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PubMed2005

High polymorphism in genes encoding antigen B from human infecting strains of Echinococcus granulosus.

Echinococcus granulosus antigen B (AgB) is encoded by a gene family and is involved in the evasion of the host immune response. E. granulosus exists as a number of strains (G1-G10) that differ in biological characteristics. We used PCR-SSCP followed by DNA sequencing to evaluate sequence variation and transcription profile of AgB in 5 E. granulosus strains. Twenty-four genomic sequences were isolated and clustered in 3 groups related to 2 of the 5 reported AgB genes. AgB4 genes were present in almost all strains, whereas AgB2 were present as functional genes exclusively in G1/G2 cluster, and as non-functional genes in G5 and the G6/G7 cluster, suggesting inter-strain variation. The AgB transcription patterns, analysed by RT-PCR, showed that AgB2 and AgB4 genes were transcribed in G1, while only the AgB4 gene was transcribed in G7 strain. Cysts from the same strain or cluster shared more genomic and cDNA variants than cysts from different strain or cluster. The level of nucleotide and deduced amino acid sequence variation observed is higher than that reported so far for coding genes of other helminths. Neutrality was rejected for AgB2 genes. These data show the genetic polymorphism of antigen-coding genes among genetically characterized strains of E. granulosus.

Amino Acid Sequence↗
PubMed1999

Inhibition of luciferase expression in transgenic Aedes aegypti mosquitoes by Sindbis virus expression of antisense luciferase RNA.

A rapid and reproducible method of inhibiting the expression of specific genes in mosquitoes should further our understanding of gene function and may lead to the identification of mosquito genes that determine vector competence or are involved in pathogen transmission. We hypothesized that the virus expression system based on the mosquito-borne Alphavirus, Sindbis (Togaviridae), may efficiently transcribe effector RNAs that inhibit expression of a targeted mosquito gene. To test this hypothesis, germ-line-transformed Aedes aegypti that express luciferase (LUC) from the mosquito Apyrase promoter were intrathoracically inoculated with a double subgenomic Sindbis (dsSIN) virus TE/3'2J/anti-luc (Anti-luc) that transcribes RNA complementary to the 5' end of the LUC mRNA. LUC activity was monitored in mosquitoes infected with either Anti-luc or control dsSIN viruses expressing unrelated antisense RNAs. Mosquitoes infected with Anti-luc virus exhibited 90% reduction in LUC compared with uninfected and control dsSIN-infected mosquitoes at 5 and 9 days postinoculation. We demonstrate that a gene expressed from the mosquito genome can be inhibited by using an antisense strategy. The dsSIN antisense RNA expression system is an important tool for studying gene function in vivo.

Aedes↗
PubMed2004

Evolution of bitter taste receptors in humans and apes.

Bitter taste perception is crucial for the survival of organisms because it enables them to avoid the ingestion of potentially harmful substances. Bitter taste receptors are encoded by a gene family that in humans has been shown to contain 25 putatively functional genes and 8 pseudogenes and in mouse 33 putatively functional genes and 3 pseudogenes. Lineage-specific expansions of bitter taste receptors have taken place in both mouse and human, but very little is known about the evolution of these receptors in primates. We report the analysis of the almost complete repertoires of bitter taste receptor genes in human, great apes, and two Old World monkeys. As a group, these genes seem to be under little selective constraint compared with olfactory receptors and other genes in the studied species. However, in contrast to the olfactory receptor gene repertoire, where humans have a higher proportion of pseudogenes than apes, there is no evidence that the rate of loss of bitter taste receptor genes varies among humans and apes.

Animals↗
PubMed1975

Temperature-sensitive mutants of influenza WSN virus defective in virus-specific RNA synthesis.

Influenza WSN virus temperature-sensitive (ts) mutants were examined for defects in viral complementary RNA (cRNA) synthesis. The synthesis of viral cRNA was determined by hybridizing RNA from infected cells to radiolabeled virion RNA of known specific activity. Mutants in complementation groups I and III synthesized little, or no, cRNA at the nonpermissive temperature (39.5 C). When cells infected by these mutants were incubated for 5 h at the permissive temperature (33 C) and were then shifted to 39.5 C, net synthesis of cRNA ceased. This strongly suggests that mutants in these two complementation groups possess a ts defect in the transciptase complex. Mutants in group II and group V synthesize reduced amounts of cRNA at 39.5 C. In contrast to the group I and group III mutants, cRNA synthesis in cells infected by a group II or a group V mutant continues after a shift-up. This indicated that these mutants do not possess a ts transcriptase complex and that these mutants are most probably defective in some step in the amplification of cRNA synthesis. As will be discussed, the most likely defect in these mutants is in the synthesis of virion-type RNA. These results suggest that there are two influenza viral gene functions required for transcription and most likely two additional gene functions required for RNA replication.

Cell Line↗
PubMed1998

Visual function and gene analysis in a family with Oguchi's disease.

A family with 1 case of retinitis pigmentosa (III-1) and 2 cases of Oguchi's disease (III-2, 3) was examined in terms of electrophysiology as well as molecular biology. The proband (III-3), a 42-year-old female, and 2 older brothers (III-1, 2, aged 52 and 45 years) and 2 unaffected members in the same family participated in this study. Corrected visual acuities of the individuals with Oguchi's disease (III-2, 3) were 1.2. On funduscopy, blood vessels stood out in relief against a metallic-appearing background and a Mizuo-Nakamura phenomenon was evident. Full-field electroretinograms (ERGs) recorded from the proband were indicative of rod dystrophy, but results of other electrophysiological examinations (multifocal ERG, pattern ERG and visual-evoked cortical potential recordings) were within normal limits. Patient III-1 had corrected visual acuities of RE 20 cm/m.m. and LE 30 cm/n.d., severe chorioretinal atrophy in both fundi, and full-field ERG revealed rod-cone dystrophy. Mutation of the arrestin gene (1147de1A) was detected in all 3 patients. Visual function in each patient coincides with that of retinitis pigmentosa or Oguchi's disease, respectively.

Adult↗
PubMed1994

STV1 gene encodes functional homologue of 95-kDa yeast vacuolar H(+)-ATPase subunit Vph1p.

The Saccharomyces cerevisiae gene, VPH1 (Vacuolar pH 1), encodes a 95-kDa integral membrane subunit of the vacuolar-type H(+)-ATPase (V-ATPase) that is required for enzyme assembly; disruption of the VPH1 gene impairs vacuolar acidification (Manolson, M.F., Proteau, D., Preston, R. A., Stenbit, A., Roberts, B. T., Hoyt, M. A., Preuss, D., Mulholland, J., Botstein, D., and Jones, E. W. (1992) J. Biol. Chem. 267, 14294-14303). Here we show that STV1 (Similar To VPH1) encodes an integral membrane polypeptide of 102 kDa with 54% identity with the peptide sequence of Vph1p. High copy expression of STV1 partially restores vacuolar acidification in a delta vph1 mutant strain; solubilization and fractionation of membrane proteins from these vacuoles show that Stv1p co-purifies with bafilomycin A1-sensitive ATPase activity and with the 60- and 69-kDa V-ATPase subunits. Immunofluorescence microscopy of strains bearing a single copy of epitope-tagged STV1 reveals punctate staining of the cytoplasm; overexpression of epitope-tagged Stv1p reveals both punctate cytoplasmic staining and vacuolar membrane staining. Northern analysis shows that disruption of STV1 does not affect the level of transcription of VPH1 and that disruption of VPH1 does not affect the level of transcription of STV1. Strains bearing disruption of genes encoding other V-ATPase subunits (VMA1, VMA2, VMA3, and VMA4) fail to grow on media supplemented with 100 mM CaCl2 or 4 mM ZnCl2, media buffered to pH 7.5, or media with a glycerol carbon source. On the same types of media only a delta vph1 delta stv1 double disruption mutant has growth phenotypes equivalent to strains bearing a single disruption of the VMA1, VMA2, VMA3, and VMA4 genes; a delta vph1 strain has only moderate growth inhibition while a delta stv1 strain has wild type growth on the conditions listed above. We conclude that Stv1p is a functional homologue of Vph1p and suggest that Stv1p and Vph1p may be equivalent subunits for V-ATPases located on different organelles. The function of these 100-kDa homologues may be to target or regulate other common V-ATPase subunits for two distinct cellular locations.

Amino Acid Sequence↗
PubMed1994

The repair fidelity of restriction enzyme-induced double strand breaks in plasmid DNA correlates with radioresistance in human tumor cell lines.

PURPOSE: The accuracy of DNA repair may play a role in determining the cytotoxic effect of ionizing radiation. Repair, as measured by DNA strand breakage, often shows little difference between tumor cell lines of widely different radiosensitivity. The mechanism by which DNA fragments are rejoined is poorly understood. This study used plasmid transfection as a probe to assess the balance between correct repair and misrepair. METHODS AND MATERIALS: Using techniques described, a double-strand break was introduced into a coding sequence of circular plasmid DNA using a restriction endonuclease as a model for a radiation-induced double-strand break; it was then transfected as a linear molecule into human tumor cells, and the subsequent cell-mediated restoration of the coding sequence, evidenced by intact gene function, was documented. The plasmid used in these experiments, pPMH16, is known to integrate into genomic DNA. Gene function was tested by the ability to grow colonies in selection media. The plasmid also contains a second selectable marker gene that was used to identify transfected cells, before the function of the damaged gene was tested. The proportion of transfected cells that had correctly restored the damaged gene gave a measure of repair fidelity. RESULTS: A general trend for sensitive cells to show lower repair fidelity relative to resistant cells was observed. The type of double-strand cleavage of the plasmid (staggered or blunt) made little difference to the measured repair fidelity, in contrast to published studies in which restriction-enzyme breaks had been introduced into DNA within chromatin. Specific comparison of parent lines and their radiosensitive clones showed significant differences in repair fidelity for a relatively small change in radiation response, which was in line with the overall correlation. These same pairs have previously been shown to have no difference in the loss of DNA fragmentation with time after irradiation, and Southern analysis had confirmed the integrated plasmid copy number was similar in the cell lines compared. The number of intact copies of the damaged gene relative to the undamaged gene mirrored the observed repair fidelity. However, in one cell line out of the 10 studied, an exception to the observed trend was found. In a comparison of two equally radioresistant bladder cancer cell lines, large differences in repair fidelity were observed. Again, no difference in the integrated copy number was found, and the damaged gene was highly rearranged or deleted in the cell line with low repair fidelity. CONCLUSION: These studies have shown repair fidelity to correlate closely with radiosensitivity, including the comparison of genetically related lines. It is suggested that repair fidelity can be, but is not invariably, a measure of correct repair relative to misrepair, resulting from the processing of double-strand breaks and, hence, the response to ionizing radiation.

DNA↗
PubMed2001

Expression kinetics of the transcript and product of the UL28 homologue of bovine herpesvirus 1.

We report that the bovine herpesvirus 1 (BHV1) UL28 ORF, a homologue of the herpes simplex virus (HSV) UL28 gene, represents a functional gene encoding a viral specific protein. The BHV1 UL28 ORF, located at positions 53058-->55538 of the viral genome, encodes a viral specific transcript of 3.4 kb detected at 6 h post-infection (p.i.) after which its levels accumulated up to 12 h p.i. and then remained constant up to 24 h p.i. Transcription of the BHV1 UL28 was determined to initiate 95 bases upstream from the ORF's initiating codon, which corresponds to 33 nucleotides downstream from a putative TATA box. A BHV1 UL28 specific antiserum, generated against a T7-Tag/UL28 fusion protein expressed in E. coli, specifically reacted with a 100 kDa protein in Western blots of BHV1-infected protein cell lysates. The expression kinetics of the protein was delayed by 6 h relative to that of its transcript suggesting that the gene is regulated at the translational level. In contrast to the HSV and pseudorabies virus UL28 genes, which belong to viral genes of the early (beta) class, that of BHV1 was unambiguously classified as a gamma2 gene. Further studies will be required to determine whether these kinetic differences have any functional implications.

5' Untranslated Regions↗
PubMed1990

Molecular cloning of the human CTP synthetase gene by functional complementation with purified human metaphase chromosomes.

Successive rounds of chromosome-mediated gene transfer were used to complement a hamster cytidine auxotroph deficient in CTP synthetase activity and eventually to clone human genomic and cDNA fragments coding for the structural gene. Our approach was to isolate human Alu+ fragments from a tertiary transfectant and to utilize these fragments to screen a panel of primary transfectants. In this manner two DNA fragments, both mapping within the structural gene, were identified and used to clone a partial length cDNA. The remaining portion of the open reading frame was obtained through the RACE polymerase chain reaction technique. The open reading frame encodes 591 amino acids having a striking degree of similarity to the Escherichia coli structural gene (48% identical amino acids with 76% overall similarity including conservative substitutions) with the glutamine amide transfer domain being particularly conserved. As regulatory mutations of CTP synthetase confer both multi-drug resistance to agents widely used in cancer chemotherapy and a mutator phenotype, the cloning of the structural gene will be important in assessing the relevance of such phenotypes to the development of cellular drug resistance.

Amino Acid Sequence↗
PubMed2003

The regulatory elements of the Mycobacterium tuberculosis gene Rv3881c function efficiently in Escherichia coli.

We report efficient expression of the Mycobacterium tuberculosis gene Rv3881c in Escherichia coli from its M. tuberculosis promoter, attributable to an E. coli consensus Pribnow box and ribosome binding site. The N-terminal sequence of the recombinant E. coli-generated protein was identical to the predicted open reading frame of Rv3881c and transcription of the Rv3881c gene initiated at the same nucleotide position in both bacteria. We demonstrate the utility of this promoter for rapid analysis of expression in E. coli of heterologous gene constructs, for subsequent expression from the genomes of slow-growing mycobacteria such as Mycobacterium bovis-BCG. M. tuberculosis Rv3881c homologues were present in other pathogenic mycobacteria such as M. bovis-BCG, Mycobacterium szulgai and Mycobacterium kansasii.

Base Sequence↗
PubMed2002

Functional exploration of the C. elegans genome using DNA microarrays.

Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans development.

Animals↗
PubMed1991

The human placental lactogen genes: structure, function, evolution and transcriptional regulation.

hPL is a member of an evolutionarily related gene family including hGH and hPRL. Expression of hPL is limited to the placenta but its physiological actions are far reaching. hPL has a direct somatotropic effect on fetal tissues, it alters maternal carbohydrate and lipid metabolism to provide for fetal nutrient requirements, and aids in stimulation of mammary cell proliferation. Two hPL genes (hPL3 and hPL4) encoding identical proteins are responsible for the production of up to 1-3 g PL hormone/day. Recent studies have characterized the regulatory controls of hPL expression. At the post transcriptional level, RNA stability may contribute to variable levels of hPL3 vs. hPL4 production. In addition, non-tissue-specific protein-promoter interactions involving the Sp1 transcription factor are necessary for hPL transcription initiation. A transcriptional enhancer located 3' to the hPL3 gene is responsible for the placenta-specific expression of this gene, while an additional enhancer may be located 3' to the hPl4 gene. The hPL enhancer is bound by multiple proteins including at least one placental specific protein that interacts with a TEF-1 motif. Therefore, enhancer-protein interactions most likely play a large part in the high levels of placenta-specific hPL expression.

Amino Acid Sequence↗
PubMed1982

Globin genes: a paradigm of gene structure, function, and evolution.

Access to the detailed structure of the globin (and other) genes has taught us at least three valuable, but not necessarily expected, lessons regarding the structure and evolution of the genes. Foremost, at least in terms of its surprising nature, is the fact that many genes are interrupted, i.e., they contain discontinuous blocks of coding and noncoding information. No less surprising are the accompanying facts that chromosomal DNA changes by the movement and rearrangement of large pieces of DNA and that genetic loci are highly and unexpectedly complex, consisting of arrays of related genes and pseudo (or apparently nonfunctional) genes. Here we review some of the evidence upon which these conclusions rest, and we try to form a coherent picture of gene evolution. The evidence that we shall use is based on studies of the mouse globin. Evidence from various other genetic systems leads us to believe that these genes serve as an instructive general model rather than an idiosyncratic one.

Animals↗
PubMed1987

Differing expression patterns and evolution of the rat kininogen gene family.

The present investigation using molecular cloning and sequence analysis concerns the examination of the molecular basis for different expression patterns of two types of the rat kininogen genes. We show that the low molecular weight and high molecular weight forms of K kininogens are produced from a single gene through alternative usage of two 3'-coding regions, whereas only the low molecular weight forms of T kininogens are generated as a result of several mutational changes in the high molecular weight-specifying regions of both T-I and T-II kininogen genes. The mutational changes include a nucleotide substitution at the polyadenylation/processing signal site, nucleotide deletions resulting in the frame-shift mutation, and an insertion of the type 2 Alu-equivalent sequence. Because kininogens represent a multifunctional protein comprising the proteinase-inhibitory activity, the kinin moiety, and the clotting activity, these results present evidence indicating the molecular basis for the disappearance of a part of the gene functions. We also show that the K and T kininogen genes as well as the two T kininogen genes are extremely homologous, excluding and including the above mutational changes, respectively. These structural relationships allow us to envisage evolutionary processes for the generation of the rat kininogen gene family, particularly for the disappearance of a part of the gene functions.

Animals↗
PubMed2002

B cell-restricted human mb-1 gene: expression, function, and lineage infidelity.

The antigen receptor on B cells (B cell receptor [BCR]) consists of two noncovalently associated modules. Immunoglobulin genes created somatically during B cell development encode the antigen-specific component of the receptor. The Igalpha/beta heterodimer, encoded by the mb-1 and B29 genes, is necessary to escort the receptor complex to the plasma membrane. Following antigen engagement of the BCR, Igalpha/beta nucleates signal transduction and promotes endocytosis of bound antigen for intracellular degradation and presentation to helper T-cells. In this review, we outline the discovery of the mb-1 gene; summarize results from other laboratories on the function of Igalpha/beta in B cells; and conclude with our recent studies, which indicate that mb-1 is not a B-lineage-restricted gene as originally proposed.

Antigen Presentation↗
PubMed1996

Cloning and sequencing a human homolog (hMYH) of the Escherichia coli mutY gene whose function is required for the repair of oxidative DNA damage.

We have cloned the human mutY gene (hMYH) from both genomic and cDNA libraries. The human gene contains 15 introns and is 7.1 kb long. The 16 exons encode a protein of 535 amino acids that displays 41% identity to the Escherichia coli protein, which provides an important function in the repair of oxidative damage to DNA and helps to prevent mutations from oxidative lesions. The human mutY gene maps on the short arm of chromosome 1, between p32.1 and p34.3.

Amino Acid Sequence↗
PubMed2003

Genomic expression discovery predicts pathways and opposing functions behind phenotypes.

Discovering states of genetic expression that are true to a high degree of certainty is likely to predict gene function behind biological phenotypes. The states of expression (up- or down-regulated) of 19200 cDNAs in 10 meningiomas are compared with normal brain by an algorithm that detects only 1 false measurement per 192000; 364 genes are discovered. The expression data accurately predict activation of signaling pathways and link gene function to specific phenotypes. Meningiomas appear to acquire aberrant phenotypes by disturbing the balanced expression of molecules that promote opposing functions. The findings expose interconnected genes and propose a role of genomic expression discovery in functional genomics of living systems.

Algorithms↗
PubMed2006

Finding motifs in protein secondary structure for use in function prediction.

This paper presents a novel algorithm for the discovery of biological sequence motifs. Our motivation is the prediction of gene function. We seek to discover motifs and combinations of motifs in the secondary structure of proteins for application to the understanding and prediction of functional classes. The motifs found by our algorithm allow both flexible length structural elements and flexible length gaps and can be of arbitrary length. The algorithm is based on neither top-down nor bottom-up search, but rather is dichotomic. It is also "anytime," so that fixed termination of the search is not necessary. We have applied our algorithm to yeast sequence data to discover rules predicting function classes from secondary structure. These resultant rules are informative, consistent with known biology, and a contribution to scientific knowledge. Surprisingly, the rules also demonstrate that secondary structure prediction algorithms are effective for membrane proteins and suggest that the association between secondary structure and function is stronger in membrane proteins than globular ones. We demonstrate that our algorithm can successfully predict gene function directly from predicted secondary structure; e.g., we correctly predict the gene YGL124c to be involved in the functional class "cytoplasmic and nuclear degradation." Datasets and detailed results (generated motifs, rules, evaluation on test dataset, and predictions on unknown dataset) are available at www.aber.ac.uk/compsci/Research/bio/dss/yeast.ss.mips/, and www.genepredictions.org.

Algorithms↗