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At least 1,585 records · Page 88Linked to original sources
PubMed2001

Characterization of the myostatin gene in the gilthead seabream (Sparus aurata): sequence, genomic structure, and expression pattern.

We report on the sequence and expression analysis of the myostatin gene (MSTN) in the gilthead seabream Sparus aurata. A 2189-bp transcript was isolated, encoding an open reading frame (385 amino acids) that showed 74% to 60% protein similarity with other vertebrate myostatins. Phylogenetic analysis of MSTN and other related genes confirmed the evolutionary relationships of the isolated sequence. The complete sequences of two introns were also determined. Intron-exon boundaries were conserved when compared with those of mammalian MSTN genes, whereas intron size was smaller. Reverse transcriptase polymerase chain reaction on total RNA extracted from different tissues and developmental stages revealed MSTN expression in the skeletal muscle, but also in other tissues. The observed expression profile differed from that in mammals, suggesting possible additional functions of myostatin in the teleost fish.

Journal Article↗
PubMed2000

Elucidation of determinants of protein stability through genome sequence analysis.

Sequences of putative soluble proteins from complete genomes of eight thermophiles and 12 mesophiles were analyzed to gain insight into determinants of protein thermostability. The predator algorithm was used to assign secondary structures to each protein sequence. Based on simple statistical tests, a set of stabilizing factors was identified. These include reduced protein size, increases in number of residues involved in hydrogen bonding, beta-strand content and helix stabilization through ion pairs. There are also significant increases in the relative amounts of charged and hydrophobic beta-branched amino acids and decreases in uncharged polar amino acids in proteins from thermophiles relative to mesophilic organisms. Factors such as the relative proportion of residues in loops, proline and glycine content and helix capping do not appear to be important.

Amino Acids↗
PubMed2005

Characterization and partial genome sequence of stocky prune virus, a new member of the genus Cheravirus.

Characterization of a seemingly new spherical virus isolated from severely affected plum trees in south-western France indicated that its divided genome is composed of two single-stranded, polyadenylated RNAs of approximately 7.4 and 3.7 kb. Its particles are composed of three coat protein subunits of approximately 23, 23.5, and 24.5 kDa. Partial sequencing of the genomic RNAs indicated that this new virus, tentatively named stocky prune virus (StPV), is distantly related to the two sequenced cheraviruses, cherry rasp leaf virus (CRLV) and apple latent spherical virus (ALSV). StPV should be regarded as a new member in the unassigned genus Cheravirus.

Amino Acid Sequence↗
PubMed1995

The genomic sequence of a virulent bovine viral diarrhea virus (BVDV) from the type 2 genotype: detection of a large genomic insertion in a noncytopathic BVDV.

A second genotype of bovine viral diarrhea virus, BVDV genotype 2 or BVDV 2, has been identified based on phylogenic analysis of sequences from the 5' untranslated region of the viral RNA. In this study, we derived the complete nucleic acid sequence of a virulent BVDV 2 virus, BVDV2-890, isolated from an animal that died of an acute uncomplicated BVDV infection. BVDV2-890 is noncytopathic in cell culture and does not produce a p80 viral polypeptide. The ORF of BVDV2-890 is 11,922 nucleotide bases long and codes for 3973 amino acids. In comparison, the ORFs of other noncytopathic pestiviruses are shorter by about 250 nucleotides. The sequence identity at the amino acid level, between BVDV2-890 and published sequences for other pestiviruses, is 74% or less. The most conserved nucleotide and amino acid sequences between BVDV2-890 and other pestiviruses are located in the region coding for the nonstructural protein p80. The least conserved are in the regions coding for the structural polypeptide gp53 and nonstructural polypeptides p54 and p58. The larger size of the BVDV2-890 ORF is due to a 228-nucleotide insertion in the portion of the genome coding for the viral polypeptide p54. The location of this insertion was upstream from those reported in cytopathic pestiviruses. This insertion was not characteristic of all of the BVDV 2 viruses or all of the virulent BVDV 2 viruses.

Amino Acid Sequence↗
PubMed1998

Nucleotide sequence, genome organization, and transcription map of bovine adenovirus type 3.

The complete DNA sequence of bovine adenovirus type 3 is reported here. The size of the genome is 34,446 bp in length with a G+C content of 54%. All the genes of the early and late regions are present in the expected locations of the genome. However, the late-region genes are organized into seven families, instead of five as they are in human adenovirus type 2. The deduced amino acid sequences of open reading frames (ORFs) in the late regions and early region 2 (E2) and for IVa2 show higher degrees of homology, whereas the predicted amino acid sequences of ORFs in the E1, E3, and E4 regions and the pIX, fiber, and 33,000-molecular-weight nonstructural proteins show little or no homology with the corresponding proteins of other adenoviruses. In addition, the penton base protein lacks the integrin binding motif, RGD, but has an LDV motif instead of an MDV motif. Interestingly, as in other animal adenoviruses, the virus-associated RNA genes appear to be absent from their usual location. Sequence analysis of cDNA clones representing the early- and late-region genes identified splice acceptor and splice donor sites, polyadenylation signals and polyadenylation sites, and tripartite leader sequences.

Amino Acid Sequence↗
PubMed1991

[5-Variable genome sequence of the LIVP vaccinia virus. A possible role for short direct repeats in the formation of deletions].

HindIII-O/N DNA fragments of vaccinia virus (VV) of the LIVP strain were mapped using thirteen restriction endonucleases. Nucleotide sequences of the HindIII-O fragment (1530 bp) as well as of a site of the HindIII-N genome fragment 353 bp in size were determined. Comparison of restriction maps and nucleotide sequences of VV strains (WR and LIVP) demonstrated that DNA of VV LIVP contained % deletions and 2 insertions. "Reliable" short direct repeats were localized and their possible role in formation of DNA deletions was shown. It was suggested that VV endonuclease and DNA-ligase participate in replication and repair processes. Mechanism of formation of variable sequences of viral genomes is discussed.

Amino Acid Sequence↗
PubMed2000

The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium.

Heterochromatin, constitutively condensed chromosomal material, is widespread among eukaryotes but incompletely characterized at the nucleotide level. We have sequenced and analyzed 2.1 megabases (Mb) of Arabidopsis thaliana chromosome 4 that includes 0.5-0.7 Mb of isolated heterochromatin that resembles the chromosomal knobs described by Barbara McClintock in maize. This isolated region has a low density of expressed genes, low levels of recombination and a low incidence of genetrap insertion. Satellite repeats were absent, but tandem arrays of long repeats and many transposons were found. Methylation of these sequences was dependent on chromatin remodeling. Clustered repeats were associated with condensed chromosomal domains elsewhere. The complete sequence of a heterochromatic island provides an opportunity to study sequence determinants of chromosome condensation.

Arabidopsis↗
PubMed1996

Partial genomic sequence determination of yellow fever virus strain associated with a recent epidemic in Gabon.

A limited epidemic, with important mortality among the initial human cases, occured in a forest region in the north of Gabon by the end of 1994. It was identified as yellow fever according to first serological and reverse transcription/polymerase chain reaction (RT-PCR) results, but no virus was isolated. We received 37 sera from people who lived in the same region and presented symptoms of the disease during the period of concern. In ten of them, we were able to detect and identify yellow fever virus (YFV) RNA by RT-PCR and endonuclease digestion of the RT-PCR products. Nucleotide (nt) sequence of two regions (242 and 161 nt long) of YFV RNA was determined for three sera. As it differed from that of the Asibi strain of YFV, the presence of a new topotype (strain) of YFV is presumed.

Base Sequence↗
PubMed2026

The genome sequence of a window fly, Scenopinus jerei Pohjoismäki & Haarto, 2021 (Diptera: Scenopinidae).

We present a genome assembly from an individual male Scenopinus jerei (window fly; Arthropoda; Insecta; Diptera; Scenopinidae). The assembly contains two haplotypes with total lengths of 345.25 megabases and 232.44 megabases. Most of haplotype 1 (94.85%) is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.52 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Scenopinus jerei; window fly; genome sequence; chr↗
PubMed2006

A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis).

We obtained the complete mitochondrial genome of U.thibetanus mupinensis by DNA sequencing based on the PCR fragments of 18 primers we designed. The results indicate that the mtDNA is 16,868 bp in size, encodes 13 protein genes, 22 tRNA genes, and 2 rRNA genes, with an overall H-strand base composition of 31.2% A, 25.4% C, 15.5% G and 27.9% T. The sequence of the control region (CR) located between tRNA-Pro and tRNA-Phe is 1422 bp in size, consists of 8.43% of the whole genome, GC content is 51.9% and has a 6bp tandem repeat and two 10bp tandem repeats identified by using the Tandem Repeats Finder. U. thibetanus mupinensis mitochondrial genome shares high similarity with those of three other Ursidae: U. americanus (91.46%), U. arctos (89.25%) and U. maritimus (87.66%).

Animals↗
PubMed2006

Genome sequence diversity and clues to the evolution of variola (smallpox) virus.

Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.

DNA, Viral↗
PubMed1997

Human glutamate pyruvate transaminase (GPT): localization to 8q24.3, cDNA and genomic sequences, and polymorphic sites.

Two frequent protein variants of glutamate pyruvate transminase (GPT) (E.C.2.6.1.2) have been used as genetic markers in humans for more than two decades, although chromosomal mapping of the GPT locus in the 1980s produced conflicting results. To resolve this conflict and develop useful DNA markers for this gene, we isolated and characterized cDNA and genomic clones of GPT. We have definitively mapped human GPT to the terminus of 8q using several methods. First, two cosmids shown to contain the GPT sequence were derived from a chromosome 8-specific library. Second, by fluorescence in situ hybridization, we mapped the cosmid containing the human GPT gene to chromosome band 8q24.3. Third, we mapped the rat gpt cDNA to the syntenic region of rat chromosome 7. Finally, PCR primers specific to human GPT amplify sequences contained within a "half-YAC" from the long arm of chromosome 8, that is, a YAC containing the 8q telomere. The human GPT genomic sequence spans 2,7 kb and consists of 11 exons, ranging in size from 79 to 243 bp. The exonic sequence encodes a protein of 495 amino acids that is nearly identical to the previously reported protein sequence of human GPT-1. The two polymorphic GPT isozymes are the results of a nucleotide substitution in codon 14, coding for a histidine in GPT-1 and an asparagine in GPT-2, which causes a gain or loss of an NlaIII restriction site. In addition, a cosmid containing the GPT sequence also contains a previously unmapped, polymorphic microsatellite sequence, D8S421. The cloned GPT gene and associated polymorphisms will be useful for linkage and physical mapping of disease loci that map to the terminus of 8q, including atypical vitelliform macular dystrophy (VMD1) and epidermolysis bullosa simplex, type Ogna (EBS1). In addition, this will be a useful system for characterizing the telomeric region of 8q. Finally, determination of the molecular basis of the GPT isozyme variants will permit PCR-based detection of this world-wide polymorphism.

Alanine Transaminase↗
PubMed1995

Human herpesvirus-6: a survey of presence and distribution of genomic sequences in normal brain and neuroglial tumors.

In an attempt to study the frequency and distribution of human herpesvirus-6 (HHV-6) infection both in normal and neoplastic brain tissues in vivo, polymerase chain reaction was used to look for HHV-6 genomes: 1) in samples, obtained at necropsy, from different regions of the brain of immunocompetent adult subjects and of patients who died of AIDS; 2) in the surgical biopsies of a well-characterized series of primary brain tumors of neuroglial origin. HHV-6-specific sequences were identified in six of nine brain samples from immunocompetent subjects, and in four of seven brain samples from AIDS patients. Viral sequences were identified in the specimens derived either from the grey (frontal cortex and basal ganglia) or from the periventricular white matter. HHV-6 DNA was found only in 6 of the 37 primary brain tumor biopsies examined. This study provides for the first time molecular evidence of a wide distribution of HHV-6 infection in the brain tissues of a high proportion of subjects, both in normal and in impaired immunity. In this large series of tumor biopsies the presence of HHV-6 genomic sequences is a rare phenomenon, arguing against a major role of this herpesvirus in the pathogenesis of primary brain tumors of neuroglial origin in immunocompetent subjects.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Amino Acid Sequence↗
PubMed1989

Chicken protamine genes are intronless. The complete genomic sequence and organization of the two loci.

A positive cosmid clone obtained from a pwe15-rooster DNA library using a chicken protamine cDNA probe reveals the complete sequence of the two loci for the rooster protamine genes. The organization of these two loci within the cosmid clone matches that of genomic DNA. The copy number per haploid genome is two. The sequence for the rooster protamine predicted from the coding region shows differences from that previously determined at the protein level (Nakano, M., Tobita, T., and Ando, T. (1976) Int. J. Peptide Protein Res. 8, 565-578). A recent re-determination of the rooster protamine amino acid sequence (28 residues from the N terminus) matches that predicted from the genome rather than the sequence of Nakano et al. (1976). Both loci are intronless and the gene is extremely GC-rich (88% in the coding region). The 5' region of the gene contains a typical TATAAA box, several CG boxes, as well as other characteristic motifs. The 3' region of the gene contains the polyadenylation signal and several GT repeats of known Z-DNA forming potential. A correlation between the functional map of the gene and the tendency of the DNA to bend or to adopt the Z-conformation is presented and possible roles for these conformations in the transcription of this gene are discussed.

Amino Acid Sequence↗
PubMed2026

The genome sequence of the Eurasian common lizard, Zootoca vivipara (von Jacquin, 1787) (Squamata: Lacertidae).

We present a genome assembly from an individual male Zootoca vivipara (Eurasian common lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1 424.51 megabases and 1 423.70 megabases. Most of the haplotype 1 assembly (99.49%) and the haplotype 2 assembly (99.42%) are each scaffolded into 18 chromosomal pseudomolecules, including the Z 1 and Z 2 sex chromosomes. The mitochondrial genome has also been assembled, with a length of 17.09 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Eurasian common lizard↗