• genome
  • Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture. (biomedsearch.com)
  • CONCLUSIONS: This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. (biomedsearch.com)
  • Epigenetics most often denotes changes in a chromosome that affect gene activity and expression, but can also be used to describe any heritable phenotypic change that does not derive from a modification of the genome, such as prions. (wikipedia.org)
  • Given that the exact ancestry of genes in different organisms is difficult to ascertain due to gene duplication and genome rearrangement events, the strongest evidence that two similar genes are orthologous is usually found by carrying out phylogenetic analysis of the gene lineage. (wikipedia.org)
  • metabolism
  • Calorie restriction studies show that decreased nutrition, like sugar, increase life span (likely due to slower metabolism and thus decreased reactive oxygen species production or induced survival genes). (wikipedia.org)
  • yeast
  • A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of CLN2. (nih.gov)
  • Next, in order to test the predictive ability of the stochastic model, we focus on a recent experimental study in which forced periodic expression of CLN2 cyclin (driven by MET3 promoter in cln3 background) has been used to synchronize budding yeast cell colonies. (nih.gov)
  • Pheromone-regulated genes required for yeast mating differentiation. (nih.gov)
  • Expression of the yeast phosphoglycerate kinase gene (PGK) requires the binding of RAP1 to the activator core sequence within the upstream activating sequence (UAS) of PGK. (hku.hk)
  • The results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. (nih.gov)
  • Yeast TAF(II)145 required for transcription of G1/S cyclin genes and r" by Scott S. Walker, Wu-Cheng Shen et al. (umassmed.edu)
  • TFIID comprises the TATA box-binding protein and a set of highly conserved associated factors (TAF(II)s). yTAF(II)145, the core subunit of the yeast TAF(II) complex, is dispensable for transcription of most yeast genes but specifically required for progression through G1/S. Here we show that transcription of G1 and certain B-type cyclin genes is dependent upon yTAF(II)145. (umassmed.edu)
  • At high cell density or following nutrient deprivation, yeast cells cease division, enter a G0-like state, and terminate transcription of most genes. (umassmed.edu)
  • We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. (umassmed.edu)
  • In the budding yeast Saccharomyces cerevisiae, Mob1p interacts with the Dbf2p kinase and cells containing mutations in these genes arrest in late anaphase . (umassmed.edu)
  • Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. (nih.gov)
  • Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. (nih.gov)
  • In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. (wikipedia.org)
  • species
  • Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. (biomedsearch.com)
  • We examine conservation of functional variants across four Saccharomyces species, and find that about a third of transcription factors have target genes that are differentially expressed in a condition-specific manner that is correlated with the nucleotide at variant motif positions. (nih.gov)
  • In all three species, genes associated with the "G" BSMV (orange) are more highly expressed than genes associated with the "A" BSMV (green) in starvation conditions (glycerol). (nih.gov)
  • In all four species, genes associated with the "C" BSMV (blue) are more highly expressed than genes associated with the "T" BSMV (red) in starvation conditions (glycerol), and the opposite relationship is apparent during nitrogen starvation. (nih.gov)
  • For example, the difference in regulation of genes with "G" or "A" at position 9 for the Reb1 binding sites is highest during growth in glycerol in all three Saccharomyces species examined, and therefore these experiments cluster together in Figure 3A-C. (nih.gov)
  • Environmental Exposure Exposure to fungal species that secrete gliotoxin is common because airborne Aspergillus fungal spores are ubiquitous in many environments. (wikipedia.org)
  • The lolines are insecticidal and insect-deterrent compounds that are produced in grasses infected by endophytic fungal symbionts of the genus Epichloë (anamorphic species: Neotyphodium). (wikipedia.org)
  • Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (wikipedia.org)
  • Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. (wikipedia.org)
  • OrthoMCL OMA Roundup OrthoMaM for mammals OrthologID GreenPhylDB for plants Tree-based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in databases such as TreeFam LOFT. (wikipedia.org)
  • Peptides
  • Although they are called untranslated regions, and do not form the protein-coding region of the gene, uORFs located within the 5' UTR can be translated into peptides. (wikipedia.org)
  • In bacteria, uORFs are called leader peptides, and were originally discovered on the basis of their impact on the regulation of genes involved in the synthesis or transport of amino acids. (wikipedia.org)
  • Mitosis
  • Mob1p is required for Sid2p localization, and Mob1p localization requires the function of the cdc7, cdc11, cdc14, spg1, sid1, sid2, and sid4 genes, suggesting that together with Sid2p, Mob1p functions at the end of the signaling cascade required to regulate the onset of cytokinesis at the end of mitosis. (umassmed.edu)
  • organisms
  • In higher plants, they are used to control phototropism, chloroplast relocation, and stomatal opening, whereas in fungal organisms, they are used for adjusting the circadian temporal organization of the cells to the daily and seasonal periods. (wikipedia.org)
  • regulates
  • Mutants of in planta inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice.These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes.The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how M. oryzae regulates its pathogenesis, development, and stress responses. (nih.gov)
  • The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how M. oryzae regulates its pathogenesis, development, and stress responses. (nih.gov)
  • It regulates gene expression. (wikipedia.org)
  • Aspergillus
  • This result confirms the importance of a functional NADPH oxidase in resistance to Aspergillus infections, and suggests that increased hypoxia prevents proliferation of fungal tissue in the absence of SrbA. (nih.gov)
  • In Aspergillus fumigatus, the enzymes needed for gliotoxin biosynthesis are encoded in 13 genes within the gli gene cluster. (wikipedia.org)
  • protein
  • We analyzed the distribution of Gex1 and Gex2 in strains with the corresponding genes tagged at the chromosomal locus (at the carboxy terminus of the encoded protein) with GFP or HA. (nih.gov)
  • mid2 gene expression and protein levels fluctuate during the cell cycle in a sep1- and Skp1/Cdc53/F-box (SCF)-dependent manner, respectively, implying that Mid2p activity must be carefully regulated.Overproduction of Mid2p depolarizes cell growth and affects the organization of both the septin and actin cytoskeletons. (nih.gov)
  • mid2 gene expression and protein levels fluctuate during the cell cycle in a sep1- and Skp1/Cdc53/F-box (SCF)-dependent manner, respectively, implying that Mid2p activity must be carefully regulated. (nih.gov)
  • One key factor associated with this 3'-end structure is the poly(A)-binding protein (Pab1p) encoded by the PAB1 gene in Saccharomyces cerevisiae. (umassmed.edu)
  • Approximately 50% of human genes contain uORFs in their 5'UTR, and when present, these cause reductions in protein expression. (wikipedia.org)
  • Each subdomain contains an ACT domain that allows for complex regulation of several different protein functions. (wikipedia.org)
  • Leukocyte antigen CD37 is a protein that in humans is encoded by the CD37 gene. (wikipedia.org)
  • The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. (wikipedia.org)
  • transcription factor
  • Gex1 expression was induced under conditions of iron depletion and was principally dependent on the iron-responsive transcription factor Aft2. (nih.gov)
  • Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF) genes in the rice blast fungus Magnaporthe oryzae under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. (nih.gov)
  • Functional
  • Conserved expression patterns associated with functional binding site motif variants (BSMVs).The y-axis of each plot is the mean expression (Y6.4kv6 arrays) standard error of mean shown) of the stress condition relative to the non-stress condition and the x-axis is experimental treatment, ordered by the difference between the means of genes with each BSMV (black dashes). (nih.gov)
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor. (wikipedia.org)
  • whereas
  • Simulated return maps for successive cells with and without forced CLN2 expression.No forcing is applied in (A) and (C), whereas the forcing period is 90 min in (B) and (D). "D" and "M" stand for daughters and mothers, respectively. (nih.gov)
  • sequences
  • Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 genes. (nih.gov)
  • We searched the regions immediately upstream of the four novel FIG genes characterized in this study and found sequences matching the PRE consensus (Fig. 2). (nih.gov)
  • 1992), failed to identify sequences in the upstream regions of the FIG1-4 genes closely matching the consensus binding site. (nih.gov)
  • Many DNA-binding domains must recognize specific DNA sequences, such as DBDs of transcription factors that activate specific genes, or those of enzymes that modify DNA at specific sites, like restriction enzymes and telomerase. (wikipedia.org)
  • citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
  • Alleles
  • Transposon insertion alleles corresponding to 20 genes that are novel or had not previously been known to be pheromone regulated were examined for effects on the mating process. (nih.gov)
  • phase
  • Our model also generates a novel prediction: under frequent CLN2 expression pulses, G1 phase duration is bimodal among small-born cells. (nih.gov)
  • fungi
  • In N. crassa (and other fungi) cartenoids al genes, namely focused provide UV radiation protection. (wikipedia.org)
  • Cell Cycle
  • We demonstrate that the model correctly predicts the experimentally observed synchronization levels and cell cycle statistics of mother and daughter cells under various experimental conditions (numerical data that is not enforced in parameter optimization), in addition to correctly predicting the qualitative changes in size control due to forced CLN2 expression. (nih.gov)
  • indicate
  • Our results indicate that a variety of novel genes are expressed specifically during mating differentiation to mediate proper cell morphogenesis, cell fusion, and other steps of the mating process. (nih.gov)
  • Since several of these genes are pheromone dependent for their expression yet contain only PRE sites that differ from the consensus, these results indicate that variant PRE sites are likely to be important for Ste12p-dependent regulation of some genes (e.g. (nih.gov)
  • A model for the regulatory network controlling the expression of conidiation-specific TF genes.Solid diamonds indicate the genes deleted in ΔMohox2, ΔMohox4, ΔMoaps1, ΔMoaps2, ΔMoleu3, and ΔMonit4. (nih.gov)
  • Cdc14
  • Here we show that FEAR homologs in S. pombe do not promote release of the Cdc14 homolog Clp1p/Flp1p from the nucleolus, and that Clp1p/Flp1p is not required for nucleolar and telomeric DNA segregation suggesting that this aspect of Cdc14 regulation and function may not be universally conserved. (umassmed.edu)
  • Kinase
  • The AK-HSD gene codes for aspartate kinase, an intermediate domain (coding for the linker region between the two enzymes in the bifunctional form), and finally the coding sequence for homoserine dehydrogenase. (wikipedia.org)
  • Additionally, the aspartate kinase-homoserine dehydrogenase gene is primarily expressed in actively growing, young plant tissues, particularly in the apical and lateral meristems. (wikipedia.org)
  • Homoserine dehydrogenase and aspartate kinase are both subject to significant regulation (refer to figure 3). (wikipedia.org)
  • Another example of structural variability is seen in vertebrates, in which 3 paralogues of subunits of the cyclin-dependent kinase module have evolved by 3 independent gene duplication events followed by sequence divergence. (wikipedia.org)
  • Binding Sites
  • An additional search for Mcm1p binding sites, which can be found near PRE sites of a subset of pheromone-induced genes such as FUS1 (Herskowitz et al. (nih.gov)
  • The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5'- and 3'-extended transcripts, and de-repression of adjacent genes and intergenic regions. (nih.gov)
  • reporter
  • Of the putative interacting genes examined, PBP1 promoted the highest level of resistance to 3-aminotriazole (>100 mM) in constructs in which HIS3 was used as a reporter. (umassmed.edu)
  • evident
  • Fungal tissue remains evident on GMS stains indicating that despite surviving the infection, these mice have not entirely cleared the fungal infection. (nih.gov)
  • infection
  • These symptoms, likely due to the large inflammatory response characteristic of these mice when exposed to fungal antigens, included ruffled fur, hunched posture, and lethargic movement as early as 24 hours post-infection. (nih.gov)
  • function
  • Further, the results suggest that the attributes of Set1 required for trimethylation of histone H3 are those required for Pol II gene silencing at the rDNA and kinetochore function. (nih.gov)
  • These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. (nih.gov)
  • Since the regulation of gene expression is critical in the proper function of cells, this is an area of study that needs to be investigated further. (wikipedia.org)
  • Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. (wikipedia.org)
  • The function of DNA binding is either structural or involves transcription regulation, with the two roles sometimes overlapping. (wikipedia.org)
  • upstream
  • An upstream regulatory element termed the PRE has been identified as mediating the pheromone-induced transcription of a number of genes involved in the mating response (e.g. (nih.gov)
  • enzymes
  • When this gene cluster is activated, these enzymes mediate the production of gliotoxin from serine and phenylalanine residues. (wikipedia.org)
  • absence
  • 91,200 transformants containing random lacZ insertions were screened for beta-galactosidase (beta-gal) expression in the presence and absence of alpha factor, and 189 strains containing pheromone-regulated lacZ insertions were identified. (nih.gov)