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Sample records for ada mutant strains

  1. Mutant strain of C. acetobutylicum and process for making butanol

    DOEpatents

    Jain, Mahendra K.; Beacom, Daniel; Datta, Rathin

    1993-01-01

    A biologically pure asporogenic mutant of Clostridium acetobutylicum is produced by growing sporogenic C. acetobutylicum ATCC 4259 and treating the parent strain with ethane methane sulfonate. The mutant which as been designated C. acetobutylicum ATCC 55025 is useful in an improved ABE fermentation process, and produces high concentrations of butanol and total solvents.

  2. Ethanol production characteristics for a respiratory deficient mutant yeast strain

    SciTech Connect

    Garcia, A. III; Grilione, P.

    1982-01-01

    Barley was fermented with a defined strain of Saccharomyces cerevisiae and a chemical induced respiratory deficient mutant RD, specific gravity, pH, CO/sub 2/ production and ethanol production rates and yield were compared. RD fermentation were slower but yielded slightly more ethanol after a considerable time. Partial reversion to a respiratory capable strain occurred.

  3. Applications of mutant yeast strains with low glycogen storage capability

    NASA Technical Reports Server (NTRS)

    Petersen, G. R.; Schubert, W. W.; Stokes, B. O.

    1981-01-01

    Several strains of Hansenula polymorpha were selected for possible low glycogen storage characteristics based on a selective I2 staining procedure. The levels of storage carbohydrates in the mutant strains were found to be 44-70% of the levels in the parent strain for cultures harvested in stationary phase. Similar differences generally were not found for cells harvested in exponential phase. Yeast strains deficient in glycogen storage capability are valuable in increasing the relative protein value of microbial biomass and also may provide significant cost savings in substrate utilization in fermentative processes.

  4. Role of the Ada adaptor complex in gene activation by the glucocorticoid receptor.

    PubMed Central

    Henriksson, A; Almlöf, T; Ford, J; McEwan, I J; Gustafsson, J A; Wright, A P

    1997-01-01

    We have shown that the Ada adaptor complex is important for the gene activation capacity of the glucocorticoid receptor in yeast. The recently isolated human Ada2 protein also increases the potency of the receptor protein in mammalian cells. The Ada pathway is of key significance for the tau1 core transactivation domain (tau1c) of the receptor, which requires Ada for activity in vivo and in vitro. Ada2 can be precipitated from nuclear extracts by a glutathione S-transferase-tau1 fusion protein coupled to agarose beads, and a direct interaction between Ada2 and tau1c can be shown by using purified proteins. This interaction is strongly reduced by a mutation in tau1c that reduces transactivation activity. Mutations affecting the Ada complex do not reverse transcriptional squelching by the tau1 domain, as they do for the VP16 transactivation domain, and thus these powerful acidic activators differ in at least some important aspects of gene activation. Mutations that reduce the activity of the tau1c domain in wild-type yeast strains cause similar reductions in ada mutants that contain little or no Ada activity. Thus, gene activation mechanisms, in addition to the Ada pathway, are involved in the activity of the tau1c domain. PMID:9154805

  5. Mutants of Paracoccidioides brasiliensis strain IVIC Pb9 affected in dimorphism.

    PubMed

    San-Blas, F; San-Blas, G

    1992-01-01

    Morphological mutants were isolated after nitrosoguanidine treatment of Paracoccidioides brasiliensis strain IVIC Pb9. Two of these mutants, Pb257 and Pb258, developed a typical mycelia at 23 degrees C, however, the yeast cells which developed at 37 degrees C were indistinguishable from those of the parental strain. A third mutant, strain Pb267, was thermosensitive, grew as yeast-like cells at 23 degrees C, but was unable to survive at 37 degrees C. Morphological observations as well as serological and segregation tests confirmed that the mutant strains originated from P. brasiliensis. Cell wall chemical analyses of the mutant strains grown at 23 degrees C indicated the presence of alkali-soluble, acid-insoluble polysaccharides absent in the parental wild-type strain Pb9 grown under the same conditions. The phenotypes shown by the mutant strains may be related to deficiencies in the proper synthesis of cell wall components of the mycelial phase of this fungus. PMID:1573521

  6. Revealing Differences in Metabolic Flux Distributions between a Mutant Strain and Its Parent Strain Gluconacetobacter xylinus CGMCC 2955

    PubMed Central

    Liu, Miao; Yang, Xiao-Ning; Zhu, Hui-Xia; Jia, Yuan-Yuan; Jia, Shi-Ru; Piergiovanni, Luciano

    2014-01-01

    A better understanding of metabolic fluxes is important for manipulating microbial metabolism toward desired end products, or away from undesirable by-products. A mutant strain, Gluconacetobacter xylinus AX2-16, was obtained by combined chemical mutation of the parent strain (G. xylinus CGMCC 2955) using DEC (diethyl sulfate) and LiCl. The highest bacterial cellulose production for this mutant was obtained at about 11.75 g/L, which was an increase of 62% compared with that by the parent strain. In contrast, gluconic acid (the main byproduct) concentration was only 5.71 g/L for mutant strain, which was 55.7% lower than that of parent strain. Metabolic flux analysis indicated that 40.1% of the carbon source was transformed to bacterial cellulose in mutant strain, compared with 24.2% for parent strain. Only 32.7% and 4.0% of the carbon source were converted into gluconic acid and acetic acid in mutant strain, compared with 58.5% and 9.5% of that in parent strain. In addition, a higher flux of tricarboxylic acid (TCA) cycle was obtained in mutant strain (57.0%) compared with parent strain (17.0%). It was also indicated from the flux analysis that more ATP was produced in mutant strain from pentose phosphate pathway (PPP) and TCA cycle. The enzymatic activity of succinate dehydrogenase (SDH), which is one of the key enzymes in TCA cycle, was 1.65-fold higher in mutant strain than that in parent strain at the end of culture. It was further validated by the measurement of ATPase that 3.53–6.41 fold higher enzymatic activity was obtained from mutant strain compared with parent strain. PMID:24901455

  7. Biofilm formation by exopolysaccharide mutants of Leuconostoc mesenteroides strain NRRL B-1355

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leuconostoc mesenteroides strain NRRL B-1355 produces the soluble exopolysaccharides alternan and dextran in planktonic cultures. A set of mutants of this strain are available that are deficient in the production of alternan, dextran, or both. Another mutant of NRRL B-1355, strain R1510, produces ...

  8. Generation and Evaluation of High β-Glucan Producing Mutant Strains of Sparassis crispa

    PubMed Central

    Kim, Seung-Rak; Kang, Hyeon-Woo

    2013-01-01

    A chemical mutagenesis technique was employed for development of mutant strains of Sparassis crispa targeting the shortened cultivation time and the high β-glucan content. The homogenized mycelial fragments of S. crispa IUM4010 strain were treated with 0.2 vol% methyl methanesulfonate, an alkylating agent, yielding 199 mutant strains. Subsequent screening in terms of growth and β-glucan content yielded two mutant strains, B4 and S7. Both mutants exhibited a significant increase in β-glucan productivity by producing 0.254 and 0.236 mg soluble β-glucan/mg dry cell weight for the B4 and S7 strains, respectively, whereas the wild type strain produced 0.102 mg soluble β-glucan/mg dry cell weight. The results demonstrate the usefulness of chemical mutagenesis for generation of mutant mushroom strains. PMID:24198672

  9. Isolation of a mutant strain of Pseudomonas sp ATCC 31461 exhibiting elevated polysaccharide production.

    PubMed

    West, T P

    2002-10-01

    A mutant strain of the bacterium Pseudomonas sp. ATCC 31461 that exhibited elevated production of the polysaccharide gellan on glucose or corn syrup as a carbon source was isolated. Gellan production by the mutant strain was about twofold higher than its parent strain on glucose or corn syrup after 48 h of growth, and about 1.4-fold higher after 72 h. An increase in biomass production was not correlated with enhanced gellan synthesis by the mutant strain. The increased gellan production by the mutant strain on either carbon source resulted in an increase in its culture medium viscosity and the viscosity of the isolated polysaccharide produced by glucose-grown cells. No differences in the glucuronic acid content of the polysaccharides produced by the mutant and parent strains were observed. PMID:12355317

  10. Benomyl-resistant mutant strain of Trichoderma sp. with increased mycoparasitic activity.

    PubMed

    Olejníková, P; Ondrusová, Z; Krystofová, S; Hudecová, D

    2010-01-01

    Application of UV radiation to the strain Trichoderma sp. T-bt (isolated from lignite) resulted in the T-brm mutant which was resistant to the systemic fungicide benomyl. The tub2 gene sequence in the T-brm mutant differed from the parent as well as the collection strain (replacing tyrosine with histidine in the TUB2 protein). Under in vitro conditions this mutant exhibited a higher mycoparasitic activity toward phytopathogenic fungi. PMID:20336512

  11. Increased riboflavin production from activated bleaching earth by a mutant strain of Ashbya gossypii.

    PubMed

    Tajima, Satoshi; Itoh, Yoko; Sugimoto, Takashi; Kato, Tatsuya; Park, Enoch Y

    2009-10-01

    The production of riboflavin from vegetable oil was increased using a mutant strain of Ashbya gossypii. This mutant was generated by treating the wild-type strain with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Riboflavin production was 10-fold higher in the mutant compared to the wild-type strain. The specific intracellular catalase activity after 3 d of culture was 6-fold higher in the mutant than in the wild-type strain. For the mutant, riboflavin production in the presence of 40 mM hydrogen peroxide was 16% less than that in the absence of hydrogen peroxide, whereas it was 56% less for the wild-type strain. The isocitrate lyase (ICL) activity of the mutant was 0.26 mU/mg of protein during the active riboflavin production phase, which was 2.6-fold higher than the wild-type strain. These data indicate that the mutant utilizes the carbon flux from the TCA cycle to the glyoxylate cycle more efficiently than the wild-type strain, resulting in enhanced riboflavin production. This novel mutant has the potential to be of use for industrial-scale riboflavin production from waste-activated bleaching earth (ABE), thereby transforming a useless material into a valuable bioproduct. PMID:19716523

  12. Distributed systems and Ada

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Viewgraphs of two briefings designed to provide information to the Software I and V Study Group to help complete the I and V study task are given. The information is taken from the areas of Ada real-time processing support, Ada run-time environments, Ada program construction, object oriented design, and Ada/UNIX/POSIX interfaces. Also covered are the development, integration, and verification of Ada systems; fault tolerance and Ada; and Ada programming standards, techniques, and tools.

  13. Mutant strains of Tetrahymena thermophila defective in thymidine kinase activity: Biochemical and genetic characterization

    SciTech Connect

    Cornish, K.V.; Pearlman, R.E.

    1982-08-01

    Three mutant strains, one conditional, of Tetrahymena thermophila were defective in thymidine phosphorylating activity in vivo and in thymidine kinase activity in vitro. Nucleoside phosphotransferase activity in mutant cell extracts approached wild-type levels, suggesting that thymidine kinase is responsible for most, if not all, thymidine phosphorylation in vivo. Thymidine kinase activity in extracts of the conditional mutant strain was deficient when the cells were grown or assayed or both at the permissive temperature, implying a structural enzyme defect. Analysis of the reaction products from in vitro assays with partially purified enzymes showed that phosphorylation by thymidine kinase and nucleoside phosphotransferase occurred at the 5' position. Genetic analyses showed that the mutant phenotype was recessive and that mutations in each of the three mutant strains did not complement, suggesting allelism.

  14. Induction, isolation, and characterization of aspergillus niger mutant strains producing elevated levels of beta-galactosidase.

    PubMed Central

    Nevalainen, K M

    1981-01-01

    An Aspergillus niger mutant strain, VTT-D-80144, with an improvement of three- to fourfold in the production of extracellular beta-galactosidase was isolated after mutagenesis. The production of beta-galactosidase by this mutant was unaffected by fermentor size, and the enzyme was also suitable for immobilization. PMID:6784672

  15. Efficient production of ethanol from crude glycerol by a Klebsiella pneumoniae mutant strain.

    PubMed

    Oh, Baek-Rock; Seo, Jeong-Woo; Heo, Sun-Yeon; Hong, Won-Kyung; Luo, Lian Hua; Joe, Min-ho; Park, Don-Hee; Kim, Chul Ho

    2011-02-01

    A mutant strain of Klebsiella pneumoniae, termed GEM167, was obtained by γ irradiation, in which glycerol metabolism was dramatically affected on exposure to γ rays. Levels of metabolites of the glycerol reductive pathway, 1,3-propanediol (1,3-PD) and 3-hydroxypropionic acid (3-HP), were decreased in the GEM167 strain compared to a control strain, whereas the levels of metabolites derived from the oxidative pathway, 2,3-butanediol (2,3-BD), ethanol, lactate, and succinate, were increased. Notably, ethanol production from glycerol was greatly enhanced upon fermentation by the mutant strain, to a maximum production level of 21.5 g/l, with a productivity of 0.93 g/l/h. Ethanol production level was further improved to 25.0 g/l upon overexpression of Zymomonas mobilis pdc and adhII genes encoding pyruvate decarboxylase (Pdc) and aldehyde dehydrogenase (Adh), respectively in the mutant strain GEM167. PMID:21186120

  16. Mutant E. coli strain with increased succinic acid production

    DOEpatents

    Donnelly, Mark; Millard, Cynthia S.; Stols, Lucy

    2002-01-01

    A method for isolating succinic acid producing bacteria is provided comprising increasing the biomass of an organism which lacks the ability to catabolize pyruvate, and then subjecting the biomass to glucose-rich medium in an anaerobic environment to enable pyruvate-catabolizing mutants to grow. The invention also provides for a mutant that produces high amounts of succinic acid, which has been derived from a parent which lacked the genes for pyruvate formate lyase and lactate dehydrogenase, and which belongs to the E.coli Group of Bacteria.

  17. Mutant E. coli strain with increased succinic acid production

    DOEpatents

    Donnelly, M.; Millard, C.S.; Stols, L.

    1998-06-23

    A method for isolating succinic acid producing bacteria is provided comprising increasing the biomass of an organism which lacks the ability to catabolize pyruvate, and then subjecting the biomass to glucose-rich medium in an anaerobic environment to enable pyruvate-catabolizing mutants to grow. The invention also provides for a mutant that produces high amounts of succinic acid, which as been derived from a parent which lacked the genes for pyruvate formate lyase and lactate dehydrogenase, and which belongs to the E.coli Group of Bacteria. 2 figs.

  18. Mutant E. coli strain with increased succinic acid production

    DOEpatents

    Donnelly, Mark; Millard, Cynthia S.; Stols, Lucy

    1998-01-01

    A method for isolating succinic acid producing bacteria is provided comprising increasing the biomass of an organism which lacks the ability to catabolize pyruvate, and then subjecting the biomass to glucose-rich medium in an anaerobic environment to enable pyruvate-catabolizing mutants to grow. The invention also provides for a mutant that produces high amounts of succinic acid, which as been derived from a parent which lacked the genes for pyruvate formate lyase and lactate dehydrogenase, and which belongs to the E.coli Group of Bacteria.

  19. Mutant E. coli strain with increased succinic acid production

    DOEpatents

    Donnelly, Mark; Millard, Cynthia S.; Stols, Lucy

    2001-09-25

    A method for isolating succinic acid producing bacteria is provided comprising increasing the biomass of an organism which lacks the ability to catabolize pyruvate, and then subjecting the biomass to glucose-rich medium in an anaerobic environment to enable pyruvate-catabolizing mutants to grow. The invention also provides for a mutant that produces high amounts of succinic acid, which has been derived from a parent which lacked the genes for pyruvate formate lyase and lactate dehydrogenase, and which belongs to the E.coli Group of Bacteria.

  20. Transforming AdaPT to Ada

    NASA Technical Reports Server (NTRS)

    Goldsack, Stephen J.; Holzbach-Valero, A. A.; Waldrop, Raymond S.; Volz, Richard A.

    1991-01-01

    This paper describes how the main features of the proposed Ada language extensions intended to support distribution, and offered as possible solutions for Ada9X can be implemented by transformation into standard Ada83. We start by summarizing the features proposed in a paper (Gargaro et al, 1990) which constitutes the definition of the extensions. For convenience we have called the language in its modified form AdaPT which might be interpreted as Ada with partitions. These features were carefully chosen to provide support for the construction of executable modules for execution in nodes of a network of loosely coupled computers, but flexibly configurable for different network architectures and for recovery following failure, or adapting to mode changes. The intention in their design was to provide extensions which would not impact adversely on the normal use of Ada, and would fit well in style and feel with the existing standard. We begin by summarizing the features introduced in AdaPT.

  1. Characterization of a non-pigment producing Monascus purpureus mutant strain.

    PubMed

    Rasheva, Tanya V; Nedeva, Trayana S; Hallet, Jean-Noel; Kujumdzieva, Anna V

    2003-01-01

    A characterization of a non-pigment producing mutant Monascus purpureus M12 compared with its parental strain Monascus purpureus Went CBS 109.07 has been performed aiming to investigate the relation between pigment biosynthesis and other characteristics of these fungi. A comparison has been made of morphological features, some physiological properties and biochemical activities of both strains. The albino mutant exhibits an anamorph life cycle, high conidia forming capability, slower radial growth rate and temperature sensitivity. The assimilation capacity of both strains for mono-, disaccharides and some alcohols is in the same range (Yx/c 0.2 - 0.35), while the red strain has a higher fermentation capacity. In a selected albino mutant, the growth rate, metabolic activity and capacity for production of typical for Monascus fungi secondary metabolites were reduced considerably. Hydrolytic activity towards natural substrates expressed through glucoamylase and protease was approximately 10 fold lower in the non pigment producing strain (0.05 - 0.08 U/mg protein and 0.01 - 0.07 U/mg protein respectively) compared with the red one. Important qualitative differences between both strains was found in fatty acid composition and in the production of citrinin and monacolin. The mutant strain possessed C17, C20 and C22 fatty acids and did not produce citrinin. PMID:12777069

  2. Biological methods for archiving and maintaining mutant laboratory mice. Part I: conserving mutant strains.

    PubMed

    Fray, Martin D

    2009-01-01

    The mouse is now firmly established as the model organism of choice for scientists studying mammalian biology and human disease. Consequently, a plethora of novel, genetically altered (GA) mouse lines have been created. In addition, the output from the large scale mutagenesis programmes currently under way around the world will increase the collection of GA mouse strains still further. Because of the implications for animal welfare and the constraints on resources, it would be unreasonable to expect anything other than those strains essential for ongoing research programmes to be maintained as breeding colonies. Unfortunately, unless the redundant strains are preserved using robust procedures, which guarantee their recovery, they will be lost to future generations of researchers.This chapter describes some of the preservation methods currently used in laboratories around the world to archive novel mouse strains. PMID:19504080

  3. Effects of a Mutant Strain and a Wild Type Strain of Verticillium lecanii on Heterodera glycines Populations in the Greenhouse

    PubMed Central

    Meyer, Susan L. F.; Meyer, Robert J.

    1995-01-01

    A wild type strain ofVerticillium lecanii and a mutant strain with increased tolerance to the fungicide benomyl were evaluated in greenhouse experiments for effects on Heterodera glycines populations. Nematodes were applied at 300 eggs and juveniles per 4,550-cm³ pot (two soybean plants in 4,990 g loamy sand per pot) and at both 300 and 10,000 eggs and juveniles per 1,720-cm³ pot (one soybean plant in 2,060 g sand per pot). With 300 nematodes added per pot, both V. lecanii strains significantly reduced nematode populations in loamy sand (fungus applied at 0.02% dry weight per dry weight loamy sand) and sand (0.006% and 0.06% fungus application rates). The mutant strain applied at 0.002% to sand also significantly reduced cyst numbers. When 10,000 nematodes were added per pot, only the mutant strain at 0.06% significantly decreased population. Various media were tested for isolation of the fungus strains from prills, loamy sand, and sand, but the fungi were recovered from few of the greenhouse pots. PMID:19277306

  4. [Generation of nalidixic acid-resistant strains and signature-tagged mutants of Actinobacillus pleuropneumoniae].

    PubMed

    Shang, Lin; Li, Wei; Li, Liangjun; Li, Lu; Zhang, Sihua; Li, Tingting; Li, Yaokun; Liu, Lei; Guo, Zhiwei; Zhou, Rui; Chen, Huanchun

    2008-01-01

    Actinobacillus pleuropneumoniae is a very important respiratory pathogen for swine and causes great economic losses in pig industry worldwide. Signature-tagged mutagenesis (STM) is an effective method to identify virulence genes in bacteria. In this study, we selected nalidixic acid-resistant strains of APP serotypes 1 and 3 by in vitro cultivation, and used as receipt strains for constructing transposon mutants by mating with E. coli CC 118 lambdapir or S17-1 lambdapir containing mini-Tn10 tag plasmids pLOF/TAG1-48, with or without the help of E. coli DH5alpha (pRK2073). We screened mutant strains by antibiotics selection, PCR and Southern blot identification. Our data revealed that nalidixic acid-resistance of APP strains could easily be induced in vitro and the resistance was due to the mutation in the DNA gyrase A subunit gene gyrA. In the mating experiments, the bi-parental mating was more effective and easier than tri-parental mating. Different APP strains showed a different mating and transposon efficiency in the bi-parental mating, with the strains of serotype 1 much higher than serotype 3 and the reference strain of serotype 3 higher than the field strains. These data were helpful for the construction of STM mutants and pickup of virulence genes of APP. PMID:18338580

  5. GSFC Ada programming guidelines

    NASA Technical Reports Server (NTRS)

    Roy, Daniel M.; Nelson, Robert W.

    1986-01-01

    A significant Ada effort has been under way at Goddard for the last two years. To ease the center's transition toward Ada (notably for future space station projects), a cooperative effort of half a dozen companies and NASA personnel was started in 1985 to produce programming standards and guidelines for the Ada language. The great richness of the Ada language and the need of programmers for good style examples makes Ada programming guidelines an important tool to smooth the Ada transition. Because of the natural divergence of technical opinions, the great diversity of our government and private organizations and the novelty of the Ada technology, the creation of an Ada programming guidelines document is a difficult and time consuming task. It is also a vital one. Steps must now be taken to ensure that the guide is refined in an organized but timely manner to reflect the growing level of expertise of the Ada community.

  6. Global carbon utilization profiles of wild-type, mutant, and transformant strains of Hypocrea jecorina.

    PubMed

    Druzhinina, Irina S; Schmoll, Monika; Seiboth, Bernhard; Kubicek, Christian P

    2006-03-01

    The ascomycete Hypocrea jecorina (Trichoderma reesei), an industrial producer of cellulases and hemicellulases, can efficiently degrade plant polysaccharides. However, the catabolic pathways for the resulting monomers and their relationship to enzyme induction are not well known. Here we used the Biolog Phenotype MicroArrays technique to evaluate the growth of H. jecorina on 95 carbon sources. For this purpose, we compared several wild-type isolates, mutants producing different amounts of cellulases, and strains transformed with a heterologous antibiotic resistance marker gene. The wild-type isolates and transformed strains had the highest variation in growth patterns on individual carbon sources. The cellulase mutants were relatively similar to their parental strains. Both in the mutant and in the transformed strains, the most significant changes occurred in utilization of xylitol, erythritol, D-sorbitol, D-ribose, D-galactose, L-arabinose, N-acetyl-D-glucosamine, maltotriose, and beta-methyl-glucoside. Increased production of cellulases was negatively correlated with the ability to grow on gamma-aminobutyrate, adonitol, and 2-ketogluconate; and positively correlated with that on d-sorbitol and saccharic acid. The reproducibility, relative simplicity, and high resolution (+/-10% of increase in mycelial density) of the phenotypic microarrays make them a useful tool for the characterization of mutant and transformed strains and for a global analysis of gene function. PMID:16517662

  7. Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption

    PubMed Central

    Denes, Thomas; den Bakker, Henk C.; Tokman, Jeffrey I.; Guldimann, Claudia

    2015-01-01

    Listeria-infecting phages are readily isolated from Listeria-containing environments, yet little is known about the selective forces they exert on their host. Here, we identified that two virulent phages, LP-048 and LP-125, adsorb to the surface of Listeria monocytogenes strain 10403S through different mechanisms. We isolated and sequenced, using whole-genome sequencing, 69 spontaneous mutant strains of 10403S that were resistant to either one or both phages. Mutations from 56 phage-resistant mutant strains with only a single mutation mapped to 10 genes representing five loci on the 10403S chromosome. An additional 12 mutant strains showed two mutations, and one mutant strain showed three mutations. Two of the loci, containing seven of the genes, accumulated the majority (n = 64) of the mutations. A representative mutant strain for each of the 10 genes was shown to resist phage infection through mechanisms of adsorption inhibition. Complementation of mutant strains with the associated wild-type allele was able to rescue phage susceptibility for 6 out of the 10 representative mutant strains. Wheat germ agglutinin, which specifically binds to N-acetylglucosamine, bound to 10403S and mutant strains resistant to LP-048 but did not bind to mutant strains resistant to only LP-125. We conclude that mutant strains resistant to only LP-125 lack terminal N-acetylglucosamine in their wall teichoic acid (WTA), whereas mutant strains resistant to both phages have disruptive mutations in their rhamnose biosynthesis operon but still possess N-acetylglucosamine in their WTA. PMID:25888172

  8. Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption.

    PubMed

    Denes, Thomas; den Bakker, Henk C; Tokman, Jeffrey I; Guldimann, Claudia; Wiedmann, Martin

    2015-07-01

    Listeria-infecting phages are readily isolated from Listeria-containing environments, yet little is known about the selective forces they exert on their host. Here, we identified that two virulent phages, LP-048 and LP-125, adsorb to the surface of Listeria monocytogenes strain 10403S through different mechanisms. We isolated and sequenced, using whole-genome sequencing, 69 spontaneous mutant strains of 10403S that were resistant to either one or both phages. Mutations from 56 phage-resistant mutant strains with only a single mutation mapped to 10 genes representing five loci on the 10403S chromosome. An additional 12 mutant strains showed two mutations, and one mutant strain showed three mutations. Two of the loci, containing seven of the genes, accumulated the majority (n = 64) of the mutations. A representative mutant strain for each of the 10 genes was shown to resist phage infection through mechanisms of adsorption inhibition. Complementation of mutant strains with the associated wild-type allele was able to rescue phage susceptibility for 6 out of the 10 representative mutant strains. Wheat germ agglutinin, which specifically binds to N-acetylglucosamine, bound to 10403S and mutant strains resistant to LP-048 but did not bind to mutant strains resistant to only LP-125. We conclude that mutant strains resistant to only LP-125 lack terminal N-acetylglucosamine in their wall teichoic acid (WTA), whereas mutant strains resistant to both phages have disruptive mutations in their rhamnose biosynthesis operon but still possess N-acetylglucosamine in their WTA. PMID:25888172

  9. Debugging tasked Ada programs

    NASA Technical Reports Server (NTRS)

    Fainter, R. G.; Lindquist, T. E.

    1986-01-01

    The applications for which Ada was developed require distributed implementations of the language and extensive use of tasking facilities. Debugging and testing technology as it applies to parallel features of languages currently falls short of needs. Thus, the development of embedded systems using Ada pose special challenges to the software engineer. Techniques for distributing Ada programs, support for simulating distributed target machines, testing facilities for tasked programs, and debugging support applicable to simulated and to real targets all need to be addressed. A technique is presented for debugging Ada programs that use tasking and it describes a debugger, called AdaTAD, to support the technique. The debugging technique is presented together with the use interface to AdaTAD. The component of AdaTAD that monitors and controls communication among tasks was designed in Ada and is presented through an example with a simple tasked program.

  10. Genetics of Peripheral Vestibular Dysfunction: Lessons from Mutant Mouse Strains

    PubMed Central

    Jones, Sherri M.; Jones, Timothy A.

    2015-01-01

    Background A considerable amount of research has been published about genetic hearing impairment. Fifty to sixty percent of hearing loss is thought to have a genetic cause. Genes may also play a significant role in acquired hearing loss due to aging, noise exposure, or ototoxic medications. Between 1995 and 2012, over 100 causative genes have been identified for syndromic and nonsyndromic forms of hereditary hearing loss (see Hereditary Hearing Loss Homepage http://hereditaryhearingloss.org). Mouse models have been extremely valuable in facilitating the discovery of hearing loss genes, and in understanding inner ear pathology due to genetic mutations or elucidating fundamental mechanisms of inner ear development. Purpose Whereas much is being learned about hereditary hearing loss and the genetics of cochlear disorders, relatively little is known about the role genes may play in peripheral vestibular impairment. Here we review the literature with regard to genetics of vestibular dysfunction and discuss what we have learned from studies using mutant mouse models and direct measures of peripheral vestibular neural function. Results Several genes are considered that when mutated lead to varying degrees of inner ear vestibular dysfunction due to deficits in otoconia, stereocilia, hair cells, or neurons. Behavior often does not reveal the inner ear deficit. Many of the examples presented are also known to cause human disorders. Conclusions Knowledge regarding the roles of particular genes in the operation of the vestibular sensory apparatus is growing and it is clear that gene products co-expressed in the cochlea and vestibule may play different roles in the respective end organs. The discovery of new genes mediating critical inner ear vestibular function carries the promise of new strategies in diagnosing, treating and managing patients as well as predicting the course and level of morbidity in human vestibular disease. PMID:25032973

  11. Frequency-dependent viability in mutant strains of Drosophila melanogaster.

    PubMed

    Curtsinger, J W; Sheen, F M

    1991-01-01

    We investigated the effects of genotypic frequencies on egg-to-adult viabilities in pairwise combinations of four strains of Drosophila melanogaster. The experiments involved mixture of a total of 42,000 eggs in varying proportions under controlled densities and observation of surviving adults. Viabilities were found to depend on frequencies in several genotypic combinations. In the most extreme case, the absolute viability of cn;bw females increased monotonically from 54% when common to 70% when rare. The results illustrate several statistical and methodological problems that might explain why some experiments have failed to detect frequency-dependent viabilities. These problems include heterogeneity between replications, sex differences in susceptibility to competition, and strong dependence of the experimental outcome on the choice of competitor genotypes. PMID:1901577

  12. Derepression of colicin E1 synthesis in the constitutive tif mutant strain (spr tif sfi) and in a tif sfi mutant strain of Escherichia coli K-12.

    PubMed Central

    Tessman, E S; Gritzmacher, C A; Peterson, P K

    1978-01-01

    We show here that expression of the colicin gene of the ColE1 plasmid is greatly derepressed in Escherichia coli K-12 strain DM1187 spr tif sfi, which is a constitutive tif mutant, altered in the lexA gene, and which shows constitutive expression of various pathways of the recA-dependent, lexA-blocked (SOS) repair system. In this strain colicin E1 synthesis is at least 100-fold greater than that observed in uninduced control strains (spr+ tif sfi and spr+ tif+ sfi). This result confirms the regulatory role of the lexA product in colicin E1 synthesis. Colicin yields by the uninduced strain DM1187 are as high as the maximum yields from mitomycin-induced control strains and often are several-fold higher. When the nonconstitutive tif sfi strain GC467 is raised to 43 degrees C to induce the SOS system, a low level of colicin synthesis is observed which is less than one-tenth of the yield obtained by induction with mitomycin C. Addition of adenine at the time of shift-up can increase the colicin yield of tif sfi to about one-third of the yield obtained with mitomycin C. We have also found that colicin overproduction can be detected by altered colony appearance in an overlay assay with colicin-sensitive bacteria. In addition, the lethality of the process of colicin synthesis is observed here without the use of bacteriostatic inducing agents. Images PMID:353034

  13. ART/Ada and CLIPS/Ada

    NASA Technical Reports Server (NTRS)

    Culbert, Chris

    1990-01-01

    Although they have reached a point of commercial viability, expert systems were originally developed in artificial intelligence (AI) research environments. Many of the available tools still work best in such environments. These environments typically utilize special hardware such as LISP machines and relatively unfamiliar languages such as LISP or Prolog. Space Station applications will require deep integration of expert system technology with applications developed in conventional languages, specifically Ada. The ability to apply automation to Space Station functions could be greatly enhanced by widespread availability of state-of-the-art expert system tools based on Ada. Although there have been some efforts to examine the use of Ada for AI applications, there are few, if any, existing products which provide state-of-the-art AI capabilities in an Ada tool. The goal of the ART/Ada Design Project is to conduct research into the implementation in Ada of state-of-the-art hybrid expert systems building tools (ESBT's). This project takes the following approach: using the existing design of the ART-IM ESBT as a starting point, analyze the impact of the Ada language and Ada development methodologies on that design; redesign the system in Ada; and analyze its performance. The research project will attempt to achieve a comprehensive understanding of the potential for embedding expert systems in Ada systems for eventual application in future Space Station Freedom projects. During Phase 1 of the project, initial requirements analysis, design, and implementation of the kernel subset of ART-IM functionality was completed. During Phase 2, the effort has been focused on the implementation and performance analysis of several versions with increasing functionality. Since production quality ART/Ada tools will not be available for a considerable time, and additional subtask of this project will be the completion of an Ada version of the CLIPS expert system shell developed by NASA

  14. Mechanical properties of elytra from Tribolium castaneum wild-type and body color mutant strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cuticle tanning in insects involves simultaneous cuticular hardening and pigmentation. The dynamic mechanical properties of the highly modified and cuticle-rich forewings (elytra) from Tribolium castaneum (red flour beetle) body color mutant strains were investigated to determine the relationship b...

  15. Large scale parallel pyrosequencing technology: PRRSV strain VR-2332 nsp2 deletion mutant stability in swine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomes from fifteen porcine reproductive and respiratory syndrome virus (PRRSV) isolates were derived simultaneously using 454 pyrosequencing technology. The viral isolates sequenced were from a recent swine study, in which engineered Type 2 prototype PRRSV strain VR-2332 mutants, with 87, 184, 200...

  16. [Saccharomyces cerevisiae: porphobilinogenase activity in a wild-type strain and its heme-deficient mutant].

    PubMed

    Araujo, L S; Lombardo, M E; Rossetti, M V; Batlle, A M

    1987-01-01

    Properties of Porphobilinogenase (PBGase), the enzyme complex converting porphobilinogen (PBG) into uroporphyrinogens, were comparatively studied in a wild strain D273-10B and its mutant B231 of Saccharomyces cerevisiae, Figure 1 shows the growth curves for both strains. The basic pattern of growth was observed but, although S. cerevisiae is a facultative aerobe and was grown on dextrose, a diauxic growth curve was not observed. The beginning of the exponential phase was slightly delayed for the mutant, so, its generation time (G = 3.20 h) was greater than that for the wild strain (G = 1.26 h). Optimum conditions for extracting the enzyme from both strains were found to be sonication at 10 mu for 3 min (Table 1). Table 2 shows the effect of centrifugation at 24,000 xg for 30 min on activity. For both strains the amount of porphyrins formed was the same either in the absence or presence of air. It was found (Figure 2) that urogen formation was linear with protein over a wide range of concentrations and with incubation time up to 2h in agreement with previous results for the enzyme of different sources. Figure 3 shows the effect of pH on PBGase activity. An optimum pH of 7.4 was found for both strains employing sodium phosphate buffer pH 8.0. The shape of the pH curve as well as optimum pH were the same in both Tris-HCl and phosphate buffer, however PBGase was 15% less active in the former. When plots of velocity against PBG concentration were analyzed for PBGase, it was found that measuring the rate of the reaction on the basis of total urogen formation, saturation curves for wild and mutant strains harvested at the exponential phase, followed classical Michaelis-Menten kinetics. Saturation was reached at PBG concentration of about 70-90 microM. Therefore, double reciprocal plots (Figure 4) were linear and from these plots apparent Km's values of 20 and 14 microM were obtained for the wild and mutant strain respectively. It is known that in some organisms, the

  17. Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins.

    PubMed

    Larsen, Sasha; Weaver, Jun; de Sa Campos, Katherine; Bulahan, Rhobe; Nguyen, Jackson; Grove, Heather; Huang, Amy; Low, Lauren; Tran, Namphuong; Gomez, Seth; Yau, Jennifer; Ilustrisimo, Thomas; Kawilarang, Jessica; Lau, Jonathan; Tranphung, Maivi; Chen, Irene; Tran, Christina; Fox, Marcia; Lin-Cereghino, Joan; Lin-Cereghino, Geoff P

    2013-11-01

    Although Pichia pastoris is a popular protein expression system, it exhibits limitations in its ability to secrete heterologous proteins. Therefore, a REMI (restriction enzyme mediated insertion) strategy was utilized to select mutant beta-g alactosidase s upersecretion (bgs) strains that secreted increased levels of a β-galactosidase reporter. Many of the twelve BGS genes may have functions in intracellular signaling or vesicle transport. Several of these strains also appeared to contain a more permeable cell wall. Preliminary characterization of four bgs mutants showed that they differed in the ability to enhance the export of other reporter proteins. bgs13, which has a disruption in a gene homologous to Saccharomyces cerevisiae protein kinase C (PKC1), gave enhanced secretion of most recombinant proteins that were tested, raising the possibility that it has the universal super-secreter phenotype needed in an industrial production strain of P. pastoris. PMID:23881328

  18. Biotransformation of ethanol to acetaldehyde by wild and mutant strains of methylotrophic yeast

    SciTech Connect

    Moroz, O.M.; Sibirnyi, A.A.; Ksheminskaya, G.P. |

    1995-05-01

    The conversion of ethanol to acetaldehyde by intact cells of wild and mutant strains of methylotrophic yeast Hansenula polymorpha was studied. It was established that mutations that lower the activity of aldehyde reductase and acetaldehyde dehydrogenase stimulate acetaldehyde accumulation. The highest accumulation of acetaldehyde was found in a mutant that possessed increased alcohol oxidase activity in growth on a medium with glucose. A decrease in formaldehyde dehydrogenase did not stimulate acetaldehyde accumulation. Bioconversion of ethanol to acetaldehyde was most effective at lowered temperatures due to marked suppression of catabolic alcohol oxidase inactivation, but not to the activity of this enzyme under indicated conditions. 27 refs., 4 figs., 3 tabs.

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

    PubMed

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

    2011-11-01

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

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

    SciTech Connect

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

    2011-01-01

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

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

    SciTech Connect

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

    2011-01-01

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

  2. Managing Ada development

    NASA Technical Reports Server (NTRS)

    Green, James R.

    1986-01-01

    The Ada programming language was developed under the sponsorship of the Department of Defense to address the soaring costs associated with software development and maintenance. Ada is powerful, and yet to take full advantage of its power, it is sufficiently complex and different from current programming approaches that there is considerable risk associated with committing a program to be done in Ada. There are also few programs of any substantial size that have been implemented using Ada that may be studied to determine those management methods that resulted in a successful Ada project. The items presented are the author's opinions which have been formed as a result of going through an experience software development. The difficulties faced, risks assumed, management methods applied, and lessons learned, and most importantly, the techniques that were successful are all valuable sources of management information for those managers ready to assume major Ada developments projects.

  3. Experiments with Ada

    NASA Technical Reports Server (NTRS)

    Roy, D.; Mcclimens, M.; Agresti, W.

    1985-01-01

    A 1200-line Ada source code project simulating the most basic functions of an operations control center was developed. We selected George Cherry's Process Abstraction Methodology for Embedded Large Applications (PAMELA) and DEC's Ada Compilation System (ACS) under VAX/VMS to build the software from requirements to acceptance test. The system runs faster than its FORTRAN implementation and was produced on schedule and under budget with an overall productivity in excess of 30 lines of Ada source code per day.

  4. Development of a mutant strain of Bacillus polymyxa showing enhanced production of 2,3-butanediol

    SciTech Connect

    Mallonee, D.H.; Speckman, R.A.

    1988-01-01

    2,3-Butanediol is a feedstock chemical of potential industrial importance. It can serve as a monomer for many polymers of consumer interest that are currently supplied by the fossil fuel industry. Bacillus polymyxa can grow on inexpensive waste products of the food-processing industry and produce this glycol. This paper describes a mutant strain of B. polymyxa which displays constitutive production of catabolic ..cap alpha..-acetolactate synthase, an enzyme in the 2,3-butanediol pathway which is normally produced only in the late log or stationary phase of growth. The mutant was obtained by treating the wild type with nitrosoguanidine and subjecting it to a penicillin counterselection procedure. One of the selected mutant strains produced four times as much of the glycol as the wild type and utilized approximately 25% of the energy source, compared with essentially complete utilization of the energy source by the wild type. Studies are under way to optimize the production of the glycol by the mutant.

  5. Software development in Ada

    NASA Technical Reports Server (NTRS)

    Basili, V. R.; Katz, E. E.

    1985-01-01

    Ada will soon become a part of systems developed for the US Department of Defense. NASA must determine whether it will become part of its environment and particularly whether it will become a part fo the space station development. However, there are several issues about Ada which should be considered before this decision is made. One means of considering these issues is the examination of other developments in Ada. Unfortunately, few full scale developments have been completed or made publicly available for observation. Therefore, it will probably be necessary to study an Ada development in a NASA environment. Another means related to the first is the development of Ada metrics which can be used to characterize and evaluate Ada developments. These metrics need not be confined to full scale developments and could be used to evaluate on going projects as well. An early development in Ada, some observations from that development, metrics which were developed for use with Ada, and future directions for research into the use of Ada in software development in general and in the NASA Goddard environment in particular are described.

  6. Live Attenuated Borrelia burgdorferi Targeted Mutants in an Infectious Strain Background Protect Mice from Challenge Infection.

    PubMed

    Hahn, Beth L; Padmore, Lavinia J; Ristow, Laura C; Curtis, Michael W; Coburn, Jenifer

    2016-08-01

    Borrelia burgdorferi, B. garinii, and B. afzelii are all agents of Lyme disease in different geographic locations. If left untreated, Lyme disease can cause significant and long-term morbidity, which may continue after appropriate antibiotic therapy has been administered and live bacteria are no longer detectable. The increasing incidence and geographic spread of Lyme disease are renewing interest in the vaccination of at-risk populations. We took the approach of vaccinating mice with two targeted mutant strains of B. burgdorferi that, unlike the parental strain, are avirulent in mice. Mice vaccinated with both strains were protected against a challenge with the parental strain and a heterologous B. burgdorferi strain by either needle inoculation or tick bite. In ticks, the homologous strain was eliminated but the heterologous strain was not, suggesting that the vaccines generated a response to antigens that are produced by the bacteria both early in mammalian infection and in the tick. Partial protection against B. garinii infection was also conferred. Protection was antibody mediated, and reactivity to a variety of proteins was observed. These experiments suggest that live attenuated B. burgdorferi strains may be informative regarding the identification of protective antigens produced by the bacteria and recognized by the mouse immune system in vivo Further work may illuminate new candidates that are effective and safe for the development of Lyme disease vaccines. PMID:27335385

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

    SciTech Connect

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

    2012-01-01

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

  8. Isolation and characterization of symbiotic mutants of bradyrhizobium sp. (Arachis) strain NC92: mutants with host-specific defects in nodulation and nitrogen fixation.

    PubMed Central

    Wilson, K J; Anjaiah, V; Nambiar, P T; Ausubel, F M

    1987-01-01

    Random transposon Tn5 mutagenesis of Bradyrhizobium sp. (Arachis) strain NC92, a member of the cowpea cross-inoculation group, was carried out, and kanamycin-resistant transconjugants were tested for their symbiotic phenotype on three host plants: groundnut, siratro, and pigeonpea. Two nodulation (Nod- phenotype) mutants were isolated. One is unable to nodulate all three hosts and appears to contain an insertion in one of the common nodulation genes (nodABCD); the other is a host-specific nodulation mutant that fails to nodulate pigeonpea, elicits uninvaded nodules on siratro, and elicits normal, nitrogen-fixing nodules on groundnut. In addition, nine mutants defective in nitrogen fixation (Fix- phenotype) were isolated. Three fail to supply symbiotically fixed nitrogen to all three host plants. Surprisingly, nodules elicited by one of these mutants exhibit high levels of acetylene reduction activity, demonstrating the presence of the enzyme nitrogenase. Three more mutants have partially effective phenotypes (Fix +/-) in symbiosis with all three host plants. The remaining three mutants fail to supply fixed nitrogen to one of the host plants tested while remaining partially or fully effective on the other two hosts; two of these mutants are Fix- in pigeonpea and Fix +/- on groundnut and on siratro, whereas the other one is Fix- on groundnut but Fix+ on siratro and on pigeonpea. These latter mutants also retain significant nodule acetylene reduction activity, even in the ineffective symbioses. Such bacterial host-specific fixation (Hsf) mutants have not previously been reported. Images PMID:3032910

  9. Mutants of Rhizobium tropici strain CIAT899 that do not induce chlorosis in plants.

    PubMed

    O'Connell, K P; Raffel, S J; Saville, B J; Handelsman, J

    1998-09-01

    Type B strains of Rhizobium tropici induce severe foliar chlorosis when applied at planting to seeds of symbiotic host and non-host dicotyledonous plants. A Tn5-induced mutant, designated CT4812, or R. tropici strain CIAT899 that was unable to induce chlorosis was isolated. Cloning and sequencing of the DNA flanking the transposon in CT4812 revealed that the Tn5 insertion is located in a gene similar to glnD, which encodes uridylyltransferase/uridylyl-removing enzyme in enteric bacteria. Two marker-exchange mutants with insertions in glnD also failed to induce chlorosis in bean (Phaseolus vulgaris) plants. The 5'-most insertion in glnD (in mutant strain ME330) abolished the ability of R. tropici to utilize nitrate as a sole carbon source, whereas a mutation in glnD further downstream (in mutant strain ME245) did not have an obvious effect on nitrate utilization. A gene similar to the Salmonella typhimurium virulence gene mviN overlaps the 3' end of the R. tropici glnD homologue. A mutation in mviN had no effect on the ability of CIAT899 to induce chlorosis in bean plants. Therefore the glnD homologue, but not mviN, appears to be required for induction of chlorosis in plants by R. tropici strain CIAT899. A high nitrogen: carbon ratio in the rhizosphere of bean plants also prevented R. tropici from inducing chlorosis in bean plants. Mutations in either the glnD homologue or mviN had no significant effect on root nodule formation or acetylene reduction activity. A mutation in mviN eliminated motility in R. tropici. The sequence data, the inability of the glnD mutant to utilize nitrate, and the role of the R. tropici glnD gene in chlorosis induction in plants, a process that is nitrogen regulated, suggest that glnD plays a role in nitrogen sensing in R. tropici as its homologues do in other organisms. PMID:9782510

  10. Altered Regulation of Escherichia coli Biotin Biosynthesis in BirA Superrepressor Mutant Strains

    PubMed Central

    Chakravartty, Vandana

    2012-01-01

    Transcription of the Escherichia coli biotin (bio) operon is directly regulated by the biotin protein ligase BirA, the enzyme that covalently attaches biotin to its cognate acceptor proteins. Binding of BirA to the bio operator requires dimerization of the protein, which is triggered by BirA-catalyzed synthesis of biotinoyl-adenylate (biotinoyl-5′-AMP), the obligatory intermediate of the ligation reaction. Although several aspects of this regulatory system are well understood, no BirA superrepressor mutant strains had been isolated. Such superrepressor BirA proteins would repress the biotin operon transcription in vivo at biotin concentrations well below those needed for repression by wild-type BirA. We isolated mutant strains having this phenotype by a combined selection-screening approach and resolved multiple mutations to give several birA superrepressor alleles, each having a single mutation, all of which showed repression dominant over that of the wild-type allele. All of these mutant strains repressed bio operon transcription in vivo at biotin concentrations that gave derepression of the wild-type strain and retained sufficient ligation activity for growth when overexpressed. All of the strains except that encoding G154D BirA showed derepression of bio operon transcription upon overproduction of a biotin-accepting protein. In BirA, G154D was a lethal mutation in single copy, and the purified protein was unable to transfer biotin from enzyme-bound biotinoyl-adenylate either to the natural acceptor protein or to a biotin-accepting peptide sequence. Consistent with the transcriptional repression data, each of the purified mutant proteins showed increased affinity for the biotin operator DNA in electrophoretic mobility shift assays. Surprisingly, although most of the mutations were located in the catalytic domain, all of those tested, except G154D BirA, had normal ligase activity. Most of the mutations that gave superrepressor phenotypes altered residues

  11. Ada & the Analytical Engine.

    ERIC Educational Resources Information Center

    Freeman, Elisabeth

    1996-01-01

    Presents a brief history of Ada Byron King, Countess of Lovelace, focusing on her primary role in the development of the Analytical Engine--the world's first computer. Describes the Ada Project (TAP), a centralized World Wide Web site that serves as a clearinghouse for information related to women in computing, and provides a Web address for…

  12. Comparative metabolic profiling of mce1 operon mutant vs wild-type Mycobacterium tuberculosis strains.

    PubMed

    Queiroz, Adriano; Medina-Cleghorn, Daniel; Marjanovic, Olivera; Nomura, Daniel K; Riley, Lee W

    2015-11-01

    Mycobacterium tuberculosis disrupted in a 13-gene operon (mce1) accumulates free mycolic acids (FM) in its cell wall and causes accelerated death in mice. Here, to more comprehensively analyze differences in their cell wall lipid composition, we used an untargeted metabolomics approach to compare the lipid profiles of wild-type and mce1 operon mutant strains. By liquid chromatography-mass spectrometry, we identified >400 distinct lipids significantly altered in the mce1 mutant compared to wild type. These lipids included decreased levels of saccharolipids and glycerophospholipids, and increased levels of alpha-, methoxy- and keto mycolic acids (MA), and hydroxyphthioceranic acid. The mutant showed reduced expression of mmpL8, mmpL10, stf0, pks2 and papA2 genes involved in transport and metabolism of lipids recognized to induce proinflammatory response; these lipids were found to be decreased in the mutant. In contrast, the transcripts of mmpL3, fasI, kasA, kasB, acpM and RV3451 involved in MA transport and metabolism increased; MA inhibits inflammatory response in macrophages. Since the mce1 operon is known to be regulated in intracellular M. tuberculosis, we speculate that the differences we observed in cell wall lipid metabolism and composition may affect host response to M. tuberculosis infection and determine the clinical outcome of such an infection. PMID:26319139

  13. Production and downstream processing of (1→3)-β-D-glucan from mutant strain of Agrobacterium sp. ATCC 31750

    PubMed Central

    2012-01-01

    We isolated a mutant that produced higher levels of curdlan than the wild strain Agrobacterium sp. ATCC 31750 by chemical mutagenesis using N-methyl-N-nitro-nitrosoguanidine. The mutant strain produced 66 g/L of curdlan in 120 h with a yield of (0.88) while, the wild strain produced 41 g/L in 120 h with a yield of (0.62) in a stirred bioreactor. The mutant could not produce curdlan when the pH was shifted from 7.0 to 5.5 after nitrogen depletion as followed for wild strain. In contrast, pH optimum for cell growth and curdlan production for mutant was found to be 7.0. We optimized the downstream processing of curdlan by varying different volumes of NaOH and HCl for extraction and precipitation of curdlan. The molecular weight of the purified curdlan from the wild and mutant strain was 6.6 × 105 Da and 5.8 × 105 Da respectively. The monosaccharide analyses confirm that curdlan from both wild and mutant strain contains only glucose units. From the NMR and FTIR data, it has been confirmed that curdlan was exclusively composed of β (1 → 3)-D-glucan residues. PMID:22681895

  14. A Mutant Strain of a Surfactant-Producing Bacterium with Increased Emulsification Activity

    NASA Astrophysics Data System (ADS)

    Liu, Qingmei; Yao, Jianming; Pan, Renrui; Yu, Zengliang

    2005-06-01

    As reported in this paper, a strain of oil-degrading bacterium Sp-5-3 was determined to belong to Enterobacteriaceae, which would be useful for microbial enhanced oil recovery (MEOR). The aim of our study was to generate a mutant using low energy N+ beam implantation. With 10 keV of energy and 5.2 × 1014 N+/cm2 of dose - the optimum condition, a mutant, S-34, was obtained, which had nearly a 5-fold higher surface and a 13-fold higher of emulsification activity than the wild type. The surface activity was measured by two methods, namely, a surface tension measuring instrument and a recording of the repulsive circle of the oil film; the emulsification activity was scaled through measuring the separating time of the oil-fermentation mixture. The metabolic acid was determined as methane by means of gas chromatography.

  15. The ultrastructure of a Chlamydomonas reinhardtii mutant strain lacking phytoene synthase resembles that of a colorless alga.

    PubMed

    Inwood, William; Yoshihara, Corinne; Zalpuri, Reena; Kim, Kwang-Seo; Kustu, Sydney

    2008-11-01

    Chlamydomonas reinhardtii strains lacking phytoene synthase, the first enzyme of carotenoid biosynthesis, are white. They lack carotenoid pigments, have very low levels of chlorophyll, and can grow only heterotrophically in the dark. Our electron and fluorescence microscopic studies showed that such a mutant strain (lts1-204) had a proliferated plastid envelope membrane but no stacks of thylakoid membranes within the plastid. It accumulated cytoplasmic compartments that appeared to be autophagous vacuoles filled with membranous material. The lts1 mutants apparently lacked pyrenoid bodies, which normally house ribulose bisphosphate carboxylase-oxygenase (Rubisco), and accumulated many starch granules. Although these mutant strains cannot synthesize the carotenoid and carotenoid-derived pigments present in the phototactic organelle (eyespot), the mutant we examined made a vestigial eyespot that was disorganized and often mislocalized to the posterior end of the cell. The absence of a pyrenoid body, the accumulation of starch, and the disorganization of the eyespot may all result from the absence of thylakoids. The ultrastructure of lts1 mutant strains is similar to but distinct from that of previously described white and yellow mutant strains of C. reinhardtii and is similar to that of naturally colorless algae of the Polytoma group. PMID:19825593

  16. Symbiotic effectiveness of antibiotic-resistant mutants of fast- and slow-growing strains of Rhizobium nodulating Lotus species.

    PubMed

    Pankhurst, C E

    1977-08-01

    Mutants resistant ot 16 individual antibiotics were isolated from two fast-growing and two slow-growing strains of Lotus rhizobia and their symbiotic effectiveness on Lotus pedunculatus evaluated. Resistance to streptomycin, spectinomycin, chloramphenicol, and tetracycline (inhibitors of protein synthesis) was associated with little or no loss of effectiveness with all four strains but resistance to nalidixic acid and rifampicin (inhibitors of nucleic acid synthesis), and to D-cycloserine, novobiocin, and penicillin (inhibitors of cell wall-cell membrane synthesis) was associated with significant loss of effectiveness in 20-100% of the mutants. Resistance to viomycin, neomycin, kanamycin, and vibramycin was associated with loss of effectiveness with mutants of the two fast-growing strains but not with mutants of the two slow-growing strains. When tested on four alternate host legumes individual mutants of a slow-growing strain showed significantly different levels of effectiveness. The results suggest that both the inherent characteristics of the bacterium and of the host plant will influence the symbiotic effectiveness of antibiotic-resistant mutants of Rhizobium. PMID:890601

  17. Software engineering capability for Ada (GRASP/Ada Tool)

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1995-01-01

    The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada Source code. A new Motif compliant graphical user interface has been developed for the GRASP/Ada prototype.

  18. ART-Ada: An Ada-based expert system tool

    NASA Technical Reports Server (NTRS)

    Lee, S. Daniel; Allen, Bradley P.

    1990-01-01

    The Department of Defense mandate to standardize on Ada as the language for software systems development has resulted in an increased interest in making expert systems technology readily available in Ada environments. NASA's Space Station Freedom is an example of the large Ada software development projects that will require expert systems in the 1990's. Another large scale application that can benefit from Ada based expert system tool technology is the Pilot's Associate (PA) expert system project for military combat aircraft. The Automated Reasoning Tool-Ada (ART-Ada), an Ada expert system tool, is explained. ART-Ada allows applications of a C-based expert system tool called ART-IM to be deployed in various Ada environments. ART-Ada is being used to implement several prototype expert systems for NASA's Space Station Freedom program and the U.S. Air Force.

  19. Production of a thermal stress resistant mutant Euglena gracilis strain using Fe-ion beam irradiation.

    PubMed

    Yamada, Koji; Kazama, Yusuke; Mitra, Sharbanee; Marukawa, Yuka; Arashida, Ryo; Abe, Tomoko; Ishikawa, Takahiro; Suzuki, Kengo

    2016-08-01

    Euglena gracilis is a common phytoplankton species, which also has motile flagellate characteristics. Recent research and development has enabled the industrial use of E. gracilis and selective breeding of this species is expected to further expand its application. However, the production of E. gracilis nuclear mutants is difficult because of the robustness of its genome. To establish an efficient mutation induction procedure for E. gracilis, we employed Fe-ion beam irradiation in the RIKEN RI beam factory. A decrease in the survival rate was observed with the increase in irradiation dose, and the upper limit used for E. gracilis selective breeding was around 50 Gy. For a practical trial of Fe-ion irradiation, we conducted a screening to isolate high-temperature-tolerant mutants. The screening yielded mutants that proliferated faster than the wild-type strain at 32 °C. Our results demonstrate the effectiveness of heavy-ion irradiation on E. gracilis selective breeding. PMID:27075598

  20. The N-terminus region of the putative C2H2 transcription factor Ada1 harbors a species-specific activation motif that regulates asexual reproduction in Fusarium verticillioides.

    PubMed

    Malapi-Wight, Martha; Kim, Jung-Eun; Shim, Won-Bo

    2014-01-01

    Fusarium verticillioides is an important plant pathogenic fungus causing maize ear and stalk rots. In addition, the fungus is directly associated with fumonisin contamination of food and feeds. Here, we report the functional characterization of Ada1, a putative Cys2-His2 zinc finger transcription factor with a high level of similarity to Aspergillus nidulans FlbC, which is required for the activation of the key regulator of conidiation brlA. ADA1 is predicted to encode a protein with two DNA binding motifs at the C terminus and a putative activator domain at the N terminus region. Deletion of the flbC gene in A. nidulans results in "fluffy" cotton-like colonies, with a defect in transition from vegetative growth to asexual development. In this study we show that Ada1 plays a key role in asexual development in F. verticillioides. Conidia production was significantly reduced in the knockout mutantada1), in which aberrant conidia and conidiophores were also observed. We identified genes that are predicted to be downstream of ADA1, based on A. nidulans conidiation signaling pathway. Among them, the deletion of stuA homologue, FvSTUA, resulted in near absence of conidia production. To further investigate the functional conservation of this transcription factor, we complemented the Δada1 strain with A. nidulans flbC, F. verticillioides ADA1, and chimeric constructs. A. nidulans flbC failed to restore conidia production similar to the wild-type level. However, the Ada1N-terminal domain, which contains a putative activator, fused to A. nidulans FlbC C-terminal motif successfully complemented the Δada1 mutant. Taken together, Ada1 is an important transcriptional regulator of asexual development in F. verticillioides and that the N-terminus domain is critical for proper function of this transcription factor. PMID:24161731

  1. Assembling flagella in Salmonella mutant strains producing a type III export apparatus without FliO.

    PubMed

    Barker, Clive S; Meshcheryakova, Irina V; Inoue, Tomoharu; Samatey, Fadel A

    2014-12-01

    The type III export apparatus of the Salmonella flagellum consists of six transmembrane proteins (FlhA, FlhB, FliO, FliP, FliQ, and FliR) and three soluble proteins (FliH, FliI, and FliJ). Deletion of the fliO gene creates a mutant strain that is poorly motile; however, suppressor mutations in the fliP gene can partially rescue motility. To further understand the mechanism of suppression of a fliO deletion mutation, we isolated new suppressor mutant strains with partially rescued motility. Whole-genome sequence analysis of these strains found a missense mutation that localized to the clpP gene [clpP(V20F)], which encodes the ClpP subunit of the ClpXP protease, and a synonymous mutation that localized to the fliA gene [fliA(+36T→C)], which encodes the flagellar sigma factor, σ(28). Combining these suppressor mutations with mutations in the fliP gene additively rescued motility and biosynthesis of the flagella in fliO deletion mutant strains. Motility was also rescued by an flgM deletion mutation or by plasmids carrying either the flhDC or fliA gene. The fliA(+36T→C) mutation increased mRNA translation of a fliA'-lacZ gene fusion, and immunoblot analysis revealed that the mutation increased levels of σ(28). Quantitative real-time reverse transcriptase PCR showed that either the clpP(V20F) or fliA(+36T→C) mutation rescued expression of class 3 flagellar and chemotaxis genes; still, the suppressor mutations in the fliP gene had a greater effect on bypassing the loss of fliO function. This suggests that the function of FliO is closely associated with regulation of FliP during assembly of the flagellum. PMID:25201947

  2. A phenotype survey of 36 mutant mouse strains with gene-targeted defects in glycosyltransferases or glycan-binding proteins

    PubMed Central

    Orr, Sally L; Le, Dzung; Long, Jeffrey M; Sobieszczuk, Peter; Ma, Bo; Tian, Hua; Fang, Xiaoqun; Paulson, James C; Marth, Jamey D; Varki, Nissi

    2013-01-01

    The consortium for functional glycomics (CFG) was a large research initiative providing networking and resources for investigators studying the role of glycans and glycan-binding proteins in health and disease. Starting in 2001, six scientific cores were established to generate data, materials and new technologies. By the end of funding in 2011, the mouse phenotype core (MPC) submitted data to a website from the phenotype screen of 36 mutant mouse strains deficient in a gene for either a glycan-binding protein (GBP) or glycosyltransferase (GT). Each mutant strain was allotted three months for analysis and screened by standard phenotype assays used in the fields of immunology, histology, hematology, coagulation, serum chemistry, metabolism and behavior. Twenty of the deficient mouse strains had been studied in other laboratories, and additional tests were performed on these strains to confirm previous observations and discover new data. The CFG constructed 16 new homozygous mutant mouse strains and completed the initial phenotype screen of the majority of these new mutant strains. In total, >300 phenotype changes were observed, but considering the over 100 assays performed on each strain, most of the phenotypes were unchanged. Phenotype differences include abnormal testis morphology in GlcNAcT9- and Siglec-H-deficient mice and lethality in Pomgnt1-deficient mice. The numerous altered phenotypes discovered, along with the consideration of the significant findings of normality, will provide a platform for future characterization to understand the important roles of glycans and GBPs in the mechanisms of health and disease. PMID:23118208

  3. ART-Ada: An Ada-based expert system tool

    NASA Technical Reports Server (NTRS)

    Lee, S. Daniel; Allen, Bradley P.

    1991-01-01

    The Department of Defense mandate to standardize on Ada as the language for software systems development has resulted in increased interest in making expert systems technology readily available in Ada environments. NASA's Space Station Freedom is an example of the large Ada software development projects that will require expert systems in the 1990's. Another large scale application that can benefit from Ada based expert system tool technology is the Pilot's Associate (PA) expert system project for military combat aircraft. Automated Reasoning Tool (ART) Ada, an Ada Expert system tool is described. ART-Ada allow applications of a C-based expert system tool called ART-IM to be deployed in various Ada environments. ART-Ada is being used to implement several prototype expert systems for NASA's Space Station Freedom Program and the U.S. Air Force.

  4. Recovery of Nonpathogenic Mutant Bacteria from Tumors Caused by Several Agrobacterium tumefaciens Strains: a Frequent Event?▿

    PubMed Central

    Llop, Pablo; Murillo, Jesús; Lastra, Beatriz; López, María M.

    2009-01-01

    We have evaluated the interaction that bacterial genotypes and plant hosts have with the loss of pathogenicity in tumors, using seven Agrobacterium tumefaciens strains inoculated on 12 herbaceous and woody hosts. We performed a screening of the agrobacteria present inside the tumors, looking for nonpathogenic strains, and found a high variability of those strains in this niche. To verify the origin of the putative nonpathogenic mutant bacteria, we applied an efficient, reproducible, and specific randomly amplified polymorphic DNA analysis method. In contrast with previous studies, we recovered a very small percentage (0.01%) of nonpathogenic strains that can be considered true mutants. Of 5,419 agrobacterial isolates examined, 662 were nonpathogenic in tomato, although only 7 (from pepper and tomato tumors induced by two A. tumefaciens strains) could be considered to derive from the inoculated strain. Six mutants were affected in the transferred DNA (T-DNA) region; one of them contained IS426 inserted into the iaaM gene, whereas the whole T-DNA region was apparently deleted in three other mutants, and the virulence of the remaining two mutants was fully restored with the T-DNA genes as well. The plasmid profile was altered in six of the mutants, with changes in the size of the Ti plasmid or other plasmids and/or the acquisition of new plasmids. Our results also suggest that the frequent occurrence of nonpathogenic clones in the tumors is probably due to the preferential growth of nonpathogenic agrobacteria, of either endophytic or environmental origin, but different from the bacterial strain inducing the tumor. PMID:19700547

  5. Isolation, characterization and biological activities of verotetrone from a mutant strain of Streptomyces aureofaciens.

    PubMed

    Prikrylová, V; Podojil, M; Hilgert, I; Fuska, J; Vokoun, J; Vanĕk, Z

    1980-01-01

    A new metabolite denoted as verotetrone was isolated from the mycelium of the mutant strain Streptomyces aureofaciens NMG-2. Interpretations of physical data concerning verotetrone and its triacetate and, the determination of its degradation product indicate that verotetrone belongs to pretetramide-type metabolites. Verotetrone exhibits neither antibacterial nor antifungal activity. In vitro it inhibits the synthesis of nucleic acids as well as proteins in Ehrlich ascites carcinoma cells. Both verotetrone and its triacetate interfere in vivo with the metabolism of tumour and lymphoid cells, exhibiting antitumour or immunosuppressive activity. This activity, which is more intense with verotetrone than with its triacetate, is detectable in a dose which is already toxic in some animals. PMID:6774935

  6. Degradation of p-chlorotoluene by a mutant of Pseudomonas sp. strain JS6

    SciTech Connect

    Haigler, B.E.; Spain, J.C. )

    1989-02-01

    Pseudomonas sp. strain JS6 grows on chlorobenzene, p-dichlorobenzene, or toluene as a sole source of carbon and energy. It does not grow on p-chlorotoluene (p-CT). Growth on glucose in the presence of p-CT resulted in the accumulation of 4-chloro-2,3- dihydroxy-1-methyl benzene (3-chloro-6- methylcatechol), 4-chloro- 2,3-dihydroxy-1-methyl cyclohexa- 4,6-diene (p-CT dihydrodoil), and 2-methyl-4-carboxy methylenebut-2-en-4-olide (2-methyl dienelactone). Strain JS21, a spontaneous mutant capable of growth on p-CT, was isolated from cultures of strain JS6 after extended exposure to p-CT. In addition to growing on p-CT, JS21 grew on all of the substrates that supported growth of the parent strain, including p-dichlorobenzene, chlorobenzene, benzene, toluene, benzoate, p-hydroxybenzoate, phenol, and ethylbenzene. The pathway for degradation of p-CT by JS21 was investigated by respirometry, isolation of intermediates, and assay of enzymes in cell extracts. p-CT was converted to 3-chloro-6-methylcatechol by dioxygenase and dihydrodiol dehydrogenase enzymes. 3-Chloro-6-methylcatechol underwent ortho ring cleavage catalyzed by a catechol 1,2-dioxygenase to form 2-chloro-5-methyl-cis,cis-muconate, which was converted to 2-methyl dienelactone. A dienelactone hydrolase converted 2-methyl dienelactone to 2-methylmaleylacetic acid. Preliminary results indicate that a change in wild-type induction patterns allows JS21 to grow on p-CT.

  7. Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant.

    PubMed

    Kramer, Annemarie; Beck, Hans Christian; Kumar, Abhishek; Kristensen, Lars Peter; Imhoff, Johannes F; Labes, Antje

    2015-01-01

    The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum. PMID:26460745

  8. Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant

    PubMed Central

    Kramer, Annemarie; Beck, Hans Christian; Kumar, Abhishek; Kristensen, Lars Peter; Imhoff, Johannes F.; Labes, Antje

    2015-01-01

    The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum. PMID:26460745

  9. Biotransformation of L-tyrosine to Dopamine by a Calcium Alginate Immobilized Mutant Strain of Aspergillus oryzae.

    PubMed

    Ali, Sikander; Nawaz, Wajeeha

    2016-08-01

    The present research work is concerned with the biotransformation of L-tyrosine to dopamine (DA) by calcium alginate entrapped conidiospores of a mutant strain of Aspergillus oryzae. Different strains of A. oryzae were isolated from soil. Out of 13 isolated strains, isolate-2 (I-2) was found to be a better DA producer. The wild-type I-2 was chemically improved by treating it with different concentrations of ethyl methyl sulfonate (EMS). Among seven mutant variants, EMS-6 exhibiting maximal DA activity of 43 μg/ml was selected. The strain was further exposed with L-cysteine HCl to make it resistant against diversion and environmental stress. The conidiospores of selected mutant variant A. oryzae EMS-6 strain were entrapped in calcium alginate beads. Different parameters for immobilization were investigated. The activity was further improved from 44 to 62 μg/ml under optimized conditions (1.5 % sodium alginate, 2 ml inoculum, and 2 mm bead size). The best resistant mutant variable exhibited over threefold increase in DA activity (62 μg/ml) than did wild-type I-2 (21 μg/ml) in the reaction mixture. From the results presented in the study, it was observed that high titers of DA activity in vitro could effectively be achieved by the EMS-induced mutagenesis of filamentous fungus culture used. PMID:27068833

  10. Induced drought tolerance through wild and mutant bacterial strain Pseudomonas simiae in mung bean (Vigna radiata L.).

    PubMed

    Kumari, Sarita; Vaishnav, Anukool; Jain, Shekhar; Varma, Ajit; Choudhary, Devendra Kumar

    2016-01-01

    The present study focused on the overproducing mutant of a plant growth promoting rhizobacterium (PGPR) Pseudomonas simiae strain AU (MTCC-12057) for significant drought tolerance in mung bean plants. Five mutants namely AU-M1, AU-M2, AU-M3, AU-M4 and AU-M5 were made after treatment of wild type strain with N-methyl-N-nitro-N-nitrosoguanidine. Mutant strain AU-M4 was recorded for enhanced ACC deaminase (ACC-D) activity, indole acetic acid (IAA) production and inorganic phosphate (Pi) solubilization compared to wild strain and other four mutant strains under drought condition. AU-M4 showed higher phosphate solubilization index (8.17) together with higher ACC-D activity (98 nmol/mg/h) and IAA concentration (69.35 µg/ml) compared with the wild type P. simiae strain AU ACC-D activity (79 nmol/mg/h) and IAA concentration (38.98 µg/ml) respectively. In this report, we investigated the effect of both wild and mutant type bacterial strain on mung bean plants under drought stress. Results showed that mutant AU-M4 and wild type strain AU inoculated plants exhibited superior tolerance against drought stress, as shown by their enhanced plant biomass (fresh weight), higher water content, higher proline accumulation and lower osmotic stress injury. Mutant AU-M4 and wild strain AU inoculated plants reduced the ethylene level by 59 and 45% respectively, compared to the control under stress condition. Furthermore, bacterial inoculated plants showed enhanced induced systemic drought tolerance by reducing stomata size and net photosynthesis resulting higher water content in mung bean plants that may help in survival of plants during drought condition. To mitigate the effects of drought stress, use of PGPR will be needed to ensure sufficient production of food from crop plants. Taking current leads available, concerted future research is needed in this area, particularly on field evaluation with application of potential microorganisms. PMID:26712619

  11. Phage-resistant mutants of Lactobacillus delbrueckii may have functional properties that differ from those of parent strains.

    PubMed

    Vinderola, Gabriel; Marcó, Mariángeles Briggiler; Guglielmotti, Daniela M; Perdigón, Gabriela; Giraffa, Giorgio; Reinheimer, Jorge; Quiberoni, Andrea

    2007-05-01

    Three commercial phage sensitive Lactobacillus delbrueckii strains (identified as Ab(1), YSD V and Ib(3)), and four spontaneous phage-resistant mutants isolated from them were tested for their capacity to activate the gut mucosal immune response in mice, as indicated by the numbers of IgA-producing cells. Random Amplified Polymorphic DNA (RAPD) analysis revealed a strong genetic homology between the sensitive strains and their respective derivatives. The phage-resistant mutants exhibited high levels of phage resistance, elevated stability of this phenotype and technological properties comparable to those of their respective parent strains. The tolerance to acidic conditions, bile salts and lysozyme was strain dependent and total cell viability losses as a result of exposure to all three stresses ranged from 2.0 to 3.7 log units. All the strains were highly resistant to a simulated gastric solution of pH 3, while significant additional losses in cell viability were observed when acid treated cells were exposed to bile salts and lysozyme. BALB/c mice received pure cultures of Lb. delbrueckii sensitive and phage-resistant strains for 2, 5 or 7 consecutive days. The ability of the parent strains to activate the small intestine immune response was preserved or enhanced in phage-resistant mutants. The maximal proliferation of IgA(+) cells was observed at day 5 or 7, depending on the strain. Mutants isolated in this study using natural selection strategies had improved phage resistance, adequate technological properties and satisfactory gut mucosal immunostimulation ability, and so would be good candidates for industrial applications in functional foods. PMID:17307269

  12. Enhancing cellulase production by overexpression of xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus cellulase hyperproducing mutant strain.

    PubMed

    Okuda, Naoyuki; Fujii, Tatsuya; Inoue, Hiroyuki; Ishikawa, Kazuhiko; Hoshino, Tamotsu

    2016-10-01

    We obtained strains with the xylanase regulator gene, xlnR, overexpressed (HXlnR) and disrupted (DXlnR) derived from Talaromyces cellulolyticus strain C-1, which is a cellulase hyperproducing mutant. Filter paper degrading enzyme activity and cellobiohydrolase I gene expression was the highest in HXlnR, followed by C-1 and DXlnR. These results indicate that the enhancement of cellulase productivity was succeeded by xlnR overexpression. PMID:27309759

  13. A short-filament mutant of Anabaena sp. strain PCC 7120 that fragments in nitrogen-deficient medium.

    PubMed Central

    Bauer, C C; Buikema, W J; Black, K; Haselkorn, R

    1995-01-01

    Strain 129 is a fragmentation mutant of the filamentous cyanobacterium Anabaena sp. strain PCC 7120. Growing with fixed nitrogen, this mutant forms filaments that are much shorter than wild-type filaments. Following starvation for fixed nitrogen, strain 129 becomes nearly unicellular and forms few heterocysts, although electron microscopy suggests that proheterocysts form while fragmentation occurs. Starvation for sulfate, phosphate, iron, and calcium does not cause this fragmentation. The affected gene in strain 129, fraC, was cloned by complementation and characterized. It encodes a unique 179-amino-acid protein rich in phenylalanine. Insertional inactivation of the chromosomal copy of fraC results in a phenotype identical to that of strain 129, while complementation using a truncated version of FraC results in only partial complementation of the original mutant. Heterocysts could be induced to form in N-replete cultures of strain 129, as in wild-type cells, by supplying extra copies of the hetR gene on a plasmid. Thus, FraC is required for the integrity of cell junctions in general but is apparently not directly involved in normal differentiation and nitrogen fixation. PMID:7883709

  14. A LISP-Ada connection

    NASA Technical Reports Server (NTRS)

    Jaworski, Allan; Lavallee, David; Zoch, David

    1987-01-01

    The prototype demonstrates the feasibility of using Ada for expert systems and the implementation of an expert-friendly interface which supports knowledge entry. In the Ford LISP-Ada Connection (FLAC) system LISP and Ada are used in ways which complement their respective capabilities. Future investigation will concentrate on the enhancement of the expert knowledge entry/debugging interface and on the issues associated with multitasking and real-time expert systems implementation in Ada.

  15. Altered calmodulin activity in fluphenazine-resistant mutant strains. Pleiotropic effect on development and cellular organization in Volvox carteri.

    PubMed

    Kurn, N; Sela, B A

    1981-12-01

    Genetically altered calmodulin activity in spontaneously derived mutant strains, which were selected for resistance to the toxic effect of a specific inhibitor, the phenothiazine drug fluphenazine, is demonstrated. Partially purified calmodulin preparations from wild-type and fluphenazine-resistant strains of the multicellular alga Volvox carteri, were tested for the ability to activate Ca2+-ATPase of the erythrocyte membranes, and the inhibition of this stimulatory activity by fluphenazine. Unlike the preparation obtained from wild-type cells, mutant calmodulin is shown to be insensitive to fluphenazine inhibition, in one case, and calmodulin from another strain was found to be inactive in vitro, i.e. it did not activate Ca2+-ATPase. The pleiotropic phenotype of the spontaneously derived mutant strains involved aberrant multicellular organization and hormone-independent commitment of the multipotent asexual reproductive cells, gonodia, to sexual development. These results clearly implicate calmodulin in the control of development and morphogenesis in this simple multicellular eukaryote. In addition, intracellular inhibition of calmodulin in wild-type cells is shown to block the morphogenic process of embryo inversion and to arrest motility. The availability of mutant calmodulin will facilitate further investigation of the role of this ubiquitous regulatory protein in the control of development and differentiation in multicellular eukarytes, as well as the fine structure/function relationship with regard to calmodulin modulation of a wide variety of cellular processes. PMID:6459931

  16. Draft Genome Sequence of the Intermediate Rough Vaccine Strain Brucella abortus S19Δper Mutant

    PubMed Central

    Chaudhuri, Pallab; Goswami T, Tapas K.; Lalsiamthara, Jonathan; Kaur, Gurpreet; Vishnu, Udayakumar S.; Sankarasubramanian, Jagadesan; Gunasekaran, Paramasamy

    2015-01-01

    Here, we report the genome sequence of the intermediate rough vaccine strain mutant, Brucella abortus S19Δper. The length of the draft genome was 3,271,238 bp, with 57.2% G+C content. A total of 3,204 protein-coding genes and 56 RNA genes were predicted. PMID:26564050

  17. A halocin-H4 mutant Haloferax mediterranei strain retains the ability to inhibit growth of other halophilic archaea.

    PubMed

    Naor, Adit; Yair, Yael; Gophna, Uri

    2013-11-01

    Many members of the Halobacteriaceae were found to produce halocins, molecules that inhibit the growth of other halophilic archaea. Halocin H4 that is produced by Haloferax mediterranei and inhibits the growth of Halobacterium salinarum is one of the best studied halocins to date. The gene encoding this halocin had been previously identified as halH4, located on one of Hfx. mediterranei megaplasmids. We generated a mutant of the halH4 gene and examined the killing ability of the Haloferax mediterranei halH4 mutant with respect to both Halobacterium salinarum and Haloferax volcanii. We showed that both wild-type Hfx. mediterranei and the halH4 mutant strain efficiently inhibited the growth of both species, indicating halocin redundancy. Surprisingly, the halH4 deletion mutant exhibited faster growth in standard medium than the wild type, and is likely to have a better response to several nucleotides, which could explain this phenotype. PMID:24037372

  18. The effect of gamma irradiation on astaxanthin synthetase encoding gene in two mutant strains of Phaffia rhodozyma

    PubMed Central

    Najafi, Naeimeh; Hosseini, Ramin; Ahmadi, Ali-Reza

    2013-01-01

    Background and Objectives Astaxanthin, an orange-red carotenoid pigment, acts as a protective agent against oxidative damage to cells in vivo. The astaxanthin synthetase gene (crtS) size consists of 3995 bp. This gene has been suggested to catalyse β-carotene to astaxanthin in Phaffia rhodozyma. The aim of this research was to find any possible changes in this gene in two mutant strains, Gam1 and Gam2 (with high astaxanthin pigment production), previously created by gamma irradiation. Materials and Methods The astaxanthin synthetase gene sequence of Phaffia rhodozyma in the NCBI Gene bank was used to design primer. In Gam1, this gene was amplified using primers Asta F1, Asta R2, Asta F3, Asta R4. In Gam2, primers asta F1, asta R4 were used to amplify the gene. The amplified fragments were 8 sequenced using primers Asta F1, Asta R1, Asta F2, Asta R2, Asta F3, Asta R3 and Asta F4, Asta R4. Astaxanthin synthetase gene from two mutant strains, Gam1 and Gam2 were amplified using PCR. The amplified products were sequenced and aligned using the ClustalW software. Conclusion The comparison of this gene showed 98% and 99% similarities between the reference sequence and Gam1 and Gam2 mutant strains, respectively, whereas the comparison of this gene in Gam1 and Gam2 mutant strains showed 97% similarity. However, the deduced proteins showed 78% and 83% between the reference protein obtained from the wild type and Gam1 and Gam2, respectively. This similarity was 75% between the mutant strains. PMID:24475339

  19. AN ADA NAMELIST PACKAGE

    NASA Technical Reports Server (NTRS)

    Klumpp, A. R.

    1994-01-01

    The Ada Namelist Package, developed for the Ada programming language, enables a calling program to read and write FORTRAN-style namelist files. A namelist file consists of any number of assignment statements in any order. Features of the Ada Namelist Package are: the handling of any combination of user-defined types; the ability to read vectors, matrices, and slices of vectors and matrices; the handling of mismatches between variables in the namelist file and those in the programmed list of namelist variables; and the ability to avoid searching the entire input file for each variable. The principle user benefits of this software are the following: the ability to write namelist-readable files, the ability to detect most file errors in the initialization phase, a package organization that reduces the number of instantiated units to a few packages rather than to many subprograms, a reduced number of restrictions, and an increased execution speed. The Ada Namelist reads data from an input file into variables declared within a user program. It then writes data from the user program to an output file, printer, or display. The input file contains a sequence of assignment statements in arbitrary order. The output is in namelist-readable form. There is a one-to-one correspondence between namelist I/O statements executed in the user program and variables read or written. Nevertheless, in the input file, mismatches are allowed between assignment statements in the file and the namelist read procedure statements in the user program. The Ada Namelist Package itself is non-generic. However, it has a group of nested generic packages following the nongeneric opening portion. The opening portion declares a variety of useraccessible constants, variables and subprograms. The subprograms are procedures for initializing namelists for reading, reading and writing strings. The subprograms are also functions for analyzing the content of the current dataset and diagnosing errors. Two nested

  20. Initial Ada components evaluation

    NASA Technical Reports Server (NTRS)

    Moebes, Travis

    1989-01-01

    The SAIC has the responsibility for independent test and validation of the SSE. They have been using a mathematical functions library package implemented in Ada to test the SSE IV and V process. The library package consists of elementary mathematical functions and is both machine and accuracy independent. The SSE Ada components evaluation includes code complexity metrics based on Halstead's software science metrics and McCabe's measure of cyclomatic complexity. Halstead's metrics are based on the number of operators and operands on a logical unit of code and are compiled from the number of distinct operators, distinct operands, and total number of occurrences of operators and operands. These metrics give an indication of the physical size of a program in terms of operators and operands and are used diagnostically to point to potential problems. McCabe's Cyclomatic Complexity Metrics (CCM) are compiled from flow charts transformed to equivalent directed graphs. The CCM is a measure of the total number of linearly independent paths through the code's control structure. These metrics were computed for the Ada mathematical functions library using Software Automated Verification and Validation (SAVVAS), the SSE IV and V tool. A table with selected results was shown, indicating that most of these routines are of good quality. Thresholds for the Halstead measures indicate poor quality if the length metric exceeds 260 or difficulty is greater than 190. The McCabe CCM indicated a high quality of software products.

  1. Assessing benzene-induced toxicity on wild type Euglena gracilis Z and its mutant strain SMZ.

    PubMed

    Peng, Cheng; Arthur, Dionne M; Sichani, Homa Teimouri; Xia, Qing; Ng, Jack C

    2013-11-01

    Benzene is a representative member of volatile organic compounds and has been widely used as an industrial solvent. Groundwater contamination of benzene may pose risks to human health and ecosystems. Detection of benzene in the groundwater using chemical analysis is expensive and time consuming. In addition, biological responses to environmental exposures are uninformative using such analysis. Therefore, the aim of this study was to employ a microorganism, Euglena gracilis (E. gracilis) as a putative model to monitor the contamination of benzene in groundwater. To this end, we examined the wild type of E. gracilis Z and its mutant form, SMZ in their growth rate, morphology, chlorophyll content, formation of reactive oxygen species (ROS) and DNA damage in response to benzene exposure. The results showed that benzene inhibited cell growth in a dose response manner up to 48 h of exposure. SMZ showed a greater sensitivity compared to Z in response to benzene exposure. The difference was more evident at lower concentrations of benzene (0.005-5 μM) where growth inhibition occurred in SMZ but not in Z cells. We found that benzene induced morphological changes, formation of lipofuscin, and decreased chlorophyll content in Z strain in a dose response manner. No significant differences were found between the two strains in ROS formation and DNA damage by benzene at concentrations affecting cell growth. Based on these results, we conclude that E. gracilis cells were sensitive to benzene-induced toxicities for certain endpoints such as cell growth rate, morphological change, depletion of chlorophyll. Therefore, it is a potentially suitable model for monitoring the contamination of benzene and its effects in the groundwater. PMID:24034892

  2. Sequential parametric optimization of lipase production by a mutant strain Rhizopus sp. BTNT-2.

    PubMed

    Bapiraju, K V V S N; Sujatha, P; Ellaiah, P; Ramana, T

    2005-01-01

    Lipase production by the mutant strain Rhizopus sp. BTNT-2 was optimized in submerged fermentation. Different chemical and physical parameters such as carbon sources, nitrogen sources, oils, inoculum level, pH, incubation time, incubation temperature and aeration have been extensively studied to increase lipase productivity. Potato starch (1.25% w/v) as a carbon source, corn steep liquor (1.5% w/v) as a nitrogen source and olive oil (0.5% v/v) as lipid source were found to be optimal for lipase production. The optimal levels of other parameters are 4 ml of inoculum (2.6x10(8) spores/ml), initial pH of 5.5, incubation time of 48 hours, incubation temperature of 28 degrees C and aeration rate of 120 rpm. With the optimized parameters, the highest production of lipase was 59.2 U/ml while an yield of only 28.7 U/ml was obtained before optimization resulting in 206% increase in the productivity. PMID:16028198

  3. Pilin regulation in the pilT mutant of Neisseria gonorrhoeae strain MS11

    PubMed Central

    Dietrich, Manuela; Mollenkopf, Hans; So, Magdalene; Friedrich, Alexandra

    2009-01-01

    The ATPase protein PilT mediates retraction of type IV pili (Tfp). Tfp retraction of Neisseria gonorrhoeae causes many signal transduction events and changes in gene expression in infected epithelial cells. To find out whether a pilT mutation and lack of Tfp retraction, respectively, lead also to gene regulation in bacteria we performed microarrays comparing the transcriptional profiles of the N. gonorrhoeae parent strain MS11 and its isogenic pilT mutant during growth in vitro. A loss-of-function-mutation in pilT led to altered transcript levels of 63 open reading frames. Levels of pilE transcripts and its deduced protein the major Tfp subunit pilin, were increased most markedly by a mutation in pilT. Further studies revealed that pilE expression was also controlled by two other genes encoding Tfp biogenesis proteins, pilD and pilF. Our studies strongly suggest that pilE expression is a finely-tuned process. PMID:19486161

  4. Selection by Anion-Exchange Chromatography of Exopolysaccharide Mutants of the Cyanobacterium Synechocystis Strain PCC 6803

    PubMed Central

    Panoff, Jean-Michel; Joset, Françoise

    1989-01-01

    The degree of retention of whole cells of Synechocystis strain PCC 6803 on DEAE-cellulose columns was shown to depend on their content of exopolysaccharides, which are at least in part responsible for the external negative charge of the cells. This feature was used for the isolation of mutants modified in the apparent viscosity caused by these macromolecular constituents. When a wild-type suspension was loaded onto a DE52 column, the cells eluting in the two extreme fractions of a 0 to 5 M NaCl step gradient represented 10−9 to 10−7 of the total eluted population. The accuracy of the procedure was established through the analysis of four clones: Suc(0)32 and Suc(0)65 (0 M) and Suc(5)64A and Suc(5)61 (5 M). The decreased viscosity of the exopolymers of the two 0 M clones, which appeared identical, could be related to the production of molecules less charged in uronic acids and more readily liberated from the cells. The two 5 M clones exhibited a lower sedimentation velocity, correlating with either a 60% increase in uronic acid and a doubling of the specific viscosity of the exopolysaccharides [clone Suc(5)64A] or a doubling of the per-cell production of polymers otherwise identical to those from wild-type cells [clone Suc(5)61]. Images PMID:16347938

  5. Isolation and complementation of mutants of Anabaena sp. strain PCC 7120 unable to grow aerobically on dinitrogen

    SciTech Connect

    Wolk, C.P.; Cai, Y.; Cardemil, L.; Flores, E.; Hohn, B.; Murry, M.; Schmetterer, G.; Schrautemeier, B.; Wilson, R.

    1988-03-01

    Mutants of Anabaena sp. strain PCC 7120 unable to grow aerobically on dinitrogen were isolated by mutagenesis with UV irradiation, followed by a period of incubation in yellow light and then by penicillin enrichment. A cosmid vector, pRL25C, containing replicons functional in Escherichia coli and in Anabaena species was constructed. DNA from wild-type Anabaena sp. strain PCC 7120 was partially digested with Sau3AI, and size-fractionated fragments about 40 kilobases (kb) in length were ligated into the phosphatase-treated unique BamHI site of pRL25C. A library of 1054 cosmid clones was generated in E. coli DH1 bearing helper plasmid pDS4101. A derivative of conjugative plasmid RP-4 was transferred to this library by conjugation, and the library was replicated to lawns of mutant Anabaena strains with defects in the polysaccharide layer of the envelopes of the heterocysts. Mutant EF116 was complemented by five cosmids, three of which were subjected to detailed restriction mapping; a 2.8-kb fragment of DNA derived from one of the cosmids was found to complement EF116. Mutant EF113 was complemented by a single cosmid, which was also restriction mapped, and was shown to be complemented by a 4.8-kb fragment of DNA derived from this cosmid.

  6. Biological methods for archiving and maintaining mutant laboratory mice. Part II: recovery and distribution of conserved mutant strains.

    PubMed

    Fray, Martin D

    2009-01-01

    The mouse is now firmly established as the model organism of choice for scientists studying mammalian biology and human disease. Consequently, large collections of novel genetically altered mouse lines have been deposited in secure archives around the world. If these resources are to be of value to the scientific community, they must be easily accessible to all researchers regardless of their embryological skills or geographical location.This chapter describes how the archiving centres attempt to make the strains they hold visible and accessible to all interested parties, and also outlines the methods currently used in laboratories around the world to recover mouse strains previously archived using the methods highlighted in this manual (see Chapter 20). PMID:19504081

  7. Functional complementation of Leishmania (Leishmania) amazonensis AP endonuclease gene (lamap) in Escherichia coli mutant strains challenged with DNA damage agents

    PubMed Central

    Verissimo-Villela, Erika; Kitahara-Oliveira, Milene Yoko; dos Reis, Ana Beatriz de Bragança; Albano, Rodolpho Mattos; Da-Cruz, Alda Maria; Bello, Alexandre Ribeiro

    2016-01-01

    During its life cycle Leishmania spp. face several stress conditions that can cause DNA damages. Base Excision Repair plays an important role in DNA maintenance and it is one of the most conserved mechanisms in all living organisms. DNA repair in trypanosomatids has been reported only for Old World Leishmania species. Here the AP endonuclease from Leishmania (L.) amazonensis was cloned, expressed in Escherichia coli mutants defective on the DNA repair machinery, that were submitted to different stress conditions, showing ability to survive in comparison to the triple null mutant parental strain BW535. Phylogenetic and multiple sequence analyses also confirmed that LAMAP belongs to the AP endonuclease class of proteins. PMID:27223868

  8. Phenotypes of Campylobacter jejuni luxS Mutants Are Depending on Strain Background, Kind of Mutation and Experimental Conditions

    PubMed Central

    Adler, Linda; Alter, Thomas; Sharbati, Soroush; Gölz, Greta

    2014-01-01

    Since the discovery that Campylobacter (C.) jejuni produces Autoinducer 2 (AI-2), various studies have been conducted to explore the function and role of AI-2 in C. jejuni. However, the interpretation of these analyses has been complicated by differences in strain backgrounds, kind of mutation and culture conditions used. Furthermore, all research on AI-2 dependent phenotypes has been conducted with AI-2 synthase (luxS) mutants. This mutation also leads to a disruption of the activated-methyl-cycle. Most studies lack sufficient complementation resulting in not knowing whether phenotypes of luxS mutants depend on disrupted metabolism or lack of AI-2. Additionally, no AI-2 receptor has been found yet. All this contributes to an intensive discussion about the exact role of AI-2 in C. jejuni. Therefore, we examined the impact of different experiment settings on three different C. jejuni luxS mutants on growth and motility (37°C and 42°C). Our study showed that differing phenotypes of C. jejuni luxS mutants depend on strain background, mutation strategy and culture conditions. Furthermore, we complemented experiments with synthetic AI-2 or homocysteine as well as the combination of both. Complementation with AI-2 and AI-2+homocysteine significantly increased the cell number of C. jejuni NCTC 11168ΔluxS in stationary phase compared to the non-complemented C. jejuni NCTC 11168ΔluxS mutant. Genetic complementation of both C. jejuni 81-176 luxS mutants resulted in wild type comparable growth curves. Also swarming ability could be partially complemented. While genetic complementation restored swarming abilities of C. jejuni 81-176ΔluxS, it did not fully restore the phenotype of C. jejuni 81-176::luxS, which indicates that compensatory mutations in other parts of the chromosome and/or potential polar effects may appear in this mutant strain. Also with neither synthetic complementation, the phenotype of the wild type-strains was achieved, suggesting yet another reason for

  9. Dynamics of Photosynthesis in a Glycogen-Deficient glgC Mutant of Synechococcus sp. Strain PCC 7002

    PubMed Central

    Jackson, Simon A.; Eaton-Rye, Julian J.; Bryant, Donald A.; Posewitz, Matthew C.

    2015-01-01

    Cyanobacterial glycogen-deficient mutants display impaired degradation of light-harvesting phycobilisomes under nitrogen-limiting growth conditions and secrete a suite of organic acids as a putative reductant-spilling mechanism. This genetic background, therefore, represents an important platform to better understand the complex relationships between light harvesting, photosynthetic electron transport, carbon fixation, and carbon/nitrogen metabolisms. In this study, we conducted a comprehensive analysis of the dynamics of photosynthesis as a function of reductant sink manipulation in a glycogen-deficient glgC mutant of Synechococcus sp. strain PCC 7002. The glgC mutant showed increased susceptibility to photoinhibition during the initial phase of nitrogen deprivation. However, after extended periods of nitrogen deprivation, glgC mutant cells maintained higher levels of photosynthetic activity than the wild type, supporting continuous organic acid secretion in the absence of biomass accumulation. In contrast to the wild type, the glgC mutant maintained efficient energy transfer from phycobilisomes to photosystem II (PSII) reaction centers, had an elevated PSII/PSI ratio as a result of reduced PSII degradation, and retained a nitrogen-replete-type ultrastructure, including an extensive thylakoid membrane network, after prolonged nitrogen deprivation. Together, these results suggest that multiple global signals for nitrogen deprivation are not activated in the glgC mutant, allowing the maintenance of active photosynthetic complexes under conditions where photosynthesis would normally be abolished. PMID:26150450

  10. Mutant strains of Spirulina (Arthrospira) platensis to increase the efficiency of micro-ecological life support systems

    NASA Astrophysics Data System (ADS)

    Brown, Igor

    The European Micro-Ecological Life Support System Alternative (MELiSSA) is an advanced idea for organizing a bioregenerative system for long term space flights and extraterrestrial settlements (Hendrickx, De Wever et al., 2005). Despite the hostility of both lunar and Martian environments to unprotected life, it seems possible to cultivate photosynthetic bacteria using closed bioreactors illuminated and heated by solar energy. Such reactors might be employed in critical processes, e.g. air revitalization, foodcaloric and protein source, as well as an immunomodulators production. The MELiSSA team suggested cyanobacterium Spirulina as most appropriate agent to revitalize air and produce a simple "fast" food. This is right suggestion because Spirulina was recently shown to be an oxygenic organism with the highest level of O2 production per unit mass (Ananyev et al., 2005). Chemical composition of Spirulina includes proteins (55Aiming to make Spirulina cultivation in life support systems like MELiSSA more efficient, we selected Spirulina mutant strains with increased fraction of methionine in the biomass of this cyanobacterium and compared the effect of parental wild strain of Spirulina and its mutants on the tendency of such experimental illnesses as radiationinduced lesions and hemolythic anemia. Results: It was found that mutant strains 198B and 27G contain higher quantities of total protein, essential amino acids, c-phycocyanin, allophycocyanin and chlorophyll a than parental wild strain of S. platensis. The strain 198B is also characterized with increased content of carotenoids. Revealed biochemical peculiarities of mutant strains suggest that these strains can serve as an additional source of essential amino acids as well as phycobiliproteins and carotenoids for the astronauts. Feeding animals suffering from radiation-induced lesions, c-phycocyanin, extracted from strain 27G, led to a correction in deficient dehydrogenase activity and energy-rich phosphate levels

  11. Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans

    PubMed Central

    Shanmugam, Mayilvahanan; El Abbar, Faiha; Ramasubbu, Narayanan

    2015-01-01

    Exopolysaccharides have a diverse set of functions in most bacteria including a mechanistic role in protecting bacteria against environmental stresses. Among the many functions attributed to the exopolysaccharides, biofilm formation, antibiotic resistance, immune evasion and colonization have been studied most extensively. The exopolysaccharide produced by many Gram positive as well as Gram negative bacteria including the oral pathogen Aggregatibacter actinomycetemcomitans is the homopolymer of β(1,6)-linked N-acetylglucosamine. Recently, we reported that the PGA-deficient mutant of A. actinomycetemcomitans failed to colonize or induce bone resorption in a rat model of periodontal disease, and the colonization genes, apiA and aae, were significantly down regulated in the mutant strain. To understand the role of exopolysaccharide and the pga locus in the global expression of A. actinomycetemcomitans, we have used comparative transcriptome profiling to identify differentially expressed genes in the wild-type strain in relation to the PGA-deficient strain. Transcriptome analysis revealed that about 50% of the genes are differently expressed (P < 0.05 and fold change >1.5). Our study demonstrated that the absence of the pga locus affects the genes involved in peptidoglycan recycling, glycogen storage, and virulence. Further, using confocal microscopy and plating assays, we show that the viability of pga mutant strain is significantly reduced during biofilm growth. Thus, this study highlights the importance of pga genes and the exopolysaccharide in the virulence of A. actinomycetemcomitans. PMID:26221956

  12. ADAS Update and Maintainability

    NASA Technical Reports Server (NTRS)

    Watson, Leela R.

    2010-01-01

    Since 2000, both the National Weather Service Melbourne (NWS MLB) and the Spaceflight Meteorology Group (SMG) have used a local data integration system (LOIS) as part of their forecast and warning operations. The original LOIS was developed by the Applied Meteorology Unit (AMU) in 1998 (Manobianco and Case 1998) and has undergone subsequent improvements. Each has benefited from three-dimensional (3-D) analyses that are delivered to forecasters every 15 minutes across the peninsula of Florida. The intent is to generate products that enhance short-range weather forecasts issued in support of NWS MLB and SMG operational requirements within East Central Florida. The current LDIS uses the Advanced Regional Prediction System (ARPS) Data Analysis System (AD AS) package as its core, which integrates a wide variety of national, regional, and local observational data sets. It assimilates all available real-time data within its domain and is run at a finer spatial and temporal resolution than current national or regional-scale analysis packages. As such, it provides local forecasters with a more comprehensive understanding of evolving fine-scale weather features. Over the years, the LDIS has become problematic to maintain since it depends on AMU-developed shell scripts that were written for an earlier version of the ADAS software. The goals of this task were to update the NWS MLB/SMG LDIS with the latest version of ADAS, incorporate new sources of observational data, and upgrade and modify the AMU-developed shell scripts written to govern the system. In addition, the previously developed ADAS graphical user interface (GUI) was updated. Operationally, these upgrades will result in more accurate depictions of the current local environment to help with short-range weather forecasting applications, while also offering an improved initialization for local versions of the Weather Research and Forecasting (WRF) model used by both groups.

  13. Anthraquinone dyes decolorization capacity of anamorphic Bjerkandera adusta CCBAS 930 strain and its HRP-like negative mutants.

    PubMed

    Korniłłowicz-Kowalska, Teresa; Rybczyńska, Kamila

    2014-06-01

    Cultures of the anamorphic fungus Bjerkandera adusta CCBAS 930 decolorizing, in stationary cultures, 0.01 % solutions of carminic acid and Poly R-478, were characterised by a strong increase in the activity of the horseradish peroxidase (HRP-like) and manganese-dependent peroxidase (MnP) at a low activity of lignin peroxidase. Genotypically modified mutants of B. adusta CCBAS 930: 930-5 and 930-14, with total or partial loss of decolorization capabilities relative to anthraquinonic dyes, showed inhibition of the activity of HRP-like peroxidase and MnP. Whereas, compared to the parental strain, in the mutant cultures there was an increase in the activity of lignin peroxidase and laccase. The paper presents a discussion of the role of the studied enzymatic activities in the process of decolorization of anthraquinonic dyes by the strain B. adusta CCBAS 930. PMID:24415463

  14. [Study of the transcriptional and transpositional activities of the Tirant retrotransposon in Drosophila melanogaster strains mutant for the flamenco locus].

    PubMed

    Nefedova, L N; Urusov, F A; Romanova, N I; Shmel'kova, A O; Kim, A I

    2012-11-01

    Transpositions of the gypsy retrotransposon in the Drosophila melanogaster genome are controlled by the flamenco locus, which is represented as an accumulation of defective copies of transposable elements. In the present work, genetic control by the flamenco locus of the transcriptional and transpositional activities of the Tirant retrotransposon from the gypsy group was studied. Tissue-specific expression of Tirant was detected in the tissues of ovaries in a strain mutant for the flamenco locus. Tirant was found to be transpositionally active in isogenic D. melanogaster strains mutant for the flamenco locus. The sites of two new insertions have been localized by the method of subtractive hybridization. It has been concluded from the results obtained that the flamenco locus is involved in the genetic control of Tirant transpositions. PMID:23297482

  15. Generation and Characterization of an Attenuated Mutant in a Response Regulator Gene of Francisella tularensis Live Vaccine Strain (LVS)

    PubMed Central

    Sammons-Jackson, Wendy L.; McClelland, Karen; Manch-Citron, Jean N.; Metzger, Dennis W.; Bakshi, Chandra Shekhar; Garcia, Emilio; Rasley, Amy

    2008-01-01

    Francisella tularensis is a zoonotic bacterium that must exist in diverse environments ranging from arthropod vectors to mammalian hosts. To better understand how virulence genes are regulated in these different environments, a transcriptional response regulator gene (genome locus FTL0552) was deleted in F. tularensis live vaccine strain (LVS). The FTL0552 deletion mutant exhibited slightly reduced rates of extracellular growth but was unable to replicate or survive in mouse macrophages and was avirulent in the mouse model using either BALB/c or C57BL/6 mice. Mice infected with the FTL0552 mutant produced reduced levels of inflammatory cytokines, exhibited reduced histopathology, and cleared the bacteria quicker than mice infected with LVS. Mice that survived infection with the FTL0552 mutant were afforded partial protection when challenged with a lethal dose of the virulent SchuS4 strain (4 of 10 survivors, day 21 postinfection) when compared to naive mice (0 of 10 survivors by day 7 postinfection). Microarray experiments indicate that 148 genes are regulated by FTL0552. Most of the genes are downregulated, indicating that FTL0552 controls transcription of genes in a positive manner. Genes regulated by FTL0552 include genes located within the Francisella pathogenicity island that are essential for intracellular survival and virulence of F. tularensis. Further, a mutant in FTL0552 or the comparable locus in SchuS4 (FTT1557c) may be an alternative candidate vaccine for tularemia. PMID:18613792

  16. AdaNET executive summary

    NASA Technical Reports Server (NTRS)

    Digman, R. Michael

    1988-01-01

    The goal of AdaNET is to transfer existing and emerging software engineering technology from the Federal government to the private sector. The views and perspectives of the current project participants on long and short term goals for AdaNET; organizational structure; resources and returns; summary of identified AdaNET services; and the summary of the organizational model currently under discussion are presented.

  17. Characterization of oxidative phosphorylation enzymes in Euglena gracilis and its white mutant strain W(gm)ZOflL.

    PubMed

    Krnáčová, Katarína; Rýdlová, Ivana; Vinarčíková, Michaela; Krajčovič, Juraj; Vesteg, Matej; Horváth, Anton

    2015-03-12

    The enzymes involved in Euglena oxidative phosphorylation (OXPHOS) were characterized in this study. We have demonstrated that Euglena gracilis strain Z and its stable bleached non-photosynthetic mutant strain WgmZOflL both possess fully functional OXPHOS apparatus as well as pathways requiring terminal alternative oxidase(s) and alternative mitochondrial NADH-dehydrogenase(s). Light (or dark) and plastid (non)functionality seem to have little effect on oxygen consumption, the activities of the enzymes involved in OXPHOS and the action of respiration inhibitors in Euglena. This study also demonstrates biochemical properties of complex III (cytochrome c reductase) in Euglena. PMID:25660326

  18. Ada training evaluation and recommendation

    NASA Technical Reports Server (NTRS)

    Murphy, Robert; Stark, Michael

    1987-01-01

    This paper documents the Ada training experiences and recommendations of the Gamma Ray Observatory dynamics simulator Ada development team. A two month Ada training program for software developers is recommended which stresses the importance of teaching design methodologies early, as well as the use of certain training aids such as videotaped lectures and computer-aided instruction. Furthermore, a separate training program for managers is recommended, so that they may gain a better understanding of modified review products and resource allocation associated with Ada projects.

  19. AdaNET research project

    NASA Technical Reports Server (NTRS)

    Digman, R. Michael

    1988-01-01

    The components necessary for the success of the commercialization of an Ada Technology Transition Network are reported in detail. The organizational plan presents the planned structure for services development and technical transition of AdaNET services to potential user communities. The Business Plan is the operational plan for the AdaNET service as a commercial venture. The Technical Plan is the plan from which the AdaNET can be designed including detailed requirements analysis. Also contained is an analysis of user fees and charges, and a proposed user fee schedule.

  20. Constitutive expression of the tzs gene from Agrobacterium tumefaciens virG mutant strains is responsible for improved transgenic plant regeneration in cotton meristem transformation.

    PubMed

    Ye, Xudong; Chen, Yurong; Wan, Yuechun; Hong, Yun-Jeong; Ruebelt, Martin C; Gilbertson, Larry A

    2016-03-01

    KEY MESSAGE : virG mutant strains of a nopaline type of Agrobacterium tumefaciens increase the transformation frequency in cotton meristem transformation. Constitutive cytokinin expression from the tzs gene in the virG mutant strains is responsible for the improvement. Strains of Agrobacterium tumefaciens were tested for their ability to improve cotton meristem transformation frequency. Two disarmed A. tumefaciens nopaline strains with either a virGN54D constitutively active mutation or virGI77V hypersensitive induction mutation significantly increased the transformation frequency in a cotton meristem transformation system. The virG mutant strains resulted in greener explants after three days of co-culture in the presence of light, which could be attributed to a cytokinin effect of the mutants. A tzs knockout strain of virGI77V mutant showed more elongated, less green explants and decreased cotton transformation frequency, as compared to a wild type parental strain, suggesting that expression of the tzs gene is required for transformation frequency improvement in cotton meristem transformation. In vitro cytokinin levels in culture media were tenfold higher in the virGN54D strain, and approximately 30-fold higher in the virGI77V strain, in the absence of acetosyringone induction, compared to the wild type strain. The cytokinin level in the virGN54D strain is further increased upon acetosyringone induction, while the cytokinin level in the virGI77V mutant is decreased by induction, suggesting that different tzs gene expression regulation mechanisms are present in the two virG mutant strains. Based on these data, we suggest that the increased cytokinin levels play a major role in increasing Agrobacterium attachment and stimulating localized division of the attached plant cells. PMID:26650837

  1. Distributed and parallel Ada and the Ada 9X recommendations

    NASA Astrophysics Data System (ADS)

    Volz, R. A.; Theriault, R.; Waldrop, R.; Goldsack, S. J.; Holzbacher-Valero, A.

    1994-06-01

    In modern software systems development, distributed and parallel systems are of increasing importance. Much research has been done to investigate the distribution of Ada programs across a set of processors, both in loosely-coupled distributed systems and in more tightly-coupled parallel systems. To this point, however, there has been something of an idea that the support needed for distributed systems differs from that required for parallel systems. In this paper, the authors first discuss the support requirements for distributed and parallel Ada programs, and point out that the requirements for these two areas have more in common than may have been previously thought. Next, the authors discuss AdaPT (Ada plus ParTitions), a set of extensions to Ada to support distributed and fault-tolerant systems. AdaPT is used as a reference in the further discussion of the previously identified requirements for distributed systems. After this, the authors provide an in-depth discussion of the Ada 9X Distributed Systems Annex, as presented by the Ada 9X mapping/revision team in the version 5.0 draft Language Reference Manual, and the extent to which this annex fulfils the previously identified requirements.

  2. Transforming AdaPT to Ada9x

    NASA Technical Reports Server (NTRS)

    Goldsack, Stephen J.; Holzbach-Valero, A. A.; Volz, Richard A.; Waldrop, Raymond S.

    1993-01-01

    How the concepts of AdaPT can be transformed into programs using the object oriented features proposed in the preliminary mapping for Ada9x are described. Emphasizing, as they do, the importance of data types as units of program, these features match well with the development of partitions as translations into Abstract Data Types which was exploited in the Ada83 translation covered in report R3. By providing a form of polymorphic type, the Ada83 version also gives support for the conformant partition idea which could be achieved in Ada83 only by using UNCHECKED CONVERSIONS. It is assumed that the reader understands AdaPT itself, but the translation into Ada83 is briefly reviewed, by applying it to a small example. This is then used to show how the same translation would be achieved in the 9x version. It is important to appreciate that the distribution features which are proposed in current mapping are not used or discussed in any detail, as those are not well matched to the AdaPT approach. Critical evaluation and comparison of these approaches is given in a separate report.

  3. Comparative studies of lipopolysaccharide and exopolysaccharide from a virulent strain of Pseudomonas solanacearum and from three avirulent mutants.

    PubMed Central

    Drigues, P; Demery-Lafforgue, D; Trigalet, A; Dupin, P; Samain, D; Asselineau, J

    1985-01-01

    The composition of the Pseudomonas solanacearum lipolysaccharide (LPS) was found to be similar to that described for the LPS of enterobacteria. The lipid A contained fatty acids and glucosamine in a molar ratio of 5:2. The LPS fraction contained 2-keto-3-deoxyoctulosonic acid, L-glycero-D-mannoheptose, hexoses (glucose, rhamnose, and glucosamine), and a pentose (xylose). The LPSs from the wild-type strain (GMI1000), from the spontaneous rough mutant (GMI2000), and from their respective acridine orange-resistant (Acrr) mutants (GMI1178 and GMI2179) contained the same component sugars in their polysaccharide moieties, but the relative amounts of each sugar varied greatly. Spontaneous mutation to the rough type was characterized by a decrease in the ratio of rhamnose to glucose, whereas a reverse effect was seen for the acridine orange resistance mutation from the parent strains (GMI1000 and GMI2000) to the respective mutant strains (GMI1178 and GMI2179). The exopolysaccharide (EPS) from GMI1000 was found to be composed of two fractions: a heteropolysaccharide (galactosamine, glucose, and rhamnose) excluded from Sephadex G-50 and an additional glucan with a lower molecular weight. Strains GMI1000 and GMI1178 produced comparable amounts of EPS, GMI2179 synthesized less EPS, and GMI2000 produced no detectable EPS. High-pressure liquid chromatography and 13C nuclear magnetic resonance analyses revealed some differences between these EPSs. The glucan fraction seemed to be the major component of the EPS from GMI2179, whereas GMI1000 and GMI1178 EPSs contained both fractions and appeared to differ in the structures of their heteropolysaccharide fractions. Viscosity measurements confirmed differences between whole EPSs produced by the three strains. PMID:3988700

  4. Isolation of monoclonal antibodies reacting with the core component of lipopolysaccharide from Rhizobium leguminosarum strain 3841 and mutant derivatives.

    PubMed Central

    Lucas, M M; Peart, J L; Brewin, N J; Kannenberg, E L

    1996-01-01

    Monoclonal antibodies reacting with the core oligosaccharide or lipid A component of Rhizobium lipopolysaccharide (LPS) could be useful for the elucidation of the structure and biosynthesis of this group of macromolecules. Mutant derivatives of Rhizobium leguminosarum 3841 with LPS structures lacking the major O-antigen moiety were used as immunogens, and eight antibodies were selected for further study. All the antibodies reacted with the fast-migrating species known as LPS-2 following gel electrophoresis of Rhizobium cell extracts. For four of these antibodies, reactivity with affinity-purified LPS was lost after mild acid hydrolysis, indicating that they probably recognized the core oligosaccharide component. The four other antibodies still reacted with acid-treated LPS and may recognize the lipid A moiety, which is stable to mild acid hydrolysis. The pattern of antibody staining after gel electrophoresis revealed differences in LPS-2 epitope structure between each of the mutants and the wild type. Furthermore, for each of the mutants the antibodies crossreacted with a minor band that migrated more slowly than LPS-2; we have termed this more slowly migrating form LPS-3. The majority of the antibodies also reacted with LPS from strain CE109, a derivative of Rhizobium etli CE3, confirming that the LPS core antigens can be relatively conserved between strains of different Rhizobium species. One of the antibodies isolated in this study (JIM 32) was unusual because it appeared to react with all forms of LPS from strain 3841 (namely, LPS-1, LPS-2, and LPS-3). Furthermore, JIM 32 reacted positively with the LPS from many strains of Rhizobium tested (excluding the Rhizobium meliloti subgroup). JIM 32 did not react with representative strains from Bradyrhizobium, Azorhizobium or other related bacterial species. PMID:8631658

  5. Distributed and parallel Ada and the Ada 9X recommendations

    NASA Technical Reports Server (NTRS)

    Volz, Richard A.; Goldsack, Stephen J.; Theriault, R.; Waldrop, Raymond S.; Holzbacher-Valero, A. A.

    1992-01-01

    Recently, the DoD has sponsored work towards a new version of Ada, intended to support the construction of distributed systems. The revised version, often called Ada 9X, will become the new standard sometimes in the 1990s. It is intended that Ada 9X should provide language features giving limited support for distributed system construction. The requirements for such features are given. Many of the most advanced computer applications involve embedded systems that are comprised of parallel processors or networks of distributed computers. If Ada is to become the widely adopted language envisioned by many, it is essential that suitable compilers and tools be available to facilitate the creation of distributed and parallel Ada programs for these applications. The major languages issues impacting distributed and parallel programming are reviewed, and some principles upon which distributed/parallel language systems should be built are suggested. Based upon these, alternative language concepts for distributed/parallel programming are analyzed.

  6. Update of GRASP/Ada reverse engineering tools for Ada

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1992-01-01

    The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation of Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAS 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3, the prototype was evaluated by software engineering students at Auburn University and then updated with significant enhancements to the user interface including editing capabilities. Version 3.2 of the prototype was prepared for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application.

  7. [Analysis of the structure and expression of the DIP1 gene in Drosophila melanogaster strains mutant for the flamenco gene].

    PubMed

    Nefedova, L N; Potanova, M V; Romanova, N I; Kim, A I

    2009-02-01

    DIP1 gene transcription was analyzed with the use of RT-PCR in three Drosophila melanogaster strains with the flamenco- phenotype (flam(SS), flam(MS), and flam(Ore)) and in one flamenco+ strain at the stages of embryos (0-24 h), third-instar larvae, and adult flies. The mutant strains flam(SS) and flam(Ore) lack an active copy of transposon gypsy. Theflam(MS) strain was obtained by introducing an active copy of gypsy in flies of theflam(SS) strain and is characterized by a high rate of gypsy transpositions. The experiments showed that at least five forms of DIP1 gene transcripts are produced. The form of cDNA corresponding to CDS DIP1-d was discovered only in embryos. It was found that DIP1 gene transcription depends on the age of flies: at the larval stage the level of transcription is significantly reduced. However, no reduction of gene transcription is observed in theflam(Ore) strain. These results suggest that the flamenco- phenotype may be associated with an alteration of DIP1 gene transcription, as in differentflamenco- strains the DIP1 gene expression is changed differently. PMID:19334614

  8. Using Ada: The deeper challenges

    NASA Technical Reports Server (NTRS)

    Feinberg, David A.

    1986-01-01

    The Ada programming language and the associated Ada Programming Support Environment (APSE) and Ada Run Time Environment (ARTE) provide the potential for significant life-cycle cost reductions in computer software development and maintenance activities. The Ada programming language itself is standardized, trademarked, and controlled via formal validation procedures. Though compilers are not yet production-ready as most would desire, the technology for constructing them is sufficiently well known and understood that time and money should suffice to correct current deficiencies. The APSE and ARTE are, on the other hand, significantly newer issues within most software development and maintenance efforts. Currently, APSE and ARTE are highly dependent on differing implementer concepts, strategies, and market objectives. Complex and sophisticated mission-critical computing systems require the use of a complete Ada-based capability, not just the programming language itself; yet the range of APSE and ARTE features which must actually be utilized can vary significantly from one system to another. As a consequence, the need to understand, objectively evaluate, and select differing APSE and ARTE capabilities and features is critical to the effective use of Ada and the life-cycle efficiencies it is intended to promote. It is the selection, collection, and understanding of APSE and ARTE which provide the deeper challenges of using Ada for real-life mission-critical computing systems. Some of the current issues which must be clarified, often on a case-by-case basis, in order to successfully realize the full capabilities of Ada are discussed.

  9. ADA Guide for Small Businesses.

    ERIC Educational Resources Information Center

    Department of Justice, Washington, DC. Civil Rights Div.

    This guide presents an informal overview of some basic Americans with Disabilities Act (ADA) requirements for small businesses that provide goods or services to the public. References to key sections of the regulations or other information are included. The first section describes the ADA briefly. Section two lists the 12 categories of public…

  10. The effect of Clostridium perfringens type C strain CN3685 and its isogenic beta toxin null mutant in goats.

    PubMed

    Garcia, J P; Beingesser, J; Fisher, D J; Sayeed, S; McClane, B A; Posthaus, H; Uzal, F A

    2012-06-15

    Clostridium perfringens type C is an important cause of enteritis and/or enterocolitis in several animal species, including pigs, sheep, goats, horses and humans. The disease is a classic enterotoxemia and the enteric lesions and associated systemic effects are thought to be caused primarily by beta toxin (CPB), one of two typing toxins produced by C. perfringens type C. This has been demonstrated recently by fulfilling molecular Koch's postulates in rabbits and mice. We present here an experimental study to fulfill these postulates in goats, a natural host of C. perfringens type C disease. Nine healthy male or female Anglo Nubian goat kids were inoculated with the virulent C. perfringens type C wild-type strain CN3685, an isogenic CPB null mutant or a strain where the cpb null mutation had been reversed. Three goats inoculated with the wild-type strain presented abdominal pain, hemorrhagic diarrhea, necrotizing enterocolitis, pulmonary edema, hydropericardium and death within 24h of inoculation. Two goats inoculated with the CPB null mutant and two goats inoculated with sterile culture media (negative controls) remained clinically healthy during 24h after inoculation and no gross or histological abnormalities were observed in the tissues of any of them. Reversal of the null mutation to partially restore CPB production also increased virulence; 2 goats inoculated with this reversed mutant presented clinical and pathological changes similar to those observed in goats inoculated with the wild-type strain, except that spontaneous death was not observed. These results indicate that CPB is required for C. perfringens type C to induce disease in goats, supporting a key role for this toxin in natural C. perfringens type C disease pathogenesis. PMID:22296994

  11. The effect of Clostridium perfringens type C strain CN3685 and its isogenic beta toxin null mutant in goats

    PubMed Central

    Garcia, J. P.; Beingesser, J.; Fisher, D. J.; Sayeed, S.; McClane, B. A.; Posthaus, H.; Uzal, F. A.

    2012-01-01

    Clostridium perfringens type C is an important cause of enteritis and/or enterocolitis in several animal species, including pigs, sheep, goats, horses and humans. The disease is a classic enterotoxemia and the enteric lesions and associated systemic effects are thought to be caused primarily by beta toxin (CPB), one of two typing toxins produced by C. perfringens type C. This has been demonstrated recently by fulfilling molecular Koch’s postulates in rabbits and mice. We present here an experimental study to fulfill these postulates in goats, a natural host of C. perfringens type C disease. Nine healthy male or female Anglo Nubian goat kids were inoculated with the virulent C. perfringens type C wild-type strain CN3685, an isogenic CPB null mutant or a strain where the cpb null mutation had been reversed. Three goats inoculated with the wild-type strain presented abdominal pain, hemorrhagic diarrhea, necrotizing enterocolitis, pulmonary edema, hydropericardium and death within 24 h of inoculation. Two goats inoculated with the CPB null mutant and two goats inoculated with sterile culture media (negative controls) remained clinically healthy during 24 h after inoculation and no gross or histological abnormalities were observed in the tissues of any of them. Reversal of the null mutation to partially restore CPB production also increased virulence; 2 goats inoculated with this reversed mutant presented clinical and pathological changes similar to those observed in goats inoculated with the wild-type strain, except that spontaneous death was not observed. These results indicate that CPB is required for C. perfringens type C to induce disease in goats, supporting a key role for this toxin in natural C. perfringens type C disease pathogenesis. PMID:22296994

  12. Survival of Bacillus megaterium strains in water.

    PubMed

    Palmada, F M; Sanchez-Rivas, C

    1996-01-01

    Cultures of Bacillus megaterium strains, producers or not of poly-beta-hydroxy-butyrate (PHB+ and PHB-) were submitted to several shift-downs: nutritional (one hundred fold dilution in saline water S or artificial fresh water ADA) or nutritional and osmotic (one hundred fold dilution in water or W). In all conditions tested, the wild type strain survived, duplicated five times and sporulated. However, the PHB- mutant strain showed a drastic loss of viability in water (< 0.1%) not observed when the shift was only nutritional (S or ADA). Discussion was focused on the advantages of the potential use of Bacillus megaterium as host for delivering bio-insecticides in waters instead of natural hosts such as B. thuringiensis strains. PMID:9017852

  13. Strain-Dependent Anterior Segment Dysgenesis and Progression to Glaucoma in Col4a1 Mutant Mice

    PubMed Central

    Mao, Mao; Smith, Richard S.; Alavi, Marcel V.; Marchant, Jeffrey K.; Cosma, Mihai; Libby, Richard T.; John, Simon W. M.; Gould, Douglas B.

    2015-01-01

    Purpose Mutations in the gene encoding collagen type IV alpha 1 (COL4A1) cause multisystem disorders including anterior segment dysgenesis (ASD) and optic nerve hypoplasia. The penetrance and severity of individual phenotypes depends on genetic context. Here, we tested the effects of a Col4a1 mutation in two different genetic backgrounds to compare how genetic context influences ocular dysgenesis, IOP, and progression to glaucoma. Methods Col4a1 mutant mice maintained on a C57BL/6J background were crossed to either 129S6/SvEvTac or CAST/EiJ and the F1 progeny were analyzed by slit-lamp biomicroscopy and optical coherence tomography. We also measured IOPs and compared tissue sections of eyes and optic nerves. Results. We found that the CAST/EiJ inbred strain has a relatively uniform and profound suppression on the effects of Col4a1 mutation and that mutant CASTB6F1 mice were generally only very mildly affected. In contrast, mutant 129B6F1 mice had more variable and severe ASD and IOP dysregulation that were associated with glaucomatous signs including lost or damaged retinal ganglion cell axons and excavation of the optic nerve head. Conclusions. Ocular defects in Col4a1 mutant mice model ASD and glaucoma that are observed in a subset of patients with COL4A1 mutations. We demonstrate that different inbred strains of mice give graded severities of ASD and we detected elevated IOP and glaucomatous damage in 129B6F1, but not CASTB6F1 mice that carried a Col4a1 mutation. These data demonstrate that genetic context differences are one factor that may contribute to the variable penetrance and severity of ASD and glaucoma in patients with COL4A1 mutations. PMID:26567795

  14. Ada Structure Design Language (ASDL)

    NASA Technical Reports Server (NTRS)

    Chedrawi, Lutfi

    1986-01-01

    An artist acquires all the necessary tools before painting a scene. In the same analogy, a software engineer needs the necessary tools to provide their design with the proper means for implementation. Ada provide these tools. Yet, as an artist's painting needs a brochure to accompany it for further explanation of the scene, an Ada design also needs a document along with it to show the design in its detailed structure and hierarchical order. Ada could be self-explanatory in small programs not exceeding fifty lines of code in length. But, in a large environment, ranging from thousands of lines and above, Ada programs need to be well documented to be preserved and maintained. The language used to specify an Ada document is called Ada Structure Design Language (ASDL). This language sets some rules to help derive a well formatted Ada detailed design document. The rules are defined to meet the needs of a project manager, a maintenance team, a programmer and a systems designer. The design document templates, the document extractor, and the rules set forth by the ASDL are explained in detail.

  15. Update of GRASP/Ada reverse engineering tools for Ada

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1993-01-01

    The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional pretty printed Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype CSD generator (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3,e two update phases were completed. Update'92 focused on the initial analysis of evaluation data collected from software engineering students at Auburn University and the addition of significant enhancements to the user interface. Update'93 (the current update) focused on the statistical analysis of the data collected in the previous update and preparation of Version 3.4 of the prototype for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical

  16. Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors.

    PubMed Central

    Marcus, G A; Silverman, N; Berger, S L; Horiuchi, J; Guarente, L

    1994-01-01

    A selection for yeast mutants resistant to GAL4-VP16-induced toxicity previously identified two genes, ADA2 and ADA3, which may function as adaptors for some transcriptional activation domains and thereby facilitate activation. Here we identify two new genes by the same selection, one of which is identical to GCN5. We show that gcn5 mutants share properties with ada mutants, including slow growth, temperature sensitivity and reduced activation by the VP16 and GCN4 activation domains. Double mutant studies suggest that ADA2 and GCN5 function together in a complex or pathway. Moreover, we demonstrate that GCN5 binds to ADA2 both by the two-hybrid assay in vivo and by co-immunoprecipitation in vitro. This suggests that ADA2 and GCN5 are part of a heteromeric complex that mediates transcriptional activation. Finally, we demonstrate the functional importance of the bromodomain of GCN5, a sequence found in other global transcription factors such as the SWI/SNF complex and the TATA binding protein-associated factors. This domain is not required for the interaction between GCN5 and ADA2 and thus may mediate a more general activity of transcription factors. Images PMID:7957049

  17. Praxis - An alternative to Ada

    SciTech Connect

    Holloway, F.W.; Sherman, T.A.

    1987-08-01

    This report describes Praxis, a modern, complete, block structured, strongly typed, programming language, comparable to Ada, and with special emphasis toward meeting systems programming requirements on all level machines. Praxis is considered as a possible alternative to Ada in certain applications. Praxis has been used since 1980 on the distributed control system for the Nova high energy laser at Lawrence Livermore National Laboratory. A description of the intended applications, the history of development, and an overview of the features of the language with comparisons to the Pascal and Ada languages, are given. The features are described in four categories: general appearance, power, insurance of freedom from errors, and manageability.

  18. Praxis: An alternative to Ada

    SciTech Connect

    Holloway, F.W.; Sherman, T.A.

    1987-05-13

    This report describes Praxis, a modern, complete, block structures, strongly typed, programming language, comparable to Ada, and with special emphasis toward meeting systems programming requirements on all level machines. Praxis is considered as a possible alternative to Ada in certain applications. Praxis has been used since 1980 on the distributed control system for the Nova high energy laser at Lawrence Livermore National Laboratory. A description of the intended applications, the history of development, and an overview of the features of the language with comparisons to the Pascal and Ada languages, are given. The features are described in four categories: general appearance, power, insurance of freedom from errors, and manageability.

  19. Characterization of the endemic equilibrium and response to mutant injection in a multi-strain disease model.

    PubMed

    Aquino, Tomás; Bolster, Diogo; Nunes, Ana

    2015-03-01

    We explore a model of an antigenically diverse infection whose otherwise identical strains compete through cross-immunity. We assume that individuals may produce upon infection different numbers of antibody types, each of which matches the antigenic configuration of a particular epitope, and that one matching antibody type grants total immunity against a challenging strain. In order to reduce the number of equations involved in the analytic description of the dynamics, we follow the strategy proposed by Kryazhimskiy et al. (2007) and apply a low-order closure reminiscent of a pair approximation. Using this approximation, we go beyond the numerical studies of Kryazhimskiy et al. (2007) and explore the analytic properties of the ensuing model in the absence of mutation. We characterize its endemic equilibrium, comparing with the results of agent based simulations of the full model to assess the performance of the closure assumption. We show that a particular choice of immune response leads to a degenerate endemic equilibrium, where different strain prevalences may exist, breaking the symmetry of the model. Finally we study the behavior of the system under the injection of mutant strains. We find that the build up of diversity from a single founding strain is extremely unlikely for different choices of the population׳s immune response. PMID:25496729

  20. Calcofluor staining of cellulose during microcyst differentiation in wild-type and mutant strains of Polysphondylium pallidum.

    PubMed Central

    Choi, A H; O'Day, D H

    1984-01-01

    Calcofluor White ST was used to monitor the morphological events in the biogenesis of cellulose in the microcyst wall of the wild-type strain (WS-320) and two developmental mutants (mic-1 and mic-2) of Polysphondylium pallidum. During encystment, the cell surface acquires a Calcofluor-specific material which appears to be cellulose because of its sensitivity to purified cellulase. Cellulose-containing vesicles appear distributed throughout the cytoplasm of encysting cells of the three strains. Later, the cellulose-rich vesicles appear near the cell surface. Subsequently, the cell surface stains with Calcofluor, and the vesicles are no longer detectable. Intracellular vesicles resembling the cellulose-rich vesicles in size, in the timing of appearance, and in cellular location are also seen in thin sections. These vesicles are surrounded by a single unit membrane, and their amorphous matrix, which contains a dense irregular core, further implicates them as the basis for the bilayered microcyst wall. Images PMID:6197403

  1. Restoration of growth by manganese in a mutant strain of Escherichia coli lacking most known iron and manganese uptake systems.

    PubMed

    Taudte, Nadine; German, Nadezhda; Zhu, Yong-Guan; Grass, Gregor; Rensing, Christopher

    2016-06-01

    The interplay of manganese and iron homeostasis and oxidative stress in Escherichia coli can give important insights into survival of bacteria in the phagosome and under differing iron or manganese bioavailabilities. Here, we characterized a mutant strain devoid of all know iron/manganese-uptake systems relevant for growth in defined medium. Based on these results an exit strategy enabling the cell to cope with iron depletion and use of manganese as an alternative for iron could be shown. Such a strategy would also explain why E. coli harbors some iron- or manganese-dependent iso-enzymes such as superoxide dismutases or ribonucleotide reductases. The benefits for gaining a means for survival would be bought with the cost of less efficient metabolism as indicated in our experiments by lower cell densities with manganese than with iron. In addition, this strain was extremely sensitive to the metalloid gallium but this gallium toxicity can be alleviated by low concentrations of manganese. PMID:27003826

  2. Ada Linear-Algebra Program

    NASA Technical Reports Server (NTRS)

    Klumpp, A. R.; Lawson, C. L.

    1988-01-01

    Routines provided for common scalar, vector, matrix, and quaternion operations. Computer program extends Ada programming language to include linear-algebra capabilities similar to HAS/S programming language. Designed for such avionics applications as software for Space Station.

  3. Levels of Expression and Immunogenicity of Attenuated Salmonella enterica Serovar Typhimurium Strains Expressing Escherichia coli Mutant Heat-Labile Enterotoxin

    PubMed Central

    Covone, M. Giuseppina; Brocchi, Marcelo; Palla, Emanuela; da Silveira, W. Dias; Rappuoli, Rino; Galeotti, Cesira L.

    1998-01-01

    The effects of heterologous gene dosage as well as Salmonella typhimurium strain variability on immune response toward both the heterologous antigen, the nontoxic mutant of the Escherichia coli heat-labile enterotoxin LTK63, and the carrier Salmonella strain have been analyzed. Effects of a single integration into the host DNA and different-copy-number episomal vectors were compared in S. typhimurium Δcya Δcrp Δasd strains of two different serotypes, UK-1 and SR-11. Expression of the enterotoxin in the different Salmonella isolates in vitro was found to vary considerably and, for the episomal vectors, to correlate with the plasmid copy number. LTK63-specific serum immunoglobulin G (IgG) and mucosal immunoglobulin A (IgA) antibodies were highest in mice immunized with the high-level-expression strain. High anti-LTK63 IgG and IgA titers were found to correspond to higher anti-Salmonella immunity, suggesting that LTK63 exerts an adjuvant effect on response to the carrier. Statistically significant differences in anti-LTK63 immune response were observed between groups of mice immunized with the attenuated Δcya Δcrp UK-1 and SR-11 derivatives producing the antigen at the same rate. These data indicate that the same attenuation in S. typhimurium strains of different genetic backgrounds can influence significantly the immune response toward the heterologous antigen. Moreover, delivery of the LTK63 enterotoxin to the immune system by attenuated S. typhimurium strains is effective only when synthesis of the antigen is very high during the initial phase of invasion, while persistence of the S. typhimurium strain in deep tissues has only marginal influence. PMID:9423862

  4. GRASP/Ada 95: Reverse Engineering Tools for Ada

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1996-01-01

    The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped an algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD), and a new visualization for a fine-grained complexity metric called the Complexity Profile Graph (CPG). By synchronizing the CSD and the CPG, the CSD view of control structure, nesting, and source code is directly linked to the corresponding visualization of statement level complexity in the CPG. GRASP has been integrated with GNAT, the GNU Ada 95 Translator to provide a comprehensive graphical user interface and development environment for Ada 95. The user may view, edit, print, and compile source code as a CSD with no discernible addition to storage or computational overhead. The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada 95 source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. The current update has focused on the design and implementation of a new Motif compliant user interface, and a new CSD generator consisting of a tagger and renderer. The Complexity Profile Graph (CPG) is based on a set of functions that describes the context, content, and the scaling for complexity on a statement by statement basis. When combined graphicafly, the result is a composite profile of complexity for the program unit. Ongoing research includes the development and refinement of the associated functions, and the development of the CPG generator prototype. The current Version 5.0 prototype provides the capability for the user to generate CSDs and CPGs from Ada 95 source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for

  5. Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains.

    PubMed Central

    Lorenz, M C; Heitman, J

    1998-01-01

    Nitrogen-starved diploid cells of the yeast Saccharomyces cerevisiae differentiate into a filamentous, pseudohyphal growth form. Recognition of nitrogen starvation is mediated, at least in part, by the ammonium permease Mep2p and the Galpha subunit Gpa2p. Genetic activation of the pheromone-responsive MAP kinase cascade, which is also required for filamentous growth, only weakly suppresses the filamentation defect of Deltamep2/Deltamep2 and Deltagpa2/Deltagpa2 strain. Surprisingly, deletion of Mep1p, an ammonium permease not previously thought to regulate differentiation, significantly enhances the potency of MAP kinase activation, such that the STE11-4 allele induces filamentation to near wild-type levels in Deltamep1/Deltamep1 Deltamep2/Deltamep2 and Deltamep1/Deltamep1 Deltagpa2/Deltagpa2 strains. To identify additional regulatory components, we isolated high-copy suppressors of the filamentation defect of the Deltamep1/Deltamep1 Deltamep2/Deltamep2 mutant. Multicopy expression of TEC1, PHD1, PHD2 (MSS10/MSN1/FUP4), MSN5, CDC6, MSS11, MGA1, SKN7, DOT6, HMS1, HMS2, or MEP2 each restored filamentation in a Deltamep1/Deltamep1 Deltamep2/Deltamep2 strain. Overexpression of SRK1 (SSD1), URE2, DAL80, MEP1, or MEP3 suppressed only the growth defect of the Deltamep1/Deltamep1 Deltamep2/Deltamep2 mutant strain. Characterization of these genes through deletion analysis and epistasis underscores the complexity of this developmental pathway and suggests that stress conditions other than nitrogen deprivation may also promote filamentous growth. PMID:9832522

  6. An Ada programming support environment

    NASA Technical Reports Server (NTRS)

    Tyrrill, AL; Chan, A. David

    1986-01-01

    The toolset of an Ada Programming Support Environment (APSE) being developed at North American Aircraft Operations (NAAO) of Rockwell International, is described. The APSE is resident on three different hosts and must support developments for the hosts and for embedded targets. Tools and developed software must be freely portable between the hosts. The toolset includes the usual editors, compilers, linkers, debuggers, configuration magnagers, and documentation tools. Generally, these are being supplied by the host computer vendors. Other tools, for example, pretty printer, cross referencer, compilation order tool, and management tools were obtained from public-domain sources, are implemented in Ada and are being ported to the hosts. Several tools being implemented in-house are of interest, these include an Ada Design Language processor based on compilable Ada. A Standalone Test Environment Generator facilitates test tool construction and partially automates unit level testing. A Code Auditor/Static Analyzer permits the Ada programs to be evaluated against measures of quality. An Ada Comment Box Generator partially automates generation of header comment boxes.

  7. Comparative Proteomic Analysis of Streptomyces lividans Wild-Type and ppk Mutant Strains Reveals the Importance of Storage Lipids for Antibiotic Biosynthesis

    PubMed Central

    Le Maréchal, Pierre; Decottignies, Paulette; Marchand, Christophe H.; Degrouard, Jeril; Jaillard, Danièle; Dulermo, Thierry; Froissard, Marine; Smirnov, Aleksey; Chapuis, Violaine

    2013-01-01

    Streptomyces lividans TK24 is a strain that naturally produces antibiotics at low levels, but dramatic overproduction of antibiotics occurs upon interruption of the ppk gene. However, the role of the Ppk enzyme in relation to the regulation of antibiotic biosynthesis remains poorly understood. In order to gain a better understanding of the phenotype of the ppk mutant, the proteomes of the wild-type (wt) and ppk mutant strains, grown for 96 h on R2YE medium limited in phosphate, were analyzed. Intracellular proteins were separated on two-dimensional (2D) gels, spots were quantified, and those showing a 3-fold variation or more were identified by mass spectrometry. The expression of 12 proteins increased and that of 29 decreased in the ppk mutant strain. Our results suggested that storage lipid degradation rather than hexose catabolism was taking place in the mutant. In order to validate this hypothesis, the triacylglycerol contents of the wt and ppk mutant strains of S. lividans as well as that of Streptomyces coelicolor M145, a strain that produces antibiotics at high levels and is closely related to S. lividans, were assessed using electron microscopy and thin-layer chromatography. These studies highlighted the large difference in triacylglycerol contents of the three strains and confirmed the hypothetical link between storage lipid metabolism and antibiotic biosynthesis in Streptomyces. PMID:23872561

  8. Emergence of potential superbug mycobacterium tuberculosis, lessons from new delhi mutant-1 bacterial strains.

    PubMed

    Nazir, Taha; Abraham, Suraj; Islam, Azharul

    2012-01-01

    Recent reports have shown that certain bacterial strains attain the New Delhi Metallo-beta-lactamase-1 (NDM-1) enzyme and become resistant to a broad range of antibiotics. Similarly, more dangerous "superbugs" of multi-drug resistant (MDR) and extensive drug resistant (XDR) Mycobacterium tuberculosis strains are gradually emerging through rapid genetic mutation caused by prescription non-compliance or unsupervised indiscriminate use of anti-tubercular drugs or other antibiotics. Mycobacterium tuberculosis cases have been reported in highly susceptible population groups including the aboriginal communities of US and Canada. In Canada alone, the total number of reported tuberculosis cases has decreased over the past decade. However, there is a steady increase in HIV cases in certain communities including the aboriginal communities. Reintroduction of MDR/XDR strains of tuberculosis is possible in these susceptible communities, which in turn may pose serious public health situation. MDR/XDR strains of tuberculosis are virtually untreatable using current anti-tubercular medication protocols. Thus, MDR/XDR tuberculosis presents a grave global public health threat. The unpredictable genetic mechanism involved in generating MDR/XDR resistant strains of Mycobacterium tuberculosis may pose greater challenges in developing appropriate treatment strategies. In this article, we briefly review potential genetic mechanism of emerging NDM-1 bacterial strains and draw a rationale parallel to the underlying genetic mechanism of MDR/XDR Mycobacterium tuberculosis strain development. PMID:23267308

  9. Establishing a Markerless Genetic Exchange System for Methanosarcina mazei Strain Gö1 for Constructing Chromosomal Mutants of Small RNA Genes

    PubMed Central

    Ehlers, Claudia; Jäger, Dominik; Schmitz, Ruth A.

    2011-01-01

    A markerless genetic exchange system was successfully established in Methanosarcina mazei strain Gö1 using the hpt gene coding for hypoxanthine phosphoribosyltransferase. First, a chromosomal deletion mutant of the hpt gene was generated conferring resistance to the purine analog 8-aza-2,6-diaminopurine (8-ADP). The nonreplicating allelic exchange vector (pRS345) carrying the pac-resistance cassette for direct selection of chromosomal integration, and the hpt gene for counterselection was introduced into this strain. By a pop-in and ultimately pop-out event of the plasmid from the chromosome, allelic exchange is enabled. Using this system, we successfully generated a M. mazei deletion mutant of the gene encoding the regulatory non-coding RNA sRNA154. Characterizing M. mazeiΔsRNA154 under nitrogen limiting conditions demonstrated differential expression of at least three cytoplasmic proteins and reduced growth strongly arguing for a prominent role of sRNA154 in regulation of nitrogen fixation by posttranscriptional regulation. PMID:21941461

  10. Ada/POSIX binding: A focused Ada investigation

    NASA Technical Reports Server (NTRS)

    Legrand, Sue

    1988-01-01

    NASA is seeking an operating system interface definition (OSID) for the Space Station Program (SSP) in order to take advantage of the commercial off-the-shelf (COTS) products available today and the many that are expected in the future. NASA would also like to avoid the reliance on any one source for operating systems, information system, communication system, or instruction set architecture. The use of the Portable Operating System Interface for Computer Environments (POSIX) is examined as a possible solution to this problem. Since Ada is already the language of choice for SSP, the question of an Ada/POSIX binding is addressed. The intent of the binding is to provide access to the POSIX standard operation system (OS) interface and environment, by which application portability of Ada applications will be supported at the source code level. A guiding principle of Ada/POSIX binding development is a clear conformance of the Ada interface with the functional definition of POSIX. The interface is intended to be used by both application developers and system implementors. The objective is to provide a standard that allows a strictly conforming application source program that can be compiled to execute on any conforming implementation. Special emphasis is placed on first providing those functions and facilities that are needed in a wide variety of commercial applications

  11. ART-Ada design project, phase 2

    NASA Technical Reports Server (NTRS)

    Lee, S. Daniel; Allen, Bradley P.

    1990-01-01

    Interest in deploying expert systems in Ada has increased. An Ada based expert system tool is described called ART-Ada, which was built to support research into the language and methodological issues of expert systems in Ada. ART-Ada allows applications of an existing expert system tool called ART-IM (Automated Reasoning Tool for Information Management) to be deployed in various Ada environments. ART-IM, a C-based expert system tool, is used to generate Ada source code which is compiled and linked with an Ada based inference engine to produce an Ada executable image. ART-Ada is being used to implement several expert systems for NASA's Space Station Freedom Program and the U.S. Air Force.

  12. Pigmentation restored in mutant laboratory strain of the lady beetle Coleomegilla maculata through dietary supplementation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A laboratory colony of Coleomegilla maculata (DeGeer), ye, selected for a pigmentation deficiency, was restored to near wild type cuticle coloration by adding crushed heads and wings of the red colored parental strain to the diet. While the wings and other colored portions of the cuticle regained th...

  13. Multiprocessor performance modeling with ADAS

    NASA Technical Reports Server (NTRS)

    Hayes, Paul J.; Andrews, Asa M.

    1989-01-01

    A graph managing strategy referred to as the Algorithm to Architecture Mapping Model (ATAMM) appears useful for the time-optimized execution of application algorithm graphs in embedded multiprocessors and for the performance prediction of graph designs. This paper reports the modeling of ATAMM in the Architecture Design and Assessment System (ADAS) to make an independent verification of ATAMM's performance prediction capability and to provide a user framework for the evaluation of arbitrary algorithm graphs. Following an overview of ATAMM and its major functional rules are descriptions of the ADAS model of ATAMM, methods to enter an arbitrary graph into the model, and techniques to analyze the simulation results. The performance of a 7-node graph example is evaluated using the ADAS model and verifies the ATAMM concept by substantiating previously published performance results.

  14. AdaNET research plan

    NASA Technical Reports Server (NTRS)

    Mcbride, John G.

    1990-01-01

    The mission of the AdaNET research effort is to determine how to increase the availability of reusable Ada components and associated software engineering technology to both private and Federal sectors. The effort is structured to define the requirements for transfer of Federally developed software technology, study feasible approaches to meeting the requirements, and to gain experience in applying various technologies and practices. The overall approach to the development of the AdaNET System Specification is presented. A work breakdown structure is presented with each research activity described in detail. The deliverables for each work area are summarized. The overall organization and responsibilities for each research area are described. The schedule and necessary resources are presented for each research activity. The estimated cost is summarized for each activity. The project plan is fully described in the Super Project Expert data file contained on the floppy disk attached to the back cover of this plan.

  15. Modelling Hepatitis B Virus Antiviral Therapy and Drug Resistant Mutant Strains

    NASA Astrophysics Data System (ADS)

    Bernal, Julie; Dix, Trevor; Allison, Lloyd; Bartholomeusz, Angeline; Yuen, Lilly

    Despite the existence of vaccines, the Hepatitis B virus (HBV) is still a serious global health concern. HBV targets liver cells. It has an unusual replication process involving an RNA pre-genome that the reverse transcriptase domain of the viral polymerase protein translates into viral DNA. The reverse transcription process is error prone and together with the high replication rates of the virus, allows the virus to exist as a heterogeneous population of mutants, known as a quasispecies, that can adapt and become resistant to antiviral therapy. This study presents an individual-based model of HBV inside an artificial liver, and associated blood serum, undergoing antiviral therapy. This model aims to provide insights into the evolution of the HBV quasispecies and the individual contribution of HBV mutations in the outcome of therapy.

  16. Systematic mutagenesis method for enhanced production of bacitracin by Bacillus licheniformis Mutant Strain UV-MN-HN-6

    PubMed Central

    Aftab, Muhammad Nauman; Ikram-ul-Haq; Baig, Shahjahan

    2012-01-01

    The purpose of the current study was intended to obtain the enhanced production of bacitracin by Bacillus licheniformis through random mutagenesis and optimization of various parameters. Several isolates of Bacillus licheniformis were isolated from local habitat and isolate designated as GP-35 produced maximum bacitracin production (14±0.72 IU ml-1). Bacitracin production of Bacillus licheniformis GP-35 was increased to 23±0.69 IU ml-1 after treatment with ultraviolet (UV) radiations. Similarly, treatment of vegetative cells of GP-35 with chemicals like N-methyl N’-nitro N-nitroso guanidine (MNNG) and Nitrous acid (HNO2) increased the bacitracin production to a level of 31±1.35 IU ml-1 and 27±0.89 IU ml-1respectively. Treatment of isolate GP-35 with combined effect of UV and chemical treatment yield significantly higher titers of bacitracin with maximum bacitracin production of 41.6±0.92 IU ml-1. Production of bacitracin was further enhanced (59.1±1.35 IU ml-1) by optimization of different parameters like phosphate sources, organic acids as well as temperature and pH. An increase of 4.22 fold in the production of bacitracin after mutagenesis and optimization of various parameters was achieved in comparison to wild type. Mutant strain was highly stable and produced consistent yield of bacitracin even after 15 generations. On the basis of kinetic variables, notably Yp/s (IU/g substrate), Yp/x (IU/g cells), Yx/s(g/g), Yp/s, mutant strain B. licheniformis UV-MN-HN-6 was found to be a hyperproducer of bacitracin. PMID:24031806

  17. Ada style guide (version 1.1)

    NASA Technical Reports Server (NTRS)

    Seidewitz, Edwin V.; Agresti, William; Ferry, Daniel; Lavallee, David; Maresca, Paul; Nelson, Robert; Quimby, Kelvin; Rosenberg, Jacob; Roy, Daniel; Shell, Allyn

    1987-01-01

    Ada is a programming language of considerable expressive power. The Ada Language Reference Manual provides a thorough definition of the language. However, it does not offer sufficient guidance on the appropriate use of Ada's powerful features. For this reason, the Goddard Space Flight Center Ada User's Group has produced this style guide which addresses such program style issues. The guide covers three areas of Ada program style: the structural decomposition of a program; the coding and the use of specific Ada features; and the textural formatting of a program.

  18. Erythritol Metabolism in Wild-Type and Mutant Strains of Schizophyllum commune

    PubMed Central

    Braun, M. L.; Niederpruem, D. J.

    1969-01-01

    Erythritol uptake and metabolism were compared in wild-type mycelium and a dome morphological mutant of the wood-rotting mushroom Schizophyllum commune. Wild-type mycelium utilized glucose, certain hexitols, and pentitols including ribitol, as well as d-erythrose, erythritol, and glycerol as sole carbon sources for growth. The dome mutant utilized all of these compounds except d-erythrose and erythritol. Erythritol- or glycerol-grown wild-type mycelium incorporated erythritol into various cellular constituents, whereas glucose-grown cells lagged considerably before initiation of erythritol uptake. This acquisition was inhibited by cycloheximide. Dome mycelium showed behavior similar to wild-type in uptake of erythritol after growth on glucose or glycerol, except that erythritol was not further catabolized. Enzymes of carbohydrate metabolism were compared in cell extracts of glucose-cultured wild-type mycelium and dome. Enzymes of hexose monophosphate catabolism, nicotinamide adenine dinucleotide (NAD)-dependent sugar alcohol dehydrogenases, and reduced nicotinamide adenine dinucleotide phosphate (NADPH)-coupled erythrose reductase were demonstrated in both. The occurrence of erythrose reductase was unaffected by the nature of the growth carbon source, showed optimal activity at pH 7, and generated NAD phosphate and erythritol as products of the reaction. Glycerol-, d-erythrose-, or erythritol-grown wild-type mycelium contained an NAD-dependent erythritol dehydrogenase absent in glucose cells. Erythritol dehydrogenase activity was optimal at pH 8.8 and produced erythrulose during NAD reduction. Glycerol-growth of dome mycelium induced the erythritol uptake system, but a functional erythritol dehydrogenase could not be demonstrated. Neither wild-type nor dome mycelium produced erythritol dehydrogenase during growth on ribitol. Erythritol metabolism in wild-type cells of S. commune, therefore, involves an NADPH-dependent reduction of d-erythrose to produce erythritol

  19. Intracellular and Extracellular Cyclic Nucleotides in Wild-Type and White Collar Mutant Strains of Neurospora crassa

    PubMed Central

    Shaw, Nicholas M.; Harding, Roy W.

    1987-01-01

    Cyclic AMP and cyclic GMP were released into the growth medium of mycelia of Neurospora crassa wild-type strains St.L.74A and Em5297a and by white collar-1 and white collar-2 mutant strains. After growth for 6 days at 18°C, there were 2.19 (St.L.74A), 5.83 (Em5297a), 1.38 (white collar-1), and 1.10 (white collar-2) nanomoles of cyclic AMP per gram dry weight of mycelia in the growth medium. These values corresponded to concentrations of cyclic AMP of between approximately 10 and 50 nanomolar. The corresponding values for extracellular cyclic GMP were typically less than 6% of the values for cyclic AMP. Following transfer to fresh medium, cyclic AMP efflux was demonstrated for each of the strains, and the amount of cyclic AMP exported into the fresh medium was greater at 25°C than 6°C. Intracellular cyclic AMP and cyclic GMP were also measured in each of the strains. The values for cyclic AMP were in the same range as those in the literature (approximately 0.5 to 1.5 nanomoles per gram dry weight of mycelia). However, the corresponding intracellular cyclic GMP values were less than 1% of the cyclic AMP values, i.e. more than 50 times lower than the value previously reported for the St.L.74A wild-type. Transfer of mycelia after 6 days at 18°C to fresh media and incubation for 2 hours at 25°C or 6°C did not consistently affect the intracellular level of cyclic AMP or cyclic GMP in the strains examined. We could detect no change in intracellular cyclic AMP when mycelia of the St.L.74A wild-type strain were irradiated with blue light for periods of up to 3.0 hours at 18°C, or in cyclic AMP and cyclic GMP for irradiation times of up to 1 minute at 6°C. We propose that the plasma membrane of Neurospora crassa is permeable to cyclic nucleotides, and the export of cyclic nucleotides into the growth medium may be a means of regulating intracellular levels. We conclude that three factors that affect carotenogenesis in Neurospora crassa (blue light, temperature, and

  20. Safety, efficacy and efficiency of laser-assisted IVF in subfertile mutant mouse strains

    PubMed Central

    Li, Ming-Wen; Kinchen, Kristy L; Vallelunga, Jadine M; Young, Diana L; Wright, Kaleb D K; Gorano, Lisa N; Wasson, Katherine; Lloyd, K C Kent

    2013-01-01

    In the present report we studied the safety, efficacy and efficiency of using an infrared laser to facilitate IVF by assessing fertilization, development and birth rates after laser-zona drilling (LZD) in 30 subfertile genetically modified (GM) mouse lines. We determined that LZD increased the fertilization rate four to ten times that of regular IVF, thus facilitating the derivation of 26 of 30 (86.7%) GM mouse lines. Cryopreserved two-cell stage embryos derived by LZD-assisted IVF were recovered and developed to blastocysts in vitro at the same rate as frozen–thawed embryos derived by regular IVF. Surprisingly after surgical transfer to pseudopregnant recipients the birth rate of embryos derived by LZD-assisted IVF was significantly lower than that of embryos derived by regular IVF. However this result could be completely mitigated by the addition of 0.25 M sucrose to the culture medium during LZD which caused the oocyte to shrink in volume relative to the perivitelline space. By increasing the distance from the laser target site on the zona pellucida, we hypothesize that the hyperosmotic effect of sucrose reduced the potential for laser-induced cytotoxic thermal damage to the underlying oocytes. With appropriate preparation and cautious application, our results indicate that LZD-assisted IVF is a safe, efficacious and efficient assisted reproductive technology for deriving mutant mouse lines with male factor infertility and subfertility caused by sperm–zona penetration defects. PMID:23315689

  1. Software reuse issues affecting AdaNET

    NASA Technical Reports Server (NTRS)

    Mcbride, John G.

    1989-01-01

    The AdaNet program is reviewing its long-term goals and strategies. A significant concern is whether current AdaNet plans adequately address the major strategic issues of software reuse technology. The major reuse issues of providing AdaNet services that should be addressed as part of future AdaNet development are identified and reviewed. Before significant development proceeds, a plan should be developed to resolve the aforementioned issues. This plan should also specify a detailed approach to develop AdaNet. A three phased strategy is recommended. The first phase would consist of requirements analysis and produce an AdaNet system requirements specification. It would consider the requirements of AdaNet in terms of mission needs, commercial realities, and administrative policies affecting development, and the experience of AdaNet and other projects promoting the transfer software engineering technology. Specifically, requirements analysis would be performed to better understand the requirements for AdaNet functions. The second phase would provide a detailed design of the system. The AdaNet should be designed with emphasis on the use of existing technology readily available to the AdaNet program. A number of reuse products are available upon which AdaNet could be based. This would significantly reduce the risk and cost of providing an AdaNet system. Once a design was developed, implementation would proceed in the third phase.

  2. Renovating To Meet ADA Standards.

    ERIC Educational Resources Information Center

    Huber, Judy; Jones, Garry

    2003-01-01

    Using the examples of Owen D. Young School in Van Hornesville, New York, and the Tonawanda City school district in Buffalo, New York, describes how school planners should take the accessibility standards mandated by the Americans with Disabilities Act (ADA) into account when renovating. (EV)

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

    PubMed Central

    2014-01-01

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

  4. Constitutive synthesis of enzymes of the protocatechuate pathway and of the beta-ketoadipate uptake system in mutant strains of Pseudomonas putida.

    PubMed Central

    Parke, D; Ornston, L N

    1976-01-01

    Mutant Pseudomonas putida strains that produce constitutive levels of the beta-ketoadipate uptake system are selected by the sequential transfer of cultures between mineral growth media supplemented with the noninducing growth substrate succinate and growth media containing beta-ketoadipate as the sole carbon and energy source. The mutant strains also produce constitutively three catabolic enzymes that give rise to beta-ketoadipate from the metabolic precursor beta-carboxy-cis, cis-muconate, and thus a single regulatory gene appears to govern the expression of the enzymes as well as the uptake system. The three enzymes that convert beta-carboxy-cis, cis-muconate to beta-ketoadipate are induced to higher levels when the orgainisms are grown with p-hydroxybenzoate (a compound that is catabolized via beta-ketoadipate); the beta-ketoadipate uptake system is partially repressed when the cells are grwon at the expense of p-hydroxybenzoate. The transferase that acts upon beta-ketoadipate remains inducible in the constitutive mutant strains. Thus a minimum of three biosynthetic controls must be exerted over the expression of the five genes. Since the regulatory mutation does not alter the expression of the gene for the transferase, the physiological target of the selection procedure appears to be mutant strains that produce the uptake system constitutively. Levels of the uptake system are higher in uninduced constitutive mutant cultures than in induced cultures of the wild type. Hence procedures analogous to the one we employed may be of general use in obtaining mutant strains that produce high levels of uptake systems. PMID:1262305

  5. Microbial conversion of ginsenoside Rd from Rb1 by the fungus mutant Aspergillus niger strain TH-10a.

    PubMed

    Feng, Li; Xu, Chunchun; Li, Zhuo; Li, Jing; Dai, Yulin; Han, Hongxiang; Yu, Shanshan; Liu, Shuying

    2016-05-18

    Ginsenoside Rd, one of the ginsenosides with significant pharmaceutical activities, is getting more and more attractions on its biotransformation. In this study, a novel fungus mutant, the Aspergillus niger strain TH-10a, which can efficiently convert ginsenoside Rd from Rb1, was obtained through screening survival library of LiCl and ultraviolet (UV) irradiation. The transformation product ginsenoside Rd, generated by removing the outer glucose residue from the position C20 of ginsenoside Rb1, was identified through high-performance liquid chromatography (HPLC) analysis. Factors for the microbial culture and biotransformation were investigated in terms of the carbon sources, the nitrogen sources, pH values, and temperatures. This showed that maximum mycelia growth could be obtained at 28°C and pH 6.0 with cellobiose and tryptone as the carbon source and the nitrogen source, respectively. The highest transformation rate (∼86%) has been achieved at 32°C and pH 5.0 with the feeding time of substrate 48 hr. Also, Aspergillus niger strain TH-10a could tolerate even 40 mg/mL ginseng root extract as substrate with 60% bioconversion rate after 72 hr of treatment at the optimal condition. Our results highlight a novel ginsenoside Rd transformation fungus and illuminate its potentially practical application in the pharmaceutical industries. PMID:25831478

  6. Scierai ectasia associated with hereditary retinal dysplasia in a mutant strain of Japanese quail (Coturnix coturnix japonica).

    PubMed

    Shibuya, K; Nunoya, T; Tajima, M; Mizutani, M

    1997-01-01

    Ocular defects and age-related lesions in mutant (GUB strain) Japanese quail (Coturnix coturnix japonica), phenotypically characterised by silver plumage, are described. Grossly, a circular area of hypopigmentation in the posterior retina with thinning of the subjacent sciera was observed in all GUB quails. As the birds matured, the thinned sciera progressed to scierai ectasia. Histologically, the sciera at the ectatic area consisted of an outer fibrous layer and was devoid of the inner cartilaginous shell. Atypical differentiation and duplication of the retina with absence of the choroid was common at the ectatic area. The retina, choroid, ciliary body and iris were all poorly pigmented. With increasing age, the ectatic area became cystic, and the duplicated retina degenerated and atrophied. In addition, there were mononuclear cell infiltration in the stroma of the iris and ciliary body, anterior and posterior synechiae, cataract and/or glaucoma in aged GUB quails. These findings suggest that posterior scierai ectasia in the GUB strain of Japanese quails may have developed secondarily to a congenital structural defect of the posterior portion of sciera associating with general ocular defects. PMID:18483890

  7. Francisella tularensis type B ΔdsbA mutant protects against type A strain and induces strong inflammatory cytokine and Th1-like antibody response in vivo.

    PubMed

    Straskova, Adela; Spidlova, Petra; Mou, Sherry; Worsham, Patricia; Putzova, Daniela; Pavkova, Ivona; Stulik, Jiri

    2015-11-01

    Francisella tularensis subspecies tularensis is a highly virulent intracellular bacterial pathogen, causing the disease tularemia. However, a safe and effective vaccine for routine application against F. tularensis has not yet been developed. We have recently constructed the deletion mutants for the DsbA homolog protein (ΔdsbA/FSC200) and a hypothetical protein IglH (ΔiglH/FSC200) in the type B F. tularensis subsp. holarctica FSC200 strain, which exerted different protection capacity against parental virulent strain. In this study, we further investigated the immunological correlates for these different levels of protection provided by ΔdsbA/FSC200 and ΔiglH/FSC200 mutants. Our results show that ΔdsbA/FSC200 mutant, but not ΔiglH/FSC200 mutant, induces an early innate inflammatory response leading to strong Th1-like antibody response. Furthermore, vaccination with ΔdsbA/FSC200 mutant, but not with ΔiglH/FSC200, elicited protection against the subsequent challenge with type A SCHU S4 strain in mice. An immunoproteomic approach was used to map a spectrum of antigens targeted by Th1-like specific antibodies, and more than 80 bacterial antigens, including novel ones, were identified. Comparison of tularemic antigens recognized by the ΔdsbA/FSC200 post-vaccination and the SCHU S4 post-challenge sera then revealed the existence of 22 novel SCHU S4 specific antibody clones. PMID:26253078

  8. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development

    PubMed Central

    Mott, Tiffany M.; Vijayakumar, Sudhamathi; Sbrana, Elena; Endsley, Janice J.; Torres, Alfredo G.

    2015-01-01

    Background In this study, a Burkholderia mallei tonB mutant (TMM001) deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis. Methodology/Principal Findings Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 104 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001. Conclusions/Significance Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis. PMID:26114445

  9. Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus

    PubMed Central

    Gokce, Abdulmecit; Cakar, Zeynep Petek; Yucel, Meral; Ozcan, Orhan; Sencan, Sevde; Sertdemir, Ibrahim; Erguner, Bekir; Yuceturk, Betul; Sarac, Aydan; Yuksel, Bayram

    2016-01-01

    The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from Rhodobacter capsulatus DSM 1710, and with different hydrogen production levels, are reported here. These sequences may help understand the molecular basis of heat resistance and hydrogen production in R. capsulatus. PMID:27284151

  10. Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus.

    PubMed

    Gokce, Abdulmecit; Cakar, Zeynep Petek; Yucel, Meral; Ozcan, Orhan; Sencan, Sevde; Sertdemir, Ibrahim; Erguner, Bekir; Yuceturk, Betul; Sarac, Aydan; Yuksel, Bayram; Ozturk, Yavuz

    2016-01-01

    The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from Rhodobacter capsulatus DSM 1710, and with different hydrogen production levels, are reported here. These sequences may help understand the molecular basis of heat resistance and hydrogen production in R. capsulatus. PMID:27284151

  11. Ada--Programming Language of the Future.

    ERIC Educational Resources Information Center

    Rudd, David

    1983-01-01

    Ada is a programing language developed for the Department of Defense, with a registered trademark. It was named for Ada Augusta, coworker of Charles Babbage and the world's first programer. The Department of Defense hopes to prevent variations and to establish Ada as a consistent, standardized language. (MNS)

  12. Software unit testing in Ada environment

    NASA Technical Reports Server (NTRS)

    Warnock, Glenn

    1986-01-01

    A validation procedure for the Ada binding of the Graphical Kernel System (GKS) is being developed. PRIOR Data Sciences is also producing a version of the GKS written in Ada. These major software engineering projects will provide an opportunity to demonstrate a sound approach for software testing in an Ada environment. The GKS/Ada validation capability will be a collection of test programs and data, and test management guidelines. These products will be used to assess the correctness, completeness, and efficiency of any GKS/Ada implementation. The GKS/Ada developers will be able to obtain the validation software for their own use. It is anticipated that this validation software will eventually be taken over by an independent standards body to provide objective assessments of GKS/Ada implementations, using an approach similar to the validation testing currently applied to Ada compilers. In the meantime, if requested, this validation software will be used to assess GKS/Ada products. The second project, implementation of GKS using the Ada language, is a conventional software engineering tasks. It represents a large body of Ada code and has some interesting testing problems associated with automatic testing of graphics routines. Here the normal test practices which include automated regression testing, independent quality assistance, test configuration management, and the application of software quality metrics will be employed. The software testing methods emphasize quality enhancement and automated procedures. Ada makes some aspects of testing easier, and introduces some concerns. These issues are addressed.

  13. The Brucella abortus Phosphoglycerate Kinase Mutant Is Highly Attenuated and Induces Protection Superior to That of Vaccine Strain 19 in Immunocompromised and Immunocompetent Mice ▿

    PubMed Central

    Trant, Cyntia G. M. C.; Lacerda, Thais L. S.; Carvalho, Natalia B.; Azevedo, Vasco; Rosinha, Gracia M. S.; Salcedo, Suzana P.; Gorvel, Jean-Pierre; Oliveira, Sergio C.

    2010-01-01

    Brucella abortus is a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. The mechanism of virulence of Brucella spp. is not yet fully understood. Therefore, it is crucial to identify new molecules that can function as virulence factors to better understand the host-pathogen interplay. Herein, we identified the gene encoding the phosphoglycerate kinase (PGK) of B. abortus strain 2308. To test the role of PGK in Brucella pathogenesis, a pgk deletion mutant was constructed. Replacement of the wild-type pgk by recombination was demonstrated by Southern and Western blot analyses. The B. abortus Δpgk mutant strain exhibited extreme attenuation in bone marrow-derived macrophages and in vivo in BALB/c, C57BL/6, 129/Sv, and interferon regulatory factor-1 knockout (IRF-1 KO) mice. Additionally, at 24 h postinfection the Δpgk mutant was not found within the same endoplasmic reticulum-derived compartment as the wild-type bacteria, but, instead, over 60% of Brucella-containing vacuoles (BCVs) retained the late endosomal/lysosomal marker LAMP1. Furthermore, the B. abortus Δpgk deletion mutant was used as a live vaccine. Challenge experiments revealed that the Δpgk mutant strain induced protective immunity in 129/Sv or IRF-1 KO mice that was superior to the protection conferred by commercial strain 19 or RB51. Finally, the results shown here demonstrated that Brucella PGK is critical for full bacterial virulence and that a Δpgk mutant may serve as a potential vaccine candidate in future studies. PMID:20194591

  14. The Brucella abortus phosphoglycerate kinase mutant is highly attenuated and induces protection superior to that of vaccine strain 19 in immunocompromised and immunocompetent mice.

    PubMed

    Trant, Cyntia G M C; Lacerda, Thais L S; Carvalho, Natalia B; Azevedo, Vasco; Rosinha, Gracia M S; Salcedo, Suzana P; Gorvel, Jean-Pierre; Oliveira, Sergio C

    2010-05-01

    Brucella abortus is a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. The mechanism of virulence of Brucella spp. is not yet fully understood. Therefore, it is crucial to identify new molecules that can function as virulence factors to better understand the host-pathogen interplay. Herein, we identified the gene encoding the phosphoglycerate kinase (PGK) of B. abortus strain 2308. To test the role of PGK in Brucella pathogenesis, a pgk deletion mutant was constructed. Replacement of the wild-type pgk by recombination was demonstrated by Southern and Western blot analyses. The B. abortus Delta pgk mutant strain exhibited extreme attenuation in bone marrow-derived macrophages and in vivo in BALB/c, C57BL/6, 129/Sv, and interferon regulatory factor-1 knockout (IRF-1 KO) mice. Additionally, at 24 h postinfection the Delta pgk mutant was not found within the same endoplasmic reticulum-derived compartment as the wild-type bacteria, but, instead, over 60% of Brucella-containing vacuoles (BCVs) retained the late endosomal/lysosomal marker LAMP1. Furthermore, the B. abortus Delta pgk deletion mutant was used as a live vaccine. Challenge experiments revealed that the Delta pgk mutant strain induced protective immunity in 129/Sv or IRF-1 KO mice that was superior to the protection conferred by commercial strain 19 or RB51. Finally, the results shown here demonstrated that Brucella PGK is critical for full bacterial virulence and that a Delta pgk mutant may serve as a potential vaccine candidate in future studies. PMID:20194591

  15. Production of 1,3-PDO and butanol by a mutant strain of Clostridium pasteurianum with increased tolerance towards crude glycerol

    PubMed Central

    2012-01-01

    The production of biodiesel results in a concomitant production of crude glycerol (10% w/w). Clostridium pasteurianum can utilize glycerol as sole carbon source and converts it into 1,3-propanediol, ethanol, butanol, and CO2. Reduced growth and productivities on crude glycerol as compared to technical grade glycerol have previously been observed. In this study, we applied random mutagenesis mediated by ethane methyl sulfonate (EMS) to develop a mutant strain of C. pasteurianum tolerating high concentrations of crude glycerol. At an initial crude glycerol concentration of 25 g/l the amount of dry cell mass produced by the mutant strain was six times higher than the amount produced by the wild type. Growth of the mutant strain was even detected at an initial crude glycerol concentration of 105 g/l. A pH controlled reactor with in situ removal of butanol by gas-stripping was used to evaluate the performance of the mutant strain. Utilizing stored crude glycerol, the mutant strain showed significantly increased rates compared to the wild type. A maximum glycerol utilization rate of 7.59 g/l/h was observed along with productivities of 1.80 g/l/h and 1.21 g/l/h of butanol and 1,3-PDO, respectively. These rates are higher than what previously has been published for C. pasteurianum growing on technical grade glycerol in fed batch reactors. In addition, high yields of the main products (butanol and 1,3-PDO) were detected and these two products were efficiently separated in two steams using gas-stripping. PMID:22901717

  16. KRE5 Gene Null Mutant Strains of Candida albicans Are Avirulent and Have Altered Cell Wall Composition and Hypha Formation Properties

    PubMed Central

    Herrero, Ana B.; Magnelli, Paula; Mansour, Michael K.; Levitz, Stuart M.; Bussey, Howard; Abeijon, Claudia

    2004-01-01

    The UDP-glucose:glycoprotein glucosyltransferase (UGGT) is an endoplasmic reticulum sensor for quality control of glycoprotein folding. Saccharomyces cerevisiae is the only eukaryotic organism so far described lacking UGGT-mediated transient reglucosylation of N-linked oligosaccharides. The only gene in S. cerevisiae with similarity to those encoding UGGTs is KRE5. S. cerevisiae KRE5 deletion strains show severely reduced levels of cell wall β-1,6-glucan polymer, aberrant morphology, and extremely compromised growth or lethality, depending on the strain background. Deletion of both alleles of the Candida albicans KRE5 gene gives rise to viable cells that are larger than those of the wild type (WT), tend to aggregate, have enlarged vacuoles, and show major cell wall defects. C. albicans kre5/kre5 mutants have significantly reduced levels of β-1,6-glucan and more chitin and β-1,3-glucan and less mannoprotein than the WT. The remaining β-1,6-glucan, about 20% of WT levels, exhibits a β-1,6-endoglucanase digestion pattern, including a branch point-to-linear stretch ratio identical to that of WT strains, suggesting that Kre5p is not a β-1,6-glucan synthase. C. albicans KRE5 is a functional homologue of S. cerevisiae KRE5; it partially complements both the growth defect and reduced cell wall β-1,6-glucan content of S. cerevisiae kre5 viable mutants. C. albicans kre5/kre5 homozygous mutant strains are unable to form hyphae in several solid and liquid media, even in the presence of serum, a potent inducer of the dimorphic transition. Surprisingly the mutants do form hyphae in the presence of N-acetylglucosamine. Finally, C. albicans KRE5 homozygous mutant strains exhibit a 50% reduction in adhesion to human epithelial cells and are completely avirulent in a mouse model of systemic infection. PMID:15590817

  17. Ada and cyclic runtime scheduling

    NASA Technical Reports Server (NTRS)

    Hood, Philip E.

    1986-01-01

    An important issue that must be faced while introducing Ada into the real time world is efficient and prodictable runtime behavior. One of the most effective methods employed during the traditional design of a real time system is the cyclic executive. The role cyclic scheduling might play in an Ada application in terms of currently available implementations and in terms of implementations that might be developed especially to support real time system development is examined. The cyclic executive solves many of the problems faced by real time designers, resulting in a system for which it is relatively easy to achieve approporiate timing behavior. Unfortunately a cyclic executive carries with it a very high maintenance penalty over the lifetime of the software that is schedules. Additionally, these cyclic systems tend to be quite fragil when any aspect of the system changes. The findings are presented of an ongoing SofTech investigation into Ada methods for real time system development. The topics covered include a description of the costs involved in using cyclic schedulers, the sources of these costs, and measures for future systems to avoid these costs without giving up the runtime performance of a cyclic system.

  18. An Unusual Mutation Results in the Replacement of Diaminopimelate with Lanthionine in the Peptidoglycan of a Mutant Strain of Mycobacterium smegmatis†

    PubMed Central

    Consaul, Sandra A.; Wright, Lori F.; Mahapatra, Sebabrata; Crick, Dean C.; Pavelka, Martin S.

    2005-01-01

    Mycobacterial peptidoglycan contains l-alanyl-d-iso-glutaminyl-meso-diaminopimelyl-d-alanyl-d-alanine peptides, with the exception of the peptidoglycan of Mycobacterium leprae, in which glycine replaces the l-alanyl residue. The third-position amino acid of the peptides is where peptidoglycan cross-linking occurs, either between the meso-diaminopimelate (DAP) moiety of one peptide and the penultimate d-alanine of another peptide or between two DAP residues. We previously described a collection of spontaneous mutants of DAP-auxotrophic strains of Mycobacterium smegmatis that can grow in the absence of DAP. The mutants are grouped into seven classes, depending on how well they grow without DAP and whether they are sensitive to DAP, temperature, or detergent. Furthermore, the mutants are hypersusceptible to β-lactam antibiotics when grown in the absence of DAP, suggesting that these mutants assemble an abnormal peptidoglycan. In this study, we show that one of these mutants, M. smegmatis strain PM440, utilizes lanthionine, an unusual bacterial metabolite, in place of DAP. We also demonstrate that the abilities of PM440 to grow without DAP and use lanthionine for peptidoglycan biosynthesis result from an unusual mutation in the putative ribosome binding site of the cbs gene, encoding cystathionine β-synthase, an enzyme that is a part of the cysteine biosynthetic pathway. PMID:15716431

  19. Phenotype microarray analysis of a Salmonella enterica serovar Typhimurium qseC mutant compared to a qseBC mutant and the wild-type strain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Salmonella enterica serovar Typhimurium QseBC two-component system has previously been shown to regulate bacterial motility and colonization potential in the porcine gastrointestinal tract. A qseC mutant has decreased bacterial motility and decreased colonization in swine. However, in the absenc...

  20. Dataset of differentially regulated proteins in HUVECs challenged with wild type and UGM1 mutant Aspergillus fumigatus strains.

    PubMed

    Neves, Gabriela Westerlund Peixoto; Curty, Nathália; Kubitschek-Barreira, Paula Helena; Fontaine, Thierry; Souza, Gustavo Henrique Martins Ferreira; Cunha, Marcel Lyra; Goldman, Gustavo H; Beauvais, Anne; Latgé, Jean-Paul; Lopes-Bezerra, Leila M

    2016-12-01

    Invasive aspergillosis is the primary opportunistic invasive fungal infection described in neutropenic hematologic patients, caused by the angioinvasive pathogen Aspergillus fumigatus. The molecular mechanisms associated with A. fumigatus infection in the vascular endothelium are poorly understood. In this context, we used a high-throughput proteomic approach to unveil the proteins modulated in HUVECs after interaction with a wild type strain and the UGM1 mutant (Δugm1) of A. fumigatus. The proteomic analysis was also performed in HUVECs challenged with a galactosaminogalactan (GAG) purified from A. fumigatus cell wall. The dataset presented here correspond to all proteins identified that fit a 2-fold change criteria (log 2 ratio ≥ 1 or ≤ -1), disregarding the statistical validation cut off, in order to supplement the research article entitled "Modifications to the composition of the hyphal outer layer of Aspergillus fumigatus modulates the HUVEC proteins associated with inflammatory and stress responses" (G.W.P. Neves, N.A. Curty, P.H. Kubitschek-Barreira, T. Fontaine, G.H.M.F. Souza, M. Lyra Cunha, G.H. Goldman, A. Beauvais, J.P. Latgé, L.M. Lopes-Bezerra, 2016) [1]. The mass spectrometry proteomic data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002823. PMID:27622208

  1. Rapid, Sensitive, and Accurate Evaluation of Drug Resistant Mutant (NS5A-Y93H) Strain Frequency in Genotype 1b HCV by Invader Assay.

    PubMed

    Yoshimi, Satoshi; Ochi, Hidenori; Murakami, Eisuke; Uchida, Takuro; Kan, Hiromi; Akamatsu, Sakura; Hayes, C Nelson; Abe, Hiromi; Miki, Daiki; Hiraga, Nobuhiko; Imamura, Michio; Aikata, Hiroshi; Chayama, Kazuaki

    2015-01-01

    Daclatasvir and asunaprevir dual oral therapy is expected to achieve high sustained virological response (SVR) rates in patients with HCV genotype 1b infection. However, presence of the NS5A-Y93H substitution at baseline has been shown to be an independent predictor of treatment failure for this regimen. By using the Invader assay, we developed a system to rapidly and accurately detect the presence of mutant strains and evaluate the proportion of patients harboring a pre-treatment Y93H mutation. This assay system, consisting of nested PCR followed by Invader reaction with well-designed primers and probes, attained a high overall assay success rate of 98.9% among a total of 702 Japanese HCV genotype 1b patients. Even in serum samples with low HCV titers, more than half of the samples could be successfully assayed. Our assay system showed a better lower detection limit of Y93H proportion than using direct sequencing, and Y93H frequencies obtained by this method correlated well with those of deep-sequencing analysis (r = 0.85, P <0.001). The proportion of the patients with the mutant strain estimated by this assay was 23.6% (164/694). Interestingly, patients with the Y93H mutant strain showed significantly lower ALT levels (p=8.8 x 10-4), higher serum HCV RNA levels (p=4.3 x 10-7), and lower HCC risk (p=6.9 x 10-3) than those with the wild type strain. Because the method is both sensitive and rapid, the NS5A-Y93H mutant strain detection system established in this study may provide important pre-treatment information valuable not only for treatment decisions but also for prediction of disease progression in HCV genotype 1b patients. PMID:26083687

  2. QUEST/Ada (Query Utility Environment for Software Testing) of Ada: The development of a program analysis environment for Ada

    NASA Technical Reports Server (NTRS)

    Brown, David B.

    1988-01-01

    A history of the Query Utility Environment for Software Testing (QUEST)/Ada is presented. A fairly comprehensive literature review which is targeted toward issues of Ada testing is given. The definition of the system structure and the high level interfaces are then presented. The design of the three major components is described. The QUEST/Ada IORL System Specifications to this point in time are included in the Appendix. A paper is also included in the appendix which gives statistical evidence of the validity of the test case generation approach which is being integrated into QUEST/Ada.

  3. Auxin autonomy in cultured tobacco teratoma tissues transformed by an auxin-mutant strain of Agrobacterium tumefaciens.

    PubMed

    Campell, B R; Su, L Y; Pengelly, W L

    1992-08-01

    We have studied the mechanism of auxin autonomy in tobacco (Nicotiana tabacum L.) crowngall tissues transformed by the auxin-mutant (tms (-)) A66 strain of Agrobacterium tumefaciens. Normally, tms (-) tobacco tumor tissues require the formation of shoots to exhibit auxin-independent growth in culture. We have isolated from tms (-) tobacco cells several stable variants that are fully hormone-independent and grow rapidly as friable, unorganized tissues, thus mimicking the growth and morphology of tms (+) tobacco cells that produce high levels of auxin. However, none of the variants contained the high levels of auxin found in tms (+) tumor cells. The variants could be divided into two classes with respect to their response to applied auxin. The first class was highly sensitive to applied auxin: low concentrations (1 μM) of α-naphthaleneacetic acid (NAA) severely inhibited growth and markedly stimulated the accumulation of the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC). The second class of variants showed a low sensitivity to applied auxin: growth was promoted by concentrations of NAA up to 10 μM, and growth inhibition and high ACC levels were observed only at high NAA concentrations (100 μM). Unorganized variants with low auxin sensitivity were also isolated from a variant line with high auxin sensitivity. The isolation of tumor cells that exhibited the growth phenotype of tms (+) cells while retaining the low auxin content and low auxin sensitivity of tms (-) cells indicates that full hormone autonomy, characteristic of wild-type crown-gall tumors, can be achieved by a mechanism that is independent of changes in the auxin physiology of the cells. PMID:24178208

  4. Oligonucleotide-directed mutagenesis of psbB, the gene encoding CP47, employing a deletion mutant strain of the cyanobacterium Synechocystis sp. PCC 6803.

    PubMed

    Eaton-Rye, J J; Vermaas, W F

    1991-12-01

    A mutant strain of the cyanobacterium Synechocystis sp. PCC (Pasteur Culture Collection) 6803 has been developed in which psbB, the gene coding for the chlorophyl alpha-binding protein CP47 in Photosystem II (PSII), has been deleted. This deletion mutant can be used for the reintroduction of modified psbB into the cyanobacterium. To study the role of a large hydrophilic region in CP47, presumably located on the lumenal side of the thylakoid membrane between the fifth and sixth membrane-spanning regions, specific deletions have been introduced in psbB coding for regions within this domain. One psbB mutation leads to deletion of Gly-351 to Thr-365 in CP47, another psbB mutation was targeted towards deletion of Arg-384 to Val-392 in this protein. The deletion from Gly-351 to Thr-365 results in a loss of PSII activity and of photoautotrophic growth of the mutant, but the deletion between Arg-384 and Val-392 retains PSII activity and the ability to grow photoautotrophically. The mutant strain with the deletion from Gly-351 to Thr-365 does not assemble a stable PSII reaction center complex in its thylakoid membranes, and exhibits diminished levels of CP47 and of the reaction center proteins D1 and D2. In contrast to the Arg-384 to Val-392 portion of this domain, the region between Gly-351 and Thr-365 appears essential for the normal structure and function of photosystem II. PMID:1932693

  5. C Language Integrated Production System, Ada Version

    NASA Technical Reports Server (NTRS)

    Culbert, Chris; Riley, Gary; Savely, Robert T.; Melebeck, Clovis J.; White, Wesley A.; Mcgregor, Terry L.; Ferguson, Melisa; Razavipour, Reza

    1992-01-01

    CLIPS/Ada provides capabilities of CLIPS v4.3 but uses Ada as source language for CLIPS executable code. Implements forward-chaining rule-based language. Program contains inference engine and language syntax providing framework for construction of expert-system program. Also includes features for debugging application program. Based on Rete algorithm which provides efficient method for performing repeated matching of patterns. Written in Ada.

  6. Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation

    PubMed Central

    Kumar, Ritesh; Mukhopadhyay, Asish K.; Ghosh, Prachetash; Rao, Desirazu N.

    2012-01-01

    Helicobacter pylori is an important human pathogen and one of the most successful chronic colonizers of the human body. H. pylori uses diverse mechanisms to modulate its interaction with the host in order to promote chronic infection and overcome host immune response. Restriction-modification genes are a major part of strain-specific genes present in H. pylori. The role of N6 - adenine methylation in bacterial gene regulation and virulence is well established but not much is known about the effect of C5 -cytosine methylation on gene expression in prokaryotes. In this study, it was observed by microarray analysis and RT-PCR, that deletion of an orphan C5 -cytosine methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a significant effect on the expression of number of genes belonging to motility, adhesion and virulence. AM5ΔhpyAVIBM mutant strain has a different LPS profile and is able to induce high IL-8 production compared to wild-type. hpyAVIBM from strain 26695 is able to complement mutant SS1 and AM5 strains. This study highlights a possible significance of cytosine methylation in the physiology of H. pylori. PMID:22879937

  7. Production of fumaric acid by simultaneous saccharification and fermentation of starchy materials with 2-deoxyglucose-resistant mutant strains of Rhizopus oryzae.

    PubMed

    Deng, Yuefang; Li, Shuang; Xu, Qing; Gao, Min; Huang, He

    2012-03-01

    A mutant strain with high glucoamylase activity and insensitive to catabolite repression was developed to produce fumaric acid by simultaneous saccharification and fermentation (SSF) of starch without additional commercial glucoamylase supplementation. A series of mutant strains resistant to the non-metabolizable and toxic glucose analog 2-deoxyglucose (2-DG) were obtained by implanting nitrogen ion (N(+)) into Rhizopus oryzae ME-F12. Among them, the best mutant strain DG-3 produced 39.80 g/L fumaric acid, which is 1.28-fold of that produced by ME-F12, and exhibited higher glucoamylase activity during SSF. Higher fumaric acid production (44.10 g/L) was achieved when the initial total sugar concentration of cornstarch was 100g/L. During SSF of cheap, raw bioresource-degermed corn powder (100g/L total sugar) by DG-3, the maximum fumaric acid concentration and productivity were 32.18 g/L and 0.44 g/(Lh), respectively. PMID:22217732

  8. ART/Ada design project, phase 1

    NASA Technical Reports Server (NTRS)

    1989-01-01

    An Ada-Based Expert System Building Tool Design Research Project was conducted. The goal was to investigate various issues in the context of the design of an Ada-based expert system building tool. An attempt was made to achieve a comprehensive understanding of the potential for embedding expert systems in Ada systems for eventual application in future projects. The current status of the project is described by introducing an operational prototype, ART/Ada. How the project was conducted is explained. The performance of the prototype is analyzed and compared with other related works. Future research directions are suggested.

  9. Ada training evaluation and recommendations from the Gamma Ray Observatory Ada Development Team

    NASA Technical Reports Server (NTRS)

    1985-01-01

    The Ada training experiences of the Gamma Ray Observatory Ada development team are related, and recommendations are made concerning future Ada training for software developers. Training methods are evaluated, deficiencies in the training program are noted, and a recommended approach, including course outline, time allocation, and reference materials, is offered.

  10. Proceedings of the 2nd NASA Ada User's Symposium

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Several presentations, mostly in viewgraph form, on various topics relating to Ada applications are given. Topics covered include the use of Ada in NASA, Ada and the Space Station, the software support environment, Ada in the Software Engineering Laboratory, Ada at the Jet Propulsion Laboratory, the Flight Telerobotic Servicer, and lessons learned in prototyping the Space Station Remote Manipulator System control.

  11. UDP-N-Acetylmuramic Acid l-Alanine Ligase (MurC) Inhibition in a tolC Mutant Escherichia coli Strain Leads to Cell Death

    PubMed Central

    Humnabadkar, Vaishali; Prabhakar, K. R.; Narayan, Ashwini; Sharma, Sreevalli; Guptha, Supreeth; Manjrekar, Praveena; Chinnapattu, Murugan; Ramachandran, Vasanthi; Hameed, Shahul P.; Ravishankar, Sudha

    2014-01-01

    The Mur ligases play an essential role in the biosynthesis of bacterial peptidoglycan and hence are attractive antibacterial targets. A screen of the AstraZeneca compound library led to the identification of compound A, a pyrazolopyrimidine, as a potent inhibitor of Escherichia coli and Pseudomonas aeruginosa MurC. However, cellular activity against E. coli or P. aeruginosa was not observed. Compound A was active against efflux pump mutants of both strains. Experiments using an E. coli tolC mutant revealed accumulation of the MurC substrate and a decrease in the level of product upon treatment with compound A, indicating inhibition of MurC enzyme in these cells. Such a modulation was not observed in the E. coli wild-type cells. Further, overexpression of MurC in the E. coli tolC mutant led to an increase in the compound A MIC by ≥16-fold, establishing a correlation between MurC inhibition and cellular activity. In addition, estimation of the intracellular compound A level showed an accumulation of the compound over time in the tolC mutant strain. A significant compound A level was not detected in the wild-type E. coli strain even upon treatment with high concentrations of the compound. Therefore, the lack of MIC and absence of MurC inhibition in wild-type E. coli were possibly due to suboptimal compound concentration as a consequence of a high efflux level and/or poor permeativity of compound A. PMID:25114134

  12. Systematic strain construction and process development: Xylitol production by Saccharomyces cerevisiae expressing Candida tenuis xylose reductase in wild-type or mutant form.

    PubMed

    Pratter, S M; Eixelsberger, T; Nidetzky, B

    2015-12-01

    A novel Saccharomyces cerevisiae whole-cell biocatalyst for xylitol production based on Candida tenuis xylose reductase (CtXR) is presented. Six recombinant strains expressing wild-type CtXR or an NADH-specific mutant were constructed and evaluated regarding effects of expression mode, promoter strength, biocatalyst concentration and medium composition. Intracellular XR activities ranged from 0.09 U mgProt(-1) to 1.05 U mgProt(-1) but did not correlate with the strains' xylitol productivities, indicating that other factors limited xylose conversion in the high-activity strains. The CtXR mutant decreased the biocatalyst's performance, suggesting use of the NADPH-preferring wild-type enzyme when (semi-)aerobic conditions are applied. In a bioreactor process, the best-performing strain converted 40 g L(-1) xylose with an initial productivity of 1.16 g L(-1)h(-1) and a xylitol yield of 100%. The obtained results underline the potential of CtXR wild-type for xylose reduction and point out parameters to improve "green" xylitol production. PMID:26452180

  13. [The accumulation of proteins with chitinase activity in the culture media of the parent and mutant Serratia marcescens strain grown in the presence of mitomycin C].

    PubMed

    Iusupova, D V; Petukhova, E V; Sokolova, R B; Gabdrakhmanova, L A

    2002-01-01

    The study of the accumulation pattern of extracellular proteins with chitinase activity in the parent Serratia marcescens strain Bú 211 (ATCC 9986) grown in the presence of mitomycin C and its mutant strain with the constitutive synthesis of chitinases grown in the absence of the inducer showed that chitinase activity appeared in the culture liquids of both strains at the end of the exponential phase (4 h of growth) and reached a maximum in the stationary phase (18-20 h of growth). The analysis of the culture liquids (12 h of growth) by denaturing electrophoresis in PAAG followed by the protein renaturation step revealed the presence of four extracellular proteins with chitinase activity and molecular masses of 21, 38, 52, and 58 kDa. PMID:12449629

  14. A small evaluation suite for Ada compilers

    NASA Technical Reports Server (NTRS)

    Wilke, Randy; Roy, Daniel M.

    1986-01-01

    After completing a small Ada pilot project (OCC simulator) for the Multi Satellite Operations Control Center (MSOCC) at Goddard last year, the use of Ada to develop OCCs was recommended. To help MSOCC transition toward Ada, a suite of about 100 evaluation programs was developed which can be used to assess Ada compilers. These programs compare the overall quality of the compilation system, compare the relative efficiencies of the compilers and the environments in which they work, and compare the size and execution speed of generated machine code. Another goal of the benchmark software was to provide MSOCC system developers with rough timing estimates for the purpose of predicting performance of future systems written in Ada.

  15. Oxidation of d-Malic and β-Alkylmalic Acids by Wild-Type and Mutant Strains of Salmonella typhimurium and by Aerobacter aerogenes

    PubMed Central

    Stern, Joseph R.; O'Brien, R. W.

    1969-01-01

    A mutant strain of Salmonella typhimurium (SL 1634 dml-51) capable of growth on d-malate as sole carbon source was shown to produce d-malic enzyme. This enzyme was absent in the parent wild-type strain which was unable to grow on d-malate. Growth of the mutant on d-malate also resulted in a greatly increased level of β-isopropylmalic enzyme compared with its level in the wild-type strain grown on citrate or l-malate. The d-malic and β-isopropylmalic enzymes, both of which catalyze a nicotinamide adenine dinucleotide- and Mg++-dependent oxidative decarboxylation of their respective substrates, were shown to be distinct enzymes by selective inhibition with erythro-dl-β-hydroxyaspartate and by other methods. Cell extracts of the mutant strain also oxidized dl-β-methyl-, dl-β-ethyl-, dl-β-propyl- and dl-ββ-dimethylmalates, in order of decreasing activity. dl-β-Methyl-malate was shown to be oxidized by both the d-malic and the β-isopropylmalic enzymes, whereas the oxidation of the other β-alkylmalates appeared to be effected exclusively by the β-isopropylmalic enzyme. β-Isopropylmalic enzyme activity was induced by d-malate but not by l-malate, showing that it behaved as a d-malictype enzyme. Growth of Aerobacter aerogenes on d-malate, which caused induction of d malic enzyme, resulted in only a small increase in the activity of β-isopropylmalic enzyme. PMID:4889267

  16. Comparison of wild-type and UV-mutant beta-glucanase-producing strains of Talaromyces emersonii with potential in brewing applications.

    PubMed

    McCarthy, Tracey C; Lalor, Eoin; Hanniffy, Orla; Savage, Angela V; Tuohy, Maria G

    2005-04-01

    A screen of 46 UV-mutant strains of the moderately thermophilic fungus Talaromyces emersonii yielded two mutants (TC2, TC5) that displayed gross morphological differences to the parent strain and enhanced activity against mixed linkage cereal beta-glucans. Activity against beta-(1, 3)(1, 4)-D: -glucan from barley (BBGase) was measured during growth of the mutant and wild-type strains on a variety of carbon sources, ranging from solka floc to crude cereal fractions. In liquid culture, TC2 and TC5 secreted 1.2- to 8.6-fold more BBGase than the parent strain and markedly less beta-glucosidase (exo-activity); enzyme levels were dependent on the carbon source. Cellulose induced high BBGase. However, beet pulp, wheat bran, carob and tea-leaves were cheap and effective inducers. T. emersonii wild-type, TC2 and TC5 crude enzyme preparations achieved similar end-points during the hydrolysis of commercial barley beta-glucan (13.0-16.9%), but were more active against crude beta-glucan from barley (16.0-24.2% hydrolysis). The products of hydrolysis were quantified by high-performance anion-exchange chromatography. Mash trials indicated that enzyme preparations from all three organisms effected a significant reduction in wort viscosity and residual mash beta-glucan. Finally, TC2 and TC5 produce more efficient beta-glucan-depolymerizing enzymes; and wheat bran and solka floc can be used to provide inexpensive and potent enzyme cocktails with potential in brewing applications. PMID:15856354

  17. Construction of upp deletion mutant strains of Lactobacillus casei and Lactococcus lactis based on counterselective system using temperature-sensitive plasmid.

    PubMed

    Song, Li; Cui, Hongyu; Tang, Lijie; Qiao, Xinyuan; Liu, Min; Jiang, Yanping; Cui, Wen; Li, Yijing

    2014-07-01

    Integration plasmids are often used in constructing chromosomal mutations, as it enables the alternation of genes at any location by integration or replacement. Food-grade integration vectors can integrate into the host genome without introducing any selectable markers or residual bases, and the recombination often happens in non-coding region. In this study we used the temperature-sensitive pWV01 replicon to construct 2 chloramphenicol-resistant integration plasmids (pGBHC32-upp) containing the uracil phosphoribosyl transferase (upp) gene as a counterselective marker for Lactobacillus casei (L. casei) ATCC393 and Lactococcus lactis (L. lactis) MG1363. We then ligated the designed homologous arms to the pGBHC32-upp plasmids to allow their integration to the bacterial chromosome, and selected upp deletion mutants of L. casei ATCC393 and L. lactis MG1363 in the presence of 5-fluorouracil (5-FU). Analysis of genetic stability, growth curve, carbon utilization and scanning electronic microscopy showed that, except for 5-FU resistance, there were no significant differences between the wild type and mutant lactic acid bacteria. The integration system and the upp deletion strains could be used in the insertion or deletion of genes at any location of the chromosome of both L. casei ATCC 393 and L. lactis MG1363, and the homologous recombination would not introduce any selectable markers or residual bases. These mutant strains can be further investigated for heterologous protein expression and construction of a live mucosal vaccine carrier. PMID:24798148

  18. The development of a program analysis environment for Ada: Reverse engineering tools for Ada

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1991-01-01

    The Graphical Representations of Algorithms, Structures, and Processes for Ada (GRASP/Ada) has successfully created and prototyped a new algorithm level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and thus improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under the Virtual Memory System (VMS) on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. In Phase 3 of the project, the prototype was prepared for limited distribution (GRASP/Ada Version 3.0) to facilitate evaluation. The user interface was extensively reworked. The current prototype provides the capability for the user to generate CSD from Ada source code in a reverse engineering mode with a level of flexibility suitable for practical application.

  19. Correlation between biofilm production, antibiotic susceptibility and exopolysaccharide composition in Burkholderia pseudomallei bpsI, ppk, and rpoS mutant strains.

    PubMed

    Mongkolrob, Rungrawee; Taweechaisupapong, Suwimol; Tungpradabkul, Sumalee

    2015-11-01

    Burkholderia pseudomallei is the cause of melioidosis, a fatal tropical infectious disease, which has been reported to have a high rate of recurrence, even when an intensive dose of antibiotics is used. Biofilm formation is believed to be one of the possible causes of relapse because of its ability to increase drug resistance. EPS in biofilms have been reported to be related to the limitation of antibiotic penetration in B. pseudomallei. However, the mechanisms by which biofilms restrict the diffusion of antibiotics remain unclear. The present study presents a correlation between exopolysaccharide production in biofilm matrix and antibiotic resistance in B. pseudomallei using bpsI, ppk, and rpoS mutant strains. CLSM revealed a reduction in exopolysaccharide production and disabled micro-colony formation in B. pseudomallei mutants, which paralleled the antibiotic resistance. Different ratios of carbohydrate contents in the exopolysaccharides of the mutants were detected, although they have the same components, including glucose, galactose, mannose, and rhamnose, with the exception being that no detectable rhamnose peak was observed in the bpsI mutant. These results indicate that the correlation between these phenomena in the B. pseudomallei biofilm at least results from the exopolysaccharide, which may be under the regulation of bpsI, ppk, or rpoS genes. PMID:26486518

  20. Growth on D-lyxose of a mutant strain of Escherichia coli K12 using a novel isomerase and enzymes related to D-xylase metabolism.

    PubMed

    Stevens, F J; Wu, T T

    1976-12-01

    Escherichia coli K12 cannot grow on D-lyxose, but a mutant was isolated which can utilize D-lyxose as sole source of carbon and energy for growth. D-Lyxose is transported into the bacteria by the D-xylose permease. The mutant constitutively synthesizes a new isomerase which is not inducible in the parent strain under any of the conditions tested. This enzyme, whose native substrate appears to be D-mannose, fortuitously converts D-lyxose into D-xylulose. Its structural gene is located at around 85 min on the E. coli genetic map, away from other known isomerase genes. D-Xylulose is subsequently catabolized by the enzymes of the normal D-xylose metabolic pathway. D-Mannose isomerase was partially purified and some of its properties were examined. PMID:796410

  1. Genetic analysis of developmental mechanisms in hydra. XVI. Effect of food on budding and developmental gradients in a mutant strain L4.

    PubMed

    Takano, J; Sugiyama, T

    1985-12-01

    Effect of food was examined on the budding rate and the developmental gradients of a mutant hydra strain L4. This mutant strain has very high levels of head-inhibition potential gradient along its body axis (Takano & Sugiyama, 1983). It also has a reduced budding capacity when it is cultured using brine shrimp nauplii as food, but its budding capacity is significantly improved when a small amount of tubifex worm tissue is added to its diet of brine shrimp (Takano, 1984). To test whether or not this change of budding rate is correlated with the change in the levels of the head-activation or head-inhibition potential gradients, L4 animals were cultured on the diet of brine shrimp with or without addition of tubifex worm tissue and the budding rates and the gradient levels were examined in these animals. The results showed that food affected the budding rate in L4 without affecting its gradient levels. This suggests that the gradient levels and the budding rate in L4 are are uncorrelated to each other, and that therefore the high levels of head-inhibition potential are not the cause for the low budding rate in this strain (cf., Takano & Sugiyama, 1983). PMID:3834025

  2. Sulphide Resistance in the Cyanobacterium Microcystis aeruginosa: a Comparative Study of Morphology and Photosynthetic Performance Between the Sulphide-Resistant Mutant and the Wild-Type Strain.

    PubMed

    Bañares-España, Elena; del Mar Fernández-Arjona, María; García-Sánchez, María Jesús; Hernández-López, Miguel; Reul, Andreas; Mariné, Mariona Hernández; Flores-Moya, Antonio

    2016-05-01

    The cyanobacterium Microcystis aeruginosa is a mesophilic freshwater organism, which cannot tolerate sulphide. However, it was possible to isolate a sulphide-resistant (S(r)) mutant strain that was able to survive in a normally lethal medium sulphide. In order to evaluate the cost of the mutation conferring sulphide resistance in the S(r) strain of M. aeruginosa, the morphology and the photosynthetic performance were compared to that found in the wild-type, sulphide-sensitive (S(s)) strain. An increase in size and a disrupted morphology was observed in S(r) cells in comparison to the S(s) counterpart. Phycoerythrin and phycocyanin levels were higher in the S(r) than in the S(s) cells, whereas a higher carotenoid content, per unit volume, was found in the S(s) strain. The irradiance-saturated photosynthetic oxygen-production rate (GPR max) and the photosynthetic efficiency (measured both by oxygen production and fluorescence, α(GPR) and α(ETR)) were lower in the S(r) strain than in the wild-type. These results appear to be the result of package effect. On the other hand, the S(r) strain showed higher quantum yield of non-photochemical quenching, especially those regulated mechanisms (estimated throughout qN and Y(NPQ)) and a significantly lower slope in the maximum quantum yield of light-adapted samples (Fv'/Fm') compared to the S(s) strain. These findings point to a change in the regulation of the quenching of the transition states (qT) in the S(r) strain which may be generated by a change in the distribution of thylakoidal membranes, which somehow could protect metalloenzymes of the electron transport chain from the lethal effect of sulphide. PMID:26677166

  3. Biological characteristics of the rtA181T/sW172* mutant strain of Hepatitis B virus in animal model

    PubMed Central

    2012-01-01

    Background The effects of Hepatitis B virus (HBV) rtA181T/sW172* mutation on viral replication and pathogenicity was concerned recently. This study aimed to investigate the biological characteristics of rtA181T/sW172* mutant strain of HBV in animal model. Methods The rtA181T/sW172* mutant plasmid was constructed using the pHBV4.1 (wild type HBV) as a template. The wild and mutant HBV replication mouse models were established utilizing a hydrodynamic technique. The titers of hepatitis B surface antigen (HBsAg), hepatitis B e antigen, and HBV DNA in serum, and the levels of HBsAg, hepatitis B core antigen(HBcAg), HBV DNA replication intermediates (HBV DNA RI) and HBV RNA in liver were measured after 1, 3, 5, 7, 10, 12 and 15 days of plasmid injection. Results In wild-type HBV replication mouse model, serum HBsAg was high on day 1, 3, and 5, but became lower since day 7; while in mutant HBV mouse model, serum HBsAg was always at very low level. In liver tissues, HBV DNA RI of wild type HBV was detected on day 1 after transfection. The level subsequently peaked on day 3, gradually declined after day 5, and was almost undetectable on day 10. However, the HBV DNA RI levels of the mutant strain were always higher and lasted longer until day 15. Consistently, the expression levels of HBsAg and HBcAg in liver of the mutant group were significantly increased. Conclusions In the case of the HBV rtA181T/sW172* mutation, the secretion of serum HBsAg was impaired, whereas HBV DNA replication and HBsAg/HBcAg expression were increased in liver. These results suggest that the mutation can impair HBsAg secretion, and may cause the accumulation of viral core particles in liver. PMID:23171829

  4. NAD(P)+-Malic Enzyme Mutants of Sinorhizobium sp. Strain NGR234, but Not Azorhizobium caulinodans ORS571, Maintain Symbiotic N2 Fixation Capabilities

    PubMed Central

    Zhang, Ye; Aono, Toshihiro; Poole, Phillip

    2012-01-01

    C4-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (TCA) cycle in N2-fixing bacteria (bacteroids) within legume nodules. In Sinorhizobium meliloti bacteroids from alfalfa, NAD+-malic enzyme (DME) is required for N2 fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. In contrast, in the pea symbiont Rhizobium leguminosarum, pyruvate synthesis occurs via either DME or a pathway catalyzed by phosphoenolpyruvate carboxykinase (PCK) and pyruvate kinase (PYK). Here we report that dme mutants of the broad-host-range Sinorhizobium sp. strain NGR234 formed nodules whose level of N2 fixation varied from 27 to 83% (plant dry weight) of the wild-type level, depending on the host plant inoculated. NGR234 bacteroids had significant PCK activity, and while single pckA and single dme mutants fixed N2 at reduced rates, a pckA dme double mutant had no N2-fixing activity (Fix−). Thus, NGR234 bacteroids appear to synthesize pyruvate from TCA cycle intermediates via DME or PCK pathways. These NGR234 data, together with other reports, suggested that the completely Fix− phenotype of S. meliloti dme mutants may be specific to the alfalfa-S. meliloti symbiosis. We therefore examined the ME-like genes azc3656 and azc0119 from Azorhizobium caulinodans, as azc3656 mutants were previously shown to form Fix− nodules on the tropical legume Sesbania rostrata. We found that purified AZC3656 protein is an NAD(P)+-malic enzyme whose activity is inhibited by acetyl-coenzyme A (acetyl-CoA) and stimulated by succinate and fumarate. Thus, whereas DME is required for symbiotic N2 fixation in A. caulinodans and S. meliloti, in other rhizobia this activity can be bypassed via another pathway(s). PMID:22307295

  5. Development of an Ada programming support environment database SEAD (Software Engineering and Ada Database) administration manual

    NASA Technical Reports Server (NTRS)

    Liaw, Morris; Evesson, Donna

    1988-01-01

    Software Engineering and Ada Database (SEAD) was developed to provide an information resource to NASA and NASA contractors with respect to Ada-based resources and activities which are available or underway either in NASA or elsewhere in the worldwide Ada community. The sharing of such information will reduce duplication of effort while improving quality in the development of future software systems. SEAD data is organized into five major areas: information regarding education and training resources which are relevant to the life cycle of Ada-based software engineering projects such as those in the Space Station program; research publications relevant to NASA projects such as the Space Station Program and conferences relating to Ada technology; the latest progress reports on Ada projects completed or in progress both within NASA and throughout the free world; Ada compilers and other commercial products that support Ada software development; and reusable Ada components generated both within NASA and from elsewhere in the free world. This classified listing of reusable components shall include descriptions of tools, libraries, and other components of interest to NASA. Sources for the data include technical newletters and periodicals, conference proceedings, the Ada Information Clearinghouse, product vendors, and project sponsors and contractors.

  6. Development of an Ada package library

    NASA Technical Reports Server (NTRS)

    Burton, Bruce; Broido, Michael

    1986-01-01

    A usable prototype Ada package library was developed and is currently being evaluated for use in large software development efforts. The library system is comprised of an Ada-oriented design language used to facilitate the collection of reuse information, a relational data base to store reuse information, a set of reusable Ada components and tools, and a set of guidelines governing the system's use. The prototyping exercise is discussed and the lessons learned from it have led to the definition of a comprehensive tool set to facilitate software reuse.

  7. A distributed programming environment for Ada

    NASA Technical Reports Server (NTRS)

    Brennan, Peter; Mcdonnell, Tom; Mcfarland, Gregory; Timmins, Lawrence J.; Litke, John D.

    1986-01-01

    Despite considerable commercial exploitation of fault tolerance systems, significant and difficult research problems remain in such areas as fault detection and correction. A research project is described which constructs a distributed computing test bed for loosely coupled computers. The project is constructing a tool kit to support research into distributed control algorithms, including a distributed Ada compiler, distributed debugger, test harnesses, and environment monitors. The Ada compiler is being written in Ada and will implement distributed computing at the subsystem level. The design goal is to provide a variety of control mechanics for distributed programming while retaining total transparency at the code level.

  8. Experiences with Ada in an embedded system

    NASA Technical Reports Server (NTRS)

    Labaugh, Robert J.

    1988-01-01

    Recent experiences with using Ada in a real time environment are described. The application was the control system for an experimental robotic arm. The objectives of the effort were to experiment with developing embedded applications in Ada, evaluating the suitability of the language for the application, and determining the performance of the system. Additional objectives were to develop a control system based on the NASA/NBS Standard Reference Model for Telerobot Control System Architecture (NASREM) in Ada, and to experiment with the control laws and how to incorporate them into the NASREM architecture.

  9. Software engineering and Ada in design

    NASA Technical Reports Server (NTRS)

    Oneill, Don

    1986-01-01

    Modern software engineering promises significant reductions in software costs and improvements in software quality. The Ada language is the focus for these software methodology and tool improvements. The IBM FSD approach, including the software engineering practices that guide the systematic design and development of software products and the management of the software process are examined. The revised Ada design language adaptation is revealed. This four level design methodology is detailed including the purpose of each level, the management strategy that integrates the software design activity with the program milestones, and the technical strategy that maps the Ada constructs to each level of design. A complete description of each design level is provided along with specific design language recording guidelines for each level. Finally, some testimony is offered on education, tools, architecture, and metrics resulting from project use of the four level Ada design language adaptation.

  10. Lessons learned from an Ada conversion project

    NASA Technical Reports Server (NTRS)

    Porter, Tim

    1988-01-01

    Background; SAVVAS architecture; software portability; history of Ada; isolation of non-portable code; simple terminal interface package; constraints of language features; and virtual interfaces are outlined. This presentation is represented by viewgraphs only.

  11. Cross-Resistance between Triclosan and Antibiotics in Pseudomonas aeruginosa Is Mediated by Multidrug Efflux Pumps: Exposure of a Susceptible Mutant Strain to Triclosan Selects nfxB Mutants Overexpressing MexCD-OprJ

    PubMed Central

    Chuanchuen, Rungtip; Beinlich, Kerry; Hoang, Tung T.; Becher, Anna; Karkhoff-Schweizer, RoxAnn R.; Schweizer, Herbert P.

    2001-01-01

    Triclosan is an antiseptic frequently added to items as diverse as soaps, lotions, toothpaste, and many commonly used household fabrics and plastics. Although wild-type Pseudomonas aeruginosa expresses the triclosan target enoyl-acyl carrier protein reductase, it is triclosan resistant due to expression of the MexAB-OprM efflux system. Exposure of a susceptible Δ(mexAB-oprM) strain to triclosan selected multidrug-resistant bacteria at high frequencies. These bacteria hyperexpressed the MexCD-OprJ efflux system due to mutations in its regulatory gene, nfxB. The MICs of several drugs for these mutants were increased up to 500-fold, including the MIC of ciprofloxacin, which was increased 94-fold. Whereas the MexEF-OprN efflux system also participated in triclosan efflux, this antimicrobial was not a substrate for MexXY-OprM. PMID:11158736

  12. Cross-resistance between triclosan and antibiotics in Pseudomonas aeruginosa is mediated by multidrug efflux pumps: exposure of a susceptible mutant strain to triclosan selects nfxB mutants overexpressing MexCD-OprJ.

    PubMed

    Chuanchuen, R; Beinlich, K; Hoang, T T; Becher, A; Karkhoff-Schweizer, R R; Schweizer, H P

    2001-02-01

    Triclosan is an antiseptic frequently added to items as diverse as soaps, lotions, toothpaste, and many commonly used household fabrics and plastics. Although wild-type Pseudomonas aeruginosa expresses the triclosan target enoyl-acyl carrier protein reductase, it is triclosan resistant due to expression of the MexAB-OprM efflux system. Exposure of a susceptible Delta(mexAB-oprM) strain to triclosan selected multidrug-resistant bacteria at high frequencies. These bacteria hyperexpressed the MexCD-OprJ efflux system due to mutations in its regulatory gene, nfxB. The MICs of several drugs for these mutants were increased up to 500-fold, including the MIC of ciprofloxacin, which was increased 94-fold. Whereas the MexEF-OprN efflux system also participated in triclosan efflux, this antimicrobial was not a substrate for MexXY-OprM. PMID:11158736

  13. Ada programming guidelines for deterministic storage management

    NASA Technical Reports Server (NTRS)

    Auty, David

    1988-01-01

    Previous reports have established that a program can be written in the Ada language such that the program's storage management requirements are determinable prior to its execution. Specific guidelines for ensuring such deterministic usage of Ada dynamic storage requirements are described. Because requirements may vary from one application to another, guidelines are presented in a most-restrictive to least-restrictive fashion to allow the reader to match appropriate restrictions to the particular application area under investigation.

  14. Parallel Ada benchmarks for the SVMS

    NASA Technical Reports Server (NTRS)

    Collard, Philippe E.

    1990-01-01

    The use of parallel processing paradigm to design and develop faster and more reliable computers appear to clearly mark the future of information processing. NASA started the development of such an architecture: the Spaceborne VHSIC Multi-processor System (SVMS). Ada will be one of the languages used to program the SVMS. One of the unique characteristics of Ada is that it supports parallel processing at the language level through the tasking constructs. It is important for the SVMS project team to assess how efficiently the SVMS architecture will be implemented, as well as how efficiently Ada environment will be ported to the SVMS. AUTOCLASS II, a Bayesian classifier written in Common Lisp, was selected as one of the benchmarks for SVMS configurations. The purpose of the R and D effort was to provide the SVMS project team with the version of AUTOCLASS II, written in Ada, that would make use of Ada tasking constructs as much as possible so as to constitute a suitable benchmark. Additionally, a set of programs was developed that would measure Ada tasking efficiency on parallel architectures as well as determine the critical parameters influencing tasking efficiency. All this was designed to provide the SVMS project team with a set of suitable tools in the development of the SVMS architecture.

  15. Guanine nucleotide metabolism in a mutant strain of Escherichia coli with a temperature sensitive lesion in rRNA synthesis.

    PubMed

    Harris, J S; Chaney, S G

    1978-12-21

    We have described a mutant of Escherichia coli (designated 2S142) which shows specific inhibition of rRNA synthesis at 42 degrees C. ppGpp levels increase at the restrictive temperature, as expected. However, when the cells are returned to 30 degrees C, rRNA synthesis resumes before ppGpp levels have returned to normal. Furthermore, when ppGpp levels are decreased by the addition of tetracycline or choramphenicol, rRNA synthesis does not resume at 42 degrees C. Also, a derivative of 2S142 with a temperature-sensitive G factor (which cannot synthesize either protein or ppGpp at 42 degrees C) shows identical kinetics of rRNA shut-off at 42 degrees C as 2S142. Thus, the elevated ppGpp levels in this mutant do not appear to be directly responsible for the cessation of rRNA synthesis at 42 degrees C. PMID:367439

  16. Comparative Evaluation of Agroindustrial Byproducts for the Production of Alkaline Protease by Wild and Mutant Strains of Bacillus subtilis in Submerged and Solid State Fermentation

    PubMed Central

    Haq, Ikramul

    2013-01-01

    The present study describes the screening of different agroindustrial byproducts for enhanced production of alkaline protease by a wild and EMS induced mutant strain of Bacillus subtilis IH-72EMS8. During submerged fermentation, different agro-industrial byproducts were tested which include defatted seed meals of rape, guar, sunflower, gluten, cotton, soybean, and gram. In addition to these meals, rice bran, wheat bran, and wheat flour were also evaluated for protease production. Of all the byproducts tested, soybean meal at a concentration of 20 g/L gave maximum production of the enzyme, that is, 5.74  ±  0.26 U/mL from wild and 11.28  ±  0.45 U/mL from mutant strain, during submerged fermentation. Different mesh sizes (coarse, medium, and fine) of the soybean meal were also evaluated, and a finely ground soybean meal (fine mesh) was found to be the best. In addition to the defatted seed meals, their alkali extracts were also tested for the production of alkaline protease by Bacillus subtilis, but these were proved nonsignificant for enhanced production of the enzyme. The production of the enzyme was also studied in solid state fermentation, and different agro-industrial byproducts were also evaluated for enzyme production. Wheat bran partially replaced with guar meal was found as the best substrate for maximum enzyme production under solid state fermentation conditions. PMID:24294129

  17. Comparative evaluation of agroindustrial byproducts for the production of alkaline protease by wild and mutant strains of Bacillus subtilis in submerged and solid state fermentation.

    PubMed

    Mukhtar, Hamid; Haq, Ikramul

    2013-01-01

    The present study describes the screening of different agroindustrial byproducts for enhanced production of alkaline protease by a wild and EMS induced mutant strain of Bacillus subtilis IH-72(EMS8). During submerged fermentation, different agro-industrial byproducts were tested which include defatted seed meals of rape, guar, sunflower, gluten, cotton, soybean, and gram. In addition to these meals, rice bran, wheat bran, and wheat flour were also evaluated for protease production. Of all the byproducts tested, soybean meal at a concentration of 20 g/L gave maximum production of the enzyme, that is, 5.74  ±  0.26 U/mL from wild and 11.28  ±  0.45 U/mL from mutant strain, during submerged fermentation. Different mesh sizes (coarse, medium, and fine) of the soybean meal were also evaluated, and a finely ground soybean meal (fine mesh) was found to be the best. In addition to the defatted seed meals, their alkali extracts were also tested for the production of alkaline protease by Bacillus subtilis, but these were proved nonsignificant for enhanced production of the enzyme. The production of the enzyme was also studied in solid state fermentation, and different agro-industrial byproducts were also evaluated for enzyme production. Wheat bran partially replaced with guar meal was found as the best substrate for maximum enzyme production under solid state fermentation conditions. PMID:24294129

  18. Comparative genomic analysis of Klebsiella pneumonia (LCT-KP214) and a mutant strain (LCT-KP289) obtained after spaceflight

    PubMed Central

    2014-01-01

    Background With the development of space science, it is important to analyze the relationship between the space environment and genome variations that might cause phenotypic changes in microbes. Klebsiella pneumoniae is commonly found on the human body and is resistant to multiple drugs. To study space-environment-induced genome variations and drug resistance changes, K. pneumoniae was carried into outer space by the Shenzhou VIII spacecraft. Results The K. pneumoniae strain LCT-KP289 was selected after spaceflight based on its phenotypic differences compared to the ground-control strain. Analysis of genomic structural variations revealed one inversion, 25 deletions, fifty-nine insertions, two translocations and six translocations with inversions. In addition, 155 and 400 unique genes were observed in LCT-KP214 and LCT-KP289, respectively, including the gene encoding dihydroxyacetone kinase, which generates the ATP and NADH required for microbial growth. Furthermore, a large number of mutant genes were related to transport and metabolism. Phylogenetic analysis revealed that most genes in these two strains had a dN/dS value greater than 1, indicating that the strain diversity increased after spaceflight. Analysis of drug-resistance phenotypes revealed that the K. pneumoniae strain LCT-KP289 was resistant to sulfamethoxazole, whereas the control strain, LCT-KP214, was not; both strains were resistant to benzylpenicillin, ampicillin, lincomycin, vancomycin, chloramphenicol and streptomycin. The sulfamethoxazole resistance may be associated with sequences in Scaffold7 in LCT-KP289, which were not observed in LCT-K214; this scaffold contained the gene sul1. In the strain LCT-KP289, we also observed a drug-resistance integron containing emrE (confers multidrug resistance) and ant (confers resistance to spectinomycin, streptomycin, tobramycin, kanamycin, sisomicin, dibekacin, and gentamicin). The gene ampC (confers resistance to penicillin, cephalosporin-ii and

  19. Open fermentative production of fuel ethanol from food waste by an acid-tolerant mutant strain of Zymomonas mobilis.

    PubMed

    Ma, Kedong; Ruan, Zhiyong; Shui, Zongxia; Wang, Yanwei; Hu, Guoquan; He, Mingxiong

    2016-03-01

    The aim of present study was to develop a process for open ethanol fermentation from food waste using an acid-tolerant mutant of Zymomonas mobilis (ZMA7-2). The mutant showed strong tolerance to acid condition of food waste hydrolysate and high ethanol production performance. By optimizing fermentation parameters, ethanol fermentation with initial glucose concentration of 200 g/L, pH value around 4.0, inoculum size of 10% and without nutrient addition was considered as best conditions. Moreover, the potential of bench scales fermentation and cell reusability was also examined. The fermentation in bench scales (44 h) was faster than flask scale (48 h), and the maximum ethanol concentration and ethanol yield (99.78 g/L, 0.50 g/g) higher than that of flask scale (98.31 g/L, 0.49 g/g). In addition, the stable cell growth and ethanol production profile in five cycles successive fermentation was observed, indicating the mutant was suitable for industrial ethanol production. PMID:26744803

  20. Cloning of Bordetella bronchiseptica urease genes and analysis of colonization by a urease-negative mutant strain in a guinea-pig model.

    PubMed

    Monack, D M; Falkow, S

    1993-11-01

    The genes encoding urease were cloned from Bordetella bronchiseptica and the 5.2 kb of DNA essential for expression analysed in a T7 RNA polymerase transcription-translation system. At least four polypeptides with predicted molecular weights of 69,000, 26,000, 12,200 and 11,000 were found. Partial DNA sequence of the gene encoding the 69,000 Da polypeptide revealed high amino acid identity to the alpha-subunit of Proteus mirabilis urease, UreC and jack bean urease. A stable, unmarked deletion was constructed in this gene to create a urease-negative mutant of B. bronchiseptica. To assess colonization in a guinea-pig model, the urease-negative strain was inoculated with the urease-positive parental strain in a mixed infection. The urease-negative strain out competed the urease-positive strain in the trachea, lungs and caecum. We demonstrate that urease is not essential for B. bronchiseptica colonization of the guinea-pig respiratory and digestive tracts. PMID:7968532

  1. Development of a Nuclear Transformation System for Oleaginous Green Alga Lobosphaera (Parietochloris) incisa and Genetic Complementation of a Mutant Strain, Deficient in Arachidonic Acid Biosynthesis

    PubMed Central

    Khozin-Goldberg, Inna; Leu, Stefan; Shapira, Michal; Kaye, Yuval; Tourasse, Nicolas; Vallon, Olivier; Boussiba, Sammy

    2014-01-01

    Microalgae are considered a promising source for various high value products, such as carotenoids, ω-3 and ω-6 polyunsaturated fatty acids (PUFA). The unicellular green alga Lobosphaera (Parietochloris) incisa is an outstanding candidate for the efficient phototrophic production of arachidonic acid (AA), an essential ω-6 PUFA for infant brain development and a widely used ingredient in the baby formula industry. Although phototrophic production of such algal products has not yet been established, estimated costs are considered to be 2–5 times higher than competing heterotrophic production costs. This alga accumulates unprecedented amounts of AA within triacylglycerols and the molecular pathway of AA biosynthesis in L. incisa has been previously elucidated. Thus, progress in transformation and metabolic engineering of this high value alga could be exploited for increasing the efficient production of AA at competitive prices. We describe here the first successful transformation of L. incisa using the ble gene as a selection marker, under the control of the endogenous RBCS promoter. Furthermore, we have succeeded in the functional complementation of the L. incisa mutant strain P127, containing a mutated, inactive version of the delta-5 (Δ5) fatty acid desaturase gene. A copy of the functional Δ5 desaturase gene, linked to the ble selection marker, was transformed into the P127 mutant. The resulting transformants selected for zeocine resistant, had AA biosynthesis partially restored, indicating the functional complementation of the mutant strain with the wild-type gene. The results of this study present a platform for the successful genetic engineering of L. incisa and its long-chain PUFA metabolism. PMID:25133787

  2. Metabolic Engineering of Light and Dark Biochemical Pathways in Wild-Type and Mutant Strains of Synechocystis PCC 6803 for Maximal, 24-Hour Production of Hydrogen Gas

    SciTech Connect

    Ely, Roger L.; Chaplen, Frank W.R.

    2014-03-11

    enhanced H2 production profiles using selected culture conditions and inhibitors of specific pathways in WT cells and an NDH-1 mutant; 3. Create Synechocystis PCC 6803 mutant strains with modified hydrogenases exhibiting increased O2 tolerance and greater H2 production; and 4. Integrate enhanced hydrogenase mutants and culture and metabolic factor studies to maximize 24-hour H2 production.

  3. Toward the efficient implementation of expert systems in Ada

    NASA Technical Reports Server (NTRS)

    Lee, S. Daniel

    1990-01-01

    Here, the authors describe Ada language issues encountered during the development of ART-Ada, an expert system tool for Ada deployment. ART-Ada is being used to implement several expert system applications for the Space Station Freedom and the U.S. Air Force. Additional information is given on dynamic memory allocation.

  4. An Embedded Rule-Based Diagnostic Expert System in Ada

    NASA Technical Reports Server (NTRS)

    Jones, Robert E.; Liberman, Eugene M.

    1992-01-01

    Ada is becoming an increasingly popular programming language for large Government-funded software projects. Ada with it portability, transportability, and maintainability lends itself well to today's complex programming environment. In addition, expert systems have also assumed a growing role in providing human-like reasoning capability expertise for computer systems. The integration is discussed of expert system technology with Ada programming language, especially a rule-based expert system using an ART-Ada (Automated Reasoning Tool for Ada) system shell. NASA Lewis was chosen as a beta test site for ART-Ada. The test was conducted by implementing the existing Autonomous Power EXpert System (APEX), a Lisp-based power expert system, in ART-Ada. Three components, the rule-based expert systems, a graphics user interface, and communications software make up SMART-Ada (Systems fault Management with ART-Ada). The rules were written in the ART-Ada development environment and converted to Ada source code. The graphics interface was developed with the Transportable Application Environment (TAE) Plus, which generates Ada source code to control graphics images. SMART-Ada communicates with a remote host to obtain either simulated or real data. The Ada source code generated with ART-Ada, TAE Plus, and communications code was incorporated into an Ada expert system that reads the data from a power distribution test bed, applies the rule to determine a fault, if one exists, and graphically displays it on the screen. The main objective, to conduct a beta test on the ART-Ada rule-based expert system shell, was achieved. The system is operational. New Ada tools will assist in future successful projects. ART-Ada is one such tool and is a viable alternative to the straight Ada code when an application requires a rule-based or knowledge-based approach.

  5. The ADA Library Kit: Sample ADA-Related Documents to Help You Implement the Law.

    ERIC Educational Resources Information Center

    Mayo, Kathleen, Ed.; O'Donnell, Ruth, Ed.

    The Association of Specialized and Cooperative Library Agencies (ASCLA) formed an Americans with Disabilities Act (ADA) Assembly in 1992, and one of its first projects was to prepare this publication by collecting samples of library-produced ADA-related documents. Its aim is to help libraries increase levels of compliance and public awareness. The…

  6. Ada Run Time Support Environments and a common APSE Interface Set. [Ada Programming Support Environment

    NASA Technical Reports Server (NTRS)

    Mckay, C. W.; Bown, R. L.

    1985-01-01

    The paper discusses the importance of linking Ada Run Time Support Environments to the Common Ada Programming Support Environment (APSE) Interface Set (CAIS). A non-stop network operating systems scenario is presented to serve as a forum for identifying the important issues. The network operating system exemplifies the issues involved in the NASA Space Station data management system.

  7. An Ada inference engine for expert systems

    NASA Technical Reports Server (NTRS)

    Lavallee, David B.

    1986-01-01

    The purpose is to investigate the feasibility of using Ada for rule-based expert systems with real-time performance requirements. This includes exploring the Ada features which give improved performance to expert systems as well as optimizing the tradeoffs or workarounds that the use of Ada may require. A prototype inference engine was built using Ada, and rule firing rates in excess of 500 per second were demonstrated on a single MC68000 processor. The knowledge base uses a directed acyclic graph to represent production lines. The graph allows the use of AND, OR, and NOT logical operators. The inference engine uses a combination of both forward and backward chaining in order to reach goals as quickly as possible. Future efforts will include additional investigation of multiprocessing to improve performance and creating a user interface allowing rule input in an Ada-like syntax. Investigation of multitasking and alternate knowledge base representations will help to analyze some of the performance issues as they relate to larger problems.

  8. Proceedings of the First NASA Ada Users' Symposium

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Ada has the potential to be a part of the most significant change in software engineering technology within NASA in the last twenty years. Thus, it is particularly important that all NASA centers be aware of Ada experience and plans at other centers. Ada activity across NASA are covered, with presenters representing five of the nine major NASA centers and the Space Station Freedom Program Office. Projects discussed included - Space Station Freedom Program Office: the implications of Ada on training, reuse, management and the software support environment; Johnson Space Center (JSC): early experience with the use of Ada, software engineering and Ada training and the evaluation of Ada compilers; Marshall Space Flight Center (MSFC): university research with Ada and the application of Ada to Space Station Freedom, the Orbital Maneuvering Vehicle, the Aero-Assist Flight Experiment and the Secure Shuttle Data System; Lewis Research Center (LeRC): the evolution of Ada software to support the Space Station Power Management and Distribution System; Jet Propulsion Laboratory (JPL): the creation of a centralized Ada development laboratory and current applications of Ada including the Real-time Weather Processor for the FAA; and Goddard Space Flight Center (GSFC): experiences with Ada in the Flight Dynamics Division and the Extreme Ultraviolet Explorer (EUVE) project and the implications of GSFC experience for Ada use in NASA. Despite the diversity of the presentations, several common themes emerged from the program: Methodology - NASA experience in general indicates that the effective use of Ada requires modern software engineering methodologies; Training - It is the software engineering principles and methods that surround Ada, rather than Ada itself, which requires the major training effort; Reuse - Due to training and transition costs, the use of Ada may initially actually decrease productivity, as was clearly found at GSFC; and real-time work at LeRC, JPL and GSFC shows

  9. Live Attenuated Mutants of Francisella tularensis Protect Rabbits against Aerosol Challenge with a Virulent Type A Strain

    PubMed Central

    Smith, Le'Kneitah P.; Cole, Kelly Stefano; Santiago, Araceli E.; Mann, Barbara J.; Barry, Eileen M.

    2014-01-01

    Francisella tularensis, a Gram-negative bacterium, is the causative agent of tularemia. No licensed vaccine is currently available for protection against tularemia, although an attenuated strain, dubbed the live vaccine strain (LVS), is given to at-risk laboratory personnel as an investigational new drug (IND). In an effort to develop a vaccine that offers better protection, recombinant attenuated derivatives of a virulent type A strain, SCHU S4, were evaluated in New Zealand White (NZW) rabbits. Rabbits vaccinated via scarification with the three attenuated derivatives (SCHU S4 ΔguaBA, ΔaroD, and ΔfipB strains) or with LVS developed a mild fever, but no weight loss was detected. Twenty-one days after vaccination, all vaccinated rabbits were seropositive for IgG to F. tularensis lipopolysaccharide (LPS). Thirty days after vaccination, all rabbits were challenged with aerosolized SCHU S4 at doses ranging from 50 to 500 50% lethal doses (LD50). All rabbits developed fevers and weight loss after challenge, but the severity was greater for mock-vaccinated rabbits. The ΔguaBA and ΔaroD SCHU S4 derivatives provided partial protection against death (27 to 36%) and a prolonged time to death compared to results for the mock-vaccinated group. In contrast, LVS and the ΔfipB strain both prolonged the time to death, but there were no survivors from the challenge. This is the first demonstration of vaccine efficacy against aerosol challenge with virulent type A F. tularensis in a species other than a rodent since the original work with LVS in the 1960s. The ΔguaBA and ΔaroD SCHU S4 derivatives warrant further evaluation and consideration as potential vaccines for tularemia and for identification of immunological correlates of protection. PMID:24614653

  10. Applying Ada to Beech Starship avionics

    NASA Technical Reports Server (NTRS)

    Funk, David W.

    1986-01-01

    As Ada solidified in its development, it became evident that it offered advantages for avionics systems because of it support for modern software engineering principles and real time applications. An Ada programming support environment was developed for two major avionics subsystems in the Beech Starship. The two subsystems include electronic flight instrument displays and the flight management computer system. Both of these systems use multiple Intel 80186 microprocessors. The flight management computer provides flight planning, navigation displays, primary flight display of checklists and other pilot advisory information. Together these systems represent nearly 80,000 lines of Ada source code and to date approximately 30 man years of effort. The Beech Starship avionics systems are in flight testing.

  11. A database management capability for Ada

    NASA Technical Reports Server (NTRS)

    Chan, Arvola; Danberg, SY; Fox, Stephen; Landers, Terry; Nori, Anil; Smith, John M.

    1986-01-01

    The data requirements of mission critical defense systems have been increasing dramatically. Command and control, intelligence, logistics, and even weapons systems are being required to integrate, process, and share ever increasing volumes of information. To meet this need, systems are now being specified that incorporate data base management subsystems for handling storage and retrieval of information. It is expected that a large number of the next generation of mission critical systems will contain embedded data base management systems. Since the use of Ada has been mandated for most of these systems, it is important to address the issues of providing data base management capabilities that can be closely coupled with Ada. A comprehensive distributed data base management project has been investigated. The key deliverables of this project are three closely related prototype systems implemented in Ada. These three systems are discussed.

  12. EXAFS of Klebsiella pneumoniae nitrogenase MoFe protein from wild-type and nif V mutant strains

    SciTech Connect

    Eidsness, M.K.; Flank, A.M.; Smith, B.E.; Flood, A.C.; Garner, C.D.; Cramer. S.P.

    1986-05-14

    The enzyme nitrogenase catalyzes the biological reduction of N/sub 2/ to NH/sub 3/. In Klebsiella pneumoniae a cluster of 17 genes in seven transcriptional units has been associated with nitrogen fixation. The nitrogenase enzyme from the nif V mutants is relatively ineffective at dinitrogen reduction, is more efficient than the wild-type enzyme at HCN reduction, and has its hydrogen evolution activity inhibited up to 80% by CO. This altered substrate specificity has been shown to be associated with the iron-molybdenum cofactor, FeMo-co, of the enzyme. X-ray absorption spectroscopy has been a valuable tool for probing the molybdenum environment of wild-type nitrogenase, and the authors report here similar studies on the Nif V/sup -/ enzyme.

  13. Novel mutant human immunodeficiency virus type 1 strains with high degree of resistance to cynomolgus macaque TRIMCyp generated by random mutagenesis.

    PubMed

    Sultana, Tahmina; Nakayama, Emi E; Tobita, Satoshi; Yokoyama, Masaru; Seki, Yohei; Saito, Akatsuki; Nomaguchi, Masako; Adachi, Akio; Akari, Hirofumi; Sato, Hironori; Shioda, Tatsuo

    2016-04-01

    Old World monkey TRIM5α strongly suppresses human immunodeficiency virus type 1 (HIV-1) replication. A fusion protein comprising cynomolgus macaque (CM) TRIM5 and cyclophilin A (CM TRIMCyp) also potently suppresses HIV-1 replication. However, CM TRIMCyp fails to suppress a mutant HIV-1 that encodes a mutant capsid protein containing a SIVmac239-derived loop between α-helices 4 and 5 (L4/5). There are seven amino acid differences between L4/5 of HIV-1 and SIVmac239. Here, we investigated the minimum numbers of amino acid substitutions that would allow HIV-1 to evade CM TRIMCyp-mediated suppression. We performed random PCR mutagenesis to construct a library of HIV-1 variants containing mutations in L4/5, and then we recovered replication-competent viruses from CD4+ MT4 cells that expressed high levels of CM TRIMCyp. CM TRIMCyp-resistant viruses were obtained after three rounds of selection in MT4 cells expressing CM TRIMCyp and these were found to contain four amino acid substitutions (H87R, A88G, P90D and P93A) in L4/5. We then confirmed that these substitutions were sufficient to confer CM TRIMCyp resistance to HIV-1. In a separate experiment using a similar method, we obtained novel CM TRIM5α-resistant HIV-1 strains after six rounds of selection and rescue. Analysis of these mutants revealed that V86A and G116E mutations in the capsid region conferred partial resistance to CM TRIM5α without substantial fitness cost when propagated in MT4 cells expressing CM TRIM5α. These results confirmed and further extended the previous notion that CM TRIMCyp and CM TRIM5α recognize the HIV-1 capsid in different manners. PMID:26795727

  14. Ada software productivity prototypes: A case study

    NASA Technical Reports Server (NTRS)

    Hihn, Jairus M.; Habib-Agahi, Hamid; Malhotra, Shan

    1988-01-01

    A case study of the impact of Ada on a Command and Control project completed at the Jet Propulsion Laboratory (JPL) is given. The data for this study was collected as part of a general survey of software costs and productivity at JPL and other NASA sites. The task analyzed is a successful example of the use of rapid prototyping as applied to command and control for the U.S. Air Force and provides the U.S. Air Force Military Airlift Command with the ability to track aircraft, air crews and payloads worldwide. The task consists of a replicated database at several globally distributed sites. The local databases at each site can be updated within seconds after changes are entered at any one site. The system must be able to handle up to 400,000 activities per day. There are currently seven sites, each with a local area network of computers and a variety of user displays; the local area networks are tied together into a single wide area network. Using data obtained for eight modules, totaling approximately 500,000 source lines of code, researchers analyze the differences in productivities between subtasks. Factors considered are percentage of Ada used in coding, years of programmer experience, and the use of Ada tools and modern programming practices. The principle findings are the following. Productivity is very sensitive to programmer experience. The use of Ada software tools and the use of modern programming practices are important; without such use Ada is just a large complex language which can cause productivity to decrease. The impact of Ada on development effort phases is consistent with earlier reports at the project level but not at the module level.

  15. Synthesis and biological properties of novel 2-aminopyrimidin-4(3H)-ones highly potent against HIV-1 mutant strains.

    PubMed

    Mai, Antonello; Artico, Marino; Rotili, Dante; Tarantino, Domenico; Clotet-Codina, Imma; Armand-Ugón, Mercedes; Ragno, Rino; Simeoni, Silvia; Sbardella, Gianluca; Nawrozkij, Maxim B; Samuele, Alberta; Maga, Giovanni; Esté, José A

    2007-11-01

    Following the disclosure of dihydro-alkoxy-, dihydro-alkylthio-, and dihydro-alkylamino-benzyl-oxopyrimidines (DABOs, S-DABOs, and NH-DABOs) as potent and selective anti-HIV-1 agents belonging to the non-nucleoside reverse transcriptase inhibitor (NNRTI) class, we report here the synthesis and biological evaluation of a novel series of DABOs bearing a N,N-disubstituted amino group or a cyclic amine at the pyrimidine-C2 position, a hydrogen atom or a small alkyl group at C5 and/or at the benzylic position, and the favorable 2,6-difluorobenzyl moiety at the C6 position (F2-N,N-DABOs). The new compounds were highly active up to the subnanomolar level against both wt HIV-1 and the Y181C mutant and at the submicromolar to nanomolar range against the K103N and Y188L mutant strains. Such derivatives were more potent than S-DABOs, NH-DABOs, and nevirapine and efavirenz were chosen as reference drugs. The higher inhibitor adaptability to the HIV-1 RT non-nucleoside binding site (NNBS) may account for the higher inhibitory effect exerted by the new molecules against the mutated RTs. PMID:17910429

  16. Characterization of the sodF gene region of Frankia sp. strain ACN14a and complementation of Escherichia coli sod mutant.

    PubMed

    Maréchal, Joëlle; Santos, Renata; Hammad, Yasser; Alloisio, Nicole; Domenach, Anne-Marie; Normand, Philippe

    2003-04-01

    The Frankia sp. strain ACN14a superoxide dismutase SodF was previously shown to be induced in response to Alnus glutinosa root exudates, and its gene was sequenced. We report here the sequence of the 9-kb genomic segment surrounding the sodF gene and further characterize this gene and its product. Nine ORFs coding for various proteins, such as regulators, acetyl-CoA transferases, and a bacterioferritin A next to the sodF gene, were found. Northern blot analysis showed that the sodF gene was expressed as a major 1-kb transcript, which indicates that it has its own promoter. The sodF gene strongly complemented an Escherichia coli triple mutant (sodA sodB recA), restoring aerobic growth when the gene was expressed from the synthetic tac promoter but when expressed from its own promoter showed only slight rescue, suggesting that it was poorly recognized by the E. coli RNA polymerase. It is noteworthy that this is the first time that a Frankia gene has been reported to complement an E. coli mutant. The superoxide dismutase activity of the protein was inactivated by hydrogen peroxide, indicating that the metal ligand is iron, which is supported by analysis of the protein sequence. Thus, the SodF protein induced in Frankia by root exudates is an iron-containing enzyme similar to the one present in the nodules. PMID:12897839

  17. Proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of Paracoccus denitrificans.

    PubMed

    Pernikářová, Vendula; Sedláček, Vojtěch; Potěšil, David; Procházková, Iva; Zdráhal, Zbyněk; Bouchal, Pavel; Kučera, Igor

    2015-07-01

    FerB is a cytoplasmic flavoprotein from the soil bacterium Paracoccus denitrificans with a putative role in defense against oxidative stress. To further explore this hypothesis, we compared protein variations upon methyl viologen treatment in wild-type and FerB mutant strains by a quantitative proteomic analysis based on iTRAQ-3DLC-MS/MS analysis. The proteins showing the most prominent increase in abundance were assigned to carbon fixation and sulfur assimilatory pathways. By employing these proteins as indirect markers, oxidative stress was found to be 15% less severe in the wild-type than in the FerB-deficient mutant cells. Oxidative stress altered the levels of proteins whose expression is dependent on the transcriptional factor FnrP. The observed down-regulation of the fnrP regulon members, most notably that of nitrous oxide reductase, was tentatively explained by an oxidative degradation of the [4Fe-4S] center of FnrP leading to a protein form which no longer activates transcription. While the level of FerB remained relatively constant, two proteins homologous to FerB accumulated during oxidative stress. When their genes were expressed in Escherichia coli, neither of the protein products contained a bound flavin, whereas they both had a high activity of flavin reductase, one preferentially utilizing NADH and the other NADPH. PMID:25976748

  18. Knowledge representation into Ada parallel processing

    NASA Technical Reports Server (NTRS)

    Masotto, Tom; Babikyan, Carol; Harper, Richard

    1990-01-01

    The Knowledge Representation into Ada Parallel Processing project is a joint NASA and Air Force funded project to demonstrate the execution of intelligent systems in Ada on the Charles Stark Draper Laboratory fault-tolerant parallel processor (FTPP). Two applications were demonstrated - a portion of the adaptive tactical navigator and a real time controller. Both systems are implemented as Activation Framework Objects on the Activation Framework intelligent scheduling mechanism developed by Worcester Polytechnic Institute. The implementations, results of performance analyses showing speedup due to parallelism and initial efficiency improvements are detailed and further areas for performance improvements are suggested.

  19. [Characteristics of the structural organization of the DIP1 gene in Drosophila melanogaster strains mutant for the flamenco gene].

    PubMed

    Nefedova, L N; Romanova, N I; Kim, A I

    2007-01-01

    Molecular cloning of the DIP1 gene located in the 20A4-5 region has been performed from the following strains with the flamenco phenotype: flamSS (SS) and flamMS (MS) characterized by a high transposition rate of retrotransposon gypsy (mdg4), flampy + (P) carrying the insertion of a construction based on the P element into the region of the flamenco gene, and flamenco+. The results of restriction analysis and sequencing cloned DNA fragments has shown that strains flamSS, flamMS, flampy +(P), and flamenco+ considerably differ from one another in the structure of DIP1. Strains flamss and flamMS have no Dral restriction site at position 1765 in the coding region of the gene, specifically, in the domain determining the signal of the nuclear localization of the DIP1 protein. This mutation has been found to consist in a nucleotide substitution in the recognition site of DraI restriction endonuclease, which is transformed from TTTAAA into TTTAAG and, hence, is not recognized by the enzyme. This substitution changes codon AAA into AAG and is translationally insignificant, because both triplets encode the same amino acid, lysine. The Dral gene of strainsflamSS andflamMS has been found to contain a 182-bp insertion denoted IdSS (insertion in DIP1 strain SS); it is located in the second intron of the gene. The IdSS sequence is part of the open reading frame encoding the putative transposase of the mobile genetic element HB1 belonging to the Tcl/mariner family. This insertion is presumed to disturb the conformations of DNA and the chromosome, in particular, by forming loops, which alters the expression of DIPI and, probably, neighboring genes. In strains flamenco+ and flampy + (P), the IdSS insertion within the HB1 sequence is deleted. The deletion encompasses five C-terminal amino acid residues of the conserved domain and the entire C-terminal region of the putative HB1 transposase. The obtained data suggest that DIP1 is involved in the control of gypsy transpositions either

  20. Ada in AI or AI in Ada. On developing a rationale for integration

    NASA Technical Reports Server (NTRS)

    Collard, Philippe E.; Goforth, Andre

    1988-01-01

    The use of Ada as an Artificial Intelligence (AI) language is gaining interest in the NASA Community, i.e., by parties who have a need to deploy Knowledge Based-Systems (KBS) compatible with the use of Ada as the software standard for the Space Station. A fair number of KBS and pseudo-KBS implementations in Ada exist today. Currently, no widely used guidelines exist to compare and evaluate these with one another. The lack of guidelines illustrates a fundamental problem inherent in trying to compare and evaluate implementations of any sort in languages that are procedural or imperative in style, such as Ada, with those in languages that are functional in style, such as Lisp. Discussed are the strengths and weakness of using Ada as an AI language and a preliminary analysis provided of factors needed for the development of criteria for the integration of these two families of languages and the environments in which they are implemented. The intent for developing such criteria is to have a logical rationale that may be used to guide the development of Ada tools and methodology to support KBS requirements, and to identify those AI technology components that may most readily and effectively be deployed in Ada.

  1. Gamma ray observatory dynamics simulator in Ada (GRODY)

    NASA Technical Reports Server (NTRS)

    1990-01-01

    This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.

  2. A protein kinase screen of Neurospora crassa mutant strains reveals that the SNF1 protein kinase promotes glycogen synthase phosphorylation.

    PubMed

    Candido, Thiago De Souza; Gonçalves, Rodrigo Duarte; Felício, Ana Paula; Freitas, Fernanda Zanolli; Cupertino, Fernanda Barbosa; De Carvalho, Ana Carolina Gomes Vieira; Bertolini, Maria Célia

    2014-12-15

    Glycogen functions as a carbohydrate reserve in a variety of organisms and its metabolism is highly regulated. The activities of glycogen synthase and glycogen phosphorylase, the rate-limiting enzymes of the synthesis and degradation processes, respectively, are regulated by allosteric modulation and reversible phosphorylation. To identify the protein kinases affecting glycogen metabolism in Neurospora crassa, we performed a screen of 84 serine/threonine kinase knockout strains. We identified multiple kinases that have already been described as controlling glycogen metabolism in different organisms, such as NcSNF1, NcPHO85, NcGSK3, NcPKA, PSK2 homologue and NcATG1. In addition, many hypothetical kinases have been implicated in the control of glycogen metabolism. Two kinases, NcIME-2 and NcNIMA, already functionally characterized but with no functions related to glycogen metabolism regulation, were also identified. Among the kinases identified, it is important to mention the role of NcSNF1. We showed in the present study that this kinase was implicated in glycogen synthase phosphorylation, as demonstrated by the higher levels of glycogen accumulated during growth, along with a higher glycogen synthase (GSN) ±glucose 6-phosphate activity ratio and a lesser set of phosphorylated GSN isoforms in strain Ncsnf1KO, when compared with the wild-type strain. The results led us to conclude that, in N. crassa, this kinase promotes phosphorylation of glycogen synthase either directly or indirectly, which is the opposite of what is described for Saccharomyces cerevisiae. The kinases also play a role in gene expression regulation, in that gdn, the gene encoding the debranching enzyme, was down-regulated by the proteins identified in the screen. Some kinases affected growth and development, suggesting a connection linking glycogen metabolism with cell growth and development. PMID:25253091

  3. The Courts, the ADA, and the Academy

    ERIC Educational Resources Information Center

    Cope, David D.

    2005-01-01

    Litigation influences what goes on in the classroom. The Americans with Disabilities Act (ADA), other statutes, and legal precedent have defined reasonable restrictions on what qualifies as a handicap. Still, universities tend to go overboard--out of ignorance, and influenced by a culture that seems to champion every conceivable victim--in…

  4. Using ADA Tasks to Simulate Operating Equipment

    NASA Technical Reports Server (NTRS)

    DeAcetis, Louis A.; Schmidt, Oron; Krishen, Kumar

    1990-01-01

    A method of simulating equipment using ADA tasks is discussed. Individual units of equipment are coded as concurrently running tasks that monitor and respond to input signals. This technique has been used in a simulation of the space-to-ground Communications and Tracking subsystem of Space Station Freedom.

  5. AdaNET prototype library administration manual

    NASA Technical Reports Server (NTRS)

    Hanley, Lionel

    1989-01-01

    The functions of the AdaNET Prototype Library of Reusable Software Parts is described. Adopted from the Navy Research Laboratory's Reusability Guidebook (V.5.0), this is a working document, customized for use the the AdaNET Project. Within this document, the term part is used to denote the smallest unit controlled by a library and retrievable from it. A part may have several constituents, which may not be individually tracked. Presented are the types of parts which may be stored in the library and the relationships among those parts; a concept of trust indicators which provide measures of confidence that a user of a previously developed part may reasonably apply to a part for a new application; search and retrieval, configuration management, and communications among those who interact with the AdaNET Prototype Library; and the AdaNET Prototype, described from the perspective of its three major users: the part reuser and retriever, the part submitter, and the librarian and/or administrator.

  6. Is Your Queuing System ADA-Compliant?

    ERIC Educational Resources Information Center

    Lawrence, David

    2002-01-01

    Discusses the Americans with Disabilities (ADA) and Uniform Federal Accessibility Standards (UFAS) regulations regarding public facilities' crowd control stanchions and queuing systems. The major elements are protruding objects and wheelchair accessibility. Describes how to maintain compliance with the regulations and offers a list of additional…

  7. Alma Flor Ada: Writer, Translator, Storyteller.

    ERIC Educational Resources Information Center

    Brodie, Carolyn S.

    2003-01-01

    Discusses the work of children's author Alma Flor Ada, a Cuban native who has won awards honoring Latino writers and illustrators. Includes part of an interview that explores her background, describes activity ideas, and presents a bibliography of works written by her (several title published in both English and Spanish) as well as sources of…

  8. Degradation of trichloroethylene by Pseudomonas cepacia G4 and the constitutive mutant strain G4 5223 PR1 in aquifer microcosms.

    PubMed

    Krumme, M L; Timmis, K N; Dwyer, D F

    1993-08-01

    Pseudomonas cepacia G4 degrades trichloroethylene (TCE) via a degradation pathway for aromatic compounds which is induced by substrates such as phenol and tryptophan. P. cepacia G4 5223 PR1 (PR1) is a Tn5 insertion mutant which constitutively expresses the toluene ortho-monooxygenase responsible for TCE degradation. In groundwater microcosms, phenol-induced strain G4 and noninduced strain PR1 degraded TCE (20 and 50 microM) to nondetectable levels (< 0.1 microM) within 24 h at densities of 10(8) cells per ml; at lower densities, degradation of TCE was not observed after 48 h. In aquifer sediment microcosms, TCE was reduced from 60 to < 0.1 microM within 24 h at 5 x 10(8) PR1 organisms per g (wet weight) of sediment and from 60 to 26 microM over a period of 10 weeks at 5 x 10(7) PR1 organisms per g. Viable G4 and PR1 cells decreased from approximately 10(7) to 10(4) per g over the 10-week period. PMID:7690223

  9. Use of a genetically defined double mutant strain of Bordetella bronchiseptica lacking adenylate cyclase and type III secretion as a live vaccine.

    PubMed

    Mann, Paul; Goebel, Elizabeth; Barbarich, James; Pilione, Mylisa; Kennett, Mary; Harvill, Eric

    2007-07-01

    While most vaccines consisting of killed bacteria induce high serum antibody titers, they do not always confer protection as effective as that induced by infection, particularly against mucosal pathogens. Bordetella bronchiseptica is a gram-negative respiratory pathogen that is endemic in many nonhuman mammalian populations and causes substantial disease in a variety of animals. At least 14 different live attenuated vaccines against this pathogen are available for use in a variety of livestock and companion animals. However, there are few published data on the makeup or efficacy of these vaccines. Here we report the use of a genetically engineered double mutant of B. bronchiseptica, which lacks adenylate cyclase and type III secretion, as a vaccine candidate. This strain is safe at high doses, even for highly immunocompromised animals, and induces immune responses that are protective against highly divergent B. bronchiseptica strains, preventing colonization in the lower respiratory tract and decreasing the bacterial burden in the upper respiratory tract. This novel B. bronchiseptica vaccine candidate induces strong local immunity while eliminating damage caused by the two predominant cytotoxic mechanisms. PMID:17452472

  10. Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

    PubMed Central

    DiChiara, Jeanne M.; Liu, Bo; Figaro, Sabine; Condon, Ciarán; Bechhofer, David H.

    2016-01-01

    The recent findings that the narrow-specificity endoribonuclease RNase III and the 5′ exonuclease RNase J1 are not essential in the Gram-positive model organism, Bacillus subtilis, facilitated a global analysis of internal 5′ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5′ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions appeared to be direct targets of RNase III. These target sites were, in most cases, not associated with a known antisense RNA. The PARE analysis also revealed an accumulation of 3′-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. A significant result from the PARE analysis was the discovery of an endonuclease cleavage just 2 nts downstream of the 16S rRNA 3′ end. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic versus endonucleolytic nature of 16S rRNA maturation. PMID:26883633

  11. Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains.

    PubMed

    DiChiara, Jeanne M; Liu, Bo; Figaro, Sabine; Condon, Ciarán; Bechhofer, David H

    2016-04-20

    The recent findings that the narrow-specificity endoribonuclease RNase III and the 5' exonuclease RNase J1 are not essential in the Gram-positive model organism,Bacillus subtilis, facilitated a global analysis of internal 5' ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5' monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions appeared to be direct targets of RNase III. These target sites were, in most cases, not associated with a known antisense RNA. The PARE analysis also revealed an accumulation of 3'-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. A significant result from the PARE analysis was the discovery of an endonuclease cleavage just 2 nts downstream of the 16S rRNA 3' end. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic versus endonucleolytic nature of 16S rRNA maturation. PMID:26883633

  12. Differential activities of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine derivatives against different human immunodeficiency virus type 1 mutant strains.

    PubMed Central

    Balzarini, J; Baba, M; De Clercq, E

    1995-01-01

    A series of 23 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine derivatives that were highly potent inhibitors of wild-type human immunodeficiency virus type 1 strain IIIB (HIV-1/IIIB) replication in CEM cells were evaluated against a panel of HIV-1 mutant strains containing the replacement of leucine by isoleucine at position 100 (100-Leu-->Ile), 103-Lys-->Asn, 106-Val-->Ala, 138-Glu-->Lys, 181-Tyr-->Cys, 181-Tyr-->Ile, or 188-Tyr-->His in their reverse transcriptase (RT). A different structure-antiviral activity relationship was found, depending on the nature of the mutated amino acid in the HIV-1 RT. The results show that 5-ethyl-1-ethoxymethyl-6-(3,5-dimethylbenzyl)uracil, 5-ethyl-1-ethoxymethyl-6-(3,5-dimethylphenylthio)uracil, and 5-ethyl-1-ethoxymethyl-6-(3,5-dimethylphenylthio)-2-thiouracil remain active against the majority of viruses containing single mutations which confer resistance to nonnucleoside RT inhibitors. PMID:7540384

  13. Growth, ethanol production, and inulinase activity on various inulin substrates by mutant Kluyveromyces marxianus strains NRRL Y-50798 and NRRL Y-50799.

    PubMed

    Galindo-Leva, Luz Ángela; Hughes, Stephen R; López-Núñez, Juan Carlos; Jarodsky, Joshua M; Erickson, Adam; Lindquist, Mitchell R; Cox, Elby J; Bischoff, Kenneth M; Hoecker, Eric C; Liu, Siqing; Qureshi, Nasib; Jones, Marjorie A

    2016-07-01

    Economically important plants contain large amounts of inulin. Disposal of waste resulting from their processing presents environmental issues. Finding microorganisms capable of converting inulin waste to biofuel and valuable co-products at the processing site would have significant economic and environmental impact. We evaluated the ability of two mutant strains of Kluyveromyces marxianus (Km7 and Km8) to utilize inulin for ethanol production. In glucose medium, both strains consumed all glucose and produced 0.40 g ethanol/g glucose at 24 h. In inulin medium, Km7 exhibited maximum colony forming units (CFU)/mL and produced 0.35 g ethanol/g inulin at 24 h, while Km8 showed maximum CFU/mL and produced 0.02 g ethanol/g inulin at 96 h. At 24 h in inulin + glucose medium, Km7 produced 0.40 g ethanol/g (inulin + glucose) and Km8 produced 0.20 g ethanol/g (inulin + glucose) with maximum CFU/mL for Km8 at 72 h, 40 % of that for Km7 at 36 h. Extracellular inulinase activity at 6 h for both Km7 and Km8 was 3.7 International Units (IU)/mL. PMID:27130462

  14. Programming fault-tolerant distributed systems in Ada

    NASA Technical Reports Server (NTRS)

    Voigt, Susan J.

    1985-01-01

    Viewgraphs on the topic of programming fault-tolerant distributed systems in the Ada programming language are presented. Topics covered include project goals, Ada difficulties and solutions, testbed requirements, and virtual processors.

  15. Growth on D-arabitol of a mutant strain of Escherichia coli K12 using a novel dehydrogenase and enzymes related to L-1,2-propanediol and D-xylose metabolism.

    PubMed

    Wu, T T

    1976-06-01

    Escherichia coli K12 cannot grow on D-arabitol, L-arabitol, ribitol or xylitol (Reiner, 1975). Using a mutant of E. coli K12 (strain 3; Sridhara et al., 1969) that can grow on L-1,2-propanediol, a second-stage mutant was isolated which can utilize D-arabitol as sole source of carbon and energy for growth. D-Arabitol is probably transported into the bacteria by the same system as that used for the transport of L-1,2-propanediol. The second-stage mutant constitutively synthesizes a new dehydrogenase, which is not present in the parent strain 3. This enzyme, whose native substrate may be D-galactose, apparently dehydrogenates D-arabitol to D-xylulose, and its structural gene is located at 68.5 +/- 1 min on the E. coli genetic map. D-Xylulose is subsequently catabolized by the enzymes of the D-xylose metabolic pathway. PMID:181526

  16. The computerization of programming: Ada (R) lessons learned

    NASA Technical Reports Server (NTRS)

    Struble, Dennis D.

    1986-01-01

    One of the largest systems yet written in Ada has been constructed. This system is the Intermetrics Ada compiler. Many lessons have been learned during the implementation of this Ada compiler. Some of these lessons, concentrating on those lessons relevant to large system implementations are described. The characteristics of the Ada compiler implementation project at Intermetrics are also described. Some specific experiences during the implementation are pointed out.

  17. Knowledge, programming, and programming cultures: LISP, C, and Ada

    NASA Technical Reports Server (NTRS)

    Rochowiak, Daniel

    1990-01-01

    The results of research 'Ada as an implementation language for knowledge based systems' are presented. The purpose of the research was to compare Ada to other programming languages. The report focuses on the programming languages Ada, C, and Lisp, the programming cultures that surround them, and the programming paradigms they support.

  18. Screening of High-Level 4-Hydroxy-2 (or 5)-Ethyl-5 (or 2)-Methyl-3(2H)-Furanone-Producing Strains from a Collection of Gene Deletion Mutants of Saccharomyces cerevisiae

    PubMed Central

    Watanabe, Jun; Akao, Takeshi; Watanabe, Daisuke; Mogi, Yoshinobu; Shimoi, Hitoshi

    2014-01-01

    4-Hydroxy-2 (or 5)-ethyl-5 (or 2)-methyl-3(2H)-furanone (HEMF) is an important flavor compound that contributes to the sensory properties of many natural products, particularly soy sauce and soybean paste. The compound exhibits a caramel-like aroma and several important physiological activities, such as strong antioxidant activity. HEMF is produced by yeast species in soy sauce manufacturing; however, the enzymes involved in HEMF production remain unknown, hindering efforts to breed yeasts with high-level HEMF production. In this study, we identified high-level HEMF-producing mutants among a Saccharomyces cerevisiae gene deletion mutant collection. Fourteen deletion mutants were screened as high-level HEMF-producing mutants, and the ADH1 gene deletion mutant (adh1Δ) exhibited the maximum HEMF production capacity. Further investigations of the adh1Δ mutant implied that acetaldehyde accumulation contributes to HEMF production, agreeing with previous findings. Therefore, acetaldehyde might be a precursor for HEMF. The ADH1 gene deletion mutant of Zygosaccharomyces rouxii, which is the dominant strain of yeast found during soy sauce fermentation, also produces HEMF effectively, suggesting that acetaldehyde accumulation might be a benchmark for breeding industrial yeasts with excellent HEMF production abilities. PMID:25362059

  19. Screening of high-level 4-hydroxy-2 (or 5)-ethyl-5 (or 2)-methyl-3(2H)-furanone-producing strains from a collection of gene deletion mutants of Saccharomyces cerevisiae.

    PubMed

    Uehara, Kenji; Watanabe, Jun; Akao, Takeshi; Watanabe, Daisuke; Mogi, Yoshinobu; Shimoi, Hitoshi

    2015-01-01

    4-Hydroxy-2 (or 5)-ethyl-5 (or 2)-methyl-3(2H)-furanone (HEMF) is an important flavor compound that contributes to the sensory properties of many natural products, particularly soy sauce and soybean paste. The compound exhibits a caramel-like aroma and several important physiological activities, such as strong antioxidant activity. HEMF is produced by yeast species in soy sauce manufacturing; however, the enzymes involved in HEMF production remain unknown, hindering efforts to breed yeasts with high-level HEMF production. In this study, we identified high-level HEMF-producing mutants among a Saccharomyces cerevisiae gene deletion mutant collection. Fourteen deletion mutants were screened as high-level HEMF-producing mutants, and the ADH1 gene deletion mutant (adh1Δ) exhibited the maximum HEMF production capacity. Further investigations of the adh1Δ mutant implied that acetaldehyde accumulation contributes to HEMF production, agreeing with previous findings. Therefore, acetaldehyde might be a precursor for HEMF. The ADH1 gene deletion mutant of Zygosaccharomyces rouxii, which is the dominant strain of yeast found during soy sauce fermentation, also produces HEMF effectively, suggesting that acetaldehyde accumulation might be a benchmark for breeding industrial yeasts with excellent HEMF production abilities. PMID:25362059

  20. ADAS: Asiago-DLR Asteroid Survey

    NASA Astrophysics Data System (ADS)

    Barbieri, C.; Bertini, I.; Magrin, S.; Salvadori, L.; Calvani, M.; Claudi, R.; Pignata, G.; Hahn, G.; Mottola, S.; Hoffmann, M.

    The Asiago-DLR Asteroid Survey is the joint program among the Department of Astronomy and Astronomical Observatory of Padova and the DLR Berlin, dedicated to the search of asteroids. The Minor Planet Center has attributed to ADAS the survey code 209. The project is carried out since the end of December 2000 with the S67/92cm telescope at Asiago - Cima Ekar equipped with the SCAM-1 camera of DLR, in Time Delay Integration mode, in a strip from -5o to +15o around the celestial equator. The camera has a front illuminated Loral chip of 2048x2048 pixels of 15 mu m each, covering a field of 49'x49' with a resolution of 1.4'' pixel-1. This paper presents the main results obtained till March 15, 2002, when the telescope has been closed for a complete overhaul. ADAS will resume presumably at the end of June 2002.

  1. Ada and software management in NASA: Assessment and recommendations

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Recent NASA missions have required software systems that are larger, more complex, and more critical than NASA software systems of the past. The Ada programming language and the software methods and support environments associated with it are seen as potential breakthroughs in meeting NASA's software requirements. The findings of a study by the Ada and Software Management Assessment Working Group (ASMAWG) are presented. The study was chartered to perform three tasks: (1) assess the agency's ongoing and planned Ada activities; (2) assess the infrastructure (standards, policies, and internal organizations) supporting software management and the Ada activities; and (3) present an Ada implementation and use strategy appropriate for NASA over the next 5 years.

  2. Comparing host and target environments for distributed Ada programs

    NASA Technical Reports Server (NTRS)

    Paulk, Mark C.

    1986-01-01

    The Ada programming language provides a means of specifying logical concurrency by using multitasking. Extending the Ada multitasking concurrency mechanism into a physically concurrent distributed environment which imposes its own requirements can lead to incompatibilities. These problems are discussed. Using distributed Ada for a target system may be appropriate, but when using the Ada language in a host environment, a multiprocessing model may be more suitable than retargeting an Ada compiler for the distributed environment. The tradeoffs between multitasking on distributed targets and multiprocessing on distributed hosts are discussed. Comparisons of the multitasking and multiprocessing models indicate different areas of application.

  3. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

    PubMed Central

    2012-01-01

    Background The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDNA sequencing (RNA-seq). ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae, where it regulates a considerable number of genes involved in environmental adaptation and virulence. In P. profundum the abundance and activity of this protein is influenced by hydrostatic pressure and its role is related to the regulation of genes in a pressure-dependent manner. Results To better characterize the ToxR regulon, we compared the expression profiles of wt and toxR strains in response to pressure changes. Our results revealed a complex expression pattern with a group of 22 genes having expression profiles similar to OmpH that is an outer membrane protein transcribed in response to high hydrostatic pressure. Moreover, RNA-seq allowed a deep characterization of the transcriptional landscape that led to the identification of 460 putative small RNA genes and the detection of 298 protein-coding genes previously unknown. We were also able to perform a genome-wide prediction of operon structure, transcription start and termination sites, revealing an unexpected high number of genes (992) with large 5′-UTRs, long enough to harbour cis-regulatory RNA structures, suggesting a correlation between intergenic region size and UTR length. Conclusion This work led to a better understanding of high-pressure response in P. profundum. Furthermore, the high-resolution RNA-seq analysis revealed several unexpected features about transcriptional landscape and general mechanisms of controlling bacterial gene expression. PMID:23107454

  4. Hydrogen production by hup(-) mutant and wild-type strains of Rhodobacter capsulatus from dark fermentation effluent of sugar beet thick juice in batch and continuous photobioreactors.

    PubMed

    Uyar, Basar; Gürgan, Muazzez; Özgür, Ebru; Gündüz, Ufuk; Yücel, Meral; Eroglu, Inci

    2015-10-01

    Photofermentative production of hydrogen is a promising and sustainable process; however, it should be coupled to dark fermentation to become cost effective. In order to integrate dark fermentation and photofermentation, the suitability of dark fermenter effluents for the photofermentative hydrogen production must be demonstrated. In this study, thermophilic dark fermenter effluent (DFE) of sugar beet thick juice was used as a substrate in photofermentation process to compare wild-type and uptake hydrogenase-deficient (hup (-)) mutant strains of Rhodobacter capsulatus by means of hydrogen production and biomass growth. The tests were conducted in small-scale (50 mL) batch and large-scale (4 L) continuous photobioreactors in indoor conditions under continuous illumination. In small scale batch conditions, maximum cell concentrations were 0.92 gdcw/L c and 1.50 gdcw/L c, hydrogen yields were 34 % and 31 %, hydrogen productivities were 0.49 mmol/(L c·h) and 0.26 mmol/(Lc·h), for hup (-) and wild-type cells, respectively. In large-scale continuous conditions, maximum cell concentrations were 1.44 gdcw/L c and 1.87 gdcw/L c, hydrogen yields were 48 and 46 %, and hydrogen productivities were 1.01 mmol/(L c·h) and 1.05 mmol/(L c·h), for hup (-) and wild-type cells, respectively. Our results showed that Rhodobacter capsulatus hup (-) cells reached to a lower maximum cell concentration but their hydrogen yield and productivity were in the same range or superior compared to the wild-type cells in both batch and continuous operating modes. The maximum biomass concentration, yield and productivity of hydrogen were higher in continuous mode compared to the batch mode with both bacterial strains. PMID:26164274

  5. SEL Ada reuse analysis and representations

    NASA Technical Reports Server (NTRS)

    Kester, Rush

    1990-01-01

    Overall, it was revealed that the pattern of Ada reuse has evolved from initial reuse of utility components into reuse of generalized application architectures. Utility components were both domain-independent utilities, such as queues and stacks, and domain-specific utilities, such as those that implement spacecraft orbit and attitude mathematical functions and physics or astronomical models. The level of reuse was significantly increased with the development of a generalized telemetry simulator architecture. The use of Ada generics significantly increased the level of verbatum reuse, which is due to the ability, using Ada generics, to parameterize the aspects of design that are configurable during reuse. A key factor in implementing generalized architectures was the ability to use generic subprogram parameters to tailor parts of the algorithm embedded within the architecture. The use of object oriented design (in which objects model real world entities) significantly improved the modularity for reuse. Encapsulating into packages the data and operations associated with common real world entities creates natural building blocks for reuse.

  6. SDI satellite autonomy using AI and Ada

    NASA Technical Reports Server (NTRS)

    Fiala, Harvey E.

    1990-01-01

    The use of Artificial Intelligence (AI) and the programming language Ada to help a satellite recover from selected failures that could lead to mission failure are described. An unmanned satellite will have a separate AI subsystem running in parallel with the normal satellite subsystems. A satellite monitoring subsystem (SMS), under the control of a blackboard system, will continuously monitor selected satellite subsystems to become alert to any actual or potential problems. In the case of loss of communications with the earth or the home base, the satellite will go into a survival mode to reestablish communications with the earth. The use of an AI subsystem in this manner would have avoided the tragic loss of the two recent Soviet probes that were sent to investigate the planet Mars and its moons. The blackboard system works in conjunction with an SMS and a reconfiguration control subsystem (RCS). It can be shown to be an effective way for one central control subsystem to monitor and coordinate the activities and loads of many interacting subsystems that may or may not contain redundant and/or fault-tolerant elements. The blackboard system will be coded in Ada using tools such as the ABLE development system and the Ada Production system.

  7. Evolving impact of Ada on a production software environment

    NASA Technical Reports Server (NTRS)

    Mcgarry, F.; Esker, L.; Quimby, K.

    1988-01-01

    Many aspects of software development with Ada have evolved as our Ada development environment has matured and personnel have become more experienced in the use of Ada. The Software Engineering Laboratory (SEL) has seen differences in the areas of cost, reliability, reuse, size, and use of Ada features. A first Ada project can be expected to cost about 30 percent more than an equivalent FORTRAN project. However, the SEL has observed significant improvements over time as a development environment progresses to second and third uses of Ada. The reliability of Ada projects is initially similar to what is expected in a mature FORTRAN environment. However, with time, one can expect to gain improvements as experience with the language increases. Reuse is one of the most promising aspects of Ada. The proportion of reusable Ada software on our Ada projects exceeds the proportion of reusable FORTRAN software on our FORTRAN projects. This result was noted fairly early in our Ada projects, and experience shows an increasing trend over time.

  8. Ada education in a software life-cycle context

    NASA Technical Reports Server (NTRS)

    Clough, Anne J.

    1986-01-01

    Some of the experience gained from a comprehensive educational program undertaken at The Charles Stark Draper Lab. to introduce the Ada language and to transition modern software engineering technology into the development of Ada and non-Ada applications is described. Initially, a core group, which included manager, engineers and programmers, received training in Ada. An Ada Office was established to assume the major responsibility for training, evaluation, acquisition and benchmarking of tools, and consultation on Ada projects. As a first step in this process, and in-house educational program was undertaken to introduce Ada to the Laboratory. Later, a software engineering course was added to the educational program as the need to address issues spanning the entire software life cycle became evident. Educational efforts to date are summarized, with an emphasis on the educational approach adopted. Finally, lessons learned in administering this program are addressed.

  9. Ada (trademark) projects at NASA. Runtime environment issues and recommendations

    NASA Technical Reports Server (NTRS)

    Roy, Daniel M.; Wilke, Randall W.

    1988-01-01

    Ada practitioners should use this document to discuss and establish common short term requirements for Ada runtime environments. The major current Ada runtime environment issues are identified through the analysis of some of the Ada efforts at NASA and other research centers. The runtime environment characteristics of major compilers are compared while alternate runtime implementations are reviewed. Modifications and extensions to the Ada Language Reference Manual to address some of these runtime issues are proposed. Three classes of projects focusing on the most critical runtime features of Ada are recommended, including a range of immediately feasible full scale Ada development projects. Also, a list of runtime features and procurement issues is proposed for consideration by the vendors, contractors and the government.

  10. Effect of multiple short highly energetic X-ray pulses on the synthesis of endoglucanase by a mutant strain of Trichoderma reesei-M7

    PubMed Central

    Gemishev, Orlin; Zapryanov, Stanislav; Blagoev, Alexander; Markova, Maya; Savov, Valentin

    2014-01-01

    Bioconversion of cellulose-containing substrate to glucose represents an important area of modern biotechnology. Enzymes for the degradation of the polysaccharide part of biomass have been produced, mostly by fungi belonging to genus Trichoderma. Studies were carried out with the mutant strain Trichoderma reesei-M7, a cellulase producer. Spores of the enzyme producer were irradiated with different doses of characteristic X-ray radiation from metallic tungsten (mainly the W Kα1 and Kα2 lines) with a high dose rate. The latter is a specific property of the dense plasma focus (DPF) device, which has pulsed operation and thus gives short and highly energetic pulses of multiple types of rays and particles. In this case, we focused our study on the influence of hard X-rays. The doses of X-rays absorbed by the spores varied in the range of approximately 5–11,000 mSv measured with thermoluminescent dosimeters (TLD). The influence of the applied doses in combination with exceptionally high dose rates (in the order of tens of millisieverts per microsecond) on the activity of the produced endoglucanase, amount of biomass and extra-cellular protein, was studied in batch cultivation conditions. In the dose range of 200–1200 mSv, some enhancement of endoglucanase activity was obtained: around 18%–32%, despite the drop of the biomass amount, compared with the untreated material. PMID:26019569