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Sample records for engineering clostridium strain

  1. Physiology, Genomics, and Pathway Engineering of an Ethanol-Tolerant Strain of Clostridium phytofermentans.

    PubMed

    Tolonen, Andrew C; Zuroff, Trevor R; Ramya, Mohandass; Boutard, Magali; Cerisy, Tristan; Curtis, Wayne R

    2015-08-15

    Novel processing strategies for hydrolysis and fermentation of lignocellulosic biomass in a single reactor offer large potential cost savings for production of biocommodities and biofuels. One critical challenge is retaining high enzyme production in the presence of elevated product titers. Toward this goal, the cellulolytic, ethanol-producing bacterium Clostridium phytofermentans was adapted to increased ethanol concentrations. The resulting ethanol-tolerant (ET) strain has nearly doubled ethanol tolerance relative to the wild-type level but also reduced ethanol yield and growth at low ethanol concentrations. The genome of the ET strain has coding changes in proteins involved in membrane biosynthesis, the Rnf complex, cation homeostasis, gene regulation, and ethanol production. In particular, purification of the mutant bifunctional acetaldehyde coenzyme A (CoA)/alcohol dehydrogenase showed that a G609D variant abolished its activities, including ethanol formation. Heterologous expression of Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase in the ET strain increased cellulose consumption and restored ethanol production, demonstrating how metabolic engineering can be used to overcome disadvantageous mutations incurred during adaptation to ethanol. We discuss how genetic changes in the ET strain reveal novel potential strategies for improving microbial solvent tolerance.

  2. Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain

    SciTech Connect

    Yee, Kelsey L; Rodriguez Jr, Miguel; Thompson, Olivia A; Fu, Chunxiang; Wang, Zeng-Yu; Davison, Brian H; Mielenz, Jonathan R

    2014-01-01

    Background: Switchgrass is an abundant and dedicated bioenergy feedstock however its inherent recalcitrance is one of the economic hurdles for producing biofuels. The down-regulation of the caffeic acid O-methyl transferase (COMT) gene in the lignin pathway of switchgrass reduced lignin content and S/G ratio, and the transgenic lines showed improved fermentation yield with S. cerevisiae and C. thermocellum (ATCC 27405) in comparison to the wild-type switchgrass. Results: Here we examine the fermentation potential of the COMT transgenic switchgrass and its wild-type line, with an engineered and evolved Clostridium thermocellum (M1570) strain. The fermentation of the transgenic switchgrass had superior conversion relative to the control line with an increase of 20% and ethanol was the primary metabolite accounting for 90% of the total metabolites measured by HPLC. Conclusions: The down-regulation of the COMT gene in switchgrass reduced recalcitrance and improved microbial bioconversion yield. Moreover, these results showed ethanol as the main fermentation metabolite produced by an engineered and evolved C. thermocellum strain grown on a transgenic switchgrass.

  3. Converting Carbon Dioxide to Butyrate with an Engineered Strain of Clostridium ljungdahlii

    SciTech Connect

    Ueki, T; Nevin, KP; Woodard, TL; Lovley, DR

    2014-08-26

    Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H-2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. IMPORTANCE The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors

  4. Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii.

    PubMed

    Ueki, Toshiyuki; Nevin, Kelly P; Woodard, Trevor L; Lovley, Derek R

    2014-10-21

    Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. Importance: The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors

  5. Process engineering and scale-up of autotrophic Clostridium strain P11 syngas fermentation

    NASA Astrophysics Data System (ADS)

    Kundiyana, Dimple Kumar Aiyanna

    Scope and Method of Study. Biomass gasification followed by fermentation of syngas to ethanol is a potential process to produce bioenergy. The process is currently being researched under laboratory- and pilot-scale in an effort to optimize the process conditions and make the process feasible for commercial production of ethanol and other biofuels such as butanol and propanol. The broad research objectives for the research were to improve ethanol yields during syngas fermentation and to design a economical fermentation process. The research included four statistically designed experimental studies in serum bottles, bench-scale and pilot-scale fermentors to screen alternate fermentation media components, to determine the effect of process parameters such as pH, temperature and buffer on syngas fermentation, to determine the effect of key limiting nutrients of the acetyl-CoA pathway in a continuous series reactor design, and to scale-up the syngas fermentation in a 100-L pilot scale fermentor. Findings and Conclusions. The first experimental study identified cotton seed extract (CSE) as a feasible medium for Clostridium strain P11 fermentation. The study showed that CSE at 0.5 g L-1 can potentially replace all the standard Clostridium strain P11 fermentation media components while using a media buffer did not significantly improve the ethanol production when used in fermentation with CSE. Scale-up of the CSE fermentation in 2-L and 5-L stirred tank fermentors showed 25% increase in ethanol yield. The second experimental study showed that syngas fermentation at 32°C without buffer was associated with higher ethanol concentration and reduced lag time in switching to solventogenesis. Conducting fermentation at 40°C or by lowering incubation pH to 5.0 resulted in reduced cell growth and no production of ethanol or acetic acid. The third experiment studied the effect of three limiting nutrients, calcium pantothenate, vitamin B12 and CoCl2 on syngas fermentation. Results

  6. Genomic diversity of Clostridium difficile strains.

    PubMed

    Janezic, Sandra; Rupnik, Maja

    2015-05-01

    Approaches to exploring Clostridium difficile genomic diversity have ranged from molecular typing methods to use of comparative genome microarrays and whole genome sequence comparisons. The C. difficile population structure is clonal and distributed into six clades, which correlate well with MLST STs (multilocus sequence types) and PCR ribotypes. However, toxigenic strains and strains with increased virulence are distributed throughout several clades. Here we summarize studies on C. difficile genomic diversity, with emphasis on phylogenetic aspects, epidemiological aspect and variability of some virulence factors.

  7. Genomic diversity of Clostridium difficile strains.

    PubMed

    Janezic, Sandra; Rupnik, Maja

    2015-05-01

    Approaches to exploring Clostridium difficile genomic diversity have ranged from molecular typing methods to use of comparative genome microarrays and whole genome sequence comparisons. The C. difficile population structure is clonal and distributed into six clades, which correlate well with MLST STs (multilocus sequence types) and PCR ribotypes. However, toxigenic strains and strains with increased virulence are distributed throughout several clades. Here we summarize studies on C. difficile genomic diversity, with emphasis on phylogenetic aspects, epidemiological aspect and variability of some virulence factors. PMID:25700631

  8. Secretome analysis of Clostridium difficile strains.

    PubMed

    Boetzkes, Alexander; Felkel, Katharina Wiebke; Zeiser, Johannes; Jochim, Nelli; Just, Ingo; Pich, Andreas

    2012-08-01

    Clostridium difficile causes infections ranging from mild C. difficile-associated diarrhea to severe pseudomembranous colitis. Since 2003 new hypervirulent C. difficile strains (PCR ribotype 027) emerged characterized by a dramatically increased mortality. The secretomes of the three C. difficile strains CDR20291, CD196, and CD630 were analyzed and compared. Proteins were separated and analyzed by means of SDS--PAGE and LC-MS. MS data were analyzed using Mascot and proteins were checked for export signals with SecretomeP and SignalP. LC-MS analysis revealed 158 different proteins in the supernatant of C. difficile. Most of the identified proteins originate from the cytoplasm. Thirty-two proteins in CDR20291, 36 in CD196 and 26 in CD630 were identified to be secreted by C. difficile strains. Those were mainly S-layer proteins, substrate-binding proteins of ABC-transporters, cell wall hydrolases, pilin and unknown hypothetical proteins. Toxin A and toxin B were identified after growth in brain heart infusion medium using immunological techniques. The ADP-ribosyltransferase-binding component protein, which is a part of the binary toxin CDT, was only identified in the hypervirulent ribotype 027 strains. Further proteins that are secreted specifically by hypervirulent strains were identified. PMID:22398929

  9. Draft Genome Sequences of Clostridium Strains Native to Colombia with the Potential To Produce Solvents

    PubMed Central

    Rosas-Morales, Juan Pablo; Perez-Mancilla, Ximena; López-Kleine, Liliana

    2015-01-01

    Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria, isolated from crop soil in Colombia, with a strong potential to produce alcohols like 1,3-propanediol, were analyzed. We present the draft genome of these strains, which will be useful for developing genetic engineering strategies. PMID:25999575

  10. [Cellulose degradation and ethanol production of different Clostridium strain].

    PubMed

    Fang, Zhi-guo; Ouyang, Zhi-yun

    2010-08-01

    Cellulose degradation and ethanol production of two types of cellulosic materials with different concentration were evaluated in batch system of mono-cultures of cellulolytic ethanol producing strains (Clostridium thermocellum strain LQRI and Clostridium thermocellum strain VPI), and co-cultures of LQRI or VPI in combination with one of the non-cellulolytic ethanol producing strains (Thermoanaerobacter ethanolicus strains X514 or Thermoanaerobacter ethanolicus 39E). Results demonstrated that higher cellulose degradation abilities about 1.2 times were detected in LQRI mono-culture than in VPI mono-culture, while no significant difference of ethanol yields was found between the two mono-cultures. Abilities of cellulose degradation and ethanol production decreased significantly with the increasing of substrate cellulose concentration (1%, 2%, 5%). In the co-culture system, cellulose degradation abilities of LQRI were also significantly higher than VPI, the former is 1.28-1.58 times of the latter. Cellulose degradation rate of LQRI + Thermoanaerobacter and VPI + Thermoanaerobacter decreased gradually with the increasing of substrate cellulose concentration, while the absolute value of cellulose degradation was also affected by the partner Thermoanaerobacter strain. Additionally, the ethanol yields in the co-cultures of LQRI + Thermoanaerobacter were significantly higher than that in the co-cultures of VPI + Thermoanaerobacter with same Thermoanaerobaeter partner, the former is 1.27-1.77 times of the latter. However, ethanol yields in the co-cultures have not significantly declined with the increasing of substrate cellulose concentration.

  11. Traits of selected Clostridium strains for syngas fermentation to ethanol.

    PubMed

    Martin, Michael E; Richter, Hanno; Saha, Surya; Angenent, Largus T

    2016-03-01

    Syngas fermentation is an anaerobic bioprocess that could become industrially relevant as a biorefinery platform for sustainable production of fuels and chemicals. An important prerequisite for commercialization is adequate performance of the biocatalyst (i.e., sufficiently high production rate, titer, selectivity, yield, and stability of the fermentation). Here, we compared the performance of three potential candidate Clostridium strains in syngas-to-ethanol conversion: Clostridium ljungdahlii PETC, C. ljungdahlii ERI-2, and Clostridium autoethanogenum JA1-1. Experiments were conducted in a two-stage, continuously fed syngas-fermentation system that had been optimized for stable ethanol production. The two C. ljungdahlii strains performed similar to each other but different from C. autoethanogenum. When the pH value was lowered from 5.5 to 4.5 to induce solventogenesis, the cell-specific carbon monoxide and hydrogen consumption (similar rate for all strains at pH 5.5), severely decreased in JA1-1, but hardly in PETC and ERI-2. Ethanol production in strains PETC and ERI-2 remained relatively stable while the rate of acetate production decreased, resulting in a high ethanol/acetate ratio, but lower overall productivities. With JA1-1, lowering the pH severely lowered rates of both ethanol and acetate production; and as a consequence, no pronounced shift to solventogenesis was observed. The highest overall ethanol production rate of 0.301 g · L(-1)  · h(-1) was achieved with PETC at pH 4.5 with a corresponding 19 g/L (1.9% w/v) ethanol concentration and a 5.5:1 ethanol/acetate molar ratio. A comparison of the genes relevant for ethanol metabolism revealed differences between C. ljungdahlii and C. autoethanogenum that, however, did not conclusively explain the different phenotypes.

  12. Biodegradation of trinitrotoluene (TNT) by a strain of Clostridium bifermentans

    SciTech Connect

    Shin, C.Y.; Crawford, D.L.

    1995-12-31

    A Clostridium capable of degrading 2,4,6-trinitrotoluene (TNT) cometabolically was isolated from a mixed culture obtained from a bioreactor fed TNT. This bacterium, identified as a strain of Clostridium bifermentans, and designated strain CYS-1, was able to degrade TNT via 4-amino-2,6-dinitrotoluene (4-ADNT) and 2,4-diamino-6-nitrotoluene (2,4-DANT) to aliphatic polar products which are now being identified and are assumed to be organic acids. CYS 1 cells are tolerant of TNT and capable of degrading it at starting concentrations of up to {ge}100 mg/L TNT. The number of cells inoculated and the availability of cosubstrate nutrients are significant factors influencing TNT degradation, as are TNT tolerance and survival of the cells at high TNT concentrations. In liquid media, at high TNT concentrations, TNT toxicity could be overcome by increasing the amount of inoculum and supplementing the culture with appropriate rich organic cosubstrates. Under these conditions, the reduction of 4-ADNT to 2,4-DANT occurred very fast, whereas the further degradation of 2,4-DANT proceeded more slowly.

  13. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum

    DOE PAGES

    Lo, Jonathan; Olson, Daniel G.; Murphy, Sean Jean-Loup; Tian, Liang; Hon, Shuen; Lanahan, Anthony; Guss, Adam M.; Lynd, Lee R.

    2016-10-28

    Here, the NfnAB (NADH-dependent reduced ferredoxin:NADP+ oxidoreductase) and Rnf (Rhodobacter nitrogen fixation) complexes are thought to catalyze electron transfer between reduced ferredoxin and NAD(P)+. Efficient electron flux is critical for engineering fuel production pathways, but little is known about the relative importance of these enzymes in vivo. In this study we investigate the importance of the NfnAB and Rnf complexes in Clostridium thermocellum for growth on cellobiose and Avicel using gene deletion, enzyme assays, and fermentation product analysis. The NfnAB complex does not seem to play a major role in metabolism, since deletion of nfnAB genes had little effect onmore » the distribution of fermentation products. By contrast, the Rnf complex appears to play an important role in ethanol formation. Deletion of rnf genes resulted in a decrease in ethanol formation. Overexpression of rnf genes resulted in an increase in ethanol production of about 30%, but only in strains where the hydG hydrogenase maturation gene was also deleted.« less

  14. Draft Genome Sequences of 17 French Clostridium botulinum Group III Strains.

    PubMed

    Woudstra, Cédric; Le Maréchal, Caroline; Souillard, Rozenn; Bayon-Auboyer, Marie-Hélène; Mermoud, Isabelle; Desoutter, Denise; Fach, Patrick

    2015-01-01

    Animal botulism is mainly associated with Clostridium botulinum group III strains producing neurotoxin types C, C/D, D, and D/C. In this report, we present the draft genome sequences of fourteen strains of Clostridium botulinum producing type C/D and two strains producing type D/C isolated in France, and one strain producing type D/C that originated from New Caledonia. PMID:26430029

  15. Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk

    PubMed Central

    La Torre, Angela; Zotta, Teresa; Orrù, Luigi; Lamontanara, Antonella; Cocconcelli, Pier Sandro

    2016-01-01

    Clostridium sporogenes is a causative agent of food spoilage and is often used as the nontoxigenic surrogate for Clostridium botulinum. Here, we described the draft genome sequence and annotation of C. sporogenes strain UC9000 isolated from raw milk. PMID:27081128

  16. Hydrogen production from wastewater sludge using a Clostridium strain.

    PubMed

    Wang, C C; Chang, C W; Chu, C P; Lee, D J; Chang, B V; Liao, C S

    2003-09-01

    Limited data in literature revealed a relatively low hydrogen yield from wastewater sludge, ca. 0.16 mg/g-dried solids, using anaerobic fermentation. We demonstrated in this work a much higher hydrogen yield, around 1.1 mg-H2/g-dried solids using a clostridium strain isolated from the sludge sample. The formed hydrogen would be consumed after passing the peak value at around 30-36 h of fermentation. We examined the effects of employing five different pre-treatments on substrate sludge, but noted no appreciable enhancement in hydrogen yield as commonly expected for methane production. Since a vast amount of organic matters had been released to water after hydrogen fermentation, we externally dosed methanogenic bacteria to the fermented liquor to produce methane. The fermented liquor could produce more methane than the non-fermented sample, indicating that the dosed methanogenic bacteria readily utilized the organic matters derived from the fermentation test.

  17. Spores of Clostridium engineered for clinical efficacy and safety cause regression and cure of tumors in vivo

    PubMed Central

    Ehsaan, Muhammad; Kubiak, Aleksandra M; Dubois, Ludwig; Paesmans, Kim; Van Mellaert, Lieve; Knox, Richard; Kuehne, Sarah A.; Lambin, Phillipe; Minton, Nigel P.

    2014-01-01

    Spores of some species of the strictly anaerobic bacteria Clostridium naturally target and partially lyse the hypoxic cores of tumors, which tend to be refractory to conventional therapies. The anti-tumor effect can be augmented by engineering strains to convert a non-toxic prodrug into a cytotoxic drug specifically at the tumor site by expressing a prodrug-converting enzyme (PCE). Safe doses of the favored prodrug CB1954 lead to peak concentrations of 6.3 μM in patient sera, but at these concentration(s) known nitroreductase (NTR) PCEs for this prodrug show low activity. Furthermore, efficacious and safe Clostridium strains that stably express a PCE have not been reported. Here we identify a novel nitroreductase from Neisseria meningitidis, NmeNTR, which is able to activate CB1954 at clinically-achievable serum concentrations. An NmeNTR expression cassette, which does not contain an antibiotic resistance marker, was stably localized to the chromosome of Clostridium sporogenes using a new integration method, and the strain was disabled for safety and containment by making it a uracil auxotroph. The efficacy of Clostridium-Directed Enzyme Prodrug Therapy (CDEPT) using this system was demonstrated in a mouse xenograft model of human colon carcinoma. Substantial tumor suppression was achieved, and several animals were cured. These encouraging data suggest that the novel enzyme and strain engineering approach represent a promising platform for the clinical development of CDEPT. PMID:24732092

  18. Genomic characterization of Italian Clostridium botulinum group I strains.

    PubMed

    Giordani, Francesco; Fillo, Silvia; Anselmo, Anna; Palozzi, Anna Maria; Fortunato, Antonella; Gentile, Bernardina; Azarnia Tehran, Domenico; Ciammaruconi, Andrea; Spagnolo, Ferdinando; Pittiglio, Valentina; Anniballi, Fabrizio; Auricchio, Bruna; De Medici, Dario; Lista, Florigio

    2015-12-01

    Clostridium botulinum is a gram-positive bacterium capable of producing the botulinum neurotoxin, a powerful poison that causes botulism, a severe neuroparalytic disease. Its genome has been sequenced entirely and its gene content has been analyzed. To date, 19 full genomes and 64 draft genomes are available. The geographical origin of these genomes is predominantly from the US. In the present study, 10 Italian genomes of C. botulinum group I were analyzed and compared with previously sequenced group I genomes, in order to genetically characterize the Italian population of C. botulinum group I and to investigate the phylogenetic relationships among different lineages. Using the suites of software ClonalFrame and ClonalOrigin to perform genomic analysis, we demonstrated that Italian C. botulinum group I population is phylogenetically heterogeneous encompassing different and distant lineages including overseas strains, too. Moreover, a high recombination rate was demonstrated in the evolution of C. botulinum group I species. Finally, genome sequencing of the strain 357 led us to identify a novel botulinum neurotoxin subtype, F8. PMID:26341861

  19. Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellumto utilize hemicellulose and unpretreated plant material

    SciTech Connect

    Izquierdo, Javier A.; Pattathil, Sivakumar; Guseva, Anna; Hahn, Michael G.; Lynd, Lee R.

    2014-11-18

    Among themophilic consolidated bioprocessing (CBP) candidate organisms, environmental isolates of Clostridium clariflavum have demonstrated the ability to grow on xylan, and the genome of C. clariflavum DSM 19732 has revealed a number of mechanisms that foster solubilization of hemicellulose that are distinctive relative to the model cellulolytic thermophile Clostridium thermocellum. Growth experiments on xylan, xylooligosaccharides, and xylose reveal that C. clariflavum strains are able to completely break down xylan to xylose and that the environmental strain C. clariflavum sp. 4-2a is able to grow on monomeric xylose. C. clariflavum strains were able to utilize a larger proportion of unpretreated switchgrass, and solubilize a higher proportion of glucan, xylan, and arabinan, with strain 4-2a reaching the highest extent of solubilization of these components (64.7 to 69.4%) compared to C. thermocellum (29.5 to 42.5%). In addition, glycome immunoanalyses of residual plant biomass reveal differences in the extent of degradation of easily accessible xylans, with C. clariflavum strains having increased solubilization of this fraction of xylans relative to C. thermocellum. In conclusion, C. clariflavum strains exhibit higher activity than C. thermocellum in the breakdown of hemicellulose and are capable of degrading xylan to xylooligomers and xylose. This capability seems to also play a role in the higher levels of utilization of unpretreated plant material.

  20. Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellumto utilize hemicellulose and unpretreated plant material

    DOE PAGES

    Izquierdo, Javier A.; Pattathil, Sivakumar; Guseva, Anna; Hahn, Michael G.; Lynd, Lee R.

    2014-11-18

    Among themophilic consolidated bioprocessing (CBP) candidate organisms, environmental isolates of Clostridium clariflavum have demonstrated the ability to grow on xylan, and the genome of C. clariflavum DSM 19732 has revealed a number of mechanisms that foster solubilization of hemicellulose that are distinctive relative to the model cellulolytic thermophile Clostridium thermocellum. Growth experiments on xylan, xylooligosaccharides, and xylose reveal that C. clariflavum strains are able to completely break down xylan to xylose and that the environmental strain C. clariflavum sp. 4-2a is able to grow on monomeric xylose. C. clariflavum strains were able to utilize a larger proportion of unpretreated switchgrass,more » and solubilize a higher proportion of glucan, xylan, and arabinan, with strain 4-2a reaching the highest extent of solubilization of these components (64.7 to 69.4%) compared to C. thermocellum (29.5 to 42.5%). In addition, glycome immunoanalyses of residual plant biomass reveal differences in the extent of degradation of easily accessible xylans, with C. clariflavum strains having increased solubilization of this fraction of xylans relative to C. thermocellum. In conclusion, C. clariflavum strains exhibit higher activity than C. thermocellum in the breakdown of hemicellulose and are capable of degrading xylan to xylooligomers and xylose. This capability seems to also play a role in the higher levels of utilization of unpretreated plant material.« less

  1. Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

    PubMed Central

    Weigand, Michael R.; Pena-Gonzalez, Angela; Shirey, Timothy B.; Broeker, Robin G.; Ishaq, Maliha K.; Konstantinidis, Konstantinos T.

    2015-01-01

    Taxonomic classification of Clostridium botulinum is based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified as Clostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of C. botulinum group I and C. sporogenes clearly separated these two species into discrete clades which showed ∼93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143 C. sporogenes clade-specific genetic signatures, a subset of which were further evaluated for their ability to correctly classify a panel of presumptive C. sporogenes strains by PCR. Genome sequencing of several C. sporogenes strains lacking these signatures confirmed that they clustered with C. botulinum strains in a core genome phylogenetic tree. Our analysis also identified C. botulinum strains that contained C. sporogenes clade-specific signatures and phylogenetically clustered with C. sporogenes strains. The genome sequences of two bont/B2-containing strains belonging to the C. sporogenes clade contained regions with similarity to a bont-bearing plasmid (pCLD), while two different strains belonging to the C. botulinum clade carried bont/B2 on the chromosome. These results indicate that bont/B2 was likely acquired by C. sporogenes strains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification. PMID:26048939

  2. Metabolic engineering of Clostridium acetobutylicum for the enhanced production of isopropanol-butanol-ethanol fuel mixture.

    PubMed

    Jang, Yu-Sin; Malaviya, Alok; Lee, Joungmin; Im, Jung Ae; Lee, Sang Yup; Lee, Julia; Eom, Moon-Ho; Cho, Jung-Hee; Seung, Do Young

    2013-01-01

    Butanol is considered as a superior biofuel, which is conventionally produced by clostridial acetone-butanol-ethanol (ABE) fermentation. Among ABE, only butanol and ethanol can be used as fuel alternatives. Coproduction of acetone thus causes lower yield of fuel alcohols. Thus, this study aimed at developing an improved Clostridium acetobutylicum strain possessing enhanced fuel alcohol production capability. For this, we previously developed a hyper ABE producing BKM19 strain was further engineered to convert acetone into isopropanol. The BKM19 strain was transformed with the plasmid pIPA100 containing the sadh (primary/secondary alcohol dehydrogenase) and hydG (putative electron transfer protein) genes from the Clostridium beijerinckii NRRL B593 cloned under the control of the thiolase promoter. The resulting BKM19 (pIPA100) strain produced 27.9 g/l isopropanol-butanol-ethanol (IBE) as a fuel alcohols with negligible amount of acetone (0.4 g/l) from 97.8 g/l glucose in lab-scale (2 l) batch fermentation. Thus, this metabolically engineered strain was able to produce 99% of total solvent produced as fuel alcohols. The scalability and stability of BKM19 (pIPA100) were evaluated at 200 l pilot-scale fermentation, which showed that the fuel alcohol yield could be improved to 0.37 g/g as compared to 0.29 g/g obtained at lab-scale fermentation, while attaining a similar titer. To the best of our knowledge, this is the highest titer of IBE achieved and the first report on the large scale fermentation of C. acetobutylicum for IBE production.

  3. Strain Engineering in Graphene

    NASA Astrophysics Data System (ADS)

    Castro Neto, Antonio

    2011-03-01

    Graphene is a unique example of a one atom thick metallic membrane. Hence, graphene brings together properties of soft and hard condensed matter systems. The elementary electronic excitations in graphene, the Dirac quasiparticles, couple in a singular way to structural distortions in the form of scalar and vector potentials. Therefore, graphene has an effective electrodynamics where structural deformations couple to the Dirac particles at equal footing to electric and magnetic fields. This so-called strain engineering of the electronic properties of graphene opens doors for a new paradigm in terms of electronic devices, where electronic properties can be manipulated at will using its membrane-like properties. I thank partial support from from DOE Grant DE-FG02-08ER46512 and ONR Grant MURI N00014-09-1-1063.

  4. Draft Genome Sequence of Clostridium tyrobutyricum Strain DIVETGP, Isolated from Cow's Milk for Grana Padano Production.

    PubMed

    Soggiu, Alessio; Piras, Cristian; Gaiarsa, Stefano; Bendixen, Emøke; Panitz, Frank; Bendixen, Christian; Sassera, Davide; Brasca, Milena; Bonizzi, Luigi; Roncada, Paola

    2015-01-01

    We announce the draft genome sequence of Clostridium tyrobutyricum strain DIVETGP. This strain was isolated from cow's milk used for Grana Padano cheese production. The genome was obtained using Illumina HiSeq technology and comprises 45 contigs for 3,018,999 bp, with a G+C content of 30.8%.

  5. Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.

    PubMed

    Lancaster, W Andrew; Utturkar, Sagar M; Poole, Farris L; Klingeman, Dawn M; Elias, Dwayne A; Adams, Michael W W; Brown, Steven D

    2016-05-05

    Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile isolated from the municipal sewage treatment plant in Athens, GA. We report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained by using PacBio DNA sequencing and Pilon for sequence assembly refinement with Illumina data.

  6. Near complete genome sequence of Clostridium paradoxum strain JW-YL-7

    DOE PAGES

    Lancaster, Andrew; Utturkar, Sagar M.; Poole, Farris; Klingeman, Dawn Marie; Elias, Dwayne A.; Adams, Michael W. W.; Brown, Steven D.

    2016-05-05

    Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile isolated from the municipal sewage treatment plant in Athens, GA. We report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained by using PacBio DNA sequencing and Pilon for sequence assembly refinement with Illumina data.

  7. Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7

    PubMed Central

    Lancaster, W. Andrew; Utturkar, Sagar M.; Poole, Farris L.; Klingeman, Dawn M.; Elias, Dwayne A.

    2016-01-01

    Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile isolated from the municipal sewage treatment plant in Athens, GA. We report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained by using PacBio DNA sequencing and Pilon for sequence assembly refinement with Illumina data. PMID:27151784

  8. Butyric acid from anaerobic fermentation of lignocellulosic biomass hydrolysates by Clostridium tyrobutyricum strain RPT-4213

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A newly isolated Clostridium sp. strain RPT-4213 was found to produce butyrate under anaerobic conditions. Fermentations using Lactobacilli MRS Broth produced 9.47 g L-1 butyric acid from glucose (0.48 g/g glucose). However, the strain was not capable of utilizing five carbon sugars. To assess the a...

  9. Butyric acid from anaerobic fermentation of lignocellulosic biomass hydrolysates by Clostridium sp. strain RPT-4213

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel Clostridium sp. strain RPT-4213 was found producing butyrate under strict anaerobic conditions. This strain produced 9.47 g L-1 butyric acid from MRS media (0.48 g/g glucose). RPT-4213 was also used to ferment dilute acid pretreated hydrolysates including wheat straw (WSH), corn fiber (CFH...

  10. Multidisciplinary Analysis of a Nontoxigenic Clostridium difficile Strain with Stable Resistance to Metronidazole

    PubMed Central

    Moura, Ines; Monot, Marc; Tani, Chiara; Barbanti, Fabrizio; Norais, Nathalie; Dupuy, Bruno; Bouza, Emilio; Mastrantonio, Paola

    2014-01-01

    Stable resistance to metronidazole in a nontoxigenic Clostridium difficile strain was investigated at both the genomic and proteomic levels. Alterations in the metabolic pathway involving the pyruvate-ferredoxin oxidoreductase were found, suggesting that reduction of metronidazole, required for its activity, may be less efficient in this strain. Proteomic studies also showed a cellular response to oxidative stress. PMID:24913157

  11. Isolation and characterization of a hydrogen- and ethanol-producing Clostridium sp. strain URNW.

    PubMed

    Ramachandran, Umesh; Wrana, Nathan; Cicek, Nazim; Sparling, Richard; Levin, David B

    2011-03-01

    Identification, characterization, and end-product synthesis patterns were analyzed in a newly identified mesophilic, anaerobic Clostridium sp. strain URNW, capable of producing hydrogen (H₂) and ethanol. Metabolic profiling was used to characterize putative end-product synthesis pathways of the Clostridium sp. strain URNW, which was found to grow on cellobiose; on hexose sugars, such as glucose, sucrose, and mannose; and on sugar alcohols, like mannitol and sorbitol. When grown in batch cultures on 2 g cellobiose·L⁻¹, Clostridium sp. strain URNW showed a cell generation time of 1.5 h, and the major end-products were H2, formate, carbon dioxide (CO₂), lactate, butyrate, acetate, pyruvate, and ethanol. The total volumetric H₂ production was 14.2 mmol·(L culture)⁻¹ and the total production of ethanol was 0.4 mmol·(L culture)⁻¹. The maximum yield of H₂ was 1.3 mol·(mol glucose equivalent)⁻¹ at a carbon recovery of 94%. The specific production rates of H₂, CO₂, and ethanol were 0.45, 0.13, and 0.003 mol·h⁻¹·(g dry cell mass)-1, respectively. BLAST analyses of 16S rDNA and chaperonin 60 (cpn60) sequences from Clostridium sp. strain URNW revealed a 98% nucleotide sequence identity with the 16S rDNA and cpn60 sequences from Clostridium intestinale ATCC 49213. Phylogenetic analyses placed Clostridium sp. strain URNW within the butyrate-synthesizing clostridia.

  12. Characterization of the spore surface and exosporium proteins of Clostridium sporogenes; implications for Clostridium botulinum group I strains.

    PubMed

    Janganan, Thamarai K; Mullin, Nic; Tzokov, Svetomir B; Stringer, Sandra; Fagan, Robert P; Hobbs, Jamie K; Moir, Anne; Bullough, Per A

    2016-10-01

    Clostridium sporogenes is a non-pathogenic close relative and surrogate for Group I (proteolytic) neurotoxin-producing Clostridium botulinum strains. The exosporium, the sac-like outermost layer of spores of these species, is likely to contribute to adhesion, dissemination, and virulence. A paracrystalline array, hairy nap, and several appendages were detected in the exosporium of C. sporogenes strain NCIMB 701792 by EM and AFM. The protein composition of purified exosporium was explored by LC-MS/MS of tryptic peptides from major individual SDS-PAGE-separated protein bands, and from bulk exosporium. Two high molecular weight protein bands both contained the same protein with a collagen-like repeat domain, the probable constituent of the hairy nap, as well as cysteine-rich proteins CsxA and CsxB. A third cysteine-rich protein (CsxC) was also identified. These three proteins are also encoded in C. botulinum Prevot 594, and homologues (75-100% amino acid identity) are encoded in many other Group I strains. This work provides the first insight into the likely composition and organization of the exosporium of Group I C. botulinum spores. PMID:27375261

  13. Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923)

    PubMed Central

    Clément, Benjamin; Lopes Ferreira, Nicolas

    2016-01-01

    Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776 (IFP923), an efficient producer of butyric acid. The genome consists of a single chromosome of 3.19 Mb and provides useful data concerning the metabolic capacities of the strain. PMID:26941139

  14. Complete Genome Sequence of the Hypervirulent Bacterium Clostridium difficile Strain G46, Ribotype 027

    PubMed Central

    Gaulton, Tom; Rose, Graham; Baybayan, Primo; Hall, Richard; Freeman, Jane; Turton, Jane; Picton, Steve; Korlach, Jonas; Gharbia, Saheer; Shah, Haroun

    2015-01-01

    Clostridium difficile is one of the leading causes of antibiotic-associated diarrhea in health care facilities worldwide. Here, we report the genome sequence of C. difficile strain G46, ribotype 027, isolated from an outbreak in Glamorgan, Wales, in 2006. PMID:25814591

  15. Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii

    SciTech Connect

    Banerjee, A; Leang, C; Ueki, T; Nevin, KP; Lovley, DR

    2014-03-25

    The development of tools for genetic manipulation of Clostridium ljungdahlii has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for C. ljungdahlii, the possibility of adapting a lactose-inducible system for gene expression, previously reported for Clostridium perfringens, was investigated. The plasmid pAH2, originally developed for C. perfringens with a gusA reporter gene, functioned as an effective lactose-inducible system in C. ljungdahlii. Lactose induction of C. ljungdahlii containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of adhE1 30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of adhE1 in a strain in which adhE1 and the adhE1 homolog adhE2 had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of adhE2 similarly failed to restore ethanol production, suggesting that adhE1 is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.

  16. Enhanced butanol fermentation using metabolically engineered Clostridium acetobutylicum with ex situ recovery of butanol.

    PubMed

    Lee, Sang-Hyun; Kim, Sooah; Kim, Jung Yeon; Cheong, Nam Yong; Kim, Kyoung Heon

    2016-10-01

    In this study, metabolic target reactions for strain engineering were searched via intracellular coenzyme A (CoA) metabolite analysis. The metabolic reactions catalyzed by thiolase (AtoB) and aldehyde-alcohol dehydrogenase (AdhE1) were considered potential rate-limiting steps. In addition, CoA transferase (CtfAB) was highlighted as being important for the assimilation of organic acids, in order to achieve high butanol production. Based on this quantitative analysis, the BEKW_E1AB-atoB strain was constructed by overexpressing the thl (atoB), adhE1, and ctfAB genes in Clostridium acetobutylicum strain BEKW, which has the phosphotransacetylase (pta) and butyrate kinase (buk) genes knocked out. After 100h of continuous fermentation coupled with adsorptive ex situ butanol recovery, the concentrations found after considering desorption, yield, and productivity for the BEKW_E1AB-atoB strain were 55.7g/L, 0.38g/g, and 2.64g/L/h, respectively. The level of butanol production achieved (2.64g/L/h) represents the highest reported value obtained after adsorptive, long-term fermentation. PMID:27441828

  17. Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge.

    PubMed

    Wong, Y M; Juan, J C; Gan, H M; Austin, C M

    2014-01-01

    Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the metabolic pathways involved in efficient biohydrogen production. PMID:24604639

  18. Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge

    PubMed Central

    Wong, Y. M.; Gan, H. M.; Austin, C. M.

    2014-01-01

    Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the metabolic pathways involved in efficient biohydrogen production. PMID:24604639

  19. Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge.

    PubMed

    Wong, Y M; Juan, J C; Gan, H M; Austin, C M

    2014-03-06

    Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the metabolic pathways involved in efficient biohydrogen production.

  20. Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes

    PubMed Central

    Mazuet, Christelle; Legeay, Christine; Sautereau, Jean; Ma, Laurence; Bouchier, Christiane; Bouvet, Philippe; Popoff, Michel R.

    2016-01-01

    In France, human botulism is mainly food-borne intoxication, whereas infant botulism is rare. A total of 99 group I and II Clostridium botulinum strains including 59 type A (12 historical isolates [1947–1961], 43 from France [1986–2013], 3 from other countries, and 1 collection strain), 31 type B (3 historical, 23 recent isolates, 4 from other countries, and 1 collection strain), and 9 type E (5 historical, 3 isolates, and 1 collection strain) were investigated by botulinum locus gene sequencing and multilocus sequence typing analysis. Historical C. botulinum A strains mainly belonged to subtype A1 and sequence type (ST) 1, whereas recent strains exhibited a wide genetic diversity: subtype A1 in orfX or ha locus, A1(B), A1(F), A2, A2b2, A5(B2′) A5(B3′), as well as the recently identified A7 and A8 subtypes, and were distributed into 25 STs. Clostridium botulinum A1(B) was the most frequent subtype from food-borne botulism and food. Group I C. botulinum type B in France were mainly subtype B2 (14 out of 20 historical and recent strains) and were divided into 19 STs. Food-borne botulism resulting from ham consumption during the recent period was due to group II C. botulinum B4. Type E botulism is rare in France, 5 historical and 1 recent strains were subtype E3. A subtype E12 was recently identified from an unusual ham contamination. Clostridium botulinum strains from human botulism in France showed a wide genetic diversity and seems to result not from a single evolutionary lineage but from multiple and independent genetic rearrangements. PMID:27189984

  1. Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes.

    PubMed

    Mazuet, Christelle; Legeay, Christine; Sautereau, Jean; Ma, Laurence; Bouchier, Christiane; Bouvet, Philippe; Popoff, Michel R

    2016-01-01

    In France, human botulism is mainly food-borne intoxication, whereas infant botulism is rare. A total of 99 group I and II Clostridium botulinum strains including 59 type A (12 historical isolates [1947-1961], 43 from France [1986-2013], 3 from other countries, and 1 collection strain), 31 type B (3 historical, 23 recent isolates, 4 from other countries, and 1 collection strain), and 9 type E (5 historical, 3 isolates, and 1 collection strain) were investigated by botulinum locus gene sequencing and multilocus sequence typing analysis. Historical C. botulinum A strains mainly belonged to subtype A1 and sequence type (ST) 1, whereas recent strains exhibited a wide genetic diversity: subtype A1 in orfX or ha locus, A1(B), A1(F), A2, A2b2, A5(B2') A5(B3'), as well as the recently identified A7 and A8 subtypes, and were distributed into 25 STs. Clostridium botulinum A1(B) was the most frequent subtype from food-borne botulism and food. Group I C. botulinum type B in France were mainly subtype B2 (14 out of 20 historical and recent strains) and were divided into 19 STs. Food-borne botulism resulting from ham consumption during the recent period was due to group II C. botulinum B4. Type E botulism is rare in France, 5 historical and 1 recent strains were subtype E3. A subtype E12 was recently identified from an unusual ham contamination. Clostridium botulinum strains from human botulism in France showed a wide genetic diversity and seems to result not from a single evolutionary lineage but from multiple and independent genetic rearrangements. PMID:27189984

  2. Mechanisms of hypervirulent Clostridium difficile ribotype 027 displacement of endemic strains: an epidemiological model.

    PubMed

    Yakob, Laith; Riley, Thomas V; Paterson, David L; Marquess, John; Magalhaes, Ricardo J Soares; Furuya-Kanamori, Luis; Clements, Archie C A

    2015-07-28

    Following rapid, global clonal dominance of hypervirulent ribotypes, Clostridium difficile now constitutes the primary infectious cause of nosocomial diarrhoea. Evidence indicates at least three possible mechanisms of hypervirulence that facilitates the successful invasion of these atypical strains: 1) increased infectiousness relative to endemic strains; 2) increased symptomatic disease rate relative to endemic strains; and 3) an ability to outcompete endemic strains in the host's gut. Stochastic simulations of an infection transmission model demonstrate clear differences between the invasion potentials of C. difficile strains utilising the alternative hypervirulence mechanisms, and provide new evidence that favours certain mechanisms (1 and 2) more than others (3). Additionally, simulations illustrate that direct competition between strains (inside the host's gut) is not a prerequisite for the sudden switching that has been observed in prevailing ribotypes; previously dominant C. difficile strains can be excluded by hypervirulent ribotypes through indirect (exploitative) competition.

  3. Metabolic and process engineering of Clostridium cellulovorans for biofuel production from cellulose.

    PubMed

    Yang, Xiaorui; Xu, Mengmeng; Yang, Shang-Tian

    2015-11-01

    Production of cellulosic biofuels has drawn increasing attention. However, currently no microorganism can produce biofuels, particularly butanol, directly from cellulosic biomass efficiently. Here we engineered a cellulolytic bacterium, Clostridium cellulovorans, for n-butanol and ethanol production directly from cellulose by introducing an aldehyde/alcohol dehydrogenase (adhE2), which converts butyryl-CoA to n-butanol and acetyl-CoA to ethanol. The engineered strain was able to produce 1.42 g/L n-butanol and 1.60 g/L ethanol directly from cellulose. Moreover, the addition of methyl viologen as an artificial electron carrier shifted the metabolic flux from acid production to alcohol production, resulting in a high biofuel yield of 0.39 g/g from cellulose, comparable to ethanol yield from corn dextrose by yeast fermentation. This study is the first metabolic engineering of C. cellulovorans for n-butanol and ethanol production directly from cellulose with significant titers and yields, providing a promising consolidated bioprocessing (CBP) platform for biofuel production from cellulosic biomass.

  4. The same clade of Clostridium botulinum strains is causing avian botulism in southern and northern Europe.

    PubMed

    Anza, Ibone; Skarin, Hanna; Vidal, Dolors; Lindberg, Anna; Båverud, Viveca; Mateo, Rafael

    2014-04-01

    Avian botulism is a paralytic disease caused by Clostridium botulinum-produced botulinum neurotoxins (BoNTs), most commonly of type C/D. It is a serious disease of waterbirds and poultry flocks in many countries in Europe. The objective of this study was to compare the genetic relatedness of avian C. botulinum strains isolated in Spain with strains isolated in Sweden using pulsed-field gel electrophoresis (PFGE). Fifteen strains were isolated from Spanish waterbirds using an immunomagnetic separation technique. Isolates were characterized by PCR, and all were identified as the genospecies Clostridium novyi sensu lato and eight harboured the gene coding for the BoNT type C/D. PFGE analysis of the strains revealed four highly similar pulsotypes, out of which two contained strains from both countries. It also showed that outbreaks in wild and domestic birds can be caused by the same strains. These results support a clonal spreading of the mosaic C. botulinum type C/D through Europe and give relevant information for future epidemiological studies.

  5. Acetone-butanol-ethanol production from substandard and surplus dates by Egyptian native Clostridium strains.

    PubMed

    Abd-Alla, Mohamed Hemida; Zohri, Abdel-Naser Ahmed; El-Enany, Abdel-Wahab Elsadek; Ali, Shimaa Mohamed

    2015-04-01

    One hundred and seven mesophilic isolates of Clostridium were isolated from agricultural soils cultivated with different plants in Assuit Governorate, Egypt. Eighty isolates (out of 107) showed the ability to produce ABE (Acetone, butanol and ethanol) on T6 medium ranging from 0.036 to 31.89 g/L. The highest numbers of ABE producing isolates were obtained from soil samples of potato contributing 27 isolates, followed by 18 isolates from wheat and 10 isolates from onion. On the other hand, there were three native isolates that produced ABE more than those produced by the reference isolate Clostridium acetobutylicum ATCC 824 (11.543 g/L). The three isolates were identified based on phenotypic and gene encoding 16S rRNA as Clostridium beijerinckii ASU10 (KF372577), Clostridium chauvoei ASU55 (KF372580) and Clostridium roseum ASU58 (KF372581). The highest ABE level from substandard and surplus dates was produced by C. beijerinckii ASU10 (24.07 g/L) comprising butanol 67.15% (16.16 g/L), acetone 30.73% (7.4 g/L) and ethanol 2.12% (0.51 g/L), while C. roseum ASU58 and C. chauvoei ASU55 produced ABE contributing 20.20 and 13.79 g/L, respectively. ABE production by C. acetobutylicum ATCC 824 was 15.01 g/L. This study proved that the native strains C. beijerinckii ASU10 and C. roseum ASU58 have high competitive efficacy on ABE production from economical substrate as substandard and surplus date fruits. Additionally, using this substrate without any nutritional components is considered to be a commercial substrate for desired ABE production.

  6. Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota.

    PubMed

    Benamar, Samia; Cassir, Nadim; Caputo, Aurélia; Cadoret, Frédéric; La Scola, Bernard

    2016-01-01

    Clostridium septicum is one of the first pathogenic anaerobes to be identified. Here, we announce the genome draft sequence of C. septicum strain CSUR P1044 isolated from the gut of a healthy adult. Its chromosome genome consists of 3.2 Mbp with a plasmid of 32 Kbp. C. septicum strain CSUR P1044 has a G+C content of 27.5%, and is composed of 3,125 protein-coding genes together with 103 RNA genes, including 22 rRNA genes. PMID:27609912

  7. Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota.

    PubMed

    Benamar, Samia; Cassir, Nadim; Caputo, Aurélia; Cadoret, Frédéric; La Scola, Bernard

    2016-01-01

    Clostridium septicum is one of the first pathogenic anaerobes to be identified. Here, we announce the genome draft sequence of C. septicum strain CSUR P1044 isolated from the gut of a healthy adult. Its chromosome genome consists of 3.2 Mbp with a plasmid of 32 Kbp. C. septicum strain CSUR P1044 has a G+C content of 27.5%, and is composed of 3,125 protein-coding genes together with 103 RNA genes, including 22 rRNA genes.

  8. Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota

    PubMed Central

    Benamar, Samia; Cassir, Nadim; Caputo, Aurélia; Cadoret, Frédéric

    2016-01-01

    Clostridium septicum is one of the first pathogenic anaerobes to be identified. Here, we announce the genome draft sequence of C. septicum strain CSUR P1044 isolated from the gut of a healthy adult. Its chromosome genome consists of 3.2 Mbp with a plasmid of 32 Kbp. C. septicum strain CSUR P1044 has a G+C content of 27.5%, and is composed of 3,125 protein-coding genes together with 103 RNA genes, including 22 rRNA genes. PMID:27609912

  9. Clostridium perfringens: Comparative effects of heat and osmotic stress on non-enterotoxigenic and enterotoxigenic strains.

    PubMed

    Abbona, Cinthia Carolina; Stagnitta, Patricia Virginia

    2016-06-01

    Clostridium perfringens isolates associated with food poisoning carries a chromosomal cpe gene, while non-foodborne human gastrointestinal disease isolates carry a plasmid cpe gene. The enterotoxigenic strains tested produced vegetative cells and spores with significantly higher resistance than non-enterotoxigenic strains. These results suggest that the vegetative cells and spores have a competitive advantage over non-enterotoxigenic strains. However, no explanation has been provided for the significant associations between chromosomal cpe genotypes with the high resistance, which could explain the strong relationship between chromosomal cpe isolates and C. perfringens type A food poisoning. Here, we analyse the action of physical and chemical agent on non-enterotoxigenic and enterotoxigenic regional strains. And this study tested the relationship between the sensitivities of spores and their levels SASPs (small acid soluble proteins) production in the same strains examined. PMID:27012900

  10. Identification of toxigenic Clostridium difficile strains by using a toxin A gene-specific probe.

    PubMed Central

    Wren, B W; Clayton, C L; Castledine, N B; Tabaqchali, S

    1990-01-01

    A 4.5-kilobase PstI fragment encoding part of the toxin A gene was isolated and used as a DNA probe in colony hybridization studies with 58 toxigenic and 17 nontoxigenic Clostridium difficile strains. All 58 toxigenic strains showed positive hybridization, in contrast to the 17 nontoxigenic strains. Southern blot analysis with the toxin A gene probe showed hybridization to a single fragment of equal intensities for HindIII-digested genomic DNAs isolated from C. difficile strains of wide-ranging toxin production. The positive hybridization signals were due to fragments of heterogeneous lengths (9 to 13 kilobases) for toxigenic strains of different types but were absent for the nontoxigenic strains. These results suggest the presence of a single copy of the toxin A gene on the genome of C. difficile strains, and the wide variation of toxin expression is not a reflection of gene copy number. The lack of toxin activity for nontoxigenic strains can be explained by the absence of at least part of the toxin A gene. The toxin A gene probe was tested against clostridial strains from 18 other species, of which only toxigenic C. sordellii strains showed positive hybridization. The specificity of the toxin A gene probe for toxigenic strains may lead to improved methods for the specific identification of toxigenic C. difficile strains from clinical specimens. Images PMID:2118549

  11. Neutralization of Clostridium difficile Toxin B Mediated by Engineered Lactobacilli That Produce Single-Domain Antibodies

    PubMed Central

    Andersen, Kasper Krogh; Strokappe, Nika M.; Hultberg, Anna; Truusalu, Kai; Smidt, Imbi; Mikelsaar, Raik-Hiio; Mikelsaar, Marika; Verrips, Theo; Hammarström, Lennart

    2015-01-01

    Clostridium difficile is the primary cause of nosocomial antibiotic-associated diarrhea in the Western world. The major virulence factors of C. difficile are two exotoxins, toxin A (TcdA) and toxin B (TcdB), which cause extensive colonic inflammation and epithelial damage manifested by episodes of diarrhea. In this study, we explored the basis for an oral antitoxin strategy based on engineered Lactobacillus strains expressing TcdB-neutralizing antibody fragments in the gastrointestinal tract. Variable domain of heavy chain-only (VHH) antibodies were raised in llamas by immunization with the complete TcdB toxin. Four unique VHH fragments neutralizing TcdB in vitro were isolated. When these VHH fragments were expressed in either secreted or cell wall-anchored form in Lactobacillus paracasei BL23, they were able to neutralize the cytotoxic effect of the toxin in an in vitro cell-based assay. Prophylactic treatment with a combination of two strains of engineered L. paracasei BL23 expressing two neutralizing anti-TcdB VHH fragments (VHH-B2 and VHH-G3) delayed killing in a hamster protection model where the animals were challenged with spores of a TcdA− TcdB+ strain of C. difficile (P < 0.05). Half of the hamsters in the treated group survived until the termination of the experiment at day 5 and showed either no damage or limited inflammation of the colonic mucosa despite having been colonized with C. difficile for up to 4 days. The protective effect in the hamster model suggests that the strategy could be explored as a supplement to existing therapies for patients. PMID:26573738

  12. Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2

    SciTech Connect

    Brown, Steven D; Lamed, Raphael; Morag, Ely; Borovok, Ilya; Shoham, Yuval; Klingeman, Dawn Marie; Johnson, Courtney M; Yang, Zamin; Land, Miriam L; Utturkar, Sagar M; Keller, Martin; Bayer, Edward A

    2012-01-01

    Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain AD2 played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.

  13. Synergistic inactivation of spores of proteolytic Clostridium botulinum strains by high pressure and heat is strain and product dependent.

    PubMed

    Bull, M K; Olivier, S A; van Diepenbeek, R J; Kormelink, F; Chapman, B

    2009-01-01

    The combined high pressure and heat resistances of spores of five proteolytic Clostridium botulinum strains and of the nonpathogenic surrogate strain Clostridium sporogenes PA3679 were compared with their heat-only resistances on the basis of equivalent accumulated thermal lethality, expressed as equivalent minutes at a reference temperature of 105 degrees C (F(105 degrees C). Comparisons were made with three model (i.e., diluted) products, namely, 30% (wt/wt) Bolognese sauce, 50% (wt/wt) cream sauce, and rice water agar. Pressure was determined to act synergistically with heat during high-pressure thermal (HPT) processing for C. botulinum FRRB 2802 (NCTC 7273) and C. botulinum FRRB 2804 (NCTC 3805 and 62A) in the Bolognese and cream sauces and for C. botulinum FRRB 2807 (213B) in the Bolognese sauce only. No synergy was observed for C. botulinum FRRB 2803 (NCTC 2916) or FRRB 2806 (62A) or C. sporogenes FRRB 2790 (NCTC 8594 and PA3679) in any of the model products. No significant protective effect of pressure against spore inactivation was determined for any Clostridium strain in any product. Because synergy was not consistently observed among strains of C. botulinum or among products, the prediction of inactivation of C. botulinum spores by HPT sterilization (HPTS) for the present must assume a complete lack of synergy. Therefore, any HPTS process for low-acid shelf-stable foods must be at least thermally equivalent to an F(0) process of 2.8 min, in line with current good manufacturing practices. The results of this study suggest that the use of C. sporogenes PA3679 as a surrogate organism may risk overestimating inactivation of C. botulinum by HPT processing.

  14. Clinical Utility of Laboratory Detection of Clostridium difficile Strain BI/NAP1/027

    PubMed Central

    Gerding, Dale N.

    2015-01-01

    Clostridium difficile strain BI/NAP1/027 is associated with increased C. difficile infection (CDI) rates and severity, and the efficacy of some CDI therapies may be strain dependent. Although cultured C. difficile isolates can be reliably subtyped by various methods, the long turnaround times, high cost, and limited availability of strain typing preclude their routine use. Nucleic acid amplification tests identify BI/NAP1/027 rapidly from stool, but the emergence of closely related strains compromises test specificity. Although detection of epidemiologically significant pathogens is generally useful for infection control programs, specific data supporting use of rapid detection of BI/NAP1/027 as an infection control tool are still awaited. PMID:26511742

  15. Clinical Utility of Laboratory Detection of Clostridium difficile Strain BI/NAP1/027.

    PubMed

    Kociolek, Larry K; Gerding, Dale N

    2016-01-01

    Clostridium difficile strain BI/NAP1/027 is associated with increased C. difficile infection (CDI) rates and severity, and the efficacy of some CDI therapies may be strain dependent. Although cultured C. difficile isolates can be reliably subtyped by various methods, the long turnaround times, high cost, and limited availability of strain typing preclude their routine use. Nucleic acid amplification tests identify BI/NAP1/027 rapidly from stool, but the emergence of closely related strains compromises test specificity. Although detection of epidemiologically significant pathogens is generally useful for infection control programs, specific data supporting use of rapid detection of BI/NAP1/027 as an infection control tool are still awaited. PMID:26511742

  16. Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways

    SciTech Connect

    Van Der Veen, Douwe; Lo, Jonathan; Brown, Steven D; Johnson, Courtney M; Tschaplinski, Timothy J; Martin, Madhavi Z; Engle, Nancy L; Van den Berg, Robert A; Argyros, Aaron; Caiazza, Nicky; Guss, Adam M; Lynd, Lee R

    2013-01-01

    Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Dldh) and/or acetate (Dpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Dldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Dhpt Dspo0A). The Dpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol. A Dldh Dpta double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Dpta. Free amino acids were secreted by all examined strains, with both Dpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Dldh Dpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Dpta and 16-fold in the Dldh Dpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP* through increased production of amino acids.

  17. Characterization of Clostridium thermocellum strains with disrupted fermentation end product pathways

    SciTech Connect

    Van Der Veen, Douwe; Lo, Jonathan; Brown, Steven D; Johnson, Courtney M; Tschaplinski, Timothy J; Martin, Madhavi Z; Engle, Nancy L; Argyros, Aaron; Van den Berg, Robert A; Caiazza, Nicky; Guss, Adam M; Lynd, Lee R

    2013-01-01

    Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of Llactate ( ldh) and/or acetate ( pta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end products. Cellobiose-grown cultures of the ldh strain had identical biomass accumulation, fermentation end products, transcription profile and intracellular metabolite concentrations compared to its parent strain (DSM1313 hpt spo0A). The pta-deficient strain grew slower and had 30% lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol. A ldh pta double mutant strain evolved for faster growth had growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to pta. Free amino acids were secreted by all examined strains, with both pta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for ldh pta reached 5 mM by the end of growth, or 2.7% of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to 6-fold in the pta and 16-fold in the ldh pta strain. We hypothesize that the deletions in fermentation end product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP+ through increased production of amino acids.

  18. The molecular-genetic analysis of Clostridium perfringens strains isolated from broilers on farms in Central Russia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the research was to perform phenotypic and molecular-genetic typing of Clostridium perfringens strains commonly spread on poultry farms in Central Russia. Samples of homogenized iliac and cecal contents from 760 broilers were assayed and 325 C. perfringens strains (42.8 %) were isol...

  19. Variations in virulence and molecular biology among emerging strains of Clostridium difficile.

    PubMed

    Hunt, Jonathan J; Ballard, Jimmy D

    2013-12-01

    Clostridium difficile is a Gram-positive, spore-forming organism which infects and colonizes the large intestine, produces potent toxins, triggers inflammation, and causes significant systemic complications. Treating C. difficile infection (CDI) has always been difficult, because the disease is both caused and resolved by antibiotic treatment. For three and a half decades, C. difficile has presented a treatment challenge to clinicians, and the situation took a turn for the worse about 10 years ago. An increase in epidemic outbreaks related to CDI was first noticed around 2003, and these outbreaks correlated with a sudden increase in the mortality rate of this illness. Further studies discovered that these changes in CDI epidemiology were associated with the rapid emergence of hypervirulent strains of C. difficile, now collectively referred to as NAP1/BI/027 strains. The discovery of new epidemic strains of C. difficile has provided a unique opportunity for retrospective and prospective studies that have sought to understand how these strains have essentially replaced more historical strains as a major cause of CDI. Moreover, detailed studies on the pathogenesis of NAP1/BI/027 strains are leading to new hypotheses on how this emerging strain causes severe disease and is more commonly associated with epidemics. In this review, we provide an overview of CDI, discuss critical mechanisms of C. difficile virulence, and explain how differences in virulence-associated factors between historical and newly emerging strains might explain the hypervirulence exhibited by this pathogen during the past decade. PMID:24296572

  20. Variations in Virulence and Molecular Biology among Emerging Strains of Clostridium difficile

    PubMed Central

    Hunt, Jonathan J.

    2013-01-01

    SUMMARY Clostridium difficile is a Gram-positive, spore-forming organism which infects and colonizes the large intestine, produces potent toxins, triggers inflammation, and causes significant systemic complications. Treating C. difficile infection (CDI) has always been difficult, because the disease is both caused and resolved by antibiotic treatment. For three and a half decades, C. difficile has presented a treatment challenge to clinicians, and the situation took a turn for the worse about 10 years ago. An increase in epidemic outbreaks related to CDI was first noticed around 2003, and these outbreaks correlated with a sudden increase in the mortality rate of this illness. Further studies discovered that these changes in CDI epidemiology were associated with the rapid emergence of hypervirulent strains of C. difficile, now collectively referred to as NAP1/BI/027 strains. The discovery of new epidemic strains of C. difficile has provided a unique opportunity for retrospective and prospective studies that have sought to understand how these strains have essentially replaced more historical strains as a major cause of CDI. Moreover, detailed studies on the pathogenesis of NAP1/BI/027 strains are leading to new hypotheses on how this emerging strain causes severe disease and is more commonly associated with epidemics. In this review, we provide an overview of CDI, discuss critical mechanisms of C. difficile virulence, and explain how differences in virulence-associated factors between historical and newly emerging strains might explain the hypervirulence exhibited by this pathogen during the past decade. PMID:24296572

  1. Subinhibitory concentrations of metronidazole increase biofilm formation in Clostridium difficile strains.

    PubMed

    Vuotto, Claudia; Moura, Ines; Barbanti, Fabrizio; Donelli, Gianfranco; Spigaglia, Patrizia

    2016-03-01

    Resistance mechanism to metronidazole is still poorly understood, even if the number of reports on Clostridium difficile strains with reduced susceptibility to this antibiotic is increasing. In this study, we investigated the ability of the C. difficile strains 7032994, 7032985 and 7032989, showing different susceptibility profiles to metronidazole but all belonging to the PCR ribotype 010, to form biofilm in vitro in presence and absence of subinhibitory concentrations of metronidazole. The quantitative biofilm production assay performed in presence of metronidazole revealed a significant increase in biofilm formation in both the susceptible strain 7032994 and the strain 7032985 exhibiting a reduced susceptibility to this antibiotic, while antibiotic pressure did not affect the biofilm-forming ability of the stable-resistant strain 7032989. Moreover, confocal microscopy analysis showed an abundant biofilm matrix production by the strains 7032994 and 7032885, when grown in presence of metronidazole, but not in the stable-resistant one. These results seem to demonstrate that subinhibitory concentrations of metronidazole are able to enhance the in vitro biofilm production of the above-mentioned PCR ribotype 010 C. difficile strains, susceptible or with reduced susceptibility to this antibiotic, suggesting a possible role of biofilm formation in the multifactorial mechanism of metronidazole resistance developed by C. difficile.

  2. Systemic colonization of clover (Trifolium repens) by Clostridium botulinum strain 2301

    PubMed Central

    Zeiller, Matthias; Rothballer, Michael; Iwobi, Azuka N.; Böhnel, Helge; Gessler, Frank; Hartmann, Anton; Schmid, Michael

    2015-01-01

    In recent years, cases of botulism in cattle and other farm animals and also in farmers increased dramatically. It was proposed, that these cases could be affiliated with the spreading of compost or other organic manures contaminated with Clostridium botulinum spores on farm land. Thus, soils and fodder plants and finally farm animals could be contaminated. Therefore, the colonization behavior and interaction of the botulinum neurotoxin (BoNT D) producing C. botulinum strain 2301 and the non-toxin producing Clostridium sporogenes strain 1739 were investigated on clover (Trifolium repens) in a field experiment as well as in phytochamber experiments applying axenic and additionally soil based systems under controlled conditions. Plants were harvested and divided into root and shoot parts for further DNA isolation and polymerase chain reaction (PCR) assays; subsamples were fixed for fluorescence in situ hybridization analysis in combination with confocal laser scanning microscopy. In addition, we observed significant differences in the growth behavior of clover plants when inoculated with clostridial spores, indicating a plant growth promoting effect. Inoculated plants showed an increased growth index (shoot size, wet and dry weight) and an enlarged root system induced by the systemic colonization of clover by C. botulinum strain 2301. To target C. botulinum and C. sporogenes, 16S rDNA directed primers were used and to specifically detect C. botulinum, BoNT D toxin genes targeted primers, using a multiplex PCR approach, were applied. Our results demonstrate an effective colonization of roots and shoots of clover by C. botulinum strain 2301 and C. sporogenes strain 1739. Detailed analysis of colonization behavior showed that C. botulinum can occur as individual cells, in cell clusters and in microcolonies within the rhizosphere, lateral roots and within the roots tissue of clover. PMID:26583010

  3. Systemic colonization of clover (Trifolium repens) by Clostridium botulinum strain 2301.

    PubMed

    Zeiller, Matthias; Rothballer, Michael; Iwobi, Azuka N; Böhnel, Helge; Gessler, Frank; Hartmann, Anton; Schmid, Michael

    2015-01-01

    In recent years, cases of botulism in cattle and other farm animals and also in farmers increased dramatically. It was proposed, that these cases could be affiliated with the spreading of compost or other organic manures contaminated with Clostridium botulinum spores on farm land. Thus, soils and fodder plants and finally farm animals could be contaminated. Therefore, the colonization behavior and interaction of the botulinum neurotoxin (BoNT D) producing C. botulinum strain 2301 and the non-toxin producing Clostridium sporogenes strain 1739 were investigated on clover (Trifolium repens) in a field experiment as well as in phytochamber experiments applying axenic and additionally soil based systems under controlled conditions. Plants were harvested and divided into root and shoot parts for further DNA isolation and polymerase chain reaction (PCR) assays; subsamples were fixed for fluorescence in situ hybridization analysis in combination with confocal laser scanning microscopy. In addition, we observed significant differences in the growth behavior of clover plants when inoculated with clostridial spores, indicating a plant growth promoting effect. Inoculated plants showed an increased growth index (shoot size, wet and dry weight) and an enlarged root system induced by the systemic colonization of clover by C. botulinum strain 2301. To target C. botulinum and C. sporogenes, 16S rDNA directed primers were used and to specifically detect C. botulinum, BoNT D toxin genes targeted primers, using a multiplex PCR approach, were applied. Our results demonstrate an effective colonization of roots and shoots of clover by C. botulinum strain 2301 and C. sporogenes strain 1739. Detailed analysis of colonization behavior showed that C. botulinum can occur as individual cells, in cell clusters and in microcolonies within the rhizosphere, lateral roots and within the roots tissue of clover. PMID:26583010

  4. Clonal Spread of a Clostridium difficile Strain with a Complete Set of Toxin A, Toxin B, and Binary Toxin Genes among Polish Patients with Clostridium difficile-Associated Diarrhea

    PubMed Central

    Pituch, Hanna; Kreft, Deborah; Obuch-Woszczatyński, Piotr; Wultańska, Dorota; Meisel-Mikołajczyk, Felicja; Łuczak, Mirosław; van Belkum, Alex

    2005-01-01

    Clinically relevant Clostridium difficile strains usually produce toxins A and B. Some C. difficile strains can produce an additional binary toxin. We report clonality among five strains carrying all toxin genes from Polish patients with C. difficile-associated diarrhea. In another strain, possible recombination between binary toxin genes is documented. PMID:15635019

  5. Direct bioconversion of raw corn stalk to hydrogen by a new strain Clostridium sp. FS3.

    PubMed

    Song, Zhao-Xia; Li, Xiao-Hu; Li, Wei-Wei; Bai, Yan-Xia; Fan, Yao-Ting; Hou, Hong-Wei

    2014-04-01

    A new strain FS3 which could achieve an efficient bioconversion of raw corn stalk to hydrogen had been isolated from anaerobic acclimated sludge, and identified as Clostridium butyricum on the basis of a series of physiological and biochemical experiments and 16S rDNA gene sequence. The strain could utilize various carbon sources to produce hydrogen. On the basis of single-factor experiments, the response surface methodology (RSM) was performed to optimize the media for hydrogen production. The maximum hydrogen yield of 92.9ml/g was observed under the optimal conditions: 20g/l raw corn stalk, 1.76g/l NH4HCO3, 0.91g/l KH2PO4 and 10.4ml/l nutrient solution. This finding opens a new avenue for direct conversion of raw cellulosic biomass to bio-hydrogen.

  6. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum

    SciTech Connect

    Shao, Xiongjun; Raman, Babu; Zhu, Mingjun; Mielenz, Jonathan R; Brown, Steven D; Guss, Adam M; Lynd, Lee R

    2011-01-01

    Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1-2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.

  7. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum

    SciTech Connect

    Lynd, Lee R; Shao, Xiongjun; Raman, Babu; Mielenz, Jonathan R; Brown, Steven D; Guss, Adam M; Zhu, Mingjun

    2011-01-01

    Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1 2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.

  8. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum.

    PubMed

    Shao, Xiongjun; Raman, Babu; Zhu, Mingjun; Mielenz, Jonathan R; Brown, Steven D; Guss, Adam M; Lynd, Lee R

    2011-11-01

    Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1-2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed. PMID:21874277

  9. Phenotypic characterization of Clostridium botulinum strains isolated from infant botulism cases in Argentina.

    PubMed

    Sagua, M D; Lúquez, C; Barzola, C P; Bianco, M I; Fernández, R A

    2009-01-01

    Infant botulism is the most common form of human botulism; however, its transmission has not been completely explained yet. Some of the most recognized potential sources of Clostridium botulinum spores are the soil, dust, honey and medicinal herbs. In Argentina, 456 cases of infant botulism were reported between 1982 and 2007. C. botulinum type A was identified in 455 of these cases whereas type B was identified in just one case. However, in Argentina, types A, B, E, F, G, and Af have been isolated from environmental sources. It is not clearly known if strains isolated from infant botulism cases have different characteristics from strains isolated from other sources. During this study, 46 C. botulinum strains isolated from infant botulism cases and from environmental sources were typified according to phenotypic characteristics. Biochemical tests, antimicrobial activity, and haemagglutinin-negative botulinum neurotoxin production showed uniformity among all these strains. Despite the variability observed in the botulinum neurotoxin's binding to cellular receptors, no correlation was found between these patterns and the source of the botulinum neurotoxin. However, an apparent geographical clustering was observed, since strains isolated from Argentina had similar characteristics to those isolated from Italy and Japan, but different to those isolated from the United States. PMID:19831311

  10. Identification and genetic characterization of Clostridium botulinum serotype A strains from commercially pasteurized carrot juice.

    PubMed

    Marshall, Kristin M; Nowaczyk, Louis; Raphael, Brian H; Skinner, Guy E; Rukma Reddy, N

    2014-12-01

    Clostridium botulinum is an important foodborne pathogen capable of forming heat resistant endospores and producing deadly botulinum neurotoxins (BoNTs). In 2006, C. botulinum was responsible for an international outbreak of botulism attributed to the consumption of commercially pasteurized carrot juice. The purpose of this study was to isolate and characterize strains of C. botulinum from the adulterated product. Carrot juice bottles retrieved from the manufacturing facility were analyzed for the presence of BoNT and BoNT-producing isolates using DIG-ELISA. Toxigenic isolates from the carrot juice were analyzed using pulsed-field gel electrophoresis (PFGE) and DNA microarray analysis to determine their genetic relatedness to the original outbreak strains CDC51348 and CDC51303. PFGE revealed that isolates CJ4-1 and CJ10-1 shared an identical pulsotype with strain CDC51303, whereas isolate CJ5-1 displayed a unique restriction banding pattern. DNA microarray analysis identified several phage related genes unique to strain CJ5-1, and Southern hybridization analysis of XhoI digested and nondigested DNA showed their chromosomal location, while a homolog to pCLI_A009 of plasmid pCLI of C. botulinum serotype Langeland F, was located on a small plasmid. The acquisition or loss of bacteriophages and other mobile genetic elements among C. botulinum strains has epidemiological and evolutionary implications.

  11. Butyric acid fermentation from pretreated and hydrolysed wheat straw by an adapted Clostridium tyrobutyricum strain

    PubMed Central

    Baroi, G N; Baumann, I; Westermann, P; Gavala, H N

    2015-01-01

    Butyric acid is a valuable building-block for the production of chemicals and materials and nowadays it is produced exclusively from petroleum. The aim of this study was to develop a suitable and robust strain of Clostridium tyrobutyricum that produces butyric acid at a high yield and selectivity from lignocellulosic biomasses. Pretreated (by wet explosion) and enzymatically hydrolysed wheat straw (PHWS), rich in C6 and C5 sugars (71.6 and 55.4 g l−1 of glucose and xylose respectively), was used as substrate. After one year of serial selections, an adapted strain of C. tyrobutyricum was developed. The adapted strain was able to grow in 80% (v v−1) PHWS without addition of yeast extract compared with an initial tolerance to less than 10% PHWS and was able to ferment both glucose and xylose. It is noticeable that the adapted C. tyrobutyricum strain was characterized by a high yield and selectivity to butyric acid. Specifically, the butyric acid yield at 60–80% PHWS lie between 0.37 and 0.46 g g−1 of sugar, while the selectivity for butyric acid was as high as 0.9–1.0 g g−1 of acid. Moreover, the strain exhibited a robust response in regards to growth and product profile at pH 6 and 7. PMID:26230610

  12. Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge.

    PubMed

    Wong, Y M; Juan, J C; Gan, H M; Austin, C M

    2014-01-01

    Clostridium perfringens strain JJC is an effective biohydrogen and biochemical producer that was isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the gene interactions involved in efficient biohydrogen production. PMID:24604637

  13. Draft Genome Sequences of Two Clostridium botulinum Group II (Nonproteolytic) Type B Strains (DB-2 and KAPB-3).

    PubMed

    Petronella, Nicholas; Kenwell, Robyn; Pagotto, Franco; Pightling, Arthur W

    2014-01-01

    Clostridium botulinum is important for food safety and studies of neurotoxins associated with human botulism. We present the draft genome sequences of two strains belonging to group II type B: one collected from Pacific Ocean sediments (DB-2) and another obtained during a botulism outbreak (KAPB-3). PMID:25377702

  14. Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge

    PubMed Central

    Wong, Y. M.; Gan, H. M.; Austin, C. M.

    2014-01-01

    Clostridium perfringens strain JJC is an effective biohydrogen and biochemical producer that was isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the gene interactions involved in efficient biohydrogen production. PMID:24604637

  15. Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese

    PubMed Central

    Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

    2015-01-01

    Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. PMID:25767226

  16. Mechanisms of microbial oil recovery by Clostridium acetobutylicum and Bacillus strain JF-2

    SciTech Connect

    Marsh, T.L.; Zhang, X.; Knapp, R.M.; McInerney, M.J.; Sharma, P.K.; Jackson, B.E.

    1995-12-31

    Core displacement experiments at elevated pressures were conducted to determine whether microbial processes are effective under conditions that simulate those found in an actual oil reservoir. The in-situ growth of Clostridium acetobutylicum and Bacillus strain JF-2 resulted in the recovery of residual oil. About 21 and 23% of the residual oil was recovered by C. acetobutylicum and Bacillus strain JF-2, respectively. Flooding cores with cell-free culture fluids of C. acetobutylicum with and without the addition of 50 mM acetone and 100 mM butanol did not result in the recovery of residual oil. Mathematical simulations showed that the amount of gas produced by the clostridial fermentation was not showed that the amount of gas produced by the clostridial fermentation was not sufficient to recover residual oil. Oil recovery by Bacillus strain JF-2 was highly correlated to surfactant production. A biosurfactant-deficient mutant of strain JF-2 was not capable of recovering residual oil. These data show that surfactant production is an important mechanism for microbially enhanced oil recovery. The mechanism for oil recovery by C. acetobutylicum is not understood at this time, but the production of acids, solvents, or gases alone cannot explain the observed increases in oil recovery by this organism.

  17. Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children

    NASA Astrophysics Data System (ADS)

    Ling, Zongxin; Liu, Xia; Jia, Xiaoyun; Cheng, Yiwen; Luo, Yueqiu; Yuan, Li; Wang, Yuezhu; Zhao, Chunna; Guo, Shu; Li, Lanjuan; Xu, Xiwei; Xiang, Charlie

    2014-12-01

    Increasing evidence suggests that altered intestinal microbial composition and function result in an increased risk of Clostridium difficile-associated diarrhoea (CDAD); however, the specific changes of intestinal microbiota in children suffering from CDAD and their associations with C. difficile strain toxigenicity are poorly understood. High-throughput pyrosequencing showed that reduced faecal bacterial diversity and dramatic shifts of microbial composition were found in children with CDAD. The Firmicutes/Bacteroidetes ratio was increased significantly in patients with CDAD, which indicated that dysbiosis of faecal microbiota was closely associated with CDAD. C. difficile infection resulted in an increase in lactate-producing phylotypes, with a corresponding decrease in butyrate-producing bacteria. The decrease in butyrate and lactate buildup impaired intestinal colonisation resistance, which increased the susceptibility to C. difficile colonisation. Strains of C. difficile which were positive for both toxin A and toxin B reduced faecal bacterial diversity to a greater degree than strains that were only toxin B-positive, and were associated with unusually abundant Enterococcus, which implies that the C. difficile toxins have different impacts on the faecal microbiota of children. Greater understanding of the relationships between disruption of the normal faecal microbiota and colonisation with C. difficile that produces different toxins might lead to improved treatment.

  18. Isolation of a bile salt sulfatase-producing Clostridium strain from rat intestinal microflora.

    PubMed Central

    Huijghebaert, S M; Mertens, J A; Eyssen, H J

    1982-01-01

    Bile acid sulfates, formed in human and rat livers, are desulfated by the intestinal microflora. In our study we first isolated from conventional rat feces an unnamed bacterium, termed strain S1, which desulfated the 5 beta-bile salt 3 alpha-sulfates in vitro and in vivo after association with gnotobiotic rats. Strain S1 also possessed 12 alpha-hydroxysteroid dehydrogenase and bile salt-deconjugating activities. The strain was a strict anaerobic, CO2-requiring, gram-negative, sporeforming rod and was designated as belonging to the genus Clostridium. Growth was scarce in culture media, unless in the presence of 0.1% taurine, a sulfur-containing amino acid. Addition of this substance raised the number of bacteria in thioglycolate and peptone yeast media from 10(4) per ml to 10(6) to 10(7) per ml and increased the colony diameter on agar medium from 0.2 mm to 0.5 to 0.9 mm. Sulfatase activity was specific for the 5 beta-bile salt sulfates, leaving the 5 alpha-bile salt sulfates unchanged. In addition, the sulfatase activity was cell bound, and its production was dependent on the composition of the culture medium, although no minimal sulfur medium was required for sulfatase activity. Images PMID:7055372

  19. Flagellin Diversity in Clostridium botulinum Groups I and II: a New Strategy for Strain Identification▿

    PubMed Central

    Paul, Catherine J.; Twine, Susan M.; Tam, Kevin J.; Mullen, James A.; Kelly, John F.; Austin, John W.; Logan, Susan M.

    2007-01-01

    Strains of Clostridium botulinum are traditionally identified by botulinum neurotoxin type; however, identification of an additional target for typing would improve differentiation. Isolation of flagellar filaments and analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that C. botulinum produced multiple flagellin proteins. Nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis of in-gel tryptic digests identified peptides in all flagellin bands that matched two homologous tandem flagellin genes identified in the C. botulinum Hall A genome. Designated flaA1 and flaA2, these open reading frames encode the major structural flagellins of C. botulinum. Colony PCR and sequencing of flaA1/A2 variable regions classified 80 environmental and clinical strains into group I or group II and clustered isolates into 12 flagellar types. Flagellar type was distinct from neurotoxin type, and epidemiologically related isolates clustered together. Sequencing a larger PCR product, obtained during amplification of flaA1/A2 from type E strain Bennett identified a second flagellin gene, flaB. LC-MS analysis confirmed that flaB encoded a large type E-specific flagellin protein, and the predicted molecular mass for FlaB matched that observed by SDS-PAGE. In contrast, the molecular mass of FlaA was 2 to 12 kDa larger than the mass predicted by the flaA1/A2 sequence of a given strain, suggesting that FlaA is posttranslationally modified. While identification of FlaB, and the observation by SDS-PAGE of different masses of the FlaA proteins, showed the flagellin proteins of C. botulinum to be diverse, the presence of the flaA1/A2 gene in all strains examined facilitates single locus sequence typing of C. botulinum using the flagellin variable region. PMID:17351097

  20. Strain engineering of graphene: a review

    NASA Astrophysics Data System (ADS)

    Si, Chen; Sun, Zhimei; Liu, Feng

    2016-02-01

    Graphene has intrigued the science community by many unique properties not found in conventional materials. In particular, it is the strongest two-dimensional material ever measured, being able to sustain reversible tensile elastic strain larger than 20%, which yields an interesting possibility to tune the properties of graphene by strain and thus opens a new field called ``straintronics''. In this article, the current progress in the strain engineering of graphene is reviewed. We first summarize the strain effects on the electronic structure and Raman spectra of graphene. We then highlight the electron-phonon coupling greatly enhanced by the biaxial strain and the strong pseudomagnetic field induced by the non-uniform strain with specific distribution. Finally, the potential application of strain-engineering in the self-assembly of foreign atoms on the graphene surface is also discussed. Given the short history of graphene straintronics research, the current progress has been notable, and many further advances in this field are expected.

  1. Spo0A differentially regulates toxin production in evolutionarily diverse strains of Clostridium difficile.

    PubMed

    Mackin, Kate E; Carter, Glen P; Howarth, Pauline; Rood, Julian I; Lyras, Dena

    2013-01-01

    Clostridium difficile is an important pathogen of humans and animals, representing a significant global healthcare problem. The last decade has seen the emergence of epidemic BI/NAP1/027 and ribotype 078 isolates, associated with the onset of more severe disease and higher rates of morbidity and mortality. However, little is known about these isolates at the molecular level, partly due to difficulties in the genetic manipulation of these strains. Here we report the development of an optimised Tn916-mediated plasmid transfer system, and the use of this system to construct and complement spo0A mutants in a number of different C. difficile strain backgrounds. Spo0A is a global regulator known to control sporulation, but may also be involved in the regulation of potential virulence factors and other phenotypes. Recent studies have failed to elucidate the role of Spo0A in toxin A and toxin B production by C. difficile, with conflicting data published to date. In this study, we aimed to clarify the role of Spo0A in production of the major toxins by C. difficile. Through the construction and complementation of spo0A mutants in two ribotype 027 isolates, we demonstrate that Spo0A acts as a negative regulator of toxin A and toxin B production in this strain background. In addition, spo0A was disrupted and subsequently complemented in strain 630Δerm and, for the first time, in a ribotype 078 isolate, JGS6133. In contrast to the ribotype 027 strains, Spo0A does not appear to regulate toxin production in strain 630Δerm. In strain JGS6133, Spo0A appears to negatively regulate toxin production during early stationary phase, but has little effect on toxin expression during late stationary phase. These data suggest that Spo0A may differentially regulate toxin production in phylogenetically distinct C. difficile strain types. In addition, Spo0A may be involved in regulating some aspects of C. difficile motility. PMID:24236153

  2. Spo0A Differentially Regulates Toxin Production in Evolutionarily Diverse Strains of Clostridium difficile

    PubMed Central

    Mackin, Kate E.; Carter, Glen P.; Howarth, Pauline; Rood, Julian I.; Lyras, Dena

    2013-01-01

    Clostridium difficile is an important pathogen of humans and animals, representing a significant global healthcare problem. The last decade has seen the emergence of epidemic BI/NAP1/027 and ribotype 078 isolates, associated with the onset of more severe disease and higher rates of morbidity and mortality. However, little is known about these isolates at the molecular level, partly due to difficulties in the genetic manipulation of these strains. Here we report the development of an optimised Tn916-mediated plasmid transfer system, and the use of this system to construct and complement spo0A mutants in a number of different C. difficile strain backgrounds. Spo0A is a global regulator known to control sporulation, but may also be involved in the regulation of potential virulence factors and other phenotypes. Recent studies have failed to elucidate the role of Spo0A in toxin A and toxin B production by C. difficile, with conflicting data published to date. In this study, we aimed to clarify the role of Spo0A in production of the major toxins by C. difficile. Through the construction and complementation of spo0A mutants in two ribotype 027 isolates, we demonstrate that Spo0A acts as a negative regulator of toxin A and toxin B production in this strain background. In addition, spo0A was disrupted and subsequently complemented in strain 630Δerm and, for the first time, in a ribotype 078 isolate, JGS6133. In contrast to the ribotype 027 strains, Spo0A does not appear to regulate toxin production in strain 630Δerm. In strain JGS6133, Spo0A appears to negatively regulate toxin production during early stationary phase, but has little effect on toxin expression during late stationary phase. These data suggest that Spo0A may differentially regulate toxin production in phylogenetically distinct C. difficile strain types. In addition, Spo0A may be involved in regulating some aspects of C. difficile motility. PMID:24236153

  3. Spo0A differentially regulates toxin production in evolutionarily diverse strains of Clostridium difficile.

    PubMed

    Mackin, Kate E; Carter, Glen P; Howarth, Pauline; Rood, Julian I; Lyras, Dena

    2013-01-01

    Clostridium difficile is an important pathogen of humans and animals, representing a significant global healthcare problem. The last decade has seen the emergence of epidemic BI/NAP1/027 and ribotype 078 isolates, associated with the onset of more severe disease and higher rates of morbidity and mortality. However, little is known about these isolates at the molecular level, partly due to difficulties in the genetic manipulation of these strains. Here we report the development of an optimised Tn916-mediated plasmid transfer system, and the use of this system to construct and complement spo0A mutants in a number of different C. difficile strain backgrounds. Spo0A is a global regulator known to control sporulation, but may also be involved in the regulation of potential virulence factors and other phenotypes. Recent studies have failed to elucidate the role of Spo0A in toxin A and toxin B production by C. difficile, with conflicting data published to date. In this study, we aimed to clarify the role of Spo0A in production of the major toxins by C. difficile. Through the construction and complementation of spo0A mutants in two ribotype 027 isolates, we demonstrate that Spo0A acts as a negative regulator of toxin A and toxin B production in this strain background. In addition, spo0A was disrupted and subsequently complemented in strain 630Δerm and, for the first time, in a ribotype 078 isolate, JGS6133. In contrast to the ribotype 027 strains, Spo0A does not appear to regulate toxin production in strain 630Δerm. In strain JGS6133, Spo0A appears to negatively regulate toxin production during early stationary phase, but has little effect on toxin expression during late stationary phase. These data suggest that Spo0A may differentially regulate toxin production in phylogenetically distinct C. difficile strain types. In addition, Spo0A may be involved in regulating some aspects of C. difficile motility.

  4. Clostridium difficile infection in patients with haematological malignant disease. Risk factors, faecal toxins and pathogenic strains.

    PubMed Central

    Heard, S. R.; Wren, B.; Barnett, M. J.; Thomas, J. M.; Tabaqchali, S.

    1988-01-01

    Two hundred and forty-eight patients from shared oncology and general medical wards were prospectively studied over a 6-month period for carriage of Clostridium difficile during an outbreak of clinical disease with an epidemic strain of the organism. Risk factors for infection were assessed. Acute leukaemia and/or its treatment were identified as significantly increasing the risk of infection. The relationship between the type of C. difficile isolated (as defined by a typing system based on the incorporation of [35S]methionine into bacterial proteins followed by gel electrophoresis), the presence of faecal toxins A and B and clinical symptoms were analysed. Carriage of the epidemic strain, type X, had a significant association with symptoms amongst oncology patients, with two thirds of these patients having detectable faecal toxin A and one third detectable faecal toxin B. During an outbreak of C. difficile-associated disease, typing the organism and assaying for both faecal toxins in symptomatic patients may be of benefit in determining which patients require specific, urgent treatment. PMID:3123260

  5. In vitro activity of MCB3681 against Clostridium difficile strains.

    PubMed

    Rashid, Mamun-Ur; Dalhoff, Axel; Weintraub, Andrej; Nord, Carl Erik

    2014-08-01

    One hundred fourteen Clostridium difficile strains were collected from 67 patients and analyzed for the presence of C. difficile toxin B by the cell cytotoxoicity neutralization assay, genes for toxin A, toxin B, binary toxin and TcdC deletion by PCR. All strains were also PCR-ribotyped. The MICs of the isolates were determined against MCB3681 and nine other antimicrobial agents by the agar dilution method. All isolates were positive for toxin B as well as for toxin A and B genes. In addition, 13 isolates were positive for the binary toxin genes. Thirty-two different ribotypes were identified. No strain of ribotype 027 was found. All 114 isolates were sensitive to MCB3681 (0.008-0.5 mg/l), cadazolid (0.064-0.5 mg/l), fidaxomicin (0.008-0.125 mg/l), metronidazole (0.125-2 mg/l), vancomycin (0.125-1 mg/l) and tigecycline (0.032-0.25 mg/l). Three isolates were resistant to linezolid (8 mg/l), 12 isolates were resistant to moxifloxacin (8-32 mg/l), 87 isolates were resistant to clindamycin (8-256 mg/l) and 107 isolates were resistant to ciprofloxacin (8-256 mg/l). No association between toxins A, B and binary toxin, ribotypes and the sensitivity to MCB3681 could be found. MCB3681 has a potent in vitro activity against C. difficile.

  6. Purification and characterization of a primary-secondary alcohol dehydrogenase from two strains of Clostridium beijerinckii.

    PubMed Central

    Ismaiel, A A; Zhu, C X; Colby, G D; Chen, J S

    1993-01-01

    Two primary alcohols (1-butanol and ethanol) are major fermentation products of several clostridial species. In addition to these two alcohols, the secondary alcohol 2-propanol is produced to a concentration of about 100 mM by some strains of Clostridium beijerinckii. An alcohol dehydrogenase (ADH) has been purified to homogeneity from two strains (NRRL B593 and NESTE 255) of 2-propanol-producing C. beijerinckii. When exposed to air, the purified ADH was stable, whereas the partially purified ADH was inactivated. The ADHs from the two strains had similar structural and kinetic properties. Each had a native M(r) of between 90,000 and 100,000 and a subunit M(r) of between 38,000 and 40,000. The ADHs were NADP(H) dependent, but a low level of NAD(+)-linked activity was detected. They were equally active in reducing aldehydes and 2-ketones, but a much lower oxidizing activity was obtained with primary alcohols than with secondary alcohols. The kcat/Km value for the alcohol-forming reaction appears to be a function of the size of the larger alkyl substituent on the carbonyl group. ADH activities measured in the presence of both acetone and butyraldehyde did not exceed activities measured with either substrate present alone, indicating a common active site for both substrates. There was no similarity in the N-terminal amino acid sequence between that of the ADH and those of fungi and several other bacteria. However, the N-terminal sequence had 67% identity with those of two other anaerobes, Thermoanaerobium brockii and Methanobacterium palustre. Furthermore, conserved glycine and tryptophan residues are present in ADHs of these three anaerobic bacteria and ADHs of mammals and green plants. Images PMID:8349550

  7. Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk.

    PubMed

    La Torre, Angela; Bassi, Daniela; Zotta, Teresa; Orrù, Luigi; Lamontanara, Antonella; Cocconcelli, Pier Sandro

    2016-01-01

    Clostridium sporogenesis a causative agent of food spoilage and is often used as the nontoxigenic surrogate forClostridium botulinum Here, we described the draft genome sequence and annotation ofC. sporogenesstrain UC9000 isolated from raw milk. PMID:27081128

  8. [Comparison of susceptibility of spores of Bacillus subtilis and Czech strains of Clostridium difficile to disinfectants].

    PubMed

    Votava, M; Slitrová, B

    2009-02-01

    An important factor in the prevention of nosocomial outbreaks caused by Clostridium difficile ribotype 027 is the disinfection of a patient environment by reliable sporicidal disinfectants. Sporicidal activity of particular agents is tested on spores of Bacillus subtilis. Questions are brought up if the disinfectant which works on B. subtilis spores will be equally effective on the spores of C. difficile. Therefore we have compared the effects of five disinfectants available on the Czech market on the spores of collection strains of both microbes and on the spores of ten C. difficile field strains isolated from feces of hospitalized patients. The effective substances were: disinfectant No. 1 chloramine B, No. 2 chlorine dioxide, No. 3 formaldehyde and ethan-2-dion, No. 4 peracetic and acetic acids and hydrogen peroxide, No. 5 ethanol and propan-2-ol. The testing was performed using the dilution neutralization method according to (SN EN 13704, the agent reducing the number of spores by more than 3 orders was considered sporicidal. In addition to the standard time 60 min a 15-minutes exposition was used and the effect was tested also under the protein burden. Disinfectant No. 1 showed better effect on the C. difficile than B. subtilis spores, even in lower (1%) concentration. Similarly, the sensitivity of the C. difficile spores to disinfectants No. 2 and 3 was somewhat higher. The sporicidity of the disinfectant No. 4 was so high that it reduced the number of spores of all strains within 15 minutes by more than 4 orders; possible difference in the susceptibility of spores was not observed. Whereas the disinfectant No. 5 was not reliably effective on the spores of B. subtilis, surprisingly it showed the sporicidal effect on the spores of field C. difficile strains. We conclude that spores of field C. difficile strains in particular turned out to be more sensitive to disinfectants than the spores of the collection strain ofB. subtilis. Therefore B. subtilis remains

  9. [Comparison of susceptibility of spores of Bacillus subtilis and Czech strains of Clostridium difficile to disinfectants].

    PubMed

    Votava, M; Slitrová, B

    2009-02-01

    An important factor in the prevention of nosocomial outbreaks caused by Clostridium difficile ribotype 027 is the disinfection of a patient environment by reliable sporicidal disinfectants. Sporicidal activity of particular agents is tested on spores of Bacillus subtilis. Questions are brought up if the disinfectant which works on B. subtilis spores will be equally effective on the spores of C. difficile. Therefore we have compared the effects of five disinfectants available on the Czech market on the spores of collection strains of both microbes and on the spores of ten C. difficile field strains isolated from feces of hospitalized patients. The effective substances were: disinfectant No. 1 chloramine B, No. 2 chlorine dioxide, No. 3 formaldehyde and ethan-2-dion, No. 4 peracetic and acetic acids and hydrogen peroxide, No. 5 ethanol and propan-2-ol. The testing was performed using the dilution neutralization method according to (SN EN 13704, the agent reducing the number of spores by more than 3 orders was considered sporicidal. In addition to the standard time 60 min a 15-minutes exposition was used and the effect was tested also under the protein burden. Disinfectant No. 1 showed better effect on the C. difficile than B. subtilis spores, even in lower (1%) concentration. Similarly, the sensitivity of the C. difficile spores to disinfectants No. 2 and 3 was somewhat higher. The sporicidity of the disinfectant No. 4 was so high that it reduced the number of spores of all strains within 15 minutes by more than 4 orders; possible difference in the susceptibility of spores was not observed. Whereas the disinfectant No. 5 was not reliably effective on the spores of B. subtilis, surprisingly it showed the sporicidal effect on the spores of field C. difficile strains. We conclude that spores of field C. difficile strains in particular turned out to be more sensitive to disinfectants than the spores of the collection strain ofB. subtilis. Therefore B. subtilis remains

  10. Biodiversity of Clostridium botulinum Type E Strains Isolated from Fish and Fishery Products

    PubMed Central

    Hyytiä, Eija; Hielm, Sebastian; Björkroth, Johanna; Korkeala, Hannu

    1999-01-01

    The genetic biodiversity of Clostridium botulinum type E strains was studied by pulsed-field gel electrophoresis (PFGE) with two macrorestriction enzymes (SmaI-XmaI and XhoI) and by randomly amplified polymorphic DNA (RAPD) analysis with two primers (OPJ 6 and OPJ 13) to characterize 67 Finnish isolates from fresh fish and fishery products, 15 German isolates from farmed fish, and 10 isolates of North American or North Atlantic origin derived mainly from different types of seafood. The effects of fish species, processing, and geographical origin on the epidemiology of the isolates were evaluated. Cluster analysis based on macrorestriction profiles was performed to study the genetic relationships of the isolates. PFGE and RAPD analyses were combined and resulted in the identification of 62 different subtypes among the 92 type E isolates analyzed. High genetic biodiversity among the isolates was observed regardless of their source. Finnish and North American or North Atlantic isolates did not form distinctly discernible clusters, in contrast with the genetically homogeneous group of German isolates. On the other hand, indistinguishable or closely related genetic profiles among epidemiologically unrelated samples were detected. It was concluded that the high genetic variation was probably a result of a lack of strong selection factors that would influence the evolution of type E. The wide genetic biodiversity observed among type E isolates indicates the value of DNA-based typing methods as a tool in contamination studies in the food industry and in investigations of botulism outbreaks. PMID:10224001

  11. Comparative Transcriptional Analysis of Clinically Relevant Heat Stress Response in Clostridium difficile Strain 630

    PubMed Central

    Ternan, Nigel G.; Jain, Shailesh; Srivastava, Malay; McMullan, Geoff

    2012-01-01

    Clostridium difficile is considered to be one of the most important causes of health care-associated infections worldwide. In order to understand more fully the adaptive response of the organism to stressful conditions, we examined transcriptional changes resulting from a clinically relevant heat stress (41°C versus 37°C) in C. difficile strain 630 and identified 341 differentially expressed genes encompassing multiple cellular functional categories. While the transcriptome was relatively resilient to the applied heat stress, we noted upregulation of classical heat shock genes including the groEL and dnaK operons in addition to other stress-responsive genes. Interestingly, the flagellin gene (fliC) was downregulated, yet genes encoding the cell-wall associated flagellar components were upregulated suggesting that while motility may be reduced, adherence – to mucus or epithelial cells – could be enhanced during infection. We also observed that a number of phage associated genes were downregulated, as were genes associated with the conjugative transposon Tn5397 including a group II intron, thus highlighting a potential decrease in retromobility during heat stress. These data suggest that maintenance of lysogeny and genome wide stabilisation of mobile elements could be a global response to heat stress in this pathogen. PMID:22860125

  12. Elimination of acetate production to improve ethanol yield during continuous synthesis gas fermentation by engineered biocatalyst Clostridium sp. MTEtOH550.

    PubMed

    Berzin, Vel; Kiriukhin, Michael; Tyurin, Michael

    2012-05-01

    Acetogen strain Clostridum sp. MT653 produced acetate 273 mM (p < 0.005) and ethanol 250 mM (p < 0.005) from synthesis gas blend mixture of 64% CO and 36% H(2). Clostridum sp. MT653 was metabolically engineered to the biocatalyst strain Clostridium sp. MTEtOH550. The biocatalyst increased ethanol yield to 590 mM with no acetate production during single-stage continuous syngas fermentation due to expression of synthetic adh cloned in a multi-copy number expression vector. The acetate production was eliminated by inactivation of the pta gene in Clostridium sp. MTEtOH550. Gene introduction and gene elimination were achieved only using Syngas Biofuels Energy, Inc. electroporation generator. The electrotransformation efficiencies were 8.0 ± 0.2 × 10(6) per microgram of transforming DNA of the expression vector at cell viability ~15%. The frequency of suicidal vector integration to inactivate pta was ~10(-5) per the number of recipient cells. This is the first report on elimination of acetate production and overexpression of synthetic adh gene to engineer acetogen biocatalyst for selective biofuel ethanol production during continuous syngas fermentation.

  13. Detection of nosocomial Clostridium difficile infections with toxigenic strains despite negative toxin A and B testing on stool samples.

    PubMed

    Stahlmann, J; Schönberg, M; Herrmann, M; von Müller, L

    2014-09-01

    A two-step diagnostic algorithm is recommended to detect Clostridium difficile infections; however, samples are regularly found that are glutamate dehydrogenase (GDH) positive but stool toxin negative. In the present single-centre prospective study we focused on these 'difficult-to-interpret' samples and characterized them by anaerobic culture, toxigenic culture, slpA sequence typing and multiplex PCR (GenoType CDiff). The majority of stool toxin A and B-negative samples have been caused by toxigenic strains including ribotype 027. The multiplex PCR was faster and more sensitive compared with culture and allowed preliminary identification of hypervirulent strains in stool samples on the same day.

  14. Purification and characterization of thermostable glucose isomerase from Clostridium thermosulfurogenes and Thermoanaerobacter strain B6A.

    PubMed Central

    Lee, C Y; Zeikus, J G

    1991-01-01

    Glucose isomerases produced by Thermoanaerobacter strain B6A and Clostridium thermosulfurogenes strain 4B were purified 10-11-fold to homogeneity and their physicochemical and catalytic properties were determined. Both purified enzymes displayed very similar properties (native Mr 200,000, tetrameric subunit composition, and apparent pH optima 7.0-7.5). The enzymes were stable at pH 5.5-12.0, and maintained more than 90% activity after incubation at high temperature (85 degrees C) for 1 h in the presence of metal ions. The N-terminal amino acid sequences of both thermostable glucose isomerases were Met-Asn-Lys-Tyr-Phe-Glu-Asn and were not similar to that of the thermolabile Bacillus subtilis enzyme. The glucose isomerase from C. thermosulfurogenes and Thermoanaerobacter displayed pI values of 4.9 and 4.8, and their kcat. and Km values for D-glucose at 65 degrees C were 1040 and 1260 min-1 and 140 and 120 mM respectively. Both enzymes displayed higher kcat. and lower Km values for D-xylose than for D-glucose. The C. thermosulfurogenes enzyme required Co2+ or Mg2+ for thermal stability and glucose isomerase activity, and Mn2+ or these metals for xylose isomerase activity. Crystals of C. thermosulfurogenes glucose isomerase were formed at room temperature by the hanging-drop method using 16-18% poly(ethylene glycol) (PEG) 4000 in 0.1 M-citrate buffer. Images Fig. 1. Fig. 5. PMID:1996956

  15. Control of surface wettability via strain engineering

    NASA Astrophysics Data System (ADS)

    Xiong, Wei; Liu, Jefferson Zhe; Zhang, Zhi-Liang; Zhen, Quan-Shui

    2013-08-01

    Reversible control of surface wettability has wide applications in lab-on-chip systems, tunable optical lenses, and microfluidic tools. Using a graphene sheet as a sample material and molecular dynamic simulations, we demonstrate that strain engineering can serve as an effective way to control the surface wettability. The contact angles θ of water droplets on a graphene vary from 72.5° to 106° under biaxial strains ranging from -10% to 10% that are applied on the graphene layer. For an intrinsic hydrophilic surface (at zero strain), the variation of θ upon the applied strains is more sensitive, i.e., from 0° to 74.8°. Overall the cosines of the contact angles exhibit a linear relation with respect to the strains. In light of the inherent dependence of the contact angle on liquid-solid interfacial energy, we develop an analytic model to show the cos θ as a linear function of the adsorption energy E ads of a single water molecule over the substrate surface. This model agrees with our molecular dynamic results very well. Together with the linear dependence of E ads on biaxial strains, we can thus understand the effect of strains on the surface wettability. Thanks to the ease of reversibly applying mechanical strains in micro/nano-electromechanical systems, we believe that strain engineering can be a promising means to achieve the reversibly control of surface wettability.

  16. Immunoprecipitation of Native Botulinum Neurotoxin Complexes from Clostridium botulinum Subtype A Strains

    PubMed Central

    Lin, Guangyun; Tepp, William H.; Bradshaw, Marite; Fredrick, Chase M.

    2014-01-01

    Botulinum neurotoxins (BoNTs) naturally exist as components of protein complexes containing nontoxic proteins. The nontoxic proteins impart stability of BoNTs in the gastrointestinal tract and during purification and handling. The two primary neurotoxin complexes (TCs) are (i) TC1, consisting of BoNT, nontoxin-nonhemagglutinin (NTNH), and hemagglutinins (HAs), and (ii) TC2, consisting of BoNT and NTNH (and possibly OrfX proteins). In this study, BoNT/A subtypes A1, A2, A3, and A5 were examined for the compositions of their TCs in culture extracts using immunoprecipitation (IP). IP analyses showed that BoNT/A1 and BoNT/A5 form TC1s, while BoNT/A2 and BoNT/A3 form TC2s. A Clostridium botulinum host strain expressing recombinant BoNT/A4 (normally present as a TC2) from an extrachromosomal plasmid formed a TC1 with complexing proteins from the host strain, indicating that the HAs and NTNH encoded on the chromosome associated with the plasmid-encoded BoNT/A4. Strain NCTC 2916 (A1/silent B1), which carries both an ha silent bont/b cluster and an orfX bont/a1 cluster, was also examined. IP analysis revealed that NCTC 2916 formed only a TC2 containing BoNT/A1 and its associated NTNH. No association between BoNT/A1 and the nontoxic proteins from the silent bont/b cluster was detected, although the HAs were expressed as determined by Western blotting analysis. Additionally, NTNH and HAs from the silent bont/b cluster did not form a complex in NCTC 2916. The stabilities of the two types of TC differed at various pHs and with addition of KCl and NaCl. TC1 complexes were more stable than TC2 complexes. Mouse serum stabilized TC2, while TC1 was unaffected. PMID:25362065

  17. [Progress on engineered strains for ethanol production].

    PubMed

    Wang, Fan-qiang; Xu, Ping

    2006-08-01

    With the 21 century's coming, the era of cheap oil is coming to the end. There has been an increasing worldwide interest in fuel ethanol. In the last two decades, lots of work has been done to develop strains for ethanol producing. Research progress on metabolic engineering of strains for fuel ethanol production is summarized, including genetically engineered Saccharomyces cerevisiae to utilize starch, pentose and cellulose, Zymomonas mobilis to ferment arabinose and xylose, Escherichia coli and Klebsiella oxytoca to introduce heterogenous ethanol production pathway. The aim of engineering these strains is to obtain an ideal microorganism which can converse the available carbon sources to ethanol rapidly and efficiently with high tolerance to ethanol and to inhibitory components in the cheap materials such as lignocellulose hydrolysate. The importance of fuel ethanol will be a stimulus to develop engineered hardy strains to utilize cheap materials for high ethanol concentration production. Since both Saccharomyces cerevisiae and Zymomonas mobilis are generally regarded as safe (GRAS), genetically engineered Saccharomyces cerevisiae which can utilize raw starch directly and recombinant Zymomonas mobilis which can ferment glucose, arabinose and xylose in the lignocellulose hydrolysate have potential application to industry in the near future.

  18. Membrane vesicles of Clostridium perfringens Type A strains induce innate and adaptive immunity

    PubMed Central

    Jiang, Yanlong; Kong, Qingke; Roland, Kenneth L.; Curtiss, Roy

    2014-01-01

    Vesicle shedding from bacteria is a universal process in most Gram-negative bacteria and a few Gram-positive bacteria. In this report, we isolate extracellular membrane vesicles (MVs) from the supernatants of Gram-positive pathogen Clostridium perfringens (C. perfringens). We demonstrated vesicle production in a variety of virulent and nonvirulent type A strains. MVs did not contain alpha-toxin and NetB toxin demonstrated by negative reaction to specific antibody and absence of specific proteins identified by LC-MS/MS. C. perfringens MVs contained DNA components such as 16S ribosomal RNA gene (16S rRNA), alpha-toxin gene (plc) and the perfringolysin O gene (pfoA) demonstrated by PCR. We also identified a total of 431 proteins in vesicles by 1-D gel separation and LC-MS/MS analysis. In vitro studies demonstrated that vesicles could be internalized into murine macrophage RAW264.7 cells without direct cytotoxicity effects, causing release of inflammation cytokines including granulocyte colony stimulating factor (G-CSF), tumor necrosis factor-alpha (TNF-α) and interleukin-1 (IL-1), which could also be detected in mice injected with MVs through intraperitoneal (i.p.) route. Mice immunized with C. perfringens MVs produced high titer IgG, especially IgG1, antibodies against C. perfringens membrane proteins. However, this kind of antibody could not provide protection in mice following challenge, though it could slightly postpone the time of death. Our results indicate that release of MVs from C. perfringens could provide a previously unknown mechanism to induce release of inflammatory cytokines, especially TNF-α, these findings may contribute to a better understanding of the pathogenesis of C. perfringens infection. PMID:24631214

  19. Whole-Genome Sequence of Clostridium botulinum A2B3 87, a Highly Virulent Strain Involved in a Fatal Case of Foodborne Botulism in Italy

    PubMed Central

    Giordani, Francesco; Fillo, Silvia; Anselmo, Anna; Palozzi, Anna Maria; Fortunato, Antonella; Gentile, Bernardina; Pittiglio, Valentina; Spagnolo, Ferdinando; Anniballi, Fabrizio; Fiore, Alfonsina; Auricchio, Bruna; De Medici, Dario

    2015-01-01

    Here, we report the genome sequence of a rare bivalent strain of Clostridium botulinum, A2B3 87. The strain was isolated from a foodborne botulism case that occurred in Italy in 1995. The case was characterized by rapid evolution of the illness and failure of conventional treatments. PMID:25814616

  20. Engineering Clostridium beijerinckii with the Cbei_4693 gene knockout for enhanced ferulic acid tolerance.

    PubMed

    Liu, Jun; Guo, Ting; Shen, Xiaoning; Xu, Jiahui; Wang, Junzhi; Wang, Yanyan; Liu, Dong; Niu, Huanqing; Liang, Lei; Ying, Hanjie

    2016-07-10

    A mutant strain of Clostridium beijerinckii NCIMB 8052, C. beijerinckii M11, which exhibited ferulic acid tolerance up to 0.9g/L, was generated using atmospheric pressure glow discharge and high-throughput screening. Comparative genomic analysis revealed that this strain harbored a mutation of the Cbei_4693 gene, which encodes a hypothetical protein suspected to be an NADPH-dependent FMN reductase. After disrupting the Cbei_4693 gene in C. beijerinckii NCIMB 8052 using the ClosTron group II intron-based gene inactivation system, we obtained the Cbei_4693 gene inactivated mutant strain, C. beijerinckii 4693::int. Compared with C. beijerinckii NCIMB 8052, 6.23g/L of butanol was produced in P2 medium containing 0.5g/L of ferulic acid by 4693::int, and the ferulic acid tolerance was also significantly increased up to 0.8g/L. These data showed, for the first time, that the Cbei_4693 gene plays an important role in regulating ferulic acid tolerance in ABE fermentation by C. beijerinckii. PMID:27164255

  1. Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile strains isolated from swine and dogs in Italy.

    PubMed

    Spigaglia, Patrizia; Drigo, Ilenia; Barbanti, Fabrizio; Mastrantonio, Paola; Bano, Luca; Bacchin, Cosetta; Puiatti, Cinzia; Tonon, Elena; Berto, Giacomo; Agnoletti, Fabrizio

    2015-02-01

    Recent studies suggest animals, in particular farm and companion animals, as possible reservoir for Clostridium difficile human pathogenic strains. The aim of this study was to give a first characterization of C. difficile isolates from Italian swine and dogs. In total, 10 different PCR-ribotypes were identified among porcine strains and six among canine strains. The predominant type found among porcine strains was 078 (50%), whereas the most frequently detected among canine strains was the non-toxinogenic 010 (64%). Considering the CLSI breakpoints, 60% of porcine isolates was resistant to ERY, 35% to MXF, 15% to CLI, 5% to RIF, and none to MTZ or VAN. Among dogs, 51% of strains was resistant to CLI, 46% to ERY, 21% to MTZ and 5% to MXF or RIF, and none to VAN. Five porcine strains (10%) and 9 canine isolates (41%) were MDR. Interestingly, 8 MDR canine strains were highly resistant to MTZ, with MICs ≥32 mg/L. Considering the EUCAST cut-off for MTZ (MIC >2 mg/L), 13 canine isolates and one porcine strain were found with reduced susceptibility to MTZ (MICs ranging from 3 to ≥256 mg/L). Swine and canine strains showing resistance or reduced susceptibility to MTZ belonged to PCR-ribotype 010 and 078. These PCR-ribotypes have been associated to reduced susceptibility to MTZ also in human, suggesting a potential risk for the emergence of C. difficile strains resistant to the current first-line antibiotic for CDI treatment. The agar incorporation method (AIM) was confirmed as the best method to detect C. difficile strains with this phenotype also after strains manipulations. The results obtained add further evidences about the possible role of animals as source of MDR C. difficile strains and reservoir of antibiotic resistance determinants.

  2. Genetic, physiological and nutritional studies on Clostridium strains isolated and screened for characteristics useful in enhanced oil recovery, with special reference to high salt tolerance

    SciTech Connect

    Grula, M.M.; Russell, H.H.

    1990-03-01

    This work is concerned with a group of microorganisms generally thought to have the highest potential for usefulness in microbial enhancement of oil recovery (MEOR), namely, fermentative species of the genus Clostridium. The report consists of two parts: (1) a study of the effects of various environmental factors (mainly chemical) on growth, gas production, sporulation, and spore germination of several strains of Clostridium in laboratory media; and (2) a study of the effects of core minerals and pore volume on solvent, acid, and gas production and refeedability (in cores) of similar freshly isolated Clostridium strains. In addition, the bacterial strains were characterized, and their basic nutritional requirements were determined. 15 refs., 27 figs., 37 tabs.

  3. Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Guess, Adam

    2013-03-01

    Adam Guss of Oak Ridge National Lab on "Metabolic engineering of Clostridium thermocellum for biofuel production" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  4. Effect of hospital disinfectants on spores of clinical Brazilian Clostridium difficile strains.

    PubMed

    Ferreira, Thaís Gonçalves; Barbosa, Thaís Flecher; Teixeira, Felipe Lopes; Ferreira, Eliane de Oliveira; Duarte, Rafael Silva; Domingues, Regina Maria Cavalcanti Pilotto; de Paula, Geraldo Renato

    2013-08-01

    The aim of this study was to evaluate the sporicidal activity of hospital disinfectants against spores of two Brazilian Clostridium difficile ribotypes and the BI/NAP1/027. Our results showed that CloroRio(®) and Cidex Opa(®) were the most efficient agents for eliminating spores of C difficile.

  5. Characteristics of a strain of Clostridium carnis causing septicaemia in a young infant.

    PubMed

    Wort, A J; Ozere, R L

    1976-11-01

    Clostridium carnis is a species which is only rarely isolated from man or animals and is occasionally found in the soil. This paper is an account of a single isolate found in blood cultures obtained from an 8-week-old boy who was suffering from gastroenteritis.

  6. Characteristics of a strain of Clostridium carnis causing septicaemia in a young infant.

    PubMed Central

    Wort, A J; Ozere, R L

    1976-01-01

    Clostridium carnis is a species which is only rarely isolated from man or animals and is occasionally found in the soil. This paper is an account of a single isolate found in blood cultures obtained from an 8-week-old boy who was suffering from gastroenteritis. PMID:1002832

  7. Ethanol production from syngas by Clostridium strain P11 using corn steep liquor as a nutrient replacement to yeast extract.

    PubMed

    Maddipati, Prasanth; Atiyeh, Hasan K; Bellmer, Danielle D; Huhnke, Raymond L

    2011-06-01

    The feasibility of replacing yeast extract (YE) by corn steep liquor (CSL), a low cost nutrient source, for syngas fermentation to produce ethanol using Clostridium strain P11 was investigated. About 32% more ethanol (1.7 g L(-1)) was produced with 20 g L(-1) CSL media in 250-mL bottle fermentations compared to media with 1 g L(-1) YE after 360 h. Maximum ethanol concentrations after 360 h of fermentation in a 7.5-L fermentor with 10 and 20 g L(-1) CSL media were 8.6 and 9.6 g L(-1), respectively, which represent 57% and 60% of the theoretical ethanol yields from CO. Only about 6.1 g L(-1) of ethanol was obtained in the medium with 1 g L(-1) YE after 360 h, which represents 53% of the theoretical ethanol yield from CO. The use of CSL also enhanced butanol production by sevenfold compared to YE in bottle fermentations. These results demonstrate that CSL can replace YE as the primary medium component and significantly enhance ethanol production by Clostridium strain P11.

  8. Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression

    PubMed Central

    Scalfaro, Concetta; Iacobino, Angelo; Grande, Laura; Morabito, Stefano; Franciosa, Giovanna

    2016-01-01

    Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E. PMID:26941734

  9. Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression.

    PubMed

    Scalfaro, Concetta; Iacobino, Angelo; Grande, Laura; Morabito, Stefano; Franciosa, Giovanna

    2016-01-01

    Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E. PMID:26941734

  10. Three enzymatically active neurotoxins of Clostridium botulinum strain Af84: BoNT/A2, /F4, and /F5.

    PubMed

    Kalb, Suzanne R; Baudys, Jakub; Smith, Theresa J; Smith, Leonard A; Barr, John R

    2014-04-01

    Botulinum neurotoxins (BoNTs) are produced by various species of clostridia and are potent neurotoxins which cause the disease botulism, by cleaving proteins needed for successful nerve transmission. There are currently seven confirmed serotypes of BoNTs, labeled A-G, and toxin-producing clostridia typically only produce one serotype of BoNT. There are a few strains (bivalent strains) which are known to produce more than one serotype of BoNT, producing either both BoNT/A and /B, BoNT/A and /F, or BoNT/B and /F, designated as Ab, Ba, Af, or Bf. Recently, it was reported that Clostridium botulinum strain Af84 has three neurotoxin gene clusters: bont/A2, bont/F4, and bont/F5. This was the first report of a clostridial organism containing more than two neurotoxin gene clusters. Using a mass spectrometry based proteomics approach, we report here that all three neurotoxins, BoNT/A2, /F4, and /F5, are produced by C. botulinum Af84. Label free MS(E) quantification of the three toxins indicated that toxin composition is 88% BoNT/A2, 1% BoNT/F4, and 11% BoNT/F5. The enzymatic activity of all three neurotoxins was assessed by examining the enzymatic activity of the neurotoxins upon peptide substrates, which mimic the toxins' natural targets, and monitoring cleavage of the substrates by mass spectrometry. We determined that all three neurotoxins are enzymatically active. This is the first report of three enzymatically active neurotoxins produced in a single strain of Clostridium botulinum.

  11. Purification and Characterization of Botulinum Neurotoxin FA from a Genetically Modified Clostridium botulinum Strain

    PubMed Central

    Pellett, Sabine; Tepp, William H.; Bradshaw, Marite; Kalb, Suzanne R.; Dykes, Janet K.; Lin, Guangyun; Nawrocki, Erin M.; Pier, Christina L.; Barr, John R.; Maslanka, Susan E.

    2016-01-01

    ABSTRACT Botulinum neurotoxins (BoNTs), produced by neurotoxigenic clostridial species, are the cause of the severe disease botulism in humans and animals. Early research on BoNTs has led to their classification into seven serotypes (serotypes A to G) based upon the selective neutralization of their toxicity in mice by homologous antibodies. Recently, a report of a potential eighth serotype of BoNT, designated “type H,” has been controversial. This novel BoNT was produced together with BoNT/B2 in a dual-toxin-producing Clostridium botulinum strain. The data used to designate this novel toxin as a new serotype were derived from culture supernatant containing both BoNT/B2 and novel toxin and from sequence information, although data from two independent laboratories indicated neutralization by antibodies raised against BoNT/A1, and classification as BoNT/FA was proposed. The sequence data indicate a chimeric structure consisting of a BoNT/A1 receptor binding domain, a BoNT/F5 light-chain domain, and a novel translocation domain most closely related to BoNT/F1. Here, we describe characterization of this toxin purified from the native strain in which expression of the second BoNT (BoNT/B) has been eliminated. Mass spectrometry analysis indicated that the toxin preparation contained only BoNT/FA and confirmed catalytic activity analogous to that of BoNT/F5. The in vivo mouse bioassay indicated a specific activity of this toxin of 3.8 × 107 mouse 50% lethal dose (mLD50) units/mg, whereas activity in cultured human neurons was very high (50% effective concentration [EC50] = 0.02 mLD50/well). Neutralization assays in cells and mice both indicated full neutralization by various antibodies raised against BoNT/A1, although at 16- to 20-fold-lower efficiency than for BoNT/A1. IMPORTANCE Botulinum neurotoxins (BoNTs), produced by anaerobic bacteria, are the cause of the potentially deadly, neuroparalytic disease botulism. BoNTs have been classified into seven serotypes

  12. Purification and Characterization of Botulinum Neurotoxin FA from a Genetically Modified Clostridium botulinum Strain.

    PubMed

    Pellett, Sabine; Tepp, William H; Bradshaw, Marite; Kalb, Suzanne R; Dykes, Janet K; Lin, Guangyun; Nawrocki, Erin M; Pier, Christina L; Barr, John R; Maslanka, Susan E; Johnson, Eric A

    2016-01-01

    Botulinum neurotoxins (BoNTs), produced by neurotoxigenic clostridial species, are the cause of the severe disease botulism in humans and animals. Early research on BoNTs has led to their classification into seven serotypes (serotypes A to G) based upon the selective neutralization of their toxicity in mice by homologous antibodies. Recently, a report of a potential eighth serotype of BoNT, designated "type H," has been controversial. This novel BoNT was produced together with BoNT/B2 in a dual-toxin-producing Clostridium botulinum strain. The data used to designate this novel toxin as a new serotype were derived from culture supernatant containing both BoNT/B2 and novel toxin and from sequence information, although data from two independent laboratories indicated neutralization by antibodies raised against BoNT/A1, and classification as BoNT/FA was proposed. The sequence data indicate a chimeric structure consisting of a BoNT/A1 receptor binding domain, a BoNT/F5 light-chain domain, and a novel translocation domain most closely related to BoNT/F1. Here, we describe characterization of this toxin purified from the native strain in which expression of the second BoNT (BoNT/B) has been eliminated. Mass spectrometry analysis indicated that the toxin preparation contained only BoNT/FA and confirmed catalytic activity analogous to that of BoNT/F5. The in vivo mouse bioassay indicated a specific activity of this toxin of 3.8 × 10(7) mouse 50% lethal dose (mLD50) units/mg, whereas activity in cultured human neurons was very high (50% effective concentration [EC50] = 0.02 mLD50/well). Neutralization assays in cells and mice both indicated full neutralization by various antibodies raised against BoNT/A1, although at 16- to 20-fold-lower efficiency than for BoNT/A1. IMPORTANCE Botulinum neurotoxins (BoNTs), produced by anaerobic bacteria, are the cause of the potentially deadly, neuroparalytic disease botulism. BoNTs have been classified into seven serotypes, serotypes A

  13. Deciphering Adaptation Strategies of the Epidemic Clostridium difficile 027 Strain during Infection through In Vivo Transcriptional Analysis

    PubMed Central

    Kansau, Imad; Barketi-Klai, Amira; Monot, Marc; Hoys, Sandra; Dupuy, Bruno; Janoir, Claire; Collignon, Anne

    2016-01-01

    Clostridium difficile is responsible for a wide spectrum of infection from asymptomatic carriage to severe, relapsing colitis. Since 2003, C. difficile infections have increased with a higher morbidity and mortality due to the emergence of epidemic and hypervirulent C. difficile strains such as those of the epidemic lineage 027/BI/NAP1. To decipher the hypervirulence and epidemicity of 027 strains, we analyzed gene expression profiles of the R20291 027 strain using a monoxenic mouse model during the first 38h of infection. A total of 741 genes were differentially expressed during the course of infection. They are mainly distributed in functional categories involved in host adaptation. Several genes of PTS and ABC transporters were significantly regulated during the infection, underlying the ability of strain R20291 to adapt its metabolism according to nutrient availability in the digestive tract. In this animal model, despite the early sporulation process, sporulation efficiency seems to indicate that growth of R20291 vegetative cells versus spores were favored during infection. The bacterial mechanisms associated to adaptability and flexibility within the gut environment, in addition to the virulence factor expression and antibiotic resistance, should contribute to the epidemicity and hypervirulence of the C. difficile 027 strains. PMID:27351947

  14. Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential.

    PubMed

    Koeck, Daniela E; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

    2014-07-01

    Clostridium thermocellum is among the most prevalent of known anaerobic cellulolytic bacteria. In this study, genetic and phenotypic variations among C. thermocellum strains isolated from different biogas plants were determined and different genotyping methods were evaluated on these isolates. At least two C. thermocellum strains were isolated independently from each of nine different biogas plants via enrichment on cellulose. Various DNA-based genotyping methods such as ribotyping, RAPD (Random Amplified Polymorphic DNA) and VNTR (Variable Number of Tandem Repeats) were applied to these isolates. One novel approach - the amplification of unknown target sequences between copies of a previously discovered Random Inserted Mobile Element (RIME) - was also tested. The genotyping method with the highest discriminatory power was found to be the amplification of the sequences between the insertion elements, where isolates from each biogas plant yielded a different band pattern. Cellulolytic potentials, optimal growth conditions and substrate spectra of all isolates were characterized to help identify phenotypic variations. Irrespective of the genotyping method used, the isolates from each individual biogas plant always exhibited identical patterns. This is suggestive of a single C. thermocellum strain exhibiting dominance in each biogas plant. The genotypic groups reflect the results of the physiological characterization of the isolates like substrate diversity and cellulase activity. Conversely, strains isolated across a range of biogas plants differed in their genotyping results and physiological properties. Both strains isolated from one biogas plant had the best specific cellulose-degrading properties and might therefore achieve superior substrate utilization yields in biogas fermenters.

  15. Enhanced expression of recombinant beta toxin of Clostridium perfringens type B using a commercially available Escherichia coli strain.

    PubMed

    Bakhshi, Fatemah; Pilehchian Langroudi, Reza; Eimani, Bahram Golestani

    2016-01-01

    Clostridium perfringens beta toxin is only produced by types B and C and plays an important role in many human and animal diseases, causing fatal conditions that originate in the intestines. We compared the expression of C. perfringens type B vaccine strain recombinant beta toxin gene in the Escherichia coli strains Rosetta(DE3) and BL21(DE3). The beta toxin gene was extracted from pJETβ and ligated with pET22b(+). pET22β was transformed into E. coli strains BL21(DE3) and Rosetta(DE3). Recombinant protein was expressed as a soluble protein after isopropyl β-D-1-thiogalactopyranoside (IPTG) induction in strain Rosetta(DE3) but not in BL21(DE3). Expression was optimised by growing recombinant cells at 37 °C and at an induction of 0.5 mM, 1 mM, 1.5 mM IPTG. Expression was evaluated using sodium dodecyl sulfate Polyacrylamide gel electrophoresis (SDS-PAGE). The recombinant protein was purified via Ni-NTA and was analysed using western blot. We concluded that E. coli strain RosettaTM(DE3) can enhance the expression of C. perfringens recombinant beta toxin. PMID:27380656

  16. Global Phenotypic Characterization of Effects of Fluoroquinolone Resistance Selection on the Metabolic Activities and Drug Susceptibilities of Clostridium perfringens Strains.

    PubMed

    Park, Miseon; Rafii, Fatemeh

    2014-01-01

    Fluoroquinolone resistance affects toxin production of Clostridium perfringens strains differently. To investigate the effect of fluoroquinolone resistance selection on global changes in metabolic activities and drug susceptibilities, four C. perfringens strains and their norfloxacin-, ciprofloxacin-, and gatifloxacin-resistant mutants were compared in nearly 2000 assays, using phenotype microarray plates. Variations among mutant strains resulting from resistance selection were observed in all aspects of metabolism. Carbon utilization, pH range, osmotic tolerance, and chemical sensitivity of resistant strains were affected differently in the resistant mutants depending on both the bacterial genotype and the fluoroquinolone to which the bacterium was resistant. The susceptibilities to gentamicin and erythromycin of all resistant mutants except one increased, but some resistant strains were less susceptible to amoxicillin, cefoxitin, ceftriaxone, chloramphenicol, and metronidazole than their wild types. Sensitivity to ethidium bromide decreased in some resistant mutants and increased in others. Microarray analysis of two gatifloxacin-resistant mutants showed changes in metabolic activities that were correlated with altered expression of various genes. Both the chemical structures of fluoroquinolones and the genomic makeup of the wild types influenced the changes found in resistant mutants, which may explain some inconsistent reports of the effects of therapeutic use of fluoroquinolones on clinical isolates of bacteria. PMID:25587280

  17. Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.

    PubMed

    Wong, Y M; Juan, J C; Ting, Adeline; Wu, T Y; Gan, H M; Austin, C M

    2014-01-01

    Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production. PMID:24604640

  18. Draft Genome Sequence of an Oxalate-Degrading Strain of Clostridium sporogenes from the Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula)

    PubMed Central

    Miller, Aaron; Dale, Colin; Dearing, Denise

    2016-01-01

    The gastrointestinal tract of the white-throated woodrat Neotoma albigula harbors a diverse microbial population that functions in the degradation of ingested plant secondary compounds. Here, we present the draft genome sequence and annotation of Clostridium sporogenes strain 8-O, a novel oxalate-degrading bacterium isolated from the feces of N. albigula. PMID:27198026

  19. Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm.

    PubMed

    Ransom-Jones, Emma; McDonald, James E

    2016-01-01

    Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic, cellulolytic biofilm of a cotton string sample incubated in a landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510 bp, 51.5% G+C content, and 4,119 predicted coding domain sequences. PMID:27660778

  20. Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge

    PubMed Central

    Wong, Y. M.; Ting, Adeline; Wu, T. Y.; Gan, H. M.; Austin, C. M.

    2014-01-01

    Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production. PMID:24604640

  1. Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.

    PubMed

    Wong, Y M; Juan, J C; Ting, Adeline; Wu, T Y; Gan, H M; Austin, C M

    2014-03-06

    Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production.

  2. Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm

    PubMed Central

    2016-01-01

    Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic, cellulolytic biofilm of a cotton string sample incubated in a landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510 bp, 51.5% G+C content, and 4,119 predicted coding domain sequences. PMID:27660778

  3. Reexamining the Germination Phenotypes of Several Clostridium difficile Strains Suggests Another Role for the CspC Germinant Receptor

    PubMed Central

    Bhattacharjee, Disha; Francis, Michael B.; Ding, Xicheng; McAllister, Kathleen N.; Shrestha, Ritu

    2015-01-01

    ABSTRACT Clostridium difficile spore germination is essential for colonization and disease. The signals that initiate C. difficile spore germination are a combination of taurocholic acid (a bile acid) and glycine. Interestingly, the chenodeoxycholic acid class (CDCA) bile acids competitively inhibit taurocholic acid-mediated germination, suggesting that compounds that inhibit spore germination could be developed into drugs that prophylactically prevent C. difficile infection or reduce recurring disease. However, a recent report called into question the utility of such a strategy to prevent infection by describing C. difficile strains that germinated in the apparent absence of bile acids or germinated in the presence of the CDCA inhibitor. Because the mechanisms of C. difficile spore germination are beginning to be elucidated, the mechanism of germination in these particular strains could yield important information on how C. difficile spores initiate germination. Therefore, we quantified the interaction of these strains with taurocholic acid and CDCA, the rates of spore germination, the release of DPA from the spore core, and the abundance of the germinant receptor complex (CspC, CspB, and SleC). We found that strains previously observed to germinate in the absence of taurocholic acid correspond to more potent 50% effective concentrations (EC50 values; the concentrations that achieve a half-maximum germination rate) of the germinant and are still inhibited by CDCA, possibly explaining the previous observations. By comparing the germination kinetics and the abundance of proteins in the germinant receptor complex, we revised our original model for CspC-mediated activation of spore germination and propose that CspC may activate spore germination and then inhibit downstream processes. IMPORTANCE Clostridium difficile forms metabolically dormant spores that persist in the health care environment. In susceptible hosts, C. difficile spores germinate in response to certain

  4. Regulation of Type IV Pili Contributes to Surface Behaviors of Historical and Epidemic Strains of Clostridium difficile

    PubMed Central

    Purcell, Erin B.; McKee, Robert W.; Bordeleau, Eric; Burrus, Vincent

    2015-01-01

    ABSTRACT The intestinal pathogen Clostridium difficile is an urgent public health threat that causes antibiotic-associated diarrhea and is a leading cause of fatal nosocomial infections in the United States. C. difficile rates of recurrence and mortality have increased in recent years due to the emergence of so-called “hypervirulent” epidemic strains. A great deal of the basic biology of C. difficile has not been characterized. Recent findings that flagellar motility, toxin synthesis, and type IV pilus (TFP) formation are regulated by cyclic diguanylate (c-di-GMP) reveal the importance of this second messenger for C. difficile gene regulation. However, the function(s) of TFP in C. difficile remains largely unknown. Here, we examine TFP-dependent phenotypes and the role of c-di-GMP in controlling TFP production in the historical 630 and epidemic R20291 strains of C. difficile. We demonstrate that TFP contribute to C. difficile biofilm formation in both strains, but with a more prominent role in R20291. Moreover, we report that R20291 is capable of TFP-dependent surface motility, which has not previously been described in C. difficile. The expression and regulation of the pilA1 pilin gene differs between R20291 and 630, which may underlie the observed differences in TFP-mediated phenotypes. The differences in pilA1 expression are attributable to greater promoter-driven transcription in R20291. In addition, R20291, but not 630, upregulates c-di-GMP levels during surface-associated growth, suggesting that the bacterium senses its substratum. The differential regulation of surface behaviors in historical and epidemic C. difficile strains may contribute to the different infection outcomes presented by these strains. IMPORTANCE How Clostridium difficile establishes and maintains colonization of the host bowel is poorly understood. Surface behaviors of C. difficile are likely relevant during infection, representing possible interactions between the bacterium and the

  5. Clostridium difficile in goats and sheep in Slovenia: characterisation of strains and evidence of age-related shedding.

    PubMed

    Avberšek, Jana; Pirš, Tina; Pate, Mateja; Rupnik, Maja; Ocepek, Matjaž

    2014-08-01

    Diversity of Clostridium difficile in different age groups of goats (n = 109) and sheep (n = 105) was investigated. C. difficile was detected in 9.2% of goats and 5.7% of sheep. None of the adult animals were positive. Isolates belonged to four toxinotypes (0, V, XIa, XII), six PCR-ribotypes (010, 014/020, 045, 056, SLO 061, SLO 151) and six pulsotypes. PCR-ribotypes 010, 014/020, 045 and 056 were found previously in other animal species and humans in Slovenia. Additionally, three pulsotypes were indistinguishable from restriction patterns in our PFGE database of animal isolates. All strains were susceptible to metronidazol, vancomycin, moxifloxacin, and with the exception of a single non-toxigenic strain also to clindamycin and erythromycin. While all strains were resistant to ciprofloxacin and levofloxacin, oxacillin-resistance was observed only in strains of PCR-ribotype 045. This first study on C. difficile in small ruminants in Slovenia revealed the evidence of age-related shedding as the highest was demonstrated in neonatal goats and sheep aged up to 16 days.

  6. Clostridium botulinum Group I Strain Genotyping by 15-Locus Multilocus Variable-Number Tandem-Repeat Analysis ▿ †

    PubMed Central

    Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M.; Scholz, Holger C.; Splettstoesser, Wolf D.; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

    2011-01-01

    Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse. PMID:22012011

  7. Clostridium botulinum group I strain genotyping by 15-locus multilocus variable-number tandem-repeat analysis.

    PubMed

    Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M; Scholz, Holger C; Splettstoesser, Wolf D; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

    2011-12-01

    Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse.

  8. Antimicrobial susceptibility patterns of Clostridium difficile strains belonging to different polymerase chain reaction ribotypes isolated in Poland in 2012.

    PubMed

    Lachowicz, Dominika; Pituch, Hanna; Obuch-Woszczatyński, Piotr

    2015-02-01

    In the beginning of 2012, a study was conducted to obtain an overview of Clostridium difficile infections (CDIs) in Polish hospitals. The collection of 83 toxigenic C. difficile isolates obtained from this hospital-based survey was used to identify antimicrobial susceptibility patterns. Among the C. difficile isolates analyzed, 48 (57.8%) belonged to PCR ribotype 027, 21 (25.3%) to its closely related PCR ribotype 176, and 14 (16.9%) to different PCR ribotypes. Seventy one (85.5%) isolates were resistant to erythromycin, whereas 23 (27.7%) had high-level clindamycin resistance, having minimum inhibitory concentrations (MICs) greater than 256 mg/L. All strains were ciprofloxacin resistant and 69 (83.1%) were moxifloxacin resistant. Seventy-three (87.9%) strains were imipenem resistant, but only 2 (2.4%) strains were resistant to tetracycline. All strains were sensitive to tigecycline. Metronidazole and vancomycin were generally effective against the C. difficile isolates, both having an MIC90 value of 0.75 mg/L. Isolates belonging to PCR ribotype 027 and the closely related PCR ribotype 176, showed higher resistance. All ribotype 027 and 176 C. difficile isolates demonstrated high-level resistance to erythromycin (MIC ≥ 256 mg/L), and 95,2% of ribotype 176 isolates were co-resistant to erythromycin and clindamycin. The MIC of moxifloxacin for this epidemic strain was very high (≥32 mg/L). Resistance to erythromycin, moxifloxacin, and rifampicin was observed in 15 (18%) of the isolates, all of which belonged to PCR ribotype 027. Multidrug resistance (MDR), defined as resistance at least to three classes of antimicrobial agents was observed in 85.5% (n = 71) of toxigenic C. difficile strains.

  9. EDITORIAL: Excelling under strain: band engineering in nanomaterials Excelling under strain: band engineering in nanomaterials

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2013-08-01

    A little stress or strain has been known to improve the performance of athletes, actors and of course nanomaterials alike. In fact strain in silicon is now a major engineering tool for improving the performance of devices, and is ubiquitously used in device design and fabrication. Strain engineering alters a material's band structure, a model of electron behaviour that describes how as atoms come together in a solid, their discrete electron orbitals overlap to ultimately give rise to bands of allowed energy levels. In a strained crystal lattice of silicon or silicon germanium the distance between atoms in the lattice is greater than usual and the bands of allowed energy levels change. This July marks 100 years since Bohr submitted his paper 'On the constitution of atoms and molecules' [1] where he describes the structure of the atom in terms of discrete allowed energy levels. The paper was a seminal contribution to the development of quantum mechanics and laid the initial theoretical precepts for band gap engineering in devices. In this issue Nrauda and a collaboration of researchers in Europe and Australia study the growth of defect-free SiGe islands on pre-patterned silicon [2]. They analyse the strain in the islands and determine at what point lattice dislocations set in with a view to informing implementation of strain engineering in devices. The effects of strain on band structure in silicon and germanium were already studied and reported in the 1950s [3, 4]. Since then the increasing focus on nanoscale materials and the hunger for control of electronic properties has prompted further study of strain effects. The increased surface area to volume ratio in nanostructures changes the strain behaviour with respect to bulk materials, and this can also be exploited for handling and fine tuning strain to manipulate material properties. It is perhaps no surprise that graphene, one of the most high-profile materials in current nanotechnology research, has attracted

  10. Conversion of acids to alcohols by Clostridium ragsdalei strain P11: Process optimization and biochemistry

    NASA Astrophysics Data System (ADS)

    Isom, Catherine E.

    Research focus was directed toward the development of a biocatalyst that can be used to produce commodity chemicals and transportation fuels from volatile fatty acids ubiquitous in waste biomass. Clostridium ragsdalei was introduced to serve as an exemplar carboxidotrophic acetogen that reduces VFAs to alcohols of the same carbon structure with only acetate and ethanol as by-products of the fermentation. This dissertation developed a better understanding of this process in C. ragsdalei and, in turn, other similar bacteria and to supported previous discoveries as they relate to carboxylate reduction in acetogens. Additionally, pure culture studies allowed for a more detailed understanding of the biochemical behavior response to different compounds without skewing the results due to the influence of other species.

  11. Alanine as an end product during fermentation of monosaccharides by Clostridium strain P2.

    PubMed

    Orlygsson, J; Anderson, R; Svensson, B H

    1995-11-01

    The thermophilic Clostridium P2 was isolated from a semi-continuously fed reactor with high ammonium concentration. This bacterium formed substantial amounts of L-alanine as a major fermentation product from glucose, fructose and mannose. Low amounts of acetate, butyrate, carbon dioxide and hydrogen were also formed. A high partial pressure of hydrogen inhibited the degradation of the monosaccharides, whereas hydrogen removal, in the form of methanogenesis was found to be stimulatory. However, the amount of alanine produced per mole of hexose degraded did not change. Hexose degradation and alanine production were favoured by high ammonium concentrations. Nuclear magnetic resonance spectroscopy studies provided strong evidence that an active Embden-Meyerhof-Parnas pathway existed and that alanine was produced via an amination of pyruvate.

  12. Characterization of Clostridium difficile Strains in British Columbia, Canada: A Shift from NAP1 Majority (2008) to Novel Strain Types (2013) in One Region

    PubMed Central

    Jassem, Agatha N.; Prystajecky, Natalie; Marra, Fawziah; Kibsey, Pamela; Tan, Kennard; Umlandt, Patricia; Janz, Loretta; Champagne, Sylvie; Gamage, Bruce; Golding, George R.; Mulvey, Michael R.; Henry, Bonnie

    2016-01-01

    Background. Clostridium difficile is a major cause of gastrointestinal illness. Epidemic NAP1 strains contain toxins A and B, a deletion in repressor tcdC, and a binary toxin. Objectives. To determine the molecular epidemiology of C. difficile in British Columbia and compare between two time points in one region. Methods. C. difficile isolates from hospital and community laboratories (2008) and one Island Health hospital laboratory (2013) were characterized by pulsed-field gel electrophoresis, PCR-ribotyping, toxin possession, tcdC genotype, and antimicrobial susceptibility. Results. In 2008, 42.7% of isolates had NAP1 designation. Hospital-collected isolates were associated with older patients and more NAP1 types. Unlike other isolates, most NAP1 isolates possessed binary toxin and a 19 bp loss in tcdC. All isolates were susceptible to metronidazole and vancomycin. A 2013 follow-up revealed a 28.9% decrease in NAP1 isolates and 20.0% increase in isolates without NAP designation in one region. Then, community-associated cases were seen in younger patients, while NAP types were evenly distributed. Isolates without NAP designation did not cluster with a PFGE pattern or ribotype. Conclusions. Evaluation of C. difficile infections within British Columbia revealed demographic associations, epidemiological shifts, and characteristics of strain types. Continuous surveillance of C. difficile will enable detection of emerging strains. PMID:27366181

  13. Putative function of hypothetical proteins expressed by Clostridium perfringens type A strains and their protective efficacy in mouse model.

    PubMed

    Alam, Syed Imteyaz; Dwivedi, Pratistha

    2016-10-01

    The whole genome sequencing and annotation of Clostridium perfringens strains revealed several genes coding for proteins of unknown function with no significant similarities to genes in other organisms. Our previous studies clearly demonstrated that hypothetical proteins CPF_2500, CPF_1441, CPF_0876, CPF_0093, CPF_2002, CPF_2314, CPF_1179, CPF_1132, CPF_2853, CPF_0552, CPF_2032, CPF_0438, CPF_1440, CPF_2918, CPF_0656, and CPF_2364 are genuine proteins of C. perfringens expressed in high abundance. This study explored the putative role of these hypothetical proteins using bioinformatic tools and evaluated their potential as putative candidates for prophylaxis. Apart from a group of eight hypothetical proteins (HPs), a putative function was predicted for the rest of the hypothetical proteins using one or more of the algorithms used. The phylogenetic analysis did not suggest an evidence of a horizontal gene transfer event except for HP CPF_0876. HP CPF_2918 is an abundant extracellular protein, unique to C. perfringens species with maximum strain coverage and did not show any significant match in the database. CPF_2918 was cloned, recombinant protein was purified to near homogeneity, and probing with mouse anti-CPF_2918 serum revealed surface localization of the protein in C. perfringens ATCC13124 cultures. The purified recombinant CPF_2918 protein induced antibody production, a mixed Th1 and Th2 kind of response, and provided partial protection to immunized mice in direct C. perfringens challenge.

  14. Direct degradation of cellulosic biomass to bio-hydrogen from a newly isolated strain Clostridium sartagoforme FZ11.

    PubMed

    Zhang, Jing-Nan; Li, Yan-Hong; Zheng, Hui-Qin; Fan, Yao-Ting; Hou, Hong-Wei

    2015-09-01

    A mesophilic hydrogen-producing strain, Clostridium sartagoforme FZ11, had been newly isolated from cow dung compost acclimated using microcrystalline cellulose (MCC) for at least 30 rounds in an anaerobic bioreactor, and identified by the 16S rDNA gene sequencing, which could directly utilized various carbon sources, especially cellulosic biomass, to produce hydrogen. The maximum hydrogen yields from MCC (10 g/l) and carboxymethyl cellulose (CMC, 10 g/l) were 77.2 and 64.6 ml/g, separately. Furthermore, some key parameters of affecting hydrogen production from raw corn stalk were also optimized. The maximal hydrogen yield and substrate degradation rate from raw corn stalk were 87.2 ml/g and 41.2% under the optimized conditions with substrate concentration of 15 g/l, phosphate buffer of 0.15 M, urea of 6 g/l and initial pH of 6.47 at 35 °C. The result showed that the strain FZ11 would be an ideal candidate to directly convert cellulosic biomass into bio-hydrogen without substrate pretreatment.

  15. A penicillin- and metronidazole-resistant Clostridium botulinum strain responsible for an infant botulism case.

    PubMed

    Mazuet, C; Yoon, E-J; Boyer, S; Pignier, S; Blanc, T; Doehring, I; Meziane-Cherif, D; Dumant-Forest, C; Sautereau, J; Legeay, C; Bouvet, P; Bouchier, C; Quijano-Roy, S; Pestel-Caron, M; Courvalin, P; Popoff, M R

    2016-07-01

    The clinical course of a case of infant botulism was characterized by several relapses despite therapy with amoxicillin and metronidazole. Botulism was confirmed by identification of botulinum toxin and Clostridium botulinum in stools. A C. botulinum A2 strain resistant to penicillins and with heterogeneous resistance to metronidazole was isolated from stool samples up to 110 days after onset. Antibiotic susceptibility was tested by disc agar diffusion and MICs were determined by Etest. Whole genome sequencing allowed detection of a gene cluster composed of blaCBP for a novel penicillinase, blaI for a regulator, and blaR1 for a membrane-bound penicillin receptor in the chromosome of the C. botulinum isolate. The purified recombinant penicillinase was assayed. Resistance to β-lactams was in agreement with the kinetic parameters of the enzyme. In addition, the β-lactamase gene cluster was found in three C. botulinum genomes in databanks and in two of 62 genomes of our collection, all the strains belonging to group I C. botulinum. This is the first report of a C. botulinum isolate resistant to penicillins. This stresses the importance of antibiotic susceptibility testing for adequate therapy of botulism. PMID:27108966

  16. Industrial Robustness: Understanding the Mechanism of Tolerance for the Populus Hydrolysate-Tolerant Mutant Strain of Clostridium thermocellum

    PubMed Central

    Linville, Jessica L.; Rodriguez, Miguel; Land, Miriam; Syed, Mustafa H.; Engle, Nancy L.; Tschaplinski, Timothy J.; Mielenz, Jonathan R.; Cox, Chris D.

    2013-01-01

    Background An industrially robust microorganism that can efficiently degrade and convert lignocellulosic biomass into ethanol and next-generation fuels is required to economically produce future sustainable liquid transportation fuels. The anaerobic, thermophilic, cellulolytic bacterium Clostridium thermocellum is a candidate microorganism for such conversions but it, like many bacteria, is sensitive to potential toxic inhibitors developed in the liquid hydrolysate produced during biomass processing. Microbial processes leading to tolerance of these inhibitory compounds found in the pretreated biomass hydrolysate are likely complex and involve multiple genes. Methodology/Principal Findings In this study, we developed a 17.5% v/v Populus hydrolysate tolerant mutant strain of C. thermocellum by directed evolution. The genome of the wild type strain, six intermediate population samples and seven single colony isolates were sequenced to elucidate the mechanism of tolerance. Analysis of the 224 putative mutations revealed 73 high confidence mutations. A longitudinal analysis of the intermediate population samples, a pan-genomic analysis of the isolates, and a hotspot analysis revealed 24 core genes common to all seven isolates and 8 hotspots. Genetic mutations were matched with the observed phenotype through comparison of RNA expression levels during fermentation by the wild type strain and mutant isolate 6 in various concentrations of Populus hydrolysate (0%, 10%, and 17.5% v/v). Conclusion/Significance The findings suggest that there are multiple mutations responsible for the Populus hydrolysate tolerant phenotype resulting in several simultaneous mechanisms of action, including increases in cellular repair, and altered energy metabolism. To date, this study provides the most comprehensive elucidation of the mechanism of tolerance to a pretreated biomass hydrolysate by C. thermocellum. These findings make important contributions to the development of industrially

  17. Evaluation of the Cepheid Xpert C. difficile/Epi and meridian bioscience illumigene C. difficile assays for detecting Clostridium difficile ribotype 033 strains.

    PubMed

    Androga, Grace O; McGovern, Alan M; Elliott, Briony; Chang, Barbara J; Perkins, Timothy T; Foster, Niki F; Riley, Thomas V

    2015-03-01

    Clostridium difficile PCR ribotype 033 (RT033) is found in the gastrointestinal tracts of production animals and, occasionally, humans. The illumigene C. difficile assay (Meridian Bioscience, Inc.) failed to detect any of 52 C. difficile RT033 isolates, while all strains signaled positive for the binary toxin genes but were reported as negative for C. difficile by the Xpert C. difficile/Epi assay (Cepheid).

  18. In vitro activity of cadazolid against Clostridium difficile strains isolated from primary and recurrent infections in Stockholm, Sweden.

    PubMed

    Rashid, Mamun-Ur; Lozano, Helena Martinez; Weintraub, Andrej; Nord, Carl Erik

    2013-04-01

    One hundred thirty-three Clostridium difficile strains were collected from 71 patients and analyzed for the presence of C. difficile toxin B by the cell cytotoxicity neutralization assay, genes for toxin A, toxin B, binary toxin and TcdC deletion by PCR. All strains were also PCR-ribotyped and analyzed for sporulation frequency. The MICs of the isolates were determined against cadazolid and seven other antimicrobial agents by the agar dilution method. All isolates were positive for toxin B by the cell cytotoxicity neutralization assay. One hundred fourteen isolates were positive for toxin A and B and 16 isolates were positive for toxin A, toxin B and binary toxin by PCR. Three isolates were negative for toxin A but positive for toxin B. Thirty-three different ribotypes were identified. No strain of ribotype 027 was found. No differences in sporulation were noticed between the primary and recurrent isolates. All 133 isolates were sensitive to cadazolid (0.064-0.5 mg/l), fidaxomicin (0.008-0.125 mg/l), metronidazole (0.125-2 mg/l), vancomycin (0.125-1 mg/l) and tigecycline (0.032-0.25 mg/l). Three isolates were resistant to linezolid (8 mg/l), 15 isolates were resistant to moxifloxacin (8-32 mg/l) and 103 isolates were resistant to clindamycin (8-256 mg/l). No association between toxins A, B and binary toxin, ribotypes or the sporulation and the sensitivity to cadazolid could be found. Cadazolid has a potent in vitro activity against C. difficile.

  19. Distribution of Clostridium botulinum Type E Strains in Nunavik, Northern Quebec, Canada

    PubMed Central

    Leclair, Daniel; Farber, Jeffrey M.; Doidge, Bill; Blanchfield, Burke; Suppa, Sandy; Pagotto, Franco

    2013-01-01

    The distribution and levels of Clostridium botulinum type E were determined from field sites used by Inuit hunters for butchering seals along the coast of Nunavik. The incidence rates of C. botulinum type E in shoreline soil along the coast were 0, 50, and 87.5% among samples tested for the Hudson Strait, Hudson Bay, and Ungava Bay regions, respectively. Spores were detected in seawater or coastal rock surfaces from 17.6% of butchering sites, almost all of which were located in southern Ungava Bay. Concentrations of C. botulinum type E along the Ungava Bay coast were significantly higher than on the coasts of Hudson Strait and Hudson Bay, with the highest concentrations (270 to 1,800/kg of sample) found near butchering sites located along the mouths of large rivers. The Koksoak River contained high levels of C. botulinum type E, with the highest median concentration (270/kg) found in sediments of the marine portion of the river. C. botulinum type E was found in the intestinal contents (4.4%) and skins (1.4%) of seals. A high genetic biodiversity of C. botulinum type E isolates was observed among the 21 butchering sites and their surroundings along the Nunavik coastline, with 83% of isolates (44/53) yielding distinct pulsed-field gel electrophoresis genotypes. Multiple sources of C. botulinum type E may be involved in the contamination of seal meat during butchering in this region, but the risk of contamination appears to be much higher from environmental sources along the shoreline of southern Ungava Bay and the sediments of the Koksoak River. PMID:23160120

  20. Multilocus sequence typing analysis and antibiotic resistance of Clostridium difficile strains isolated from retail meat and humans in Belgium.

    PubMed

    Rodriguez, C; Taminiau, B; Avesani, V; Van Broeck, J; Delmée, M; Daube, G

    2014-09-01

    Clostridium difficile has been isolated from food animals and meat, specially ground pork and ground beef. The recovered isolates were closely related to C. difficile human strains, indicating that animals and food are possible transmission routes of human C. difficile infection. The main objective of this study was to characterize C. difficile isolates from retail meat and to compare with human isolates recovered from hospital patients in Belgium. Raw meat (beef and pork) was obtained from the retail trade. C. difficile was recovered from 2.3% of the beef samples and from 4.7% of the pork samples. A total of 4 different PCR-ribotypes were identified with a large percentage of types 078 and 014. Resistance to moxifloxacin and erythromycin was detected. The multi-locus sequence typing (MLST) analysis showed that meat and human isolates cluster in the same lineage. This study reveals the presence of toxigenic C. difficile in retail meat in Belgium with predominance PCR-ribotypes 078 and 014, which are among the four most prevalent ribotypes of C. difficile isolated from humans in Europe.

  1. Characterisation of Clostridium difficile strains isolated from Groote Schuur Hospital, Cape Town, South Africa.

    PubMed

    Kullin, B; Brock, T; Rajabally, N; Anwar, F; Vedantam, G; Reid, S; Abratt, V

    2016-10-01

    The C. difficile infection rate in South Africa is concerning. Many strains previously isolated from diarrhetic patients at Groote Schuur Hospital were ribotype 017. This study further characterised these strains with respect to their clonal relationships, antibiotic susceptibility, toxin production and various attributes impacting on pathogen colonisation. Multilocus variable-number tandem-repeat analysis (MLVA) was used to characterise all C. difficile isolates. Antibiotic susceptibility was determined by E-test and PCR-based analysis of the ermB, gyrA and gyrB genes. Auto-aggregation of cells was measured in broth, and biofilm formation observed in 24-well plates. Toxins were measured using the Wampole C DIFF TOX A/B II kit. Most isolates belonged to the ribotype 017 group. Identical MLVA types occurred in different wards over time, and several patients were infected with identical strains. All isolates were susceptible to vancomycin and metronidazole, but some ribotype 017 isolates showed reduced metronidazole susceptibility (≥2 mg l(-1)). Sixty-nine percent of ribotype 017 isolates were resistant to moxifloxacin, and 94 % to erythromycin, compared to 0 % and 17 % resistance, respectively, in non-ribotype 017 isolates. The ermB gene and mutations in the gyrA and/or gyrB genes were linked to erythromycin and moxifloxacin resistance, respectively. Ribotype 017 isolates auto-aggregated more strongly than other isolates and produced lower levels of the TcdB toxin than a reference strain. Certain strains produced strong biofilms. Patient-to-patient transfer and unique infection events could cause the predominance of ribotype 017 strains in the cohort. Multi-drug resistant strains are a potential reservoir for future infections.

  2. Rapid spread of Clostridium difficile NAP1/027/ST1 in Chile confirms the emergence of the epidemic strain in Latin America.

    PubMed

    Aguayo, C; Flores, R; Lévesque, S; Araya, P; Ulloa, S; Lagos, J; Hormazabal, J C; Tognarelli, J; Ibáñez, D; Pidal, P; Duery, O; Olivares, B; Fernández, J

    2015-10-01

    Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains. This study reports the molecular epidemiology of C. difficile obtained from hospitalized patients in Chile. Seven hundred and nineteen isolates of toxigenic C. difficile from 45 hospitals across the country were characterized through toxin profile, pulsed-field gel electrophoresis (PFGE), and sequencing of the tcdC gene. In addition, polymerase chain reaction (PCR) ribotyping and multilocus sequence typing (MLST) were performed on a subset of selected strains. PFGE typing of 719 isolates of C. difficile produced 60 PFGE patterns (subtypes). Subtype 1 was predominant (79% of isolates) and related to the hypervirulent strain (NAP1). Subtype 1 showed 73% relatedness with nine other subtypes, which had a similar tcdC deletion. Subtype 1 corresponded to ribotype 027 and ST1. This report shows the wide dissemination of the hypervirulent strain NAP1/027/ST1 in Chile.

  3. Deletions in the repeating sequences of the toxin A gene of toxin A-negative, toxin B-positive Clostridium difficile strains.

    PubMed

    Kato, H; Kato, N; Katow, S; Maegawa, T; Nakamura, S; Lyerly, D M

    1999-06-15

    The repeating sequences of the toxin A gene from toxin A-negative, toxin B-positive (toxin A-, toxin B+) strains of Clostridium difficile which were isolated in geographically separated facilities in Japan and Indonesia were determined. All six strains tested had identical repeating sequences with two deletions (1548 and 273 nucleotides in size) in the toxin A gene. A PCR method was designed to detect the deletions and the deletions were confirmed in all 50 toxin A-, toxin B+ strains examined by this method. Western immunoblot analysis revealed that polyclonal antiserum against native toxin A did not react with the concentrated culture filtrates of the toxin A-, toxin B+ strains. These results may suggest that toxin A-, toxin B+ strains have deletions of the two thirds of the repeating regions of the toxin A gene, which encodes the epitopes fully responsible for the reaction with the polyclonal antiserum.

  4. Strain Engineering of Transition Metal Dichalcogenides

    NASA Astrophysics Data System (ADS)

    Dadgar, Ali; Pasupathy, Abhay; Herman, Irving; Wang, Dennis; Kang, Kyungnam; Yang, Eui-Hyeok

    The application of strain to materials can cause changes to bandwidth, effective masses, degeneracies and even structural phases. In the case of the transition metal dichalcogenide (TMD) semiconductors, small strain (around 1 percent) is expected to change band gaps and mobilities, while larger strains are expected to cause phase changes from the triangular 2H phase to orthorhombic 1T' phases. We will describe experimental techniques to apply small and large (around 10 percent) strains to one or few layer samples of the TMD semiconductors, and describe the effect of the strain using optical (Raman, photoluminescence) and cryogenic transport techniques.

  5. EDITORIAL: Excelling under strain: band engineering in nanomaterials Excelling under strain: band engineering in nanomaterials

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2013-08-01

    A little stress or strain has been known to improve the performance of athletes, actors and of course nanomaterials alike. In fact strain in silicon is now a major engineering tool for improving the performance of devices, and is ubiquitously used in device design and fabrication. Strain engineering alters a material's band structure, a model of electron behaviour that describes how as atoms come together in a solid, their discrete electron orbitals overlap to ultimately give rise to bands of allowed energy levels. In a strained crystal lattice of silicon or silicon germanium the distance between atoms in the lattice is greater than usual and the bands of allowed energy levels change. This July marks 100 years since Bohr submitted his paper 'On the constitution of atoms and molecules' [1] where he describes the structure of the atom in terms of discrete allowed energy levels. The paper was a seminal contribution to the development of quantum mechanics and laid the initial theoretical precepts for band gap engineering in devices. In this issue Nrauda and a collaboration of researchers in Europe and Australia study the growth of defect-free SiGe islands on pre-patterned silicon [2]. They analyse the strain in the islands and determine at what point lattice dislocations set in with a view to informing implementation of strain engineering in devices. The effects of strain on band structure in silicon and germanium were already studied and reported in the 1950s [3, 4]. Since then the increasing focus on nanoscale materials and the hunger for control of electronic properties has prompted further study of strain effects. The increased surface area to volume ratio in nanostructures changes the strain behaviour with respect to bulk materials, and this can also be exploited for handling and fine tuning strain to manipulate material properties. It is perhaps no surprise that graphene, one of the most high-profile materials in current nanotechnology research, has attracted

  6. Strain engineering in graphene by laser irradiation

    SciTech Connect

    Papasimakis, N.; Mailis, S.; Huang, C. C.; Al-Saab, F.; Hewak, D. W.; Luo, Z.; Shen, Z. X.

    2015-02-09

    We demonstrate that the Raman spectrum of graphene on lithium niobate can be controlled locally by continuous exposure to laser irradiation. We interpret our results in terms of changes to doping and mechanical strain and show that our observations are consistent with light-induced gradual strain relaxation in the graphene layer.

  7. A MLST Clade 2 Clostridium difficile strain with a variant TcdB induces severe inflammatory and oxidative response associated with mucosal disruption.

    PubMed

    Costa, Cecília Leite; López-Ureña, Diana; de Oliveira Assis, Thiago; Ribeiro, Ronaldo A; Silva, Rodrigo Otávio Silveira; Rupnik, Maja; Wilcox, Mark H; de Carvalho, Alex Fiorini; do Carmo, Anderson Oliveira; Dias, Adriana Abalen Martins; de Carvalho, Cibele Barreto Mano; Chaves-Olarte, Esteban; Rodríguez, César; Quesada-Gómez, Carlos; de Castro Brito, Gerly Anne

    2016-08-01

    The epidemiology of Clostridium difficile infections is highly dynamic as new strains continue to emerge worldwide. Here we present a detailed analysis of a new C. difficile strain (ICC-45) recovered from a cancer patient in Brazil that died from severe diarrhea. A polyphasic approach assigned a new PCR-ribotype and PFGE macrorestriction pattern to strain ICC-45, which is toxigenic (tcdA(+), tcdB(+) and ctdB(+)) and classified as ST41 from MLST Clade 2 and toxinotype IXb. Strain ICC-45 encodes for a variant TcdB that induces a distinct CPE in agreement with its toxinotype. Unlike epidemic NAP1/027 strains, which are also classified to MLST Clade 2, strain ICC-45 is susceptible to fluoroquinolones and does not overproduce toxins TcdA and TcdB. However, supernatants from strain ICC-45 and a NAP1/027 strain produced similar expression of pro-inflammatory cytokines, epithelial damage, and oxidative stress response in the mouse ileal loop model. These results highlight inflammation and oxidative stress as common features in the pathogenesis of C. difficile Clade 2 strains. Finally, this work contributes to the description of differences in virulence among various C. difficile strains. PMID:27311833

  8. Biaxial Compressive Strain Engineering in Graphene/Boron Nitride Heterostructures

    PubMed Central

    Pan, Wei; Xiao, Jianliang; Zhu, Junwei; Yu, Chenxi; Zhang, Gang; Ni, Zhenhua; Watanabe, K.; Taniguchi, T.; Shi, Yi; Wang, Xinran

    2012-01-01

    Strain engineered graphene has been predicted to show many interesting physics and device applications. Here we study biaxial compressive strain in graphene/hexagonal boron nitride heterostructures after thermal cycling to high temperatures likely due to their thermal expansion coefficient mismatch. The appearance of sub-micron self-supporting bubbles indicates that the strain is spatially inhomogeneous. Finite element modeling suggests that the strain is concentrated on the edges with regular nano-scale wrinkles, which could be a playground for strain engineering in graphene. Raman spectroscopy and mapping is employed to quantitatively probe the magnitude and distribution of strain. From the temperature-dependent shifts of Raman G and 2D peaks, we estimate the TEC of graphene from room temperature to above 1000K for the first time. PMID:23189242

  9. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain

    PubMed Central

    2014-01-01

    Background The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum. Results In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell

  10. Tuning Surface Properties of Low Dimensional Materials via Strain Engineering.

    PubMed

    Yang, Shengchun; Liu, Fuzhu; Wu, Chao; Yang, Sen

    2016-08-01

    The promising and versatile applications of low dimensional materials are largely due to their surface properties, which along with their underlying electronic structures have been well studied. However, these materials may not be directly useful for applications requiring properties other than their natal ones. In recent years, strain has been shown to be an additionally useful handle to tune the physical and chemical properties of materials by changing their geometric and electronic structures. The strategies for producing strain are summarized. Then, the electronic structure of quasi-two dimensional layered non-metallic materials (e.g., graphene, MX2, BP, Ge nanosheets) under strain are discussed. Later, the strain effects on catalytic properties of metal-catalyst loaded with strain are focused on. Both experimental and computational perspectives for dealing with strained systems are covered. Finally, an outlook on engineering surface properties utilizing strain is provided. PMID:27376498

  11. Tuning Surface Properties of Low Dimensional Materials via Strain Engineering.

    PubMed

    Yang, Shengchun; Liu, Fuzhu; Wu, Chao; Yang, Sen

    2016-08-01

    The promising and versatile applications of low dimensional materials are largely due to their surface properties, which along with their underlying electronic structures have been well studied. However, these materials may not be directly useful for applications requiring properties other than their natal ones. In recent years, strain has been shown to be an additionally useful handle to tune the physical and chemical properties of materials by changing their geometric and electronic structures. The strategies for producing strain are summarized. Then, the electronic structure of quasi-two dimensional layered non-metallic materials (e.g., graphene, MX2, BP, Ge nanosheets) under strain are discussed. Later, the strain effects on catalytic properties of metal-catalyst loaded with strain are focused on. Both experimental and computational perspectives for dealing with strained systems are covered. Finally, an outlook on engineering surface properties utilizing strain is provided.

  12. Combinatorial and high-throughput screening approaches for strain engineering.

    PubMed

    Liu, Wenshan; Jiang, Rongrong

    2015-03-01

    Microbes have long been used in the industry to produce valuable biochemicals. Combinatorial engineering approaches, new strain engineering tools derived from inverse metabolic engineering, have started to attract attention in recent years, including genome shuffling, error-prone DNA polymerase, global transcription machinery engineering (gTME), random knockout/overexpression libraries, ribosome engineering, multiplex automated genome engineering (MAGE), customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER), and library construction of "tunable intergenic regions" (TIGR). Since combinatorial approaches and high-throughput screening methods are fundamentally interconnected, color/fluorescence-based, growth-based, and biosensor-based high-throughput screening methods have been reviewed. We believe that with the help of metabolic engineering tools and new combinatorial approaches, plus effective high-throughput screening methods, researchers will be able to achieve better results on improving microorganism performance under stress or enhancing biochemical yield.

  13. Nanoscale strain engineering of graphene and graphene-based devices

    NASA Astrophysics Data System (ADS)

    Yeh, N.-C.; Hsu, C.-C.; Teague, M. L.; Wang, J.-Q.; Boyd, D. A.; Chen, C.-C.

    2016-06-01

    Structural distortions in nano-materials can induce dramatic changes in their electronic properties. This situation is well manifested in graphene, a two-dimensional honeycomb structure of carbon atoms with only one atomic layer thickness. In particular, strained graphene can result in both charging effects and pseudo-magnetic fields, so that controlled strain on a perfect graphene lattice can be tailored to yield desirable electronic properties. Here, we describe the theoretical foundation for strain-engineering of the electronic properties of graphene, and then provide experimental evidence for strain-induced pseudo-magnetic fields and charging effects in monolayer graphene. We further demonstrate the feasibility of nano-scale strain engineering for graphene-based devices by means of theoretical simulations and nano-fabrication technology.

  14. Protein design in systems metabolic engineering for industrial strain development.

    PubMed

    Chen, Zhen; Zeng, An-Ping

    2013-05-01

    Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.

  15. Metabolically engineered glucose-utilizing Shewanella strains under anaerobic conditions.

    PubMed

    Choi, Donggeon; Lee, Sae Bom; Kim, Sohyun; Min, Byoungnam; Choi, In-Geol; Chang, In Seop

    2014-02-01

    Comparative genome analysis of Shewanella strains predicted that the strains metabolize preferably two- and three-carbon carbohydrates as carbon/electron source because many Shewanella genomes are deficient of the key enzymes in glycolysis (e.g., glucokinase). In addition, all Shewanella genomes are known to have only one set of genes associated with the phosphotransferase system required to uptake sugars. To engineer Shewanella strains that can utilize five- and six-carbon carbohydrates, we constructed glucose-utilizing Shewanella oneidensis MR-1 by introducing the glucose facilitator (glf; ZMO0366) and glucokinase (glk; ZMO0369) genes of Zymomonas mobilis. The engineered MR-1 strain was able to grow on glucose as a sole carbon/electron source under anaerobic conditions. The glucose affinity (Ks) and glucokinase activity in the engineered MR-1 strain were 299.46 mM and 0.259 ± 0.034 U/g proteins. The engineered strain was successfully applied to a microbial fuel cell system and exhibited current generation using glucose as the electron source.

  16. Strain Engineering to Modify the Electrochemistry of Energy Storage Electrodes

    PubMed Central

    Muralidharan, Nitin; Carter, Rachel; Oakes, Landon; Cohn, Adam P.; Pint, Cary L.

    2016-01-01

    Strain engineering has been a critical aspect of device design in semiconductor manufacturing for the past decade, but remains relatively unexplored for other applications, such as energy storage. Using mechanical strain as an input parameter to modulate electrochemical potentials of metal oxides opens new opportunities intersecting fields of electrochemistry and mechanics. Here we demonstrate that less than 0.1% strain on a Ni-Ti-O based metal-oxide formed on superelastic shape memory NiTi alloys leads to anodic and cathodic peak potential shifts by up to ~30 mV in an electrochemical cell. Moreover, using the superelastic properties of NiTi to enable strain recovery also recovers the electrochemical potential of the metal oxide, providing mechanistic evidence of strain-modified electrochemistry. These results indicate that mechanical energy can be coupled with electrochemical systems to efficiently design and optimize a new class of strain-modulated energy storage materials. PMID:27283872

  17. Strain Engineering to Modify the Electrochemistry of Energy Storage Electrodes

    NASA Astrophysics Data System (ADS)

    Muralidharan, Nitin; Carter, Rachel; Oakes, Landon; Cohn, Adam P.; Pint, Cary L.

    2016-06-01

    Strain engineering has been a critical aspect of device design in semiconductor manufacturing for the past decade, but remains relatively unexplored for other applications, such as energy storage. Using mechanical strain as an input parameter to modulate electrochemical potentials of metal oxides opens new opportunities intersecting fields of electrochemistry and mechanics. Here we demonstrate that less than 0.1% strain on a Ni-Ti-O based metal-oxide formed on superelastic shape memory NiTi alloys leads to anodic and cathodic peak potential shifts by up to ~30 mV in an electrochemical cell. Moreover, using the superelastic properties of NiTi to enable strain recovery also recovers the electrochemical potential of the metal oxide, providing mechanistic evidence of strain-modified electrochemistry. These results indicate that mechanical energy can be coupled with electrochemical systems to efficiently design and optimize a new class of strain-modulated energy storage materials.

  18. Strain Engineering to Modify the Electrochemistry of Energy Storage Electrodes.

    PubMed

    Muralidharan, Nitin; Carter, Rachel; Oakes, Landon; Cohn, Adam P; Pint, Cary L

    2016-06-10

    Strain engineering has been a critical aspect of device design in semiconductor manufacturing for the past decade, but remains relatively unexplored for other applications, such as energy storage. Using mechanical strain as an input parameter to modulate electrochemical potentials of metal oxides opens new opportunities intersecting fields of electrochemistry and mechanics. Here we demonstrate that less than 0.1% strain on a Ni-Ti-O based metal-oxide formed on superelastic shape memory NiTi alloys leads to anodic and cathodic peak potential shifts by up to ~30 mV in an electrochemical cell. Moreover, using the superelastic properties of NiTi to enable strain recovery also recovers the electrochemical potential of the metal oxide, providing mechanistic evidence of strain-modified electrochemistry. These results indicate that mechanical energy can be coupled with electrochemical systems to efficiently design and optimize a new class of strain-modulated energy storage materials.

  19. Draft Genome Sequence of Clostridium difficile Strain IT1118, an Epidemic Isolate Belonging to the Emerging PCR Ribotype 018

    PubMed Central

    Wasels, François; Barbanti, Fabrizio

    2016-01-01

    Clostridium difficile PCR ribotype 018 has emerged in Italy, South Korea, and Japan, causing severe infections and outbreaks. In this study, we sequenced the genome of IT1118, an Italian clinical isolate, to clarify the molecular features contributing to the success of this epidemic type. PMID:27445391

  20. Impact strain engineering on gate stack quality and reliability

    NASA Astrophysics Data System (ADS)

    Claeys, C.; Simoen, E.; Put, S.; Giusi, G.; Crupi, F.

    2008-08-01

    Strain engineering based on either a global approach using high-mobility substrates or the implementation of so-called processing-induced stressors has become common practice for 90 nm and below CMOS technologies. Although the main goal is to improve the performance by increasing the drive current, other electrical parameters such as the threshold voltage, the multiplication current, the low frequency noise and the gate oxide quality in general may be influenced. This paper reviews the impact of different global and local strain engineering techniques on the gate stack quality and its reliability, including hot carrier performance, negative bias temperature instabilities, time dependent dielectric breakdown and radiation hardness. Recent insights will be discussed and the influence of different strain engineering approaches illustrated.

  1. The non-toxigenic Clostridium difficile CD37 protects mice against infection with a BI/NAP1/027 type of C. difficile strain.

    PubMed

    Zhang, Keshan; Zhao, Song; Wang, Yuankai; Zhu, Xuejun; Shen, Hong; Chen, Yugen; Sun, Xingmin

    2015-12-01

    Clostridium difficile CD37, a clinical isolate from the USA, does not produce toxin A, B or binary toxin. The aim of this study was to determine whether strain CD37 can protect mice against infection from a challenge with a toxigenic C. difficile strain. Three groups of mice (n = 10) were pretreated with a antibiotics cocktail for 5 days, switched to sterile water for 2 days, and given one dose of clindamycin (10 mg/kg) one day (day-1) before challenge (day 0) with a toxigenic C. difficile strain. Group 1 (CD37 + UK6) was given 10(7)C. difficile CD37 vegetative cells by gavage twice a day on days -1 and -2, followed by challenge with 10(6) spores of the toxigenic C. difficile UK6 (BI/NAPI/027) on day 0; Group 2 (UK6) was infected with 10(6)C. difficile UK6 spores on day 0; Group 3 (CD37) was challenged with 10(6) CD37 vegetative cells on day 0. Our data show that pre-inoculation of strain CD37 provided mice significant protection (survival, p < 0.001 between groups CD37 + UK6 and UK6) against subsequent infection with the strain UK6, while mice infected with CD37 only did not develop any symptoms of C. difficile infection (CDI). Our results highlight the potential use of CD37 as a therapeutic strain for the prevention of primary and recurrent CDI in humans.

  2. Understanding the Current State of Infection Prevention to Prevent Clostridium difficile Infection: A Human Factors and Systems Engineering Approach

    PubMed Central

    Yanke, Eric; Zellmer, Caroline; Van Hoof, Sarah; Moriarty, Helene; Carayon, Pascale; Safdar, Nasia

    2015-01-01

    Background Achieving and sustaining high levels of healthcare worker (HCW) compliance with contact isolation precautions is challenging. The aim of this study was to determine HCW work system barriers to, and facilitators of, adherence to contact isolation for patients with suspected or confirmed Clostridium difficile infection (CDI) using a human factors and systems engineering approach. Methods Prospective cohort study from September 2013 to November 2013 at a large academic medical center (hospital A) and an affiliated Veterans Administration (VA) hospital (hospital B). A human factors engineering (HFE) model for patient safety – the Systems Engineering Initiative for Patient Safety (SEIPS) model – was used to guide work system analysis and direct observation data collection. 288 observations were conducted. HCWs and visitors were assessed for compliance with all components of contact isolation precautions (hand hygiene, gowning, and gloving) before and after patient contact. Time required to complete contact isolation precautions was measured and adequacy of contact isolation supplies was assessed. Results Full compliance with contact isolation precautions was low at both hospitals: hospital A, 7%; hospital B, 22%. Lack of appropriate hand hygiene prior to room entry (Compliance: hospital A, 18%; hospital B, 29%) was the most common reason for lack of full compliance. More time was required for full compliance as compared to compliance with no components of contact isolation precautions before patient room entry, inside patient room, and after patient room exit (59.9 sec vs. 3.2 sec; P < .001; 507.3 sec vs. 149.7 sec; P = .006; 15.2 sec vs. 1.3 sec; P < .001). Compliance was lower when contact isolation supplies were inadequate (4% vs. 16%; P = .005). Conclusions Adherence to contact isolation precautions for CDI is a complex, time-consuming process. HFE analysis indicates multiple work system components serve as barriers and facilitators to full compliance

  3. Strain engineering in semiconducting two-dimensional crystals.

    PubMed

    Roldán, Rafael; Castellanos-Gomez, Andrés; Cappelluti, Emmanuele; Guinea, Francisco

    2015-08-12

    One of the fascinating properties of the new families of two-dimensional crystals is their high stretchability and the possibility to use external strain to manipulate, in a controlled manner, their optical and electronic properties. Strain engineering, understood as the field that study how the physical properties of materials can be tuned by controlling the elastic strain fields applied to it, has a perfect platform for its implementation in the atomically thin semiconducting materials. The object of this review is to give an overview of the recent progress to control the optical and electronics properties of 2D crystals, by means of strain engineering. We will concentrate on semiconducting layered materials, with especial emphasis in transition metal dichalcogenides (MoS2, WS2, MoSe2 and WSe2). The effect of strain in other atomically thin materials like black phosphorus, silicene, etc, is also considered. The benefits of strain engineering in 2D crystals for applications in nanoelectronics and optoelectronics will be revised, and the open problems in the field will be discussed. PMID:26199038

  4. Field Performance of a Genetically Engineered Strain of Pink Bollworm

    PubMed Central

    Simmons, Gregory S.; McKemey, Andrew R.; Morrison, Neil I.; O'Connell, Sinead; Tabashnik, Bruce E.; Claus, John; Fu, Guoliang; Tang, Guolei; Sledge, Mickey; Walker, Adam S.; Phillips, Caroline E.; Miller, Ernie D.; Rose, Robert I.; Staten, Robert T.; Donnelly, Christl A.; Alphey, Luke

    2011-01-01

    Pest insects harm crops, livestock and human health, either directly or by acting as vectors of disease. The Sterile Insect Technique (SIT) – mass-release of sterile insects to mate with, and thereby control, their wild counterparts – has been used successfully for decades to control several pest species, including pink bollworm, a lepidopteran pest of cotton. Although it has been suggested that genetic engineering of pest insects provides potential improvements, there is uncertainty regarding its impact on their field performance. Discrimination between released and wild moths caught in monitoring traps is essential for estimating wild population levels. To address concerns about the reliability of current marking methods, we developed a genetically engineered strain of pink bollworm with a heritable fluorescent marker, to improve discrimination of sterile from wild moths. Here, we report the results of field trials showing that this engineered strain performed well under field conditions. Our data show that attributes critical to SIT in the field – ability to find a mate and to initiate copulation, as well as dispersal and persistence in the release area – were comparable between the genetically engineered strain and a standard strain. To our knowledge, these represent the first open-field experiments with a genetically engineered insect. The results described here provide encouragement for the genetic control of insect pests. PMID:21931649

  5. Strain engineered barium strontium titanate for tunable thin film resonators

    SciTech Connect

    Khassaf, H.; Khakpash, N.; Sun, F.; Sbrockey, N. M.; Tompa, G. S.; Kalkur, T. S.; Alpay, S. P.

    2014-05-19

    Piezoelectric properties of epitaxial (001) barium strontium titanate (BST) films are computed as functions of composition, misfit strain, and temperature using a non-linear thermodynamic model. Results show that through adjusting in-plane strains, a highly adaptive rhombohedral ferroelectric phase can be stabilized at room temperature with outstanding piezoelectric response exceeding those of lead based piezoceramics. Furthermore, by adjusting the composition and the in-plane misfit, an electrically tunable piezoelectric response can be obtained in the paraelectric state. These findings indicate that strain engineered BST films can be utilized in the development of electrically tunable and switchable surface and bulk acoustic wave resonators.

  6. Delay time and Hartman effect in strain engineered graphene

    SciTech Connect

    Chen, Xi Deng, Zhi-Yong; Ban, Yue

    2014-05-07

    Tunneling times, including group delay and dwell time, are studied for massless Dirac electrons transmitting through a one-dimensional barrier in strain-engineered graphene. The Hartman effect, the independence of group delay on barrier length, is induced by the strain effect, and associated with the transmission gap and the evanescent mode. The influence of barrier height/length and strain modulus/direction on the group delay is also discussed, which provides the flexibility to control the group delay with applications in graphene-based devices. The relationship between group delay and dwell time is finally derived to clarify the nature of the Hartman effect.

  7. Strain engineering of magnetic state in vacancy-doped phosphorene

    NASA Astrophysics Data System (ADS)

    Ren, Jie; Zhang, Chunxiao; Li, Jin; Guo, Zhixin; Xiao, Huaping; Zhong, Jianxin

    2016-09-01

    Inducing and manipulating the magnetism in two-dimensional materials play an important role for the development of the next-generation spintronics. In this letter, the effects of the biaxial strain on magnetic properties of vacancy-doped phosphorene are investigated using first-principles calculation. We find although only SV956 doping induces magnetism for unstrained phosphorene, the biaxial strain induces nonzero magnetic moment for SV5566 and DVa doped phosphorene. The biaxial strain also modulates the magnetic state for SV956, SV5566 and DVa doped phosphorene. The local magnetic moment derives from the spin polarization of the dangling bonds near the vacancy. The biaxial strain influences the local bonding configuration near the vacancy which determines the presence of dangling bonds, and then modulates the magnetic state. Our findings promise the synergistic effect of strain engineering and vacancy decoration is an effective method for the operation of phosphorene-based spintronic devices.

  8. Genome engineering and gene expression control for bacterial strain development.

    PubMed

    Song, Chan Woo; Lee, Joungmin; Lee, Sang Yup

    2015-01-01

    In recent years, a number of techniques and tools have been developed for genome engineering and gene expression control to achieve desired phenotypes of various bacteria. Here we review and discuss the recent advances in bacterial genome manipulation and gene expression control techniques, and their actual uses with accompanying examples. Genome engineering has been commonly performed based on homologous recombination. During such genome manipulation, the counterselection systems employing SacB or nucleases have mainly been used for the efficient selection of desired engineered strains. The recombineering technology enables simple and more rapid manipulation of the bacterial genome. The group II intron-mediated genome engineering technology is another option for some bacteria that are difficult to be engineered by homologous recombination. Due to the increasing demands on high-throughput screening of bacterial strains having the desired phenotypes, several multiplex genome engineering techniques have recently been developed and validated in some bacteria. Another approach to achieve desired bacterial phenotypes is the repression of target gene expression without the modification of genome sequences. This can be performed by expressing antisense RNA, small regulatory RNA, or CRISPR RNA to repress target gene expression at the transcriptional or translational level. All of these techniques allow efficient and rapid development and screening of bacterial strains having desired phenotypes, and more advanced techniques are expected to be seen.

  9. Enhanced expression of recombinant beta toxin of Clostridium perfringens type B using a commercially available Escherichia coli strain.

    PubMed

    Bakhshi, Fatemah; Pilehchian Langroudi, Reza; Imani, Bahram Golestani

    2016-06-30

    Clostridium perfringens beta toxin is only produced by types B and C and plays an important role in many human and animal diseases, causing fatal conditions that originate in the intestines. We compared the expression of C. perfringens type B vaccine strain recombinant beta toxin gene in the Escherichia coli strains RosettaTM(DE3) and BL21(DE3). The beta toxin gene was extracted from pJETβ and ligated with pET22b(+). pET22β was transformed into E. coli strains BL21(DE3) and RosettaTM(DE3). Recombinant protein was expressed as a soluble protein after isopropyl β-D-1-thiogalactopyranoside (IPTG) induction in strain RosettaTM(DE3) but not in BL21(DE3). Expression was optimised by growing recombinant cells at 37 °C and at an induction of 0.5 mM, 1 mM, 1.5 mM IPTG. Expression was evaluated using sodium dodecyl sulfate Polyacrylamide gel electrophoresis (SDS-PAGE). The recombinant protein was purified via Ni-NTA and was analysed using western blot. We concluded that E. coli strain RosettaTM(DE3) can enhance the expression of C. perfringens recombinant beta toxin.

  10. Differences in biomass degradation between newly isolated environmental strains of Clostridium thermocellum and heterogeneity in the size of the cellulosomal scaffoldin.

    PubMed

    Koeck, D E; Koellmeier, T; Zverlov, V V; Liebl, W; Schwarz, W H

    2015-09-01

    Cellulolytic bacterial strains with high activity were isolated from cellulose degrading enrichment cultures derived from thermophilic biogas plants and environmental samples. The 16S rRNA gene sequences of the strains revealed >99.8% sequence identity and affiliation with the species Clostridium thermocellum. The strains differed in their ability to degrade crystalline cellulose, especially at an elevated temperature of up to 67 °C and at relatively low pH values (pH 6.5). To evaluate the influence of amino acid sequences on the discrepancies in cellulose degradation efficacy, the gene for the major cellulosomal component CelR was sequenced for all strains. The sequences were found to be almost identical (>99%). In contrast, the cellulosomal scaffoldin gene cipA showed more differences in the amino acid sequence and contained 8 or 9 cohesin modules, which indicated a different size of the cellulosome depending on the isolate. Based on MALDI-TOF MS analysis the relative abundance of important cellulosomal enzyme classes was determined. The strains with better biomass degradation properties (BC1 and NB2) had a significantly higher fraction of xylanases.

  11. Enhanced expression of recombinant beta toxin of Clostridium perfringens type B using a commercially available Escherichia coli strain.

    PubMed

    Bakhshi, Fatemah; Pilehchian Langroudi, Reza; Imani, Bahram Golestani

    2016-01-01

    Clostridium perfringens beta toxin is only produced by types B and C and plays an important role in many human and animal diseases, causing fatal conditions that originate in the intestines. We compared the expression of C. perfringens type B vaccine strain recombinant beta toxin gene in the Escherichia coli strains RosettaTM(DE3) and BL21(DE3). The beta toxin gene was extracted from pJETβ and ligated with pET22b(+). pET22β was transformed into E. coli strains BL21(DE3) and RosettaTM(DE3). Recombinant protein was expressed as a soluble protein after isopropyl β-D-1-thiogalactopyranoside (IPTG) induction in strain RosettaTM(DE3) but not in BL21(DE3). Expression was optimised by growing recombinant cells at 37 °C and at an induction of 0.5 mM, 1 mM, 1.5 mM IPTG. Expression was evaluated using sodium dodecyl sulfate Polyacrylamide gel electrophoresis (SDS-PAGE). The recombinant protein was purified via Ni-NTA and was analysed using western blot. We concluded that E. coli strain RosettaTM(DE3) can enhance the expression of C. perfringens recombinant beta toxin. PMID:27543150

  12. Toxigenicity of Clostridium histolyticum

    PubMed Central

    Nishida, Shoki; Imaizumi, Masaaki

    1966-01-01

    Nishida, Shoki (Kanazawa University, Kanazawa, Japan), and Masaaki Imaizumi. Toxigenicity of Clostridium histolyticum. J. Bacteriol. 91:477–483. 1966.—From 234 soil samples, 21 strains of Clostridium histolyticum of different levels of α-toxigenicity were isolated by a new method specially designed for the isolation of this species. The α-toxigenicity of freshly isolated strains and of stock strains was closely associated with the potentiality for sporulation, growth, and smooth-colony formation. The presence of sugars, particularly xylose and arabinose, was inhibitory for growth. A few controversies on the biological properties of this species seem to be due to disregard for the growth-inhibiting effects of these sugars. PMID:5935337

  13. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    SciTech Connect

    Bao, Guanhui; Dong, Hongjun; Zhu, Yan; Mao, Shaoming; Zhang, Tianrui; Zhang, Yanping; Chen, Zugen; Li, Yin

    2014-08-08

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance.

  14. Nontoxigenic Clostridium difficile protects hamsters against challenge with historic and epidemic strains of toxigenic BI/NAP1/027 C. difficile.

    PubMed

    Nagaro, Kristin J; Phillips, S Tyler; Cheknis, Adam K; Sambol, Susan P; Zukowski, Walter E; Johnson, Stuart; Gerding, Dale N

    2013-11-01

    Nontoxigenic Clostridium difficile (NTCD) has been shown to prevent fatal C. difficile infection in the hamster model when hamsters are challenged with standard toxigenic C. difficile strains. The purpose of this study was to determine if NTCD can prevent C. difficile infection in the hamster model when hamsters are challenged with restriction endonuclease analysis group BI C. difficile strains. Groups of 10 hamsters were given oral clindamycin, followed on day 2 by 10(6) CFU of spores of NTCD strain M3 or T7, and were challenged on day 5 with 100 CFU of spores of BI1 or BI6. To conserve animals, results for control hamsters challenged with BI1 or BI6 from the present study and controls from previous identical experiments were combined for statistical comparisons. NTCD strains M3 and T7 achieved 100% colonization and were 100% protective against challenge with BI1 (P ≤ 0.001). M3 colonized 9/10 hamsters and protected against BI6 challenge in the colonized hamsters (P = 0.0003). T7 colonized 10/10 hamsters, but following BI6 challenge, cocolonization occurred in 5 hamsters, 4 of which died, for protection of 6/10 animals (P = 0.02). NTCD colonization provides protection against challenge with toxigenic BI group strains. M3 is more effective than T7 in preventing C. difficile infection caused by the BI6 epidemic strain. Prevention of C. difficile infection caused by the epidemic BI6 strain may be more challenging than that of infections caused by historic BI1 and non-BI C. difficile strains.

  15. Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

    PubMed

    Kwon, Man Jae; Wei, Na; Millerick, Kayleigh; Popovic, Jovan; Finneran, Kevin

    2014-06-01

    A fermentative, non-spore forming, motile, rod-shaped bacterium, designated strain MJ1(T), was isolated from an RDX contaminated aquifer at a live-fire training site in Northwest NJ, United States. On the basis of 16S rRNA gene sequencing and DNA base composition, strain MJ1(T) was assigned to the Firmicutes. The DNA G+C content was 42.8 mol%. Fermentative growth was supported by glucose and citrate in a defined basal medium. The bacterium is a strict anaerobe that grows between at pH 6.0 and pH 8.0 and 18 and 37 °C. The culture did not grow with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) as the electron acceptor or mineralize RDX under these conditions. However, MJ1(T) transformed RDX into MNX, methylenedinitramine, formaldehyde, formate, ammonium, nitrous oxide, and nitrate. The nearest phylogenetic relative with a validly published name was Desulfotomaculum guttoideum (95 % similarity). However, MJ1(T) was also related to Clostridium celerecrescens DSM 5628 (95 %), Clostridium indolis DSM 755 (94 %), and Clostridium sphenoides DSM 632 (94 %). DNA:DNA hybridization with these strains was between 6.7 and 58.7 percent. The dominant cellular fatty acids (greater than 5 % of the total, which was 99.0 % recovery) were 16:0 fatty acid methyl ester (FAME) (32.12 %), 18:1cis 11 dimethyl acetal (DMA) (16.47 %), 16:1cis 9 DMA (10.28 %), 16:1cis 9 FAME (8.10 %), and 18:1cis 9 DMA (5.36 %). On the basis of morphological, physiological, and phylogenetic data, Clostridium geopurificans is proposed as a new species in genus Clostridium, with strain MJ1(T) as the type strain. PMID:24522483

  16. Functional Characterization of an Extended Binding Component of the Actin-ADP-Ribosylating C2 Toxin Detected in Clostridium botulinum Strain (C) 2300 ▿

    PubMed Central

    Sterthoff, Charlott; Lang, Alexander E.; Schwan, Carsten; Tauch, Andreas; Aktories, Klaus

    2010-01-01

    Clostridium botulinum C2 toxin consists of the binding component C2II and the enzyme component C2I, which ADP-ribosylates G-actin of eukaryotic cells. Trypsin-activated C2II (C2IIa) forms heptamers that mediate cell binding and translocation of C2I from acidic endosomes into the cytosol of target cells. By genome sequencing of C. botulinum strain (C) 2300, we found that C2II from this strain carries a C-terminal extension of 129 amino acids, unlike its homologous counterparts from strains (C) 203U28, (C) 468, and (D) 1873. This extension shows a high similarity to the C-terminal receptor-binding domain of C2II and is presumably the result of a duplication of this domain. The C2II extension facilitates the binding to cell surface receptors, which leads to an increased intoxication efficiency compared to that of C2II proteins from other C. botulinum strains. PMID:20145093

  17. Clostridium difficile infection among immunocompromised patients in Rio de Janeiro, Brazil and detection of moxifloxacin resistance in a ribotype 014 strain.

    PubMed

    Secco, Danielle Angst; Balassiano, Ilana Teruszkin; Boente, Renata Ferreira; Miranda, Karla Rodrigues; Brazier, Jon; Hall, Val; dos Santos-Filho, Joaquim; Lobo, Leandro Araujo; Nouér, Simone Aranha; Domingues, Regina Maria Cavalcanti Pilotto

    2014-08-01

    Clostridium difficile is a Gram-positive spore forming anaerobic bacterium, often associated with nosocomial diarrhea and pseudomembranous colitis. The acquisition of this organism occurs primarily in hospitals through accidental ingestion of spores, and its establishment and proliferation in the colon results from the removal of members of the normal intestinal flora during or after antibiotic therapy. In this study, stool samples from patients admitted to the University Hospital Clementino Fraga Filho (HUCCF/UFRJ) were screened for C. difficile toxins with an ELISA test and cultured with standard techniques for C. difficile isolation. A total of 74 stool samples were collected from patients undergoing antibiotic therapy between August 2009 and November 2010, only two (2.7%) were positive in the ELISA test and culture. A third isolate was obtained from a negative ELISA test sample. All cases of CDI were identified in patients with acute lymphoid or myeloid leukemia. Genotypic and phenotypic characterization showed that all strains carried toxins A and B genes, and belonged to PCR-ribotypes 014, 043 and 046. The isolated strains were sensitive to metronidazole and vancomycin, and resistant to ciprofloxacin and levofloxacin. Resistance to moxifloxacin, was present in the strain from PCR-ribotype 014, that showed an amino acid substitution in gyrB gene (Asp 426 → Asn). This is the first time that this mutation in a PCR-ribotype 014 strain has been described in Brazil.

  18. Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene).

    PubMed

    Bhushan, Ashish; Mukherjee, Tanmoy; Joshi, Jayadev; Shankar, Pratap; Kalia, Vipin Chandra

    2015-06-01

    Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho. PMID:25805900

  19. Clostridium Difficile Colonization in Hematopoietic Stem Cell Transplant Recipients: A Prospective Study of the Epidemiology and Outcomes Involving Toxigenic and Nontoxigenic Strains.

    PubMed

    Jain, Tania; Croswell, Christopher; Urday-Cornejo, Varinia; Awali, Reda; Cutright, Jessica; Salimnia, Hossein; Reddy Banavasi, Harsha Vardhan; Liubakka, Alyssa; Lephart, Paul; Chopra, Teena; Revankar, Sanjay G; Chandrasekar, Pranatharthi; Alangaden, George

    2016-01-01

    Clostridium difficile is a leading cause of infectious diarrhea in hematopoietic stem cell transplant (HSCT) recipients. Asymptomatic colonization of the gastrointestinal tract occurs before development of C. difficile infection (CDI). This prospective study examines the rates, risk factors, and outcomes of colonization with toxigenic and nontoxigenic strains of C. difficile in HSCT patients. This 18-month study was conducted in the HSCT unit at the Karmanos Cancer Center and Wayne State University in Detroit. Stool samples from the patients who consented for the study were taken at admission and weekly until discharge. Anaerobic culture for C. difficile and identification of toxigenic strains by PCR were performed on the stool samples. Demographic information and clinical and laboratory data were collected. Of the 150 patients included in the study, 29% were colonized with C. difficile at admission; 12% with a toxigenic strain and 17% with a nontoxigenic strain. Over a 90-day follow-up, 12 of 44 (26%) patients colonized with any C. difficile strain at admission developed CDI compared with 13 of 106 (12%) of patients not colonized (odds ratio [OR], 2.70; 95% confidence interval [95% CI], 1.11 to 6.48; P = .025). Eleven of 18 (61%) patients colonized with the toxigenic strain and 1 of 26 (4%) of those colonized with nontoxigenic strain developed CDI (OR, 39.30; 95% CI, 4.30 to 359.0; P < .001) at a median of 12 days. On univariate and multivariate analyses, none of the traditional factors associated with high risk for C. difficile colonization or CDI were found to be significant. Recurrent CDI occurred in 28% of cases. Asymptomatic colonization with C. difficile at admission was high in our HSCT population. Colonization with toxigenic C. difficile was predictive of CDI, whereas colonization with a nontoxigenic C. difficile appeared protective. These findings may have implications for infection control strategies and for novel approaches for the prevention and

  20. MESSI: metabolic engineering target selection and best strain identification tool.

    PubMed

    Kang, Kang; Li, Jun; Lim, Boon Leong; Panagiotou, Gianni

    2015-01-01

    Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae's ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae's metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains' natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels.Database URL: http://sbb.hku.hk/MESSI/.

  1. Engineering related neutron diffraction measurements probing strains, texture and microstructure

    SciTech Connect

    Clausen, Bjorn; Brown, Donald W; Tome, Carlos N; Balogh, Levente; Vogel, Sven C

    2010-01-01

    Neutron diffraction has been used for engineering applications for nearly three decades. The basis of the technique is powder diffraction following Bragg's Law. From the measured diffraction patterns information about internal, or residual, strain can be deduced from the peak positions, texture information can be extracted from the peak intensities, and finally the peak widths can provide information about the microstructure, e.g. dislocation densities and grain sizes. The strains are measured directly from changes in lattice parameters, however, in many cases it is non-trivial to determine macroscopic values of stress or strain from the measured data. The effects of intergranular strains must be considered, and combining the neutron diffraction measurements with polycrystal deformation modeling has proven invaluable in determining the overall stress and strain values of interest in designing and dimensioning engineering components. Furthelmore, the combined use of measurements and modeling has provided a tool for elucidating basic material properties, such as critical resolved shear stresses for the active deformation modes and their evolution as a function of applied deformation.

  2. [Comparison of AP-PCR methods, ribotyping (PCR-ribotyping) and pulsed-field electrophoresis (PFGE) for strains of Clostridium difficile producing toxin B and not producing toxin A].

    PubMed

    Pituch, Hanna; van Belkum, Alex; Obuch-Woszczatyński, Piotr; Meisel-Mikołajczyk, Felicja; Łuczak, Miroslaw

    2003-01-01

    In this study were used AP-PCR, PCR-ribotyping and pulsed-field elecrophoresis (PFGE) for comparative study of toxin A-negative/toxin B-posi-tive Clostridium difficile strains with deletion in toxin A gen. We investigated nine unrelated clinical strains, isolated from different units and different time from patients suffering to antibiotic associated diarrhea (AAD). We found that toxin A-negative/toxin B-positive C. difficile strains isolated in Poland belonging to a single genotype A, are being similar to the Japanese strains.

  3. Broad coverage of genetically diverse strains of Clostridium difficile by actoxumab and bezlotoxumab predicted by in vitro neutralization and epitope modeling.

    PubMed

    Hernandez, Lorraine D; Racine, Fred; Xiao, Li; DiNunzio, Edward; Hairston, Nichelle; Sheth, Payal R; Murgolo, Nicholas J; Therien, Alex G

    2015-02-01

    Clostridium difficile infections (CDIs) are the leading cause of hospital-acquired infectious diarrhea and primarily involve two exotoxins, TcdA and TcdB. Actoxumab and bezlotoxumab are human monoclonal antibodies that neutralize the cytotoxic/cytopathic effects of TcdA and TcdB, respectively. In a phase II clinical study, the actoxumab-bezlotoxumab combination reduced the rate of CDI recurrence in patients who were also treated with standard-of-care antibiotics. However, it is not known whether the antibody combination will be effective against a broad range of C. difficile strains. As a first step toward addressing this, we tested the ability of actoxumab and bezlotoxumab to neutralize the activities of toxins from a number of clinically relevant and geographically diverse strains of C. difficile. Neutralization potencies, as measured in a cell growth/survival assay with purified toxins from various C. difficile strains, correlated well with antibody/toxin binding affinities. Actoxumab and bezlotoxumab neutralized toxins from culture supernatants of all clinical isolates tested, including multiple isolates of the BI/NAP1/027 and BK/NAP7/078 strains, at antibody concentrations well below plasma levels observed in humans. We compared the bezlotoxumab epitopes in the TcdB receptor binding domain across known TcdB sequences and found that key substitutions within the bezlotoxumab epitopes correlated with the relative differences in potencies of bezlotoxumab against TcdB of some strains, including ribotypes 027 and 078. Combined with in vitro neutralization data, epitope modeling will enhance our ability to predict the coverage of new and emerging strains by actoxumab-bezlotoxumab in the clinic. PMID:25451052

  4. Complete nucleotide sequence of a plasmid containing the botulinum neurotoxin gene in Clostridium botulinum type B strain 111 isolated from an infant patient in Japan.

    PubMed

    Hosomi, Koji; Sakaguchi, Yoshihiko; Kohda, Tomoko; Gotoh, Kazuyoshi; Motooka, Daisuke; Nakamura, Shota; Umeda, Kaoru; Iida, Tetsuya; Kozaki, Shunji; Mukamoto, Masafumi

    2014-12-01

    Botulinum neurotoxins (BoNTs) are highly potent toxins that are produced by Clostridium botulinum. We determined the complete nucleotide sequence of a plasmid containing the botulinum neurotoxin gene in C. botulinum type B strain 111 in order to obtain an insight into the toxigenicity and evolution of the bont gene in C. botulinum. Group I C. botulinum type B strain 111 was isolated from the first case of infant botulism in Japan in 1995. In previous studies, botulinum neurotoxin subtype B2 (BoNT/B2) produced by strain 111 exhibited different antigenic properties from those of authentic BoNT/B1 produced by strain Okra. We have recently shown that the isolates of strain 111 that lost toxigenicity were cured of the plasmid containing the bont/B2 gene. In the present study, the plasmid (named pCB111) was circular 265,575 bp double-stranded DNA and contained 332 predicted open reading frames (ORFs). 85 gene products of these ORFs could be functionally assigned on the basis of sequence homology to known proteins. The bont/B2 complex genes were located on pCB111 and some gene products may be involved in the conjugative plasmid transfer and horizontal transfer of bont genes. pCB111 was similar to previously identified plasmids containing bont/B1, /B5, or/A3 complex genes in other group I C. botulinum strains. It was suggested that these plasmids had been derived from a common ancestor and had played important roles for the bont gene transfer between C. botulinum. PMID:25149145

  5. High temperature strain gage technology for gas turbine engines

    NASA Astrophysics Data System (ADS)

    Fichtel, Edward J.; McDaniel, Amos D.

    1994-08-01

    This report summarizes the results of a six month study that addressed specific issues to transfer the Pd-13Cr static strain sensor to a gas turbine engine environment. The application issues that were addressed include: (1) evaluation of a miniature, variable potentiometer for use as the ballast resistor, in conjunction with a conventional strain gage signal conditioning unit; (2) evaluation of a metal sheathed, platinum conductor leadwire assembly for use with the three-wire sensor; and (3) subjecting the sensor to dynamic strain cyclic testing to determine fatigue characteristics. Results indicate a useful static strain gage system at all temperature levels up to 1350 F. The fatigue characteristics also appear to be very promising, indicating a potential use in dynamic strain measurement applications. The procedure, set-up, and data for all tests are presented in this report. This report also discusses the specific strain gage installation technique for the Pd-13Cr gage because of its potential impact on the quality of the output data.

  6. High temperature strain gage technology for gas turbine engines

    NASA Technical Reports Server (NTRS)

    Fichtel, Edward J.; Mcdaniel, Amos D.

    1994-01-01

    This report summarizes the results of a six month study that addressed specific issues to transfer the Pd-13Cr static strain sensor to a gas turbine engine environment. The application issues that were addressed include: (1) evaluation of a miniature, variable potentiometer for use as the ballast resistor, in conjunction with a conventional strain gage signal conditioning unit; (2) evaluation of a metal sheathed, platinum conductor leadwire assembly for use with the three-wire sensor; and (3) subjecting the sensor to dynamic strain cyclic testing to determine fatigue characteristics. Results indicate a useful static strain gage system at all temperature levels up to 1350 F. The fatigue characteristics also appear to be very promising, indicating a potential use in dynamic strain measurement applications. The procedure, set-up, and data for all tests are presented in this report. This report also discusses the specific strain gage installation technique for the Pd-13Cr gage because of its potential impact on the quality of the output data.

  7. Semiconductor nanomembranes: a platform for new properties via strain engineering

    PubMed Central

    2012-01-01

    New phenomena arise in single-crystal semiconductors when these are fabricated in very thin sheets, with thickness at the nanometer scale. We review recent research on Si and Ge nanomembranes, including the use of elastic strain sharing, layer release, and transfer, that demonstrate new science and enable the fabrication of materials with unique properties. Strain engineering produces new strained forms of Si or Ge not possible in nature, new layered structures, defect-free SiGe sheets, and new electronic band structure and photonic properties. Through-membrane elastic interactions cause the double-sided ordering of epitaxially grown nanostressors on Si nanomembranes, resulting in a spatially and periodically varying strain field in the thin crystalline semiconductor sheet. The inherent influence of strain on the band structure creates band gap modulation, thereby creating effectively a single-element electronic superlattice. Conversely, large-enough externally applied strain can make Ge a direct-band gap semiconductor, giving promise for Group IV element light sources. PMID:23153167

  8. Acetone production with metabolically engineered strains of Acetobacterium woodii.

    PubMed

    Hoffmeister, Sabrina; Gerdom, Marzena; Bengelsdorf, Frank R; Linder, Sonja; Flüchter, Sebastian; Öztürk, Hatice; Blümke, Wilfried; May, Antje; Fischer, Ralf-Jörg; Bahl, Hubert; Dürre, Peter

    2016-07-01

    Expected depletion of oil and fossil resources urges the development of new alternative routes for the production of bulk chemicals and fuels beyond petroleum resources. In this study, the clostridial acetone pathway was used for the formation of acetone in the acetogenic bacterium Acetobacterium woodii. The acetone production operon (APO) containing the genes thlA (encoding thiolase A), ctfA/ctfB (encoding CoA transferase), and adc (encoding acetoacetate decarboxylase) from Clostridium acetobutylicum were cloned under the control of the thlA promoter into four vectors having different replicons for Gram-positives (pIP404, pBP1, pCB102, and pCD6). Stable replication was observed for all constructs. A. woodii [pJIR_actthlA] achieved the maximal acetone concentration under autotrophic conditions (15.2±3.4mM). Promoter sequences of the genes ackA from A. woodii and pta-ack from C. ljungdahlii were determined by primer extension (PEX) and cloned upstream of the APO. The highest acetone production in recombinant A. woodii cells was achieved using the promoters PthlA and Ppta-ack. Batch fermentations using A. woodii [pMTL84151_actthlA] in a bioreactor revealed that acetate concentration had an effect on the acetone production, due to the high Km value of the CoA transferase. In order to establish consistent acetate concentration within the bioreactor and to increase biomass, a continuous fermentation process for A. woodii was developed. Thus, acetone productivity of the strain A. woodii [pMTL84151_actthlA] was increased from 1.2mgL(-1)h(-1) in bottle fermentation to 26.4mgL(-1)h(-1) in continuous gas fermentation. PMID:26971669

  9. Acetone production with metabolically engineered strains of Acetobacterium woodii.

    PubMed

    Hoffmeister, Sabrina; Gerdom, Marzena; Bengelsdorf, Frank R; Linder, Sonja; Flüchter, Sebastian; Öztürk, Hatice; Blümke, Wilfried; May, Antje; Fischer, Ralf-Jörg; Bahl, Hubert; Dürre, Peter

    2016-07-01

    Expected depletion of oil and fossil resources urges the development of new alternative routes for the production of bulk chemicals and fuels beyond petroleum resources. In this study, the clostridial acetone pathway was used for the formation of acetone in the acetogenic bacterium Acetobacterium woodii. The acetone production operon (APO) containing the genes thlA (encoding thiolase A), ctfA/ctfB (encoding CoA transferase), and adc (encoding acetoacetate decarboxylase) from Clostridium acetobutylicum were cloned under the control of the thlA promoter into four vectors having different replicons for Gram-positives (pIP404, pBP1, pCB102, and pCD6). Stable replication was observed for all constructs. A. woodii [pJIR_actthlA] achieved the maximal acetone concentration under autotrophic conditions (15.2±3.4mM). Promoter sequences of the genes ackA from A. woodii and pta-ack from C. ljungdahlii were determined by primer extension (PEX) and cloned upstream of the APO. The highest acetone production in recombinant A. woodii cells was achieved using the promoters PthlA and Ppta-ack. Batch fermentations using A. woodii [pMTL84151_actthlA] in a bioreactor revealed that acetate concentration had an effect on the acetone production, due to the high Km value of the CoA transferase. In order to establish consistent acetate concentration within the bioreactor and to increase biomass, a continuous fermentation process for A. woodii was developed. Thus, acetone productivity of the strain A. woodii [pMTL84151_actthlA] was increased from 1.2mgL(-1)h(-1) in bottle fermentation to 26.4mgL(-1)h(-1) in continuous gas fermentation.

  10. MESSI: metabolic engineering target selection and best strain identification tool

    PubMed Central

    Kang, Kang; Li, Jun; Lim, Boon Leong; Panagiotou, Gianni

    2015-01-01

    Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae’s ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae’s metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains’ natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels. Database URL: http://sbb.hku.hk/MESSI/ PMID:26255308

  11. Tunable thermoelectric transport in nanomeshes via elastic strain engineering

    SciTech Connect

    Piccione, Brian; Gianola, Daniel S.

    2015-03-16

    Recent experimental explorations of silicon nanomeshes have shown that the unique metastructures exhibit reduced thermal conductivity while preserving bulk electrical conductivity via feature sizes between relevant phonon and electron mean free paths, aiding in the continued promise that nanometer-scale engineering may further enhance thermoelectric behavior. Here, we introduce a strategy for tuning thermoelectric transport phenomena in semiconductor nanomeshes via heterogeneous elastic strain engineering, using silicon as a model material for demonstration of the concept. By combining analytical models for electron mobility in uniformly stressed silicon with finite element analysis of strained silicon nanomeshes in a lumped physical model, we show that the nonuniform and multiaxial strain fields defined by the nanomesh geometry give rise to spatially varying band shifts and warping, which in aggregate accelerate electron transport along directions of applied stress. This allows for global electrical conductivity and Seebeck enhancements beyond those of homogenous samples under equivalent far-field stresses, ultimately increasing thermoelectric power factor nearly 50% over unstrained samples. The proposed concept and structures—generic to a wide class of materials with large dynamic ranges of elastic strain in nanoscale volumes—may enable a new pathway for active and tunable control of transport properties relevant to waste heat scavenging and thermal management.

  12. Simulating MEMS Chevron Actuator for Strain Engineering 2D Materials

    NASA Astrophysics Data System (ADS)

    Vutukuru, Mounika; Christopher, Jason; Bishop, David; Swan, Anna

    2D materials pose an exciting paradigm shift in the world of electronics. These crystalline materials have demonstrated high electric and thermal conductivities and tensile strength, showing great potential as the new building blocks of basic electronic circuits. However, strain engineering 2D materials for novel devices remains a difficult experimental feat. We propose the integration of 2D materials with MEMS devices to investigate the strain dependence on material properties such as electrical and thermal conductivity, refractive index, mechanical elasticity, and band gap. MEMS Chevron actuators, provides the most accessible framework to study strain in 2D materials due to their high output force displacements for low input power. Here, we simulate Chevron actuators on COMSOL to optimize actuator design parameters and accurately capture the behavior of the devices while under the external force of a 2D material. Through stationary state analysis, we analyze the response of the device through IV characteristics, displacement and temperature curves. We conclude that the simulation precisely models the real-world device through experimental confirmation, proving that the integration of 2D materials with MEMS is a viable option for constructing novel strain engineered devices. The authors acknowledge support from NSF DMR1411008.

  13. Genomic Sequence of Bacteriophage ATCC 8074-B1 and Activity of Its Endolysin and Engineered Variants against Clostridium sporogenes

    PubMed Central

    Gasson, Michael J.; Narbad, Arjan

    2012-01-01

    Lytic bacteriophage ATCC 8074-B1 produces large plaques on its host Clostridium sporogenes. Sequencing of the 47,595-bp genome allowed the identification of 82 putative open reading frames, including those encoding proteins for head and tail morphogenesis and lysis. However, sequences commonly associated with lysogeny were absent. ORF 22 encodes an endolysin, CS74L, that shows homology to N-acetylmuramoyl-l-alanine amidases, and when expressed in Escherichia coli, the protein causes effective lysis of C. sporogenes cells when added externally. CS74L was also active on Clostridium tyrobutyricum and Clostridium acetobutylicum. The catalytic domain expressed alone (CS74L1–177) exhibited a similar activity and the same host range as the full-length endolysin. A chimeric endolysin consisting of the CS74L catalytic domain fused to the C-terminal domain of endolysin CD27L, derived from Clostridium difficile bacteriophage ΦCD27, was produced. This chimera (CSCD) lysed C. sporogenes cells with an activity equivalent to that of the catalytic domain alone. In contrast, the CD27L C-terminal domain reduced the efficacy of the CS74L catalytic domain when tested against C. tyrobutyricum. The addition of the CD27L C-terminal domain did not enable the lysin to target C. difficile or other CD27L-sensitive bacteria. PMID:22427494

  14. The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective

    PubMed Central

    Ihekwaba, Adaoha E. C.; Mura, Ivan; Peck, Michael W.; Barker, G. C.

    2015-01-01

    Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most poisonous substances known to mankind. However, toxin regulation and signals triggering synthesis as well as the regulatory network and actors controlling toxin production are unknown. Experiments show that the neurotoxin gene is growth phase dependent for C. botulinum type A1 strain ATCC 19397, and toxin production is influenced both by culture conditions and nutritional status of the medium. Building mathematical models to describe the genetic and molecular machinery that drives the synthesis and release of BoNT requires a simultaneous description of the growth of the bacterium in culture. Here, we show four plausible modelling options which could be considered when constructing models describing the pattern of growth observed in a botulinum growth medium. Commonly used bacterial growth models are unsuitable to fit the pattern of growth observed, since they only include monotonic growth behaviour. We find that a model that includes both the nutritional status and the ability of the cells to sense their surroundings in a quorum-sensing manner is most successful at explaining the pattern of growth obtained for C. botulinum type A1 strain ATCC 19397. PMID:26449712

  15. Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.

    PubMed

    Cairns, M D; Preston, M D; Lawley, T D; Clark, T G; Stabler, R A; Wren, B W

    2015-10-01

    Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.

  16. The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective.

    PubMed

    Ihekwaba, Adaoha E C; Mura, Ivan; Peck, Michael W; Barker, G C

    2015-12-01

    Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most poisonous substances known to mankind. However, toxin regulation and signals triggering synthesis as well as the regulatory network and actors controlling toxin production are unknown. Experiments show that the neurotoxin gene is growth phase dependent for C. botulinum type A1 strain ATCC 19397, and toxin production is influenced both by culture conditions and nutritional status of the medium. Building mathematical models to describe the genetic and molecular machinery that drives the synthesis and release of BoNT requires a simultaneous description of the growth of the bacterium in culture. Here, we show four plausible modelling options which could be considered when constructing models describing the pattern of growth observed in a botulinum growth medium. Commonly used bacterial growth models are unsuitable to fit the pattern of growth observed, since they only include monotonic growth behaviour. We find that a model that includes both the nutritional status and the ability of the cells to sense their surroundings in a quorum-sensing manner is most successful at explaining the pattern of growth obtained for C. botulinum type A1 strain ATCC 19397.

  17. Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.

    PubMed

    Cairns, M D; Preston, M D; Lawley, T D; Clark, T G; Stabler, R A; Wren, B W

    2015-10-01

    Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified. PMID:26179308

  18. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism.

    PubMed

    Kim, Soo Rin; Park, Yong-Cheol; Jin, Yong-Su; Seo, Jin-Ho

    2013-11-01

    Efficient and rapid fermentation of all sugars present in cellulosic hydrolysates is essential for economic conversion of renewable biomass into fuels and chemicals. Xylose is one of the most abundant sugars in cellulosic biomass but it cannot be utilized by wild type Saccharomyces cerevisiae, which has been used for industrial ethanol production. Therefore, numerous technologies for strain development have been employed to engineer S. cerevisiae capable of fermenting xylose rapidly and efficiently. These include i) optimization of xylose-assimilating pathways, ii) perturbation of gene targets for reconfiguring yeast metabolism, and iii) simultaneous co-fermentation of xylose and cellobiose. In addition, the genetic and physiological background of host strains is an important determinant to construct efficient and rapid xylose-fermenting S. cerevisiae. Vibrant and persistent researches in this field for the last two decades not only led to the development of engineered S. cerevisiae strains ready for industrial fermentation of cellulosic hydrolysates, but also deepened our understanding of operational principles underlying yeast metabolism. PMID:23524005

  19. Comparative neuropathology of ovine enterotoxemia produced by Clostridium perfringens type D wild-type strain CN1020 and its genetically modified derivatives.

    PubMed

    Garcia, J P; Giannitti, F; Finnie, J W; Manavis, J; Beingesser, J; Adams, V; Rood, J I; Uzal, F A

    2015-05-01

    Clostridium perfringens type D causes enterotoxemia in sheep and goats. The disease is mediated by epsilon toxin (ETX), which affects the cerebrovascular endothelium, increasing vascular permeability and leading to cerebral edema. In the present study, we compared the distribution and severity of the cerebrovascular changes induced in lambs by C. perfringens type D strain CN1020, its isogenic etx null mutant, and the ETX-producing complemented mutant. We also applied histochemical and immunohistochemical markers to further characterize the brain lesions induced by ETX. Both ETX-producing strains induced extensive cerebrovascular damage that did not differ significantly between each other in nature, neuroanatomic distribution, or severity. By contrast, lambs inoculated with the etx mutant or sterile, nontoxic culture medium did not develop detectable brain lesions, confirming that the neuropathologic effects observed in these infections are dependent on ETX production. Lambs treated with the wild-type and complemented strains showed perivascular and mural vascular edema, as well as serum albumin extravasation, particularly severe in the cerebral white matter, midbrain, medulla oblongata, and cerebellum. Brains of animals inoculated with the ETX-producing strains showed decreased expression of glial fibrillary acidic protein and increased expression of aquaporin-4 in the end-feet processes of the astrocytes around blood vessels. Early axonal injury was demonstrated with anti-amyloid precursor protein immunohistochemistry. Perivascular accumulation of macrophages/microglia with intracytoplasmic albumin globules was also observed in these animals. This study demonstrates that ETX is responsible for the major cerebrovascular changes in C. perfringens type D-induced disease.

  20. Strain engineered high reflectivity DBRs in the deep UV

    NASA Astrophysics Data System (ADS)

    Franke, A.; Hoffmann, M. P.; Hernandez-Balderrama, L.; Kaess, F.; Bryan, I.; Washiyama, S.; Bobea, M.; Tweedie, J.; Kirste, R.; Gerhold, M.; Collazo, R.; Sitar, Z.

    2016-02-01

    The maximum achievable reflectivity of current III-nitride Bragg reflectors in the UV-C spectral range is limited due to plastic relaxation of thick multilayer structures. Cracking due to a large mismatch of the thermal expansion and lattice constants between AlxGa1-xN/AlyGa1-yN alloys of different composition and the substrate at the heterointerface is the common failure mode. Strain engineering and strain relaxation concepts by the growth on a strain reduced Al0.85Ga0.15N template and the implementation of low temperature interlayers is demonstrated. A significant enhancement of the maximum reflectivity above 97% at a resonance wavelength of 270 nm due to an increase of the critical thickness of our AlN/Al0.65Ga0.35N DBRs to 1.45 μm (25.5 pairs) prove their potential. By comparing the growth of identical Bragg reflectors on different pseudo-templates, the accumulated mismatch strain energy in the DBR, not the dislocation density provided by the template/substrate, was identified to limit the critical thickness. To further enhance the reflectivity low temperature interlays were implemented into the DBR to partially relief the misfit strain. Relaxation is enabled by the nucleation of small surface domains facilitating misfit dislocation injection and glide. Detailed structural and optical investigations will be conducted to prove the influence of the LT-AlN interlayers on the strain state, structural integrity and reflectivity properties. Coherent growth and no structural and optical degradation of the Bragg mirror properties was observed proving the fully applicability of the relaxation concept to fabricate thick high reflectivity DBR and vertical cavity laser structures.

  1. Clostridium difficile Infection

    PubMed Central

    Heinlen, Latisha; Ballard, Jimmy D.

    2010-01-01

    Clostridium difficile is the leading cause of hospital-acquired diarrhea in Europe and North America and is a serious re-emerging pathogen. Recent outbreaks have led to increasing morbidity and mortality and have been associated with a new strain (BI/NAP1/027) of C. difficile that produces more toxin than historical strains. With the increasing incidence of C. difficile infection, clinicians have also seen a change in the epidemiology with increased infections in previously low-risk populations. This chapter highlights the current knowledge on C. difficile virulence, human disease, epidemic outbreaks, and optimal treatment strategies. PMID:20697257

  2. Crystallization engineering as a route to epitaxial strain control

    SciTech Connect

    Akbashev, Andrew R.; Plokhikh, Aleksandr V.; Barbash, Dmitri; Lofland, Samuel E.; Spanier, Jonathan E.

    2015-10-01

    The controlled synthesis of epitaxial thin films offers opportunities for tuning their functional properties via enabling or suppressing strain relaxation. Examining differences in the epitaxial crystallization of amorphous oxide films, we report on an alternate, low-temperature route for strain engineering. Thin films of amorphous Bi–Fe–O were grown on (001)SrTiO{sub 3} and (001)LaAlO{sub 3} substrates via atomic layer deposition. In situ X-ray diffraction and X-ray photoelectron spectroscopy studies of the crystallization of the amorphous films into the epitaxial (001)BiFeO{sub 3} phase reveal distinct evolution profiles of crystallinity with temperature. While growth on (001)SrTiO{sub 3} results in a coherently strained film, the same films obtained on (001)LaAlO{sub 3} showed an unstrained, dislocation-rich interface, with an even lower temperature onset of the perovskite phase crystallization than in the case of (001)SrTiO{sub 3}. Our results demonstrate how the strain control in an epitaxial film can be accomplished via its crystallization from the amorphous state.

  3. Fluoroquinolone and Macrolide Exposure Predict Clostridium difficile Infection with the Highly Fluoroquinolone- and Macrolide-Resistant Epidemic C. difficile Strain BI/NAP1/027.

    PubMed

    Wieczorkiewicz, Jeffrey T; Lopansri, Bert K; Cheknis, Adam; Osmolski, James R; Hecht, David W; Gerding, Dale N; Johnson, Stuart

    2015-11-02

    Antibiotics have been shown to influence the risk of infection with specific Clostridium difficile strains as well as the risk of C. difficile infection (CDI). We performed a retrospective case-control study of patients infected with the epidemic BI/NAP1/027 strain in a U.S. hospital following recognition of increased CDI severity and culture of stools positive by C. difficile toxin immunoassay. Between 2005 and 2007, 72% (103/143) of patients with first-episode CDIs were infected with the BI strain by restriction endonuclease analysis (REA) typing. Most patients received multiple antibiotics within 6 weeks of CDI onset (median of 3 antibiotic classes). By multivariate analysis, fluoroquinolone and macrolide exposure was more frequent among BI cases than among non-BI-infected controls (odds ratio [OR] for fluoroquinolones, 3.2; 95% confidence interval [CI], 1.3 to 7.5; (P < 0.001; OR for macrolides, 5.2; 95% CI, 1.1 to 24.0; P = 0.04)). In contrast, clindamycin use was less frequent among the BI cases than among the controls (OR, 0.1; 95% CI, 0.03 to 0.4; P = 0.001). High-level resistance to moxifloxacin and azithromycin was more frequent among BI strains (moxifloxacin, 49/102 [48%] BI versus 0/40 non-BI, P = 0.0001; azithromycin, 100/102 [98%] BI versus 22/40 [55%] non-BI, P = 0.0001). High-level resistance to clindamycin was more frequent among non-BI strains (22/40 [55%] non-BI versus 7/102 [7%] BI, P = 0.0001). Fluoroquinolone use, macrolide use, and C. difficile resistance to these antibiotic classes were associated with infection by the epidemic BI strain of C. difficile in a U.S. hospital during a time when CDI rates were increasing nationally due to the highly fluoroquinolone-resistant BI/NAP1/027 strain.

  4. Fluoroquinolone and Macrolide Exposure Predict Clostridium difficile Infection with the Highly Fluoroquinolone- and Macrolide-Resistant Epidemic C. difficile Strain BI/NAP1/027

    PubMed Central

    Wieczorkiewicz, Jeffrey T.; Lopansri, Bert K.; Cheknis, Adam; Osmolski, James R.; Hecht, David W.; Gerding, Dale N.

    2015-01-01

    Antibiotics have been shown to influence the risk of infection with specific Clostridium difficile strains as well as the risk of C. difficile infection (CDI). We performed a retrospective case-control study of patients infected with the epidemic BI/NAP1/027 strain in a U.S. hospital following recognition of increased CDI severity and culture of stools positive by C. difficile toxin immunoassay. Between 2005 and 2007, 72% (103/143) of patients with first-episode CDIs were infected with the BI strain by restriction endonuclease analysis (REA) typing. Most patients received multiple antibiotics within 6 weeks of CDI onset (median of 3 antibiotic classes). By multivariate analysis, fluoroquinolone and macrolide exposure was more frequent among BI cases than among non-BI-infected controls (odds ratio [OR] for fluoroquinolones, 3.2; 95% confidence interval [CI], 1.3 to 7.5; (P < 0.001; OR for macrolides, 5.2; 95% CI, 1.1 to 24.0; P = 0.04)). In contrast, clindamycin use was less frequent among the BI cases than among the controls (OR, 0.1; 95% CI, 0.03 to 0.4; P = 0.001). High-level resistance to moxifloxacin and azithromycin was more frequent among BI strains (moxifloxacin, 49/102 [48%] BI versus 0/40 non-BI, P = 0.0001; azithromycin, 100/102 [98%] BI versus 22/40 [55%] non-BI, P = 0.0001). High-level resistance to clindamycin was more frequent among non-BI strains (22/40 [55%] non-BI versus 7/102 [7%] BI, P = 0.0001). Fluoroquinolone use, macrolide use, and C. difficile resistance to these antibiotic classes were associated with infection by the epidemic BI strain of C. difficile in a U.S. hospital during a time when CDI rates were increasing nationally due to the highly fluoroquinolone-resistant BI/NAP1/027 strain. PMID:26525793

  5. Bio-Engineering High Performance Microbial Strains for MEOR

    SciTech Connect

    Xiangdong Fang; Qinghong Wang; Patrick Shuler

    2007-12-30

    The main objectives of this three-year research project are: (1) to employ the latest advances in genetics and bioengineering, especially Directed Protein Evolution technology, to improve the effectiveness of the microbial enhanced oil recovery (MEOR) process. (2) to improve the surfactant activity and the thermal stability of bio-surfactant systems for MEOR; and (3) to develop improved laboratory methods and tools that screen quickly candidate bio-systems for EOR. Biosurfactants have been receiving increasing attention as Enhanced Oil Recovery (EOR) agents because of their unique properties (i.e., mild production conditions, lower toxicity, and higher biodegradability) compared to their synthetic chemical counterparts. Rhamnolipid as a potent natural biosurfactant has a wide range of potential applications, including EOR and bioremediation. During the three-year of the project period, we have successfully cloned the genes involved in the rhamnolipid bio-synthesis. And by using the Transposon containing Rhamnosyltransferase gene rhlAB, we engineered the new mutant strains P. aeruginosa PEER02 and E. coli TnERAB so they can produce rhamnolipid biosurfactans. We were able to produce rhamnolipds in both P. aeroginosa PAO1-RhlA- strain and P. fluorescens ATCC15453 strain, with the increase of 55 to 175 fold in rhamnolipid production comparing with wild type bacteria strain. We have also completed the first round direct evolution studies using Error-prone PCR technique and have constructed the library of RhlAB-containing Transposon to express mutant gene in heterologous hosts. Several methods, such as colorimetric agar plate assay, colorimetric spectrophotometer assay, bioactive assay and oil spreading assay have been established to detect and screen rhamnolipid production. Our engineered P. aeruginosa PEER02 strain can produce rhamnolipids with different carbon sources as substrate. Interfacial tension analysis (IFT) showed that different rhamnolipids from different

  6. Computational methods in metabolic engineering for strain design.

    PubMed

    Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L

    2015-08-01

    Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms.

  7. Strain-engineered manufacturing of freeform carbon nanotube microstructures

    NASA Astrophysics Data System (ADS)

    de Volder, M.; Park, S.; Tawfick, S.; Hart, A. J.

    2014-07-01

    The skins of many plants and animals have intricate microscale surface features that give rise to properties such as directed water repellency and adhesion, camouflage, and resistance to fouling. However, engineered mimicry of these designs has been restrained by the limited capabilities of top-down fabrication processes. Here we demonstrate a new technique for scalable manufacturing of freeform microstructures via strain-engineered growth of aligned carbon nanotubes (CNTs). Offset patterning of the CNT growth catalyst is used to locally modulate the CNT growth rate. This causes the CNTs to collectively bend during growth, with exceptional uniformity over large areas. The final shape of the curved CNT microstructures can be designed via finite element modeling, and compound catalyst shapes produce microstructures with multidirectional curvature and unusual self-organized patterns. Conformal coating of the CNTs enables tuning of the mechanical properties independently from the microstructure geometry, representing a versatile principle for design and manufacturing of complex microstructured surfaces.

  8. Computational methods in metabolic engineering for strain design.

    PubMed

    Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L

    2015-08-01

    Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms. PMID:25576846

  9. Comparative genomic analysis of single-molecule sequencing and hybrid approaches for finishing the Clostridium autoethanogenum JA1-1 strain DSM 10061 genome

    SciTech Connect

    Brown, Steven D; Nagaraju, Shilpa; Utturkar, Sagar M; De Tissera, Sashini; Segovia, Simón; Mitchell, Wayne; Land, Miriam L; Dassanayake, Asela; Köpke, Michael

    2014-01-01

    Background Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. Results A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a

  10. Engineering of Bacillus subtilis Strains To Allow Rapid Characterization of Heterologous Diguanylate Cyclases and Phosphodiesterases

    PubMed Central

    Gao, Xiaohui; Dong, Xiao; Subramanian, Sundharraman; Matthews, Paige M.; Cooper, Caleb A.; Kearns, Daniel B.

    2014-01-01

    Microbial processes, including biofilm formation, motility, and virulence, are often regulated by changes in the available concentration of cyclic dimeric guanosine monophosphate (c-di-GMP). Generally, high c-di-GMP concentrations are correlated with decreased motility and increased biofilm formation and low c-di-GMP concentrations are correlated with an increase in motility and activation of virulence pathways. The study of c-di-GMP is complicated, however, by the fact that organisms often encode dozens of redundant enzymes that synthesize and hydrolyze c-di-GMP, diguanylate cyclases (DGCs), and c-di-GMP phosphodiesterases (PDEs); thus, determining the contribution of any one particular enzyme is challenging. In an effort to develop a facile system to study c-di-GMP metabolic enzymes, we have engineered a suite of Bacillus subtilis strains to assess the effect of individual heterologously expressed proteins on c-di-GMP levels. As a proof of principle, we characterized all 37 known genes encoding predicted DGCs and PDEs in Clostridium difficile using parallel readouts of swarming motility and fluorescence from green fluorescent protein (GFP) expressed under the control of a c-di-GMP-controlled riboswitch. We found that 27 of the 37 putative C. difficile 630 c-di-GMP metabolic enzymes had either active cyclase or phosphodiesterase activity, with agreement between our motility phenotypes and fluorescence-based c-di-GMP reporter. Finally, we show that there appears to be a threshold level of c-di-GMP needed to inhibit motility in Bacillus subtilis. PMID:25085482

  11. Environmental Factors Influencing the Prevalence of a Clostridium botulinum Type C/D Mosaic Strain in Nonpermanent Mediterranean Wetlands

    PubMed Central

    Anza, Ibone; Taggart, Mark A.; Pérez-Ramírez, Elisa; Crespo, Elena; Hofle, Ursula; Mateo, Rafael

    2013-01-01

    Between 1978 and 2008, 13 avian botulism outbreaks were recorded in the wetlands of Mancha Húmeda (central Spain). These outbreaks caused the deaths of around 20,000 birds from over 50 species, including globally endangered white-headed ducks (Oxyura leucoceophala). Here, a significant association was found between the number of dead birds recorded in each botulism outbreak and the mean temperature in July (always >26°C). The presence of Clostridium botulinum type C/D in wetland sediments was detected by real-time PCR (quantitative PCR [qPCR]) in 5.8% of 207 samples collected between 2005 and 2008. Low concentrations of Cl− and high organic matter content in sediments were significantly associated with the presence of C. botulinum. Seventy-five digestive tracts of birds found dead during botulism outbreaks were analyzed; C. botulinum was present in 38.7% of them. The prevalence of C. botulinum was 18.2% (n = 22 pools) in aquatic invertebrates (Chironomidae and Corixidae families) and 33.3% (n = 18 pools) in necrophagous invertebrates (Sarcophagidae and Calliphoridae families), including two pools of adult necrophagous flies collected around bird carcasses. The presence of the bacteria in the adult fly form opens up new perspectives in the epidemiology of avian botulism, since these flies may be transporting C. botulinum from one carcass to another. PMID:23645197

  12. Predominance of PCR-ribotypes, 018 (smz) and 369 (trf) of Clostridium difficile in Japan: a potential relationship with other global circulating strains?

    PubMed

    Senoh, Mitsutoshi; Kato, Haru; Fukuda, Tadashi; Niikawa, Akiko; Hori, Yoshiko; Hagiya, Hideharu; Ito, Yoichiro; Miki, Hiroshi; Abe, Yoshifumi; Furuta, Kiyoshi; Takeuchi, Hideki; Tajima, Hirokazu; Tominaga, Harumi; Satomura, Hideyuki; Kato, Hideaki; Morita, Sayuri; Tanada, Ai; Hara, Toshinori; Kawada, Miki; Sato, Yuka; Takahashi, Masahiko; Higuchi, Akiko; Nakajima, Tomoko; Wakamatsu, Yukiko; Toyokawa, Masahiro; Ueda, Akiko; Roberts, Paul; Miyajima, Fabio; Shibayama, Keigo

    2015-10-01

    Global spread and evolutionary links of an epidemic Clostridium difficile strain (PCR-ribotype 027) have been noted in recent decades. However, in Japan, no outbreaks caused by type 027 have been reported to date. A total of 120 C. difficile isolates from patients at 15 hospitals during non-outbreak seasons between 2011 and 2013 as well as 18 and 21 isolates collected from two hospitals in 2010 and 2009, respectively, in outbreak periods in Japan, were examined. Among these 120 isolates, Japan-ribotypes smz and ysmz (subtype variant of smz) were the most predominant (39.2 %) followed by Japan-ribotype trf (15.8 %). Types smz/ysmz and trf were also concurrently predominant at two hospitals in the outbreak settings. Out of the five binary toxin-positive isolates observed, only one was PCR-ribotype 027 and another PCR-ribotype 078. Type smz was later found to correspond to PCR-ribotype 018. High rates of resistance against gatifloxacin, moxifloxacin, erythromycin and clindamycin were observed in the PCR-ribotype 018 isolates. Interestingly, all trf isolates were toxin A-negative, toxin B-positive, but they did not correspond to PCR-ribotype 017, thus being assigned a new ribotype (PCR-ribotype 369). In conclusion, PCR-ribotypes 018 (smz) and 369 (trf) were identified as major circulating strains in both outbreak and non-outbreak settings in Japan. Given their epidemiological relevance, molecular investigations are warranted to clarify potential evolutionary links with related strains found elsewhere, such as PCR-ribotypes 018 and 017 from Europe and North America.

  13. Secreted Compounds of the Probiotic Bacillus clausii Strain O/C Inhibit the Cytotoxic Effects Induced by Clostridium difficile and Bacillus cereus Toxins.

    PubMed

    Ripert, Gabrielle; Racedo, Silvia M; Elie, Anne-Marie; Jacquot, Claudine; Bressollier, Philippe; Urdaci, Maria C

    2016-06-01

    Although the use of probiotics based on Bacillus strains to fight off intestinal pathogens and antibiotic-associated diarrhea is widespread, the mechanisms involved in producing their beneficial effects remain unclear. Here, we studied the ability of compounds secreted by the probiotic Bacillus clausii strain O/C to counteract the cytotoxic effects induced by toxins of two pathogens, Clostridium difficile and Bacillus cereus, by evaluating eukaryotic cell viability and expression of selected genes. Coincubation of C. difficile and B. cereus toxic culture supernatants with the B. clausii supernatant completely prevented the damage induced by toxins in Vero and Caco-2 cells. The hemolytic effect of B. cereus was also avoided by the probiotic supernatant. Moreover, in these cells, the expression of rhoB, encoding a Rho GTPase target for C. difficile toxins, was normalized when C. difficile supernatant was pretreated using the B. clausii supernatant. All of the beneficial effects observed with the probiotic were abolished by the serine protease inhibitor phenylmethylsulfonyl fluoride (PMSF). Suspecting the involvement of a secreted protease in this protective effect, a protease was purified from the B. clausii supernatant and identified as a serine protease (M-protease; GenBank accession number Q99405). Experiments on Vero cells demonstrated the antitoxic activity of the purified protease against pathogen supernatants. This is the first report showing the capacity of a protease secreted by probiotic bacteria to inhibit the cytotoxic effects of toxinogenic C. difficile and B. cereus strains. This extracellular compound could be responsible, at least in part, for the protective effects observed for this human probiotic in antibiotic-associated diarrhea.

  14. Secreted Compounds of the Probiotic Bacillus clausii Strain O/C Inhibit the Cytotoxic Effects Induced by Clostridium difficile and Bacillus cereus Toxins.

    PubMed

    Ripert, Gabrielle; Racedo, Silvia M; Elie, Anne-Marie; Jacquot, Claudine; Bressollier, Philippe; Urdaci, Maria C

    2016-06-01

    Although the use of probiotics based on Bacillus strains to fight off intestinal pathogens and antibiotic-associated diarrhea is widespread, the mechanisms involved in producing their beneficial effects remain unclear. Here, we studied the ability of compounds secreted by the probiotic Bacillus clausii strain O/C to counteract the cytotoxic effects induced by toxins of two pathogens, Clostridium difficile and Bacillus cereus, by evaluating eukaryotic cell viability and expression of selected genes. Coincubation of C. difficile and B. cereus toxic culture supernatants with the B. clausii supernatant completely prevented the damage induced by toxins in Vero and Caco-2 cells. The hemolytic effect of B. cereus was also avoided by the probiotic supernatant. Moreover, in these cells, the expression of rhoB, encoding a Rho GTPase target for C. difficile toxins, was normalized when C. difficile supernatant was pretreated using the B. clausii supernatant. All of the beneficial effects observed with the probiotic were abolished by the serine protease inhibitor phenylmethylsulfonyl fluoride (PMSF). Suspecting the involvement of a secreted protease in this protective effect, a protease was purified from the B. clausii supernatant and identified as a serine protease (M-protease; GenBank accession number Q99405). Experiments on Vero cells demonstrated the antitoxic activity of the purified protease against pathogen supernatants. This is the first report showing the capacity of a protease secreted by probiotic bacteria to inhibit the cytotoxic effects of toxinogenic C. difficile and B. cereus strains. This extracellular compound could be responsible, at least in part, for the protective effects observed for this human probiotic in antibiotic-associated diarrhea. PMID:27001810

  15. Ethanol and Acetic Acid Production from Carbon Monoxide in a Clostridium Strain in Batch and Continuous Gas-Fed Bioreactors

    PubMed Central

    Nalakath Abubackar, Haris; Veiga, María C.; Kennes, Christian

    2015-01-01

    The effect of different sources of nitrogen as well as their concentrations on the bioconversion of carbon monoxide to metabolic products such as acetic acid and ethanol by Clostridium autoethanogenum was studied. In a first set of assays, under batch conditions, either NH4Cl, trypticase soy broth or yeast extract (YE) were used as sources of nitrogen. The use of YE was found statistically significant (p < 0.05) on the product spectrum in such batch assays. In another set of experiments, three bioreactors were operated with continuous CO supply, in order to estimate the effect of running conditions on products and biomass formation. The bioreactors were operated under different conditions, i.e., EXP1 (pH = 5.75, YE 1g/L), EXP2 (pH = 4.75, YE 1 g/L) and EXP3 (pH = 5.75, YE 0.2 g/L). When compared to EXP2 and EXP3, it was found that EXP1 yielded the maximum biomass accumulation (302.4 mg/L) and products concentrations, i.e., acetic acid (2147.1 mg/L) and ethanol (352.6 mg/L). This can be attributed to the fact that the higher pH and higher YE concentration used in EXP1 stimulated cell growth and did, consequently, also enhance metabolite production. However, when ethanol is the desired end-product, as a biofuel, the lower pH used in EXP2 was more favourable for solventogenesis and yielded the highest ethanol/acetic acid ratio, reaching a value of 0.54. PMID:25608591

  16. Multiple effects of Escherichia coli Nissle 1917 on growth, biofilm formation, and inflammation cytokines profile of Clostridium perfringens type A strain CP4.

    PubMed

    Jiang, Yanlong; Kong, Qingke; Roland, Kenneth L; Wolf, Amanda; Curtiss, Roy

    2014-04-01

    Clostridium perfringens is an important Gram-positive pathogen responsible for food poisoning, necrotic enteritis, gas gangrene, and even death. Escherichia coli Nissle 1917 (EcN) is a well-characterized probiotic strain with demonstrated benefits. In this study, we evaluated the effects of EcN on growth, toxin production, biofilm formation, and inflammatory cytokine responses of C. perfringens. In vitro co-culture experiments demonstrated that EcN inhibited growth, gas production, and toxin production (α-toxin and NetB) of C. perfringens in a dose-dependent manner. The growth inhibition effect was not observed when C. perfringens was incubated with EcN cell-free supernatants (CFSE), suggesting that growth inhibition was caused by nutrition competition during co-incubation. In vitro studies demonstrated that pre-incubation with EcN did not inhibit C. perfringens attachment to Caco-2 cells, but did reduce C. perfringens total number, toxin production, and cytotoxicity after 24 h. The similar growth inhibition results were also observed during the formation of C. perfringens biofilm. Finally, pre-incubation of EcN with RAW264.7 cells significantly decreased the production of inflammatory cytokines caused by the introduction of C. perfringens. Our results indicate that EcN can inhibit many of the pathological effects of C. perfringens in vitro conditions. PMID:24532573

  17. Functional Heterologous Expression of an Engineered Full Length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum

    SciTech Connect

    Currie, Devin; Herring, Christopher; Guss, Adam M; Olson, Daniel G.; Hogsett, David; Lynd, Lee R

    2013-01-01

    BACKGROUND: Cellulose is highly recalcitrant and thus requires a specialized suite of enzymes to solubilize it into fermentable sugars. In C. thermocellum, these extracellular enzymes are present as a highly active multi-component system known as the cellulosome. This study explores the expression of a critical C. thermocellum cellulosomal component in T. saccharolyticum as a step toward creating a thermophilic bacterium capable of consolidated bioprocessing by employing heterologously expressed cellulosomes. RESULTS: We developed an inducible promoter system based on the native T. saccharolyticum xynA promoter, which was shown to be induced by xylan and xylose. The promoter was used to express the cellulosomal component cipA*, an engineered form of the wild-type cipA from C. thermocellum. Expression and localization to the supernatant were both verified for CipA*. When a cipA mutant C. thermocellum strain was cultured with a CipA*-expressing T. saccharolyticum strain, hydrolysis and fermentation of 10 grams per liter SigmaCell 101, a highly crystalline cellulose, were observed. This trans-species complementation of a cipA deletion demonstrated the ability for CipA* to assemble a functional cellulosome. CONCLUSION: This study is the first example of an engineered thermophile heterologously expressing a structural component of a cellulosome. To achieve this goal we developed and tested an inducible promoter for controlled expression in T. saccharolyticum as well as a synthetic cipA. In addition, we demonstrate a high degree of hydrolysis (up to 93%) on microcrystalline cellulose.

  18. The Clostridium difficile Cell Wall Protein CwpV is Antigenically Variable between Strains, but Exhibits Conserved Aggregation-Promoting Function

    PubMed Central

    Reynolds, Catherine B.; Emerson, Jenny E.; de la Riva, Lucia; Fagan, Robert P.; Fairweather, Neil F.

    2011-01-01

    Clostridium difficile is the main cause of antibiotic-associated diarrhea, leading to significant morbidity and mortality and putting considerable economic pressure on healthcare systems. Current knowledge of the molecular basis of pathogenesis is limited primarily to the activities and regulation of two major toxins. In contrast, little is known of mechanisms used in colonization of the enteric system. C. difficile expresses a proteinaceous array on its cell surface known as the S-layer, consisting primarily of the major S-layer protein SlpA and a family of SlpA homologues, the cell wall protein (CWP) family. CwpV is the largest member of this family and is expressed in a phase variable manner. Here we show CwpV promotes C. difficile aggregation, mediated by the C-terminal repetitive domain. This domain varies markedly between strains; five distinct repeat types were identified and were shown to be antigenically distinct. Other aspects of CwpV are, however, conserved. All CwpV types are expressed in a phase variable manner. Using targeted gene knock-out, we show that a single site-specific recombinase RecV is required for CwpV phase variation. CwpV is post-translationally cleaved at a conserved site leading to formation of a complex of cleavage products. The highly conserved N-terminus anchors the CwpV complex to the cell surface. Therefore CwpV function, regulation and processing are highly conserved across C. difficile strains, whilst the functional domain exists in at least five antigenically distinct forms. This hints at a complex evolutionary history for CwpV. PMID:21533071

  19. Growth Patterns of Clostridium difficile – Correlations with Strains, Binary Toxin and Disease Severity: A Prospective Cohort Study

    PubMed Central

    Tschudin-Sutter, Sarah; Braissant, Olivier; Erb, Stefan; Stranden, Anne; Bonkat, Gernot; Frei, Reno; Widmer, Andreas F.

    2016-01-01

    A broad spectrum of symptoms has been associated with C. difficile infection (CDI). Several studies indicate that toxin-production correlates with growth rates of C. difficile. This study aimed to correlate growth rates of C. difficile with disease severity and strain characteristics. From 01/2003 to 10/2011, strains from a prospective cohort of all inpatients with CDI at the University Hospital Basel, Switzerland were analyzed regarding binary toxin, presence of the tcdC deletion and ribotype. Isothermal microcalorimetry was performed to determine growth rates, quantified by the Gompertz function. Ordered logistic regression models were used to correlate disease severity with strain features and clinical characteristics. Among 199 patients, 31 (16%) were infected with binary toxin-producing strains, of which the tcdC gene-deletion nt117 was detected in 9 (4%). Disease severity was classified as mild in 130 patients (65.3%), as severe in 59 patients (29.7%) and as severe/complicated in 10 patients (5.0%). Growth rates were inversely associated with disease severity in univariable (OR 0.514, 95%CI 0.29–0.91, p = 0.023) and multivariable analyses (OR 0.51, 95%CI 0.26–0.97, p = 0.040). While none of the strain characteristics such as presence of the tcdC gene deletion or binary toxin predicted CDI severity, growth rates were inversely correlated with disease severity. Further investigations are needed to analyze growth-regulators and respective correlations with the level of toxin production in C. difficile, which may be important determinants of disease severity. PMID:27598309

  20. Growth Patterns of Clostridium difficile - Correlations with Strains, Binary Toxin and Disease Severity: A Prospective Cohort Study.

    PubMed

    Tschudin-Sutter, Sarah; Braissant, Olivier; Erb, Stefan; Stranden, Anne; Bonkat, Gernot; Frei, Reno; Widmer, Andreas F

    2016-01-01

    A broad spectrum of symptoms has been associated with C. difficile infection (CDI). Several studies indicate that toxin-production correlates with growth rates of C. difficile. This study aimed to correlate growth rates of C. difficile with disease severity and strain characteristics. From 01/2003 to 10/2011, strains from a prospective cohort of all inpatients with CDI at the University Hospital Basel, Switzerland were analyzed regarding binary toxin, presence of the tcdC deletion and ribotype. Isothermal microcalorimetry was performed to determine growth rates, quantified by the Gompertz function. Ordered logistic regression models were used to correlate disease severity with strain features and clinical characteristics. Among 199 patients, 31 (16%) were infected with binary toxin-producing strains, of which the tcdC gene-deletion nt117 was detected in 9 (4%). Disease severity was classified as mild in 130 patients (65.3%), as severe in 59 patients (29.7%) and as severe/complicated in 10 patients (5.0%). Growth rates were inversely associated with disease severity in univariable (OR 0.514, 95%CI 0.29-0.91, p = 0.023) and multivariable analyses (OR 0.51, 95%CI 0.26-0.97, p = 0.040). While none of the strain characteristics such as presence of the tcdC gene deletion or binary toxin predicted CDI severity, growth rates were inversely correlated with disease severity. Further investigations are needed to analyze growth-regulators and respective correlations with the level of toxin production in C. difficile, which may be important determinants of disease severity. PMID:27598309

  1. Construction of an environmental safe Bacillus thuringiensis engineered strain against Coleoptera.

    PubMed

    Yu, Yajun; Yuan, Yihui; Gao, Meiying

    2016-05-01

    Cloning of new toxic genes from Bacillus thuringiensis (Bt) and construction of Bt engineered strains are two key strategies for bio-control of coleopteran pests in agriculture and forestry. In this study, we cloned a new cry3Aa-type gene, cry3Aa8, from wild Bt strain YC-03 against coleopteran, and constructed a Bt engineered strain, ACE-38, containing insecticidal protein-encoding gene cry3Aa8. The engineered strain, with almost four times of Cry3Aa yield compared with strain YC-03, was an antibiotic marker-free strain. Though no selective pressure was presented in the medium, cry3Aa8 in the engineered strain ACE-38 remained stable. The yield of Cry3Aa by strain ACE-38 reached 2.09 mg/ml in the optimized fermentation medium. The activity of strain ACE-38 against Plagiodera versicolora was tested, and the LC50 of ACE-38 cultures in the optimized fermentation medium was 1.13 μl/ml. Strain ACE-38 is a non-antibiotic Bt engineered strain with high Chrysomelidae toxicity and exhibits good fermentation property. The modified indigenous site-specific recombination system constructed in this study might be useful for the construction of Bt engineered strains containing genes that cannot be expressed in the indigenous site-specific recombination system using plasmid pBMB1205R. PMID:26767987

  2. Complete genome sequence of a malodorant-producing acetogen, Clostridium scatologenes ATCC 25775(T).

    PubMed

    Zhu, Zhengang; Guo, Ting; Zheng, Huajun; Song, Tianshun; Ouyang, Pingkai; Xie, Jingjing

    2015-10-20

    Clostridium scatologenes ATCC 25775(T) is an acetogenic anaerobic bacteria known to be capable of synthesizing volatile fatty acids and solvents from CO2 or CO on its autotrophic mode and producing 3-methylindole and 4-methylphenol on its heterotrophic mode. Here, we report the complete genome sequence of this strain, which might provide a lot of valuable information for developing metabolic engineering strategies to produce biofuels or chemicals from greenhouse gases. PMID:26210291

  3. A New Type of Toxin A-Negative, Toxin B-Positive Clostridium difficile Strain Lacking a Complete tcdA Gene

    PubMed Central

    Marín, Mercedes; Martín, Adoración; Rupnik, Maja

    2014-01-01

    Toxins A and B are the main virulence factors of Clostridium difficile and are the targets for molecular diagnostic tests. Here, we describe a new toxin A-negative, toxin B-positive, binary toxin CDT (Clostridium difficile transferase)-negative (A− B+ CDT−) toxinotype (XXXII) characterized by a variant type of pathogenicity locus (PaLoc) without tcdA and with atypical organization of the PaLoc integration site. PMID:25428159

  4. Engineered biosealant strains producing inorganic and organic biopolymers.

    PubMed

    Bergdale, Terran E; Pinkelman, Rebecca J; Hughes, Stephen R; Zambelli, Barbara; Ciurli, Stefano; Bang, Sookie S

    2012-10-31

    Microbiologically induced calcium carbonate precipitation (MICCP) is a naturally occurring biological process that has shown its potential in remediation of a wide range of structural damages including concrete cracks. In this study, genetically engineered microorganisms, capable of producing extracellular polymeric substances (EPSs) as well as inducing MICCP, were developed based on the assumption that the complex of inorganic CaCO(3) and organic EPS would provide a stronger matrix than MICCP alone as biosealant. In order to develop a recombinant biosealant microorganism, the entire Sporosarcina pasteurii urease gene sequences including ureA, ureB, ureC, ureD, ureE, ureF, and ureG from plasmid pBU11 were sub-cloned into the shuttle vector, pUCP18. The newly constructed plasmid, pUBU1, was transformed into two Pseudomonas aeruginosa strains, 8821 and PAO1, to develop recombinants capable of inducing calcite precipitation in addition to their own ability to produce EPS. Nickel-dependent urease activities were expressed from the recombinant P. aeruginosa 8821 (pUBU1) and P. aeruginosa PAO1 (pUBU1), at 99.4% and 60.9% of the S. pasteurii urease activity, respectively, in a medium containing 2mM NiCl(2). No urease activities were detected from the wild type P. aeruginosa 8821 and P. aeruginosa PAO1 under the same growth conditions. Recombinant Pseudomonas strains induced CaCO(3) precipitation at a comparable rate as S. pasteurii and scanning electron microscopy evidenced the complex of CaCO(3) crystals and EPS layers surrounding the cells. The engineered strains produced in this study are expected to serve as a valuable reference to future biosealants that could be applied in the environment. However, the pathogenic potential of P. aeruginosa, used here only as a model system to show the proof of principle, prevents the use of this recombinant organism as a biosealant. In practical applications, other recombinant organisms should be used. PMID:22789480

  5. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation

    DOE PAGES

    Sander, Kyle B.; Wilson, Charlotte M.; M. Rodriquez, Jr.; Klingeman, Dawn Marie; Davison, Brian H.; Brown, Steven D.; Rydzak, T.

    2015-12-12

    Clostridium thermocellum is a promising consolidated bioprocessing candidate organism capable of directly converting lignocellulosic biomass to ethanol. Current ethanol yields, productivities, and growth inhibitions are industrial deployment impediments for commodity fuel production by this bacterium. Redox imbalance under certain conditions and in engineered strains may contribute to incomplete substrate utilization and may direct fermentation products to undesirable overflow metabolites. As a result, towards a better understanding of redox metabolism in C. thermocellum, we established continuous growth conditions and analyzed global gene expression during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which changed the fermentation redox potential.

  6. Isolation of a solventogenic Clostridium sp. strain: fermentation of glycerol to n-butanol, analysis of the bcs operon region and its potential regulatory elements.

    PubMed

    Panitz, J C; Zverlov, V V; Pham, V T T; Stürzl, S; Schieder, D; Schwarz, W H

    2014-02-01

    A new solventogenic bacterium, strain GT6, was isolated from standing water sediment. 16S-rRNA gene analysis revealed that GT6 belongs to the heterogeneous Clostridium tetanomorphum group of bacteria exhibiting 99% sequence identity with C. tetanomorphum 4474(T). GT6 can utilize a wide range of carbohydrate substrates including glucose, fructose, maltose, xylose and glycerol to produce mainly n-butanol without any acetone. Additional products of GT6 metabolism were ethanol, butyric acid, acetic acid, and trace amounts of 1,3-propanediol. Medium and substrate composition, and culture conditions such as pH and temperature influenced product formation. The major fermentation product from glycerol was n-butanol with a final concentration of up to 11.5 g/L. 3% (v/v) glycerol lead to a total solvent concentration of 14 g/L within 72 h. Growth was not inhibited by glycerol concentrations as high as 15% (v/v). The solventogenesis genes crt, bcd, etfA/B and hbd composing the bcs (butyryl-CoA synthesis) operon of C. tetanomorphum GT6 were sequenced. They occur in a genomic arrangement identical to those in other solventogenic clostridia. Furthermore, the sequence of a potential regulator gene highly similar to that of the NADH-sensing Rex family of regulatory genes was found upstream of the bcs operon. Potential binding sites for Rex have been identified in the promoter region of the bcs operon of solvent producing clostridia as well as upstream of other genes involved in NADH oxidation. This indicates a fundamental role of Rex in the regulation of fermentation products in anaerobic, and especially in solventogenic bacteria.

  7. Strain and process development for poly(3HB-co-3HP) fermentation by engineered Shimwellia blattae from glycerol.

    PubMed

    Sato, Shunsuke; Andreeßen, Björn; Steinbüchel, Alexander

    2015-01-01

    Poly(3-hydroxybytyrate-co-3-hydroxypropionate), poly(3HB-co-3HP), is a possible alternative to synthetic polymers such as polypropylene, polystyrene and polyethylene due to its low crystallinity and fragility. We already reported that recombinant strains of Shimwellia blattae expressing 1,3-propanediol dehydrogenase DhaT as well as aldehyde dehydrogenase AldD of Pseudomonas putida KT2442, propionate-CoA transferase Pct of Clostridium propionicum X2 and PHA synthase PhaC1 of Ralstonia eutropha H16 are able to accumulate up to 14.5% (wtPHA/wtCDW) of poly(3-hydroxypropionate), poly(3HP), homopolymer from glycerol as a sole carbon source (Appl Microbiol Biotechnol 98:7409-7422, 2014a). However, the cell density was rather low. In this study, we optimized the medium aiming at a more efficient PHA synthesis, and we engineered a S. blattae strain accumulating poly(3HB-co-3HP) with varying contents of the constituent 3-hydroxypropionate (3HP) depending on the cultivation conditions. Consequently, 7.12, 0.77 and 0.32 gPHA/L of poly(3HB-co-3HP) containing 2.1, 8.3 and 18.1 mol% 3HP under anaerobic/aerobic (the first 24 hours under anaerobic condition, thereafter, aerobic condition), low aeration/agitation (the minimum stirring rate required in medium mixing and small amount of aeration) and anaerobic conditions (the minimum stirring rate required in medium mixing without aeration), respectively, were synthesized from glycerol by the genetically modified S. blattae ATCC33430 strains in optimized culture medium. PMID:25852995

  8. Enhanced succinate production from glycerol by engineered Escherichia coli strains.

    PubMed

    Li, Qing; Wu, Hui; Li, Zhimin; Ye, Qin

    2016-10-01

    In this study, an engineered strain Escherichia coli MLB (ldhA(-)pflB(-)) was constructed for production of succinate from glycerol. The succinate yield was 0.37mol/mol in anaerobic culture, however, the growth and glycerol consumption rates were very slow, resulting in a low succinate level. Two-stage fermentation was performed in flasks, and the succinate yield reached 0.93mol/mol, but the succinate titer was still low. Hence, overexpression of malate dehydrogenase, malic enzyme, phosphoenolpyruvate (PEP) carboxylase and PEP carboxykinase (PCK) from E. coli, and pyruvate carboxylase from Corynebacterium glutamicum in MLB was investigated for improving succinate production. Overexpression of PCK resulted in remarkable enhancement of glycerol consumption and succinate production. In flask experiments, the succinate concentration reached 118.1mM, and in a 1.5-L bioreactor the succinate concentration further increased to 360.2mM. The highest succinate yield achieved 0.93mol/mol, which was 93% of the theoretical yield, in the anaerobic stage. PMID:27371794

  9. Reducing β-glucosidase supplementation during cellulase recovery using engineered strain for successive lignocellulose bioconversion.

    PubMed

    Guo, Hong; Zou, Shaolan; Liu, Boshi; Su, Rongxin; Huang, Renliang; Qi, Wei; Zhang, Minhua; He, Zhimin

    2015-01-01

    Enzyme recycling by re-adsorption is one of the primary methods for reducing enzyme usage in lignocellulose conversion. This work proposes the combination of an engineered yeast strain that expresses β-glucosidase with enzyme recycling to reduce the amount of supplemented β-glucosidase in enzyme recycling experiments. Using the engineered strain, a slight increase in ethanol concentration was obtained after a 96-h fermentation of pretreated corncobs. Ethanol concentrations increased by 34.7% and 62.7% in the following two recycle rounds using the engineered strain compared with those using its parental strain without β-glucosidase addition. Furthermore, with the addition of β-glucosidase at 30CBU/g cellulose, the ethanol concentration after two recycle rounds exceeded 90% of that observed in the first SSF round with the engineered strain at a high initial cellulase loading of 45FPU/g cellulose.

  10. [Clostridium perfringens].

    PubMed

    Komatsu, Haruki; Inui, Ayano; Sogo, Tsuyoshi; Fujisawa, Tomoo

    2012-08-01

    In Japan, Clostridium perfringens (C. perfringens) is the top 5th or 6th pathogen of foodborne illnesses. Annually between 2006 and 2010, there were between 20 and 40 reported outbreaks of foodborne illnesses caused by C. perfringens. C. perfringens is found in soil and dust, in the intestinal tract humans and animals, on the surface of vegetable products. C. perfringens produces an enterotoxin that causes diarrhea and abdominal pain. Inappropriate food handing practice (inadequate heating, cooling and reheating) can lead to an outbreak. In general, clinical symptoms are mild and short duration. The diagnosis of C. perfringens food poisoning is based on either quantitative cultures of implicated foods or enterotoxin-positive stool specimens. Antibiotics are not indicated.

  11. An integrated approach: advances in the use of Clostridium for biofuel.

    PubMed

    Kök, M Samil

    2015-01-01

    Almost 90% of our energy comes from fossil fuels, which are both limited and polluting, hence the need to find alternative sources. Biofuels can provide a sustainable and renewable source of energy for the future. Recent significant advances in genetic engineering and fermentation technology have made microbial bio-based production of chemicals from renewable resources more viable. Clostridium species are considered as promising micro-organisms for the production of a wide range of chemicals for industrial use. However, a number of scientific challenges still need to be overcome to facilitate an economically viable production system. These include the use of cheap non-food-based substrates, a better understanding of the metabolic processes involved, improvement of strains through genetic engineering and innovation in process technology. This paper reviews recent developments in these areas, advancing the use of Clostridium within an industrial context especially for the production of biofuels.

  12. An integrated approach: advances in the use of Clostridium for biofuel.

    PubMed

    Kök, M Samil

    2015-01-01

    Almost 90% of our energy comes from fossil fuels, which are both limited and polluting, hence the need to find alternative sources. Biofuels can provide a sustainable and renewable source of energy for the future. Recent significant advances in genetic engineering and fermentation technology have made microbial bio-based production of chemicals from renewable resources more viable. Clostridium species are considered as promising micro-organisms for the production of a wide range of chemicals for industrial use. However, a number of scientific challenges still need to be overcome to facilitate an economically viable production system. These include the use of cheap non-food-based substrates, a better understanding of the metabolic processes involved, improvement of strains through genetic engineering and innovation in process technology. This paper reviews recent developments in these areas, advancing the use of Clostridium within an industrial context especially for the production of biofuels. PMID:27160660

  13. Strain engineering of diamond silicon vacancy centers in MEMS cantilevers

    NASA Astrophysics Data System (ADS)

    Meesala, Srujan; Sohn, Young-Ik; Atikian, Haig; Holzgrafe, Jeffrey; Zhang, Mian; Burek, Michael; Loncar, Marko

    2016-05-01

    The silicon vacancy (SiV) center in diamond has recently attracted attention as a solid state quantum emitter due to its attractive optical properties. We fabricate diamond MEMS cantilevers, and use electrostatic actuation to apply controlled strain fields to single SiV centers implanted in these devices. The strain response of the four electronic transitions of the SiV at 737 nm is measured via cryogenic (4 K) photoluminescence excitation. We demonstrate over 300 GHz of tuning for the mean transition frequency between the ground and excited states, and over 100 GHz of tuning for the orbital splittings within the ground and excited states. The interaction Hamiltonian for strain fields is inferred, and large strain susceptibilities of the order 1 PHz/strain are measured. We discuss prospects to utilize our device to reduce phonon-induced decoherence in SiV spin qubits, and to exploit the large strain susceptibilities for hybrid quantum systems based on nanomechanical resonators.

  14. Metabolism of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine by Clostridium bifermentans strain HAW-1 and several other H2-producing fermentative anaerobic bacteria.

    PubMed

    Zhao, Jian-Shen; Paquet, Louise; Halasz, Annamaria; Manno, Dominic; Hawari, Jalal

    2004-08-01

    Several H2-producing fermentative anaerobic bacteria including Clostridium, Klebsiella and Fusobacteria degraded octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) (36 microM) to formaldehyde (HCHO) and nitrous oxide (N2O) with rates ranging from 5 to 190 nmol h(-1)g [dry weight] of cells(-1). Among these strains, C. bifermentans strain HAW-1 grew and transformed HMX rapidly with the detection of the two key intermediates the mononitroso product and methylenedinitramine. Its cellular extract alone did not seem to degrade HMX appreciably, but degraded much faster in the presence of H2, NADH or NADPH. The disappearance of HMX was concurrent with the release of nitrite without the formation of the nitroso derivative(s). Results suggest that two types of enzymes were involved in HMX metabolism: one for denitration and the second for reduction to the nitroso derivative(s).

  15. A unique restriction site in the flaA gene allows rapid differentiation of group I and group II Clostridium botulinum strains by PCR-restriction fragment length polymorphism analysis.

    PubMed

    Paul, Catherine J; Tran, Shulin; Tam, Kevin J; Austin, John W

    2007-09-01

    Clostridium botulinum produces the potent botulinum neurotoxin, the causative agent of botulism. Based on distinctive physiological traits, strains of C. botulinum can be divided into four groups: however, only groups I and II are associated with human illness. Alignment of the flaA gene sequences from 40 group I and 40 group II strains identified a single BsrG1 restriction cut site that was present at base pair 283 in all group II flaA sequences and was not found in any group I sequence. The flaA gene was amplified by rapid colony PCR from 22 group I strains and 18 group II strains and digested with BsrGI restriction enzyme. Standard agarose gel electrophoresis with ethidium bromide staining showed two fragments, following restriction digestion of group II flaA gene amplicons with BsrGI, but only a single band of uncut flaA from group I strains. Combining rapid colony PCR with BsrGI restriction digest of the flaA gene at 60 degrees C is a significant improvement over current methods, such as meat digestion or amplified fragment length polymorphism, as a strain can be identified as either group I or group II in under 5 h when starting with a visible plated C. botulinum colony.

  16. 36. PHOTOGRAPHY OF W.P.A. PROJECT (MINNEAPOLIS CITY ENGINEER) STRAIN SHEET ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    36. PHOTOGRAPHY OF W.P.A. PROJECT (MINNEAPOLIS CITY ENGINEER) STRAIN SHEET (4 x 5 negative) - Steel Arch Bridge, Hennepin Avenue spanning west channel of Mississippi River, Minneapolis, Hennepin County, MN

  17. Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae.

    PubMed

    Inoue, Hiroyuki; Hashimoto, Seitaro; Matsushika, Akinori; Watanabe, Seiya; Sawayama, Shigeki

    2014-12-01

    The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.

  18. Engineering industrial Saccharomyces cerevisiae strains for xylose fermentation and comparison for switchgrass conversion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Saccharomyces physiology and fermentation related properties vary broadly among industrial strains. In this study, six industrial strains of varied genetic background were engineered to ferment xylose. Aerobic growth rates on xylose were 0.040 h**-1 to 0.167 h**-1. Fermentation of xylose, glucose/xy...

  19. Phase-Change Memory Materials by Design: A Strain Engineering Approach.

    PubMed

    Zhou, Xilin; Kalikka, Janne; Ji, Xinglong; Wu, Liangcai; Song, Zhitang; Simpson, Robert E

    2016-04-20

    Van der Waals heterostructure superlattices of Sb2 Te1 and GeTe are strain-engineered to promote switchable atomic disordering, which is confined to the GeTe layer. Careful control of the strain in the structures presents a new degree of freedom to design the properties of functional superlattice structures for data storage and photonics applications.

  20. Strain-displacement relations for strain engineering in single-layer 2d materials

    NASA Astrophysics Data System (ADS)

    Midtvedt, Daniel; Lewenkopf, Caio H.; Croy, Alexander

    2016-03-01

    We investigate the electromechanical coupling in single-layer 2d materials. For non-Bravais lattices, we find important corrections to the standard macroscopic strain-microscopic atomic-displacement theory. We put forward a general and systematic approach to calculate strain-displacement relations for several classes of 2d materials. We apply our findings to graphene as a study case, by combining a tight binding and a valence force-field model to calculate electronic and mechanical properties of graphene nanoribbons under strain. The results show good agreement with the predictions of the Dirac equation coupled to continuum mechanics. For this long wave-limit effective theory, we find that the strain-displacement relations lead to a renormalization correction to the strain-induced pseudo-magnetic fields. A similar renormalization is found for the strain-induced band-gap of black phosphorous. Implications for nanomechanical properties and electromechanical coupling in 2d materials are discussed.

  1. Strain engineering the work function in monolayer metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Lanzillo, Nicholas A.; Simbeck, Adam J.; Nayak, Saroj K.

    2015-05-01

    We use first-principles density functional theory to investigate the effect of both tensile and compressive strain on the work functions of various metal dichalcogenide monolayers. We find that for all six species considered, including MoS2, WS2, SnS2, VS2, MoSe2 and MoTe2, that compressive strain of up to 10% decreases the work function continuously by as much as 1.0 eV. Large enough tensile strain is also found to decrease the work function, although in some cases we observe an increase in the work function for intermediate values of tensile strain. This work function modulation is attributed to a weakening of the chalcogenide-metal bonds and an increase in total energy of each system as a function of strain. Values of strain which bring the metal atoms closer together lead to an increase in electrostatic potential energy, which in turn results in an increase in the vacuum potential level. The net effect on the work function can be explained in terms of the balance between the increases in the vacuum potential levels and Fermi energy.

  2. Strain engineering the work function in monolayer metal dichalcogenides.

    PubMed

    Lanzillo, Nicholas A; Simbeck, Adam J; Nayak, Saroj K

    2015-05-01

    We use first-principles density functional theory to investigate the effect of both tensile and compressive strain on the work functions of various metal dichalcogenide monolayers. We find that for all six species considered, including MoS2, WS2, SnS2, VS2, MoSe2 and MoTe2, that compressive strain of up to 10% decreases the work function continuously by as much as 1.0 eV. Large enough tensile strain is also found to decrease the work function, although in some cases we observe an increase in the work function for intermediate values of tensile strain. This work function modulation is attributed to a weakening of the chalcogenide-metal bonds and an increase in total energy of each system as a function of strain. Values of strain which bring the metal atoms closer together lead to an increase in electrostatic potential energy, which in turn results in an increase in the vacuum potential level. The net effect on the work function can be explained in terms of the balance between the increases in the vacuum potential levels and Fermi energy. PMID:25836754

  3. Strain Engineering for Transition Metal Dichalcogenides Based Field Effect Transistors.

    PubMed

    Shen, Tingting; Penumatcha, Ashish V; Appenzeller, Joerg

    2016-04-26

    Using electrical characteristics from three-terminal field-effect transistors (FETs), we demonstrate substantial strain induced band gap tunability in transition metal dichalcogenides (TMDs) in line with theoretical predictions and optical experiments. Devices were fabricated on flexible substrates, and a cantilever sample holder was used to apply uniaxial tensile strain to the various multilayer TMD FETs. Analyzing in particular transfer characteristics, we argue that the modified device characteristics under strain are clear evidence of a band gap reduction of 100 meV in WSe2 under 1.35% uniaxial tensile strain at room temperature. Furthermore, the obtained device characteristics imply that the band gap does not shrink uniformly under strain relative to a reference potential defined by the source/drain contacts. Instead, the band gap change is only related to a change of the conduction band edge of WSe2, resulting in a decrease in the Schottky barrier (SB) for electrons without any change for hole injection into the valence band. Simulations of SB device characteristics are employed to explain this point and to quantify our findings. Last, our experimental results are compared with DFT calculations under strain showing excellent agreement between theoretical predictions and the experimental data presented here. PMID:27043387

  4. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum.

    PubMed

    Lin, Paul P; Mi, Luo; Morioka, Amy H; Yoshino, Kouki M; Konishi, Sawako; Xu, Sharon C; Papanek, Beth A; Riley, Lauren A; Guss, Adam M; Liao, James C

    2015-09-01

    Consolidated bioprocessing (CBP) has the potential to reduce biofuel or biochemical production costs by processing cellulose hydrolysis and fermentation simultaneously without the addition of pre-manufactured cellulases. In particular, Clostridium thermocellum is a promising thermophilic CBP host because of its high cellulose decomposition rate. Here we report the engineering of C. thermocellum to produce isobutanol. Metabolic engineering for isobutanol production in C. thermocellum is hampered by enzyme toxicity during cloning, time-consuming pathway engineering procedures, and slow turnaround in production tests. In this work, we first cloned essential isobutanol pathway genes under different promoters to create various plasmid constructs in Escherichia coli. Then, these constructs were transformed and tested in C. thermocellum. Among these engineered strains, the best isobutanol producer was selected and the production conditions were optimized. We confirmed the expression of the overexpressed genes by their mRNA quantities. We also determined that both the native ketoisovalerate oxidoreductase (KOR) and the heterologous ketoisovalerate decarboxylase (KIVD) expressed were responsible for isobutanol production. We further found that the plasmid was integrated into the chromosome by single crossover. The resulting strain was stable without antibiotic selection pressure. This strain produced 5.4 g/L of isobutanol from cellulose in minimal medium at 50(o)C within 75 h, corresponding to 41% of theoretical yield.

  5. Alignment of the diamond nitrogen vacancy center by strain engineering

    SciTech Connect

    Karin, Todd; Dunham, Scott; Fu, Kai-Mei

    2014-08-04

    The nitrogen vacancy (NV) center in diamond is a sensitive probe of magnetic field and a promising qubit candidate for quantum information processing. The performance of many NV-based devices improves by aligning the NV(s) parallel to a single crystallographic direction. Using ab initio theoretical techniques, we show that NV orientation can be controlled by high-temperature annealing in the presence of strain under currently accessible experimental conditions. We find that (89 ± 7)% of NVs align along the [111] crystallographic direction under 2% compressive biaxial strain (perpendicular to [111]) and an annealing temperature of 970 °C.

  6. Dihydrodaidzein-producing Clostridium-like intestinal bacterium, strain TM-40, affects in vitro metabolism of daidzein by fecal microbiota of human male equol producer and non-producers

    PubMed Central

    TAMURA, Motoi; HORI, Sachiko; NAKAGAWA, Hiroyuki

    2011-01-01

    Much attention has been focused on the biological effects of equol, a metabolite of daidzein produced by intestinal microbiota. However, little is known about the role of isoflavone metabolizing bacteria in the intestinal microbiota. Recently, we isolated a dihydrodaidzein (DHD)-producing Clostridium-like bacterium, strain TM-40, from human feces. We investigated the effects of strain TM-40 on in vitro daidzein metabolism by human fecal microbiota from a male equol producer and two male equol non-producers. In the fecal suspension from the male equol non-producer and DHD producer, DHD was detected in the in vitro fecal incubation of daidzein after addition of TM-40. The DHD concentration increased as the concentration of strain TM-40 increased. In the fecal suspension from the equol producer, the fecal equol production was increased by the addition of strain TM-40. The occupation ratios of Bifidobacterium and Lactobacillales were higher in the equol non-producers than in the equol producer. Adding isoflavone-metabolizing bacteria to the fecal microbiota should facilitate the estimation of the metabolism of isoflavonoids by fecal microbiota. Studies on the interactions among equol-producing microbiota and DHD-producing bacteria might lead to clarification of some of the mechanisms regulating the production of equol by fecal microbiota. PMID:25045313

  7. Improved performance of graphene transistors by strain engineering.

    PubMed

    Nguyen, V Hung; Nguyen, Huy-Viet; Dollfus, P

    2014-04-25

    By means of numerical simulation, in this work we study the effects of uniaxial strain on the transport properties of strained graphene heterojunctions and explore the possibility of achieving good performance of graphene transistors using these hetero-channels. It is shown that a finite conduction gap can open in the strain junctions due to strain-induced deformation of the graphene bandstructure. These hetero-channels are then demonstrated to significantly improve the operation of graphene field-effect transistors (FETs). In particular, the ON/OFF current ratio can reach a value of over 10(5). In graphene normal FETs, the transconductance, although reduced compared to the case of unstrained devices, is still high, while good saturation of current can be obtained. This results in a high voltage gain and a high transition frequency of a few hundreds of GHz for a gate length of 80 nm. In graphene tunneling FETs, subthreshold swings lower than 30 mV /dec, strong nonlinear effects such as gate-controllable negative differential conductance, and current rectification are observed.

  8. Elimination of formate production in Clostridium thermocellum

    DOE PAGES

    Rydzak, Thomas; Lynd, Lee R.; Guss, Adam M.

    2015-07-11

    We study the ability of Clostridium thermocellum to rapidly degrade cellulose and ferment resulting hydrolysis products into ethanol makes it a promising platform organism for cellulosic biofuel production via consolidated bioprocessing. Currently, however, ethanol yield are far below theoretical maximum due to branched product pathways that divert carbon and electrons towards formate, H2, lactate, acetate, and secreted amino acids. To redirect carbon and electron flux away from formate, pyruvate:formate lyase (pfl) and respective PFL-activating enzyme were deleted. Formate production in the resulting Δpfl strain was eliminated and acetate production decreased by 50% on both complex and defined medium. Growth ratemore » of Δpfl decreased by 2.9-fold on defined medium and diauxic growth was observed on complex medium. Supplementation of defined medium with 2 mM formate restored Δpfl growth rate to 80% of the parent strain. Finally, we discuss the role of pfl in metabolic engineering strategies and C1 metabolism.« less

  9. Phylogeny of the ammonia-producing ruminal bacteria Peptostreptococcus anaerobius, Clostridium sticklandii, and Clostridium aminophilum sp. nov

    NASA Technical Reports Server (NTRS)

    Paster, B. J.; Russell, J. B.; Yang, C. M.; Chow, J. M.; Woese, C. R.; Tanner, R.

    1993-01-01

    In previous studies, gram-positive bacteria which grew rapidly with peptides or an amino acid as the sole energy source were isolated from bovine rumina. Three isolates, strains C, FT (T = type strain), and SR, were considered to be ecologically important since they produced up to 20-fold more ammonia than other ammonia-producing ruminal bacteria. On the basis of phenotypic criteria, the taxonomic position of these new isolates was uncertain. In this study, the 16S rRNA sequences of these isolates and related bacteria were determined to establish the phylogenetic positions of the organisms. The sequences of strains C, FT, and SR and reference strains of Peptostreptococcus anaerobius, Clostridium sticklandii, Clostridium coccoides, Clostridium aminovalericum, Acetomaculum ruminis, Clostridium leptum, Clostridium lituseburense, Clostridium acidiurici, and Clostridium barkeri were determined by using a modified Sanger dideoxy chain termination method. Strain C, a large coccus purported to belong to the genus Peptostreptococcus, was closely related to P. anaerobius, with a level of sequence similarity of 99.6%. Strain SR, a heat-resistant, short, rod-shaped organism, was closely related to C. sticklandii, with a level of sequence similarity of 99.9%. However, strain FT, a heat-resistant, pleomorphic, rod-shaped organism, was only distantly related to some clostridial species and P. anaerobius. On the basis of the sequence data, it was clear that strain FT warranted designation as a separate species. The closest known relative of strain FT was C. coccoides (level of similarity, only 90.6%). Additional strains that are phenotypically similar to strain FT were isolated in this study.(ABSTRACT TRUNCATED AT 250 WORDS).

  10. Clostridium jejuense sp. nov., isolated from soil.

    PubMed

    Jeong, Hyunyoung; Yi, Hana; Sekiguchi, Yuji; Muramatsu, Mizuho; Kamagata, Yoichi; Chun, Jongsik

    2004-09-01

    A strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 degrees C, pH 7.0 and 0-0.5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G + C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96.65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (= IMSNU 40003T = KCTC 5026T = DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.

  11. Clostridium difficile in poultry and poultry meat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence and severity of disease associated with toxigenic Clostridium difficile have increased in hospitals in North America from the emergence of newer, more virulent strains. Toxigenic C. difficile has been isolated from food animals and retail meat with potential implications of transfer t...

  12. Tuning the hydrogen evolution activity of MS2 (M = Mo or Nb) monolayers by strain engineering.

    PubMed

    Chen, Xiaobo; Wang, Guangjin

    2016-04-14

    Strain engineering is an effective strategy to tune the electronic, magnetic and optical properties of atomically thin materials like graphene and monolayer transition-metal dichalcogenides (m-TMDs). Using first-principles calculations, we show that strain is also effective for tuning the catalytic activity of m-MS2 (M = Mo or Nb) towards the hydrogen evolution reaction (HER), which is essential for electrochemical hydrogen generation from water splitting. A wide strain range covering both compressive (0-6%) and tensile (0-10%) regions is considered. It is found that biaxial tensile strain can enhance the HER activity more effectively than uniaxial tensile strain, while compressive strain deteriorates the HER activity. Compared with monolayer 1T-NbS2, monolayers 1T-MoS2 and 1H-NbS2 exhibit better strain tunability towards their HER activities since more active sites can be induced with increasing strain. In contrast, monolayer 1H-MoS2 is catalytically inert in the considered strain range because H adsorption is too weak. We demonstrate that tensile strain can lead to decrease of the adiabatic proton affinity but simultaneously a larger magnitude of increase of the adiabatic electron affinity, thus enhancing the catalytic activity. Electronic structure calculations show that tensile strain can activate the relatively inert inner valence electrons and enlarge the d-band exchange splitting, both of which induce destabilization of the system and enhancement of catalytic activity. PMID:26878108

  13. Strain-Engineering of Graphene Based Topological Quantum Devices

    NASA Astrophysics Data System (ADS)

    Diniz, Ginetom S.; Guassi, Marcos R.; Qu, Fanyao

    2015-03-01

    We have investigated the spin-charge transport in quantum devices based on graphene nanoribbons (GNR). Our calculation is based on the surface Green's function technique, considering the presence of an uniform uniaxial strain, spin-orbit interactions (SOIs), exchange field and a smooth staggered potential. We propose the use of uniaxial strain as an efficient mechanism to tune the conductance profiles of GNR with different edge terminations. Our results show that distinct behaviors can be achieved: for armchair GNR there is a complete suppression of the conductance close to the Fermi level with the formation of a band gap that depends on the direction and strength of the strain deformation, while for zigzag GNR there is only a small conductance suppression. We also discuss the effects of SOIs and the appearance of spin-resolved conductance oscillations, and the local density of states of these GNR devices in the quantum anomalous Hall regime. Furthermore, we demonstrate that the local density of states show that depending on the smoothness of the staggered potential, the edge states of AGNR can either emerge or be suppressed. These emerging states can be probed by scanning tunneling microscope. Our findings can be potentially used in novel GNR based topological quantum devices. Supported by FAP-DF, CNPq and CAPES.

  14. Electrotransformation of Clostridium thermocellum.

    PubMed

    Tyurin, Michael V; Desai, Sunil G; Lynd, Lee R

    2004-02-01

    Electrotransformation of several strains of Clostridium thermocellum was achieved using plasmid pIKm1 with selection based on resistance to erythromycin and lincomycin. A custom-built pulse generator was used to apply a square 10-ms pulse to an electrotransformation cuvette consisting of a modified centrifuge tube. Transformation was verified by recovery of the shuttle plasmid pIKm1 from presumptive transformants of C. thermocellum with subsequent PCR specific to the mls gene on the plasmid, as well as by retransformation of Escherichia coli. Optimization carried out with strain DSM 1313 increased transformation efficiencies from <1 to (2.2 +/- 0.5) x 10(5) transformants per micro g of plasmid DNA. Factors conducive to achieving high transformation efficiencies included optimized periods of incubation both before and after electric pulse application, chilling during cell collection and washing, subculture in the presence of isoniacin prior to electric pulse application, a custom-built cuvette embedded in an ice block during pulse application, use of a high (25-kV/cm) field strength, and induction of the mls gene before plating the cells on selective medium. The protocol and preferred conditions developed for strain DSM 1313 resulted in transformation efficiencies of (5.0 +/- 1.8) x 10(4) transformants per micro g of plasmid DNA for strain ATCC 27405 and approximately 1 x 10(3) transformants per micro g of plasmid DNA for strains DSM 4150 and 7072. Cell viability under optimal conditions was approximately 50% of that of controls not exposed to an electrical pulse. Dam methylation had a beneficial but modest (7-fold for strain ATCC 27405; 40-fold for strain DSM 1313) effect on transformation efficiency. The effect of isoniacin was also strain specific. The results reported here provide for the first time a gene transfer method functional in C. thermocellum that is suitable for molecular manipulations involving either the introduction of genes associated with foreign

  15. Tunable gaps and enhanced mobilities in strain-engineered silicane

    SciTech Connect

    Restrepo, Oscar D.; Mishra, Rohan; Windl, Wolfgang; Goldberger, Joshua E.

    2014-01-21

    The recent demonstration of single-atom thick, sp{sup 3}-hybridized group 14 analogues of graphene enables the creation of materials with electronic structures that are manipulated by the nature of the covalently bound substituents above and below the sheet. These analogues can be electronically derived from isolated (111) layers of the bulk diamond lattice. Here, we perform systematic Density Functional Theory calculations to understand how the band dispersions, effective masses, and band gaps change as the bulk silicon (111) layers are continuously separated from each other until they are electronically isolated, and then passivated with hydrogen. High-level calculations based on HSE06 hybrid functionals were performed on each endpoint to compare directly with experimental values. We find that the change in the electronic structure due to variations in the Si-H bond length, Si-Si-Si bond angle, and most significantly the Si-Si bond length can tune the nature of the band gap from indirect to direct with dramatic effects on the transport properties. First-principles calculations of the phonon-limited electron mobility predict a value of 464 cm{sup 2}/Vs for relaxed indirect band gap Si-H monolayers at room temperature. However, for 1.6% tensile strain, the band gap becomes direct, which increases the mobility significantly (8 551 cm{sup 2}/Vs at 4% tensile strain). In total, this analysis of Si-based monolayers suggests that strain can change the nature of the band gap from indirect to direct and increase the electron mobility more than 18-fold.

  16. Quantum pumping of valley current in strain engineered graphene

    SciTech Connect

    Wang, Jing; Chan, K. S. E-mail: zjlin@ustc.edu.cn; Lin, Zijing E-mail: zjlin@ustc.edu.cn

    2014-01-06

    We studied the generation of valley dependent current by adiabatic quantum pumping in monolayer graphene in the presence of electric potential barriers, ferromagnetic field and strain. The pumped currents in the two valleys have same magnitudes and opposite directions; thus, a pure valley current is generated. The oscillation of the pumped pure valley current is determined by the Fabry-Perot resonances formed in the structure. In our calculation, the pumped pure valley current can be as high as 50 nA, which is measurable using present technologies. The proposed device is useful for the development of graphene valleytronic devices.

  17. Application of fiber optic distributed sensor for strain measurement in civil engineering

    NASA Astrophysics Data System (ADS)

    Kurashima, Toshio; Usu, Tomonori; Tanaka, Kuniaki; Nobiki, Atsushi; Sato, Masashi; Nakai, Kenji

    1997-11-01

    We report on civil engineering applications of a fiber optic distributed strain sensor. It consists of a sensing fiber and a high performance optical time domain reflectometer (OTDR), for measuring both strain and optical loss distribution along optical fibers by accessing only one end of the fiber. The OTDR can measure distributed strain with an accuracy of better than +/- 60 X 10-6 and a high spatial resolution of up to 1 m over a 10 km long fiber. In model experiments using the OTDR, we measured the strain changes in fibers attached to the surface of a concrete test beam. The performance of the fiber strain sensor was tested by measuring the strain distribution in optical fibers and comparing the results with resistance strain gage measurements for several loads. We found that the two sets of results were similar, and in addition, we demonstrated experimentally that the sensor was able to measure an induced strain change of less than 100 by 10-6, which is nearly the elastic limit of the concrete material. These results show the potential of the OTDR to extend the application of monitoring systems to such areas as large building diagnostics for civil engineering.

  18. Antipathogenic activity of probiotics against Salmonella Typhimurium and Clostridium difficile in anaerobic batch culture systems: is it due to synergies in probiotic mixtures or the specificity of single strains?

    PubMed

    Tejero-Sariñena, Sandra; Barlow, Janine; Costabile, Adele; Gibson, Glenn R; Rowland, Ian

    2013-12-01

    Probiotics are currently being investigated for prevention of infections caused by enteric pathogens. The aim of this in vitro study was to evaluate the influence of three single probiotics: Lactobacillus casei NCIMB 30185 (PXN 37), Lactobacillus acidophilus NCIMB 30184 (PXN 35), Bifidobacterium breve NCIMB 30180 (PXN 25) and a probiotic mixture containing the above strains plus twelve other strains belonging to the Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus and Bacillus genera on the survival of Salmonella Typhimurium and Clostridium difficile using pH-controlled anaerobic batch cultures containing mixed faecal bacteria. Changes in relevant bacterial groups and effects of probiotic addition on survival of the two pathogens were assessed over 24 h. Quantitative analysis of bacterial populations revealed that there was a significant increase in lactobacilli and/or bifidobacteria numbers, depending on probiotic addition, compared with the control (no added probiotic). There was also a significant reduction in S. Typhimurium and C. difficile numbers in the presence of certain probiotics compared with controls. Of the probiotic treatments, two single strains namely L. casei NCIMB 30185 (PXN 37), and B. breve NCIMB 30180 (PXN 25) were the most potent in reducing the numbers of S. Typhimurium and C. difficile. In addition, the supplementation with probiotics into the systems influenced some fermentations parameters. Acetate was found in the largest concentrations in all vessels and lactate and formate were generally detected in higher amounts in vessels with probiotic addition compared to controls.

  19. Metabolic engineering of Saccharomyces cerevisiae ethanol strains PE-2 and CAT-1 for efficient lignocellulosic fermentation.

    PubMed

    Romaní, Aloia; Pereira, Filipa; Johansson, Björn; Domingues, Lucília

    2015-03-01

    In this work, Saccharomyces cerevisiae strains PE-2 and CAT-1, commonly used in the Brazilian fuel ethanol industry, were engineered for xylose fermentation, where the first fermented xylose faster than the latter, but also produced considerable amounts of xylitol. An engineered PE-2 strain (MEC1121) efficiently consumed xylose in presence of inhibitors both in synthetic and corn-cob hydrolysates. Interestingly, the S. cerevisiae MEC1121 consumed xylose and glucose simultaneously, while a CEN.PK based strain consumed glucose and xylose sequentially. Deletion of the aldose reductase GRE3 lowered xylitol production to undetectable levels and increased xylose consumption rate which led to higher final ethanol concentrations. Fermentation of corn-cob hydrolysate using this strain, MEC1133, resulted in an ethanol yield of 0.47 g/g of total sugars which is 92% of the theoretical yield.

  20. Strain- and twist-engineered optical absorption of few-layer black phosphorus

    NASA Astrophysics Data System (ADS)

    Jia, Qian; Kong, XiangHua; Qiao, JingSi; Ji, Wei

    2016-09-01

    Density functional and many-body perturbation theories calculations were carried out to investigate fundamental and optical bandgap, exciton binding energy and optical absorption property of normal and strain- and twist-engineered few-layer black phosphorus (BP). We found that the fundamental bandgaps of few layer BP can be engineered by layer stacking and in-plane strain, with linear relationships to their associated exciton binding energies. The strain-dependent optical absorption behaviors are also anisotropic that the position of the first absorption peak monotonically blue-shifts as the strain applies to either direction for incident light polarized along the armchair direction, but this is not the case for that along the zigzag direction. Given those striking properties, we proposed two prototype devices for building potentially more balanced light absorbers and light filter passes, which promotes further applications and investigations of BP in nanoelectronics and optoelectronics.

  1. Enhanced Seebeck effect in graphene devices by strain and doping engineering

    NASA Astrophysics Data System (ADS)

    Nguyen, M. Chung; Nguyen, V. Hung; Nguyen, Huy-Viet; Saint-Martin, J.; Dollfus, P.

    2015-09-01

    In this work, we investigate the possibility of enhancing the thermoelectric power (Seebeck coefficient) in graphene devices by strain and doping engineering. While a local strain can result in the misalignment of Dirac cones of different graphene sections in the k-space, doping engineering leads to their displacement in energy. By combining these two effects, we demonstrate that a conduction gap as large as a few hundred meV can be achieved and hence the enhanced Seebeck coefficient can reach a value higher than 1.4 mV/K in graphene doped heterojunctions with a locally strained area. Such hetero-channels appear to be very promising for enlarging the applications of graphene devices as in strain and thermal sensors.

  2. Metabolic engineering of Saccharomyces cerevisiae ethanol strains PE-2 and CAT-1 for efficient lignocellulosic fermentation.

    PubMed

    Romaní, Aloia; Pereira, Filipa; Johansson, Björn; Domingues, Lucília

    2015-03-01

    In this work, Saccharomyces cerevisiae strains PE-2 and CAT-1, commonly used in the Brazilian fuel ethanol industry, were engineered for xylose fermentation, where the first fermented xylose faster than the latter, but also produced considerable amounts of xylitol. An engineered PE-2 strain (MEC1121) efficiently consumed xylose in presence of inhibitors both in synthetic and corn-cob hydrolysates. Interestingly, the S. cerevisiae MEC1121 consumed xylose and glucose simultaneously, while a CEN.PK based strain consumed glucose and xylose sequentially. Deletion of the aldose reductase GRE3 lowered xylitol production to undetectable levels and increased xylose consumption rate which led to higher final ethanol concentrations. Fermentation of corn-cob hydrolysate using this strain, MEC1133, resulted in an ethanol yield of 0.47 g/g of total sugars which is 92% of the theoretical yield. PMID:25536512

  3. Clostridium difficile in mixed populations of animals and humans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objectives: Since 2003, there has been an emergence of BI/NAP1 strain of Clostridium difficile (Cd) in North American hospitals. The origins of this epidemic strain have yet to be determined. However, PFGE analysis has shown ~80% similarity between this strain and some swine isolates. The objecti...

  4. Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition

    PubMed Central

    Velmurugan, Punitha; Jonnalagadda, Raghava Rao; Unni Nair, Balachandran

    2015-01-01

    Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of DAla in collagen like peptide (imino-poor region of type I collagen) on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD). Our findings suggest that, DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins. PMID:25973613

  5. Analysis of strain gage reliability in F-100 jet engine testing at NASA Lewis Research Center

    NASA Technical Reports Server (NTRS)

    Holanda, R.

    1983-01-01

    A reliability analysis was performed on 64 strain gage systems mounted on the 3 rotor stages of the fan of a YF-100 engine. The strain gages were used in a 65 hour fan flutter research program which included about 5 hours of blade flutter. The analysis was part of a reliability improvement program. Eighty-four percent of the strain gages survived the test and performed satisfactorily. A post test analysis determined most failure causes. Five failures were caused by open circuits, three failed gages showed elevated circuit resistance, and one gage circuit was grounded. One failure was undetermined.

  6. Controlling thermal and electrical properties of graphene by strain-engineering its flexural phonons

    NASA Astrophysics Data System (ADS)

    Conley, Hiram; Nicholl, Ryan; Bolotin, Kirill

    2014-03-01

    We explore the effects of flexural phonons on the thermal and electrical properties of graphene. To control the amplitude of flexural phonons, we developed a technique to engineer uniform mechanical strain between 0 and 1% in suspended graphene. We determine the level of strain, thermal conductivity and carrier mobility of graphene through a combination of mechanical resonance and electrical transport measurements. Depending on strain, we find significant changes in the thermal expansion coefficient, thermal conductivity, and carrier mobility of suspended graphene. These changes are consistent with the expected contribution of flexural phonons.

  7. Defect-free single-crystal SiGe: a new material from nanomembrane strain engineering.

    PubMed

    Paskiewicz, Deborah M; Tanto, Boy; Savage, Donald E; Lagally, Max G

    2011-07-26

    Many important materials cannot be grown as single crystals in bulk form because strain destroys long-range crystallinity. Among them, alloys of group IV semiconductors, specifically SiGe alloys, have significant technological value. Using nanomembrane strain engineering methods, we demonstrate the fabrication of fully elastically relaxed Si(1-x)Ge(x) nanomembranes (NMs) for use as growth substrates for new materials. To do so, we grow defect-free, uniformly and elastically strained SiGe layers on Si substrates and release the SiGe layers to allow them to relax this strain completely as free-standing NMs. These SiGe NMs are transferred to new hosts and bonded there. We confirm the high structural quality of these new materials and demonstrate their use as substrates for technologically relevant epitaxial films by growing strained-Si layers and thick, lattice-matched SiGe alloy layers on them.

  8. Strain and Cracking Surveillance in Engineered Cementitious Composites by Piezoresistive Properties

    NASA Astrophysics Data System (ADS)

    Yu, Jia Huan; Hou, Tsung Chan

    2010-12-01

    Engineered Cementitious Composites (ECCs) are novel cement-based ultraductile materials which is crack resistant and undergoes strain hardening when loaded in tension. In particular, the material is piezoresistive with changes in electrical resistance correlated with mechanical strain. The unique electrical properties of ECC render them a smart material capable of measuring strain and the evolution of structural damage. In this study, the conductivity of the material prior to loading was quantified. The piezoresistive property of ECC structural specimens are exploited to directly measure levels of cracking pattern and tensile strain. Changes in ECC electrical resistance are measured using a four-probe direct-current (DC) resistance test as specimens are monotonically loaded in tension. The change in piezoresistivity correlates the cracking and strain in the ECC matrix and results in a nonlinear change in the material conductivity.

  9. Enhanced isopropanol and n-butanol production by supplying exogenous acetic acid via co-culturing two clostridium strains from cassava bagasse hydrolysate.

    PubMed

    Zhang, Shaozhi; Qu, Chunyun; Huang, Xiaoyan; Suo, Yukai; Liao, Zhengping; Wang, Jufang

    2016-07-01

    The focus of this study was to produce isopropanol and butanol (IB) from dilute sulfuric acid treated cassava bagasse hydrolysate (SACBH), and improve IB production by co-culturing Clostridium beijerinckii (C. beijerinckii) with Clostridium tyrobutyricum (C. tyrobutyricum) in an immobilized-cell fermentation system. Concentrated SACBH could be converted to solvents efficiently by immobilized pure culture of C. beijerinckii. Considerable solvent concentrations of 6.19 g/L isopropanol and 12.32 g/L butanol were obtained from batch fermentation, and the total solvent yield and volumetric productivity were 0.42 g/g and 0.30 g/L/h, respectively. Furthermore, the concentrations of isopropanol and butanol increased to 7.63 and 13.26 g/L, respectively, under the immobilized co-culture conditions when concentrated SACBH was used as the carbon source. The concentrations of isopropanol and butanol from the immobilized co-culture fermentation were, respectively, 42.62 and 25.45 % higher than the production resulting from pure culture fermentation. The total solvent yield and volumetric productivity increased to 0.51 g/g and 0.44 g/L/h when co-culture conditions were utilized. Our results indicated that SACBH could be used as an economically favorable carbon source or substrate for IB production using immobilized fermentation. Additionally, IB production could be significantly improved by co-culture immobilization, which provides extracellular acetic acid to C. beijerinckii from C. tyrobutyricum. This study provided a technically feasible and cost-efficient way for IB production using cassava bagasse, which may be suitable for industrial solvent production. PMID:27116556

  10. Enhanced isopropanol and n-butanol production by supplying exogenous acetic acid via co-culturing two clostridium strains from cassava bagasse hydrolysate.

    PubMed

    Zhang, Shaozhi; Qu, Chunyun; Huang, Xiaoyan; Suo, Yukai; Liao, Zhengping; Wang, Jufang

    2016-07-01

    The focus of this study was to produce isopropanol and butanol (IB) from dilute sulfuric acid treated cassava bagasse hydrolysate (SACBH), and improve IB production by co-culturing Clostridium beijerinckii (C. beijerinckii) with Clostridium tyrobutyricum (C. tyrobutyricum) in an immobilized-cell fermentation system. Concentrated SACBH could be converted to solvents efficiently by immobilized pure culture of C. beijerinckii. Considerable solvent concentrations of 6.19 g/L isopropanol and 12.32 g/L butanol were obtained from batch fermentation, and the total solvent yield and volumetric productivity were 0.42 g/g and 0.30 g/L/h, respectively. Furthermore, the concentrations of isopropanol and butanol increased to 7.63 and 13.26 g/L, respectively, under the immobilized co-culture conditions when concentrated SACBH was used as the carbon source. The concentrations of isopropanol and butanol from the immobilized co-culture fermentation were, respectively, 42.62 and 25.45 % higher than the production resulting from pure culture fermentation. The total solvent yield and volumetric productivity increased to 0.51 g/g and 0.44 g/L/h when co-culture conditions were utilized. Our results indicated that SACBH could be used as an economically favorable carbon source or substrate for IB production using immobilized fermentation. Additionally, IB production could be significantly improved by co-culture immobilization, which provides extracellular acetic acid to C. beijerinckii from C. tyrobutyricum. This study provided a technically feasible and cost-efficient way for IB production using cassava bagasse, which may be suitable for industrial solvent production.

  11. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation

    SciTech Connect

    Sander, Kyle B.; Wilson, Charlotte M.; M. Rodriquez, Jr.; Klingeman, Dawn Marie; Davison, Brian H.; Brown, Steven D.; Rydzak, T.

    2015-12-12

    Clostridium thermocellum is a promising consolidated bioprocessing candidate organism capable of directly converting lignocellulosic biomass to ethanol. Current ethanol yields, productivities, and growth inhibitions are industrial deployment impediments for commodity fuel production by this bacterium. Redox imbalance under certain conditions and in engineered strains may contribute to incomplete substrate utilization and may direct fermentation products to undesirable overflow metabolites. As a result, towards a better understanding of redox metabolism in C. thermocellum, we established continuous growth conditions and analyzed global gene expression during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which changed the fermentation redox potential.

  12. FT-IR spectroscopic analysis for studying Clostridium cell response to conversion of enzymatically hydrolyzed hay

    NASA Astrophysics Data System (ADS)

    Grube, Mara; Gavare, Marita; Nescerecka, Alina; Tihomirova, Kristina; Mezule, Linda; Juhna, Talis

    2013-07-01

    Grass hay is one of assailable cellulose containing non-food agricultural wastes that can be used as a carbohydrate source by microorganisms producing biofuels. In this study three Clostridium strains Clostridium acetobutylicum, Clostridium beijerinckii and Clostridium tetanomorphum, capable of producing acetone, butanol and ethanol (ABE) were adapted to convert enzymatically hydrolyzed hay used as a growth media additive. The results of growth curves, substrate degradation kinetics and FT-IR analyses of bacterial biomass macromolecular composition showed diverse strain-specific cell response to the growth medium composition.

  13. Height control of self-assembled quantum dots by strain engineering during capping

    SciTech Connect

    Grossi, D. F. Koenraad, P. M.; Smereka, P.; Keizer, J. G.; Ulloa, J. M.

    2014-10-06

    Strain engineering during the capping of III-V quantum dots has been explored as a means to control the height of strained self-assembled quantum dots. Results of Kinetic Monte Carlo simulations are confronted with cross-sectional Scanning Tunnel Microscopy (STM) measurements performed on InAs quantum dots grown by molecular beam epitaxy. We studied InAs quantum dots that are capped by In{sub x}Ga{sub (1−x)}As layers of different indium compositions. Both from our realistic 3D kinetic Monte Carlo simulations and the X-STM measurements on real samples, a trend in the height of the capped quantum dot is found as a function of the lattice mismatch between the quantum dot material and the capping layer. Results obtained on additional material combinations show a generic role of the elastic energy in the control of the quantum dot morphology by strain engineering during capping.

  14. Bandgap engineering of strained monolayer and bilayer MoS2.

    PubMed

    Conley, Hiram J; Wang, Bin; Ziegler, Jed I; Haglund, Richard F; Pantelides, Sokrates T; Bolotin, Kirill I

    2013-08-14

    We report the influence of uniaxial tensile mechanical strain in the range 0-2.2% on the phonon spectra and bandstructures of monolayer and bilayer molybdenum disulfide (MoS2) two-dimensional crystals. First, we employ Raman spectroscopy to observe phonon softening with increased strain, breaking the degeneracy in the E' Raman mode of MoS2, and extract a Grüneisen parameter of ~1.06. Second, using photoluminescence spectroscopy we measure a decrease in the optical band gap of MoS2 that is approximately linear with strain, ~45 meV/% strain for monolayer MoS2 and ~120 meV/% strain for bilayer MoS2. Third, we observe a pronounced strain-induced decrease in the photoluminescence intensity of monolayer MoS2 that is indicative of the direct-to-indirect transition of the character of the optical band gap of this material at applied strain of ~1%. These observations constitute a demonstration of strain engineering the band structure in the emergent class of two-dimensional crystals, transition-metal dichalcogenides.

  15. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

    PubMed

    Brunk, Elizabeth; George, Kevin W; Alonso-Gutierrez, Jorge; Thompson, Mitchell; Baidoo, Edward; Wang, George; Petzold, Christopher J; McCloskey, Douglas; Monk, Jonathan; Yang, Laurence; O'Brien, Edward J; Batth, Tanveer S; Martin, Hector Garcia; Feist, Adam; Adams, Paul D; Keasling, Jay D; Palsson, Bernhard O; Lee, Taek Soon

    2016-05-25

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks. PMID:27211860

  16. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

    PubMed

    Brunk, Elizabeth; George, Kevin W; Alonso-Gutierrez, Jorge; Thompson, Mitchell; Baidoo, Edward; Wang, George; Petzold, Christopher J; McCloskey, Douglas; Monk, Jonathan; Yang, Laurence; O'Brien, Edward J; Batth, Tanveer S; Martin, Hector Garcia; Feist, Adam; Adams, Paul D; Keasling, Jay D; Palsson, Bernhard O; Lee, Taek Soon

    2016-05-25

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.

  17. Mechanical Self-Assembly of a Strain-Engineered Flexible Layer: Wrinkling, Rolling, and Twisting

    NASA Astrophysics Data System (ADS)

    Chen, Zi; Huang, Gaoshan; Trase, Ian; Han, Xiaomin; Mei, Yongfeng

    2016-01-01

    Self-shaping of curved structures, especially those involving flexible thin layers, is attracting increasing attention because of their broad potential applications in, e.g., nanoelectromechanical andmicroelectromechanical systems, sensors, artificial skins, stretchable electronics, robotics, and drug delivery. Here, we provide an overview of recent experimental, theoretical, and computational studies on the mechanical self-assembly of strain-engineered thin layers, with an emphasis on systems in which the competition between bending and stretching energy gives rise to a variety of deformations, such as wrinkling, rolling, and twisting. We address the principle of mechanical instabilities, which is often manifested in wrinkling or multistability of strain-engineered thin layers. The principles of shape selection and transition in helical ribbons are also systematically examined. We hope that a more comprehensive understanding of the mechanical principles underlying these rich phenomena can foster the development of techniques for manufacturing functional three-dimensional structures on demand for a broad spectrum of engineering applications.

  18. Production of cellobionate from cellulose using an engineered Neurospora crassa strain with laccase and redox mediator addition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report a novel production process for cellobionic acid from cellulose using an engineered fungal strain with the exogenous addition of laccase and a redox mediator. A previously engineered strain of Neurospora crassa (F5'ace-1'cre-1'ndvB) was shown to produce cellobionate directly from cellulose ...

  19. Novel Real-Time PCR Assay for Simultaneous Detection and Differentiation of Clostridium chauvoei and Clostridium septicum in Clostridial Myonecrosis▿

    PubMed Central

    Halm, Anna; Wagner, Martin; Köfer, Josef; Hein, Ingeborg

    2010-01-01

    A real-time PCR assay based on the 16S rRNA gene sequence was designed for differentiation of blackleg-causing Clostridium chauvoei and Clostridium septicum, a phylogenetically closely related bacterium responsible for malignant edema. In order to exclude false-negative results, an internal amplification control was included in the assay. A set of three probes, one specific for C. chauvoei, one specific for C. septicum, and one specific for both species, permitted unequivocal detection of C. chauvoei in tests of 32 Clostridium sp. strains and 10 non-Clostridium strains. The assay proved to be sensitive, detecting one genome of C. chauvoei or C. septicum per PCR and 1.79 × 103 C. chauvoei cells/g artificially contaminated muscle tissue. In tests of 11 clinical specimens, the real-time PCR assay yielded the same results as an established conventional PCR method. PMID:20129968

  20. Strain-engineered diffusive atomic switching in two-dimensional crystals

    NASA Astrophysics Data System (ADS)

    Kalikka, Janne; Zhou, Xilin; Dilcher, Eric; Wall, Simon; Li, Ju; Simpson, Robert E.

    2016-06-01

    Strain engineering is an emerging route for tuning the bandgap, carrier mobility, chemical reactivity and diffusivity of materials. Here we show how strain can be used to control atomic diffusion in van der Waals heterostructures of two-dimensional (2D) crystals. We use strain to increase the diffusivity of Ge and Te atoms that are confined to 5 Å thick 2D planes within an Sb2Te3-GeTe van der Waals superlattice. The number of quintuple Sb2Te3 2D crystal layers dictates the strain in the GeTe layers and consequently its diffusive atomic disordering. By identifying four critical rules for the superlattice configuration we lay the foundation for a generalizable approach to the design of switchable van der Waals heterostructures. As Sb2Te3-GeTe is a topological insulator, we envision these rules enabling methods to control spin and topological properties of materials in reversible and energy efficient ways.

  1. Engineering and Analysis of a Saccharomyces cerevisiae Strain That Uses Formaldehyde as an Auxiliary Substrate▿

    PubMed Central

    Baerends, Richard J. S.; de Hulster, Erik; Geertman, Jan-Maarten A.; Daran, Jean-Marc; van Maris, Antonius J. A.; Veenhuis, Marten; van der Klei, Ida J.; Pronk, Jack T.

    2008-01-01

    We demonstrated that formaldehyde can be efficiently coutilized by an engineered Saccharomyces cerevisiae strain that expresses Hansenula polymorpha genes encoding formaldehyde dehydrogenase (FLD1) and formate dehydrogenase (FMD), in contrast to wild-type strains. Initial chemostat experiments showed that the engineered strain coutilized formaldehyde with glucose, but these mixed-substrate cultures failed to reach steady-state conditions and did not exhibit an increased biomass yield on glucose. Subsequent transcriptome analyses of chemostat cultures of the engineered strain, grown on glucose-formaldehyde mixtures, indicated that the presence of formaldehyde in the feed caused biotin limitations. Further transcriptome analysis demonstrated that this biotin inactivation was prevented by using separate formaldehyde and vitamin feeds. Using this approach, steady-state glucose-limited chemostat cultures were obtained that coutilized glucose and formaldehyde. Coutilization of formaldehyde under these conditions resulted in an enhanced biomass yield of the glucose-limited cultures. The biomass yield was quantitatively consistent with the use of formaldehyde as an auxiliary substrate that generates NADH and subsequently, via oxidative phosphorylation, ATP. On an electron pair basis, the biomass yield increase observed with formaldehyde was larger than that observed previously for formate, which is tentatively explained by different modes of formate and formaldehyde transport in S. cerevisiae. PMID:18378663

  2. Electrostatic actuated strain engineering in monolithically integrated VLS grown silicon nanowires

    NASA Astrophysics Data System (ADS)

    Wagesreither, Stefan; Bertagnolli, Emmerich; Kawase, Shinya; Isono, Yoshitada; Lugstein, Alois

    2014-11-01

    In this paper we demonstrate the fabrication and application of an electrostatic actuated tensile straining test (EATEST) device enabling strain engineering in individual suspended nanowires (NWs). Contrary to previously reported approaches, this special setup guarantees the application of pure uniaxial tensile strain with no shear component of the stress while e.g. simultaneously measuring the resistance change of the NW. To demonstrate the potential of this approach we investigated the piezoresistivity of about 3 μm long and 100 nm thick SiNWs but in the same way one can think about the application of such a device on other geometries, other materials beyond Si as well as the use of other characterization techniques beyond electrical measurements. Therefore single-crystal SiNWs were monolithically integrated in a comb drive actuated MEMS device based on a silicon-on-insulator (SOI) wafer using the vapor-liquid-solid (VLS) growth technique. Strain values were verified by a precise measurement of the NW elongation with scanning electron microscopy (SEM). Further we employed confocal μ-Raman microscopy for in situ, high spatial resolution measurements of the strain in individual SiNWs during electrical characterization. A giant piezoresistive effect was observed, resulting in a fivefold increase in conductivity for 3% uniaxially strained SiNWs. As the EATEST approach can be easily integrated into an existing Si technology platform this architecture may pave the way toward a new generation of nonconventional devices by leveraging the strain degree of freedom.

  3. Strain-engineered band parameters of graphene-like SiC monolayer

    SciTech Connect

    Behera, Harihar; Mukhopadhyay, Gautam

    2014-10-06

    Using full-potential density functional theory (DFT) calculations we show that the band gap and effective masses of charge carriers in SiC monolayer (ML-SiC) in graphene-like two-dimensional honeycomb structure are tunable by strain engineering. ML-SiC was found to preserve its flat 2D graphene-like structure under compressive strain up to 7%. A transition from indirect-to-direct gap-phase is predicted to occur for a strain value lying within the interval (1.11 %, 1.76%). In both gap-phases band gap decreases with increasing strain, although the rate of decrease is different in the two gap-phases. Effective mass of electrons show a non-linearly decreasing trend with increasing tensile strain in the direct gap-phase. The strain-sensitive properties of ML-SiC, may find applications in future strain-sensors, nanoelectromechanical systems (NEMS) and nano-optomechanical systems (NOMS) and other nano-devices.

  4. Clostridium vulturis sp. nov., isolated from the intestine of the cinereous vulture (Aegypius monachus).

    PubMed

    Paek, Jayoung; Lee, Mi-Hwa; Kim, Byung-Chun; Sang, Byoung-In; Paek, Woon Kee; Jin, Tae-Eun; Shin, Yeseul; Park, In-Soon; Chang, Young-Hyo

    2014-09-01

    A Gram-stain positive, strict anaerobe, spore-forming, motile rod-shaped bacterial strain with peritrichous flagella, designated YMB-57(T), was isolated from the intestine of a cinereous vulture (Aegypius monachus) in Korea. Strain YMB-57(T) was found to show optimal growth at 37 °C, pH 7.5 and 1.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain YMB-57(T) belongs to the genus Clostridium and is most closely related to the type strains of Clostridium subterminale (96.9 % sequence similarity), Clostridium thiosulfatireducens (96.7 %) and Clostridium sulfidigenes (96.6 %). The main fermentation end-products identified following growth in PYG medium were acetate, butyrate, ethanol, propanol, carbon dioxide and hydrogen. Peptone was converted to ethanol, and butanol, whereas glucose was fermented to ethanol. The major cellular fatty acids were identified as C16:0, C18:1 ω9c, and C18:1 ω9c DMA and the DNA G+C content was determined to be 34.0 mol%. Phenotypic and phylogenetic differences indicate that strain YMB-57(T) is distinct from other Clostridium species. It is proposed that strain YMB-57(T) be classified as the type strain of a novel species of the genus Clostridium, with the name Clostridium vulturis sp. nov. The type strain is YMB-57(T) (=KCTC 15114(T) = JCM 17998(T)).

  5. Multicenter clinical evaluation of the portrait toxigenic C. difficile assay for detection of toxigenic Clostridium difficile strains in clinical stool specimens.

    PubMed

    Buchan, Blake W; Mackey, Tami-Lea A; Daly, Judy A; Alger, Garrison; Denys, Gerald A; Peterson, Lance R; Kehl, Sue C; Ledeboer, Nathan A

    2012-12-01

    We compared the Portrait Toxigenic C. difficile Assay, a new semiautomated sample-to-result molecular test, to a toxigenic bacterial culture/cell cytotoxin neutralization assay (TBC/CCNA) for the detection of toxigenic Clostridium difficile in 549 stool specimens. Stool specimens were also tested by one of three alternative FDA-cleared molecular tests for toxigenic C. difficile (Xpert C. difficile, Illumigene C. difficile, or GeneOhm Cdiff). The sensitivities and specificities of the molecular tests compared to TBC/CCNA were as follows: 98.2% and 92.8% for the Portrait assay, 100% and 91.7% for the Xpert assay, 93.3% and 95.1% for the Illumigene assay, and 97.4% and 98.5% for the GeneOhm assay, respectively. The majority of Portrait false-positive results (20/31; 64.5%) were also positive for C. difficile by an alternative molecular test, suggesting an increased sensitivity compared to the culture-based "gold standard" method. The Portrait test detected an assay input of 30 CFU in 100% of spiked samples and detected an input of 10 CFU in 96.7% of samples tested.

  6. Memory B Cells Encode Neutralizing Antibody Specific for Toxin B from the Clostridium difficile Strains VPI 10463 and NAP1/BI/027 but with Superior Neutralization of VPI 10463 Toxin B.

    PubMed

    Devera, T Scott; Lang, Gillian A; Lanis, Jordi M; Rampuria, Pragya; Gilmore, Casey L; James, Judith A; Ballard, Jimmy D; Lang, Mark L

    2016-01-01

    Secreted toxin B (TcdB) substantially contributes to the pathology observed during Clostridium difficile infection. To be successfully incorporated into a vaccine, TcdB-based immunogens must stimulate the production of neutralizing antibody (Ab)-encoding memory B cells (Bmem cells). Despite numerous investigations, a clear analysis of Bmem cellular responses following vaccination against TcdB is lacking. B6 mice were therefore used to test the ability of a nontoxigenic C-terminal domain (CTD) fragment of TcdB to induce Bmem cells that encode TcdB-neutralizing antibody. CTD was produced from the historical VPI 10463 strain (CTD1) and from the hypervirulent strain NAP1/BI/027 (CTD2). It was then demonstrated that CTD1 induced strong recall IgG antibody titers, and this led to the development of functional Bmem cells that could be adoptively transferred to naive recipients. Bmem cell-driven neutralizing Ab responses conferred protection against lethal challenge with TcdB1. Further experiments revealed that an experimental adjuvant (Imject) and a clinical adjuvant (Alhydrogel) were compatible with Bmem cell induction. Reactivity of human Bmem cells to CTD1 was also evident in human peripheral blood mononuclear cells (PBMCs), suggesting that CTD1 could be a good vaccine immunogen. However, CTD2 induced strong Bmem cell-driven antibody titers, and the CTD2 antibody was neutralizing in vitro, but its protection against lethal challenge with TcdB2 was limited to delaying time to death. Therefore, CTD from different C. difficile strains may be a good immunogen for stimulating B cell memory that encodes in vitro neutralizing Ab but may be limited by variable protection against intoxication in vivo. PMID:26502913

  7. Memory B Cells Encode Neutralizing Antibody Specific for Toxin B from the Clostridium difficile Strains VPI 10463 and NAP1/BI/027 but with Superior Neutralization of VPI 10463 Toxin B

    PubMed Central

    Devera, T. Scott; Lang, Gillian A.; Lanis, Jordi M.; Rampuria, Pragya; Gilmore, Casey L.; James, Judith A.; Ballard, Jimmy D.

    2015-01-01

    Secreted toxin B (TcdB) substantially contributes to the pathology observed during Clostridium difficile infection. To be successfully incorporated into a vaccine, TcdB-based immunogens must stimulate the production of neutralizing antibody (Ab)-encoding memory B cells (Bmem cells). Despite numerous investigations, a clear analysis of Bmem cellular responses following vaccination against TcdB is lacking. B6 mice were therefore used to test the ability of a nontoxigenic C-terminal domain (CTD) fragment of TcdB to induce Bmem cells that encode TcdB-neutralizing antibody. CTD was produced from the historical VPI 10463 strain (CTD1) and from the hypervirulent strain NAP1/BI/027 (CTD2). It was then demonstrated that CTD1 induced strong recall IgG antibody titers, and this led to the development of functional Bmem cells that could be adoptively transferred to naive recipients. Bmem cell-driven neutralizing Ab responses conferred protection against lethal challenge with TcdB1. Further experiments revealed that an experimental adjuvant (Imject) and a clinical adjuvant (Alhydrogel) were compatible with Bmem cell induction. Reactivity of human Bmem cells to CTD1 was also evident in human peripheral blood mononuclear cells (PBMCs), suggesting that CTD1 could be a good vaccine immunogen. However, CTD2 induced strong Bmem cell-driven antibody titers, and the CTD2 antibody was neutralizing in vitro, but its protection against lethal challenge with TcdB2 was limited to delaying time to death. Therefore, CTD from different C. difficile strains may be a good immunogen for stimulating B cell memory that encodes in vitro neutralizing Ab but may be limited by variable protection against intoxication in vivo. PMID:26502913

  8. Characterization of the Adherence of Clostridium difficile Spores: The Integrity of the Outermost Layer Affects Adherence Properties of Spores of the Epidemic Strain R20291 to Components of the Intestinal Mucosa

    PubMed Central

    Mora-Uribe, Paola; Miranda-Cárdenas, Camila; Castro-Córdova, Pablo; Gil, Fernando; Calderón, Iván; Fuentes, Juan A.; Rodas, Paula I.; Banawas, Saeed; Sarker, Mahfuzur R.; Paredes-Sabja, Daniel

    2016-01-01

    Clostridium difficile is the causative agent of the most frequently reported nosocomial diarrhea worldwide. The high incidence of recurrent infection is the main clinical challenge of C. difficile infections (CDI). Formation of C. difficile spores of the epidemic strain R20291 has been shown to be essential for recurrent infection and transmission of the disease in a mouse model. However, the underlying mechanisms of how these spores persist in the colonic environment remains unclear. In this work, we characterized the adherence properties of epidemic R20291 spores to components of the intestinal mucosa, and we assessed the role of the exosporium integrity in the adherence properties by using cdeC mutant spores with a defective exosporium layer. Our results showed that spores and vegetative cells of the epidemic R20291 strain adhered at high levels to monolayers of Caco-2 cells and mucin. Transmission electron micrographs of Caco-2 cells demonstrated that the hair-like projections on the surface of R20291 spores are in close proximity with the plasma membrane and microvilli of undifferentiated and differentiated monolayers of Caco-2 cells. Competitive-binding assay in differentiated Caco-2 cells suggests that spore-adherence is mediated by specific binding sites. By using spores of a cdeC mutant we demonstrated that the integrity of the exosporium layer determines the affinity of adherence of C. difficile spores to Caco-2 cells and mucin. Binding of fibronectin and vitronectin to the spore surface was concentration-dependent, and depending on the concentration, spore-adherence to Caco-2 cells was enhanced. In the presence of an aberrantly-assembled exosporium (cdeC spores), binding of fibronectin, but not vitronectin, was increased. Notably, independent of the exosporium integrity, only a fraction of the spores had fibronectin and vitronectin molecules binding to their surface. Collectively, these results demonstrate that the integrity of the exosporium layer of

  9. Metabolic engineering of Synechocystis sp. strain PCC 6803 for isobutanol production.

    PubMed

    Varman, Arul M; Xiao, Yi; Pakrasi, Himadri B; Tang, Yinjie J

    2013-02-01

    Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium Synechocystis sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl β-d-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer = 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed in situ removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions.

  10. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.

    PubMed

    Sun, Jie; Alper, Hal S

    2015-03-01

    A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.

  11. Biofuels and bio-based chemicals from lignocellulose: metabolic engineering strategies in strain development.

    PubMed

    Chen, Rachel; Dou, Jennifer

    2016-02-01

    Interest in developing a sustainable technology for fuels and chemicals has unleashed tremendous creativity in metabolic engineering for strain development over the last few years. This is driven by the exceptionally recalcitrant substrate, lignocellulose, and the necessity to keep the costs down for commodity products. Traditional methods of gene expression and evolutionary engineering are more effectively used with the help of synthetic biology and -omics techniques. Compared to the last biomass research peak during the 1980s oil crisis, a more diverse range of microorganisms are being engineered for a greater variety of products, reflecting the broad applicability and effectiveness of today's gene technology. We review here several prominent and successful metabolic engineering strategies with emphasis on the following four areas: xylose catabolism, inhibitor tolerance, synthetic microbial consortium, and cellulosic oligomer assimilation. PMID:26466596

  12. Strain engineering for mechanical properties in graphene nanoribbons revisited: The warping edge effect

    NASA Astrophysics Data System (ADS)

    Jiang, Jin-Wu

    2016-06-01

    We investigate the strain engineering and the edge effect for mechanical properties in graphene nanoribbons. The free edges of the graphene nanoribbons are warped due to compressive edge stresses. There is a structural transformation for the free edges from the three-dimensional warping configuration to the two-dimensional planar structure at the critical strain ɛc = 0.7%, at which the applied mechanical stress is equal to the intrinsic compressive edge stress. This structural transformation leads to step-like changes in several mechanical properties studied in the present work, including the Young's modulus, the Poisson's ratio, the quality factor of nanomechanical resonators, and the phonon edge mode.

  13. Engineering single-valley forward transport in strained graphene by magnetic-electric modulation

    NASA Astrophysics Data System (ADS)

    Wang, Yu

    2013-08-01

    Based on the distinct response of valley transport in graphene under the uniform strain, magnetic barrier, and electrostatic barrier manipulation, completely single-valley forward transport has been theoretically demonstrated by aligning deliberately the field profile of magnetic barrier and strain field. Further imposing electrostatic engineering, the receiving single-valley transport can be flexibly tuned to adapt much realistic field modulation, improve its ability to resist the temperature-induced thermal smooth, and even turn on or off this single-valley transport mode, displaying the appealing features for valleytronic device application.

  14. Electrically integrated SU-8 clamped graphene drum resonators for strain engineering

    NASA Astrophysics Data System (ADS)

    Lee, Sunwoo; Chen, Changyao; Deshpande, Vikram V.; Lee, Gwan-Hyoung; Lee, Ilkyu; Lekas, Michael; Gondarenko, Alexander; Yu, Young-Jun; Shepard, Kenneth; Kim, Philip; Hone, James

    2013-04-01

    Graphene mechanical resonators are the ultimate two-dimensional nanoelectromechanical systems (NEMS) with applications in sensing and signal processing. While initial devices have shown promising results, an ideal graphene NEMS resonator should be strain engineered, clamped at the edge without trapping gas underneath, and electrically integratable. In this Letter, we demonstrate fabrication and direct electrical measurement of circular SU-8 polymer-clamped chemical vapor deposition graphene drum resonators. The clamping increases device yield and responsivity, while providing a cleaner resonance spectrum from eliminated edge modes. Furthermore, the clamping induces a large strain in the resonator, increasing its resonant frequency.

  15. Clostridium Difficile Infections

    MedlinePlus

    Clostridium difficile (C. difficile) is a bacterium that causes diarrhea and more serious intestinal conditions such as colitis. Symptoms include Watery ... Nausea Abdominal pain or tenderness You might get C. difficile disease if you have an illness that ...

  16. Combining Protein and Strain Engineering for the Production of Glyco-Engineered Horseradish Peroxidase C1A in Pichia pastoris

    PubMed Central

    Capone, Simona; Ćorajević, Lejla; Bonifert, Günther; Murth, Patrick; Maresch, Daniel; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

    2015-01-01

    Horseradish peroxidase (HRP), conjugated to antibodies and lectins, is widely used in medical diagnostics. Since recombinant production of the enzyme is difficult, HRP isolated from plant is used for these applications. Production in the yeast Pichia pastoris (P. pastoris), the most promising recombinant production platform to date, causes hyperglycosylation of HRP, which in turn complicates conjugation to antibodies and lectins. In this study we combined protein and strain engineering to obtain an active and stable HRP variant with reduced surface glycosylation. We combined four mutations, each being beneficial for either catalytic activity or thermal stability, and expressed this enzyme variant as well as the unmutated wildtype enzyme in both a P. pastoris benchmark strain and a strain where the native α-1,6-mannosyltransferase (OCH1) was knocked out. Considering productivity in the bioreactor as well as enzyme activity and thermal stability, the mutated HRP variant produced in the P. pastoris benchmark strain turned out to be interesting for medical diagnostics. This variant shows considerable catalytic activity and thermal stability and is less glycosylated, which might allow more controlled and efficient conjugation to antibodies and lectins. PMID:26404235

  17. Engineering human neo-tendon tissue in vitro with human dermal fibroblasts under static mechanical strain.

    PubMed

    Deng, Dan; Liu, Wei; Xu, Feng; Yang, Yang; Zhou, Guangdong; Zhang, Wen Jie; Cui, Lei; Cao, Yilin

    2009-12-01

    Proper cell source is one of the key issues for tendon engineering. Our previous study showed that dermal fibroblasts could be used to successfully engineer tendon in vivo and tenocytes could engineer neo-tendon in vitro with static strain. This study further investigated the possibility of engineering human neo-tendon tissue in vitro using dermal fibroblasts. Human dermal fibroblasts were seeded on polyglycolic acid (PGA) fibers pre-fixed on a U-shape as a mechanical loading group, or simply cultured in a dish as a tension-free group. In addition, human tenocytes were also seeded on PGA fibers with tension as a comparison to human dermal fibroblasts. The results showed that human neo-tendon tissue could be generated using dermal fibroblasts during in vitro culture under static strain and the tissue structure became more mature with the increase of culture time. Longitudinally aligned collagen fibers and spindle shape cells were observed histologically and collagen fibril diameter and tensile strength increased with time and reached a peak at 14 weeks. In contrast, the dermal fibroblast-PGA constructs failed to form neo-tendon, but formed disorganized fibrous tissue in tension-free condition with significantly weaker strength and poor collagen fiber formation. Interestingly, neo-tendon tissues generated with human dermal fibroblasts were indistinguishable from the counterpart engineered with human tenocytes, which supports the viewpoint that human dermal fibroblasts is likely to replace tenocytes for future tendon graft development in vitro with dynamic mechanical loading in a bioreactor system.

  18. Clostridium difficile prevalence in an integrated swine operation in Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently there has been an epidemic of human disease in North America caused by the bacterium Clostridium difficile (Cd). It appears to be a new strain that is more virulent than previous strains, produces more toxins, and causes more severe disease (McDonald et al., 2005). The origin of the new s...

  19. A national survey of the molecular epidemiology of Clostridium difficile in Israel: the dissemination of the ribotype 027 strain with reduced susceptibility to vancomycin and metronidazole.

    PubMed

    Adler, Amos; Miller-Roll, Tamar; Bradenstein, Rita; Block, Colin; Mendelson, Bracha; Parizade, Miriam; Paitan, Yossi; Schwartz, David; Peled, Nehama; Carmeli, Yehuda; Schwaber, Mitchell J

    2015-09-01

    Our goals were to study the molecular epidemiology and antimicrobial susceptibilities of C. difficile strains in Israel. Microbiology laboratories serving 6 general hospitals (GH) and 10 long-term care facilities (LTCF) were asked to submit all stool samples in January-February 2014 that tested positive for C. difficile. Toxigenic C. difficile isolates were recovered in 208 out of 217 samples (95.8%), of which 50 (23.6%) were from LTCFs. Ribotype 027 was the most common type overall, identified in 65 samples (31.8%), and was the predominant strain in the 3 GHs with the highest incidence of C. difficile infections. Other common strains were slpA types cr-02 (n = 45) and hr-02 (n = 18). The proportions of vancomycin and metronidazole MIC values >2mg/L were high in ribotype 027 (87.7% and 44.6%, respectively) and slpA-cr-02 strains (88.8% and 17.8%, respectively). This study demonstrates that the ribotype 027 strain has disseminated across Israel and is now the most common strain.

  20. Multidrug-resistant North American pulsotype 2 Clostridium difficile was the predominant toxigenic hospital-acquired strain in the province of Manitoba, Canada, in 2006-2007.

    PubMed

    Karlowsky, James A; Zhanel, George G; Hammond, Greg W; Rubinstein, Ethan; Wylie, John; Du, Tim; Mulvey, Michael R; Alfa, Michelle J

    2012-05-01

    The objective of the current study was to determine whether the antimicrobial susceptibility profile or genotype of hospital-acquired isolates of Clostridium difficile differed from isolates causing community-acquired disease. Five hundred diarrhoeal stool samples (one >2 ml sample per patient) from patients across Manitoba, Canada, in 2006-2007 that were reported as C. difficile toxin positive were cultured, resulting in 432 isolates of toxin-positive C. difficile for analysis. Of these 432 isolates, acquisition status could be determined for 235 (54.4%); 182 (77.4%) isolates were hospital acquired and 53 (22.6%) were community acquired. North American pulsotype (NAP) designations based on SmaI PFGE could be defined for 52.3% of the 432 isolates, with NAP2 (n=122) being the most common. Ninety-one per cent (71/78) of NAP2 isolates were recovered from patients with hospital-acquired C. difficile disease. Other NAP types and isolates with non-NAP-type PFGE patterns were less frequently associated with hospital-acquired disease. Community-acquired disease (35.3% of isolates) was associated with a wide variety of NAP types. NAP2 isolates were homogeneous (85.5% had SmaI PFGE pattern 0003) and demonstrated low susceptibility to moxifloxacin (6.6%) and clindamycin (1.6%) compared with non-NAP2 isolates (64.1-93.2% moxifloxacin susceptible; 14.1-28.2% clindamycin susceptible). All isolates of C. difficile in Manitoba were susceptible to metronidazole, piperacillin-tazobactam, amoxicillin-clavulanate and meropenem. NAP2 isolates of toxigenic C. difficile were approximately three times more common than NAP1 isolates (28.2 vs 9.1%) in Manitoba in 2006-2007, and these isolates demonstrated high levels of clonality and multidrug resistance, and were associated with hospital acquisition. PMID:22301615

  1. Recovery of succinic acid produced by fermentation of a metabolically engineered Mannheimia succiniciproducens strain.

    PubMed

    Song, Hyohak; Huh, Yun Suk; Lee, Sang Yup; Hong, Won Hi; Hong, Yeon Ki

    2007-12-01

    There have recently been much advances in the production of succinic acid, an important four-carbon dicarboxylic acid for many industrial applications, by fermentation of several natural and engineered bacterial strains. Mannheimia succiniciproducens MBEL55E isolated from bovine rumen is able to produce succinic acid with high efficiency, but also produces acetic, formic and lactic acids just like other anaerobic succinic acid producers. We recently reported the development of an engineered M. succiniciproducens LPK7 strain which produces succinic acid as a major fermentation product while producing much reduced by-products. Having an improved succinic acid producer developed, it is equally important to develop a cost-effective downstream process for the recovery of succinic acid. In this paper, we report the development of a simpler and more efficient method for the recovery of succinic acid. For the recovery of succinic acid from the fermentation broth of LPK7 strain, a simple process composed of a single reactive extraction, vacuum distillation, and crystallization yielded highly purified succinic acid (greater than 99.5% purity, wt%) with a high yield of 67.05wt%. When the same recovery process or even multiple reactive extraction steps were applied to the fermentation broth of MBEL55E, lower purity and yield of succinic acid were obtained. These results suggest that succinic acid can be purified in a cost-effective manner by using the fermentation broth of engineered LPK7 strain, showing the importance of integrating the strain development, fermentation and downstream process for optimizing the whole processes for succinic acid production. PMID:17765349

  2. Room Temperature Semiconductor-Metal Transition of MoTe2 Thin Films Engineered by Strain.

    PubMed

    Song, Seunghyun; Keum, Dong Hoon; Cho, Suyeon; Perello, David; Kim, Yunseok; Lee, Young Hee

    2016-01-13

    We demonstrate a room temperature semiconductor-metal transition in thin film MoTe2 engineered by strain. Reduction of the 2H-1T' phase transition temperature of MoTe2 to room temperature was realized by introducing a tensile strain of 0.2%. The observed first-order SM transition improved conductance ∼10 000 times and was made possible by an unusually large temperature-stress coefficient, which results from a large volume change and small latent heat. The demonstrated strain-modulation of the phase transition temperature is expected to be compatible with other TMDs enabling the 2D electronics utilizing polymorphism of TMDs along with the established materials. PMID:26713902

  3. Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering

    PubMed Central

    Derntl, Christian; Kiesenhofer, Daniel P.; Mach, Robert L.

    2015-01-01

    The state-of-the-art procedure for gene insertions into Trichoderma reesei is a cotransformation of two plasmids, one bearing the gene of interest and the other a marker gene. This procedure yields up to 80% transformation efficiency, but both the number of integrated copies and the loci of insertion are unpredictable. This can lead to tremendous pleiotropic effects. This study describes the development of a novel transformation system for site-directed gene insertion based on auxotrophic markers. For this purpose, we tested the applicability of the genes asl1 (encoding an enzyme of the l-arginine biosynthesis pathway), the hah1 (encoding an enzyme of the l-lysine biosynthesis pathway), and the pyr4 (encoding an enzyme of the uridine biosynthesis pathway). The developed transformation system yields strains with an additional gene at a defined locus that are prototrophic and ostensibly isogenic compared to their parental strain. A positive transformation rate of 100% was achieved due to the developed split-marker system. Additionally, a double-auxotrophic strain that allows multiple genomic manipulations was constructed, which facilitates metabolic engineering purposes in T. reesei. By employing goxA of Aspergillus niger as a reporter system, the influence on the expression of an inserted gene caused by the orientation of the insertion and the transformation strategy used could be demonstrated. Both are important aspects to be considered during strain engineering. PMID:26150462

  4. Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering

    PubMed Central

    2010-01-01

    Background Cost-effective fermentation of lignocellulosic hydrolysate to ethanol by Saccharomyces cerevisiae requires efficient mixed sugar utilization. Notably, the rate and yield of xylose and arabinose co-fermentation to ethanol must be enhanced. Results Evolutionary engineering was used to improve the simultaneous conversion of xylose and arabinose to ethanol in a recombinant industrial Saccharomyces cerevisiae strain carrying the heterologous genes for xylose and arabinose utilization pathways integrated in the genome. The evolved strain TMB3130 displayed an increased consumption rate of xylose and arabinose under aerobic and anaerobic conditions. Improved anaerobic ethanol production was achieved at the expense of xylitol and glycerol but arabinose was almost stoichiometrically converted to arabitol. Further characterization of the strain indicated that the selection pressure during prolonged continuous culture in xylose and arabinose medium resulted in the improved transport of xylose and arabinose as well as increased levels of the enzymes from the introduced fungal xylose pathway. No mutation was found in any of the genes from the pentose converting pathways. Conclusion To the best of our knowledge, this is the first report that characterizes the molecular mechanisms for improved mixed-pentose utilization obtained by evolutionary engineering of a recombinant S. cerevisiae strain. Increased transport of pentoses and increased activities of xylose converting enzymes contributed to the improved phenotype. PMID:20550651

  5. Metabolic engineering of Corynebacterium glutamicum strain ATCC13032 to produce L-methionine.

    PubMed

    Qin, Tianyu; Hu, Xiaoqing; Hu, Jinyu; Wang, Xiaoyuan

    2015-01-01

    L-Methionine-producing strain QW102/pJYW-4-hom(m) -lysC(m) -brnFE was developed from Corynebacterium glutamicum strain ATCC13032, using metabolic engineering strategies. These strategies involved (i) deletion of the gene thrB encoding homoserine kinase to increase the precursor supply, (ii) deletion of the gene mcbR encoding the regulator McbR to release the transcriptional repression to various genes in the l-methionine biosynthetic pathway, (iii) overexpression of the gene lysC(m) encoding feedback-resistant aspartate kinase and the gene hom(m) encoding feedback-resistant homoserine dehydrogenase to further increase the precursor supply, and (iv) overexpression of the gene cluster brnF and brnE encoding the export protein complex BrnFE to increase extracellular l-methionine concentration. QW102/pJYW-4-hom(m) -lysC(m) -brnFE produced 42.2 mM (6.3 g/L) l-methionine after 64-H fed-batch fermentation. These results suggest that l-methionine-producing strains can be developed from wild-type C. glutamicum strains by rationally metabolic engineering.

  6. Monolithically Integrated Microelectromechanical Systems for On-Chip Strain Engineering of Quantum Dots.

    PubMed

    Zhang, Yang; Chen, Yan; Mietschke, Michael; Zhang, Long; Yuan, Feifei; Abel, Stefan; Hühne, Ruben; Nielsch, Kornelius; Fompeyrine, Jean; Ding, Fei; Schmidt, Oliver G

    2016-09-14

    Elastic strain fields based on single crystal piezoelectric elements represent an effective way for engineering the quantum dot (QD) emission with unrivaled precision and technological relevance. However, pioneering researches in this direction were mainly based on bulk piezoelectric substrates, which prevent the development of chip-scale devices. Here, we present a monolithically integrated Microelectromechanical systems (MEMS) device with great potential for on-chip quantum photonic applications. High-quality epitaxial PMN-PT thin films have been grown on SrTiO3 buffered Si and show excellent piezoelectric responses. Dense arrays of MEMS with small footprints are then fabricated based on these films, forming an on-chip strain tuning platform. After transferring the QD-containing nanomembranes onto these MEMS, the nonclassical emissions (e.g., single photons) from single QDs can be engineered by the strain fields. We envision that the strain tunable QD sources on the individually addressable and monolithically integrated MEMS pave the way toward complex quantum photonic applications on chip. PMID:27574953

  7. Novel Clostridium difficile Anti-Toxin (TcdA and TcdB) Humanized Monoclonal Antibodies Demonstrate In Vitro Neutralization across a Broad Spectrum of Clinical Strains and In Vivo Potency in a Hamster Spore Challenge Model

    PubMed Central

    Qiu, Hongyu; Cassan, Robyn; Johnstone, Darrell; Han, Xiaobing; Joyee, Antony George; McQuoid, Monica; Masi, Andrea; Merluza, John; Hrehorak, Bryce; Reid, Ross; Kennedy, Kieron; Tighe, Bonnie; Rak, Carla; Leonhardt, Melanie; Dupas, Brian; Saward, Laura; Berry, Jody D.; Nykiforuk, Cory L.

    2016-01-01

    Clostridium difficile (C. difficile) infection (CDI) is the main cause of nosocomial antibiotic-associated colitis and increased incidence of community-associated diarrhea in industrialized countries. At present, the primary treatment of CDI is antibiotic administration, which is effective but often associated with recurrence, especially in the elderly. Pathogenic strains produce enterotoxin, toxin A (TcdA), and cytotoxin, toxin B (TcdB), which are necessary for C. difficile induced diarrhea and gut pathological changes. Administration of anti-toxin antibodies provides an alternative approach to treat CDI, and has shown promising results in preclinical and clinical studies. In the current study, several humanized anti-TcdA and anti-TcdB monoclonal antibodies were generated and their protective potency was characterized in a hamster infection model. The humanized anti-TcdA (CANmAbA4) and anti-TcdB (CANmAbB4 and CANmAbB1) antibodies showed broad spectrum in vitro neutralization of toxins from clinical strains and neutralization in a mouse toxin challenge model. Moreover, co-administration of humanized antibodies (CANmAbA4 and CANmAbB4 cocktail) provided a high level of protection in a dose dependent manner (85% versus 57% survival at day 22 for 50 mg/kg and 20 mg/kg doses, respectively) in a hamster gastrointestinal infection (GI) model. This study describes the protective effects conferred by novel neutralizing anti-toxin monoclonal antibodies against C. difficile toxins and their potential as therapeutic agents in treating CDI. PMID:27336843

  8. Novel Clostridium difficile Anti-Toxin (TcdA and TcdB) Humanized Monoclonal Antibodies Demonstrate In Vitro Neutralization across a Broad Spectrum of Clinical Strains and In Vivo Potency in a Hamster Spore Challenge Model.

    PubMed

    Qiu, Hongyu; Cassan, Robyn; Johnstone, Darrell; Han, Xiaobing; Joyee, Antony George; McQuoid, Monica; Masi, Andrea; Merluza, John; Hrehorak, Bryce; Reid, Ross; Kennedy, Kieron; Tighe, Bonnie; Rak, Carla; Leonhardt, Melanie; Dupas, Brian; Saward, Laura; Berry, Jody D; Nykiforuk, Cory L

    2016-01-01

    Clostridium difficile (C. difficile) infection (CDI) is the main cause of nosocomial antibiotic-associated colitis and increased incidence of community-associated diarrhea in industrialized countries. At present, the primary treatment of CDI is antibiotic administration, which is effective but often associated with recurrence, especially in the elderly. Pathogenic strains produce enterotoxin, toxin A (TcdA), and cytotoxin, toxin B (TcdB), which are necessary for C. difficile induced diarrhea and gut pathological changes. Administration of anti-toxin antibodies provides an alternative approach to treat CDI, and has shown promising results in preclinical and clinical studies. In the current study, several humanized anti-TcdA and anti-TcdB monoclonal antibodies were generated and their protective potency was characterized in a hamster infection model. The humanized anti-TcdA (CANmAbA4) and anti-TcdB (CANmAbB4 and CANmAbB1) antibodies showed broad spectrum in vitro neutralization of toxins from clinical strains and neutralization in a mouse toxin challenge model. Moreover, co-administration of humanized antibodies (CANmAbA4 and CANmAbB4 cocktail) provided a high level of protection in a dose dependent manner (85% versus 57% survival at day 22 for 50 mg/kg and 20 mg/kg doses, respectively) in a hamster gastrointestinal infection (GI) model. This study describes the protective effects conferred by novel neutralizing anti-toxin monoclonal antibodies against C. difficile toxins and their potential as therapeutic agents in treating CDI. PMID:27336843

  9. Cultures of "Clostridium acetobutylicum" from various collections comprise Clostridium acetobutylicum, Clostridium beijerinckii, and two other distinct types based on DNA-DNA reassociation.

    PubMed

    Johnson, J L; Toth, J; Santiwatanakul, S; Chen, J S

    1997-04-01

    The best-known acetone-butanol (solvent)-producing bacterium is the Weizmann organism, Clostridium acetobutylicum, which was used for starch-based industrial fermentation. In the past two decades, cultures of "C. acetobutylicum" from various culture collections have included organisms that were isolated for sugar (molasses)-based industrial solvent production. Recent biochemical and genetic studies have revealed significant differences among some of these "C. acetobutylicum" strains. We used DNA-DNA reassociation to analyze 39 cultures of "C. acetobutylicum" and phenotypically similar organisms from major collections. The results of this study clearly identified four groups intergroup reassociation values of less than 30%. All of the intragroup values except the value for one strain were 68% or more, which supported species status for each group. The C. acetobutylicum group (with ATCC 824 as the type strain) consisted of 17 cultures and had average reassociation values of 10% with the other three groups. All strains of C. acetobutylicum produced riboflavin in milk, and the cultures were bright yellow, which is useful for differentiating this species from the other three groups. The Clostridium beijerinckii group (with VPI 5481 [= ATCC 25752] as the type strain) consisted of 16 cultures and included strains NCIMB 8052 and NCP 270. Strains NCP 262 and NRRL B643 constituted the third group, whereas strain N1-4 ("Clostridium saccharoperbutylacetonicum") and its derivative, strain N1-4081, formed the fourth group. At present, the last two groups are each represented by only one independent strain; definitive descriptions of these two groups as two new or revived species will require further phenotypic characterization, as well as identification of additional strains. C. beijerinckii NCP 270, Clostridium sp. strain NRRL B643, and "C. saccharoperbutylacetonicum" were used in industrial solvent production from molasses, which confirms that the new organisms used for the

  10. Acetone-butanol-ethanol fermentation of corn stover by Clostridium species: present status and future perspectives.

    PubMed

    Li, Jianzheng; Baral, Nawa Raj; Jha, Ajay Kumar

    2014-04-01

    Sustainable vehicle fuel is indispensable in future due to worldwide depletion of fossil fuel reserve, oil price fluctuation and environmental degradation. Microbial production of butanol from renewable biomass could be one of the possible options. Renewable biomass such as corn stover has no food deficiency issues and is also cheaper in most of the agricultural based countries. Thus it can effectively solve the existing issue of substrate cost. In the last 30 years, a few of Clostridium strains have been successfully implemented for biobutanol fermentation. However, the commercial production is hindered due to their poor tolerance to butanol and inhibitors. Metabolic engineering of Clostridia strains is essential to solve above problems and ultimately enhance the solvent production. An effective and efficient pretreatment of raw material as well as optimization of fermentation condition could be another option. Furthermore, biological approaches may be useful to optimize both the host and pathways to maximize butanol production. In this context, this paper reviews the existing Clostridium strains and their ability to produce butanol particularly from corn stover. This study also highlights possible fermentation pathways and biological approaches that may be useful to optimize fermentation pathways. Moreover, challenges and future perspectives are also discussed.

  11. MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

    PubMed

    Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

    2016-08-01

    All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species.

  12. MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

    PubMed

    Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

    2016-08-01

    All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species. PMID:27296834

  13. High strain rate and high temperature behaviour of metallic materials for jet engine turbine containment

    NASA Astrophysics Data System (ADS)

    Gálvez, F.; Cendón, D.; Enfedaque, A.; Sánchez-Gálvez, V.

    2006-08-01

    This work presents a study on the mechanical characterisation of the materials involved in air jet engine turbines. The final objective is to analyse the phenomenon of a turbine blade off failure, to verify the requirements of the case containment. The materials in the turbine are under high temperatures, ranging from 400circC to 800circC and when the fail of the blade occurs if impacts against the case, reaching strain rates up to 103 s - 1. To obtain the behaviour of the materials, testing at high strain rate and high temperature at one time is necessary. The experimental set-up used was a split Hopkinson pressure bar, with a high temperature furnace adapted. The bars used on the device were high strength nickel alloys with a cooling system to decrease the temperature of the measurement devices. The effect of wave dispersion due to the temperature gradient has been also studied to correct the measurements if necessary. The material tested has been the FV535 stainless steel used on the case. The full stress-strain curves at different temperatures and at strain rates up to 103 s-1 have been obtained. The experimental results show a marked influence of the strain rate and the temperature that cannot be neglected. The Johnson-Cook material model has been used to fit the results of the material tests.

  14. Effect of growth rate on plasmid DNA production and metabolic performance of engineered Escherichia coli strains.

    PubMed

    Wunderlich, Martin; Taymaz-Nikerel, Hilal; Gosset, Guillermo; Ramírez, Octavio T; Lara, Alvaro R

    2014-03-01

    Two engineered Escherichia coli strains, designated VH33 and VH34, were compared to their parent strain W3110 in chemostat mode during plasmid DNA (pDNA) production. In strain VH33 the glucose uptake system was modified with the aim of reducing overflow metabolism. The strain VH34 has an additional deletion of the pyruvate kinase A gene (pykA) to increase pDNA formation. pDNA formation rates as well as kinetic and stoichiometric parameters were investigated in dependence of the growth rate within a range from 0.02 to 0.25 h(-1). Differences between strains were found in terms of the biomass yields on nitrogen and oxygen, as well as on the cell maintenance coefficients. The deletion of pykA led to a significantly increased pDNA yield and productivity. At an optimal growth rate of 0.20 h(-1) it was nearly 60% higher than that of W3110 and VH33. Metabolic fluxes calculated by metabolite balance analysis showed differences mainly in reactions catalyzed by pyruvate kinase and glucose 6-phosphate dehydrogenase. The obtained data are useful for the design of cultivation schemes for pDNA production by E. coli. PMID:24012107

  15. Strain engineering of selective chemical adsorption on monolayer MoS2.

    PubMed

    Kou, Liangzhi; Du, Aijun; Chen, Changfeng; Frauenheim, Thomas

    2014-05-21

    Nanomaterials are prone to influence by chemical adsorption because of their large surface to volume ratios. This enables sensitive detection of adsorbed chemical species which, in turn, can tune the properties of the host material. Recent studies discovered that single and multi-layer molybdenum disulfide (MoS2) films are ultra-sensitive to several important environmental molecules. Here we report new findings from ab inito calculations that reveal substantially enhanced adsorption of NO and NH3 on strained monolayer MoS2 with significant impact on the properties of the adsorbates and the MoS2 layer. The magnetic moment of adsorbed NO can be tuned between 0 and 1 μB; strain also induces an electronic phase transition between the half-metal and the metal. Adsorption of NH3 weakens the MoS2 layer considerably, which explains the large discrepancy between the experimentally measured strength and breaking strain of MoS2 films and previous theoretical predictions. On the other hand, adsorption of NO2, CO, and CO2 is insensitive to the strain conditions in the MoS2 layer. This contrasting behavior allows sensitive strain engineering of selective chemical adsorption on MoS2 with effective tuning of mechanical, electronic, and magnetic properties. These results suggest new design strategies for constructing MoS2-based ultrahigh-sensitivity nanoscale sensors and electromechanical devices.

  16. Tuning the optical, magnetic, and electrical properties of ReSe2 by nanoscale strain engineering.

    PubMed

    Yang, Shengxue; Wang, Cong; Sahin, Hasan; Chen, Hui; Li, Yan; Li, Shu-Shen; Suslu, Aslihan; Peeters, Francois M; Liu, Qian; Li, Jingbo; Tongay, Sefaattin

    2015-03-11

    Creating materials with ultimate control over their physical properties is vital for a wide range of applications. From a traditional materials design perspective, this task often requires precise control over the atomic composition and structure. However, owing to their mechanical properties, low-dimensional layered materials can actually withstand a significant amount of strain and thus sustain elastic deformations before fracture. This, in return, presents a unique technique for tuning their physical properties by "strain engineering". Here, we find that local strain induced on ReSe2, a new member of the transition metal dichalcogenides family, greatly changes its magnetic, optical, and electrical properties. Local strain induced by generation of wrinkle (1) modulates the optical gap as evidenced by red-shifted photoluminescence peak, (2) enhances light emission, (3) induces magnetism, and (4) modulates the electrical properties. The results not only allow us to create materials with vastly different properties at the nanoscale, but also enable a wide range of applications based on 2D materials, including strain sensors, stretchable electrodes, flexible field-effect transistors, artificial-muscle actuators, solar cells, and other spintronic, electromechanical, piezoelectric, photonic devices.

  17. Toxin plasmids of Clostridium perfringens.

    PubMed

    Li, Jihong; Adams, Vicki; Bannam, Trudi L; Miyamoto, Kazuaki; Garcia, Jorge P; Uzal, Francisco A; Rood, Julian I; McClane, Bruce A

    2013-06-01

    In both humans and animals, Clostridium perfringens is an important cause of histotoxic infections and diseases originating in the intestines, such as enteritis and enterotoxemia. The virulence of this Gram-positive, anaerobic bacterium is heavily dependent upon its prolific toxin-producing ability. Many of the ∼16 toxins produced by C. perfringens are encoded by large plasmids that range in size from ∼45 kb to ∼140 kb. These plasmid-encoded toxins are often closely associated with mobile elements. A C. perfringens strain can carry up to three different toxin plasmids, with a single plasmid carrying up to three distinct toxin genes. Molecular Koch's postulate analyses have established the importance of several plasmid-encoded toxins when C. perfringens disease strains cause enteritis or enterotoxemias. Many toxin plasmids are closely related, suggesting a common evolutionary origin. In particular, most toxin plasmids and some antibiotic resistance plasmids of C. perfringens share an ∼35-kb region containing a Tn916-related conjugation locus named tcp (transfer of clostridial plasmids). This tcp locus can mediate highly efficient conjugative transfer of these toxin or resistance plasmids. For example, conjugative transfer of a toxin plasmid from an infecting strain to C. perfringens normal intestinal flora strains may help to amplify and prolong an infection. Therefore, the presence of toxin genes on conjugative plasmids, particularly in association with insertion sequences that may mobilize these toxin genes, likely provides C. perfringens with considerable virulence plasticity and adaptability when it causes diseases originating in the gastrointestinal tract.

  18. Recombinant protein expression in Pichia pastoris strains with an engineered methanol utilization pathway

    PubMed Central

    2012-01-01

    Βackground The methylotrophic yeast Pichia pastoris has become an important host organism for recombinant protein production and is able to use methanol as a sole carbon source. The methanol utilization pathway describes all the catalytic reactions, which happen during methanol metabolism. Despite the importance of certain key enzymes in this pathway, so far very little is known about possible effects of overexpressing either of these key enzymes on the overall energetic behavior, the productivity and the substrate uptake rate in P. pastoris strains. Results A fast and easy-to-do approach based on batch cultivations with methanol pulses was used to characterize different P. pastoris strains. A strain with MutS phenotype was found to be superior over a strain with Mut+ phenotype in both the volumetric productivity and the efficiency in expressing recombinant horseradish peroxidase C1A. Consequently, either of the enzymes dihydroxyacetone synthase, transketolase or formaldehyde dehydrogenase, which play key roles in the methanol utilization pathway, was co-overexpressed in MutS strains harboring either of the reporter enzymes horseradish peroxidase or Candida antarctica lipase B. Although the co-overexpression of these enzymes did not change the stoichiometric yields of the recombinant MutS strains, significant changes in the specific growth rate, the specific substrate uptake rate and the specific productivity were observed. Co-overexpression of dihydroxyacetone synthase yielded a 2- to 3-fold more efficient conversion of the substrate methanol into product, but also resulted in a reduced volumetric productivity. Co-overexpression of formaldehyde dehydrogenase resulted in a 2-fold more efficient conversion of the substrate into product and at least similar volumetric productivities compared to strains without an engineered methanol utilization pathway, and thus turned out to be a valuable strategy to improve recombinant protein production. Conclusions Co

  19. Clostridium difficile in paediatric populations

    PubMed Central

    Allen, Upton D

    2014-01-01

    An increase in Clostridium difficile infection incidence has been observed among hospitalized children in the United States. The present statement, targeted at clinicians caring for infants and children in community and institutional settings, summarizes the relevant information relating to the role of C difficile in childhood diarrhea and provides recommendations for diagnosis, prevention and treatment. Significant differences between adult and paediatric risk factors and disease are discussed, along with emerging therapies. The relationship between age and disease severity in children with a newly emergent and more fluoroqinolone-resistant strain of C difficile (North American Pulse-field type-1 [NAP1]) remains unknown. The importance of antimicrobial stewardship as a preventive strategy is highlighted. This statement replaces a previous Canadian Paediatric Society position statement on C difficile published in 2000. PMID:24627655

  20. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

    DOE PAGES

    Dash, Satyakam; Mueller, Thomas J.; Venkataramanan, Keerthi P.; Papoutsakis, Eleftherios T.; Maranas, Costas D.

    2014-10-14

    Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.

  1. Ultrasound Elastography for Estimation of Regional Strain of Multilayered Hydrogels and Tissue-Engineered Cartilage.

    PubMed

    Chung, Chen-Yuan; Heebner, Joseph; Baskaran, Harihara; Welter, Jean F; Mansour, Joseph M

    2015-12-01

    Tissue-engineered (TE) cartilage constructs tend to develop inhomogeneously, thus, to predict the mechanical performance of the tissue, conventional biomechanical testing, which yields average material properties, is of limited value. Rather, techniques for evaluating regional and depth-dependent properties of TE cartilage, preferably non-destructively, are required. The purpose of this study was to build upon our previous results and to investigate the feasibility of using ultrasound elastography to non-destructively assess the depth-dependent biomechanical characteristics of TE cartilage while in a sterile bioreactor. As a proof-of-concept, and to standardize an assessment protocol, a well-characterized three-layered hydrogel construct was used as a surrogate for TE cartilage, and was studied under controlled incremental compressions. The strain field of the construct predicted by elastography was then validated by comparison with a poroelastic finite-element analysis (FEA). On average, the differences between the strains predicted by elastography and the FEA were within 10%. Subsequently engineered cartilage tissue was evaluated in the same test fixture. Results from these examinations showed internal regions where the local strain was 1-2 orders of magnitude greater than that near the surface. These studies document the feasibility of using ultrasound to evaluate the mechanical behaviors of maturing TE constructs in a sterile environment.

  2. Band structure engineering via piezoelectric fields in strained anisotropic CdSe/CdS nanocrystals

    PubMed Central

    Christodoulou, Sotirios; Rajadell, Fernando; Casu, Alberto; Vaccaro, Gianfranco; Grim, Joel Q.; Genovese, Alessandro; Manna, Liberato; Climente, Juan I.; Meinardi, Francesco; Rainò, Gabriele; Stöferle, Thilo; Mahrt, Rainer F.; Planelles, Josep; Brovelli, Sergio; Moreels, Iwan

    2015-01-01

    Strain in colloidal heteronanocrystals with non-centrosymmetric lattices presents a unique opportunity for controlling optoelectronic properties and adds a new degree of freedom to existing wavefunction engineering and doping paradigms. We synthesized wurtzite CdSe nanorods embedded in a thick CdS shell, hereby exploiting the large lattice mismatch between the two domains to generate a compressive strain of the CdSe core and a strong piezoelectric potential along its c-axis. Efficient charge separation results in an indirect ground-state transition with a lifetime of several microseconds, almost one order of magnitude longer than any other CdSe/CdS nanocrystal. Higher excited states recombine radiatively in the nanosecond time range, due to increasingly overlapping excited-state orbitals. k̇p calculations confirm the importance of the anisotropic shape and crystal structure in the buildup of the piezoelectric potential. Strain engineering thus presents an efficient approach to highly tunable single- and multiexciton interactions, driven by a dedicated core/shell nanocrystal design. PMID:26219691

  3. Band structure engineering via piezoelectric fields in strained anisotropic CdSe/CdS nanocrystals.

    PubMed

    Christodoulou, Sotirios; Rajadell, Fernando; Casu, Alberto; Vaccaro, Gianfranco; Grim, Joel Q; Genovese, Alessandro; Manna, Liberato; Climente, Juan I; Meinardi, Francesco; Rainò, Gabriele; Stöferle, Thilo; Mahrt, Rainer F; Planelles, Josep; Brovelli, Sergio; Moreels, Iwan

    2015-07-29

    Strain in colloidal heteronanocrystals with non-centrosymmetric lattices presents a unique opportunity for controlling optoelectronic properties and adds a new degree of freedom to existing wavefunction engineering and doping paradigms. We synthesized wurtzite CdSe nanorods embedded in a thick CdS shell, hereby exploiting the large lattice mismatch between the two domains to generate a compressive strain of the CdSe core and a strong piezoelectric potential along its c-axis. Efficient charge separation results in an indirect ground-state transition with a lifetime of several microseconds, almost one order of magnitude longer than any other CdSe/CdS nanocrystal. Higher excited states recombine radiatively in the nanosecond time range, due to increasingly overlapping excited-state orbitals. k˙p calculations confirm the importance of the anisotropic shape and crystal structure in the buildup of the piezoelectric potential. Strain engineering thus presents an efficient approach to highly tunable single- and multiexciton interactions, driven by a dedicated core/shell nanocrystal design.

  4. A Pseudomonas putida Strain Genetically Engineered for 1,2,3-Trichloropropane Bioremediation

    PubMed Central

    Samin, Ghufrana; Pavlova, Martina; Arif, M. Irfan; Postema, Christiaan P.; Damborsky, Jiri

    2014-01-01

    1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacterium Pseudomonas putida MC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutive dhlA promoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium, P. putida MC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon. PMID:24973068

  5. An Update on Clostridium difficile Toxinotyping

    PubMed Central

    Janezic, Sandra

    2015-01-01

    Toxinotyping is a PCR-restriction fragment length polymorphism (RFLP)-based method for differentiation of Clostridium difficile strains according to the changes in the pathogenicity locus (PaLoc), a region coding for toxins A and B. Toxinotypes are a heterogenous group of strains that are important in the development of molecular diagnostic tests and vaccines and are a good basis for C. difficile phylogenetic studies. Here we describe an overview of the 34 currently known toxinotypes (I to XXXIV) and some changes in nomenclature. PMID:26511734

  6. [Construction and evaluation of an engineered bacterial strain for producing lipopeptide under anoxic conditions].

    PubMed

    Liang, Xiao-long; Zhao, Feng; Shi, Rong-jiu; Ban, Yun-he; Zhou, Ji-dong; Han, Si-qin; Zhang, Ying

    2015-08-01

    Biosurfactant-facilitated oil recovery is one of the most important aspects of microbial enhanced oil recovery (MEOR). However, the biosurfactant production by biosurfactant-producing microorganisms, most of which are aerobes, is severely suppressed due to the in-situ anoxic conditions within oil reservoirs. In this research, we successfully engineered a strain JD-3, which could grow rapidly and produce lipopeptide under anoxic conditions, by protoplast confusion using a Bacillus amyloliquefaciens strain BQ-2 which produces biosurfactant aerobically, and a facultative anaerobic Pseudomonas stutzeri strain DQ-1 as parent strains. The alignment of 16S rDNA sequence (99% similarity) and comparisons of cell colony morphology showed that fusant JD-3 was closer to the parental strain B. amyloliquefaciens BQ-2. The surface tension of culture broth of fusant JD-3, after 36-hour cultivation under anaerobic conditions, decreased from initially 63.0 to 32.5 mN · m(-1). The results of thin layer chromatography and infrared spectrum analysis demonstrated that the biosurfactant produced by JD-3 was lipopeptide. The surface-active lipopeptide had a low critical micelle concentration (CMC) of 90 mg · L(-1) and presented a good ability to emulsify various hydrocarbons such as crude oil, liquid paraffin, and kerosene. Strain JD-3 could utilize peptone as nitrogen source and sucrose, glucose, glycerin or other common organics as carbon sources for anaerobic lipopeptide synthesis. The subculture of fusant JD-3 showed a stable lipopeptide-producing ability even after ten serial passages. All these results indicated that fusant JD-3 holds a great potential to microbially enhance oil recovery under anoxic conditions. PMID:26685621

  7. Evaluation results of the 700 deg C Chinese strain gauges. [for gas turbine engine

    NASA Technical Reports Server (NTRS)

    Hobart, H. F.

    1985-01-01

    Gauges fabricated from specially developed Fe-Cr-Al-V-Ti-Y alloy wire in the Republic of China were evaluated for use in static strain measurement of hot gas turbine engines. Gauge factor variation with temperature, apparent strain, and drift were included. Results of gauge factor versus temperature tests show gauge factor decreasing with increasing temperature. The average slope is -3-1/2 percent/100 K, with an uncertainty band of + or - 8 percent. Values of room temperature gauge factor for the Chinese and Kanthal A-1 gauges averaged 2.73 and 2.12, respectively. The room temperature gauge factor of the Chinese gauges was specified to be 2.62. The apparent strain data for both the Chinese alloy and Kanthal A-1 showed large cycle to cycle nonrepeatability. All apparent strain curves had a similar S-shape, first going negative and then rising to positive value with increasing temperatures. The mean curve for the Chinese gauges between room temperature and 100 K had a total apparent strain of 1500 microstrain. The equivalent value for Kanthal A-1 was about 9000 microstrain. Drift tests at 950 K for 50 hr show an average drift rate of about -9 microstrain/hr. Short-term (1 hr) rates are higher, averaging about -40 microstrain for the first hour. In the temperature range 700 to 870 K, however, short-term drift rates can be as high as 1700 microstrain for the first hour. Therefore, static strain measurements in this temperature range should be avoided.

  8. Strain-engineered diffusive atomic switching in two-dimensional crystals

    PubMed Central

    Kalikka, Janne; Zhou, Xilin; Dilcher, Eric; Wall, Simon; Li, Ju; Simpson, Robert E.

    2016-01-01

    Strain engineering is an emerging route for tuning the bandgap, carrier mobility, chemical reactivity and diffusivity of materials. Here we show how strain can be used to control atomic diffusion in van der Waals heterostructures of two-dimensional (2D) crystals. We use strain to increase the diffusivity of Ge and Te atoms that are confined to 5 Å thick 2D planes within an Sb2Te3–GeTe van der Waals superlattice. The number of quintuple Sb2Te3 2D crystal layers dictates the strain in the GeTe layers and consequently its diffusive atomic disordering. By identifying four critical rules for the superlattice configuration we lay the foundation for a generalizable approach to the design of switchable van der Waals heterostructures. As Sb2Te3–GeTe is a topological insulator, we envision these rules enabling methods to control spin and topological properties of materials in reversible and energy efficient ways. PMID:27329563

  9. Single photons on-demand from light-hole excitons in strain-engineered quantum dots.

    PubMed

    Zhang, Jiaxiang; Huo, Yongheng; Rastelli, Armando; Zopf, Michael; Höfer, Bianca; Chen, Yan; Ding, Fei; Schmidt, Oliver G

    2015-01-14

    We demonstrate for the first time on-demand and wavelength-tunable single-photon emission from light-hole (LH) excitons in strain engineered GaAs quantum dots (QDs). The LH photon emission from tensile-strained GaAs QDs is systematically investigated with polarization-resolved, power-dependent photoluminescence spectroscopy, and photon-correlation measurements. By integrating QD-containing nanomembranes onto a piezo-actuator and driving single QDs with picosecond laser pulses, we achieve triggered and wavelength-tunable LH single-photon emission. Fourier transform spectroscopy is also performed, from which the coherence time of the LH single-photon emission is studied. We envision that this new type of LH exciton-based single-photon source (SPS) can be applied to realize an all-semiconductor based quantum interface in distributed quantum networks [Phys. Rev. Lett. 2008, 100, 096602]. PMID:25471544

  10. Chronic septic arthritis and osteomyelitis in a prosthetic knee joint due to Clostridium difficile.

    PubMed

    Pron, B; Merckx, J; Touzet, P; Ferroni, A; Poyart, C; Berche, P; Gaillard, J L

    1995-07-01

    A case of chronic septic arthritis and osteomyelitis in a prosthetic knee joint due to Clostridium difficile is reported. A knee prosthesis was installed in a 16-year-old boy for surgical treatment of an osteosarcoma of the femur. Later, the patient suffered a traumatic closed fracture of his patella, and a sterile fluid was aspirated. One month later, the joint displayed inflammation. Culture of the articular fluid yielded a nontoxigenic Clostridium difficile strain. Despite several attempts using conservative medical treatment with penicillins and ornidazole, Clostridium difficile strains with the same antibiotic susceptibility pattern were repeatedly isolated from the joint over an eight-month period. The foreign material was then ablated, and finally, the patient's leg was amputated one year after Clostridium difficile was first isolated. The possible sources of contamination in our case and other reported cases of extraintestinal infection due to Clostridium difficile are discussed.

  11. Three new milbemycins from a genetically engineered strain S. avermitilis MHJ1011.

    PubMed

    Pan, Jun-jie; Wan, Xu; Zhang, Hui; Chen, Zhen; Huang, Jun; Yang, Bo; Chen, An-liang; Wang, Ji-dong

    2016-02-01

    Three new β-class milbemycins, 13α-hydroxy-4-ethy1 milbemycin β3 (1), 13α-hydroxy-25-ethy1 milbemycin β3 (2), 13α-hydroxy milbemycin β3 (3), were isolated from the broth of the genetically engineered strains Streptomyces avermitilis MHJ1011, whose aveA1 gene was replaced by milA1 gene seamlessly. Their structures were determined on the basis of extensive spectroscopic analysis and comparison with data from the literature. These three compounds, especially compound 1, exhibited potent acaricidal activity. PMID:26328934

  12. Escherichia coli strains engineered for homofermentative production of D-lactic acid from glycerol.

    PubMed

    Mazumdar, Suman; Clomburg, James M; Gonzalez, Ramon

    2010-07-01

    Given its availability and low price, glycerol has become an ideal feedstock for the production of fuels and chemicals. We recently reported the pathways mediating the metabolism of glycerol in Escherichia coli under anaerobic and microaerobic conditions. In this work, we engineer E. coli for the efficient conversion of glycerol to d-lactic acid (d-lactate), a negligible product of glycerol metabolism in wild-type strains. A homofermentative route for d-lactate production was engineered by overexpressing pathways involved in the conversion of glycerol to this product and blocking those leading to the synthesis of competing by-products. The former included the overexpression of the enzymes involved in the conversion of glycerol to glycolytic intermediates (GlpK-GlpD and GldA-DHAK pathways) and the synthesis of d-lactate from pyruvate (d-lactate dehydrogenase). On the other hand, the synthesis of succinate, acetate, and ethanol was minimized through two strategies: (i) inactivation of pyruvate-formate lyase (DeltapflB) and fumarate reductase (DeltafrdA) (strain LA01) and (ii) inactivation of fumarate reductase (DeltafrdA), phosphate acetyltransferase (Deltapta), and alcohol/acetaldehyde dehydrogenase (DeltaadhE) (strain LA02). A mutation that blocked the aerobic d-lactate dehydrogenase (Deltadld) also was introduced in both LA01 and LA02 to prevent the utilization of d-lactate. The most efficient strain (LA02Deltadld, with GlpK-GlpD overexpressed) produced 32 g/liter of d-lactate from 40 g/liter of glycerol at a yield of 85% of the theoretical maximum and with a chiral purity higher than 99.9%. This strain exhibited maximum volumetric and specific productivities for d-lactate production of 1.5 g/liter/h and 1.25 g/g cell mass/h, respectively. The engineered homolactic route generates 1 to 2 mol of ATP per mol of d-lactate and is redox balanced, thus representing a viable metabolic pathway.

  13. Identification of toxigenic Clostridium difficile by the polymerase chain reaction.

    PubMed Central

    Kato, N; Ou, C Y; Kato, H; Bartley, S L; Brown, V K; Dowell, V R; Ueno, K

    1991-01-01

    Toxigenic strains of Clostridium difficile are causative agents of pseudomembranous colitis and antimicrobial agent-associated diarrhea and colitis. The toxigenicity is routinely assayed by using highly sensitive cell cultures. We used a simple and rapid polymerase chain reaction (PCR) assay to differentiate toxigenic and nontoxigenic strains of C. difficile. Two sets of oligonucleotide primer pairs derived from nonrepeating sequences of the toxin A gene were used to amplify 546- and 252-bp DNA fragments. A primer pair derived from repeating sequences of the toxin A gene was used to amplify a 1,266-bp DNA product. Amplified products were visualized by polyacrylamide gel electrophoresis followed by ethidium bromide staining. All 35 cytotoxic strains of C. difficile tested generated the expected amplified DNA. In contrast, none of the 26 noncytotoxic strains tested gave positive results. Although the toxins of C. difficile have been demonstrated to cross-react serologically with the toxins of Clostridium sordellii, we did not detect any amplified DNA in two cytotoxic strains or seven noncytotoxic strains of C. sordellii. PCR was negative in all 30 strains of 20 other Clostridium species. Southern hybridization of HindIII-digested genomic DNA by use of subgenomic probes showed a single hybridization band in toxigenic strains but not in nontoxigenic strains. PCR appears to be a sensitive and specific assay for the rapid identification of toxigenic C. difficile. Nontoxigenic C. difficile appeared to lack the C. difficile toxin A gene. Images PMID:1993763

  14. Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake.

    PubMed

    McLaughlin, Richard W; Cochran, Philip A; Dowd, Scot E; Andersen, Kylie; Anderson, Nichole; Brennan, Rachel; Brook, Nicole; Callaway, Tracie; Diamante, Kimberly; Duberstine, Annie; Fitch, Karla; Freiheit, Heidi; Godlewski, Chantel; Gorman, Kelly; Haubrich, Mark; Hernandez, Mercedes; Hirtreiter, Amber; Ivanoski, Beth; Jaminet, Xochitl; Kirkpatrick, Travis; Kratowicz, Jennifer; Latus, Casey; Leable, Tiegen; Lingafelt, Nicole; Lowe, Deanna; Lowrance, Holly; Malsack, Latiffa; Mazurkiewicz, Julie; Merlos, Persida; Messley, Jamie; Montemurro, Dawn; Nakitare, Samora; Nelson, Christine; Nye, Amber; Pazera, Valerie; Pierangeli, Gina; Rellora, Ashley; Reyes, Angelica; Roberts, Jennifer; Robins, Shadara; Robinson, Jeshannah; Schultz, Alissa; Seifert, Sara; Sigler, Elona; Spangler, Julie; Swift, Ebony; Tencate, Rebecca; Thurber, Jessica; Vallee, Kristin; Wamboldt, Jennifer; Whitten, Shannon; Woods, De'andrea; Wright, Amanda; Yankunas, Darin

    2014-01-01

    Here, we report the draft genome sequence of Clostridium mangenotii strain TR, which was isolated from the fecal material of a timber rattlesnake. This bacterium is nonpathogenic but contains 68 genes involved in virulence, disease, and defense. PMID:24407632

  15. Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake

    PubMed Central

    Cochran, Philip A.; Dowd, Scot E.; Andersen, Kylie; Anderson, Nichole; Brennan, Rachel; Brook, Nicole; Callaway, Tracie; Diamante, Kimberly; Duberstine, Annie; Fitch, Karla; Freiheit, Heidi; Godlewski, Chantel; Gorman, Kelly; Haubrich, Mark; Hernandez, Mercedes; Hirtreiter, Amber; Ivanoski, Beth; Jaminet, Xochitl; Kirkpatrick, Travis; Kratowicz, Jennifer; Latus, Casey; Leable, Tiegen; Lingafelt, Nicole; Lowe, DeAnna; Lowrance, Holly; Malsack, Latiffa; Mazurkiewicz, Julie; Merlos, Persida; Messley, Jamie; Montemurro, Dawn; Nakitare, Samora; Nelson, Christine; Nye, Amber; Pazera, Valerie; Pierangeli, Gina; Rellora, Ashley; Reyes, Angelica; Roberts, Jennifer; Robins, Shadara; Robinson, Jeshannah; Schultz, Alissa; Seifert, Sara; Sigler, Elona; Spangler, Julie; Swift, Ebony; TenCate, Rebecca; Thurber, Jessica; Vallee, Kristin; Wamboldt, Jennifer; Whitten, Shannon; Woods, De’andrea; Wright, Amanda; Yankunas, Darin

    2014-01-01

    Here, we report the draft genome sequence of Clostridium mangenotii strain TR, which was isolated from the fecal material of a timber rattlesnake. This bacterium is nonpathogenic but contains 68 genes involved in virulence, disease, and defense. PMID:24407632

  16. Lactic acid bacteria as protective cultures in fermented pork meat to prevent Clostridium spp. growth.

    PubMed

    Di Gioia, Diana; Mazzola, Giuseppe; Nikodinoska, Ivana; Aloisio, Irene; Langerholc, Tomaz; Rossi, Maddalena; Raimondi, Stefano; Melero, Beatriz; Rovira, Jordi

    2016-10-17

    In meat fermented foods, Clostridium spp. growth is kept under control by the addition of nitrite. The growing request of consumers for safer products has led to consider alternative bio-based approaches, the use of protective cultures being one of them. This work is aimed at checking the possibility of using two Lactobacillus spp. strains as protective cultures against Clostridium spp. in pork ground meat for fermented salami preparation. Both Lactobacillus strains displayed anti-clostridia activity in vitro using the spot agar test and after co-culturing them in liquid medium with each Clostridium strain. Only one of them, however, namely L. plantarum PCS20, was capable of effectively surviving in ground meat and of performing anti-microbial activity in carnis in a challenge test where meat was inoculated with the Clostridium strain. Therefore, this work pointed out that protective cultures can be a feasible approach for nitrite reduction in fermented meat products. PMID:27400453

  17. Lactic acid bacteria as protective cultures in fermented pork meat to prevent Clostridium spp. growth.

    PubMed

    Di Gioia, Diana; Mazzola, Giuseppe; Nikodinoska, Ivana; Aloisio, Irene; Langerholc, Tomaz; Rossi, Maddalena; Raimondi, Stefano; Melero, Beatriz; Rovira, Jordi

    2016-10-17

    In meat fermented foods, Clostridium spp. growth is kept under control by the addition of nitrite. The growing request of consumers for safer products has led to consider alternative bio-based approaches, the use of protective cultures being one of them. This work is aimed at checking the possibility of using two Lactobacillus spp. strains as protective cultures against Clostridium spp. in pork ground meat for fermented salami preparation. Both Lactobacillus strains displayed anti-clostridia activity in vitro using the spot agar test and after co-culturing them in liquid medium with each Clostridium strain. Only one of them, however, namely L. plantarum PCS20, was capable of effectively surviving in ground meat and of performing anti-microbial activity in carnis in a challenge test where meat was inoculated with the Clostridium strain. Therefore, this work pointed out that protective cultures can be a feasible approach for nitrite reduction in fermented meat products.

  18. Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin

    PubMed Central

    2011-01-01

    Background The xanthophyll astaxanthin is a high-value compound with applications in the nutraceutical, cosmetic, food, and animal feed industries. Besides chemical synthesis and extraction from naturally producing organisms like Haematococcus pluvialis, heterologous biosynthesis in non-carotenogenic microorganisms like Escherichia coli, is a promising alternative for sustainable production of natural astaxanthin. Recent achievements in the metabolic engineering of E. coli strains have led to a significant increase in the productivity of carotenoids like lycopene or β-carotene by increasing the metabolic flux towards the isoprenoid precursors. For the heterologous biosynthesis of astaxanthin in E. coli, however, the conversion of β-carotene to astaxanthin is obviously the most critical step towards an efficient biosynthesis of astaxanthin. Results Here we report the construction of the first plasmid-free E. coli strain that produces astaxanthin as the sole carotenoid compound with a yield of 1.4 mg/g cdw (E. coli BW-ASTA). This engineered E. coli strain harbors xanthophyll biosynthetic genes from Pantoea ananatis and Nostoc punctiforme as individual expression cassettes on the chromosome and is based on a β-carotene-producing strain (E. coli BW-CARO) recently developed in our lab. E. coli BW-CARO has an enhanced biosynthesis of the isoprenoid precursor isopentenyl diphosphate (IPP) and produces β-carotene in a concentration of 6.2 mg/g cdw. The expression of crtEBIY along with the β-carotene-ketolase gene crtW148 (NpF4798) and the β-carotene-hydroxylase gene (crtZ) under controlled expression conditions in E. coli BW-ASTA directed the pathway exclusively towards the desired product astaxanthin (1.4 mg/g cdw). Conclusions By using the λ-Red recombineering technique, genes encoding for the astaxanthin biosynthesis pathway were stably integrated into the chromosome of E. coli. The expression levels of chromosomal integrated recombinant biosynthetic genes were

  19. Strain engineering of selective chemical adsorption on monolayer MoS2

    NASA Astrophysics Data System (ADS)

    Kou, Liangzhi; Du, Aijun; Chen, Changfeng; Frauenheim, Thomas

    2014-04-01

    Nanomaterials are prone to influence by chemical adsorption because of their large surface to volume ratios. This enables sensitive detection of adsorbed chemical species which, in turn, can tune the properties of the host material. Recent studies discovered that single and multi-layer molybdenum disulfide (MoS2) films are ultra-sensitive to several important environmental molecules. Here we report new findings from ab inito calculations that reveal substantially enhanced adsorption of NO and NH3 on strained monolayer MoS2 with significant impact on the properties of the adsorbates and the MoS2 layer. The magnetic moment of adsorbed NO can be tuned between 0 and 1 μB strain also induces an electronic phase transition between the half-metal and the metal. Adsorption of NH3 weakens the MoS2 layer considerably, which explains the large discrepancy between the experimentally measured strength and breaking strain of MoS2 films and previous theoretical predictions. On the other hand, adsorption of NO2, CO, and CO2 is insensitive to the strain conditions in the MoS2 layer. This contrasting behavior allows sensitive strain engineering of selective chemical adsorption on MoS2 with effective tuning of mechanical, electronic, and magnetic properties. These results suggest new design strategies for constructing MoS2-based ultrahigh-sensitivity nanoscale sensors and electromechanical devices.Nanomaterials are prone to influence by chemical adsorption because of their large surface to volume ratios. This enables sensitive detection of adsorbed chemical species which, in turn, can tune the properties of the host material. Recent studies discovered that single and multi-layer molybdenum disulfide (MoS2) films are ultra-sensitive to several important environmental molecules. Here we report new findings from ab inito calculations that reveal substantially enhanced adsorption of NO and NH3 on strained monolayer MoS2 with significant impact on the properties of the adsorbates and the

  20. MoS2/MX2 heterobilayers: bandgap engineering via tensile strain or external electrical field

    NASA Astrophysics Data System (ADS)

    Lu, Ning; Guo, Hongyan; Li, Lei; Dai, Jun; Wang, Lu; Mei, Wai-Ning; Wu, Xiaojun; Zeng, Xiao Cheng

    2014-02-01

    We have performed a comprehensive first-principles study of the electronic and magnetic properties of two-dimensional (2D) transition-metal dichalcogenide (TMD) heterobilayers MX2/MoS2 (M = Mo, Cr, W, Fe, V; X = S, Se). For M = Mo, Cr, W; X = S, Se, all heterobilayers show semiconducting characteristics with an indirect bandgap with the exception of the WSe2/MoS2 heterobilayer which retains the direct-bandgap character of the constituent monolayer. For M = Fe, V; X = S, Se, the MX2/MoS2 heterobilayers exhibit metallic characters. Particular attention of this study has been focused on engineering the bandgap of the TMD heterobilayer materials via application of either a tensile strain or an external electric field. We find that with increasing either the biaxial or uniaxial tensile strain, the MX2/MoS2 (M = Mo, Cr, W; X = S, Se) heterobilayers can undergo a semiconductor-to-metal transition. For the WSe2/MoS2 heterobilayer, a direct-to-indirect bandgap transition may occur beyond a critical biaxial or uniaxial strain. For M (=Fe, V) and X (=S, Se), the magnetic moments of both metal and chalcogen atoms are enhanced when the MX2/MoS2 heterobilayers are under a biaxial tensile strain. Moreover, the bandgap of MX2/MoS2 (M = Mo, Cr, W; X = S, Se) heterobilayers can be reduced by the vertical electric field. For two heterobilayers MSe2/MoS2 (M = Mo, Cr), PBE calculations suggest that the indirect-to-direct bandgap transition may occur under an external electric field. The transition is attributed to the enhanced spontaneous polarization. The tunable bandgaps in general and possible indirect-direct bandgap transitions due to tensile strain or external electric field make the TMD heterobilayer materials a viable candidate for optoelectronic applications.We have performed a comprehensive first-principles study of the electronic and magnetic properties of two-dimensional (2D) transition-metal dichalcogenide (TMD) heterobilayers MX2/MoS2 (M = Mo, Cr, W, Fe, V; X = S, Se). For

  1. Increased resveratrol production in wines using engineered wine strains Saccharomyces cerevisiae EC1118 and relaxed antibiotic or auxotrophic selection.

    PubMed

    Sun, Ping; Liang, Jing-Long; Kang, Lin-Zhi; Huang, Xiao-Yan; Huang, Jia-Jun; Ye, Zhi-Wei; Guo, Li-Qiong; Lin, Jun-Fang

    2015-01-01

    Resveratrol is a polyphenolic compound with diverse beneficial effects on human health. Red wine is the major dietary source of resveratrol but the amount that people can obtain from wines is limited. To increase the resveratrol production in wines, two expression vectors carrying 4-coumarate: coenzyme A ligase gene (4CL) from Arabidopsis thaliana and resveratrol synthase gene (RS) from Vitis vinifera were transformed into industrial wine strain Saccharomyces cerevisiae EC1118. When cultured with 1 mM p-coumaric acid, the engineered strains grown with and without the addition of antibiotics produced 8.249 and 3.317 mg/L of trans-resveratrol in the culture broth, respectively. Resveratrol content of the wine fermented with engineered strains was twice higher than that of the control, indicating that our engineered strains could increase the production of resveratrol during wine fermentation.

  2. MoS2/MX2 heterobilayers: bandgap engineering via tensile strain or external electrical field.

    PubMed

    Lu, Ning; Guo, Hongyan; Li, Lei; Dai, Jun; Wang, Lu; Mei, Wai-Ning; Wu, Xiaojun; Zeng, Xiao Cheng

    2014-03-01

    We have performed a comprehensive first-principles study of the electronic and magnetic properties of two-dimensional (2D) transition-metal dichalcogenide (TMD) heterobilayers MX2/MoS2 (M = Mo, Cr, W, Fe, V; X = S, Se). For M = Mo, Cr, W; X = S, Se, all heterobilayers show semiconducting characteristics with an indirect bandgap with the exception of the WSe2/MoS2 heterobilayer which retains the direct-bandgap character of the constituent monolayer. For M = Fe, V; X = S, Se, the MX2/MoS2 heterobilayers exhibit metallic characters. Particular attention of this study has been focused on engineering the bandgap of the TMD heterobilayer materials via application of either a tensile strain or an external electric field. We find that with increasing either the biaxial or uniaxial tensile strain, the MX2/MoS2 (M = Mo, Cr, W; X = S, Se) heterobilayers can undergo a semiconductor-to-metal transition. For the WSe2/MoS2 heterobilayer, a direct-to-indirect bandgap transition may occur beyond a critical biaxial or uniaxial strain. For M (=Fe, V) and X (=S, Se), the magnetic moments of both metal and chalcogen atoms are enhanced when the MX2/MoS2 heterobilayers are under a biaxial tensile strain. Moreover, the bandgap of MX2/MoS2 (M = Mo, Cr, W; X = S, Se) heterobilayers can be reduced by the vertical electric field. For two heterobilayers MSe2/MoS2 (M = Mo, Cr), PBE calculations suggest that the indirect-to-direct bandgap transition may occur under an external electric field. The transition is attributed to the enhanced spontaneous polarization. The tunable bandgaps in general and possible indirect-direct bandgap transitions due to tensile strain or external electric field make the TMD heterobilayer materials a viable candidate for optoelectronic applications.

  3. Bacteriophages of Clostridium perfringens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The specific aims of the book chapter are to: (1) Briefly review the nomenclature of bacteriophages and how these agents are classified. (2) Discuss the problems associated with addition/removal of antibiotics in commercial animal feeds. (3) Provide a brief overview of Clostridium perfringens biolog...

  4. Strain response of thermal barrier coatings captured under extreme engine environments through synchrotron X-ray diffraction.

    PubMed

    Knipe, Kevin; Manero, Albert; Siddiqui, Sanna F; Meid, Carla; Wischek, Janine; Okasinski, John; Almer, Jonathan; Karlsson, Anette M; Bartsch, Marion; Raghavan, Seetha

    2014-01-01

    The mechanical behaviour of thermal barrier coatings in operation holds the key to understanding durability of jet engine turbine blades. Here we report the results from experiments that monitor strains in the layers of a coating subjected to thermal gradients and mechanical loads representing extreme engine environments. Hollow cylindrical specimens, with electron beam physical vapour deposited coatings, were tested with internal cooling and external heating under various controlled conditions. High-energy synchrotron X-ray measurements captured the in situ strain response through the depth of each layer, revealing the link between these conditions and the evolution of local strains. Results of this study demonstrate that variations in these conditions create corresponding trends in depth-resolved strains with the largest effects displayed at or near the interface with the bond coat. With larger temperature drops across the coating, significant strain gradients are seen, which can contribute to failure modes occurring within the layer adjacent to the interface. PMID:25078347

  5. Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents.

    PubMed

    Anton, Brian P; Fomenkov, Alexey; Raleigh, Elisabeth A; Berkmen, Mehmet

    2016-01-01

    SHuffle strains are genetically engineeredEscherichia colistrains that are capable of oxidizing cysteines within proteins to form disulfide bonds. Here we present the complete genome of both the K-12 and B versions of SHuffle strains along with their parental ancestors. These strains have been of significant use to both the general scientific community and the biotech industry, interested in producing novel disulfide-bonded proteins that were hitherto unable to be expressed in standardE. coliexpression strains. PMID:27034504

  6. Strong Modulation of Optical Properties in Black Phosphorus through Strain-Engineered Rippling.

    PubMed

    Quereda, Jorge; San-Jose, Pablo; Parente, Vincenzo; Vaquero-Garzon, Luis; Molina-Mendoza, Aday J; Agraït, Nicolás; Rubio-Bollinger, Gabino; Guinea, Francisco; Roldán, Rafael; Castellanos-Gomez, Andres

    2016-05-11

    Controlling the bandgap through local-strain engineering is an exciting avenue for tailoring optoelectronic materials. Two-dimensional crystals are particularly suited for this purpose because they can withstand unprecedented nonhomogeneous deformations before rupture; one can literally bend them and fold them up almost like a piece of paper. Here, we study multilayer black phosphorus sheets subjected to periodic stress to modulate their optoelectronic properties. We find a remarkable shift of the optical absorption band-edge of up to ∼0.7 eV between the regions under tensile and compressive stress, greatly exceeding the strain tunability reported for transition metal dichalcogenides. This observation is supported by theoretical models that also predict that this periodic stress modulation can yield to quantum confinement of carriers at low temperatures. The possibility of generating large strain-induced variations in the local density of charge carriers opens the door for a variety of applications including photovoltaics, quantum optics, and two-dimensional optoelectronic devices. PMID:27042865

  7. Strong Modulation of Optical Properties in Black Phosphorus through Strain-Engineered Rippling.

    PubMed

    Quereda, Jorge; San-Jose, Pablo; Parente, Vincenzo; Vaquero-Garzon, Luis; Molina-Mendoza, Aday J; Agraït, Nicolás; Rubio-Bollinger, Gabino; Guinea, Francisco; Roldán, Rafael; Castellanos-Gomez, Andres

    2016-05-11

    Controlling the bandgap through local-strain engineering is an exciting avenue for tailoring optoelectronic materials. Two-dimensional crystals are particularly suited for this purpose because they can withstand unprecedented nonhomogeneous deformations before rupture; one can literally bend them and fold them up almost like a piece of paper. Here, we study multilayer black phosphorus sheets subjected to periodic stress to modulate their optoelectronic properties. We find a remarkable shift of the optical absorption band-edge of up to ∼0.7 eV between the regions under tensile and compressive stress, greatly exceeding the strain tunability reported for transition metal dichalcogenides. This observation is supported by theoretical models that also predict that this periodic stress modulation can yield to quantum confinement of carriers at low temperatures. The possibility of generating large strain-induced variations in the local density of charge carriers opens the door for a variety of applications including photovoltaics, quantum optics, and two-dimensional optoelectronic devices.

  8. Controlling the thermal conductance of graphene/h -BN lateral interface with strain and structure engineering

    NASA Astrophysics Data System (ADS)

    Ong, Zhun-Yong; Zhang, Gang; Zhang, Yong-Wei

    2016-02-01

    Although phonon-mediated thermal conduction in pristine graphene and hexagonal boron nitride is well understood, less is known about phonon transport in single-sheet graphene-hexagonal boron nitride (Gr /h -BN ) lateral heterostructures, where the thermal resistance of the interfaces plays an important role in the overall thermal conductivity. We apply the newly developed extended atomistic Green's function method to analyze with detail the effect of strain and structure engineering on the thermal conductance Gint of the Gr /h -BN interface. Our calculations show that longitudinal tensile strain leads to significant Gint enhancement (up to 25 % at 300 K) primarily through the improved alignment of the flexural acoustic phonon bands, despite the reduction in the longitudinal acoustic (LA) and transverse acoustic phonon velocities. In addition, we find that alternating C-N zigzag bonds along the zigzag interface lead to a greater Gint than C-B bonds through more effective transmission of high-frequency LA and transverse optical phonons, especially at high strain levels. We also demonstrate how the interfacial structure dramatically affects the orientation of the transmitted optical phonons, a phenomenon that is neither seen for acoustic phonons nor predictable from conventional acoustic wave scattering theory. Insights from our paper can provide the basis for manipulating the interfacial thermal conductance in other two-dimensional heterostructures.

  9. [The Engineering of a Yarrowia lipolytica Yeast Strain Capable of Homologous Recombination of the Mitochondrial Genome].

    PubMed

    Isakova, E P; Epova, E Yu; Sekova, V Yu; Trubnikova, E V; Kudykina, Yu K; Zylkova, M V; Guseva, M A; Deryabina, Yu I

    2015-01-01

    None of the studied eukaryotic species has a natural system for homologous recombination of the mitochondrial genome. We propose an integrated genetic construct pQ-SRUS, which allows introduction of the recA gene from Bacillus subtilis into the nuclear genome of an extremophilic yeast, Yarrowia lipolytica. The targeting of recombinant RecA to the yeast mitochondria is provided by leader sequences (5'-UTR and 3'-UTR) derived from the SOD2 gene mRNA, which exhibits affinity to the outer mitochondrial membrane and thus provides cotranslational transport of RecA to the inner space of the mitochondria. The Y. lipolytica strain bearing the pQ-SRUS construct has the unique ability to integrate DNA constructs into the mitochondrial genome. This fact was confirmed using a tester construct, pQ-NIHN, intended for the introduction of the EYFP gene into the translation initiation region of the Y. lipolytica ND1 mitochondrial gene. The Y. lipolytica strain bearing pQ-SRUS makes it possible to engineer recombinant producers based on Y. lipolytica bearing transgenes in the mitochondrial genome. They are promising for the construction of a genetic system for in vivo replication and modification of the human mitochondrial genome. These strains may be used as a tool for the treatment of human mitochondrial diseases (including genetically inherited ones). PMID:26204776

  10. Wrinkling instability in nanoparticle-supported graphene: implications for strain engineering

    NASA Astrophysics Data System (ADS)

    Cullen, William; Yamamoto, Mahito; Pierre-Louis, Olivier; Huang, Jia; Fuhrer, Michael; Einstein, Theodore

    2013-03-01

    We have carried out a systematic study of the wrinkling instability of graphene membranes supported on SiO2 substrates with randomly placed silica nanoparticles. At small nanoparticle density, monolayer graphene adheres to the substrate and is highly conformal over the nanoparticles. With increasing nanoparticle density, and decreasing nanoparticle separation to ~100 nm, graphene's elastic response dominates substrate adhesion, and elastic stretching energy is reduced by the formation of wrinkles which connect protrusions. Above a critical nanoparticle density, the wrinkles form a percolating network through the sample. As the graphene membrane is made thicker, delamination from the substrate is observed. Since the wrinkling instability acts to remove inhomogeneous in-plane elastic strains through out-of-plane buckling, our results can be used to place limits on the possible in-plane strain magnitudes that may be created in graphene to realized strain-engineered electronic structures.[2] Supported by the UMD NSF-MRSEC under Grant No. DMR 05-20471, the US ONR MURI and UMD CNAM.

  11. Strong Modulation of Optical Properties in Black Phosphorus through Strain-Engineered Rippling

    NASA Astrophysics Data System (ADS)

    Quereda, Jorge; San-Jose, Pablo; Parente, Vincenzo; Vaquero-Garzon, Luis; Molina-Mendoza, Aday J.; Agraït, Nicolás; Rubio-Bollinger, Gabino; Guinea, Francisco; Roldán, Rafael; Castellanos-Gomez, Andres

    2016-05-01

    Controlling the bandgap through local-strain engineering is an exciting avenue for tailoring optoelectronic materials. Two-dimensional crystals are particularly suited for this purpose because they can withstand unprecedented non-homogeneous deformations before rupture: one can literally bend them and fold them up almost like a piece of paper. Here, we study multi-layer black phosphorus sheets subjected to periodic stress to modulate their optoelectronic properties. We find a remarkable shift of the optical absorption band-edge of up to ~0.7 eV between the regions under tensile and compressive stress, greatly exceeding the strain tunability reported for transition metal dichalcogenides. This observation is supported by theoretical models which also predict that this periodic stress modulation can yield to quantum confinement of carriers at low temperatures. The possibility of generating large strain-induced variations in the local density of charge carriers opens the door for a variety of applications including photovoltaics, quantum optics and two-dimensional optoelectronic devices.

  12. Expression and delivery of an endolysin to combat Clostridium perfringens.

    PubMed

    Gervasi, Teresa; Horn, Nikki; Wegmann, Udo; Dugo, Giacomo; Narbad, Arjan; Mayer, Melinda J

    2014-03-01

    Clostridium perfringens is a cause for increasing concern due to its responsibility for severe infections both in humans and animals, especially poultry. To find new control strategies to treat C. perfringens infection, we investigated the activity and delivery of a bacteriophage endolysin. We identified a new endolysin, designated CP25L, which shows similarity to an N-acetylmuramoyl-L-alanine amidase domain and is distinct from other C. perfringens endolysins whose activity has been demonstrated in vitro. The cp25l gene was cloned and expressed in Escherichia coli, and the gene product demonstrated lytic activity against all 25 C. perfringens strains tested. The probiotic strain Lactobacillus johnsonii FI9785 was engineered to deliver the endolysin to the gastrointestinal tract. The integration of the nisRK two-component regulatory system from the Lactococcus lactis nisin A biosynthesis operon into the chromosome of L. johnsonii allowed constitutive expression of the endolysin under the control of the nisA promoter (P nisA ), while the use of a signal peptide (SLPmod) led to successful secretion of the active endolysin to the surrounding media. The high specificity and activity of the endolysin suggest that it may be developed as an effective tool to enhance the control of C. perfringens by L. johnsonii in the gastrointestinal tract. PMID:23942878

  13. Clostridium kogasensis sp. nov., a novel member of the genus Clostridium, isolated from soil under a corroded gas pipeline.

    PubMed

    Shin, Yeseul; Kang, Seok-Seong; Paek, Jayoung; Jin, Tae Eun; Song, Hong Seok; Kim, Hongik; Park, Hee-Moon; Chang, Young-Hyo

    2016-06-01

    Two bacterial strains, YHK0403(T) and YHK0508, isolated from soil under a corroded gas pipe line, were revealed as Gram-negative, obligately anaerobic, spore-forming and mesophilic bacteria. The cells were rod-shaped and motile by means of peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were members of the genus Clostridium and were the most closely related to Clostridium scatologenes KCTC 5588(T) (95.8% sequence similarity), followed by Clostridium magnum KCTC 15177(T) (95.8%), Clostridium drakei KCTC 5440(T) (95.7%) and Clostridium tyrobutyricum KCTC 5387(T) (94.9%). The G + C contents of the isolates were 29.6 mol%. Peptidoglycan in the cell wall was of the A1γ type with meso-diaminopimelic acid. The major polar lipid was diphosphatidylglycerol (DPG), and other minor lipids were revealed as phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unknown glycolipids (GL1 and GL2), an unknown aminoglycolipid (NGL), two unknown aminophospholipids (PN1 and PN2) and four unknown phospholipids (PL1 to PL4). Predominant fatty acids were C16:0 and C16:1cis9 DMA. The major end products from glucose fermentation were identified as butyrate (12.2 mmol) and acetate (9.8 mmol). Collectively, the results from a wide range of phenotypic tests, chemotaxonomic tests, and phylogenetic analysis indicated that the two isolates represent novel species of the genus Clostridium, for which the name Clostridium kogasensis sp. nov. (type strain, YHK0403(T) = KCTC 15258(T) = JCM 18719(T)) is proposed. PMID:26899448

  14. Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.

    PubMed

    Lee, Kang-Hoon; Lim, Debora; Chiu, Sophia; Greenhalgh, David; Cho, Kiho

    2016-04-01

    Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.

  15. Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.

    PubMed

    Lee, Kang-Hoon; Lim, Debora; Chiu, Sophia; Greenhalgh, David; Cho, Kiho

    2016-04-01

    Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans. PMID:26779669

  16. Clostridium difficile in retail meat and processing plants in Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence and severity of disease associated with toxigenic Clostridium difficile (Cd) have increased in hospitals in North America from the emergence of newer, more virulent strains of Cd. Toxigenic Cd has been isolated from food animals and retail meat with potential implications of transfer ...

  17. Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates.

    PubMed

    Baums, Christoph G; Schotte, Ulrich; Amtsberg, Gunter; Goethe, Ralph

    2004-05-20

    In this study we provide a protocol for genotyping Clostridium perfringens with a new multiplex PCR. This PCR enables reliable and specific detection of the toxin genes cpa, cpb, etx, iap, cpe and cpb2 from heat lysed bacterial suspensions. The efficiency of the protocol was demonstrated by typing C. perfringens reference strains and isolates from veterinary bacteriological routine diagnostic specimens.

  18. Isolation process of industrially useful Clostridium bifermentans from natural samples.

    PubMed

    Myszka, Kamila; Leja, Katarzyna; Olejnik-Schmidt, Agnieszka K; Czaczyk, Katarzyna

    2012-05-01

    A selective isolation procedure of clostridial strains from natural samples able to convert glycerol to 1,3-propanediol (1,3-PD) and organic acids was investigated. The modified PY medium of high concentration of NaHCO(3) was shown to be highly selective for Clostridium bifermentans. Obtained isolates produced mainly 1,3-PD, lactic, acetic, and formic acids from glycerol.

  19. Genetically Engineered Immunomodulatory Streptococcus thermophilus Strains Producing Antioxidant Enzymes Exhibit Enhanced Anti-Inflammatory Activities

    PubMed Central

    del Carmen, Silvina; de Moreno de LeBlanc, Alejandra; Martin, Rebeca; Chain, Florian; Langella, Philippe; Bermúdez-Humarán, Luis G.

    2014-01-01

    The aims of this study were to develop strains of lactic acid bacteria (LAB) having both immunomodulatory and antioxidant properties and to evaluate their anti-inflammatory effects both in vitro, in different cellular models, and in vivo, in a mouse model of colitis. Different Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains were cocultured with primary cultures of mononuclear cells. Analysis of the pro- and anti-inflammatory cytokines secreted by these cells after coincubation with candidate bacteria revealed that L. delbrueckii subsp. bulgaricus CRL 864 and S. thermophilus CRL 807 display the highest anti-inflammatory profiles in vitro. Moreover, these results were confirmed in vivo by the determination of the cytokine profiles in large intestine samples of mice fed with these strains. S. thermophilus CRL 807 was then transformed with two different plasmids harboring the genes encoding catalase (CAT) or superoxide dismutase (SOD) antioxidant enzymes, and the anti-inflammatory effects of recombinant streptococci were evaluated in a mouse model of colitis induced by trinitrobenzenesulfonic acid (TNBS). Our results showed a decrease in weight loss, lower liver microbial translocation, lower macroscopic and microscopic damage scores, and modulation of the cytokine production in the large intestines of mice treated with either CAT- or SOD-producing streptococci compared to those in mice treated with the wild-type strain or control mice without any treatment. Furthermore, the greatest anti-inflammatory activity was observed in mice receiving a mixture of both CAT- and SOD-producing streptococci. The addition of L. delbrueckii subsp. bulgaricus CRL 864 to this mixture did not improve their beneficial effects. These findings show that genetically engineering a candidate bacterium (e.g., S. thermophilus CRL 807) with intrinsic immunomodulatory properties by introducing a gene expressing an antioxidant enzyme enhances its anti

  20. Toxin Plasmids of Clostridium perfringens

    PubMed Central

    Li, Jihong; Adams, Vicki; Bannam, Trudi L.; Miyamoto, Kazuaki; Garcia, Jorge P.; Uzal, Francisco A.; Rood, Julian I.

    2013-01-01

    SUMMARY In both humans and animals, Clostridium perfringens is an important cause of histotoxic infections and diseases originating in the intestines, such as enteritis and enterotoxemia. The virulence of this Gram-positive, anaerobic bacterium is heavily dependent upon its prolific toxin-producing ability. Many of the ∼16 toxins produced by C. perfringens are encoded by large plasmids that range in size from ∼45 kb to ∼140 kb. These plasmid-encoded toxins are often closely associated with mobile elements. A C. perfringens strain can carry up to three different toxin plasmids, with a single plasmid carrying up to three distinct toxin genes. Molecular Koch's postulate analyses have established the importance of several plasmid-encoded toxins when C. perfringens disease strains cause enteritis or enterotoxemias. Many toxin plasmids are closely related, suggesting a common evolutionary origin. In particular, most toxin plasmids and some antibiotic resistance plasmids of C. perfringens share an ∼35-kb region containing a Tn916-related conjugation locus named tcp (transfer of clostridial plasmids). This tcp locus can mediate highly efficient conjugative transfer of these toxin or resistance plasmids. For example, conjugative transfer of a toxin plasmid from an infecting strain to C. perfringens normal intestinal flora strains may help to amplify and prolong an infection. Therefore, the presence of toxin genes on conjugative plasmids, particularly in association with insertion sequences that may mobilize these toxin genes, likely provides C. perfringens with considerable virulence plasticity and adaptability when it causes diseases originating in the gastrointestinal tract. PMID:23699255

  1. Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine

    PubMed Central

    Báez-Viveros, José Luis; Flores, Noemí; Juárez, Katy; Castillo-España, Patricia; Bolivar, Francisco; Gosset, Guillermo

    2007-01-01

    Background The rational design of L-phenylalanine (L-Phe) overproducing microorganisms has been successfully achieved by combining different genetic strategies such as inactivation of the phosphoenolpyruvate: phosphotransferase transport system (PTS) and overexpression of key genes (DAHP synthase, transketolase and chorismate mutase-prephenate dehydratase), reaching yields of 0.33 (g-Phe/g-Glc), which correspond to 60% of theoretical maximum. Although genetic modifications introduced into the cell for the generation of overproducing organisms are specifically targeted to a particular pathway, these can trigger unexpected transcriptional responses of several genes. In the current work, metabolic transcription analysis (MTA) of both L-Phe overproducing and non-engineered strains using Real-Time PCR was performed, allowing the detection of transcriptional responses to PTS deletion and plasmid presence of genes related to central carbon metabolism. This MTA included 86 genes encoding enzymes of glycolysis, gluconeogenesis, pentoses phosphate, tricarboxylic acid cycle, fermentative and aromatic amino acid pathways. In addition, 30 genes encoding regulatory proteins and transporters for aromatic compounds and carbohydrates were also analyzed. Results MTA revealed that a set of genes encoding carbohydrate transporters (galP, mglB), gluconeogenic (ppsA, pckA) and fermentative enzymes (ldhA) were significantly induced, while some others were down-regulated such as ppc, pflB, pta and ackA, as a consequence of PTS inactivation. One of the most relevant findings was the coordinated up-regulation of several genes that are exclusively gluconeogenic (fbp, ppsA, pckA, maeB, sfcA, and glyoxylate shunt) in the best PTS- L-Phe overproducing strain (PB12-ev2). Furthermore, it was noticeable that most of the TCA genes showed a strong up-regulation in the presence of multicopy plasmids by an unknown mechanism. A group of genes exhibited transcriptional responses to both PTS inactivation

  2. Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement.

    PubMed

    Lakshmanan, Meiyappan; Chung, Bevan Kai-Sheng; Liu, Chengcheng; Kim, Seon-Won; Lee, Dong-Yup

    2013-12-01

    Cofactors, such as NAD(H) and NADP(H), play important roles in energy transfer within the cells by providing the necessary redox carriers for a myriad of metabolic reactions, both anabolic and catabolic. Thus, it is crucial to establish the overall cellular redox balance for achieving the desired cellular physiology. Of several methods to manipulate the intracellular cofactor regeneration rates, altering the cofactor specificity of a particular enzyme is a promising one. However, the identification of relevant enzyme targets for such cofactor specificity engineering (CSE) is often very difficult and labor intensive. Therefore, it is necessary to develop more systematic approaches to find the cofactor engineering targets for strain improvement. Presented herein is a novel mathematical framework, cofactor modification analysis (CMA), developed based on the well-established constraints-based flux analysis, for the systematic identification of suitable CSE targets while exploring the global metabolic effects. The CMA algorithm was applied to E. coli using its genome-scale metabolic model, iJO1366, thereby identifying the growth-coupled cofactor engineering targets for overproducing four of its native products: acetate, formate, ethanol, and lactate, and three non-native products: 1-butanol, 1,4-butanediol, and 1,3-propanediol. Notably, among several target candidates for cofactor engineering, glyceraldehyde-3-phosphate dehydrogenase (GAPD) is the most promising enzyme; its cofactor modification enhanced both the desired product and biomass yields significantly. Finally, given the identified target, we further discussed potential mutational strategies for modifying cofactor specificity of GAPD in E. coli as suggested by in silico protein docking experiments.

  3. Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses

    PubMed Central

    Lee, Joungmin; Jang, Yu-Sin; Han, Mee-Jung; Kim, Jin Young

    2016-01-01

    ABSTRACT Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain. PMID:27302759

  4. Metabolic process engineering of Clostridium tyrobutyricum Δack-adhE2 for enhanced n-butanol production from glucose: effects of methyl viologen on NADH availability, flux distribution, and fermentation kinetics.

    PubMed

    Du, Yinming; Jiang, Wenyan; Yu, Mingrui; Tang, I-Ching; Yang, Shang-Tian

    2015-04-01

    Butanol biosynthesis through aldehyde/alcohol dehydrogenase (adhE2) is usually limited by NADH availability, resulting in low butanol titer, yield, and productivity. To alleviate this limitation and improve n-butanol production by Clostridium tyrobutyricum Δack-adhE2 overexpressing adhE2, the NADH availability was increased by using methyl viologen (MV) as an artificial electron carrier to divert electrons from ferredoxin normally used for H2 production. In the batch fermentation with the addition of 500 μM MV, H2 , acetate, and butyrate production was reduced by more than 80-90%, while butanol production increased more than 40% to 14.5 g/L. Metabolic flux analysis revealed that butanol production increased in the fermentation with MV because of increased NADH availability as a result of reduced H2 production. Furthermore, continuous butanol production of ∼55 g/L with a high yield of ∼0.33 g/g glucose and extremely low ethanol, acetate, and butyrate production was obtained in fed-batch fermentation with gas stripping for in situ butanol recovery. This study demonstrated a stable and reliable process for high-yield and high-titer n-butanol production by metabolically engineered C. tyrobutyricum by applying MV as an electron carrier to increase butanol biosynthesis. PMID:25363722

  5. Metabolic process engineering of Clostridium tyrobutyricum Δack-adhE2 for enhanced n-butanol production from glucose: effects of methyl viologen on NADH availability, flux distribution, and fermentation kinetics.

    PubMed

    Du, Yinming; Jiang, Wenyan; Yu, Mingrui; Tang, I-Ching; Yang, Shang-Tian

    2015-04-01

    Butanol biosynthesis through aldehyde/alcohol dehydrogenase (adhE2) is usually limited by NADH availability, resulting in low butanol titer, yield, and productivity. To alleviate this limitation and improve n-butanol production by Clostridium tyrobutyricum Δack-adhE2 overexpressing adhE2, the NADH availability was increased by using methyl viologen (MV) as an artificial electron carrier to divert electrons from ferredoxin normally used for H2 production. In the batch fermentation with the addition of 500 μM MV, H2 , acetate, and butyrate production was reduced by more than 80-90%, while butanol production increased more than 40% to 14.5 g/L. Metabolic flux analysis revealed that butanol production increased in the fermentation with MV because of increased NADH availability as a result of reduced H2 production. Furthermore, continuous butanol production of ∼55 g/L with a high yield of ∼0.33 g/g glucose and extremely low ethanol, acetate, and butyrate production was obtained in fed-batch fermentation with gas stripping for in situ butanol recovery. This study demonstrated a stable and reliable process for high-yield and high-titer n-butanol production by metabolically engineered C. tyrobutyricum by applying MV as an electron carrier to increase butanol biosynthesis.

  6. Band gap engineering in polymers through chemical doping and applied mechanical strain

    NASA Astrophysics Data System (ADS)

    Lanzillo, Nicholas A.; Breneman, Curt M.

    2016-08-01

    We report simulations based on density functional theory and many-body perturbation theory exploring the band gaps of common crystalline polymers including polyethylene, polypropylene and polystyrene. Our reported band gaps of 8.6 eV for single-chain polyethylene and 9.1 eV for bulk crystalline polyethylene are in excellent agreement with experiment. The effects of chemical doping along the polymer backbone and side-groups are explored, and the use mechanical strain as a means to modify the band gaps of these polymers over a range of several eV while leaving the dielectric constant unchanged is discussed. This work highlights some of the opportunities available to engineer the electronic properties of polymers with wide-reaching implications for polymeric dielectric materials used for capacitive energy storage.

  7. Mechanical Strain Using 2D and 3D Bioreactors Induces Osteogenesis: Implications for Bone Tissue Engineering

    NASA Astrophysics Data System (ADS)

    van Griensven, M.; Diederichs, S.; Roeker, S.; Boehm, S.; Peterbauer, A.; Wolbank, S.; Riechers, D.; Stahl, F.; Kasper, C.

    Fracture healing is a complicated process involving many growth factors, cells, and physical forces. In cases, where natural healing is not able, efforts have to be undertaken to improve healing. For this purpose, tissue engineering may be an option. In order to stimulate cells to form a bone tissue several factors are needed: cells, scaffold, and growth factors. Stem cells derived from bone marrow or adipose tissues are the most useful in this regard. The differentiation of the cells can be accelerated using mechanical stimulation. The first part of this chapter describes the influence of longitudinal strain application. The second part uses a sophisticated approach with stem cells on a newly developed biomaterial (Sponceram) in a rotating bed bioreactor with the administration of bone morphogenetic protein-2. It is shown that such an approach is able to produce bone tissue constructs. This may lead to production of larger constructs that can be used in clinical applications.

  8. Band gap engineering in polymers through chemical doping and applied mechanical strain.

    PubMed

    Lanzillo, Nicholas A; Breneman, Curt M

    2016-08-17

    We report simulations based on density functional theory and many-body perturbation theory exploring the band gaps of common crystalline polymers including polyethylene, polypropylene and polystyrene. Our reported band gaps of 8.6 eV for single-chain polyethylene and 9.1 eV for bulk crystalline polyethylene are in excellent agreement with experiment. The effects of chemical doping along the polymer backbone and side-groups are explored, and the use mechanical strain as a means to modify the band gaps of these polymers over a range of several eV while leaving the dielectric constant unchanged is discussed. This work highlights some of the opportunities available to engineer the electronic properties of polymers with wide-reaching implications for polymeric dielectric materials used for capacitive energy storage.

  9. Three new 16-membered macrolide compounds from a genetically engineered strain S. avermitilis MHJ1011.

    PubMed

    Pan, Jun-Jie; Wan, Xu; Zhang, Shao-Yong; Huang, Jun; Zhang, Hui; Chen, An-Liang; Wang, Ji-Dong

    2016-07-15

    Three new 16-membered macrolide compounds, 13α-O-α-l-oleandrosyl milbemycin β3 (1), 13α-O-α-l-oleandrosyl-25-ethyl milbemycin β3 (2), 13α-O-α-l-oleandrosyl-25-isopropyl milbemycin β3 (3), were isolated from the genetically engineered strains Streptomyces avermitilis MHJ1011. Their structures were determined on the basis of spectroscopic analysis, including 1D and 2D NMR techniques as well as ESI-MS and comparison with data from the literature. Both compounds 1-3 displayed impressive acaricidal activity against larval mites with the IC50 values of 0.0327, 0.0276 and 0.0235mg/L, respectively, which are higher than those of 13α-hydroxy milbemycin β3 and 13α-hydroxy-25-ethyl milbemycin β3. PMID:27246617

  10. Strain-induced band-gap engineering of graphene monoxide and its effect on graphene

    NASA Astrophysics Data System (ADS)

    Pu, H. H.; Rhim, S. H.; Hirschmugl, C. J.; Gajdardziska-Josifovska, M.; Weinert, M.; Chen, J. H.

    2013-02-01

    Using first-principles calculations we demonstrate the feasibility of band-gap engineering in two-dimensional crystalline graphene monoxide (GMO), a recently reported graphene-based material with a 1:1 carbon/oxygen ratio. The band gap of GMO, which can be switched between direct and indirect, is tunable over a large range (0-1.35 eV) for accessible strains. Electron and hole transport occurs predominantly along the zigzag and armchair directions (armchair for both) when GMO is a direct- (indirect-) gap semiconductor. A band gap of ˜0.5 eV is also induced in graphene at the K' points for GMO/graphene hybrid systems.

  11. Band gap engineering in polymers through chemical doping and applied mechanical strain.

    PubMed

    Lanzillo, Nicholas A; Breneman, Curt M

    2016-08-17

    We report simulations based on density functional theory and many-body perturbation theory exploring the band gaps of common crystalline polymers including polyethylene, polypropylene and polystyrene. Our reported band gaps of 8.6 eV for single-chain polyethylene and 9.1 eV for bulk crystalline polyethylene are in excellent agreement with experiment. The effects of chemical doping along the polymer backbone and side-groups are explored, and the use mechanical strain as a means to modify the band gaps of these polymers over a range of several eV while leaving the dielectric constant unchanged is discussed. This work highlights some of the opportunities available to engineer the electronic properties of polymers with wide-reaching implications for polymeric dielectric materials used for capacitive energy storage. PMID:27324304

  12. Molecular characterization and antimicrobial susceptibilities of Clostridium difficile clinical isolates from Victoria, Australia.

    PubMed

    Mackin, Kate E; Elliott, Briony; Kotsanas, Despina; Howden, Benjamin P; Carter, Glen P; Korman, Tony M; Riley, Thomas V; Rood, Julian I; Jenkin, Grant A; Lyras, Dena

    2015-08-01

    Some Australian strain types of Clostridium difficile appear unique, highlighting the global diversity of this bacterium. We examined recent and historic local isolates, finding predominantly toxinotype 0 strains, but also toxinotypes V and VIII. All isolates tested were susceptible to vancomycin and metronidazole, while moxifloxacin resistance was only detected in recent strains.

  13. Inducing and Quantifying Clostridium difficile Spore Formation.

    PubMed

    Shen, Aimee; Fimlaid, Kelly A; Pishdadian, Keyan

    2016-01-01

    The Gram-positive nosocomial pathogen Clostridium difficile induces sporulation during growth in the gastrointestinal tract. Sporulation is necessary for this obligate anaerobe to form metabolically dormant spores that can resist antibiotic treatment, survive exit from the mammalian host, and transmit C. difficile infections. In this chapter, we describe a method for inducing C. difficile sporulation in vitro. This method can be used to study sporulation and maximize spore purification yields for a number of C. difficile strain backgrounds. We also describe procedures for visualizing spore formation using phase-contrast microscopy and for quantifying the efficiency of sporulation using heat resistance as a measure of functional spore formation. PMID:27507338

  14. Biosynthesis of poly(3-hydroxypropionate) from glycerol using engineered Klebsiella pneumoniae strain without vitamin B12

    PubMed Central

    Feng, Xinjun; Xian, Mo; Liu, Wei; Xu, Chao; Zhang, Haibo; Zhao, Guang

    2015-01-01

    Poly(3-hydroxypropionate) (P3HP) is a biodegradable and biocompatible thermoplastic. Previous studies demonstrated that engineered Escherichia coli strains can produce P3HP with supplementation of expensive vitamin B12. The present study examined the production of P3HP from glycerol in the recombinant Klebsiella pneumoniae strain, which naturally synthesizes vitamin B12. The genes glycerol dehydratase and its reactivation factor (dhaB123, gdrA, and gdrB from K. pneumoniae), aldehyde dehydrogenase (aldH from E. coli) were cloned and expressed in K. pneumoniae to produce 3-hydroxypropionate (3HP), with 2 genes (dhaT and yqhD) for biosynthesis of 1,3-propanediol were deleted. To obtain P3HP production, propionyl-CoA synthetase (prpE from E. coli) and polyhydroxyalkanoate synthase (phaC from Ralstonia eutropha) were introduced. Under the appropriate aeration condition, the cell yield and P3HP content were 0.24 g/L and 12.7% (wt/wt [cell dry weight]) respectively along with 2.03 g/L 3HP after 48 h cultivation. Although the yield is relatively low, this study shows the feasibility of producing P3HP in K. pneumoniae from glycerol without vitamin B12 for the first time. The results also suggest that the aeration conditions should be optimized carefully for the efficient production of P3HP. PMID:25621933

  15. Biomass, strain engineering, and fermentation processes for butanol production by solventogenic clostridia.

    PubMed

    Lee, Sang-Hyun; Yun, Eun Ju; Kim, Jungyeon; Lee, Sang Jun; Um, Youngsoon; Kim, Kyoung Heon

    2016-10-01

    Butanol is considered an attractive biofuel and a commercially important bulk chemical. However, economical production of butanol by solventogenic clostridia, e.g., via fermentative production of acetone-butanol-ethanol (ABE), is hampered by low fermentation performance, mainly as a result of toxicity of butanol to microorganisms and high substrate costs. Recently, sugars from marine macroalgae and syngas were recognized as potent carbon sources in biomass feedstocks that are abundant and do not compete for arable land with edible crops. With the aid of systems metabolic engineering, many researchers have developed clostridial strains with improved performance on fermentation of these substrates. Alternatively, fermentation strategies integrated with butanol recovery processes such as adsorption, gas stripping, liquid-liquid extraction, and pervaporation have been designed to increase the overall titer of butanol and volumetric productivity. Nevertheless, for economically feasible production of butanol, innovative strategies based on recent research should be implemented. This review describes and discusses recent advances in the development of biomass feedstocks, microbial strains, and fermentation processes for butanol production. PMID:27531513

  16. Doping, strain engineering, and interlayer interaction in bilayer hexagonal boron nitride sheets

    NASA Astrophysics Data System (ADS)

    Saito, Susumu; Fujimoto, Yoshitaka

    We study electronic properties of bilayer hexagonal boron nitride (h-BN) sheets with different stacking sequences in the framework of the density-functional theory. The bulk h-BN material usually takes the so-called AA (or AA') stacking, corresponding to the ''non-polar'' bilayer h-BN sheet. On the other hand, the rhombohedral BN takes the ABC stacking, and the corresponding bilayer sheet has ''upper'' and ''lower'' layers which are not equivalent with each other. Interestingly, the energetics of stacking sequences for bilayer h-BN sheets is found to be different from that for bulk h-BN materials. We report that strain engineering for bilayer h-BN sheets can possess much wider possibilities than that for monolayer h-BN due to the modification of the interlayer interaction. We also study the substitutional C doping into bilayer h-BN sheets, and report the energetics and the strain effect for these C-doped sheets. Finally we discuss the similarities and differences between bilayer h-BN sheets and double-wall h-BN nanotubes. This work was partly supported by the MEXT Elements Strategy Initiative to Form Core Research Center, Grant in Aid for Scientific Research, MEXT Japan, ``Science of Atomic Layers'', and JSPS KAKENHI Grant No. 26390062.

  17. Xylitol production by genetically engineered Trichoderma reesei strains using barley straw as feedstock.

    PubMed

    Dashtban, Mehdi; Kepka, Greg; Seiboth, Bernhard; Qin, Wensheng

    2013-01-01

    Xylitol, a naturally occurring five-carbon sugar alcohol derived from D-xylose, is currently in high demand by industries. Trichoderma reesei, a prolific industrial cellulase and hemicellulase producing fungus, is able to selectively use D-xylose from hemicelluloses for xylitol production. The xylitol production by T. reesei can be enhanced by genetic engineering of blocking further xylitol metabolism in the D-xylose pathway. We have used two different T. reesei strains which are impaired in the further metabolism of xylitol including a single mutant in which the xylitol dehydrogenase gene was deleted (∆xdh1) and a double mutant where additionally L-arabinitol-4-dehydrogenase, an enzyme which can partially compensate for xylitol dehydrogenase function, was deleted (∆lad1∆xdh1). Barely straw was first pretreated using NaOH and Organosolv pretreatment methods. The highest xylitol production of 6.1 and 13.22 g/L was obtained using medium supplemented with 2 % Organosolv-pretreated barley straw and 2 % D-xylose by the ∆xdh1 and ∆lad1∆xdh1 strains, respectively.

  18. Biosynthesis of poly(3-hydroxypropionate) from glycerol using engineered Klebsiella pneumoniae strain without vitamin B12.

    PubMed

    Feng, Xinjun; Xian, Mo; Liu, Wei; Xu, Chao; Zhang, Haibo; Zhao, Guang

    2015-01-01

    Poly(3-hydroxypropionate) (P3HP) is a biodegradable and biocompatible thermoplastic. Previous studies demonstrated that engineered Escherichia coli strains can produce P3HP with supplementation of expensive vitamin B12. The present study examined the production of P3HP from glycerol in the recombinant Klebsiella pneumoniae strain, which naturally synthesizes vitamin B12. The genes glycerol dehydratase and its reactivation factor (dhaB123, gdrA, and gdrB from K. pneumoniae), aldehyde dehydrogenase (aldH from E. coli) were cloned and expressed in K. pneumoniae to produce 3-hydroxypropionate (3HP), with 2 genes (dhaT and yqhD) for biosynthesis of 1,3-propanediol were deleted. To obtain P3HP production, propionyl-CoA synthetase (prpE from E. coli) and polyhydroxyalkanoate synthase (phaC from Ralstonia eutropha) were introduced. Under the appropriate aeration condition, the cell yield and P3HP content were 0.24 g/L and 12.7% (wt/wt [cell dry weight]) respectively along with 2.03 g/L 3HP after 48 h cultivation. Although the yield is relatively low, this study shows the feasibility of producing P3HP in K. pneumoniae from glycerol without vitamin B12 for the first time. The results also suggest that the aeration conditions should be optimized carefully for the efficient production of P3HP. PMID:25621933

  19. Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress

    PubMed Central

    2013-01-01

    Background Organisms of the genus Clostridium are Gram-positive endospore formers of great importance to the carbon cycle, human normo- and pathophysiology, but also in biofuel and biorefinery applications. Exposure of Clostridium organisms to chemical and in particular toxic metabolite stress is ubiquitous in both natural (such as in the human microbiome) and engineered environments, engaging both the general stress response as well as specialized programs. Yet, despite its fundamental and applied significance, it remains largely unexplored at the systems level. Results We generated a total of 96 individual sets of microarray data examining the transcriptional changes in C. acetobutylicum, a model Clostridium organism, in response to three levels of chemical stress from the native metabolites, butanol and butyrate. We identified 164 significantly differentially expressed transcriptional regulators and detailed the cellular programs associated with general and stressor-specific responses, many previously unexplored. Pattern-based, comparative genomic analyses enabled us, for the first time, to construct a detailed picture of the genetic circuitry underlying the stress response. Notably, a list of the regulons and DNA binding motifs of the stress-related transcription factors were identified: two heat-shock response regulators, HrcA and CtsR; the SOS response regulator LexA; the redox sensor Rex; and the peroxide sensor PerR. Moreover, several transcriptional regulators controlling stress-responsive amino acid and purine metabolism and their regulons were also identified, including ArgR (arginine biosynthesis and catabolism regulator), HisR (histidine biosynthesis regulator), CymR (cysteine metabolism repressor) and PurR (purine metabolism repressor). Conclusions Using an exceptionally large set of temporal transcriptional data and regulon analyses, we successfully built a STRING-based stress response network model integrating important players for the general and

  20. Predictive Synthesis of Freeform Carbon Nanotube Microarchitectures by Strain-Engineered Chemical Vapor Deposition.

    PubMed

    Park, Sei Jin; Zhao, Hangbo; Kim, Sanha; De Volder, Michael; John Hart, A

    2016-08-01

    High-throughput fabrication of microstructured surfaces with multi-directional, re-entrant, or otherwise curved features is becoming increasingly important for applications such as phase change heat transfer, adhesive gripping, and control of electromagnetic waves. Toward this goal, curved microstructures of aligned carbon nanotubes (CNTs) can be fabricated by engineered variation of the CNT growth rate within each microstructure, for example by patterning of the CNT growth catalyst partially upon a layer which retards the CNT growth rate. This study develops a finite-element simulation framework for predictive synthesis of complex CNT microarchitectures by this strain-engineered growth process. The simulation is informed by parametric measurements of the CNT growth kinetics, and the anisotropic mechanical properties of the CNTs, and predicts the shape of CNT microstructures with impressive fidelity. Moreover, the simulation calculates the internal stress distribution that results from extreme deformation of the CNT structures during growth, and shows that delamination of the interface between the differentially growing segments occurs at a critical shear stress. Guided by these insights, experiments are performed to study the time- and geometry-depended stress development, and it is demonstrated that corrugating the interface between the segments of each microstructure mitigates the interface failure. This study presents a methodology for 3D microstructure design based on "pixels" that prescribe directionality to the resulting microstructure, and show that this framework enables the predictive synthesis of more complex architectures including twisted and truss-like forms. PMID:27378165

  1. Heterologous production of α-farnesene in metabolically engineered strains of Yarrowia lipolytica.

    PubMed

    Yang, Xia; Nambou, Komi; Wei, Liujing; Hua, Qiang

    2016-09-01

    Herein, we studied the heterologous production of α-farnesene, a valuable sesquiterpene with various biotechnological applications, by metabolic engineering of Yarrowia lipolytica. Different overexpression vectors harboring combinations of tHMG1, IDI, ERG20 and codon-optimized α-farnesene synthase (OptFS) genes were constructed and integrated into the genome of Y. lipolytica Po1h. The engineered strain produced 57.08±1.43mg/L of α-farnesene corresponding to 20.8-fold increase over the initial production of 2.75±0.29mg/L in the YPD medium in shake flasks. Bioreactor scale-up in PM medium led to α-farnesene concentration of 259.98±2.15mg/L with α-farnesene to biomass ratio of 33.98±1.51mg/g, which was a 94.5-fold increase over the initial production. This first report on α-farnesene synthesis in Y. lipolytica lays a foundation for future research on production of sesquitepenes in Y. lipolytica and other closest yeast species and will potentially contribute in its industrial production. PMID:27347651

  2. Predictive Synthesis of Freeform Carbon Nanotube Microarchitectures by Strain-Engineered Chemical Vapor Deposition.

    PubMed

    Park, Sei Jin; Zhao, Hangbo; Kim, Sanha; De Volder, Michael; John Hart, A

    2016-08-01

    High-throughput fabrication of microstructured surfaces with multi-directional, re-entrant, or otherwise curved features is becoming increasingly important for applications such as phase change heat transfer, adhesive gripping, and control of electromagnetic waves. Toward this goal, curved microstructures of aligned carbon nanotubes (CNTs) can be fabricated by engineered variation of the CNT growth rate within each microstructure, for example by patterning of the CNT growth catalyst partially upon a layer which retards the CNT growth rate. This study develops a finite-element simulation framework for predictive synthesis of complex CNT microarchitectures by this strain-engineered growth process. The simulation is informed by parametric measurements of the CNT growth kinetics, and the anisotropic mechanical properties of the CNTs, and predicts the shape of CNT microstructures with impressive fidelity. Moreover, the simulation calculates the internal stress distribution that results from extreme deformation of the CNT structures during growth, and shows that delamination of the interface between the differentially growing segments occurs at a critical shear stress. Guided by these insights, experiments are performed to study the time- and geometry-depended stress development, and it is demonstrated that corrugating the interface between the segments of each microstructure mitigates the interface failure. This study presents a methodology for 3D microstructure design based on "pixels" that prescribe directionality to the resulting microstructure, and show that this framework enables the predictive synthesis of more complex architectures including twisted and truss-like forms.

  3. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

    SciTech Connect

    Dash, Satyakam; Mueller, Thomas J.; Venkataramanan, Keerthi P.; Papoutsakis, Eleftherios T.; Maranas, Costas D.

    2014-10-14

    Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.

  4. Production of a bacteriocin by a poultry derived Campylobacter jejuni isolate with antimicrobial activity against Clostridium perfringens and other Gram positive bacteria.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have purified a bacteriocin peptide (termed CUV-3), produced by a poultry cecal isolate of Campylobacter jejuni (strain CUV-3) with inhibitory activity against Gram positive bacteria including Clostridium perfringens (38 strains), Staphylococcus aureus, Staphylococcus epidermidis and Listeria mon...

  5. Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater.

    PubMed

    Bowman, Kimberly S; Dupré, Rachael E; Rainey, Fred A; Moe, William M

    2010-02-01

    Four hydrogen-producing, aerotolerant, anaerobic bacterial strains isolated from chlorinated solvent-contaminated groundwater were characterized using a polyphasic approach. Three of the strains, designated BL-18, BL-19 and BL-20(T), were found to be identical in 16S rRNA gene sequences and in phenotypic properties. Cells of these strains are Gram-positive-staining, spore-forming, motile rods with peritrichous flagella. Growth occurred at 15-40 degrees C, pH 5.0-10.0 and at NaCl concentrations up to 5 % (w/v). Acid was produced in fermentation of cellobiose, fructose, galactose (weak), glucose, maltose and salicin. Products of fermentation in PYG medium were acetate, butyrate, ethanol, formate, carbon dioxide and hydrogen. Dominant cellular fatty acids when grown in PYG medium were C(13 : 0) iso, C(16 : 0), C(13 : 0) anteiso, C(15 : 0) iso and C(15 : 0) anteiso. The genomic DNA G+C content was 30.4 mol%. These isolates can be differentiated from their closest phylogenetic relative, the cluster I Clostridium species Clostridium frigidicarnis (97.2 % similar to the type strain in 16S rRNA gene sequence), on the basis of phenotypic and chemotaxonomic properties. The other strain characterized in this study, BL-28(T), was Gram-positive-staining with spore-forming, rod-shaped cells. Growth occurred at 15-46 degrees C, pH 6.0-8.5 and at NaCl concentrations up to 3 % (w/v). Acid was produced from cellobiose, dextran, fructose (weak), glucose, maltose, salicin and trehalose. End products of PYG fermentation included acetate, butyrate, pyruvate, carbon dioxide and hydrogen. Dominant cellular fatty acids from cells grown in PYG medium at 30 degrees C were C(14 : 0), C(14 : 0) dimethyl aldehyde, C(16 : 0) and C(12 : 0). The DNA G+C content was 28.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BL-28(T) falls within cluster I of the genus Clostridium, but with

  6. Industrial Saccharomyces cerevisiae Yeast Strain Engineered to Convert Glucose, Mannose, Arabinose, and Xylose (GMAX) to Ethanol Anaerobically

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technology for engineering an industrial yeast strain for production of ethanol from glucose, mannose, arabinose, and xylose (GMAX-yeast) using both corn starch and cellulosic feedstocks with simultaneous production of valuable coproducts, including biodiesel, will be discussed. A stable industrial...

  7. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum.

    PubMed

    Brown, Steven D; Guss, Adam M; Karpinets, Tatiana V; Parks, Jerry M; Smolin, Nikolai; Yang, Shihui; Land, Miriam L; Klingeman, Dawn M; Bhandiwad, Ashwini; Rodriguez, Miguel; Raman, Babu; Shao, Xiongjun; Mielenz, Jonathan R; Smith, Jeremy C; Keller, Martin; Lynd, Lee R

    2011-08-16

    Clostridium thermocellum is a thermophilic, obligately anaerobic, gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. Biochemical assays confirm a complete loss of NADH-dependent activity with concomitant acquisition of NADPH-dependent activity, which likely affects electron flow in the mutant. The simplicity of the genetic basis for the ethanol-tolerant phenotype observed here informs rational engineering of mutant microbial strains for cellulosic ethanol production.

  8. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum

    SciTech Connect

    Brown, Steven D; Guss, Adam M; Karpinets, Tatiana V; Parks, Jerry M; Smolin, Nikolai; Yang, Shihui; Land, Miriam L; Klingeman, Dawn Marie; Bhandiwad, Ashwini; Rodriguez, Jr., Miguel; Raman, Babu; Shao, Xiongjun; Mielenz, Jonathan R; Smith, Jeremy C; Keller, Martin; Lynd, Lee R

    2011-01-01

    Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. Biochemical assays confirm a complete loss of NADH-dependent activity with concomitant acquisition of NADPH-dependent activity, which likely affects electron flow in the mutant. The simplicity of the genetic basis for the ethanol-tolerant phenotype observed here informs rational engineering of mutant microbial strains for cellulosic ethanol production.

  9. Fidaxomicin: in Clostridium difficile infection.

    PubMed

    Duggan, Sean T

    2011-12-24

    Fidaxomicin is a first-in-class macrocyclic antibacterial that primarily demonstrates activity against species of clostridia, predominantly Clostridium difficile, while having limited or no activity against normal faecal microflora. Fidaxomicin is minimally absorbed following oral administration and is excreted almost solely in the faeces. Fidaxomicin displayed a high level of antibacterial activity against C. difficile in vitro, with a minimum inhibitory concentration required to inhibit 90% of C. difficile strains of 0.125-0.5 μg/mL, and was ≈2- to 8-fold more active than vancomycin or metronidazole. Fidaxomicin demonstrated a prolonged postantibiotic effect against C. difficile relative to vancomycin and metronidazole. In two randomized, double-blind, phase III trials, oral fidaxomicin 200 mg every 12 hours for 10 days was no less effective than oral vancomycin 125 mg every 6 hours for 10 days in the treatment of C. difficile infection, based on noninferiority analyses of clinical cure rates (primary endpoint). Fidaxomicin therapy was associated with a significantly lower rate of recurrence, as well as a significantly higher rate of global cure (i.e. sustained clinical response; resolution of diarrhoea without recurrence) compared with vancomycin therapy in the two clinical trials. Fidaxomicin was generally well tolerated in patients with C. difficile infection, with a tolerability profile generally similar to that of vancomycin.

  10. Retaining large and adjustable elastic strains of kilogram-scale Nb nanowires [Better Superconductor by Elastic Strain Engineering: Kilogram-scale Free-Standing Niobium Metal Composite with Large Retained Elastic Strains

    DOE PAGES

    Hao, Shijie; Cui, Lishan; Wang, Hua; Jiang, Daqiang; Liu, Yinong; Yan, Jiaqiang; Ren, Yang; Han, Xiaodong; Brown, Dennis E.; Li, Ju

    2016-02-10

    Crystals held at ultrahigh elastic strains and stresses may exhibit exceptional physical and chemical properties. Individual metallic nanowires can sustain ultra-large elastic strains of 4-7%. However, retaining elastic strains of such magnitude in kilogram-scale nanowires is challenging. Here, we find that under active load, ~5.6% elastic strain can be achieved in Nb nanowires in a composite material. Moreover, large tensile (2.8%) and compressive (-2.4%) elastic strains can be retained in kilogram-scale Nb nanowires when the composite is unloaded to a free-standing condition. It is then demonstrated that the retained tensile elastic strains of Nb nanowires significantly increase their superconducting transitionmore » temperature and critical magnetic fields, corroborating ab initio calculations based on BCS theory. This free-standing nanocomposite design paradigm opens new avenues for retaining ultra-large elastic strains in great quantities of nanowires and elastic-strain-engineering at industrial scale.« less

  11. Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses

    PubMed Central

    Rusk, Anthony W.; Tung, David; Miller, Maria; Roix, Jeffrey; Khanna, Kristen V.; Murthy, Ravi; Benjamin, Robert S.; Helgason, Thorunn; Szvalb, Ariel D.; Bird, Justin E.; Roy-Chowdhuri, Sinchita; Zhang, Halle H.; Qiao, Yuan; Karim, Baktiar; McDaniel, Jennifer; Elpiner, Amanda; Sahora, Alexandra; Lachowicz, Joshua; Phillips, Brenda; Turner, Avenelle; Klein, Mary K.; Post, Gerald; Diaz, Luis A.; Riggins, Gregory J.; Papadopoulos, Nickolas; Kinzler, Kenneth W.; Vogelstein, Bert; Bettegowda, Chetan; Huso, David L.; Varterasian, Mary

    2015-01-01

    Species of Clostridium bacteria are notable for their ability to lyse tumor cells growing in hypoxic environments. We show that an attenuated strain of Clostridium novyi (C. novyi-NT) induces a microscopically precise, tumor-localized response in a rat orthotopic brain tumor model after intratumoral injection. It is well known, however, that experimental models often do not reliably predict the responses of human patients to therapeutic agents. We therefore used naturally occurring canine tumors as a translational bridge to human trials. Canine tumors are more like those of humans because they occur in animals with heterogeneous genetic backgrounds, are of host origin, and are due to spontaneous rather than engineered mutations. We found that intratumoral injection of C. novyi-NT spores was well tolerated in companion dogs bearing spontaneous solid tumors, with the most common toxicities being the expected symptoms associated with bacterial infections. Objective responses were observed in 6 of 16 dogs (37.5%), with three complete and three partial responses. On the basis of these encouraging results, we treated a human patient who had an advanced leiomyosarcoma with an intratumoral injection of C. novyi-NT spores. This treatment reduced the tumor within and surrounding the bone. Together, these results show that C. novyi-NT can precisely eradicate neoplastic tissues and suggest that further clinical trials of this agent in selected patients are warranted. PMID:25122639

  12. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru

    PubMed Central

    O’Neal, Lindsey; Obregón-Tito, Alexandra J.; Tito, Raul Y.; Ozga, Andrew T.; Polo, Susan I.; Lewis, Cecil M.; Lawson, Paul A.

    2015-01-01

    A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08VT, was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth on glucose were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08VT (DSM 23598T = CCUG 59712T). PMID:26123611

  13. Engineered vaginal lactobacillus strain for mucosal delivery of the human immunodeficiency virus inhibitor cyanovirin-N.

    PubMed

    Liu, Xiaowen; Lagenaur, Laurel A; Simpson, David A; Essenmacher, Kirsten P; Frazier-Parker, Courtney L; Liu, Yang; Tsai, Daniel; Rao, Srinivas S; Hamer, Dean H; Parks, Thomas P; Lee, Peter P; Xu, Qiang

    2006-10-01

    Women are at significant risk of human immunodeficiency virus (HIV) infection, with the cervicovaginal mucosa serving as a major portal for virus entry. Female-initiated preventatives, including topical microbicides, are urgently needed to help curtail the HIV/AIDS pandemic. Here we report on the development of a novel, live microbicide that employs a natural vaginal strain of Lactobacillus jensenii engineered to deliver the potent HIV inhibitor cyanovirin-N (CV-N). To facilitate efficient expression of CV-N by this bacterium, the L. jensenii 1153 genome was sequenced, allowing identification of native regulatory elements and sites for the chromosomal integration of heterologous genes. A CV-N expression cassette was optimized and shown to produce high levels of structurally intact CV-N when expressed in L. jensenii. Lactobacillus-derived CV-N was capable of inhibiting CCR5-tropic HIV(BaL) infectivity in vitro with a 50% inhibitory concentration of 0.3 nM. The CV-N expression cassette was stably integrated as a single copy into the bacterial chromosome and resolved from extraneous plasmid DNA without adversely affecting the bacterial phenotype. This bacterial strain was capable of colonizing the vagina and producing full-length CV-N when administered intravaginally to mice during estrus phase. The CV-N-producing Lactobacillus was genetically stable when propagated in vitro and in vivo. This work represents a major step towards the development of an inexpensive yet durable protein-based microbicide to block the heterosexual transmission of HIV in women. PMID:17005802

  14. Genetic and biochemical analysis of solvent formation in Clostridium acetobutylicum

    SciTech Connect

    Bennett, G.N.; Rudolph, F.B.

    1998-05-01

    The anaerobic organism Clostridium acetobutylicum has been used for commercial production of important organic solvents due to its ability to convert a wide variety of crude substrates to acids and alcohols. Current knowledge concerning the molecular genetics, cell regulation and metabolic engineering of this organism is still rather limited. The objectives are to improve the knowledge of the molecular genetics and enzymology of Clostridia in order to make genetic alterations which will more effectively channel cell metabolism toward production of desired products. Two factors that limit butanol production in continuous cultures are: (1) The degeneration of the culture, with an increase in the proportion of cells which are incapable of solvent production. Currently isolated degenerate strains are being evaluated to analyze the molecular mechanism of degeneration to determine if it is due to a genetic loss of solvent related genes, loss of a regulatory element, or an increase in general mutagenesis. Recent studies show two general types of degenerates, one which seems to have lost essential solvent pathway genes and another which has not completely lost all solvent production capability and retains the DNA bearing solvent pathway genes. (2) The production of hydrogen which uses up reducing equivalents in the cell. If the reducing power were more fully directed to the reduction reactions involved in butanol production, the process would be more efficient. The authors have studied oxidation reduction systems related to this process. These studies focus on ferredoxin and rubredoxin and their oxidoreductases.

  15. Genetic engineering of industrial Saccharomyces cerevisiae strains using a selection/counter-selection approach.

    PubMed

    Kutyna, Dariusz R; Cordente, Antonio G; Varela, Cristian

    2014-01-01

    Gene modification of laboratory yeast strains is currently a very straightforward task thanks to the availability of the entire yeast genome sequence and the high frequency with which yeast can incorporate exogenous DNA into its genome. Unfortunately, laboratory strains do not perform well in industrial settings, indicating the need for strategies to modify industrial strains to enable strain development for industrial applications. Here we describe approaches we have used to genetically modify industrial strains used in winemaking.

  16. Septicemia in Neutropenic Patients Infected with Clostridium tertium Resistant to Cefepime and Other Expanded-Spectrum Cephalosporins

    PubMed Central

    Steyaert, Sophia; Peleman, Renaat; Vaneechoutte, Mario; De Baere, Thierry; Claeys, Geert; Verschraegen, Gerda

    1999-01-01

    Clostridium tertium was isolated from two immunocompromised patients with septicemia, fever, and gastrointestinal symptoms. The strains were resistant to ceftazidime, cefepime, and clindamycin; intermediately resistant to penicillin; and susceptible to metronidazole, quinolones, and vancomycin. PMID:10523601

  17. Electronic structure and magnetism in g-C{sub 4}N{sub 3} controlled by strain engineering

    SciTech Connect

    Liu, L. Z.; Liu, X. X.; Wu, X. L. E-mail: paul.chu@cityu.edu.hk; Chu, Paul K. E-mail: paul.chu@cityu.edu.hk

    2015-03-30

    Regulation of magnetism and half-metallicity has attracted much attention because of its potential in spintronics. The magnetic properties and electronic structure of graphitic carbon nitride (g-C{sub 4}N{sub 3}) with external strain are determined theoretically based on the density function theory and many-body perturbation theory (G{sub 0}W{sub 0}). Asymmetric deformation induced by uniaxial strain not only regulates the magnetic characteristics but also leads to a transformation from half-metallicity to metallicity. However, this transition cannot occur in the structure with symmetric deformation induced by biaxial strain. Our results suggest the use of strain engineering in metal-free spintronics applications.

  18. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum

    SciTech Connect

    Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M.; Olson, Daniel G.; Lynd, Lee R.; Trinh, Cong T.

    2015-10-21

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model s capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. Furthermore, the model can be applied to design C. thermocellum as a platform microbe for

  19. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum

    DOE PAGES

    Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M.; Olson, Daniel G.; Lynd, Lee R.; Trinh, Cong T.

    2015-10-21

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model smore » capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. Furthermore, the model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol

  20. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum.

    PubMed

    Thompson, R Adam; Layton, Donovan S; Guss, Adam M; Olson, Daniel G; Lynd, Lee R; Trinh, Cong T

    2015-11-01

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model's capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. The model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol and other reduced

  1. Clostridium oryzae sp. nov., from soil of a Japanese rice field.

    PubMed

    Horino, Haruka; Ito, Miyuki; Tonouchi, Akio

    2015-03-01

    An obligately anaerobic bacterial strain designated KC3(T) was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3(T) were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8-1×4-25 µm. Endospores were formed at a terminal position in elongated cells (12-25 µm, mean 15 µm). The temperature range for growth was 20-50 °C, with an optimum at 37 °C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.0 (slightly acidophilic). Strain KC3(T) fermented cellobiose to lactate, butyrate, acetate, formate, hydrogen and carbon dioxide. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and C19 : 0 cyclo 11,12 dimethylacetal. The DNA G+C content of strain KC3(T) was 37.5 mol%. 16S rRNA gene sequence analysis revealed that strain KC3(T) shared low sequence similarity (<93 %) with type strains of the genus Clostridium sensu stricto (Clostridium rRNA cluster I). Analyses of the DNA gyrase A and ATP synthase beta subunit sequences supported the affiliation of strain KC3(T) to the genus Clostridium sensu stricto. The evidence presented here indicates that strain KC3(T) represents a novel species of the genus Clostridium, for which the name Clostridium oryzae sp. nov. is proposed. The type strain of Clostridium oryzae is KC3(T) ( = DSM 28571(T) = NBRC 110163(T)).

  2. III-V strain layer superlattice based band engineered avalanche photodiodes (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Ghosh, Sid

    2015-08-01

    Laser detection and ranging (LADAR)-based systems operating in the Near Infrared (NIR) and Short Wave Infrared (SWIR) have become popular optical sensors for remote sensing, medical, and environmental applications. Sophisticated laser-based radar and weapon systems used for long-range military and astronomical applications need to detect, recognize, and track a variety of targets under a wide spectrum of atmospheric conditions. Infrared APDs play an important role in LADAR systems by integrating the detection and gain stages in a single device. Robust silicon-APDs are limited to visible and very near infrared region (< 1 um), while InGaAs works well up to wavelengths of about 1.5um. Si APDs have low multiplication or excess noise but are limited to below 1um due very poor quantum efficiency above 0.8um. InGaAs and Ge APDs operate up to wavelengths of 1.5um but have poor multiplication or excess noise due to a low impact ionization coefficient ratio between electrons and holes. For the past several decades HgCdTe has been traditionally used in longer wavelength (> 3um) infrared photon detection applications. Recently, various research groups (including Ghosh et. al.) have reported SWIR and MWIR HgCdTe APDs on CdZnTe and Si substrates. However, HgCdTe APDs suffer from low breakdown fields due to material defects, and excess noise increases significantly at high electric fields. During the past decade, InAs/GaSb Strain Layer Superlattice (SLS) material system has emerged as a potential material for the entire infrared spectrum because of relatively easier growth, comparable absorption coefficients, lower tunneling currents and longer Auger lifetimes resulting in enhanced detectivities (D*). Band engineering in type II SLS allows us to engineer avalanche properties of electrons and holes. This is a great advantage over bulk InGaAs and HgCdTe APDs where engineering avalanche properties is not possible. The talk will discuss the evolution of superlattice based avalanche

  3. Band gap engineering via electrostatic chemical strain in cation ordered LaSrAlO4

    NASA Astrophysics Data System (ADS)

    Balachandran, Prasanna V.; Rondinelli, James M.

    2014-03-01

    In this work, we employ density functional theory to examine a novel design route that employs A-site cation ordering to engineer the band gaps of (A,A')BO4 Ruddlesden-Popper (RP) oxides. Using LaSrAlO4 as a model material, we show that the band gap is highly sensitive to the A-site cation ordering ranging from 3-4.5 eV. When the [AlO2]-1 layers are interleaved between two chemically equivalent [LaO]1+ or [SrO]0+ layers, we obtain the smallest band gap with a reduction of ~1 eV determined from the Heyd, Scuseria, and Ernzerhof (HSE) hybrid exchange-correlation functional. We relate the observed band gap reduction to the local bond distortions arising from electrostatic chemical strain induced changes to the O 2 p and La 5 d states in the valence and conduction bands, respectively. The project was supported by The Defense Advanced Research Projects Agency (grant no. N66001-12-4224). The views, opinions, and/or findings reported here are solely those of the authors and do not represent official views of DARPA or DOD.

  4. Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic pathway engineering.

    PubMed Central

    Deanda, K; Zhang, M; Eddy, C; Picataggio, S

    1996-01-01

    The substrate fermentation range of the ethanologenic bacterium Zymomonas mobilis was expanded to include the pentose sugar, L-arabinose, which is commonly found in agricultural residues and other lignocellulosic biomass. Five genes, encoding L-arabinose isomerase (araA), L-ribulokinase (araB), L-ribulose-5-phosphate-4-epimerase (araD), transaldolase (talB), and transketolase (tktA), were isolated from Escherichia coli and introduced into Z. mobilis under the control of constitutive promoters that permitted their expression even in the presence of glucose. The engineered strain grew on and produced ethanol from L-arabinose as a sole C source at 98% of the maximum theoretical ethanol yield, based on the amount of consumed sugar. This indicates that arabinose was metabolized almost exclusively to ethanol as the sole fermentation product, with little by-product formation. Although no diauxic growth pattern was evident, the microorganism preferentially utilized glucose before arabinose, apparently reflecting the specificity of the indigenous facilitated diffusion transport system. This microorganism may be useful, along with the previously developed xylose-fermenting Z. mobilis (M. Zhang, C. Eddy, K. Deanda, M. Finkelstein, and S. Picataggio, Science 267:240-243, 1995), in a mixed culture for efficient fermentation of the predominant hexose and pentose sugars in agricultural residues and other lignocellulosic feedstocks to ethanol. PMID:8953718

  5. [Decoloration and bioaugmentation on azo dye by immobilized genetically engineered strain].

    PubMed

    Jin, Ruo-Fei; Zhou, Ji-Ti; Wang, Jing; Cao, Tong-Chuan

    2007-11-01

    Decoloration and bioaugmentation on azo dye are investigated by using immobilized genetically engineered strain Escherichia coli JM109 (pGEX-AZR) on marcroporous foam carriers. The kinetics of the acid red GR decolorization by the immobilized E. coli JM109 (pGEX-AZR) accords with Andrews model proved by our experiments, and the kinetic parameters, mu(max,c), K(c) and K(ic), are found to be 49.2 mg x (g x h)(-1), 710.43 mg x L(-1) and 681.62 mg x L(-1) respectively. For continuous operating in the anaerobic SBRs with 10% inoculation of Escherichia coli JM109 (pGEX-AZR) on marcroporous foam carriers for 32 d, both the tolerance to red GR concentration shock and the colorific removal in the bioaugmented anaerobic SBRs are higher than the control system, and the acid red GR decoloration rate reached 90%. Changes in microbial community have been detected by the RISA, in which the introduced immobilized GEM and preponderant mixed culture were subsisted steadily in sludge systems.

  6. [Engineering by reverse genetics and characterization of the new reassortant influenza virus strain H5N1].

    PubMed

    Zeberezhnyĭ, A D; Grebennikova, T V; Vorkunova, G K; Yuzhakov, A G; Kostina, L V; Norkina, S N; Aliper, T I; Nepoklonov, E A; Lvov, D K

    2014-01-01

    Reverse genetics was applied to engineering of the reassortantvaccine candidate strain against highly pathogenic avian influenza viruses (HPAIVs) of the H5 subtype. The new strain recPR8-H5N1 contains the HA gene from the Russian HPAIV A/Kurgan/05/2005 (H5N1), the NA and internal genes from A/Puerto Rico/8/34 (H1N1). The strain recPR8-H5N1 demonstrated the antigenic specificity (H5), high proliferation rate in 12 days chicken embryos, and was lethal for the embryos in 36 hours. An inactivated emulsified vaccine based on the strain recPR8-H5N1 elicited high antibody titers and protected 6-week-old chickens from lethal challenge with the HPAIV A/Kurgan/05/2005 (H5N1) on day 21 after single immunization. Infection of non-vaccinated birds with the strain recPR8-H5N1 did not cause any pathology, and the virus was not detected using PCR in blood and cloacal swabs on day 7 p.i. Specific weak seroconversion caused by infection with the strain recPR8-H5N1 was detected on day 14 p.i. As a result, a new influenza virus strain was obtained with modified properties.

  7. Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum

    DOE PAGES

    Papanek, Beth A.; Biswas, Ranjita; Rydzak, Thomas; Guss, Adam M.

    2015-09-12

    Clostridium thermocellum has the natural ability to convert cellulose to ethanol, making it a promising candidate for consolidated bioprocessing (CBP) of cellulosic biomass to biofuels. To further improve its CBP capabilities, we study a mutant strain of C. thermocellum that was constructed (strain AG553; C. thermocellum Δhpt ΔhydG Δldh Δpfl Δpta-ack) to increase flux to ethanol by removing side product formation. Strain AG553 showed a two- to threefold increase in ethanol yield relative to the wild type on all substrates tested. On defined medium, strain AG553 exceeded 70% of theoretical ethanol yield on lower loadings of the model crystalline cellulosemore » Avicel, effectively eliminating formate, acetate, and lactate production and reducing H2 production by fivefold. On 5 g/L Avicel, strain AG553 reached an ethanol yield of 63.5% of the theoretical maximum compared with 19.9% by the wild type, and it showed similar yields on pretreated switchgrass and poplar. The elimination of organic acid production suggested that the strain might be capable of growth under higher substrate loadings in the absence of pH control. Final ethanol titer peaked at 73.4 mM in mutant AG553 on 20 g/L Avicel, at which point the pH decreased to a level that does not allow growth of C. thermocellum, likely due to CO2 accumulation. In comparison, the maximum titer of wild type C. thermocellum was 14.1 mM ethanol on 10 g/L Avicel. In conclusion, with the elimination of the metabolic pathways to all traditional fermentation products other than ethanol, AG553 is the best ethanol-yielding CBP strain to date and will serve as a platform strain for further metabolic engineering for the bioconversion of lignocellulosic biomass.« less

  8. Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum.

    PubMed

    Papanek, Beth; Biswas, Ranjita; Rydzak, Thomas; Guss, Adam M

    2015-11-01

    Clostridium thermocellum has the natural ability to convert cellulose to ethanol, making it a promising candidate for consolidated bioprocessing (CBP) of cellulosic biomass to biofuels. To further improve its CBP capabilities, a mutant strain of C. thermocellum was constructed (strain AG553; C. thermocellum Δhpt ΔhydG Δldh Δpfl Δpta-ack) to increase flux to ethanol by removing side product formation. Strain AG553 showed a two- to threefold increase in ethanol yield relative to the wild type on all substrates tested. On defined medium, strain AG553 exceeded 70% of theoretical ethanol yield on lower loadings of the model crystalline cellulose Avicel, effectively eliminating formate, acetate, and lactate production and reducing H2 production by fivefold. On 5 g/L Avicel, strain AG553 reached an ethanol yield of 63.5% of the theoretical maximum compared with 19.9% by the wild type, and it showed similar yields on pretreated switchgrass and poplar. The elimination of organic acid production suggested that the strain might be capable of growth under higher substrate loadings in the absence of pH control. Final ethanol titer peaked at 73.4mM in mutant AG553 on 20 g/L Avicel, at which point the pH decreased to a level that does not allow growth of C. thermocellum, likely due to CO2 accumulation. In comparison, the maximum titer of wild type C. thermocellum was 14.1mM ethanol on 10 g/L Avicel. With the elimination of the metabolic pathways to all traditional fermentation products other than ethanol, AG553 is the best ethanol-yielding CBP strain to date and will serve as a platform strain for further metabolic engineering for the bioconversion of lignocellulosic biomass.

  9. Carbohydrate metabolism in Corynebacterium glutamicum and applications for the metabolic engineering of L-lysine production strains.

    PubMed

    Blombach, Bastian; Seibold, Gerd M

    2010-05-01

    Carbohydrates exclusively serve as feedstock for industrial amino acid production with Corynebacterium glutamicum. Due to the industrial interest, knowledge about the pathways for carbohydrate metabolization in C. glutamicum steadily increases, enabling the rational design of optimized strains and production processes. In this review, we provide an overview of the metabolic pathways for utilization of hexoses (glucose, fructose), disaccharides (sucrose, maltose), pentoses (D-ribose, L-arabinose, D-xylose), gluconate, and beta-glucosides present in C. glutamicum. Recent approaches of metabolic engineering of L: -lysine production strains based on the known pathways are described and evaluated with respect to L: -lysine yields.

  10. Band gap tuning of epitaxial SrTiO{sub 3-δ}/Si(001) thin films through strain engineering

    SciTech Connect

    Cottier, Ryan J.; Steinle, Nathan A.; Currie, Daniel A.; Theodoropoulou, Nikoleta

    2015-11-30

    We investigate the effect of strain and oxygen vacancies (V{sub O}) on the crystal and optical properties of oxygen deficient, ultra-thin (4–30 nm) films of SrTiO{sub 3-δ} (STO) grown heteroepitaxially on p-Si(001) substrates by molecular beam epitaxy. We demonstrate that STO band gap tuning can be achieved through strain engineering and show that the energy shift of the direct energy gap transition of SrTiO{sub 3-δ}/Si films has a quantifiable dimensional and doping dependence that correlates well with the changes in crystal structure.

  11. Characteristics and Adaptability of Some New Isolates of Clostridium thermocellum

    PubMed Central

    Bender, Judith; Vatcharapijarn, Y.; Jeffries, T. W.

    1985-01-01

    Six strains of Clostridium thermocellum isolated from various environments were characterized as to growth rate, production of reducing sugars, ethanol, and acetic acid from cellulose, base composition of DNA, and the abilities to adapt to ethanol and to grow at 45°C. Five of the six new isolates produced 7 to 15% more ethanol and two produced about 45% more reducing sugars than a standard reference strain. One strain (MC-6) adapted more readily to growth in 2% ethanol than the others. PMID:16346740

  12. [Clostridium difficile infecion--diagnostics, prevention and treatment].

    PubMed

    Piekarska, Marta; Wandałowicz, Alicja D; Miigoć, Henryka

    2014-04-01

    Clostridium difficile is the most common cause of an antibiotic-associated diarrhoea. Frequency of Clostridium difficile infections (CDI) increased in the last decade. This study presents current preventive measure i.e. hand washing, disposable gloves. Additionally, the article presents diagnostic methods: detection glutamine dehydrogenase (GDH), toxins A and B, cytotoxicity neutralization test, polymerase chain reaction methods (PCR) i.e. nucleic acid amplification test (NAAT) and stool culture. Moreover available methods of treatment were presented depending on severity of CDI e.i. metronidazole, vancomycin, fidaxomicin, rifaximin. Furthermore, the review provides information about alternative methods of treatment in view of new hypervirulent strains of C. difficile and increasing resistance to commonly used antibiotics, including: fuscid acid, bacitracin, probiotics, non-toxigenic strains, immunoglobulins, monoclonal antibodies, vaccines, toxins binders and fecal transplant. PMID:24868904

  13. Engineering the quantum anomalous Hall effect in graphene with uniaxial strains

    NASA Astrophysics Data System (ADS)

    Diniz, G. S.; Guassi, M. R.; Qu, F.

    2013-12-01

    We theoretically investigate the manipulation of the quantum anomalous Hall effect (QAHE) in graphene by means of the uniaxial strain. The values of Chern number and Hall conductance demonstrate that the strained graphene in presence of Rashba spin-orbit coupling and exchange field, for vanishing intrinsic spin-orbit coupling, possesses non-trivial topological phase, which is robust against the direction and modulus of the strain. Besides, we also find that the interplay between Rashba and intrinsic spin-orbit couplings results in a topological phase transition in the strained graphene. Remarkably, as the strain strength is increased beyond approximately 7%, the critical parameters of the exchange field for triggering the quantum anomalous Hall phase transition show distinct behaviors—decrease (increase) for strains along zigzag (armchair) direction. Our findings open up a new platform for manipulation of the QAHE by an experimentally accessible strain deformation of the graphene structure, with promising application on novel quantum electronic devices with high efficiency.

  14. Electrostatic Chemical Strain: An Approach to Electronic Structure Engineering in Layered Oxides

    NASA Astrophysics Data System (ADS)

    Rondinelli, James

    2015-03-01

    Traditional approaches to create and control functional electronic materials have focused on new phases in previously unknown bulk minerals. More recently, interlayer physics has spawned interest in known materials in unexplored atomic scale geometries, especially in complex transition metal oxides (TMO), where heterostructures and superlattices with abrupt interfaces can be created on demand. The interfaces between TMO overs a handle to direct the electrostatic field exerted on the transition metal centers via the coordinating oxygen ligands, which alter the M cation's d-orbital occupancies and spin state, thereby imparting desirable electronic functionality. In this talk, I describe an atomistic engineering approach that makes use of long-range electrostatic interactions between atomic metal-monoxide planes (AO and A'O) in naturally occurring superlattices, e.g., Ruddlesden-Popper (RP), phases, to tune interlayer atomic structure, orbital degeneracies, and magnetic properties. Using first-principles electronic structure calculations, I show how this electrostatic chemical strain (ECS) effect can be used to tune both crystal field energies and the frontier orbital structure in correlated (La, A)NiO4 RP phases at fixed stoichiometry. I describe how to enhance the Ni eg orbital polarization, resulting in NiO6 units that exhibit a single d (x2 -y2) band at the Fermi level--electronic features similar to the layered superconducting cuprates. This approach is generic in construction, making it applicable to any layered topology supporting heterovalent cation substitutions. I conclude by showing it is a realistic strategy to tailor the electronic properties of known materials, and discover yet-to-be realized novel functional oxides without resorting to complex assembly of multi-component heterostructures. Funding for this work is provided by the Defense Advanced Research Projects Agency (DARPA), Grant No. N66001-12-4224 and performed in collaboration with P

  15. Xylose fermentation with Clostridium thermohydrosulfuricum

    SciTech Connect

    Mancuso, A.; Wilke, C.R.; Blanch, H.W.

    1982-12-01

    In this study, the fermentation of xylose to ethanol with a thermophilic, strictly anaerobic bacterium, Clostridium thermohydrosulfuricum, was examined. The focus of this investigation was on the physiological parameters which most strongly affect the economic feasibility of using this bacterium for industrial ethanol production. In rich medium (containing economically impractical concentrations of yeast extract) yields as high as 0.43 gm ethanol/gm xylose and growth rates of 0.4 to 0.5 hr/sup -1/ were observed. The predominant by-products of the fermentation were acetate and lactate. Nutritional studies indicated that the cost of the growth medium could be dramatically reduced by replacing most of the yeast extract used with nicotinic acid and vitamin B/sup 12/. Ethanol was found to be very inhibitory to growth and ethanol formation. To overcome the problem of inhibition, cells were gradually adapted to high concentrations (up to 4.2%) of ethanol. However, the ethanol yield of adapted cells was typically 30 to 40% less than the yield of non-adapted cells. Environmental parameters such as pH and by-product concentrations had only a slight effect on the ethanol yield produced by tolerant cells. A mutant, selected from an adapted strain, was found to produce 60% less lactate than its parent. This low-lactate producing mutant had a slightly improved ethanol yield. The results obtained with the tolerant, low-lactate producing mutant were used in the design of an industrial-scale fermentation process. An economic evaluation of the process indicates that ethanol production with this bacterium is currently uneconomical.

  16. Clostridium difficile phages: still difficult?

    PubMed Central

    Hargreaves, Katherine R.; Clokie, Martha R. J.

    2014-01-01

    Phages that infect Clostridium difficile were first isolated for typing purposes in the 1980s, but their use was short lived. However, the rise of C. difficile epidemics over the last decade has triggered a resurgence of interest in using phages to combat this pathogen. Phage therapy is an attractive treatment option for C. difficile infection, however, developing suitable phages is challenging. In this review we summarize the difficulties faced by researchers in this field, and we discuss the solutions and strategies used for the development of C. difficile phages for use as novel therapeutics. Epidemiological data has highlighted the diversity and distribution of C. difficile, and shown that novel strains continue to emerge in clinical settings. In parallel with epidemiological studies, advances in molecular biology have bolstered our understanding of C. difficile biology, and our knowledge of phage–host interactions in other bacterial species. These three fields of biology have therefore paved the way for future work on C. difficile phages to progress and develop. Benefits of using C. difficile phages as therapeutic agents include the fact that they have highly specific interactions with their bacterial hosts. Studies also show that they can reduce bacterial numbers in both in vitro and in vivo systems. Genetic analysis has revealed the genomic diversity among these phages and provided an insight into their taxonomy and evolution. No strictly virulent C. difficile phages have been reported and this contributes to the difficulties with their therapeutic exploitation. Although treatment approaches using the phage-encoded endolysin protein have been explored, the benefits of using “whole-phages” are such that they remain a major research focus. Whilst we don’t envisage working with C. difficile phages will be problem-free, sufficient study should inform future strategies to facilitate their development to combat this problematic pathogen. PMID:24808893

  17. Strain properties analysis and wireless collection system of PVDF for structural local health monitoring of civil engineering structures

    NASA Astrophysics Data System (ADS)

    Yu, Yan; Wang, Yang; Dong, Weijie; Jin, Yajing; Ou, Jinping

    2009-07-01

    For large civil engineering structures and base establishments, for example, bridges, super-high buildings, long-span space structures, offshore platforms and pipe systems of water & gas supply, their lives are up to a few decades or centuries. Damaged by environmental loads, fatigue effects, corrosion effects and material aging, these structures experience inevitably such side effects as damage accumulation, resistance reduction and even accidents. The traditional civil structure is a kind of passive one, whose performance and status are unpredictable to a great extent, but the informatics' introduction breaks a new path to obtain the status of the structure, thus it is an important research direction to evaluate and improve reliability of civil structures by the use of monitoring and health diagnosis technique, and this also assures the security of service for civil engineering structures. Smart material structure, originated from the aerospace sector, has been a research hotspot in civil engineering, medicine, shipping, and so on. For structural health monitoring of civil engineering, the research about high-performance sensing unit of smart material structure is very important, and this will possibly push further the development and application of monitoring and health diagnosis techniques. At present, piezoelectric materials are one of the most widely used sensing materials among the research of smart material structures. As one of the piezoelectric materials, PVDF(Polyvinylidene Fluoride)film is widely considered for the advantages of low cost, good mechanical ability, high sensibility, the ability of being easily placed and resistance of corrosion. However, only a few studies exit about building a mature monitoring system using PVDF. In this paper, for the sake of using PVDF for sensing unit for structural local monitoring of civil engineering, the strain sensing properties of PVDF are studied in detail. Firstly, the operating mechanism of PVDF is analyzed

  18. Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering.

    PubMed

    Cotten, Cameron; Reed, Jennifer L

    2013-05-01

    In recent years, a growing number of metabolic engineering strain design techniques have employed constraint-based modeling to determine metabolic and regulatory network changes which are needed to improve chemical production. These methods use systems-level analysis of metabolism to help guide experimental efforts by identifying deletions, additions, downregulations, and upregulations of metabolic genes that will increase biological production of a desired metabolic product. In this work, we propose a new strain design method with continuous modifications (CosMos) that provides strategies for deletions, downregulations, and upregulations of fluxes that will lead to the production of the desired products. The method is conceptually simple and easy to implement, and can provide additional strategies over current approaches. We found that the method was able to find strain design strategies that required fewer modifications and had larger predicted yields than strategies from previous methods in example and genome-scale networks. Using CosMos, we identified modification strategies for producing a variety of metabolic products, compared strategies derived from Escherichia coli and Saccharomyces cerevisiae metabolic models, and examined how imperfect implementation may affect experimental outcomes. This study gives a powerful and flexible technique for strain engineering and examines some of the unexpected outcomes that may arise when strategies are implemented experimentally.

  19. Strain engineering the charged-impurity-limited carrier mobility in phosphorene

    NASA Astrophysics Data System (ADS)

    Mohammadi, Yawar; Nia, Borhan Arghavani

    2016-01-01

    We investigate, based on the tight-binding model and in the linear deformation regime, the strain dependence of the electronic band structure of phosphorene, exposed to a uniaxial strain in one of its principle directions, the normal, the armchair and the zigzag directions. We show that the electronic band structure of strained phosphorene, for the experimentally accessible carrier densities and the uniaxial strains, is well described by a strain-dependent decoupled electron-hole Hamiltonian. Then, employing the decoupled Hamiltonian, we consider the strain dependence of the charged-impurity-limited carrier mobility in phosphorene, for both types of carriers, arbitrary carrier densities and in both armchair and zigzag directions. We show that a uniaxial tensile (compressive) strain in the normal direction enhances (weakens) the anisotropy of the carrier mobility, while a uniaxial strain in the zigzag direction acts inversely. Moreover applying a uniaxial strain in the armchair direction is shown to be ineffective on the anisotropy of the carrier mobility. These will be explained based on the effects of the strains on the carrier effective masses.

  20. Lung stress, strain, and energy load: engineering concepts to understand the mechanism of ventilator-induced lung injury (VILI).

    PubMed

    Nieman, Gary F; Satalin, Joshua; Andrews, Penny; Habashi, Nader M; Gatto, Louis A

    2016-12-01

    It was recently shown that acute respiratory distress syndrome (ARDS) mortality has not been reduced in over 15 years and remains ~40 %, even with protective low tidal volume (LVt) ventilation. Thus, there is a critical need to develop novel ventilation strategies that will protect the lung and reduce ARDS mortality. Protti et al. have begun to analyze the impact of mechanical ventilation on lung tissue using engineering methods in normal pigs ventilated for 54 h. They used these methods to assess the impact of a mechanical breath on dynamic and static global lung strain and energy load. Strain is the change in lung volume in response to an applied stress (i.e., Tidal Volume-Vt). This study has yielded a number of exciting new concepts including the following: (1) Individual mechanical breath parameters (e.g., Vt or Plateau Pressure) are not directly correlated with VILI but rather any combination of parameters that subject the lung to excessive dynamic strain and energy/power load will cause VILI; (2) all strain is not equal; dynamic strain resulting in a dynamic energy load (i.e., kinetic energy) is more damaging to lung tissue than static strain and energy load (i.e., potential energy); and (3) a critical consideration is not just the size of the Vt but the size of the lung that is being ventilated by this Vt. This key concept merits attention since our current protective ventilation strategies are fixated on the priority of keeping the Vt low. If the lung is fully inflated, a large Vt is not necessarily injurious. In conclusion, using engineering concepts to analyze the impact of the mechanical breath on the lung is a novel new approach to investigate VILI mechanisms and to help design the optimally protective breath. Data generated using these methods have challenged some of the current dogma surrounding the mechanisms of VILI and of the components in the mechanical breath necessary for lung protection.

  1. Secretion of clostridium cellulase by E. coli

    DOEpatents

    Yu, Ida Kuo

    1998-01-01

    A gene, encoding an endocellulase from a newly isolated mesophilic Clostridium strain IY-2 which can digest bamboo fibers, cellulose, rice straw, and sawdust, was isolated by shotgun cloning in an E. coli expression plasmid pLC2833. E. coli positive clones were selected based on their ability to hydrolyze milled bamboo fibers and cellulose present in agar plates. One clone contained a 2.8 kb DNA fragment that was responsible for cellulase activity. Western blot analyses indicated that the positive clone produced a secreted cellulase with a mass of about 58,000 daltons that was identical in size to the subunit of one of the three major Clostridium cellulases. The products of cellulose digestion by this cloned cellulase were cellotetraose and soluble higher polymers. The cloned DNA contained signal sequences capable of directing the secretion of heterologous proteins from an E. coli host. The invention describes a bioprocess for the treatment of cellulosic plant materials to produce cellular growth substrates and fermentation end products suitable for production of liquid fuels, solvents, and acids.

  2. Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum.

    PubMed

    Zhang, Lei; Leyn, Semen A; Gu, Yang; Jiang, Weihong; Rodionov, Dmitry A; Yang, Chen

    2012-03-01

    The transcription factor AraR controls utilization of L-arabinose in Bacillus subtilis. In this study, we combined a comparative genomic reconstruction of AraR regulons in nine Clostridium species with detailed experimental characterization of AraR-mediated regulation in Clostridium acetobutylicum. Based on the reconstructed AraR regulons, a novel ribulokinase, AraK, present in all analyzed Clostridium species was identified, which was a nonorthologous replacement of previously characterized ribulokinases. The predicted function of the araK gene was confirmed by inactivation of the araK gene in C. acetobutylicum and biochemical assays using purified recombinant AraK. In addition to the genes involved in arabinose utilization and arabinoside degradation, extension of the AraR regulon to the pentose phosphate pathway genes in several Clostridium species was revealed. The predicted AraR-binding sites in the C. acetobutylicum genome and the negative effect of L-arabinose on DNA-regulator complex formation were verified by in vitro binding assays. The predicted AraR-controlled genes in C. acetobutylicum were experimentally validated by testing gene expression patterns in both wild-type and araR-inactivated mutant strains during growth in the absence or presence of L-arabinose.

  3. CRISPR Diversity and Microevolution in Clostridium difficile.

    PubMed

    Andersen, Joakim M; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E P; Barrangou, Rodolphe

    2016-01-01

    Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes.

  4. CRISPR Diversity and Microevolution in Clostridium difficile.

    PubMed

    Andersen, Joakim M; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E P; Barrangou, Rodolphe

    2016-01-01

    Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes. PMID:27576538

  5. Inhibitory activity of reuterin, nisin, lysozyme and nitrite against vegetative cells and spores of dairy-related Clostridium species.

    PubMed

    Avila, Marta; Gómez-Torres, Natalia; Hernández, Marta; Garde, Sonia

    2014-02-17

    The butyric acid fermentation, responsible for late blowing of cheese, is caused by the outgrowth in cheese of some species of Clostridium, resulting in texture and flavor defects and economical losses. The aim of this study was to evaluate the effectiveness of different antimicrobial compounds against vegetative cells and spores of C. tyrobutyricum, C. butyricum, C. beijerinckii and C. sporogenes strains isolated from cheeses with late blowing defect. Minimal inhibitory concentration (MIC) for reuterin, nisin, lysozyme and sodium nitrite were determined against Clostridium strains in milk and modified RCM (mRCM) after 7d exposure. Although the sensitivity of Clostridium to the tested antimicrobials was strain-dependent, C. sporogenes and C. beijerinckii generally had higher MIC values than the rest of Clostridium species. The majority of Clostridium strains were more resistant to antimicrobials in milk than in mRCM, and vegetative cells exhibited higher sensitivity than spores. Reuterin (MIC values 0.51-32.5 mM) and nisin (MIC values 0.05-12.5 μg/ml) were able to inhibit the growth of vegetative cells and spores of all assayed Clostridium strains in milk and mRCM. Strains of C. tyrobutyricum exhibited the highest sensitivity to lysozyme (MIC values<0.20-400 μg/ml) and sodium nitrite (MIC values 18.75-150 μg/ml). These results suggest that reuterin and nisin, with a broad inhibitory activity spectrum against Clostridium spp. spores and vegetative cells, may be the best options to control Clostridium growth in dairy products and to prevent associated spoilage, such as late blowing defect of cheese. However, further studies in cheese would be necessary to validate this hypothesis.

  6. Inhibitory activity of reuterin, nisin, lysozyme and nitrite against vegetative cells and spores of dairy-related Clostridium species.

    PubMed

    Avila, Marta; Gómez-Torres, Natalia; Hernández, Marta; Garde, Sonia

    2014-02-17

    The butyric acid fermentation, responsible for late blowing of cheese, is caused by the outgrowth in cheese of some species of Clostridium, resulting in texture and flavor defects and economical losses. The aim of this study was to evaluate the effectiveness of different antimicrobial compounds against vegetative cells and spores of C. tyrobutyricum, C. butyricum, C. beijerinckii and C. sporogenes strains isolated from cheeses with late blowing defect. Minimal inhibitory concentration (MIC) for reuterin, nisin, lysozyme and sodium nitrite were determined against Clostridium strains in milk and modified RCM (mRCM) after 7d exposure. Although the sensitivity of Clostridium to the tested antimicrobials was strain-dependent, C. sporogenes and C. beijerinckii generally had higher MIC values than the rest of Clostridium species. The majority of Clostridium strains were more resistant to antimicrobials in milk than in mRCM, and vegetative cells exhibited higher sensitivity than spores. Reuterin (MIC values 0.51-32.5 mM) and nisin (MIC values 0.05-12.5 μg/ml) were able to inhibit the growth of vegetative cells and spores of all assayed Clostridium strains in milk and mRCM. Strains of C. tyrobutyricum exhibited the highest sensitivity to lysozyme (MIC values<0.20-400 μg/ml) and sodium nitrite (MIC values 18.75-150 μg/ml). These results suggest that reuterin and nisin, with a broad inhibitory activity spectrum against Clostridium spp. spores and vegetative cells, may be the best options to control Clostridium growth in dairy products and to prevent associated spoilage, such as late blowing defect of cheese. However, further studies in cheese would be necessary to validate this hypothesis. PMID:24361835

  7. Production of d-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains.

    PubMed

    Utrilla, José; Vargas-Tah, Alejandra; Trujillo-Martínez, Berenice; Gosset, Guillermo; Martinez, Alfredo

    2016-11-01

    In this study, the lactogenic Escherichia coli strain JU15 was used and modified to produce d-lactate (d-LA) from plant hydrolysates with a minimal nutrient addition in pH controlled fermenters. Results showed that strain JU15 produces d-LA with high yield and productivity in laboratory simulated hydrolysate media and actual sugar cane bagasse hemicellulosic hydrolysate. Strain JU15 showed sequential carbon source utilization and acetic acid production. The l-lactic and acetic acid production pathways were deleted in JU15, resulting strain AV03 (JU15 ΔpoxB, ΔackA-pta, ΔmgsA), which showed simultaneous consumption of glucose and xylose and no acetic acid production in the simulated hydrolysate. The d-LA yield from hydrolysate sugars was close to 0.95gD-LA/gsugars in all cases. Our results show that d-LA can be produced from plant hydrolysates in simple batch fermentation processes with a high productivity using engineered E. coli strains at fermenter scales from 0.2 up to 10L.

  8. Production of d-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains.

    PubMed

    Utrilla, José; Vargas-Tah, Alejandra; Trujillo-Martínez, Berenice; Gosset, Guillermo; Martinez, Alfredo

    2016-11-01

    In this study, the lactogenic Escherichia coli strain JU15 was used and modified to produce d-lactate (d-LA) from plant hydrolysates with a minimal nutrient addition in pH controlled fermenters. Results showed that strain JU15 produces d-LA with high yield and productivity in laboratory simulated hydrolysate media and actual sugar cane bagasse hemicellulosic hydrolysate. Strain JU15 showed sequential carbon source utilization and acetic acid production. The l-lactic and acetic acid production pathways were deleted in JU15, resulting strain AV03 (JU15 ΔpoxB, ΔackA-pta, ΔmgsA), which showed simultaneous consumption of glucose and xylose and no acetic acid production in the simulated hydrolysate. The d-LA yield from hydrolysate sugars was close to 0.95gD-LA/gsugars in all cases. Our results show that d-LA can be produced from plant hydrolysates in simple batch fermentation processes with a high productivity using engineered E. coli strains at fermenter scales from 0.2 up to 10L. PMID:27573474

  9. Roles of human sulfotransferases in genotoxicity of carcinogens using genetically engineered umu test strains.

    PubMed

    Oda, Yoshimitsu; Zhang, Yu; Buchinger, Sebastian; Reifferscheid, Georg; Yang, Min

    2012-03-01

    Human sulfotransferase (SULT) 1A1, 1A2, and 1A3 cDNA genes were subcloned separately into the pTrc99A(KM) vector. The generated plasmids were introduced into the Salmonella typhimurium O-acetyltransferase-deficient strain NM6000 (TA1538/1,8-DNP/pSK1002), resulting in the new strains NM7001, NM7002, and NM7003. We compared the sensitivities of these three strains with the parental strain NM7000 against 51 chemicals including aromatic amines, nitroarenes, alkenylbenzenes, estrogens-like chemicals, and other compounds with and without S9 mix by making use of the umu test system that is based on the bacterial SOS induction. 2-Amino-6-methyl-dipyrido[1,2-α:3',2'-d]imidazole, 3-methoxy-4-aminoazobenzene, 3-nitrobenzanthrone, 5-nitroacenaphthene, and 3,9-dinitrofluoranthene caused high genotoxicity in the NM7001 strain. The genotoxic effects of 2-aminofluorene, 2-acetylaminofluorene, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, 2-nitrofluorene, 1-nitropyrene, and 2-nitropropane were stronger in the NM7002 strain compared with the NM7001 and NM7003 strains. Among the tested benzylic and allylic compounds, 1-hydroxymethylpyrene was detected in the NM7001 strain with the highest sensitivity. Estragole and 1'-hydroxysafrole exhibited strong genotoxicity in the NM7003 strain. The estrogen-like chemicals such as bisphenol A, genistein, p,n-nonylphenol, and 4-hydroxytamoxifen were not detected as genotoxins in any strain used. Collectively, the present results suggest that the generated test strains are valuable tools in order to elucidate the role of SULT enzymes in the bioactivation of chemicals to environmental carcinogens. PMID:22072630

  10. Engineering electronic properties of armchair graphene nanoribbons using strain and functional species

    NASA Astrophysics Data System (ADS)

    Peng, Xihong; Tang, Fu; Velasquez, Selina; Copple, Andrew

    2012-02-01

    First principles density-functional theory calculations were performed to study effects of strain, edge passivation, and surface functional species on structural and electronic properties. Particularly band gap and work function, of armchair graphene nanoribbons (AGNRs), are addressed. It was found that the band gap of the O-passivated AGNRs experiences a direct-to-indirect transition with sufficient tensile strain. The indirect band gap reduces to zero with further increased strain. The work function was found to increase with uniaxial tensile strain while decreasing with compression. The variation of the work function under strain is primarily due to the shift of the Fermi energy with strain. For AGNRs with edge carbon atoms passivated by oxygen, the work function is higher than that of nanoribbons with edge passivated by hydrogen under a moderate strain. The difference between work functions in these two edge passivations is enlarged (reduced) under a sufficient tensile (compressive) strain. Furthermore, the effect of surface species decoration, such as H, F, or OH with different covering density, was investigated. It was found the work function varies with the type and coverage of surface functional species. F and OH decoration increase the work function while H decreases it. The surface functional species were decorated on either one side or both sides of AGNRs. The difference in the work functions between one-side and two-side decorations was found to be relatively small, which may suggest the introduced surface dipole plays a minor role.

  11. Clostridium beijerinckii and Clostridium difficile Detoxify Methylglyoxal by a Novel Mechanism Involving Glycerol Dehydrogenase

    PubMed Central

    Liyanage, Hemachandra; Kashket, Shelby; Young, Michael; Kashket, Eva R.

    2001-01-01

    In contrast to gram-negative bacteria, little is known about the mechanisms by which gram-positive bacteria degrade the toxic metabolic intermediate methylglyoxal (MG). Clostridium beijerinckii BR54, a Tn1545 insertion mutant of the NCIMB 8052 strain, formed cultures that contained significantly more (free) MG than wild-type cultures. Moreover, BR54 was more sensitive to growth inhibition by added MG than the wild type, suggesting that it has a reduced ability to degrade MG. The single copy of Tn1545 in this strain lies just downstream from gldA, encoding glycerol dehydrogenase. As a result of antisense RNA production, cell extracts of BR54 possess significantly less glycerol dehydrogenase activity than wild-type cell extracts (H. Liyanage, M. Young, and E. R. Kashket, J. Mol. Microbiol. Biotechnol. 2:87–93, 2000). Inactivation of gldA in both C. beijerinckii and Clostridium difficile gave rise to pinpoint colonies that could not be subcultured, indicating that glycerol dehydrogenase performs an essential function in both organisms. We propose that this role is detoxification of MG. To our knowledge, this is the first report of targeted gene disruption in the C. difficile chromosome. PMID:11319074

  12. Subband engineering in n-type silicon nanowires using strain and confinement.

    PubMed

    Stanojević, Zlatan; Sverdlov, Viktor; Baumgartner, Oskar; Kosina, Hans

    2012-04-01

    We present a model based on k · p theory which is able to capture the subband structure effects present in ultra-thin strained silicon nanowires. For electrons, the effective mass and valley minima are calculated for different crystal orientations, thicknesses, and strains. The actual enhancement of the transport properties depends highly on the crystal orientation of the nanowire axis; for certain orientations strain and confinement can play together to give a significant increase of the electron mobility. We also show that the effects of both strain and confinement on mobility are generally more pronounced in nanowires than in thin films. We show that optimal transport properties can be expected to be achieved through a mix of confinement and strain. Our results are in good agreement with recent experimental findings.

  13. Local strain effect on the band gap engineering of graphene by a first-principles study

    SciTech Connect

    Gui, Gui; Booske, John; Ma, Zhenqiang E-mail: mazq@engr.wisc.edu; Morgan, Dane; Zhong, Jianxin E-mail: mazq@engr.wisc.edu

    2015-02-02

    We have systematically investigated the effect of local strain on electronic properties of graphene by first-principles calculations. Two major types of local strain, oriented along the zigzag and the armchair directions, have been studied. We find that local strain with a proper range and strength along the zigzag direction results in opening of significant band gaps in graphene, on the order of 10{sup −1 }eV; whereas, local strain along the armchair direction cannot open a significant band gap in graphene. Our results show that appropriate local strain can effectively open and tune the band gap in graphene; therefore, the electronic and transport properties of graphene can also be modified.

  14. Adherence of Clostridium thermocellum to cellulose.

    PubMed Central

    Bayer, E A; Kenig, R; Lamed, R

    1983-01-01

    The adherence of Clostridium thermocellum, a cellulolytic, thermophilic anaerobe, to its insoluble substrate (cellulose) was studied. The adherence phenomenon was determined to be selective for cellulose. The observed adherence was not significantly affected by various parameters, including salts, pH, temperature, detergents, or soluble sugars. A spontaneous adherence-defective mutant strain (AD2) was isolated from the wild-type strain YS. Antibodies were prepared against the bacterial cell surface and rendered specific to the cellulose-binding factor (CBF) by adsorption to mutant AD2 cells. By using these CBF-specific antibodies, crossed immunoelectrophoresis of cell extracts revealed a single discrete precipitation peak in the parent strain which was absent in the mutant. This difference was accompanied by an alteration in the polypeptide profile whereby sonicates of strain YS contained a 210,000-molecular-weight band which was missing in strain AD2. The CBF antigen could be removed from cell extracts by adsorption to cellulose. A combined gel-overlay--immunoelectrophoretic technique demonstrated that the cellulose-binding properties of the CBF were accompanied by carboxymethylcellulase activity. During the exponential phase of growth, a large part of the CBF antigen and related carboxymethylcellulase activity was associated with the cells of wild-type strain YS. However, the amounts decreased in stationary-phase cells. Cellobiose-grown mutant AD2 cells lacked the cell-associated CBF, but the latter was detected in the extracellular fluid. Increased levels of CBF were observed when cells were grown on cellulose. In addition, mutant AD2 regained cell-associated CBF together with the property of cellulose adherence. The presence of the CBF antigen and related adherence characteristics appeared to be a phenomenon common to other naturally occurring strains of this species. Images PMID:6630152

  15. Clostridium difficile colitis.

    PubMed

    Trnka, Y M; Lamont, J T

    1984-01-01

    Clostridium difficile has become one of the commonest pathogens of the lower intestinal tract. This organism appears unique in that infection almost always occurs during or after antibiotic therapy, suggesting that some component of the normal microflora prevents colonization by C. difficile. Once it has overgrown in the colon, C. difficile releases several toxins which cause tissue damage and diarrhea. Infection can range from a simple self-limited diarrheal illness to fulminant colitis with perforation and megacolon. Assay of stool filtrates reveals the presence of cytotoxin in nearly all patients with antibiotic-associated pseudomembranous colitis, and in approximately one third to one half of those with less severe infections. Effective therapy is available in the form of oral vancomycin, although the expense of this antibiotic has led to the use of oral metronidazole or bacitracin, which appear to be equally efficacious and considerably cheaper. Although we have learned a great deal about C. difficile in the past decade, a number of fascinating puzzles remain. We know very little about the immune response to this organism or its toxin, or whether a vaccine might someday be feasible. Similarly, we have very little insight into what effects antibodies exert on the normal colonic flora and how these effects allow C. difficile infection in a small percentage of patients. Studies of this pathogen will undoubtedly lead to a fuller understanding of the enormously complex and still mysterious microbial ferment which lives within our gastrointestinal tract. PMID:6369936

  16. Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica

    PubMed Central

    Nambou, Komi; Jian, Xingxing; Zhang, Xinkai; Wei, Liujing; Lou, Jiajia; Madzak, Catherine; Hua, Qiang

    2015-01-01

    Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA) and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y. lipolytica. Lycopene concentrations of 126 and 242 mg/L were achieved correspondingly from the FBA-independent and the FBA-assisted designed media in fed-batch cultivation mode. Transcriptional studies revealed upregulations of heterologous genes in media designed according to FBA, thus implying the efficiency of model predictions. Our study will potentially support upgraded lycopene and other terpenoids production from existing or prospect bioengineered strains of Y. lipolytica and/or closely related yeast species. PMID:26703753

  17. Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica.

    PubMed

    Nambou, Komi; Jian, Xingxing; Zhang, Xinkai; Wei, Liujing; Lou, Jiajia; Madzak, Catherine; Hua, Qiang

    2015-01-01

    Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA) and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y. lipolytica. Lycopene concentrations of 126 and 242 mg/L were achieved correspondingly from the FBA-independent and the FBA-assisted designed media in fed-batch cultivation mode. Transcriptional studies revealed upregulations of heterologous genes in media designed according to FBA, thus implying the efficiency of model predictions. Our study will potentially support upgraded lycopene and other terpenoids production from existing or prospect bioengineered strains of Y. lipolytica and/or closely related yeast species. PMID:26703753

  18. Reverse biological engineering of hrdB to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis

    PubMed Central

    Zhuo, Ying; Zhang, Wenquan; Chen, Difei; Gao, Hong; Tao, Jun; Liu, Mei; Gou, Zhongxuan; Zhou, Xianlong; Ye, Bang-Ce; Zhang, Qing; Zhang, Siliang; Zhang, Li-Xin

    2010-01-01

    Avermectin and its analogues are produced by the actinomycete Streptomyces avermitilis and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene, aveR, were up-regulated in the high-producing strain. The upstream promoter region of aveR was predicted and proved to be directly recognized by σhrdB in vitro. A mutant library of hrdB gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved hrdB expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of aveR was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the hrdB gene can not only elicit the overexpression of aveR but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems. PMID:20534557

  19. [Construction of the flavinogenic yeast Candida famata strains with high riboflavin kinase activity using gene engineering].

    PubMed

    Ishchuk, O P; Iatsyshyn, V Iu; Dmytruk, K V; Voronovs'kyĭ, A Ia; Fedorovych, D V; Sybirnyĭ, A A

    2006-01-01

    The recombinant strains of the flavinogenic yeast Candida famata, which contain the DNA fragment consisting of the FMN1 gene (encoding the riboflavin kinase, enzyme that converts riboflavin to flavinmononucleotide) driven by the strong promoters (the regulated RIB1 or constitutive TEF1 promoter) were isolated. Riboflavin kinase activity in the isolated transformants was tested. The 6-8-fold increase of the riboflavin kinase activity was shown in the recombinant strains containing the integrated Debaryomyces hansenii FMN1 gene under the strong constitutive TEF1 promoter. The recombinant strains can be used for the following construction of flavinmononucleotide overproducers. PMID:17290783

  20. Expression of a Heterologous Xylose Transporter in a Saccharomyces cerevisiae Strain Engineered to Utilize Xylose Improves Aerobic Xylose Co-consumption

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strains of Saccharomyces cerevisiae have been engineered to utilize xylose by expression of the genes for xylose reductase and xylitol dehydrogenase, or xylose isomerase. These strains are still limited in their ability to efficiently use xylose. Unlike native xylose assimilating yeasts such as Pi...

  1. Expression of a heterologous xylose transporter in a Saccharomyces cerevisiae strain engineered to utilize xylose increases xylose uptake and improves xylose/glucose co-consumption

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strains of Saccharomyces cerevisiae have been engineered to utilize xylose by expressing either the genes for xylose reductase and xylitol dehydrogenase, or for xylose isomerase. These strains still use xylose at sub-optimal rates for industrial fermentation. Unlike natural xylose fermenting yeast...

  2. Carrier Mobility Enhancement of Tensile Strained Si and SiGe Nanowires via Surface Defect Engineering.

    PubMed

    Ma, J W; Lee, W J; Bae, J M; Jeong, K S; Oh, S H; Kim, J H; Kim, S-H; Seo, J-H; Ahn, J-P; Kim, H; Cho, M-H

    2015-11-11

    Changes in the carrier mobility of tensile strained Si and SiGe nanowires (NWs) were examined using an electrical push-to-pull device (E-PTP, Hysitron). The changes were found to be closely related to the chemical structure at the surface, likely defect states. As tensile strain is increased, the resistivity of SiGe NWs deceases in a linear manner. However, the corresponding values for Si NWs increased with increasing tensile strain, which is closely related to broken bonds induced by defects at the NW surface. Broken bonds at the surface, which communicate with the defect state of Si are critically altered when Ge is incorporated in Si NW. In addition, the number of defects could be significantly decreased in Si NWs by incorporating a surface passivated Al2O3 layer, which removes broken bonds, resulting in a proportional decrease in the resistivity of Si NWs with increasing strain. Moreover, the presence of a passivation layer dramatically increases the extent of fracture strain in NWs, and a significant enhancement in mobility of about 2.6 times was observed for a tensile strain of 5.7%.

  3. Band Gap Engineering with Ultralarge Biaxial Strains in Suspended Monolayer MoS2.

    PubMed

    Lloyd, David; Liu, Xinghui; Christopher, Jason W; Cantley, Lauren; Wadehra, Anubhav; Kim, Brian L; Goldberg, Bennett B; Swan, Anna K; Bunch, J Scott

    2016-09-14

    We demonstrate the continuous and reversible tuning of the optical band gap of suspended monolayer MoS2 membranes by as much as 500 meV by applying very large biaxial strains. By using chemical vapor deposition (CVD) to grow crystals that are highly impermeable to gas, we are able to apply a pressure difference across suspended membranes to induce biaxial strains. We observe the effect of strain on the energy and intensity of the peaks in the photoluminescence (PL) spectrum and find a linear tuning rate of the optical band gap of 99 meV/%. This method is then used to study the PL spectra of bilayer and trilayer devices under strain and to find the shift rates and Grüneisen parameters of two Raman modes in monolayer MoS2. Finally, we use this result to show that we can apply biaxial strains as large as 5.6% across micron-sized areas and report evidence for the strain tuning of higher level optical transitions.

  4. Band Gap Engineering with Ultralarge Biaxial Strains in Suspended Monolayer MoS2.

    PubMed

    Lloyd, David; Liu, Xinghui; Christopher, Jason W; Cantley, Lauren; Wadehra, Anubhav; Kim, Brian L; Goldberg, Bennett B; Swan, Anna K; Bunch, J Scott

    2016-09-14

    We demonstrate the continuous and reversible tuning of the optical band gap of suspended monolayer MoS2 membranes by as much as 500 meV by applying very large biaxial strains. By using chemical vapor deposition (CVD) to grow crystals that are highly impermeable to gas, we are able to apply a pressure difference across suspended membranes to induce biaxial strains. We observe the effect of strain on the energy and intensity of the peaks in the photoluminescence (PL) spectrum and find a linear tuning rate of the optical band gap of 99 meV/%. This method is then used to study the PL spectra of bilayer and trilayer devices under strain and to find the shift rates and Grüneisen parameters of two Raman modes in monolayer MoS2. Finally, we use this result to show that we can apply biaxial strains as large as 5.6% across micron-sized areas and report evidence for the strain tuning of higher level optical transitions. PMID:27509768

  5. Strain-engineering the anisotropic electrical conductance in ReS2 monolayer

    NASA Astrophysics Data System (ADS)

    Yu, Sheng; Zhu, Hao; Eshun, Kwesi; Shi, Chen; Zeng, Min; Li, Qiliang

    2016-05-01

    Rhenium disulfide (ReS2) is a semiconducting layered transition metal dichalcogenide that exhibits a stable distorted 1 T (Re in octahedral coordination) phase. The reduced symmetry in ReS2 leads to in-plane anisotropy in various material properties. In this work, we performed a comprehensive first-principle computational study of strain effect on the anisotropic mechanical and electronic properties of ReS2 monolayers. We found that the anisotropic ratio in electron mobility along two principle axes is 2.36 while the ratio in hole mobility reaches 7.76. The study of strain applied along different directions shows that the elastic modulus is largest for out-of-plane direction, and the strain along a-direction induces indirect bandgap while strain along b- or c-direction does not. In addition, the carrier mobility can be significantly improved by the c-direction tensile strain. This study indicates that the ReS2 monolayer has promising applications in nanoscale strain sensor and conductance-switch FETs.

  6. Sorbitol synthesis by an engineered Lactobacillus casei strain expressing a sorbitol-6-phosphate dehydrogenase gene within the lactose operon.

    PubMed

    Nissen, Lorenzo; Pérez-Martínez, Gaspar; Yebra, María J

    2005-08-01

    Sorbitol is claimed to have important health-promoting effects and Lactobacillus casei is a lactic acid bacterium relevant as probiotic and used as a cheese starter culture. A sorbitol-producing L. casei strain might therefore be of considerable interest in the food industry. A recombinant strain of L. casei was constructed by the integration of a d-sorbitol-6-phosphate dehydrogenase-encoding gene (gutF) in the chromosomal lactose operon (strain BL232). gutF expression in this strain followed the same regulation as that of the lac genes, that is, it was repressed by glucose and induced by lactose. (13)C-nuclear magnetic resonance analysis of supernatants of BL232 resting cells demonstrated that, when pre-grown on lactose, cells were able to synthesize sorbitol from glucose. Inactivation of the l-lactate dehydrogenase gene in BL232 led to an increase in sorbitol production, suggesting that the engineered route provides an alternative pathway for NAD(+) regeneration. PMID:16002237

  7. Effect of fiber volume fraction on the off-crack-plane fracture energy in strain-hardening engineered cementitious composites

    SciTech Connect

    Maalej, M.; Hashida, Toshiyuki; Li, V.C.

    1995-12-01

    In this paper, the results of an experimental study on the effect of fiber volume fraction on the off-crack-plane fracture energy in a strain-hardening engineered cementitious composite (ECC) are presented. Unlike the well-known quasi-brittle behavior of fiber-reinforced concrete, ECC exhibits quasi-ductile response by developing a large damage zone prior to fracture localization. In the damage zone, the material is microcracked but continues to strain-harden locally. The areal dimension of the damage zone has been observed to be on the order of 1,000 cm{sup 2} in double cantilever beam specimens. The energy absorption of the off-crack-plane inelastic deformation process has been measured to be more than 50% of the total fracture energy of up to 34 kJ/m{sup 2}. This magnitude of fracture energy is the highest ever reported for a fiber cementitious composite.

  8. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

    DOE PAGES

    Dickinson, Quinn; Bottoms, Scott; Hinchman, Li; McIlwain, Sean; Li, Sheena; Myers, Chad L.; Boone, Charles; Coon, Joshua J.; Hebert, Alexander; Sato, Trey K.; et al

    2016-01-20

    In this study, imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae. As a result, we found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effectsmore » of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2Δ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance. In conclusion, this work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.« less

  9. A Killed, Genetically Engineered Derivative of a Wild-Type Extraintestinal Pathogenic E. coli strain is a Vaccine Candidate

    PubMed Central

    Russo, Thomas A.; Beanan, Janet M.; Olson, Ruth; Genagon, Stacy A.; MacDonald, Ulrike; Cope, John J.; Davidson, Bruce A.; Johnston, Brian; Johnson, James R.

    2007-01-01

    Infections due to extraintestinal pathogenic E. coli (ExPEC) result in significant morbidity, mortality and increased healthcare costs. An efficacious vaccine against ExPEC would be desirable. In this report we explore the use of killed-whole E. coli as a vaccine immunogen. Given the diversity of capsule and O-antigens in ExPEC we have hypothesized that alternative targets are viable vaccine candidates. We have also hypothesized that immunization with a genetically engineered strain that is deficient in the capsule and O-antigen will generate a greater immune response against antigens other than the capsular and O-antigen epitopes than a wild-type strain. Lastly, we hypothesize that mucosal immunization with killed E. coli has the potential to generate a significant immune response. In this study we demonstrated that nasal immunization with a formalin-killed ExPEC derivative deficient in capsule and O-antigen results in a significantly greater overall humoral response compared to its wild-type derivative (which demonstrates that capsule and/or the O-antigen impede the development of an optimal humoral immune response) and a significantly greater immune response against non-capsular and O-antigen epitopes. These antibodies also bound to a subset of heterologous ExPEC strains and enhanced neutrophil-mediated bactericidal activity against the homologous and a heterologous strain. Taken together these studies support the concept that formalin-killed genetically engineered ExPEC derivatives are whole cell vaccine candidates to prevent infections due to ExPEC. PMID:17306426

  10. Interfacially engineered oxygen octahedral rotations and their impact on strain relief in coherently grown SrRu O3 films

    NASA Astrophysics Data System (ADS)

    Kan, Daisuke; Wakabayashi, Yusuke; Tajiri, Hiroo; Shimakawa, Yuichi

    2016-07-01

    We report synchrotron x-ray diffraction investigations of interfacially engineered oxygen octahedral rotations and their impact on strain relief in perovskite SrRu O3 films. We show that octahedral rotations with distinct patterns and magnitudes can be accommodated into coherently grown films. The SrRu O3 film grown directly on the GdSc O3 substrate has the Ru O6 octahedral rotation with the a-b+c- pattern in the Glazer notation and the rotation angles of αrot=6.6 ±0 .2∘ , βrot=5.5 ±0 .2∘ , and γrot=3.6 ±0 .2∘ . On the other hand, when a 1-nm-thick BaTi O3 layer without Ti O6 rotations is inserted between the SrRu O3 and GdSc O3 , the SrRu O3 has the Ru O6 rotation with a-b0c+ , and αrot=5.6 ±0 .8∘ and γrot=3.6 ±0 .8∘ . These results indicate that there are some degrees of freedom in the octahedral rotations accommodated in SrRu O3 depending on the interface structure and that the γrot rotations play the important roles in the film's structural properties when the rotation about the [010] pc axis is blocked. We also found that the strain relief in the film is influenced by the interfacially engineered octahedral rotations. The interfacial BaTi O3 layer results in the in-plane periodic lattice modulation in the t-SRO film, allowing for the anisotropic relief of the substrate-induced strain. The results highlight the importance of the interface structure as a factor, determining not only octahedral rotations in coherently grown SRO films but also the strain reliefs in them.

  11. Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks.

    PubMed

    Chen, Yun; Nielsen, Jens

    2013-12-01

    Bio-based production of chemical building blocks from renewable resources is an attractive alternative to petroleum-based platform chemicals. Metabolic pathway and strain engineering is the key element in constructing robust microbial chemical factories within the constraints of cost effective production. Here we discuss how the development of computational algorithms, novel modules and methods, omics-based techniques combined with modeling refinement are enabling reduction in development time and thus advance the field of industrial biotechnology. We further discuss how recent technological developments contribute to the development of novel cell factories for the production of the building block chemicals: adipic acid, succinic acid and 3-hydroxypropionic acid.

  12. Autism and Clostridium tetani.

    PubMed

    Bolte, E R

    1998-08-01

    Autism is a severe developmental disability believed to have multiple etiologies. This paper outlines the possibility of a subacute, chronic tetanus infection of the intestinal tract as the underlying cause for symptoms of autism observed in some individuals. A significant percentage of individuals with autism have a history of extensive antibiotic use. Oral antibiotics significantly disrupt protective intestinal microbiota, creating a favorable environment for colonization by opportunistic pathogens. Clostridium tetani is an ubiquitous anaerobic bacillus that produces a potent neurotoxin. Intestinal colonization by C. tetani, and subsequent neurotoxin release, have been demonstrated in laboratory animals which were fed vegetative cells. The vagus nerve is capable of transporting tetanus neurotoxin (TeNT) and provides a route of ascent from the intestinal tract to the CNS. This route bypasses TeNT's normal preferential binding sites in the spinal cord, and therefore the symptoms of a typical tetanus infection are not evident. Once in the brain, TeNT disrupts the release of neurotransmitters by the proteolytic cleavage of synaptobrevin, a synaptic vesicle membrane protein. This inhibition of neurotransmitter release would explain a wide variety of behavioral deficits apparent in autism. Lab animals injected in the brain with TeNT have exhibited many of these behaviors. Some children with autism have also shown a significant reduction in stereotyped behaviors when treated with antimicrobials effective against intestinal clostridia. When viewed as sequelae to a subacute, chronic tetanus infection, many of the puzzling abnormalities of autism have a logical basis. A review of atypical tetanus cases, and strategies to test the validity of this paper's hypothesis, are included. PMID:9881820

  13. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain.

    PubMed

    Florea, Michael; Hagemann, Henrik; Santosa, Gabriella; Abbott, James; Micklem, Chris N; Spencer-Milnes, Xenia; de Arroyo Garcia, Laura; Paschou, Despoina; Lazenbatt, Christopher; Kong, Deze; Chughtai, Haroon; Jensen, Kirsten; Freemont, Paul S; Kitney, Richard; Reeve, Benjamin; Ellis, Tom

    2016-06-14

    Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell. To further its use as an organism for biotechnology, we sequenced its genome and demonstrate genetic circuits that enable functionalization and patterning of heterologous gene expression within the cellulose matrix. This work lays the foundations for using genetic engineering to produce cellulose-based materials, with numerous applications in basic science, materials engineering, and biotechnology.

  14. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain

    PubMed Central

    Florea, Michael; Hagemann, Henrik; Santosa, Gabriella; Micklem, Chris N.; Spencer-Milnes, Xenia; de Arroyo Garcia, Laura; Paschou, Despoina; Lazenbatt, Christopher; Kong, Deze; Chughtai, Haroon; Jensen, Kirsten; Freemont, Paul S.; Kitney, Richard; Reeve, Benjamin; Ellis, Tom

    2016-01-01

    Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae. Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell. To further its use as an organism for biotechnology, we sequenced its genome and demonstrate genetic circuits that enable functionalization and patterning of heterologous gene expression within the cellulose matrix. This work lays the foundations for using genetic engineering to produce cellulose-based materials, with numerous applications in basic science, materials engineering, and biotechnology. PMID:27247386

  15. Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum.

    PubMed

    Jang, Yu-Sin; Lee, Jin Young; Lee, Joungmin; Park, Jin Hwan; Im, Jung Ae; Eom, Moon-Ho; Lee, Julia; Lee, Sang-Hyun; Song, Hyohak; Cho, Jung-Hee; Seung, Do Young; Lee, Sang Yup

    2012-10-23

    Butanol is an important industrial solvent and advanced biofuel that can be produced by biphasic fermentation by Clostridium acetobutylicum. It has been known that acetate and butyrate first formed during the acidogenic phase are reassimilated to form acetone-butanol-ethanol (cold channel). Butanol can also be formed directly from acetyl-coenzyme A (CoA) through butyryl-CoA (hot channel). However, little is known about the relative contributions of the two butanol-forming pathways. Here we report that the direct butanol-forming pathway is a better channel to optimize for butanol production through metabolic flux and mass balance analyses. Butanol production through the hot channel was maximized by simultaneous disruption of the pta and buk genes, encoding phosphotransacetylase and butyrate kinase, while the adhE1(D485G) gene, encoding a mutated aldehyde/alcohol dehydrogenase, was overexpressed. The ratio of butanol produced through the hot channel to that produced through the cold channel increased from 2.0 in the wild type to 18.8 in the engineered BEKW(pPthlAAD(**)) strain. By reinforcing the direct butanol-forming flux in C. acetobutylicum, 18.9 g/liter of butanol was produced, with a yield of 0.71 mol butanol/mol glucose by batch fermentation, levels which are 160% and 245% higher than those obtained with the wild type. By fed-batch culture of this engineered strain with in situ recovery, 585.3 g of butanol was produced from 1,861.9 g of glucose, with the yield of 0.76 mol butanol/mol glucose and productivity of 1.32 g/liter/h. Studies of two butanol-forming routes and their effects on butanol production in C. acetobutylicum described here will serve as a basis for further metabolic engineering of clostridia aimed toward developing a superior butanol producer. IMPORTANCE Renewable biofuel is one of the answers to solving the energy crisis and climate change problems. Butanol produced naturally by clostridia has superior liquid fuel characteristics and thus has

  16. Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor.

    PubMed

    Hahnke, Sarah; Striesow, Jutta; Elvert, Marcus; Mollar, Xavier Prieto; Klocke, Michael

    2014-08-01

    A novel anaerobic, mesophilic, hydrogen-producing bacterium, designated strain M2/40(T), was isolated from a mesophilic, two-phase, laboratory-scale biogas reactor fed continuously with maize silage supplemented with 5% wheat straw. 16S rRNA gene sequence comparison revealed an affiliation to the genus Clostridium sensu stricto (cluster I of the clostridia), with Clostridium cellulovorans as the closest characterized species, showing 93.8% sequence similarity to the type strain. Cells of strain M2/40(T) were rods to elongated filamentous rods that showed variable Gram staining. Optimal growth occurred at 35 °C and at pH 7. Grown on glucose, the main fermentation products were H2, CO2, formate, lactate and propionate. The DNA G+C content was 29.6 mol%. The major fatty acids (>10 %) were C(16 : 0), summed feature 10 (C(18 : 1)ω11c/ω9t/ω6t and/or unknown ECL 17.834) and C(18 : 1)ω11c dimethylacetal. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain M2/40(T) represents a novel species within the genus Clostridium, for which we propose the name Clostridium bornimense sp. nov. The type strain is M2/40(T) ( = DSM 25664(T) = CECT 8097(T)).

  17. Characterization of a symbiotic coculture of Clostridium thermohydrosulfuricum YM3 and clostridium thermocellum YM4

    SciTech Connect

    Mori, Yutaka )

    1990-01-01

    Clostridium thermohydrosulfuricum YM3 and C. thermocellum YM4 were isolated from a coculture which was obtained from an enrichment culture inoculated with volcanic soil in Izu Peninsula, Japan. Strain YM3 had advantages over reported C. thermohydrosulfuricum strains in that it fermented inulin and could accumulate ethanol up to 1.3% (wt/vol). The highest ethanol yield obtained was 1.96 mol/mol of anhydroglucose unit in cellobiose. Strain YM4 had features different from those reported in C. thermocellum strains: it formed spores rarely (at a frequency of <10{sup {minus}5}), it required CO{sub 2} and Na{sub 2}CO{sub 3} for growth, and it fermented sucrose. Strain YM4 completely decomposed 1% Avicel within 25 h when the inoculum constituted 2 % of the culture medium volume, and it produced 0.22 U of Avicelase and 2.21 U of carboxymethylcellulase per ml of the medium. The doubling times on Avicel, cellobiose, and glucose were 2.7, 1.1, and 1.6 h, respectively. Reconstructed cocultures of strains YM3 and YM4 were very stable and degraded Avicel more rapidly than did strain YM4 monoculture. Without yeast extract, neither microorganism was able to grow. However, the coculture grew on cellulose without yeast extract and produced ethanol in high yield. Moreover, cell-free spent culture broth of strain YM3 could replace yeast extract in supporting the growth of strain YM4. The symbiotic relationship of the two bacteria in cellulose fermentation is probably a case of mutualism.

  18. Strain-Engineered Graphene Grown on Hexagonal Boron Nitride by Molecular Beam Epitaxy.

    PubMed

    Summerfield, Alex; Davies, Andrew; Cheng, Tin S; Korolkov, Vladimir V; Cho, YongJin; Mellor, Christopher J; Foxon, C Thomas; Khlobystov, Andrei N; Watanabe, Kenji; Taniguchi, Takashi; Eaves, Laurence; Novikov, Sergei V; Beton, Peter H

    2016-01-01

    Graphene grown by high temperature molecular beam epitaxy on hexagonal boron nitride (hBN) forms continuous domains with dimensions of order 20 μm, and exhibits moiré patterns with large periodicities, up to ~30 nm, indicating that the layers are highly strained. Topological defects in the moiré patterns are observed and attributed to the relaxation of graphene islands which nucleate at different sites and subsequently coalesce. In addition, cracks are formed leading to strain relaxation, highly anisotropic strain fields, and abrupt boundaries between regions with different moiré periods. These cracks can also be formed by modification of the layers with a local probe resulting in the contraction and physical displacement of graphene layers. The Raman spectra of regions with a large moiré period reveal split and shifted G and 2D peaks confirming the presence of strain. Our work demonstrates a new approach to the growth of epitaxial graphene and a means of generating and modifying strain in graphene.

  19. Strain Engineering of the Band Gap of HgTe Quantum Wells Using Superlattice Virtual Substrates

    NASA Astrophysics Data System (ADS)

    Leubner, Philipp; Lunczer, Lukas; Brüne, Christoph; Buhmann, Hartmut; Molenkamp, Laurens W.

    2016-08-01

    The HgTe quantum well (QW) is a well-characterized two-dimensional topological insulator (2D TI). Its band gap is relatively small (typically on the order of 10 meV), which restricts the observation of purely topological conductance to low temperatures. Here, we utilize the strain dependence of the band structure of HgTe QWs to address this limitation. We use CdTe-Cd 0.5Zn0.5Te strained-layer superlattices on GaAs as virtual substrates with adjustable lattice constant to control the strain of the QW. We present magnetotransport measurements, which demonstrate a transition from a semimetallic to a 2D-TI regime in wide QWs, when the strain is changed from tensile to compressive. Most notably, we demonstrate a much enhanced energy gap of 55 meV in heavily compressively strained QWs. This value exceeds the highest possible gap on common II-VI substrates by a factor of 2-3, and extends the regime where the topological conductance prevails to much higher temperatures.

  20. Strain Engineering of the Band Gap of HgTe Quantum Wells Using Superlattice Virtual Substrates.

    PubMed

    Leubner, Philipp; Lunczer, Lukas; Brüne, Christoph; Buhmann, Hartmut; Molenkamp, Laurens W

    2016-08-19

    The HgTe quantum well (QW) is a well-characterized two-dimensional topological insulator (2D TI). Its band gap is relatively small (typically on the order of 10 meV), which restricts the observation of purely topological conductance to low temperatures. Here, we utilize the strain dependence of the band structure of HgTe QWs to address this limitation. We use CdTe-Cd_{0.5}Zn_{0.5}Te strained-layer superlattices on GaAs as virtual substrates with adjustable lattice constant to control the strain of the QW. We present magnetotransport measurements, which demonstrate a transition from a semimetallic to a 2D-TI regime in wide QWs, when the strain is changed from tensile to compressive. Most notably, we demonstrate a much enhanced energy gap of 55 meV in heavily compressively strained QWs. This value exceeds the highest possible gap on common II-VI substrates by a factor of 2-3, and extends the regime where the topological conductance prevails to much higher temperatures. PMID:27588871

  1. Strain-Engineered Graphene Grown on Hexagonal Boron Nitride by Molecular Beam Epitaxy

    PubMed Central

    Summerfield, Alex; Davies, Andrew; Cheng, Tin S.; Korolkov, Vladimir V.; Cho, YongJin; Mellor, Christopher J.; Foxon, C. Thomas; Khlobystov, Andrei N.; Watanabe, Kenji; Taniguchi, Takashi; Eaves, Laurence; Novikov, Sergei V.; Beton, Peter H.

    2016-01-01

    Graphene grown by high temperature molecular beam epitaxy on hexagonal boron nitride (hBN) forms continuous domains with dimensions of order 20 μm, and exhibits moiré patterns with large periodicities, up to ~30 nm, indicating that the layers are highly strained. Topological defects in the moiré patterns are observed and attributed to the relaxation of graphene islands which nucleate at different sites and subsequently coalesce. In addition, cracks are formed leading to strain relaxation, highly anisotropic strain fields, and abrupt boundaries between regions with different moiré periods. These cracks can also be formed by modification of the layers with a local probe resulting in the contraction and physical displacement of graphene layers. The Raman spectra of regions with a large moiré period reveal split and shifted G and 2D peaks confirming the presence of strain. Our work demonstrates a new approach to the growth of epitaxial graphene and a means of generating and modifying strain in graphene. PMID:26928710

  2. Lung stress, strain, and energy load: engineering concepts to understand the mechanism of ventilator-induced lung injury (VILI).

    PubMed

    Nieman, Gary F; Satalin, Joshua; Andrews, Penny; Habashi, Nader M; Gatto, Louis A

    2016-12-01

    It was recently shown that acute respiratory distress syndrome (ARDS) mortality has not been reduced in over 15 years and remains ~40 %, even with protective low tidal volume (LVt) ventilation. Thus, there is a critical need to develop novel ventilation strategies that will protect the lung and reduce ARDS mortality. Protti et al. have begun to analyze the impact of mechanical ventilation on lung tissue using engineering methods in normal pigs ventilated for 54 h. They used these methods to assess the impact of a mechanical breath on dynamic and static global lung strain and energy load. Strain is the change in lung volume in response to an applied stress (i.e., Tidal Volume-Vt). This study has yielded a number of exciting new concepts including the following: (1) Individual mechanical breath parameters (e.g., Vt or Plateau Pressure) are not directly correlated with VILI but rather any combination of parameters that subject the lung to excessive dynamic strain and energy/power load will cause VILI; (2) all strain is not equal; dynamic strain resulting in a dynamic energy load (i.e., kinetic energy) is more damaging to lung tissue than static strain and energy load (i.e., potential energy); and (3) a critical consideration is not just the size of the Vt but the size of the lung that is being ventilated by this Vt. This key concept merits attention since our current protective ventilation strategies are fixated on the priority of keeping the Vt low. If the lung is fully inflated, a large Vt is not necessarily injurious. In conclusion, using engineering concepts to analyze the impact of the mechanical breath on the lung is a novel new approach to investigate VILI mechanisms and to help design the optimally protective breath. Data generated using these methods have challenged some of the current dogma surrounding the mechanisms of VILI and of the components in the mechanical breath necessary for lung protection. PMID:27316442

  3. Clostridium punense sp. nov., an obligate anaerobe isolated from healthy human faeces.

    PubMed

    Lanjekar, Vikram Bholanath; Marathe, Nachiket Prakash; Shouche, Yogesh Shreepad; Ranade, Dilip Ramchandra

    2015-12-01

    An obligately anaerobic, rod-shaped (0.5-1.0 × 2.0-10.0 μm), Gram-stain-positive bacterium, occurring mainly singly or in pairs, and designated BLPYG-8T, was isolated from faeces of a healthy human volunteer aged 56 years. Cells were non-motile. Oval, terminal spores were formed that swell the cells. The strain was affiliated with the genus Clostridium sensu stricto (Clostridium rRNA cluster I) as revealed by 16S rRNA gene sequence analysis. Strain BLPYG-8T showed 97.3 to 97.4 % 16S rRNA gene sequence similarity with Clostridium sulfidigenes DSM 18982T, Clostridium subterminale DSM 6970T and Clostridium thiosulfatireducens DSM 13105T. DNA-DNA hybridization and phenotypic analysis showed that the strain was distinct from its closest relatives, C. sulfidigenes DSM 18982T, C. subterminale DSM 6970T, C. thiosulfatireducens DSM 13105T with 54.2, 53.9 and 53.3 % DNA-DNA relatedness, respectively. Strain BLPYG-8T grew in PYG broth at temperatures between 20 and 40 °C (optimum 37 °C). The strain utilized a range of amino acids as well as carbohydrates as a source of carbon and energy. Glucose fermentation resulted in the formation of volatile fatty acids mainly acetic acid, n-butyric acid and organic acids such as succinic and lactic acid. The DNA G+C content of strain BLPYG-8T was 44.1 mol%. The major fatty acids (>10 %) were C14 : 0, iso-C15 : 0, C16 : 1ω7c and C16 : 0. Phylogenetic analysis and specific phenotypic characteristics and/or DNA G+C content differentiated the strain from its closest relatives. On the basis of these data, strain BLPYG-8T represents a novel species of the genus Clostridium, for which the name Clostridium punense sp. nov. is proposed. The type strain is BLPYG-8T ( = DSM 28650T = CCUG 64195T = MCC 2737T).

  4. Artificial symbiosis for acetone-butanol-ethanol (ABE) fermentation from alkali extracted deshelled corn cobs by co-culture of Clostridium beijerinckii and Clostridium cellulovorans

    PubMed Central

    2014-01-01

    Background Butanol is an industrial commodity and also considered to be a more promising gasoline substitute compared to ethanol. Renewed attention has been paid to solvents (acetone, butanol and ethanol) production from the renewable and inexpensive substrates, for example, lignocellulose, on account of the depletion of oil resources, increasing gasoline prices and deteriorating environment. Limited to current tools for genetic manipulation, it is difficult to develop a genetically engineered microorganism with combined ability of lignocellulose utilization and solvents production. Mixed culture of cellulolytic microorganisms and solventogenic bacteria provides a more convenient and feasible approach for ABE fermentation due to the potential for synergistic utilization of the metabolic pathways of two organisms. But few bacteria pairs succeeded in producing biobutanol of high titer or high productivity without adding butyrate. The aim of this work was to use Clostridium cellulovorans 743B to saccharify lignocellulose and produce butyric acid, instead of adding cellulase and butyric acid to the medium, so that the soluble sugars and butyric acid generated can be subsequently utilized by Clostridium beijerinckii NCIMB 8052 to produce butanol in one pot reaction. Results A stable artificial symbiotic system was constructed by co-culturing a celluloytic, anaerobic, butyrate-producing mesophile (C. cellulovorans 743B) and a non-celluloytic, solventogenic bacterium (C. beijerinckii NCIMB 8052) to produce solvents by consolidated bioprocessing (CBP) with alkali extracted deshelled corn cobs (AECC), a low-cost renewable feedstock, as the sole carbon source. Under optimized conditions, the co-culture degraded 68.6 g/L AECC and produced 11.8 g/L solvents (2.64 g/L acetone, 8.30 g/L butanol and 0.87 g/L ethanol) in less than 80 h. Besides, a real-time PCR assay based on the 16S rRNA gene sequence was performed to study the dynamics of the abundance of each strain

  5. High energy white beam x-ray diffraction studies of residual strains in engineering components

    NASA Astrophysics Data System (ADS)

    Zhang, S. Y.; Vorster, W.; Jun, T. S.; Song, X.; Golshan, M.; Laundy, D.; Walsh, M. J.; Korsunsky, A. M.

    2008-09-01

    In order to predict the durability of engineering components and improve performance, it is mandatory to understand residual stresses. The last decade has witnessed a significant increase of residual stress evaluation using diffraction of penetrating radiation, such as neutrons or high energy X-rays. They provide a powerful non-destructive method for determining the level of residual stresses in engineering components through precise characterisation of interplanar crystal lattice spacing. The unique non-destructive nature of these measurement techniques is particularly beneficial in the context of engineering design, since it allows the evaluation of a variety of structural and deformational parameters inside real components without material removal, or at worst with minimal interference. However, while most real engineering components have complex shape and are often large in size, leading to measurement and interpretation difficulties, since experimental facilities usually have limited space for mounting the sample, limited sample travel range, limited loading capacity of the sample positioning system, etc. Consequently, samples often have to be sectioned, requiring appropriate corrections on measured data; or facilities must be improved. Our research group has contributed to the development of engineering applications of high-energy X-ray diffraction methods for residual stress evaluation, both at synchrotron sources and in the lab setting, including multiple detector setup, large engineering component manipulation and measurement at the UK Synchrotron Radiation Source (SRS Daresbury), and in our lab at Oxford. A nickel base superalloy combustion casing and a large MIG welded Al alloy plate were successfully studied.

  6. Sexual recombination as a tool for engineering industrial Penicillium chrysogenum strains.

    PubMed

    Dahlmann, Tim A; Böhm, Julia; Becker, Kordula; Kück, Ulrich

    2015-11-01

    The recent discovery and functional characterization of opposite mating-type loci in the industrial penicillin producer Penicillium chrysogenum demonstrated their regulatory role in sexual as well as asexual development. Subsequent experiments further showed that a sexual life cycle can be induced in P. chrysogenum that was for long believed to reproduce exclusively by asexual propagation. Finally, crossing of wild type and production strains resulted in the generation of recombinant ascospore isolates. We predict from these recent findings that recombinant progeny for industrial applications can be obtained by sexual crossings and discuss experimental difficulties that occur when parental strains with karyotype heterogeneity are used for mating.

  7. Strain-engineering the anisotropic electrical conductance of few-layer black phosphorus.

    PubMed

    Fei, Ruixiang; Yang, Li

    2014-05-14

    Newly fabricated few-layer black phosphorus and its monolayer structure, phosphorene, are expected to be promising for electronic and optical applications because of their finite direct band gaps and sizable but anisotropic electronic mobility. By first-principles simulations, we show that this unique anisotropic free-carrier mobility can be controlled by using simple strain conditions. With the appropriate biaxial or uniaxial strain (4-6%), we can rotate the preferred conducting direction by 90°. This will be useful for exploring unusual quantum Hall effects and exotic electronic and mechanical applications based on phosphorene.

  8. Comparison of melibiose utilizing baker's yeast strains produced by genetic engineering and classical breeding.

    PubMed

    Vincent, S F; Bell, P J; Bissinger, P; Nevalainen, K M

    1999-02-01

    Yeast strains currently used in the baking industry cannot fully utilize the trisaccharide raffinose found in beet molasses due to the absence of melibiase (alpha-galactosidase) activity. To overcome this deficiency, the MEL1 gene encoding melibiase enzyme was introduced into baker's yeast by both classical breeding and recombinant DNA technology. Both types of yeast strains were capable of vigorous fermentation in the presence of high levels of sucrose, making them suitable for the rapidly developing Asian markets where high levels of sugar are used in bread manufacture. Melibiase expression appeared to be dosage-dependent, with relatively low expression sufficient for complete melibiose utilization in a model fermentation system.

  9. Strain-Engineering the Anisotropic Electrical Conductance of Few-Layer Black Phosphorus

    NASA Astrophysics Data System (ADS)

    Fei, Ruixiang; Yang, Li

    2014-05-01

    Newly fabricated monolayer phosphorene and its few-layer structures are expected to be promising for electronic and optical applications because of their finite direct band gaps and sizable but anisotropic electronic mobility. By first-principles simulations, we show that this unique anisotropic conductance can be controlled by using simple strain conditions. With the appropriate biaxial or uniaxial strain, we can rotate the preferred conducting direction by 90 degrees. This will be of useful for exploring quantum Hall effects, and exotic electronic and mechanical applications based on phosphorene.

  10. Germanium-on-Silicon Strain Engineered Materials for Improved Device Performance Grown by Chemical Vapor Deposition

    NASA Astrophysics Data System (ADS)

    Bharathan, Jayesh Moorkoth

    The primary goal of this research is to develop a chemical vapor deposition process for growing epitaxial films of germanium on silicon (001) substrates with two-dimensional (2-D) morphology, and a low density of threading dislocations. Growth was carried out in a reduced-pressure chemical vapor deposition (RPCVD) system by a two-step growth technique. An accurate knowledge of elastic constants of thin films is important in understanding the effect of strain on material properties. Residual thermal strain was used to measure the Poisson ratio of Ge films grown on Si(001) substrates, by the sin2Psi method and highresolution x-ray diffraction. The Poisson ratio of the Ge films was measured to be 0.25, compared to the bulk value of 0.27. The result was found to be independent of film thickness and defect density, which confirmed that the strain is associated with the elastic response of the film. The study showed that the use of Poisson ratio instead of bulk compliance values yields a more accurate description of the state of in-plane strain present in the film. The experimentally measured in-plane strain in Ge films was found to be lower than the theoretical calculations based on the differential thermal expansion coefficients of Si and Ge. The mechanism of thermal misfit strain relaxation in epitaxial Ge films grown on Si(001) substrates was investigated by x-ray diffraction, and transmission electron microscopy. Lattice misfit strain associated with Ge/(001)Si mismatched epitaxy is relieved by a network of Lomer edge misfit dislocations during the first step of the growth technique. However, thermal misfit strain energy during growth is relieved by interdiffusion mechanism at the heterointerface. Two SiGe compositions containing 0.5 and 6.0 atomic percent Si were detected that relieve the thermal mismatch strain associated with the two steps of the growth process. This study discusses the importance of interdiffusion mechanism in relieving small misfit strains

  11. Molecular epidemiology of endemic Clostridium difficile infection.

    PubMed Central

    Fawley, W. N.; Wilcox, M. H.

    2001-01-01

    This is the first study to provide a comprehensive insight into the molecular epidemiology of endemic Clostridium difficile and particularly that associated with a recently recognized epidemic strain. We DNA fingerprinted all C. difficile isolates from the stools of patients with symptomatic antibiotic-associated diarrhoea and from repeated samples of the inanimate ward environment on two elderly medicine hospital wards over a 22-month period. Notably, C. difficile was not recoverable from either ward immediately before opening, but was found on both wards within 1-3 weeks of opening, and the level of environmental contamination rose markedly during the first 6 months of the study period. C. difficile infection (CDI) incidence data correlated significantly with the prevalence of environmental C. difficile on ward B (r = 0.76, P < 0.05) but not on ward A (r = 0.26, P > 0.05). We found that RAPD and RS-PCR typing had similar discriminatory power, although, despite fingerprinting over 200 C. difficile isolates, we identified only six distinct types. Only two distinct C. difficile strains were identified as causing both patient infection and ward contamination. Attempts to determine whether infected patients or contaminated environments are the prime source for cross-infection by C. difficile had limited success, as over 90% of C. difficile isolates were the UK epidemic clone. However, a non-epidemic strain caused a cluster of six cases of CDI, but was only isolated from the environment after the sixth patient became symptomatic. The initial absence of this strain from the environment implies patient-to-patient and/or staff-to-patient spread. In general, routine cleaning with detergent was unsuccessful at removing C. difficile from the environment. Understanding the epidemiology and virulence of prevalent strains is important if CDI is to be successfully controlled. PMID:11467790

  12. Production of Cellobionate from Cellulose Using an Engineered Neurospora crassa Strain with Laccase and Redox Mediator Addition

    PubMed Central

    Hildebrand, Amanda; Kasuga, Takao; Fan, Zhiliang

    2015-01-01

    We report a novel production process for cellobionic acid from cellulose using an engineered fungal strain with the exogenous addition of laccase and a redox mediator. A previously engineered strain of Neurospora crassa (F5∆ace-1∆cre-1∆ndvB) was shown to produce cellobionate directly from cellulose without the addition of exogenous cellulases. Specifically, N. crassa produces cellulases, which hydrolyze cellulose to cellobiose, and cellobiose dehydrogenase (CDH), which oxidizes cellobiose to cellobionate. However, the conversion of cellobiose to cellobionate is limited by the slow re-oxidation of CDH by molecular oxygen. By adding low concentrations of laccase and a redox mediator to the fermentation, CDH can be efficiently oxidized by the redox mediator, with in-situ re-oxidation of the redox mediator by laccase. The conversion of cellulose to cellobionate was optimized by evaluating pH, buffer, and laccase and redox mediator addition time on the yield of cellobionate. Mass and material balances were performed, and the use of the native N. crassa laccase in such a conversion system was evaluated against the exogenous Pleurotus ostreatus laccase. This paper describes a working concept of cellobionate production from cellulose using the CDH-ATBS-laccase system in a fermentation system. PMID:25849253

  13. Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum

    SciTech Connect

    Biswas, Ranjita; Prabhu, Sandeep; Lynd, Lee R; Guss, Adam M

    2014-01-01

    Large-scale production of lignocellulosic biofuel is a potential solution to sustainably meet global energy needs. One-step consolidated bioprocessing (CBP) is a potentially advantageous approach for the production of biofuels, but requires an organism capable of hydrolyzing biomass to sugars and fermenting the sugars to ethanol at commercially viable titers and yields. Clostridium thermocellum, a thermophilic anaerobe, can ferment cellulosic biomass to ethanol and organic acids, but low yield, low titer, and ethanol sensitivity remain barriers to industrial production. Here, we deleted the hypoxanthine phosphoribosyltransferase gene in ethanol tolerant strain of C. thermocellum adhE*(EA) in order to allow use of previously developed gene deletion tools, then deleted lactate dehydrogenase (ldh) to redirect carbon flux towards ethanol. Upon deletion of ldh, the adhE*(EA) ldh strain produced 30% more ethanol than wild type on minimal medium. The adhE*(EA) ldh strain retained tolerance to 5% v/v ethanol, resulting in an ethanol tolerant platform strain of C. thermocellum for future metabolic engineering efforts.

  14. Quantitative real-time PCR assay for Clostridium septicum in poultry gangrenous dermatitis associated samples.

    PubMed

    Neumann, A P; Dunham, S M; Rehberger, T G; Siragusa, G R

    2010-08-01

    Clostridium septicum is a spore-forming anaerobe frequently implicated in cases of gangrenous dermatitis (GD) and other spontaneously occurring myonecrotic infections of poultry. Although C. septicum is readily cultured from diseased tissues it can be difficult to enumerate due to its tendency to swarm over the surface of agar plates. In this study a quantitative real-time PCR assay was developed in order to more accurately measure the levels of C. septicum in healthy as well as GD associated poultry samples. The assay was specifically designed to target the C. septicum alpha toxin gene, csa, which is, to our knowledge, carried by all strains of C. septicum and has been shown to be essential for virulence. Genomic DNAs from a diverse collection of bacterial species, including closely related Clostridium chauvoei, Clostridium carnis, Clostridium tertium as well as several strains of Clostridium perfringens, all failed to produce a positive reaction. An approximate reproducible limit of detection in spiked extracts of at least 10(3) cfu/g of C. septicum was observed for a variety of different sample types. C. septicum levels in broiler chicken field samples estimated from the results of qPCR were statistically correlated to culture based enumerations obtained from those same tissues.

  15. Clostridium difficile infection in horses: a review.

    PubMed

    Diab, S S; Songer, G; Uzal, F A

    2013-11-29

    Clostridium difficile is considered one of the most important causes of diarrhea and enterocolitis in horses. Foals and adult horses are equally susceptible to the infection. The highly resistant spore of C. difficile is the infectious unit of transmission, which occurs primarily via the fecal-oral route, with sources of infection including equine feces, contaminated soil, animal hospitals, and feces of other animals. Two major risk factors for the development of C. difficile associated disease (CDAD) in adult horses are hospitalization and antimicrobial treatment, although sporadically, cases of CDAD can occur in horses that have not received antimicrobials or been hospitalized. The most common antibiotics associated with CDAD in horses are erythromycin, trimethoprim/sulfonamides, β-lactam antimicrobials, clindamycin, rifampicin, and gentamicin. Clinical signs and intestinal lesions of CDAD infection are not specific and they cannot be used to distinguish infections by C. difficile from infections by other agents, such as Clostridium perfringens or Salmonella sp. The distribution of lesions throughout the intestinal tract seems to be age-dependent. Small intestine is invariably affected, and colon and cecum may or may not have lesions in foals<1-month old. Naturally acquired disease in older foals and adult horses has a more aboral distribution, affecting colon and sometimes cecum, but rarely the small intestine. Detection of toxin A, toxin B or both in intestinal contents or feces is considered the most reliable diagnostic criterion for CDAD in horses. Isolation of toxigenic strains of C. difficile from horses with intestinal disease is highly suggestive of CDAD. A better understanding of pathogenesis, reservoirs of infection, and vaccines and other methods of control is needed. Also further studies are recommended to investigate other possible predisposing factors and/or etiological agents of enteric diseases of horses. PMID:23642413

  16. Purification and characterization of Clostridium difficile toxin.

    PubMed Central

    Rolfe, R D; Finegold, S M

    1979-01-01

    Recent evidence indicates that toxigenic Clostridium difficile strains are a major cause of antimicrobial-associated ileocecitis in laboratory animals and pseudomembranous colitis in humans. C. difficile ATCC 9689 was cultivated in a synthetic medium to which 3% ultrafiltrated proteose peptone was added. Purification of the toxin from broth filtrate was accomplished through ultrafiltration (100,000 nominal-molecular-weight-limit membrane), precipitation with 75% (NH4)2SO4, and chromatographic separation using Bio-Gel A 5m followed by ion-exchange chromatography on a diethylaminoethyl-Sephadex A-25 column. The purified toxin displayed only one band on polyacrylamide gel electrophoresis, and approximately 170 pg was cytopathic for human amnion cells. The isolated toxin was neutralized by Clostridium sordelli antitoxin, heat labile (56 degrees C for 30 min), and inactivated at pH 4 and 9; it had an isoelectric point of 5.0, increased vascular permeability in rabbits, and caused ileocecitis in hamsters when injected intracecally. Treatment of the toxin with trypsin, chymotrypsin, pronase, amylase, or ethylmercurithiosalicylate caused inactivation, whereas lipase had no effect. By gel filtration, its molecular weight was estimated as 530,000. Upon reduction and denaturation, the toxin dissociated into 185,000- and 50,000-molecular-weight components, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Extensive dissociation yielded only the 50,000-molecular-weight component. The toxin appears to be protoplasmic and is released into the surrounding environment upon autolysis of the cells. Attempts to correlate specific enzymatic activity with the toxin have been unsuccessful. These studies will help delineate the role of C. difficile toxin in antimicrobial-associated colitis and diarrhea. Images PMID:478634

  17. Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering.

    PubMed

    Park, Jin Hwan; Jang, Yu-Sin; Lee, Jeong Wook; Lee, Sang Yup

    2011-05-01

    A less frequently employed Escherichia coli strain W, yet possessing useful metabolic characteristics such as less acetic acid production and high L-valine tolerance, was metabolically engineered for the production of L-valine. The ilvA gene was deleted to make more pyruvate, a key precursor for L-valine, available for enhanced L-valine biosynthesis. The lacI gene was deleted to allow constitutive expression of genes under the tac or trc promoter. The ilvBN(mut) genes encoding feedback-resistant acetohydroxy acid synthase (AHAS) I and the L-valine biosynthetic ilvCED genes encoding acetohydroxy acid isomeroreductase, dihydroxy acid dehydratase, and branched chain amino acid aminotransferase, respectively, were amplified by plasmid-based overexpression. The global regulator Lrp and L-valine exporter YgaZH were also amplified by plasmid-based overexpression. The engineered E. coli W (ΔlacI ΔilvA) strain overexpressing the ilvBN(mut) , ilvCED, ygaZH, and lrp genes was able to produce an impressively high concentration of 60.7 g/L L-valine by fed-batch culture in 29.5 h, resulting in a high volumetric productivity of 2.06 g/L/h. The most notable finding is that there was no other byproduct produced during L-valine production. The results obtained in this study suggest that E. coli W can be a good alternative to Corynebacterium glutamicum and E. coli K-12, which have so far been the most efficient L-valine producer. Furthermore, it is expected that various bioproducts including other amino acids might be more efficiently produced by this revisited platform strain of E. coli.

  18. Elimination of formate production in Clostridium thermocellum

    SciTech Connect

    Rydzak, Thomas; Lynd, Lee R.; Guss, Adam M.

    2015-07-11

    We study the ability of Clostridium thermocellum to rapidly degrade cellulose and ferment resulting hydrolysis products into ethanol makes it a promising platform organism for cellulosic biofuel production via consolidated bioprocessing. Currently, however, ethanol yield are far below theoretical maximum due to branched product pathways that divert carbon and electrons towards formate, H2, lactate, acetate, and secreted amino acids. To redirect carbon and electron flux away from formate, pyruvate:formate lyase (pfl) and respective PFL-activating enzyme were deleted. Formate production in the resulting Δpfl strain was eliminated and acetate production decreased by 50% on both complex and defined medium. Growth rate of Δpfl decreased by 2.9-fold on defined medium and diauxic growth was observed on complex medium. Supplementation of defined medium with 2 mM formate restored Δpfl growth rate to 80% of the parent strain. Finally, we discuss the role of pfl in metabolic engineering strategies and C1 metabolism.

  19. Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum.

    PubMed

    Wu, Yu-Fan; Zheng, Hui; Wu, Qing-Long; Yang, Hong; Liu, Shuang-Jiang

    2014-11-01

    Two anaerobic bacterial strains, MB9-7(T) and MB9-9, were isolated from decomposing algal scum and were characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strains MB9-7(T) and MB9-9 are closely related to each other (99.7% similarity) and they are also closely related to Clostridium tyrobutyricum (96.5%). The two strains were Gram-stain positive and rod-shaped. Growth occurred at 20-45 °C, at pH 4.0-8.0 and at NaCl concentrations of up to 2% (w/v). Acid was produced from glucose, xylose and mannose. Products of fermentation in PYG medium were mainly butyrate, acetate, carbon dioxide and hydrogen. The predominant cellular fatty acids were C(14:0) and C(16:0). The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two glycolipids, one phospholipid, one aminophospholipid and two aminolipids. The DNA G+C contents of strain MB9-7(T) and MB9-9 were 27.9 and 28.7 mol%, respectively. These results support the assignment of the new isolates to the genus Clostridium and also distinguish them from other species of the genus Clostridium. Hence, it is proposed that strains MB9-7(T) and MB9-9 represent a novel species of the genus Clostridium, with the suggested name Clostridium algifaecis sp. nov. The type strain is MB9-7(T) ( =CGMCC 1.5188(T) =DSM 28783(T)).

  20. Direct selection of Clostridium acetobutylicum fermentation mutants by a proton suicide method

    SciTech Connect

    Cueto, P.H.; Mendez, B.S. )

    1990-02-01

    Clostridium acetobutylicum ATCC 10132 mutants altered in acetic acid synthesis or in the shift to solventogenesis were directly selected by a proton suicide method after mutagenic treatment, by using bromide and bromate as selective agents. The mutants were characterized according to their solvent and acid production. On the selection plates they differed in colony phenotype from the parent strain.

  1. Draft Genome Sequence of Clostridium aceticum DSM 1496, a Potential Butanol Producer through Syngas Fermentation

    PubMed Central

    Song, Yoseb; Hwang, Soonkyu

    2015-01-01

    Clostridium aceticum DSM 1496 is a Gram-negative anaerobic chemolithoautotrophic acetogenic bacterium that is capable of producing commodity chemicals from syngas fermentation. In this study, we report the draft genome sequence of the C. aceticum DSM 1496 strain (4.16 Mb) to elucidate the syngas fermentation metabolic pathway. PMID:25931594

  2. First report of an infant botulism case due to Clostridium botulinum type Af.

    PubMed

    de Jong, Laura I T; Fernández, Rafael A; Pareja, Virtudes; Giaroli, Gabriel; Guidarelli, Sergio R; Dykes, Janet K; Lúquez, Carolina

    2015-02-01

    Most infant botulism cases worldwide are due to botulinum toxin types A and B. Rarely, Clostridium botulinum strains that produce two serotypes (Ab, Ba, and Bf) have also been isolated from infant botulism cases. This is the first reported case of infant botulism due to C. botulinum type Af worldwide.

  3. Survey of Clostridium difficile in retail seafood in College Station, Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence and severity of disease associated with toxigenic Clostridium difficile have increased in hospitals in North America with the emergence of newer, more virulent strains. Toxigenic C. difficile has been isolated from food animals and retail meat with potential implications of transfer t...

  4. Antibiotic profiling of Clostridium difficile ribotype 176--A multidrug resistant relative to C. difficile ribotype 027.

    PubMed

    Krutova, Marcela; Matejkova, Jana; Tkadlec, Jan; Nyc, Otakar

    2015-12-01

    Antibiotic profiling of twenty Czech Clostridium difficile PCR-ribotype 176 isolates revealed a high level of resistance to erythromycin, ciprofloxacin and moxifloxacin (n = 20) and to rifampicin (n = 13). Accumulation of resistance mechanisms to multiple antibiotics highlight that PCR-ribotype 176 belong to problematic epidemic strains.

  5. Prevalence of Clostridium difficile in pork and retail meat in Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence and severity of disease associated with toxigenic Clostridium difficile (Cd) have increased in hospitals in North America from the emergence of newer, more virulent strains of Cd. Toxigenic Cd has been isolated from food animals and retail meat with potential implications of transfer ...

  6. Prevalence of Clostridium difficile from Commercial Beef Processing Plants in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clostridium difficile-associated disease has recently increased in both illness and relapse rates in North American and European countries. This increase has been attributed to the emergence of a toxigenic strain designated as North America pulsed-field gel electrophoresis type 1 or NAP-1. The NAP-1...

  7. Products of anaerobic 2,4,6-trinitrotoluene (TNT) transformation by Clostridium bifermentans

    SciTech Connect

    Lewis, T.A.; Goszczynski, S.; Crawford, R.L.

    1996-12-01

    Studies of bacterial transformation of TNT have shown reduction of the nitrogroups to be a ubiquitous activity. Both anaerobic and aerobic bacterial transformations have been studied to find ways to exploit the biochemical incorporation of molecular oxygen or to avoid oxidative polymerizations. This study describes TNT transformation activities of one bioreactor isolate, Clostridium bifermentans strain LJP-1. 25 refs., 4 figs.

  8. Transfer of Clostridium difficile Genetic Elements Conferring Resistance to Macrolide-Lincosamide-Streptogramin B (MLSB) Antibiotics.

    PubMed

    Barbanti, Fabrizio; Wasels, François; Spigaglia, Patrizia

    2016-01-01

    Molecular analysis is an important tool to investigate Clostridium difficile resistance to macrolide-lincosamide-streptogramin B (MLSB). In particular, the protocols described in this chapter have been designed to investigate the genetic organization of erm(B)-containing elements and to evaluate the capability of these elements to transfer in C. difficile recipient strains using filter mating assay. PMID:27507342

  9. Creation of High-Yield Polyhydroxyalkanoates Engineered Strains by Low Energy Ion Implantation

    NASA Astrophysics Data System (ADS)

    Qian, Shiquan; Cheng, Ying; Zhu, Suwen; Cheng, Beijiu

    2008-12-01

    Polyhydroxyalkanoates (PHAs), as a candidate for biodegradable plastic materials, can be synthesized by numerous microorganisms. However, as its production cost is high in comparison with those of chemically synthesized plastics, a lot of research has been focused on the efficient production of PHAs using different methods. In the present study, the mutation effects of PHAs production in strain pCB4 were investigated with implantation of low energy ions. It was found that under the implantation conditions of 7.8 × 1014 N+/cm2 at 10 keV, a high-yield PHAs strain with high genetic stability was generated from many mutants. After optimizing its fermentation conditions, the biomass, PHAs concentration and PHAs content of pCBH4 reached 2.26 g/L, 1.81 g/L, and 80.08% respectively, whereas its wild type controls were about 1.24 g/L, 0.61 g/L, and 49.20%. Moreover, the main constituent of PHAs was identified as poly-3-hydroxybutyrates (PHB) in the mutant stain and the yield of this compound was increased up to 41.33% in contrast to that of 27.78% in the wild type strain.

  10. Overexpression of a homogeneous oligosaccharide with 13C labeling by genetically engineered yeast strain.

    PubMed

    Kamiya, Yukiko; Yamamoto, Sayoko; Chiba, Yasunori; Jigami, Yoshifumi; Kato, Koichi

    2011-08-01

    This report describes a novel method for overexpression of (13)C-labeled oligosaccharides using genetically engineered Saccharomyces cerevisiae cells, in which a homogeneous high-mannose-type oligosaccharide accumulates because of deletions of genes encoding three enzymes involved in the processing pathway of asparagine-linked oligosaccharides in the Golgi complex. Using uniformly (13)C-labeled glucose as the sole carbon source in the culture medium of these engineered yeast cells, high yields of the isotopically labeled Man(8)GlcNAc(2) oligosaccharide could be successfully harvested from glycoprotein extracts of the cells. Furthermore, (13)C labeling at selected positions of the sugar residues in the oligosaccharide could be achieved using a site-specific (13)C-enriched glucose as the metabolic precursor, facilitating NMR spectral assignments. The (13)C-labeling method presented provides the technical basis for NMR analyses of structures, dynamics, and interactions of larger, branched oligosaccharides.

  11. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Bibi, Fehmida; Ramasamy, Dhamodharan; Azhar, Esam I.; Robert, Catherine; Yasir, Muhammad; Jiman-Fatani, Asif A.; Alshali, Khalid Z.; Fournier, Pierre-Edouard

    2014-01-01

    Clostridium jeddahense strain JCDT (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m2). Clostridium jeddahense strain JCDT is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462 protein-coding and 53 RNA genes, including 4 rRNA genes. PMID:25197479

  12. In vitro susceptibility of Clostridium difficile isolates from patients with antibiotic-associated diarrhea or colitis.

    PubMed Central

    Dzink, J; Bartlett, J G

    1980-01-01

    In vitro susceptibility tests were performed on 84 strains of Clostridium difficile to 11 antimicrobial agents. All isolates were from the stools of patients with antibiotic-associated diarrhea or colitis in which there was a cytopathic toxin that was neutralized by Clostridium sordellii antitoxin. Over 95% of the strains were susceptible to vancomycin, penicillin G, ampicillin, and metronidazole at concentrations of 4 microgram/ml. Susceptibility to clindamycin was variable; 60% of the strains were susceptible at 1 microgram/ml, and 9% were resistant at 128 microgram/ml. Studies of individual isolates showed that a major portion of the strains were relatively susceptible to the antimicrobial agent implicated in causing the disease. PMID:7396460

  13. Clostridium perfringens type A enteritis in blue and yellow macaw (Ara ararauna).

    PubMed

    Guimarães, Marta Brito; Torres, Luciana Neves; Mesquita, Ramon Gomes; Ampuero, Fernanda; Cunha, Marcos Paulo Vieira; Ferreira, Thais Sebastiana Porfida; Ferreira, Antonio José Piantino; Catão-Dias, José Luiz; Moreno, Andrea Micke; Knöbl, Terezinha

    2014-12-01

    This study describes an outbreak of necrotic enteritis caused by Clostridium perfringens type A in captive macaws (Ara ararauna). Two psittacine birds presented a history of prostration and died 18 hr after manifestation of clinical signs. The necropsy findings and histopathologic lesions were indicative of necrotic enteritis. Microbiologic assays resulted in the growth of large gram-positive bacilli that were identified as C. perfringens. PCR was used to identify clostridium toxinotypes and confirmed the identification of isolated strains as C pefringens type A, positive to gene codifying beta 2 toxin. The infection source and predisposing factors could not be ascertained.

  14. Electrophoretic study of Clostridium species.

    PubMed Central

    Cato, E P; Hash, D E; Holdeman, L V; Moore, W E

    1982-01-01

    Polyacrylamide gel electrophoretic analysis of soluble cellular proteins (without sodium dodecyl sulfate) of 70 Clostridium species indicated that the procedure was readily applicable to the differentiation of species in the genus. The protein patterns correlated well with the available DNA homology data and with most accepted differential tests. Results indicated that several earlier names for species were synonyms of those of accepted species and that two accepted species may be synonymous. Images PMID:6175658

  15. The acquisition of Clostridium tyrobutyricum mutants with improved bioproduction under acidic conditions after two rounds of heavy-ion beam irradiation

    PubMed Central

    Zhou, Xiang; Yang, Zhen; Jiang, Ting-Ting; Wang, Shu-Yang; Liang, Jian-Ping; Lu, Xi-Hong; Wang, Liang

    2016-01-01

    End-product inhibition is a key factor limiting the production of organic acid during fermentation. Two rounds of heavy-ion beam irradiation may be an inexpensive, indispensable and reliable approach to increase the production of butyric acid during industrial fermentation processes. However, studies of the application of heavy ion radiation for butyric acid fermentation engineering are lacking. In this study, a second 12C6+ heavy-ion irradiation-response curve is used to describe the effect of exposure to a given dose of heavy ions on mutant strains of Clostridium tyrobutyricum. Versatile statistical elements are introduced to characterize the mechanism and factors contributing to improved butyric acid production and enhanced acid tolerance in adapted mutant strains harvested from the fermentations. We characterized the physiological properties of the strains over a large pH value gradient, which revealed that the mutant strains obtained after a second round of radiation exposure were most resistant to harsh external pH values and were better able to tolerate external pH values between 4.5 and 5.0. A customized second round of heavy-ion beam irradiation may be invaluable in process engineering. PMID:27426447

  16. The acquisition of Clostridium tyrobutyricum mutants with improved bioproduction under acidic conditions after two rounds of heavy-ion beam irradiation.

    PubMed

    Zhou, Xiang; Yang, Zhen; Jiang, Ting-Ting; Wang, Shu-Yang; Liang, Jian-Ping; Lu, Xi-Hong; Wang, Liang

    2016-01-01

    End-product inhibition is a key factor limiting the production of organic acid during fermentation. Two rounds of heavy-ion beam irradiation may be an inexpensive, indispensable and reliable approach to increase the production of butyric acid during industrial fermentation processes. However, studies of the application of heavy ion radiation for butyric acid fermentation engineering are lacking. In this study, a second (12)C(6+) heavy-ion irradiation-response curve is used to describe the effect of exposure to a given dose of heavy ions on mutant strains of Clostridium tyrobutyricum. Versatile statistical elements are introduced to characterize the mechanism and factors contributing to improved butyric acid production and enhanced acid tolerance in adapted mutant strains harvested from the fermentations. We characterized the physiological properties of the strains over a large pH value gradient, which revealed that the mutant strains obtained after a second round of radiation exposure were most resistant to harsh external pH values and were better able to tolerate external pH values between 4.5 and 5.0. A customized second round of heavy-ion beam irradiation may be invaluable in process engineering. PMID:27426447

  17. Formation of ripples in atomically thin MoS₂ and local strain engineering of electrostatic properties.

    PubMed

    Luo, Siwei; Hao, Guolin; Fan, Yinping; Kou, Liangzhi; He, Chaoyu; Qi, Xiang; Tang, Chao; Li, Jin; Huang, Kai; Zhong, Jianxin

    2015-03-13

    Ripple is a common deformation in two-dimensional materials due to localized strain, which is expected to greatly influence the physical properties. The effects of the ripple deformation in the MoS2 layer on their physics, however, are rarely addressed experimentally. We here grow atomically thin MoS2 nanostructures by employing a vapor phase deposition method without any catalyst and observed the ripples in MoS2 nanostructures. The MoS2 ripples exhibit quasi-periodical ripple structures in the MoS2 surface. The heights of the ripples vary from several angstroms to tens of nanometers and the wavelength is in the range of several hundred nanometers. The growth mechanism of rippled MoS2 nanostructures is elucidated. We have also simultaneously investigated the electrostatic properties of MoS2 ripples by using Kelvin probe force microscopy, which shows inhomogeneous surface potential and charge distributions for MoS2 ripple nanostructures with different local strains.

  18. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover

    PubMed Central

    Parreiras, Lucas S.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman; Higbee, Alan J.; La Reau, Alex; Tremaine, Mary; Qin, Li; Willis, Laura B.; Bice, Benjamin D.; Bonfert, Brandi L.; Pinhancos, Rebeca C.; Balloon, Allison J.; Uppugundla, Nirmal; Liu, Tongjun; Li, Chenlin; Tanjore, Deepti; Ong, Irene M.; Li, Haibo; Pohlmann, Edward L.; Serate, Jose; Withers, Sydnor T.; Simmons, Blake A.; Hodge, David B.; Westphall, Michael S.; Coon, Joshua J.; Dale, Bruce E.; Balan, Venkatesh; Keating, David H.; Zhang, Yaoping; Landick, Robert; Gasch, Audrey P.; Sato, Trey K.

    2014-01-01

    The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH. PMID:25222864

  19. Community-Acquired Clostridium Difficile Infection: Awareness and Clinical Implications

    PubMed Central

    Juneau, Cheryl; Mendias, Elnora (Nonie) P.; Wagal, Nihas; Loeffelholz, Michael; Savidge, Tor; Croisant, Sharon; Dann, Sara

    2013-01-01

    The epidemiology of Clostridium difficile infection (CDI) is changing. CDI, usually depicted as a nosocomial infection in the elderly, is now occurring in community-dwelling persons who are younger and otherwise dissimilar. A more virulent isolate (North American Pulsed Field type 1 (NAP1) associated with increased morbidity and mortality, has been identified. In 2005, similar strains were associated with severe disease in community-dwelling patients at a rate of 7.6/100,000. Screening patients with potential CDI symptoms and implementing preventative measures, including judicious use of antibiotics, can reduce disease burden. PMID:23814528

  20. Clostridium perfringens type A-E toxin plasmids.

    PubMed

    Freedman, John C; Theoret, James R; Wisniewski, Jessica A; Uzal, Francisco A; Rood, Julian I; McClane, Bruce A

    2015-05-01

    Clostridium perfringens relies upon plasmid-encoded toxin genes to cause intestinal infections. These toxin genes are associated with insertion sequences that may facilitate their mobilization and transfer, giving rise to new toxin plasmids with common backbones. Most toxin plasmids carry a transfer of clostridial plasmids locus mediating conjugation, which likely explains the presence of similar toxin plasmids in otherwise unrelated C. perfringens strains. The association of many toxin genes with insertion sequences and conjugative plasmids provides virulence flexibility when causing intestinal infections. However, incompatibility issues apparently limit the number of toxin plasmids maintained by a single cell.