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Sakkie Pretorius Professor. Designing wine yeast for the future Pretorius, I. Holzapfel, W. Cambridge: Woodhead Publishing , p. Influence of diammonium phosphate addition to fermentation on wine biologicals Vilanova, M. Preedy, V. London: Academic Press , p.

Bioinformatics and Functional Genomics

Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae Borneman, A. Eckwahl, M. Toronto: Apple Academic Press , p. Wine, beer and cider: Unravelling the aroma profile Gamero, A. Berlin; Heidelberg: Springer, Springer Nature , p. Alcoholic Beverages. Controlling the highs and the lows of alcohol in wine Stockley, C. Peeters, A. New York: Nova Science Publishers , p. Three tests—regular t -test, Welch's test t -test modification assuming unequal variances and Wilcoxon Rank Sum Mann—Whitney test—were simultaneously applied to assess how possible violations of the assumptions underlying t -test homoscedasticity and normality affect statistical inference outcomes for the data.

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Raw p -values for each test statistic were corrected for multiplicity of comparisons using Benjamini—Hochberg correction. P -values indicated on graphs are derived from regular t -tests, with Welch and Wilcoxon Rank Sum test results which are more robust but more conservative in terms of adjusted p -values usually in agreement with regular t -tests Table S1. To identify the biological attributes required for DMSO tolerance, enrichment analyses for the 40 sensitive strains was performed with FunSpec at a corrected p -value of 0.

Table 1. Table 2. Overrepresentation analyses suggested that subunits of COG, a protein complex that mediates fusion of transport vesicles to Golgi compartments, were required for DMSO tolerance. Growth curve assays also confirmed sensitivity of the individual COG deletions under non-competitive conditions Figure 1B. Figure 1. Mutant strains were grown in competition with a GFP-expressing wild-type strain in the indicated DMSO concentrations and relative growth ratios treatment vs.

The ratio means and standard errors are shown for three independent cultures. Growth curves for three independent cultures were obtained for the indicated strains and doses of DMSO. Figure 2. Relative growth ratios were obtained for three independent cultures and analyzed as described in Materials and Methods. Growth curves were acquired from three independent cultures at the indicated doses.

Figure 3. Various chromatin remodeling mutants are sensitive to DMSO. For A—C,E , relative growth ratios were obtained and averaged for three independent cultures, while D displays average area under the curve data for growth curves acquired from three cultures. Figure 4. Relative growth assays were performed for three independent cultures. Figure 5.

Growth curves for three independent cultures were obtained in the indicated doses of DMSO. The area under the curve AUC means and standard error are shown. DMSO is a polar and aprotic solvent commonly utilized to solubilize chemicals during toxicological or pharmaceutical inquiries Santos et al.

Compared to other solvents within its class such as sulfolane, N,N -dimethylformamide, N -methyl-pyrrolidinone, or N,N -dimethyl acetamide, DMSO exhibits relatively limited acute toxicity Tilstam, , thus affording it preferred status within these fields. Despite its universality, DMSO's molecular mechanism s of action remain ambiguous, thus requiring investigations into the cellular processes and pathways it may perturb.

Here we conducted a genome-wide functional screen in the model eukaryote S. These results may indicate that DMSO's mechanism of toxicity in yeast is different from that exhibited in nematodes or human cells. However, if the toxic mechanism remains similar, it is feasible that compensatory cellular processes or genes are present in these mutants. During the preparation of this manuscript, a report was published describing functional profiling of yeast mutants in DMSO Zhang et al.

In this section, we discuss various aspects differentiating our investigation from Zhang et al.

Meeting report

First, while these researchers assessed growth of individual yeast mutants via colony size on solid media, we performed functional profiling in pooled liquid cultures under competitive growth conditions. Our analyses, in which DNA sequences unique to each strain are hybridized to a microarray after toxicant exposure, are able to discern small growth defects and can identify sensitive strains overlooked by other methods Table 4. However, the stringency of our DSSA may hinder identification of slow growing strains or those close to background levels.

Nevertheless, these data are extremely relevant to those conducting pooled growth assays, especially considering the increased popularity of automated screens and high-throughput multiplexed barcode sequencing to examine strain growth in DMSO-soluble toxicants or drugs Smith et al. The contrasting choice of doses may also account for differences in the DMSO-sensitive strains identified by each screen.

Finally, our overexpression data demonstrates that increased levels of Htz1p or Arp6p can rescue the growth of various deletion strains in DMSO Figure 5. Table 4. A comparison between studies identifying yeast genes responsible for DMSO tolerance. Microarray analyses assessing the response of S. Consistent with these findings, Pommier et al. Z deposition into chromatin Meneghini et al. Z Morillo-Huesca et al. Z at double-stranded DNA breaks Kalocsay et al. To separate effects of DMSO from a compound of interest, it is crucial for future yeast profiling studies to recognize that various deletion strains may fall out of pooled cultures during treatment with DMSO-solubilized drugs or toxicants.

Data gathered by our study can direct additional experimentation to decipher the cellular and molecular mechanisms of DMSO action. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Smith, Chris D. Vulpe is leader on Project 2]. The content is solely the responsibility of the authors and does not represent the official views of the funding agencies.

Brandon D. Conceived and designed the experiments: Brandon D. De La Rosa, and Chris D. Performed the experiments: Brandon D. Analyzed the data: Brandon D. Loguinov, Vanessa Y.

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  • Wrote the paper: Brandon D. Instead, you will look for proteins that physically interact with Nud1. While there are many ways to do this, we will consider just two of them. First, you could take a two-hybrid screening approach Chien et al. If the bait and prey proteins interact in a transformant, they form a protein complex that stimulates transcription of reporter genes. Alternatively, you could look for proteins that form a complex with Nud1, via direct or indirect interactions, by constructing a tandem affinity protein TAP —tagged version of Nud1 using cassettes that tag either the N- or C-terminus of the protein Tasto et al.

    The tagged Nud1 protein then can be isolated together with its binding partners by applying sequentially two different affinity purification methods, leading to a highly purified protein complex. You can determine the individual binding partners or detect all copurified proteins via mass spectrometry Tasto et al.

    Either approach helps to identify the role of Nud1 by revealing binding partners that may have been studied by other laboratories. The main tools provided by PomBase are summarized in Table 3.

    Ashkan Golshani

    PomBase is structured around gene pages that provide comprehensively curated data for each gene product. Here we describe the use of PomBase to find tentative clues for the cellular role of the elusive Nud1, identified in your studies. The GO controlled vocabulary is used to consistently describe the gene product attributes of molecular functions, biological processes, and cellular component localization or complex Ashburner et al. Because neither Nud1 nor its orthologs have been studied previously, no molecular function or biological process data are available.

    • Investigations in Yeast Functional Genomics and Molecular Biology.
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    • You see that Nud1 is found in the mitochondria along with other gene products. The gene page also provides phenotype data using the Fission Yeast Phenotype Ontology FYPO together with supporting information describing alleles and experimental conditions Harris et al. In addition, a visual screen of this deletion resource for mutants affecting cell cycle detected by effects on cell length and cell shape has provided broad morphology phenotype annotations for many gene products representing both viable cells and the terminal phenotypes of nonviable deletions Hayles et al.

      Because mutations in functionally related genes often confer the same phenotype, studying a list of the genes coannotated to your ontology term of interest may shed some light on the biological role of Nud1. In addition to GO terms and phenotypes, a wide range of other features can be queried, including intron number, protein length, modifications, protein families, and domains.

      The protein motifs and domains predicted by the InterPro Consortium databases can be powerful functional indicators Mitchell et al. Even if your protein of interest only contains a domain of unknown function DUF , it may be a member of a superfamily with a known fold, which can indicate some broad classification such as a catalytic activity or transport function. The protein level during vegetative growth or quiescence is also available for most proteins Marguerat et al.

      This expression level and the presence or absence at specific cell cycle or life cycle stages may give insight into possible roles of your gene of interest. Physical interactions can link a gene product to processes based on the roles of interacting partners. There are no high-throughput physical interaction data sets for fission yeast at the time of this writing, so it is highly unlikely that there would be any physical interaction data for an unstudied gene.

      An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System

      However, genome-wide genetic interaction data sets are becoming available Ryan et al. Other information presented on the gene pages includes protein features, protein modifications, human and S. A link from each gene page provides access to an Ensembl browser hosting sequence-based features including nucleosome positioning, polyadenylation sites, and transcriptomics data displayed in the context of the genome sequence.