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Biomedical subjects

L E Hood

Publications and source records attributed to L E Hood.

At least 37 records · Page 2Linked to original sources
PubMed1991

Imaging as a tool for improving length and accuracy of sequence analysis in automated fluorescence-based DNA sequencing.

A new method of signal analysis for automated fluorescence-based DNA sequencing is presented. Signal resolution is a limiting factor in obtaining accurate sequence information beyond 400-450 nucleotides per gel lane. We have developed a computer program for the imaging of DNA bands in sequencing gels. The image analysis shows that distortions in the shapes of the bands decrease resolution of peaks observed served in the standard data plots. Reconstruction of the undistorted band shape prior to signal analysis substantially improves the resolution of peaks and may improve the accuracy and length of the contiguous sequence read. Image analysis identified other factors limiting the accuracy and length of automated DNA sequence analysis and provided a tool for evaluating various remedies. Our techniques should also be applicable in other systems, for example, in gel electrophoresis of proteins and DNA restriction fragments, and in scranning densitometry.

Base Sequence↗
PubMed1991

Germline repertoire of T-cell receptor beta-chain genes in patients with insulin-dependent diabetes mellitus.

We have investigated the genotype and allelic distribution of germline restriction fragment length polymorphisms of the T-cell receptor beta chain, segment C beta, and two variable segments which are in linkage disequilibrium, V beta 8 and V beta 11, in 42 insulin-dependent diabetes mellitus (IDDM) patients and in 51 healthy blood donors used as controls. Recently, several works have reported contradictory results showing or not showing an association between polymorphic alleles of the C beta gene and diabetes type I. We found no significant differences in the allele, genotype, and haplotype distribution of the gene segments studied, between IDDM patients and control populations.

Adolescent↗
PubMed1991

The Human Genome Project: creating an infrastructure for biology and medicine.

The Human Genome Project (HGP) is an international effort to map and sequence the human genome. It combines skills from diverse fields of biological and technological research, thus establishing deeper interactions between scientific disciplines. The combination of these skills should stimulate many advances in both pure and applied fields of research and give rise to new, interdisciplinary training programs. Some critics say that the HGP will damage biomedical research; however, we argue that it will bring new funds to the field and create a large ripple effect by providing new research opportunities through its discoveries.

Chromosome Mapping↗
PubMed1990

Molecular signals for phosphatidylinositol modification of the Qa-2 antigen.

Most cell surface proteins are anchored to the cell bilayer by hydrophobic membrane-spanning domains. Recently it has been shown that a small class of molecules are attached to cell surfaces via a phosphatidylinositol moiety covalently linked to the C-terminus of the mature processed polypeptide. The molecular signals that identify a polypeptide for phosphatidylinositol (PI) attachment have not been well defined in any system, but are thought to reside in the C-terminus of the primary translation product. We report that all the signals responsible for PI anchoring of Qa-2 Ag are confined to the 36 C-terminal residues of the precursor proteins. To investigate further the features that signal cleavage and PI addition, we have studied mutants of two closely related murine class I MHC molecules: the PI-linked Ag, Q9b, from the Qa-2 Ag family, and the integral membrane transplantation antigen, H-2Ld. The addition of 15 amino acids to the three residue long cytoplasmic domain of Q9b or the mutation of Asp295 found in its C-terminal hydrophobic domain to Val converts this molecule into an integral membrane protein. However, the introduction of a short three residue cytoplasmic tail and Asp295 into the transmembrane domain of H-2Ld does not convert this molecule to a PI-linked one. The results of these analyses suggest that the PI-processing signals may depend on overall conformation, hydrophobicity, and length of the C-terminal domain of the precursor protein. In addition these data indicate that PI anchoring of class I Ag requires more than two mutational steps and may have been selected during the evolution.

Amino Acid Sequence↗
PubMed1990

Identification of cellular proteins binding to the scrapie prion protein.

The scrapie prion protein (PrPSc) is an abnormal isoform of the cellular protein PrPc. PrPSc is found only in animals with scrapie or other prion diseases. The invariable association of PrPSc with infectivity suggests that PrPSc is a component of the infectious particle. In this study, we report the identification of two proteins from hamster brain of 45 and 110 kDa (denoted PrP ligands Pli 45 and Pli 110) which were able to bind to PrP 27-30, the protease-resistant core of PrPSc on ligand blots. Pli 45 and Pli 110 also bound PrPC. Both Pli's had isoelectric points of approximately 5. The dissociation rate constant of the Pli 45/PrP 27-30 complex was 3 x 10(-6) s-1. Amino acid and protein sequence analyses were performed on purified Pli 45. Both the composition and the sequence were almost identical with those predicted for mouse glial fibrillary acidic protein (GFAP). Furthermore, antibodies to Pli 45 reacted with recombinant GFAP. The identification of proteins which interact with the PrP isoforms in normal and diseased brain may provide new insights into the function of PrPC and into the molecular mechanisms underlying prion diseases.

Amino Acid Sequence↗
PubMed1990

Covalent attachment of peptides for high sensitivity solid-phase sequence analysis.

We have developed a method for the high efficiency covalent immobilization of picomole to nanomole quantities of peptides in a form compatible with high sensitivity gas-liquid or solid-phase sequence analysis. Glass fiber filter paper was derivatized with amino-phenyltriethoxysilane and peptides were applied to circular disks cut to 1-cm diameters. Peptides were covalently immobilized on the aminophenyl-glass fiber paper through their terminal alpha-carboxyl groups and amino acid side-chain carboxyl groups by activation with the water-soluble reagent N-ethyl-N'-(3-dimethylaminopropyl)carbodiimide. Disks containing the covalently attached peptide were directly inserted into the cartridge of an automated sequenator for sequence analysis by the Edman degradation. Peptides prepared in this way could be routinely sequenced through to and including the C-terminal amino acid residue, at extraordinarily low backgrounds. The covalent immobilization of peptide fragments allowed far more flexibility in sequencing conditions, including the use of polar extraction solvents to increase the yield of phenylthiohydantoin (PTH)-His and PTH-Arg and the use of alternative Edman-type sequencing reagents with enhanced detectability, such as the chromophoric compound 4- (N,N'-dimethylamino)azobenzene-4'-isothiocyanate. The potential of this high efficiency immobilization method for contributing to the development of sequencing chemistries with enhanced sensitivity is discussed.

Amino Acid Sequence↗
PubMed1990

DNA length polymorphism 5' to the myelin basic protein gene is associated with multiple sclerosis.

A site of DNA polymorphism linked to the myelin basic protein gene, identified as restriction fragment length polymorphism, was analyzed in a population-based study comparing patients with clinically definite multiple sclerosis (MS) and population-matched control subjects. A 0.9-kilobase (kb) genomic DNA fragment (EcoG) encompassing the first exon of the human myelin basic protein gene, located on the long arm of chromosome 18, identified ten alleles arising from a region of DNA, 1.5 kb 5' to the myelin basic protein gene first exon coding region. Produced by RsaI digests and ranging in length from 2.05 to 2.15 kb, these alleles vary in size by up to 100 base pairs due to insertion or deletion, or both, from a 1-kb length of repetitive DNA. Allele frequencies among 65 patients with MS were compared with those of 63 control subjects. Chi square for these data was significant (p less than 0.001), largely due to a preponderance in the patients with MS of alleles in the 2.14- to 2.15-kb range. Comparison of the numbers of patients with MS and control subjects bearing specific alleles showed that 45% of the patients carried at least one allele of 2.14 to 2.15 kb as opposed to 19% of control subjects (p less than 0.005). These data, while preliminary, suggest that patients with MS differ from population-matched control subjects with respect to DNA polymorphism linked to the myelin basic protein gene. Although no pathogenic relationship between this polymorphism and MS can be presupposed, this finding raises the possibility that the myelin basic protein gene or some other myelin basic protein-linked locus may be a factor in susceptibility to MS.

Adult↗
PubMed1990

Activated T cells transcribe an alternatively spliced mRNA encoding a soluble form of Qa-2 antigen.

Among the best characterized non-classical mouse major histocompatibility antigens are the Qa-2 molecules. These proteins can serve as targets for allogenic cytotoxic T cells and as signal transducing molecules. They are structurally similar to H-2 transplantation antigens in their N-terminal and beta 2-microglobulin binding domains but differ at their C-termini. While the H-2 antigens span the cell membrane, the Qa-2 molecules are attached to the cell surface via phospholipid anchors. The genetic information encoding this attachment is contained in exon 5. In concanavalin A activated splenocytes the expression of membrane bound Qa-2 antigens declines and, simultaneously, soluble forms of Qa-2 molecules are secreted. We demonstrate here that the soluble Qa-2 polypeptides are translated from alternatively spliced mRNAs lacking exon 5, while the membrane forms are encoded by the full-size transcripts. In cultured cells the alternative splicing of the Qa-2 message is induced by T-cell activation splicing of the Qa-2 message is induced by T-cell activation with concanavalin A. The canonical mRNA encoding the membrane form of Qa-2 predominates in unstimulated mouse tissues but the cultured cell lines, like activated T cells, express enhanced levels of the truncated mRNA. In some cell lines almost all Qa-2 transcripts lack exon 5. For example, in L cells, mRNAs encoding soluble Qa-2 molecules are at least 10 times more abundant than Qa-2 transcripts encoding phospholipid anchored antigens. These findings are discussed in terms of potential functions of membrane bound and secreted Qa-2 molecules.

Amino Acid Sequence↗
PubMed1990

Repetitive DNA (TGGA)n 5' to the human myelin basic protein gene: a new form of oligonucleotide repetitive sequence showing length polymorphism.

DNA 5' to the human myelin basic protein (MBP) gene, mapped to 18q22----qter, is known to manifest multiallelic DNA length variation with heterozygosity of at least 45%. Isolation of genomic DNA containing the MBP gene first exon and its 5' flanking region reveals that this polymorphism arises from a 994-bp region of the diverged tandem repeat (TGGA)249. This sequence is located from 1082 to 2075 bp upstream of the MBP initiator methionine. The repetitive sequence is 18% diverged from (TGGA)249 and from analysis of higher order subsequence reiterations appears to have undergone extensive recombination. The pattern of higher order repetition suggests that multiple crossover and gene conversion events have occurred within a 1.0-kb region. Molecular clones of this sequence represent essentially the longest allelic form of this region seen in Southern transfer analysis. This repetitive DNA is similar to a sequence 5' to the human myoglobin gene.

Base Sequence↗
PubMed1990

Rapid preimplantation detection of mutant (shiverer) and normal alleles of the mouse myelin basic protein gene allowing selective implantation and birth of live young.

As a model for the detection of human genetic disease in preimplantation embryos, we describe a method in which trophectoderm biopsy samples from viable mouse blastocysts are simultaneously analyzed for the presence of a normal or mutant allele of the myelin basic protein gene by the polymerase chain reaction. The biopsied embryos are kept in culture during analysis of biopsied material and later reintroduced to a foster mother. Prenatal diagnosis can be completed in less than 7 hr. The identity of either amplification product was proved conclusively by direct sequence analysis of amplified products. Ninety-six percent of recovered blastocysts survived biopsy, as judged by re-formation of a blastocyst cavity in culture. Fifty-nine percent of the biopsied embryos established pregnancy by day 6.5, compared to 88% of unmanipulated controls. This approach can be applied to preimplantation diagnosis of human genetic diseases by using extraembryonic cells from blastocysts obtained after in vitro fertilization or uterine lavage. It will make possible the elimination of a mutant allele from a family in a single generation.

Alleles↗
PubMed1989

Specific-primer-directed DNA sequencing using automated fluorescence detection.

Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approach in conjunction with automated fluorescence detection on a commercial instrument (ABI 370A DNA sequencer). This includes procedures for the rapid chemical synthesis and purification of labeled primers, the design of primer sequences that are compatible with the commercial analysis software, and automated DNA sequence analysis using such primers. A set of four fluorophore-labeled primers can be reliably synthesized in a twenty-four hour period, and greater than 300 nucleotides of analyzed new sequence obtained using this set in an additional twenty-four hours. Scale-up of these procedures to take advantage of the full capabilities of the sequencer is, at present, too slow and costly to be suitable for routine sequencing, and therefore the use of specific-primers is best suited to the closure of gaps in extended sequence produced using random cloning and sequencing strategies.

Autoanalysis↗
PubMed1989

The class II genes of the rat MHC.

Genes that encode class II Ag from the MHC of the rat, the RT1 region, have been isolated as a series of cosmid clones. The cosmids define two clusters, each of which contains three identifiable sequences; one homologous to alpha-chain and two to beta-chain genes. Both the serologically identified rat class II Ag have been expressed in mouse L cell fibroblasts after the introduction of each alpha-chain gene along with a beta-chain gene from the same cluster. There are substantial homologies to the I region of the mouse H-2 complex in the presence, location, orientation, and expression of the six identified sequences from the rat RT1, supporting the view that the overall organization of the two gene complexes has remained conserved since the species separated.

Animals↗
PubMed1989

Effect of electric field switching on the electrophoretic mobility of single-stranded DNA molecules in polyacrylamide gels.

We have examined the effects of pulsed electric fields on the separation of single-stranded DNA molecules in polyacrylamide sequencing gels. Using different electric field pulsing regimens, the mobilities of single-stranded DNA molecules can be retarded or increased as compared to conventional electrophoresis. These results indicated that pulsed field techniques can be applied to gel electrophoresis of small single-stranded DNA molecules.

DNA, Single-Stranded↗
PubMed1989

Restriction fragment length polymorphisms of the mouse T-cell receptor gene families.

We have studied the restriction fragment length polymorphisms (RFLPs) found in the germline T-cell receptor genes of 25 inbred Mus musculus strains and 8 wild Mus species. Included in the inbred mice tested were several strains which spontaneously develop systemic autoimmune disease. Extensive polymorphism was evident for the variable (V) gene segments of the alpha gene family for both the inbred strains and wild mouse species. Changes in the total number of bands hybridizing with probes for V alpha gene segments suggest that members of a V alpha gene segment subfamily are not closely linked, but are interspersed with members of other subfamilies; that expansion and contraction of the multimembered subfamilies may be an important diversifying factor. Our data obtained with beta gene probes revealed genomic diversity that is much more limited than that seen for the alpha locus. Analysis of inbred mice with probes for the gamma gene locus revealed some RFLPs, but little evidence of expansion or contraction in the numbers of gene segments. Among the autoimmune mice, NZW, NZB, and BXSB/MpJ all display distinctive differences with alpha gene probes. NZW mice have a large deletion of the beta gene family, which has been reported previously. We found no differences to distinguish the MRL/MpJ lpr/lpr mice from non-autoimmune strains.

Animals↗
PubMed1989

Expression of the Q8/9d gene by T cells of the mouse.

The Q genes, specifying Qa antigens and situated in the extended part of the major histocompatibility complex (MHC) of the mouse, comprise a subgroup of MHC class I genes whose significance and function are still largely unknown. In screening a cDNA library made from the BALB/c inducer T-cell line Cl.Ly1-T1, we isolated 11 clones representing Q8/9, but none representing Q6 or Q7. Confirmatory evidence is given that the Q8/9 gene originated from fusion of the 5' region of the Q8 gene with the 3' region of the Q9 gene at a recombination site or hot spot in the vicinity of intron 4. Contrary to previous impressions that Q8/9 is an inert pseudogene, we find that the Q8/9 gene can be functional and encode a Qa-2, 3 antigen. One variety of the 11 Q8/9 clones isolated lacked exon 5, which encodes the transmembrane domain of class I glycoproteins, and thus may account for secretion of a soluble form of Qa-2, 3 antigen thought to be released by activated T cells.

Amino Acid Sequence↗
PubMed1989

The germline repertoire of T cell receptor beta-chain genes in patients with chronic progressive multiple sclerosis.

The T cell receptor (TcR) beta-chain germline gene repertoire of multiple sclerosis (MS) patients was compared to that of 100 normal individuals. No differences in the number of gene segments defined by probes representing 14 different human V beta subfamilies and the constant region genes were found. The distribution of haplotypes defined by restriction fragment length polymorphism (RFLP) alleles detected with V beta 8, V beta 11, and C beta probes in the MS patients was significantly different from that found in normal individuals. Because 84% of the MS patients were DR2+, the findings in these patients were compared to a second group of 43 normals who were DR2+. The distribution of TcR haplotypes in MS patients was also significantly different from that in the DR2+ normals. The data suggest that an MS susceptibility gene(s) may be located in the region of the TcR beta-chain gene complex.

Alleles↗