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Sample records for kadi ilves kadri

  1. The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence.

    PubMed

    Oliver, Jason D; Kaye, Sarah J; Tuckwell, Danny; Johns, Anna E; Macdonald, Darel A; Livermore, Joanne; Warn, Peter A; Birch, Mike; Bromley, Michael J

    2012-01-01

    Dihydroxyacid dehydratase (DHAD) is a key enzyme in the branched-chain amino acid biosynthetic pathway that exists in a variety of organisms, including fungi, plants and bacteria, but not humans. In this study we identified four putative DHAD genes from the filamentous fungus Aspergillus fumigatus by homology to Saccharomyces cerevisiae ILV3. Two of these genes, AFUA_2G14210 and AFUA_1G03550, initially designated AfIlv3A and AfIlv3B for this study, clustered in the same group as S. cerevisiae ILV3 following phylogenetic analysis. To investigate the functions of these genes, AfIlv3A and AfIlv3B were knocked out in A. fumigatus. Deletion of AfIlv3B gave no apparent phenotype whereas the Δilv3A strain required supplementation with isoleucine and valine for growth. Thus, AfIlv3A is required for branched-chain amino acid synthesis in A. fumigatus. A recombinant AfIlv3A protein derived from AFUA_2G14210 was shown to have DHAD activity in an in vitro assay, confirming that AfIlv3A is a DHAD. In addition we show that mutants lacking AfIlv3A and ilv3B exhibit reduced levels of virulence in murine infection models, emphasising the importance of branched-chain amino acid biosynthesis in fungal infections, and hence the potential of targeting this pathway with antifungal agents. Here we propose that AfIlv3A/AFUA_2G2410 be named ilvC.

  2. The Branched-Chain Amino Acid Aminotransferase Encoded by ilvE Is Involved in Acid Tolerance in Streptococcus mutans

    PubMed Central

    Santiago, Brendaliz; MacGilvray, Matthew; Faustoferri, Roberta C.

    2012-01-01

    The ability of Streptococcus mutans to produce and tolerate organic acids from carbohydrate metabolism represents a major virulence factor responsible for the formation of carious lesions. Pyruvate is a key metabolic intermediate that, when rerouted to other metabolic pathways such as amino acid biosynthesis, results in the alleviation of acid stress by reducing acid end products and aiding in maintenance of intracellular pH. Amino acid biosynthetic genes such as ilvC and ilvE were identified as being upregulated in a proteome analysis of Streptococcus mutans under acid stress conditions (A. C. Len, D. W. Harty, and N. A. Jacques, Microbiology 150:1353–1366, 2004). In Lactococcus lactis and Staphylococcus carnosus, the ilvE gene product is involved with biosynthesis and degradation of branched-chain amino acids, as well as in the production of branched-chain fatty acids (B. Ganesan and B. C. Weimer, Appl. Environ. Microbiol. 70:638–641, 2004; S. M. Madsen et al., Appl. Environ. Microbiol. 68:4007–4014, 2002; and M. Yvon, S. Thirouin, L. Rijnen, D. Fromentier, and J. C. Gripon, Appl. Environ. Microbiol. 63:414–419, 1997). Here we constructed and characterized an ilvE deletion mutant of S. mutans UA159. Growth experiments revealed that the ilvE mutant strain has a lag in growth when nutritionally limited for branched-chain amino acids. We further demonstrated that the loss of ilvE causes a decrease in acid tolerance. The ilvE strain exhibits a defect in F1-Fo ATPase activity and has reduced catabolic activity for isoleucine and valine. Results from transcriptional studies showed that the ilvE promoter is upregulated during growth at low pH. Collectively, the results of this investigation show that amino acid metabolism is a component of the acid-adaptive repertoire of S. mutans. PMID:22328677

  3. Acetohydroxyacid synthase FgIlv2 and FgIlv6 are involved in BCAA biosynthesis, mycelial and conidial morphogenesis, and full virulence in Fusarium graminearum.

    PubMed

    Liu, Xin; Han, Qi; Xu, Jianhong; Wang, Jian; Shi, Jianrong

    2015-11-10

    In this study, we characterized FgIlv2 and FgIlv6, the catalytic and regulatory subunits of acetohydroxyacid synthase (AHAS) from the important wheat head scab fungus Fusarium graminearum. AHAS catalyzes the first common step in the parallel pathways toward branched-chain amino acids (BCAAs: isoleucine, leucine, valine) and is the inhibitory target of several commercialized herbicides. Both FgILV2 and FgILV6 deletion mutants were BCAA-auxotrophic and showed reduced aerial hyphal growth and red pigmentation when cultured on PDA plates. Conidial formation was completely blocked in the FgILV2 deletion mutant ΔFgIlv2-4 and significantly reduced in the FgILV6 deletion mutant ΔFgIlv6-12. The auxotrophs of ΔFgIlv2-4 and ΔFgIlv6-12 could be restored by exogenous addition of BCAAs but relied on the designated nitrogen source the medium contained. Deletion of FgILV2 or FgILV6 also leads to hypersensitivity to various cellular stresses and reduced deoxynivalenol production. ΔFgIlv2-4 lost virulence completely on flowering wheat heads, whereas ΔFgIlv6-12 could cause scab symptoms in the inoculated spikelet but lost its aggressiveness. Taken together, our study implies the potential value of antifungals targeting both FgIlv2 and FgIlv6 in F. graminearum.

  4. Internal promoter in the ilvGEDA transcription unit of Escherichia coli K-12.

    PubMed Central

    Calhoun, D H; Wallen, J W; Traub, L; Gray, J E; Kung, H F

    1985-01-01

    Segments of the ilvGEDA transcription unit have been cloned into the promoter tester plasmid pMC81. This vector contains cloning sites situated upstream of the lacZ gene coding for beta-galactosidase. Using this method we have quantitatively evaluated in vivo (i) the activity of previously described promoter, pG, preceding ilvG; (ii) the relative activity of pE promoter, previously postulated to be located between ilvG and ilvE; and (iii) the effect of the frameshift site present in the wild-type ilvG gene by comparison with mutant derivatives lacking this frameshift site. Isogenic derivatives of strain MC1000 were constructed by transduction with phage P1 grown on rho-120, delta(ilvGEDA), delta(ilvED), and ilvA538 hosts. The potential effects of these alleles that were previously postulated to affect ilvGEDA expression were assessed in vivo by monitoring beta-galactosidase production directed by ilv DNA fragments. Cloned ilv segments were also tested for activity in vitro with a DNA-directed coupled transcription and translation system. The production in vitro of ilv-directed ilv gene expression and beta-galactosidase expression with ara-ilv-lac fusions paralleled the in vivo activity. Images PMID:3917997

  5. Molecular cloning and expression of the ilvGEDAY genes from Salmonella typhimurium.

    PubMed Central

    Blazey, D L; Kim, R; Burns, R O

    1981-01-01

    The ilvGEDAY genes of Salmonella typhimurium were cloned in Escherichia coli K-12 by in vitro recombination techniques. A single species of recombinant plasmid, designated pDU1, was obtained by selecting for Valr Ampr transformants of strain SK1592. pDU1 was shown to contain a 14-kilobase EcoRI partial digestion product of the S. typhimurium chromosome inserted into the EcoRI site of the pVH2124 cloning vector. The ilvGEDAY genes were found to occupy a maximum length of 7.5 kilobases. Restriction endonuclease analysis of the S. typhimurium ilv gene cluster provided another demonstration of the gene order as well as established the location of ilv Y between ilvA and ilvC. The presence of a ribosomal ribonucleic acid operon on the pDU1 insert, about 3 kilobases from the 5' end of ilvG, was shown by Southern hybridization. The expression of the ilvGEDA operon from pDU1 was found to be elevated, reflecting the increased gene dosage of the multicopy plasmid. A polarity was observed with respect to ilvEDA expression which is discussed in terms of the possible translational effects of the two internal promoter sequences, one located proximal to ilvE and the other located proximal to ilvD. Images PMID:6167564

  6. Targeting of mitochondrial Saccharomyces cerevisiae Ilv5p to the cytosol and its effect on vicinal diketone formation in brewing.

    PubMed

    Omura, Fumihiko

    2008-03-01

    Vicinal diketones (VDK) cause butter-like off-flavors in beer and are formed by a non-enzymatic oxidative decarboxylation of alpha-aceto-alpha-hydroxybutyrate and alpha-acetolactate, which are intermediates in isoleucine and valine biosynthesis taking place in the mitochondria. On the assumption that part of alpha-acetolactate can be formed also in the cytosol due to a mislocalization of the responsible acetohydroxyacid synthase encoded by ILV2 and ILV6, functional expression in the cytosol of acetohydroxyacid reductoisomerase (Ilv5p) was explored. Using the cytosolic Ilv5p, I aimed to metabolize the cytosolically formed alpha-aetolactate, thereby lowering the total VDK production. Among mutant Ilv5p enzymes with varying degrees of N-terminal truncation, one with a 46-residue deletion (Ilv5pDelta46) exhibited an unequivocal localization in the cytosol judged from microscopy of the Ilv5pDelta46-green fluorescent protein fusion protein and the inability of Ilv5pDelta46 to remedy the isoleucine/valine requirement of an ilv5Delta strain. When introduced into an industrial lager brewing strain, a robust expression of Ilv5pDelta46 was as effective as that of a wild-type Ilv5p in lowering the total VDK production in a 2-l scale fermentation trial. Unlike the case of the wild-type Ilv5p, an additional expression of Ilv5pDelta46 did not alter the quality of the resultant beer in terms of contents of aromatic compounds and organic acids.

  7. The 1.9 A Structure of the Branched-Chain Amino-Acid Transaminase (IlvE) from Mycobacterium tuberculosis

    SciTech Connect

    Tremblay, L.; Blanchard, J

    2009-01-01

    Unlike mammals, bacteria encode enzymes that synthesize branched-chain amino acids. The pyridoxal 5'-phosphate-dependent transaminase performs the final biosynthetic step in these pathways, converting keto acid precursors into {alpha}-amino acids. The branched-chain amino-acid transaminase from Mycobacterium tuberculosis (MtIlvE) has been crystallized and its structure has been solved at 1.9 {angstrom} resolution. The MtIlvE monomer is composed of two domains that interact to form the active site. The biologically active form of IlvE is a homodimer in which each monomer contributes a substrate-specificity loop to the partner molecule. Additional substrate selectivity may be imparted by a conserved N-terminal Phe30 residue, which has previously been observed to shield the active site in the type IV fold homodimer. The active site of MtIlvE contains density corresponding to bound PMP, which is likely to be a consequence of the presence of tryptone in the crystallization medium. Additionally, two cysteine residues are positioned at the dimer interface for disulfide-bond formation under oxidative conditions. It is unknown whether they are involved in any regulatory activities analogous to those of the human mitochondrial branched-chain amino-acid transaminase.

  8. Isoleucine and Valine Metabolism in Escherichia coli K-12: Detection and Measurement of ilv-Specific Messenger Ribonucleic Acid

    PubMed Central

    Haar, R. A. Vonder; Umbarger, H. E.

    1974-01-01

    Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of messenger RNA transcribed from the ilv gene cluster of Escherichia coli K-12. Strains with derepressed levels of the isoleucine and valine biosynthetic enzymes owing to linked or unlinked genetic lesions were found to exhibit ilv messenger RNA levels from 1.5- to 4-fold higher than did their isogenic parents. When grown under conditions that specifically repressed the synthesis of isoleucine- and valine-forming enzymes, most strains exhibited drastically reduced ilv messenger RNA levels. Hybridization performed with the separated strands of ilv DNA showed that all the ilv genes are transcribed from the same strand, the “l strand” of λφ80CI857St68dilv DNA. Sucrose gradient analyses of RNA extracted from cells starved for isoleucine, valine, or leucine resulted in the detection of at least two distinct types of ilv messenger RNA. PMID:4616946

  9. Doa4 function in ILV budding is restricted through its interaction with the Vps20 subunit of ESCRT-III

    PubMed Central

    Richter, Caleb M.; West, Matthew; Odorizzi, Greg

    2013-01-01

    Summary Assembly of the endosomal sorting complex required for transport (ESCRT)-III executes the formation of intralumenal vesicles (ILVs) at endosomes. Repeated cycles of ESCRT-III function requires disassembly of the complex by Vps4, an ATPase with a microtubule interaction and trafficking (MIT) domain that binds MIT-interacting motifs (MIM1 or MIM2) in ESCRT-III subunits. We identified a putative MIT domain at the N-terminus of Doa4, which is the ubiquitin (Ub) hydrolase in Saccharomyces cerevisiae that deubiquitinates ILV cargo proteins. The Doa4 N-terminus is predicted to have the α-helical structure common to MIT domains, and it binds directly to a MIM1-like sequence in the Vps20 subunit of ESCRT-III. Disrupting this interaction does not prevent endosomal localization of Doa4 but enhances the defect in ILV cargo protein deubiquitination observed in cells lacking Bro1, which is an ESCRT-III effector protein that stimulates Doa4 catalytic activity. Deletion of the BRO1 gene (bro1Δ) blocks ILV budding, but ILV budding was rescued upon disrupting the interaction between Vps20 and Doa4. This rescue in ILV biogenesis requires Doa4 expression but is independent of its Ub hydrolase activity. Thus, binding of Vps20 to the Doa4 N-terminus inhibits a non-catalytic function of Doa4 that promotes ILV formation. PMID:23444383

  10. Cytosolic Localization of Acetohydroxyacid Synthase Ilv2 and Its Impact on Diacetyl Formation during Beer Fermentation▿

    PubMed Central

    Dasari, Suvarna; Kölling, Ralf

    2011-01-01

    Diacetyl (2,3-butanedione) imparts an unpleasant “butterscotch-like” flavor to alcoholic beverages such as beer, and therefore its concentration needs to be reduced below the sensory threshold before packaging. We examined the mechanisms that lead to highly elevated diacetyl formation in petite mutants of Saccharomyces cerevisiae during beer fermentations. We present evidence that elevated diacetyl formation is tightly connected to the mitochondrial import of acetohydroxyacid synthase (Ilv2), the key enzyme in the production of diacetyl. Our data suggest that accumulation of the matrix-targeted Ilv2 preprotein in the cytosol is responsible for the observed high diacetyl levels. We could show that the Ilv2 preprotein accumulates in the cytosol of petite yeasts. Furthermore, expression of an Ilv2 variant that lacks the N-terminal mitochondrial targeting sequence and thus cannot be imported into mitochondria led to highly elevated diacetyl levels comparable to a petite strain. We further show that expression of a mutant allele of the γ-subunit of the F1-ATPase (ATP3-5) could be an attractive way to reduce diacetyl formation by petite strains. PMID:21131528

  11. Cytosolic localization of acetohydroxyacid synthase Ilv2 and its impact on diacetyl formation during beer fermentation.

    PubMed

    Dasari, Suvarna; Kölling, Ralf

    2011-02-01

    Diacetyl (2,3-butanedione) imparts an unpleasant "butterscotch-like" flavor to alcoholic beverages such as beer, and therefore its concentration needs to be reduced below the sensory threshold before packaging. We examined the mechanisms that lead to highly elevated diacetyl formation in petite mutants of Saccharomyces cerevisiae during beer fermentations. We present evidence that elevated diacetyl formation is tightly connected to the mitochondrial import of acetohydroxyacid synthase (Ilv2), the key enzyme in the production of diacetyl. Our data suggest that accumulation of the matrix-targeted Ilv2 preprotein in the cytosol is responsible for the observed high diacetyl levels. We could show that the Ilv2 preprotein accumulates in the cytosol of petite yeasts. Furthermore, expression of an Ilv2 variant that lacks the N-terminal mitochondrial targeting sequence and thus cannot be imported into mitochondria led to highly elevated diacetyl levels comparable to a petite strain. We further show that expression of a mutant allele of the γ-subunit of the F(1)-ATPase (ATP3-5) could be an attractive way to reduce diacetyl formation by petite strains.

  12. Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli

    PubMed Central

    Rhee, Kyu Y.; Opel, Michael; Ito, Elaine; Hung, She-pin; Arfin, Stuart M.; Hatfield, G. Wesley

    1999-01-01

    The twin-domain model [Liu, L. F. & Wang, J. C. (1987) Proc. Natl. Acad. Sci. USA 84, 7024–7027] suggests that closely spaced, divergent, superhelically sensitive promoters can affect the transcriptional activity of one another by transcriptionally induced negative DNA supercoiling generated in the divergent promoter region. This gene arrangement is observed for many LysR-type-regulated operons in bacteria. We have examined the effects of divergent transcription in the prototypic LysR-type system, the ilvYC operon of Escherichia coli. Double-reporter constructs with the lacZ gene under transcriptional control of the ilvC promoter and the galK gene under control of the divergent ilvY promoter were used to demonstrate that a down-promoter mutation in the ilvY promoter severely decreases in vivo transcription from the ilvC promoter. However, a down-promoter mutation in the ilvC promoter only slightly affects transcription from the ilvY promoter. In vitro transcription assays with DNA topoisomers showed that transcription from the ilvC promoter increases over the entire range of physiological superhelical densities, whereas transcription initiation from the ilvY promoter exhibits a broad optimum at a midphysiological superhelical density. Evidence that this promoter coupling is DNA supercoiling-dependent is provided by the observation that a novobiocin-induced decrease in global negative superhelicity results in an increase in ilvY promoter activity and a decrease in ilvC promoter activity predicted by the in vitro data. We suggest that this transcriptional coupling is important for coordinating basal level expression of the ilvYC operon with the nutritional and environmental conditions of cell growth. PMID:10588699

  13. Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli.

    PubMed

    Rhee, K Y; Opel, M; Ito, E; Hung, S p; Arfin, S M; Hatfield, G W

    1999-12-07

    The twin-domain model [Liu, L. F. & Wang, J. C. (1987) Proc. Natl. Acad. Sci. USA 84, 7024-7027] suggests that closely spaced, divergent, superhelically sensitive promoters can affect the transcriptional activity of one another by transcriptionally induced negative DNA supercoiling generated in the divergent promoter region. This gene arrangement is observed for many LysR-type-regulated operons in bacteria. We have examined the effects of divergent transcription in the prototypic LysR-type system, the ilvYC operon of Escherichia coli. Double-reporter constructs with the lacZ gene under transcriptional control of the ilvC promoter and the galK gene under control of the divergent ilvY promoter were used to demonstrate that a down-promoter mutation in the ilvY promoter severely decreases in vivo transcription from the ilvC promoter. However, a down-promoter mutation in the ilvC promoter only slightly affects transcription from the ilvY promoter. In vitro transcription assays with DNA topoisomers showed that transcription from the ilvC promoter increases over the entire range of physiological superhelical densities, whereas transcription initiation from the ilvY promoter exhibits a broad optimum at a midphysiological superhelical density. Evidence that this promoter coupling is DNA supercoiling-dependent is provided by the observation that a novobiocin-induced decrease in global negative superhelicity results in an increase in ilvY promoter activity and a decrease in ilvC promoter activity predicted by the in vitro data. We suggest that this transcriptional coupling is important for coordinating basal level expression of the ilvYC operon with the nutritional and environmental conditions of cell growth.

  14. The product of the Rhizobium meliloti ilvC gene is required for isoleucine and valine synthesis and nodulation of alfalfa.

    PubMed Central

    Aguilar, O M; Grasso, D H

    1991-01-01

    Tn5-induced mutants of Rhizobium meliloti that require the amino acids isoleucine and valine for growth on minimal medium were studied. In one mutant, 1028, the defect is associated with an inability to induce nodules on alfalfa. The Tn5 mutation in 1028 is located in a chromosomal 5.5-kb EcoRI fragment. Complementation analysis with cloned DNA indicated that 2.0 kb of DNA from the 5.5-kb EcoRI fragment restored the wild-type phenotype in the Ilv- Nod- mutant. This region was further characterized by DNA sequence analysis and was shown to contain a coding sequence homologous to those for Escherichia coli IlvC and Saccharomyces cerevisiae Ilv5. Genes ilvC and ilv5 code for the enzyme acetohydroxy acid isomeroreductase (isomeroreductase), the second enzyme in the parallel pathways for the biosynthesis of isoleucine and valine. Enzymatic assays confirmed that strain 1028 was a mutant defective in isomeroreductase activity. In addition, it was shown that the ilvC genes of Rhizobium meliloti and E. coli are functionally equivalent. We demonstrated that in ilvC mutant 1028 the common nodulation genes nodABC are not activated by the inducer luteolin. E. coli ilvC complemented both defective properties (Ilv- and Nod-) found in mutant 1028. These findings demonstrate that R. meliloti requires an active isomeroreductase enzyme for successful nodulation of alfalfa. PMID:1744032

  15. Overexpression of the truncated version of ILV2 enhances glycerol production in Saccharomyces cerevisiae.

    PubMed

    Murashchenko, Lidiia; Abbas, Charles; Dmytruk, Kostyantyn; Sibirny, Andriy

    2016-08-01

    Acetolactate synthase is a mitochondrial enzyme that catalyses the conversion of two pyruvate molecules to an acetolactate molecule with release of carbon dioxide. The overexpression of the truncated version of the corresponding gene, ILV2, that codes for presumably cytosolic acetolactate synthase in the yeast Saccharomyces cerevisiae, led to a decrease in intracellular pyruvate concentration. This recombinant strain was also characterized by a four-fold increase in glycerol production, with a concomitant 1.8-fold reduction in ethanol production, when compared to that of the wild-type strain under anaerobic conditions in a glucose alcoholic fermentation. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Construction of self-cloning bottom-fermenting yeast with low vicinal diketone production by the homo-integration of ILV5.

    PubMed

    Kusunoki, K; Ogata, T

    2012-10-01

    The vicinal diketones (VDK), such as diacetyl and 2,3-pentandione, impart an unpleasant butter-like flavour to beer. Typically, these are required to be reduced below the flavour thresholds during the maturation (lagering) stages of the brewing process. To shorten beer maturation time, we constructed a self-cloning, bottom-fermenting yeast with low VDK production by integrating ILV5, a gene encoding a protein that metabolizes α-acetolactate and α-aceto-α-hydroxybutyrate (precursors of VDK). A DNA fragment containing Saccharomyces cerevisiae-type ILV5 was inserted upstream of S. cerevisiae-type ILV2 in bottom-fermenting yeast to construct self-cloning strains with an increased copy number of ILV5. Via transformation, ILV2 was replaced with the sulfometuron methyl (SM) resistance gene SMR1B, which differs by a single nucleotide, to create SM-resistant transformants. The wort fermentation test, using the SC-ILV5-homo inserted transformant, confirmed a consecutive reduction in VDK and a shortening period during which VDK was reduced to within the threshold. The concentrations of ethyl acetate, isoamyl acetate, isoamyl alcohol, 1-propanol, isobutyl alcohol and active isoamyl alcohol (flavour components) were not changed when compared with the parent strain. We successfully constructed self-cloning brewer's yeast in which SC-ILV5 was homo-inserted. Using the transformed yeast, the concentration of VDK in fermenting wort was reduced, whereas the concentrations of flavour components were not affected. This genetically stable, low VDK-producing, self-cloning bottom-fermenting yeast would contribute to the shortening of beer maturation time without affecting important flavour components produced by brewer's yeast.

  17. The minimum activation peptide from ilvH can activate the catalytic subunit of AHAS from different species.

    PubMed

    Zhao, Yuefang; Niu, Congwei; Wen, Xin; Xi, Zhen

    2013-04-15

    Acetohydroxyacid synthases (AHASs), which catalyze the first step in the biosynthesis of branched-chain amino acids, are composed of a catalytic subunit (CSU) and a regulatory subunit (RSU). The CSU harbors the catalytic site, and the RSU is responsible for the activation and feedback regulation of the CSU. Previous results from Chipman and co-workers and our lab have shown that heterologous activation can be achieved among isozymes of Escherichia coli AHAS. It would be interesting to find the minimum peptide of ilvH (the RSU of E. coli AHAS III) that could activate other E. coli CSUs, or even those of ## species. In this paper, C-terminal, N-terminal, and C- and N-terminal truncation mutants of ilvH were constructed. The minimum peptide to activate ilvI (the CSU of E. coli AHAS III) was found to be ΔN 14-ΔC 89. Moreover, this peptide could not only activate its homologous ilvI and heterologous ilvB (CSU of E. coli AHAS I), but also heterologously activate the CSUs of AHAS from Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana plumbaginifolia. However, this peptide totally lost its ability for feedback regulation by valine, thus suggesting different elements for enzymatic activation and feedback regulation. Additionally, the apparent dissociation constant (Kd ) of ΔN 14-ΔC 89 when binding CSUs of different species was found to be 9.3-66.5 μM by using microscale thermophoresis. The ability of this peptide to activate different CSUs does not correlate well with its binding ability (Kd ) to these CSUs, thus implying that key interactions by specific residues is more important than binding ability in promoting enzymatic reactions. The high sequence similarity of the peptide ΔN 14-ΔC 89 to RSUs across species hints that this peptide represents the minimum activation motif in RSU and that it regulates all AHASs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli.

    PubMed Central

    Fisher, K E; Eisenstein, E

    1993-01-01

    High-level expression of the regulatory enzyme threonine deaminase in Escherichia coli strains grown on minimal medium that are deficient in the activities of enzymes needed for branched-chain amino acid biosynthesis result in growth inhibition, possibly because of the accumulation of toxic levels of alpha-ketobutyrate, the product of the committed step in isoleucine biosynthesis. This condition affords a means for selecting genetic variants of threonine deaminase that are deficient in catalysis by suppression of growth inhibition. Strains harboring mutations in ilvA that decreased the catalytic activity of threonine deaminase were found to grow more rapidly than isogenic strains containing wild-type ilvA. Modification of the ilvA gene to introduce additional unique, evenly spaced restriction enzyme sites facilitated the identification of suppressor mutations by enabling small DNA fragments to be subcloned for sequencing. The 10 mutations identified in ilvA code for enzymes with significantly reduced activity relative to that of wild-type threonine deaminase. Values for their specific activities range from 40% of that displayed by wild-type enzyme to complete inactivation as evidenced by failure to complement an ilvA deletion strain to isoleucine prototrophy. Moreover, some mutant enzymes showed altered allosteric properties with respect to valine activation and isoleucine inhibition. The location of the 10 mutations in the 5' two-thirds of the ilvA gene is consistent with suggestions that threonine deaminase is organized functionally with an amino-terminal domain that is involved in catalysis and a carboxy-terminal domain that is important for regulation. Images PMID:8407838

  19. Datin, a yeast poly(dA:dT)-binding protein, behaves as an activator of the wild-type ILV1 promoter and interacts synergistically with Reb1p.

    PubMed

    Moreira, J M; Remacle, J E; Kielland-Brandt, M C; Holmberg, S

    1998-04-01

    A cis-acting element required for GCN4-independent basal-level transcription of ILV1 was previously identified in our laboratories as a binding site for the REB1 protein (Reb1p). Further deletion analysis of the ILV1 promoter region identified a second element also required for GCN4-independent basal-level ILV1 expression. This second element is an A.T-rich tract (26 As out of 32 nucleotides) situated 15 bp downstream of the Reb1p-binding site. Deletion of both the Reblp site and the poly(dA:dT) element totally eliminates basal activity of the ILV1 promoter. We show that the two elements act synergistically to control ILV1 expression and that the synergistic effect is distance dependent. We demonstrate that (i) datin (Dat1p), the only known poly (dA:dT)-binding protein in yeast, specifically binds to the ILV1 poly(dA:dT) element in vitro; (ii) Dat1p functions as a trans-activating factor in the ILV1 context; and (iii) the synergistic activation observed in vivo between the Reb1p site and the poly(dA:dT) element depends on the presence of the structural gene for Dat1p, DAT1.

  20. DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths.

    PubMed

    Opel, M L; Hatfield, G W

    2001-01-01

    The twin-domain model of Liu and Wang suggested that high levels of DNA supercoiling generated in the region between closely spaced divergently transcribed promoters could serve to couple the activities of these promoters transcriptionally. In this report, we use topoisomer sets of defined superhelical densities as DNA templates in a purified in vitro transcription system to demonstrate transcriptional coupling between the divergently transcribed ilvY and ilvC promoters of the ilvYC operon of Escherichia coli. Current evidence for this type of DNA supercoiling-dependent transcriptional coupling, based largely on the in vivo activities of promoters contained in engineered DNA constructs, suggests that the transcription complex must be physically hindered to generate DNA supercoils and to prevent their diffusion throughout the DNA duplex. However, the in vitro results presented here demonstrate that (i) transcriptional coupling is observed between the divergent promoters of the ilvYC operon in the absence of transcript anchoring; (ii) the magnitude of the negative DNA supercoiling generated in the divergent promoter region is proportional to the sum of the global and transcription-induced superhelicity; and (iii) the magnitude of this transcription-induced superhelicity is proportional to promoter strengths and transcript lengths.

  1. The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons.

    PubMed

    Opel, M L; Arfin, S M; Hatfield, G W

    2001-03-01

    Transcriptional activities of closely spaced divergent promoters are affected by the accumulation of local negative superhelicity in the region between transcribing RNA polymerase molecules (transcriptional coupling). The effect of this transcription-induced DNA supercoiling on these promoters depends on their intrinsic properties. As the global superhelical density of the chromosome is controlled by the energy charge of the cell, which is affected by environmental stresses and transitions from one growth state to another, the transcriptional coupling that occurs between divergently transcribed promoters is likely to serve a physiological purpose. Here, we suggest that transcriptional coupling between the divergent promoters of the ilvYC operon of Escherichia coli serves to co-ordinate the expression of this operon with other operons of the ilv regulon during metabolic adjustments associated with growth state transitions. As DNA supercoiling-dependent transcriptional coupling between the promoters of other divergently transcribed operons is investigated, additional global gene regulatory mechanisms and physiological roles are sure to emerge.

  2. Cofactor engineering of ketol-acid reductoisomerase (IlvC) and alcohol dehydrogenase (YqhD) improves the fusel alcohol yield in algal protein anaerobic fermentation

    SciTech Connect

    Wu, Weihua; Tran-Gyamfi, Mary Bao; Jaryenneh, James Dekontee; Davis, Ryan W.

    2016-08-24

    Recently the feasibility of conversion of algal protein to mixed alcohols has been demonstrated with an engineered E.coli strain, enabling comprehensive utilization of the biomass for biofuel applications. However, the yield and titers of mixed alcohol production must be improved for market adoption. A major limiting factor for achieving the necessary yield and titer improvements is cofactor imbalance during the fermentation of algal protein. To resolve this problem, a directed evolution approach was applied to modify the cofactor specificity of two key enzymes (IlvC and YqhD) from NADPH to NADH in the mixed alcohol metabolic pathway. Using high throughput screening, more than 20 YqhD mutants were identified to show activity on NADH as a cofactor. Of these 20 mutants, the top five of YqhD mutants were selected for combination with two IlvC mutants with NADH as a cofactor for the modification of the protein conversion strain. The combination of the IlvC and YqhD mutants yielded a refined E.coli strain, subtype AY3, with increased fusel alcohol yield of ~60% compared to wild type under anaerobic fermentation on amino acid mixtures. When applied to real algal protein hydrolysates, the strain AY3 produced 100% and 38% more total mixed alcohols than the wild type strain on two different algal hydrolysates, respectively. The results indicate that cofactor engineering is a promising approach to improve the feasibility of bioconversion of algal protein into mixed alcohols as advanced biofuels.

  3. Cofactor engineering of ketol-acid reductoisomerase (IlvC) and alcohol dehydrogenase (YqhD) improves the fusel alcohol yield in algal protein anaerobic fermentation

    SciTech Connect

    Wu, Weihua; Tran-Gyamfi, Mary Bao; Jaryenneh, James Dekontee; Davis, Ryan W.

    2016-08-24

    Recently the feasibility of conversion of algal protein to mixed alcohols has been demonstrated with an engineered E.coli strain, enabling comprehensive utilization of the biomass for biofuel applications. However, the yield and titers of mixed alcohol production must be improved for market adoption. A major limiting factor for achieving the necessary yield and titer improvements is cofactor imbalance during the fermentation of algal protein. To resolve this problem, a directed evolution approach was applied to modify the cofactor specificity of two key enzymes (IlvC and YqhD) from NADPH to NADH in the mixed alcohol metabolic pathway. Using high throughput screening, more than 20 YqhD mutants were identified to show activity on NADH as a cofactor. Of these 20 mutants, the top five of YqhD mutants were selected for combination with two IlvC mutants with NADH as a cofactor for the modification of the protein conversion strain. The combination of the IlvC and YqhD mutants yielded a refined E.coli strain, subtype AY3, with increased fusel alcohol yield of ~60% compared to wild type under anaerobic fermentation on amino acid mixtures. When applied to real algal protein hydrolysates, the strain AY3 produced 100% and 38% more total mixed alcohols than the wild type strain on two different algal hydrolysates, respectively. The results indicate that cofactor engineering is a promising approach to improve the feasibility of bioconversion of algal protein into mixed alcohols as advanced biofuels.

  4. Cofactor engineering of ketol-acid reductoisomerase (IlvC) and alcohol dehydrogenase (YqhD) improves the fusel alcohol yield in algal protein anaerobic fermentation

    DOE PAGES

    Wu, Weihua; Tran-Gyamfi, Mary Bao; Jaryenneh, James Dekontee; ...

    2016-08-24

    Recently the feasibility of conversion of algal protein to mixed alcohols has been demonstrated with an engineered E.coli strain, enabling comprehensive utilization of the biomass for biofuel applications. However, the yield and titers of mixed alcohol production must be improved for market adoption. A major limiting factor for achieving the necessary yield and titer improvements is cofactor imbalance during the fermentation of algal protein. To resolve this problem, a directed evolution approach was applied to modify the cofactor specificity of two key enzymes (IlvC and YqhD) from NADPH to NADH in the mixed alcohol metabolic pathway. Using high throughput screening,more » more than 20 YqhD mutants were identified to show activity on NADH as a cofactor. Of these 20 mutants, the top five of YqhD mutants were selected for combination with two IlvC mutants with NADH as a cofactor for the modification of the protein conversion strain. The combination of the IlvC and YqhD mutants yielded a refined E.coli strain, subtype AY3, with increased fusel alcohol yield of ~60% compared to wild type under anaerobic fermentation on amino acid mixtures. When applied to real algal protein hydrolysates, the strain AY3 produced 100% and 38% more total mixed alcohols than the wild type strain on two different algal hydrolysates, respectively. The results indicate that cofactor engineering is a promising approach to improve the feasibility of bioconversion of algal protein into mixed alcohols as advanced biofuels.« less

  5. Wolbachia-induced loss of male fertility is likely related to branch chain amino acid biosynthesis and iLvE in Laodelphax striatellus.

    PubMed

    Ju, Jia-Fei; Hoffmann, Ary A; Zhang, Yan-Kai; Duan, Xing-Zhi; Guo, Yan; Gong, Jun-Tao; Zhu, Wen-Chao; Hong, Xiao-Yue

    2017-06-01

    Wolbachia are endosymbionts that infect many species of arthropods and nematodes. Wolbachia-induced cytoplasmic incompatibility (CI) is the most common phenotype in affected hosts, involving embryonic lethality in crosses between Wolbachia-infected males and uninfected females. The molecular mechanisms underlying this phenomenon are currently unclear. Here we examine the molecular correlates of the Wolbachia infection in Laodelphax striatellus (Fallén), an important rice pest, where embryonic lethality is strong and almost complete. We compared the gene expression of 4-day-old Wolbachia-infected and uninfected L. striatellus testes to identify candidate genes for paternal-effect embryonic lethality induction. Based on microarray analysis, iLvE was the most down-regulated gene; this gene mediates branched-chain amino acid (BCAA) biosynthesis and participates in many processes related to reproductive performance. After knocking down iLvE by RNAi in uninfected male L. striatellus, male fertility was reduced, leading to a decrease in embryo hatching rates, but fertility was rescued in crosses between these males and Wolbachia-infected females. Removal of BCAA in chemically-defined diets of uninfected males also led to a loss of male fertility. Low amino acid nutrition may enhance exposure time of sperm to Wolbachia in the testes to affect adult reproduction in L. striatellus by reducing the number of sperm transferred per mating by males. These results indicate that Wolbachia may decrease male fertility in L. striatellus by acting on iLvE, a key factor of BCAA biosynthesis, and delaying sperm maturation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Barriers and facilitators to enrollment and re-enrollment into the community health funds/Tiba Kwa Kadi (CHF/TIKA) in Tanzania: a cross-sectional inquiry on the effects of socio-demographic factors and social marketing strategies.

    PubMed

    Kapologwe, Ntuli A; Kagaruki, Gibson B; Kalolo, Albino; Ally, Mariam; Shao, Amani; Meshack, Manoris; Stoermer, Manfred; Briet, Amena; Wiedenmayer, Karin; Hoffman, Axel

    2017-04-27

    Introduction of a health insurance scheme is one of the ways to enhance access to health care services and to protect individuals from catastrophic health expenditures. Little is known on the influence of socio-demographic and social marketing strategies on enrollment and re-enrollment in the Community Health Fund/Tiba Kwa Kadi (CHF/TIKA) in Tanzania. This cross-sectional study employed quantitative methods for data collection between November 2014 and March 2015 in Singida and Shinyanga regions. Relationship between variables was obtained through Chi-square test and multivariate logistic regression. We recruited 496 participants in the study. Majority (92.7%) of participants consented to participate, with 229 (49.8%) and 231 (50.2%) members and non members of CHF/TIKA respectively. Majority (90.9%) were aware of CHF/TIKA. Majority of CHF/TIKA members and non-members (90% and 68.3% respectively) reported health facility-based sensitization as the most common social marketing approach employed to market the CHF/TIKA. The most popular marketing strategies in the country including traditional dances, football games, radio, television, news papers, and mosques/church were reported by few CHF and non CHF members. Multivariate Logistic regression models revealed no significant association between social marketing strategies and enrollment, but only socio-demographics; including marital status (AOR = 2.0, 95% CI 1.1-3.8) and family size (household with ≥ 6 members) (AOR = 1.5, 95% CI 1.0-2.5), were significant factors associated with enrollment/re-enrollment rate. This study indicated that low level of utilization of available social marketing strategies and socio-demographic factors are the barriers for attracting members to join the schemes. There is a need for applying various social marketing strategies and considering different facilitating and impending socio-demographic factors for the growth and sustainability of the scheme as we move towards

  7. Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in (15)N-(13)C-ILV methyl labeled proteins.

    PubMed

    Frueh, Dominique P; Leed, Alison; Arthanari, Haribabu; Koglin, Alexander; Walsh, Christopher T; Wagner, Gerhard

    2009-11-01

    We present a time-shared 3D HSQC-NOESY experiment that enables one to simultaneously record (13)C- and (15)N-dispersed spectra in Ile, Leu and Val (ILV) methyl-labeled samples. This experiment is designed to delineate the two spectra which would otherwise overlap with one another when acquired together. These spectra display nOe correlations in the detected proton dimension, i.e. with maximum resolution. This is in contrast to NOESY-HSQC types of experiments that provide cross-peaks in the indirect dimension with low resolution due to limits in experimental time. The technique is particularly advantageous at high field where even longer experimental times would be required for comparable resolution in NOESY-HSQC experiments. The method is demonstrated at 900 MHz and at 750 MHz on 37 and 31 kDa proteins, respectively. The resolution and time saving provided in this experiment was crucial for solving the structures of these two proteins.

  8. Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in 15N-13C-ILV methyl labeled proteins

    PubMed Central

    Frueh, Dominique P.; Leed, Alison; Arthanari, Haribabu; Koglin, Alexander; Walsh, Christopher T.; Wagner, Gerhard

    2009-01-01

    We present a time-shared 3D HSQC-NOESY experiment that enables one to simultaneously record 13C- and 15N-dispersed spectra in Ile, Leu and Val (ILV) methyl-labeled samples. This experiment is designed to delineate the two spectra which would otherwise overlap with one another when acquired together. These spectra display nOe correlations in the detected proton dimension, i.e. with maximum resolution. This is in contrast to NOESY-HSQC types of experiments that provide cross-peaks in the indirect dimension with low resolution due to limits in experimental time. The technique is particularly advantageous at high field where even longer experimental times would be required for comparable resolution in NOESY-HSQC experiments. The method is demonstrated at 900 MHz and at 750 MHz on 37 kDa and 31 kDa proteins, respectively. The resolution and time saving provided in this experiment was crucial for solving the structures of these two proteins. PMID:19728110

  9. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism

    PubMed Central

    2011-01-01

    Background Isobutanol can be a better biofuel than ethanol due to its higher energy density and lower hygroscopicity. Furthermore, the branched-chain structure of isobutanol gives a higher octane number than the isomeric n-butanol. Saccharomyces cerevisiae was chosen as the production host because of its relative tolerance to alcohols, robustness in industrial fermentations, and the possibility for future combination of isobutanol production with fermentation of lignocellulosic materials. Results The yield of isobutanol was improved from 0.16 to 0.97 mg per g glucose by simultaneous overexpression of biosynthetic genes ILV2, ILV3, and ILV5 in valine metabolism in anaerobic fermentation of glucose in mineral medium in S. cerevisiae. Isobutanol yield was further improved by twofold by the additional overexpression of BAT2, encoding the cytoplasmic branched-chain amino-acid aminotransferase. Overexpression of ILV6, encoding the regulatory subunit of Ilv2, in the ILV2 ILV3 ILV5 overexpression strain decreased isobutanol production yield by threefold. In aerobic cultivations in shake flasks in mineral medium, the isobutanol yield of the ILV2 ILV3 ILV5 overexpression strain and the reference strain were 3.86 and 0.28 mg per g glucose, respectively. They increased to 4.12 and 2.4 mg per g glucose in yeast extract/peptone/dextrose (YPD) complex medium under aerobic conditions, respectively. Conclusions Overexpression of genes ILV2, ILV3, ILV5, and BAT2 in valine metabolism led to an increase in isobutanol production in S. cerevisiae. Additional overexpression of ILV6 in the ILV2 ILV3 ILV5 overexpression strain had a negative effect, presumably by increasing the sensitivity of Ilv2 to valine inhibition, thus weakening the positive impact of overexpression of ILV2, ILV3, and ILV5 on isobutanol production. Aerobic cultivations of the ILV2 ILV3 ILV5 overexpression strain and the reference strain showed that supplying amino acids in cultivation media gave a substantial

  10. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism.

    PubMed

    Chen, Xiao; Nielsen, Kristian F; Borodina, Irina; Kielland-Brandt, Morten C; Karhumaa, Kaisa

    2011-07-28

    Isobutanol can be a better biofuel than ethanol due to its higher energy density and lower hygroscopicity. Furthermore, the branched-chain structure of isobutanol gives a higher octane number than the isomeric n-butanol. Saccharomyces cerevisiae was chosen as the production host because of its relative tolerance to alcohols, robustness in industrial fermentations, and the possibility for future combination of isobutanol production with fermentation of lignocellulosic materials. The yield of isobutanol was improved from 0.16 to 0.97 mg per g glucose by simultaneous overexpression of biosynthetic genes ILV2, ILV3, and ILV5 in valine metabolism in anaerobic fermentation of glucose in mineral medium in S. cerevisiae. Isobutanol yield was further improved by twofold by the additional overexpression of BAT2, encoding the cytoplasmic branched-chain amino-acid aminotransferase. Overexpression of ILV6, encoding the regulatory subunit of Ilv2, in the ILV2 ILV3 ILV5 overexpression strain decreased isobutanol production yield by threefold. In aerobic cultivations in shake flasks in mineral medium, the isobutanol yield of the ILV2 ILV3 ILV5 overexpression strain and the reference strain were 3.86 and 0.28 mg per g glucose, respectively. They increased to 4.12 and 2.4 mg per g glucose in yeast extract/peptone/dextrose (YPD) complex medium under aerobic conditions, respectively. Overexpression of genes ILV2, ILV3, ILV5, and BAT2 in valine metabolism led to an increase in isobutanol production in S. cerevisiae. Additional overexpression of ILV6 in the ILV2 ILV3 ILV5 overexpression strain had a negative effect, presumably by increasing the sensitivity of Ilv2 to valine inhibition, thus weakening the positive impact of overexpression of ILV2, ILV3, and ILV5 on isobutanol production. Aerobic cultivations of the ILV2 ILV3 ILV5 overexpression strain and the reference strain showed that supplying amino acids in cultivation media gave a substantial improvement in isobutanol production

  11. A lumenal domain-dependent pathway for sorting to intralumenal vesicles of multivesicular endosomes involved in organelle morphogenesis.

    PubMed

    Theos, Alexander C; Truschel, Steven T; Tenza, Daniele; Hurbain, Ilse; Harper, Dawn C; Berson, Joanne F; Thomas, Penelope C; Raposo, Graça; Marks, Michael S

    2006-03-01

    Cargo partitioning into intralumenal vesicles (ILVs) of multivesicular endosomes underlies such cellular processes as receptor downregulation, viral budding, and biogenesis of lysosome-related organelles such as melanosomes. We show that the melanosomal protein Pmel17 is sorted into ILVs by a mechanism that is dependent upon lumenal determinants and conserved in non-pigment cells. Pmel17 targeting to ILVs does not require its native cytoplasmic domain or cytoplasmic residues targeted by ubiquitylation and, unlike sorting of ubiquitylated cargo, is insensitive to functional inhibition of Hrs and ESCRT complexes. Chimeric protein and deletion analyses indicate that two N-terminal lumenal subdomains are necessary and sufficient for ILV targeting. Pmel17 fibril formation, which occurs during melanosome maturation in melanocytes, requires a third lumenal subdomain and proteolytic processing that itself requires ILV localization. These results establish an Hrs- and perhaps ESCRT-independent pathway of ILV sorting by lumenal determinants and a requirement for ILV sorting in fibril formation.

  12. Oahu Groundwater Flow Model

    DOE Data Explorer

    Nicole Lautze

    2015-01-01

    Groundwater flow model for the island of Oahu. Data is from the following sources: Rotzoll, K., A.I. El-Kadi. 2007. Numerical Ground-Water Flow Simulation for Red Hill Fuel Storage Facilities, NAVFAC Pacific, Oahu, Hawaii - Prepared TEC, Inc. Water Resources Research Center, University of Hawaii, Honolulu.; Whittier, R.B., K. Rotzoll, S. Dhal, A.I. El-Kadi, C. Ray, G. Chen, and D. Chang. 2004. Hawaii Source Water Assessment Program Report – Volume VII – Island of Oahu Source Water Assessment Program Report. Prepared for the Hawaii Department of Health, Safe Drinking Water Branch. University of Hawaii, Water Resources Research Center. Updated 2008.; and Whittier, R. and A.I. El-Kadi. 2009. Human and Environmental Risk Ranking of Onsite Sewage Disposal Systems – Final. Prepared by the University of Hawaii, Dept. of Geology and Geophysics for the State of Hawaii Dept. of Health, Safe Drinking Water Branch. December 2009.

  13. An Analysis of United States-Albanian Security Relations in Light of the War on Terrorism

    DTIC Science & Technology

    2004-12-01

    between Albania and Allied governments.80 77 The Albanian representative in Caserta, Mr. Kadri Hoxha...Nationalist Leader (Gani Kryeziu ) opposed to Hoxha; a Greek minister of press had claimed Northern Epirus (Southern Albania) and forces of a rightist

  14. Interactions between large and small subunits of different acetohydroxyacid synthase isozymes of Escherichia coli.

    PubMed

    Vyazmensky, Maria; Zherdev, Yuri; Slutzker, Alex; Belenky, Inna; Kryukov, Olga; Barak, Ze'ev; Chipman, David M

    2009-09-15

    The large, catalytic subunits (LSUs; ilvB, ilvG and ilvI, respectively) of enterobacterial acetohydroxyacid synthases isozymes (AHAS I, II and III) have molecular weights approximately 60 kDa and are paralogous with a family of other thiamin diphosphate dependent enzymes. The small, regulatory subunits (SSUs) of AHAS I and AHAS III (ilvN and ilvH) are required for valine inhibition, but ilvN and ilvH can only confer valine sensitivity on their own LSUs. AHAS II is valine resistant. The LSUs have only approximately 15, <1 and approximately 3%, respectively, of the activity of their respective holoenzymes, but the holoenzymes can be reconstituted with complete recovery of activity. We have examined the activation of each of the LSUs by SSUs from different isozymes and ask to what extent such activation is specific; that is, is effective nonspecific interaction possible between LSUs and SSUs of different isozymes? To our surprise, the AHAS II SSU ilvM is able to activate the LSUs of all three of the isozymes, and the truncated AHAS III SSUs ilvH-Delta80, ilvH-Delta86 and ilvH-Delta89 are able to activate the LSUs of both AHAS I and AHAS III. However, none of the heterologously activated enzymes have any feedback sensitivity. Our results imply the existence of a common region in all three LSUs to which regulatory subunits may bind, as well as a similarity between the surfaces of ilvM and the other SSUs. This surface must be included within the N-terminal betaalphabetabetaalphabeta-domain of the SSUs, probably on the helical face of this domain. We suggest hypotheses for the mechanism of valine inhibition, and reject one involving induced dissociation of subunits.

  15. A novel pathway for sorting to intralumenal vesicles of multivesicular endosomes involved in organelle morphogenesis

    PubMed Central

    Theos, Alexander C.; Truschel, Steven T.; Tenza, Danielle; Hurbain, Ilse; Harper, Dawn C.; Berson, Joanne F.; Thomas, Penelope C.; Raposo, Graça; Marks, Michael S.

    2006-01-01

    SUMMARY Cargo partitioning into intralumenal vesicles (ILVs) of multivesicular endosomes underlies such cellular processes as growth factor down-regulation, viral budding, and biogenesis of lysosome-related organelles including melanosomes. Here we show that the melanosomal protein, Pmel17, is sorted into ILVs by a novel mechanism that is conserved in non-pigment cells and is dependent upon lumenal determinants. ILV targeting of Pmel17 is unaffected by mutagenesis of cytoplasmic lysine and cysteine residues or replacement of the cytoplasmic domain, indicating independence of ubiquitylation, and unlike ILV targeting of ubiquitylated cargo, is insensitive to functional inhibition of Hrs and ESCRT complexes. Chimeric protein and deletion analyses indicate that two N-terminal lumenal sub-domains are necessary and sufficient for ILV targeting. Pmel17 fibril formation, which occurs during melanosome maturation in melanocytes, requires a third lumenal sub-domain and proteolytic processing that itself requires ILV localization. These results establish a novel Hrs- and perhaps ESCRT-independent pathway of ILV sorting by lumenal determinants and a requirement for ILV sorting in fibril formation. PMID:16516837

  16. An enzyme in yeast mitochondria that catalyzes a step in branched-chain amino acid biosynthesis also functions in mitochondrial DNA stability.

    PubMed Central

    Zelenaya-Troitskaya, O; Perlman, P S; Butow, R A

    1995-01-01

    The yeast mitochondrial high mobility group protein Abf2p is required, under certain growth conditions, for the maintenance of wild-type (rho+) mitochondrial DNA (mtDNA). We have identified a multicopy suppressor of the mtDNA instability phenotype of cells with a null allele of the ABF2 gene (delta abf2). The suppressor is a known gene, ILV5, encoding the mitochondrial protein, acetohydroxy acid reductoisomerase, which catalyzes a step in branched-chain amino acid biosynthesis. Efficient suppression occurs with just a 2- to 3-fold increase in ILV5 copy number. Moreover, in delta abf2 cells with a single copy of ILV5, changes in mtDNA stability correlate directly with changes in conditions that are known to affect ILV5 expression. Wild-type mtDNA is unstable in cells with an ILV5 null mutation (delta ilv5), leading to the production of mostly rho- petite mutants. The instability of rho+ mtDNA in delta ilv5 cells is not simply a consequence of a block in branched-chain amino acid biosynthesis, since mtDNA is stable in cells with a null allele of the ILV2 gene, which encodes another enzyme of that pathway. The most severe instability of rho+ mtDNA is observed in cells with null alleles of both ABF2 and ILV5. We suggest that ILV5 encodes a bifunctional protein required for branched-chain amino acid biosynthesis and for the maintenance of rho+ mtDNA. Images PMID:7621838

  17. Production of 2-ketoisocaproate with Corynebacterium glutamicum strains devoid of plasmids and heterologous genes

    PubMed Central

    Vogt, Michael; Haas, Sabine; Polen, Tino; van Ooyen, Jan; Bott, Michael

    2015-01-01

    2-Ketoisocaproate (KIC), the last intermediate in l-leucine biosynthesis, has various medical and industrial applications. After deletion of the ilvE gene for transaminase B in l-leucine production strains of Corynebacterium glutamicum, KIC became the major product, however, the strains were auxotrophic for l-isoleucine. To avoid auxotrophy, reduction of IlvE activity by exchanging the ATG start codon of ilvE by GTG was tested instead of an ilvE deletion. The resulting strains were indeed able to grow in glucose minimal medium without amino acid supplementation, but at the cost of lowered growth rates and KIC production parameters. The best production performance was obtained with strain MV-KICF1, which carried besides the ilvE start codon exchange three copies of a gene for a feedback-resistant 2-isopropylmalate synthase, one copy of a gene for a feedback-resistant acetohydroxyacid synthase and deletions of ltbR and iolR encoding transcriptional regulators. In the presence of 1 mM l-isoleucine, MV-KICF1 accumulated 47 mM KIC (6.1 g l−1) with a yield of 0.20 mol/mol glucose and a volumetric productivity of 1.41 mmol KIC l−1 h−1. Since MV-KICF1 is plasmid free and lacks heterologous genes, it is an interesting strain for industrial application and as platform for the production of KIC-derived compounds, such as 3-methyl-1-butanol. PMID:25488800

  18. Production of 2-ketoisocaproate with Corynebacterium glutamicum strains devoid of plasmids and heterologous genes.

    PubMed

    Vogt, Michael; Haas, Sabine; Polen, Tino; van Ooyen, Jan; Bott, Michael

    2015-03-01

    2-Ketoisocaproate (KIC), the last intermediate in l-leucine biosynthesis, has various medical and industrial applications. After deletion of the ilvE gene for transaminase B in l-leucine production strains of Corynebacterium glutamicum, KIC became the major product, however, the strains were auxotrophic for l-isoleucine. To avoid auxotrophy, reduction of IlvE activity by exchanging the ATG start codon of ilvE by GTG was tested instead of an ilvE deletion. The resulting strains were indeed able to grow in glucose minimal medium without amino acid supplementation, but at the cost of lowered growth rates and KIC production parameters. The best production performance was obtained with strain MV-KICF1, which carried besides the ilvE start codon exchange three copies of a gene for a feedback-resistant 2-isopropylmalate synthase, one copy of a gene for a feedback-resistant acetohydroxyacid synthase and deletions of ltbR and iolR encoding transcriptional regulators. In the presence of 1 mM l-isoleucine, MV-KICF1 accumulated 47 mM KIC (6.1 g l(-1)) with a yield of 0.20 mol/mol glucose and a volumetric productivity of 1.41 mmol KIC l(-1)  h(-1). Since MV-KICF1 is plasmid free and lacks heterologous genes, it is an interesting strain for industrial application and as platform for the production of KIC-derived compounds, such as 3-methyl-1-butanol. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  19. Association of Computed Tomography Ischemic Lesion Location With Functional Outcome in Acute Large Vessel Occlusion Ischemic Stroke.

    PubMed

    Ernst, Marielle; Boers, Anna M M; Aigner, Annette; Berkhemer, Olvert A; Yoo, Albert J; Roos, Yvo B; Dippel, Diederik W J; van der Lugt, Aad; van Oostenbrugge, Robert J; van Zwam, Wim H; Fiehler, Jens; Marquering, Henk A; Majoie, Charles B L M

    2017-09-01

    Ischemic lesion volume (ILV) assessed by follow-up noncontrast computed tomography correlates only moderately with clinical end points, such as the modified Rankin Scale (mRS). We hypothesized that the association between follow-up noncontrast computed tomography ILV and outcome as assessed with mRS 3 months after stroke is strengthened when taking the mRS relevance of the infarct location into account. An anatomic atlas with 66 areas was registered to the follow-up noncontrast computed tomographic images of 254 patients from the MR CLEAN trial (Multicenter Randomized Clinical Trial of Endovascular Treatment of Acute Ischemic Stroke in the Netherlands). The anatomic brain areas were divided into brain areas of high, moderate, and low mRS relevance as reported in the literature. Based on this distinction, the ILV in brain areas of high, moderate, and low mRS relevance was assessed for each patient. Binary and ordinal logistic regression analyses with and without adjustment for known confounders were performed to assess the association between the ILVs of different mRS relevance and outcome. The odds for a worse outcome (higher mRS) were markedly higher given an increase of ILV in brain areas of high mRS relevance (odds ratio, 1.42; 95% confidence interval, 1.31-1.55 per 10 mL) compared with an increase in total ILV (odds ratios, 1.16; 95% confidence interval, 1.12-1.19 per 10 mL). Regression models using ILV in brain areas of high mRS relevance instead of total ILV showed a higher quality. The association between follow-up noncontrast computed tomography ILV and outcome as assessed with mRS 3 months after stroke is strengthened by accounting for the mRS relevance of the affected brain areas. Future prediction models should account for the ILV in brain areas of high mRS relevance. © 2017 American Heart Association, Inc.

  20. Regulation of yeast ESCRT-III membrane scission activity by the Doa4 ubiquitin hydrolase.

    PubMed

    Johnson, Natalie; West, Matt; Odorizzi, Greg

    2017-03-01

    ESCRT-III executes membrane scission during the budding of intralumenal vesicles (ILVs) at endosomes. The scission mechanism is unknown but appears to be linked to the cycle of assembly and disassembly of ESCRT-III complexes at membranes. Regulating this cycle is therefore expected to be important for determining the timing of ESCRT-III-mediated membrane scission. We show that in Saccharomyces cerevisiae, ESCRT-III complexes are stabilized and ILV membrane scission is delayed by Doa4, which is the ubiquitin hydrolase that deubiquitinates transmembrane proteins sorted as cargoes into ILVs. These results suggest a mechanism to delay ILV budding while cargoes undergo deubiquitination. We further show that deubiquitination of ILV cargoes is inhibited via Doa4 binding to Vps20, which is the subunit of ESCRT-III that initiates assembly of the complex. Current models suggest that ESCRT-III complexes surround ubiquitinated cargoes to trap them at the site of ILV budding while the cargoes undergo deubiquitination. Thus our results also propose a mechanism to prevent the onset of ILV cargo deubiquitination at the initiation of ESCRT-III complex assembly.

  1. MRA_1571 is required for isoleucine biosynthesis and improves Mycobacterium tuberculosis H37Ra survival under stress

    PubMed Central

    Sharma, Rishabh; Keshari, Deepa; Singh, Kumar Sachin; Yadav, Shailendra; Singh, Sudheer Kumar

    2016-01-01

    Threonine dehydratase is a pyridoxal 5-phosphate dependent enzyme required for isoleucine biosynthesis. Threonine dehydratase (IlvA) participates in conversion of threonine to 2-oxobutanoate and ammonia is released as a by-product. MRA_1571 is annotated to be coding for IlvA in Mycobacterium tuberculosis H37Ra (Mtb-Ra). We developed a recombinant (KD) Mtb-Ra strain by down-regulating IlvA. The growth studies on different carbon sources suggested reduced growth of KD compared to wild-type (WT), also, isoleucine concentration dependent KD growth restoration was observed. The expression profiling of IlvA suggested increased expression of IlvA during oxygen, acid and oxidative stress. In addition, KD showed reduced survival under pH, starvation, nitric oxide and peroxide stresses. KD was more susceptible to antimycobacterial agents such as streptomycin (STR), rifampicin (RIF) and levofloxacin (LVF), while, no such effect was noticeable when exposed to isoniazid. Also, an increase in expression of IlvA was observed when exposed to STR, RIF and LVF. The dye accumulation studies suggested increased permeability of KD to ethidium bromide and Nile Red as compared to WT. TLC and Mass studies confirmed altered lipid profile of KD. In summary down-regulation of IlvA affects Mtb growth, increases its susceptibility to stress and leads to altered cell wall lipid profile. PMID:27353854

  2. Increase in the serum bile acid level predicts the effective hypertrophy of the nonembolized hepatic lobe after right portal vein embolization.

    PubMed

    Hayashi, Hiromitsu; Beppu, Toru; Sugita, Hiroki; Horino, Kei; Komori, Hiroyuki; Masuda, Toshiro; Okabe, Hirohisa; Takamori, Hiroshi; Baba, Hideo

    2009-09-01

    The purpose of the present study was to investigate the clinical association between serum bile acid level changes and liver hypertrophy in portal vein embolization (PVE). In 31 patients, the serum total bile acid level was prospectively measured before and 1, 3, 5, 7, and 14 days after right PVE. Computed tomographic volumetry was performed before and 25.0 +/- 3.6 days after PVE. Portal vein embolization induced the liver hypertrophy with a median increase in the left lobe volume (ILV) of 165 cm(3) and a median percentage ILV (%ILV) of 29%. Compared with the pretreatment level, the serum bile acid levels significantly increased on day 3 and day 14 after PVE (p = 0.017 and p = 0.003, respectively). In patients with greater hypertrophy after PVE (ILV > 165 cm(3) and %ILV > 30%), the increases in the bile acid level on day 3 were larger than that in those with lesser hypertrophy (p = 0.008 and p = 0.002, respectively). The increase on day 3 positively correlated with the ILV and %ILV (p = 0.003 and p = 0.004, respectively). The serum bile acid levels on day 3, 5, and 7 after PVE increased in patients with %ILV > 30% but not in those with %ILV < or = 30%. Portal vein embolization increases the serum bile acid level in patients with effective liver hypertrophy in the nonembolized lobe. The increase on day 3 is a useful predictor of effective hypertrophy of the nonembolized lobe. Thus, bile acid signaling may be important for liver regeneration post-PVE.

  3. West Maui Groundwater Flow Model

    SciTech Connect

    Nicole Lautze

    2015-01-01

    Groundwater flow model for West Maui. Data is from the following sources: Whittier, R. and A.I. El-Kadi. 2014. Human and Environmental Risk Ranking of Onsite Sewage Disposal Systems For the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final. Prepared by the University of Hawaii, Dept. of Geology and Geophysics for the State of Hawaii Dept. of Health, Safe Drinking Water Branch. September 2014; and Whittier, R.B., K. Rotzoll, S. Dhal, A.I. El-Kadi, C. Ray, G. Chen, and D. Chang. 2004. Hawaii Source Water Assessment Program Report – Volume V – Island of Maui Source Water Assessment Program Report. Prepared for the Hawaii Department of Health, Safe Drinking Water Branch. University of Hawaii, Water Resources Research Center. Updated 2008.

  4. Kauai Groundwater Flow Model

    SciTech Connect

    Nicole Lautze

    2015-01-01

    Groundwater flow model for Kauai. Data is from the following sources: Whittier, R. and A.I. El-Kadi. 2014. Human and Environmental Risk Ranking of Onsite Sewage Disposal Systems For the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final. Prepared by the University of Hawaii, Dept. of Geology and Geophysics for the State of Hawaii Dept. of Health, Safe Drinking Water Branch. September 2014.; and Whittier, R.B., K. Rotzoll, S. Dhal, A.I. El-Kadi, C. Ray, G. Chen, and D. Chang. 2004. Hawaii Source Water Assessment Program Report – Volume IV – Island of Kauai Source Water Assessment Program Report. Prepared for the Hawaii Department of Health, Safe Drinking Water Branch. University of Hawaii, Water Resources Research Center. Updated 2015.

  5. East Maui Groundwater Flow Model

    DOE Data Explorer

    Nicole Lautze

    2015-01-01

    Groundwater flow model for East Maui. Data is from the following sources: Whittier, R. and A.I. El-Kadi. 2014. Human and Environmental Risk Ranking of Onsite Sewage Disposal Systems For the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final. Prepared by the University of Hawaii, Dept. of Geology and Geophysics for the State of Hawaii Dept. of Health, Safe Drinking Water Branch. September 2014; and Whittier, R.B., K. Rotzoll, S. Dhal, A.I. El-Kadi, C. Ray, G. Chen, and D. Chang. 2004. Hawaii Source Water Assessment Program Report – Volume V – Island of Maui Source Water Assessment Program Report. Prepared for the Hawaii Department of Health, Safe Drinking Water Branch. University of Hawaii, Water Resources Research Center. Updated 2008.

  6. Hawaii Island Groundwater Flow Model

    DOE Data Explorer

    Nicole Lautze

    2015-01-01

    Groundwater flow model for Hawaii Island. Data is from the following sources: Whittier, R.B., K. Rotzoll, S. Dhal, A.I. El-Kadi, C. Ray, G. Chen, and D. Chang. 2004. Hawaii Source Water Assessment Program Report – Volume II – Island of Hawaii Source Water Assessment Program Report. Prepared for the Hawaii Department of Health, Safe Drinking Water Branch. University of Hawaii, Water Resources Research Center. Updated 2008; and Whittier, R. and A.I. El-Kadi. 2014. Human and Environmental Risk Ranking of Onsite Sewage Disposal Systems For the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final. Prepared by the University of Hawaii, Dept. of Geology and Geophysics for the State of Hawaii Dept. of Health, Safe Drinking Water Branch. September 2014.

  7. Associations of Ischemic Lesion Volume With Functional Outcome in Patients With Acute Ischemic Stroke: 24-Hour Versus 1-Week Imaging.

    PubMed

    Bucker, Amber; Boers, Anna M; Bot, Joseph C J; Berkhemer, Olvert A; Lingsma, Hester F; Yoo, Albert J; van Zwam, Wim H; van Oostenbrugge, Robert J; van der Lugt, Aad; Dippel, Diederik W J; Roos, Yvo B W E M; Majoie, Charles B L M; Marquering, Henk A

    2017-05-01

    Ischemic lesion volume (ILV) on noncontrast computed tomography at 1 week can be used as a secondary outcome measure in patients with acute ischemic stroke. Twenty-four-hour ILV on noncontrast computed tomography has greater availability and potentially allows earlier estimation of functional outcome. We aimed to assess lesion growth 24 hours after stroke onset and compare the associations of 24-hour and 1-week ILV with functional outcome. We included 228 patients from MR CLEAN trial (Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands), who received noncontrast computed tomography at 24-hour and 1-week follow-up on which ILV was measured. Relative and absolute lesion growth was determined. Logistic regression models were constructed either including the 24-hour or including the 1-week ILV. Ordinal and dichotomous (0-2 and 3-6) modified Rankin scale scores were, respectively, used as primary and secondary outcome measures. Median ILV was 42 mL (interquartile range, 21-95 mL) and 64 mL (interquartile range: 30-120 mL) at 24 hours and 1 week, respectively. Relative lesion growth exceeding 30% occurred in 121 patients (53%) and absolute lesion growth exceeding 20 mL occurred in 83 patients (36%). Both the 24-hour and 1-week ILVs were similarly significantly associated with functional outcome (both P<0.001). In the logistic analyses, the areas under the curve of the receiver-operator characteristic curves were similar: 0.85 (95% confidence interval, 0.80-0.90) and 0.87 (95% confidence interval, 0.82-0.91) for including the 24-hour and 1-week ILV, respectively. Growth of ILV is common 24-hour poststroke onset. Nevertheless, the 24-hour ILV proved to be a valuable secondary outcome measure as it is equally strongly associated with functional outcome as the 1-week ILV. URL: http://www.isrctn.com. Unique identifier: ISRCTN10888758. © 2017 American Heart Association, Inc.

  8. Membrane fatty acid composition as a determinant of Listeria monocytogenes sensitivity to trans-cinnamaldehyde.

    PubMed

    Rogiers, Gil; Kebede, Biniam T; Van Loey, Ann; Michiels, Chris W

    2017-03-23

    Trans-cinnamaldehyde, the major compound of cinnamon essential oil, is a potentially interesting natural antimicrobial food preservative. Although a number of studies have addressed its mode of action, the factors that determine bacterial sensitivity or tolerance to trans-cinnamaldehyde are poorly understood. We report the detailed characterization of a Listeria monocytogenes Scott A trans-cinnamaldehyde hypersensitive mutant defective in IlvE, which catalyzes the reversible transamination of branched-chain amino acids to the corresponding short-chain α-ketoacids. This mutant showed an 8.4 fold extended lag phase during growth in sublethal concentrations (4 mM), and faster inactivation in lethal concentrations of trans-cinnamaldehyde (6 mM). Trans-cinnamaldehyde hypersensitivity could be corrected by genetic complementation with the ilvE gene and supplementation with branched-chain α-ketoacids. Whole-cell fatty acid analyses revealed an almost complete loss of anteiso branched-chain fatty acids (BCFAs), which was compensated by elevated levels of unbranched saturated fatty acids and iso-BCFAs. Sub-inhibitory concentrations of trans-cinnamaldehyde induced membrane fatty acid adaptations predicted to reduce membrane fluidity, possibly as a response to counteract the membrane fluidizing effect of trans-cinnamaldehyde. These results demonstrate the role of IlvE in BCFA production and the role of membrane composition as an important determinant of trans-cinnamaldehyde sensitivity in L. monocytogenes.

  9. 78 FR 25446 - Notice of Intent To Prepare a Supplemental Environmental Impact Statement for the San Ysidro Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-01

    ..., Portfolio Management Division, Pacific Rim Region, Public Buildings Service. BILLING CODE 6820-YF-P ... Port of Entry (LPOE) Modernization and Expansion Project AGENCY: General Services Administration (GSA... Expansion Project (Project). FOR FURTHER INFORMATION CONTACT: Osmahn A. Kadri, NEPA Project Manager,...

  10. Coordinated binding of Vps4 to ESCRT-III drives membrane neck constriction during MVB vesicle formation.

    PubMed

    Adell, Manuel Alonso Y; Vogel, Georg F; Pakdel, Mehrshad; Müller, Martin; Lindner, Herbert; Hess, Michael W; Teis, David

    2014-04-14

    Five endosomal sorting complexes required for transport (ESCRTs) mediate the degradation of ubiquitinated membrane proteins via multivesicular bodies (MVBs) in lysosomes. ESCRT-0, -I, and -II interact with cargo on endosomes. ESCRT-II also initiates the assembly of a ringlike ESCRT-III filament consisting of Vps20, Snf7, Vps24, and Vps2. The AAA-adenosine triphosphatase Vps4 disassembles and recycles the ESCRT-III complex, thereby terminating the ESCRT pathway. A mechanistic role for Vps4 in intraluminal vesicle (ILV) formation has been unclear. By combining yeast genetics, biochemistry, and electron tomography, we find that ESCRT-III assembly on endosomes is required to induce or stabilize the necks of growing MVB ILVs. Yet, ESCRT-III alone is not sufficient to complete ILV biogenesis. Rather, binding of Vps4 to ESCRT-III, coordinated by interactions with Vps2 and Snf7, is coupled to membrane neck constriction during ILV formation. Thus, Vps4 not only recycles ESCRT-III subunits but also cooperates with ESCRT-III to drive distinct membrane-remodeling steps, which lead to efficient membrane scission at the end of ILV biogenesis in vivo.

  11. Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity

    PubMed Central

    Verdel-Aranda, Karina; López-Cortina, Susana T; Hodgson, David A; Barona-Gómez, Francisco

    2015-01-01

    The 6-phosphogluconate dehydrogenase superfamily oxidize and reduce a wide range of substrates, making their functional annotation challenging. Ketol-acid reductoisomerase (KARI), encoded by the ilvC gene in branched-chain amino acids biosynthesis, is a promiscuous reductase enzyme within this superfamily. Here, we obtain steady-state enzyme kinetic parameters for 10 IlvC homologues from the genera Streptomyces and Corynebacterium, upon eight selected chemically diverse substrates, including some not normally recognized by enzymes of this superfamily. This biochemical data suggested a Streptomyces biosynthetic interlock between proline and the branched-chain amino acids, mediated by enzyme substrate promiscuity, which was confirmed via mutagenesis and complementation analyses of the proC, ilvC1 and ilvC2 genes in Streptomyces coelicolor. Moreover, both ilvC orthologues and paralogues were analysed, such that the relationship between gene duplication and functional diversification could be explored. The KARI paralogues present in S. coelicolor and Streptomyces lividans, despite their conserved high sequence identity (97%), were shown to be more promiscuous, suggesting a recent functional diversification. In contrast, the KARI paralogue from Streptomyces viridifaciens showed selectivity towards the synthesis of valine precursors, explaining its recruitment within the biosynthetic gene cluster of valanimycin. These results allowed us to assess substrate promiscuity indices as a tool to annotate new molecular functions with metabolic implications. PMID:25296650

  12. Hijacking multivesicular bodies enables long-term and exosome-mediated long-distance action of anthrax toxin.

    PubMed

    Abrami, Laurence; Brandi, Lucia; Moayeri, Mahtab; Brown, Michael J; Krantz, Bryan A; Leppla, Stephen H; van der Goot, F Gisou

    2013-11-27

    Anthrax lethal toxin is a classical AB toxin comprised of two components: protective antigen (PA) and lethal factor (LF). Here, we show that following assembly and endocytosis, PA forms a channel that translocates LF, not only into the cytosol, but also into the lumen of endosomal intraluminal vesicles (ILVs). These ILVs can fuse and release LF into the cytosol, where LF can proteolyze and disable host targets. We find that LF can persist in ILVs for days, fully sheltered from proteolytic degradation, both in vitro and in vivo. During this time, ILV-localized LF can be transmitted to daughter cells upon cell division. In addition, LF-containing ILVs can be delivered to the extracellular medium as exosomes. These can deliver LF to the cytosol of naive cells in a manner that is independent of the typical anthrax toxin receptor-mediated trafficking pathway, while being sheltered from neutralizing extracellular factors of the immune system. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Effects of unilateral PEEP on biomechanics of both lungs during independent lung ventilation in patients anaesthetised for thoracic surgery.

    PubMed

    Trela-Stachurska, Katarzyna; Nestorowicz, Andrzej; Kotlińska-Hasiec, Edyta; Sawulski, Sławomir; Dąbrowski, Wojciech

    2015-01-01

    Synchronous independent lung ventilation (ILV) is the treatment of choice for unilateral pathology of lung parenchyma. Numerous studies have documented the improved blood oxygenation and clinical efficacy of this procedure. The aim of the present study was to evaluate the effects of ILV on the selected biomechanical parameters of the lungs. The study involved ASA I-II patients undergoing thoracic surgery in the lateral decubitus position under the standard conditions of general anaesthesia with the thoracic cavity closed. ILV with equal separation of the tidal volume was performed with a prototype volume separator, using incremental a PEEP of 0-15 cm H₂O in the dependent lung. Peak pressures, dynamic compliance and airway resistance of both lungs were evaluated. The study included 36 patients. In all of the patients, a PEEP of 5-15 cm H₂O in one lung increased its peak pressures, dynamic compliance and resistances, and variably affected the biomechanical parameters of the other lung. Irrespective of patient positioning on the right or left side, the highest compliance was recorded at a PEEP of 10 cm H₂O. In ILV, peak pressures and airway resistances are higher in the dependent lung compared to compliances in the non-dependent lung. ILV with a PEEP of 5-15 cm H₂O increases the biomechanical parameters of the dependent lung while variably influencing the parameters in the non-dependent lung.

  14. Constitutively active ESCRT-II suppresses the MVB-sorting phenotype of ESCRT-0 and ESCRT-I mutants.

    PubMed

    Mageswaran, Shrawan Kumar; Johnson, Natalie K; Odorizzi, Greg; Babst, Markus

    2015-02-01

    The endosomal sorting complex required for transport (ESCRT) protein complexes function at the endosome in the formation of intraluminal vesicles (ILVs) containing cargo proteins destined for the vacuolar/lysosomal lumen. The early ESCRTs (ESCRT-0 and -I) are likely involved in cargo sorting, whereas ESCRT-III and Vps4 function to sever the neck of the forming ILVs. ESCRT-II links these functions by initiating ESCRT-III formation in an ESCRT-I-regulated manner. We identify a constitutively active mutant of ESCRT-II that partially suppresses the phenotype of an ESCRT-I or ESCRT-0 deletion strain, suggesting that these early ESCRTs are not essential and have redundant functions. However, the ESCRT-III/Vps4 system alone is not sufficient for ILV formation but requires cargo sorting mediated by one of the early ESCRTs.

  15. Biosynthesis of branched-chain amino acids is essential for effective symbioses between betarhizobia and Mimosa pudica.

    PubMed

    Chen, Wen-Ming; Prell, Jurgen; James, Euan K; Sheu, Der-Shyan; Sheu, Shih-Yi

    2012-07-01

    Burkholderia phymatum STM815 and Cupriavidus taiwanensis LMG19424 are betaproteobacterial strains that can effectively nodulate several species of the large legume genus Mimosa. A Tn5 mutant, derived from B. phymatum STM815 (KM60), and another derived from C. taiwanensis LMG19424 (KM184-55) induced Fix(-) nodules on Mimosa pudica. The Tn5-interrupted genes of the mutants showed strong homologies to ilvE, which encodes a branched-chain amino acid aminotransferase, and leuC, which encodes the large subunit of isopropylmalate isomerase. Both enzymes are known to be involved in the biosynthetic pathways for branched-chain amino acids (BCAAs) (leucine, valine and isoleucine). The B. phymatum ilvE mutant, KM60, was not auxotrophic for BCAAs and could grow well on minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source. However, it grew less efficiently than the wild-type (WT) strain when ammonia was substituted with valine or isoleucine as a nitrogen source. The BCAA aminotransferase activity of KM60 was significantly reduced relative to the WT strain, especially with isoleucine and valine as amino group donors. The C. taiwanensis leuC mutant, KM184-55, could not grow on a minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source, but its growth was restored when leucine was added to the medium. The isopropylmalate isomerase activity of KM184-55 was completely lost compared with the WT strain. Both mutants recovered their respective enzyme activities after complementation with the WT ilvE or leuC genes and were subsequently able to grow as well as their parental strains on minimal medium. They were also able to form nitrogen-fixing nodules on M. pudica. We conclude that the biosynthesis of BCAAs is essential for the free-living growth of betarhizobia, as well as for their ability to form effective symbioses with their host plant.

  16. Cytosolic re-localization and optimization of valine synthesis and catabolism enables inseased isobutanol production with the yeast Saccharomyces cerevisiae

    PubMed Central

    2012-01-01

    Background The branched chain alcohol isobutanol exhibits superior physicochemical properties as an alternative biofuel. The yeast Saccharomyces cerevisiae naturally produces low amounts of isobutanol as a by-product during fermentations, resulting from the catabolism of valine. As S. cerevisiae is widely used in industrial applications and can easily be modified by genetic engineering, this microorganism is a promising host for the fermentative production of higher amounts of isobutanol. Results Isobutanol production could be improved by re-locating the valine biosynthesis enzymes Ilv2, Ilv5 and Ilv3 from the mitochondrial matrix into the cytosol. To prevent the import of the three enzymes into yeast mitochondria, N-terminally shortened Ilv2, Ilv5 and Ilv3 versions were constructed lacking their mitochondrial targeting sequences. SDS-PAGE and immunofluorescence analyses confirmed expression and re-localization of the truncated enzymes. Growth tests or enzyme assays confirmed enzymatic activities. Isobutanol production was only increased in the absence of valine and the simultaneous blockage of the mitochondrial valine synthesis pathway. Isobutanol production could be even more enhanced after adapting the codon usage of the truncated valine biosynthesis genes to the codon usage of highly expressed glycolytic genes. Finally, a suitable ketoisovalerate decarboxylase, Aro10, and alcohol dehydrogenase, Adh2, were selected and overexpressed. The highest isobutanol titer was 0.63 g/L at a yield of nearly 15 mg per g glucose. Conclusion A cytosolic isobutanol production pathway was successfully established in yeast by re-localization and optimization of mitochondrial valine synthesis enzymes together with overexpression of Aro10 decarboxylase and Adh2 alcohol dehydrogenase. Driving forces were generated by blocking competition with the mitochondrial valine pathway and by omitting valine from the fermentation medium. Additional deletion of pyruvate decarboxylase genes

  17. Cytosolic re-localization and optimization of valine synthesis and catabolism enables inseased isobutanol production with the yeast Saccharomyces cerevisiae.

    PubMed

    Brat, Dawid; Weber, Christian; Lorenzen, Wolfram; Bode, Helge B; Boles, Eckhard

    2012-09-06

    The branched chain alcohol isobutanol exhibits superior physicochemical properties as an alternative biofuel. The yeast Saccharomyces cerevisiae naturally produces low amounts of isobutanol as a by-product during fermentations, resulting from the catabolism of valine. As S. cerevisiae is widely used in industrial applications and can easily be modified by genetic engineering, this microorganism is a promising host for the fermentative production of higher amounts of isobutanol. Isobutanol production could be improved by re-locating the valine biosynthesis enzymes Ilv2, Ilv5 and Ilv3 from the mitochondrial matrix into the cytosol. To prevent the import of the three enzymes into yeast mitochondria, N-terminally shortened Ilv2, Ilv5 and Ilv3 versions were constructed lacking their mitochondrial targeting sequences. SDS-PAGE and immunofluorescence analyses confirmed expression and re-localization of the truncated enzymes. Growth tests or enzyme assays confirmed enzymatic activities. Isobutanol production was only increased in the absence of valine and the simultaneous blockage of the mitochondrial valine synthesis pathway. Isobutanol production could be even more enhanced after adapting the codon usage of the truncated valine biosynthesis genes to the codon usage of highly expressed glycolytic genes. Finally, a suitable ketoisovalerate decarboxylase, Aro10, and alcohol dehydrogenase, Adh2, were selected and overexpressed. The highest isobutanol titer was 0.63 g/L at a yield of nearly 15 mg per g glucose. A cytosolic isobutanol production pathway was successfully established in yeast by re-localization and optimization of mitochondrial valine synthesis enzymes together with overexpression of Aro10 decarboxylase and Adh2 alcohol dehydrogenase. Driving forces were generated by blocking competition with the mitochondrial valine pathway and by omitting valine from the fermentation medium. Additional deletion of pyruvate decarboxylase genes and engineering of co

  18. Endosomally stored MHC class II does not contribute to antigen presentation by dendritic cells at inflammatory conditions.

    PubMed

    ten Broeke, Toine; van Niel, Guillaume; Wauben, Marca H M; Wubbolts, Richard; Stoorvogel, Willem

    2011-08-01

    Major histocompatibility complex (MHC) class II (MHCII) is constitutively expressed by immature dendritic cells (DC), but has a short half-life as a consequence of its transport to and degradation in lysosomes. For its transfer to lysosomes, MHCII is actively sorted to the intraluminal vesicles (ILV) of multivesicular bodies (MVB), a process driven by its ubiquitination. ILV have, besides their role as an intermediate compartment in lysosomal transfer, also been proposed to function as a site for MHCII antigen loading and temporal storage. In that scenario, DC would recruit antigen-loaded MHCII to the cell surface in response to a maturation stimulus by allowing ILV to fuse back with the MVB delimiting membrane. Other studies, however, explained the increase in cell surface expression during DC maturation by transient upregulation of MHCII synthesis and reduced sorting of newly synthesized MHCII to lysosomes. Here, we have characterized the relative contributions from the biosynthetic and endocytic pathways and found that the vast majority of antigen-loaded MHCII that is stably expressed at the plasma membrane by mature DC is synthesized after exposure to inflammatory stimuli. Pre-existing endosomal MHCII contributed only when it was not yet sorted to ILV at the moment of DC activation. Together with previous records, our current data are consistent with a model in which passage of MHCII through ILV is not required for antigen loading in maturing DC and in which sorting to ILV in immature DC provides a one-way ticket for lysosomal degradation. © 2011 John Wiley & Sons A/S.

  19. Maternal morbidity associated with violence and maltreatment from husbands and in-laws: findings from Indian slum communities.

    PubMed

    Silverman, Jay G; Balaiah, Donta; Ritter, Julie; Dasgupta, Anindita; Boyce, Sabrina C; Decker, Michele R; Naik, D D; Nair, Saritha; Saggurti, Niranjan; Raj, Anita

    2016-09-08

    Intimate partner violence (IPV) victimization is linked to a broad range of negative maternal health outcomes. However, it is unclear whether IPV is directly related to poor maternal outcomes or whether IPV is a marker for other forms of chronic, mundane maltreatment of women that stem from the culture of gender inequity that also gives rise to IPV. To determine the prevalence of non-violent forms of gender-based household maltreatment by husbands and in-laws (GBHM), and violence from in-laws (ILV) and husbands (IPV) against women during the peripregnancy period (during and in the year prior to pregnancy); to assess relative associations of GBHM, ILV and IPV with maternal health. Cross-sectional data were collected from women <6 months postpartum (n = 1,039, ages 15-35 years) seeking child immunization in Mumbai, India. Associations of IPV, ILV and GBHM during the peripregnancy period with maternal health (prenatal care in first trimester, no weight gain, pain during intercourse, high blood pressure, vaginal bleeding, premature rupture of membranes, premature birth) were evaluated. One in three women (34.0 %) reported IPV, 4.8 % reported ILV, and 48.5 % reported GBHM during the peripregnancy period. After adjusting for other forms of abuse, IPV related to pain during intercourse (AOR = 1.79); ILV related to not receiving first trimester antenatal care (AOR = 0.49), and GBHM remained associated with premature rupture of membranes (AOR = 2.28), pain during intercourse (AOR = 1.60), and vaginal bleeding (AOR = 1.80). After adjusting for ILV and IPV, peripregnancy GBHM remained significantly associated with multiple forms of maternal morbidity, suggesting that GBHM is a prevalent and reliable indicator of maternal health risk.

  20. Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria

    SciTech Connect

    Kazakov, Alexey E.; Rodionov, Dmitry A.; Arkin, Adam Paul; Dubchak, Inna; Gelfand, Mikhail S.; Alm, Eric

    2008-10-31

    Bacteria can use branched-chain amino acids (ILV, i.e. isoleucine, leucine, valine) and fatty acids (FA) as sole carbon and energy sources convering ILV into acetyl-CoA, propanoyl-CoA and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR and GntR families binding to eleven distinct DNA motifs. The ILV degradation genes in gamma- and beta-proteobacteria are mainly regulated by anovel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species), in addition, the TetR-type regulator LiuQ was identified in some beta-proteobacteria (8 species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in the Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gamma-proteobacteria (34 species), PsrA in gamma- and beta-proteobacteria (45 species), FadP in beta-proteobacteria (14 species), and LiuR orthologs in alpha-proteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from the functional and evolutionary points of view.

  1. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

    PubMed

    Kazakov, Alexey E; Rodionov, Dmitry A; Alm, Eric; Arkin, Adam Paul; Dubchak, Inna; Gelfand, Mikhail S

    2009-01-01

    Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA), propanoyl-CoA, and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR, and GntR families binding to 11 distinct DNA motifs. The ILV degradation genes in gamma- and betaproteobacteria are regulated mainly by a novel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species); in addition, the TetR-type regulator LiuQ was identified in some betaproteobacteria (eight species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gammaproteobacteria (34 species), PsrA in gamma- and betaproteobacteria (45 species), FadP in betaproteobacteria (14 species), and LiuR orthologs in alphaproteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from functional and evolutionary points of view.

  2. Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria▿ †

    PubMed Central

    Kazakov, Alexey E.; Rodionov, Dmitry A.; Alm, Eric; Arkin, Adam Paul; Dubchak, Inna; Gelfand, Mikhail S.

    2009-01-01

    Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA), propanoyl-CoA, and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR, and GntR families binding to 11 distinct DNA motifs. The ILV degradation genes in gamma- and betaproteobacteria are regulated mainly by a novel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species); in addition, the TetR-type regulator LiuQ was identified in some betaproteobacteria (eight species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gammaproteobacteria (34 species), PsrA in gamma- and betaproteobacteria (45 species), FadP in betaproteobacteria (14 species), and LiuR orthologs in alphaproteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from functional and evolutionary points of view. PMID:18820024

  3. Impact location of objects hitting the water surface

    NASA Astrophysics Data System (ADS)

    Kadri, Usama

    2017-04-01

    Analysis of data, recorded on March 8th 2014 at the Comprehensive Test ban Treaty Organisation's hydroacoustic station off Cape Leeuwin Western Australia, reveal pressure signatures of objects impacting at the sea surface which could be associated with falling meteorites as well as the missing Malaysian MH370 airplane. The location of the sources are identified analytically by an inverse solution based on acoustic-gravity wave theory (e.g. see references below) which have been developed and validated experimentally. Apart from the direct contribution to the search efforts after the missing airplane, the method we describe here is very efficient for identifying the location of sources that result in a sudden change in the water pressure in general. References 1. T.Yamamoto,1982.Gravity waves and acoustic waves generated by submarine earthquakes, Soil Dyn. Earthquake Eng., 1, 75-82. 2. M. Stiassnie, 2010. Tsunamis and acoustic-gravity waves from underwater earthquakes, J. Eng. Math., 67, 23-32, doi:10.1007/s10665-009-9323-x. 3. U. Kadri and M. Staissnie, 2012. Acoustic-gravity waves interacting with the shelf break. J. Geophys. Res., 117, C03035, doi: 10.1029/2011JC007674. 4. E. Eyov, A. Klar, U. Kadri and M. Stiassnie, 2013. Progressive waves in a compressible ocean with elastic bottom, Wave Motion 50, 929-939. doi: 10.1016/j.wavemoti.2013.03.003 5. G. Hendin and M. Stiassnie, 2013. Tsunami and acoustic-gravity waves in water of constant depth, Phys. Fluids 25, 086103, doi: 10.1063/1.481799. 6. U. Kadri, 2016. Acoustic-gravity waves from an oscillating ice-block in arctic zones. Advances in Acoustics and Vibration, 8076108, http://dx.doi.org/10.1155/2016/8076108 7. T.C.A. Oliveira, U. Kadri, 2016. Acoustic-gravity waves from the 2004 Indian Ocean earthquake and tsunami. Journal of Geophysical Research: Oceans. doi: 10.1002/2016JC011742

  4. The tetraspanin CD63 regulates ESCRT-independent and dependent endosomal sorting during melanogenesis

    PubMed Central

    van Niel, Guillaume; Charrin, Stéphanie; Simoes, Sabrina; Romao, Maryse; Rochin, Leila; Saftig, Paul; Marks, Michael S.; Rubinstein, Eric; Raposo, Graça

    2011-01-01

    Summary Cargo sorting to intraluminal vesicles (ILVs) of multivesicular endosomes is required for numerous physiological processes including lysosome-related organelle (LRO) biogenesis. PMEL – a component of melanocyte LROs (melanosomes) – is sorted to ILVs in an ESCRT-independent manner, where it is proteolytically processed and assembled into functional amyloid fibrils during melanosome maturation. Here we show that the tetraspanin CD63 directly participates in ESCRT-independent sorting of the PMEL luminal domain, but not of traditional ESCRT-dependent cargoes, to ILVs. Inactivating CD63 in cell culture or in mice impairs amyloidogenesis and downstream melanosome morphogenesis. Whereas CD63 is required for normal PMEL luminal domain sorting, the disposal of the remaining PMEL transmembrane fragment requires functional ESCRTs but not CD63. In the absence of CD63, the PMEL luminal domain follows this fragment and is targeted for ESCRT-dependent degradation. Our data thus reveal a tight interplay regulated by CD63 between two distinct endosomal ILV sorting processes for a single cargo during LRO biogenesis. PMID:21962903

  5. A Review of Education and Training for Officers (RETO). Volume 5. Special Groups

    DTIC Science & Technology

    1978-06-30

    274MOC 121 L~o Bav Vic’Co’,wi Co’~._’.V ofIs’~vn2 P1JWOS: TOPD Veaw Off.v 00 IN. Pew," con’oo~ws122 Leg. Bam m4 "~ -~ . Onl oW duty ilv* &’Iq b.f’tr- s of

  6. Topographic Stress in the Oceans

    DTIC Science & Technology

    1990-03-20

    tilt witnd stress, Itldeed, ilves ’s, takmla- 0 A AQ 1 1) - rb tions described by D. Olbcrs of the Alfred 6 similar to the zonal momentum budget...issue Wegener Institut. Bremerhaven. Federal Re- ’ r’ , in ACC channel geometry.:.L~:-b- "T qg)"-7 in channel.geometry public of Germany, suggest that

  7. A dual-input nonlinear system analysis of autonomic modulation of heart rate

    NASA Technical Reports Server (NTRS)

    Chon, K. H.; Mullen, T. J.; Cohen, R. J.

    1996-01-01

    Linear analyses of fluctuations in heart rate and other hemodynamic variables have been used to elucidate cardiovascular regulatory mechanisms. The role of nonlinear contributions to fluctuations in hemodynamic variables has not been fully explored. This paper presents a nonlinear system analysis of the effect of fluctuations in instantaneous lung volume (ILV) and arterial blood pressure (ABP) on heart rate (HR) fluctuations. To successfully employ a nonlinear analysis based on the Laguerre expansion technique (LET), we introduce an efficient procedure for broadening the spectral content of the ILV and ABP inputs to the model by adding white noise. Results from computer simulations demonstrate the effectiveness of broadening the spectral band of input signals to obtain consistent and stable kernel estimates with the use of the LET. Without broadening the band of the ILV and ABP inputs, the LET did not provide stable kernel estimates. Moreover, we extend the LET to the case of multiple inputs in order to accommodate the analysis of the combined effect of ILV and ABP effect on heart rate. Analyzes of data based on the second-order Volterra-Wiener model reveal an important contribution of the second-order kernels to the description of the effect of lung volume and arterial blood pressure on heart rate. Furthermore, physiological effects of the autonomic blocking agents propranolol and atropine on changes in the first- and second-order kernels are also discussed.

  8. Functional analysis of all aminotransferase proteins inferred from the genome sequence of Corynebacterium glutamicum.

    PubMed

    Marienhagen, Jan; Kennerknecht, Nicole; Sahm, Hermann; Eggeling, Lothar

    2005-11-01

    Twenty putative aminotransferase (AT) proteins of Corynebacterium glutamicum, or rather pyridoxal-5'-phosphate (PLP)-dependent enzymes, were isolated and assayed among others with L-glutamate, L-aspartate, and L-alanine as amino donors and a number of 2-oxo-acids as amino acceptors. One outstanding AT identified is AlaT, which has a broad amino donor specificity utilizing (in the order of preference) L-glutamate > 2-aminobutyrate > L-aspartate with pyruvate as acceptor. Another AT is AvtA, which utilizes L-alanine to aminate 2-oxo-isovalerate, the L-valine precursor, and 2-oxo-butyrate. A second AT active with the L-valine precursor and that of the other two branched-chain amino acids, too, is IlvE, and both enzyme activities overlap partially in vivo, as demonstrated by the analysis of deletion mutants. Also identified was AroT, the aromatic AT, and this and IlvE were shown to have comparable activities with phenylpyruvate, thus demonstrating the relevance of both ATs for L-phenylalanine synthesis. We also assessed the activity of two PLP-containing cysteine desulfurases, supplying a persulfide intermediate. One of them is SufS, which assists in the sulfur transfer pathway for the Fe-S cluster assembly. Together with the identification of further ATs and the additional analysis of deletion mutants, this results in an overview of the ATs within an organism that may not have been achieved thus far.

  9. Incomplete inside-out growth pattern in invasive breast carcinoma: association with lymph vessel invasion and recurrence-free survival.

    PubMed

    Kuba, Sayaka; Ohtani, Hiroshi; Yamaguchi, Junzo; Hayashi, Hiroko; Uga, Tatsuya; Kanematsu, Takashi; Shimokawa, Isao

    2011-02-01

    Invasive micropapillary carcinoma (IMPC) is a rare subtype of epithelial tumor of the breast listed in the 2003 World Health Organization histologic classification of tumors of the breast. It is characterized by inside-out micropapillary morphology, frequent lymph vessel invasion (LVI), and lymph node metastasis; however, its etiology remains unknown. This study investigated the incomplete inside-out growth pattern (IGP) in invasive ductal carcinoma, not otherwise specified (NOS), and examined the association between incomplete IGP and clinicopathologic features, including the presence of intratumoral lymph vessels (ILV), LVI, nodal metastasis, and prognosis. Tumor tissues from 166 invasive duct carcinomas NOS and 10 IMPCs were immunostained using an anti-epithelial membrane antigen antibody to detect IGP and with D2-40 antibody to determine the presence of ILV and LVI. Incomplete IGP was detected focally in 88 (53%) of 166 invasive duct carcinomas NOS. Transition areas between IMPC and invasive duct carcinoma NOS also showed prominent incomplete IGP in 9 (90%) of 10 IMPCs. Incomplete IGP in invasive duct carcinomas NOS was associated with larger tumor size, higher frequencies of ILV, LVI, nodal metastasis, and poorer recurrence-free survival by univariate analysis. Incomplete IGP, ILV, and tumor size independently affected LVI by multivariate analysis. These findings indicate that incomplete IGP of tumor cell clusters is not uncommon and is a useful tool for predicting LVI in invasive duct carcinoma NOS of the breast.

  10. A dual-input nonlinear system analysis of autonomic modulation of heart rate

    NASA Technical Reports Server (NTRS)

    Chon, K. H.; Mullen, T. J.; Cohen, R. J.

    1996-01-01

    Linear analyses of fluctuations in heart rate and other hemodynamic variables have been used to elucidate cardiovascular regulatory mechanisms. The role of nonlinear contributions to fluctuations in hemodynamic variables has not been fully explored. This paper presents a nonlinear system analysis of the effect of fluctuations in instantaneous lung volume (ILV) and arterial blood pressure (ABP) on heart rate (HR) fluctuations. To successfully employ a nonlinear analysis based on the Laguerre expansion technique (LET), we introduce an efficient procedure for broadening the spectral content of the ILV and ABP inputs to the model by adding white noise. Results from computer simulations demonstrate the effectiveness of broadening the spectral band of input signals to obtain consistent and stable kernel estimates with the use of the LET. Without broadening the band of the ILV and ABP inputs, the LET did not provide stable kernel estimates. Moreover, we extend the LET to the case of multiple inputs in order to accommodate the analysis of the combined effect of ILV and ABP effect on heart rate. Analyzes of data based on the second-order Volterra-Wiener model reveal an important contribution of the second-order kernels to the description of the effect of lung volume and arterial blood pressure on heart rate. Furthermore, physiological effects of the autonomic blocking agents propranolol and atropine on changes in the first- and second-order kernels are also discussed.

  11. Human heart rate variability relation is unchanged during motion sickness

    NASA Technical Reports Server (NTRS)

    Mullen, T. J.; Berger, R. D.; Oman, C. M.; Cohen, R. J.

    1998-01-01

    In a study of 18 human subjects, we applied a new technique, estimation of the transfer function between instantaneous lung volume (ILV) and instantaneous heart rate (HR), to assess autonomic activity during motion sickness. Two control recordings of ILV and electrocardiogram (ECG) were made prior to the development of motion sickness. During the first, subjects were seated motionless, and during the second they were seated rotating sinusoidally about an earth vertical axis. Subjects then wore prism goggles that reverse the left-right visual field and performed manual tasks until they developed moderate motion sickness. Finally, ILV and ECG were recorded while subjects maintained a relatively constant level of sickness by intermittent eye closure during rotation with the goggles. Based on analyses of ILV to HR transfer functions from the three conditions, we were unable to demonstrate a change in autonomic control of heart rate due to rotation alone or due to motion sickness. These findings do not support the notion that moderate motion sickness is manifested as a generalized autonomic response.

  12. Human heart rate variability relation is unchanged during motion sickness

    NASA Technical Reports Server (NTRS)

    Mullen, T. J.; Berger, R. D.; Oman, C. M.; Cohen, R. J.

    1998-01-01

    In a study of 18 human subjects, we applied a new technique, estimation of the transfer function between instantaneous lung volume (ILV) and instantaneous heart rate (HR), to assess autonomic activity during motion sickness. Two control recordings of ILV and electrocardiogram (ECG) were made prior to the development of motion sickness. During the first, subjects were seated motionless, and during the second they were seated rotating sinusoidally about an earth vertical axis. Subjects then wore prism goggles that reverse the left-right visual field and performed manual tasks until they developed moderate motion sickness. Finally, ILV and ECG were recorded while subjects maintained a relatively constant level of sickness by intermittent eye closure during rotation with the goggles. Based on analyses of ILV to HR transfer functions from the three conditions, we were unable to demonstrate a change in autonomic control of heart rate due to rotation alone or due to motion sickness. These findings do not support the notion that moderate motion sickness is manifested as a generalized autonomic response.

  13. A dual-input nonlinear system analysis of autonomic modulation of heart rate.

    PubMed

    Chon, K H; Mullen, T J; Cohen, R J

    1996-05-01

    Linear analyses of fluctuations in heart rate and other hemodynamic variables have been used to elucidate cardiovascular regulatory mechanisms. The role of nonlinear contributions to fluctuations in hemodynamic variables has not been fully explored. This paper presents a nonlinear system analysis of the effect of fluctuations in instantaneous lung volume (ILV) and arterial blood pressure (ABP) on heart rate (HR) fluctuations. To successfully employ a nonlinear analysis based on the Laguerre expansion technique (LET), we introduce an efficient procedure for broadening the spectral content of the ILV and ABP inputs to the model by adding white noise. Results from computer simulations demonstrate the effectiveness of broadening the spectral band of input signals to obtain consistent and stable kernel estimates with the use of the LET. Without broadening the band of the ILV and ABP inputs, the LET did not provide stable kernel estimates. Moreover, we extend the LET to the case of multiple inputs in order to accommodate the analysis of the combined effect of ILV and ABP effect on heart rate. Analyzes of data based on the second-order Volterra-Wiener model reveal an important contribution of the second-order kernels to the description of the effect of lung volume and arterial blood pressure on heart rate. Furthermore, physiological effects of the autonomic blocking agents propranolol and atropine on changes in the first- and second-order kernels are also discussed.

  14. Identification and evaluation of novel acetolactate synthase inhibitors as antifungal agents.

    PubMed

    Richie, Daryl L; Thompson, Katherine V; Studer, Christian; Prindle, Vivian C; Aust, Thomas; Riedl, Ralph; Estoppey, David; Tao, Jianshi; Sexton, Jessica A; Zabawa, Thomas; Drumm, Joseph; Cotesta, Simona; Eichenberger, Jürg; Schuierer, Sven; Hartmann, Nicole; Movva, N Rao; Tallarico, John A; Ryder, Neil S; Hoepfner, Dominic

    2013-05-01

    High-throughput phenotypic screening against the yeast Saccharomyces cerevisiae revealed a series of triazolopyrimidine-sulfonamide compounds with broad-spectrum antifungal activity, no significant cytotoxicity, and low protein binding. To elucidate the target of this series, we have applied a chemogenomic profiling approach using the S. cerevisiae deletion collection. All compounds of the series yielded highly similar profiles that suggested acetolactate synthase (Ilv2p, which catalyzes the first common step in branched-chain amino acid biosynthesis) as a possible target. The high correlation with profiles of known Ilv2p inhibitors like chlorimuron-ethyl provided further evidence for a similar mechanism of action. Genome-wide mutagenesis in S. cerevisiae identified 13 resistant clones with 3 different mutations in the catalytic subunit of acetolactate synthase that also conferred cross-resistance to established Ilv2p inhibitors. Mapping of the mutations into the published Ilv2p crystal structure outlined the chlorimuron-ethyl binding cavity, and it was possible to dock the triazolopyrimidine-sulfonamide compound into this pocket in silico. However, fungal growth inhibition could be bypassed through supplementation with exogenous branched-chain amino acids or by the addition of serum to the medium in all of the fungal organisms tested except for Aspergillus fumigatus. Thus, these data support the identification of the triazolopyrimidine-sulfonamide compounds as inhibitors of acetolactate synthase but suggest that targeting may be compromised due to the possibility of nutrient bypass in vivo.

  15. Disposal Analysis of I-129 Bearing Waste Streams at the Intermediate Level Vault

    SciTech Connect

    Collard, L.B.

    2001-01-25

    This report examines the effects of new waste-specific sorption characteristics reported for I-129 bearing wastes on inventory limits in the Intermediate Level Vault (ILV). Inventory limits are described based on the revised performance assessment model using the waste-specific Kd's. Results are compared with inventory projections of waste streams for the next ten years.

  16. Platform Engineering of Corynebacterium glutamicum with Reduced Pyruvate Dehydrogenase Complex Activity for Improved Production of l-Lysine, l-Valine, and 2-Ketoisovalerate

    PubMed Central

    Buchholz, Jens; Schwentner, Andreas; Brunnenkan, Britta; Gabris, Christina; Grimm, Simon; Gerstmeir, Robert; Takors, Ralf; Eikmanns, Bernhard J.

    2013-01-01

    Exchange of the native Corynebacterium glutamicum promoter of the aceE gene, encoding the E1p subunit of the pyruvate dehydrogenase complex (PDHC), with mutated dapA promoter variants led to a series of C. glutamicum strains with gradually reduced growth rates and PDHC activities. Upon overexpression of the l-valine biosynthetic genes ilvBNCE, all strains produced l-valine. Among these strains, C. glutamicum aceE A16 (pJC4 ilvBNCE) showed the highest biomass and product yields, and thus it was further improved by additional deletion of the pqo and ppc genes, encoding pyruvate:quinone oxidoreductase and phosphoenolpyruvate carboxylase, respectively. In fed-batch fermentations at high cell densities, C. glutamicum aceE A16 Δpqo Δppc (pJC4 ilvBNCE) produced up to 738 mM (i.e., 86.5 g/liter) l-valine with an overall yield (YP/S) of 0.36 mol per mol of glucose and a volumetric productivity (QP) of 13.6 mM per h [1.6 g/(liter × h)]. Additional inactivation of the transaminase B gene (ilvE) and overexpression of ilvBNCD instead of ilvBNCE transformed the l-valine-producing strain into a 2-ketoisovalerate producer, excreting up to 303 mM (35 g/liter) 2-ketoisovalerate with a YP/S of 0.24 mol per mol of glucose and a QP of 6.9 mM per h [0.8 g/(liter × h)]. The replacement of the aceE promoter by the dapA-A16 promoter in the two C. glutamicum l-lysine producers DM1800 and DM1933 improved the production by 100% and 44%, respectively. These results demonstrate that C. glutamicum strains with reduced PDHC activity are an excellent platform for the production of pyruvate-derived products. PMID:23835179

  17. Improvement of the Redox Balance Increases l-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions

    PubMed Central

    Hasegawa, Satoshi; Uematsu, Kimio; Natsuma, Yumi; Suda, Masako; Hiraga, Kazumi; Jojima, Toru; Inui, Masayuki

    2012-01-01

    Production of l-valine under oxygen deprivation conditions by Corynebacterium glutamicum lacking the lactate dehydrogenase gene ldhA and overexpressing the l-valine biosynthesis genes ilvBNCDE was repressed. This was attributed to imbalanced cofactor production and consumption in the overall l-valine synthesis pathway: two moles of NADH was generated and two moles of NADPH was consumed per mole of l-valine produced from one mole of glucose. In order to solve this cofactor imbalance, the coenzyme requirement for l-valine synthesis was converted from NADPH to NADH via modification of acetohydroxy acid isomeroreductase encoded by ilvC and introduction of Lysinibacillus sphaericus leucine dehydrogenase in place of endogenous transaminase B, encoded by ilvE. The intracellular NADH/NAD+ ratio significantly decreased, and glucose consumption and l-valine production drastically improved. Moreover, l-valine yield increased and succinate formation decreased concomitantly with the decreased intracellular redox state. These observations suggest that the intracellular NADH/NAD+ ratio, i.e., reoxidation of NADH, is the primary rate-limiting factor for l-valine production under oxygen deprivation conditions. The l-valine productivity and yield were even better and by-products derived from pyruvate further decreased as a result of a feedback resistance-inducing mutation in the acetohydroxy acid synthase encoded by ilvBN. The resultant strain produced 1,470 mM l-valine after 24 h with a yield of 0.63 mol mol of glucose−1, and the l-valine productivity reached 1,940 mM after 48 h. PMID:22138982

  18. Acetohydroxyacid Synthase, a Novel Target for Improvement of l-Lysine Production by Corynebacterium glutamicum▿ †

    PubMed Central

    Blombach, Bastian; Hans, Stephan; Bathe, Brigitte; Eikmanns, Bernhard J.

    2009-01-01

    The influence of acetohydroxy acid synthase (AHAS) on l-lysine production by Corynebacterium glutamicum was investigated. An AHAS with a deleted C-terminal domain in the regulatory subunit IlvN was engineered by truncating the ilvN gene. Compared to the wild-type AHAS, the newly constructed enzyme showed altered kinetic properties, i.e., (i) an about twofold-lower Km for the substrate pyruvate and an about fourfold-lower Vmax; (ii) a slightly increased Km for the substrate α-ketobutyrate with an about twofold-lower Vmax; and (iii) insensitivity against the inhibitors l-valine, l-isoleucine, and l-leucine (10 mM each). Introduction of the modified AHAS into the l-lysine producers C. glutamicum DM1729 and DM1933 increased l-lysine formation by 43% (30 mM versus 21 mM) and 36% (51 mM versus 37 mM), respectively, suggesting that decreased AHAS activity is linked to increased l-lysine formation. Complete inactivation of the AHAS in C. glutamicum DM1729 and DM1933 by deletion of the ilvB gene, encoding the catalytic subunit of AHAS, led to l-valine, l-isoleucine, and l-leucine auxotrophy and to further-improved l-lysine production. In batch fermentations, C. glutamicum DM1729 ΔilvB produced about 85% more l-lysine (70 mM versus 38 mM) and showed an 85%-higher substrate-specific product yield (0.180 versus 0.098 mol C/mol C) than C. glutamicum DM1729. Comparative transcriptome analysis of C. glutamicum DM1729 and C. glutamicum DM1729 ΔilvB indicated transcriptional differences for about 50 genes, although not for those encoding enzymes involved in the l-lysine biosynthetic pathway. PMID:19047397

  19. Branched-Chain Amino Acids Are Required for the Survival and Virulence of Actinobacillus pleuropneumoniae in Swine▿

    PubMed Central

    Subashchandrabose, Sargurunathan; LeVeque, Rhiannon M.; Wagner, Trevor K.; Kirkwood, Roy N.; Kiupel, Matti; Mulks, Martha H.

    2009-01-01

    In Actinobacillus pleuropneumoniae, which causes porcine pleuropneumonia, ilvI was identified as an in vivo-induced (ivi) gene and encodes the enzyme acetohydroxyacid synthase (AHAS) required for branched-chain amino acid (BCAA) biosynthesis. ilvI and 7 of 32 additional ivi promoters were upregulated in vitro when grown in chemically defined medium (CDM) lacking BCAA. Based on these observations, we hypothesized that BCAA would be found at limiting concentrations in pulmonary secretions and that A. pleuropneumoniae mutants unable to synthesize BCAA would be attenuated in a porcine infection model. Quantitation of free amino acids in porcine pulmonary epithelial lining fluid showed concentrations of BCAA ranging from 8 to 30 μmol/liter, which is 10 to 17% of the concentration in plasma. The expression of both ilvI and lrp, a global regulator that is required for ilvI expression, was strongly upregulated in CDM containing concentrations of BCAA similar to those found in pulmonary secretions. Deletion-disruption mutants of ilvI and lrp were both auxotrophic for BCAA in CDM and attenuated compared to wild-type A. pleuropneumoniae in competitive index experiments in a pig infection model. Wild-type A. pleuropneumoniae grew in CDM+BCAA but not in CDM−BCAA in the presence of sulfonylurea AHAS inhibitors. These results clearly demonstrate that BCAA availability is limited in the lungs and support the hypothesis that A. pleuropneumoniae, and potentially other pulmonary pathogens, uses limitation of BCAA as a cue to regulate the expression of genes required for survival and virulence. These results further suggest a potential role for AHAS inhibitors as antimicrobial agents against pulmonary pathogens. PMID:19703979

  20. Interaction of acoustic-gravity waves with an elastic shelf-break

    NASA Astrophysics Data System (ADS)

    Tian, Miao; Kadri, Usama

    2016-04-01

    In contrast to surface gravity waves that induce flow field which decays exponentially with depth, acoustic-gravity waves oscillate throughout the water column. Their oscillatory profile exerts stresses to the ground which provides a natural explanation for the earth's microseism (Longuet-Higgins, 1950). This work is an extension of the shelf-break problem by Kadri and Stiassnie (2012) who considered the sea floor and the shelf-break to be rigid, and the elastic problem by Eyov et al. (2013) who illustrated the importance of the sea-floor elasticity. In this study we formulate and solve the two-dimensional problem of an incident acoustic-gravity wave mode propagating over an elastic wall and interacting with a shelf-break in a weakly compressible fluid. As the modes approach the shelf-break, part of the energy is reflected whereas the other part is transmitted. A mathematical model is formulated by matching particular solutions for each subregion of constant depth along vertical boundaries; the resulting matrix equation is then solved numerically. The physical properties of these waves are studied, and compared with those for waves over a rigid bottom. The present work broadens our knowledge of acoustic-gravity-waves propagation in realistic environment and can potentially benefit the early detection of tsunami, generated from landslides or submarine earthquakes. References Eyov E., Klar A., Kadri U. , Stiassnie M. 2013 Progressive waves in a compressible-ocean with an elastic bottom. Wave Motion 50, 929-939. Kadri, U., and M. Stiassnie, 2012 Acoustic-Gravity waves interacting with the shelf break. J. Geophys. Res. 117, C03035. Longuet-Higgins, M.S. 1950 A theory of the origin of microseisms. Philos. Trans. R. Soc. Lond. A 243, 1-35.

  1. Wavemaker theories for acoustic-gravity waves over a finite depth

    NASA Astrophysics Data System (ADS)

    Tian, Miao; Kadri, Usama

    2016-04-01

    Acoustic-gravity waves (hereafter AGWs) in ocean have received much interest recently, mainly with respect to early detection of tsunamis as they travel at near the speed of sound in water which makes them ideal candidates for early detection of tsunamis. While the generation mechanisms of AGWs have been studied from the perspective of vertical oscillations of seafloor (Yamamoto, 1982; Stiassnie, 2010) and triad wave-wave interaction (Longuet-Higgins 1950; Kadri and Stiassnie 2013; Kadri and Akylas 2016), in the current study we are interested in their generation by wave-structure interaction with possible application to the energy sector. Here, we develop two wavemaker theories to analyze different wave modes generated by impermeable (the classic Havelock's theory) and porous (porous wavemaker theory) plates in weakly compressible fluids. Slight modification has been made to the porous theory so that, unlike the previous theory (Chwang, 1983), the new solution depends on the geometry of the plate. The expressions for three different types of plates (piston, flap, delta-function) are introduced. Analytical solutions are also derived for the potential amplitude of the gravity, evanescent, and acoustic-gravity waves, as well as the surface elevation, velocity distribution, and pressure for AGWs. Both theories reduce to previous results for incompressible flow when the compressibility is negligible. We also show numerical examples for AGW generated in a wave flume as well as in deep ocean. Our current study sets the theoretical background towards remote sensing by AGWs, for optimized deep ocean wave-power harnessing, among others. References Chwang, A.T. 1983 A porous-wavemaker theory. Journal of Fluid Mechanics, 132, 395- 406. Kadri, U., Stiassnie, M. 2013 Generation of an acoustic-gravity wave by two gravity waves, and their subsequent mutual interaction. J. Fluid Mech. 735, R6. Kadri U., Akylas T.R. 2016 On resonant triad interactions of acoustic-gravity waves. J

  2. Excimer Lasers

    DTIC Science & Technology

    1976-06-01

    CONTINUE 46 C HATE CONSTANTS - ELCTRONIC VD=SQRT(2*TE/MASXE)* 3E10 J=NE*E*VD VDISC=V-H*J*A-L*A*E*VD*(NE-NEP)/DT NEP=NE RC=6.38E7*(5QRT(2*TE))**3...TG)/ 3E10 +CSTMDE*P**2*EXP(-VüXE/ +TG)*.25/3EI0 BETAD=CSTMD*P**2*EXP(-VDX/TG)*.25/ 3E10 GAJNE=CSTME*(PX1*EXP(-VEA/TG)/(KAEX*1.5)-2*P*XE*EXP(-VEX/TG...3EI0 +-CSTMDE*(P**2*EXP(-VDXE/TG)*.25)/ 3E10 GAIND=CSTMD*(PD1*EXP(-VDA/TG)/(KADI*12)-P**2*EXP(-VDX/TG)*.25) +/3EI0 C OUTPUT IF(ISTEP/IPrMNT-FL()AT

  3. Assessment of groundwater quality with respect to fluoride.

    PubMed

    Salve, P R; Maurya, A; Kumbhare, P S; Ramteke, D S; Wate, S R

    2008-09-01

    The study was conducted in the summer season (April-May 2007). The fluoride concentration along with physico-chemical parameters in ground water samples was determined in various villages of Kadi tehsil at Mehsana district of Gujarat state (India), since in most of the villages it is the only source of drinking water. The fluoride concentrations in these villages varied from 0.94 to 2.81 mg/L (1.37+/-0.56) with highest fluoride level at Visalpur (2.08 mg/L) and lowest at Adaraj (0.91 mg/L). There was found a positive correlation of pH with fluoride and a negative relationship of fluoride with bicarbonate which is generally observed in deep ground water.

  4. Recharge Data for Hawaii Island

    DOE Data Explorer

    Nicole Lautze

    2015-01-01

    Recharge data for Hawaii Island in shapefile format. The data are from the following sources: Whittier, R.B and A.I. El-Kadi. 2014. Human Health and Environmental Risk Ranking of On-Site Sewage Disposal systems for the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final, Prepared for Hawaii Dept. of Health, Safe Drinking Water Branch by the University of Hawaii, Dept. of Geology and Geophysics. Oki, D. S. 1999. Geohydrology and Numerical Simulation of the Ground-Water Flow System of Kona, Island of Hawaii. U.S. Water-Resources Investigation Report: 99-4073. Oki, D. S. 2002. Reassessment of Ground-water Recharge and Simulated Ground-Water Availability for the Hawi Area of North Kohala, Hawaii. U.S. Geological Survey Water-Resources Investigation report 02-4006.

  5. RBANS Memory Indices Are Related to Medial Temporal Lobe Volumetrics in Healthy Older Adults and Those with Mild Cognitive Impairment

    PubMed Central

    England, Heather B.; Gillis, M. Meredith; Hampstead, Benjamin M.

    2014-01-01

    The current study (i) determined whether NeuroQuant® volumetrics are reflective of differences in medial temporal lobe (MTL) volumes between healthy older adults and those with mild cognitive impairment (MCI) and (ii) examined the relationship between RBANS indices and MTL volumes. Forty-three healthy older adults and 57 MCI patients completed the RBANS and underwent structural MRI. Hippocampal and inferior lateral ventricle (ILV) volumes were obtained using NeuroQuant®. Results revealed significantly smaller hippocampal and larger ILV volumes in MCI patients. MTL volumes were significantly related to the RBANS Immediate and Delayed Memory and Language indices but not the Attention or Visuoconstruction indices; findings that demonstrate anatomical specificity. Following discriminant function analysis, we calculated a cutpoint that may prove clinically useful for integrating MTL volumes into the diagnosis of MCI. These findings demonstrate the potential clinical utility of NeuroQuant® and are the first to document the relationship between RBANS indices and MTL volumes. PMID:24709384

  6. Assessment of the state of the gibel carp Carassius auratus gibelio in the Amur River Basin: heavy-metal and arsenic concentrations and histopathology of internal organs.

    PubMed

    Syasina, Iraida G; Khlopova, Anna V; Chukhlebova, Lyubov M

    2012-04-01

    This study describes the concentrations of heavy metals and arsenic (As) and the basic histopathological changes in the internal organs of gibel carp Carassius auratus gibelio from five sites of the Amur River basin. Gibel carp from Sindinskaya Passage had the highest liver concentrations of zinc (Zn) (31.95 ± 13.443), copper (Cu) (12.52 ± 5.746), manganese (9.22 ± 8.121), and cadmium (0.37 ± 0.660 mg/kg wet weight [ww]) compared with fish captured from the Bol'shoi Ussuriiskii Island area and Kadi Lake; however, concentrations of nickel (0.22 ± 0.156 mg/kg ww) were not significantly different, and concentrations of lead (0.19 ± 0.121 mg/kg ww) were higher than those in fish from Kadi Lake. Mean concentrations of metals and As in muscles were lower than Russia's recommended limits for food products; however, concentrations of Cu, Zn, and Hg in individual fish were greater than the limit. Kidney disease was detected in 100% of sampled carp. Kidney disease was characterized by the formation of numerous granulomas in kidney tissues between the renal tubules. The degree of granulomatosis varied among sites. Granulomatous kidney disease in gibel carp is widespread in many reservoirs of the lower Amur River basin. The following histopathological changes were detected in liver: vacuolization of hepatocytes, hypertrophy of multiple hepatocytes, binuclearity, presence of numerous irregularly shaped nuclei in hepatocytes, karyopyknosis, diffuse necrosis of hepatocytes (in some cases focal), and edema. Necrotic changes in hepatocytes, which are important indices of the toxic effect of pollutants, were found in the majority of investigated carp from the lower Amur River basin. Some fish had simultaneous pathological alterations in multiple organs.

  7. Enhanced production of branched-chain amino acids by Gluconacetobacter europaeus with a specific regional deletion in a leucine responsive regulator.

    PubMed

    Akasaka, Naoki; Ishii, Yuri; Hidese, Ryota; Sakoda, Hisao; Fujiwara, Shinsuke

    2014-12-01

    Vinegar with increased amounts of branched-chain amino acids (BCAAs; valine, leucine and isoleucine) is favorable for human health as BCAAs decrease diet-induced obesity and hyperglycemia. To construct Gluconacetobacter europaeus which produces BCAAs, leucine responsive regulator (GeLrp) is focused and two Gelrp mutants were constructed. Wild-type KGMA0119 didn't produce significant amount of valine (0.13 mM) and leucine (0 mM) and strain KGMA7110 which lacks complete Gelrp accumulated valine (0.48 mM) and leucine (0.11 mM) but showed impaired growth, and it was fully restored in the presence of essential amino acids. Strain KGMA7203 was then constructed with a nonsense mutation at codon Trp132 in the Gelrp, which leads a specific deletion at an estimated ligand-sensing region in the C-terminal domain. KGMA7203 produced greater quantities of valine (0.80 mM) and leucine (0.26 mM) and showed the same growth characteristics as KGMA0119. mRNA levels of BCAAs biosynthesis genes (ilvI and ilvC) and probable BCAAs efflux pump (leuE) were determined by quantitative reverse-transcription PCR. Expression rates of ilvI and ilvC in the two Gelrp disruptants were greater than those in KGMA0119. leuE was highly expressed in KGMA7110 only, suggesting that the accumulation in KGMA7110 culture was caused by increased expression of the biosynthesis genes and abnormal enhanced export of amino acids resulting in impaired cell growth. In contrast, KGMA7203 would achieve the high level production through enhanced expression of the biosynthesis genes without enhancing that for the efflux pump. KGMA7203 was considered advantageous for production of vinegar with higher amounts of valine and leucine.

  8. Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2.

    PubMed

    Xiao, Yao; Warner, Lisa R; Latham, Michael P; Ahn, Natalie G; Pardi, Arthur

    2015-07-21

    Resonance assignments are the first step in most NMR studies of protein structure, function, and dynamics. Standard protein assignment methods employ through-bond backbone experiments on uniformly (13)C/(15)N-labeled proteins. For larger proteins, this through-bond assignment procedure often breaks down due to rapid relaxation and spectral overlap. The challenges involved in studies of larger proteins led to efficient methods for (13)C labeling of side chain methyl groups, which have favorable relaxation properties and high signal-to-noise. These methyls are often still assigned by linking them to the previously assigned backbone, thus limiting the applications for larger proteins. Here, a structure-based procedure is described for assignment of (13)C(1)H3-labeled methyls by comparing distance information obtained from three-dimensional methyl-methyl nuclear Overhauser effect (NOE) spectroscopy with the X-ray structure. The Ile, Leu, or Val (ILV) methyl type is determined by through-bond experiments, and the methyl-methyl NOE data are analyzed in combination with the known structure. A hierarchical approach was employed that maps the largest observed "NOE-methyl cluster" onto the structure. The combination of identification of ILV methyl type with mapping of the NOE-methyl clusters greatly simplifies the assignment process. This method was applied to the inactive and active forms of the 42-kDa ILV (13)C(1)H3-methyl labeled extracellular signal-regulated kinase 2 (ERK2), leading to assignment of 60% of the methyls, including 90% of Ile residues. A series of ILV to Ala mutants were analyzed, which helped confirm the assignments. These assignments were used to probe the local and long-range effects of ligand binding to inactive and active ERK2.

  9. Eliminating the isoleucine biosynthetic pathway to reduce competitive carbon outflow during isobutanol production by Saccharomyces cerevisiae.

    PubMed

    Ida, Kengo; Ishii, Jun; Matsuda, Fumio; Kondo, Takashi; Kondo, Akihiko

    2015-04-29

    Isobutanol is an important biorefinery target alcohol that can be used as a fuel, fuel additive, or commodity chemical. Baker's yeast, Saccharomyces cerevisiae, is a promising organism for the industrial manufacture of isobutanol because of its tolerance for low pH and resistance to autolysis. It has been reported that gene deletion of the pyruvate dehydrogenase complex, which is directly involved in pyruvate metabolism, improved isobutanol production by S. cerevisiae. However, the engineering strategies available for S. cerevisiae are immature compared to those available for bacterial hosts such as Escherichia coli, and several pathways in addition to pyruvate metabolism compete with isobutanol production. The isobutyrate, pantothenate or isoleucine biosynthetic pathways were deleted to reduce the outflow of carbon competing with isobutanol biosynthesis in S. cerevisiae. The judicious elimination of these competing pathways increased isobutanol production. ILV1 encodes threonine ammonia-lyase, the enzyme that converts threonine to 2-ketobutanoate, a precursor for isoleucine biosynthesis. S. cerevisiae mutants in which ILV1 had been deleted displayed 3.5-fold increased isobutanol productivity. The ΔILV1 strategy was further combined with two previously established engineering strategies (activation of two steps of the Ehrlich pathway and the transhydrogenase-like shunt), providing 11-fold higher isobutanol productivity as compared to the parent strain. The titer and yield of this engineered strain was 224 ± 5 mg/L and 12.04 ± 0.23 mg/g glucose, respectively. The deletion of competitive pathways to reduce the outflow of carbon, including ILV1 deletion, is an important strategy for increasing isobutanol production by S. cerevisiae.

  10. Symposium of Naval Hydrodynamics (14th) held at Ann Arbor, Michigan on August 23-27, 1982,

    DTIC Science & Technology

    1982-01-01

    Chahine -Viscous Effects on the Stability of Cavitating Line Vortices -. 195 Jaakko V. Pylkknen Nuclei and Cavitation 215 Jean -Pierre Le G9fu and Yves...the sectional area of the sheet cavity at • ,this position. . .~ . . * , ILv ’. - ,’ 4 4- ,*-. . ... . 4.4 K"% Nuclei and Cavitation Jean -Pierre Le Goff...the experiments, with analysing .- the results and with running computer programs. Thanks are also due to U H Pinto who developed a substantial part of

  11. Advanced Actuation Systems Development. Volume 2

    DTIC Science & Technology

    1989-08-01

    servovalve was constructed with discrete high-speed solenoid valve , Ito cotroI thie flow to a control actuator, The solenoid valves were a poppet design...was constructed with discrete high-speed solenoid valves to control the flow to a control actuator. The solenoih vaIlves were a poppet design using a...controlled high-speed solenoid valves , (3) the performance evaltiation of an F- 15 rudder actuator tinder applied loads, (4) the performance

  12. Genome-Based Analysis and Gene Dosage Studies Provide New Insight into 3-Hydroxy-4-Methylvalerate Biosynthesis in Ralstonia eutropha

    PubMed Central

    Ushimaru, Kazunori; Mizuno, Shoji

    2015-01-01

    Recombinant Ralstonia eutropha strain PHB−4 expressing the broad-substrate-specificity polyhydroxyalkanoate (PHA) synthase 1 from Pseudomonas sp. strain 61-3 (PhaC1Ps) synthesizes a PHA copolymer containing the branched side-chain unit 3-hydroxy-4-methylvalerate (3H4MV), which has a carbon backbone identical to that of leucine. Mutant strain 1F2 was derived from R. eutropha strain PHB−4 by chemical mutagenesis and shows higher levels of 3H4MV production than does the parent strain. In this study, to understand the mechanisms underlying the enhanced production of 3H4MV, whole-genome sequencing of strain 1F2 was performed, and the draft genome sequence was compared to that of parent strain PHB−4. This analysis uncovered four point mutations in the 1F2 genome. One point mutation was found in the ilvH gene at amino acid position 36 (A36T) of IlvH. ilvH encodes a subunit protein that regulates acetohydroxy acid synthase III (AHAS III). AHAS catalyzes the conversion of pyruvate to 2-acetolactate, which is the first reaction in the biosynthesis of branched amino acids such as leucine and valine. Thus, the A36T IlvH mutation may show AHAS tolerance to feedback inhibition by branched amino acids, thereby increasing carbon flux toward branched amino acid and 3H4MV biosynthesis. Furthermore, a gene dosage study and an isotope tracer study were conducted to investigate the 3H4MV biosynthesis pathway. Based on the observations in these studies, we propose a 3H4MV biosynthesis pathway in R. eutropha that involves a condensation reaction between isobutyryl coenzyme A (isobutyryl-CoA) and acetyl-CoA to form the 3H4MV carbon backbone. PMID:25645560

  13. Functional Analysis of All Aminotransferase Proteins Inferred from the Genome Sequence of Corynebacterium glutamicum

    PubMed Central

    Marienhagen, Jan; Kennerknecht, Nicole; Sahm, Hermann; Eggeling, Lothar

    2005-01-01

    Twenty putative aminotransferase (AT) proteins of Corynebacterium glutamicum, or rather pyridoxal-5′-phosphate (PLP)-dependent enzymes, were isolated and assayed among others with l-glutamate, l-aspartate, and l-alanine as amino donors and a number of 2-oxo-acids as amino acceptors. One outstanding AT identified is AlaT, which has a broad amino donor specificity utilizing (in the order of preference) l-glutamate > 2-aminobutyrate > l-aspartate with pyruvate as acceptor. Another AT is AvtA, which utilizes l-alanine to aminate 2-oxo-isovalerate, the l-valine precursor, and 2-oxo-butyrate. A second AT active with the l-valine precursor and that of the other two branched-chain amino acids, too, is IlvE, and both enzyme activities overlap partially in vivo, as demonstrated by the analysis of deletion mutants. Also identified was AroT, the aromatic AT, and this and IlvE were shown to have comparable activities with phenylpyruvate, thus demonstrating the relevance of both ATs for l-phenylalanine synthesis. We also assessed the activity of two PLP-containing cysteine desulfurases, supplying a persulfide intermediate. One of them is SufS, which assists in the sulfur transfer pathway for the Fe-S cluster assembly. Together with the identification of further ATs and the additional analysis of deletion mutants, this results in an overview of the ATs within an organism that may not have been achieved thus far. PMID:16267288

  14. Population Structure and Evolution of the Bacillus cereus Group

    DTIC Science & Technology

    2004-12-01

    nucleotide sequence differences within subdivisions of the B. cereus group Subdivision No. of variable sites in gene All loci glpF gmk ilvD pta pur...thuringiensis (53 isolates from 17 serovars), and Bacillus weihenstephanensis (2 isolates) were assigned to 59 sequence types (STs) derived from the nucleotide ...increasing scientific and political importance in recent years. MLST studies that employ nucleotide sequence analysis to identify genetic variation

  15. Cooperative Networked Control of Dynamical Peer-to-Peer Vehicle Systems

    DTIC Science & Technology

    2007-12-28

    34 StrUcture- thro1uh pro-b;1biliStiC cotitifexts. Siam.Jourvial ovn Computinf], 37(zl):977-1013: 2006. 187] M,. 5, largailiot and D. Liberzon. Lie-lgebraiic...S. La.1l. A characterization of convex problems in decentralized control. ILV"’’ Transa.ction_q ovn Aidwaatic Conrol, 51 (2):27zl-28G, 2006. [1261 ’.M

  16. Completed Chromosomes in Thymine-Requiring Bacillus subtilis Spores

    PubMed Central

    Callister, Heather; Wake, R. G.

    1974-01-01

    Origin:terminus genetic marker ratios (both purA: metB and purA:ilvA) were measured in extracts of spores of Bacillus subtilis strains W23 thy his and 168 thy. For strain W23 thy his, normalized to W23 spore deoxyribonucleic acid, both ratios were equal to unity and were consistent with the presence of only completed chromosomes in the spores. The same ratios in extracts of spores of 168 thy, normalized to strain 168 or the prototroph SB19, were abnormal, i.e., 2.26 ± 0.10 and 0.71 ± 0.06 for purA:metB and purA:ilvA, respectively. These values were unaffected by the extent of extraction of the spore deoxyribonucleic acid, the richness of the medium on which they are formed, and the thymine phenotype. The high ratio for purA:metB is in agreement with the results of earlier workers but, because of the low purA:ilvA ratio, cannot be explained simply by the presence of partially replicated chromosomes in spores of strain 168 thy. Furthermore, purA:leuA in such extracts is 1.01 ± 0.06, consistent with the presence of only completed chromosomes. It is concluded that the abnormal origin:terminus marker ratios are only apparent and result from non-isogenicity between strains 168 thy and 168 in the metB thyB ilvA chromosome region introduced during construction of 168 thy by transformation of strain 168 with W23 thy deoxyribonucleic acid. It is concluded further that the chromosomes of strain 168 thy spores are in a completed form. PMID:4218227

  17. Enhanced valine production in Corynebacterium glutamicum with defective H+-ATPase and C-terminal truncated acetohydroxyacid synthase.

    PubMed

    Wada, Masaru; Hijikata, Nowaki; Aoki, Ryo; Takesue, Nobuchika; Yokota, Atsushi

    2008-11-01

    We have reported increased glutamate production by a mutant of Corynebacterium glutamicum ATCC14067 (strain F172-8) with reduced H(+)-ATPase activity under biotin-limiting culture conditions (Aoki et al. Biosci. Biotechnol. Biochem., 69, 1466-1472 (2005)). In the present study, we examined valine production by an H(+)-ATPase-defective mutant of C. glutamicum. Using the double-crossover chromosome replacement technique, we constructed a newly defined H(+)-ATPase-defective mutant from ATCC13032. After transforming the new strain (A-1) with a C-terminal truncation of acetohydroxyacid synthase gene (ilvBN), valine production increased from 21.7 mM for the wild-type strain to 46.7 mM for the A-1 in shaking flask cultures with 555 mM glucose. Increased production of the valine intermediate acetoin was also observed in A-1, and was reduced by inserting acetohydroxyacid isomeroreductase gene (ilvC) into the ilvBN plasmid. After transformation with this new construct, valine production increased from 38.3 mM for the wild-type strain to 95.7 mM for A-1 strain. To the best of our knowledge, this is the first report indicating that an H(+)-ATPase-defective mutant of C. glutamicum is capable of valine production. Our combined results with glutamate and valine suggest that the H(+)-ATPase defect is also effective in the fermentative production of other practical compounds.

  18. Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides

    PubMed Central

    Sun, Hong; Tanowitz, Michael; Liang, Xue-hai; Crooke, Stanley T.

    2017-01-01

    Abstract Antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages are broadly used as research tools and therapeutic agents. Chemically modified PS-ASOs can mediate efficient target reduction by site-specific cleavage of RNA through RNase H1. PS-ASOs are known to be internalized via a number of endocytotic pathways and are released from membrane-enclosed endocytotic organelles, mainly late endosomes (LEs). This study was focused on the details of PS-ASO trafficking through endocytic pathways. It was found that lysobisphosphatidic acid (LBPA) is required for release of PS-ASOs from LEs. PS-ASOs exited early endosomes (EEs) rapidly after internalization and became co-localized with LBPA by 2 hours in LEs. Inside LEs, PS-ASOs and LBPA were co-localized in punctate, dot-like structures, likely intraluminal vesicles (ILVs). Deactivation of LBPA using anti-LBPA antibody significantly decreased PS-ASO activities without affecting total PS-ASO uptake. Reduction of Alix also substantially decreased PS-ASO activities without affecting total PS-ASO uptake. Furthermore, Alix reduction decreased LBPA levels and limited co-localization of LBPA with PS-ASOs at ILVs inside LEs. Thus, the fusion properties of ILVs, which are supported by LBPA, contribute to PS-ASO intracellular release from LEs. PMID:28379543

  19. Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides.

    PubMed

    Wang, Shiyu; Sun, Hong; Tanowitz, Michael; Liang, Xue-Hai; Crooke, Stanley T

    2017-05-19

    Antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages are broadly used as research tools and therapeutic agents. Chemically modified PS-ASOs can mediate efficient target reduction by site-specific cleavage of RNA through RNase H1. PS-ASOs are known to be internalized via a number of endocytotic pathways and are released from membrane-enclosed endocytotic organelles, mainly late endosomes (LEs). This study was focused on the details of PS-ASO trafficking through endocytic pathways. It was found that lysobisphosphatidic acid (LBPA) is required for release of PS-ASOs from LEs. PS-ASOs exited early endosomes (EEs) rapidly after internalization and became co-localized with LBPA by 2 hours in LEs. Inside LEs, PS-ASOs and LBPA were co-localized in punctate, dot-like structures, likely intraluminal vesicles (ILVs). Deactivation of LBPA using anti-LBPA antibody significantly decreased PS-ASO activities without affecting total PS-ASO uptake. Reduction of Alix also substantially decreased PS-ASO activities without affecting total PS-ASO uptake. Furthermore, Alix reduction decreased LBPA levels and limited co-localization of LBPA with PS-ASOs at ILVs inside LEs. Thus, the fusion properties of ILVs, which are supported by LBPA, contribute to PS-ASO intracellular release from LEs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. System identification of closed-loop cardiovascular control: effects of posture and autonomic blockade

    NASA Technical Reports Server (NTRS)

    Mullen, T. J.; Appel, M. L.; Mukkamala, R.; Mathias, J. M.; Cohen, R. J.

    1997-01-01

    We applied system identification to the analysis of fluctuations in heart rate (HR), arterial blood pressure (ABP), and instantaneous lung volume (ILV) to characterize quantitatively the physiological mechanisms responsible for the couplings between these variables. We characterized two autonomically mediated coupling mechanisms [the heart rate baroreflex (HR baroreflex) and respiratory sinus arrhythmia (ILV-HR)] and two mechanically mediated coupling mechanisms [the blood pressure wavelet generated with each cardiac contraction (circulatory mechanics) and the direct mechanical effects of respiration on blood pressure (ILV-->ABP)]. We evaluated the method in humans studied in the supine and standing postures under control conditions and under conditions of beta-sympathetic and parasympathetic pharmacological blockades. Combined beta-sympathetic and parasympathetic blockade abolished the autonomically mediated couplings while preserving the mechanically mediated coupling. Selective autonomic blockade and postural changes also altered the couplings in a manner consistent with known physiological mechanisms. System identification is an "inverse-modeling" technique that provides a means for creating a closed-loop model of cardiovascular regulation for an individual subject without altering the underlying physiological control mechanisms.

  1. Metabolic engineering of Saccharomyces cerevisiae for the production of isobutanol and 3-methyl-1-butanol.

    PubMed

    Park, Seong-Hee; Kim, Sujin; Hahn, Ji-Sook

    2014-11-01

    Saccharomyces cerevisiae naturally produces small amounts of isobutanol and 3-methyl-1-butanol via Ehrlich pathway from the catabolism of valine and leucine, respectively. In this study, we engineered CEN.PK2-1C, a leucine auxotrophic strain having a LEU2 gene mutation, for the production of isobutanol and 3-methyl-1-butanol. First, ALD6 encoding aldehyde dehydrogenase and BAT1 involved in valine synthesis were deleted to eliminate competing pathways. We also increased transcription of endogenous genes in the valine and leucine biosynthetic pathways by expressing Leu3Δ601, a constitutively active form of Leu3 transcriptional activator. For the production of isobutanol, genes involved in isobutanol production (ILV2, ILV3, ILV5, ARO10, and ADH2) were additionally overexpressed in ald6Δbat1Δ strain expressing LEU3Δ601, resulting in 376.9 mg/L isobutanol production from 100 g/L glucose. To increase 3-methyl-1-butanol production, leucine biosynthetic genes were additionally overexpressed in the final isobutanol-production strain. The resulting strain overexpressing LEU2 and LEU4 (D578Y) , a feedback inhibition-insensitive mutant of LEU4, showed a 34-fold increase in 3-methyl-1-butanol synthesis compared with CEN.PK2-1C control strain, producing 765.7 mg/L 3-methyl-1-butanol.

  2. Isobutanol production in engineered Saccharomyces cerevisiae by overexpression of 2-ketoisovalerate decarboxylase and valine biosynthetic enzymes.

    PubMed

    Lee, Won-Heong; Seo, Seung-Oh; Bae, Yi-Hyun; Nan, Hong; Jin, Yong-Su; Seo, Jin-Ho

    2012-11-01

    Engineering of Saccharomyces cerevisiae to produce advanced biofuels such as isobutanol has received much attention because this yeast has a natural capacity to produce higher alcohols. In this study, construction of isobutanol production systems was attempted by overexpression of effective 2-keto acid decarboxylase (KDC) and combinatorial overexpression of valine biosynthetic enzymes in S. cerevisiae D452-2. Among the six putative KDC enzymes from various microorganisms, 2-ketoisovalerate decarboxylase (Kivd) from L. lactis subsp. lactis KACC 13877 was identified as the most suitable KDC for isobutanol production in the yeast. Isobutanol production by the engineered S. cerevisiae was assessed in micro-aerobic batch fermentations using glucose as a sole carbon source. 93 mg/L isobutanol was produced in the Kivd overexpressing strain, which corresponds to a fourfold improvement as compared with the control strain. Isobutanol production was further enhanced to 151 mg/L by additional overexpression of acetolactate synthase (Ilv2p), acetohydroxyacid reductoisomerase (Ilv5p), and dihydroxyacid dehydratase (Ilv3p) in the cytosol.

  3. System identification of closed-loop cardiovascular control: effects of posture and autonomic blockade

    NASA Technical Reports Server (NTRS)

    Mullen, T. J.; Appel, M. L.; Mukkamala, R.; Mathias, J. M.; Cohen, R. J.

    1997-01-01

    We applied system identification to the analysis of fluctuations in heart rate (HR), arterial blood pressure (ABP), and instantaneous lung volume (ILV) to characterize quantitatively the physiological mechanisms responsible for the couplings between these variables. We characterized two autonomically mediated coupling mechanisms [the heart rate baroreflex (HR baroreflex) and respiratory sinus arrhythmia (ILV-HR)] and two mechanically mediated coupling mechanisms [the blood pressure wavelet generated with each cardiac contraction (circulatory mechanics) and the direct mechanical effects of respiration on blood pressure (ILV-->ABP)]. We evaluated the method in humans studied in the supine and standing postures under control conditions and under conditions of beta-sympathetic and parasympathetic pharmacological blockades. Combined beta-sympathetic and parasympathetic blockade abolished the autonomically mediated couplings while preserving the mechanically mediated coupling. Selective autonomic blockade and postural changes also altered the couplings in a manner consistent with known physiological mechanisms. System identification is an "inverse-modeling" technique that provides a means for creating a closed-loop model of cardiovascular regulation for an individual subject without altering the underlying physiological control mechanisms.

  4. Identification of the Actinobacillus pleuropneumoniae Leucine-Responsive Regulatory Protein and Its Involvement in the Regulation of In Vivo-Induced Genes▿

    PubMed Central

    Wagner, Trevor K.; Mulks, Martha H.

    2007-01-01

    Actinobacillus pleuropneumoniae is a gram-negative bacterial pathogen that causes a severe hemorrhagic pneumonia in swine. We have previously shown that the limitation of branched-chain amino acids (BCAAs) is a cue that induces the expression of a subset of A. pleuropneumoniae genes identified as specifically induced during infection of the natural host animal by using an in vivo expression technology screen. Leucine-responsive regulatory protein (Lrp) is a global regulator and has been shown in Escherichia coli to regulate many genes, including genes involved in BCAA biosynthesis. We hypothesized that A. pleuropneumoniae contains a regulator similar to Lrp and that this protein is involved in the regulation of a subset of genes important during infection and recently shown to have increased expression in the absence of BCAAs. We report the identification of an A. pleuropneumoniae serotype 1 gene encoding a protein with similarity to amino acid sequence and functional domains of other reported Lrp proteins. We further show that purified A. pleuropneumoniae His6-Lrp binds in vitro to the A. pleuropneumoniae promoter regions for ilvI, antisense cps1AB, lrp, and nqr. A genetically defined A. pleuropneumoniae lrp mutant was constructed using an allelic replacement and sucrose counterselection method. Analysis of expression from the ilvI and antisense cps1AB promoters in wild-type, lrp mutant, and complemented lrp mutant strains indicated that Lrp is required for induction of expression of ilvI under BCAA limitation. PMID:17060463

  5. Clusters of isoleucine, leucine, and valine side chains define cores of stability in high‐energy states of globular proteins: Sequence determinants of structure and stability

    PubMed Central

    Kathuria, Sagar V.; Chan, Yvonne H.; Nobrega, R. Paul; Özen, Ayşegül

    2015-01-01

    Abstract Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high‐energy states that populate their folding free‐energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high‐energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high‐energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates. PMID:26660714

  6. Divergent evolution of a bifunctional de novo protein.

    PubMed

    Smith, Betsy A; Mularz, Ann E; Hecht, Michael H

    2015-02-01

    Primordial proteins, the evolutionary ancestors of modern sequences, are presumed to have been minimally active and nonspecific. Following eons of selective pressure, these early progenitors evolved into highly active and specific proteins. While evolutionary trajectories from poorly active and multifunctional generalists toward highly active specialists likely occurred many times in evolutionary history, such pathways are difficult to reconstruct in natural systems, where primordial sequences are lost to time. To test the hypothesis that selection for enhanced activity leads to a loss of promiscuity, we evolved a de novo designed bifunctional protein. The parental protein, denoted Syn-IF, was chosen from a library of binary patterned 4-helix bundles. Syn-IF was shown previously to rescue two different auxotrophic strains of E. coli: ΔilvA and Δfes. These two strains contain deletions for proteins with very different biochemical functions; IlvA is involved in isoleucine biosynthesis, while Fes is involved in iron assimilation. In two separate experiments, Syn-IF, was evolved for faster rescue of either ΔilvA or Δfes. Following multiple rounds of mutagenesis, two new proteins were selected, each capable of rescuing the selected function significantly faster than the parental protein. In each case, the evolved protein also lost the ability to rescue the unselected function. In both evolutionary trajectories, the original bifunctional generalist was evolved into a monofunctional specialist with enhanced activity. © 2014 The Protein Society.

  7. Divergent evolution of a bifunctional de novo protein

    PubMed Central

    Smith, Betsy A; Mularz, Ann E; Hecht, Michael H

    2015-01-01

    Primordial proteins, the evolutionary ancestors of modern sequences, are presumed to have been minimally active and nonspecific. Following eons of selective pressure, these early progenitors evolved into highly active and specific proteins. While evolutionary trajectories from poorly active and multifunctional generalists toward highly active specialists likely occurred many times in evolutionary history, such pathways are difficult to reconstruct in natural systems, where primordial sequences are lost to time. To test the hypothesis that selection for enhanced activity leads to a loss of promiscuity, we evolved a de novo designed bifunctional protein. The parental protein, denoted Syn-IF, was chosen from a library of binary patterned 4-helix bundles. Syn-IF was shown previously to rescue two different auxotrophic strains of E. coli: ΔilvA and Δfes. These two strains contain deletions for proteins with very different biochemical functions; IlvA is involved in isoleucine biosynthesis, while Fes is involved in iron assimilation. In two separate experiments, Syn-IF, was evolved for faster rescue of either ΔilvA or Δfes. Following multiple rounds of mutagenesis, two new proteins were selected, each capable of rescuing the selected function significantly faster than the parental protein. In each case, the evolved protein also lost the ability to rescue the unselected function. In both evolutionary trajectories, the original bifunctional generalist was evolved into a monofunctional specialist with enhanced activity. PMID:25420677

  8. ESCRTs regulate amyloid precursor protein sorting in multivesicular bodies and intracellular amyloid-β accumulation.

    PubMed

    Edgar, James R; Willén, Katarina; Gouras, Gunnar K; Futter, Clare E

    2015-07-15

    Intracellular amyloid-β (Aβ) accumulation is a key feature of early Alzheimer's disease and precedes the appearance of Aβ in extracellular plaques. Aβ is generated through proteolytic processing of amyloid precursor protein (APP), but the intracellular site of Aβ production is unclear. APP has been localized to multivesicular bodies (MVBs) where sorting of APP onto intraluminal vesicles (ILVs) could promote amyloidogenic processing, or reduce Aβ production or accumulation by sorting APP and processing products to lysosomes for degradation. Here, we show that APP localizes to the ILVs of a subset of MVBs that also traffic EGF receptor (EGFR), and that it is delivered to lysosomes for degradation. Depletion of the endosomal sorting complexes required for transport (ESCRT) components, Hrs (also known as Hgs) or Tsg101, inhibited targeting of APP to ILVs and the subsequent delivery to lysosomes, and led to increased intracellular Aβ accumulation. This was accompanied by dramatically decreased Aβ secretion. Thus, the early ESCRT machinery has a dual role in limiting intracellular Aβ accumulation through targeting of APP and processing products to the lysosome for degradation, and promoting Aβ secretion.

  9. Endosomal type Iγ PIP 5-kinase controls EGF receptor lysosomal sorting.

    PubMed

    Sun, Yue; Hedman, Andrew C; Tan, Xiaojun; Schill, Nicholas J; Anderson, Richard A

    2013-04-29

    Endosomal trafficking and degradation of epidermal growth factor receptor (EGFR) play an essential role in the control of its signaling. Phosphatidylinositol-4,5-bisphosphate (PtdIns4,5P(2)) is an established regulator of endocytosis, whereas PtdIns3P modulates endosomal trafficking. However, we demonstrate here that type I gamma phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme that synthesizes PtdIns4,5P(2), controls endosome-to-lysosome sorting of EGFR. In this pathway, PIPKIγi5 interacts with sorting nexin 5 (SNX5), a protein that binds PtdIns4,5P(2) and other phosphoinositides. PIPKIγi5 and SNX5 localize to endosomes, and loss of either protein blocks EGFR sorting into intraluminal vesicles (ILVs) of the multivesicular body. Loss of ILV sorting greatly enhances and prolongs EGFR signaling. PIPKIγi5 and SNX5 prevent Hrs ubiquitination, and this facilitates the Hrs association with EGFR that is required for ILV sorting. These findings reveal that PIPKIγi5 and SNX5 form a signaling nexus that controls EGFR endosomal sorting, degradation, and signaling.

  10. Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes.

    PubMed Central

    Blomqvist, K; Nikkola, M; Lehtovaara, P; Suihko, M L; Airaksinen, U; Stråby, K B; Knowles, J K; Penttilä, M E

    1993-01-01

    The genes involved in the 2,3-butanediol pathway coding for alpha-acetolactate decarboxylase, alpha-acetolactate synthase (alpha-ALS), and acetoin (diacetyl) reductase were isolated from Klebsiella terrigena and shown to be located in one operon. This operon was also shown to exist in Enterobacter aerogenes. The budA gene, coding for alpha-acetolactate decarboxylase, gives in both organisms a protein of 259 amino acids. The amino acid similarity between these proteins is 87%. The K. terrigena genes budB and budC, coding for alpha-ALS and acetoin reductase, respectively, were sequenced. The 559-amino-acid-long alpha-ALS enzyme shows similarities to the large subunits of the Escherichia coli anabolic alpha-ALS enzymes encoded by the genes ilvB, ilvG, and ilvI. The K. terrigena alpha-ALS is also shown to complement an anabolic alpha-ALS-deficient E. coli strain for valine synthesis. The 243-amino-acid-long acetoin reductase has the consensus amino acid sequence for the insect-type alcohol dehydrogenase/ribitol dehydrogenase family and has extensive similarities with the N-terminal and internal regions of three known dehydrogenases and one oxidoreductase. Images PMID:8444801

  11. A Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation.

    PubMed

    Leong-Morgenthaler, P; Oliver, S G; Hottinger, H; Söll, D

    1994-01-01

    The nifS gene was first identified in nitrogen-fixing bacteria where its protein product is essential for efficient nitrogen fixation. Here, we demonstrate that a nifS-like gene also occurs in Lactobacillus bulgaricus, an organism which does not fix nitrogen, and that the nifS gene product suppresses the leucine auxotrophy of an ilvD, ilvE Escherichia coli strain. The known nifS genes from prokaryotes and eukaryotes exhibit a high degree of sequence conservation although the genes have diverse functions, as shown by their ability to complement or suppress dissimilar mutations. It was suggested that the nifS gene products represent a group of enzymes which mediate a specific chemical reaction common to diverse metabolic pathways. The purified NifS protein from Azotobacter vinelandii was experimentally shown to be a pyridoxal phosphate-dependent cysteine desulfurase. Curiously, the NifS proteins exhibit also a remarkable sequence homology to a new class of pyridoxal phoshate-dependent aminotransferases. We show that the L bulgaricus NifS-like protein is able to replace in vivo transaminase B in E coli. This experimental observation supports the prediction that some NifS-like proteins may be aminotransferases.

  12. A Family of Tetraspans Organizes Cargo for Sorting into Multivesicular Bodies

    PubMed Central

    MacDonald, Chris; Payne, Johanna A.; Aboian, Mariam; Smith, William; Katzmann, David J.; Piper, Robert C.

    2015-01-01

    SUMMARY The abundance of cell surface membrane proteins is regulated by internalization and delivery into intralumenal vesicles (ILVs) of multivesicular bodies (MVB). Many cargoes are ubiquitinated, allowing access to an ESCRT-dependent pathway into MVBs. Yet, how non-ubiquitinated proteins, such as Glycosylphosphatidylinisotol-anchored proteins, enter MVBs is unclear, supporting the possibility of mechanistically distinct ILV biogenesis pathways. Here we show a family of highly ubiquitinated tetraspan Cos proteins provide a Ub-signal in trans, allowing sorting of non-ubiquitinated MVB cargo into the canonical ESCRT- and Ub-dependent pathway. Cos proteins create discrete endosomal subdomains that concentrate Ub-cargo prior to their envelopment into ILVs and the activity of Cos proteins is required not only for efficient sorting of canonical Ub-cargo but is also essential for sorting non-ubiquitinated cargo into MVBs. Expression of these proteins increases during nutrient stress though a NAD+/Sir2-dpendent mechanism that in turn accelerates the down-regulation of a broad range of cell surface proteins. PMID:25942624

  13. Characterization and modification of enzymes in the 2-ketoisovalerate biosynthesis pathway of Ralstonia eutropha H16

    SciTech Connect

    Lu, JN; Brigham, CJ; Plassmeier, JK; Sinskey, AJ

    2014-08-01

    2-Ketoisovalerate is an important cellular intermediate for the synthesis of branched-chain amino acids as well as other important molecules, such as pantothenate, coenzyme A, and glucosinolate. This ketoacid can also serve as a precursor molecule for the production of biofuels, pharmaceutical agents, and flavor agents in engineered organisms, such as the betaproteobacterium Ralstonia eutropha. The biosynthesis of 2-ketoisovalerate from pyruvate is carried out by three enzymes: acetohydroxyacid synthase (AHAS, encoded by ilvBH), acetohydroxyacid isomeroreductase (AHAIR, encoded by ilvC), and dihydroxyacid dehydratase (DHAD, encoded by ilvD). In this study, enzymatic activities and kinetic parameters were determined for each of the three R. eutropha enzymes as heterologously purified proteins. AHAS, which serves as a gatekeeper for the biosynthesis of all three branched-chain amino acids, demonstrated the tightest regulation through feedback inhibition by l-valine (IC50 = 1.2 mM), l-isoleucine (IC50 = 2.3 mM), and l-leucine (IC50 = 5.4 mM). Intermediates in the valine biosynthesis pathway also exhibit feedback inhibitory control of the AHAS enzyme. In addition, AHAS has a very weak affinity for pyruvate (K-M = 10.5 mu M) and is highly selective towards 2-ketobutyrate (R = 140) as a second substrate. AHAIR and DHAD are also inhibited by the branched-chain amino acids, although to a lesser extent when compared to AHAS. Experimental evolution and rational site-directed mutagenesis revealed mutants of the regulatory subunit of AHAS (IlvH) (N11S, T34I, A36V, T104S, N11F, G14E, and N29H), which, when reconstituted with wild-type IlvB, lead to AHAS having reduced valine, leucine, and isoleucine sensitivity. The study of the kinetics and inhibition mechanisms of R. eutropha AHAS, AHAIR, and DHAD has shed light on interactions between these enzymes and the products they produce; it, therefore, can be used to engineer R. eutropha strains with optimal production of 2

  14. Tsunami mitigation - redistribution of energy

    NASA Astrophysics Data System (ADS)

    Kadri, Usama

    2017-04-01

    .1007/1-4020-3607-8 3 3. E. Check, 2005. Natural disasters: Roots of recovery. Nature 438, 910-911, doi:10.1038/438910a. 4. A. M. Fridman, L. S. Alperovich, L. Shemer, L. Pustil'nik, D. Shtivelman, A. G. Marchuk, D. Liberzon, 2010. Tsunami wave suppression using submarine barriers. Phys. Usp. 53 809-816, doi:10.3367/UFNe.0180.201008d.0843. 5. U. Kadri, M. Stiassnie, 2013. Generation of an acoustic-gravity wave by two gravity waves, and their mutual interaction. J. Fluid Mech. 735, R6, doi:10.1017/jfm.2013.539. 6. U. Kadri, 2015. Wave motion in a heavy compressible fluid: revisited. European Journal of Mechanics - B/Fluids, 49(A), 50-57, doi:10.1016/j.euromechflu.2014.07.008 7. U. Kadri, T.R. Akylas, 2016. On resonant triad interactions of acoustic-gravity waves. J. Fluid Mech., 788, R1(12 pages), doi:10.1017/jfm.2015.721. 8. U. Kadri, 2016. Triad resonance between a surface-gravity wave and two high frequency hydro-acoustic waves. Eur. J. Mech. B/Fluid, 55(1), 157-161, doi:10.1016/j.euromechflu.2015.09.008.

  15. Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E. coli strain.

    PubMed

    Miyanoiri, Yohei; Ishida, Yojiro; Takeda, Mitsuhiro; Terauchi, Tsutomu; Inouye, Masayori; Kainosho, Masatsune

    2016-06-01

    We recently developed a practical protocol for preparing proteins bearing stereo-selectively (13)C-methyl labeled leucines and valines, instead of the commonly used (13)C-methyl labeled precursors for these amino acids, by E. coli cellular expression. Using this protocol, proteins with any combinations of isotope-labeled or unlabeled Leu and Val residues were prepared, including some that could not be prepared by the precursor methods. However, there is still room for improvement in the labeling efficiencies for Val residues, using the methods with labeled precursors or Val itself. This is due to the fact that the biosynthesis of Val could not be sufficiently suppressed, even by the addition of large amounts of Val or its precursors. In this study, we completely solved this problem by using a mutant strain derived from E. coli BL21(DE3), in which the metabolic pathways depending on two enzymes, dihydroxy acid dehydratase and β-isopropylmalate dehydrogenase, are completely aborted by deleting the ilvD and leuB genes, which respectively encode these enzymes. The ΔilvD E. coli mutant terminates the conversion from α,β-dihydroxyisovalerate to α-ketoisovalerate, and the conversion from α,β-dihydroxy-α-methylvalerate to α-keto-β-methylvalerate, which produce the preceding precursors for Val and Ile, respectively. By the further deletion of the leuB gene, the conversion from Val to Leu was also fully terminated. Taking advantage of the double-deletion mutant, ΔilvDΔleuB E. coli BL21(DE3), an efficient and residue-selective labeling method with various isotope-labeled Ile, Leu, and Val residues was established.

  16. Enhanced biosynthetically directed fractional carbon-13 enrichment of proteins for backbone NMR Assignments

    PubMed Central

    Wenrich, Broc R.; Sonstrom, Reilly E.; Gupta, Riju A.; Rovnyak, David

    2015-01-01

    Routes to carbon-13 enrichment of bacterially expressed proteins include achieving uniform or positionally selective (e.g. ILV-Me, or 13C′, etc.) enrichment. We consider the potential for biosynthetically directed fractional enrichment (e.g. carbon-13 incorporation in the protein less than 100%) for performing routine n-(D)dimensional NMR spectroscopy of proteins. First, we demonstrate an approach to fractional isotope addition where the initial growth media containing natural abundance glucose is replenished at induction with a small amount (e.g. 10%w/w u-13C-glucose) of enriched nutrient. The approach considered here is to add 10% (e.g. 200 mg for a 2 g/L culture) u-13C-glucose at the induction time (OD600=0.8), resulting in a protein with enhanced 13C incorporation that gives almost the same NMR signal levels as an exact 20% 13C sample. Second, whereas fractional enrichment is used for obtaining stereospecific methyl assignments, we find that 13C incorporation levels no greater than 20%w/w yield 13C and 13C-13C spin pair incorporation sufficient to conduct typical 3D-bioNMR backbone experiments on moderate instrumentation (600 MHz, RT probe). Typical 3D-bioNMR experiments of a fractionally enriched protein yield expected backbone connectivities, and did not show amino acid biases in this work, with one exception. When adding 10% u-13C glucose to expression media at induction, there is poor preservation of 13Cα-13Cβ spin pairs in the amino acids ILV, leading to the absence of Cβ signals in HNCACB spectra for ILV, a potentially useful editing effect. Enhanced fractional carbon-13 enrichment provides lower-cost routes to high throughput protein NMR studies, and makes modern protein NMR more cost-accessible. PMID:26256059

  17. Interplay between Drying and Stability of a TIM Barrel Protein: A Combined Simulation-Experimental Study

    PubMed Central

    Das, Payel; Kapoor, Divya; Halloran, Kevin T.; Zhou, Ruhong; Matthews, C. Robert

    2013-01-01

    Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting on the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validate this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation on experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids, isoleucines, leucines and valines (ILV), were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with the less hydrophobic alanine showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with the isosteric and polar asparagine enhanced the wetting of the N- and C-terminal clusters. Experimental results on the stability, secondary structure and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster only experiences partial drying in the intermediate and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying in hydrophobic ILV clusters to the folding and stability of the αTS TIM barrel. PMID:23293932

  18. Downregulation of Rv0189c, encoding a dihydroxyacid dehydratase, affects growth of Mycobacterium tuberculosis in vitro and in mice.

    PubMed

    Singh, Vinayak; Chandra, Deepak; Srivastava, Brahm S; Srivastava, Ranjana

    2011-01-01

    Dihydroxyacid dehydratase (DHAD), a key enzyme involved in branched-chain amino acid (BCAA) biosynthesis, catalyses the synthesis of 2-ketoacids from dihydroxyacids. In Mycobacterium tuberculosis, DHAD is encoded by gene Rv0189c, and it shares 40% amino acid sequence identity and conserved motifs with DHAD of Escherichia coli encoded by ilvD. In this study, Rv0189c was overexpressed in E. coli and the resultant protein was characterized as a homodimer (~155 kDa). Functional characterization of Rv0189c was established by biochemical testing and by genetic complementation of an intron-disrupted ilvD-auxotrophic mutant of E. coli to prototrophy. Growth of M. tuberculosis, E. coli BL21(DE3) and recombinant E. coli BL21(DE3) ΔilvD carrying Rv0189c was inhibited by transient nitric oxide (NO) exposure in minimal medium but growth was restored if the medium was supplemented with BCAA (isoleucine, leucine and valine). This suggested that inactivation of Rv0189c by NO probably inhibited bacterial growth. The role of Rv0189c in M. tuberculosis was elucidated by antisense and sense RNA constructs. Growth of M. tuberculosis transformed with a plasmid encoding antisense mRNA was markedly poor in the lungs of infected mice and in Middlebrook 7H9 broth compared to that of sense and vector-alone transformants, but growth was normal when the medium was supplemented with BCAA. Upregulation of Rv0189c was observed during the early exponential phase of growth, under acid stress and ex vivo, suggesting that Rv0189c has a role in the survival of M. tuberculosis during normal and stress conditions. It may be concluded that the DHAD encoded by Rv0189c is essential for the survival of M. tuberculosis and could be a potential drug/vaccine target, as it is absent in mammals.

  19. Corynebacterium glutamicum tailored for efficient isobutanol production.

    PubMed

    Blombach, Bastian; Riester, Tanja; Wieschalka, Stefan; Ziert, Christian; Youn, Jung-Won; Wendisch, Volker F; Eikmanns, Bernhard J

    2011-05-01

    We recently engineered Corynebacterium glutamicum for aerobic production of 2-ketoisovalerate by inactivation of the pyruvate dehydrogenase complex, pyruvate:quinone oxidoreductase, transaminase B, and additional overexpression of the ilvBNCD genes, encoding acetohydroxyacid synthase, acetohydroxyacid isomeroreductase, and dihydroxyacid dehydratase. Based on this strain, we engineered C. glutamicum for the production of isobutanol from glucose under oxygen deprivation conditions by inactivation of l-lactate and malate dehydrogenases, implementation of ketoacid decarboxylase from Lactococcus lactis, alcohol dehydrogenase 2 (ADH2) from Saccharomyces cerevisiae, and expression of the pntAB transhydrogenase genes from Escherichia coli. The resulting strain produced isobutanol with a substrate-specific yield (Y(P/S)) of 0.60 ± 0.02 mol per mol of glucose. Interestingly, a chromosomally encoded alcohol dehydrogenase rather than the plasmid-encoded ADH2 from S. cerevisiae was involved in isobutanol formation with C. glutamicum, and overexpression of the corresponding adhA gene increased the Y(P/S) to 0.77 ± 0.01 mol of isobutanol per mol of glucose. Inactivation of the malic enzyme significantly reduced the Y(P/S), indicating that the metabolic cycle consisting of pyruvate and/or phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme is responsible for the conversion of NADH + H+ to NADPH + H+. In fed-batch fermentations with an aerobic growth phase and an oxygen-depleted production phase, the most promising strain, C. glutamicum ΔaceE Δpqo ΔilvE ΔldhA Δmdh(pJC4ilvBNCD-pntAB)(pBB1kivd-adhA), produced about 175 mM isobutanol, with a volumetric productivity of 4.4 mM h⁻¹, and showed an overall Y(P/S) of about 0.48 mol per mol of glucose in the production phase.

  20. Corynebacterium glutamicum Tailored for Efficient Isobutanol Production ▿ †

    PubMed Central

    Blombach, Bastian; Riester, Tanja; Wieschalka, Stefan; Ziert, Christian; Youn, Jung-Won; Wendisch, Volker F.; Eikmanns, Bernhard J.

    2011-01-01

    We recently engineered Corynebacterium glutamicum for aerobic production of 2-ketoisovalerate by inactivation of the pyruvate dehydrogenase complex, pyruvate:quinone oxidoreductase, transaminase B, and additional overexpression of the ilvBNCD genes, encoding acetohydroxyacid synthase, acetohydroxyacid isomeroreductase, and dihydroxyacid dehydratase. Based on this strain, we engineered C. glutamicum for the production of isobutanol from glucose under oxygen deprivation conditions by inactivation of l-lactate and malate dehydrogenases, implementation of ketoacid decarboxylase from Lactococcus lactis, alcohol dehydrogenase 2 (ADH2) from Saccharomyces cerevisiae, and expression of the pntAB transhydrogenase genes from Escherichia coli. The resulting strain produced isobutanol with a substrate-specific yield (YP/S) of 0.60 ± 0.02 mol per mol of glucose. Interestingly, a chromosomally encoded alcohol dehydrogenase rather than the plasmid-encoded ADH2 from S. cerevisiae was involved in isobutanol formation with C. glutamicum, and overexpression of the corresponding adhA gene increased the YP/S to 0.77 ± 0.01 mol of isobutanol per mol of glucose. Inactivation of the malic enzyme significantly reduced the YP/S, indicating that the metabolic cycle consisting of pyruvate and/or phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme is responsible for the conversion of NADH+H+ to NADPH+H+. In fed-batch fermentations with an aerobic growth phase and an oxygen-depleted production phase, the most promising strain, C. glutamicum ΔaceE Δpqo ΔilvE ΔldhA Δmdh(pJC4ilvBNCD-pntAB)(pBB1kivd-adhA), produced about 175 mM isobutanol, with a volumetric productivity of 4.4 mM h−1, and showed an overall YP/S of about 0.48 mol per mol of glucose in the production phase. PMID:21441331

  1. Relationship between Cognitive Performance and Measures of Neurodegeneration among Hispanic and White Non-Hispanic Individuals with Normal Cognition, Mild Cognitive Impairment, and Dementia.

    PubMed

    Burke, Shanna L; Rodriguez, Miriam J; Barker, Warren; Greig-Custo, Maria T; Rosselli, Monica; Loewenstein, David A; Duara, Ranjan

    2017-09-18

    The aim of this study was to determine the presence and severity of potential cultural and language bias in widely used cognitive and other assessment instruments, using structural MRI measures of neurodegeneration as biomarkers of disease stage and severity. Hispanic (n=75) and White non-Hispanic (WNH) (n=90) subjects were classified as cognitively normal (CN), amnestic mild cognitive impairment (aMCI) and mild dementia. Performance on the culture-fair and educationally fair Fuld Object Memory Evaluation (FOME) and Clinical Dementia Rating Scale (CDR) between Hispanics and WNHs was equivalent, in each diagnostic group. Volumetric and visually rated measures of the hippocampus entorhinal cortex, and inferior lateral ventricles (ILV) were measured on structural MRI scans for all subjects. A series of analyses of covariance, controlling for age, depression, and education, were conducted to compare the level of neurodegeneration on these MRI measures between Hispanics and WNHs in each diagnostic group. Among both Hispanics and WNH groups there was a progressive decrease in volume of the hippocampus and entorhinal cortex, and an increase in volume of the ILV (indicating increasing atrophy in the regions surrounding the ILV) from CN to aMCI to mild dementia. For equivalent levels of performance on the FOME and CDR, WNHs had greater levels of neurodegeneration than did Hispanic subjects. Atrophy in medial temporal regions was found to be greater among WNH than Hispanic diagnostic groups, despite the lack of statistical differences in cognitive performance between these two ethnic groups. Presumably, unmeasured factors result in better cognitive performance among WNH than Hispanics for a given level of neurodegeneration. (JINS, 2017, 23, 1-12).

  2. A unique plant ESCRT component, FREE1, regulates multivesicular body protein sorting and plant growth.

    PubMed

    Gao, Caiji; Luo, Ming; Zhao, Qiong; Yang, Renzhi; Cui, Yong; Zeng, Yonglun; Xia, Jun; Jiang, Liwen

    2014-11-03

    Tight control of membrane protein homeostasis by selective degradation is crucial for proper cell signaling and multicellular organismal development. Membrane proteins destined for degradation, such as misfolded proteins or activated receptors, are usually ubiquitinated and sorted into the intraluminal vesicles (ILVs) of prevacuolar compartments/multivesicular bodies (PVCs/MVBs), which then fuse with vacuoles/lysosomes to deliver their contents to the lumen for degradation by luminal proteases. The formation of ILVs and the sorting of ubiquitinated membrane cargoes into them are facilitated by the endosomal sorting complex required for transport (ESCRT) machinery. Plants possess most evolutionarily conserved members of the ESCRT machinery but apparently lack orthologs of ESCRT-0 subunits and the ESCRT-I component Mvb12. Here, we identified a unique plant ESCRT component called FYVE domain protein required for endosomal sorting 1 (FREE1). FREE1 binds to phosphatidylinositol-3-phosphate (PI3P) and ubiquitin and specifically interacts with Vps23 via PTAP-like tetrapeptide motifs to be incorporated into the ESCRT-I complex. Arabidopsis free1 mutant is seedling lethal and defective in the formation of ILVs in MVBs. Consequently, endocytosed plasma membrane (PM) proteins destined for degradation, such as the auxin efflux carrier PIN2, cannot reach the lumen of the vacuole and mislocalize to the tonoplast. Collectively, our findings provide the first functional characterization of a plant FYVE domain protein, which is essential for plant growth via its role as a unique evolutionary ESCRT component for MVB biogenesis and vacuolar sorting of membrane proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Old world arenaviruses enter the host cell via the multivesicular body and depend on the endosomal sorting complex required for transport.

    PubMed

    Pasqual, Giulia; Rojek, Jillian M; Masin, Mark; Chatton, Jean-Yves; Kunz, Stefan

    2011-09-01

    The highly pathogenic Old World arenavirus Lassa virus (LASV) and the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) use α-dystroglycan as a cellular receptor and enter the host cell by an unusual endocytotic pathway independent of clathrin, caveolin, dynamin, and actin. Upon internalization, the viruses are delivered to acidified endosomes in a Rab5-independent manner bypassing classical routes of incoming vesicular trafficking. Here we sought to identify cellular factors involved in the unusual and largely unknown entry pathway of LASV and LCMV. Cell entry of LASV and LCMV required microtubular transport to late endosomes, consistent with the low fusion pH of the viral envelope glycoproteins. Productive infection with recombinant LCMV expressing LASV envelope glycoprotein (rLCMV-LASVGP) and LCMV depended on phosphatidyl inositol 3-kinase (PI3K) as well as lysobisphosphatidic acid (LBPA), an unusual phospholipid that is involved in the formation of intraluminal vesicles (ILV) of the multivesicular body (MVB) of the late endosome. We provide evidence for a role of the endosomal sorting complex required for transport (ESCRT) in LASV and LCMV cell entry, in particular the ESCRT components Hrs, Tsg101, Vps22, and Vps24, as well as the ESCRT-associated ATPase Vps4 involved in fission of ILV. Productive infection with rLCMV-LASVGP and LCMV also critically depended on the ESCRT-associated protein Alix, which is implicated in membrane dynamics of the MVB/late endosomes. Our study identifies crucial cellular factors implicated in Old World arenavirus cell entry and indicates that LASV and LCMV invade the host cell passing via the MVB/late endosome. Our data further suggest that the virus-receptor complexes undergo sorting into ILV of the MVB mediated by the ESCRT, possibly using a pathway that may be linked to the cellular trafficking and degradation of the cellular receptor.

  4. Reconnaissance exploration geochemistry in the central Brooks Range, northern Alaska: Implications for exploration of sediment-hosted zinc-lead-silver deposits

    USGS Publications Warehouse

    Kelley, K.D.; Kelley, D.L.

    1992-01-01

    A reconnaissance geochemical survey was conducted in the southern Killik River quadrangle, central Brooks Range, northern Alaska. The Brooks Range lies within the zone of continuous permafrost which may partially inhibit chemical weathering and oxidation. The minus 30-mesh and nonmagnetic heavy-mineral concentrate fractions of sediment samples were chosen as the sample media for the survey so that mechanical rather than chemical dispersion patterns would be enhanced. A total of 263 sites were sampled within the southern half of the Killik River quadrangle at an average sample density of approximately one sample per 12 km2. All samples were submitted for multi-element analyses. In the western and central Brooks Range, several known sediment-hosted Zn-Pb-Ag(-Ba) deposits occur within a belt of Paleozoic rocks of the Endicott Mountains allochthon. Exploration for this type of deposit in the Brook Range is difficult, due to the inherently high background values for Ba, Zn and Pb in shale and the common occurrence of metamorphic quartz-calcite veins, many of which contain traces of sulfide minerals. Stream sediments derived from these sources produce numerous geochemical anomalies which are not necessarily associated with significant mineralization. R-mode factor analysis provides a means of distinguishing between element associations related to lithology and those related to possible mineralization. Factor analysis applied to the multi-element data from the southern Killik River quadrangle resulted in the discovery of two additional Zn-Pb-Ag mineral occurrences of considerable areal extent which are 80-100 km east of any previously known deposit. These have been informally named the Kady and Vidlee. Several lithogeochemical element associations, or factors, and three factors which represent sulfide mineralization were identified: Ag-Pb-Zn (galena and sphalerite) and Fe-Ni-Co-Cu (pyrite ?? chalcopyrite) in the concentrate samples and Cd-Zn-Pb-As-Mn in the sediment

  5. Propagation of acoustic-gravity waves in arctic zones with elastic ice-sheets

    NASA Astrophysics Data System (ADS)

    Kadri, Usama; Abdolali, Ali; Kirby, James T.

    2017-04-01

    We present an analytical solution of the boundary value problem of propagating acoustic-gravity waves generated in the ocean by earthquakes or ice-quakes in arctic zones. At the surface, we assume elastic ice-sheets of a variable thickness, and show that the propagating acoustic-gravity modes have different mode shape than originally derived by Ref. [1] for a rigid ice-sheet settings. Computationally, we couple the ice-sheet problem with the free surface model by Ref. [2] representing shrinking ice blocks in realistic sea state, where the randomly oriented ice-sheets cause inter modal transition at the edges and multidirectional reflections. We then derive a depth-integrated equation valid for spatially slowly varying thickness of ice-sheet and water depth. Surprisingly, and unlike the free-surface setting, here it is found that the higher acoustic-gravity modes exhibit a larger contribution. These modes travel at the speed of sound in water carrying information on their source, e.g. ice-sheet motion or submarine earthquake, providing various implications for ocean monitoring and detection of quakes. In addition, we found that the propagating acoustic-gravity modes can result in orbital displacements of fluid parcels sufficiently high that may contribute to deep ocean currents and circulation, as postulated by Refs. [1, 3]. References [1] U. Kadri, 2016. Generation of Hydroacoustic Waves by an Oscillating Ice Block in Arctic Zones. Advances in Acoustics and Vibration, 2016, Article ID 8076108, 7 pages http://dx.doi.org/10.1155/2016/8076108 [2] A. Abdolali, J. T. Kirby and G. Bellotti, 2015, Depth-integrated equation for hydro-acoustic waves with bottom damping, J. Fluid Mech., 766, R1 doi:10.1017/jfm.2015.37 [3] U. Kadri, 2014. Deep ocean water transportation by acoustic?gravity waves. J. Geophys. Res. Oceans, 119, doi:10.1002/ 2014JC010234

  6. Linerarised Optimal Control and Application to a Gliding Projectile

    DTIC Science & Technology

    1981-01-01

    the D)epartment of Defence or the Minister for Defence. S!ii ;]i Preface T’he stuidi es which Led to this paper were carried out under t he Defence...art i llery rockeis, eattcrg Iik ~ZZZ*Iiest, ne ilvelI opmteatt S have IP (’might %,it i 1t litei leW now ) a roat lit’s I0 colit t 1- I SV St (󈧏...reason why all state variablIes are led back i.n the optimal case. 5.1 Properties of Riccati Matrix R At this stage it is worth examining the

  7. Shipboard Medical Department Information Flows.

    DTIC Science & Technology

    1987-12-11

    operational commitments, and: (3) Members who do not have an eating disorder diagnosis, e.g., bulimia or anorexia nervosa, and; (4) Members who desire to...IDENTIFICATION-- CODE+ IF-F7LNl-N OT -NEGATIVE,--SM ALL-OPACIT IES- ROUNDED(SOR)-TYPE+SOR-PROFUSION+SOF-ONES+Sr1IALL- OPACITIES-IRREGULAR( SOI -TYPE+SOI...who hav’e nn; ot pi! ipaIdt ilv j c I the last three years, and; (7) Members %;ho haVe onE? ’e a I uIC-iniiog ont active duty Itiom he da te of starting

  8. Isobutanol and 2-ketoisovalerate production by Klebsiella pneumoniae via a native pathway.

    PubMed

    Gu, Jinjie; Zhou, Jidong; Zhang, Zhongxi; Kim, Chul Ho; Jiang, Biao; Shi, Jiping; Hao, Jian

    2017-09-01

    Isobutanol is a valuable chemical and is considered a new generation biofuel. Construction of isobutanol synthesis pathways in bacteria is a hot topic in isobutanol production. Here, we show that an isobutanol synthesis pathway exists naturally in Klebsiella pneumoniae; however, this pathway is dormant in the wild-type bacterium. K. pneumoniae is a 2,3-butanediol producer, and the synthesis pathways of 2,3-butanediol, valine and isobutanol all start from condensation of two pyruvate molecules to yield α-acetolactate. Inactivation of α-acetolactate decarboxylase (encoded by budA) resulted in α-acetolactate flowing into the valine pathway, which led to synthesis of isobutanol and 2-ketoisovalerate (a precursor of isobutanol). ldhA (lactate dehydrogenase) deletion further increased the isobutanol and 2-ketoisovalerate production. In the first step of this pathway, BudB (α-acetolactate synthase) was identified as responsible for most of the α-acetolactate synthesis. Complementation of ilvBN or ilvIH (isoenzymes of budB) both resulted in a remarkable increase in 2-ketoisovalerate production. Thus, α-acetolactate formation is the rate-limiting step of 2-ketoisovalerate production. ilvC (acetohydroxy acid isomeroreductase) and ilvD (dihydroxy acid dehydratase) were identified responsible for 2-ketoisovalerate synthesis from α-acetolactate. ipdC, which encodes an indole-3-pyruvate decarboxylase, was identified responsible for most of the isobutyraldehyde formation from 2-ketoisovalerate, and isobutanol production was increased 15.7 fold in the ipdC complementation strain, with a final titer of 2.45g/L. Isobutanol dehydrogenase activity is distributed across multiple alcohol dehydrogenase enzymes expressed by K. pneumoniae. BudC, DhaT, DhaD and YqhD all had isobutanol dehydrogenase activity in vitro. YqhD uses NADPH as the coenzyme, while the other dehydrogenases use NADH. However, inactivating one or two of these dehydrogenases had no effect on isobutanol production

  9. Isobutanol production from D-xylose by recombinant Saccharomyces cerevisiae.

    PubMed

    Brat, Dawid; Boles, Eckhard

    2013-03-01

    Simultaneous overexpression of an optimized, cytosolically localized valine biosynthesis pathway together with overexpression of xylose isomerase XylA from Clostridium phytofermentans, transaldolase Tal1 and xylulokinase Xks1 enabled recombinant Saccharomyces cerevisiae cells to complement the valine auxotrophy of ilv2,3,5 triple deletion mutants for growth on D-xylose as the sole carbon source. Moreover, after additional overexpression of ketoacid decarboxylase Aro10 and alcohol dehydrogenase Adh2, the cells were able to ferment D-xylose directly to isobutanol. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  10. Infrared Detector Array Test Program for the Kuiper Infrared Technology Experiment (KITE)

    DTIC Science & Technology

    1987-04-01

    3.179 2.990 3.017 2.733 2.787 2.775 2.477 2.778 2.877 2.814 2.883 2.940 B-10 Table B- R2a Rockwell BIBIB Array Background Run #2 (BG #2) AVERAGE COUNT...q0 pCA so p.4 t IV.0 a00 p. 4 p CIA .4 0 0 00 .P p.0 a 0 C4................ ....--.. !C IlV !. . . .. !. . . .. !.........0 91 W94 01V4 0 0 -WN 940 0

  11. I-129 Desorption from SRS Water Treatment Media from the Effluent Treatment Facility and the F-Area Groundwater Treatment Facility

    SciTech Connect

    Kaplan, D.I.

    2001-01-26

    The objective of this study was to quantify I-129 desorption of four waste materials and to provide reasonably conservative Kd values for modeling efforts. Since the ILV PA considers dose thousands of years in the future, additional attention was directed at evaluating how I-129 desorption changed as a function of time. The scope of this work involved evaluating four waste materials (F-WTU Dowex 21K, F-WTU Sludge, ETF Carbon, and ETF GT-73) under two aqueous conditions (acid rain and cement simulants) by two different experimental protocols (static batch and dynamic flow column experiments).

  12. National Dam Safety Program. Mach Lake Dam (MO 30133), Mississippi - Kaskaskia - St. Louis River Basin, Perry County, Missouri. Phase I Inspection Report.

    DTIC Science & Technology

    1981-04-01

    embankment was in fair condition. Deficiencies vilcuallv Ubse (rvrd by the inspection team were: (1) brUSh and briar ’rowth on upf [rem and~ rdownst-r-tm face...The slopes of the embankment were briar and )rush covered. Several ]is.. (12 to 15 inches diameter) tree stumps were noted on the upstream fare. No...perfriri ILV ai(n ~er~Me 0 in the construction of dams. (2) The slough area at midhei’Lht on rhe do)wustfre--ir fiS o Sa 1 (3) The briar and brush

  13. Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

    PubMed

    Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

    2016-03-22

    Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

  14. [Hernia surgeons of Scutari, Istanbul].

    PubMed

    Sahillioglu, H

    1998-01-01

    The Ottoman capital was constituted of four judicial regions (mevleviyet, molla kursusu): Istanbul (within the citywalls), Galata (the Roumelian side of Bosphorous from Kasimpasha to Rumelifeneri), Eyup (western bank of the Golden Horn and Scutari. Since one judicial court did not suffice for this spacious area, each region was subdivided into districts (niyabets) called Mamure and Cedide where a large collection of records registered chronologically were reserved at the law court archives. I have studied 168 judicial records of Scutari. Among them, a document with the record number of 139, attracted my attention because of its interesting content. In view of this document of the 17th century, a physician could not be blamed or legally responsible for a risky operation if the patient had given his consent in advance. In this case, the patient was a man called Yanni from Agriboz Island. He was suffering from inguinal hernia. The healer was a woman called Saliha Sultan binti Kupeli, a Coptic, who practiced as a surgeon. Since some risk is inherent in medical operations, a contract was made between the patient and the surgeon, while the consent was given in case of any legal actions for damages. Therefore the surgeon was in need of a guarantee which was to be stated in the contract and confirmed by the judge (kadi). This article gives examples of this kind of case.

  15. Recharge Data for the Islands of Kauai, Lanai and Molokai, Hawaii

    DOE Data Explorer

    Nicole Lautze

    2015-01-01

    Recharge data for the islands of Kauai, Lanai and Molokai in shapefile format. These data are from the following sources: Whittier, R.B and A.I. El-Kadi. 2014. Human Health and Environmental Risk Ranking of On-Site Sewage Disposal systems for the Hawaiian Islands of Kauai, Molokai, Maui, and Hawaii – Final, Prepared for Hawaii Dept. of Health, Safe Drinking Water Branch by the University of Hawaii, Dept. of Geology and Geophysics. (for Kauai, Lanai, Molokai). Shade, P.J., 1995, Water Budget for the Island of Kauai, Hawaii, USGS Water-Resources Investigations Report 95-4128, 25 p. (for Kauai). Izuka, S.K. and D.S. Oki, 2002 Numerical simulation of ground-water withdrawals in the Southern Lihue Basin, Kauai, Hawaii, U.S. Geologic Survey Water-Resources Investigations Report 01-4200, 52 pgs. (for Kauai). Hardy, W.R., 1996, A Numerical Groundwater Model for the Island of Lanai, Hawaii - CWRM Report No., CWRM-1, Commission on Water Resources Management, Department of Natural Resources, State of Hawaii, Honolulu, HI. (for Lanai). Oki, D.S., 1997, Geohydrology and numerical Simulation of the Ground-Water Flow System of Molokai, Hawaii, USGS Water-Resources Investigations Report 97-4176, 62 p. (for Molokai).

  16. Metabolic engineering of acetoin and meso-2, 3-butanediol biosynthesis in E. coli.

    PubMed

    Nielsen, David R; Yoon, Sang-Hwal; Yuan, Clara J; Prather, Kristala L J

    2010-03-01

    The functional reconstruction of acetoin and meso-2,3-butanediol (meso-2,3-BD) biosynthetic pathways in Escherichia coli have been explored systematically. Pathway construction involved the in vsivo screening of prospective pathway isozymes of yeast and bacterial origin. After substantial engineering of the host background to increase pyruvate availability, E. coli YYC202(DE3) ldhA(() ilvC( expressing ilvBN from E. coli and aldB from L. lactis (encoding acetolactate synthase and acetolactate decarboxylase activities, respectively) was able to produce up to 870 mg/L acetoin, with no coproduction of diacetyl observed. These strains were also found to produce small quantities of meso-2,3-BD, suggesting the existence of endogenous 2,3-BD dehydrogenase activity. Finally, the coexpression of bdh1 from S. cerevisiae, encoding 2,3-BD dehydrogenase, in this strain resulted in the production of up to 1120 mg/L meso-2,3-BD, with glucose a yield of 0.29 g/g. While disruption of the native lactate biosynthesis pathway increased pyruvate precursor availability to this strain, increased availability of NADH for acetoin reduction to meso-2,3-BD was found to be the most important consequence of ldhA deletion.

  17. System identification of closed-loop cardiovascular control mechanisms: diabetic autonomic neuropathy

    NASA Technical Reports Server (NTRS)

    Mukkamala, R.; Mathias, J. M.; Mullen, T. J.; Cohen, R. J.; Freeman, R.

    1999-01-01

    We applied cardiovascular system identification (CSI) to characterize closed-loop cardiovascular regulation in patients with diabetic autonomic neuropathy (DAN). The CSI method quantitatively analyzes beat-to-beat fluctuations in noninvasively measured heart rate, arterial blood pressure (ABP), and instantaneous lung volume (ILV) to characterize four physiological coupling mechanisms, two of which are autonomically mediated (the heart rate baroreflex and the coupling of respiration, measured in terms of ILV, to heart rate) and two of which are mechanically mediated (the coupling of ventricular contraction to the generation of the ABP wavelet and the coupling of respiration to ABP). We studied 37 control and 60 diabetic subjects who were classified as having minimal, moderate, or severe DAN on the basis of standard autonomic tests. The autonomically mediated couplings progressively decreased with increasing severity of DAN, whereas the mechanically mediated couplings were essentially unchanged. CSI identified differences between the minimal DAN and control groups, which were indistinguishable based on the standard autonomic tests. CSI may provide a powerful tool for assessing DAN.

  18. System identification of closed-loop cardiovascular control mechanisms: diabetic autonomic neuropathy

    NASA Technical Reports Server (NTRS)

    Mukkamala, R.; Mathias, J. M.; Mullen, T. J.; Cohen, R. J.; Freeman, R.

    1999-01-01

    We applied cardiovascular system identification (CSI) to characterize closed-loop cardiovascular regulation in patients with diabetic autonomic neuropathy (DAN). The CSI method quantitatively analyzes beat-to-beat fluctuations in noninvasively measured heart rate, arterial blood pressure (ABP), and instantaneous lung volume (ILV) to characterize four physiological coupling mechanisms, two of which are autonomically mediated (the heart rate baroreflex and the coupling of respiration, measured in terms of ILV, to heart rate) and two of which are mechanically mediated (the coupling of ventricular contraction to the generation of the ABP wavelet and the coupling of respiration to ABP). We studied 37 control and 60 diabetic subjects who were classified as having minimal, moderate, or severe DAN on the basis of standard autonomic tests. The autonomically mediated couplings progressively decreased with increasing severity of DAN, whereas the mechanically mediated couplings were essentially unchanged. CSI identified differences between the minimal DAN and control groups, which were indistinguishable based on the standard autonomic tests. CSI may provide a powerful tool for assessing DAN.

  19. Cargo-dependent degradation of ESCRT-I as a feedback mechanism to modulate endosomal sorting.

    PubMed

    Malerød, Lene; Pedersen, Nina Marie; Sem Wegner, Catherine Elisabeth; Lobert, Viola Hélène; Leithe, Edward; Brech, Andreas; Rivedal, Edgar; Liestøl, Knut; Stenmark, Harald

    2011-09-01

    Ligand-mediated lysosomal degradation of growth factor receptors, mediated by the endosomal sorting complex required for transport (ESCRT) machinery, is a mechanism that attenuates the cellular response to growth factors. In this article, we present a novel regulatory mechanism that involves ligand-mediated degradation of a key component of the sorting machinery itself. We have investigated the endosomal localization of subunits of the four ESCRTs-Hrs (ESCRT-0), Tsg101 (ESCRT-I), EAP30/Vps22 (ESCRT-II) and charged multivesicular body protein 3/Vps24 (ESCRT-III). All the components were detected on the limiting membrane of multivesicular endosomes (MVEs). Surprisingly, however, Tsg101 and other ESCRT-I subunits were also detected within intraluminal vesicles (ILVs) of MVEs. Tsg101 was sequestered along with cargo during endosomal sorting into ILVs and further degraded in lysosomes. Importantly, ESCRT-mediated downregulation of two distinct cargoes, epidermal growth factor receptor (EGFR) and connexin43, mutually made cells refractory to degradation of the other cargo. Our observations indicate that the degradation of a key ESCRT component along with cargo represents a novel feedback control of endosomal sorting by preventing collateral degradation of cell surface receptors following stimulation of one specific pathway.

  20. Branched-chain amino acid supplementation promotes aerobic growth of Salmonella Typhimurium under nitrosative stress conditions.

    PubMed

    Park, Yoon Mee; Lee, Hwa Jeong; Jeong, Jae-Ho; Kook, Joong-Ki; Choy, Hyon E; Hahn, Tae-Wook; Bang, Iel Soo

    2015-12-01

    Nitric oxide (NO) inactivates iron-sulfur enzymes in bacterial amino acid biosynthetic pathways, causing amino acid auxotrophy. We demonstrate that exogenous supplementation with branched-chain amino acids (BCAA) can restore the NO resistance of hmp mutant Salmonella Typhimurium lacking principal NO-metabolizing enzyme flavohemoglobin, and of mutants further lacking iron-sulfur enzymes dihydroxy-acid dehydratase (IlvD) and isopropylmalate isomerase (LeuCD) that are essential for BCAA biosynthesis, in an oxygen-dependent manner. BCAA supplementation did not affect the NO consumption rate of S. Typhimurium, suggesting the BCAA-promoted NO resistance independent of NO metabolism. BCAA supplementation also induced intracellular survival of ilvD and leuCD mutants at wild-type levels inside RAW 264.7 macrophages that produce constant amounts of NO regardless of varied supplemental BCAA concentrations. Our results suggest that the NO-induced BCAA auxotrophy of Salmonella, due to inactivation of iron-sulfur enzymes for BCAA biosynthesis, could be rescued by bacterial taking up exogenous BCAA available in oxic environments.

  1. ALIX binds a YPX(3)L motif of the GPCR PAR1 and mediates ubiquitin-independent ESCRT-III/MVB sorting.

    PubMed

    Dores, Michael R; Chen, Buxin; Lin, Huilan; Soh, Unice J K; Paing, May M; Montagne, William A; Meerloo, Timo; Trejo, JoAnn

    2012-04-30

    The sorting of signaling receptors to lysosomes is an essential regulatory process in mammalian cells. During degradation, receptors are modified with ubiquitin and sorted by endosomal sorting complex required for transport (ESCRT)-0, -I, -II, and -III complexes into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs). However, it remains unclear whether a single universal mechanism mediates MVB sorting of all receptors. We previously showed that protease-activated receptor 1 (PAR1), a G protein-coupled receptor (GPCR) for thrombin, is internalized after activation and sorted to lysosomes independent of ubiquitination and the ubiquitin-binding ESCRT components hepatocyte growth factor-regulated tyrosine kinase substrate and Tsg101. In this paper, we report that PAR1 sorted to ILVs of MVBs through an ESCRT-III-dependent pathway independent of ubiquitination. We further demonstrate that ALIX, a charged MVB protein 4-ESCRT-III interacting protein, bound to a YPX(3)L motif of PAR1 via its central V domain to mediate lysosomal degradation. This study reveals a novel MVB/lysosomal sorting pathway for signaling receptors that bypasses the requirement for ubiquitination and ubiquitin-binding ESCRTs and may be applicable to a subset of GPCRs containing YPX(n)L motifs.

  2. Remnants of an ancient pathway to L-phenylalanine and L-tyrosine in enteric bacteria: Evolutionary implications and biotechnological impact. [Escherichia coli; Salmonella typhimurium; Neurospora crassa

    SciTech Connect

    Bonner, C.A.; Fischer, R.S.; Ahmad, S.; Jensen, R.A. )

    1990-12-01

    The pathway construction for biosynthesis of aromatic amino acids in Escherichia coli is atypical of the phylogenetic subdivision of gram-negative bacteria to which it belongs. Related organisms possess second pathways to phenylalanine and tyrosine which depend upon the expression of a monofunctional chorismate mutase (CM-F) and cyclohexadienyl dehydratase (CDT). Some enteric bacteria, unlike E. coli, possess either CM-F or CDT. These essentially cryptic remnants of an ancestral pathway can be a latent source of biochemical potential under certain conditions. As one example of advantageous biochemical potential, the presence of CM-F in Salmonella typhimurium increases the capacity for prephenate accumulation in a tyrA auxotroph. We report the finding that a significant fraction of the latter prephenate is transaminated to L-arogenate. The tyrA19 mutant is now the organism of choice for isolation of L-arogenate, uncomplicated by the presence of other cyclohexadienyl products coaccumulated by a Neurospora crassa mutant that had previously served as the prime biological source of L-arogenate. Prephenate aminotransferase activity was not conferred by a discrete enzyme, but rather was found to be synonymous with the combined activities of aspartate aminotransferase (aspC), aromatic aminotransferase (tyrB), and branched-chain aminotransferase (ilvE).

  3. Engineering alternative isobutanol production platforms.

    PubMed

    Felpeto-Santero, Carmen; Rojas, Antonia; Tortajada, Marta; Galán, Beatriz; Ramón, Daniel; García, José L

    2015-12-01

    A synthetic inducible operon (IbPSO) expressing alsS, ilvC, ilvD and kivD genes encoding a pathway capable to transform pyruvate into 2-isobutyraldehyde has been designed and two recombinant plasmids named pIZIbPSO and p424IbPSO were constructed. The IbPSO containing plasmids can generate in a single transformation event new recombinant isobutanol producer strains and are useful for testing as suitable hosts wild type bacteria in different culture media. In this way we found that Shimwellia blattae (p424IbPSO) was able to produce in flasks up to 6 g l(-1) of isobutanol using glucose as carbon source. Moreover, for the first time, we have demonstrated that isobutanol can be produced from sucrose using Escherichia coli W (ATCC9367) transformed with pIZIbPSO. These robust recombinant strains were also able to produce isobutanol from a raw carbon source like hydrolysed lignocellulosic biomass.

  4. Engineering Corynebacterium glutamicum for isobutanol production.

    PubMed

    Smith, Kevin Michael; Cho, Kwang-Myung; Liao, James C

    2010-07-01

    The production of isobutanol in microorganisms has recently been achieved by harnessing the highly active 2-keto acid pathways. Since these 2-keto acids are precursors of amino acids, we aimed to construct an isobutanol production platform in Corynebacterium glutamicum, a well-known amino-acid-producing microorganism. Analysis of this host's sensitivity to isobutanol toxicity revealed that C. glutamicum shows an increased tolerance to isobutanol relative to Escherichia coli. Overexpression of alsS of Bacillus subtilis, ilvC and ilvD of C. glutamicum, kivd of Lactococcus lactis, and a native alcohol dehydrogenase, adhA, led to the production of 2.6 g/L isobutanol and 0.4 g/L 3-methyl-1-butanol in 48 h. In addition, other higher chain alcohols such as 1-propanol, 2-methyl-1-butanol, 1-butanol, and 2-phenylethanol were also detected as byproducts. Using longer-term batch cultures, isobutanol titers reached 4.0 g/L after 96 h with wild-type C. glutamicum as a host. Upon the inactivation of several genes to direct more carbon through the isobutanol pathway, we increased production by approximately 25% to 4.9 g/L isobutanol in a pycldh background. These results show promise in engineering C. glutamicum for higher chain alcohol production using the 2-keto acid pathways.

  5. Genotoxicity and antigenotoxicity evaluation of non-photoactivated hypericin.

    PubMed

    Miadokova, Eva; Chalupa, Ivan; Vlckova, Viera; Sevcovicova, Andrea; Nadova, Slavomira; Kopaskova, Marcela; Hercegova, Alena; Gasperova, Patricia; Alfoldiova, Lubica; Komjatiova, Monika; Csanyiova, Zuzana; Galova, Eliska; Cellarova, Eva; Vlcek, Daniel

    2010-01-01

    The potential genotoxicity and antigenotoxicity of non-photoactivated hypericin was investigated in five experimental models. Hypericin was non-mutagenic in the Ames assay, with and without metabolic activation. It did not exert a protective effect against mutagenicity induced by 9-aminoacridine. In a yeast (Saccharomyces cerevisiae) assay, hypericin did not increase the frequency of mitotic crossovers or total aberrants at the ade(2) locus, the number of convertants at the trp5 locus, or the number of revertants at the ilv1 locus. In combined application with 4-nitroquinoline-1-oxide, it significantly enhanced the number of revertants at the ilv1 locus at the highest concentration used. Hypericin was not mutagenic in the alga Chlamydomonas reinhardtii. However, in combined application with methyl methane sulfonate, toxicity and mutagenicity were slightly reduced. In a chromosome aberration assay using three mammalian cell lines, hypericin did not alter the frequency of structural chromosome aberrations, and in the DPPH radical scavenging assay, it did not exert any antioxidant effects.

  6. Crystal structures of RidA, an important enzyme for the prevention of toxic side products

    PubMed Central

    Liu, Xiwen; Zeng, Jianhua; Chen, Xiaolei; Xie, Wei

    2016-01-01

    The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5′-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants. PMID:27458092

  7. Functional analysis to identify genes in wine yeast adaptation to low-temperature fermentation.

    PubMed

    Salvadó, Z; Chiva, R; Rozès, N; Cordero-Otero, R; Guillamón, J M

    2012-07-01

      To identify genes and proteins involved in adaptation to low-temperature fermentations in a commercial wine yeast.   Nine proteins were identified as representing the most significant changes in proteomic maps during the first 24 h of fermentation at low (13°C) and standard temperature (25°C). These proteins were mainly involved in stress response and in glucose and nitrogen metabolism. Transcription analysis of the genes encoding most of these proteins within the same time frame of wine fermentation presented a good correlation with proteomic data. Knockout and overexpressing strains of some of these genes were constructed and tested to evaluate their ability to start the fermentation process. The strain overexpressing ILV5 improved its fermentation activity in the first hours of fermentation. This strain showed a quicker process of mitochondrial degeneration, an altered intracellular amino acid profile and laxer nitrogen catabolite repression regulation.   The proteomic and transcriptomic analysis is useful to detect key molecular adaptation mechanisms of biotechnological interest for industrial processes. ILV5 gene seems to be important in wine yeast adaptation to low-temperature fermentation.   This study provides information that might help improve the future performance of wine yeast, either by genetic modification or by adaptation during industrial production. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

  8. High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

    PubMed

    Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

    2014-07-01

    Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.

  9. AP-3 regulates PAR1 ubiquitin-independent MVB/lysosomal sorting via an ALIX-mediated pathway

    PubMed Central

    Dores, Michael R.; Paing, May M.; Lin, Huilan; Montagne, William A.; Marchese, Adriano; Trejo, JoAnn

    2012-01-01

    The sorting of signaling receptors within the endocytic system is important for appropriate cellular responses. After activation, receptors are trafficked to early endosomes and either recycled or sorted to lysosomes and degraded. Most receptors trafficked to lysosomes are modified with ubiquitin and recruited into an endosomal subdomain enriched in hepatocyte growth factor–regulated tyrosine kinase substrate (HRS), a ubiquitin-binding component of the endosomal-sorting complex required for transport (ESCRT) machinery, and then sorted into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs)/lysosomes. However, not all receptors use ubiquitin or the canonical ESCRT machinery to sort to MVBs/lysosomes. This is exemplified by protease-activated receptor-1 (PAR1), a G protein–coupled receptor for thrombin, which sorts to lysosomes independent of ubiquitination and HRS. We recently showed that the adaptor protein ALIX binds to PAR1, recruits ESCRT-III, and mediates receptor sorting to ILVs of MVBs. However, the mechanism that initiates PAR1 sorting at the early endosome is not known. We now report that the adaptor protein complex-3 (AP-3) regulates PAR1 ubiquitin-independent sorting to MVBs through an ALIX-dependent pathway. AP-3 binds to a PAR1 cytoplasmic tail–localized tyrosine-based motif and mediates PAR1 lysosomal degradation independent of ubiquitination. Moreover, AP-3 facilitates PAR1 interaction with ALIX, suggesting that AP-3 functions before PAR1 engagement of ALIX and MVB/lysosomal sorting. PMID:22833563

  10. GPCR sorting at multivesicular endosomes.

    PubMed

    Dores, Michael Robert; Trejo, JoAnn

    2015-01-01

    The lysosomal degradation of G protein-coupled receptors (GPCRs) is essential for receptor signaling and down regulation. Once internalized, GPCRs are sorted within the endocytic pathway and packaged into intraluminal vesicles (ILVs) that bud inward to form the multivesicular endosome (MVE). The mechanisms that control GPCR sorting and ILV formation are poorly understood. Quantitative strategies are important for evaluating the function of adaptor and scaffold proteins that regulate sorting of GPCRs at MVEs. In this chapter, we outline two strategies for the quantification and visualization of GPCR sorting into the lumen of MVEs. The first protocol utilizes a biochemical approach to assay the sorting of GPCRs in a population of cells, whereas the second strategy examines GPCR sorting in individual cells using immunofluorescence confocal microscopy. Combined, these assays can be used to establish the kinetics of activated GPCR lysosomal trafficking in response to specific ligands, as well as evaluate the contribution of endosomal adaptors to GPCR sorting at MVEs. The protocols presented in this chapter can be adapted to analyze GPCR sorting in a myriad of cell types and tissues, and expanded to analyze the mechanisms that regulate MVE sorting of other cargoes.

  11. Production of 2-methyl-1-butanol and 3-methyl-1-butanol in engineered Corynebacterium glutamicum.

    PubMed

    Vogt, Michael; Brüsseler, Christian; Ooyen, Jan van; Bott, Michael; Marienhagen, Jan

    2016-11-01

    The pentanol isomers 2-methyl-1-butanol and 3-methyl-1-butanol represent commercially interesting alcohols due to their potential application as biofuels. For a sustainable microbial production of these compounds, Corynebacterium glutamicum was engineered for producing 2-methyl-1-butanol and 3-methyl-1-butanol via the Ehrlich pathway from 2-keto-3-methylvalerate and 2-ketoisocaproate, respectively. In addition to an already available 2-ketoisocaproate producer, a 2-keto-3-methylvalerate accumulating C. glutamicum strain was also constructed. For this purpose, we reduced the activity of the branched-chain amino acid transaminase in an available C. glutamicuml-isoleucine producer (K2P55) via a start codon exchange in the ilvE gene enabling accumulation of up to 3.67g/l 2-keto-3-methylvalerate. Subsequently, nine strains expressing different gene combinations for three 2-keto acid decarboxylases and three alcohol dehydrogenases were constructed and characterized. The best strains accumulated 0.37g/l 2-methyl-1-butanol and 2.76g/l 3-methyl-1-butanol in defined medium within 48h under oxygen deprivation conditions, making these strains ideal candidates for additional strain and process optimization.

  12. Production of 2-methyl-1-butanol in engineered Escherichia coli.

    PubMed

    Cann, Anthony F; Liao, James C

    2008-11-01

    Recent progress has been made in the production of higher alcohols by harnessing the power of natural amino acid biosynthetic pathways. Here, we describe the first strain of Escherichia coli developed to produce the higher alcohol and potential new biofuel 2-methyl-1-butanol (2MB). To accomplish this, we explored the biodiversity of enzymes catalyzing key parts of the isoleucine biosynthetic pathway, finding that AHAS II (ilvGM) from Salmonella typhimurium and threonine deaminase (ilvA) from Corynebacterium glutamicum improve 2MB production the most. Overexpression of the native threonine biosynthetic operon (thrABC) on plasmid without the native transcription regulation also improved 2MB production in E. coli. Finally, we knocked out competing pathways upstream of threonine production (DeltametA, Deltatdh) to increase its availability for further improvement of 2MB production. This work led to a strain of E. coli that produces 1.25 g/L 2MB in 24 h, a total alcohol content of 3 g/L, and with yields of up to 0.17 g 2MB/g glucose.

  13. Characterization of hybrid plasmids carrying individual ribosomal ribonucleic acid transcription units of Escherichia coli.

    PubMed Central

    Kenerley, M E; Morgan, E A; Post, L; Lindahl, L; Nomura, M

    1977-01-01

    We have screened the strains with ColE1 hybrid plasmids constructed by Clarke and Carbon (Cell 9:91-99, 1976) for the presence of ribosomal ribonucleic acid (rRNA) genes on the plasmids and identified 16 strains whose plasmids carry rRNA genes. The structures of these 16 plasmids were compared by heteroduplex analysis, and the plasmids were classified into six groups on the basis of their chromosomal origins. Homology with known transducing-phage deoxyribonucleic acids and genetic mapping have assigned locations on the Escherichia coli chromosome to three of the six groups. These are rrnB near rif at 88 min, rrnC near ilvE at 83 min, and rrnD near aroE at 71 min. A fourth group is probably rrnA at 85 min (T. Ikemura and M. Nomura, Cell, 11:779-793, 1977). We conclude that the minimum number of rRNA transcription units per haploid chromosomes is seven, that is, the six groups identified in this work plus a known operon (rrnE near metA at 89 min) that we failed to find among the hybrid plasmids. This heteroduplex analysis also suggests that there are only two kinds of rRNA operons with respect to their spacer region; three of the six rRNA operon groups studied here have one kind, whereas the remaining three have the other kind. Images PMID:336613

  14. Proteins involved in wine aroma compounds metabolism by a Saccharomyces cerevisiae flor-velum yeast strain grown in two conditions.

    PubMed

    Moreno-García, Jaime; García-Martínez, Teresa; Millán, M Carmen; Mauricio, Juan Carlos; Moreno, Juan

    2015-10-01

    A proteomic and exometabolomic study was conducted on Saccharomyces cerevisiae flor yeast strain growing under biofilm formation condition (BFC) with ethanol and glycerol as carbon sources and results were compared with those obtained under no biofilm formation condition (NBFC) containing glucose as carbon source. By using modern techniques, OFFGEL fractionator and LTQ-Orbitrap for proteome and SBSE-TD-GC-MS for metabolite analysis, we quantified 84 proteins including 33 directly involved in the metabolism of glycerol, ethanol and 17 aroma compounds. Contents in acetaldehyde, acetic acid, decanoic acid, 1,1-diethoxyethane, benzaldehyde and 2-phenethyl acetate, changed above their odor thresholds under BFC, and those of decanoic acid, ethyl octanoate, ethyl decanoate and isoamyl acetate under NBFC. Of the twenty proteins involved in the metabolism of ethanol, acetaldehyde, acetoin, 2,3-butanediol, 1,1-diethoxyethane, benzaldehyde, organic acids and ethyl esters, only Adh2p, Ald4p, Cys4p, Fas3p, Met2p and Plb1p were detected under BFC and as many Acs2p, Ald3p, Cem1p, Ilv2p, Ilv6p and Pox1p, only under NBFC. Of the eight proteins involved in glycerol metabolism, Gut2p was detected only under BFC while Pgs1p and Rhr2p were under NBFC. Finally, of the five proteins involved in the metabolism of higher alcohols, Thi3p was present under BFC, and Aro8p and Bat2p were under NBFC.

  15. RAZOR EX anthrax air detection system.

    PubMed

    Spaulding, Usha K; Christensen, Clarissa J; Crisp, Robert J; Vaughn, Michael B; Trauscht, Robert C; Gardner, Jordan R; Thatcher, Stephanie A; Clemens, Kristine M; Teng, David H F; Bird, Abigail; Ota, Irene M; Hadfield, Ted; Ryan, Valorie; Brunelle, Sharon L

    2012-01-01

    The RAZOR EX Anthrax Air Detection System, developed by Idaho Technology, Inc. (ITI), is a qualitative method for the detection of Bacillus anthracis spores collected by air collection devices. This system comprises a DNA extraction kit, a freeze-dried PCR reagent pouch, and the RAZOR EX real-time PCR instrument. Each pouch contains three assays, which distinguish potentially virulent B. anthracis from avirulent B. anthracis and other Bacillus species. These assays target the pXO1 and pXO2 plasmids and chromosomal DNA. When all targets are detected, the instrument makes an "anthrax detected" call, meaning that virulence genes of the anthrax bacillus are present. This report describes results from AOAC Method Developer (MD) and Independent Laboratory Validation (ILV) studies, which include matrix, inclusivity/exclusivity, environmental interference, upper and lower LOD of DNA, robustness, product consistency and stability, and instrument variation testing. In the MD studies, the system met the acceptance criteria for sensitivity and specificity, and the performance was consistent, stable, and robust for all components of the system. For the matrix study, the acceptance criteria of 95/96 expected calls was met for three of four matrixes, clean dry filters being the exception. Ninety-four of the 96 clean dry filter samples tested gave the expected calls. The nucleic acid limit of detection was 5-fold lower than AOAC's acceptable minimum detection limit. The system demonstrated no tendency for false positives when tested with Bacillus cereus. Environmental substances did not inhibit accurate detection of B. anthracis. The ILV studies yielded similar results for the matrix and inclusivity/exclusivity studies. The ILV environmental interference study included environmental substances and environmental organisms. Subsoil at a high concentration was found to negatively interfere with the pXO1 reaction. No interference was observed from the environmental organisms. The

  16. Acoustic Gravity Waves Generated by an Oscillating Ice Sheet in Arctic Zone

    NASA Astrophysics Data System (ADS)

    Abdolali, A.; Kadri, U.; Kirby, J. T., Jr.

    2016-12-01

    We investigate the formation of acoustic-gravity waves due to oscillations of large ice blocks, possibly triggered by atmospheric and ocean currents, ice block shrinkage or storms and ice-quakes.For the idealized case of a homogeneous weakly compressible water bounded at the surface by ice sheet and a rigid bed, the description of the infinite family of acoustic modes is characterized by the water depth h and angular frequency of oscillating ice sheet ω ; The acoustic wave field is governed by the leading mode given by: Nmax=\\floor {(ω h)/(π c)} where c is the sound speed in water and the special brackets represent the floor function (Fig1). Unlike the free-surface setting, the higher acoustic modes might exhibit a larger contribution and therefore all progressive acoustic modes have to be considered.This study focuses on the characteristics of acoustic-gravity waves generated by an oscillating elastic ice sheet in a weakly compressible fluid coupled with a free surface model [Abdolali et al. 2015] representing shrinking ice blocks in realistic sea state, where the randomly oriented ice sheets cause inter modal transition and multidirectional reflections. A theoretical solution and a 3D numerical model have been developed for the study purposes. The model is first validated against the theoretical solution [Kadri, 2016]. To overcome the computational difficulties of 3D models, we derive a depth-integrated equation valid for spatially varying ice sheet thickness and water depth. We show that the generated acoustic-gravity waves contribute significantly to deep ocean currents compared to other mechanisms. In addition, these waves travel at the sound speed in water carrying information on ice sheet motion, providing various implications for ocean monitoring and detection of ice-quakes. Fig1:Snapshots of dynamic pressure given by an oscillating ice sheet; h=4500m, c=1500m/s, semi-length b=10km, ζ =1m, omega=π rad/s. Abdolali, A., Kirby, J. T. and Bellotti, G

  17. Sulfometuron resistance as a genetic marker for yeast populations in wine fermentations.

    PubMed

    Ambrona, Jesús; Maqueda, Matilde; Zamora, Emiliano; Ramírez, Manuel

    2005-09-21

    Winemaking with selected yeasts requires simple and cheap techniques to monitor the yeast population dynamics. We obtained new sulfometuron (smr) resistant mutants, easy to detect by replica-plate assay, from selected wine yeasts. The mutations were dominant and were located at the ilv2 locus that encodes for acetolactate synthase enzyme. The mutants were genetically stable and maintained the killer phenotype of the parent yeast strain. They were genetically improved by elimination of recessive growth-retarding alleles followed by spore clone selection according to the must fermentation kinetics and the organoleptic quality of the wine. Some mutants were tested in industrial winemaking and were easily monitored during must fermentation using a simple plate assay. They accounted for more than 95% of the total yeasts in the must, and the resulting wine had as good a quality as those made with standard commercial wine yeasts.

  18. Diacetyl and acetoin production from whey permeate using engineered Lactobacillus casei.

    PubMed

    Nadal, Inmaculada; Rico, Juan; Pérez-Martínez, Gaspar; Yebra, María J; Monedero, Vicente

    2009-09-01

    The capability of Lactobacillus casei to produce the flavor-related compounds diacetyl and acetoin from whey permeate has been examined by a metabolic engineering approach. An L. casei strain in which the ilvBN genes from Lactococcus lactis, encoding acetohydroxyacid synthase, were expressed from the lactose operon was mutated in the lactate dehydrogenase gene (ldh) and in the pdhC gene, which codes for the E2 subunit of the pyruvate dehydrogenase complex. The introduction of these mutations resulted in an increased capacity to synthesize diacetyl/acetoin from lactose in whey permeate (1,400 mg/l at pH 5.5). The results showed that L. casei can be manipulated to synthesize added-value metabolites from dairy industry by-products.

  19. dnaA acts before dnaC in the initiation of DNA replication.

    PubMed Central

    Kung, F C; Glaser, D A

    1978-01-01

    We constructed a double mutant of Escherichia coli K-12 carrying dnaA(Ts) and dnaC(Cs) lesions. In this mutant DNA synthesis proeceeds normally at 32 degrees C and initiation is inhibited at both 41 and 20 degrees C. By shifting this culture grown at 32 degrees C to the two restrictive temperatures in different time sequences and assaying protein and DNA synthesis of cells growing at different temperatures, we found that dnaA and dnaC genes work independently with dnaA acting before dnaC. While preparing special strains for this work, we also showed that the order of genes in the neighborhood of dnaA is dnaA-tnaA-phoS-ilv. PMID:627535

  20. Role of the host cell in bacteriophage T4 development. II. Characterization of host mutants that have pleiotropic effects on T4 growth.

    PubMed Central

    Stitt, B L; Revel, H R; Lielausis, I; Wood, W B

    1980-01-01

    Mutant host-defective Escherichi coli that fail to propagate bacteriophage T4 and have a pleiotropic effect on T4 development have been isolated and characterized. In phage-infected mutant cells, specific early phage proteins are absent or reduced in amount, phage DNA synthesis is depressed by about 50%, specific structural phage proteins, including some tail and collar components, are deficient or missing, and host-cell lysis is delayed and slow. Almost all phage that can overcome the host block carry mutantions that map in functionally undefined 'nonessential' regions of the T4 genome, most near gene 39. The mutant host strains are temperature sensitive for growth and show simultaneous reversion of the ts phenotype and the inability to propagate T4+. The host mutations are cotransduced with ilv (83 min) and may lie in the gene for transcription termination factor rho. Images PMID:6999171

  1. Topics in Optical Materials and Device Research - II. Volume I.

    DTIC Science & Technology

    1982-01-01

    O & K1 v~~ o I T (, d T o -) a ( ,28L) 00t f jv C’i 6 a. a a.( yo V-1 r I 41rc (cra𔃻A eI- TI Il(v \\J) T21f TV */ o ,)vL Tc& 2~ IP LO/ Y.& ( Cr ...Region" Electron Lett. 14, pp 345-347 (1978). 4. K. Aoyama and J. Minowa "Low-Loss Optical Demultiplexer for WDM Systems in the O .8-pm Wavelength...rsnlzoeplt 41 TRASPAENTPHASE~r SHIFTING ZONES 00r Fig. 2 Phase reversal Fresnel zone plate d zn is the refractive index. 42 Fig. 3 Blazed Fresnel

  2. HUGO (Hydrographic Upgrade to Oceanis) Software Modules: User’s Maintenance Manuals

    DTIC Science & Technology

    1989-02-01

    DBMS. PROMPTS ACCEPTABLE RESPONSES SHIP NAME ? H OR C PRIMARY SHEET NUMBER? A two digit number (0-99) SECONDARY SHEET ID? One character (A- Z ) PLATFORM...0 19 47 S 2842 2850 8 5 50 41 E 0 19 45 S 2853 2853 0 Table 3.3.1 Ship Track Crossing Points 12 I I 3 CIO- ( C-I C- l ! ,, -. - ,4, C . * il i ’ Z ...U U U /c w -O cc m I 0 m S~~~~~~ ~ ~ ~ ~ itt i Sc S9Sf -Jiiu Fiue2.DPH OTUS LTTDA HL mm C I _ I,__ 3 -~ -~~ Z - ILV .= t Figure 2b. DEPTH CONTOURS

  3. Activation of satellite cells and the regeneration of human skeletal muscle are expedited by ingestion of nonsteroidal anti-inflammatory medication

    PubMed Central

    Mackey, Abigail L.; Rasmussen, Lotte K.; Kadi, Fawzi; Schjerling, Peter; Helmark, Ida C.; Ponsot, Elodie; Aagaard, Per; Durigan, João Luiz Q.; Kjaer, Michael

    2016-01-01

    With this study we investigated the role of nonsteroidal anti-inflammatory drugs (NSAIDs) in human skeletal muscle regeneration. Young men ingested NSAID [1200 mg/d ibuprofen (IBU)] or placebo (PLA) daily for 2 wk before and 4 wk after an electrical stimulation–induced injury to the leg extensor muscles of one leg. Muscle biopsies were collected from the vastus lateralis muscles before and after stimulation (2.5 h and 2, 7, and 30 d) and were assessed for satellite cells and regeneration by immunohistochemistry and real-time RT-PCR, and we also measured telomere length. After injury, and compared with PLA, IBU was found to augment the proportion of ActiveNotch1+ satellite cells at 2 d [IBU, 29 ± 3% vs. PLA, 19 ± 2% (means ± sem)], satellite cell content at 7 d [IBU, 0.16 ± 0.01 vs. PLA, 0.12 ± 0.01 (Pax7+ cells/fiber)], and to expedite muscle repair at 30 d. The PLA group displayed a greater proportion of embryonic myosin+ fibers and a residual ∼2-fold increase in mRNA levels of matrix proteins (all P < 0.05). Endomysial collagen was also elevated with PLA at 30 d. Minimum telomere length shortening was not observed. In conclusion, ingestion of NSAID has a potentiating effect on Notch activation of satellite cells and muscle remodeling during large-scale regeneration of injured human skeletal muscle.—Mackey, A. L., Rasmussen, L. K., Kadi, F., Schjerling, P., Helmark, I. C., Ponsot, E., Aagaard, P., Durigan, J. L. Q., Kjaer, M. Activation of satellite cells and the regeneration of human skeletal muscle are expedited by ingestion of nonsteroidal anti-inflammatory medication. PMID:26936358

  4. Ultraviolet-Sensitive Mutator Strain of Escherichia coli K-12

    PubMed Central

    Siegel, Eli C.

    1973-01-01

    An ultraviolet (UV)-sensitive mutator gene, mutU, was identified in Escherichia coli K-12. The mutation mutU4 is very close to uvrD, between metE and ilv, on the E. coli chromosome. It was recessive as a mutator and as a UV-sensitive mutation. The frequency of reversion of trpA46 on an F episome was increased by mutU4 on the chromosome. The mutator gene did not increase mutation frequencies in virulent phages or in lytically grown phage λ. The mutU4 mutation predominantly induced transitional base changes. Mutator strains were normal for recombination and host-cell reactivation of UV-irradiated phage T1. They were normally resistant to methyl methanesulfonate and were slightly more sensitive to gamma irradiation than Mut+ strains. UV irradiation induced mutations in a mutU4 strain, and phage λ was UV-inducible. Double mutants containing mutU4 and recA, B, or C were extremely sensitive to UV irradiation; a mutU4 uvrA6 double mutant was only slightly more sensitive than a uvrA6 strain. The mutU4 uvrA6 and mutU4 recA, B, or C double mutants had mutation rates similar to that of a mutU4 strain. Two UV-sensitive mutators, mut-9 and mut-10, isolated by Liberfarb and Bryson in E. coli B/UV, were found to be co-transducible with ilv in the same general region as mutU4. PMID:4345920

  5. Delineating bacteriostatic and bactericidal targets in mycobacteria using IPTG inducible antisense expression.

    PubMed

    Kaur, Parvinder; Agarwal, Saurabh; Datta, Santanu

    2009-06-15

    In order to identify novel high value antibacterial targets it is desirable to delineate whether the inactivation of the target enzyme will lead to bacterial death or stasis. This knowledge is particularly important in slow growing organisms, like mycobacteria, where most of the viable anti-tubercular agents are bactericidal. A bactericidal target can be identified through the conditional deletion or inactivation of the target gene at a relatively high cell number and subsequently following the time course of survival for the bacteria. A simple protocol to execute conditional inactivation of a gene is by antisense expression. We have developed a mycobacteria specific IPTG inducible vector system and monitored the effect of antisense inhibition of several known essential genes in mycobacteria by following their survival kinetics. By this method, we could differentiate between genes whose down regulation lead to bacteriostatic or bactericidal effect. Targets for standard anti-tubercular drugs like inhA for isoniazid, rpoB and C for rifampicin, and gyr A/B for flouroquinolones were shown to be bactericidal. In contrast targets like FtsZ behaved in a bacteriostatic manner. Induction of antisense expression in embB and ribosomal RNA genes, viz., rplJ and rpsL showed only a marginal growth inhibition. The specificity of the antisense inhibition was conclusively shown in the case of auxotrophic gene ilvB. The bactericidal activity following antisense expression of ilvB was completely reversed when the growth media was supplemented with the isoleucine, leucine, valine and pantothenate. Additionally, under these conditions the expression of several genes in branched chain amino acid pathway was severely suppressed indicating targeted gene inactivation.

  6. Delineating Bacteriostatic and Bactericidal Targets in Mycobacteria Using IPTG Inducible Antisense Expression

    PubMed Central

    Kaur, Parvinder; Agarwal, Saurabh; Datta, Santanu

    2009-01-01

    In order to identify novel high value antibacterial targets it is desirable to delineate whether the inactivation of the target enzyme will lead to bacterial death or stasis. This knowledge is particularly important in slow growing organisms, like mycobacteria, where most of the viable anti-tubercular agents are bactericidal. A bactericidal target can be identified through the conditional deletion or inactivation of the target gene at a relatively high cell number and subsequently following the time course of survival for the bacteria. A simple protocol to execute conditional inactivation of a gene is by antisense expression. We have developed a mycobacteria specific IPTG inducible vector system and monitored the effect of antisense inhibition of several known essential genes in mycobacteria by following their survival kinetics. By this method, we could differentiate between genes whose down regulation lead to bacteriostatic or bactericidal effect. Targets for standard anti-tubercular drugs like inhA for isoniazid, rpoB and C for rifampicin, and gyr A/B for flouroquinolones were shown to be bactericidal. In contrast targets like FtsZ behaved in a bacteriostatic manner. Induction of antisense expression in embB and ribosomal RNA genes, viz., rplJ and rpsL showed only a marginal growth inhibition. The specificity of the antisense inhibition was conclusively shown in the case of auxotrophic gene ilvB. The bactericidal activity following antisense expression of ilvB was completely reversed when the growth media was supplemented with the isoleucine, leucine, valine and pantothenate. Additionally, under these conditions the expression of several genes in branched chain amino acid pathway was severely suppressed indicating targeted gene inactivation. PMID:19526063

  7. Construction of amylolytic industrial brewing yeast strain with high glutathione content for manufacturing beer with improved anti-staling capability and flavor.

    PubMed

    Wang, Jinjing; Wang, Zhao-Yue; He, Xiu-Ping; Zhang, Bo-Run

    2010-11-01

    Glutathione in beer works as the main antioxidant compounds which correlates with beer flavor stability. High residual sugars in beer contribute to major non-volatile components which correlate to high caloric content. In this work, Saccharomyces cerevisiae GSH1 gene encoding glutamylcysteine synthetase and Scharomycopsis fibuligera ALP1 gene encoding alpha-amylase were co-expressed in industrial brewing yeast strain Y31 targeting at alpha-acetolactate synthase (AHAS) gene (ILV2) and alcohol dehydrogenase gene (ADH2), and new recombinant strain TY3 was constructed. The glutathione content from the fermentation broth of TY3 increased to 43.83 mg/l compared to 33.34 mg/l from Y31. The recombinant strain showed high alpha-amylase activity and utilized more than 46% of starch after 5 days growing on starch as sole carbon source. European Brewery Convention tube fermentation tests comparing the fermentation broth of TY3 and Y31 showed that the flavor stability index increased to 1.3 fold and residual sugar concentration were reduced by 76.8%, respectively. Due to the interruption of ILV2 gene and ADH2 gene, the amounts of off-flavor compounds diacetyl and acetaldehyde were reduced by 56.93% and 31.25%, comparing with the amounts of these from Y31 fermentation broth. In addition, as no drug-resistance genes were introduced to new recombinant strain, consequently, it should be more suitable for use in beer industry because of its better flavor stability and other beneficial characteristics.

  8. The Neutral Sphingomyelinase Pathway Regulates Packaging of the Prion Protein into Exosomes*

    PubMed Central

    Guo, Belinda B.; Bellingham, Shayne A.; Hill, Andrew F.

    2015-01-01

    Prion diseases are a group of transmissible, fatal neurodegenerative disorders associated with the misfolding of the host-encoded prion protein, PrPC, into a disease-associated form, PrPSc. The transmissible prion agent is principally formed of PrPSc itself and is associated with extracellular vesicles known as exosomes. Exosomes are released from cells both in vitro and in vivo, and have been proposed as a mechanism by which prions spread intercellularly. The biogenesis of exosomes occurs within the endosomal system, through formation of intraluminal vesicles (ILVs), which are subsequently released from cells as exosomes. ILV formation is known to be regulated by the endosomal sorting complexes required for transport (ESCRT) machinery, although an alternative neutral sphingomyelinase (nSMase) pathway has been suggested to also regulate this process. Here, we investigate a role for the nSMase pathway in exosome biogenesis and packaging of PrP into these vesicles. Inhibition of the nSMase pathway using GW4869 revealed a role for the nSMase pathway in both exosome formation and PrP packaging. In agreement, targeted knockdown of nSMase1 and nSMase2 in mouse neurons using lentivirus-mediated RNAi also decreases exosome release, demonstrating the nSMase pathway regulates the biogenesis and release of exosomes. We also demonstrate that PrPC packaging is dependent on nSMase2, whereas the packaging of disease-associated PrPSc into exosomes occurs independently of nSMase2. These findings provide further insight into prion transmission and identify a pathway which directly assists exosome-mediated transmission of prions. PMID:25505180

  9. Covalent structure of biodegradative threonine dehydratase of Escherichia coli: homology with other dehydratases.

    PubMed

    Datta, P; Goss, T J; Omnaas, J R; Patil, R V

    1987-01-01

    The 987-base-pair coding region of the tdc gene of Escherichia coli K-12 encoding biodegradative threonine dehydratase [Tdc; L-threonine hydro-lyase (deaminating), EC 4.2.1.16], previously cloned in this laboratory, was sequenced. The deduced polypeptide consists of 329 amino acid residues with a calculated Mr of 35,238. Although the purified enzyme was shown to contain tryptophan, no tryptophan codon was found in the tdc reading frame. Incubation of purified Tdc with [14C]tryptophan revealed apparent "covalent" binding of tryptophan, indicating posttranslational modification of the enzyme. A heptapeptide, 54Thr-55Gly-56Ser-57Phe-58Lys-59Ile- 60Arg, was found to contain Lys-58, which binds pyridoxal phosphate coenzyme. A comparison of amino acid sequences between the Tdc polypeptide and the biosynthetic threonine dehydratases of yeast (encoded by ILV1) and E. coli (encoded by ilvA) and the E. coli D-serine dehydratase (DsdA, encoded by dsdA) revealed various extents of homology: five domains of the Tdc polypeptide were 63-93% homologous with the yeast enzyme, and three of these same regions were 80% homologous with the biosynthetic E. coli dehydratase; two different domains showed 67% and 83% homology with DsdA. In addition, two other sequences were highly conserved in all four proteins, one of which was shown to contain the conserved lysine residue that binds pyridoxal phosphate in the Tdc and DsdA polypeptides. These observations suggest that, despite their diverse origin and metabolic significance, these enzymes may have evolved from a common ancestral protein.

  10. Covalent structure of biodegradative threonine dehydratase of Escherichia coli: homology with other dehydratases.

    PubMed Central

    Datta, P; Goss, T J; Omnaas, J R; Patil, R V

    1987-01-01

    The 987-base-pair coding region of the tdc gene of Escherichia coli K-12 encoding biodegradative threonine dehydratase [Tdc; L-threonine hydro-lyase (deaminating), EC 4.2.1.16], previously cloned in this laboratory, was sequenced. The deduced polypeptide consists of 329 amino acid residues with a calculated Mr of 35,238. Although the purified enzyme was shown to contain tryptophan, no tryptophan codon was found in the tdc reading frame. Incubation of purified Tdc with [14C]tryptophan revealed apparent "covalent" binding of tryptophan, indicating posttranslational modification of the enzyme. A heptapeptide, 54Thr-55Gly-56Ser-57Phe-58Lys-59Ile- 60Arg, was found to contain Lys-58, which binds pyridoxal phosphate coenzyme. A comparison of amino acid sequences between the Tdc polypeptide and the biosynthetic threonine dehydratases of yeast (encoded by ILV1) and E. coli (encoded by ilvA) and the E. coli D-serine dehydratase (DsdA, encoded by dsdA) revealed various extents of homology: five domains of the Tdc polypeptide were 63-93% homologous with the yeast enzyme, and three of these same regions were 80% homologous with the biosynthetic E. coli dehydratase; two different domains showed 67% and 83% homology with DsdA. In addition, two other sequences were highly conserved in all four proteins, one of which was shown to contain the conserved lysine residue that binds pyridoxal phosphate in the Tdc and DsdA polypeptides. These observations suggest that, despite their diverse origin and metabolic significance, these enzymes may have evolved from a common ancestral protein. PMID:3540965

  11. F'-plasmid transfer from Escherichia coli to Pseudomonas fluorescens.

    PubMed Central

    Mergeay, M; Gerits, J

    1978-01-01

    Various F' plasmids of Escherichia coli K-12 could be transferred into mutants of the soil strain 6.2, classified herein as a Pseudomonas fluorescens biotype IV. This strain was previously found to receive Flac plasmid (N. Datta and R.W. Hedges, J. Gen Microbiol. 70:453-460, 1972). ilv, leu, met, arg, and his auxotrophs were complemented by plasmids carrying isofunctional genes; trp mutants were not complemented or were very poorly complemented. The frequency of transfer was 10(-5). Subsequent transfer into other P. fluorescens recipients was of the same order of magnitude. Some transconjugants were unable to act as donors, and these did not lose the received information if subcultured on nonselective media. Use of F' plasmids helped to discriminate metabolic blocks in P. fluorescens. In particular, metA, metB, and argH mutants were so distinguished. In addition, F131 plasmid carrying the his operon and a supD mutation could partially relieve the auxotrophy of thr, ilv, and metA13 mutants, suggesting functional expression of E. coli tRNA in P. fluorescens. In P. fluorescens metA Rifr mutants carrying the F110 plasmid, which carried the E. coli metA gene and the E. coli rifs allele, sensitivity to rifampin was found to be dominant at least temporarily over resistance. This suggests interaction of E. coli and P. fluorescens subunits of RNA polymerase. his mutations were also complemented by composite P plasmids containing the his-nif region of Klebsiella pneumoniae (plasmids FN68 and RP41). nif expression could be detected by acetylene reduction in some his+ transconjugants. The frequency of transfer of these P plasmids was 5 X 10(-4). PMID:97267

  12. Proteomics of FACS-sorted heterogeneous Corynebacterium glutamicum populations.

    PubMed

    Harst, Andreas; Albaum, Stefan P; Bojarzyn, Tanja; Trötschel, Christian; Poetsch, Ansgar

    2017-05-08

    The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS. A proteomics workflow optimized for small cell numbers was used to quantitatively compare proteomes of a ΔaceE mutant, lacking functional pyruvate dehydrogenase (PD), and the wild type. About 800 proteins could be quantified from 1,000,000 cells. In the ΔaceE mutant BCAA production was coordinated with upregulation of the glyoxylate cycle and TCA cycle to counter the lack of acetyl CoA resulting from the deletion of aceE. Metabolic pathways in C. glutamicum WT and ΔaceE, devoid of functional pyruvate dehydrogenase, were compared to understand proteome changes that contribute to the high production of branched chain amino acids (BCAA) in the ΔaceE strain. The data complements previous metabolome studies and corroborates the role of malate provided by the glyoxylate cycle and increased activity of glycolysis and pyruvate carboxylase reaction to replenish the TCA cycle. A slight increase in acetohydroxyacid synthase (ILV subunit B) substantiates the previously reported increased pyruvate pool in C. glutamicumΔaceE, and the benefit of additional ilv gene cluster overexpression for BCAA production. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. [System metabolic engineering strategies for 2,3-butandione production by Torulopsis glabrata].

    PubMed

    Gao, Xiang; Xu, Nan; Li, Shubo; Liu, Liming

    2014-04-04

    We regulated the carbon flux distribution of Torulopsis glabrata CCTCC M202019, an efficient pyruvate-producing microorganism, for improved 2, 3-butandione production. We overexpressed the acetolactate synthase (ALS) from Bacillus subtilis and then used the genome-scale metabolic model (GSMM) for T. glabrata (named iNX804) to evaluate the importance of deleting the ILV5 gene. In addition, the BDH gene was deleted to restrict the degradation of 2,3-butanedione. Overexpression of the ALS resulted in a 4.6-fold increase in ALS activity and increased the extracellular concentration of 2,3-butanedione to 0.57 g/L from 0.01 g/L. The deletion of the ILV5 gene was found to increase the 2,3-butanedione accumulation level by 28.1%, attributed to the disruption of L-valine and L-leucine biosynthetic pathway. With the deletion of the BDH gene, the enzyme activity levels of butanedione reductase and butanediol dehydrogenase were decreased by 74.4% and 76.1%, respectively. And the accumulations of 3-hydroxybutanone and 2,3-butanediol were decreased by 52.2% and 71.4%, respectively. The final 2,3-butanedione concentration was 0.95 g/L, which was 30.1% higher than that of the control strain. The GSMM based system metabolic engineering can be a functional strategy to redistribute the carbon flux from pyruvate node to 2,3-butanedione and achieve efficient accumulation of 2,3-butanedione.

  14. A non-canonical ESCRT pathway, including histidine domain phosphotyrosine phosphatase (HD-PTP), is used for down-regulation of virally ubiquitinated MHC class I.

    PubMed

    Parkinson, Michael D J; Piper, Siân C; Bright, Nicholas A; Evans, Jennifer L; Boname, Jessica M; Bowers, Katherine; Lehner, Paul J; Luzio, J Paul

    2015-10-01

    The Kaposi's sarcoma-associated herpes virus (KSHV) K3 viral gene product effectively down-regulates cell surface MHC class I. K3 is an E3 ubiquitin ligase that promotes Lys(63)-linked polyubiquitination of MHC class I, providing the signal for clathrin-mediated endocytosis. Endocytosis is followed by sorting into the intralumenal vesicles (ILVs) of multivesicular bodies (MVBs) and eventual delivery to lysosomes. The sorting of MHC class I into MVBs requires many individual proteins of the four endosomal sorting complexes required for transport (ESCRTs). In HeLa cells expressing the KSHV K3 ubiquitin ligase, the effect of RNAi-mediated depletion of individual proteins of the ESCRT-0 and ESCRT-I complexes and three ESCRT-III proteins showed that these are required to down-regulate MHC class I. However, depletion of proteins of the ESCRT-II complex or of the ESCRT-III protein, VPS20 (vacuolar protein sorting 20)/CHMP6 (charged MVB protein 6), failed to prevent the loss of MHC class I from the cell surface. Depletion of histidine domain phosphotyrosine phosphatase (HD-PTP) resulted in an increase in the cell surface concentration of MHC class I in HeLa cells expressing the KSHV K3 ubiquitin ligase. Rescue experiments with wild-type (WT) and mutant HD-PTP supported the conclusion that HD-PTP acts as an alternative to ESCRT-II and VPS20/CHMP6 as a link between the ESCRT-I and those ESCRT-III protein(s) necessary for ILV formation. Thus, the down-regulation of cell surface MHC class I, polyubiquitinated by the KSHV K3 ubiquitin ligase, does not employ the canonical ESCRT pathway, but instead utilizes an alternative pathway in which HD-PTP replaces ESCRT-II and VPS20/CHMP6.

  15. Activation and repression of transcription initiation by a distant DNA structural transition.

    PubMed

    Sheridan, S D; Opel, M L; Hatfield, G W

    2001-05-01

    Negative superhelical tension can drive local transitions to alternative DNA structures. Long regions of DNA may contain several sites that are susceptible to forming alternative structures. Their relative propensities to undergo transition are ordered according to the energies required for their formation. These energies have two components - the energy needed to drive the transition and the energy relieved by the partial relaxation of superhelicity that the transition provides. This coupling can cause a complex competition among the possible transitions, in which the formation of one energetically favourable alternative structure may inhibit the formation of another within the same domain. In principle, DNA structural competitions can affect the structural and energetic requirements for the initiation of transcription at distant promoter sites. We have tested this possibility by examining the effects of structural transitions on transcription initiation from promoter sites in the same superhelical domain. Specifically, we describe the effects of the presence of a Z-DNA-forming DNA sequence on the basal levels of expression of two supercoiling-sensitive promoters of Escherichia coli, ilvPG and gyrA. We demonstrate transcriptional repression of the ilvPG promoter and activation of the gyrA promoter. We present evidence that this regulation is effected by the superhelically induced B- to Z-DNA transition in a manner that is both orientation and distance independent. We discuss the mechanism of topological coupling between left-handed Z-DNA and the regulation of promoter activity. We also discuss the possibility that the coupling of DNA structural transitions and transcriptional activity might be used as a general regulatory mechanism for gene expression.

  16. Engineering Corynebacterium glutamicum for isobutanol production

    PubMed Central

    Smith, Kevin Michael; Cho, Kwang-Myung

    2010-01-01

    The production of isobutanol in microorganisms has recently been achieved by harnessing the highly active 2-keto acid pathways. Since these 2-keto acids are precursors of amino acids, we aimed to construct an isobutanol production platform in Corynebacterium glutamicum, a well-known amino-acid-producing microorganism. Analysis of this host’s sensitivity to isobutanol toxicity revealed that C. glutamicum shows an increased tolerance to isobutanol relative to Escherichia coli. Overexpression of alsS of Bacillus subtilis, ilvC and ilvD of C. glutamicum, kivd of Lactococcus lactis, and a native alcohol dehydrogenase, adhA, led to the production of 2.6 g/L isobutanol and 0.4 g/L 3-methyl-1-butanol in 48 h. In addition, other higher chain alcohols such as 1-propanol, 2-methyl-1-butanol, 1-butanol, and 2-phenylethanol were also detected as byproducts. Using longer-term batch cultures, isobutanol titers reached 4.0 g/L after 96 h with wild-type C. glutamicum as a host. Upon the inactivation of several genes to direct more carbon through the isobutanol pathway, we increased production by ∼25% to 4.9 g/L isobutanol in a ∆pyc∆ldh background. These results show promise in engineering C. glutamicum for higher chain alcohol production using the 2-keto acid pathways. Electronic supplementary material The online version of this article (doi:10.1007/s00253-010-2522-6) contains supplementary material, which is available to authorized users. PMID:20376637

  17. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha.

    PubMed

    Lu, Jingnan; Brigham, Christopher J; Gai, Claudia S; Sinskey, Anthony J

    2012-10-01

    Wild-type Ralstonia eutropha H16 produces polyhydroxybutyrate (PHB) as an intracellular carbon storage material during nutrient stress in the presence of excess carbon. In this study, the excess carbon was redirected in engineered strains from PHB storage to the production of isobutanol and 3-methyl-1-butanol (branched-chain higher alcohols). These branched-chain higher alcohols can directly substitute for fossil-based fuels and be employed within the current infrastructure. Various mutant strains of R. eutropha with isobutyraldehyde dehydrogenase activity, in combination with the overexpression of plasmid-borne, native branched-chain amino acid biosynthesis pathway genes and the overexpression of heterologous ketoisovalerate decarboxylase gene, were employed for the biosynthesis of isobutanol and 3-methyl-1-butanol. Production of these branched-chain alcohols was initiated during nitrogen or phosphorus limitation in the engineered R. eutropha. One mutant strain not only produced over 180 mg/L branched-chain alcohols in flask culture, but also was significantly more tolerant of isobutanol toxicity than wild-type R. eutropha. After the elimination of genes encoding three potential carbon sinks (ilvE, bkdAB, and aceE), the production titer improved to 270 mg/L isobutanol and 40 mg/L 3-methyl-1-butanol. Semicontinuous flask cultivation was utilized to minimize the toxicity caused by isobutanol while supplying cells with sufficient nutrients. Under this semicontinuous flask cultivation, the R. eutropha mutant grew and produced more than 14 g/L branched-chain alcohols over the duration of 50 days. These results demonstrate that R. eutropha carbon flux can be redirected from PHB to branched-chain alcohols and that engineered R. eutropha can be cultivated over prolonged periods of time for product biosynthesis.

  18. Variation in the OC Locus of Acinetobacter baumannii Genomes Predicts Extensive Structural Diversity in the Lipooligosaccharide

    PubMed Central

    Kenyon, Johanna J.; Nigro, Steven J.; Hall, Ruth M.

    2014-01-01

    Lipooligosaccharide (LOS) is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC) component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B) was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs). OCL1 (Group A) was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates. PMID:25247305

  19. TROSY NMR with a 52 kDa sugar transport protein and the binding of a small-molecule inhibitor.

    PubMed

    Kalverda, Arnout P; Gowdy, James; Thompson, Gary S; Homans, Steve W; Henderson, Peter J F; Patching, Simon G

    2014-06-01

    Using the sugar transport protein, GalP, from Escherichia coli, which is a homologue of human GLUT transporters, we have overcome the challenges for achieving high-resolution [(15)N-(1)H]- and [(13)C-(1)H]-methyl-TROSY NMR spectra with a 52 kDa membrane protein that putatively has 12 transmembrane-spanning α-helices and used the spectra to detect inhibitor binding. The protein reconstituted in DDM detergent micelles retained structural and functional integrity for at least 48 h at a temperature of 25 °C as demonstrated by circular dichroism spectroscopy and fluorescence measurements of ligand binding, respectively. Selective labelling of tryptophan residues reproducibly gave 12 resolved signals for tryptophan (15)N backbone positions and also resolved signals for (15)N side-chain positions. For improved sensitivity isoleucine, leucine and valine (ILV) methyl-labelled protein was prepared, which produced unexpectedly well resolved [(13)C-(1)H]-methyl-TROSY spectra showing clear signals for the majority of methyl groups. The GalP/GLUT inhibitor forskolin was added to the ILV-labelled sample inducing a pronounced chemical shift change in one Ile residue and more subtle changes in other methyl groups. This work demonstrates that high-resolution TROSY NMR spectra can be achieved with large complex α-helical membrane proteins without the use of elevated temperatures. This is a prerequisite to applying further labelling strategies and NMR experiments for measurement of dynamics, structure elucidation and use of the spectra to screen ligand binding.

  20. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha

    SciTech Connect

    Lu, JN; Brigham, CJ; Gai, CS; Sinskey, AJ

    2012-08-04

    Wild-type Ralstonia eutropha H16 produces polyhydroxybutyrate (PHB) as an intracellular carbon storage material during nutrient stress in the presence of excess carbon. In this study, the excess carbon was redirected in engineered strains from PHB storage to the production of isobutanol and 3-methyl-1-butanol (branched-chain higher alcohols). These branched-chain higher alcohols can directly substitute for fossil-based fuels and be employed within the current infrastructure. Various mutant strains of R. eutropha with isobutyraldehyde dehydrogenase activity, in combination with the overexpression of plasmid-borne, native branched-chain amino acid biosynthesis pathway genes and the overexpression of heterologous ketoisovalerate decarboxylase gene, were employed for the biosynthesis of isobutanol and 3-methyl-1-butanol. Production of these branched-chain alcohols was initiated during nitrogen or phosphorus limitation in the engineered R. eutropha. One mutant strain not only produced over 180 mg/L branched-chain alcohols in flask culture, but also was significantly more tolerant of isobutanol toxicity than wild-type R. eutropha. After the elimination of genes encoding three potential carbon sinks (ilvE, bkdAB, and aceE), the production titer improved to 270 mg/L isobutanol and 40 mg/L 3-methyl-1-butanol. Semicontinuous flask cultivation was utilized to minimize the toxicity caused by isobutanol while supplying cells with sufficient nutrients. Under this semicontinuous flask cultivation, the R. eutropha mutant grew and produced more than 14 g/L branched-chain alcohols over the duration of 50 days. These results demonstrate that R. eutropha carbon flux can be redirected from PHB to branched-chain alcohols and that engineered R. eutropha can be cultivated over prolonged periods of time for product biosynthesis.

  1. The neutral sphingomyelinase pathway regulates packaging of the prion protein into exosomes.

    PubMed

    Guo, Belinda B; Bellingham, Shayne A; Hill, Andrew F

    2015-02-06

    Prion diseases are a group of transmissible, fatal neurodegenerative disorders associated with the misfolding of the host-encoded prion protein, PrP(C), into a disease-associated form, PrP(Sc). The transmissible prion agent is principally formed of PrP(Sc) itself and is associated with extracellular vesicles known as exosomes. Exosomes are released from cells both in vitro and in vivo, and have been proposed as a mechanism by which prions spread intercellularly. The biogenesis of exosomes occurs within the endosomal system, through formation of intraluminal vesicles (ILVs), which are subsequently released from cells as exosomes. ILV formation is known to be regulated by the endosomal sorting complexes required for transport (ESCRT) machinery, although an alternative neutral sphingomyelinase (nSMase) pathway has been suggested to also regulate this process. Here, we investigate a role for the nSMase pathway in exosome biogenesis and packaging of PrP into these vesicles. Inhibition of the nSMase pathway using GW4869 revealed a role for the nSMase pathway in both exosome formation and PrP packaging. In agreement, targeted knockdown of nSMase1 and nSMase2 in mouse neurons using lentivirus-mediated RNAi also decreases exosome release, demonstrating the nSMase pathway regulates the biogenesis and release of exosomes. We also demonstrate that PrP(C) packaging is dependent on nSMase2, whereas the packaging of disease-associated PrP(Sc) into exosomes occurs independently of nSMase2. These findings provide further insight into prion transmission and identify a pathway which directly assists exosome-mediated transmission of prions.

  2. Characterization and Pathogenic Significance of Vibrio vulnificus Antigens Preferentially Expressed in Septicemic Patients

    PubMed Central

    Kim, Young Ran; Lee, Shee Eun; Kim, Choon Mee; Kim, Soo Young; Shin, Eun Kyoung; Shin, Dong Hyeon; Chung, Sun Sik; Choy, Hyon E.; Progulske-Fox, Ann; Hillman, Jeffrey D.; Handfield, Martin; Rhee, Joon Haeng

    2003-01-01

    Many important virulence genes of pathogenic bacteria are preferentially expressed in vivo. We used the recently developed in vivo-induced antigen technology (IVIAT) to identify Vibrio vulnificus genes induced in vivo. An expression library of V. vulnificus was screened by colony blot analysis by using pooled convalescent-phase serum that had been thoroughly adsorbed with in vitro-expressed V. vulnificus whole cells and lysates. Twelve clones were selected, and the sequences of the insert DNAs were analyzed. The DNA sequences showed homologies with genes encoding proteins of diverse functions: these functions included chemotaxis (a methyl-accepting chemotaxis protein), signaling (a GGDEF-containing protein and a putative serine/threonine kinase), biosynthesis and metabolism (PyrH, PurH, and IlvC), secretion (TatB and plasmid Achromobacter secretion [PAS] factor), transcriptional activation (IlvY and HlyU), and the activity of a putative lipoprotein (YaeC). In addition, one identified open reading frame encoded a hypothetical protein. Isogenic mutants of the 12 in vivo-expressed (ive) genes were constructed and tested for cytotoxicity. Cytotoxic activity of the mutant strains, as measured by lactate dehydrogenase release from HeLa cells, was nearly abolished in pyrH, purH, and hlyU mutants. The intraperitoneal 50% lethal dose in mice increased by ca. 10- to 50-fold in these three mutants. PyrH and PurH seem to be essential for in vivo growth. HlyU appears to be one of the master regulators of in vivo virulence expression. The successful identification of ive genes responsible for the in vivo bacterial virulence, as done in the present study, demonstrates the usefulness of IVIAT for the detection of new virulence genes. PMID:14500463

  3. Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients.

    PubMed

    Kim, Young Ran; Lee, Shee Eun; Kim, Choon Mee; Kim, Soo Young; Shin, Eun Kyoung; Shin, Dong Hyeon; Chung, Sun Sik; Choy, Hyon E; Progulske-Fox, Ann; Hillman, Jeffrey D; Handfield, Martin; Rhee, Joon Haeng

    2003-10-01

    Many important virulence genes of pathogenic bacteria are preferentially expressed in vivo. We used the recently developed in vivo-induced antigen technology (IVIAT) to identify Vibrio vulnificus genes induced in vivo. An expression library of V. vulnificus was screened by colony blot analysis by using pooled convalescent-phase serum that had been thoroughly adsorbed with in vitro-expressed V. vulnificus whole cells and lysates. Twelve clones were selected, and the sequences of the insert DNAs were analyzed. The DNA sequences showed homologies with genes encoding proteins of diverse functions: these functions included chemotaxis (a methyl-accepting chemotaxis protein), signaling (a GGDEF-containing protein and a putative serine/threonine kinase), biosynthesis and metabolism (PyrH, PurH, and IlvC), secretion (TatB and plasmid Achromobacter secretion [PAS] factor), transcriptional activation (IlvY and HlyU), and the activity of a putative lipoprotein (YaeC). In addition, one identified open reading frame encoded a hypothetical protein. Isogenic mutants of the 12 in vivo-expressed (ive) genes were constructed and tested for cytotoxicity. Cytotoxic activity of the mutant strains, as measured by lactate dehydrogenase release from HeLa cells, was nearly abolished in pyrH, purH, and hlyU mutants. The intraperitoneal 50% lethal dose in mice increased by ca. 10- to 50-fold in these three mutants. PyrH and PurH seem to be essential for in vivo growth. HlyU appears to be one of the master regulators of in vivo virulence expression. The successful identification of ive genes responsible for the in vivo bacterial virulence, as done in the present study, demonstrates the usefulness of IVIAT for the detection of new virulence genes.

  4. Fluvial dike breaching due to overtopping: how different is it from dam breaching?

    NASA Astrophysics Data System (ADS)

    Rifai, Ismail; Erpicum, Sébastien; Archambeau, Pierre; Violeau, Damien; Pirotton, Michel; El kadi Abderrezzak, Kamal; Dewals, Benjamin

    2017-04-01

    .g., seven times faster for a 150 % increase in the inflow discharge). When an equilibrium state is reached at the end of the test, the breach centreline orientation is found consistent with the theory of flow over a lateral weir. In the experiments, the boundary condition at the downstream end of the main channel is a lumped representation of river characteristics downstream of the breach section. In real-world conditions, these river characteristics influence the flow partition between the breach and the main channel. Therefore, we tested several downstream boundary conditions (perforated plane, rectilinear weir and sluice gate). For the same inflow discharge and water levels, they lead to significantly different breach geometries. The findings of this research shed light on key mechanisms occurring in fluvial dike breaching, which differ substantially from those in dam breaching. These specific features need to be incorporated in flood risk analyses involving fluvial dike breaching. This research also delivers a unique experimental database of high resolution continuous monitoring of the breach geometry under various flow conditions. The datasets are freely available for engineers and researchers willing to assess the performance of numerical models to simulate dike breaching and resulting flood. References Müller, C., Frank, P.-J., Hager, W.H. (2016). Dyke overtopping: effects of shape and headwater elevation. Journal of Hydraulic Research, 54(4), 410-422. Rifai, I., Erpicum, S., Archambeau, P., Violeau, D., Pirotton, M., El kadi Abderrezzak, K., Dewals, B. (2016). Monitoring topography of laboratory fluvial dike models subjected to breaching based on a laser profilometry technique. Proc. International Symposium on River Sedimentation (ISRS), 19-22 September 2016, Stuttgart. Rifai, I., Erpicum, S., Archambeau, P., Violeau, D., Pirotton, M., El kadi Abderrezzak, K., Dewals, B. (2017a). Overtopping induced failure of non-cohesive, homogenous fluvial dikes. Water Resources

  5. Avoiding the Water-Climate-Poverty Trap: Adaptive Risk Management for Bangladesh's Coastal Embankments

    NASA Astrophysics Data System (ADS)

    Hall, J. W.

    2015-12-01

    ., Aerts, J.C.J.H., Ait-Kadi, M., Brown, C., Cox, A., Dadson, S., Garrick, D., Kelman, J., McCornick, P., Ringler, C., Rosegrant, M., Whittington, D. and Wiberg, D. Securing Water, Sustaining Growth: Report of the GWP/OECD Task Force on Water Security and Sustainable Growth, University of Oxford, April 2015, 180pp.

  6. Deep water velocities and particle displacements induced by acoustic-gravity waves from submarine earthquakes

    NASA Astrophysics Data System (ADS)

    Oliveira, T. C. A.; Kadri, U.

    2016-02-01

    An uplift of the ocean bottom caused by a submarine earthquake can generate Acoustic-Gravity Waves (AGW), progressive compression-type waves that travel at near the speed of sound in water. The role of AGW for oceans hydrodynamics has recently became a topic of increasing scientific interest. Kadri [Deep ocean water transport by acoustic-gravity waves, J.Geo. Res. Oceans, 119, (2014)] showed theoretically that AGW can contribute to deep ocean currents and circulation. We analyze and simulate the fundamental AGW modes generated by a submarine earthquake. We consider the first five AGW modes and show that they may all induce comparable temporal variations in water particle velocities at different depths in regions far from the epicenter. Results of temporal variations of horizontal and vertical fluid parcel velocities induced by AGW confirm chaotic flow trajectories at different water depths. A realistic example based on the 2004 Indian Ocean earthquake shows that vertical water particle displacements of O(10-2 ) m can be generated at 1 Km depth in a 4 km water depth ocean. We show that the velocity field depends on the presence of the leading AGW modes. Each AGW mode becomes evanescent at a critical time, at which energy is transferred to the next higher modes. Consequently, the main pattern of the velocity field changes as the leading mode change. As an example, for a reference point located at 1000 Km from the epicenter, the first five AGW become evanescent after 1.6, 4.6, 7.7, 10.8 and 13.8 hours, respectively. Our analysis and simulations shed light on the spatio-temporal evolution of the deep water velocities and particle displacements induced by AGW that radiate during submarine earthquakes. Thus, this work is a contribution to understand the role of high moment magnitude submarine earthquakes in deep water mixing mechanism.

  7. [Histoplasmosis story from Tennessee, U.S.A. to Turkey].

    PubMed

    Turhan, Vedat

    2009-04-01

    Histoplasmosis is a mycotic disease that is acquired by inhalation of spores of the dimorphic fungus Histoplasma capsulatum. It is an acute, subacute or chronic, localized or systemic, sporadic, granulomatous infectious disease caused by yeast form of the fungus, and can present just like pulmonary tuberculosis. Originally thought to be a rare tropical disease, histoplasmosis has been recorded from the whole America continent mainly the central zone of the United States, whole continents except Antarctica and more than 60 countries. In this article the discovery and identification story of H. capsulatum and histoplasmosis in United States especially by the researchers in Vanderbilt University Hospital (VUMC) in Nashville-Tennessee, was reminded. The first antemortem diagnosis of histoplasmosis was made at VUMC in 1932 by MDs Edna Tomkins and Katherine Dodd, who found the organism in peripheral blood monocytes of an infant. The man who succeeded in growing and defining the H. copsulatum for the first time in the world is Dr William A. DeMonbreun. VUMC has been closely associated with progress in the understanding of the disease ever since. Ekrem Kadri Unat was the researcher who initiated the pivotal systemic mycological studies for histoplasmosis in Turkey. First human histoplasmosis case was reported by Tevfik Saglam, MD in 1945 and first feline case was reported by DVM Reşat S. Akün in 1949. This feline case was the first histoplasmosis case defined in a cat not only in Turkey but also in the world. Ayhan Yücel MD and Kantarcloğlu isolated H. capsulatum from environmental samples in 1989 for the first time in Turkey. Owing to these data, it is believed that Turkey is a possible endemic region for this fungal disease. Therefore it is aimed to make a concise review of histoplasmosis in U.S.A., Europe and Turkey in this article.

  8. Effective Trapping of Fruit Flies with Cultures of Metabolically Modified Acetic Acid Bacteria

    PubMed Central

    Ishii, Yuri; Akasaka, Naoki; Goda, Itsuko; Sakoda, Hisao

    2015-01-01

    Acetoin in vinegar is an attractant to fruit flies when combined with acetic acid. To make vinegar more effective in attracting fruit flies with increased acetoin production, Komagataeibacter europaeus KGMA0119 was modified by specific gene disruption of the acetohydroxyacid isomeroreductase gene (ilvC). A previously constructed mutant lacking the putative ligand-sensing region in the leucine-responsive regulatory protein (KeLrp, encoded by Kelrp) was also used. The ilvC and Kelrp disruptants (KGMA5511 and KGMA7203, respectively) produced greater amounts of acetoin (KGMA5511, 0.11%; KGMA7203, 0.13%) than the wild-type strain KGMA0119 (0.069%). KGMA7203 produced a trace amount of isobutyric acid (0.007%), but the other strains did not. These strains produced approximately equal amounts of acetic acid (0.7%). The efficiency of fruit fly attraction was investigated with cultured Drosophila melanogaster. D. melanogaster flies (approximately 1,500) were released inside a cage (2.5 m by 2.5 m by 1.5 m) and were trapped with a device containing vinegar and a sticky sheet. The flies trapped on the sticky sheet were counted. The cell-free supernatant from KGMA7203 culture captured significantly more flies (19.36 to 36.96% of released flies) than did KGMA0119 (3.25 to 11.40%) and KGMA5511 (6.87 to 21.50%) cultures. Contrastingly, a 0.7% acetic acid solution containing acetoin (0.13%) and isobutyric acid (0.007%), which mimicked the KGMA7203 supernatant, captured significantly fewer flies (0.88 to 4.57%). Furthermore, the KGMA0119 supernatant with additional acetoin (0.13%) and isobutyric acid (0.007%) captured slightly more flies than the original KGMA0119 supernatant but fewer than the KGMA7203 supernatant, suggesting that the synergistic effects of acetic acid, acetoin, isobutyric acid, and unidentified metabolites achieved the efficient fly trapping of the KGMA7203 supernatant. PMID:25595769

  9. Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

    SciTech Connect

    Rahman, Mohammad Mubinur; Andberg, Martina; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina

    2016-07-13

    l-Arabinonate dehydratase and d-xylonate dehydratase from the IlvD/EDD family were crystallized by the vapour-diffusion method. Diffraction data sets were collected to resolutions of 2.40 and 2.66 Å from crystals of l-arabinonate dehydratase and d-xylonate dehydratase, respectively. l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P2{sub 1}, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V{sub M} value of 3.2 Å{sup 3} Da{sup −1} and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V{sub M

  10. Effective trapping of fruit flies with cultures of metabolically modified acetic acid bacteria.

    PubMed

    Ishii, Yuri; Akasaka, Naoki; Goda, Itsuko; Sakoda, Hisao; Fujiwara, Shinsuke

    2015-04-01

    Acetoin in vinegar is an attractant to fruit flies when combined with acetic acid. To make vinegar more effective in attracting fruit flies with increased acetoin production, Komagataeibacter europaeus KGMA0119 was modified by specific gene disruption of the acetohydroxyacid isomeroreductase gene (ilvC). A previously constructed mutant lacking the putative ligand-sensing region in the leucine-responsive regulatory protein (KeLrp, encoded by Kelrp) was also used. The ilvC and Kelrp disruptants (KGMA5511 and KGMA7203, respectively) produced greater amounts of acetoin (KGMA5511, 0.11%; KGMA7203, 0.13%) than the wild-type strain KGMA0119 (0.069%). KGMA7203 produced a trace amount of isobutyric acid (0.007%), but the other strains did not. These strains produced approximately equal amounts of acetic acid (0.7%). The efficiency of fruit fly attraction was investigated with cultured Drosophila melanogaster. D. melanogaster flies (approximately 1,500) were released inside a cage (2.5 m by 2.5 m by 1.5 m) and were trapped with a device containing vinegar and a sticky sheet. The flies trapped on the sticky sheet were counted. The cell-free supernatant from KGMA7203 culture captured significantly more flies (19.36 to 36.96% of released flies) than did KGMA0119 (3.25 to 11.40%) and KGMA5511 (6.87 to 21.50%) cultures. Contrastingly, a 0.7% acetic acid solution containing acetoin (0.13%) and isobutyric acid (0.007%), which mimicked the KGMA7203 supernatant, captured significantly fewer flies (0.88 to 4.57%). Furthermore, the KGMA0119 supernatant with additional acetoin (0.13%) and isobutyric acid (0.007%) captured slightly more flies than the original KGMA0119 supernatant but fewer than the KGMA7203 supernatant, suggesting that the synergistic effects of acetic acid, acetoin, isobutyric acid, and unidentified metabolites achieved the efficient fly trapping of the KGMA7203 supernatant. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  11. The Saccharomyces cerevisiae Leu3 protein activates expression of GDH1, a key gene in nitrogen assimilation.

    PubMed

    Hu, Y; Cooper, T G; Kohlhaw, G B

    1995-01-01

    The Leu3 protein of Saccharomyces cerevisiae has been shown to be a transcriptional regulator of genes encoding enzymes of the branched-chain amino acid biosynthetic pathways. Leu3 binds to upstream activating sequences (UASLEU) found in the promoters of LEU1, LEU2, LEU4, ILV2, and ILV5. In vivo and in vitro studies have shown that activation by Leu3 requires the presence of alpha-isopropylmalate. In at least one case (LEU2), Leu3 actually represses basal-level transcription when alpha-isopropylmalate is absent. Following identification of a UASLEU-homologous sequence in the promoter of GDH1, the gene encoding NADP(+)-dependent glutamate dehydrogenase, we demonstrate that Leu3 specifically interacts with this UASLEU element. We then show that Leu3 is required for full activation of the GDH1 gene. First, the expression of a GDH1-lacZ fusion gene is three- to sixfold lower in a strain lacking the LEU3 gene than in an isogenic LEU3+ strain. Expression is restored to near-normal levels when the leu3 deletion cells are transformed with a LEU3-bearing plasmid. Second, a significant decrease in GDH1-lacZ expression is also seen when the UASLEU of the GDH1-lacZ construct is made nonfunctional by mutation. Third, the steady-state level of GDH1 mRNA decreases about threefold in leu3 null cells. The decrease in GDH1 expression in leu3 null cells is reflected in a diminished specific activity of NADP(+)-dependent glutamate dehydrogenase. We also demonstrate that the level of GDH1-lacZ expression correlates with the cells' ability to generate alpha-isopropylmalate and is lowest in cells unable to produce alpha-isopropylmalate. We conclude that GDH1, which plays an important role in the assimilation of ammonia in yeast cells, is, in part, activated by a Leu3-alpha-isopropylmalate complex. This conclusion suggests that Leu3 participates in transcriptional regulation beyond the branched-chain amino acid biosynthetic pathways.

  12. Tipranavir-Ritonavir Genotypic Resistance Score in Protease Inhibitor-Experienced Patients▿

    PubMed Central

    Marcelin, Anne-Genevieve; Masquelier, Bernard; Descamps, Diane; Izopet, Jacques; Charpentier, Charlotte; Alloui, Chakib; Bouvier-Alias, Magali; Signori-Schmuck, Anne; Montes, Brigitte; Chaix, Marie-Laure; Amiel, Corinne; Santos, Georges Dos; Ruffault, Annick; Barin, Francis; Peytavin, Gilles; Lavignon, Marc; Flandre, Philippe; Calvez, Vincent

    2008-01-01

    To identify mutations associated with the virological response (VR) to a tipranavir-ritonavir (TPV/r)-based regimen, 143 patients previously treated with protease inhibitor (PI) were studied. VR was defined by a decrease of at least 1 log10 in, or undetectable, human immunodeficiency virus (HIV) RNA at month 3. The effect of each mutation in the protease, considering all variants at a residue as a single variable, on the VR to TPV/r was investigated. Mutations at six residues were associated with a lower VR (E35D/G/K/N, M36I/L/V, Q58E, Q61D/E/G/H/N/R, H69I/K/N/Q/R/Y, and L89I/M/R/T/V), and one mutation was associated with a higher VR (F53L/W/Y). The genotypic score M36I/L/V − F53L/W/Y + Q58E + H69I/K/N/Q/R/Y + L89I/M/R/T/V was selected as providing a strong association with VR. For the seven patients with a genotypic score of −1 (viruses with only mutation at codon 53), the percentage of responders was 100% and the percentages were 79%, 56%, 33%, 21%, and 0% for those with scores of 0, 1, 2, 3, and 4, respectively. The percentage of patients showing a response to TPV/r was lower for patients infected with non-clade B viruses (n = 16, all non-B subtypes considered together) than for those infected with clade B viruses (n = 127) (25% and 59%, respectively; P = 0.015). Most mutations associated with VR to TPV/r had not previously been associated with PI resistance. This is consistent with phenotypic analysis showing that TPV has a unique resistance profile. Mutations at five positions (35, 36, 61, 69, and 89) were observed significantly more frequently in patients infected with a non-B subtype than in those infected with the B subtype, probably explaining the lower VR observed in these patients. PMID:18625773

  13. Estimate of Gaseous 14Carbon Concentrations Emanating from the Intermediate-Level Vault Disposal Facility

    SciTech Connect

    Kaplan, D

    2005-08-31

    {sup 14}Carbon-bearing resin waste will be disposed in the Low-Activity Waste (LAW) Intermediate Level Vaults (ILV) located in E-Area on the Savannah River Site (SRS). This waste will be buried in a cementitious environment in the vadose zone, i.e., the subsurface zone above the aquifer. As the resin ages, and equilibrates with slowly infiltrating water, it is expected that the {sup 14}C will partition to the solid, liquid, and gaseous phases. The objective of this task was to estimate the concentration of gaseous {sup 14}C in the waste pore space that is in contact with the resin leachate. The approach used to estimate this value was built largely around data generated from lysimeter studies that were conducted for 9 years. These lysimeters contained the same type of used resins (mixed-bed deionizer resins used in the purification of the heavy water moderator of SRS reactors) as are being disposed in the ILV. During the 9 year period, pore water {sup 14}C leaching concentrations were monitored to provide an excellent estimate of the long-term behavior of {sup 14}C release rates from the resins. Thermodynamic calculations were conducted to calculate {sup 14}CO{sub 2(g)} concentrations. These calculations included the {sup 14}C pore water data from the lysimeter study, and data from a field study that was a natural analogue to a long-term cementitious environment (Khoury et al. 1992). The calculations predicted an extremely low {sup 14}CO{sub 2(g)} concentration of 1.9 x 10{sup -7} Ci/m{sup 3} {sup 14}CO{sub 2(g)} in the air spaces above the resin leachate. This low concentrations is not surprising in light of both laboratory and field observations that concrete acts as a strong sorbent of CO{sub 2(g)}. This calculated {sup 14}CO{sub 2(g)} concentration will now be included in future risk calculations.

  14. A laser profilometry technique for monitoring fluvial dike breaching in laboratory experiments

    NASA Astrophysics Data System (ADS)

    Dewals, Benjamin; Rifai, Ismail; Erpicum, Sébastien; Archambeau, Pierre; Violeau, Damien; Pirotton, Michel; El kadi Abderrezzak, Kamal

    2017-04-01

    laser are merged to generate a cloud of points. The DLT-based image processing method uses control points and reference axes, so that no prior knowledge is needed on the position, orientation and intrinsic characteristics of the camera, nor on the laser position. Refraction of the light and laser rays across the water surface needs to be taken into account, because the dike is partially submerged during the experiments. An ad hoc correction is therefore applied using the Snell-Descartes law. For this purpose, planar approximations are used to describe the shape of the water surface. In the presentation, we will discuss the resulting uncertainty and will detail the validation of the developed method based on configurations of known geometry with various complexity. The presented laser profilometry technique allows for a rapid non-intrusive measurement of the dike geometry evolution. It is readily available for laboratory experiments and has proven its performance (Rifai et al. 2017). Further adjustments are needed for its application to cohesive dike material due to the reduced visibility resulting from the higher turbidity of water. References Frank, P.-J., Hager, W.H. (2014). Spatial dike breach: Accuracy of photogrammetric measurement system. Proc. of the International Conference on Fluvial Hydraulics, River Flow 2014, 1647-1654. Pickert, G., Weitbrecht, V., Bieberstein A. (2011). Beaching of overtopped river embankments controlled by apparent cohesion. Journal of Hydraulic Research 49:143-156. Rifai, I., Erpicum, S., Archambeau, P., Violeau, D., Pirotton, M., El kadi Abderrezzak, K., Dewals, B. (2016). Monitoring topography of laboratory fluvial dike models subjected to breaching based on a laser profilometry technique. Proc. of the International Symposium on River Sedimentation (ISRS): Stuttgart, 19-22 September 2016. Rifai, I., Erpicum, S., Archambeau, P., Violeau, D., Pirotton, M., El kadi Abderrezzak, K., Dewals, B. (2017). Overtopping induced failure of non

  15. Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo.

    PubMed

    Suter, B; Schnappauf, G; Thoma, F

    2000-11-01

    Poly(dA.dT) sequences (T-tracts) are abundant genomic DNA elements with unusual properties in vitro and an established role in transcriptional regulation of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CPDs (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photofootprint). In eukaryotic cells, where DNA is packaged in chromatin, the DNA structure of T-tracts is unknown. Here we have used in vivo UV photofootprinting and DNA repair by photolyase to investigate the structure and accessibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same characteristic photofootprints were obtained in yeast and in naked DNA, demonstrating that the unusual T-tract structure exists in living cells. Rapid repair of CPDs in the T-tracts demonstrates that these T-tracts were not folded in nucleosomes. Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, showed an influence on the structure and accessibility of T-tracts. The data support a contribution of this unusual DNA structure to transcriptional regulation.

  16. Mutations producing resistance to norfloxacin in Pseudomonas aeruginosa.

    PubMed Central

    Hirai, K; Suzue, S; Irikura, T; Iyobe, S; Mitsuhashi, S

    1987-01-01

    Two genetically distinct classes of norfloxacin-resistant Pseudomonas aeruginosa PAO4009 mutants were isolated spontaneously. Two norfloxacin resistance genes, nfxA and nfxB, were mapped hex-9001 and leu-9005 and between pro-9031 and ilv-9023, respectively, on the P. aeruginosa PAO chromosome. The nfxA gene was shown to be an allele of nalA by transductional analysis with bacteriophage F116L. The nfxB mutant showed a 16-fold increase in resistance to norfloxacin and a slight increase in resistance to nalidixic acid. The nfxB mutant was unique in that it showed hypersusceptibility to beta-lactam and aminoglycoside antibiotics. This mutant had about a threefold-lower rate of norfloxacin uptake than that of the wild-type strain or nfxA mutant. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of outer membrane proteins demonstrated the appearance of a 54,000-dalton protein in the nfxB mutant. These findings suggested that the norfloxacin resistance mechanism in the nfxB mutant might be an alteration in outer membrane permeability to norfloxacin. Images PMID:3111356

  17. Analysis and Phylogeny of Small Heat Shock Proteins from Marine Viruses and Their Cyanobacteria Host

    PubMed Central

    Maaroufi, Halim; Tanguay, Robert M.

    2013-01-01

    Small heat shock proteins (sHSPs) are oligomeric stress proteins characterized by an α-crystallin domain (ACD) surrounded by a N-terminal arm and C-terminal extension. Publications on sHSPs have reported that they exist in prokaryotes and eukaryotes but, to our knowledge, not in viruses. Here we show that sHSPs are present in some cyanophages that infect the marine unicellular cyanobacteria, Synechococcus and Prochlorococcus. These phage sHSPs contain a conserved ACD flanked by a relatively conserved N-terminal arm and a short C-terminal extension with or without the conserved C-terminal anchoring module (CAM) L-X-I/V, suggested to be implicated in the oligomerization. In addition, cyanophage sHSPs have the signature pattern, P-P-[YF]-N-[ILV]-[IV]-x(9)-[EQ], in the predicted β2 and β3 strands of the ACD. Phylogenetically, cyanophage sHSPs form a monophyletic clade closer to bacterial class A sHSPs than to cyanobacterial sHSPs. Furthermore, three sHSPs from their cellular host, Synechococcus, are phylogenetically close to plants sHSPs. Implications of evolutionary relationships between the sHSPs of cyanophages, bacterial class A, cyanobacteria, and plants are discussed. PMID:24265841

  18. Deep extractive and oxidative desulfurization of dibenzothiophene with C5H9NO·SnCl2 coordinated ionic liquid.

    PubMed

    Li, Fa-tang; Kou, Cheng-guang; Sun, Zhi-min; Hao, Ying-juan; Liu, Rui-hong; Zhao, Di-shun

    2012-02-29

    A new C5H9NO·SnCl2 coordinated ionic liquid (IL) was prepared by reacting N-methyl-pyrrolidone with anhydrous SnCl2. Desulfurization of dibenzothiophene (DBT) via extraction and oxidation with C5H9NO·SnCl2 IL as extractant, H2O2 and equal mol of CH3COOH as oxidants was investigated. The Nernst partition coefficients k(N) of C5H9NO·SnCl2 IL for the DBT in n-octane was above 5.0, showing its excellent extraction ability. During the oxidative desulfurization process, the optimal molar ratio of H2O2/DBT was six. Sulfur removal of DBT in n-octane was 94.8% in 30 min at 30 °C under the conditions of H2O2/DBT molar ratio of six and V (IL):V (oil)=1:3. Moreover, the sulfur removal increased with increasing temperature because of the high reaction rate constant, low viscosity, and high solubility of dibenzothiophene-sulfone in the IL. The kinetics of oxidative desulfurization of DBT was also investigated, and the apparent activation energy was found to be 32.5 kJ/mol. The IL could be recycled six times without a significant decrease in activity.

  19. The Corynebacterium xerosis composite transposon Tn5432 consists of two identical insertion sequences, designated IS1249, flanking the erythromycin resistance gene ermCX.

    PubMed

    Tauch, A; Kassing, F; Kalinowski, J; Pühler, A

    1995-09-01

    Analysis of the 50-kb R-plasmid pTP10 from the clinical isolate Corynebacterium xerosis M82B revealed that the erythromycin resistance gene, ermCX, is located on a 4524-bp composite transposable element, Tn5432. The ends of Tn5432 are identical, direct repeats of an insertion sequence, designated IS1249, encoding a putative transposase of the IS256 family. IS1249 consists of 1385 bp with 45/42 imperfect terminal inverted repeats. The nucleotide sequence of the 1754-bp Tn5432 central region is 99% identical to the previously sequenced erythromycin resistance region of the Corynebacterium diphtheriae plasmid pNG2. It encodes the erythromycin resistance gene, ermCX, and an ORF homologous to the amino-terminal end of the transposase of IS31831 from Corynebacterium glutamicum. Transposons with regions flanking the insertion sites were recovered from the C. glutamicum chromosome by a plasmid rescue technique. Insertion of Tn5432 created 8-bp target site duplications. A Tn5432-induced isoleucine/valine-auxotrophic mutant was found to carry the transposon in the 5' region of the ilvBNC cluster; in pTP10 the transposon is inserted in a region similar to replication and partitioning functions of the Enterococcus faecalis plasmid pAD1 and the Agrobacterium tumefaciens plasmid pTAR.

  20. Independent lung ventilation combined with HFOV for a patient suffering from tracheo-gastric roll fistula.

    PubMed

    Ichinose, Maki; Sakai, Hiroaki; Miyazaki, Ikuo; Muraoka, Akihiro; Aizawa, Miyuki; Igarashi, Kaigen; Okazaki, Atsushi

    2008-01-01

    This case report describes the difficult respiratory management of an esophageal cancer patient with acute respiratory distress syndrome (ARDS) and systemic inflammatory response syndrome (SIRS) caused by a postoperative tracheogastric roll fistula. A single-lumen tracheal tube could not seal the fistula, and therefore a double-lumen tracheal tube (DLT) for the left side was used. Although the proximal cuff of the DLT failed to seal the fistula, independent lung ventilation (ILV) improved blood gas levels. During right thoracotomy, the left lung was ventilated conventionally with 5 cmH2O positive end-expiratory pressure (PEEP), and in addition, high-frequency oscillation ventilation (HFOV) to the right lung was employed. This combination allowed the maintenance of adequate oxygenation, and the HFOV to the right lung decreased the PaCO2 level during surgery without interruption of the surgical field. These techniques provided the opportunity to successfully remove a necrotic gastric roll and achieve closure of the fistula using an intercostal muscle flap. This report documents and discusses the difficulty of performing appropriate anesthetic management of a patient with these complex complications after esophageal surgery.

  1. Multilocus sequence analysis of Bacillus thuringiensis serovars navarrensis, bolivia and vazensis and Bacillus weihenstephanensis reveals a common phylogeny.

    PubMed

    Soufiane, Brahim; Baizet, Mathilde; Côté, Jean-Charles

    2013-01-01

    The Bacillus cereus group sensu lato includes six closely-related bacterial species: Bacillus cereus, Bacillus anthracis, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides and Bacillus weihenstephanensis. B. thuringiensis is distinguished from the other species mainly by the appearance of an inclusion body upon sporulation. B. weihenstephanensis is distinguished based on its psychrotolerance and the presence of specific signature sequences in the 16S rRNA gene and cspA genes. A total of seven housekeeping genes (glpF, gmK, ilvD, pta, purH, pycA and tpi) from different B. thuringiensis serovars and B. weihenstephanensis strains were amplified and their nucleotide sequences determined. A maximum likelihood phylogenetic tree was inferred from comparisons of the concatenated sequences. B. thuringiensis serovars navarrensis, bolivia and vazensis clustered not with the other B. thuringiensis serovars but rather with the B. weihenstephanensis strains, indicative of a common phylogeny. In addition, specific signature sequences and single nucleotide polymorphisms common to B. thuringiensis serovars navarrensis, bolivia and vazensis and the B. weihenstephanensis strains, and absent in the other B. thuringiensis serovars, were identified.

  2. Bacillithiol has a role in Fe-S cluster biogenesis in Staphylococcus aureus

    PubMed Central

    Rosario-Cruz, Zuelay; Chahal, Harsimranjit K.; Mike, Laura A.; Skaar, Eric P.; Boyd, Jeffrey M.

    2015-01-01

    Summary Staphylococcus aureus does not produce the low-molecular-weight (LMW) thiol glutathione, but it does produce the LMW thiol bacillithiol (BSH). To better understand the roles that BSH plays in staphylococcal metabolism we constructed and examined strains lacking BSH. Phenotypic analysis found that the BSH-deficient strains cultured either aerobically or anaerobically had growth defects that were alleviated by the addition of exogenous iron (Fe) or the amino acids leucine and isoleucine. The activity of the iron-sulfur (Fe-S) cluster-dependent enzymes LeuCD and IlvD, which are required for the biosynthesis of leucine and isoleucine, were decreased in strains lacking BSH. The BSH-deficient cells also had decreased aconitase and glutamate synthase activities suggesting a general defect in Fe-S cluster biogenesis. The phenotypes of the BSH-deficient strains were exacerbated in strains lacking the Fe-S cluster carrier Nfu and partially suppressed by multicopy expression of either sufA or nfu suggesting functional overlap between BSH and Fe-S carrier proteins. Biochemical analysis found that SufA bound and transferred Fe-S clusters to apo-aconitase verifying that it serves as an Fe-S cluster carrier. The results presented are consistent with the hypothesis that BSH has roles in Fe homeostasis and the carriage of Fe-S clusters to apo-proteins in S. aureus. PMID:26135358

  3. A SPOPL/Cullin-3 ubiquitin ligase complex regulates endocytic trafficking by targeting EPS15 at endosomes

    PubMed Central

    Gschweitl, Michaela; Ulbricht, Anna; Barnes, Christopher A; Enchev, Radoslav I; Stoffel-Studer, Ingrid; Meyer-Schaller, Nathalie; Huotari, Jatta; Yamauchi, Yohei; Greber, Urs F; Helenius, Ari; Peter, Matthias

    2016-01-01

    Cullin-3 (CUL3)-based ubiquitin ligases regulate endosome maturation and trafficking of endocytic cargo to lysosomes in mammalian cells. Here, we report that these functions depend on SPOPL, a substrate-specific CUL3 adaptor. We find that SPOPL associates with endosomes and is required for both the formation of multivesicular bodies (MVBs) and the endocytic host cell entry of influenza A virus. In SPOPL-depleted cells, endosomes are enlarged and fail to acquire intraluminal vesicles (ILVs). We identify a critical substrate ubiquitinated by CUL3-SPOPL as EPS15, an endocytic adaptor that also associates with the ESCRT-0 complex members HRS and STAM on endosomes. Indeed, EPS15 is ubiquitinated in a SPOPL-dependent manner, and accumulates with HRS in cells lacking SPOPL. Together, our data indicates that a CUL3-SPOPL E3 ubiquitin ligase complex regulates endocytic trafficking and MVB formation by ubiquitinating and degrading EPS15 at endosomes, thereby influencing influenza A virus infection as well as degradation of EGFR and other EPS15 targets. DOI: http://dx.doi.org/10.7554/eLife.13841.001 PMID:27008177

  4. Candida albicans PROTEIN PROFILE CHANGES IN RESPONSE TO THE BUTANOLIC EXTRACT OF Sapindus saponariaL.

    PubMed Central

    FIORINI, Adriana; ROSADO, Fabio Rogério; BETTEGA, Eliane Martins da Silva; MELO, Kátia Cristina Sibin; KUKOLJ, Caroline; BONFIM-MENDONÇA, Patrícia de Souza; SHINOBU-MESQUITA, Cristiane Suemi; GHIRALDI, Luciana Dias; CAMPANERUT, Paula Aline Zanetti; CAPOCI, Isis Regina Grenier; GODOY, Janine Silva Ribeiro; FERREIRA, Izabel Cristina Piloto; SVIDZINSKI, Terezinha Inez Estivalet

    2016-01-01

    Candida albicans is an opportunistic human pathogen that is capable of causing superficial and systemic infections in immunocompromised patients. Extracts of Sapindus saponaria have been used as antimicrobial agents against various organisms. In the present study, we used a combination of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify the changes in protein abundance of C. albicans after exposure to the minimal inhibitory concentration (MIC) and sub-minimal inhibitory concentration (sub-MIC) of the butanolic extract (BUTE) of S. saponaria and also to fluconazole. A total of six different proteins with greater than 1.5 fold induction or repression relative to the untreated control cells were identified among the three treatments. In general, proteins/enzymes involved with the glycolysis (GPM1, ENO1, FBA1), amino acid metabolism (ILV5, PDC11) and protein synthesis (ASC1) pathways were detected. In conclusion, our findings reveal antifungal-induced changes in protein abundance of C. albicans. By using the previously identified components of the BUTE of S. saponaria(e.g., saponins and sesquiterpene oligoglycosides), it will be possible to compare the behavior of compounds with unknown mechanisms of action, and this knowledge will help to focus the subsequent biochemical work aimed at defining the effects of these compounds. PMID:27074319

  5. Candida albicans PROTEIN PROFILE CHANGES IN RESPONSE TO THE BUTANOLIC EXTRACT OF Sapindus saponariaL.

    PubMed

    Fiorini, Adriana; Rosado, Fabio Rogério; Bettega, Eliane Martins da Silva; Melo, Kátia Cristina Sibin; Kukolj, Caroline; Bonfim-Mendonça, Patrícia de Souza; Shinobu-Mesquita, Cristiane Suemi; Ghiraldi, Luciana Dias; Campanerut, Paula Aline Zanetti; Capoci, Isis Regina Grenier; Godoy, Janine Silva Ribeiro; Ferreira, Izabel Cristina Piloto; Svidzinski, Terezinha Inez Estivalet

    2016-01-01

    Candida albicans is an opportunistic human pathogen that is capable of causing superficial and systemic infections in immunocompromised patients. Extracts of Sapindus saponaria have been used as antimicrobial agents against various organisms. In the present study, we used a combination of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify the changes in protein abundance of C. albicans after exposure to the minimal inhibitory concentration (MIC) and sub-minimal inhibitory concentration (sub-MIC) of the butanolic extract (BUTE) of S. saponaria and also to fluconazole. A total of six different proteins with greater than 1.5 fold induction or repression relative to the untreated control cells were identified among the three treatments. In general, proteins/enzymes involved with the glycolysis (GPM1, ENO1, FBA1), amino acid metabolism (ILV5, PDC11) and protein synthesis (ASC1) pathways were detected. In conclusion, our findings reveal antifungal-induced changes in protein abundance of C. albicans. By using the previously identified components of the BUTE of S. saponaria(e.g., saponins and sesquiterpene oligoglycosides), it will be possible to compare the behavior of compounds with unknown mechanisms of action, and this knowledge will help to focus the subsequent biochemical work aimed at defining the effects of these compounds.

  6. ESCRT-0 is not required for ectopic Notch activation and tumor suppression in Drosophila.

    PubMed

    Tognon, Emiliana; Wollscheid, Nadine; Cortese, Katia; Tacchetti, Carlo; Vaccari, Thomas

    2014-01-01

    Multivesicular endosome (MVE) sorting depends on proteins of the Endosomal Sorting Complex Required for Transport (ESCRT) family. These are organized in four complexes (ESCRT-0, -I, -II, -III) that act in a sequential fashion to deliver ubiquitylated cargoes into the internal luminal vesicles (ILVs) of the MVE. Drosophila genes encoding ESCRT-I, -II, -III components function in sorting signaling receptors, including Notch and the JAK/STAT signaling receptor Domeless. Loss of ESCRT-I, -II, -III in Drosophila epithelia causes altered signaling and cell polarity, suggesting that ESCRTs genes are tumor suppressors. However, the nature of the tumor suppressive function of ESCRTs, and whether tumor suppression is linked to receptor sorting is unclear. Unexpectedly, a null mutant in Hrs, encoding one of the components of the ESCRT-0 complex, which acts upstream of ESCRT-I, -II, -III in MVE sorting is dispensable for tumor suppression. Here, we report that two Drosophila epithelia lacking activity of Stam, the other known components of the ESCRT-0 complex, or of both Hrs and Stam, accumulate the signaling receptors Notch and Dome in endosomes. However, mutant tissue surprisingly maintains normal apico-basal polarity and proliferation control and does not display ectopic Notch signaling activation, unlike cells that lack ESCRT-I, -II, -III activity. Overall, our in vivo data confirm previous evidence indicating that the ESCRT-0 complex plays no crucial role in regulation of tumor suppression, and suggest re-evaluation of the relationship of signaling modulation in endosomes and tumorigenesis.

  7. ESCRT-III on endosomes: new functions, new activation pathway.

    PubMed

    Woodman, Philip

    2016-01-15

    The multivesicular body (MVB) pathway sorts ubiquitinated membrane cargo to intraluminal vesicles (ILVs) within the endosome, en route to the lysosomal lumen. The pathway involves the sequential action of conserved protein complexes [endosomal sorting complexes required for transport (ESCRTs)], culminating in the activation by ESCRT-II of ESCRT-III, a membrane-sculpting complex. Although this linear pathway of ESCRT activation is widely accepted, a study by Luzio and colleagues in a recent issue of the Biochemical Journal suggests that there is greater complexity in ESCRT-III activation, at least for some MVB cargoes. They show that ubiquitin-dependent sorting of major histocompatibility complex (MHC) class I to the MVB requires the central ESCRT-III complex but does not involve either ESCRT-II or functional links between ESCRT-II and ESCRT-III. Instead, they propose that MHC class I utilizes histidine-domain protein tyrosine phosphatase (HD-PTP), a non-canonical ESCRT interactor, to promote ESCRT-III activation.

  8. Repression of nitrogen catabolic genes by ammonia and glutamine in nitrogen-limited continuous cultures of Saccharomyces cerevisiae.

    PubMed

    ter Schure, E G; Silljé, H H; Vermeulen, E E; Kalhorn, J W; Verkleij, A J; Boonstra, J; Verrips, C T

    1998-05-01

    Growth of Saccharomyces cerevisiae on ammonia and glutamine decreases the expression of many nitrogen catabolic genes to low levels. To discriminate between ammonia- and glutamine-driven repression of GAP1, PUT4, GDH1 and GLN1, a gln1-37 mutant was used. This mutant is not able to convert ammonia into glutamine. Glutamine-limited continuous cultures were used to completely derepress the expression of GAP1, PUT4, GDH1 and GLN1. Following an ammonia pulse, the expression of GAP1, PUT4 and GDH1 decreased while the intracellular glutamine concentration remained constant, both in the cytoplasm and in the vacuole. Therefore, it was concluded that ammonia causes gene repression independent of the intracellular glutamine concentration. The expression of GLN1 was not decreased by an ammonia pulse but solely by a glutamine pulse. Analysis of the mRNA levels of ILV5 and HIS4 showed that the response of the two biosynthetic genes, GDH1 and GLN1, to ammonia and glutamine in the wild-type and gln1-37 was not due to changes in general transcription of biosynthetic genes. Ure2p has been shown to be an essential element for nitrogen-regulated gene expression. Deletion of URE2 in the gln1-37 background prevented repression of gene expression by ammonia, showing that the ammonia-induced repression is not caused by a general stress response but represents a specific signal for nitrogen catabolite regulation.

  9. Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici.

    PubMed

    Sidhu, Y S; Cairns, T C; Chaudhari, Y K; Usher, J; Talbot, N J; Studholme, D J; Csukai, M; Haynes, K

    2015-06-01

    The lack of techniques for rapid assembly of gene deletion vectors, paucity of selectable marker genes available for genetic manipulation and low frequency of homologous recombination are major constraints in construction of gene deletion mutants in Zymoseptoria tritici. To address these issues, we have constructed ternary vectors for Agrobacterium tumefaciens mediated transformation of Z. tritici, which enable the single step assembly of multiple fragments via yeast recombinational cloning. The sulfonylurea resistance gene, which is a mutated allele of the Magnaporthe oryzae ILV2 gene, was established as a new dominant selectable marker for Z. tritici. To increase the frequency of homologous recombination, we have constructed Z. tritici strains deficient in the non-homologous end joining pathway of DNA double stranded break repair by inactivating the KU70 and KU80 genes. Targeted gene deletion frequency increased to more than 85% in both Z. tritici ku70 and ku80 null strains, compared to ⩽10% seen in the wild type parental strain IPO323. The in vitro growth and in planta pathogenicity of the Z. tritici ku70 and ku80 null strains were comparable to strain IPO323. Together these molecular tools add significantly to the platform available for genomic analysis through targeted gene deletion or promoter replacements and will facilitate large-scale functional characterization projects in Z. tritici. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Metabolic Engineering of Candida glabrata for Diacetyl Production

    PubMed Central

    Gao, Xiang; Xu, Nan; Li, Shubo; Liu, Liming

    2014-01-01

    In this study, Candida glabrata, an efficient pyruvate-producing strain, was metabolically engineered for the production of the food ingredient diacetyl. A diacetyl biosynthetic pathway was reconstructed based on genetic modifications and medium optimization. The former included (i) channeling carbon flux into the diacetyl biosynthetic pathway by amplification of acetolactate synthase, (ii) elimination of the branched pathway of α-acetolactate by deleting the ILV5 gene, and (iii) restriction of diacetyl degradation by deleting the BDH gene. The resultant strain showed an almost 1∶1 co-production of α-acetolactate and diacetyl (0.95 g L−1). Furthermore, addition of Fe3+ to the medium enhanced the conversion of α-acetolactate to diacetyl and resulted in a two-fold increase in diacetyl production (2.1 g L−1). In addition, increased carbon flux was further channeled into diacetyl biosynthetic pathway and a titer of 4.7 g L−1 of diacetyl was achieved by altering the vitamin level in the flask culture. Thus, this study illustrates that C. glabrata could be tailored as an attractive platform for enhanced biosynthesis of beneficial products from pyruvate by metabolic engineering strategies. PMID:24614328

  11. Cloning of Bacillus subtilis leucina A, B and C genes with Escherichia coli plasmids and expression of the leuC gene in E. coli.

    PubMed

    Nagahari, K; Sakaguchi, K

    1978-01-17

    The leucine genes of Bacillus subtilis have been cloned directly from the chromosomal DNA into Escherichia coli leuB cells by selection for the Leu+ phenotype using RSF2124 as a vector plasmid. The hybrid plasmid designated RSF2124-B.leu contained a 4.2 megadalton fragment derived from B. subtilis DNA, including the leu genes. The fragment had one site susceptible to EcoRI* and another site susceptible to BamNI endonuclease. Among the three fragments produced by EcoRI* and BamNI endonucleases, the 1.2 megadalton fragment had the ability to transform B. subtilis leuA, leuB and leuC auxotrophs to leu+. However, B. subtilis ilvB and ilvc auxotrophs were not rescued even by the whole 4.2 megadalton fragment present in the hybrid plasmid. beta-Isopropylmalate dehydrogenase (leuB gene product) activity found in E. coli cells containing the hybrid plasmid was about 60% of that in E. coli wild type cells, despite the high copy number (7.8) of the plasmid per chromosome observed.

  12. Systems metabolic engineering of Escherichia coli for L-threonine production.

    PubMed

    Lee, Kwang Ho; Park, Jin Hwan; Kim, Tae Yong; Kim, Hyun Uk; Lee, Sang Yup

    2007-01-01

    Amino-acid producers have traditionally been developed by repeated random mutagenesis owing to the difficulty in rationally engineering the complex and highly regulated metabolic network. Here, we report the development of the genetically defined L-threonine overproducing Escherichia coli strain by systems metabolic engineering. Feedback inhibitions of aspartokinase I and III (encoded by thrA and lysC, respectively) and transcriptional attenuation regulations (located in thrL) were removed. Pathways for Thr degradation were removed by deleting tdh and mutating ilvA. The metA and lysA genes were deleted to make more precursors available for Thr biosynthesis. Further target genes to be engineered were identified by transcriptome profiling combined with in silico flux response analysis, and their expression levels were manipulated accordingly. The final engineered E. coli strain was able to produce Thr with a high yield of 0.393 g per gram of glucose, and 82.4 g/l Thr by fed-batch culture. The systems metabolic engineering strategy reported here may be broadly employed for developing genetically defined organisms for the efficient production of various bioproducts.

  13. Analysis and phylogeny of small heat shock proteins from marine viruses and their cyanobacteria host.

    PubMed

    Maaroufi, Halim; Tanguay, Robert M

    2013-01-01

    Small heat shock proteins (sHSPs) are oligomeric stress proteins characterized by an α-crystallin domain (ACD) surrounded by a N-terminal arm and C-terminal extension. Publications on sHSPs have reported that they exist in prokaryotes and eukaryotes but, to our knowledge, not in viruses. Here we show that sHSPs are present in some cyanophages that infect the marine unicellular cyanobacteria, Synechococcus and Prochlorococcus. These phage sHSPs contain a conserved ACD flanked by a relatively conserved N-terminal arm and a short C-terminal extension with or without the conserved C-terminal anchoring module (CAM) L-X-I/V, suggested to be implicated in the oligomerization. In addition, cyanophage sHSPs have the signature pattern, P-P-[YF]-N-[ILV]-[IV]-x(9)-[EQ], in the predicted β2 and β3 strands of the ACD. Phylogenetically, cyanophage sHSPs form a monophyletic clade closer to bacterial class A sHSPs than to cyanobacterial sHSPs. Furthermore, three sHSPs from their cellular host, Synechococcus, are phylogenetically close to plants sHSPs. Implications of evolutionary relationships between the sHSPs of cyanophages, bacterial class A, cyanobacteria, and plants are discussed.

  14. Iron regulation through the back door: iron-dependent metabolite levels contribute to transcriptional adaptation to iron deprivation in Saccharomyces cerevisiae.

    PubMed

    Ihrig, Jessica; Hausmann, Anja; Hain, Anika; Richter, Nadine; Hamza, Iqbal; Lill, Roland; Mühlenhoff, Ulrich

    2010-03-01

    Budding yeast (Saccharomyces cerevisiae) responds to iron deprivation both by Aft1-Aft2-dependent transcriptional activation of genes involved in cellular iron uptake and by Cth1-Cth2-specific degradation of certain mRNAs coding for iron-dependent biosynthetic components. Here, we provide evidence for a novel principle of iron-responsive gene expression. This regulatory mechanism is based on the modulation of transcription through the iron-dependent variation of levels of regulatory metabolites. As an example, the LEU1 gene of branched-chain amino acid biosynthesis is downregulated under iron-limiting conditions through depletion of the metabolic intermediate alpha-isopropylmalate, which functions as a key transcriptional coactivator of the Leu3 transcription factor. Synthesis of alpha-isopropylmalate involves the iron-sulfur protein Ilv3, which is inactivated under iron deficiency. As another example, decreased mRNA levels of the cytochrome c-encoding CYC1 gene under iron-limiting conditions involve heme-dependent transcriptional regulation via the Hap1 transcription factor. Synthesis of the iron-containing heme is directly correlated with iron availability. Thus, the iron-responsive expression of genes that are downregulated under iron-limiting conditions is conferred by two independent regulatory mechanisms: transcriptional regulation through iron-responsive metabolites and posttranscriptional mRNA degradation. Only the combination of the two processes provides a quantitative description of the response to iron deprivation in yeast.

  15. High-level expression in Corynebacterium glutamicum of nitrile hydratase from Rhodococcus rhodochrous for acrylamide production.

    PubMed

    Kang, Mi-Suk; Han, Sang-Soo; Kim, Mi-Young; Kim, Bu-Youn; Huh, Jong-Pil; Kim, Hak-Sung; Lee, Jin-Ho

    2014-05-01

    The nhhBAG gene of Rhodococcus rhodochrous M33 that encodes nitrile hydratase (NHase), converting acrylonitrile into acrylamide, was cloned and expressed in Corynebacterium glutamicum under the control of an ilvC promoter. The specific enzyme activity in recombinant C. glutamicum cells was about 13.6 μmol/min/mg dry cell weight (DCW). To overexpress the NHase, five types of plasmid variants were constructed by introducing mutations into 80 nucleotides near the translational initiation region (TIR) of nhhB. Of them, pNBM4 with seven mutations showed the highest NHase activity, exhibiting higher expression levels of NhhB and NhhA than wild-type pNBW33, mainly owing to decreased secondary-structure stability and an introduction of a conserved Shine-Dalgarno sequence in the translational initiation region. In a fed-batch culture of recombinant Corynebacterium cells harboring pNBM4, the cell density reached 53.4 g DCW/L within 18 h, and the specific and total enzyme activities were estimated to be 37.3 μmol/min/mg DCW and 1,992 μmol/min/mL, respectively. The use of recombinant Corynebacterium cells for the production of acrylamide from acrylonitrile resulted in a conversion yield of 93 % and a final acrylamide concentration of 42.5 % within 6 h when the total amount of fed acrylonitrile was 456 g.

  16. Linear and nonlinear ARMA model parameter estimation using an artificial neural network

    NASA Technical Reports Server (NTRS)

    Chon, K. H.; Cohen, R. J.

    1997-01-01

    This paper addresses parametric system identification of linear and nonlinear dynamic systems by analysis of the input and output signals. Specifically, we investigate the relationship between estimation of the system using a feedforward neural network model and estimation of the system by use of linear and nonlinear autoregressive moving-average (ARMA) models. By utilizing a neural network model incorporating a polynomial activation function, we show the equivalence of the artificial neural network to the linear and nonlinear ARMA models. We compare the parameterization of the estimated system using the neural network and ARMA approaches by utilizing data generated by means of computer simulations. Specifically, we show that the parameters of a simulated ARMA system can be obtained from the neural network analysis of the simulated data or by conventional least squares ARMA analysis. The feasibility of applying neural networks with polynomial activation functions to the analysis of experimental data is explored by application to measurements of heart rate (HR) and instantaneous lung volume (ILV) fluctuations.

  17. Genetic engineering to enhance the Ehrlich pathway and alter carbon flux for increased isobutanol production from glucose by Saccharomyces cerevisiae.

    PubMed

    Kondo, Takashi; Tezuka, Hironori; Ishii, Jun; Matsuda, Fumio; Ogino, Chiaki; Kondo, Akihiko

    2012-05-31

    The production of higher alcohols by engineered bacteria has received significant attention. The budding yeast, Saccharomyces cerevisiae, has considerable potential as a producer of higher alcohols because of its capacity to naturally fabricate fusel alcohols, in addition to its robustness and tolerance to low pH. However, because its natural productivity is not significant, we considered a strategy of genetic engineering to increase production of the branched-chain higher alcohol isobutanol, which is involved in valine biosynthesis. Initially, we overexpressed 2-keto acid decarboxylase (KDC) and alcohol dehydrogenase (ADH) in S. cerevisiae to enhance the endogenous activity of the Ehrlich pathway. We then overexpressed Ilv2, which catalyzes the first step in the valine synthetic pathway, and deleted the PDC1 gene encoding a major pyruvate decarboxylase with the intent of altering the abundant ethanol flux via pyruvate. Through these engineering steps, along with modification of culture conditions, the isobutanol titer of S. cerevisiae was elevated 13-fold, from 11 mg/l to 143 mg/l, and the yield was 6.6 mg/g glucose, which is higher than any previously reported value for S. cerevisiae. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Secretion of 2,3-dihydroxyisovalerate as a limiting factor for isobutanol production in Saccharomyces cerevisiae.

    PubMed

    Generoso, Wesley Cardoso; Brinek, Martin; Dietz, Heiko; Oreb, Mislav; Boles, Eckhard

    2017-05-01

    Isobutanol is a superior biofuel compared to ethanol, and it is naturally produced by yeasts. Previously, Saccharomyces cerevisiae has been genetically engineered to improve isobutanol production. We found that yeast cells engineered for a cytosolic isobutanol biosynthesis secrete large amounts of the intermediate 2,3-dihydroxyisovalerate (DIV). This indicates that the enzyme dihydroxyacid dehydratase (Ilv3) is limiting the isobutanol pathway and/or yeast exhibit effective transport systems for the secretion of the intermediate, competing with isobutanol synthesis. Moreover, we found that DIV cannot be taken up by the cells again. To identify the responsible transporters, microarray analysis was performed with a DIV producing strain compared to a wild type. Altogether, 19 genes encoding putative transporters were upregulated under DIV-producing conditions. Thirteen of these were deleted together with five homologous genes. A yro2 mrh1 deletion strain showed reduced DIV secretion, while a hxt5 deletion mutant showed increased isobutanol production. However, a strain deleted for all the 18 genes secreted even slightly increased amounts of the intermediates and less isobutanol. The lactate transporter Jen1 turned out to transport the intermediate 2-ketoisovalerate, but not DIV. The results suggest that the transport of DIV is a rather complex process and several unspecific transporters seem to be involved. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. All Prime Contract Awards by State or Country, Place, and Contractor, FY 88. Part 16. (Bristol, Rhode Island-Woodbury, Tennessee)

    DTIC Science & Technology

    1988-01-01

    1 r- tn 0 0 Ln 0 C7) 0 1 cnm>u I OLn 0-4 Oqq*-*v"-q 0 .4 -* v v v -4-4-4 -* -:T v 0 r4 N 0 N 0 C14 -0 t-Ixo- 0 00 CN*- Nmr - r-mL -4 C-UCo4 C() LA...00 140 l l - W I ( 1 00 000 (00 xxi o( UUULI ~ 4 4f(144lf0 .nL n t ninL nmr - .t . 0 (0, 0 1 (o 1 (0 ( (0 w1 qt0~01c~01- V 14Vwtq *r- r.- (ilV IW 0V...4tc coo I I I-S I UCO .J 0I .J C) .4n zI O I ca 4 01 144 OIOON I0 C 4 1- I- LA) I-01 qIOON M 0 InCl 0 0)0 L z l ooN I C.L- 0 0) I- z I n 1.- 1 4 ( DNP

  20. Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

    PubMed

    Zhang, Lei; Wang, Xumin; Liu, Tao; Wang, Guoliang; Chi, Shan; Liu, Cui; Wang, Haiyang

    2015-01-01

    In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

  1. Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici

    PubMed Central

    Sidhu, Y.S.; Cairns, T.C.; Chaudhari, Y.K.; Usher, J.; Talbot, N.J.; Studholme, D.J.; Csukai, M.; Haynes, K.

    2015-01-01

    The lack of techniques for rapid assembly of gene deletion vectors, paucity of selectable marker genes available for genetic manipulation and low frequency of homologous recombination are major constraints in construction of gene deletion mutants in Zymoseptoria tritici. To address these issues, we have constructed ternary vectors for Agrobacterium tumefaciens mediated transformation of Z. tritici, which enable the single step assembly of multiple fragments via yeast recombinational cloning. The sulfonylurea resistance gene, which is a mutated allele of the Magnaporthe oryzae ILV2 gene, was established as a new dominant selectable marker for Z. tritici. To increase the frequency of homologous recombination, we have constructed Z. tritici strains deficient in the non-homologous end joining pathway of DNA double stranded break repair by inactivating the KU70 and KU80 genes. Targeted gene deletion frequency increased to more than 85% in both Z. tritici ku70 and ku80 null strains, compared to ⩽10% seen in the wild type parental strain IPO323. The in vitro growth and in planta pathogenicity of the Z. tritici ku70 and ku80 null strains were comparable to strain IPO323. Together these molecular tools add significantly to the platform available for genomic analysis through targeted gene deletion or promoter replacements and will facilitate large-scale functional characterization projects in Z. tritici. PMID:26092796

  2. Isolation of transposon Tn551 insertions near chromosomal markers of interest in Staphylococcus aureus.

    PubMed Central

    Luchansky, J B; Pattee, P A

    1984-01-01

    A procedure was developed to isolate insertions of transposon Tn551 near other markers of interest on the chromosome of Staphylococcus aureus NCTC 8325. When an inoculum of strain 8325-4 carrying a thermosensitive mutant of plasmid pI258 (on which Tn551 resides) was inoculated into brain heart infusion agar plus erythromycin and grown to saturation at 43 degrees C, the transforming DNA extracted from this population of cells contained a random collection of different chromosomal insertions of Tn551; this DNA is referred to as pooled Tn551 DNA. When erythromycin-sensitive recipient strains containing chromosomal markers of interest were transformed with pooled Tn551 DNA, and the resulting Emr transformants were screened for coinheritance of the donor allele of the marker of interest, insertions of Tn551 were isolated near several markers, including fus-149, tet-3490, mec-4916, pig-131, ilv-129, pur-140, and uraA141. Many of the insertions were within the linkage groups that contained these markers, and several insertions occupied different positions between the linkage groups in heretofore undefined regions of the circular chromosomal map of S. aureus. These insertions of transposon Tn551 extend the known limits of the existing linkage groups, provide linkage data and map locations for markers not previously mapped, and provide a means to map markers which cannot be directly selected. PMID:6090397

  3. Integrative Food-Grade Expression System Based on the Lactose Regulon of Lactobacillus casei

    PubMed Central

    Gosalbes, María José; Esteban, Carlos David; Galán, José Luis; Pérez-Martínez, Gaspar

    2000-01-01

    The lactose operon from Lactobacillus casei is regulated by very tight glucose repression and substrate induction mechanisms, which made it a tempting candidate system for the expression of foreign genes or metabolic engineering. An integrative vector was constructed, allowing stable gene insertion in the chromosomal lactose operon of L. casei. This vector was based on the nonreplicative plasmid pRV300 and contained two DNA fragments corresponding to the 3′ end of lacG and the complete lacF gene. Four unique restriction sites were created, as well as a ribosome binding site that would allow the cloning and expression of new genes between these two fragments. Then, integration of the cloned genes into the lactose operon of L. casei could be achieved via homologous recombination in a process that involved two selection steps, which yielded highly stable food-grade mutants. This procedure has been successfully used for the expression of the E. coli gusA gene and the L. lactis ilvBN genes in L. casei. Following the same expression pattern as that for the lactose genes, β-glucuronidase activity and diacetyl production were repressed by glucose and induced by lactose. This integrative vector represents a useful tool for strain improvement in L. casei that could be applied to engineering fermentation processes or used for expression of genes for clinical and veterinary uses. PMID:11055930

  4. High-energy water sites determine peptide binding affinity and specificity of PDZ domains.

    PubMed

    Beuming, Thijs; Farid, Ramy; Sherman, Woody

    2009-08-01

    PDZ domains have well known binding preferences for distinct C-terminal peptide motifs. For most PDZ domains, these motifs are of the form [S/T]-W-[I/L/V]. Although the preference for S/T has been explained by a specific hydrogen bond interaction with a histidine in the PDZ domain and the (I/L/V) is buried in a hydrophobic pocket, the mechanism for Trp specificity at the second to last position has thus far remained unknown. Here, we apply a method to compute the free energies of explicit water molecules and predict that potency gained by Trp binding is due to a favorable release of high-energy water molecules into bulk. The affinities of a series of peptides for both wild-type and mutant forms of the PDZ domain of Erbin correlate very well with the computed free energy of binding of displaced waters, suggesting a direct relationship between water displacement and peptide affinity. Finally, we show a correlation between the magnitude of the displaced water free energy and the degree of Trp-sensitivity among subtypes of the HTRA PDZ family, indicating a water-mediated mechanism for specificity of peptide binding.

  5. Construction and application of an efficient multiple-gene-deletion system in Corynebacterium glutamicum.

    PubMed

    Hu, Jinyu; Tan, Yanzhen; Li, Yanyan; Hu, Xiaoqing; Xu, Daqing; Wang, Xiaoyuan

    2013-11-01

    Gene deletion techniques are important for modifying Corynebacterium glutamicum, the bacterium for industrial production of amino acids. In this study, a novel multiple-gene-deletion system for C. glutamicum was developed. The system is composed of three plasmids pDTW109, pDTW201 and pDTW202. pDTW109 is a temperature-sensitive vector which harbors a cat gene under the tacM promoter, a cre gene under the tac promoter, an origin oriE for replicating in Escherichia coli, and another origin rep(TS) for replicating in C. glutamicum only at low temperatures; it has high transformation efficiency in C. glutamicum and can be easily eliminated by growing at 37°C. pDTW201 and pDTW202 carry loxp-flanked or mutant lox-flanked kan, respectively. This deletion system combines homologous recombination and Cre/lox site-specific recombination, could efficiently delete the aceE gene from the chromosome of C. glutamicum ATCC13032, ATCC13869 or ATCC14067, respectively, and could also delete both genes of aceE and ilvA from the chromosome of C. glutamicum ATCC14067. The system is simple and efficient, and can be easily implemented for multiple-gene-deletion in C. glutamicum. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Systems metabolic engineering of Escherichia coli for L-threonine production

    PubMed Central

    Lee, Kwang Ho; Park, Jin Hwan; Kim, Tae Yong; Kim, Hyun Uk; Lee, Sang Yup

    2007-01-01

    Amino-acid producers have traditionally been developed by repeated random mutagenesis owing to the difficulty in rationally engineering the complex and highly regulated metabolic network. Here, we report the development of the genetically defined L-threonine overproducing Escherichia coli strain by systems metabolic engineering. Feedback inhibitions of aspartokinase I and III (encoded by thrA and lysC, respectively) and transcriptional attenuation regulations (located in thrL) were removed. Pathways for Thr degradation were removed by deleting tdh and mutating ilvA. The metA and lysA genes were deleted to make more precursors available for Thr biosynthesis. Further target genes to be engineered were identified by transcriptome profiling combined with in silico flux response analysis, and their expression levels were manipulated accordingly. The final engineered E. coli strain was able to produce Thr with a high yield of 0.393 g per gram of glucose, and 82.4 g/l Thr by fed-batch culture. The systems metabolic engineering strategy reported here may be broadly employed for developing genetically defined organisms for the efficient production of various bioproducts. PMID:18059444

  7. De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth

    PubMed Central

    Fisher, Michael A.; McKinley, Kara L.; Bradley, Luke H.; Viola, Sara R.; Hecht, Michael H.

    2011-01-01

    A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >106 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles. We probed the capacity of proteins from this library to function in vivo by testing their abilities to rescue 27 different knockout strains of Escherichia coli, each deleted for a conditionally essential gene. Four different strains – ΔserB, ΔgltA, ΔilvA, and Δfes – were rescued by specific sequences from our library. Further experiments demonstrated that a strain simultaneously deleted for all four genes was rescued by co-expression of four novel sequences. Thus, cells deleted for ∼0.1% of the E. coli genome (and ∼1% of the genes required for growth under nutrient-poor conditions) can be sustained by sequences designed de novo. PMID:21245923

  8. Structural and functional analysis of the GABARAP interaction motif (GIM)

    DOE PAGES

    Rogov, Vladimir V.; Stolz, Alexandra; Ravichandran, Arvind C.; ...

    2017-06-27

    Through the canonical LC3 interaction motif (LIR), [W/F/Y]–X1–X2[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a GABARAP Interaction Motif (GIM) sequence ([W/F]–[V/I]–X2–V) that the adaptor protein PLEKHM1 tightly conforms to. Using biophysical and structural approaches, we show that the PLEKHM1–LIR is indeed 11–fold more specific for GABARAP than LC3B. Selective mutation of the X1 and X2more » positions either completely abolished the interaction with all LC3 and GABARAPs or increased PLEKHM1–GIM selectivity 20–fold towards LC3B. Finally, we show that conversion of p62/SQSTM1, FUNDC1 and FIP200 LIRs into our newly defined GIM, by introducing two valine residues, enhances their interaction with endogenous GABARAP over LC3B. In conclusion, the identification of a GABARAP–specific interaction motif will aid the identification and characterization of the expanding array of autophagy receptor and adaptor proteins and their in vivo functions.« less

  9. Linear and nonlinear ARMA model parameter estimation using an artificial neural network

    NASA Technical Reports Server (NTRS)

    Chon, K. H.; Cohen, R. J.

    1997-01-01

    This paper addresses parametric system identification of linear and nonlinear dynamic systems by analysis of the input and output signals. Specifically, we investigate the relationship between estimation of the system using a feedforward neural network model and estimation of the system by use of linear and nonlinear autoregressive moving-average (ARMA) models. By utilizing a neural network model incorporating a polynomial activation function, we show the equivalence of the artificial neural network to the linear and nonlinear ARMA models. We compare the parameterization of the estimated system using the neural network and ARMA approaches by utilizing data generated by means of computer simulations. Specifically, we show that the parameters of a simulated ARMA system can be obtained from the neural network analysis of the simulated data or by conventional least squares ARMA analysis. The feasibility of applying neural networks with polynomial activation functions to the analysis of experimental data is explored by application to measurements of heart rate (HR) and instantaneous lung volume (ILV) fluctuations.

  10. Activity of exporters of Escherichia coli in Corynebacterium glutamicum, and their use to increase L-threonine production.

    PubMed

    Diesveld, Ramon; Tietze, Nadine; Fürst, Oliver; Reth, Alexander; Bathe, Brigitte; Sahm, Hermann; Eggeling, Lothar

    2009-01-01

    L-Threonine is an important biotechnological product and Corynebacterium glutamicum is able to synthesize and accumulate this amino acid to high intracellular levels. We here use four exporters of Escherichia coli and show that three of them operate in C. glutamicum, with RhtA and RhtC being the most effective. Whereas RhtA was unspecific, resulting in L-homoserine together with L-threonine excretion, this was not the case with RhtC. Expression of rhtC reduced the intracellular L-threonine concentration from 140 to 11 mM and resulted in maximal excretion rates of 11.2 nmol min(-1) mg(-1) as compared to 2.3 nmol min(-1) mg(-1) obtained without rhtC expression. In combination with an ilvA mutation generated and introduced into the chromosome, an accumulation of up to 54 mM L-threonine was achieved as compared to 21 mM obtained with the ancestor strain. This shows that expression of rhtC is the pivotal point for industrial relevant L-threonine production with C. glutamicum, and might encourage in general the use of heterologous exporters in the field of white biotechnology to make full use of biosynthesis pathways.

  11. Metabolic engineering for high glycerol production by the anaerobic cultures of Saccharomyces cerevisiae.

    PubMed

    Semkiv, Marta V; Dmytruk, Kostyantyn V; Abbas, Charles A; Sibirny, Andriy A

    2017-03-09

    Glycerol is used by the cosmetic, paint, automotive, food, and pharmaceutical industries and for production of explosives. Currently, glycerol is available in commercial quantities as a by-product from biodiesel production, but the purity and the cost of its purification are prohibitive. The industrial production of glycerol by glucose aerobic fermentation using osmotolerant strains of the yeasts Candida sp. and Saccharomyces cerevisiae has been described. A major drawback of the aerobic process is the high cost of production. For this reason, the development of yeast strains that effectively convert glucose to glycerol anaerobically is of great importance. Due to its ability to grow under anaerobic conditions, the yeast S. cerevisiae is an ideal system for the development of this new biotechnological platform. To increase glycerol production and accumulation from glucose, we lowered the expression of TPI1 gene coding for triose phosphate isomerase; overexpressed the fused gene consisting the GPD1 and GPP2 parts coding for glycerol-3-phosphate dehydrogenase and glycerol-3-phosphate phosphatase, respectively; overexpressed the engineered FPS1 gene that codes for aquaglyceroporin; and overexpressed the truncated gene ILV2 that codes for acetolactate synthase. The best constructed strain produced more than 20 g of glycerol/L from glucose under micro-aerobic conditions and 16 g of glycerol/L under anaerobic conditions. The increase in glycerol production led to a drop in ethanol and biomass accumulation.

  12. LAPTM4B is a PtdIns(4,5)P2 effector that regulates EGFR signaling, lysosomal sorting, and degradation.

    PubMed

    Tan, Xiaojun; Sun, Yue; Thapa, Narendra; Liao, Yihan; Hedman, Andrew C; Anderson, Richard A

    2015-02-12

    Lysosomal degradation is essential for the termination of EGF-stimulated EGF receptor (EGFR) signaling. This requires EGFR sorting to the intraluminal vesicles (ILVs) of multi-vesicular endosomes (MVEs). Cytosolic proteins including the ESCRT machineries are key regulators of EGFR intraluminal sorting, but roles for endosomal transmembrane proteins in receptor sorting are poorly defined. Here, we show that LAPTM4B, an endosomal transmembrane oncoprotein, inhibits EGF-induced EGFR intraluminal sorting and lysosomal degradation, leading to enhanced and prolonged EGFR signaling. LAPTM4B blocks EGFR sorting by promoting ubiquitination of Hrs (an ESCRT-0 subunit), which inhibits the Hrs association with ubiquitinated EGFR. This is counteracted by the endosomal PIP kinase, PIPKIγi5, which directly binds LAPTM4B and neutralizes the inhibitory function of LAPTM4B in EGFR sorting by generating PtdIns(4,5)P2 and recruiting SNX5. PtdIns(4,5)P2 and SNX5 function together to protect Hrs from ubiquitination, thereby promoting EGFR intraluminal sorting. These results reveal an essential layer of EGFR trafficking regulated by LAPTM4B, PtdIns(4,5)P2 signaling, and the ESCRT complex and define a mechanism by which the oncoprotein LAPTM4B can transform cells and promote tumor progression.

  13. MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis.

    PubMed

    Buschow, Sonja I; van Balkom, Bas W M; Aalberts, Marian; Heck, Albert J R; Wauben, Marca; Stoorvogel, Willem

    2010-01-01

    Professional antigen-presenting cells secrete major histocompatibility complex class II (MHC II) carrying exosomes with unclear physiological function(s). Exosomes are first generated as the intraluminal vesicles (ILVs) of a specific type of multivesicular body, and are then secreted by fusion of this compartment with the plasma membrane. We have previously shown that in contrast to the sorting of MHC II at lysosomally targeted multivesicular bodies, sorting of MHC II into exosomes does not rely on MHC II ubiquitination. In search for proteins that drive the incorporation of MHC II into exosomes or functionally discriminate exosomal from plasma membrane MHC II, we first analyzed the total proteome of highly purified B cell-derived exosomes using sensitive and accurate mass spectrometry (MS), and identified 539 proteins, including known and not previously identified constituents. Using quantitative MS, we then identified a small subset of proteins that were specifically co-immunoprecipitated with MHC II from detergent-solubilized exosomes. These include HSC71, HSP90, 14-3-3ɛ, CD20 and pyruvate kinase type M2 (PKM2), and we speculate on the functionality of their interaction with exosomal MHC II.

  14. More precise mapping of the replication origin in Escherichia coli K-12.

    PubMed

    Louarn, J; Funderburgh, M; Bird, R E

    1974-10-01

    The origin of replication in Escherichia coli K-12 was mapped by determining the rate of marker replication during a synchronous round of replication. Four isogenic strains were made lysogenic for lambdaind(-) and for phage Mu-1, with Mu-1 integrated into a different chromosomal location in each strain. Cultures were starved for amino acids to allow completion of chromosome replication cycles and then starved for thymine in the presence of amino acids, and a synchronous cycle of replication was initiated by the addition of thymine. Samples were exposed to radioactive thymidine at intervals, deoxyribonucleic acid was extracted, and the rate of marker replication was determined by deoxyribonucleic acid-deoxyribonucleic acid hybridization to filters containing Mu-1, lambda, and E. coli deoxyribonucleic acid. The results confirm that the origin of replication is near ilv. The travel times of the replication forks, calculated from the data obtained for cultures with doubling times of approximately 40 and 61 min, are 40 and 52 min, respectively.

  15. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.

    PubMed

    Lambrecht, Jennifer A; Flynn, Jeffrey M; Downs, Diana M

    2012-01-27

    The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life, suggesting that the role of these proteins arose early and was maintained throughout evolution. Metabolic consequences of lacking this protein in Salmonella enterica and other organisms have been described, but the biochemical function of YjgF remained unknown. This work provides the first description of a conserved biochemical activity for the YjgF protein family. Our data support the conclusion that YjgF proteins have enamine/imine deaminase activity and accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Results from structure-guided mutagenesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia release by positioning a critical water molecule in the active site. YjgF is renamed RidA (reactive intermediate/imine deaminase A) to reflect the conserved activity of the protein family described here. This study, combined with previous physiological studies on yjgF mutants, suggests that intermediates of pyridoxal 5'-phosphate-mediated reactions may have metabolic consequences in vivo that were previously unappreciated. The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms.

  16. Bacterial production of isobutanol without expensive reagents.

    PubMed

    Akita, Hironaga; Nakashima, Nobutaka; Hoshino, Tamotsu

    2015-01-01

    Isobutanol is attracting attention as a potential biofuel because it has higher energy density and lower hygroscopicity than ethanol. To date, several effective methods for microbial production of isobutanol have been developed, but they require expensive reagents to maintain expression plasmids and induce expression, which is not suitable for practical production. Here, we describe a simple and efficient method for isobutanol production in Escherichia coli. It is noteworthy that no expression plasmids or inducers were used during the production. Instead, heterologous genes necessary for isobutanol production were all knocked into the genome, and the expression of those genes was induced by xylose, which is present in most biomass feedstocks. The constructed strain (mlcXT7-LAFC-AAKCD) contains Bacillus subtilis alsS, E. coli ilvCD, Lactococcus lactis adhA, and L. lactis kivd genes in its genome and efficiently produced isobutanol from glucose and xylose in flask batch cultures. Under conditions in which the temperature and pH of the medium and the aeration in the culture were all optimized, the final isobutanol concentration reached 8.4 g L(-1) after 48 h. Isobutanol was also produced using hydrolysate from Japanese cedar as the carbon source without supplemented glucose, xylose, or yeast extract. Under those conditions, isobutanol (3.7 g L(-1)) was produced in 96 h. Taken together, these results indicate that the developed strain is potentially useful for industrial isobutanol production.

  17. Proteomic analysis of cell wall in four pathogenic species of Candida exposed to oxidative stress.

    PubMed

    Ramírez-Quijas, Mayra Denisse; López-Romero, Everardo; Cuéllar-Cruz, Mayra

    2015-10-01

    In order for Candida species to adhere and colonize human host cells they must express cell wall proteins (CWP) and adapt to reactive oxygen species (ROS) generated by phagocytic cells of the human host during the respiratory burst. However, how these pathogens change the expression of CWP in response to oxidative stress (OSR) is not known. Here, fifteen moonlight-like CWP were identified that expressed differentially in four species of Candida after they were exposed to H2O2 or menadione (O2(-)). These proteins included: (i) glycolytic enzymes, such as glyceraldehyde-3-phosphate dehydrogenase (Gapdh), fructose-bisphosphate aldolase (Fba1), phosphoglycerate mutase (Gpm1), phosphoglycerate kinase (Pgk), pyruvate kinase (Pk) and enolase (Eno1); (ii) the heat shock proteins Ssb1 and Ssa2; (iii) OSR proteins such as peroxyredoxin (Tsa1), the stress protein Ddr48 (Ddr48) and glutathione reductase (Glr1); (iv) other metabolic enzymes such as ketol-acid reductoisomerase (Ilv5) and pyruvate decarboxylase (Pdc1); and (v) other proteins such as elongation factor 1-beta (Efb1) and the 14-3-3 protein homolog. RT-PCR revealed that transcription of the genes coding for some of the identified CWP are differentially regulated. To our knowledge this is the first report showing that moonlight-like CWP are the first line of defense of Candida against ROS, and that they are differentially regulated in each of these pathogens. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Effect of a water soluble derivative of alpha-tocopherol on radiation response of Saccharomyces cerevisiae.

    PubMed

    Singh, R K; Verma, N C; Kagiya, V T

    2001-12-01

    The radioprotection conferred by a highly water soluble glucose derivative of alpha-tocopherol, namely, 2-(alpha-D-glucopyranosyl) methyl-2,5,7,8-tetramethylchroman-6-ol (TMG) in Saccharomyces cerevisiae was studied. Cells grown in standard YEPD-agar medium and irradiated in the presence of TMG showed a concentration dependent higher survival up to 10 mM of TMG in comparison to cells irradiated in distilled water. Treatment of TMG to cells given either before or immediately after irradiation but not during irradiation, had no effect on their radiation response. S. cerevisiae strain LP1383 (rad52) which is defective in recombination repair showed enhanced radioresistance only when subjected to irradiation in presence of TMG. Cells of rad52 strain grown in the medium containing TMG showed a radiation response similar to that of cells grown in the medium without TMG. The nature of TMG dependent enhanced radioresistance was studied by scoring the mutations in the strain D-7, which behaved like wild type strain in complete medium, at trp and ilv loci. Our study indicated that TMG confers radioresistance in S. cerevisiae possibly by two mechanisms viz. (i), by eliminating radiation induced reactive free radicals when the irradiation is carried out in the presence of TMG and (ii), by activating an error prone repair process involving RAD52 gene, when the cells are grown in the medium containing TMG.

  19. Monitoring the influence of high-gravity brewing and fermentation temperature on flavour formation by analysis of gene expression levels in brewing yeast.

    PubMed

    Saerens, S M G; Verbelen, P J; Vanbeneden, N; Thevelein, J M; Delvaux, F R

    2008-10-01

    During fermentation, the yeast Saccharomyces cerevisiae produces a broad range of aroma-active substances, which are vital for the complex flavour of beer. In order to obtain insight into the influence of high-gravity brewing and fermentation temperature on flavour formation, we analysed flavour production and the expression level of ten genes (ADH1, BAP2, BAT1, BAT2, ILV5, ATF1, ATF2, IAH1, EHT1 and EEB1) during fermentation of a lager and an ale yeast. Higher initial wort gravity increased acetate ester production, while the influence of higher fermentation temperature on aroma compound production was rather limited. In addition, there is a good correlation between flavour production and the expression level of specific genes involved in the biosynthesis of aroma compounds. We conclude that yeasts with desired amounts of esters and higher alcohols, in accordance with specific consumer preferences, may be identified based on the expression level of flavour biosynthesis genes. Moreover, these results demonstrate that the initial wort density can determine the final concentration of important volatile aroma compounds, thereby allowing beneficial adaptation of the flavour of beer.

  20. Efficient acquisition of high-resolution 4-D diagonal-suppressed methyl-methyl NOESY for large proteins

    NASA Astrophysics Data System (ADS)

    Wen, Jie; Zhou, Pei; Wu, Jihui

    2012-05-01

    The methyl-methyl NOESY experiment plays an important role in determining the global folds of large proteins. Despite the high sensitivity of this experiment, the analysis of methyl-methyl NOEs is frequently hindered by the limited chemical shift dispersion of methyl groups, particularly methyl protons. This makes it difficult to unambiguously assign all of the methyl-methyl NOE crosspeaks using 3-D spectroscopy. The recent development of sparse sampling methods enables highly efficient acquisition of high-resolution 4-D spectra, which provides an excellent solution to resolving the degeneracy of methyl signals. However, many reconstruction algorithms for processing sparsely-sampled NMR data do not provide adequate suppression of aliasing artifacts in the presence of strong NOE diagonal signals. In order to overcome this limitation, we present a 4-D diagonal-suppressed methyl-methyl NOESY experiment specifically optimized for ultrasparse sampling and evaluate it using a deuterated, ILV methyl-protonated sample of the 42 kDa Escherichia coli maltose binding protein (MBP). Suppression of diagonal signals removes the dynamic range barrier of the methyl-methyl NOESY experiment such that residual aliasing artifacts in the CLEAN-reconstructed high-resolution 4-D spectrum can be further reduced. At an ultrasparse sampling rate of less than 1%, we were able to identify and unambiguously assign the vast majority of expected NOE crosspeaks between methyl groups separated by less than 5 Å and to detect very weak NOE crosspeaks from methyl groups that are over 7 Å apart.

  1. Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

    PubMed Central

    Liu, Tao; Wang, Guoliang; Chi, Shan; Liu, Cui; Wang, Haiyang

    2015-01-01

    In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome. PMID:26426800

  2. 40Ar/39Ar Dating of Zn-Pb-Ag Mineralization in the Northern Brooks Range, Alaska

    USGS Publications Warehouse

    Werdon, Melanie B.; Layer, Paul W.; Newberry, Rainer J.

    2004-01-01

    The 40Ar/39Ar laser step-heating method potentially can be used to provide absolute ages for a number of formerly undatable, low-temperature ore deposits. This study demonstrates the use of this method by determining absolute ages for Zn-Pb-Ag sediment-hosted massive sulfide deposits and vein-breccia occurrences found throughout a 300-km-long, east-west-trending belt in the northern Brooks Range, Alaska. Massive sulfide deposits are hosted by Mississippian to Pennsylvanian(?) black carbonaceous shale, siliceous mudstone, and lesser chert and carbonate turbidites of the Kuna Formation (e.g., Red Dog, Anarraaq, Lik (Su), and Drenchwater). The vein-breccia occurrences (e.g., Husky, Story Creek, West Kivliktort Mountain, Vidlee, and Kady) are hosted by a deformed but only weakly metamorphosed package of Upper Devonian to Lower Mississippian mixed continental and marine clastic rocks (the Endicott Group) that stratigraphically underlie the Kuna Formation. The vein-breccias are mineralogically similar to, but not spatially associated with, known massive sulfide deposits. The region's largest shale-hosted massive sulfide deposit is Red Dog; it has reserves of 148 Mt grading 16.6 percent zinc, 4.5 percent lead, and 77 g of silver per tonne. Hydrothermally produced white mica in a whole-rock sample from a sulfide-bearing igneous sill within the Red Dog deposit yielded a plateau age of 314.5 Ma. The plateau age of this whole-rock sample records the time at which temperatures cooled below the argon closure temperature of the white mica and is interpreted to represent the minimum age limit for massive sulfide-related hydrothermal activity in the Red Dog deposit. Sulfide-bearing quartz veins at Drenchwater crosscut a hypabyssal intrusion with a maximum biotite age of 337.0 Ma. Despite relatively low sulfide deposition temperatures in the vein-breccia occurrences (162°-251°C), detrital white mica in sandstone immediately adjacent to large vein-breccia zones was partially to

  3. Sulfur-, oxygen-, and carbon-isotope studies of Ag-Pb-Zn vein-breccia occurrences, sulfide-bearing concretions, and barite deposits in the north-central Brooks Range, with comparisons to shale-hosted stratiform massive sulfide deposits: A section in Geologic studies in Alaska by the U.S. Geological Survey, 1998

    USGS Publications Warehouse

    Kelley, Karen D.; Leach, David L.; Johnson, Craig A.

    2000-01-01

    Stratiform shale-hosted massive sulfide deposits, sulfidebearing concretions and vein breccias, and barite deposits are widespread in sedimentary rocks of Late Devonian to Permian age in the northern Brooks Range. All of the sulfide-bearing concretions and vein breccias are hosted in mixed continental-marine clastic rocks of the Upper Devonian to Lower Mississippian Endicott Group. The clastic rocks and associated sulfide occurrences underlie chert and shale of Mississippian-Pennsylvanian(?) age that contain large stratiform massive sulfide deposits like that at Red Dog. The relative stratigraphic position of the vein breccias, as well as previously published mineralogical, geochemical, and lead-isotope data, suggest that the vein breccias formed coevally with overlying shale-hosted massive sulfide deposits and that they may represent pathways of oreforming hydrothermal fluids. Barite deposits are hosted either in Mississippian chert and limestone (at essentially the same stratigraphic position as the shale-hosted massive sulfide deposits) or Permian chert and shale. Although most barite deposits have no associated base-metal mineralization, barite occurs with massive sulfide deposits at the Red Dog deposit.Galena and sphalerite from most vein breccias have δ34S values from –7.3 to –0.7‰ (per mil) and –5.1 to 3.6‰, respectively; sphalerite from sulfide-bearing concretions have δ34S values of 0.7 and 4.7‰. This overall range in δ34S values largely overlaps with the range previously determined for galena and sphalerite from shale-hosted massive sulfide deposits at Red Dog and Drenchwater. The Kady vein-breccia occurrence is unusual in having higher δ34S values for sphalerite (12.1 to 12.9‰) and pyrite (11.3‰), consistent with previously published values for the shale-hosted Lik deposit. The correspondence in sulfur isotopic compositions between the stratiform and vein-breccia deposits suggests that they share a common source of reduced sulfur, or

  4. Photographing Internal Fractures of the Archaeological Statues with 3D Visualization of Ground Penetrating Radar Data

    NASA Astrophysics Data System (ADS)

    Kadioglu, S.; Kadioglu, Y. K.

    2009-04-01

    PHOTOGRAPHING INTERNAL FRACTURES OF THE ARCHAEOLOGICAL STATUES WITH 3D VISUALIZATION OF GROUND PENETRATING RADAR DATA Selma KADIOGLU1 and Yusuf K. KADIOGLU2 1Ankara University, Faculty of Engineering, Department of Geophysical Engineering, 06100 Tandogan/ANKARA-TURKEY kadioglu@eng.ankara.edu.tr 2Ankara University, Faculty of Engineering, Department of Geological Engineering, 06100 Tandogan/ANKARA-TURKEY kadi@eng.ankara.edu.tr The aim of the study is to illustrate a new approach to image the discontinuities in the archaeological statues before restoration studies using ground penetrating radar (GPR) method. The method was successfully applied to detect and map the fractures and cavities of the two monument groups and lion statues in Mustafa Kemal ATATURK's tumb (ANITKABIR) in Ankara-Turkey. The tumb, which has been started to build in 1944 and completed in 1953, represents Turkish people and Ataturk, who is founder of the Republic of Turkey. Therefore this monument is very important for Turkish people. The monument groups and lion statues have been built from travertine rocks. These travertine have vesicular textures with the percent of 12. They have been mainly composed of calcite, aragonite with rare amount of plant relict and clay minerals. The concentrations of Fe, Mg, Cl and Mn may lead to verify their colours changing from white through pale green to beige. The atmospheric contamination of Ankara has been caused to cover some parts of the surface of these travertine with a thin film of Pb as blackish in colour. The micro fractures have been observed specially at the rim of the vesicular of the rocks by the polarizing microscope. Parallel two dimensional (2D) GPR profile data with 10cm profile space were acquired by RAMAC CU II system with 1600 MHz shielded antenna on the monument groups (three women, three men and 24 lion statues) and then a three dimensional (3D) data volume were built using parallel 2D GPR data. Air-filled fractures and cavities in the

  5. Secretion expression of SOD1 and its overlapping function with GSH in brewing yeast strain for better flavor and anti-aging ability.

    PubMed

    Wang, Zhaoyue; Bai, Xuejing; He, Xiuping; Zhang, Borun

    2014-09-01

    Superoxide dismutase (SOD) is a significant antioxidant, but unlike glutathione (GSH), SOD cannot be secreted into beer by yeast cells during fermentation, this directly leads to the limited application of SOD in beer anti-aging. In this investigation, we constructed the SOD1 secretion cassette in which strong promoter PGK1p and the sequence of secreting signal factor from Saccharomyces cerevisiae were both harbored to the upstream of coding sequence of SOD1 gene, as a result, the obtained strains carrying this cassette successfully realized the secretion of SOD1. In order to overcome the limitation of previous genetic modification on yeast strains, one new comprehensive strategy was adopted targeting the suitable homologous sites by gene deletion and SOD1 + GSH1 co-overexpression, and the new strain ST31 (Δadh2::SOD1 + Δilv2::GSH1) was constructed. The results of the pilot-scale fermentation showed that the diacetyl content of ST31 was lower by 42 % than that of the host, and the acetaldehyde content decreased by 29 %, the GSH content in the fermenting liquor of ST31 increased by 29 % compared with the host. Both SOD activity test and the positive and negative staining assay after native PAGE indicated that the secreted active SOD in the fermenting liquor of ST31 was mainly a dimer with the size of 32,500 Da. The anti-aging indexes such as the thiobarbituric acid and the resistance staling value further proved that the flavor stability of the beer brewed with strain ST31 was not only better than that of the original strain, but also better than that of the previous engineering strains. The multi-modification and comprehensive improvement of the beer yeast strain would greatly enhance beer quality than ever, and the self-cloning strain would be attractive to the public due to its bio-safety.

  6. Construction of an industrial brewing yeast strain to manufacture beer with low caloric content and improved flavor.

    PubMed

    Wang, Jin-Jing; Wang, Zhao-Yue; Liu, Xi-Feng; Guo, Xue-Na; He, Xiu-Ping; Wensel, Pierre Christian; Zhang, Bo-Run

    2010-04-01

    In this study, the problems of high caloric content, increased maturation time and off-flavors in commercial beer manufacture arising from residual sugar, diacetyl, and acetaldehyde levels were addressed. A recombinant industrial brewing yeast strain (TQ1) was generated from T1 [Lipomyces starkeyi dextranase gene (LSD1) introduced, alpha-acetohydroxyacid synthase gene (ILV2) disrupted] by introducing Saccharomyces cerevisiae glucoamylase (SGA1) and a strong promoter PGK1 while disrupting the genes coding alcohol dehydrogenase (ADH2). The highest glucoamylase activity for TQ1 was 93.26 U/ml compared with host strain T1 (12.36 U/ml) and wild-type industrial yeast strain YSF5 (10.39 U/ml), respectively. European Brewery Convention (EBC) tube fermentation tests comparing the fermentation broths of TQ1 with T1 and YSF5 showed that the real extract were reduced by 15.79% and 22.47%; the main residual maltotriose concentration were reduced by 13.75% and 18.82%; the caloric content were reduced by 27.18 and 35.39 calories per 12 oz. Due to the disruption of ADH2 gene in TQ1, the off-flavor acetaldehyde concentration in the fermentation broth were 9.43% and 13.28% respectively lower than that of T1 and YSF5. No heterologous DNA sequences or drug-resistance genes were introduced into TQ1. So, the gene manipulations in this work properly solved the addressed problems in commercial beer manufacture.

  7. Prevalence of F107 fimbriae on Escherichia coli isolated from pigs with oedema disease or postweaning diarrhoea.

    PubMed

    Imberechts, H; Bertschinger, H U; Stamm, M; Sydler, T; Pohl, P; De Greve, H; Hernalsteens, J P; Van Montagu, M; Lintermans, P

    1994-06-01

    The study comprises fifty 4 to 12 weeks old pigs that died from oedema disease or severe diarrhoea. Smears were prepared from the mucosa of duodenum, jejunum and ileum, and by immunofluorescence F107 fimbrial antigens were detected. E. coli strains were isolated from the intestines and were characterised by slide agglutination (serogroup and F107 fimbriae production), by their cytotoxicity for Vero cells, and by gene amplification (genes coding for the major F107 subunit FedA, the toxin causing oedema disease SLT-IIv, and enterotoxins LTI, STIa and STII). F107 fimbriae were demonstrated in association with E. coli of serogroups O139:K12 and O141:K85a,b but not of serogroup O149:K91:F4a,c. Expression in culture of F107 fimbriae by some isolates gave additional evidence for production of these fimbriae by ETEC strains. The genetic determinant of SLT-Ilv was found in association with F107, and could not be detected in serogroup O149:K91:F4a,c. Gene fedA was demonstrated in two isolates which were devoid of SLT-IIv. Most isolates from cases of oedema disease belonged to serogroup O139:K12 and did not contain enterotoxin genes. Isolates from pigs that suffered from diarrhoea were serotyped O141:K85a,b or O149:K91:F4a,c, and carried at least two enterotoxin genes in their genomes. In a small proportion of the cases F107 antigens were demonstrated in intestinal smears although gene fedA was not detected in the corresponding isolates. The results confirm the importance of F107 fimbriae as virulence factor in oedema disease E. coli strains, but also demonstrate that F107 fimbriae can be found in association with postweaning diarrhoea isolates. In these latter strains enterotoxins were always demonstrated, irrespective of the presence of toxin SLT-IIv.

  8. Attenuating l-lysine production by deletion of ddh and lysE and their effect on l-threonine and l-isoleucine production in Corynebacterium glutamicum.

    PubMed

    Dong, Xunyan; Zhao, Yue; Hu, Jinyu; Li, Ye; Wang, Xiaoyuan

    2016-11-01

    The fermentative production of l-threonine and l-isoleucine with Corynebacterium glutamicum is usually accompanied by the by-production of l-lysine, which shares partial biosynthesis pathway with l-threonine and l-isoleucine. Since the direct precursor for l-lysine synthesis, diaminopimelate, is a component of peptidoglycan and thus essential for cell wall synthesis, reducing l-lysine by-production could be troublesome. Here, a basal strain with eliminated l-lysine production was constructed from the wild type C. glutamicum ATCC13869 by deleting the chromosomal ddh and lysE. Furthermore, the basal strain as well as the ddh single mutant strain was engineered for l-threonine production by over-expressing lysC1, hom1 and thrB, and for l-isoleucine production by over-expressing lysC1, hom1, thrB and ilvA1. Fermentation experiments with the engineered strains showed that (i) deletion of ddh improved l-threonine production by 17%, and additional deletion of lysE further improved l-threonine production by 28%; (ii) deletion of ddh improved l-isoleucine production by 8% and improved cell growth by 21%, whereas additional deletion of lysE had no further influence on both l-isoleucine production and cell growth; (iii) l-lysine by-production was reduced by 95% and 86% in l-threonine and l-isoleucine production, respectively, by deletion of ddh and lysE. This is the first report on improving l-threonine and l-isoleucine production by deleting ddh and lysE in C. glutamicum. The results demonstrate deletion of ddh and lysE as an effective strategy to reduce l-lysine by-production without surrendering the cell growth of C. glutamicum. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum

    PubMed Central

    Kitamura, Takuya; Seki, Naoya

    2017-01-01

    Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation pathway, PHS is converted to 2-OH palmitic acid and then to pentadecanoic acid (C15:0-COOH) via FA α-oxidation. However, the detailed reactions and genes involved in the α-oxidation reactions of the PHS degradation pathway have yet to be determined. In the present study, we reveal the entire PHS degradation pathway: PHS is converted to C15:0-COOH via six reactions [phosphorylation, cleavage, oxidation, CoA addition, cleavage (C1 removal), and oxidation], in which the last three reactions correspond to the α-oxidation. The aldehyde dehydrogenase ALDH3A2 catalyzes both the first and second oxidation reactions (fatty aldehydes to FAs). In Aldh3a2-deficient cells, the unmetabolized fatty aldehydes are reduced to fatty alcohols and are incorporated into ether-linked glycerolipids. We also identify HACL2 (2-hydroxyacyl-CoA lyase 2) [previous name, ILVBL; ilvB (bacterial acetolactate synthase)-like] as the major 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the FA α-oxidation of the PHS degradation pathway. HACL2 is localized in the endoplasmic reticulum. Thus, in addition to the already-known FA α-oxidation in the peroxisomes, we have revealed the existence of FA α-oxidation in the endoplasmic reticulum in mammals. PMID:28289220

  10. Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum.

    PubMed

    Kitamura, Takuya; Seki, Naoya; Kihara, Akio

    2017-03-28

    Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation pathway, PHS is converted to 2-OH palmitic acid and then to pentadecanoic acid (C15:0-COOH) via FA α-oxidation. However, the detailed reactions and genes involved in the α-oxidation reactions of the PHS degradation pathway have yet to be determined. In the present study, we reveal the entire PHS degradation pathway: PHS is converted to C15:0-COOH via six reactions [phosphorylation, cleavage, oxidation, CoA addition, cleavage (C1 removal), and oxidation], in which the last three reactions correspond to the α-oxidation. The aldehyde dehydrogenase ALDH3A2 catalyzes both the first and second oxidation reactions (fatty aldehydes to FAs). In Aldh3a2-deficient cells, the unmetabolized fatty aldehydes are reduced to fatty alcohols and are incorporated into ether-linked glycerolipids. We also identify HACL2 (2-hydroxyacyl-CoA lyase 2) [previous name, ILVBL; ilvB (bacterial acetolactate synthase)-like] as the major 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the FA α-oxidation of the PHS degradation pathway. HACL2 is localized in the endoplasmic reticulum. Thus, in addition to the already-known FA α-oxidation in the peroxisomes, we have revealed the existence of FA α-oxidation in the endoplasmic reticulum in mammals.

  11. Adaptive response to hydrogen peroxide in yeast: induction, time course, and relationship to dose-response models.

    PubMed

    Hoffmann, George R; Moczula, Andrew V; Laterza, Amanda M; Macneil, Lindsey K; Tartaglione, Jason P

    2013-07-01

    The assay for trp5 gene conversion and ilv1-92 reversion in Saccharomyces cerevisiae strain D7 was used to characterize the induction of an adaptive response by hydrogen peroxide (H(2)O(2)). Effects of a small priming dose on the genotoxic effects of a larger challenge dose were measured in exponential cultures and in early stationary phase. An adaptive response, indicated by smaller convertant and revertant frequencies after the priming dose, occurred at lower priming and challenge doses in young, well-aerated cultures. Closely spaced priming doses from 0.000975 to 2 mM, followed by a 1 mM challenge, showed that the induction of the adaptive response is biphasic. In exponential cultures it was maximal with a priming dose of 0.125-0.25 mM. Very small priming doses were insufficient to induce the adaptive response, whereas higher doses contributed to damage. A significant adaptive response was detected when the challenge dose was administered 10-20 min after the priming exposure. It was fully expressed within 45 min, and the yeast began to return to the nonadapted state after 4-6 hr. Because of the similarity of the biphasic induction to hormetic curves and the proposal that adaptive responses are a manifestation of hormesis, we evaluated whether the low doses of H(2)O(2) that induce the adaptive response show a clear hormetic response without a subsequent challenge dose. Hormesis was not evident, but there was an apparent threshold for genotoxicity at or slightly below 0.125 mM. The results are discussed with respect to linear, threshold, and hormesis dose-response models.

  12. E-Area Performance Assessment Interim Measures Assessment FY2005

    SciTech Connect

    Stallings, M

    2006-01-31

    After major changes to the limits for various disposal units of the E-Area Low Level Waste Facility (ELLWF) last year, no major changes have been made during FY2005. A Special Analysis was completed which removes the air pathway {sup 14}C limit from the Intermediate Level Vault (ILV). This analysis will allow the disposal of reactor moderator deionizers which previously had no pathway to disposal. Several studies have also been completed providing groundwater transport input for future special analyses. During the past year, since Slit Trenches No.1 and No.2 were nearing volumetric capacity, they were operationally closed under a preliminary closure analysis. This analysis was performed using as-disposed conditions and data and showed that concrete rubble from the demolition of 232-F was acceptable for disposal in the STs even though the latest special analysis for the STs had reduced the tritium limits so that the inventory in the rubble exceeded limits. A number of special studies are planned during the next years; perhaps the largest of these will be revision of the Performance Assessment (PA) for the ELLWF. The revision will be accomplished by incorporating special analyses performed since the last PA revision as well as revising analyses to include new data. Projected impacts on disposal limits of more recent studies have been estimated. No interim measures will be applied during this year. However, it is being recommended that tritium disposals to the Components-in-Grout (CIG) Trenches be suspended until a limited Special Analysis (SA) currently in progress is completed. This SA will give recommendations for optimum placement of tritiated D-Area tower waste. Further recommendations for tritiated waste placement in the CIG Trenches will be given in the upcoming PA revision.

  13. Expanding the Regulatory Network Governed by the Extracytoplasmic Function Sigma Factor σH in Corynebacterium glutamicum

    PubMed Central

    Toyoda, Koichi; Teramoto, Haruhiko; Yukawa, Hideaki

    2014-01-01

    The extracytoplasmic function sigma factor σH is responsible for the heat and oxidative stress response in Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, previous transcriptome analyses have not been able to discriminate between direct and indirect targets of σH. Here, we determined the direct genome-wide targets of σH using chromatin immunoprecipitation with microarray technology (ChIP-chip) for analysis of a deletion mutant of rshA, encoding an anti-σ factor of σH. Seventy-five σH-dependent promoters, including 39 new ones, were identified. σH-dependent, heat-inducible transcripts for several of the new targets, including ilvD encoding a labile Fe-S cluster enzyme, dihydroxy-acid dehydratase, were detected, and their 5′ ends were mapped to the σH-dependent promoters identified. Interestingly, functional internal σH-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin and affected expression of Zn-responsive genes, possibly through intracellular Zn overload, indicating new physiological roles of σH. Furthermore, sigA encoding the primary σ factor was identified as a new target of σH. Reporter assays demonstrated that the σH-dependent promoter upstream of sigA was highly heat inducible but much weaker than the known σA-dependent one. Our ChIP-chip analysis also detected the σH-dependent promoters upstream of rshA within the sigH-rshA operon and of sigB encoding a group 2 σ factor, supporting the previous findings of their σH-dependent expression. Taken together, these results reveal an additional layer of the sigma factor regulatory network in C. glutamicum. PMID:25404703

  14. Optimization of carbon source and glucose feeding strategy for improvement of L-isoleucine production by Escherichia coli

    PubMed Central

    Wang, Jian; Wen, Bing; Xu, Qingyang; Xie, Xixian; Chen, Ning

    2015-01-01

    Fed-batch cultivations of L-isoleucine-producing Escherichia coli TRFP (SGr, α-ABAr, with a pTHR101 plasmid containing a thr operon and ilvA) were carried out on different carbon sources: glucose, sucrose, fructose, maltose and glycerol. The results indicated that sucrose was the best initial carbon source for L-isoleucine production and then sucrose concentration of 30 g·L−1 was determined in the production medium. The results of different carbon sources feeding showed that the glucose solution was the most suitable feeding media. The dissolved oxygen (DO) of L-isoleucine fermentation was maintained at 5%, 15% and 30% with DO-stat feeding, respectively. The results indicated that when the DO level was maintained at 30%, the highest biomass and L-isoleucine production were obtained. The accumulation of acetate was decreased and the production of L-isoleucine was increased markedly, when the glucose concentration was maintained at 0.15 g·L−1 by using glucose-stat feeding. Finally, the glucose concentration was maintained at 0.10 g·L−1 and the DO level was controlled at approximately 30% during the whole fermentation period, using the combined feeding strategy of glucose-stat feeding and DO feedback feeding. The acetate accumulation was decreased to 7.23 g·L−1, and biomass and production of L-isoleucine were increased to 46.8 and 11.95 g·L−1, respectively. PMID:26019655

  15. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

    PubMed

    Kosina, Suzanne M; Danielewicz, Megan A; Mohammed, Mujahid; Ray, Jayashree; Suh, Yumi; Yilmaz, Suzan; Singh, Anup K; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

    2016-07-15

    Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.

  16. Exosome Biogenesis, Regulation, and Function in Viral Infection

    PubMed Central

    Alenquer, Marta; Amorim, Maria João

    2015-01-01

    Exosomes are extracellular vesicles released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. They originate as intraluminal vesicles (ILVs) during the process of MVB formation. Exosomes were shown to contain selectively sorted functional proteins, lipids, and RNAs, mediating cell-to-cell communications and hence playing a role in the physiology of the healthy and diseased organism. Challenges in the field include the identification of mechanisms sustaining packaging of membrane-bound and soluble material to these vesicles and the understanding of the underlying processes directing MVBs for degradation or fusion with the plasma membrane. The investigation into the formation and roles of exosomes in viral infection is in its early years. Although still controversial, exosomes can, in principle, incorporate any functional factor, provided they have an appropriate sorting signal, and thus are prone to viral exploitation. This review initially focuses on the composition and biogenesis of exosomes. It then explores the regulatory mechanisms underlying their biogenesis. Exosomes are part of the endocytic system, which is tightly regulated and able to respond to several stimuli that lead to alterations in the composition of its sub-compartments. We discuss the current knowledge of how these changes affect exosomal release. We then summarize how different viruses exploit specific proteins of endocytic sub-compartments and speculate that it could interfere with exosome function, although no direct link between viral usage of the endocytic system and exosome release has yet been reported. Many recent reports have ascribed functions to exosomes released from cells infected with a variety of animal viruses, including viral spread, host immunity, and manipulation of the microenvironment, which are discussed. Given the ever-growing roles and importance of exosomes in viral infections, understanding what regulates their composition and levels, and

  17. Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism.

    PubMed

    Opel, Michael L; Aeling, Kimberly A; Holmes, Walter M; Johnson, Reid C; Benham, Craig J; Hatfield, G Wesley

    2004-07-01

    The leuV operon of Escherichia coli encodes three of the four genes for the tRNA1Leu isoacceptors. Transcription from this and other stable RNA promoters is known to be affected by a cis-acting UP element and by Fis protein interactions with the carboxyl-terminal domain of the alpha-subunits of RNA polymerase. In this report, we suggest that transcription from the leuV promoter also is activated by a Fis-mediated, DNA supercoiling-dependent mechanism similar to the IHF-mediated mechanism described previously for the ilvP(G) promoter (S. D. Sheridan et al., 1998, J Biol Chem 273: 21298-21308). We present evidence that Fis binding results in the translocation of superhelical energy from the promoter-distal portion of a supercoiling-induced DNA duplex destabilized (SIDD) region to the promoter-proximal portion of the leuV promoter that is unwound within the open complex. A mutant Fis protein, which is defective in contacting the carboxyl-terminal domain of the alpha-subunits of RNA polymerase, remains competent for stimulating open complex formation, suggesting that this DNA supercoiling-dependent component of Fis-mediated activation occurs in the absence of specific protein interactions between Fis and RNA polymerase. Fis-mediated translocation of superhelical energy from upstream binding sites to the promoter region may be a general feature of Fis-mediated activation of transcription at stable RNA promoters, which often contain A+T-rich upstream sequences.

  18. Geochemical Data Package for Performance Assessment Calculations Related to the Savannah River Site

    SciTech Connect

    Kaplan, Daniel I.

    2016-07-22

    The Savannah River Site (SRS) disposes of low-level radioactive waste (LLW) and stabilizes high-level radioactive waste (HLW) tanks in the subsurface environment. Calculations used to establish the radiological limits of these facilities are referred to as Performance Assessments (PA), Special Analyses (SA), and Composite Analyses (CA). The objective of this document is to revise existing geochemical input values used for these calculations. This work builds on earlier compilations of geochemical data (2007, 2010), referred to a geochemical data packages. This work is being conducted as part of the on-going maintenance program of the SRS PA programs that periodically updates calculations and data packages when new information becomes available. Because application of values without full understanding of their original purpose may lead to misuse, this document also provides the geochemical conceptual model, the approach used for selecting the values, the justification for selecting data, and the assumptions made to assure that the conceptual and numerical geochemical models are reasonably conservative (i.e., bias the recommended input values to reflect conditions that will tend to predict the maximum risk to the hypothetical recipient). This document provides 1088 input parameters for geochemical parameters describing transport processes for 64 elements (>740 radioisotopes) potentially occurring within eight subsurface disposal or tank closure areas: Slit Trenches (ST), Engineered Trenches (ET), Low Activity Waste Vault (LAWV), Intermediate Level (ILV) Vaults, Naval Reactor Component Disposal Areas (NRCDA), Components-in-Grout (CIG) Trenches, Saltstone Facility, and Closed Liquid Waste Tanks. The geochemical parameters described here are the distribution coefficient, Kd value, apparent solubility concentration, ks value, and the cementitious leachate impact factor.

  19. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli.

    PubMed Central

    Calvo, J M; Matthews, R G

    1994-01-01

    The leucine-responsive regulatory protein (Lrp) regulates the expression of more than 40 genes and proteins in Escherichia coli. Among the operons that are positively regulated by Lrp are operons involved in amino acid biosynthesis (ilvIH, serA)), in the biosynthesis of pili (pap, fan, fim), and in the assimilation of ammonia (glnA, gltBD). Negatively regulated operons include operons involved in amino acid catabolism (sdaA, tdh) and peptide transport (opp) and the operon coding for Lrp itself (lrp). Detailed studies of a few members of the regulon have shown that Lrp can act directly to activate or repress transcription of target operons. A substantial fraction of operons regulated by Lrp are also regulated by leucine, and the effect of leucine on expression of these operons requires a functional Lrp protein. The patterns of regulation are surprising and interesting: in some cases activation or repression mediated by Lrp is antagonized by leucine, in other cases Lrp-mediated activation or repression is potentiated by leucine, and in still other cases leucine has no effect on Lrp-mediated regulation. Current research is just beginning to elucidate the detailed mechanisms by which Lrp can mediate such a broad spectrum of regulatory effects. Our view of the role of Lrp in metabolism may change as more members of the regulon are identified and their regulation characterized, but at this point Lrp seems to be important in regulating nitrogen metabolism and one-carbon metabolism, permitting adaptations to feast and to famine. PMID:7968922

  20. Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol.

    PubMed

    Lian, Jiazhang; Chao, Ran; Zhao, Huimin

    2014-05-01

    2,3-Butanediol (BDO) is an important chemical with broad industrial applications and can be naturally produced by many bacteria at high levels. However, the pathogenicity of these native producers is a major obstacle for large scale production. Here we report the engineering of an industrially friendly host, Saccharomyces cerevisiae, to produce BDO at high titer and yield. By inactivation of pyruvate decarboxylases (PDCs) followed by overexpression of MTH1 and adaptive evolution, the resultant yeast grew on glucose as the sole carbon source with ethanol production completely eliminated. Moreover, the pdc- strain consumed glucose and galactose simultaneously, which to our knowledge is unprecedented in S. cerevisiae strains. Subsequent introduction of a BDO biosynthetic pathway consisting of the cytosolic acetolactate synthase (cytoILV2), Bacillus subtilis acetolactate decarboxylase (BsAlsD), and the endogenous butanediol dehydrogenase (BDH1) resulted in the production of enantiopure (2R,3R)-butanediol (R-BDO). In shake flask fermentation, a yield over 70% of the theoretical value was achieved. Using fed-batch fermentation, more than 100g/L R-BDO (1100mM) was synthesized from a mixture of glucose and galactose, two major carbohydrate components in red algae. The high titer and yield of the enantiopure R-BDO produced as well as the ability to co-ferment glucose and galactose make our engineered yeast strain a superior host for cost-effective production of bio-based BDO from renewable resources. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  1. Overexpression of PrfA Leads to Growth Inhibition of Listeria monocytogenes in Glucose-Containing Culture Media by Interfering with Glucose Uptake

    PubMed Central

    Marr, A. K.; Joseph, B.; Mertins, S.; Ecke, R.; Müller-Altrock, S.; Goebel, W.

    2006-01-01

    Listeria monocytogenes strains expressing high levels of the virulence regulator PrfA (mutant PrfA* or wild-type PrfA) show strong growth inhibition in minimal media when they are supplemented with glucose but not when they are supplemented with glucose-6-phosphate compared to the growth of isogenic strains expressing low levels of PrfA. A significantly reduced rate of glucose uptake was observed in a PrfA*-overexpressing strain growing in LB supplemented with glucose. Comparative transcriptome analyses were performed with RNA isolated from a prfA mutant and an isogenic strain carrying multiple copies of prfA or prfA* on a plasmid. These analyses revealed that in addition to high transcriptional up-regulation of the known PrfA-regulated virulence genes (group I), there was less pronounced up-regulation of the expression of several phage and metabolic genes (group II) and there was strong down-regulation of several genes involved mainly in carbon and nitrogen metabolism in the PrfA*-overexpressing strain (group III). Among the latter genes are the nrgAB, gltAB, and glnRA operons (involved in nitrogen metabolism), the ilvB operon (involved in biosynthesis of the branched-chain amino acids), and genes for some ABC transporters. Most of the down-regulated genes have been shown previously to belong to a class of genes in Bacillus subtilis whose expression is negatively affected by impaired glucose uptake. Our results lead to the conclusion that excess PrfA (or PrfA*) interferes with a component(s) essential for phosphotransferase system-mediated glucose transport. PMID:16707681

  2. Formate and Nitrate Utilization in Enterobacter aerogenes for Semi-Anaerobic Production of Isobutanol.

    PubMed

    Jung, Hwi-Min; Kim, Yong Hwan; Oh, Min-Kyu

    2017-07-21

    Anaerobic bioprocessing is preferred because of its economic advantages. However, low productivity and decreased growth of the host strain have limited the use of the anaerobic process. Anaerobic respiration can be applied to anoxic processing using formate and nitrate metabolism to improve the productivity of value-added metabolites. A isobutanol-producing strains is constructed using Enterobacter aerogenes as a host strain by metabolic engineering approaches. The byproduct pathway (ldhA, budA, and pflB) is knocked out, and heterologous keto-acid decarboxylase (kivD) and alcohol dehydrogenase (adhA) are expressed along with the L-valine synthesis pathway (ilvCD and budB). The pyruvate formate-lyase mutant shows decreased growth rates when cultivated in semi-anaerobic conditions, which results in a decline in productivity. When formate and nitrate are supplied in the culture medium, the growth rates and amount of isobutanol production is restored (4.4 g L(-1) , 0.23 g g(-1) glucose, 0.18 g L(-1)  h(-1) ). To determine the function of the formate and nitrate coupling reaction system, the mutant strains that could not utilize formate or nitrate is contructed. Decreased growth and productivity are observed in the nitrate reductase (narG) mutant strain. This is the first report of engineering isobutanol-producing E. aerogenes to increase strain fitness via augmentation of formate and nitrate metabolism during anaerobic cultivation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Characterization of TPP-binding proteins in Methanococci archaeal species

    PubMed Central

    Harris, Laura K.

    2016-01-01

    Acetolactate synthase (ALS) is a highly conserved protein family responsible for producing branched chain amino acids. In Methanocaldococcus jannaschii, two ALS proteins, MJ0277 and MJ0663 exist though variations in features between them are noted. Researchers are quick to examine MJ0277 homologs due to their increased function and close relationship, but few have characterized MJ0663 homologs. This study identified homologs for both MJ0277 and MJ0663 in all 15 Methanococci species with fully sequenced genomes. EggNOG database does not define four of the MJ0663 homologs, JH146_1236, WP_004591614, WP_018154400, and EHP89635. BLASTP comparisons suggest these four proteins had around 30% identity to MJ0277 homologs, close to the identity similarities between other MJ0663 homologs to the MJ0277 homologous group. ExPASY physiochemical characterization shows a statistically significant difference in molecular weight and grand average hydropathy between homologous groups. CDD-BLAST showed distinct domains between homologous groups. MJ0277 homologs had TPP_AHAS and PRL06276 while MJ0663 homologs had TPP_enzymes super family and IlvB domains instead. Multiple sequence alignment using PROMALS3D showed the MJ0277 homologs a tighter group than MJ0663 and its homologs. PHYLIP showed these homologous groups as evolutionarily distinct yet equal distance from bacterial ALS proteins of established structure. The four proteins EggNOG did not define had the same features as other MJ0663 homologs. This indicates that JH146_1236, WP_004591614, WP_018154400, and EHP89635, should be included in EggNOG database cluster arCOG02000 with the other MJ0663 homologs. PMID:28275290

  4. Rapid Protein Global Fold Determination Using Ultrasparse Sampling, High-Dynamic Range Artifact Suppression, and Time-Shared NOESY

    PubMed Central

    Coggins, Brian E.; Werner-Allen, Jonathan W.; Yan, Anthony; Zhou, Pei

    2012-01-01

    In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target’s topology and reducing assignment ambiguity in NOESY spectra of fully-protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in 2H/13C/15N-labeled protein samples with selectively-protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal, but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and lineshapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data. PMID:22946863

  5. [Standard algorithm of molecular typing of Yersinia pestis strains].

    PubMed

    Eroshenko, G A; Odinokov, G N; Kukleva, L M; Pavlova, A I; Krasnov, Ia M; Shavina, N Iu; Guseva, N P; Vinogradova, N A; Kutyrev, V V

    2012-01-01

    Development of the standard algorithm of molecular typing of Yersinia pestis that ensures establishing of subspecies, biovar and focus membership of the studied isolate. Determination of the characteristic strain genotypes of plague infectious agent of main and nonmain subspecies from various natural foci of plague of the Russian Federation and the near abroad. Genotyping of 192 natural Y. pestis strains of main and nonmain subspecies was performed by using PCR methods, multilocus sequencing and multilocus analysis of variable tandem repeat number. A standard algorithm of molecular typing of plague infectious agent including several stages of Yersinia pestis differentiation by membership: in main and nonmain subspecies, various biovars of the main subspecies, specific subspecies; natural foci and geographic territories was developed. The algorithm is based on 3 typing methods--PCR, multilocus sequence typing and multilocus analysis of variable tandem repeat number using standard DNA targets--life support genes (terC, ilvN, inv, glpD, napA, rhaS and araC) and 7 loci of variable tandem repeats (ms01, ms04, ms06, ms07, ms46, ms62, ms70). The effectiveness of the developed algorithm is shown on the large number of natural Y. pestis strains. Characteristic sequence types of Y. pestis strains of various subspecies and biovars as well as MLVA7 genotypes of strains from natural foci of plague of the Russian Federation and the near abroad were established. The application of the developed algorithm will increase the effectiveness of epidemiologic monitoring of plague infectious agent, and analysis of epidemics and outbreaks of plague with establishing the source of origin of the strain and routes of introduction of the infection.

  6. PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis

    PubMed Central

    Wu, Cheng-Guo; Chen, Hui; Guo, Feng; Yadav, Vikash K; Mcilwain, Sean J; Rowse, Michael; Choudhary, Alka; Lin, Ziqing; Li, Yitong; Gu, Tingjia; Zheng, Aiping; Xu, Qingge; Lee, Woojong; Resch, Eduard; Johnson, Benjamin; Day, Jenny; Ge, Ying; Ong, Irene M; Burkard, Mark E; Ivarsson, Ylva; Xing, Yongna

    2017-01-01

    Protein phosphatase 2A (PP2A) is a major Ser/Thr phosphatase; it forms diverse heterotrimeric holoenzymes that counteract kinase actions. Using a peptidome that tiles the disordered regions of the human proteome, we identified proteins containing [LMFI]xx[ILV]xEx motifs that serve as interaction sites for B′-family PP2A regulatory subunits and holoenzymes. The B′-binding motifs have important roles in substrate recognition and in competitive inhibition of substrate binding. With more than 100 novel ligands identified, we confirmed that the recently identified LxxIxEx B′α-binding motifs serve as common binding sites for B′ subunits with minor variations, and that S/T phosphorylation or D/E residues at positions 2, 7, 8 and 9 of the motifs reinforce interactions. Hundreds of proteins in the human proteome harbor intrinsic or phosphorylation-responsive B′-interaction motifs, and localize at distinct cellular organelles, such as midbody, predicting kinase-facilitated recruitment of PP2A-B′ holoenzymes for tight spatiotemporal control of phosphorylation at mitosis and cytokinesis. Moroever, Polo-like kinase 1-mediated phosphorylation of Cyk4/RACGAP1, a centralspindlin component at the midbody, facilitates binding of both RhoA guanine nucleotide exchange factor (epithelial cell transforming sequence 2 (Ect2)) and PP2A-B′ that in turn dephosphorylates Cyk4 and disrupts Ect2 binding. This feedback signaling loop precisely controls RhoA activation and specifies a restricted region for cleavage furrow ingression. Our results provide a framework for further investigation of diverse signaling circuits formed by PP2A-B′ holoenzymes in various cellular processes. PMID:28884018

  7. Recognition of p63 by the E3 ligase ITCH: Effect of an ectodermal dysplasia mutant.

    PubMed

    Bellomaria, A; Barbato, Gaetano; Melino, G; Paci, M; Melino, Sonia

    2010-09-15

    The E3 ubiquitin ligase Itch mediates the degradation of the p63 protein. Itch contains four WW domains which are pivotal for the substrate recognition process. Indeed, this domain is implicated in several signalling complexes crucially involved in human diseases including Muscular Dystrophy, Alzheimer's Disease and Huntington Disease. WW domains are highly compact protein-protein binding modules that interact with short proline-rich sequences. The four WW domains present in Itch belong to the Group I type, which binds polypeptides with a PY motif characterized by a PP xY consensus sequence, where x can be any residue. Accordingly, the Itch-p63 interaction results from a direct binding of Itch-WW2 domain with the PY motif of p63. Here, we report a structural analysis of the Itch-p63 interaction by fluorescence, CD and NMR spectroscopy. Indeed, we studied the in vitro interaction between Itch-WW2 domain and p63(534-551), an 18-mer peptide encompassing a fragment of the p63 protein including the PY motif. In addition, we evaluated the conformation and the interaction with Itch-WW2 of a site specific mutant of p63, I549T, that has been reported in both Hay-Wells syndrome and Rapp-Hodgkin syndrome. Based on our results, we propose an extended PP xY motif for the Itch recognition motif (P-P-P-Y-x(4)-[ST]-[ILV]), which includes these C-terminal residues to the PP xY motif.

  8. Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY.

    PubMed

    Coggins, Brian E; Werner-Allen, Jonathan W; Yan, Anthony; Zhou, Pei

    2012-11-14

    In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target's topology and reducing assignment ambiguity in NOESY spectra of fully protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in (2)H/(13)C/(15)N-labeled protein samples with selectively protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and line shapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than those of diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data.

  9. Potentiation of the mutagenicity and recombinagenicity of bleomycin in yeast by unconventional intercalating agents.

    PubMed

    Hoffmann, George R; Laterza, Amanda M; Sylvia, Katelyn E; Tartaglione, Jason P

    2011-03-01

    Interactions between bleomycin (BLM) and conventional or unconventional intercalating agents were analyzed in an assay for mitotic gene conversion at the trp5 locus and reversion of the ilv1-92 allele in Saccharomyces cerevisiae strain D7. BLM is a potent recombinagen and mutagen in the assay. Various chemicals modulate the genetic activity of BLM, producing either antimutagenic effects or enhanced genotoxicity. Effects of cationic amino compounds include enhancement of BLM activity by aminoacridines and protection against BLM by aliphatic amines. The potentiation of BLM is similar to findings in a micronucleus-based BLM amplification assay in Chinese hamster V79 cells. In this study, the amplification of BLM activity was explored in yeast using known intercalators, compounds structurally related to known intercalators, and unconventional intercalators that were identified on the basis of computer modeling or results in the Chinese hamster BLM amplification assay. As shown in previous studies, the classical intercalator 9-aminoacridine (9AA) caused dose-dependent enhancement of BLM activity. Other compounds found to enhance the induction of mitotic recombination and point mutations in strain D7 were chlorpromazine, chloroquine, mefloquine, tamoxifen, diphenhydramine, benzophenone, and 3-hydroxybenzophenone. The increased activity was detectable by cotreatment of yeast with BLM and the modulator compound in growth medium or by separate interaction of the intercalator with DNA followed by BLM treatment of nongrowing cells in buffer. The data support the interpretation drawn from micronucleus assays in mammalian cells that BLM enhancement results from DNA intercalation and may be useful in detecting noncovalent interactions with DNA. Environ. Copyright © 2010 Wiley-Liss, Inc.

  10. Integrons in Xanthomonas: A source of species genome diversity

    PubMed Central

    Gillings, Michael R.; Holley, Marita P.; Stokes, H. W.; Holmes, Andrew J.

    2005-01-01

    Integrons are best known for assembling antibiotic resistance genes in clinical bacteria. They capture genes by using integrase-mediated site-specific recombination of mobile gene cassettes. Integrons also occur in the chromosomes of many bacteria, notably β- and γ-Proteobacteria. In a survey of Xanthomonas, integrons were found in all 32 strains representing 12 pathovars of two species. Their chromosomal location was downstream from the acid dehydratase gene, ilvD, suggesting that an integron was present at this site in the ancestral xanthomonad. There was considerable sequence and structural diversity among the extant integrons. The majority of integrase genes were predicted to be inactivated by frameshifts, stop codons, or large deletions, suggesting that the associated gene cassettes can no longer be mobilized. In support, groups of strains with the same deletions or stop codons/frameshifts in their integrase gene usually contained identical arrays of gene cassettes. In general, strains within individual pathovars had identical cassettes, and these exhibited no similarity to cassettes detected in other pathovars. The variety and characteristics of contemporary gene cassettes suggests that the ancestral integron had access to a diverse pool of these mobile elements, and that their genes originated outside the Xanthomonas genome. Subsequent inactivation of the integrase gene in particular lineages has largely fixed the gene cassette arrays in particular pathovars during their differentiation and specialization into ecological niches. The acquisition of diverse gene cassettes by different lineages within Xanthomonas has contributed to the species-genome diversity of the genus. The role of gene cassettes in survival on plant surfaces is currently unknown. PMID:15755815

  11. Mycobacterium tuberculosis Type VII Secreted Effector EsxH Targets Host ESCRT to Impair Trafficking

    PubMed Central

    Thompson, Victor; Sirisaengtaksin, Natalie; Wells, Ashley; Porto, Maura; Köster, Stefan; Penberthy, Kristen; Kubota, Yoshihisha; Dricot, Amelie; Rogan, Daniel; Vidal, Marc; Hill, David E.; Bean, Andrew J.; Philips, Jennifer A.

    2013-01-01

    Mycobacterium tuberculosis (Mtb) disrupts anti-microbial pathways of macrophages, cells that normally kill bacteria. Over 40 years ago, D'Arcy Hart showed that Mtb avoids delivery to lysosomes, but the molecular mechanisms that allow Mtb to elude lysosomal degradation are poorly understood. Specialized secretion systems are often used by bacterial pathogens to translocate effectors that target the host, and Mtb encodes type VII secretion systems (TSSSs) that enable mycobacteria to secrete proteins across their complex cell envelope; however, their cellular targets are unknown. Here, we describe a systematic strategy to identify bacterial virulence factors by looking for interactions between the Mtb secretome and host proteins using a high throughput, high stringency, yeast two-hybrid (Y2H) platform. Using this approach we identified an interaction between EsxH, which is secreted by the Esx-3 TSSS, and human hepatocyte growth factor-regulated tyrosine kinase substrate (Hgs/Hrs), a component of the endosomal sorting complex required for transport (ESCRT). ESCRT has a well-described role in directing proteins destined for lysosomal degradation into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs), ensuring degradation of the sorted cargo upon MVB-lysosome fusion. Here, we show that ESCRT is required to deliver Mtb to the lysosome and to restrict intracellular bacterial growth. Further, EsxH, in complex with EsxG, disrupts ESCRT function and impairs phagosome maturation. Thus, we demonstrate a role for a TSSS and the host ESCRT machinery in one of the central features of tuberculosis pathogenesis. PMID:24204276

  12. Exosome Biogenesis, Regulation, and Function in Viral Infection.

    PubMed

    Alenquer, Marta; Amorim, Maria João

    2015-09-17

    Exosomes are extracellular vesicles released upon fusion of multivesicular bodies(MVBs) with the cellular plasma membrane. They originate as intraluminal vesicles (ILVs) during the process of MVB formation. Exosomes were shown to contain selectively sorted functional proteins, lipids, and RNAs, mediating cell-to-cell communications and hence playing a role in the physiology of the healthy and diseased organism. Challenges in the field include the identification of mechanisms sustaining packaging of membrane-bound and soluble material to these vesicles and the understanding of the underlying processes directing MVBs for degradation or fusion with the plasma membrane. The investigation into the formation and roles of exosomes in viral infection is in its early years. Although still controversial, exosomes can, in principle, incorporate any functional factor, provided they have an appropriate sorting signal, and thus are prone to viral exploitation.This review initially focuses on the composition and biogenesis of exosomes. It then explores the regulatory mechanisms underlying their biogenesis. Exosomes are part of the endocytic system,which is tightly regulated and able to respond to several stimuli that lead to alterations in the composition of its sub-compartments. We discuss the current knowledge of how these changes affect exosomal release. We then summarize how different viruses exploit specific proteins of endocytic sub-compartments and speculate that it could interfere with exosome function, although no direct link between viral usage of the endocytic system and exosome release has yet been reported. Many recent reports have ascribed functions to exosomes released from cells infected with a variety of animal viruses, including viral spread, host immunity, and manipulation of the microenvironment, which are discussed. Given the ever-growing roles and importance of exosomes in viral infections, understanding what regulates their composition and levels, and

  13. Molecular cloning and characterization of genes required for ribose transport and utilization in Escherichia coli K-12.

    PubMed Central

    Iida, A; Harayama, S; Iino, T; Hazelbauer, G L

    1984-01-01

    We isolated spontaneous and transposon insertion mutants of Escherichia coli K-12 that were specifically defective in utilization or in high-affinity transport of D-ribose (or in both). Cotransduction studies located all of the mutations near ilv, at the same position as previously identified mutations causing defects in ribokinase ( rbsK ) or ribose transport ( rbsP ). Plasmids that complemented the rbs mutations were isolated from the collection of ColE1 hybrid plasmids constructed by Clarke and Carbon. Analysis of those plasmids as well as of fragments cloned into pBR322 and pACYC184 allowed definition of the rbs region. Products of rbs genes were identified by examination of the proteins produced in minicells containing various rbs plasmids. We identified four rbs genes: rbsB , which codes for the 29-kilodalton ribose-binding protein; rbsK , which codes for the 34-kilodalton ribokinase ; rbsA , which codes for a 50-kilodalton protein required for high-affinity transport; and rbsC , which codes for a 27-kilodalton protein likely to be a transport system component. Our studies showed that these genes are transcribed from a common promoter in the order rbsA rbsC rbsB rbsK . It appears that the high-affinity transport system for ribose consists of the three components, ribose-binding protein, the 50-kilodalton RbsA protein, and the 27-kilodalton RbsC protein, although a fourth, unidentified component could exist. Mutants defective in this transport system, but normal for ribokinase , are able to grow normally on high concentrations of the sugar, indicating that there is at least a second, low-affinity transport system for ribose in E. coli K-12. Images PMID:6327617

  14. Monitoring yeast physiology during very high gravity wort fermentations by frequent analysis of gene expression.

    PubMed

    Rautio, Jari J; Huuskonen, Anne; Vuokko, Heikki; Vidgren, Virve; Londesborough, John

    2007-09-01

    Brewer's yeast experiences constantly changing environmental conditions during wort fermentation. Cells can rapidly adapt to changing surroundings by transcriptional regulation. Changes in genomic expression can indicate the physiological condition of yeast in the brewing process. We monitored, using the transcript analysis with aid of affinity capture (TRAC) method, the expression of some 70 selected genes relevant to wort fermentation at high frequency through 9-10 day fermentations of very high gravity wort (25 degrees P) by an industrial lager strain. Rapid changes in expression occurred during the first hours of fermentations for several genes, e.g. genes involved in maltose metabolism, glycolysis and ergosterol synthesis were strongly upregulated 2-6 h after pitching. By the time yeast growth had stopped (72 h) and total sugars had dropped by about 50%, most selected genes had passed their highest expression levels and total mRNA was less than half the levels during growth. There was an unexpected upregulation of some genes of oxygen-requiring pathways during the final fermentation stages. For five genes, expression of both the Saccharomyces cerevisiae and S. bayanus components of the hybrid lager strain were determined. Expression profiles were either markedly different (ADH1, ERG3) or very similar (MALx1, ILV5, ATF1) between these two components. By frequent analysis of a chosen set of genes, TRAC provided a detailed and dynamic picture of the physiological state of the fermenting yeast. This approach offers a possible way to monitor and optimize the performance of yeast in a complex process environment.

  15. Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.

    PubMed

    Neshat, Armin; Mentz, Almut; Rückert, Christian; Kalinowski, Jörn

    2014-11-20

    The Gram-positive bacterium Corynebacterium glutamicum belongs to the order Corynebacteriales and is used as a producer of amino acids at industrial scales. Due to its economic importance, gene expression and particularly the regulation of amino acid biosynthesis has been investigated extensively. Applying the high-resolution technique of transcriptome sequencing (RNA-seq), recently a vast amount of data has been generated that was used to comprehensively analyze the C. glutamicum transcriptome. By analyzing RNA-seq data from a small RNA cDNA library of C. glutamicum, short transcripts in the known transcriptional attenuators sites of the trp operon, the ilvBNC operon and the leuA gene were verified. Furthermore, whole transcriptome RNA-seq data were used to elucidate the transcriptional organization of these three amino acid biosynthesis operons. In addition, we discovered and analyzed the novel attenuator aroR, located upstream of the aroF gene (cg1129). The DAHP synthase encoded by aroF catalyzes the first step in aromatic amino acid synthesis. The AroR leader peptide contains the amino acid sequence motif F-Y-F, indicating a regulatory effect by phenylalanine and tyrosine. Analysis by real-time RT-PCR suggests that the attenuator regulates the transcription of aroF in dependence of the cellular amount of tRNA loaded with phenylalanine when comparing a phenylalanine-auxotrophic C. glutamicum mutant fed with limiting and excess amounts of a phenylalanine-containing dipeptide. Additionally, the very interesting finding was made that all analyzed attenuators are leaderless transcripts. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. [Ramadan and bipolar disorder: Example of circadian rhythm disturbance and its impact on patients with bipolar disorders].

    PubMed

    Eddahby, S; Kadri, N; Moussaoui, D

    2013-09-01

    Fasting during the Ramadan month is a cornerstone of Islam. Several disorders of the chronobiological rhythms occur during this month and impact on mood. Through this paper the authors provide a literature review of the impact of fasting on patients with bipolar disorders. A literature review using Mesh keywords through Medline database. From 1970 to 2011, articles in French and English were selected. Circadian rhythm refers to the approximately 24-hour cycles that are generated by an organism. Most physiological systems demonstrate circadian variations. Many hormones and other metabolisms, such as gastric pH, insulin, glucose, calcium and plasmatic gastrine, have been shown to exhibit circadian oscillation. The role of social rhythm in behaviors and its influence on circadian rhythms in humans is now obvious. It has been shown that the lack of concentration and irritability increased continuously during Ramadan month and reached its peak at the end of the month. Mood and vigilance are significantly decreased during the fasting month. Several authors have stated that the course of bipolar illness may be affected by the changes in social rhythm that occur during Ramadan (fasting month). Studies which have been devoted to this topic are sparse. Kadri et al., in 2000, studied 20 bipolar patients during the fasting month of Ramadan of 1417 (Hegirian calendar, corresponding to January 1997). Diagnosis of bipolar disorder was made according to ICD-10 criteria. Patients were assessed during the week before Ramadan, the second and the fourth weeks of the fasting month and the first week after its end, with the Hamilton Depression and Bech-Rafaelsen scales. The plasma concentration of lithium was also assessed. The main finding of the study was that 45% of the patients relapsed, 70% during the second week, and the remaining patients at the end of Ramadan. These relapses were not related to plasma concentration of lithium. Most of the relapses were manic (71

  17. Avibactam and Inhibitor-Resistant SHV β-Lactamases

    PubMed Central

    Winkler, Marisa L.; Papp-Wallace, Krisztina M.; Taracila, Magdalena A.

    2015-01-01

    β-Lactamase enzymes (EC 3.5.2.6) are a significant threat to the continued use of β-lactam antibiotics to treat infections. A novel non-β-lactam β-lactamase inhibitor with activity against many class A and C and some class D β-lactamase variants, avibactam, is now available in the clinic in partnership with ceftazidime. Here, we explored the activity of avibactam against a variety of characterized isogenic laboratory constructs of β-lactamase inhibitor-resistant variants of the class A enzyme SHV (M69I/L/V, S130G, K234R, R244S, and N276D). We discovered that the S130G variant of SHV-1 shows the most significant resistance to inhibition by avibactam, based on both microbiological and biochemical characterizations. Using a constant concentration of 4 mg/liter of avibactam as a β-lactamase inhibitor in combination with ampicillin, the MIC increased from 1 mg/liter for blaSHV-1 to 256 mg/liter for blaSHV S130G expressed in Escherichia coli DH10B. At steady state, the k2/K value of the S130G variant when inactivated by avibactam was 1.3 M−1 s−1, versus 60,300 M−1 s−1 for the SHV-1 β-lactamase. Under timed inactivation conditions, we found that an approximately 1,700-fold-higher avibactam concentration was required to inhibit SHV S130G than the concentration that inhibited SHV-1. Molecular modeling suggested that the positioning of amino acids in the active site of SHV may result in an alternative pathway of inactivation when complexed with avibactam, compared to the structure of CTX-M-15–avibactam, and that S130 plays a role in the acylation of avibactam as a general acid/base. In addition, S130 may play a role in recyclization. As a result, we advance that the lack of a hydroxyl group at position 130 in the S130G variant of SHV-1 substantially slows carbamylation of the β-lactamase by avibactam by (i) removing an important proton acceptor and donator in catalysis and (ii) decreasing the number of H bonds. In addition, recyclization is most likely

  18. Organic electronic devices via interface engineering

    NASA Astrophysics Data System (ADS)

    Xu, Qianfei

    This dissertation focuses on interface engineering and its influence on organic electronic devices. A comprehensive review of interface studies in organic electronic devices is presented in Chapter 1. By interface engineering at the cathode contact, an ultra-high efficiency green polymer light emitting diode is demonstrated in Chapter 2. The interface modification turns out to be solution processable by using calcium acetylacetonate, donated by Ca(acac)2. The device structure is Induim Tin Oxide (ITO)/3,4-polyethylenedioxythiophene-polystyrene-sulfonate (PEDOT)/Green polyfluorene/Ca(acac) 2/Al. Based on this structure, we obtained device efficiencies as high as 28 cd/A at 2650 cd/m2, which is about a 3 times improvement over previous devices. The mechanism of this nano-layer has been studied by I-L-V measurements, photovoltaic measurements, XPS/UPS studies, impedance measurements as well as transient EL studies. The interfacial layer plays a crucial role for the efficiency improvement. It is believed to work as a hole blocking layer as well as an electron injection layer. Meanwhile, a systematic study on ITO electrodes is also carried out in Chapter 4. By engineering the interface at ITO electrode, the device lifetime has been improved. In Chapter 5, very bright white emission PLEDs are fabricated based on blue polyfluorene (PF) doped with 1 wt% 6, 8, 15, 17-tetraphyenyl-1.18, 4.5, 9.10, 13.14-tetrabenzoheptacene (TBH). The maximum luminance exceeds 20,000 cd/m2. The maximum luminance efficiency is 3.55 cd/A at 4228 cd/m2 while the maximum power efficiency is 1.6 lm/W at 310 cd/m2. The white color is achieved by an incomplete energy transfer from blue PF to TBH. The devices show super stable CIE coordinates as a function of current density. The interface engineering is also applied to memory devices. In Chapter 6, a novel nonvolatile memory device is fabricated by inserting a buffer layer at the anode contact. Devices with the structure of Cu

  19. Search for genes responsible for the remarkably high acetic acid tolerance of a Zygosaccharomyces bailii-derived interspecies hybrid strain.

    PubMed

    Palma, Margarida; Roque, Filipa de Canaveira; Guerreiro, Joana Fernandes; Mira, Nuno Pereira; Queiroz, Lise; Sá-Correia, Isabel

    2015-12-16

    Zygosaccharomyces bailii is considered the most problematic acidic food spoilage yeast species due to its exceptional capacity to tolerate high concentrations of weak acids used as fungistatic preservatives at low pH. However, the mechanisms underlying its intrinsic remarkable tolerance to weak acids remain poorly understood. The identification of genes and mechanisms involved in Z. bailii acetic acid tolerance was on the focus of this study. For this, a genomic library from the highly acetic acid tolerant hybrid strain ISA1307, derived from Z. bailii and a closely related species and isolated from a sparkling wine production plant, was screened for acetic acid tolerance genes. This screen was based on the transformation of an acetic acid susceptible Saccharomyces cerevisiae mutant deleted for the gene encoding the acetic acid resistance determinant transcription factor Haa1. The expression of 31 different DNA inserts from ISA1307 strain genome was found to significantly increase the host cell tolerance to acetic acid. The in silico analysis of these inserts was facilitated by the recently available genome sequence of this strain. In total, 65 complete or truncated ORFs were identified as putative determinants of acetic acid tolerance and an S. cerevisiae gene homologous to most of them was found. These include genes involved in cellular transport and transport routes, protein fate, protein synthesis, amino acid metabolism and transcription. The role of strong candidates in Z. bailii and S. cerevisiae acetic acid tolerance was confirmed based on homologous and heterologous expression analyses. ISA1307 genes homologous to S. cerevisiae genes GYP8, WSC4, PMT1, KTR7, RKR1, TIF3, ILV3 and MSN4 are proposed as strong candidate determinants of acetic acid tolerance. The ORF ZBAI_02295 that contains a functional domain associated to the uncharacterised integral membrane proteins of unknown function of the DUP family is also suggested as a relevant tolerance determinant

  20. Primary biliary cirrhosis is characterized by IgG3 antibodies cross-reactive with the major mitochondrial autoepitope and its Lactobacillus mimic.

    PubMed

    Bogdanos, Dimitrios-Petrou; Baum, Harold; Okamoto, Manabu; Montalto, Paolo; Sharma, Umesh C; Rigopoulou, Eirini I; Vlachogiannakos, John; Ma, Yun; Burroughs, Andrew K; Vergani, Diego

    2005-08-01

    The serological hallmark of primary biliary cirrhosis (PBC) is the presence of pyruvate dehydrogenase complex E2 subunit (PDC-E2) antimitochondrial antibodies (AMAs). Anti-PDC-E2 antibodies cross-react specifically with mycobacterial hsp65, and we have demonstrated that the motif SxGDL[ILV]AE shared by PDC-E2(212-226) and hsp's is a cross-reactive target. Having found that this same motif is present only in beta-galactosidase of Lactobacillus delbrueckii (BGAL LACDE), we hypothesized that this homology would also lead to cross-reactivity. The mimics were tested via ELISA for reactivity and competitive cross-reactivity using sera from 100 AMA-positive and 23 AMA-negative PBC patients and 190 controls. An Escherichia coli (ECOLI) PDC-E2 mimic that has been pathogenetically linked to PBC but lacks this motif has been also tested. Anti-BGAL(266-280) LACDE antibodies were restricted to AMA-positive patients (54 of 95, 57%) and belonged to immunoglobulin (Ig) G3. Of the 190 controls, 22 (12%; P < .001) had anti-BGAL(266-280) antibodies, mainly of the IgG4 subclass. ECOLI PDC-E2 reactivity was virtually absent. BGAL(266-280)/PDC-E2(212-226) reactivity of the IgG3 isotype was found in 52 (52%) AMA-positive PBC patients but in only 1 of the controls (P < .001). LACDE BGAL(266-280)/PDC-E2(212-226) reactivity was due to cross-reactivity as confirmed via competition ELISA. Antibody affinity for BGAL(266-280) was greater than for PDC-E2 mimics. Preincubation of a multireactive serum with BGAL(266-280) reduced the inhibition of enzymatic activity by 40%, while marginal effect (12%) or no effect (2%) was observed in human or ECOLI PDC-E2 mimics. In conclusion, IgG3 antibodies to BGAL LACDE cross-react with the major mitochondrial autoepitope and are characteristic of PBC.

  1. An expanded two-state model accounts for homotropic cooperativity in biosynthetic threonine deaminase from Escherichia coli.

    PubMed

    Eisenstein, E; Yu, H D; Fisher, K E; Iacuzio, D A; Ducote, K R; Schwarz, F P

    1995-07-25

    The linkage between substrate and regulatory effector binding to separate sites on allosteric enzymes results in shifts in their sigmoidal kinetics to regulate metabolism. Control of branched chain amino acid biosynthesis in Escherichia coli occurs in part through shifts in the sigmoidal dependence of alpha-ketobutyrate production promoted by isoleucine and valine binding to biosynthetic threonine deaminase. The structural similarity of threonine, valine, and isoleucine have given rise to suggestions that there may be competition among different ligands for the same sites on this tetrameric enzyme, resulting in a complex pattern of regulation. In an effort to provide a coherent interpretation of the cooperative association of ligands to the active sites and to the effector sites of threonine deaminase, binding studies using single amino acid variants were undertaken. A previously-isolated, feedback-resistant mutant identified in Salmonella typhimurium, ilvA219, has been cloned and sequenced. The phenotype is attributable to a single amino acid substitution in the regulatory domain of the enzyme in which leucine at position 447 is substituted with phenylalanine. The mutant exhibits hyperbolic saturation curves in both ligand binding and steady-state kinetics. These results, in addition to calorimetric and spectroscopic measurements of isoleucine and valine binding, indicate that the low affinity (T) state is destabilized in the mutant and that it exists predominantly in the high affinity (R) conformation in the absence of ligands, providing an explanation for its resistance to isoleucine. Chemical and spectroscopic analyses of another mutant, in which alanine has replaced an essential lysine at position 62 that forms a Schiff base with pyridoxal phosphate, indicate that the cofactor is complexed to exogenous threonine and is therefore unable to bind additional amino acids at the active sites. Isoleucine and valine binding to this inactive, active site

  2. Unravelling the Secrets of Mycobacterial Cidality through the Lens of Antisense

    PubMed Central

    Datta, Santanu; Shandil, Radha Krishan; Kumar, Naveen; Robert, Nanduri; Sokhi, Upneet K.; Guptha, Supreeth; Narayanan, Shridhar; Anbarasu, Anand; Ramaiah, Sudha

    2016-01-01

    One of the major impediments in anti-tubercular drug discovery is the lack of a robust grammar that governs the in-vitro to the in-vivo translation of efficacy. Mycobacterium tuberculosis (Mtb) is capable of growing both extracellular as well as intracellular; encountering various hostile conditions like acidic milieu, free radicals, starvation, oxygen deprivation, and immune effector mechanisms. Unique survival strategies of Mtb have prompted researchers to develop in-vitro equivalents to simulate in-vivo physiologies and exploited to find efficacious inhibitors against various phenotypes. Conventionally, the inhibitors are screened on Mtb under the conditions that are unrelated to the in-vivo disease environments. The present study was aimed to (1). Investigate cidality of Mtb targets using a non-chemical inhibitor antisense-RNA (AS-RNA) under in-vivo simulated in-vitro conditions.(2). Confirm the cidality of the targets under in-vivo in experimental tuberculosis. (3). Correlate in-vitro vs. in-vivo cidality data to identify the in-vitro condition that best predicts in-vivo cidality potential of the targets. Using cidality as a metric for efficacy, and AS-RNA as a target-specific inhibitor, we delineated the cidality potential of five target genes under six different physiological conditions (replicating, hypoxia, low pH, nutrient starvation, nitrogen depletion, and nitric oxide).In-vitro cidality confirmed in experimental tuberculosis in BALB/c mice using the AS-RNA allowed us to identify cidal targets in the rank order of rpoB>aroK>ppk>rpoC>ilvB. RpoB was used as the cidality control. In-vitro and in-vivo studies feature aroK (encoding shikimate kinase) as an in-vivo mycobactericidal target suitable for anti-TB drug discovery. In-vitro to in-vivo cidality correlations suggested the low pH (R = 0.9856) in-vitro model as best predictor of in-vivo cidality; however, similar correlation studies in pathologically relevant (Kramnik) mice are warranted. In the acute

  3. Selected amino acid changes in HIV-1 subtype-C gp41 are associated with specific gp120(V3) signatures in the regulation of co-receptor usage.

    PubMed

    Dimonte, Salvatore; Babakir-Mina, Muhammed; Mercurio, Fabio; Di Pinto, Domenico; Ceccherini-Silberstein, Francesca; Svicher, Valentina; Perno, Carlo-Federico

    2012-09-01

    The majority of studies have characterized the tropism of HIV-1 subtype-B isolates, but little is known about the determinants of tropism in other subtypes. So, the goal of the present study was to genetically characterize the envelope of viral proteins in terms of co-receptor usage by analyzing 356 full-length env sequences derived from HIV-1 subtype-C infected individuals. The co-receptor usage of V3 sequences was inferred by using the Geno2Pheno and PSSM algorithms, and also analyzed to the "11/25 rule". All reported env sequences were also analyzed with regard to N-linked glycosylation sites, net charge and hydrophilicity, as well as the binomial correlation phi coefficient to assess covariation among gp120(V3) and gp41 signatures and the average linkage hierarchical agglomerative clustering were also performed. Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2V(V3) and G24T(V3) (bootstrap=1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GR(V3), 13-14insIG/LG(V3), P16RQ(V3), Q18KR(V3), F20ILV(V3), D25KRQ(V3), Q32KR(V3) along with A30T(gp41), S107N(gp41), D148E(gp41), A189S(gp41) was identified (bootstrap=0.86). Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41

  4. Unravelling the Secrets of Mycobacterial Cidality through the Lens of Antisense.

    PubMed

    Kaur, Parvinder; Datta, Santanu; Shandil, Radha Krishan; Kumar, Naveen; Robert, Nanduri; Sokhi, Upneet K; Guptha, Supreeth; Narayanan, Shridhar; Anbarasu, Anand; Ramaiah, Sudha

    2016-01-01

    One of the major impediments in anti-tubercular drug discovery is the lack of a robust grammar that governs the in-vitro to the in-vivo translation of efficacy. Mycobacterium tuberculosis (Mtb) is capable of growing both extracellular as well as intracellular; encountering various hostile conditions like acidic milieu, free radicals, starvation, oxygen deprivation, and immune effector mechanisms. Unique survival strategies of Mtb have prompted researchers to develop in-vitro equivalents to simulate in-vivo physiologies and exploited to find efficacious inhibitors against various phenotypes. Conventionally, the inhibitors are screened on Mtb under the conditions that are unrelated to the in-vivo disease environments. The present study was aimed to (1). Investigate cidality of Mtb targets using a non-chemical inhibitor antisense-RNA (AS-RNA) under in-vivo simulated in-vitro conditions.(2). Confirm the cidality of the targets under in-vivo in experimental tuberculosis. (3). Correlate in-vitro vs. in-vivo cidality data to identify the in-vitro condition that best predicts in-vivo cidality potential of the targets. Using cidality as a metric for efficacy, and AS-RNA as a target-specific inhibitor, we delineated the cidality potential of five target genes under six different physiological conditions (replicating, hypoxia, low pH, nutrient starvation, nitrogen depletion, and nitric oxide).In-vitro cidality confirmed in experimental tuberculosis in BALB/c mice using the AS-RNA allowed us to identify cidal targets in the rank order of rpoB>aroK>ppk>rpoC>ilvB. RpoB was used as the cidality control. In-vitro and in-vivo studies feature aroK (encoding shikimate kinase) as an in-vivo mycobactericidal target suitable for anti-TB drug discovery. In-vitro to in-vivo cidality correlations suggested the low pH (R = 0.9856) in-vitro model as best predictor of in-vivo cidality; however, similar correlation studies in pathologically relevant (Kramnik) mice are warranted. In the acute

  5. Geochemical Data Package for Performance Assessment Calculations Related to the Savannah River Site

    SciTech Connect

    Kaplan, D

    2006-02-28

    The Savannah River Site disposes of certain types of radioactive waste within subsurface-engineered facilities. One of the tools used to establish the capacity of a given site to safely store radioactive waste (i.e., that a site does not exceed its Waste Acceptance Criteria) is the Performance Assessment (PA). The objective of this document is to provide the geochemical values for the PA calculations. This work is being conducted as part of the on-going maintenance program that permits the PA to periodically update existing calculations when new data becomes available. Because application of values without full understanding of their original purpose may lead to misuse, this document also provides the geochemical conceptual model, approach used for selecting the values, the justification for selecting data, and the assumptions made to assure that the conceptual and numerical geochemical models are reasonably conservative (i.e., reflect conditions that will tend to predict the maximum risk to the hypothetical recipient). The geochemical parameters describe transport processes for 38 elements (>90 radioisotopes) potentially occurring within eight disposal units (Slit Trenches, Engineered Trenches, Low Activity Waste (LAW) Vault, Intermediate Level (ILV) Vaults, TRU-Pad-1, Naval Reactor Waste Pads, Components-in-Grout Trenches, and Saltstone Facility). This work builds upon well-documented work from previous PA calculations (McDowell-Boyer et al. 2000). The new geochemical concepts introduced in this data package are: (1) In the past, solubility products were used only in a few conditions (element existing in a specific environmental setting). This has been expanded to >100 conditions. (2) Radionuclide chemistry in cementitious environments is described through the use of both the Kd and apparent solubility concentration limit. Furthermore, the solid phase is assumed to age during the assessment period (thousands of years), resulting in three main types of controlling

  6. Application of an oxygen-inducible nar promoter system in metabolic engineering for production of biochemicals in Escherichia coli.

    PubMed

    Hwang, Hee J; Kim, Jin W; Ju, Si Y; Park, Jin H; Lee, Pyung C

    2017-02-01

    The nar promoter, a dissolved oxygen (DO)-dependent promoter in Escherichia coli, is simply induced and functional in any cell growth phase, which are advantageous for producing biochemicals/fuels on an industrial scale. To demonstrate the feasibility of using the nar promoter in the metabolic engineering of biochemicals/biofuels in E. coli, three target pathways were examined: the d-lactate, 2,3-butandiol (2,3-BDO), and 1,3-propanediol (1,3-PDO) pathways consisting of one, three, and six genes, respectively. Each pathway gene was expressed under the control of the nar promoter. When the ldhD gene was expressed in fed-batch culture, the titer, yield, and productivity of d-lactate were 113.12 ± 2.37 g/L, 0.91 ± 0.07 g/g-glucose, and 4.19 ± 0.09 g/L/h, respectively. When three 2,3-BDO pathway genes (ilvBN, aldB, bdh1) were expressed in fed-batch culture, the titer, yield, and productivity of (R,R)-2,3-BDO were 48.0 ± 8.48 g/L, 0.43 ± 0.07 g/g glucose, and 0.76 ± 0.13 g/L/h, respectively. When six 1,3-PDO pathway genes (dhaB1B2B3, yqhD, gdrA, and gdrB) were expressed in fed-batch culture, the titer, yield, and productivity of 1,3-PDO were 15.8 ± 0.62 g/L, 0.35 ± 0.01 g/g-glycerol, and 0.25 ± 0.01 g/L/h, respectively. Based on the reasonable performance comparable to that observed in previous studies using different promoters in metabolic engineering, the nar promoter can serve as a controlled expression tool for developing a microbial system to efficiently produce biochemicals and biofuels. Biotechnol. Bioeng. 2017;114: 468-473. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Use of the valine biosynthetic pathway to convert glucose into isobutanol.

    PubMed

    Savrasova, Ekaterina A; Kivero, Aleksander D; Shakulov, Rustem S; Stoynova, Nataliya V

    2011-09-01

    Microbiological synthesis of higher alcohols (1-butanol, isobutanol, 2-methyl-1-butanol, etc.) from plant biomass is critically important due to their advantages over ethanol as a motor fuel. In recent years, the use of branched-chain amino acid (BCAA) biosynthesis pathways together with heterologous Ehrlich pathway enzyme system (Hazelwood et al. in Appl Environ Microbiol 74:2259-2266, 2008) has been proposed by the Liao group as an alternative approach to aerobic production of higher alcohols as new-generation biofuels (Atsumi et al. in Nature 451:86-90, 2008; Atsumi et al. in Appl Microbiol Biotechnol 85:651-657, 2010; Cann and Liao in Appl Microbiol Biotechnol 81:89-98, 2008; Connor and Liao in Appl Environ Microbiol 74:5769-5775, 2008; Shen and Liao in Metab Eng 10:312-320, 2008; Yan and Liao in J Ind Microbiol Biotechnol 36:471-479, 2009). On the basis of these remarkable investigations, we re-engineered Escherichia coli valine-producing strain H-81, which possess overexpressed ilvGMED operon, for the aerobic conversion of sugar into isobutanol. To redirect valine biosynthesis to the production of alcohol, we also--as has been demonstrated previously (Atsumi et al. in Nature 451:86-90, 2008; Atsumi et al. in Appl Microbiol Biotechnol 85:651-657, 2010; Cann and Liao in Appl Microbiol Biotechnol 81:89-98, 2008; Connor and Liao in Appl Environ Microbiol 74:5769-5775, 2008; Shen and Liao in Metab Eng 10:312-320, 2008; Yan and Liao in J Ind Microbiol Biotechnol 36:471-479, 2009)--used enzymes of Ehrlich pathway. In particular, in our study, the following heterologous proteins were exploited: branched-chain 2-keto acid decarboxylase (BCKAD) encoded by the kdcA gene from Lactococcus lactis with rare codons substituted, and alcohol dehydrogenase (ADH) encoded by the ADH2 gene from Saccharomyces cerevisiae. We show that expression of both of these genes in the valine-producing strain H-81 results in accumulation of isobutanol instead of valine. Expression of BCKAD

  8. Discovery and Confirmation of Ligand Binding Specificities of the Schistosoma japonicum Polarity Protein Scribble

    PubMed Central

    Piao, Xianyu; Hou, Nan; Liu, Shuai; Gao, Youhe; Wang, Heng; Chen, Qijun

    2014-01-01

    Background Schistosomiasis is a chronic debilitating parasitic disease that afflicts more than 200 million individuals worldwide. Long-term administration of chemotherapy with the single available drug, praziquantel, has led to growing concerns about drug resistance. The PSD-95/Dlg/ZO-1 (PDZ) domain is an important module found in many scaffolding proteins, which has been recognized as promising targets for the development of novel drugs. However, the parasite-derived PDZ domains and their associated functions are still largely unknown. Methodology/Principal Findings The gene encoding the Schistosoma japonicum Scribble protein (SjScrib) was identified by homologous search with the S. mansoni Scrib sequence. By screening an arbitrary peptide library in yeast two-hybrid (Y2H) assays, we identified and confirmed the ligand binding specificity for each of the four PDZ domains of SjScrib. Both SjScrib-PDZ1 and SjScrib-PDZ3 recognize type I C-terminal PDZ-domain binding motifs (PBMs), which can be deduced as consensus sequences of -[Φ][x][E][TS][x][ILF] and -[x][RKx][ETS][T][WΦ][ILV], respectively. SjScrib-PDZ2 prefers stringent type II C-terminal PBMs, which significantly differs from that of its human ortholog. SjScrib-PDZ4 binds to typical II C-terminal PBMs with a consensus sequence -[x][FW][x][LI][x][LIV], in which the aromatic residue Phe is predominantly selected at position -4. The irregular and unconventional internal ligand binding specificities for the PDZ domains of SjScrib were confirmed by point mutations of the key amino acids within the ligand binding motifs. We also compared the differences in ligand specificities between SjScrib-PDZs and hScrib-PDZs, and explored the structural basis for the ligand binding properties of SjScrib-PDZs. Conclusions/Significance In this study, we characterized and confirmed the ligand binding specificities of all four PDZ domains of SjScrib for the first time. We denoted the differential ligand binding specificities

  9. Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

    PubMed Central

    Rahman, Mohammad Mubinur; Andberg, Martina; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina

    2016-01-01

    l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V M value of 3.2 Å3 Da−1 and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V M value of 4.0 Å3 Da−1 and a solvent content of 69%. PMID:27487924

  10. Evaluation of a Shuttle Derived Vehicle (SDV) for Cargo Transportation

    NASA Technical Reports Server (NTRS)

    Roman, Jose M.; Meacham, Stephen B.; Krupp, Donald R.; Threet, G. E.; Best, Joel; Davis, Stephan R.; Crumbly, Christopher; Olsen, Ronald A.; Engler, Leah M.; Garner, Tim

    2005-01-01

    In this new era of space exploration, a host of launch vehicles are being examined for possible use in transporting cargo and crew to low Earth orbit and beyond. Launch vehicles derived from the Space Shuttle Program (SSP), known as Shuttle Derived Vehicles (SDVs), are prime candidates for heavy-lift duty because of their potential to minimize non-recurring costs and because the Shuttle can leverage off proven high-performance flight systems with established ground and flight support. To determine the merits of SDVs, a detailed evaluation was performed. This evaluation included a trade study and risk assessment of options based on performance, safety reliability, cost, operations, and evolution. The purpose of this paper is to explain the approach, processes, and tools used to evaluate launch vehicles for heavy lift cargo transportation. The process included defining the trade space, characterizing the concepts, analyzing the systems, and scoring the options. The process also included a review by subject experts from NASA and industry to compare past and recent study data and assess the risks. A set of technical performance measures (TPMs) was generated based on the study requirements and constraints. Tools such as INTROS and POST were used to calculate performance, FIRST was used for prediction of reliability, and other software packages, both commercial and NASA-owned, were applied to study the trade space. By following a clear process and using the right tools a thorough assessment was performed. An SDV can be classified as either a side-mount vehicle (SMV) or an in-line vehicle OLV). An SMV is a Space Shuttle where the Orbiter is replaced by a cargo carrier. An ILV is comprised of a modified Shuttle External Tank (ET) with engines mounted to the bottom and cargo mounted atop. For both families of vehicles, Solid Rocket Boosters (SRBs) are attached to the ET. The first derivate of Shuttle is defined as the vehicle with minimum changes necessary to transform the

  11. Characteristics and phylogeny of Bacillus cereus strains isolated from Maari, a traditional West African food condiment.

    PubMed

    Thorsen, Line; Kando, Christine Kere; Sawadogo, Hagrétou; Larsen, Nadja; Diawara, Bréhima; Ouédraogo, Georges Anicet; Hendriksen, Niels Bohse; Jespersen, Lene

    2015-03-02

    Maari is a spontaneously fermented food condiment made from baobab tree seeds in West African countries. This type of product is considered to be safe, being consumed by millions of people on a daily basis. However, due to the spontaneous nature of the fermentation the human pathogen Bacillus cereus occasionally occurs in Maari. This study characterizes succession patterns and pathogenic potential of B. cereus isolated from the raw materials (ash, water from a drilled well (DW) and potash), seed mash throughout fermentation (0-96h), after steam cooking and sun drying (final product) from two production sites of Maari. Aerobic mesophilic bacterial (AMB) counts in raw materials were of 10(5)cfu/ml in DW, and ranged between 6.5×10(3) and 1.2×10(4)cfu/g in potash, 10(9)-10(10)cfu/g in seed mash during fermentation and 10(7) - 10(9) after sun drying. Fifty three out of total 290 AMB isolates were identified as B. cereus sensu lato by use of ITS-PCR and grouped into 3 groups using PCR fingerprinting based on Escherichia coli phage-M13 primer (M13-PCR). As determined by panC gene sequencing, the isolates of B. cereus belonged to PanC types III and IV with potential for high cytotoxicity. Phylogenetic analysis of concatenated sequences of glpF, gmk, ilvD, pta, pur, pycA and tpi revealed that the M13-PCR group 1 isolates were related to B. cereus biovar anthracis CI, while the M13-PCR group 2 isolates were identical to cereulide (emetic toxin) producing B. cereus strains. The M13-PCR group 1 isolates harboured poly-γ-D-glutamic acid capsule biosynthesis genes capA, capB and capC showing 99-100% identity with the environmental B. cereus isolate 03BB108. Presence of cesB of the cereulide synthetase gene cluster was confirmed by PCR in M13-PCR group 2 isolates. The B. cereus harbouring the cap genes were found in potash, DW, cooking water and at 8h fermentation. The "emetic" type B. cereus were present in DW, the seed mash at 48-72h of fermentation and in the final product

  12. Cardiovascular Deconditioning in Humans: Alteration in Cardiovascular Regulation and Function During Simulated Microgravity

    NASA Technical Reports Server (NTRS)

    Cohen, Richard

    1999-01-01

    Alterations in cardiovascular regulation and function that occur during and after space flight have been reported. These alterations are manifested, for example, by reduced orthostatic tolerance upon reentry to the earth's gravity from space. However, the precise physiologic mechanisms responsible for these alterations remain to be fully elucidated. Perhaps, as a result, effective countermeasures have yet to be developed. In this project we apply a powerful, new method - cardiovascular system identification (CSI) - for the study of the effects of space flight on the cardiovascular system so that effective countermeasures can be developed. CSI involves the mathematical analysis of second-to-second fluctuations in non-invasively measured heart rate, arterial blood pressure (ABP), and instantaneous lung volume (ILV - respiratory activity) in order to characterize quantitatively the physiologic mechanisms responsible for the couplings between these signals. Through the characterization of all the physiologic mechanisms coupling these signals, CSI provides a model of the closed-loop cardiovascular regulatory state in an individual subject. The model includes quantitative descriptions of the heart rate baroreflex, autonomic function, as well as other important physiologic mechanisms. We are in the process of incorporating beat-to-beat fluctuations of stroke volume into the CSI technique in order to quantify additional physiologic mechanisms such as those involved in control of peripheral vascular resistance and alterations in cardiac contractility. We apply CSI in conjunction with the two general protocols of the Human Studies Core project. The first protocol involves ground-based, human head down tilt bed rest to simulate microgravity and acute stressors - upright tilt, standing and bicycle exercise - to provide orthostatic and exercise challenges. The second protocol is intended to be the same as the first but with the addition of sleep deprivation to determine whether

  13. Cardiovascular Deconditioning in Humans: Alteration in Cardiovascular Regulation and Function During Simulated Microgravity

    NASA Technical Reports Server (NTRS)

    Cohen, Richard

    1999-01-01

    Alterations in cardiovascular regulation and function that occur during and after space flight have been reported. These alterations are manifested, for example, by reduced orthostatic tolerance upon reentry to the earth's gravity from space. However, the precise physiologic mechanisms responsible for these alterations remain to be fully elucidated. Perhaps, as a result, effective countermeasures have yet to be developed. In this project we apply a powerful, new method - cardiovascular system identification (CSI) - for the study of the effects of space flight on the cardiovascular system so that effective countermeasures can be developed. CSI involves the mathematical analysis of second-to-second fluctuations in non-invasively measured heart rate, arterial blood pressure (ABP), and instantaneous lung volume (ILV - respiratory activity) in order to characterize quantitatively the physiologic mechanisms responsible for the couplings between these signals. Through the characterization of all the physiologic mechanisms coupling these signals, CSI provides a model of the closed-loop cardiovascular regulatory state in an individual subject. The model includes quantitative descriptions of the heart rate baroreflex, autonomic function, as well as other important physiologic mechanisms. We are in the process of incorporating beat-to-beat fluctuations of stroke volume into the CSI technique in order to quantify additional physiologic mechanisms such as those involved in control of peripheral vascular resistance and alterations in cardiac contractility. We apply CSI in conjunction with the two general protocols of the Human Studies Core project. The first protocol involves ground-based, human head down tilt bed rest to simulate microgravity and acute stressors - upright tilt, standing and bicycle exercise - to provide orthostatic and exercise challenges. The second protocol is intended to be the same as the first but with the addition of sleep deprivation to determine whether

  14. EDITORIAL: Focus on Mechanical Systems at the Quantum Limit FOCUS ON MECHANICAL SYSTEMS AT THE QUANTUM LIMIT

    NASA Astrophysics Data System (ADS)

    Aspelmeyer, Markus; Schwab, Keith

    2008-09-01

    progress was reported almost on a monthly basis and new groups entered the field. We intend to keep submission to this Focus Issue open for some time and invite everyone to share their latest results with us. And finally, a note to our fellow colleagues: keep up the good work! We would like to call the next Focus Issue 'Mechanical Systems IN the Quantum Regime'. Focus on Mechanical Systems at the Quantum Limit Contents Parametric coupling between macroscopic quantum resonators L Tian, M S Allman and R W Simmonds Quantum noise in a nanomechanical Duffing resonator E Babourina-Brooks, A Doherty and G J Milburn Creating and verifying a quantum superposition in a micro-optomechanical system Dustin Kleckner, Igor Pikovski, Evan Jeffrey, Luuk Ament, Eric Eliel, Jeroen van den Brink and Dirk Bouwmeester Ground-state cooling of a nanomechanical resonator via a Cooper-pair box qubit Konstanze Jaehne, Klemens Hammerer and Margareta Wallquist Dissipation in circuit quantum electrodynamics: lasing and cooling of a low-frequency oscillator Julian Hauss, Arkady Fedorov, Stephan André, Valentina Brosco, Carsten Hutter, Robin Kothari, Sunil Yeshwanth, Alexander Shnirman and Gerd Schön Route to ponderomotive entanglement of light via optically trapped mirrors Christopher Wipf, Thomas Corbitt, Yanbei Chen and Nergis Mavalvala Nanomechanical-resonator-assisted induced transparency in a Cooper-pair box system Xiao-Zhong Yuan, Hsi-Sheng Goan, Chien-Hung Lin, Ka-Di Zhu and Yi-Wen Jiang High-sensitivity monitoring of micromechanical vibration using optical whispering gallery mode resonators A Schliesser, G Anetsberger, R Rivière, O Arcizet and T J Kippenberg Optomechanical to mechanical entanglement transformation Giovanni Vacanti, Mauro Paternostro, G Massimo Palma and Vlatko Vedral The optomechanical instability in the quantum regime Max Ludwig, Björn Kubala and Florian Marquardt Quantum limits of photothermal and radiation pressure cooling of a movable mirror M Pinard and A Dantan

  15. Engineering Ralstonia eutropha for Production of Isobutanol (IBT) Motor Fuel from Carbon Dioxide, Hydrogen, and Oxygen Project Final Report

    SciTech Connect

    Sinskey, Anthony J.; Worden, Robert Mark; Brigham, Christopher; Lu, Jingnan; Quimby, John Westlake; Gai, Claudia; Speth, Daan; Elliott, Sean; Fei, John Qiang; Bernardi, Amanda; Li, Sophia; Grunwald, Stephan; Grousseau, Estelle; Maiti, Soumen; Liu, Chole

    2013-12-16

    into complex cellular molecules using the energy from hydrogen. In this research project, engineered strains of R. eutropha redirected the excess carbon from PHB storage into the production of isobutanol and 3-methyl-1-butanol (branched-chain higher alcohols). These branched-chain higher alcohols can be used directly as substitutes for fossil-based fuels and are seen as alternative biofuels to ethanol and biodiesel. Importantly, these alcohols have approximately 98 % of the energy content of gasoline, 17 % higher than the current gasoline additive ethanol, without impacting corn market production for feed or food. Unlike ethanol, these branched-chain alcohols have low vapor pressure, hygroscopicity, and water solubility, which make them readily compatible with the existing pipelines, gasoline pumps, and engines in our transportation infrastructure. While the use of alternative energies from solar, wind, geothermal, and hydroelectric has spread for stationary power applications, these energy sources cannot be effectively or efficiently employed in current or future transportation systems. With the ongoing concerns of fossil fuel availability and price stability over the long term, alternative biofuels like branched-chain higher alcohols hold promise as a suitable transportation fuel in the future. We showed in our research that various mutant strains of R. eutropha with isobutyraldehyde dehydrogenase activity, in combination with the overexpression of plasmid-borne, native branched-chain amino acid biosynthesis pathway genes and the overexpression of heterologous ketoisovalerate decarboxylase gene, would produce isobutanol and 3-methyl-1-butanol when initiated during nitrogen or phosphorus limitation. Early on, we isolated one mutant R. eutropha strain which produced over 180 mg/L branched-chain alcohols in flask culture while being more tolerant of isobutanol toxicity. After the targeted elimination of genes encoding several potential carbon sinks (ilvE, bkdAB, and ace

  16. [Bottom-up analysis of the case costs of stem cell transplantation and selected chemotherapies].

    PubMed

    Stäbler, W; Wagner, B

    2003-01-01

    multiplicity of treatment sessions is manifested in the compact "establishment of the diagnosis" to determine a therapy protocol which entails very elaborate inpatient measures under hospitalization, in the expensive and individual "stays due to complications" which usually take place between the "chemotherapy blocks", and the expensive long-term care of the SCT patients after the end of the residence limit (GVD). Owing to the small and divergent numbers of cases in Germany (2000 new patients in 50 centers and 330 SCT per year) and per center, this problem cannot be dealt with by means of a quantity compensation argumentation, as is doubtless justified elsewhere. The actual individual case costs of oncological patients would be 166,72 euro; per outpatient contact and covered by 459,30 euro; per day of hospital care and 808,20 euro; per inpatient treatment day (admission plus discharge day calculated separately and comprised stem cell transplantation patients beyond the residence limit) is covered. The level of the currently applicable case flat rate payments for stem cell transplantations and heterologous donors, mismatched heterologous donors and family donors appear appropriate in relation to the GVD. (The true costs of all oncological patients would indeed be even higher if the GOA payment of the ILV did not only relate to a house-internal low pricing of the GOA scoring value, but would also relate to HLA typing, unpaid physician overtime and the costs of the study centers to the individual cases. From 2002, there will be changes consequent on the judgment of the European Court that stand-by is working time, so that more physicians must be employed and there are expensive changes in the infrastructure owing to the need for a GMP clean area laboratory to process stem cells according to the medical products law.) The indeterminate bound-aries between the three treatment categories place in question the dual financing by the Panel Doctor's Association and the health insurance