Showing papers on "Cloning published in 1996"

Cell cycle co-ordination in embryo cloning by nuclear transfer

Abstract: Exciting new opportunities in embryo cloning have been made possible by recent studies on the interaction of the donor nucleus with the recipient cytoplasm after embryo reconstruction. This article reviews information regarding the co-ordination of nuclear and cytoplasmic events during embryo reconstruction, in particular the direct and indirect effects of maturation/ meiosis/mitosis-promoting factor (MPF), upon the transferred nucleus. This will be discussed in relation to DNA replication, the maintenance of correct ploidy, the occurrence of chromosomal abnormalities and development of reconstructed embryos. Although this review is primarily concerned with the reconstruction of mammalian embryos, specific examples from amphibians will also be cited.

Molecular Cloning and Functional Analysis of Sialyltransferases

Abstract: To elucidate the regulatory mechanism for carbohydrate expression and to understand the meaning of the carbohydrate-structural diversity, we started to clone sialyltransferase (ST) genes based on two different strategies, i.e. expression and homology cloning. So far, 13 STs have been cloned in our laboratory, 7 of which turned out to be new ones. The primary enzyme structures deduced from all the cloned ST genes suggest a putative domain structure with a type II transmembrane topology. There are no significant amino acid sequence similarities among these cloned STs, except for in two sialyl motifs, L and S, which are proposed to be the CMP-sialic acid recognition and/or catalytic sites. Northern blot analysis revealed the developmental stage-dependent and/or tissue-specific expression of most of the cloned STs. The cloned STs are classified into four families according to the carbohydrate linkages they synthesize, i.e. the ST3Gal-, ST6Gal-, ST6GalNAc-, and ST8Sia-families. Generally, enzymes in these families exhibit strong activity toward certain acceptor groups but show very weak activity toward other acceptor groups, and the substrate specificities of the enzymes overlap one another, as indicated by in vitro experiments. Enzymes in the ST3Gal-family are expressed mainly in a tissue-specific manner. However, those in the ST6GalNAc- and ST8Sia-families are expressed in a tissue-as well as developmental stage-specific manner. In vivo conditions are supposed to be more complex. Therefore, it is quite important to examine their substrate specificities in vivo and the mechanism of their expression to elucidate the physiological role of each enzyme and the meaning of the diversity in carbohydrate structure. Using cloned cDNAs and expressed enzymes, we have been studying how sialylcarbohydrate expression is regulated and what the functions of sialylcarbohydrate chains are. Recently, we found that transfection of the GD3 synthase, an alpha 2,8-ST (ST8Sia I), gene triggers cholinergic neuritogenesis in Neuro2a cells through the de novo expression of GD3, suggesting that the GD3 synthase gene behaves as a neural differentiation inducer.

Insertional mutagenesis and rapid cloning of essential genes in zebrafish

Abstract: Large-scale chemical mutagenesis screens in zebrafish have led to the isolation of thousands of lethal mutations in genes that are essential for embryonic development. However, the cloning of these mutated genes is difficult at present as it requires positional cloning methods. In Drosophila, chemical mutagenesis screens were complemented with P-element insertional mutagenesis which facilitated the cloning of many genes that had been identified by chemical lesions. To facilitate the cloning of vertebrate genes that are important during embryogenesis, we have developed an insertional mutagenesis strategy in zebrafish using a retroviral vector. Here, in a pilot screen of 217 proviral insertions, we obtained three insertional mutants with embryonic lethal phenotypes, and identified two of the disrupted genes. One of these, no arches, is essential for normal pharyngeal arch development, and is homologous to the recently characterized Drosophila zinc-finger gene, clipper, which encodes a novel type of ribonuclease. As it is easy to generate tens to hundreds of thousands of proviral transgenes in zebrafish, it should now be possible to use this screening method to mutate and then rapidly clone a large number of genes affecting vertebrate developmental and cellular processes.

The cloning and clinical implications of HGV and HGBV-C.

Abstract: The cloning of the hepatitis C virus (HCV)1 established that important human pathogens, which could not be seen microscopically, grown in cell culture, or detected serologically, could nonetheless ...

Recombinational cloning using engineered recombination sites

Abstract: Recombinational cloning is provided by the use of nucleic acids, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins to provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s).

Cloning and characterization of KAP2 : a novel kinesin superfamily associated protein of KIF3A/3B

Abstract: We previously reported that KIF3A and KIF3B form a heterodimer that functions as a microtubule-based fast anterograde translocator of membranous organelles. We have also shown that this KIF3A/3B forms a complex with other associated polypeptides, named kinesin superfamily-associated protein 3 (KAP3). In the present study, we purified KAP3 protein by immunoprecipitation using anti-KIF3B antibody from mouse testis. Microsequencing was carried out, and we cloned the full-length KAP3 cDNA from a mouse brain cDNA library. Two isoforms of KAP3 exist [KAP3A (793 aa) and KAP3B (772 aa)], generated by alternative splicing in the carboxyl terminus region. Their amino acid sequences have no homology with those of any other known proteins, and prediction of their secondary structure indicated that almost the entire KAP3 molecule is alpha-helical. We produced recombinant KAP3 and KIF3A/3B using a baculovirus-Sf9 expression system. A reconstruction study in Sf9 cells revealed that KAP3 is a globular protein that binds to the tail domain of KIF3A/3B. The immunolocalization pattern of KAP3 was similar to that of KIF3A/3B in nerve cells. In addition, we found that KAP3 does not affect the motor activity of KIF3A/3B. KAP3 was associated with a membrane-bound form of KIF3A/3B in a fractional immunoprecipitation experiment, and since the KIF3 complex was found to bind to membranous organelles in an EM study, KAP3 may regulate membrane binding of the KIF3 complex.

Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination

Abstract: DNA molecules undergoing transformation into yeast are highly recombinogenic, even when diverged. We reasoned that transformation-associated recombination (TAR) could be employed to clone large DNAs containing repeat sequences, thereby eliminating the need for in vitro enzymatic reactions such as restriction and ligation and reducing the amount of DNA handling. Gently isolated human DNA was transformed directly into yeast spheroplasts along with two genetically marked (M1 and M2) linearized vectors that contained a human Alu sequence at one end and a telomere sequence at the other end (Alu-CEN-M1-TEL and Alu-M2-TEL). Nearly all the M1-selected transformants had yeast artificial chromosomes (YACs) containing human DNA inserts that varied in size from 70 kb to > 600 kb. Approximately half of these had also acquired the unselected M2 marker. The mitotic segregational stability of YACs generated from one (M1) or two (M1 and M2) vector(s) was comparable, suggesting de novo generation of telomeric ends. Since no YACs were isolated when rodent DNAs or a vector lacking an Alu sequence was used, the YACs were most likely the consequence of TAR between the repeat elements on the vector(s) and the human DNA. Using the BLUR13 Alu-containing vector, we demonstrated that human DNA could be efficiently cloned from mouse cells that contained a single human chromosome 16. The distribution of cloned DNAs on chromosome 16 was determined by fluorescence in situ hybridization. We propose that TAR cloning can provide an efficient means for generating YACs from specific chromosomes and subchromosome fragments and that TAR cloning may be useful for isolating families of genes and specific genes from total genome DNA.

Cloning and tissue distribution of the human P2Y1 receptor

Abstract: Sets of degenerate oligonucleotide primers synthesized on the basis of the best conserved regions of the chick brain P2Y/P2Y1 and the murine neuroblastoma P2U/P2Y2 receptors were used in polymerase chain reaction experiments on human genomic DNA. An amplified fragment of 712 base pairs was then used as a probe to screen a human genomic DNA library. Several clones were isolated and sequencing revealed an intronless 1122 base pair open reading frame. The corresponding amino acid sequence revealed 83% identity with the chick brain P2Y1 receptor and 34% with the murine neuroblastoma P2Y2 receptor. In COS-7 cells transfected with the coding sequence inserted into the pcDNA3 expression vector, 2-methylthioATP and ATP produced a strong stimulation of inositol phosphates, a typical response of a P2Y1 receptor. Northern blot analysis detected a 6.7 kilobase messenger RNA in most human tissues, the strongest signals being observed in prostate and ovary.

Phage display shot-gun cloning of ligand-binding domains of prokaryotic receptors approaches 100% correct clones.

Abstract: We recently presented an application of the phage display technique enabling cloning of DNA encoding ligand-binding domain(s) of prokaryotic receptors directly from chromosomal DNA. Here we show that the use of a gene VIII-based, instead of a gene III-based, phagemid vector system results in a much more efficient selection for phage displaying a binding capacity. A phagemid library was made by insertion of randomly fragmented chromosomal DNA from Staphylococcus aureus strain 8325-4 into gene VIII in the constructed phagemid vector pG8H6. The library, which in theory should express parts of all proteins encoded by the bacterial genome, was affinity panned against the ligands IgG, fibronectin and fibrinogen, respectively. After a second panning against the same ligand, a significant increase in the number of eluted phagemid particles was observed, and 75%-100% of randomly picked clones contained inserts derived from genes encoding proteins with a binding affinity for the respective ligand. The results show that this technique can be used for cloning prokaryotic receptor genes without any prior knowledge of the receptor, thus eliminating the need for probes in the identification of receptor genes.

Cloning of the mouse fusin gene, homologue to a human HIV-1 co-factor

Abstract: Previous studies have demonstrated that mouse cells do not become infected with HIV-1 despite transfection with human CD4. Recently, a human protein termed "fusin" with characteristics of a seven-transmembrane-spanning receptor was found to be a co-factor required for the entry and fusion of HIV-1 with human CD4-bearing lymphocytes. Thus, cloning of the murine homologue of the human fusin (also termed CXCR-4) gene could provide an important comparative tool for identification of the structures crucial for fusin function. Using degenerate PCR, the mouse homologue of human fusin was cloned from a peritoneal exudate cell cDNA library. The predicted amino acid sequence is 91% identical to human fusin. Twenty-eight of the 37 amino acid differences between mouse and human fusin are located in the ectodomains, suggesting that the intracytoplasmic components that mediate G protein binding and signaling are highly conserved. Northern blot analysis showed a message of 2.2 kb in thymus, spleen, neutrophils, and primary astrocyte cultures. Lymphoid and monocyte cell lines also expressed message for fusin. The coding regions of most chemokine receptors lack introns. In contrast, cloning of genomic DNA for mouse fusin revealed the presence of a 2.3-Kb intron separating the first seven amino acids from the remaining 352 residues. Therefore, the mouse fusin gene has a unique genomic organization compared with other chemokine receptors.

Cloning, characterization, and steroid-dependent posttranscriptional processing of RUSH-1 alpha and beta, two uteroglobin promoter-binding proteins.

Abstract: We previously used gel shift assays, Southwestern blots, and UV cross-linking to identify four proteins that bind to the 203-bp 5'-flanking region (-194/ +9) of the rabbit uteroglobin gene. Here we report cloning, by recognition site screening, the cDNAs for two of the uteroglobin promoter-binding proteins (95 kDa and 113 kDa). Their presumptive nucleotide-binding motifs share 61% identity with the SWI2/SNF2 helicase superfamily, and each protein has the novel C3HC4 (RING) zinc-finger signature near its C terminus. RUSH-1 alpha, the 113-kDa protein, is the rabbit homolog of human HIP116, a protein that binds to the human immunodeficiency virus-1 promoter. RUSH-1 beta is a 95-kDa truncated version of RUSH-1 alpha that results from alternative splicing of a 57-bp exon as confirmed by genomic cloning. Northern analysis showed mRNA expression (5.2 kb) was induced by progesterone +/- PRL and antagonized by estrogen. However, because the two proteins result from alternative splicing of a 57-bp exon, the small d...

A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing.

Abstract: We describe here the cloning and sequencing of a new auxiliary gene identified by Tn551 insertional mutagenesis of the highly and homogeneously methicillin-resistant Staphylococcus aureus ...

Highly selective isolation of human DNAs from rodent–human hybrid cells as circular yeast artificial chromosomes by transformation-associated recombination cloning

Abstract: Transformation-associated recombination (TAR) can be exploited in yeast to clone human DNAs. TAR cloning was previously accomplished using one or two telomere-containing vectors with a common human repeat(s) that could recombine with human DNA during transformation to generate yeast artificial chromosomes (YACs). On basis of the proposal that broken DNA ends are more recombinogenic than internal sequences, we have investigated if TAR cloning could be applied to the generation of circular YACs by using a single centromere vector containing various human repeats at opposite ends. Transformation with these vectors along with human DNA led to the efficient isolation of circular YACs with a mean size of approximately 150 kb. The circular YACs are stable and they can be easily separated from yeast chromosomes or moved into bacterial cells if the TAR vector contains an Escherichia coli F-factor cassette. More importantly, circular TAR cloning enabled the selective isolation of human DNAs from monochromosomal human-rodent hybrid cell lines. Although < 2% of the DNA in the hybrid cells was human, as much as 80% of transformants had human DNA YACs when a TAR cloning vector contained Alu repeats. The level of enrichment of human DNA was nearly 3000-fold. A comparable level of enrichment was demonstrated with DNA isolated from a radiation hybrid cell line containing only 5 Mb of human DNA. A high selectivity of human DNA cloning was also observed for linear TAR cloning with two telomere vectors. No human-rodent chimeras were detected among YACs generated by TAR cloning. The results with a circular TAR cloning vector or two vectors differed from results with a single-telomere vector in that the latter often resulted in a series of terminal deletions in linear YACs. This could provide a means for physical mapping of cloned material.

Cloning and Characterization of a cDNA Encoding the Collagen-Binding Stress Protein hsp47 in Zebrafish

Abstract: Hsp47 is a major stress-inducible protein that is localized to the endoplasmic reticulum of avian and mammalian cells and is thought to act as a molecular chaperone specific for the processing of procollagen. Although hsp47 is coordinately expressed together with several collagen types, and vertebrate embryos are known to express collagen genes in complex spatial and temporal patterns, limited information is available regarding the function or regulation of hsp47 during early embryonic development. We have initiated an examination of hsp47 in the zebrafish, Danio rerio, which offers a number of features that make it attractive as a model developmental system with which to examine the expression and function of hsp47. A polymerase chain reaction (PCR)-based cloning strategy was used to isolate a hsp47 cDNA from an embryonic zebrafish cDNA library. The deduced translation product of the cDNA is a 404-amino-acid polypeptide that is 72% identical to chicken, 64% identical to mouse and rat, and 69% identical to human hsp47. The protein contains a typical hydrophobic signal sequence, an RDEL endoplasmic reticulum retention signal, and a serine protease inhibitor signature sequence, all of which are characteristic of hsp47 in higher vertebrates. Thus, it is likely that hsp47 in zebrafish is also localized to the endoplasmic reticulum and may play a similar role to its counterpart in higher vertebrates. Northern blot analysis revealed that the hsp47 gene is expressed at relatively low levels in embryos during normal development but is strongly induced following exposure to heat shock at the gastrula, midsomitogenesis, 2-day, and 3-day larval stages. The level of induction was much higher than has previously been reported in chicken and mouse cells.

Cloning, expression, and uses of human lactoferrin

Abstract: Disclosed is human lactoferrin expressed using recombinant DNA, its method of production and purification.

Rapid cloning of any rearranged mouse immunoglobulin variable genes

Abstract: Immunoglobulins (Ig) have been the focus of extensive study for several decades and have become an important research area for immunologists and molecular biologists. The use of polymerase chain reaction (PCR) technology has accelerated the cloning, sequencing, and characterization of genes of the immune system. However, cloning and sequencing the Ig variable (V) genes using the PCR technology has been a challenging task, primarily due to the very diverse nature of Ig V region genes. We have developed a simple, rapid, and reproducible PCR-based technique to clone any rearranged mouse Ig heavy or light chain genes. A close examination of all Ig heavy and light chain V gene families has resulted in the design of 5' and 3' universal primers from regions that are highly conserved across all heavy or light chain V gene families, and the joining or constant regions, respectively. We present our strategy for designing universal primers for Ig V gene families. These primers were able to rapidly amplify the rearranged Ig V genes, belonging to diverse Ig V gene families from very different cell lines, i.e., J558, MOPC-21, 36-60, and a chicken ovalbumin specific B-cell hybridoma. In addition, the present study provides the complete alignment of nucleotide sequences of all heavy and light chain variable gene families. This powerful method of cloning Ig V genes, therefore, allows rapid and precise analysis of B-cell hybridomas, B-cell repertoire, and B-cell ontogeny.

Cloning and characterization of the first two genes of the non-oxidative part of the saccharomyces cerevisiae pentose-phosphate pathway

Abstract: We have cloned and characterized the two remaining unknown genes of the non-oxidative part of the pentose-phosphate pathway of Saccharomyces cerevisiae encoding the enzymes D-ribulose-5-phosphate 3-epimerase (Rpe1p) and D-ribose-5-phosphate ketol-isomerase (Rki1p). Rpe1p has an unexpected high specific activity of 2148 mU x (mg protein)-1 in crude extracts. Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose. Unexpectedly, haploid rki1 deletion mutants are not viable. Functional expression of RKI1 was demonstrated following an increase of gene dosage in the haploid rki1 deletion mutant, which restored viability and specific D-ribose-5-phosphate ketol-isomerase activity. Both enzymes show high similarity to the deduced protein sequences of various open reading frames, expressed sequence tags or cDNAs from different organisms.