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PubMed1993

Molecular cloning and sequence analysis of two porcine seminal proteins, PSP-I and PSP-II: new members of the spermadhesin family.

Two full-length cDNAs encoding porcine seminal proteins, PSP-I and PSP-II, have been isolated from a porcine seminal vesicle cDNA library. Nucleotide sequence analysis of the 706-bp PSP-I cDNA predicts a precursor protein of 133 amino acid residues, which includes a 21-residue signal peptide and a 112-residue secreted protein. On the other hand, the complete sequence of the 686-bp PSP-II cDNA reveals a coding sequence for a 21-residue signal peptide and a 116-residue secreted protein. The predicted amino acid sequences agree very well with those determined by conventional amino acid sequence analysis. Alignment of the two cDNA sequences shows an overall 66% sequence homology throughout their entire length. However, the sequence homology is much higher in the 3' untranslated region (72%) than in the coding region (61%). This suggests that these two genes evolved by duplication and divergence from a common ancestral gene. They share about 50% amino acid sequence homology and a similar overall structure with three members of the spermadhesin family.

Amino Acid Sequence↗
PubMed2005

LT, VP1 and TCR-BKV sequence analysis in a patient with post-transplant BKV nephropathy associated with EBV-related PTLD.

A 10-year-old boy kidney transplant recipient (KTR) developed an abdominal post-transplant lymphoproliferative syndrome (PTLD) followed by BK virus nephropathy (BKVN). BK virus (BKV) and Epstein-Barr virus (EBV) were studied in renal and PTLD tissue by polymerase chain reaction (PCR) assay. Afterwards, the patient was monitored in relation to BKV in urine and serum; transcription control region (TCR)-BK polymorphism sequence analysis was also performed. In the PCR assay, both early large T antigen (LT) and late (VP1) transcriptional BKV coding regions were found in renal tissue, whereas EBV and only LT-BK were detected in PTLD abdominal tissue. On the other hand, TCR sequence analysis revealed the AS genomic BK variant.

Antigens, Viral, Tumor↗
PubMed2005

Visfatin: gene expression in isolated adipocytes and sequence analysis in obese WOKW rats compared with lean control rats.

Recently, Fukuhara et al. have shown that the novel visfatin is predominantly released from visceral adipocytes and shares metabolic functions with insulin. The authors suggested that there is a relationship between visfatin and the metabolic syndrome in humans. These findings prompted us to clarify the visfatin gene expression from visceral and subcutaneous adipocytes in WOKW rats, as an animal model for polygenically inherited metabolic syndrome, compared to lean Dark Agouti (DA) rats. Moreover, visfatin sequence analysis was performed in WOKW, DA rats, and disease-resistant Fisher 344, Lewis, Brown Norway, and Karlsburg wild rats. The relative gene expression of visfatin displays no significant changes in adipocytes from WOKW rats compared with DA and visfatin sequence analysis of the coding region was identical to the GenBank. But, we found length differences of two repeats, GT and GA, in intron 2 between the strains. In summary, the relative visfatin gene expression is not associated with the metabolic syndrome in WOKW rats.

Adipocytes↗
PubMed2000

Cloning and sequence analysis of lily and tobacco guanylate kinases.

Guanylate kinase is an essential enzyme in the nucleotide biosynthetic pathway, catalyzing the reversible transfer of the terminal phosphoryl group of ATP to GMP or dGMP. This enzyme has been well studied from several organisms and many structural and functional details have been characterized. Animal GMP kinases have also been implicated in signal transduction pathways. However, the corresponding role by plant derived GMP kinases remains to be elucidated. Full-length cDNA clones encoding enzymatically active guanylate kinases were isolated from cDNA libraries of lily and tobacco. Lily cDNA is predicted to encode a 392-amino acid protein with a molecular mass of 43.1 kDa and carries amino- and carboxy- terminal extensions of the guanylate kinase (GK)-like domain. But tobacco cDNA is predicted to encode a smaller protein of 297-amino acids with a molecular mass of 32.7 kDa. The amino acid residues known to participate in the catalytic activity of functionally characterized GMP kinases, are also conserved in GK domains of LGK-1 and NGK-1. The GK domains of NGK-1, LGK-1 and previously characterized AGK-1 from Arabidopsis exhibit 74-84% identity, whereas their N- and C-terminal domains are more divergent with amino acid conservation in the order of 48-55%. Phylogenetic analysis on the deduced amino acid sequences reveals that NGK-1 and LGK-1 form one distinct subgroup along with AGK-1 and AGK-2 homologues from Arabidopsis. Isolation of GMP kinases from diverse plant species like lily and tobacco adds a new dimension in understanding their role in cell signaling pathways that are associated with plant growth and development.

Amino Acid Sequence↗
PubMed1992

Differential Expression and Sequence Analysis of Ribosomal Protein Genes Induced in Stolon Tips of Potato (Solanum tuberosum L.) during the Early Stages of Tuberization.

cDNA clones of two genes, TUBS19 and TUBL7, which show a 15- to 20-fold increase in transcript level in the stolon tip during the early stages of tuberization, have been isolated by differential screening. These genes are also expressed in leaves, stems, and roots, and the expression pattern in these organs changes on tuberization. Southern analysis shows that there are similar sequences in the genome of nontuberizing wild-type potato species Solanum brevidens and in Lycopersicon esculentum (tomato). Sequence analysis reveals a high degree of similarity between the TUBS19 cDNA and the eukaryotic S19 ribosomal protein gene. TUBL7 cDNA shows similarity to another eukaryotic ribosomal protein gene, L7.

Journal Article↗
PubMed1990

Covalent attachment of peptides for high sensitivity solid-phase sequence analysis.

We have developed a method for the high efficiency covalent immobilization of picomole to nanomole quantities of peptides in a form compatible with high sensitivity gas-liquid or solid-phase sequence analysis. Glass fiber filter paper was derivatized with amino-phenyltriethoxysilane and peptides were applied to circular disks cut to 1-cm diameters. Peptides were covalently immobilized on the aminophenyl-glass fiber paper through their terminal alpha-carboxyl groups and amino acid side-chain carboxyl groups by activation with the water-soluble reagent N-ethyl-N'-(3-dimethylaminopropyl)carbodiimide. Disks containing the covalently attached peptide were directly inserted into the cartridge of an automated sequenator for sequence analysis by the Edman degradation. Peptides prepared in this way could be routinely sequenced through to and including the C-terminal amino acid residue, at extraordinarily low backgrounds. The covalent immobilization of peptide fragments allowed far more flexibility in sequencing conditions, including the use of polar extraction solvents to increase the yield of phenylthiohydantoin (PTH)-His and PTH-Arg and the use of alternative Edman-type sequencing reagents with enhanced detectability, such as the chromophoric compound 4- (N,N'-dimethylamino)azobenzene-4'-isothiocyanate. The potential of this high efficiency immobilization method for contributing to the development of sequencing chemistries with enhanced sensitivity is discussed.

Amino Acid Sequence↗
PubMed1998

Somatic deletion mapping on chromosome 10 and sequence analysis of PTEN/MMAC1 point to the 10q25-26 region as the primary target in low-grade and high-grade gliomas.

The 10q25-26 region between the dinucleotide markers D10S587 and D10S216 is deleted in glioblastomas and, as we have recently shown, in low-grade oligodendrogliomas. We further refined somatic mapping on 10q23-tel and simultaneously assessed the role of the candidate tumor suppressor gene PTEN/MMAC1 in glial neoplasms by sequence analysis of eight low-grade and 24 high-grade gliomas. These tumors were selected for partial or complete loss of chromosome 10 based on deletion mapping with increased microsatellite marker density at 10q23-tel. Three out of eight (38%) low-grade and 3/24 (13%) high-grade gliomas exclusively target 10q25-26. We did not find a tumor only targeting 10q23.3, and most tumors (23/32, 72%) showed large deletions on 10q including both regions. The sequence analysis of PTEN/MMAC1 revealed nucleotide alterations in 1/8 (12.5%) low-grade gliomas in a tumor with LOH at l0q21-qtel and in 5/21 (24%) high-grade gliomas displaying LOH that always included 10q23-26. Our refined mapping data point to the 10q25-26 region as the primary target on 10q, an area that also harbors the DMBT1 candidate tumor suppressor gene. The fact that we find hemizygous deletions at 10q25-qtel in low-grade astrocytomas and oligodendrogliomas - two histologically distinct entities of gliomas - suggests the existence of a putative suppressor gene involved early in glial tumorigenesis.

Amino Acid Substitution↗
PubMed2004

Identification of clinically relevant viridans group streptococci by sequence analysis of the 16S-23S ribosomal DNA spacer region.

The feasibility of sequence analysis of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (ITS) for the identification of clinically relevant viridans group streptococci (VS) was evaluated. The ITS regions of 29 reference strains (11 species) of VS were amplified by PCR and sequenced. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The ITS lengths (246 to 391 bp) and sequences were highly conserved among strains within a species. The intraspecies similarity scores for the ITS sequences ranged from 0.98 to 1.0, except for the score for S. gordonii strains. The interspecies similarity scores for the ITS sequences varied from 0.31 to 0.93. Phylogenetic analysis of the ITS regions revealed that evolution of the regions of some species of VS is not parallel to that of the 16S rRNA genes. One hundred six clinical isolates of VS were identified by the Rapid ID 32 STREP system (bioMérieux Vitek, Marcy l'Etoile, France) and by ITS sequencing, and the level of disagreement between the two methods was 18% (19 isolates). Most isolates producing discrepant results could be unambiguously assigned to a specific species by their ITS sequences. The accuracy of using ITS sequencing for identification of VS was verified by 16S rDNA sequencing for all strains except strains of S. oralis and S. mitis, which were difficult to differentiate by their 16S rDNA sequences. In conclusion, identification of species of VS by ITS sequencing is reliable and could be used as an alternative accurate method for identification of VS.

DNA, Ribosomal Spacer↗
PubMed2006

Sequence analysis of major histocompatibility complex class-II DQB1 (Patr-DQB1) alleles in chimpanzees by polymerase chain reaction-based methods.

The major histocompatibility complex (MHC) class-II genes are described as the genes that encode the antigen-presenting molecule. In particular, functional alleles of MHC class-II genes in nonhuman primates have been analyzed as part of the study of infectious and immune-mediated diseases in animal models and as part of efforts to understand the molecular evolution of human leukocyte antigen. The polymorphisms and sequence analysis of MHC class-II genes in a large number of subjects is necessary for the group management of nonhuman primates. In the present study, we attempted to analyze the DQB1 polymorphism in the common chimpanzee (Pan troglodytes) by exon 2 sequencing. For exact typing of Patr-DQB1 alleles, we carried out polymerase chain reaction-restriction fragment length polymorphism and sequence analysis. In the genomic DNA of 25 chimpanzees, 6 Patr-DQB1 alleles, including 2 new alleles, were detected. Identification and analysis of Patr-DQB1 alleles using this method may contribute to our understanding of Patr-DQB1 allelic diversity in individual chimpanzees and should be useful in facilitating colony management of chimpanzee groups in Japan.

Amino Acid Sequence↗
PubMed1990

Rapid detection of genomic variations in different strains of hantaviruses by polymerase chain reaction techniques and nucleotide sequence analysis.

The polymerase chain reaction (PCR) with subsequent nucleotide sequence analysis was employed to rapidly detect genomic variations among different Hantavirus strains. Using synthetic oligonucleotide primers derived from the M and S segment RNAs of nephropathia epidemica virus strain Hällnäs B1 (NEV) we succeeded in amplifying the corresponding sequences of Hantaan and Puumala viruses. The nucleotide sequences of the cDNAs derived from the Puumala M and S RNA segments were analyzed. It was found that the particular nucleotide sequences of Puumala M and S segments were 81% and 82% homologous to the corresponding genomic segments of NEV, respectively. The amino acid homology was 94% for both segments. In contrast, the degree of homology to the corresponding Hantaan M and S genomic RNA segments was 63% at the nucleotide level for both segments and 53 and 55% at the deduced amino acid level, respectively. This demonstrates that Puumala virus is very similar to NEV and significantly different from Hantaan virus at both the nucleotide and protein level.

Amino Acid Sequence↗
PubMed1987

DNA sequence analysis of host range mutants of the promiscuous IncP-1 plasmids R18 and R68 with Tn7 insertions in oriV.

Transposon Tn7 insertions in the origin of vegetative replication (oriV) result in host range mutants of the promiscuous IncP-1 plasmids R18 and R68 which affect plasmid replication in Escherichia coli but not in Pseudomonas aeruginosa. The sites of these insertions have been analyzed by DNA sequence analysis. In two mutants, the insertions generated direct duplications of 5'GTATT3' at the target site which included the first base at the 5' end of the fourth 17-bp direct repeat in oriV. In a third mutant the duplication of 5'GACAC3' also involved the same direct repeat also at the 5' end but contiguous with the previous duplication. DNA sequence analysis of another Tn7-induced host range mutant of R18, characterized by reduced conjugational transmissibility into P. stutzeri while retaining normal transmissibility within P. aeruginosa, showed that the insertion generated a 474-bp deletion which brought the insertion 20 bp 5' to the 17-bp direct repeat between oriV and the oxytetracycline hydrochloride-resistant gene. The analysis of the DNA sequence data at the site of the Tn7 insertions shows that particular segments of the DNA sequence in oriV are differentially required for the replication of these plasmids in different bacterial hosts and thus of importance to the promiscuity of these plasmids.

Base Sequence↗
PubMed1998

Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): taxonomic implications for the Great Lakes species flock.

Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco (Coregonus zenithicus). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi, C. hoyi, C. kiyi, and C. clupeaformis. DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.

Animals↗
PubMed2005

Detection and identification of Flavobacterium psychrophilum from gill washings and benthic diatoms by PCR-based sequencing analysis.

A nested polymerase chain reaction (PCR) amplification technique was used to detect Flavobacterium psychrophilum from washings of fish gill surfaces and benthic diatoms as environmental samples. Gill washing samples were prepared from kawamutsu, Zacco temminckii (Temminck & Schlegel) and oikawa, Z. platypus (Temminck & Schlegel). Benthic diatom samples were collected from stone surfaces. All samples were collected from rivers in Wakayama Prefecture, Japan from November 2003 to January 2004. Following simple DNA extraction using a chelating resin, nested PCR techniques targeting 16S-rDNA and gyrB regions were performed, and PCR products were cloned and sequenced. With nested PCR amplification for the 16S-rDNA gene, ambiguous PCR products were detected from two of six samples, and by cloning and sequencing analysis were found not to be DNA fragments amplified from F. psychrophilum. Using nested PCR for the gyrB gene, however, five of six samples were clearly positive for F. psychrophilum in agarose gel electrophoresis, and were found to be identical with nucleotide sequences of F. psychrophilumgyrB deposited in DNA databases by sequencing analysis. Results indicate that nested PCR for the gyrB region is a useful technique to detect low levels of F. psychrophilum from environmental samples contaminated with many other organisms.

Animals↗