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PubMed1994

Physical and genetic mapping at the ATA/ATC locus on chromosome 11q22-23.

Genetic heterogeneity in ataxia-telangiectasia (A-T) points to four different genes responsible for this disease. The two major A-T genes, ATA and ATC, were localized by genetic analysis close to each other on chromosome 11q22-23, prompting efforts of positional cloning. Essential steps in positional cloning are long-range cloning of the genomic region of interest, and derivation of highly polymorphic markers that would allow further reduction of the interval carrying the A-T gene. We constructed genomic contigs across the D11S611-D1S424 region harbouring the ATA and ATC genes in yeast artificial chromosome (YAC) vectors. These contigs were used as a fine mapping tool and enabled us to localize along the A-T region, eight microsatellite markers generated randomly by genome mapping centres. In addition, we used specific YAC clones to generate five new microsatellite markers based on polymorphic CA repeats. Recombination mapping based on Israeli A-T families indicates that the ATC gene is distal to the locus D11S1817. Further linkage analysis using these markers is expected to reduce the major A-T locus considerably to a size appropriate for cosmid cloning and identification of transcribed sequences.

Ataxia Telangiectasia↗

PubMed1998

[Molecular analysis of peroxisomal disorders].

Peroxisome biogenesis disorders (PBD) include Zellweger syndrome (ZS), neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD). They are classified into ten complementation groups. Five pathogenic genes have been identified using different model systems of peroxisome deficient mutants. PAF-1 and 2 were identified from CHO mutants and were responsible genes for PBD group F and C. Human PEX 5, 12 and 1, responsible genes for group 2, 3 and 1, respectively, were cloned by homology search between yeast PEX genes and human genes on the cDNA data base. Adrenoleukodystrophy (ALD), the most frequent peroxisomal disorder, shows phenotypic heterogeneity. Its responsible gene was cloned by positional cloning. It encodes a 75 kDa peroxisomal membrane protein (ALDP) that is a member of the ATP-binding cassette transporter family. There are about 120 different mutations including missense, nonsense and splice mutations, as well as insertions and deletions of a few base pairs. There is no correlation between the clinical phenotype and the ALDP gene mutation. Recently, animal models have been produced by targeted mutation of the PBD and ALD genes. The mouse model should facilitate researches on PBD and ALD, especially those on regulatory factors of their phenotypic heterogeneity and on new therapeutic approaches.

Adrenoleukodystrophy↗

PubMed1998

Characterization of microsatellite loci from Elymus alaskanus and length polymorphism in several Elymus species (Triticeae: Poaceae).

A size-selected genomic library from Elymus alaskanus was screened for the presence of (GA)n, (GT)n, (CAC)n, and (TCT)n microsatellite sequences. A total of 28 positive clones were found for the two dinucleotide repeats, whereas no positive clones were found for the trinucleotide repeats. Positive clones were sequenced to validate the presence of microsatellites and to generate polymerase chain reaction (PCR) primers, based on the sequences flanking the microsatellite. Primer pairs were designed and evaluated for 18 selected microsatellites. The resulting loci were analysed by PCR for their usefulness as molecular markers in an array of 18 accessions representing E. alaskanus and 10 other Elymus species. PCR amplification revealed alleles for the 18 loci, which varied in having 1-10 alleles in these accessions. In the 18 accessions tested, 7 of the 18 loci were polymorphic, with gene diversity values ranging from 0.54 to 0.80 among all species. Within E. alaskanus, gene diversity values ranged from 0.20 to 0.72, with a mean of 0.48. Polymorphism was also detected within accessions. No clear relationship between total repeat length and the degree of polymorphism was observed in this study. Primer pairs designed to amplify microsatellites in E. alaskanus can be used to generate polymorphism products in other species within the genus. Hence, microsatellites are useful markers for studying both inter- and intra-specific genetic variability within Elymus.

Base Sequence↗

PubMed1999

L-leucine auxotrophy in Bifidobacterium globosum.

The enzymes involved in the biosynthetic pathway of L-leucine were studied in plasmid-negative and plasmid-positive clones derived from the RU 809 strain of the Bifidobacterium globosum species. The growth of plasmid-positive clones in synthetic medium required L-leucine. We have shown that no detectable activity of the beta-isopropylmalate dehydrogenase enzyme was present in plasmid-positive clones, whereas detectable and significant activity of this enzyme was found in plasmid-negative clones. The lack of activity of the beta-isopropylmalate dehydrogenase enzyme is considered responsible for the L-leucine auxotrophy in the plasmid-positive clones.

3-Isopropylmalate Dehydrogenase↗

PubMed2003

[Screening and identification for cDNA of differentially expressed genes in human primary hepatocellular carcinoma].

OBJECTIVE: Screening and identification of differentially expressed genes in human primary hepatocellular carcinoma(HCC). METHODS: The differentially expressed genes subtracted cDNA library of HCC constructed by suppression subtractive hybridization(SSH) technique was screened by colony in situ hybridization, then the positive clones were further screened with PCR amplification. The positive clones were sequenced and analyzed for homology in the Genbank databases with Basic Local Alignment Search Tool BLAST . The novel cDNA sequences were analyzed by Northern blot analysis. RESULTS: Thirteen positive clones were obtained, and 11 cDNA sequences were identified. Sequences of 11 cDNA showed that 6 cDNA were homologous with the genes published in Genbank and 5 cDNA were unknown genes. Northern blot indicated that 3 novel cDNA(>300 bp) were only expressed in HCC. CONCLUSION: The subtracted cDNA library constructed by SSH technique contains differentially expressed genes of HCC. Three novel cDNA sequences might be differentially expressed genes of HCC. Further screening the library and gaining the whole gene sequence may lay a foundation for identifying differentially expressed genes in HCC.

Base Sequence↗

PubMed2006

LINKAGE programs: linkage analysis for monogenic cardiovascular diseases.

Identification of the genes for a human disease provides significant insights into the molecular mechanism underlying the pathogenesis of the disease. A human disease gene can be identified by its chromosomal location (positional cloning). Linkage analysis is a key step in positional cloning. For monogenic disorders with a known inheritance pattern, model-based linkage analysis is effective in mapping the disease location. Therefore, model-based linkage analysis can provide a powerful tool to positional cloning of some specific molecular determinants that co-segregate with disease phenotypes in the isolated samples (e.g., large and multiplex impaired pedigrees). This chapter describes model-based human genetic linkage analysis as implemented in the LINKAGE computer package. First, we introduce the basic concepts and principles for genetic analysis of monogenic disorders. Then, we demonstrate the usages of the programs by analyzing several examples of hypothetical pedigrees with the inheritance modes of autosomal-dominant, autosomal-recessive, and genetic heterogeneity.

Cardiovascular Diseases↗

PubMed2005

Functional genomics of maize submergence tolerance and cloning of the related gene Sicyp51.

In this study, SSH (Suppression Subtractive Hybridization) and cDNA microarray were used to identify genes associated with waterlogging response of maize roots. Mo17 and Hz32 are two maize inbred lines with differential tolerance to hypoxia. Seedlings of the inbred lines with two leaves were submerged in hypoxia buffer. SSH libraries were constructed with cDNA samples from roots. Both forward and reverse subtractions were performed for each inbred line, and 105 positive clones induced by hypoxia were selected by differential screening. The treated and control message RNA were hybridized with the cDNA microarray of Mo17, sequentially, 57 of 3-fold differentially expressed clones were obtained. A total of 162 positive clones were all sequenced. Bioinformatics analysis showed these positive clones represent 85 TUGs, including genes involved in several biochemistry pathways, such as glycolysis, protection, signal transduction, cell construction and energy metabolism and 41 EST with unknown function. Comparison between Mo17 and Hz32 indicates that genes related to hypoxia tolerance have different expression patterns in submerged roots. Several positive clones' expression patterns were revealed by Northern or RT-PCR, and a new gene (Sicyp51), which may contribute to hypoxia tolerance, was identified.

Cell Hypoxia↗

PubMed1995

New ccdB positive-selection cloning vectors with kanamycin or chloramphenicol selectable markers.

Recently, we described pKIL18/19 positive-selection cloning vectors which rely on the inactivation of the cytotoxic ccdB gene [Bernard et al., Gene 148 (1994) 71-74]. They are new tools for simplifying gene cloning/sequencing procedures, as only recombinant DNA allow the formation of viable colonies. To enhance positive-selection capabilities, putative translational reinitiation codons located within the pKIL18/19 ccdB were modified by site-directed mutagenesis. New pKIL-derived vectors with kanamycin (KmR) or chloramphenicol (CmR) resistance-encoding genes were also constructed. In addition, a new host derived from the DH2 strain was developed.

Bacterial Proteins↗

PubMed2005

[Difference analysis of genome-wide DNA methylation status of CpG islands between the monozygotic twins with disconcordant phenotypes of chronic hepatitis B virus infection].

OBJECTIVE: To analyse the difference of genome-wide DNA methylation status of CpG island between the monozygotic twins with disconcordant phenotype of HBV infection and to discover possible differentially methylated genes. METHODS: Modified AIMS (amplification of inter-methylated sites) method was adopted. According to the frequent sites of CpG islands (-CGCG- and -CCGG-), three groups of isochizomers with distinct methylation sensitivity (Sma I-Xma I, Hpa II-Msp I and BssH II-Pau I/BseP I) were used to modify the AIMS method. The modified AIMS method combined with Personal Molecular Imager FX system analysis and radioautographic analysis was used to make the global detection of the methylome of CpG islands. Multiple anonymous bands were compared between the twins with the Quantity One bio-soft. The different bands were cloned into T vectors and positive clones were sequenced. BLAST analysis of positive clone sequences was conducted to give the clues for the differential methylated genes between monozygotic twins with discordant phenotype of HBV infection. RESULTS: Nearly the same bands were found between one pair of twins with concordant phenotype of HBV infection. Different methylated bands were found not only between monozygotic twins with concordant phenotype but also between those with disconcordant phenotype. More differential methylated bands were found in the latter groups. By BLAST analysis with sequences of differential methylated bands, four possible genes were got. These genes might relate to the monozygotic twins with disconcordant phenotype of chronic HBV infection. CONCLUSION: Differential methylation of genes occurs in monozygotic twins with discordant phenotype of HBV infection. Whether these changes are involved in the pathogenesis of different phenotypes needs further elucidation.

Adolescent↗

PubMed1992

Tracking disease genes by reverse genetics.

Increasingly, human genes are being identified by the "reverse genetics", or "positional cloning" approach. This molecular genetic strategy is particularly useful in mental illness, for which no readily detectable functional alterations are present to indicate candidate genes. The positional cloning procedure is briefly described. Significant examples of successful positional cloning are presented, including the fragile-X mental retardation syndrome gene. The study of gene expression may be complicated by genetic and non-genetic variability. Genomic imprinting may play a role in several mental illnesses, and may provide an explanation for the unusual inheritance pattern in fragile-X syndrome, for the phenotypic differences observed between Angelman and Prader-Willi syndromes, and for the juvenile onset form of Huntington disease. DNA instability may explain disease anticipation in fragile-X syndrome and myotonic dystrophy. Finally, the prospects of improvements in positional cloning methods for tracking genes responsible for mental illness are briefly discussed.

Chromosome Mapping↗

PubMed2005

[Isolation of maize genes related to aluminum tolerance].

To investigate gene expression profile in response to aluminum stress and to cloning the key genes related to aluminum tolerance, are crucial to genetic improvement of plant aluminum tolerance. In this study, suppression subtractive hybridization method was adopted to construct SSH-cDNA libraries at seedling stage of two maize inbred lines (Fig. 1), of which Mo17 is sensitive to aluminum toxicity and TL94B is tolerant. As a result, a forward SSH-cDNA library including 762 clones and a reverse SSH-cDNA library including 382 clones were constructed for Mo17. In the same way, a forward SSH-cDNA library including 760 clones and a reverse SSH-cDNA library including 380 clones were constructed for TL94B. Identification of these SSH-cDNA libraries shows that the length of inserted fragments ranges from 250 bp to 1.0 kb (Fig. 2), of which nearly 18% are positive clones. Through differential hybridization screening (Fig. 3), 124 and 47 positive clones were screened from forward and reverse SSH-cDNA libraries of Mo17 respectively; 103 and 64 positive clones from forward and reverse SSH-cDNA libraries of TL94B respectively. Total 338 positive clones from four SSH-cDNA libraries were sequenced, and all of the sequences of inserted fragments were analyzed using bioinformatical methods. A total of 232 kinds of EST sequences were obtained. Among these ESTs, 70.2% had significant homology with known genes, and the remaining 29.8% were function-unknown including 21 kinds of newly found ESTs (Table 1). An aluminum tolerant gene, GDP dissociation inhibitor gene, was detected its expression character by Northern hybridization (Fig. 4). These results indicate that the responses of maize to aluminum stress involve the interactions among different signal/metabolism pathways, such as signal transduction of stress-related factors, transcription and regulation of responsive genes, synthesis and transport of substances, changes in cell structures and functions.

Adaptation, Physiological↗

PubMed2005

[Expression of truncated Toxoplasma gondii GRA8 in the prokaryotic expression plasmids].

OBJECTIVE: To construct the prokaryotic recombinant expression plasmids of Toxoplasma gondii GRA8 and analyze their expression in E. coli containing the prokaryotic recombinant plasmids. METHODS: The full gene and its truncated fragment of GRA8 were amplified by PCR from T. gondii genomic DNA, and cloned into pMD18-T vector. The right genes in positive clones sequenced with ABI PRISMTM 377XL DNA Sequencer were digested with restrictive endonucleases and subcloned into pGEX-4T-2. The recombinant plasmids were transformed into E. coli JM109. The recombinant clones were characterized by PCR and digested with restriction endonucleases. Positive clones were induced with IPTG to express target protein and characterized by SDS-PAGE. The recombinant protein was purified from E. coli lysate by affinity chromatography and SDS-PAGE. The immunological activity of this protein was analyzed by Western blotting. RESULTS: The gene fragments encoding GRA8 were amplified by PCR from T. gondii genomic DNA. The inserts of GRA8 in positive clones were coincident with the original sequence of GRA8 gene from GenBank. The recombinant expression plasmids were constructed through subcloning the right inserts of GRA8 into pGEX-4T-2. The expression level of GRA8 from the recombinant expression plasmids in E. coli was low, and there was almost no full-length GRA8 expressed in E. coli. The purified protein reacted with the sera from rabbits infected with T. gondii RH strain. CONCLUSION: The expression level of GRA8 from the recombinant expression plasmids in E. coli is low and the purified truncated GRA8 shows certain antigenicity.

Animals↗

PubMed2006

[Biological significance of E-cadherin in an inflammatory breast carcinoma cell line].

OBJECTIVE: To investigate the effects of E-cadherin on the biologic behavior of SUM149, an inflammatory breast cancer cell line. METHODS: SUM149 cells were transfected with dominant-negative mutant E-cadherin expressing plasmid. The positive clones with higher expression of dominant-negative E-cadherin mutant were identified by RT-PCR and fluorescent flow cytometry method. The differences in cell growth, proliferation and invasion between positive clones and controls were compared. RESULTS: Whereas the proliferation of positive clones was of no change, compared with controls, the ability of invasion was decreased and the mRNA levels of MMP-1 and MMP-9 were downregulated. Gelatin zymography analysis also confirmed the decreasing expression of MMP-9 in the positive clones. CONCLUSION: In this cell line model, down-regulation of E-cadherin can inhibit the ability of invasion of this inflammatory breast cancer cell line.

Breast Neoplasms↗

PubMed2006

[Screening for endocrine exophthalmos-associated genes/cDNA fragments].

This study was conducted to screen the endocrine exophthalmos-associated genes or cDNA fragments and provide a basis for exploring the pathogenesis. The cDNA from the thyroid tissues of patients with hyperthyroidism and endocrine exophthalmos (HT&EE) was used as tester cDNA, and that from the thyroid tissues of patients with HT but free from EE was used as driver cDNA. The subtractive PCR products between tester and driver cDNA were obtained through two cycles of subtraction hybridization and two cycles of PCR by using suppression subtractive hybridization, and then were inserted into pT-Adv, a cloning vector. The ligated DNAs were transformed into E. coli DH5alpha competent cells and incubated for proper blue/white color development. Forty-eight white colonies were randomly picked and their inserts were colony PCR amplified. The PCR product from one of the colonies contained two inserts; the others contained single insert, having a size of 0.2 kb to 2 kb. The inserts of transformants were arrayed on nylon membrane. After cDNA/Rsa I digestion the thyroid tissues of patients with HT, and of patients with HT&EE, were labeled with digoxigenin; the nylon membranes were then hybridized respectively with the two cDNA probes for a high throughput screening for positive clones. The clones which were hybridized with the cDNA probe of HE&EE patients but not hybridized with the probe of the HT patients or showed only faint signal of hybridization, were chosen as positive clones and their inserts were candidates for the endocrine exophthalmos genes or cDNA fragments. About 50% of the clones were confirmed as positive clones. The cDNA fragments in the positive clones were the endocrine exophthalmos-associated genes or cDNA fragments. Endocrine exophthalmos

Cloning, Molecular↗

PubMed1990

SV40 T antigen alone drives karyotype instability that precedes neoplastic transformation of human diploid fibroblasts.

To define the role of SV40 large T antigen in the transformation and immortalization of human cells, we have constructed a plasmid lacking most of the unique coding sequences of small t antigen as well as the SV40 origin of replication. The promoter for T antigen, which lies within the origin of replication, was deleted and replaced by the Rous sarcoma virus promoter. This minimal construct was co-electroporated into normal human fibroblasts of neonatal origin along with a plasmid containing the neomycin resistance gene (neo). Three G418-resistant, T antigen-positive clones were expanded and compared to three T antigen-positive clones that received the pSV3neo plasmid (capable of expressing large and small T proteins and having two origins of replication). Autonomous replication of plasmid DNA was observed in all three clones that received pSV3neo but not in any of the three origin minus clones. Immediately after clonal expansion, several parameters of neoplastic transformation were assayed. Low percentages of cells in T antigen-positive populations were anchorage independent or capable of forming colonies in 1% fetal bovine serum. The T antigen-positive clones generally exhibited an extended lifespan in culture but rarely became immortalized. Large numbers of dead cells were continually generated in all T antigen-positive, pre-crisis populations. Ninety-nine percent of all T antigen-positive cells had numerical or structural chromosome aberrations. Control cells that received the neo gene did not have an extended life span, did not have noticeable numbers of dead cells, and did not exhibit karyotype instability. We suggest that the role of T antigen protein in the transformation process is to generate genetic hypervariability, leading to various consequences including neoplastic transformation and cell death.

Antigens, Viral, Tumor↗

PubMed2006

[Differentially expressed genes between a fertile patient and an infertile patient in a large Chinese androgen insensitivity syndrome pedigree].

OBJECTIVE: To screen and identify differentially expressed genes between a fertile patient and another infertile patient who belonged to a large Chinese pedigree affected with androgen insensitivity syndrome (AIS). METHODS: We constructed the forward and reversed subtracted libraries using genital skin fibroblasts (GSF), which were obtained from the fertile patient MJ and infertile patient ZGJ, as tester respectively. Candidate clones were screened with colony in situ hybridization, dot blot, and Southern blot analysis step by step and conformed with Northern blot analysis. The potential positive clones were sequenced and the homology of the sequences was analyzed. RESULTS: The forward and reversed subtracted libraries containing differentially expressed pattern of two GSF cell lines were constructed. Two positive clones identified by Northern blot were obtained in the reversed subtracted library. Eleven candidate clones from the two libraries that failed to hybridize with both RNA populations were obtained simultaneously, which might represent differentially expressed low abundance transcripts. Sequencing results and homology analysis demonstrated that the two positive clones were significantly homologous with the genes of autotaxin-t and calcium binding protein calcyclin (S100A6), respectively. CONCLUSIONS: Two positive clones and eleven clones showing no hybridization signals may represent differentially expressed genes between the two GSFs. This finding may be useful to elucidate the molecular mechanisms leading to phenotypic variation and preserved fertility of the AIS pedigree.

Androgen-Insensitivity Syndrome↗

PubMed2003

[Construction of plant expressive vector of human beta-defensin-2 gene].

OBJECTIVE: Several evidences suggested that transgenic plants would be a facile and economic bioreactor for large-scale production of industrial and pharmaceutical recombinant proteins. This study is made in an attempt to establish plant bioreactor for expression of recombinant hBD-2. METHODS: Recombinant hBD-2 gene with C terminal of bi-tags of myc and 6xHis was inserted into a plant expressive vector-pCAMBIA1304, which closely located the down-stream of CaMV35S promoter. Agrobacterium tumefaciens LBA4404 was transformed with the recombinant plant expressive vector: rpCAMBIA1304/hBD-2/His. The positive clones of LBA4404 transformed by rpCAMBIA1304/hBD-2/His were selected on a culture plate containing kanamycin. The callus tissues were transfected by positive clones of LBA4404, and positive callus were examined by using the resistant selection of hygromycin gene. RESULTS: The evidences of enzyme digestion, PCR and sequence analysis confirmed that recombinant hBD-2 gene with C terminal of bi-tags of myc and 6xHis was correctly inserted into pCAMBIA1304 and was located between CaMV35S promoter and Nos terminal cordon to construct recombinant plant expressive vector: rpCAMBIA1304/hBD-2/His, thus indicating that rpCAMBIA1304/hBD-2/His has successfully transformed Agrobacterium tumefaciens LBA4404 and positive clones have been isolated. The results from resistant selection of hygromycin gene showed that rpCAMBIA1304/hBD-2/His has been transferred into the callus of wheat, and the differentiation of callus tissue under selective pressure of hygromycin is carried out continually. CONCLUSION: The above data suggest that the technique of transgenic plant is workable for the production of recombinant hBD-2.

Base Sequence↗

PubMed1990

Identification of four subsets of human CD3-CD16+ natural killer (NK) cells by the expression of clonally distributed functional surface molecules: correlation between subset assignment of NK clones and ability to mediate specific alloantigen recognition.

In previous studies we identified a surface molecule (termed GL183) capable of mediating cell activation and selectively expressed by a subset of human CD3-CD16+ natural killer (NK) cells. In this study we analyzed whether other subset-specific functional molecules were expressed in GL183- NK cells. To this end, mice were immunized with the PE29 (CD3-CD16+GL183-) NK clone. Monoclonal antibodies (mAbs) were selected by screening the hybridoma supernatants for their ability to trigger the cytolytic activity of clone PE29 against the human myelomonocytic leukemia U937. The EB6 mAb (IgG1) triggered the PE29 clone, but not a GL183+ clone used as a control. EB6+ cells ranged between 1 and 13% of peripheral blood lymphocytes and were largely included in the CD3-CD16+CD56+ cell populations (only less than 2% of EB6+ cells were CD3+). Analysis of resting or activated CD3-CD16+ populations, or clones for the expression of EB6 or GL183 mAbs, allowed us to identify four distinct, phenotypically stable, NK subsets (EB6+GL183-; EB6+GL183+; EB6-GL183+; EB6-GL183-). Similar to GL183 mAb, the EB6 mAb selectively triggered the NK subset expressing the corresponding surface antigen to lyse human tumor cell lines including U937, IGROV-I, M14, and A549. In addition, EB6 mAb sharply inhibited the cytolytic activity of EB6+ clones against P815, M12, and P3U1 murine target cells. In EB6+GL183+ ("double-positive") clones both EB6 and GL183 mAb inhibited the redirected killing of P815 cells induced by anti-CD16, anti-CD2 mAbs and phytohemagglutinin (PHA). Similar to GL183 molecules, molecules precipitated by EB6 mAb were represented by either single 58-kD chain or double chains of 55 and 58 kD (with no detectable differences in EB6+GL183- or EB6+GL183+ clones). In sequential immunoprecipitation experiments using the double-positive clones CEG52 and CA25.50, preclearing of cell lysates with EB6 or GL183 mAb removed only EB6 or GL183 molecules, respectively, thus indicating that the two antigenic determinants are carried by two distinct molecules. Peptide map analysis indicated that EB6 (or GL183) molecules precipitated from double-positive clones were identical to the corresponding molecules isolated from single-positive ones. On the other hand, comparison of the EB6 and GL183 maps revealed peptides that were unique to each molecule, although most of the major peptides migrated to identical positions. We further investigated whether correlation existed between the phenotypic assignment of NK clones and their ability to mediate specific lysis of normal allogeneic cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗