Готові списки джерел за темами / Wzb gene

Добірка наукової літератури з теми "Wzb gene"

Автор: Grafiati
Опубліковано: 14 березня 2023

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Статті в журналах з теми "Wzb gene"

1

Reid, Anne N., and Chris Whitfield. "Functional Analysis of Conserved Gene Products Involved in Assembly of Escherichia coli Capsules and Exopolysaccharides: Evidence for Molecular Recognition between Wza and Wzc for Colanic Acid Biosynthesis." Journal of Bacteriology 187, no. 15 (August 1, 2005): 5470–81. http://dx.doi.org/10.1128/jb.187.15.5470-5481.2005.

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ABSTRACT Group 1 capsular polysaccharides (CPSs) of Escherichia coli and some loosely cell-associated exopolysaccharides (EPSs), such as colanic acid, are assembled by a Wzy-dependent polymerization system. In this biosynthesis pathway, Wza, Wzb, and Wzc homologues are required for surface expression of wild-type CPS or EPS. Multimeric complexes of Wza in the outer membrane are believed to provide a channel for polymer export; Wzc is an inner membrane tyrosine autokinase and Wzb is its cognate phosphatase. This study was performed to determine whether the Wza, Wzb, and Wzc proteins for colanic acid expression in E. coli K-12 could function in the E. coli K30 prototype group 1 capsule system. When expressed together, colanic acid Wza, Wzb, and Wzc could complement a wza-wzb-wzc defect in E. coli K30, suggesting conservation in their collective function in Wzy-dependent CPS and EPS systems. Expressed individually, colanic acid Wza and Wzb could also function in K30 CPS expression. In contrast, the structural requirements for Wzc function were more stringent because colanic acid Wzc could restore translocation of K30 CPS to the cell surface only when expressed with its cognate Wza protein. Chimeric colanic acid-K30 Wzc proteins were constructed to further study this interaction. These proteins could restore K30 biosynthesis but were unable to couple synthesis to export. The chimeric protein comprising the periplasmic domain of colanic acid Wzc was functional for effective K30 CPS surface expression only when coexpressed with colanic acid Wza. These data highlight the importance of Wza-Wzc interactions in group 1 CPS assembly.
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2

Rahn, Andrea, Kostantinos Beis, James H. Naismith, and Chris Whitfield. "A Novel Outer Membrane Protein, Wzi, Is Involved in Surface Assembly of the Escherichia coli K30 Group 1 Capsule." Journal of Bacteriology 185, no. 19 (October 1, 2003): 5882–90. http://dx.doi.org/10.1128/jb.185.19.5882-5890.2003.

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ABSTRACT Escherichia coli group 1 K antigens form a tightly associated capsule structure on the cell surface. Although the general features of the early steps in capsular polysaccharide biosynthesis have been described, little is known about the later stages that culminate in assembly of a capsular structure on the cell surface. Group 1 capsule biosynthesis gene clusters (cps) in E. coli and Klebsiella pneumoniae include a conserved open reading frame, wzi. The wzi gene is the first of a block of four conserved genes (wzi-wza-wzb-wzc) found in all group 1 K-antigen serotypes. Unlike wza, wzb, and wzc homologs that are found in gene clusters responsible for production of exopolysaccharides (i.e., predominantly cell-free polymer) in a range of bacteria, wzi is found only in systems that assemble capsular polysaccharides. The predicted Wzi protein shows no similarity to any other known proteins in the databases, but computer analysis of Wzi predicted a cleavable signal sequence. Wzi was expressed with a C-terminal hexahistidine tag, purified, and used for the production of specific antibodies that facilitated localization of Wzi to the outer membrane. Circular dichroism spectroscopy indicates that Wzi consists primarily of a β-barrel structure, and dynamic light scattering studies established that the protein behaves as a monomer in solution. A nonpolar wzi chromosomal mutant retained a mucoid phenotype and remained sensitive to lysis by a K30-specific bacteriophage. However, the mutant showed a significant reduction in cell-bound polymer, with a corresponding increase in cell-free material. Furthermore, examination of the mutant by electron microscopy showed that it lacked a coherent capsule structure. It is proposed that the Wzi protein plays a late role in capsule assembly, perhaps in the process that links high-molecular-weight capsule to the cell surface.
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3

Smith, Ben, and James D. Oliver. "In Situ Gene Expression by Vibrio vulnificus." Applied and Environmental Microbiology 72, no. 3 (March 2006): 2244–46. http://dx.doi.org/10.1128/aem.72.3.2244-2246.2006.

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ABSTRACT Strains of Vibrio vulnificus incubated in situ in natural estuarine waters during warm months continued to express katG (periplasmic catalase), rpoS (stress sigma factor), tufA (elongation factor), wza, and wzb (capsule synthesis). vvhA (hemolysin) was differentially expressed between environmental and clinical isolates. These results paralleled our in vitro findings.
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4

Nakar, David, and David L. Gutnick. "Involvement of a Protein Tyrosine Kinase in Production of the Polymeric Bioemulsifier Emulsan from the Oil-Degrading Strain Acinetobacter lwoffii RAG-1." Journal of Bacteriology 185, no. 3 (February 1, 2003): 1001–9. http://dx.doi.org/10.1128/jb.185.3.1001-1009.2003.

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ABSTRACT The genes associated with the biosynthesis of the polymeric bioemulsifier emulsan, produced by the oil-degrading Acinetobacter lwoffii RAG-1 are clustered within a 27-kbp region termed the wee cluster. This report demonstrates the involvement of two genes of the wee cluster of RAG-1, wzb and wzc, in emulsan biosynthesis. The two gene products, Wzc and Wzb were overexpressed and purified. Wzc exhibited ATP-dependent autophosphorylating protein tyrosine kinase activity. Wzb was found to be a protein tyrosine phosphatase capable of dephosphorylating the phosphorylated Wzc. Using the synthetic substrate p-nitrophenyl phosphate (PNPP) Wzb exhibited a V max of 12 μmol of PNPP min−1 mg−1 and a Km of 8 mM PNPP at 30°C. The emulsifying activity of mutants lacking either wzb or wzc was 16 and 15% of RAG-1 activity, respectively, suggesting a role for the two enzymes in emulsan production. Phosphorylation of Wzc was found to occur within a cluster of five tyrosine residues at the C terminus. Colonies from a mutant in which these five tyrosine residues were replaced by five phenylalanine residues along with those of a second mutant, which also lacked Wzb, exhibited a highly viscous colony consistency. Emulsan activity of these mutants was 25 and 24% of that of RAG-1, respectively. Neither of these mutants contained cell-associated emulsan. However, they did produce an extracellular high-molecular-mass galactosamine-containing polysaccharide. A model is proposed in which subunit polymerization, translocation and release of emulsan are all associated and coregulated by tyrosine phosphorylation.
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5

Rosche, Thomas M., Ben Smith, and James D. Oliver. "Evidence for an Intermediate Colony Morphology of Vibrio vulnificus." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4356–59. http://dx.doi.org/10.1128/aem.02937-05.

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ABSTRACT Vibrio vulnificus causes both food-borne disease and wound infections. Most V. vulnificus strains express capsular polysaccharide (CPS), which is required for the virulence of this organism. Under standard growth conditions, CPS expression is lost at a relatively high frequency (10−3 to 10−4), resulting in a switch from an opaque (Op, CPS+) colony morphology to a translucent (Tr, CPS−) colony morphology. The wzb gene, which encodes a phosphatase required for CPS expression, has been proposed to be involved in this switch through a site-specific deletion of the entire gene. In an examination of five strains, we found that the frequency of wzb deletion in Tr colonies varies by strain and therefore does not account for all the Tr colonies that are seen. In addition, we have identified a third, intermediate (Int) colony morphotype, in which the colonies appear less opaque but are not fully translucent. PCR studies have demonstrated that Int colonies still contain the wzb gene, while reverse transcriptase PCR studies have shown that although Int strains retain expression of wzb, in some cases the transcription of wzb is reduced. Int strains switch to a true Tr (wzb negative) morphotype at a very high frequency (nearly 100%) under certain conditions. Finally, Int colonies, which in some cases can easily be mistaken for Tr colonies, have been observed to occasionally revert to Op, while Tr colonies containing a wzb deletion presumably are unable to revert to the encapsulated form.
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6

Vincent, Carole, Patricia Doublet, Christophe Grangeasse, Elisabeth Vaganay, Alain J. Cozzone, and Bertrand Duclos. "Cells of Escherichia coli Contain a Protein-Tyrosine Kinase, Wzc, and a Phosphotyrosine-Protein Phosphatase, Wzb." Journal of Bacteriology 181, no. 11 (June 1, 1999): 3472–77. http://dx.doi.org/10.1128/jb.181.11.3472-3477.1999.

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ABSTRACT Two proteins of Escherichia coli, termed Wzc and Wzb, were analyzed for their capacity to participate in the reversible phosphorylation of proteins on tyrosine. First, Wzc was overproduced from its specific gene and purified to homogeneity by affinity chromatography. Upon incubation in the presence of radioactive ATP, it was found to effectively autophosphorylate. Two-dimensional analysis of its phosphoamino acid content revealed that it was modified exclusively at tyrosine. Second, Wzb was also overproduced from the corresponding gene and purified to homogeneity by affinity chromatography. It was shown to contain a phosphatase activity capable of cleaving the synthetic substrate p-nitrophenyl phosphate intop-nitrophenol and free phosphate. In addition, it was assayed on individual phosphorylated amino acids and appeared to dephosphorylate specifically phosphotyrosine, with no effect on phosphoserine or phosphothreonine. Such specificity for phosphotyrosine was confirmed by the observation that Wzb was able to dephosphorylate previously autophosphorylated Wzc. Together, these data demonstrate, for the first time, that E. coli cells contain both a protein-tyrosine kinase and a phosphotyrosine-protein phosphatase. They also provide evidence that this phosphatase can utilize the kinase as an endogenous substrate, which suggests the occurrence of a regulatory mechanism connected with reversible protein phosphorylation on tyrosine. From comparative analysis of amino acid sequences, Wzc was found to be similar to a number of proteins present in other bacterial species which are all involved in the synthesis or export of exopolysaccharides. Since these polymers are considered important virulence factors, we suggest that reversible protein phosphorylation on tyrosine may be part of the cascade of reactions that determine the pathogenicity of bacteria.
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7

Péant, B., G. LaPointe, C. Gilbert, D. Atlan, P. Ward, and D. Roy. "Comparative analysis of the exopolysaccharide biosynthesis gene clusters from four strains of Lactobacillus rhamnosus." Microbiology 151, no. 6 (June 1, 2005): 1839–51. http://dx.doi.org/10.1099/mic.0.27852-0.

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The exopolysaccharide (EPS) biosynthesis gene clusters of four Lactobacillus rhamnosus strains consist of chromosomal DNA regions of 18·5 kb encoding 17 ORFs that are highly similar among the strains. However, under identical conditions, EPS production varies considerably among these strains, from 61 to 1611 mg l−1. Fifteen genes are co-transcribed starting from the first promoter upstream of wzd. Nevertheless, five transcription start sites were identified by 5′-RACE PCR analysis, and these were associated with promoter sequences upstream of wzd, rmlA, welE, wzr and wzb. Six potential glycosyltransferase genes were identified that account for the assembly of the heptasaccharide repeat unit containing an unusually high proportion of rhamnose. Four genes involved in the biosynthesis of the sugar nucleotide precursor dTDP-l-rhamnose were identified in the EPS biosynthesis locus, which is unusual for lactic acid bacteria. These four genes are expressed from their own promoter (P2), as well as co-transcribed with the upstream EPS genes, resulting in coordinated production of the rhamnose precursor with the enzymes involved in EPS biosynthesis. This is believed to be the first report demonstrating that the sequence, original organization and transcription of genes encoding EPS production are highly similar among four strains of Lb. rhamnosus, and do not vary with the amount of EPS produced.
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8

Rahn, Andrea, Jolyne Drummelsmith, and Chris Whitfield. "Conserved Organization in the cps Gene Clusters for Expression of Escherichia coli Group 1 K Antigens: Relationship to the Colanic Acid Biosynthesis Locus and the cps Genes from Klebsiella pneumoniae." Journal of Bacteriology 181, no. 7 (April 1, 1999): 2307–13. http://dx.doi.org/10.1128/jb.181.7.2307-2313.1999.

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ABSTRACT Group 1 capsules of Escherichia coli are similar to the capsules produced by strains of Klebsiella spp. in terms of structure, genetics, and patterns of expression. The striking similarities between the capsules of these organisms prompted a more detailed investigation of the cps loci encoding group 1 capsule synthesis. Six strains of K. pneumoniae and 12 strains of E. coli were examined. PCR analysis showed that the clusters in these strains are conserved in their chromosomal locations. A highly conserved block of four genes,orfX-wza-wzb-wzc, was identified in all of the strains. Thewza and wzc genes are required for translocation and surface assembly of E. coli K30 antigen. The conservation of these genes points to a common pathway for capsule translocation. A characteristic JUMPstart sequence was identified upstream of each cluster which may function in conjunction with RfaH to inhibit transcriptional termination at a stem-loop structure found immediately downstream of the “translocation-surface assembly” region of the cluster. Interestingly, the sequence upstream of thecps clusters in five E. coli strains and oneKlebsiella strain indicated the presence of IS elements. We propose that the IS elements were responsible for the transfer of thecps locus between organisms and that they may continue to mediate recombination between strains.
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9

Pettis, Gregg S., and Aheli S. Mukerji. "Structure, Function, and Regulation of the Essential Virulence Factor Capsular Polysaccharide of Vibrio vulnificus." International Journal of Molecular Sciences 21, no. 9 (May 5, 2020): 3259. http://dx.doi.org/10.3390/ijms21093259.

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Vibrio vulnificus populates coastal waters around the world, where it exists freely or becomes concentrated in filter feeding mollusks. It also causes rapid and life-threatening sepsis and wound infections in humans. Of its many virulence factors, it is the V. vulnificus capsule, composed of capsular polysaccharide (CPS), that plays a critical role in evasion of the host innate immune system by conferring antiphagocytic ability and resistance to complement-mediated killing. CPS may also provoke a portion of the host inflammatory cytokine response to this bacterium. CPS production is biochemically and genetically diverse among strains of V. vulnificus, and the carbohydrate diversity of CPS is likely affected by horizontal gene transfer events that result in new combinations of biosynthetic genes. Phase variation between virulent encapsulated opaque colonial variants and attenuated translucent colonial variants, which have little or no CPS, is a common phenotype among strains of this species. One mechanism for generating acapsular variants likely involves homologous recombination between repeat sequences flanking the wzb phosphatase gene within the Group 1 CPS biosynthetic and transport operon. A considerable number of environmental, genetic, and regulatory factors have now been identified that affect CPS gene expression and CPS production in this pathogen.
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10

Smith, Ben, and James D. Oliver. "In Situ and In Vitro Gene Expression by Vibrio vulnificus during Entry into, Persistence within, and Resuscitation from the Viable but Nonculturable State." Applied and Environmental Microbiology 72, no. 2 (February 2006): 1445–51. http://dx.doi.org/10.1128/aem.72.2.1445-1451.2006.

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ABSTRACT Isolation of Vibrio vulnificus during winter months is difficult due to the entrance of these cells into the viable but nonculturable (VBNC) state. While several studies have investigated in vitro gene expression upon entrance into and persistence within the VBNC state, to our knowledge, no in situ studies have been reported. We incubated clinical and environmental isolates of V. vulnificus in estuarine waters during winter months to monitor the expression of several genes during the VBNC state and compared these to results from in vitro studies. katG (periplasmic catalase) was down-regulated during the VBNC state in vitro and in situ compared to the constitutively expressed gene tufA. Our results indicate that the loss of catalase activity we previously reported is a direct result of katG repression, which likely accounts for the VBNC response of this pathogen. While expression of vvhA (hemolysin) was detectable in environmental strains during in situ incubation, it ceased in all cases by ca. 1 h. These results suggest that the natural role of hemolysin in V. vulnificus may be in osmoprotection and/or the cold shock response. Differences in expression of the capsular genes wza and wzb were observed in the two recently reported genotypes of this species. Expression of rpoS, encoding the stress sigma factor RpoS, was continuous upon entry into the VBNC state during both in situ and in vitro studies. We found the half-life of mRNA to be less than 60 minutes, confirming that mRNA detection in these VBNC cells is a result of de novo RNA synthesis.
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Дисертації з теми "Wzb gene"

1

Iodice, Domenico. "Construction and characterization of probiotic Lactobacillus rhamnosus GG deletion mutant for extracellular polysaccharide (EPS) biosynthesis regulator." Doctoral thesis, Università di Siena, 2018. http://hdl.handle.net/11365/1037713.

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Lactobacillus rhamnosus GG ATCC 53103 (LGG) is a probiotic microorganism producing a galactose-rich exopolysaccharide (EPS) surrounding the cell wall involved in adhesion and biofilm formation. The EPS gene cluster is composed by 16 genes associated to EPS biosynthesis. The wzb gene is an ortholog of the Streptococcus pneumoniae cpsB, encoding a protein phosphatase involved in the regulation of capsule production. In order to study the role of wzb gene in EPS biosynthesis, a L. rhamnosus GG wzb deletion mutant was constructed. Deletion of wzb produced a 12 minutes reduction of duplication time during growth. Deletion mutant strain produced smaller colonies than wild-type strain. Alcian Blue and India Ink staining denoted a strong reduction of the halo surrounding cells likely associated to EPS in Δwzb strain. Zeta potential analysis showed 2 bacterial populations in the Δwzb strain, while a single population was present in wild type indicating different Zeta potential values and consequently different electrokinetic properties of bacterial surfaces in the isogenic strains. Flow cytometry and dot blot analyses were used to assess the binding of Wheat Germ Agglutinin (WGA) and Chum Salmon Lectin 3 (CSL-3) lectins to the Nacetylglucosamine and rhamnose residues of EPS. In presence of WGA, 2 bacterial populations were observed in Δwzb strain, while a single population in wild type strain. In Δwzb strain a strong reduction of CSL-3 binding was observed. Furthermore, deletion of wzb is responsible of a significant reduction in biofilm production as estimated by crystal violet coloration. A general reduction of gene expression level of the EPS gene cluster was observed in Δwzb strain from the mid exponential to the early stationary growth phases. The present data reported the first inactivation of wzb gene in L. rhamnosus and the functional characterization of the Δwzb strain confirmed a role of Wzb phosphatase in EPS production.
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2

Neveu, Françoise. "Des gens et des lettres, et www?" Paris 7, 1997. http://www.theses.fr/1997PA070102.

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La problématique de départ était, au travers d'une démarche ethnométhodologique, d'aller a la rencontre de professionnels de la lettre. Qui sont ces "gens" qui tournent autour de la "lettre", la dessinent, l'écrivent, la composent, la regardent, la mettent en regard de l'image, la mettent en recherche ? Sous la figure emblématique du "WWW", quels sont leurs rapports avec les objets lettre et livre, avec la macroculture environnante ? La méthodologie pour en rendre compte n'est pas du tout extérieure au champ de l'étude : elle est au contraire au cœur de la recherche. Utiliser les arguments (au sens mathématique du terme) fondamentaux des savoir-faire pour donner a voir les gens qui les utilisent. Les termes de "balisage", "navigation", "niveaux de lecture", "connotation" (sens second), sont des termes de métier. S'appuyer sur les concepts d'ethnométhodologie (notion de membre, réflexivité, indexicalitée, distance) dans une représentation qui ne soit pas simplement métaphorique : le voyage de Marco Polo, mais un parcours selon les procédures et modalités même des réseaux multimédia. La thèse est de contribuer par la pratique a une réflexion sur l'ébauche de la réalisation d'un "objet" : la cartographie d'un service web, qui pose les trois paradigmes, "gens", "lettres", "WWW" et les traverse en un syntagme qui ne soit pas linéaire mais en maillage, en réseau. Cette optique "d'objet" n'est ni en rupture (objet séparé), ni totalisante (objet auto-suffisant), mais en ouverture, en prolongements, ou les changements d'angle, la navigation, offrent la possibilité de dimensions multiples. L'objet, dont l'architecture rejoint la structure de la recherche, est mis en mouvement par une transversalité la moins linéaire possible, par le choix d'un acte d'écrire, the act of writing, et de "l'oralité". Son décryptage révèle des mots-clés dans les paradigmes, qui indiquent la possibilité d'autres parcours et l'ouverture a une complémentarité (jointe ou disjointe) en devenir
The starting point for this thesis was te use an ethnomethodological approach to look at professionals in the print trade. Who are these "people" who spend their time with "letters", drawing them, writing them, composing them, looking at them, making them into images and sending them in research ? Looking at them from the angle of the emblematic "WWW", what relation do they have with objects letter and book, and with the surrounding culture as a whole ? The methodology applied actually lies at the heart of the research field itself. It involves using the fundamental arguments (in the mathematical sense) of a set of skills to render the people who use these skills sisible. The terms "marking up", "navigation", "levels of reading", "connotation" (associated meaning) are trade terms. The ethnomethodological concepts of member, reflexivity, indexicality and distance are used to produce a representation that is not purely metaphorical - Marco Polo's travels but also a journey using the very same principle as multimedia networks. This thesis is an attempt to think practically about how "objects" are created - the cartography of a web service, based on thre paradigms of "people", "letters", "WWW", using a network-looped rather than a linear syntagmatics. This approach to "objects" neither breaks them up into separate objects nor elevated them into total self-sufficient wholes ; it broadens and extends the perspective, so that the change of angles, the process of navigation opens up a broad range of dimensions. The architecture of the objects resembles the structure of the search. It is set in motion by a cross- functionality which is maximally non-linear, trough the act of writing and "orality". Deciphering this cross-functionality reveals key-words in the paradigms, and by choosing one, one can set off on other navigation, offering an emerging form of complementarity (joint or disjoint)
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3

Santini, Marina. "Automatic identification of genre in Web pages." Thesis, University of Brighton, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439208.

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4

DEETER, ANTHONY E. Deeter. "A Web-Based Software System Utilizing Consensus Networks to Infer Gene Interactions." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron152302071289795.

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5

Bara, Olivier. "Le théâtre de l'opéra-comique entre 1822 et 1827 la difficile recherche d'un genre moyen /." Lille : A.N.R.T, Université de Lille III, 1998. http://bibpurl.oclc.org/web/24931.

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6

France, Jacques. "Theadelpheia in de Romeinse Periode : Een bijdrage op basis van onuitgegeven papyri in de universiteitsbibliotheek te Gent /." Online version, 1994. http://bibpurl.oclc.org/web/21981.

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7

Ullestad, Ove. "La légende des sept dormants les gens de la caverne (Ahl al-Kahf): exégèses islamiques d'une légende hagiographique /." Online version, 1993. http://bibpurl.oclc.org/web/25559.

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8

Kennedy, Alistair. "Automatic genre classification of home pages on the web /." Halifax, N.S. : Dalhousie University, 2004. http://torch.cs.dal.ca/%7Ekennedy/genre%5Fthesis.pdf.

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Thesis (B.C.S.)--Dalhousie University, Halifax.
"Submitted in partial fulfillment of the requirements for the degree of bachelor of computer science with honours at Dalhousie University, Halifax, Nova Scotia, April 2004." Includes bibliographical references (p. 33-35). Also available in PDF via the World Wide Web.
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9

Santa-Maria, Luis. "Visual genre conventions and user performance on the web." Thesis, University of Reading, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515751.

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10

L'Étoile, Jeannine de. "Amorce de caractérisation textuelle du genre site Web informatif." Mémoire, Université de Sherbrooke, 2003. http://savoirs.usherbrooke.ca/handle/11143/2400.

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Анотація:
La présente recherche se penche sur l'étude du cyberdocument dont la visée est d'informer. Elle se propose de reconnaître et de recenser différents mécanismes--langagiers et visuels--propres au site Web informatif afin de caractériser un modèle émergent du genre. Réalisée à partir d'un corpus de dix sites tant des secteurs public que parapublic ou privé, l'exploration s'est faite au regard de deux principaux niveaux structurels du texte, à savoir la microstructure et la superstructure. Ainsi, dans un premier temps, l'application de deux formules qui rendent compte d'approches différentes de la lisibilité (test évaluant l'indice de brouillard, de Gunning, et formule simplifiée de Flesch) a permis une évaluation nuancée de cette variable retenue au niveau microstructurel. Nous appuyant ensuite sur divers principes du modèle de l'Architecture textuelle, développé par Jacques Virbel (1985) et Elsa Pascual (1991), nous nous sommes attardés, dans un deuxième temps, à des mécanismes qui concernent la superstructure: marqueurs d'appartenance, organisateurs énumératifs, spatiaux et temporels ainsi que procédés de segmentation. Il est ressorti de l'analyse un certain défaut de lisibilité, conséquent de phrases et de mots longs. L'observation a aussi mis en lumière la forte segmentation des contenus, et ce, tant au plan local que global du cybertexte. Enfin, il apparaît que la mise en forme matérielle, tout en participant à la structuration et à la hiérarchisation des composantes textuelles, signe également l'appartenance des parties au tout qui les englobe. Sans être exhaustive, la présente recherche brosse toutefois un portrait assez précis des pratiques mises en oeuvre dans les sites du corpus par rapport aux variables observées. Sans conteste, elle ouvre la voie à la réflexion critique d'autres chercheurs du domaine.
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Книги з теми "Wzb gene"

1

Prakash, Ambegaonkar, ed. Intranet resource kit. Berkeley, CA: Osborne/McGraw-Hill, 1997.

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2

Prakash, Ambegaonkar, ed. Intranet resource kit. Berkeley, Calif: Osborne/McGraw-Hill, 1997.

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3

H, Burkman Katherine, and Roof Judith 1951-, eds. Staging the rage: The web of misogyny in modern drama. Madison [NJ]: Fairleigh Dickinson University Press, 1998.

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4

Architects of the Web: 1,000 days that built the future of business. New York: John Wiley & Sons, 1997.

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5

Andersson, Eve Astrid. Software engineering for Internet applications. Cambridge, Mass: MIT Press, 2006.

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6

Thielen, Johan Everard Dirk Marie. Man ende wyb ne hebben nen twiet gut: Man en vrouw hebben geen gedeeld goed (Sachsenspiegel I.31.1) : een studie over de geschiedenis van het huwelijksgoederenrecht in Nederlandse en Belgische gewesten. Lelystad: Koninklijke Vermande, 2001.

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7

Balagué, Christine. Facebook, Twitter et les autres--: Intégrer les réseaux sociaux dans une stratégie d'entreprise. Paris: Pearson, 2010.

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8

Hypermedia Genes. Morgan & Claypool, 2009.

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9

Wuketits, Franz M. WB-Forum, Bd.51, Gene, Kultur und Moral. Wissenschaftliche Buchgesellschaft, 1990.

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10

Fu, Junning. A Dream of Returning to 1997. Edited by Carlos Rojas and Andrea Bachner. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199383313.013.15.

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This chapter analyzes the Chinese web fantasy novelA Dream of Returning to 1997,created and serialized between 2004 and 2005 by the pseudonymous author Tonglingzhe, as a basis for reflecting upon the medial and commercial pragmatics as well as the ideological framework of web literature. With its plot of a web fantasy aficionado who achieves literary and economic success only after traveling back in time and reaping the fruits of his earlier unproductive spare-time activity, the novel offers a self-referential commentary on the genre of web fantasy and its infrastructure. Apart from fictionalizing the history of the genre and the company that runs its major platform (Qidian), the novel also reflects on, questions, and elides the binary oppositions between original and copy, as well as high literature and popular culture, thus allowing for a reflection on the real and imaginary economies and mediascapes of capitalist modernity.
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Частини книг з теми "Wzb gene"

1

Islam, A. K. M. Tauhidul, Chae-Gyun Lim, and Byeong-Soo Jeong. "Parallel Gene Clustering Using MapReduce." In Web-Age Information Management, 372–81. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11538-2_34.

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Pérez-Llantada, Carmen, and María-José Luzón. "Networks of genres in Web 2.0." In Genre Networks, 1–18. New York: Routledge, 2022. http://dx.doi.org/10.4324/9781003147732-1.

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Skaruz, Jaroslaw, and Franciszek Seredynski. "Web Application Security through Gene Expression Programming." In Lecture Notes in Computer Science, 1–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-01129-0_1.

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Zuo, Jie, Changjie Tang, and Tianqing Zhang. "Mining Predicate Association Rule by Gene Expression Programming." In Advances in Web-Age Information Management, 92–103. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45703-8_9.

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5

Zuo, Jie, Chang-jie Tang, Chuan Li, Chang-an Yuan, and An-long Chen. "Time Series Prediction Based on Gene Expression Programming." In Advances in Web-Age Information Management, 55–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-27772-9_7.

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Meyer zu Eissen, Sven, and Benno Stein. "Genre Classification of Web Pages." In KI 2004: Advances in Artificial Intelligence, 256–69. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30221-6_20.

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Badea, Liviu. "Semantic Web Reasoning for Analyzing Gene Expression Profiles." In Principles and Practice of Semantic Web Reasoning, 78–89. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11853107_6.

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8

Sun, Feixian. "Gene-Certificate Based Model for User Authentication and Access Control." In Web Information Systems and Mining, 228–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16515-3_29.

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9

Xu, Kai. "Web-Based Genomic Information Integration with Gene Ontology." In Frontiers of WWW Research and Development - APWeb 2006, 812–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11610113_78.

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10

Masseroli, Marco, and Marco Tagliasacchi. "Web Resources for Gene List Analysis in Biomedicine." In Annals of Information Systems, 117–41. Boston, MA: Springer US, 2010. http://dx.doi.org/10.1007/978-1-4419-1274-9_8.

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Тези доповідей конференцій з теми "Wzb gene"

1

Lin, Kuan-Ting, Chia-Hung Liu, Jen-Jie Chiou, Wen-Hsien Tseng, Kuang-Lung Lin, and Chun-Nan Hsu. "Gene Name Service: No-Nonsense Alias Resolution Service for Homo Sapiens Genes." In 2007 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology - Workshops. IEEE, 2007. http://dx.doi.org/10.1109/wi-iatw.2007.30.

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2

Lin, Kuan-Ting, Chia-Hung Liu, Jen-Jie Chiou, Wen-Hsien Tseng, Kuang-Lung Lin, and Chun-Nan Hsu. "Gene Name Service: No-Nonsense Alias Resolution Service for Homo Sapiens Genes." In 2007 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology - Workshops. IEEE, 2007. http://dx.doi.org/10.1109/wiiatw.2007.4427568.

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3

Azmi, Muhammad Bilal. "In Silico Basis to Understand the Molecular Interaction of Human NNATGene With Therapeutic Compounds of Anorexia Nervosa." In INTERNATIONAL CONFERENCE ON BIOLOGICAL RESEARCH AND APPLIED SCIENCE. Jinnah University for Women, Karachi,Pakistan, 2022. http://dx.doi.org/10.37962/ibras/2022/1-2.

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Introduction: Anorexia nervosa (AN)– a perplexing heritable, psychiatric eating disorder condition characterized by low body weight. The prevalence of AN is found to be high in younger age adults with a raised mortality rate. Genetic studies have been insufficient in identifying the role of specific genes that predispose an individual to AN. Objectives: The objective was to explore the role of NNAT (neuronatin) gene variants and its structure based molecular interactions with therapeutic compounds of AN. To investigate the role of structural missense pathogenic variants (SNPs: single nucleotide polymorphism) or change in the expression of NNAT with possibility of AN. Methodology: NNAT gene protein coding sequence, SNPs were extracted and validated from public databases. Gene to gene interactions, protein localization and human tissue-specific expression analysis of NNAT gene showed highest tissue-specific expression in the brain. Estimates of functional impact of SNPs using transcript sequence and machine learning based approaches (in silico algorithms) were computed to investigate the pathogenicity and protein stability of NNAT variants. Sequence alignment, ab initio 3D structure-modeling of wild-type, validation and recognition of binding cavities of NNAT through in silico web based tools were performed. Alternate model prediction for NNAT variants through residue specific mutation approach and structural validation were also done through Chimera tool. The 3D compounds involved in the management of AN were extracted from the Drug Bank database, afterwards energy minimization and rule of drug-likeness were performed. The eligible 3D compounds were docked with identified variants, to evaluate the drugs binding molecular mechanics. Results & Conclusion: Overall, 10 NNAT missense variants were extracted on the basis of minor allele frequency (MAF < 0.001) and other consequence types. Further three variants were selected among ten according to the transcript sequence, which includesrs542858994 (F26L), rs539681368 (C30Y) and rs542858994 (F53L). Structures for these variants’ protein were generated, validated and docked with AN drugs. The functional impact analyses of selected missense SNPs of NNAT showed high risk pathogenicity and can cause changes in the physical and chemical properties of amino acids, thus affecting the function of protein. The computation of binding energies of variants of NNAT with AN compounds strengthen the hypothesis that these variants strongly interact with the AN drugs, hence reducing the level of free NNAT as well as target drugs, for neuronal functioning. Therefore, constitutionally reduced level of NNAT and binding of NNAT variants with AN drugs may serve as the basis to increases the susceptibility towards AN.
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4

Almeida, Jamile Aislin Silva de, and Carla Yasmym De Carvalho Lima. "NUTRIGENÔMICA E AS DOENÇAS CRÔNICAS NÃO TRANSMISSÍVEIS: UMA REVISÃO BIBLIOGRÁFICA ENTRE OS POLIFORMISMOS E COMPOSTOS BIOATIVOS." In II Congresso Brasileiro de Biologia Molecular On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/2323.

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Introdução: A presença de poliformismos associados ao risco de Doenças Crônicas Não Transmissíveis (DCNTs) se tornou um despertar de interesse para a genômica nutricional, que tem como foco o estudo da relação gene-nutriente, uma vez que vários nutrientes e compostos bioativos podem ter um papel importante na diminuição de tais doenças nos indivíduos. Objetivo: Analisar a contribuição da nutrigenômica para precaver os casos de DCNT, como obesidade, Diabetes Mellitus II, câncer, doenças inflamatórias intestinais e outras complicações, durante os últimos 3 anos. Material e Métodos: A pesquisa foi realizada a partir de 7 estudos retirados nas bases de dados SciElo, Web of, Science e Scopus. Publicados no período de 2018 e 2020, utilizando as palavras-chaves: “doenças crônicas não transmissíveis”, “nutrição”, “nutrigenômica” e “poliformismo”. Resultados: Estudos demonstraram que existem em nosso genoma diversos tipos de poliformismos, associados a incidência de DCNTs. Dentre eles temos os Poliformismos de Nucleotídeo Único (SNps) nos genes FTO; FADS1, ADRB2, LEPR, IL-6, LPIN1, AdipoR1, PPARγ, ZnT8, TCF7L2, BRCA1, PPM1K, RVD, DIO1-2, GPX-1,3, SEPHS1, SEPSECS e TXNRD2 e FOXO3. Com relação aos alimentos, temos aqueles à base de plantas, especialmente as frutas e hortaliças, que são fontes de uma variedade de compostos bioativos, como terpenóides, polifenóis, compostos de enxofre, alcalóides e poliaminas, em que a ingestão está ligado à proteção contra doenças crônicas. Compostos polifenóis, por exemplo, quando entram na via do fator nuclear κB (NF-κB) exercem a função de transcrição de vários genes, incluindo os que se relacionam com a produção de citocinas pró-inflamatórias, quimiocinas e moléculas essenciais para a resposta inflamatória, que irão exerce importante ação no retardo de DCNTs. Conclusão: Os resultados nutrigenômicos servem como parâmetro para a análise das DCNTs no período de três anos. Mas, é necessário corroborar que elas são resultado de uma rede de fatores, não apenas genéticos e nutricionais, mas também, ambientais, como a prática de atividade física, uso de álcool e tabaco e fatores individuais. Sendo de grande relevância entender melhor a interação gene-nutriente e seu papel para a saúde da população portadora de DCNTs ou em processo de tratamento.
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Peng, Jiajie, Hongxiang Li, Yadong Wang, and Jin Chen. "A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks." In BCB '15: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2808719.2816835.

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6

Chen, Guangyu, and Ben Choi. "Web page genre classification." In the 2008 ACM symposium. New York, New York, USA: ACM Press, 2008. http://dx.doi.org/10.1145/1363686.1364247.

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7

Jiangpeng, Lin, and Li Jing. "Study of Electricity Consumption Forecasting Model Based on Gene Expression Programming." In 2009 Second Pacific-Asia Conference on Web Mining and Web-based Application (WMWA). IEEE, 2009. http://dx.doi.org/10.1109/wmwa.2009.80.

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Mizutani, Eriko, and Jun Sese. "GOMA: Web utility for direct finding of enriched Gene Ontology terms from gene expression profile." In 2008 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE). IEEE, 2008. http://dx.doi.org/10.1109/bibe.2008.4696687.

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9

Ceresa, Mario, Marco Masseroli, and Alessandro Campi. "A Web-enabled Database of Human Gene Expression Controlled Annotations for Gene List Functional Evaluation." In 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2007. http://dx.doi.org/10.1109/iembs.2007.4352307.

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Heine, Alexandre A. P., Eduardo P. S. Santos, Marcelo F. Lima, and Sérgio Lifschitz. "Aplicação Web de Processamento, Clustering e Visualização de Grafos de Genes de Workflows Científicos." In Anais Estendidos do Simpósio Brasileiro de Banco de Dados. Sociedade Brasileira de Computação - SBC, 2021. http://dx.doi.org/10.5753/sbbd_estendido.2021.18163.

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Este trabalho propõe uma aplicação web de apoio a dados provenientes de workflows científicos de genes diferencialmente expressos (DEGs) que envolvem análises de sequenciamento de RNA. Assim, procura-se contribuir com formas de manuseio desses dados, permitindo a formação de um grafo de genes, por meio de dados de interação de genes, assim como a criação de subgrafos e clusters representativos, utilizando-se de informações obtidas de dados armazenados em arquivos de string. Esses arquivos são processados conforme são realizados novos pedidos na aplicação e, então, armazenados em um banco de dados relacional, possibilitando a pesquisadores visualizarem e manusearem grafos de genes para seus estudos.
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Звіти організацій з теми "Wzb gene"

1

Wu, Alex, and Myriam Abramson. Image Classification for Web Genre Identification. Fort Belvoir, VA: Defense Technical Information Center, January 2012. http://dx.doi.org/10.21236/ada599790.

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2

Barkay, Tamar. Lateral Gene Transfer Among Subsurface Bacteria: Horizontal Gene Flow in Microbial Communities: A Special Focus Issue, Web Focus and Supplement. Office of Scientific and Technical Information (OSTI), November 2009. http://dx.doi.org/10.2172/967075.

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3

Peel, Sheila A., Karen Kopydlowski, and Roland Carel. Development of a Web-Enabled Informatics Platform for Manipulation of Gene Expression Data. Fort Belvoir, VA: Defense Technical Information Center, December 2004. http://dx.doi.org/10.21236/ada433520.

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Elizur, Abigail, Amir Sagi, Gideon Hulata, Clive Jones, and Wayne Knibb. Improving Crustacean Aquaculture Production Efficiencies through Development of Monosex Populations Using Endocrine and Molecular Manipulations. United States Department of Agriculture, June 2010. http://dx.doi.org/10.32747/2010.7613890.bard.

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Background Most of Australian prawn aquaculture production is based on P. monodon. However, the Australian industry is under intense competition from lower priced overseas imports. The availability of all-female monosex populations, by virtue of their large size and associated premium prize, will offer competitive advantage to the industry which desperately needs to counteract competitors within this market. As for the redclaw production in Israel, although it is at its infancy, the growers realized that the production of males is extremely advantageous and that such management strategy will change the economic assumptions and performances of this aquaculture to attract many more growers. Original objectives (as in original proposal) Investigating the sex inheritance mechanism in the tiger prawn. Identification of genes expressed uniquely in the androgenic gland (AG) of prawns and crayfish. The above genes and/or their products will be used to localize the AG in the prawn and manipulate the AG activity in both species. Production of monosex populations through AG manipulation. In the prawn, production of all-female populations and in the crayfish, all-male populations. Achievements In the crayfish, the AG cDNA library was further screened and a third AG specific transcript, designated Cq-AG3, had been identified. Simultaneously the two AG specific genes, which were previously identified, were further characterized. Tissue specificity of one of those genes, termed Cq-AG2, was demonstrated by northern blot hybridization and RNA in-situ hybridization. Bioinformatics prediction, which suggested a 42 amino acid long signal anchor at the N-terminus of the deduced Cq-AG2, was confirmed by immunolocalization of a recombinant protein. Cq-IAG's functionality was demonstrated by dsRNA in-vivo injections to intersex crayfish. Cq-IAGsilencing induced dramatic sex-related alterations, including male feature feminization, reduced sperm production, extensive testicular apoptosis, induction of the vitellogeningene expression and accumulation of yolk proteins in the ovaries. In the prawn, the AG was identified and a cDNA library was created. The putative P. monodonAG hormone encoding gene (Pm-IAG) was identified, isolated and characterized for time of expression and histological localization. Implantation of the AG into prawn post larvae (PL) and juveniles resulted in phenotypic transformation which included the appearance of appendix masculina and enlarged petasma. The transformation however did not result in sex change or the creation of neo males thus the population genetics stage to be executed with Prof. Hulata did not materialized. Repeated AG implantation is currently being trialed. Major conclusions and Implications, both scientific and agricultural Cq-IAG's involvement in male sexual differentiation had been demonstrated and it is strongly suggested that this gene encodes an AG hormone in this crayfish. A thorough screening of the AG cDNA library shows Cq-IAG is the prominent transcript within the library. However, the identification of two additional transcripts hints that Cq-IAG is not the only gene mediating the AG effects. The successful gene silencing of Cq-IAG, if performed at earlier developmental stages, might accomplish full and functional sex reversal which will enable the production of all-male crayfish populations. Pm-IAG is likely to play a similar role in prawns. It is possible that repeated administration of the AG into prawn will lead to the desired full sex reversal, so that WZ neo males, crossed with WZ females can result in WW females, which will form the basis for monosex all-female population.
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5

Fluhr, Robert, and Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7696517.bard.

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Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.
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Zhao, Lili, Tao Li, Meijuan Dang, Ye Li, Hong Fan, Qian Hao, Dingli Song, et al. Association of methylenetetrahydrofolate reductase (MTHFR) C677T gene polymorphism with ischemic stroke risk in different populations: an updated meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2022. http://dx.doi.org/10.37766/inplasy2022.11.0037.

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Review question / Objective: Recently, increasing evidence has implicated methylenetetrahydrofolate reductase (MTHFR) gene mutation as a risk factor for ischemic stroke (IS) in the general population. However, studies have been inconclusive and lack evidence on specific populations. We aim to determine whether the MTHFR C677T variant is linked to an increased risk of IS in different age groups andregions. Information sources: A systematic search of PubMed, EMBASE, Cochrane Library, Web of Science, and CNKI databases for relevant observational studies will be undertaken.
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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Borgwardt, Stefan, Marco Cerami, and Rafael Peñaloza. Subsumption in Finitely Valued Fuzzy EL. Technische Universität Dresden, 2015. http://dx.doi.org/10.25368/2022.212.

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Aus der Einleitung: Description Logics (DLs) are a family of knowledge representation formalisms that are successfully applied in many application domains. They provide the logical foundation for the Direct Semantics of the standard web ontology language OWL2. The light-weight DL EL, underlying the OWL2 EL profile, is of particular interest since all common reasoning problems are polynomial in this logic, and it is used in many prominent biomedical ontologies like SNOMEDCT and the Gene Ontology.
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9

Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697123.bard.

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Анотація:
Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In plants, one set of this defense system is characterized by large families of TIR–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) resistance genes. The direct interaction between plant proteins harboring the TIR domain with proteins that transmit and facilitate a signaling pathway has yet to be shown. The Arabidopsis genome encodes TIR-domain containing genes that lack NBS and LRR whose functions are unknown. Here we investigated the functional role of such protein, TLW1 (TIR LECTIN WOUNDRESPONSIVE1). The TLW1 gene encodes a protein with two domains: a TIR domain linked to a lectin-containing domain. Our specific aim in this proposal was to examine the ramifications of the TL1-glycan interaction by; A) The functional characterization of TL1 activity in the context of plant wound response and B) Examine the hypothesis that wounding induced specific polysaccharides and examine them as candidates for TL-1 interactive glycan compounds. The Weizmann group showed TLW1 transcripts are rapidly induced by wounding in a JA-independent pathway and T-DNA-tagged tlw1 mutants that lack TLW1 transcripts, fail to initiate the full systemic wound response. Transcriptome methodology analysis was set up and transcriptome analyses indicates a two-fold reduced level of JA-responsive but not JA-independent transcripts. The TIR domain of TLW1 was found to interact directly with the KAT2/PED1 gene product responsible for the final b-oxidation steps in peroxisomal-basedJA biosynthesis. To identify potential binding target(s) of TL1 in plant wound response, the CCRC group first expressed recombinant TL1 in bacterial cells and optimized conditions for the protein expression. TL1 was most highly expressed in ArcticExpress cell line. Different types of extraction buffers and extraction methods were used to prepare plant extracts for TL1 binding assay. Optimized condition for glycan labeling was determined, and 2-aminobenzamide was used to label plant extracts. Sensitivity of MALDI and LC-MS using standard glycans. THAP (2,4,6- Trihydroxyacetophenone) showed minimal background peaks at positive mode of MALDI, however, it was insensitive with a minimum detection level of 100 ng. Using LC-MS, sensitivity was highly increased enough to detect 30 pmol concentration. However, patterns of total glycans displayed no significant difference between different extraction conditions when samples were separated with Dionex ICS-2000 ion chromatography system. Transgenic plants over-expressing lectin domains were generated to obtain active lectin domain in plant cells. Insertion of the overexpression construct into the plant genome was confirmed by antibiotic selection and genomic DNA PCR. However, RT-PCR analysis was not able to detect increased level of the transcripts. Binding ability of azelaic acid to recombinant TL1. Azelaic acid was detected in GST-TL1 elution fraction, however, DHB matrix has the same mass in background signals, which needs to be further tested on other matrices. The major findings showed the importance of TLW1 in regulating wound response. The findings demonstrate completely novel and unexpected TIR domain interactions and reveal a control nexus and mechanism that contributes to the propagation of wound responses in Arabidopsis. The implications are to our understanding of the function of TIR domains and to the notion that early molecular events occur systemically within minutes of a plant sustaining a wound. A WEB site (http://genome.weizmann.ac.il/hormonometer/) was set up that enables scientists to interact with a collated plant hormone database.
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10

Harman, Gary E., and Ilan Chet. Enhancement of plant disease resistance and productivity through use of root symbiotic fungi. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7695588.bard.

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The objectives of the project were to (a) compare effects ofT22 and T-203 on growth promotion and induced resistance of maize inbred line Mol7; (b) follow induced resistance of pathogenesis-related proteins through changes in gene expression with a root and foliar pathogen in the presence or absence of T22 or T-203 and (c) to follow changes in the proteome of Mol? over time in roots and leaves in the presence or absence of T22 or T-203. The research built changes in our concepts regarding the effects of Trichoderma on plants; we hypothesized that there would be major changes in the physiology of plants and these would be reflected in changes in the plant proteome as a consequence of root infection by Trichoderma spp. Further, Trichoderma spp. differ in their effects on plants and these changes are largely a consequence of the production of different elicitors of elicitor mixtures that are produced in the zone of communication that is established by root infection by Trichoderma spp. In this work, we demonstrated that both T22 and T-203 increase growth and induce resistance to pathogens in maize. In Israel, it was shown that a hydrophobin is critical for root colonization by Trichoderma strains, and that peptaibols and an expansin-like protein from Ttrichoderma probably act as elicitors of induced resistance in plants. Further, this fungus induces the jasmonate/ethylene pathway of disease resistance and a specific cucumber MAPK is required for transduction of the resistance signal. This is the first such gene known to be induced by fungal systems. In the USA, extensive proteomic analyses of maize demonstrated a number of proteins are differentially regulated by T. harzianum strain T22. The pattern of up-regulation strongly supports the contention that this fungus induces increases in plant disease resistance, respiratory rates and photosynthesis. These are all very consistent with the observations of effects of the fungus on plants in the greenhouse and field. In addition, the chitinolytic complex of maize was examined. The numbers of maize genes encoding these enzymes was increased about 3-fold and their locations on maize chromosomes determined by sequence identification in specific BAC libraries on the web. One of the chitinolytic enzymes was determined to be a heterodimer between a specific exochitinase and different endochitinases dependent upon tissue differences (shoot or root) and the presence or absence of T. harzianum. These heterodimers, which were discovered in this work, are very strongly antifungal, especially the one from shoots in the presence of the biocontrol fungus. Finally, RNA was isolated from plants at Cornell and sent to Israel for transcriptome assessment using Affymetrix chips (the chips became available for maize at the end of the project). The data was sent back to Cornell for bioinformatic analyses and found, in large sense, to be consistent with the proteomic data. The final assessment of this data is just now possible since the full annotation of the sequences in the maize Affy chips is just now available. This work is already being used to discover more effective strains of Trichoderma. It also is expected to elucidate how we may be able to manipulate and breed plants for greater disease resistance, enhanced growth and yield and similar goals. This will be possible since the changes in gene and protein expression that lead to better plant performance can be elucidated by following changes induced by Trichoderma strains. The work was in, some parts, collaborative but in others, most specifically transcriptome analyses, fully synergistic.
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