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At least 397 records · Page 22Linked to original sources
PubMed2006

Evaluating bias due to population stratification in epidemiologic studies of gene-gene or gene-environment interactions.

Confounding by ethnicity (i.e. population stratification) can result in bias and incorrect inferences in genotype-disease association studies, but the effect of population stratification in gene-gene or gene-environment interaction studies has not been addressed. We used logistic regression models to fit multiplicative interactions between two dichotomous variables that represented genetic and/or environmental factors for a binary disease outcome in a hypothetical cohort of multiple ethnicities. Biases in main effects and interactions due to population stratification were evaluated by comparing regression coefficients in mis-specified models that ignored ethnicities with their counterparts in models that accounted for ethnicities. We showed that biases in main effects and interactions were constrained by the differences in disease risks across the ethnicities. Therefore, large biases due to population stratification are not possible when baseline disease risk differences among ethnicities are small or moderate. Numerical examples of biases in genotype-genotype and/or genotype-environment interactions suggested that biases due to population stratification for main effects were generally small but could become large for studies of interactions, particularly when strong linkage disequilibrium between genes or large correlations between genetic and environmental factors existed. However, when linkage disequilibrium among genes or correlations among genes and environments were small, biases to main effects or interaction odds ratios were small to nonexistent.

Bias↗
PubMed2006

Gene therapy for breast cancer. --Review of clinical gene therapy trials for breast cancer and MDR1 gene therapy trial in Cancer Institute Hospital.

Gene therapy for advanced breast cancer is anticipated to be a useful therapeutic approach. Strategies in ongoing clinical protocols can be divided into four groups: (1) suppression of oncogenes or transfer of tumor-suppressor genes; (2) enhancement of immunological response; (3) transfer of suicide genes; (4) protection of bone marrow using drug resistance genes. We have started a clinical study of multidrug resistance (MDR1) gene therapy. Advanced breast cancer patients received high dose chemotherapy and autologous peripheral blood stem cell transplantation(PBSCT)with MDR1-transduced hematopoietic cells, and then were treated with docetaxel. Two patients have been treated so far, and in vivo enrichment of MDR1-transduced cells with docetaxel treatment has been seen. Both patients are in complete remission and had no apparent adverse effects from the MDR1 gene transfer.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1991

Structure of the human lipoprotein-associated coagulation inhibitor gene. Intro/exon gene organization and localization of the gene to chromosome 2.

Lipoprotein-associated coagulation inhibitor (LACI) is a multivalent, Kunitz-type proteinase inhibitor which appears to play an important role in the regulation of hemostasis. LACI directly inhibits factor Xa, and, in a Xa-dependent fashion, also inhibits the factor VIIa-tissue factor catalytic complex. Hybridization of a LACI cDNA probe to DNA isolated from a panel of human-mouse somatic cell hybrids containing different human chromosomes localized the human LACI gene to chromosome 2. In situ hybridization to metaphase chromosomes further mapped the gene to the region 2q31----2q32.1. Exons of the human LACI gene were cloned from genomic or chromosome 2-specific phage libraries and sequenced, including approximately 500 base pairs of 5' upstream DNA. The 5' DNA did not contain a prototypical TATAA box or CCAAT sequence, and attempts to identify a unique site for the initiation of transcription were unsuccessful in that primer extension and S1 nuclease protection analysis indicate multiple transcription initiation sites for LACI messages. Comparing the gene sequence with LACI cDNA sequences indicates that the gene contains nine exons and that alternative splicing can occur, resulting in the absence of exon 2 in the 5' untranslated region of some messages. The three Kunitz domains in LACI are encoded on separate exons. Introns which interrupt coding sequences all occur in the same codon phase interrupting the first and second bases of the codon triplets. The data are consistent with LACI evolving by a combination of gene segment duplications and exon shuffling.

Amino Acid Sequence↗
PubMed2003

The trichothecene biosynthesis gene cluster of Fusarium graminearum F15 contains a limited number of essential pathway genes and expressed non-essential genes.

We report for the first time the complete structure and sequence of the trichothecene biosynthesis gene cluster (i.e. Tri5-cluster) from Fusarium graminearum F15, a strain that produces 3-acetyldeoxynivalenol (3-ADON). A putative tyrosinase and polysaccharide deacetylase gene flank the Tri5-cluster: the number of pathway genes between them is less than half the total number of steps necessary for 3-ADON biosynthesis. In comparison with partial Tri5-cluster sequences of strains with 15-acetyldeoxynivalenol and 4-acetylnivalenol chemotypes, the Tri5-cluster from strain F15 contains three genes that are apparently unnecessary for the biosynthesis of 3-ADON (i.e. Tri8 and Tri3, which are expressed, and pseudo-Tri13, which is not expressed). In addition, the Tri7 gene was missing from the cluster. Recombinant TRI3 protein showed limited trichothecene C-15 acetylase activity. In contrast, recombinant TRI8 protein displayed no C-3 deacetylase activity, suggesting that the loss or alteration of function contribute directly to the chemotype difference.

Fusarium↗
PubMed1997

Abnormal erythropoietin (Epo) gene expression in the murine erythroleukemia IW32 cells results from a rearrangement between the G-protein beta2 subunit gene and the Epo gene.

Abnormal production of erythropoietin (Epo) has been described in several human and murine erythroleukemia. The murine IW32 cell line is derived from an F-MuLV-induced erythroleukemia. An autocrine Epo production due to the rearrangement of one Epo allele has been previously described (Beru et al., 1989). However, the exact mechanism leading to the transcriptional activation of the abnormal Epo gene was unknown. In this study, we show that this deregulated expression results from a deletion within chromosome 5. The Epo gene in the abnormal allele is under the control of the G-protein beta2 subunit gene promoter and the expressed mRNA results from the fusion of the non coding exon 1 of the G-protein beta2 subunit gene to a truncated Epo exon 1 gene. This resulting abnormal cDNA allows the expression of a normal Epo protein.

Animals↗
PubMed2001

A polymorphism in the regulatory region of the corticotropin-releasing hormone gene in relation to cortisol secretion, obesity, and gene-gene interaction.

In recent years, a considerable body of evidence has emerged regarding the pathogenic role of cortisol in abdominal obesity. The regulation of the corticotropin-releasing hormone (CRH) gene might play an essential role because it is the primary hypothalamic neuropeptide involved in the control of adrenal secretion of cortisol. Therefore, we examined the hypothalamic-pituitary-adrenal function by repeated salivary samples for the assessment of cortisol as well as other endocrine, anthropometric, metabolic, and circulatory variables in middle-aged Swedish men (n = 284). With the restriction enzyme XmnI, a variant in the 5'-flanking region of the CRH gene was identified (T255G). The observed genotype frequencies were 89.9% and 9.7% for T/T and T/G, respectively. Only 1 subject was homozygous for the rare allele (0.4%; G/G). The results showed that the XmnI polymorphism of the CRH gene is not associated with an altered cortisol-secretory pattern or sensitivity to glucocorticoids or with obesity and its related metabolic and circulatory perturbations. However, when the interaction effect between a previously described TthlllI glucocorticoid-receptor gene polymorphism and the present XmnI CRH polymorphism was investigated, the cortisol levels before and during physiologic stress and the total diurnal cortisol secretion were significantly increased among subjects who were carriers for both variants. From these results, we conclude that an abnormal production rate of the CRH gene product in the presence of an inadequate glucocorticoid receptor density might lead to elevated cortisol levels.

Aging↗
PubMed1990

The immunoglobulin lambda-like gene cluster (14.1, 16.1 and F lambda 1) contains gene(s) selectively expressed in pre-B cells and is the human counterpart of the mouse lambda 5 gene.

A human immunoglobulin (Ig)-related gene, covering approximately 8 kb, was isolated from a cosmid genomic library, by hybridization with a C lambda probe and with a lambda-like probe. This gene was identified as 14.1 It belongs to the human lambda-like cluster which is composed of three genes (14.1, 16.1 and F lambda 1) that do not rearrange. Sequence data indicate that 14.1 is organized similarly to the mouse lambda 5 gene. It contains three exons with lengths of 69, 38, and 106 codons as compared with 65, 38, and 106 for exons 1, 2, and 3 of mouse lambda 5, respectively. The corresponding homology values were 61, 66 and 75.5%. Using a 14.1 specific probe containing exon 1, we showed that this gene was selectively expressed in human pre-B cell lines. It is likely to encode a 213-amino acid lambda-like light chain that would associate with mu chains and play an important role in the early steps of B cell differentiation.

Amino Acid Sequence↗
PubMed1992

Molecular analysis of POP2 gene, a gene required for glucose-derepression of gene expression in Saccharomyces cerevisiae.

We have isolated a new mutant of Saccharomyces cerevisiae that exhibits a glucose-derepression resistant (and sucrose-non-fermentor) phenotype. This mutant was obtained by screening for overproduction of alpha-amylase in a strain containing the mouse alpha-amylase gene under the control of the PGK promoter. The mutation designated pop2 (PGK promoter directed over production). The pop2 mutant overproduced amylase 5-6 fold and displayed several other pleiotropic defects: (1) resistance to glucose derepression, (2) temperature-sensitive growth, (3) failure of homozygous diploid cells to sporulate and (4) reduced amount of reserve carbohydrates. We mapped pop2 to chromosome XIV, distal to lys9 and SUP28, indicating that POP2 is a newly-identified locus. We isolated the POP2 gene from two yeast strains of different genetic backgrounds, S288C and A364A, and determined their nucleotide sequences. The predicted amino acid sequence of the POP2 protein contains three glutamine-rich region, a proline-rich region and a serine/threonine-rich region, characteristic of many transcription factors. Steady state levels of RNA transcribed from the PGK-amylase fusion gene and from endogenous PGK gene in stationary-phase pop2 cells were 5- to 10-fold higher than those observed in wild-type cells, showing that the pop2 mutation affects transcription of the PGK gene transcription.

Amino Acid Sequence↗
PubMed1998

Herpes simplex virus thymidine kinase-green fluorescent protein fusion gene: new tool for gene transfer studies and gene therapy.

Green fluorescent protein (GFP) and herpes simplex virus type-I thymidine kinase (TK) are commonly used markers in gene transfer studies. The latter gene has also proven to be an effective tool in cancer "suicide" gene therapy. To facilitate rapid and reliable selection of cells expressing TK, we constructed a plasmid expressing a TK-green fluorescent protein fusion gene (TK-GFP). In this fusion gene, the expression of each component is coupled to one another, permitting accurate determination of the percentage of cells expressing TK by detecting the green fluorescence produced by GFP. Transfection of the fusion plasmid to mammalian cells revealed that the construct is fully functional, making the cells both fluorescent and sensitive to ganciclovir.

Animals↗
PubMed1992

Co-deletions of the retinoblastoma gene and Wilms' tumor gene and rearrangement of the Krev-1 gene in a human insulinoma.

We found deletions of both alleles of the retinoblastoma gene (Rb) and the candidate Wilms' tumor gene (WT33) in a surgically resected human insulinoma by blot hybridization. Rearrangement of Krev-1, a transformation suppressor gene, was also detected in this case. The clinical and histological findings suggested that this tumor would be a benign insulinoma. The result suggests that the inactivation of multiple tumor suppressor genes could be involved even in the development of benign human tumors.

Aged↗
PubMed1998

The rfb genes in Azotobacter vinelandii are arranged in a rfbFGC gene cluster: a significant deviation to the arrangement of the rfb genes in Enterobacteriaceae.

We report the identification of rfbF and rfbC located adjacent to the previously identified rfbG (Gavini et. al. Biochem. Biophys. Res. Commun. 1997, 240, 153-161) from the non-symbiotic, non-pathogenic soil bacterium Azotobacter vinelandii. The rfbF open reading frame encodes a putative polypeptide of 256 amino acids. This polypeptide shares a homology of 74% with the RfbF of Synechocystis sp. and a 70% homology with the AscA of Yersinia pseudotuberculosis which function as alpha-D-glucose-1-phosphate cytidylyltransferases in the biosynthesis of the O-antigen. The rfbC encodes a putative polypeptide of 186 amino acids. It shows strongest homology to the RfbC of Synechocystis sp. (64%) and Salmonella typhimurium (40%). RfbC functions as a dTDP-4-Dehydrorhamnose 3,5-Epimerase. The genes identified here have a low G + C content (approximately 56%) as compared to the A. vinelandii chromosome (approximately 63%) which is characteristic of the rfb clusters identified in other bacteria and may be indicative of the acquisition of the rfb genes by interspecific gene transfer. Despite the high level of sequence conservation, the organization of the rfb genes in A. vinelandii deviates from the arrangement of the most thoroughly studied rfb gene clusters of Enterobacteriaceae.

Amino Acid Sequence↗
PubMed2000

Familial chylomicronemia caused by a novel type of mutation in the APOE-CI-CIV-CII gene cluster encompassing both the APOCII gene and the first APOCIV gene mutation: APOCII-CIV(Nijmegen).

Apolipoprotein CII (ApoCII) deficiency is a relatively rare cause of the chylomicronemia syndrome, a disorder characterized by severe fasting hypertriglyceridemia and massive accumulation of chylomicrons in plasma. Here we present a case which is the first example of apoCII deficiency caused by a major rearrangement in the APOCII gene. Southern blot analysis revealed an approximately 7.5-kb deletion disrupting the APOCII gene including the promotor region and first exon. Interestingly, the deletion also encompasses the APOCIV gene, a recently discovered novel gene upstream of APOCII. This deletion is the first mutation to be reported in the APOCIV gene.

Apolipoproteins C↗
PubMed1994

The pregnancy-specific glycoprotein (PSG) gene cluster on human chromosome 19: fine structure of the 11 PSG genes and identification of 6 new genes forming a third subgroup within the carcinoembryonic antigen (CEA) family.

The human pregnancy-specific glycoprotein (PSG) genes belong to the carcinoembryonic antigen (CEA) family, which in turn is a member of the immunoglobulin superfamily. We have analyzed a 700-kb cosmid contig spanning the PSG region on chromosome 19q13.2. The region contains 11 closely related PSG genes organized in tandem with a highly conserved structure and organization. Seven novel genes (CGM12 to CGM18) were found in the PSG region. CGM12 belongs to the CEA subgroup and appears to be a pseudogene. CGM13 to CGM18 forms a third new subgroup within the CEA gene family. The members of this new subgroup show 94-99% identity to each other but only 70-80% to other members of either the CEA or the PSG subgroups. They are composed of exons encoding two IgC-like domains and short hydrophilic carboxyl terminals similar to those of the PSGs. Unlike any of the known CEA family genes, however, they seem to lack the exon for an IgV-like N-terminal domain.

Amino Acid Sequence↗
PubMed1994

The legumin gene family: a reconstructed Vicia faba legumin gene encoding a high-molecular-weight subunit is related to type B genes.

Nucleotide sequence information from a partial genomic clone, a cDNA clone, a RACE clone and a PCR fragment was combined to reconstruct the first reported complete gene sequence encoding a large legumin subunit, designated LelB3. The length difference to the well-characterized major legumin subunits is caused by an extended glutamine/glutamic acid-rich region encoded by the C-terminal part of the alpha chain. Amino acid sequence comparisons reveal that gene LelB3 is more closely related to B-type than to A-type legumin genes of Vicia faba. Gene LelB3 is a member of a small gene family as indicated by published (Pich and Schubert, Biol Zbl 112 (1993); 342-350) and limited own data.

Amino Acid Sequence↗
PubMed2004

Potential regulatory sequences in the untranslated regions of the baboon MHC class Ib gene, Paan-AG, more closely resemble those in the human MHC class Ia genes than those in the class Ib gene, HLA-G.

The baboon major histocompatibility complex (MHC) class Ib gene, Paan-AG, is structurally similar to the human MHC class Ia gene, HLA-A, but exhibits characteristics similar to those of the class Ib gene HLA-G. These include limited polymorphism, alternative splicing of a single message, and restricted tissue distribution, with high expression in the placenta. In order to determine whether regulatory elements controlling expression of Paan-AG resemble those of HLA-A or HLA-G, we cloned the 5' and 3' untranslated regions of Paan-AG. Unexpectedly, sequence comparisons showed that potential regulatory elements in Paan-AG strikingly resembled those in HLA-A and differed in major respects from those in HLA-G. Unlike HLA-G, Paan-AG contained an intact interferon-gamma stimulated response element (ISRE) in the promoter. Studies using luciferase reporter assays showed that the Paan-AG ISRE was functional. The basal activity of the Paan-AG ISRE and its response to interferon-gamma was similar to that of class Ia MHC genes. Further, we identified an ISRE in the 3' untranslated region of Paan-AG that is known to be functional in HLA-A2 but is deleted in HLA-G. These experiments predict that functional studies may demonstrate differences in regulation of expression of Paan-AG and HLA-G genes, which could restrict the use of the baboon as a primate model for studying HLA-G expression and function.

Animals↗
PubMed2001

Molecular cloning and characterization of a gene expressed in mouse developing tongue, mDscr5 gene, a homolog of human DSCR5 (Down syndrome Critical Region gene 5).

For understanding the pathogenesis of Down syndrome (DS), it is important to identify and characterize the genes on Chromosome (Chr) 21, especially those in the Down syndrome critical region (DSCR) on Chr 21q22.2. Recently we have determined 33.5 Mb (more than 99%) of DNA sequence of Chr 21 and, from these sequence data, we identified a novel gene, DSCR5 (transcript = 0.8 kb), from DSCR by combination of computational gene prediction and cDNA screening. For functional analysis of DSCR5, we identified a mouse homolog of the DSCR5 cDNA, and termed it mDscr5 (transcript length = 0.8 kb). The gene was mapped to mouse Chr 16 C3-C4, the syntenic region of human Chr 21, and encodes an amino acid of 132 residues with 90% identity to DSCR5. In situ hybridization showed that mDscr5 is predominantly expressed in the developing tongue. To our best knowledge, no other gene in DSCR is reported to be expressed in tongue, so that DSCR5 may be the first candidate to elucidate the pathophysiology of tongue malformation observed in DS.

Amino Acid Sequence↗
PubMed1991

The neurotransmitter role of calcitonin gene-related peptide in the rat and guinea-pig ureter: effect of a calcitonin gene-related peptide antagonist and species-related differences in the action of omega conotoxin on calcitonin gene-related peptide release from primary afferents.

In the rat and guinea-pig isolated ureter electrical field stimulation of intrinsic nerves (10 Hz for 10 s) produces transient inhibition of evoked (20 mM KCl or 0.1-1 microM neurokinin A) rhythmic contractions by releasing transmitter(s) from peripheral endings of capsaicin-sensitive primary afferents. The C-terminal fragment of human calcitonin gene-related peptide (8-37) blocked the inhibitory effect of electrical field stimulation as well as that produced by exogenous calcitonin gene-related peptide, while leaving unaffected the inhibitory response to isoprenaline. Human calcitonin gene-related peptide (8-37) was devoid of any inhibitory activity of its own but enhanced the amplitude and frequency of KCl-evoked rhythmic contractions in the rat ureter, probably by antagonizing the inhibitory effect of endogenous calcitonin gene-related peptide released by KCl. Omega conotoxin fraction GVIA, a peptide which possesses a potent blocking activity of N-type voltage-sensitive calcium channels, prevented the inhibitory response to electrical stimulation in the guinea-pig ureter, while leaving the response unaffected in the rat ureter. Conotoxin had no effect toward the inhibition produced by exogenous calcitonin gene-related peptide indicating its prejunctional site of action, demonstrated previously in the guinea-pig ureter [Maggi et al. (1990) Neurosci, Lett. 114, 203-206]. Dermorphin, an amphibian peptide with potent agonist activity on mu-type opioid receptors, inhibited the response to electrical stimulation in the guinea-pig ureter but had no effect in the rat ureter.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗