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At least 739 records · Page 41Linked to original sources
PubMed2000

TRIPLES: a database of gene function in Saccharomyces cerevisiae.

Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm

DNA Transposable Elements↗
PubMed2006

Polymorphisms in manganese superoxide dismutase and catalase genes: functional study in Hong Kong Chinese asthma patients.

BACKGROUND: Reactive oxygen species may contribute to the pathogenesis of asthma. Functional genetic polymorphisms of antioxidant enzymes, superoxide dismutase (SOD) and catalase are good candidates for asthma susceptibility. OBJECTIVE: To investigate the association of the manganese-containing form of SOD (MnSOD) gene at amino acid position 16 (Val16Ala) and catalase gene in the promoter at A-21T and C-262T polymorphisms and asthma in a Hong Kong Chinese population. METHODS: The association study was conducted in a case-control design in asthma patients (n=251) and healthy controls (n=316) by genotyping. The functional significance was assessed by determining erythrocyte SOD and catalase activity. RESULTS: The Val allele of MnSOD at Val16Ala and the A allele of catalase gene at A-21T were not different between patients and controls, while the C allele of catalase gene at C-262T was found to be significantly different between patients and controls (P=0.033). The less frequent variant of catalase gene (-262T) was found to be protective from the development of asthma in a Hong Kong Chinese non-smoking population (adjusted odds ratio=0.35, 0.15-0.85; P=0.017). Asthma patients had elevated erythrocyte SOD and catalase activities in comparison with healthy controls (P<0.01). However, their activities were not associated with different genotypes within healthy controls or asthma patients. CONCLUSION: This is the first report showing that SOD and catalase functional activities are not associated with their respective genetic polymorphisms but related to the presence of asthma in a Hong Kong Chinese population.

Alleles↗
PubMed1984

A post-alpha gene function turns off the capacity of a host protein to bind DNA in cells infected with herpes simplex virus 1.

HEp-2 cell proteins electrophoretically separated in denaturing polyacrylamide gels and electrically transferred to nitrocellulose sheets contain a polypeptide which efficiently binds linear native DNA end labeled with 32P but not denatured DNA. The polypeptide has an apparent molecular weight of ca. 130,000. The activity of the protein was stable, and no appreciable turnover was observed after exposure of uninfected cells to inhibitory concentrations of cycloheximide for intervals of up to 24 h. However, the activity was absent from lysates of cells harvested 6 h or later postinfection with wild-type viruses. To identify the viral function involved in the loss of DNA-binding activity, we tested the lysates of cells infected with several mutants. Thus, the DNA-binding activity was unaffected in cells infected with a temperature-sensitive mutant (herpes simplex virus 1 tsLB2) in the alpha 4 gene and was maintained at a nonpermissive temperature (39 degrees C). Experiments involving (i) temperature shift-down of cells infected with tsLB2 in the presence of cycloheximide, (ii) withdrawal of cycloheximide in the presence and absence of actinomycin D from cells infected with wild-type virus, (iii) infection of cells at 33 and 39 degrees C with herpes simplex virus 1 tsHA1 carrying a temperature-sensitive lesion in the beta 8 gene, and (iv) infection of cells in the presence of inhibitory concentrations of phosphonoacetate led to the conclusion that the viral functions responsible for the loss of DNA-binding capacity were specified by either beta or gamma genes not dependent on viral DNA synthesis for their expression.

Cycloheximide↗
PubMed1999

Characterization of a cholesterol response element (CRE) in the promoter of the cholesteryl ester transfer protein gene: functional role of the transcription factors SREBP-1a, -2, and YY1.

Cholesteryl ester transfer protein (CETP) is expressed in human adipocytes, where it acts to promote selective uptake of HDL-CE (Benoist, F., M. McDonnell, P. Lau, R. Milne, and R. McPherson. 1997. J. Biol. Chem. 272: 23572;-23577). In contrast to other major sterol-responsive genes such as 3-hydroxy-3-methylglutaryl coenzyme A reductase CETP expression is up-regulated rather than down-regulated in response to cholesterol. To define elements involved in cholesterol-mediated up-regulation of CETP gene expression, deletion derivatives of the CETP promoter were cloned into a luciferase reporter construct and transfected into the human liposarcoma cell line SW872, cultured in the presence or absence of lipoproteins. A fragment associated with a positive cholesterol response was identified between nucleotides -361 and -138 (relative to the initiation site of transcription) of the promoter. This region contains a tandem repeat of a sequence known to mediate sterol dependent regulation of the hamster HMG-CoA reductase gene. We have putatively denoted this region, the cholesterol response element (CRE). Using gel mobility shift assays we demonstrate that both YY1 and SREBP-1 interact with the CRE of CETP. Furthermore, in transient co-transfection experiments, both YY1 and SREBP-1a were found to trans-activate, in a dose-dependent manner, the luciferase activity of constructs harboring the CRE. We also demonstrate that SREBP-2, is able to trans-activate a luciferase construct harboring the CRE although much less effectively as compared to SREBP-1. Finally, functional analysis of the CRE confirms its regulatory role in modulating CETP gene expression through its interaction with YY1 and SREBP-1a.

Animals↗
PubMed1988

Characterization of rat and human tyrosine hydroxylase genes: functional expression of both promoters in neuronal and non-neuronal cell types.

We describe the structure of the promoter and intron 1 of the human and rat tyrosine hydroxylase genes. The 5' flanking region of the two genes are 74% identical (+1 to -380) and contain a completely conserved cAMP response element. Although both genes are single copy, multiple splicing events of the human transcript lead to multiple mRNAs. Based on several lines of evidence alternative forms of mRNA of rat TH analogous to those in the human are not present. Both rat and human promoters direct the transcription of reporter genes when introduced into rat pheochromocytoma and fibroblast cells.

Adrenal Gland Neoplasms↗
PubMed2002

A defect of Kap104 alleviates the requirement of mitotic exit network gene functions in Saccharomyces cerevisiae.

A subgroup of the karyopherin beta (also called importin beta) protein that includes budding yeast Kap104 and human transportin/karyopherin beta2 is reported to function as a receptor for the transport of mRNA-binding proteins into the nucleus. We identified KAP104 as a responsible gene for a suppressor mutation of cdc15-2. We found that the kap104-E604K mutation suppressed the temperature-sensitive growth of cdc15-2 cells by promoting the exit from mitosis and suppressed the temperature sensitivity of various mitotic-exit mutations. The cytokinesis defect of these mitotic-exit mutants was not suppressed by kap104-E604K. Furthermore, the kap104-E604K mutation delays entry into DNA synthesis even at a permissive temperature. In cdc15-2 kap104-E604K cells, SWI5 and SIC1, but not CDH1, became essential at a high temperature, suggesting that the kap104-E604K mutation promotes mitotic exit via the Swi5-Sic1 pathway. Interestingly, SPO12, which is involved in the release of Cdc14 from the nucleolus during early anaphase, also became essential in cdc15-2 kap104-E604K cells at a high temperature. The kap104-E604K mutation caused a partial delocalization of Cdc14 from the nucleolus during interphase. This delocalization of Cdc14 was suppressed by the deletion of SPO12. These results suggest that a mutation in Kap104 stimulates exit from mitosis through the activation of Cdc14 and implies a novel role for Kap104 in cell-cycle progression in budding yeast.

Base Sequence↗
PubMed2000

[The promoter sequence of human nitric-oxide-synthase gene: functional study].

OBJECTIVE: Endothelial nitric oxide synthase (ecNOS) catalyzes the NADPH and O(2) to nitric oxide(NO). This study aimed at the regulation mechanism of the transcription of ecNOS gene. METHODS: The promoter regions of ecNOS gene were analyzed by gel mobility shift assay and DNase I footprinting assay using nuclear extract from endothelial cells. RESULTS: Three regions were protected by protein/transcription-factors. One of these regions, (-106 to -88) was demonstrated to be SP1 binding consensus sequence which was extremely rich in GC content. The other two regions, (-79 to -64) and (-58 to -44), covered the CTCF binding regions, but showed various binding modes. CONCLUSION: The protected regions are bound either with aggregated SP1/SP1- like proteins or with new transcription factor which have not been reported yet.

DNA Footprinting↗
PubMed1995

[Human papillomavirus type 16-gene functions relevant to molecular human carcinogenesis].

Human papillomavirus type 16 is a strong ethiologic agent of tumor development in human mucous epithelia such as uterine cervix. The virus two early genes, E6 and E7, have been characterized to be oncogenes that transform various cells and cell lines in vitro. Extensive analyses of E6 and E7 proteins revealed that these two oncoproteins interacted with cellular tumor suppressors, p53 and pRb, respectively. Thus, oncogenic potentials of the E6/E7-genes could be explained in part by the consequence of crosstalk of E6/E7-proteins and the cell cycle regulators. Furthermore, telomerase activation that protects telomere erosion appeared to by necessary for HPV16-oncogenesis and was demonstrated in HPV16-immortalized human epithelial cell lines. This line of evidence now enabled us to describe, but not fully, a scheme of an earlier process of human carcinogenesis induced by this virus type.

Cell Cycle↗
PubMed1998

The 3' untranslated region of a rice alpha-amylase gene functions as a sugar-dependent mRNA stability determinant.

In plants, sugar feedback regulation provides a mechanism for control of carbohydrate allocation and utilization among tissues and organs. The sugar repression of alpha-amylase gene expression in rice provides an ideal model for studying the mechanism of sugar feedback regulation. We have shown previously that sugar repression of alpha-amylase gene expression in rice suspension cells involves control of both transcription rate and mRNA stability. The alpha-amylase mRNA is significantly more stable in sucrose-starved cells than in sucrose-provided cells. To elucidate the mechanism of sugar-dependent mRNA turnover, we have examined the effect of alphaAmy3 3' untranslated region (UTR) on mRNA stability by functional analyses in transformed rice suspension cells. We found that the entire alphaAmy3 3' UTR and two of its subdomains can independently mediate sugar-dependent repression of reporter mRNA accumulation. Analysis of reporter mRNA half-lives demonstrated that the entire alphaAmy3 3' UTR and the two subdomains each functioned as a sugar-dependent destabilizing determinant in the turnover of mRNA. Nuclear run-on transcription analysis further confirmed that the alphaAmy3 3' UTR and the two subdomains did not affect the transcription rate of promoter. The identification of sequence elements in the alpha-amylase mRNA that dictate the differential stability has very important implications for the study of sugar-dependent mRNA decay mechanisms.

Base Sequence↗
PubMed2006

BIGYIN, an orthologue of human and yeast FIS1 genes functions in the control of mitochondrial size and number in Arabidopsis thaliana.

Reverse-genetics was used to evaluate the role of an Arabidopsis homologue of the human and yeast FIS1 genes, which are both involved in mitochondrial fission. Two independent T-DNA insertion mutants of gene At3g57090 were identified and genetically transformed to express mitochondria-targeted GFP to enable visualization of mitochondria in vivo. Plants homozygous for either of the recessive T-DNA mutant alleles, termed bigyin1-1 (bgy1-1) and bigyin1-2 (bgy1-2), displayed an abnormal mitochondrial morphology. Disruption of BIGYIN leads to a reduced number of mitochondria per cell, coupled to a large increase in the size of individual mitochondria, relative to wild-type. It is concluded that BIGYIN is an Arabidopsis FIS orthologue and is part of the Arabidopsis mitochondrial division apparatus.

Amino Acid Sequence↗
PubMed1995

Initial mutational steps toward loss of opsin gene function in cavefish.

The river-dwelling fishes of Astyanax fasciatus and their derivatives from Pachon and Micos caves in Mexico were collected. By comparing red (r007) and green (g103) opsin gene sequences from the three populations, we found a high frequency of C-->T changes in r007 and g103 of the eyed Micos fishes presumably due to spontaneous cytosine methylation or enzymatic deamination of the CG dinucleotide, and a deletion of 12 consecutive nucleotides in g101 of the blind Pachon fishes. Thus, high rates of nucleotide substitution and C-->T transitions, usually found for pseudogenes, may occur even before they become nonfunctional.

Animals↗
PubMed2005

Association between angiotensin I-converting enzyme insertion/deletion gene functional polymorphism and novelty seeking personality in healthy females.

A certain type of personality is at risk for developing psychiatric diseases. Several lines of evidence support the interaction between brain angiotensins and central catecholamine systems, and suggest that angiotensin I-converting enzyme (ACE) may be a reasonable candidate gene for psychiatric disorders. The present study examined the possibility that ACE insertion (I)/deletion (D) functional polymorphism might be associated with particular personality traits. Healthy Japanese subjects (N=184) were administered the Temperament and Character Inventory (TCI) and the NEO Personality Inventory Revised version (NEO-PI-R), and their ACE I/D polymorphisms were determined. There was an ethnic difference in the genetic distribution of ACE I/D between Japanese (D=34.5%) and Caucasians (D=55.2%). We found that the scores of novelty seeking (NS) in the Low-ACE group (II genotype) of healthy female subjects were significantly lower than those in the High-ACE group (ID or DD genotype) (p=0.018). Our findings suggested that the ACE I/D polymorphism might be associated with the NS personality trait in females, but not males. Taking into account the effects of multiple comparisons, this result should be interpreted with caution, and needs confirmation in a larger sample.

Adult↗
PubMed2002

The GCR1 gene function is essential for glycogen and trehalose metabolism in Saccharomyces cerevisiae.

Trehalose (Tre) and glycogen (Glg) are synthesized in response to unfavorable growth conditions from glycolytic intermediates in Saccharomyces cerevisiae. Transcription of the glycolytic genes is activated by the Gcr1p complex, the DNA binding transcription factor that directly associates with the CT-box sequences on the promoter region of the glycolytic genes. gcr1 mutant yeast cells cannot utilize glucose effectively. Glg and Tre levels in stationary-phase gcr1 mutant yeast cells were 20-50% of those in the wild-type strain. Likewise, stress-induced accumulation of Tre and Glg in gcr1 mutant cells was significantly lower than in the wild type. In addition, both the synthesis and the degradation of Tre and Glg are very slow in the gcr1 mutant. It seems that Gcr1p function is essential for the coordinated regulation of glycolysis, Tre and Glg metabolism in S. cerevisiae.

DNA-Binding Proteins↗