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At least 433 records · Page 24Linked to original sources
PubMed1995

Cloning and characterisation of an ovine interleukin-10-encoding cDNA.

Expression of the interleukin 10-encoding (IL-10) mRNA by ovine (ov-) cells, in response to mitogenic stimulation, was assessed by Northern blot and polymerase chain reaction (PCR) analyses using a human (hu) IL-10 cDNA probe and oligodeoxyribonucleotide primers based on homologous regions of the human and murine IL-10 cDNA sequences. A 315-bp cDNA generated by the PCR analysis was cloned and used to screen a lipopolysaccharide-stimulated alveolar ov-macrophage cDNA library. The full-length ov-cDNA sequence isolated translates to a protein of 177 amino acids (aa) with a predicted 18-aa leader sequence and molecular mass of 20,165 Da. Expression in a mammalian system demonstrated that the ov-cDNA encoded a protein with the expected IL-10 biological activity. Both recombinant huIL-10 and supernatants from COS cells transfected with an expression vector containing the ovIL-10 cDNA inhibited production of IL-1 and tumour necrosis factor-alpha by ov-alveolar macrophages. Genomic DNA analysis indicated ovIL-10 exists as a single gene within the ov-genome.

Amino Acid Sequence↗
PubMed1995

Cloning of the rat ErbB3 cDNA and characterization of the recombinant protein.

Three cDNA fragments that encoded all but the extreme N terminus of the rat ErbB3 protein were cloned by low-stringency screening of a rat liver cDNA library with a human ERBB3 probe. The remaining 5'-end of the cDNA was generated by a reverse transcription-polymerase chain reaction method, and a single full-length rat ErbB3 cDNA was assembled. A comparison of the deduced amino acid (aa) sequences of human and rat ErbB3 was made, and the effects of certain aa substitutions in the putative protein tyrosine kinase domain were considered. The rat ErbB3 cDNA was subsequently expressed in cultured NIH-3T3 mouse fibroblasts, in which a high level of approx. 180-kDa recombinant ErbB3 (re-ErbB3) was generated. The rat re-ErbB3 produced in transfected fibroblasts was responsive to the polypeptide, heregulin, a known ligand for ErbB3. Challenge of transfected fibroblasts with heregulin stimulated the phosphorylation of rat re-ErbB3 on Tyr residues and promoted its association with the p85 subunit of phosphatidylinositol 3-kinase. Together, these results indicate that a fully functional rat ErbB3 cDNA has been isolated, and that fibroblast cells expressing this cDNA will be suitable for investigations of the signal transduction mechanism of ErbB3.

3T3 Cells↗
PubMed1994

Optimization of subtractive hybridization in construction of subtractive cDNA libraries.

The efficiency of subtraction, integrity of residual single-stranded cDNA, and efficient recovery of nanogram quantities of double-stranded cDNA are the three most important factors affecting quality of subtractive hybridization reactions prior to subtractive cDNA library construction. Techniques for efficient isolation of single-stranded cDNA, after subtraction, have greatly improved from early protocols based on hydroxylapatite chromatography to phenol-chloroform extraction of biotin-streptavidin-crosslinked polynucleotides or oligo(dA)-cellulose affinity chromatography. Factors affecting mRNA stability at the hybridization step, however, also have consequences that directly affect the complexity of the library and the length of cDNAs recovered. We have optimized the subtractive hybridization step in subtractive cDNA library construction to ensure that single-stranded cDNAs survive hybridization as near to full length as possible. These improvements have enabled successful construction of subtractive cDNA libraries from the nanogram quantities of single-stranded cDNA remaining after extensive liquid hybridization to high calculated C(o)t values.

DNA, Complementary↗
PubMed2006

Trehalose as a good candidate for enriching full-length cDNAs in cDNA library construction.

It has been reported that the disaccharide trehalose is capable of increasing the thermostability and thermoactivity of reverse transcriptase, and therefore improving the length of cDNA synthesis. However, no test has been done on how the disaccharide trehalose performs in the context of the entire cDNA synthesis processes, or whether it can seamlessly integrate into the commercially available cDNA synthesis kit. In this report, we optimized a protocol to incorporate trehalose in the Stratagene's cDNA library construction kit in order to demonstrate great improvement in cDNA's length (average length of 1.8 kb in the trehalose group versus 1.0 kb in the control). Sequence analysis of the cDNA clones showed that the addition of trehalose did not increase the error rate of the RT products but greatly increase the quantity of full-length in cDNA library.

Animals↗
PubMed2005

Characterization of a novel cDNA encoding a short venom peptide derived from venom gland of scorpion Buthus martensii Karsch: trans-splicing may play an important role in the diversification of scorpion venom peptides.

A novel cDNA clone (named BmKT-u) which is a hybrid molecule of the 5'-terminal region of BmKT' cDNA and the 3'-terminal region of an undocumented cDNA (named BmKu), was isolated from a cDNA library made from the venom gland of scorpion Buthus martensii Karsch. BmKT-u codes for a 30 amino acid residue precursor peptide composed of a 20-residue signal sequence, and a putative 10-residue novel mature peptide. Northern blot hybridization showed BmKT-u cDNA is generated from a transcript. RT-PCR experiments excluded the possibility that BmKT-u cDNA is an artifact generated during reverse transcription. Genomic amplifications performed with three pairs of BmKT-u gene-specific primers showed the BmKT-u gene does not exist in the genome of the scorpion as a single transcriptional unit. Genomic cloning for BmKT' showed that the BmKT' gene contains an intron of 509 bp inserted into the region encoding the C-terminal region of the signal peptide. A sequence alignment comparison of the cDNA of BmKT-u with genomic BmKT' revealed that the junction site of the hybrid molecule is located at the 5'-splicing site of the intron. The data suggest that the BmKT-u transcript is a naturally occurring mature mRNA that is generated by trans-splicing. Trans-splicing may contribute to the diversity of venom peptides from venomous animals.

Amino Acid Sequence↗
PubMed2004

An mRNA amplification procedure with directional cDNA cloning and strand-specific cRNA synthesis for comprehensive gene expression analysis.

We developed an integrated system suitable for comprehensive gene expression studies including construction and analysis of cDNA microarrays starting from a small amount of mRNA. We amplified total mRNA first as cDNA mixtures by polymerase chain reaction and then as strand-specific cRNA mixtures by in vitro transcription. These amplified cDNA and cRNA enabled determination of mRNA levels by hybridization analyses such as Southern, Northern, reverse-Northern macroarray, and cDNA microarray analyses, as well as construction of the cDNA library with a unidirectional cDNA insert. By using strand-specific cRNA derived from rat primary-cultured hepatocytes, we detected putative antisense transcripts for the metallothionein gene. cDNA microarray analysis for genes regulated by glucocorticoids and glucagon in the hepatocytes revealed that a number of genes involved in signal transduction and transcriptional regulation were up- or down-regulated. The present system is widely applicable to gene expression analysis with limited amounts of RNA samples.

Animals↗
PubMed1987

Analysis of human terminal deoxynucleotidyl transferase cDNA expressible in mammalian cells.

Human Molt3 cDNA library was constructed using pcD vector system which permits the expression of cDNA inserts in mammalian cells. Nearly full-length human terminal deoxynucleotidyltransferase (TdT) cDNA was cloned using a fragment of bovine TdT cDNA as a probe. The human TdT cDNA contains an open reading frame of 1,557 bp coding for 519 amino acids, including 31 bp and 341 bp from 5' and 3' untranslated regions, respectively. The TdT cDNA was transfected into COS7 monkey fibroblasts directed the synthesis of enzymatically active protein of Mr 59,495. The cloned TdT cDNA hybridized with poly A+ RNAs of 2,100 b and 3,300 b from stable T-cell leukemia Molt3 and Molt4 cells.

Animals↗
PubMed1988

Cloning and sequencing of a cDNA for human mitochondrial ubiquinone-binding protein of complex III.

The ubiquinone-binding protein (QP-C) is a nuclear-encoded component of ubiquinol-cytochrome c oxidoreductase in the mitochondrial respiratory chain and plays an important role in electron transfer as a ubiquinone-QP-C complex. We obtained a partial cDNA for rat liver QP-C by screening a lambda gt11 rat liver cDNA library using antiserum directed against bovine heart QP-C. Using this cDNA as a probe, a cDNA clone was isolated from a human fibroblast cDNA library by colony hybridization. The total length of the cloned cDNA was 518 base pairs with an open reading frame of 333 base pairs. The 111-amino acid sequence deduced from the nucleotide sequence of the cDNA is 85% homologous to that of bovine QP-C and contains only a single additional amino-terminal methionine. This implies that the human QP-C is synthesized without a presequence which is required for import of most nuclear-encoded mitochondrial proteins into mitochondria.

Amino Acid Sequence↗
PubMed1998

cDNA cloning of Brassica napus malonyl-CoA:ACP transacylase (MCAT) (fab D) and complementation of an E. coli MCAT mutant.

The GenBank database was searched using the E. coli malonyl CoA:ACP transacylase (MCAT) sequence, for plant protein/cDNA sequences corresponding to MCAT, a component of plant fatty acid synthetase (FAS), for which the plant cDNA has not been isolated. A 272-bp Zea mays EST sequence (GenBank accession number: AA030706) was identified which has strong homology to the E. coli MCAT. A PCR derived cDNA probe from Zea mays was used to screen a Brassica napus (rape) cDNA library. This resulted in the isolation of a 1200-bp cDNA clone which encodes an open reading frame corresponding to a protein of 351 amino acids. The protein shows 47% homology to the E. coli MCAT amino acid sequence in the coding region for the mature protein. Expression of a plasmid (pMCATrap2) containing the plant cDNA sequence in Fab D89, an E. coli mutant, in MCAT activity restores growth demonstrating functional complementation and direct function of the cloned cDNA. This is the first functional evidence supporting the identification of a plant cDNA for MCAT.

Acyl-Carrier Protein S-Malonyltransferase↗
PubMed1999

Phage display of cDNA repertoires: the pVI display system and its applications for the selection of immunogenic ligands.

The selection of phage displayed cDNA repertoires on an immobilised target has been reported to be an efficient way to rapidly identify interacting partners. To date, however, only a few successful applications have been reported. Here, we present a review of the current status of the display and selection of cDNA libraries using phage. As an example, we report the construction of a set of phage display vectors suitable for cDNA display based on fusion to the minor bacteriophage coat protein 6 (pVI) of filamentous phage. We have evaluated these vectors through the display of the C(H)3 domain of human IgG and of the Escherichia coli alkaline phosphatase (PhoA) gene. Both the C(H)3 domain of IgG and PhoA are shown to be displayed on pVI, and PhoA is also shown to be enzymatically active. We have constructed primary colorectal tumor cDNA repertoires in these vectors and performed selections on both a monoclonal antibody to beta2 microglobulin (beta2M) and polyclonal antibody sera to human IgG. In both cases, relevant ligands were recovered from the phage displayed cDNA repertoire. These vectors may be used for selection of phage displayed cDNA libraries with polyclonal sera from patients. This will allow the identifying antigenic cDNA products in such diseases as cancer, viral/bacterial infections or autoimmune disease. Furthermore, by selections with other specific biomolecules, this display system may aid the identification of interacting partners in functional genomics.

Alkaline Phosphatase↗
PubMed1990

Planning the purification process of active cDNA in expression cloning strategies.

In principle, it is possible to clone the gene for any receptor that can be expressed in the Xenopus laevis frog oocyte and assayed electrophysiologically (E. S. Levitan, 1988, TINS 11, 41-43). Repeated fractionation of a lambda vector cDNA library made from mRNA which encodes the receptor protein will eventually lead to a single cDNA clone. This strategy poses the question as to how large should a lambda vector cDNA aliquot be at any fractionation stage in order that one may be relatively certain that the aliquot contains the clone of interest, and how many times should the fractionation be repeated in order that one isolate the single clone of interest? The purification of active cDNA is an iterative process. At each fractionation stage we specify the probability of at least one active cDNA in the total aliquot to be high. The required size of the aliquot taken depends upon this specified probability and the additional probability of selecting at random an individual cDNA which is active. We require an estimate of the latter probability for the initial stage. For subsequent stages Baye's estimators of these probabilities are used in the formula for calculating the aliquot size at each stage. We show how to perform this calculation when there is equal amplification of the active and remaining sequences and when the active sequence has a non-representative (unequal) amplification. When equal amplification holds a relatively simple formula is provided for calculating the expected number of stages needed in the process. When unequal amplification holds there is no simple calculation for this quantity and the entire sequence of calculations leading to termination of the process must be performed. In either case the minimum lambda vector amplification (growth) factor required at each stage to yield an adequate amount of cDNA for analysis is calculable.

Animals↗
PubMed1996

Androgenic up-regulation of androgen receptor cDNA expression in androgen-independent prostate cancer cells.

The expression of the androgen receptor (AR) gene is regulated by androgens. Although androgens down-regulate AR mRNA in most cell lines and tissues, including the prostate, up-regulation occurs in some tissues. Androgen-mediated reduction in AR mRNA is reproduced in COS1 cells and in the androgen-sensitive human prostate cancer cell line LNCaP when each expresses the AR cDNA. We have previously established that the AR cDNA contains the requisite sequences for this down-regulation. Here we shown that androgen promoted up-regulation of AR mRNA in two androgen-independent human prostate cancer cell lines, PC3 and DU145, when each was transfected with a human AR cDNA. This effect was due to the AR cDNA and not to the heterologous promoter driving AR expression. In addition to up-regulation of AR mRNA, androgen induced comparable increases in AR protein levels in PC3 cells stably expressing an AR cDNA (PC3/AR). Up-regulation of AR in PC3/AR cells was accompanied by failure of these cells to undergo desensitization or inactivation of AR following prolonged (96 h) androgen administration, whereas the same conditions resulted in desensitization of AR transactivation in LNCaP cells and in CVl cells that stably express the AR cDNA. Androgen treatment of PC3/AR cells resulted in induction of an androgen-regulated reporter gene (MMTV-CAT) as well as the native prostate-specific antigen gene, which is silent in untransfected PC3 but is androgen up-regulated in LNCaP and in the prostate. These results suggest that ectopic expression of AR in androgen-independent prostate cancer cell lines establishes both typical and atypical androgenic responses in a target gene-specific manner. Androgenic up-regulation of AR cDNA expression may be due to distinct signaling mechanisms that influence androgen action in androgen-independent prostate cancer cells.

Adenocarcinoma↗
PubMed2002

Full-length-enriched cDNA libraries from Echinococcus granulosus contain separate populations of oligo-capped and trans-spliced transcripts and a high level of predicted signal peptide sequences.

The tissue-dwelling larval stages of the cestode Echinococcus granulosus are intimately associated with the host, implying that a range of molecular mediators may be secreted by the parasite into the host environment. These mediators are being sought through a transcriptome-based analysis, using recombinant cDNA libraries. Conventional cDNA libraries of E. granulosus contain high levels of mitochondrial transcripts, as well as host (bovine) genomic DNA. In particular, 60% of a conventional protoscolex stage cDNA library corresponds to the large subunit (LSU) of mitochondrial rRNA. We attribute the presence of LSU rRNA copies to its polyadenylation in E. granulosus. To circumvent this problem, we adapted the 5' Rapid Amplification of cDNA Ends (RNA-ligase mediated RACE) technique that excludes all polynucleotides missing the 7-methyl-guanosine (7MG) cap specific to the 5' end of full-length mRNA. By ligating a specific oligonucleotide (oligo-cap) to 7MG-bearing mRNA, three cDNA libraries were made by PCR from oligo-cap and oligo-dT primers. Analysis of these libraries showed that mitochondrial RNA contaminants had been excluded. Moreover, no bovine genomic sequences were detected. In parallel, we constructed three cDNA libraries using the newly described trans-spliced leader (SL) from Echinococcus. Although these represent a smaller subset of parasite genes, mitochondrial and genomic contributions were again excluded. In both cases, a majority of cDNAs (61-92%) were judged to contain the initiation ATG codon, and 11-27% of inserts included potential N-terminal signal sequences. The 5' UTR tracts of most oligo-capped cDNAs were <100 nt, although approximately 8% were longer than this. Among the trans-spliced cDNAs, 43% potentially utilise the AUG donated by the SL, and in only 6% was the SL separated from an endogenous putative start site by >60 nt. Sequence analysis of randomly selected clones shows virtually no overlap between the oligo-capped and SL libraries, indicating that trans-spliced E. granulosus mRNAs appear to be insensitive to the enzymatic treatments used to 'oligo-cap' unspliced mRNAs. The oligo-capped and SL strategies represent efficient and complementary pathways to isolate full-length cDNA clones from this cestode parasite and, possibly, from related parasitic flatworms.

5' Untranslated Regions↗
PubMed1997

Cloning and expression of a cDNA encoding a nonintegrin laminin-binding protein from Echinococcus granulosus with localization of the laminin-binding domain.

We have isolated a cDNA from the hydatid tapeworm, Echinococcus granulosus, encoding a protein that binds laminin. This is the first report of a helminth parasite laminin-binding protein and the first description of a cDNA encoding a laminin-binding protein from a parasite. The cDNA clone (egmo3) was isolated from an E. granulosus protoscolex cDNA expression library, and identified on the basis of sequence homology to the nonintegrin mammalian metastasis-associated 67-kDa laminin receptor (67-LR). The amino acid sequence predicted from the cDNA sequence is 268 residues long with a calculated molecular mass of 29.9 kDa. Southern blot analysis suggested that many copies of the gene may occur in the E. granulosus genome. A Northern blot revealed that the gene is expressed as a single transcript of approximately 1 kb consistent with the size of the cDNA insert. Antibodies raised to the purified protein interacted with a 30 kDa protein in whole E. granulosus protoscoleces. A Western blot of the purified and refolded recombinant protein specifically bound 125I-labelled laminin, as did a synthetic peptide derived from the inferred amino acid sequence of egmo3 which is similar in homology to peptide G, the active ligand-binding site of 67-LR. We also isolated the 3' end of the cDNA encoding the homologous protein from the closely related species, E. multilocularis. The polypeptide encoded by egmo3 also shares substantial identity with the acidic class of ribosomal proteins which are involved in protein synthesis. As such, the egmo3 protein may be multifunctional in E. granulosus, acting as a laminin-binding molecule but also playing a role in cell division and growth.

Amino Acid Sequence↗
PubMed1999

Molecular analysis of the GCF gene identifies revisions to the cDNA and amino acid sequences(1).

GC factor (GCF) was reported as a transcriptional regulator that binds to a specific GC-rich sequence in the epidermal growth factor receptor (EGFR) gene promoter and represses its expression. In this paper, we present the data on three revisions of the cDNA sequence that lead to significant changes of the amino acid sequences of the published GCF. Firstly, 5'-rapid amplification of cDNA end (5'-RACE) analysis revealed that the 308 nucleotides of 5'-end of the previously published GCF cDNA does not exist at the 5'-end of the RACE product. Simultaneously, the correct 5'-end cDNA sequence of 31 nucleotides was identified. Secondly, the 'T' at the position 787 of the published GCF cDNA was not observed. Finally, a new sequence of 114 nucleotides was identified between the positions 851 and 852 of the published cDNA sequence. The revisions result in a GCF cDNA of 2661 nucleotides that encodes a protein of 781 amino acids, replacing the highly basic region of the amino-terminus of the published GCF with a new sequence of 147 amino acids. In this era of massive gene cloning and sequencing, this study is a warning to the biological research of recent years.

Alternative Splicing↗
PubMed2001

Low-density cDNA array-coupled to PCR differential display identifies new estrogen-responsive genes during the postnatal differentiation of the rat hypothalamus.

To identify estrogen (E)-responsive genes that may play important roles in the sexual differentiation and maturation of the neuroendocrine hypothalamus, we used mRNA differential display PCR to analyze hypothalamic RNA derived from estrogen-sterilized rats (ESRs). Neonatal rats were s.c.-injected with 100 microg of 17 beta-estradiol-benzoate (EB) for 5 days. Approximately 300 out of more than 2000 RNAs examined displayed a differential expression pattern between hypothalami of the ESR females compared to their 60-day-old controls. EB-dependent expression of these genes was further analyzed by low-density cDNA array using cDNA probe sets reverse-transcribed from the same groups; 98 genes were confirmed to be differentially expressed. We selected 41 clones that showed higher density differences between the two probe sets than mean density difference in control cyclophilin cDNA blots in the cDNA array. After being cloned into pGEM-T vectors, their sequences were analyzed. Homology searches identified four genes as a protein kinase C (PKC)-binding protein, NELL2 (clone 6-1), a thyroid nuclear factor, TTF-1 (9-1), Munc18-1 (17-6), and leuserpin-2 (18-5). The other 22 genes were similar to reported genes or cDNAs such as mouse kinesin-associated protein 3 (KAP3, 8b), mouse IgE binding lectin (15-1), normalized rat brain cDNA (5-1), rat cDNA (8-1) and rat embryonic cDNA (17-1). Fifteen clones such as clone 7-3 showed no match in the GenBank Database. Further characterization of eight clones (17-1, 7-3, 8-1, 5-1, NELL2, KAP3 homolog, IgE binding lectin homolog, and TTF-1) showed that their expression in the adult female rat hypothalamus is sensitive to neonatal treatment with EB. They showed brain-specific expression and moreover, showed an increase in their mRNA level before the initiation of puberty. Some of them showed gender differences in their different postnatal expression pattern. We speculate that further study will demonstrate that many of the E-regulated genes identified in the present study play important roles in the regulation of the sexual differentiation and E-dependent maturation of the hypothalamus.

Animals↗
PubMed2000

Human allantoicase gene: cDNA cloning, genomic organization and chromosome localization.

Uric-acid-degrading enzymes (uricase, allantoinase, allantoicase, ureidoglycolate lyase and urease) were lost during vertebrate evolution and the causes for this loss are still unclear. We have recently cloned the first vertebrate allantoicase cDNA from the amphibian Xenopus laevis. Surprisingly, we have found some mammalian expressed sequence tags (ESTs) that show high similarity with Xenopus allantoicase cDNA. From a human fetal spleen cDNA library and adult kidney EST clone, we have obtained a 1790 nucleotide long cDNA. The 3' end of this sequence reveals a substantial high identity with the corresponding portion of Xenopus allantoicase cDNA. In contrast, at the 5' end the human sequence diverges from that of Xenopus; since no continuous open reading frame can be found in this region, the hypothetical human protein appears truncated at its N-terminus. We proposed that such a transcript could be due to an incorrect splicing mechanism that introduces an intron portion at the 5' end of human cDNA. Allantoicase cDNA is expressed in adult testis, prostate, kidney and fetal spleen. By comparison with available genomic sequences deposited in database, we have determined that the human allantoicase gene consists of five exons and spans 8kb. We have also mapped the gene in chromosome 2.

Amino Acid Sequence↗
PubMed2001

Construction and characterization of a cDNA library from 4-week-old human embryo.

Development and differentiation studies of early human embryos have been severely impeded by general difficulties in obtaining suitable samples. In order to isolate and identify new genes expressed during early human development, we constructed and characterized a PCR-based cDNA library using a 4-week-old chorion-free human embryo. The constructed cDNA library contained 6.3 x 10(6) directional recombinants, and its insert size ranged from 0.4 to 1.8 kb. The cDNA library proportionally represents the mRNA population, containing beta-actin, tPA and LINE1 repetitive sequences at the expected frequencies as in other conventionally constructed and PCR-based cDNA libraries. PCR analyses of the library for specific genes have also revealed the presence of cDNAs for developmentally important genes such as CD59, MCP, Quox-1 and ZNF268. Among the 70 randomly selected cDNA clones, 53% encoded previously known genes, 26% matched with anonymous sequences, and 17% showed no sequence similarity and were designated as human early embryo-specific ESTs. These results demonstrate the sequence complexity and relatively low redundancy of our cDNA library. Furthermore, approximately 40% of those randomly analyzed clones contained full-length encoding regions. To our knowledge, this is the first description of the PCR-based cDNA library from a 4-week-old chorion-free human embryo, and the presence of novel sequences within this library makes it a valuable and unique resource for studying gene expression and regulatory mechanisms that underlie the early process of human embryogenesis.

Cloning, Molecular↗