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J A Lenstra

Publications and source records attributed to J A Lenstra.

At least 55 records · Page 3Linked to original sources
PubMed1995

Rapid species identification in meat by using satellite DNA probes.

A fast procedure for species identification in heated meat is described. Deoxyribonucleic acid (DNA) was isolated from meat samples by an alkaline extraction method and hybridized to a conjugate of a specific oligonucleotide and alkaline phosphatase. The oligonucleotide probes are based on satellite DNA, tandem-repeated sequences, which are highly specific for species. Probes are developed for the identification of meat from cattle, sheep/goat, horse, deer, pig, chicken and turkey. Differentiation between closely related species like chicken and turkey is possible. Admixtures of 1-5% of meat of one species in another could be detected. The complete assay of up to 50 samples takes 4 h. Heated meat samples could be analysed.

Animals↗
PubMed1995

Evolution and recombination of bovine DNA repeats.

The history of the abundant repeat elements in the bovine genome has been studied by comparative hybridization and PCR. The Bov-A and Bov-B SINE elements both emerged just after the divergence of the Camelidae and the true ruminants. A 31-bp subrepeat motif in satellites of the Bovidae species cattle, sheep, and goat is also present in Cervidae (deer) and apparently predates the Bovidae. However, the other components of the bovine satellites were amplified after the divergence of the cattle and the Caprinae (sheep and goat). A 23-bp motif, which as subrepeat of two major satellites occupies 5% of the cattle genome, emerged only after the split of the water buffalo and other cattle species. During the evolution of the Bovidae the satellite repeat units were shaped by recombination events involving subrepeats, other satellite components, and SINE elements. Differences in restriction sites of homologous satellites indicate a continuing rapid horizontal spread of new sequence variants.

Animals↗
PubMed1995

The applications of the polymerase chain reaction in the life sciences.

The polymerase chain reaction (PCR) allows the in vitro amplification of DNA fragments starting with tiny amounts of biological sample and oligonucleotide primers derived from sequence data. Since the technique is fast and easy, PCR has taken the DNA-technology to the routine laboratoria. We present a survey of the following applications of PCR: 1) The amplification of gene fragments as fast alternative of cloning. 2) The modification of DNA fragments. 3) The sensitive detection of pathogenic microorganisms, if desired followed by an accurate genotyping. 4) DNA analysis of arachaeological specimens. 5) The detection of mutations relevant for inherited diseases, malignant transformation or tissue typing. 6) The analysis of genetic markers for forensic applications, for paternity testing and for the mapping of hereditary traits. 7) The species-specific amplification of DNA segments between interspersed-repeat elements. 8) The study of gene expression.

Animals↗
PubMed1995

Optimization of the PCR test for the mutation causing bovine leukocyte adhesion deficiency.

The recent emergence of the bovine leukocyte adhesion deficiency (BLAD) demonstrated the risks of narrowing the genetic basis of a population. About 6% of the Holstein-Friesian cattle now descends from one bull who was a heterozygous BLAD carrier. Crossing his descendants resulted in the birth of homozygous BLAD calves with a life expectancy of < 1 year. The BLAD syndrome is caused by a point mutation in the gene coding for CD18, a subunit of the beta 2 integrins on the surface of leukocytes. By using a PCR-RFLP test, large numbers of cattle are now being screened in several countries to eradicate the mutant allele. We describe an optimization of the PCR primer set that has led to an improvement of the test.

Animals↗
PubMed1994

The human T-cell receptor TCRAC/TCRDC (C alpha/C delta) region: organization, sequence, and evolution of 97.6 kb of DNA.

We sequenced and analyzed 97.6 kb of new DNA sequence containing the human TCRAC (C alpha) and TCRDC (C delta) genes as well as the TCRDV3 (V delta 3) and 61 different TCRAJ (J alpha) gene segments and compared its organization and structure to the previously described mouse T-cell receptor TCRAC/TCRDC (C alpha/C delta) region. A comprehensive nomenclature, consistent with the IUIS nomenclature committee recommendations, for both human and mouse TCRAJ gene segments is presented. In the human sequence, we identified 20 new TCRAJ gene segments and obtained the germline sequence for 23 additional TCRAJ gene segments known from cDNA clones. Using the sequence data obtained from the human TCRAC/TCRDC region, we have extended a polymerase chain reaction-based assay to test for the expression of the individual TCRAJ gene segments. At least five TCRAJ pseudogene segments were identified by sequence criteria. Like the murine TCRAC/TCRDC sequence, this sequence contains a high level of coding sequence, with over 6.6% of the total sequence being transcribed. Comparison of the human sequence with the previously reported mouse DNA sequence reveals homologous counterparts for the variable and joining (J) gene segments and both constant genes. Eleven new J pseudogene segments have been identified in the mouse TCRAC/TCRDC sequence through the use of human and mouse sequence comparisons. In terms of structure and organization, this region of the human and mouse genome appears to be remarkably conserved.

Amino Acid Sequence↗
PubMed1993

Organization of the murine T-cell receptor gamma locus.

Murine T cells carry either of two antigen receptors on their surface: alpha beta or gamma delta T-cell receptors (TCR). The function of gamma delta T cells is not well understood. In this population, subsets exist with tissue-specific localization, with invariant variable regions, and with specificity for self antigens. We have analyzed the murine TCR gamma locus by field inversion gel electrophoresis and cosmid cloning. The structure of the complete TCR gamma locus, the first complete physical map of any mouse TCR locus, is reported here. The locus spans 205 kb and consists of four clusters of genes and gene segments. Each cluster contains one or more variable elements, one joining element, and one constant element. We demonstrate that the C gamma 4 gene is distinguished from the other C gamma genes in that it has an additional hinge-encoding exon. New enhancer-like elements are identified in two of the clusters, downstream from the C gamma genes. The most upstream cluster has four V elements and resembles the human TCR gamma locus. The four clusters probably arose via duplications.

Animals↗
PubMed1993

Rapid evolution of horse satellite DNA.

The major satellite of the horse genome consists of about 1 million copies of a 221-bp tandem repeat unit. By fluorescence in situ hybridization it has been localized in the centromeres of 58 of the 64 horse chromosomes. The donkey genome contains a similar but not identical satellite. Strikingly, the equine repeat did not hybridize to DNA of the Grevy zebra, despite the divergence of the horse and zebra only 3 to 5 million years ago and the ability of these species to crossbreed. The evolution of satellite DNA in the Equidae is more rapid than that in other mammalian families, which may be explained by their rapid karyotypic evolution.

Animals↗
PubMed1993

Short interspersed nuclear element (SINE) sequences of the Bovidae.

DNA sequences from Bovidae (cattle, goats and sheep) in the EMBL nucleotide database contain several short interspersed repeated sequences (SINEs). Three different SINEs have been found: Bov-A2, containing two 115-bp A elements; Bov-tA, a tRNA pseudogene coupled to an A element; and Bov-B of 560 bp or less and partially homologous to the A element. Bov-A2, Bov-tA and Bov-B occupy about 1.8%, 1.6% and 0.5%, respectively, of the bovine genome as represented in the nucleotide database. Apart from a tRNA-like sequence in both Bov-tA and the porcine SINEs, there was no similarity with the porcine SINEs. Apparently, the artiodactyle SINEs were established after the divergence leading to the Suidae and Bovidae but before the radiation within these families. Oligonucleotides were designed for a specific amplification of DNA from Bovidae.

Animals↗
PubMed1992

Isolation of sequences from a random-sequence expression library that mimic viral epitopes.

We describe the use of random peptide sequences for the mapping of antigenic determinants. An oligonucleotide with a completely degenerate sequence of 17 or 23 nucleotides was inserted into a bacterial expression vector. This resulted in an expression library producing random hexa- or octapeptides attached to a beta-galactosidase hybrid protein. Mimotopes, or antigenic sequences that mimic an epitope, were selected by immunoscreening of colonies with monoclonal antibodies, which were specific for antigenic sites on the spike protein of the coronavirus transmissible gastroenteritis virus. We report one mimotope for antigenic site II, eight for site III and one for site IV. The site III and site IV mimotopes were closely similar to the corresponding linear epitopes, localized previously in the amino acid sequence of the S protein. An alignment of the site II mimotope and the sequence of the S protein around Trp97, which is substituted in escape mutants, suggests that this mimotope mimics a conformational epitope located around residues 97-103. Applications of mimotopes to epitope mapping, serodiagnosis and vaccine development are discussed.

Amino Acid Sequence↗
PubMed1991

Conserved nucleotide sequences at the 5' end of T cell receptor variable genes facilitate polymerase chain reaction amplification.

Alignment of all available nucleotide sequences of mouse and rat alpha/beta T cell receptor (TcR) variable (V) regions revealed the presence of relatively conserved sequences at the 5' end of the V gene segments. Based on these conserved sequences, degenerate primers were developed for use in the polymerase chain reaction (PCR). The degenerate primers developed on the basis of the conserved sequences at the 5' end of rat and mouse V gene segments are expected to enable the amplification of all mouse and rat TcR alpha/beta chain V regions. To test their applicability, the primers were used for the amplification of the V region of the TcR alpha/beta expressed by rat T cell lines. After amplification, the TcR V regions expressed were cloned and sequenced. The Z1a T cell line was shown to use the same TcR V gene segments (V alpha 2 and V beta 8.2), as most other experimental allergic encephalomyelitis associated T cell lines, but had different D and J segments. In spite of these differences at the nucleotide level, a remarkable conservation of the amino acid sequence at the V beta D beta J beta junction was found. Alignment of a large number of human V alpha and V beta gene segments revealed the presence of similarly conserved sequences. Degenerate primers based on these conserved sequences enabled the amplification of TcR V regions of human T cell lines.

Amino Acid Sequence↗
PubMed1991

Residues involved in the antigenic sites of transmissible gastroenteritis coronavirus S glycoprotein.

The S glycoprotein of transmissible gastroenteritis virus (TGEV) has been shown to contain four major antigenic sites (A, B, C, and D). Site A is the main inducer of neutralizing antibodies and has been previously subdivided into the three subsites Aa, Ab, and Ac. The residues that contribute to these sites were localized by sequence analysis of 21 mutants that escaped neutralization or binding by TGEV-specific monoclonal antibodies (MAbs), and by epitope scanning (PEPSCAN). Site A contains the residues 538, 591, and 543, which are essential in the formation of subsites Aa, Ab, and Ac, respectively. In addition, mar mutant 1B.H6 with residue 586 changed had partially altered both subsite Aa and Ab, indicating that these subsites overlap in residue 586; i.e. this residue also is part of site A. The peptide 537-MKSGYGQPIA-547 represents, at least partially, subsite Ac which is highly conserved among coronaviruses. This site is relevant for diagnosis and could be of interest for protection. Other residues contribute to site B (residues 97 and 144), site C (residues 50 and 51), and site D (residue 385). The location of site D is in agreement with PEPSCAN results. Site C can be represented by the peptide 48-P-P/S-N-S-D/E-52 but is not exposed on the surface of native virus. Its accessibility can be modulated by treatment at pH greater than 11 (at 4 degrees) and temperatures greater than 45 degrees. Sites A and B are fully dependent on glycosylation for proper folding, while sites C and D are fully or partially independent of glycosylation, respectively. Once the S glycoprotein has been assembled into the virion, the carbohydrate moiety is not essential for the antigenic sites.

Amino Acid Sequence↗
PubMed1991

Immunogenicity of peptides simulating a neutralization epitope of transmissible gastroenteritis virus.

Previously, an epitope recognized by a set of neutralizing monoclonal antibodies directed against the S protein of transmissible gastroenteritis has been identified. This neutralization epitope can be simulated by a single peptide combining residues 380 to 387 and 1176 to 1184 of the S protein; this combination peptide (SFFSYGEI-QLAKDKVNE) was more antigenic than it single constituents. Here we describe the immunogenicity of this combination peptide, in comparison with monomer and tandem peptides of both constituents, and with a cyclic peptide consisting of residues 373 to 398. All antisera, raised in rabbits, bound to the peptide used as immunogen. Only sera that recognized the residues 380 to 387 bound to whole virus. Three of the four antisera with the highest binding titers to whole virus also had neutralization activity. Analysis of the fine-specificity of the antisera with PEPSCAN peptides indicated that the spectrum of antibodies induced by the 380 to 387 sequence depended on the presentation of this sequence in a peptide to the immune system. The nonbinding and nonneutralizing anti-(380 to 387)-sera appeared to contain a limited spectrum of antipeptide antibodies. Furthermore, the lack of neutralization of the antiserum against the combination peptide could be explained by the immunodominance in rabbits of the 1176 to 1184 sequence over the 380 to 387 sequence. These findings demonstrate a few fundamental problems of simulating discontinuous epitopes by single synthetic peptides.

Amino Acid Sequence↗
PubMed1991

The use of peptides to reconstruct conformational determinants; a brief review.

In many biological processes, defined regions of proteins are involved in selective recognition. These regions can often be mimicked with peptides and are the main targets for vaccine and drug development. The authors review the use of peptides, to define and ultimately mimic defined protein regions of interest. Especially the role of the Pepscan method is emphasized. This method has been proven to be a useful and fast tool in defining protein regions of interest. It is based on the simultaneously synthesis of multiple peptides coupled to solid supports. Hundreds of peptides can be produced and tested in a relatively short period of time. With the construction of random peptide libraries in recombinant DNA systems, it is now even possible to screen for peptidic determinants without the requirement of preliminary knowledge of primary structure. Having this information, the affinity of peptides can be further enhanced with the Pepscan approach. The power of this approach will be illustrated with results from studies on the development of synthetic vaccines and hormone analogues.

Biological Assay↗
PubMed1990

Mapping of viral epitopes with prokaryotic expression products.

Several systems are available for the expression of foreign gene sequences in Escherichia coli. We describe the use of prokaryotic expression products of viral gene fragments in order to identify the regions that specify the binding sites of antibodies. This approach is particularly successful if the antigenicity does not depend on the native protein, but only on the amino acid sequence, i.e., if the epitope is sequential. Combining prokaryotic expression with the use of synthetic peptides often permits a fast and accurate mapping of an epitope. The occurrence of immunodominant sequential epitopes on the surfaces of viruses seems to be a widespread phenomenon.

Antigens, Viral↗
PubMed1990

Localization of antigenic sites of the E2 glycoprotein of transmissible gastroenteritis coronavirus.

Four antigenic sites of the E2 glycoprotein of transmissible gastroenteritis virus were defined by competitive radioimmunoassays of monoclonal antibodies (MAbs). Here, we describe the localization of these sites by testing the antigenicity of protein fragments and prokaryotic expression products of E2 gene fragments, and by sequencing of MAb-resistant (mar) mutants. Partial proteolysis of purified E2 protein allowed the isolation of a 28K fragment recognized by both site A- and site C-specific MAbs. An antiserum against this fragment bound to a synthetic peptide containing residues 1 to 18 and to an expression product containing residues 1 to 325. The same expression product was recognized by site C-specific MAbs. These data indicate that residues within the sequence 1 to 325 contribute to site C and possibly also to site A. Sequencing of mar mutants that escaped neutralization by site A-specific MAbs indicated that residues 538 and 543 also belong to site A. The binding of site-specific MAbs to expression products led directly to the localization of sites B and D, between residues 1 to 325 and 379 to 529, respectively. The first 37% of the polypeptide chain of E2 appears to be more immunogenic than the rest of the sequence.

Amino Acid Sequence↗