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Results for “positional cloning”

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PubMed2005

[Screen of differentially expressed genes between gastrula embryos and tail bud embryos in gynogenetic gibel carp (Carassius auratus gibelio)].

Suppression subtractive hybridization (SSH) cDNA plasmid libraries were constructed between gastrula embryos and tail bud embryos in gynogenetic gibel carp (Carassius auratus gibelio). 739 and 816 PCR positive clones were respectively selected to perform dot blot, and 72 dot blot positive clones and 98 dot blot positive clones were obtained from the SSH plasmid libraries specific for gastrula embryos and tail bud embryos. Sequencing analysis and database searches indicated that there were 19 known genes and 31 unknown/cDNA fragments in the sequenced 72 dot blot positive clones specific for gastrula embryos, and 52 known genes and 37 unknown cDNA fragments in the sequenced 98 dot blot positive clones specific for tail bud embryos. Moreover,specific expressions of partial genes were further confirmed by virtual Northern blots and RT-PCR. The screen of these differentially expressed genes will help us to understand the molecular mechanism in gibel carp embryogenesis.

Animals↗

PubMed2003

Identification of novel genes for secreted and membrane-anchored proteins in human keratinocytes.

BACKGROUND: Both intercellular and intracellular signals are transduced primarily by interactions of secreted and/or membrane-anchored polypeptides, and they play a pivotal role in regulating proliferation, differentiation and apoptosis of keratinocytes within the epidermis. Despite recent identification of these polypeptides, it is likely that several important molecules remain undisclosed. OBJECTIVES: To identify novel genes encoding secreted or membrane-anchored polypeptides expressed by human keratinocytes. METHODS: We employed a signal sequence (SS) trap of a 5'-end-enriched cDNA library prepared from primary cultured human keratinocytes. Gene expression analysis was performed using Northern blotting. R Screening of 4018 cDNA clones yielded 82 positive clones (57 independent genes), most of which encoded SSs in their N-termini. Most of the positive clones were known genes registered in the GenBank database. Seven genes were identified in the EST database, four of which encoded novel membrane-anchored polypeptides with features of type I transmembrane proteins; the other three genes encoded novel non-type I transmembrane polypeptides. These EST genes were expressed differentially by keratinocytes subjected to low vs. high calcium concentrations and by basal vs. squamous cell carcinomas. CONCLUSIONS: Using the SS trap, we isolated many genes known to be involved in constituting epidermal structures and others that had not previously been associated with keratinocytes. In addition, we identified novel genes (EST genes) that differ in kinetics of gene expression in keratinocyte differentiation. Our results validate the effective use of this SS trap method for identifying secreted and membrane-anchored polypeptides expressed by human keratinocytes. The identification will better illuminate the molecular mechanisms responsible for co-ordinated regulation of epidermal homeostasis.

Amino Acid Sequence↗

PubMed1990

[Cloning and sequencing of hemolysin gene from clinical Aeromonas hydrophila].

Aerolysin is one of the important virulence factors for Aeromonas hydrophila infection. To understand the characteristics of the aerolysin gene in clinical A. hydrophila, a genomic library was constructed by using pUC19 as cloning vector. The positive clone containing the aerolysin gene was selected by the colony hybridization method, using the aerolysin probe (an 48 mer oligonucleotide) of aquatic A. hydrophila. Four positive out of 1,200 transformants were obtained from the primarily screened genomic library, and were further identified for specific binding capability by the dot blot hybridization method. One of three positive clones, designated as pAH-1, was further analyzed by the restriction mapping technique. For further sequencing the aerolysin gene nucleotides, the 3.0 kb fragment of A. hydrophila isolated from pAH-1 was cloned into pBluescriptII, pKS+, resulting in plasmid pKAH-1. Subclones of pKAH-1 were constructed and determined for the presence of 48 mer aerolysin gene sequence by dot blot hybridization method. These (subclones pKS+SS and pSK+SS) were selected for nucleotide sequencing by single-stranded dideoxy sequencing method. The nucleotide sequence similarity coefficient between clinical and aquatic strains of A. hydrophila was 76%; whereas between clinical strains of A. hydrophila and A. sobria was 71%. Since the length of the A. hydrophila DNA fragment cloned into pAH-1 is 3.0 kb, a larger size than the aerolysin gene of aquatic A. hydrophila (1.45 kb) and, also, includes 3' region of aerolysin gene in aquatic A. hydrophila, the indication is that the clone, pKAH-1, contains an entire aerolysin gene of A. hydrophila. The similarity between a small region (containing 8 amino acids) of the aerolysin in the clinical A. hydrophila and the alpha toxin of Staphylococcus aureus suggests that there is functional significance in this region.

Aeromonas↗

PubMed1992

Cloning and partial sequencing of the porcine growth hormone (pGH) gene from pituitary gland.

High molecular weight DNA was isolated from porcine pituitary gland, and a genomic library was constructed using lambda EMBL3 as cloning vector. Five positive clones were identified by in-situ hybridization with the full-length pGH cDNA as the probe. Dot-blot hybridization, restriction analysis, and Southern hybridization showed that one of the positive clones contained the entire pGH gene. A subclone that contained the upstream sequence from the SmaI site of pGH gene was identified, and part of it was sequenced. We also compared the sequence of our pGH gene with the corresponding sequence of the published pGH gene.

Amino Acid Sequence↗

PubMed2006

[Establishment of a reporter gene-based cell screening model for discovering new agonists of estrogen receptor beta subtype].

AIM: To establish a sensitive and efficient reporter gene-based screening model for finding agonists of estrogen receptor beta subtype. METHODS: A recombinant vector pTAL-ERE-SEAP was constructed by inserting a synthetic sequence composed of five estrogen responsive elements in front of promoter of pTAL-SEAP vector. pTAL-ERE-SEAP was then transfected into human embryonic kidney (HEK293) cells. G418 (200 microg x mL(-1)) was added to select positive clones that can be induced by E2 to express reporter gene SEAP. The speciality was tested by several ligands of relative nuclear receptors of the same family. The stability of the model, the time-effect relationship, the dose-response relationship, and the immunocytochemistry staining of ERbeta expression after transfection were observed. 2 622 compounds were screened by using this model. RESULTS: Stably transfected clones were obtained. The expression levels of reporter gene SEAP of positive clones was induced by E2 in a dose-response and time-effect relationship manners. The Z' factor value was 0.7. The expression levels of dexamethasone and other ligands were low. The result of immunocytochemistry staining showed the expression of ERbeta. E2 had no proliferating effects on stably transfected clones. CONCLUSION: Stably transfected positive clones transfected with recombinant vector pTAL-ERE-SEAP were obtained. The positive clones may be used to screen for agonists of estrogen receptor beta subtype by measurement of luminescent value of expressed SEAP in wells of microlitre plate.

Alkaline Phosphatase↗

PubMed1998

Ribonuclease-charged vector for facile direct cloning with positive selection.

Plasmid vectors for positive selection of cloned inserts in Escherichia coli were devised, based on an expression plasmid (pMT416) for the bacterial ribonuclease barnase. In addition to the barnase gene under control of a synthetic tac promoter, these plasmids carry the gene for the barnase inhibitor, barstar, the constitutive expression of which protects the bacterium from the detrimental effects of moderate barnase production. Full expression of the barnase gene overcomes protection by barstar and becomes lethal. Having a unique SmaI/XmaI site in the barnase structural gene, pMT416 itself can be used as a selective vector: uncut or religated pMT416 will preclude growth while plasmids with inserts in the barnase gene will allow the cells to survive. The entire pUC polylinker was inserted into the barnase gene in place of the Val-36 codon. This insert of nineteen largely hydrophilic amino acids does not prevent the lethal effect of full expression of the gene. The resulting plasmid, pMT440, is a generally useful selective cloning vector representing the "kill-the-rest" approach.

Amino Acid Sequence↗

PubMed1994

Generalized and mobilizable positive-selection cloning vectors.

We have modified the positive-selection cloning vector pUN121 to expand the numbers of unique cloning sites by insertion of a multiple cloning site into the lambda cI gene without disrupting its repressor function, resulting in plasmid pSKM10. Plasmid pSKM10 has seven restriction enzyme sites suitable for general cloning purposes. A mobilizable version (pSKM11) of pSKM10 was constructed by insertion of the IncP mob sequence which permitted mobilization of the plasmid into a wide variety of Gram- bacteria.

Amino Acid Sequence↗

PubMed2003

Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening.

New secondary mesenchyme specific genes, expressed exclusively in pigment cells, were isolated from sea urchin embryos using a differential screening of a macroarray cDNA library. The comparison was performed between mRNA populations of embryos having an expansion of the endo-mesodermal territory and embryos blocked in secondary mesenchyme specification. To be able to isolate transcripts with a prevalence down to five copies per cell, a subtractive hybridization procedure was employed. About 400 putative positive clones were identified and sequenced from the 5' end. Gene expression analysis was carried out on a subset of 66 clones with real time quantitative PCR and 40 clones were positive. This group of clones contained sequences highly similar to: the transcription factor glial cells missing (gcm); the polyketide synthase gene cluster (pks-gc); three different members of the flavin-containing monooxygenase gene family (fmo); and a sulfotransferase gene (sult). Using whole mount in situ hybridization, it was shown that these genes are specifically expressed in pigment cells. A functional analysis of the S. purpuratus pks and of one S. purpuratus fmo was carried out using antisense technology and it was shown that their expression is necessary for the biosynthesis of the sea urchin pigment echinochrome. The results suggest that S. purpuratus pks, fmo and sult could belong to a differentiation gene battery of pigment cells.

Animals↗

PubMed1999

[Molecular-genetic approach to congenital malformation syndromes].

The causes of congenital malformation syndromes had long remained obscure, because their biochemical bases were unknown. However, with recently developed reverse-genetic and/or Human Genome Project-derived technology, we have been able to approach such disorders. These new methods include positional cloning techniques, candidate gene approach and positional candidate strategies. Among them, positional cloning has become most reliable nowadays, and three ways are mainly available to obtain position information of disease genes, i.e., data from linkage analysis of disease families; comparative maps between different species; breakpoints of disease-related de novo chromosomal translocations. I present here some examples for each strategy: a large kindred with mesomelic dysplasia Kantaputra type for linkage data, and its seemingly allelic bone dysplasia associated with t (2; 8) for positional cloning that starts from a chromosomal translocation; Waardenburg syndrome for candidate gene approach; and the p57KIP2 gene for positional candidate approach to Wiedemann-Beckwith syndrome. I finally emphasize that a human link composed of general physicians, molecular geneticists and clinical researchers is essential to reach a goal of reverse genetics. Without such a goal, we can neither understand the genesis of diseases nor develop their therapy.

Beckwith-Wiedemann Syndrome↗

PubMed2002

Screening the proteins that interact with calpain in a human heart cDNA library using a yeast two-hybrid system.

Calpain, a cytosolic cysteine protease, requires calcium ions for activity. It has been reported that calpain is involved in the degradation of myofibrillar and neurofilament proteins, and the activation of phosphorylase b kinase and protein kinase C. More recently, calpain was shown to participate in apoptosis. In order to understand the calpain-related signal transduction pathway and its changes during hypertrophy, and especially in hypertension, we screened a human heart cDNA library to find proteins that interact with calpain. 1) Using PCR we amplified the full-length, domain II, domain III and domain IV cDNA of calpain (calcium-activated neutral protease, CANP) I large subunit respectively. 2) Then the fragments were cloned into pGBKT7 vector, resulting in 4 bait expression constructs (pGBKT7-CANP, pGBKT7-CANP II, pGBKT7-CANP III, and pG BKT7-CANP IV). 3) After 4 bait vectors were transformed into AH109 by the lithium acetate-mediated method, AH109/pGBKT7-CANP, AH109/pGBKT7-CANP II, AH109/pGBKT7-CANP III, and AH109/pGBKT7-CANP IV were obtained, respectively. 4) After the human heart cDNA library was sequentially transformed into AH109/ pGBKT7-CANP, 1000-1200 positive clones were grown on SD/Trp-Leu-Ade-His-. Only 150 positive clones were obtained through a colony-lift filter assay to detect beta-galactosidase activity. 5) Total 105 clones among above 150 positive clones were eliminated through that the duplicate, pseudopositive and autoactive detection, respectively. 6) Finally, sequencing eliminated clones with a wrong open reading frame (ORF). Eight clones were cancelled with wrong ORF. The remaining 37 positive clones were analyzed using BLAST software available on the Internet and classified as follows: 1. enzymes or proteins related to signal transduction in the cell; 2. contraction proteins 3. matrix proteins 4. unknown proteins. 7) In order to determine which domain of the calpain I large subunit was involved in the interaction with these real clones, the 37 clones were transformed into AH109/pGBKT7-CANP II, AH109/pGBKT7-CANP III or AH109/pGBKT7-CANP IV. Among these 37 clones, 29 clones could interact with domain II, 5 clones could interact with domain III and 6 clones could interact with domain IV. Thus, we successfully constructed 4 bait expression vectors, pGBKT7-CANP, pGBKT7-CANP II, pGBKT7-CANP III and pGBKT7-CANP IV, and obtained 37 real positive clones that interacted with the calpain I large subunit by screening a human heart cDNA library using pGBKT7-CANP as bait. Among them, 29 clones could interact with domain II of the calpain I large subunit, where the active site of calpain is located. Additional studies will be needed to clarify the calpain-related signal transduction pathway in greater detail.

Calpain↗

PubMed2000

[Immunoscreening of Schistosoma japonicum adult worm cDNA library by sera from rabbits vaccinated with ultraviolet-attenuated cercariae].

OBJECTIVE: To find out the major antigenic molecules of radiation-attenuated cercariae, and provide some useful candidate antigens for developing schistosomiasis vaccine. METHODS: Schistosoma japonicum (Sj) adult worm cDNA library was screened by sera of rabbits vaccinated with ultraviolet-attenuated cercariae, and the inserts of positive clones were specifically amplified by PCR and sequenced. RESULTS: Ten positive clones were obtained after three rounds of screening, and the size of Sj cDNA fragments of the positive clones ranged from 1.5 kb to 1.8 kb. Five partial sequences were got after preliminary sequencing. Two of them had significantly homology with Sj dynein light chain 5(DLC 5) gene and Sj mitochondrial gene, respectively, and the others were identified as partial sequences of novel genes for they showed only partial homology with non-schistosome genes or other organism in the database. CONCLUSIONS: The positive clones may be the genes encoding the antigens that can elicit protective immunity against Sj.

Animals↗

PubMed2004

[Immunoscreening of newborn larvae cDNA library of Trichinella spiralis].

OBJECTIVE: To obtain antigenic genes encoding newborn larvae antigens of Trichinella spiralis. METHODS: Newborn larvae (NBL) cDNA library of Trichinella spiralis was screened using the infected swine serum and positive clones were sequenced and analysed. RESULTS: 158 positive clones were obtained from 4.5 x 10(5) recombinant clones by immunoscreening. The sequence analysis of positive clones showed that there are 36 novel cDNAs, 5 reported cDNAs and 12 cDNAs without the ORF showing high similarity to the mitochondrial DNA of Trichinella spiralis. CONCLUSION: Some cDNAs encoding antigenic protein of newborn larvae of Trichinella spiralis were obtained.

Amino Acid Sequence↗

PubMed2003

[Immunoscreening of Schistosoma japonicum adult worm cDNA library with sera vaccinated with cercaria antigen and analysis of novel genes].

OBJECTIVE: To explore antigens possessing common immunogenicity with Schistosoma japonicum (Sj) cercariae antigens, and to find out new candidate antigens for schistosomiasis diagnosis and vaccine. METHODS: Sj adult cDNA library was screened using sera from rabbits vaccinated with Sj cercariae antigen, the inserts of positive clones were amplified by PCR, all positive clones were sequenced and the data were analysed using Nucleotide BLAST software of NCBI and Expert Protein Analysis System of Swiss Institute of Bioinformatics. RESULTS: Thirteen positive clones were obtained after three rounds of immunoscreening, and all amplified by PCR. Among four novel genes, SjCAI, SjCA, SjCAI-2 and SjCAI-3 (GenBank accession number: AF495883, AF515834, AY118086 and AY129303, respectively) encoded proteins with 353, 161, 137 and 72 animo acids respectively. Sj CAI protein contained six DNA-binding zinc fingers and showed some homology to gastrula zinc finger protein XLCGF48.2; proteins encoded by SjCA, SjCAI-2 and SjCAI-3 respectively contained N-glycosylation sites and phosphorylation sites. CONCLUSION: Novel genes were obtained by immunoscreening Sj adult cDNA library.

Amino Acid Sequence↗

PubMed2003

[Immunological screening of Toxoplasma tachyzoite cDNA expression libraries with serum from infected rats].

OBJECTIVE: To screen and identify the potential candidates for the development of toxoplasmosis vaccine. METHODS: Rats were infected with Toxoplasma gondii (T. gondii) RH strain and their sera were used as a probe to screen T. gondii tachyzoite cDNA expression libraries. The positive clones were analyzed by PCR amplification and DNA sequencing. RESULTS: Thirteen positive clones were obtained from about 4 x 10(5) phage plagues after three rounds of screening. The size of the inserts ranged from 0.45 kb to 2.4 kb. A BLAST search of all available sequence databases using the partial sequences from four positive clones (L1, L2, L4, L5) showed that the sequence of L2 clone was identical with T. gondii P24 major antigen gene (TgP24). Clone L4 had a high homology with Saccharum officinarum pyruvate orthophosphate dikinase. There is no significant hit of any sequences to clone L1, suggesting that L1 could be a novel gene(GenBank accession number AY180109), named T.g-R1, which encodes a non-transmembrane protein with 134 amino acid open reading frame. PROSCAN analysis of the T.g-R1 amino acid sequence showed that this gene product contains two protein kinase C phosphorylation site, two casein kinase II phosphorylation site, one N-myristoylation site and one microbodies C-terminal targeting signal. Clone L5 was a small partial fragment. CONCLUSION: The identification of positive clones provides a possible way for the development of toxoplasmosis vaccine.

Amino Acid Sequence↗

PubMed1979

Chromosomes and causation of human cancer and leukemia. XXXII. Unusual features of Ph1-positive acute myeloblastic leukemia (AML), including a review of the literature.

Five cases of Ph1-positive AML were studied. In all cases a Ph1-chromosome was shown with banding techniques to be due to a translocation between chromosomes No. 9 and No. 22. Cases 1 and 4 were found to have more than one Ph1 with evidence of only on Ph1-translocation accompanying other chromosome abnormalities. Two cases represented an unusual pattern of appearance and disappearance of the Ph1-positive clone during their clinical courses: Case No. 2 was originally Ph1-positive (46,XY,Ph1) but two months before his expiration the Ph1-positive clone was completely replaced by a newly developed Ph1-negative clone with an abnormal chromosome No. 21 (46,XY,21q+), whereas case No. 3, primarily Ph1-negative, developed a Ph1-positive clone among the previously karyotypically normal cells one month before death. The Ph1-positive AML cases presented have been discussed in relation to: 1) the genesis and significance of the Ph1-positive clone, 2) differentiation from the blastic phase of CML and 31 the general experience with Ph1-positive acute non-lymphocytic leukemia (ANLL), the world literature of which have been tabulated.

Adolescent↗

PubMed2002

Genetic analysis of jumbled spine and ribs (Jsr) mutation affecting the vertebral development in mice.

The jumbled spine and ribs (Jsr) mouse was derived from a spontaneous mutation. As the phenotype, a shortened trunk and kinky tail are characteristic Jsr traits. In this study, on high resolution mapping it was found that Lunatic fringe (Lfng) mapped at the same position as Jsr. Lfng was identified as the candidate gene for Jsr, but sequence analysis of this gene revealed no substitution in the coding region of cDNA. Therefore, we adopted the strategy of positional cloning for Jsr using a mouse bacterial artificial chromosome (BAC) library. A BAC contig was constructed from three BAC clones showing positive signals of Lfng and 11MMHAP75FRD8.seq near the Jsr locus on chromosome 5. Based on the genetic mapping of both T7 and sp6 ends of a clone of BAC382-O-7 (BAC382), the Jsr gene was considered to exist in BAC382 and to be positioned near the sp6 side.

Animals↗

PubMed1997

Le(X) structure enhances myocardial differentiation from embryonic stem cells.

alpha-1,3-Fucosyltransferase (Fuc T IV) cDNA was placed under the control of beta-actin, cytomegalovirus enhancer/promoter and transfected into embryonic stem cells. The transfected cell clones with integrated cDNA (positive clones) differentiated more efficiently into myocardial cell clones without integrated cDNA (negative clones) or parental cells. Furthermore, myocardial cells differentiated from the positive clones survived longer than those differentiated from the negative clones or parental cells. These results indicate that Lewis X structure, the product of Fuc T IV, enhances myocardial differentiation. The mechanism of the phenomenon is discussed on relation to integrin action.

Animals↗

PubMed2004

[Screening of dominant epitopes of antigens related to antibodies in the sera of patients with nasopharyngeal carcinoma].

BACKGROUND & OBJECTIVE: Epstein-Barr virus (EBV) is closely related to nasopharyngeal carcinoma (NPC). Many kinds of methods can be used to examine antibodies in NPC patients sera. This study was to screen the dominant epitopes from random peptide libraries (RPLs) displayed on phage using the EBV-related antibodies purified from the sera of NPC patients, and find new antigens at the epitope level. METHODS: The EBV-related antibodies were eluted from the sera of NPC patients using B95-8 cell EBV proteins as antigen, and the phages from 12-mer RPLs were elutriated for 3 rounds with the antibodies. The positive clones were gained by sandwich ELISA, and competitive inhibition assay from the third elution. The positive clones were sequenced, and the peptide coded by the inserted DNA were blasted with the antigen region of EBV proteins. RESULTS: Sixty-four phage clones were randomly picked up from the third eluate,25 positive clones were picked up using sandwich ELISA assay, the positive percentage was 39.06%. Thirteen clones were picked up for competitive ELISA assay,11 clones showed inhibitory phenomena,the inhibitory rates were between 18.09% and 65.94%. Five positive clones with high absorbency value, and high inhibitory rates were selected out, the sequences of peptides displayed on these clones were -A-T-S-H-L-H-V-R-L-P-W-T- (d15, and d18), -G-S-T-H-K-H-N-H-F-N-K-T- (d19), -K-P-I-H-E-H-P-H-R-F-K-S- (e8), -H-T-H-K-I-K-I-P-L-P-I-Q- (e23). These peptide sequences showed similarity with the amino acid sequences located in antigen regions of EBV integral membrane protein (d15, and d18), EBV thymidine kinase (d19), and EBV major capsid protein (e8, and e23). CONCLUSION: EBV-related epitopes could be obtained by screening the phages from RPLs with polyclonal antibodies purified from the sera of NPC patients, which may offer new methods of antigen preparation for sera diagnosis of NPC.

Amino Acid Sequence↗