the MLVA-16 profile of the B. abortus 82 strain was unique and did not change during 33 serial passages. MLVA genotyping may thus be useful for epidemiological monitoring of brucellosis, and for tracking the source(s) of infection. We suggest that countrywide application of MLVA genotyping would improve the control of brucellosis in Kazakhstan.

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening

PubMed Central

Earls, Megan R.; Kinnevey, Peter M.; Brennan, Gráinne I.; Lazaris, Alexandros; Skally, Mairead; O’Connell, Brian; Humphreys, Hilary; Shore, Anna C.

2017-01-01

Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010–2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1) (n = 46), 16 other hospitals (n = 28), four other healthcare facilities (n = 4) and community-associated sources (n = 11). Isolates underwent antimicrobial susceptibility testing, DNA microarray profiling and whole-genome sequencing. Minimum spanning trees were generated following core-genome multilocus sequence typing and pairwise single nucleotide variation (SNV) analysis was performed. All isolates were sequence type 1 MRSA staphylococcal cassette chromosome mec type IV (ST1-MRSA-IV) and 76/89 were multidrug-resistant. Fifty isolates, including 40/46 from H1, were high-level mupirocin-resistant, carrying a conjugative 39 kb iles2-encoding plasmid. Two closely related ST1-MRSA-IV strains (I and II) and multiple sporadic strains were identified. Strain I isolates (57/89), including 43/46 H1 and all high-level mupirocin-resistant isolates, exhibited ≤80 SNVs. Two strain I isolates from separate H1 healthcare workers differed from other H1/strain I isolates by 7–47 and 12–53 SNVs, respectively, indicating healthcare worker involvement in this outbreak. Strain II isolates (19/89), including the remaining H1 isolates, exhibited ≤127 SNVs. For each strain, the pairwise SNVs exhibited by healthcare-associated and community-associated isolates indicated recent transmission of ST1-MRSA-IV within and between multiple hospitals, healthcare facilities and communities in Ireland. Given the interchange between healthcare-associated and community-associated isolates in hospitals, the risk factors that inform screening for MRSA require revision. PMID:28399151

Exploring grape marc as trove for new thermotolerant and inhibitor-tolerant Saccharomyces cerevisiae strains for second-generation bioethanol production

PubMed Central

2013-01-01

Background Robust yeasts with high inhibitor, temperature, and osmotic tolerance remain a crucial requirement for the sustainable production of lignocellulosic bioethanol. These stress factors are known to severely hinder culture growth and fermentation performance. Results Grape marc was selected as an extreme environment to search for innately robust yeasts because of its limited nutrients, exposure to solar radiation, temperature fluctuations, weak acid and ethanol content. Forty newly isolated Saccharomyces cerevisiae strains gave high ethanol yields at 40°C when inoculated in minimal media at high sugar concentrations of up to 200 g/l glucose. In addition, the isolates displayed distinct inhibitor tolerance in defined broth supplemented with increasing levels of single inhibitors or with a cocktail containing several inhibitory compounds. Both the fermentation ability and inhibitor resistance of these strains were greater than those of established industrial and commercial S. cerevisiae yeasts used as control strains in this study. Liquor from steam-pretreated sugarcane bagasse was used as a key selective condition during the isolation of robust yeasts for industrial ethanol production, thus simulating the industrial environment. The isolate Fm17 produced the highest ethanol concentration (43.4 g/l) from the hydrolysate, despite relatively high concentrations of weak acids, furans, and phenolics. This strain also exhibited a significantly greater conversion rate of inhibitory furaldehydes compared with the reference strain S. cerevisiae 27P. To our knowledge, this is the first report describing a strain of S. cerevisiae able to produce an ethanol yield equal to 89% of theoretical maximum yield in the presence of high concentrations of inhibitors from sugarcane bagasse. Conclusions This study showed that yeasts with high tolerance to multiple stress factors can be obtained from unconventional ecological niches. Grape marc appeared to be an unexplored and promising substrate for the isolation of S. cerevisiae strains showing enhanced inhibitor, temperature, and osmotic tolerance compared with established industrial strains. This integrated approach of selecting multiple resistant yeasts from a single source demonstrates the potential of obtaining yeasts that are able to withstand a number of fermentation-related stresses. The yeast strains isolated and selected in this study represent strong candidates for bioethanol production from lignocellulosic hydrolysates. PMID:24286305

Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems.

PubMed

Statzell-Tallman, Adele; Scorzetti, Gloria; Fell, Jack W

2010-08-01

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

Association between specific plasmids and relapse in typhoid fever.

PubMed Central

Gotuzzo, E; Morris, J G; Benavente, L; Wood, P K; Levine, O; Black, R E; Levine, M M

1987-01-01

We studied isolates from 73 patients hospitalized with typhoid fever in Lima, Peru. Of these 73 patients, 11 (15%) suffered a clinical relapse, with fever and positive blood cultures, within 3 months of their original illness. Using plasmids as epidemiologic markers, we found that three patients who subsequently relapsed were initially infected with more than one strain of Salmonella typhi. There was a highly significant association between relapse and isolation of a strain containing either a 24- or a 38-kilobase plasmid at the time of the original infection; however, we were unable to show any evidence of homology between these two plasmids. Our data indicate that infection with multiple strains is not uncommon in this endemic area and suggest that relapse may be partly strain dependent. Images PMID:2821064

Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

PubMed

Fomukong, N G; Tang, T H; al-Maamary, S; Ibrahim, W A; Ramayah, S; Yates, M; Zainuddin, Z F; Dale, J W

1994-12-01

DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

Strain-compensated (Ga,In)N/(Al,Ga)N/GaN multiple quantum wells for improved yellow/amber light emission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lekhal, K.; Damilano, B., E-mail: bd@crhea.cnrs.fr; De Mierry, P.

2015-04-06

Yellow/amber (570–600 nm) emitting In{sub x}Ga{sub 1−x}N/Al{sub y}Ga{sub 1−y}N/GaN multiple quantum wells (QWs) have been grown by metal organic chemical vapor deposition on GaN-on- sapphire templates. When the (Al,Ga)N thickness of the barrier increases, the room temperature photoluminescence is red-shifted while its yield increases. This is attributed to an increase of the QW internal electric field and an improvement of the material quality due to the compensation of the compressive strain of the In{sub x}Ga{sub 1−x}N QWs by the Al{sub y}Ga{sub 1−y}N layers, respectively.

In Search of Multi-Peaked Reflective Spectrum with Optic Fiber Bragg Grating Sensor for Dynamic Strain Measurement

NASA Technical Reports Server (NTRS)

Tai, Hsiang

2006-01-01

In a typical optic fiber Bragg grating (FBG) strain measurement, unless in an ideal static laboratory environment, the presence of vibration or often disturbance always exists, which often creates spurious multiple peaks in the reflected spectrum, resulting in a non-unique determination of strain value. In this report we attempt to investigate the origin of this phenomenon by physical arguments and simple numerical simulation. We postulate that the fiber gratings execute small amplitude transverse vibrations changing the optical path in which the reflected light traverses slightly and non-uniformly. Ultimately, this causes the multi-peak reflected spectrum.

Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control

PubMed Central

van Helden, Paul D.; Wilson, Douglas; Colijn, Caroline; McLaughlin, Megan M.; Abubakar, Ibrahim; Warren, Robin M.

2012-01-01

Summary: Numerous studies have reported that individuals can simultaneously harbor multiple distinct strains of Mycobacterium tuberculosis. To date, there has been limited discussion of the consequences for the individual or the epidemiological importance of mixed infections. Here, we review studies that documented mixed infections, highlight challenges associated with the detection of mixed infections, and discuss possible implications of mixed infections for the diagnosis and treatment of patients and for the community impact of tuberculosis control strategies. We conclude by highlighting questions that should be resolved in order to improve our understanding of the importance of mixed-strain M. tuberculosis infections. PMID:23034327

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.

PubMed

Gangaiah, Dharanesh; Spinola, Stanley M

2016-12-01

Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities.

Comparisons of Internal Behavior after Exposure to Flavobacterium psychrophilum between Two Ayu (Plecoglossus altivelis altivelis) Strains Showing Different Cumulative Mortality to Bacterial Cold Water Disease

PubMed Central

KAGEYAMA, Tetsushi; KUWADA, Tomonori; OHARA, Kenichi; NOUNO, Aya; UMINO, Tetsuya; FURUSAWA, Shuichi

2013-01-01

ABSTRACT Bacterial cold water disease (BCWD) in ayu (Plecoglossus altivelis altivelis) has a serious impact on aquaculture and fisheries. There is known to be a significant difference among ayu strains with regard to mortality caused by BCWD. In this study, the immune response of different ayu strains against Flavobacterium psychrophilum infection was observed. One strain was resistant to infection by F. psychrophilum, and the other was susceptible to infection by the same bacteria. The number of bacteria in the body was observed in each ayu strain, and the change in bacterial counts was similar. However, there was a significant difference in bacterial count in the spleen between the two strains on days 6, 9, 12 and 15 after exposure. To observe the immune response against F. psychrophilum, agglutination assay using serum was performed. An agglutination reaction in the resistant ayu strain was observed in 4 out of 6 ayu on day 6 after exposure, while no reactions in the susceptible ayu strain were observed in any sampled fish until day 12. However, some reactions in the susceptible ayu strain were observed in surviving ayu. These results indicate that there is a correlation between the presence of bacterial multiplication and agglutination reaction against F. psychrophilum. PMID:23902927

Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.

PubMed

Garcia-Hermoso, Dea; Criscuolo, Alexis; Lee, Soo Chan; Legrand, Matthieu; Chaouat, Marc; Denis, Blandine; Lafaurie, Matthieu; Rouveau, Martine; Soler, Charles; Schaal, Jean-Vivien; Mimoun, Maurice; Mebazaa, Alexandre; Heitman, Joseph; Dromer, Françoise; Brisse, Sylvain; Bretagne, Stéphane; Alanio, Alexandre

2018-04-24

Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015). A total of 21 isolates, including 14 isolates from six BU1 patients, were analyzed by whole-genome sequencing (WGS). Phylogenetic classification based on de novo assembly and assembly free approaches showed that the clinical isolates clustered in four highly divergent clades. Clade 1 contained at least one of the strains from the six epidemiologically linked BU1 patients. The clinical isolates were specific to each patient. Two patients were infected with more than two strains from different clades, suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients from BU1 shared one strain, which could correspond to direct transmission or contamination with the same environmental source. In conclusion, WGS of several isolates per patients coupled with precise epidemiological data revealed a complex situation combining potential cross-transmission between patients and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir. IMPORTANCE Invasive wound mucormycosis (IWM) is a severe infection due to environmental molds belonging to the order Mucorales. Severely burned patients are particularly at risk for IWM. Here, we used whole-genome sequencing (WGS) analysis to resolve an outbreak of IWM due to Mucor circinelloides that occurred in our hospital (BU1). We sequenced 21 clinical isolates, including 14 from BU1 and 7 unrelated isolates, and compared them to the reference genome (1006PhL). This analysis revealed that the outbreak was mainly due to multiple strains that seemed patient specific, suggesting that the patients were more likely infected from a pool of diverse strains from the environment rather than from direct transmission among them. This study revealed the complexity of a Mucorales outbreak in the settings of IWM in burn patients, which has been highlighted based on WGS combined with careful sampling. Copyright © 2018 Garcia-Hermoso et al.

Whole genome analysis of an MDR Beijing/W strain of Mycobacterium tuberculosis with large genomic deletions associated with resistance to isoniazid.

PubMed

Zhang, Qiufen; Wan, Baoshan; Zhou, Aiping; Ni, Jinjing; Xu, Zhihong; Li, Shuxian; Tao, Jing; Yao, YuFeng

2016-05-15

Mycobacterium tuberculosis (M.tb) is one of the most prevalent bacterial pathogens in the world. With geographical wide spread and hypervirulence, Beijing/W family is the most successful M.tb lineage. China is a country of high tuberculosis (TB) and high multiple drug-resistant TB (MDR-TB) burden, and the Beijing/W family strains take the largest share of MDR strains. To study the genetic basis of Beijing/W family strains' virulence and drug resistance, we performed the whole genome sequencing of M.tb strain W146, a clinical Beijing/W genotype MDR isolated from Wuxi, Jiangsu province, China. Compared with genome sequence of M.tb strain H37Rv, we found that strain W146 lacks three large fragments and the missing of furA-katG operon confers isoniazid resistance. Besides the missing of furA-katG operon, strain W146 harbored almost all known drug resistance-associated mutations. Comparison analysis of single nucleotide polymorphisms (SNPs) and indels between strain W146 and Beijing/W genotype strains and non-Beijing/W genotype strains revealed that strain W146 possessed some unique mutations, which may be related to drug resistance, transmission and pathogenicity. These findings will help to understand the large sequence polymorphisms (LSPs) and the transmission and drug resistance related genetic characteristics of the Beijing/W genotype of M.tb. Copyright © 2016 Elsevier B.V. All rights reserved.

Non-encapsulated strains reveal novel insights in invasion and survival of Streptococcus suis in epithelial cells.

PubMed

Benga, L; Goethe, R; Rohde, M; Valentin-Weigand, P

2004-09-01

Streptococcus suis is a porcine and human pathogen causing invasive diseases, such as meningitis or septicaemia. Host cell interactions of S. suis have been studied mainly with serotype 2 strains, but multiple capsular serotypes as well as non-typeable strains exist with diverse virulence features. At present, S. suis is considered an extracellular pathogen. However, whether or not it can also invade host cells is a matter of controversial discussions. We have assessed adherence and invasion of S. suis for HEp-2 epithelial cells by comparing 10 serotype 2 strains and four non-typeable (NT) strains. Only the NT strains and a non-encapsulated serotype 2 mutant strain, but none of the serotype 2 strains, adhered strongly and were invasive. Invasion seemed to be affected by environmental signals, as suggested from comparison of strains grown in different media. Further phenotypic and genotypic characterization revealed a high diversity among the different strains. Electron microscopic analysis of invasion of selected invasive NT strains indicated different uptake mechanisms. One strain induced large invaginations comparable to those seen in 'caveolae' mediated uptake, whereas invasion of the other strains was accompanied by formation of filipodia-like membrane protrusions. Invasion of all strains, however, was similarly susceptible to hypertonic sucrose, which inhibits receptor-mediated endocytosis. Irrespective of the uptake pathway, streptococci resided in acidified phago-lysosome like vacuoles. All strains, except one, survived intracellularly as well as extracellular acidic conditions. Survival seemed to be associated with the AdiS protein, an environmentally regulated arginine deiminase of S. suis. Concluding, invasion and survival of NT strains of S. suis in epithelial cells revealed novel evidence that S. suis exhibits a broad variety of virulence-associated features depending on genetic variation and regulation.

Genetic Characterization and Comparison of Clostridium botulinum Isolates from Botulism Cases in Japan between 2006 and 2011

PubMed Central

Sekizuka, Tsuyoshi; Yamamoto, Akihiko; Iwaki, Masaaki; Komiya, Takako; Hatakeyama, Takashi; Nakajima, Hiroshi; Takahashi, Motohide; Kuroda, Makoto; Shibayama, Keigo

2014-01-01

Genetic characterization was performed for 10 group I Clostridium botulinum strains isolated from botulism cases in Japan between 2006 and 2011. Of these, 1 was type A, 2 were type B, and 7 were type A(B) {carrying a silent bont/B [bont/(B)] gene} serotype strains, based on botulinum neurotoxin (BoNT) production. The type A strain harbored the subtype A1 BoNT gene (bont/A1), which is associated with the ha gene cluster. The type B strains carried bont/B5 or bont/B6 subtype genes. The type A(B) strains carried bont/A1 identical to that of type A(B) strain NCTC2916. However, bont/(B) genes in these strains showed single-nucleotide polymorphisms (SNPs) among strains. SNPs at 2 nucleotide positions of bont/(B) enabled classification of the type A(B) strains into 3 groups. Pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem-repeat analysis (MLVA) also provided consistent separation results. In addition, the type A(B) strains were separated into 2 lineages based on their plasmid profiles. One lineage carried a small plasmid (5.9 kb), and another harbored 21-kb plasmids. To obtain more detailed genetic information about the 10 strains, we sequenced their genomes and compared them with 13 group I C. botulinum genomes in a database using whole-genome SNP analysis. This analysis provided high-resolution strain discrimination and enabled us to generate a refined phylogenetic tree that provides effective traceability of botulism cases, as well as bioterrorism materials. In the phylogenetic tree, the subtype B6 strains, Okayama2011 and Osaka05, were distantly separated from the other strains, indicating genomic divergence of subtype B6 strains among group I strains. PMID:25192986

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb

PubMed Central

Kahan, Anat; Ben-Shaul, Yoram

2016-01-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse’s strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female’s receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons. PMID:26938460

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb.

PubMed

Kahan, Anat; Ben-Shaul, Yoram

2016-03-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse's strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female's receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons.

Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing

PubMed Central

2018-01-01

ABSTRACT Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015). A total of 21 isolates, including 14 isolates from six BU1 patients, were analyzed by whole-genome sequencing (WGS). Phylogenetic classification based on de novo assembly and assembly free approaches showed that the clinical isolates clustered in four highly divergent clades. Clade 1 contained at least one of the strains from the six epidemiologically linked BU1 patients. The clinical isolates were specific to each patient. Two patients were infected with more than two strains from different clades, suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients from BU1 shared one strain, which could correspond to direct transmission or contamination with the same environmental source. In conclusion, WGS of several isolates per patients coupled with precise epidemiological data revealed a complex situation combining potential cross-transmission between patients and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir. PMID:29691339

Enterovirus D68 receptor requirements unveiled by haploid genetics

PubMed Central

Baggen, Jim; Thibaut, Hendrik Jan; Staring, Jacqueline; Jae, Lucas T.; Liu, Yue; Guo, Hongbo; Slager, Jasper J.; de Bruin, Jost W.; van Vliet, Arno L. W.; Blomen, Vincent A.; Overduin, Pieter; Sheng, Ju; de Haan, Cornelis A. M.; de Vries, Erik; Meijer, Adam; Rossmann, Michael G.; Brummelkamp, Thijn R.; van Kuppeveld, Frank J. M.

2016-01-01

Enterovirus D68 (EV-D68) is an emerging pathogen that can cause severe respiratory disease and is associated with cases of paralysis, especially among children. Heretofore, information on host factor requirements for EV-D68 infection is scarce. Haploid genetic screening is a powerful tool to reveal factors involved in the entry of pathogens. We performed a genome-wide haploid screen with the EV-D68 prototype Fermon strain to obtain a comprehensive overview of cellular factors supporting EV-D68 infection. We identified and confirmed several genes involved in sialic acid (Sia) biosynthesis, transport, and conjugation to be essential for infection. Moreover, by using knockout cell lines and gene reconstitution, we showed that both α2,6- and α2,3-linked Sia can be used as functional cellular EV-D68 receptors. Importantly, the screen did not reveal a specific protein receptor, suggesting that EV-D68 can use multiple redundant sialylated receptors. Upon testing recent clinical strains, we identified strains that showed a similar Sia dependency, whereas others could infect cells lacking surface Sia, indicating they can use an alternative, nonsialylated receptor. Nevertheless, these Sia-independent strains were still able to bind Sia on human erythrocytes, raising the possibility that these viruses can use multiple receptors. Sequence comparison of Sia-dependent and Sia-independent EV-D68 strains showed that many changes occurred near the canyon that might allow alternative receptor binding. Collectively, our findings provide insights into the identity of the EV-D68 receptor and suggest the possible existence of Sia-independent viruses, which are essential for understanding tropism and disease. PMID:26787879

A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis.

PubMed

Namouchi, Amine; Mardassi, Helmi

2006-11-01

Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.

The Phage Lysin PlySs2 Decolonizes Streptococcus suis from Murine Intranasal Mucosa.

PubMed

Gilmer, Daniel B; Schmitz, Jonathan E; Thandar, Mya; Euler, Chad W; Fischetti, Vincent A

2017-01-01

Streptococcus suis infects pigs worldwide and may be zoonotically transmitted to humans with a mortality rate of up to 20%. S. suis has been shown to develop in vitro resistance to the two leading drugs of choice, penicillin and gentamicin. Because of this, we have pursued an alternative therapy to treat these pathogens using bacteriophage lysins. The bacteriophage lysin PlySs2 is derived from an S. suis phage and displays potent lytic activity against most strains of that species including serotypes 2 and 9. At 64 μg/ml, PlySs2 reduced multiple serotypes of S. suis by 5 to 6-logs within 1 hour in vitro and exhibited a minimum inhibitory concentration (MIC) of 32 μg/ml for a S. suis serotype 2 strain and 64 μg/ml for a serotype 9 strain. Using a single 0.1-mg dose, the colonizing S. suis serotype 9 strain was reduced from the murine intranasal mucosa by >4 logs; a 0.1-mg dose of gentamicin reduced S. suis by <3-logs. A combination of 0.05 mg PlySs2 + 0.05 mg gentamicin reduced S. suis by >5-logs. While resistance to gentamicin was induced after systematically increasing levels of gentamicin in an S. suis culture, the same protocol resulted in no observable resistance to PlySs2. Thus, PlySs2 has both broad and high killing activity against multiple serotypes and strains of S. suis, making it a possible tool in the control and prevention of S. suis infections in pigs and humans.

The Phage Lysin PlySs2 Decolonizes Streptococcus suis from Murine Intranasal Mucosa

PubMed Central

Gilmer, Daniel B.; Schmitz, Jonathan E.; Thandar, Mya; Euler, Chad W.; Fischetti, Vincent A.

2017-01-01

Streptococcus suis infects pigs worldwide and may be zoonotically transmitted to humans with a mortality rate of up to 20%. S. suis has been shown to develop in vitro resistance to the two leading drugs of choice, penicillin and gentamicin. Because of this, we have pursued an alternative therapy to treat these pathogens using bacteriophage lysins. The bacteriophage lysin PlySs2 is derived from an S. suis phage and displays potent lytic activity against most strains of that species including serotypes 2 and 9. At 64 μg/ml, PlySs2 reduced multiple serotypes of S. suis by 5 to 6-logs within 1 hour in vitro and exhibited a minimum inhibitory concentration (MIC) of 32 μg/ml for a S. suis serotype 2 strain and 64 μg/ml for a serotype 9 strain. Using a single 0.1-mg dose, the colonizing S. suis serotype 9 strain was reduced from the murine intranasal mucosa by >4 logs; a 0.1-mg dose of gentamicin reduced S. suis by <3-logs. A combination of 0.05 mg PlySs2 + 0.05 mg gentamicin reduced S. suis by >5-logs. While resistance to gentamicin was induced after systematically increasing levels of gentamicin in an S. suis culture, the same protocol resulted in no observable resistance to PlySs2. Thus, PlySs2 has both broad and high killing activity against multiple serotypes and strains of S. suis, making it a possible tool in the control and prevention of S. suis infections in pigs and humans. PMID:28046082

Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA).

PubMed

Bergonier, Dominique; Sobral, Daniel; Feßler, Andrea T; Jacquet, Eric; Gilbert, Florence B; Schwarz, Stefan; Treilles, Michaël; Bouloc, Philippe; Pourcel, Christine; Vergnaud, Gilles

2014-10-02

Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes.

Different Antibiotic Resistance and Sporulation Properties within Multiclonal Clostridium difficile PCR Ribotypes 078, 126, and 033 in a Single Calf Farm

PubMed Central

Zidaric, Valerija; Pardon, Bart; dos Vultos, Tiago; Deprez, Piet; Brouwer, Michael Sebastiaan Maria; Roberts, Adam P.; Henriques, Adriano O.

2012-01-01

Clostridium difficile strains were sampled periodically from 50 animals at a single veal calf farm over a period of 6 months. At arrival, 10% of animals were C. difficile positive, and the peak incidence was determined to occur at the age of 18 days (16%). The prevalence then decreased, and at slaughter, C. difficile could not be isolated. Six different PCR ribotypes were detected, and strains within a single PCR ribotype could be differentiated further by pulsed-field gel electrophoresis (PFGE). The PCR ribotype diversity was high up to the animal age of 18 days, but at later sampling points, PCR ribotype 078 and the highly related PCR ribotype 126 predominated. Resistance to tetracycline, doxycycline, and erythromycin was detected, while all strains were susceptible to amoxicillin and metronidazole. Multiple variations of the resistance gene tet(M) were present at the same sampling point, and these changed over time. We have shown that PCR ribotypes often associated with cattle (ribotypes 078, 126, and 033) were not clonal but differed in PFGE type, sporulation properties, antibiotic sensitivities, and tetracycline resistance determinants, suggesting that multiple strains of the same PCR ribotype infected the calves and that calves were likely to be infected prior to arrival at the farm. Importantly, strains isolated at later time points were more likely to be resistant to tetracycline and erythromycin and showed higher early sporulation efficiencies in vitro, suggesting that these two properties converge to promote the persistence of C. difficile in the environment or in hosts. PMID:23001653

Genetic and phenotypic intra-species variation in Candida albicans.

PubMed

Hirakawa, Matthew P; Martinez, Diego A; Sakthikumar, Sharadha; Anderson, Matthew Z; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M; Greenberg, Joshua M; Berman, Judith; Bennett, Richard J; Cuomo, Christina A

2015-03-01

Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity. © 2015 Hirakawa et al.; Published by Cold Spring Harbor Laboratory Press.

Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees

PubMed Central

Tamarit, Daniel; Ellegaard, Kirsten M.; Wikander, Johan; Olofsson, Tobias; Vásquez, Alejandra; Andersson, Siv G.E.

2015-01-01

Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication. The phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria. PMID:25953738

Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing

PubMed Central

2014-01-01

Background Mosquito control programmes using chemical insecticides are increasingly threatened by the development of resistance. Such resistance can be the consequence of changes in proteins targeted by insecticides (target site mediated resistance), increased insecticide biodegradation (metabolic resistance), altered transport, sequestration or other mechanisms. As opposed to target site resistance, other mechanisms are far from being fully understood. Indeed, insecticide selection often affects a large number of genes and various biological processes can hypothetically confer resistance. In this context, the aim of the present study was to use RNA sequencing (RNA-seq) for comparing transcription level and polymorphism variations associated with adaptation to chemical insecticides in the mosquito Aedes aegypti. Biological materials consisted of a parental susceptible strain together with three child strains selected across multiple generations with three insecticides from different classes: the pyrethroid permethrin, the neonicotinoid imidacloprid and the carbamate propoxur. Results After ten generations, insecticide-selected strains showed elevated resistance levels to the insecticides used for selection. RNA-seq data allowed detecting over 13,000 transcripts, of which 413 were differentially transcribed in insecticide-selected strains as compared to the susceptible strain. Among them, a significant enrichment of transcripts encoding cuticle proteins, transporters and enzymes was observed. Polymorphism analysis revealed over 2500 SNPs showing > 50% allele frequency variations in insecticide-selected strains as compared to the susceptible strain, affecting over 1000 transcripts. Comparing gene transcription and polymorphism patterns revealed marked differences among strains. While imidacloprid selection was linked to the over transcription of many genes, permethrin selection was rather linked to polymorphism variations. Focusing on detoxification enzymes revealed that permethrin selection strongly affected the polymorphism of several transcripts encoding cytochrome P450 monooxygenases likely involved in insecticide biodegradation. Conclusions The present study confirmed the power of RNA-seq for identifying concomitantly quantitative and qualitative transcriptome changes associated with insecticide resistance in mosquitoes. Our results suggest that transcriptome modifications can be selected rapidly by insecticides and affect multiple biological functions. Previously neglected by molecular screenings, polymorphism variations of detoxification enzymes may play an important role in the adaptive response of mosquitoes to insecticides. PMID:24593293

Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing.

PubMed

David, Jean-Philippe; Faucon, Frédéric; Chandor-Proust, Alexia; Poupardin, Rodolphe; Riaz, Muhammad Asam; Bonin, Aurélie; Navratil, Vincent; Reynaud, Stéphane

2014-03-05

Mosquito control programmes using chemical insecticides are increasingly threatened by the development of resistance. Such resistance can be the consequence of changes in proteins targeted by insecticides (target site mediated resistance), increased insecticide biodegradation (metabolic resistance), altered transport, sequestration or other mechanisms. As opposed to target site resistance, other mechanisms are far from being fully understood. Indeed, insecticide selection often affects a large number of genes and various biological processes can hypothetically confer resistance. In this context, the aim of the present study was to use RNA sequencing (RNA-seq) for comparing transcription level and polymorphism variations associated with adaptation to chemical insecticides in the mosquito Aedes aegypti. Biological materials consisted of a parental susceptible strain together with three child strains selected across multiple generations with three insecticides from different classes: the pyrethroid permethrin, the neonicotinoid imidacloprid and the carbamate propoxur. After ten generations, insecticide-selected strains showed elevated resistance levels to the insecticides used for selection. RNA-seq data allowed detecting over 13,000 transcripts, of which 413 were differentially transcribed in insecticide-selected strains as compared to the susceptible strain. Among them, a significant enrichment of transcripts encoding cuticle proteins, transporters and enzymes was observed. Polymorphism analysis revealed over 2500 SNPs showing > 50% allele frequency variations in insecticide-selected strains as compared to the susceptible strain, affecting over 1000 transcripts. Comparing gene transcription and polymorphism patterns revealed marked differences among strains. While imidacloprid selection was linked to the over transcription of many genes, permethrin selection was rather linked to polymorphism variations. Focusing on detoxification enzymes revealed that permethrin selection strongly affected the polymorphism of several transcripts encoding cytochrome P450 monooxygenases likely involved in insecticide biodegradation. The present study confirmed the power of RNA-seq for identifying concomitantly quantitative and qualitative transcriptome changes associated with insecticide resistance in mosquitoes. Our results suggest that transcriptome modifications can be selected rapidly by insecticides and affect multiple biological functions. Previously neglected by molecular screenings, polymorphism variations of detoxification enzymes may play an important role in the adaptive response of mosquitoes to insecticides.

Method for Estimating Operational Loads on Aerospace Structures Using Span-Wisely Distributed Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2013-01-01

This report presents a new method for estimating operational loads (bending moments, shear loads, and torques) acting on slender aerospace structures using distributed surface strains (unidirectional strains). The surface strain-sensing stations are to be evenly distributed along each span-wise strain-sensing line. A depth-wise cross section of the structure along each strain-sensing line can then be considered as an imaginary embedded beam. The embedded beam was first evenly divided into multiple small domains with domain junctures matching the strain-sensing stations. The new method is comprised of two steps. The first step is to determine the structure stiffness (bending or torsion) using surface strains obtained from a simple bending (or torsion) loading case, for which the applied bending moment (or torque) is known. The second step is to use the strain-determined structural stiffness (bending or torsion), and a new set of surface strains induced by any other loading case to calculate the associated operational loads (bending moments, shear loads, or torques). Performance of the new method for estimating operational loads was studied in light of finite-element analyses of several example structures subjected to different loading conditions. The new method for estimating operational loads was found to be fairly accurate, and is very promising for applications to the flight load monitoring of flying vehicles with slender wings.

Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity

PubMed Central

Swarnkar, Mohit Kumar; Vyas, Pratibha; Rahi, Praveen; Thakur, Rishu; Thakur, Namika; Singh, Anil Kumar

2015-01-01

The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-3-acetic acid (IAA) production, and stress response. PMID:26337878

Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.

PubMed

Li, Xiang Sean; Yuan, Xiaoli Kat

2017-09-21

The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a variety of agricultural crops, such as potato, tomato, corn, barley, etc. Here, we report five new genome sequences, those of strains CFIA-Cs3N, CFIA-CsR14, LMG 3663 T , LMG 7333 T , and ATCC 33566 T , from different subspecies of Clavibacter michiganensis All these genomic data will be used for reclassification and niche-adapted feature comparisons. © Crown copyright 2017.

Microarray-based Resequencing of Multiple Bacillus anthracis Isolates

DTIC Science & Technology

2004-12-17

generated an Unweighted Pair Group Method Arithmetic Mean ( UPGMA ) tree (see methods [56]; Figure 3). The strains group together in a manner broadly similar...was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [56]. The B1 strain A0465 was used as an...distance matrix was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [57]. Additional data files The

The effect of hydrogenation on strain hardening and deformation mechanisms in <113> single crystals of Hadfield steel

NASA Astrophysics Data System (ADS)

Astafurova, Elena; Maier, Galina; Melnikov, Eugene; Koshovkina, Vera; Moskvina, Valentina; Smirnov, Alexander; Bataev, Vladimir

2015-10-01

The effect of hydrogenation on the strain-hardening behavior and the deformation mechanisms of <113>-oriented single crystals of Hadfield steel was investigated under tension at room temperature. The stages of plastic flow and deformation mechanisms for hydrogen-charged specimens are similar to one in hydrogen-free state: slip → slip + single twinning → slip + multiple twinning. Hydrogen alloying favors to mechanical twinning, micro- and macrolocalization of plastic flow.