Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “GenBank”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed2004

[Screening of differential genes between human embryonic stem cell and differentiated cell].

It is one of the core questions that how human embryonic stem cell (hESC) maintain the undifferentiated state during the propagation process. The current advance in answering this question included the studies on LIF signal transduction, Oct-4 factor and Nanog gene. But the question is far from being elucidated. In order to further understand the mechanism of maintaining the undifferentiated state of hESC, we screened out the expressed sequence tags (ESTs) which expressed highly in hESC but expressed lowly or unexpressed in the differentiated hESC's clones (dhESC) by suppression subtractive hybridization (SSH) and cDNA dot blot techniques. One hundred and five putative positive clones were screened out to be sequenced and were compared with the GenBank. Among them, seventy six clones represented sixty one identified genes that shared high homology with sequences in GenBank. Eighteen clones represented fifteen hypothetic genes, and eleven clones were function-unknown. Eight clones were picked out to analyze using semi-quantitative RT-PCR, the results confirmed that the expression of seven clones among them were higher in the hESC, and lower or no expression in the dhESC. The results showed that many differentiated expressed genes were involved before and after hESC's differentiation. Further functional analysis to those genes that expressed highly in the undifferentiated hESC and lowly in the dhESC might provide a basis to understand the mechanism of maintaining the undifferentiated state of hESC.

Cell Differentiation↗
PubMed2004

[Cloning and expression of pituitary prolactin gene in Ailuropoda melanoleuca].

The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. It has been proposed that it has a highly specialized reproductive pattern with low fecundity, but little is known about its basic reproductive biology at molecular level. In this study,the pituitary prolactin (PRL) cDNA of giant panda was amplified by RT-PCR from pituitary total RNA and then cloned, sequenced and submitted to GenBank (GenBank accession No. AY161285). The sequence analysis revealed that the giant panda prolactin cDNA contains a 687-nucleotide open reading frame encoding the prolactin prohormone of 229 amino acid residues. The signal peptide contains 30 amino acid residues and the mature prolactin is composed of 199 amino acid residues. Then the DNA fragment amplified was subcloned into pGEX-4T-1 procaryotic expression plasmid and protein expression was induced by IPTG in Escherichia coil BL21. SDS-PAGE analysis revealed the PRL protein is infusible. The multiple sequence alignments revealed that the homology of giant panda is 95% to cat and pig, 80% - 70% to human, cow and goat, 52% to rat and 45.9% to mouse at the amino acid level. The 64th amino acid of giant panda prolactin is hydrophilic serine instead of hydrophobic proline of cat, goat, and cow or hydrophobic alanine of human.

Amino Acid Sequence↗
PubMed2004

New polymorphism of FASN gene in chicken.

Sequencing, Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP) were carried out to detect polymorphism in the last intron of the FASN gene of the Campero broiler line. The analysis of the sequences presents a G to A substitution located at base 459 of the PCR product (GenBank accession number J02839, located at base Nr. 1222), resulting in a site recognized by restriction enzymes Hae III and Ava II. Also, the sequence presents a G to A substitution (located at base 603 of the PCR product and Nr. 1366 of the J02839 GenBank accession) resulting in a site recognized by restriction enzyme Pst I. Alleles and genotype frequencies were calculated for endonucleases Hae III, Ava II and Pst I for 44 broilers.

Animals↗
PubMed2004

Bovine mu-calpain (CAPN1) gene: new SNP within intron 14.

The calpain system originally comprised molecules: two Ca2+-dependent proteases, mu-calpain and m-calpain, and a third polypeptide, calpastatin, whose only known function is to inhibit the two calpains. This proteolytic system plays a key role in the tenderisation process that occurs during post-mortem storage of meat under refrigerated conditioning. Their polymorphism is examined from the point of view of their effect on corresponding production traits. The calpain genes are investigated as potential candidate genes for a quantitative trait locus (QTL) affecting meat tenderness. In this study a new single nucleotide polymorphism (SNP) was found within intron 14 of the bovine CAPN1 gene, being transition C --> T at position 4685 nt (consensus sequence - GenBank No. AF 248054), as this mutation creates a new FokI restriction site detected with PCR-RFLP analysis. This sequence fragment of the SNP position has already been deposited in the GenBank database under accession No. AY639597. The RFLP-FokI polymorphism was studied in 141 bulls of seven breeds, including the native Polish Red (PR, preserved), and Polish Black-and White (BW) breed. The frequency of alleles T and C varied between the breeds considered, the mean reaching 0.38 and 0.62, respectively. Associations between CAPN1/FokI gene polymorphism and meat production traits were studied in BW (n = 84) young bulls. In the animals of the TT genotype the lean share in valuable cuts (%) was found more favourable than in CC animals.

Animals↗
PubMed2004

[Isolation and expression of novel expressed sequence tags (ESTs) from ovarian follicles of Shaoxing ducks].

Three expressed sequence tags ( ESTs), SXDF0201 (271 bp), SXDF0202 (200 bp) and SXDF0203 (173 bp), were isolated from ovarian follicles of Shaoxing ducks by using silver staining mRNA differential display. GenBank/BLAST analysis revealed that SXDF0201 was not homologous to any of the published sequences from all species, indicating that it was a novel EST and was then registered in GenBank (GenBank Accession No.: CB072629), while SXDF0202 and SXDF0203 were found to be highly homologous to seven known chicken ESTs and chicken mRNA for gizzard smooth muscle myosin heavy chain. 5'-RACE was employed to extend the SXDF0201 to 544 bp which was confirmed as novel in BLAST search. The temporal and spatial expression of SXDF0201 and SXDF0202 were also investigated with semi-quantitative RT-PCR. The result showed that: both SXDF0201 and SXDF0202 were found to be expressed in hypothalamus, pituitary, muscle, liver, and fat tissues of Shaoxing ducks; SXDF0201 was expressed significantly higher in ovaries of 30-day-old Shaoxing ducks compared with that of 60-day-old (P < 0.05) and 90-day-old (P = 0.015), but the expression of SXDF0202 showed no difference throughout the ovarian development; granulose layers expressed higher SXDF0201 than theca layers in almost all hierarchical follicles, the expression of SXDF0202 in granulose layers increased along with follicular maturation (P < 0.01) from Fw to F3 follicles, but decreased dramatically to the lowest in F1 follicles (P < 0.01). In theca layers, the highest expression of SXDF0202 was found in Fw follicles (P < 0.01).

Animals↗
PubMed2004

Cloning and sequence analysis of genes encoding Fasciola hepatica immunodominant antigens.

Fasciola hepatica lambdagt11 cDNA expression library was immuno-screened with IPAb, two clones were isolated and identified as Fhlambda400 Fhlambda800. Both clones were sequenced, FhA400 contained 305 translated bases encoding 11.509 kDa and designated as SFh12, while Fhlambda800 contained 311 translated bases encoding protein of 11.058 kDa designated as SFh11. The DNA sequence homology search of Fhlambda400 revealed a relatively high degree of identity with F. hepatica amoebapore-like protein mRNA (GenBank accession No. AF286903). However, Fhlambda800 revealed the highest similarity with F. hepatica tegumental antigen (T1) mRNA (GenBank accession No. AF153056). The protein homology search of SFh12 gave 100% identity with amoebapore-like protein (APLP), while SFh-\11 showed 75% identity with F. hepatica tegumenttal antigen (TA). The biochemical analysis of the deduced proteins was identified; in addition the predicted T- & B-cell epitopes have been also evaluated. However, histological localization of identified antigens was achieved using the IPAb in an indirect immunoflorescent antibody assay (IFA). Results revealed that the IPAb labeled the outer glycocalyx in a characteristic, pattern, which proved that the identified antigens were tegumental in origin and that infected Fasciola subjects induced antibodies directed mainly against tegumental components.

Amino Acid Sequence↗
PubMed2004

[Structure and expression analysis of the gama-glutamylcysteine synthetase gene in rice].

Gama-glutamylcysteine synthetase (GCS) is a rate-limiting enzyme in GSH biosynthesis. The GCS gene has been cloned in Arabidopsis thaliana and other plants, but has still not been reported in rice. From rice mutant population generated from T-DNA insertion, we cloned the rice GCS gene from mutant L395 by T-DNA tag cloning method, and named it OsGCS (Genbank accession No. AJ508915). Full length OsGCS cDNA clones were obtained from a rice cDNA library by the PCR method. A comparison of the genome and cDNA sequence (Genbank accession No. AJ508916) shows that OsGCS gene is composed of 15 exons and 14 introns and coding a 493-amino acid protein. The OsGCS gene is highly homologous with the AtGCS gene in the coding region but completely different in the promoter region. The putative transcription start site (TSS) confirmed by RT-PCR was located 211 bp upstream of the translation start codon "ATG". In mutant L395, a single T-DNA copy was integrated between the second intron and second exon of OsGCS gene, causing one nucleotide deletion in the second exon and two nucleotide deletions in the second intron. No significant differences were found in Cd(2+) stress tolerance, rice GCS gene expression level and GSH content between mutant L395 and Zhonghua 11. It is possible that another GCS gene on chromosome 7 might complement function of OsGCS gene on chromosome 5.

Amino Acid Sequence↗
PubMed2004

[Identification of ESTs of genes related to compaction in preimplantation embryos of mouse].

A total of 181 8-cell embryos and 241 8-cell compacted embryos were collected respectively from Kunmingbai mouse and their cDNA was synthesized directly using SMART PCR. Genes, which expressed differently between early 8-cell embryos and 8-cell compacted embryos, were investigated using the method of suppression subtractive hybridization (SSH). Then PCR production was cloned into pUCm-T vector respectively according to the size after isolated and purified. Twenty-seven ESTs (expressed sequence tags) of genes expressed differently between early 8-cell embryos and 8-cell compacted embryos have been isolated and cloned. seventeen of those were novel ESTs after being confirmed by blaster matching in GenBank for homology analysis. And they were banked into GenBank with accession numbers. All 17 ESTs might be for novel genes related to compaction in compacted embryos. And longer ESTs may be obtained by cloning according to the size.

Animals↗
PubMed2005

Demonstration of differential gene expression between sensitive and resistant ovarian tumor cells by fluorescence differential display-PCR analysis.

Chemotherapy plays a major role in cancer management; however, acquired drug resistance remains a significant problem for ovarian cancer treatment. Chemoresistance is regulated by the coordinated expression of a set of genes. Thus, the identification of genes specifically modulated in the process provides an important step toward the discovery of underlying molecular mechanisms in drug resistance events. We recently developed five drug-resistant human ovarian carcinoma cell lines, including two cisplatin (cis) resistant cell lines, two carboplatin (car) resistant cell lines and one taxol (tax) resistant cell line. In this study, we investigated differential gene expression between these resistant cell lines and their parental cell lines by the fluorescence differential display-polymerase chain reaction (FDD-PCR) technique. We first screened and identified differentially expressed genes in the resistant ovarian cancer cell lines, and we then sequenced and analyzed these genes by bioinformatics software. A total of 33 fragments were displayed in the two resistant cell lines (S-cis and S-car) derived from the sensitive SKOV-3 cell line, and 36 fragments were displayed in the three resistant cell lines (A-cis, A-car and A-tax) derived from the sensitive A2780 cell line. After purification, cloning, sequencing, and homology analysis on the NCBI BLAST GenBank, 12 gene fragments were identified from the resistant S-cis and S-car cells, and 23 gene fragments were identified from the resistant A-cis, A-car and A-tax cells. Although a homolog search of the NIH GenBank revealed that most of the gene fragments were not significantly associated with the known drug resistance-related genes, our study conclusively demonstrates that FDD-PCR is a useful tool for analyzing the differential gene expression between resistant and sensitive tumor cells and for identifying novel chemoresistance-associated genes and potential biological markers or genetic markers of drug resistance.

Base Sequence↗
PubMed2005

[Study of gene differential display of hydatidiform moles].

OBJECTIVE: To screen the specific molecular maker of invasive hydatidiform moles (HM) by differential display analysis. METHODS: For dot hybridization, about 1.0 microg of each cDNA sample of invasive and non-invasive HM were labeled as probes using the Dig DNA labeling and Detection Kit (Boehringer Mannheim). The specific expression fragments of invasive HM recovered from PAGE gel were re-amplified by PCR, and the PCR products were dotted onto nylon membrane and hybridized by two probes of invasive and non-invasive HM cDNA respectively. Some fragments with a strong positive hybridization signal were cloned into the polylinker of lasmid PUC19 and were sequenced. The fragments' sequences were searched for homology in the NCBI data using the BLAST (Database: GenBank Human EST entries; Posted date:Aug 31, 2004; Number of letters in database: 1,697,659,032; Number of sequences in database: 3,677,722). RESULTS: The 20 fragments in 28 bands with specific expression in invasive HM were re-amplified, of which 13 showed positive hybridization signals, and 3 were cloned into the polylinker of lasmid PUC19. A fragment in the 3 was a new expressed sequence tag (EST) and the sequence was submitted to NCBI data (dbEST_Id: 10875704; GenBank_Accn: BM403211). CONCLUSION: There are more differences in gene expression between invasive and non-invasive HMs, and differential display analyses are of a potential significance to early diagnosis of invasive HM.

Adult↗
PubMed2002

[Discovery of Cervus nippon Temminck-derived sentrin/SUMO].

In order to identify unknown encoding cDNAs of Cervus nioppon Temminck (sika deer), we constructed a cDNA library of uterus from Jilin-Shuangyang Cervus nippon Temminck using PCR cDNA library kit. PCR products of the library were cloned into pGEM-Teasy vectors and the cDNAs were sequenced and analyzed by nucleotide homology comparison against GenBank Database using the BLAST network service. The results showed that the cDNA library contained cDNA fragments of different lengths and a full length encoding cDNA highly homologous to human sentrin-1/SUMO-1 (small ubiquitin-related modifier 1) was identified. The cDNA was deposited in GenBank under the accession number AF 242526. These show that Cervus nippon Temminck-derived sentrin/SUMO gene has been discovered from PCR cDNA library of uterus from Cervus nippon Temminck.

English Abstract↗
PubMed2005

[Cloning and sequence analysis of human uric acid transporter gene].

OBJECTIVE: To obtain full-length human urate transporter (hUAT) gene. METHODS: Primers was designed according to the sequence of hUAT reported in Genbank. The target fragments were obtained by reverse transcriptional (RT) PCR from the mRNA extracted from human renal tubular epithelial cell lines (HK-2), followed by cloning into pEGFP-C1 plasmid. The cloned fragment was subjected to restriction mapping and sequence analysis for confirmation. RESULTS AND CONCLUSION: hUAT gene with correct sequence is successfully cloned from HK-2 cells. The restriction maps and sequence analysis of the selected clones were consistent with the sequence reported in Genbank.

Base Sequence↗
PubMed2005

[Molecular Cloning of Smooth Muscle Calponin h1 in SHeep.].

It was found that the level of Calponin h1 (CaP h1) mRNA was significantly up-regulated by Estrogen in the myometrium of sheep towards the end pregnancy. Although the CaP h1 has been widely used as a reference gene to observe the changes of expression level of other genes, the full-length gene in sheep has not been obtained. With the oligo nucleotide primers according to human, mouse and pig CaP h1 mRNA, the full-length cDNA of CaP h1 was cloned by 5'- and 3'-RACE (Genbank accession number = AY327118). The cDNA was 1499bp in length and contained a complete open reading frame of 891 bp, encoding a protein of 297 amino acid residues. 5'-and 3'-UTR was 79 bp and 529bp, respectively. With PCR-SSP approaches,the genomic DNA of sheep CaP h1 was obtained .It showed that the gene has 7 exons and 6 introns, spanning over 8kb(Genbank accession number of introns : AY771807,AY771808, AY771809, AY771810.) Homologous comparison indicated that the cDNA sequences are highly conserved across the species. The highest homology was found in wild pig (92%), followed by human (88%), rat (81%), mouse (81%) and chicken (79%). The intron sequence and length showed a large variation among species (>50%).

Amino Acid Sequence↗
PubMed2005

[Mangrove soil community analysis using DGGE of 16S rDNA V3 fragment polymerase chain reaction products].

The 16S rDNA V3 fragment polymerase chain reaction products amplified from mangrove soil-DNA extracts were analyzed by denaturing gradient gel electrophoresis (DGGE) followed by clone technology. Regional factors and mangrove species were found to influence the soil microbe community. Two DNA slices separated on denaturing gradient gel from Sonneratia alba soil sample were recovered and the recovered DNA were used to establish two clone libraries. Some clones were sequenced and each sequence was compared with all nucleotide sequences in GenBank database. Most cloned sequences were found not in GenBank database. These results suggest that DGGE followed by clone technique is a practicable protocol to research the complex community of soil microbe.

Bacteria↗
PubMed2005

[Cloning and sequencing of heat shock protein 60 (HSP60) gene of Legionella pneumophila].

OBJECTIVE: To obtain the heat shock protein 60 (HSP60) gene of Legionella pneumophila and clone it into plasmid pUC18 for nucleotide sequencing. METHODS: The HSP60 gene of Legionella pneumophila was amplified by PCR, then inserted into pUC18 vector and transformed into Escherichia coli (E. coli) strain JM109. The recombinant plasmids were identified by restriction analysis and PCR. HSP60 gene was sequenced by the dideoxy chain termination method, then analyzed and compared with that reported in GenBank. RESULTS: The HSP60 gene of 1647 bp in length was successfully cloned. Comparison of the sequence of HSP60 gene with that reported in GenBank showed that the identities were 98%. CONCLUSION: A confirmed HSP60 gene has been obtained in this paper. The study laid a good foundation of the recombination,expression and research of the gene.

Base Sequence↗
PubMed2004

[Identification of an auxin response factor-like protein cDNA from mango cotyledon section].

Auxin-responsive elements (AuxRE) interact with a new class of plant-specific transcription factors, auxin response factors (ARFs). Some of ARFs have been shown to repress or activate expression of genes with an AuxRE promotor element. In Arabidopsis, ARFs play important roles in early embryo development and vascular strand formation (ARF5), floral patterning (ARF3) and photo- and gravitropic responses (ARF7). Two cut surfaces (distal and proximal) of mango (Mangifera indica L. var. Zi-Hua) cotyledon showed different patterns of adventitious root formation, with only the proximal cut surface, but not the distal one, could be induced to form the roots. Thus, the mango cotyledon is a good system for studying adventitious root formation. A cDNA fragment homologous to the Arabidopsis auxin response factor-like protein and relates to adventitious root formation from the cut sections were isolated using suppressive subtractive hybridization (SSH). Two cDNA clones, designated as MiARF1 (mango auxin response factor 1 gene, GenBank accession number AY255705) and MiARF2 (mango auxin response factor 2 gene, GenBank accession number is AY300808), were identified by 3'RACE. MiARF1, 3 272bp long, contains an open reading frame (ORF) of 2 523bp, 5'UTR of 285bp and 3'UTR of 464bp, MiARF2, 1 474bp long, contains an ORF of 981bp, 5' UTR of 285bp and 3'UTR of 208bp. The deduced MiARF1 and MiARF2 are homologues of auxin response factor (ARF) family of transcriptional regulators, and show high similarity to ARF of Arabidopsis in conserved domains. The motifs of MiARF1 EL-WHACAGPL in DBD (DNA binding domain) and GDDPW in IV domain are identical to that of ARF-like protein of Arabidopsis. MiARF2 is identical to MiARF1 in a large part of DBD, but lacks a carboxyl-terminal domain containing conserved motifs III and IV. Virtual Northern blot showed that the expression of MiARF2 was high in rooting tissue of cultured cotyledon sections but low in non-rooting tissue, and the MiARF1 was expressed both in the rooting and non-rooting tissues. We suggest that the MiARF2 is related to adventitious root formation of mango cotyledon section.

Base Sequence↗
PubMed2005

[Cloning and analysis of psaB cDNA of Dunaliella salina].

One pair of degenerate primer was designed according to conserved motifs of the psaB (A2 subunit of photosystem I) of Chlamydomonas reinhardtii, Chlamydomonas moewusii, Chlorella vulgaris and Mesostigma viride, and a total RNA of Dunaliella salina (D. salina) was extracted with TRIzol reagent. A cDNA fragment, about 1.8kb in length, from green algal D. salina was obtained through RT-PCR method. The resulting PCR product was cloned into T-vector and screened to determine its sequence. Homologous analysis of the deduced amino acid sequence was performed by BLAST and subsequeqtly compared with GenBank data. The obtained cDNA sequence was 1815 bp long, which encodes 605 amino acids (GenBank accession number: AY820754). The sequence shared high homologue with the following psaB: Chlamydomonas reinhardtii 92%, Chlamydomonas moewusii 91%, Chlorella vulgaris 86%, Mesostigma viride 85%, Physcomitrella patens subsp. Patens 85% and Nephroselmis olivacea 84%. It can be concluded that the cloned sequence is psaB cDNA fragment from D. salina.

Algal Proteins↗
PubMed2001

[Androgen receptor isoforms expression and its novel cDNA cloning in human prostate].

OBJECTIVE: To investigate the androgen receptor isoforms expression and its novel eDNA cloning in prostate tissue. METHODS: The tissue from a case of benign prostatic hyperplasia (BPH) was analyzed by high resolution isoelectric focusing (IEF) technique and molecular biological technique of cDNA cloning was used to determine its AR isoforms expression and genes of AR isoforms. RESULTS: From the prostatic specimen, three types of AR isoforms were detected with pI values of 6.5, 6.0 and 5.3 respectively. A novel AR subtype cDNA cloning, named as PHAR-1 and including 1 913 nucleotides was isolated from the same BPH tissue. The GenBank accession number for the nucleotide sequence of this AR cDNA was BankIT372205 AF324243. The comparison between PHAR-1 and AR nucleotide sequence registered in GenBank showed that 961 nucleotides in three part of nucleotide sequence were the same, while the other 952 nucleotides were different. CONCLUSION: These three AR isoforms may originate from the same gene. The results may be important for the study of BPH, or prostatic growth. It is also valuable in the field of pharmacotherapy for treatment of BPH and prostatic cancer.

DNA, Complementary↗