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At least 1,567 records · Page 87Linked to original sources
PubMed1996

FISH digital imaging microscopy in mosquito genomics.

The yellow fever mosquito, Aedes aegypti, transmits pathogens that affect both humans and livestock, and has been the focus of extensive research to identify genetic loci that may be useful in control strategies. Fluorescence in situ hybridization (FISH) and digital imaging microscopy have provided a rapid mechanism to populate the physical map with probes derived from genetic markers, cDNAs and recombinant genomic libraries. When the physical and genetic linkage maps are aligned, map-based cloning will allow the rapid isolation of target genomic sequences. The strategy of FISH mapping and the results of initial hybridization studies are reviewed here by Martin Ferguson, Susan Brown and Dennis Knudson. An Ae. aegypti-specific genomic database, which collates data from mapping studies, sequences, references and other relevant information, is also discussed.

Journal Article↗
PubMed1988

Sequence analysis of HLA class II genes from insulin-dependent diabetic individuals.

To examine the nature of HLA-linked genetic susceptibility to insulin-dependent diabetes mellitus (IDDM), we compared HLA class II gene sequences from IDDM patients and control individuals. Genomic libraries were constructed from two siblings with IDDM, typed serologically as DR3,w6 and DR3,4. These libraries represent the HLA haplotypes (DR3, DR4) most frequently associated with IDDM, as well as one haplotype found less often. Individual genomic clones were identified and assigned to specific loci and haplotypes. The nucleotide sequence was then determined from the variable second exon from the HLA-DQ alpha, DQ beta, and DR beta genes from all three haplotypes. Sequence variation within the DQ alpha genes could not be correlated with the disease. For all three haplotypes, the DQ alpha sequence from the IDDM patient was identical to the DR-matched control sequence. Similarly, for the DR3 haplotype, the DQ beta sequences matched all control DR3 alleles. The DQ beta sequence from the DR4 haplotype was identical to the predominant DR4 allele (DQ beta 3.2) but differed at four amino acid residues from the other major DR4 DQ beta sequence (DQ beta 3.1) found rarely among IDDM patients. Sequence analysis of the DQ beta gene from the DRw6 haplotype revealed a new allele that differed from the DQ beta allele from a control DR6 allele at two residues. The DR beta genes from these three haplotypes also did not show any sequence features uniquely associated with IDDM, although the frequency of certain allelic variants in all three of these haplotypes may be altered in the IDDM population. A particular group of amino acids was found to be shared between the DR beta-1 alleles from the DR4 and DRw6 haplotypes and may be involved in genetic susceptibility to IDDM.

Amino Acid Sequence↗
PubMed1987

A new shuttle cosmid vector, pKC505, for streptomycetes: its use in the cloning of three different spiramycin-resistance genes from a Streptomyces ambofaciens library.

A new shuttle cosmid vector, pKC505, was constructed for the cloning of Streptomyces DNA. This vector, which can be conjugally transferred between different streptomycetes, was used to construct a genomic library from a spiramycin-producing S. ambofaciens strain. By transformation of the spiramycin-sensitive S. griseofuscus with the library, three phenotypically different spiramycin-resistance genes were isolated. S. ambofaciens DNA in these clones was colinear with the chromosome, and the cloned DNA was stable in E. coli, S. griseofuscus and S. fradiae. These cosmids could be isolated easily from S. griseofuscus, an improvement over the previous shuttle cosmid vector, pKC462a [Stanzak et al., Bio/Technology 4 (1986) 229-232], which was somewhat difficult to isolate from S. lividans.

Chromosome Mapping↗
PubMed1990

(TG)n uncovers a sex-specific hybridization pattern in cattle.

Screening of a bovine genomic library with the human minisatellite 33.6 probe uncovered a family of clones that, when used to probe Southern blots of bovine genomic DNA digested with the restriction enzyme HaeIII or MboI, revealed sexually dimorphic, but otherwise virtually monomorphic, patterns among the larger DNA fragments to which they hybridized. Characterization of one of these clones revealed that it contains different minisatellite sequences. The sexual dimorphism hybridization pattern observed with this clone was found to be due to multiple copies of two tandemly interspersed repeats: the simple sequence (TG)n and a previously undescribed 29-bp sequence. Both repeats appear to share many genomic loci including autosomal loci. In contrast, Southern analysis of AluI- or HinfI-digested bovine DNA with the (TG)n repeat used as a probe yielded substantial polymorphism. These results show that (i) different minisatellites can be found in a cluster, (ii) both simple and more complex repeated sequences other than the simple quaternary (GATA)n repeat can be sexually dimorphic, and (iii) simple repeats can reveal substantial polymorphism.

Animals↗
PubMed2006

The membrane skeleton in Paramecium: Molecular characterization of a novel epiplasmin family and preliminary GFP expression results.

Previous attempts to identify the membrane skeleton of Paramecium cells have revealed a protein pattern that is both complex and specific. The most prominent structural elements, epiplasmic scales, are centered around ciliary units and are closely apposed to the cytoplasmic side of the inner alveolar membrane. We sought to characterize epiplasmic scale proteins (epiplasmins) at the molecular level. PCR approaches enabled the cloning and sequencing of two closely related genes by amplifications of sequences from a macronuclear genomic library. Using these two genes (EPI-1 and EPI-2), we have contributed to the annotation of the Paramecium tetraurelia macronuclear genome and identified 39 additional (paralogous) sequences. Two orthologous sequences were found in the Tetrahymena thermophila genome. Structural analysis of the 43 sequences indicates that the hallmark of this new multigenic family is a 79 aa domain flanked by two Q-, P- and V-rich stretches of sequence that are much more variable in amino-acid composition. Such features clearly distinguish members of the multigenic family from epiplasmic proteins previously sequenced in other ciliates. The expression of Green Fluorescent Protein (GFP)-tagged epiplasmin showed significant labeling of epiplasmic scales as well as oral structures. We expect that the GFP construct described herein will prove to be a useful tool for comparative subcellular localization of different putative epiplasmins in Paramecium.

Amino Acid Sequence↗
PubMed1997

Entamoeba histolytica contains a gene encoding a homologue to the 54 kDa subunit of the signal recognition particle.

We have determined the nucleotide sequence and predicted amino acid sequence of the 54 kDa subunit of the signal recognition particle (SRP54) from the amitochondrial protist Entamoeba histolytica. The SRP54 gene was isolated from a genomic library using a polymerase chain reaction (PCR) probe. Nucleotide sequence analysis of a 2.3 kb fragment, derived from a 7 kb genomic clone, revealed an open reading frame encoding a protein of 487 amino acids (MW 53.8 kDa). The identities of the predicted amino acid sequence with its homologues from other species were between 24 and 47%. Functional domains previously defined for the SRP54-type proteins were present in the entamoebal sequence, such as the amino-terminal GTP binding domain (G domain) and the carboxy-terminal methionine rich domain (M domain). SRP54 mRNA contains an extra G residue at the 5' end, suggesting that capping of poly-A(+) transcripts is present in E. histolytica. Evolutionary analysis of the SRP54 based on phylogenetic inference placed the E. histolytica sequence as an early divergence of the eukaryotic tree. Although the function of the entamoebal homologue remains to be elucidated, the identification of the SRP54 gene constitutes the first evidence for SRP related proteins in protozoans.

Amino Acid Sequence↗
PubMed2001

Organization, expression, and localization of the murine mdmx gene and pseudogene.

The mdmx gene is the first additional member of the mdm2 gene family to be isolated. It encodes a protein similar to MDM2 in several domains and also retains the ability to bind and inhibit p53 transactivation in vitro. However, mdmx does not appear to be transcriptionally regulated by p53. We have cloned and characterized the murine mdmx genomic locus from a 129 genomic library. The mdmx gene contains 11 exons, spans approximately 37 kb of DNA, and is located on mouse chromosome 1. The genomic organization of the mdmx gene is identical to that of mdm2 except at the 5' end of the gene near the p53 responsive element. Additionally, a pseudogene for mdmx was also identified that resides on the mouse X chromosome. Expression analysis of mdmx transcripts during mouse embryogenesis revealed constitutive and ubiquitous expression throughout development.

Amino Acid Sequence↗
PubMed2001

Human mouse mast cell protease 7-like tryptase genes are pseudogenes.

BACKGROUND: Alpha-tryptase and beta-tryptase are important clinical markers for mast cell-dependent disorders. A third family of tryptase genes on human chromosome 16 has been identified and called human mouse mast cell protease 7 (hmMCP-7)-like tryptase. OBJECTIVE: This study was designed to determine whether these tryptase genes are expressed by human mast cells. METHODS: A 2842-bp hmMCP-7-like tryptase gene was cloned and sequenced from a human placental genomic library. PCR and RT-PCR procedures, respectively, were used to determine whether this tryptase gene family was present in most genomes and whether it was expressed. RESULTS: The tryptase clone was almost identical to the hmMCP-7-like tryptase II and I genes, and therefore it was called hmMCP-7-like tryptase III. All such genes encode a Gln(-3) like alpha-tryptase. They also terminate translation after amino acid 235, whereas alpha- and beta-tryptase genes each encode a 275-amino acid protein. In this study, cell lines HMC-1, KU812, and Mono-Mac-6; mast cells derived in vitro from cord blood and fetal liver progenitors; and mast cell-enriched preparations of dispersed skin and lung cells contained hmMCP-7-like tryptases in their genomes by PCR with gene-specific primers. To identify whether such genes were transcriptionally active, RT-PCR revealed alpha- or beta-tryptase products in all mast cell preparations and cell lines and in activated skin-derived mast cells, but no hmMCP-7-like tryptase products. CONCLUSION: These results indicate hmMCP-7-like tryptase (I, II, III) genes are pseudogenes and unlikely to affect measurements of alpha- and beta-tryptases.

Animals↗
PubMed1986

Genomic cloning, characterization, and multilineage growth-promoting activity of human granulocyte-macrophage colony-stimulating factor.

Through the use of long single-sequence oligonucleotide probes, the complete gene for human granulocyte-macrophage colony-stimulating factor (hGM-CSF) has been cloned from a human genomic library. The gene is 2.5 kilobases in length, contains three introns, and is present as a single copy in the human genome. When subcloned into the mammalian expression vector pD3, the gene directs the synthesis of authentic hGM-CSF. In addition to its stimulation of in vitro granulopoiesis and monopoiesis, recombinant hGM-CSF stimulates in vitro erythropoiesis and megakaryopoiesis.

Base Sequence↗
PubMed1986

Studies on the transcription, translation, and structure of alpha-actinin in Dictyostelium discoideum.

A clone coding for the F-actin cross-linking protein alpha-actinin was obtained by screening a genomic library of Dictyostelium discoideum DNA in lambda gt11 with monoclonal antibodies specific for Dictyostelium alpha-actinin. The 1.2-kilobase (kb) genomic clone was confirmed as containing part of the alpha-actinin gene by comparing its nucleotide sequence with the amino acid sequence of tryptic peptides from purified alpha-actinin. The clone recognized a 3.0-kb message in a Northern blot. Hybridization to RNA isolated from different developmental stages of several D. discoideum strains indicated that the mRNA content increased during early development. A similar result was obtained when the alpha-actinin content of the cells was followed by Western blot analysis. Hybridization of the clone to DNA from different wild-type strains of D. discoideum indicated a polymorphism on the DNA level that coincided with a polymorphism on the protein level. The data suggest continuous transcription of the alpha-actinin gene throughout the development of D. discoideum, up- and down-regulation of the levels of alpha-actinin mRNA and protein with maximum levels at the onset of aggregation, and a high diversity of alpha-actinin at the DNA and protein level among different D. discoideum strains. The structural data make it conceivable that the highly conserved nature of alpha-actinin resides only at the functional sites, whereas the helical portions of the alpha-actinin molecule allow a higher level of diversity throughout evolution.

Actinin↗
PubMed1999

Novel endogenous type C retrovirus in baboons: complete sequence, providing evidence for baboon endogenous virus gag-pol ancestry.

A complete endogenous type C viral genome has been isolated from a baboon genomic library. The provirus, Papio cynocephalus endogenous retrovirus (PcEV), is 8,572 nucleotides long, and 38 to 59 proviral copies per baboon genome are found. The PcEV provirus possesses the typical simple retroviral gene organization, including two long terminal repeats and genes encoding gag, pol, and env proteins. The open reading frames for gag-pol and env are complete but have premature stop codons or frameshift mutations. The primer binding site of PcEV is complementary to tRNAGly. The gag and pol genes of PcEV are closely related to those of the baboon endogenous virus (BaEV). The env coding region of PcEV is related to the env genes of type C retroviruses. This suggests that PcEV is one of the ancestors of BaEV contributing the type C gag-pol genome fragment to the type C/D recombinant virus BaEV. Earlier it was shown that another endogenous type D virus (simian endogenous retrovirus) provided the env gene for BaEV (A. C. van der Kuyl et al., J. Virol. 71:3666-3676, 1997).

Animals↗
PubMed1988

Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome.

The gene for MRP7, a 40-kilodalton protein of the large subunit of the yeast mitochondrial ribosome, was identified in a lambda gt11 expression library by immunological screening with a monoclonal antibody to MRP7. An intact copy of MRP7 was then isolated from a yeast genomic library by colony hybridization. Gene disruption showed that MRP7 protein was essential for ribosomal function. Sequencing of MRP7 revealed a coding region for a basic (pI 10.6), 43.2-kilodalton protein containing 371 amino acid residues. Amino acid residues 28 to 112 of the deduced MRP7 sequence aligned with the 84 residues of the Escherichia coli ribosomal protein L27, but no significant similarity was detected between the carboxy-terminal 259 amino acids of MRP7 and other protein sequences in existing computer data bases. Within the aligned region, there was 49% amino acid identity between MRP7 and L27, compared with the 57% identity observed between L27 and its homolog in Bacillus stearothermophilus. The steady-state levels of the MRP7 protein and its mRNA were monitored in response to catabolite repression and to increased dosage of the MRP7 gene. The response to catabolite repression was characterized by a ninefold change in the level of the protein and little, if any, change in the level of the mRNA. In cells carrying the MRP7 gene on a high-copy-number plasmid, the mRNA was increased 20-fold, but there was no significant increase in MRP7 protein. Furthermore, MRP7 mRNA and protein accumulated at normal levels in [rho0] cells, which are devoid of 21S rRNA, indicating that the protein is relatively stable in the absence of ribosome assembly. Together, these results suggest that MRP7 is regulated posttranscriptionally, probably at the level of protein synthesis rather than protein turnover.

Amino Acid Sequence↗
PubMed1993

Molecular structure and transcriptional function of the rat vascular AT1a angiotensin receptor gene.

Rat vascular angiotensin receptors (AT1a receptors) are encoded by two mRNA transcripts sharing an identical receptor coding sequence but differing in their 5' and 3' untranslated sequences. We screened male Sprague-Dawley rat genomic libraries to clone the vascular AT1a receptor gene. Two sets of overlapping clones were isolated that encode over 90 kb of genomic sequence around the AT1a receptor gene. Four overlapping clones were identified from the 5' flanking portion of the gene. These contain the promoter region and two exons, 141 bp and 89 bp in size, respectively, encoding the alternatively spliced 5' untranslated mRNA sequence. Six additional clones overlap each other but do not overlap the set of clones from the 5' flanking region of the gene. These contain a single 1977-bp exon that encodes 900 bp of the 5' and 3' untranslated sequences in addition to a 1077-bp open reading frame identical to that found in vascular smooth muscle cell AT1a receptor cDNAs. Primer extension and RNase protection studies indicate that the transcription start site for this gene begins 9 bp upstream from the most 5' sequence found within the AT1a receptor cDNAs. Our mapping studies of the cloned gene, which so far includes an uncloned gap within the second intron, indicate that the transcription start site is no less than 67 kb upstream from the receptor coding exon. Promoter-reporter assays were performed by transfection of vascular smooth muscle cells with deletions of a 3.2-kb promoter region fused to a luciferase cDNA reporter plasmid. Relatively strong basal transcriptional activity is observed from the 5'-most 2 kb of the promoter and diminishes markedly with deletions within 1 kb of the early promoter region, suggesting strong promoter elements in the more upstream regions of the gene. Deletion of a 53-bp early promoter region containing the transcription start site and a putative TATA box completely abolishes the ability of upstream elements to drive transcription of the luciferase cDNA. These results indicate that we have isolated the AT1a receptor gene and its functional promoter.

Animals↗
PubMed1992

Characterization of the human gene encoding cytokeratin 17 and its expression pattern.

Among the members of the cytokeratin (CK) subfamily of intermediate filament (IF) proteins, CK 17 is remarkable as it is normally expressed in the basal cells of complex epithelia but not in stratified or simple epithelia. Because of its unusual expression pattern in normal and diseased states and because of the potential importance of CK 17 in tumor diagnosis, we have characterized the gene(s) and its cDNA-derived amino acid sequence. A cDNA clone encoding CK 17 was isolated from a HeLa cDNA library and used for the determination of the amino acid sequence, for studies of expression and for the screening of human genomic libraries. A number of lambda phage clones were isolated that covered three distinct, non-contiguous gene regions. Only one of these loci contains the functional CK 17 gene which is located only approximately 5 kbp 5'-upstream of the CK 16 gene, whereas the other two contain unprocessed CK 17 pseudogenes. Each of these genes is part of a larger CK type I gene locus the arrangement of which suggests that these genes and pseudogenes have arisen during evolution by duplication events comprising whole multigene loci. The functional CK 17 gene differs from the pseudogenes by the extent of methylation of certain DNA sequences in the 5'-upstream region. The 5 kbp CK 17 gene with 8 exons and 7 introns encodes a polypeptide of 432 amino acids with a calculated molecular weight of 48,000. Using S1-nuclease protection assays and RNAs from several cell lines we identified a single transcriptional start point 26 nucleotides down-stream from a TATA box element. Northern blot hybridization experiments showed a restricted pattern of CK 17 gene expression, supporting the notion that CK 17 synthesis is essentially regulated at the transcriptional level. From these findings and from immunohistological observations, CK 17 synthesis seems to be a marker of basal cell differentiation in complex epithelia and therefore indicative of a certain type of epithelial "stem cells".

Amino Acid Sequence↗
PubMed1988

Isolation and analysis of the Neurospora crassa Cyt-21 gene. A nuclear gene encoding a mitochondrial ribosomal protein.

The Neurospora crassa nuclear mutant cyt-21-1 (originally 297-24; Pittenger, T.H., and West, D.J. (1979) Genetics 93, 539-555) has a defect leading to gross deficiency of mitochondrial small ribosomal subunits. Here, we have cloned the cyt-21+ gene from a N. crassa genomic library, using the sib selection procedure (Akins, R. A., and Lambowitz, A. M. (1985) Mol. Cell Biol. 5, 2272-2278). The genomic clone contains a short split gene encoding a basic protein of 107 amino acid residues. This protein shows strong homology to Escherichia coli ribosomal protein S-16. Comparison of mutant and wild-type mitochondrial ribosomal proteins (Kuiper, M. T. R., Holtrop, M., Vennema, H., Lambowitz, A. M., and de Vries, H. (1988) J. Biol. Chem. 263, 2848-2852) indicates that the cyt-21 gene encodes N. crassa mitochondrial ribosomal protein S-24. The expression of the cyt-21+ gene is regulated such that the level of the putative cyt-21+ mRNA is increased about 5-fold when mitochondrial protein synthesis is inhibited. We suggest that this reflects part of a general mechanism for coordinately activating Neurospora nuclear genes that encode mitochondrial constituents in response to impaired mitochondrial function. This is the first report of the cloning and characterization of a mitochondrial ribosomal protein gene from N. crassa.

Amino Acid Sequence↗
PubMed1990

Structural analysis of the rabbit TNF locus, containing the genes encoding TNF-beta (lymphotoxin) and TNF-alpha (tumor necrosis factor).

The genes coding for 20-kDa lymphotoxin (TNF-beta) and tumor necrosis factor (TNF-alpha) have been cloned from a rabbit genomic library. The two genes are tandemly arranged and separated by only 1 kb of DNA, as previously observed in human and mouse genomes. We have sequenced the entire rabbit lymphotoxin-encoding gene and inferred the primary structure of rabbit TNF-beta, whose cDNA is not yet cloned. We also analysed the upstream sequences of the rabbit TNF-beta and TNF-alpha genes and identified a number of potential binding sites for known nuclear transcription factors, and in particular several putative kappa B-type sequences.

Amino Acid Sequence↗
PubMed2002

Three sucrose transporter genes are expressed in the developing grain of hexaploid wheat.

A family of three cDNAs, designated TaSUT1A, 1B and 1D, encoding sucrose transporter (SUT) proteins was isolated from a hexaploid wheat (Triticum aestivum) endosperm library. The cDNA sequences are 96% identical but are distinguishable from one another by virtue of a size polymorphism in the 3'-untranslated region (UTR). The predicted amino acid sequences are 98% identical and are highly similar to the sucrose transporters from rice, maize and barley. A gene for TaSUT1 was isolated from genomic libraries of Aegilops tauschii (the donor of the D genome of wheat) and the coding sequence found to be identical to that of TaSUT1D cDNA. There is only one copy of each TaSUT1 gene in hexaploid wheat and it is located on chromosome 4. Genomic Southern analysis and PCR analysis across the 3' polymorphic region of hexaploid, tetraploid and progenitor diploid wheat DNAs established that the TaSUT1A gene was present in the putative A-genome progenitor, T. monococcum, and that the TaSUT1B gene was present in the putative B-genome progenitor, T. searsii. All three TaSUT1 genes are expressed at high levels in filling grain, showing a good correlation with the developmental time course of growth. This reinforces the view that in cereals a major role of SUT1 is in the post-phloem sugar transport pathway associated with seed filling.

Base Sequence↗
PubMed1991

Characterization and mapping of human genes encoding zinc finger proteins.

The zinc finger motif, exemplified by a segment of the Drosophila gap gene Krüppel, is a nucleic acid-binding domain present in many transcription factors. To investigate the gene family encoding this motif in the human genome, a placental genomic library was screened at moderate stringency with a degenerate oligodeoxynucleotide probe designed to hybridize to the His/Cys (H/C) link region between adjoining zinc fingers. Over 200 phage clones were obtained and are being sorted into groups by partial sequencing, cross-hybridization with oligodeoxynucleotide probes, and PCR amplification. Further, the genomic clones were cross-hybridized with a set of 30 zinc finger-encoding cDNAs (Kox1-Kox30) isolated from a human T-cell cDNA library. Four cDNAs (Kox4, Kox7, Kox12, and Kox15) were identified that match one or more genomic clones; these matches were confirmed by nucleotide sequence analysis. One or more clones from each locus were mapped onto human metaphase chromosomes by chromosomal in situ suppression hybridization with fluorescent probe detection. We mapped ZNF7/Kox4 to chromosome 8qter, ZNF19/Kox12 to 16q22, ZNF22/Kox15 to 10q11, and ZNF44/Kox7 to 16p11. The results of these analyses support the conclusion that the human genome contains many, probably several hundred, zinc finger genes with consensus H/C link regions.

Amino Acid Sequence↗