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T Hunkapiller

Publications and source records attributed to T Hunkapiller.

At least 19 recordsLinked to original sources
PubMed1992

Sequence accuracy of large DNA sequencing projects.

Very little information has been accumulated regarding the likely accuracy of final or consensus DNA sequence data. With the large-scale efforts anticipated for the Human Genome Project, the subjective determination of final sequence must eventually be replaced with more objective, automatic methods. This will require a much better understanding of the nature of error in raw sequencing data and its impact on the determination of the final sequence. This paper describes a start at defining the error model of large-scale sequencing efforts based on random subcloning strategies.

Consensus Sequence↗
PubMed1991

Large-scale and automated DNA sequence determination.

DNA sequence analysis is a multistage process that includes the preparation of DNA, its fragmentation and base analysis, and the interpretation of the resulting sequence information. New technological advances have led to the automation of certain steps in this process and have raised the possibility of large-scale DNA sequencing efforts in the near future [for example, 1 million base pairs (Mb) per year]. New sequencing methodologies, fully automated instrumentation, and improvements in sequencing-related computational resources may render genome-size sequencing projects (100 Mb or larger) feasible during the next 5 to 10 years.

Animals↗
PubMed1990

Chimeric immunoglobulin-T cell receptor proteins form functional receptors: implications for T cell receptor complex formation and activation.

We constructed chimeric receptor chains in which an immunoglobulin heavy chain variable region (VH) from a phosphorylcholine-specific antibody is substituted for T cell receptor (Tcr) alpha and beta V regions. We demonstrate that the VH region joined to either the C alpha or the C beta region can form stable chimeric proteins in EL4 T cells. Both chimeric receptor chains associate with CD3 polypeptides in functional receptor complexes and respond to phosphorylcholine coupled to Sepharose beads. The VH-C alpha chimeric chain associates with the EL4 beta chain, while the VH-C beta chimeric protein appears to form either a homodimer or a heterodimer with the native EL4 beta chain. Thus, functional receptor complexes can be formed using two C beta regions, and the C alpha region may not be required for CD3 association and surface expression of Tcr complexes.

Animals↗
PubMed1989

Comparison of exon 5 sequences from 35 class I genes of the BALB/c mouse.

DNA sequences of the fifth exon, which encodes the transmembrane domain, were determined for the BALB/c mouse class I MHC genes and used to study the relationships between them. Based on nucleotide sequence similarity, the exon 5 sequences can be divided into seven groups. Although most members within each group are at least 80% similar to each other, comparison between groups reveals that the groups share little similarity. However, in spite of the extensive variation of the fifth exon sequences, analysis of their predicted amino acid translations reveals that only four class I gene fifth exons have frameshifts or stop codons that terminate their translation and prevent them from encoding a domain that is both hydrophobic and long enough to span a lipid bilayer. Exactly 27 of the remaining fifth exons could encode a domain that is similar to those of the transplantation antigens in that it consists of a proline-rich connecting peptide, a transmembrane segment, and a cytoplasmic portion with membrane-anchoring basic residues. The conservation of this motif in the majority of the fifth exon translations in spite of extensive variation suggests that selective pressure exists for these exons to maintain their ability to encode a functional transmembrane domain, raising the possibility that many of the nonclassical class I genes encode functionally important products.

Amino Acid Sequence↗
PubMed1988

Nucleotide sequence of dengue 2 RNA and comparison of the encoded proteins with those of other flaviviruses.

We have determined the complete sequence of the RNA of dengue 2 virus (S1 candidate vaccine strain derived from the PR-159 isolate) with the exception of about 15 nucleotides at the 5' end. The genome organization is the same as that deduced earlier for other flaviviruses and the amino acid sequences of the encoded dengue 2 proteins show striking homology to those of other flaviviruses. The overall amino acid sequence similarity between dengue 2 and yellow fever virus is 44.7%, whereas that between dengue 2 and West Nile virus is 50.7%. These viruses represent three different serological subgroups of mosquito-borne flaviviruses. Comparison of the amino acid sequences shows that amino acid sequence homology is not uniformly distributed among the proteins; highest homology is found in some domains of nonstructural protein NS5 and lowest homology in the hydrophobic polypeptides ns2a and 2b. In general the structural proteins are less well conserved than the nonstructural proteins. Hydrophobicity profiles, however, are remarkably similar throughout the translated region. Comparison of the dengue 2 PR-159 sequence to partial sequence data from dengue 4 and another strain of dengue 2 virus reveals amino acid sequence homologies of about 64 and 96%, respectively, in the structural protein region. Thus as a general rule for flaviviruses examined to date, members of different serological subgroups demonstrate 50% or less amino acid sequence homology, members of the same subgroup average 65-75% homology, and strains of the same virus demonstrate greater than 95% amino acid sequence similarity.

Amino Acid Sequence↗
PubMed1987

Diversity and structure of human T-cell receptor alpha-chain variable region genes.

The nucleotide sequences of 27 T-cell receptor alpha-chain variable region (V alpha)-containing cDNA clones isolated from a cDNA library derived from human peripheral blood lymphocytes were determined. Eighteen different V alpha and 26 different joining (J alpha) gene segments are utilized in these clones. The V alpha gene segments belong to 12 different subfamilies, each containing from one to seven members. Comparisons with the 16 different V alpha and 21 different J alpha sequences previously reported suggest that the germ-line repertoires for these gene segments are greater than previously estimated. Flexibility in the sites of gene segment joining and possibly N-region diversification also contribute to human alpha-chain diversity. Comparisons of human V alpha regions indicate a high degree of variability spread uniformly across the entire V alpha region without obvious hypervariable regions. However, amino acids important for the maintenance of V gene structure are conserved.

Amino Acid Sequence↗
PubMed1987

L3T4 and the immunoglobulin gene superfamily: new relationships between the immune system and the nervous system.

L3T4 is a mouse cell surface protein expressed on most thymocytes and on the subset of mature T cells that recognizes class II MHC molecules. Its primary function on T cells is most likely that of increasing the avidity of the interaction between T cells and antigen-presenting or target cells. It may accomplish this by binding to a nonpolymorphic region on class II MHC molecules. The cDNA and gene encoding L3T4 have been isolated and sequenced. Analysis of the amino acid sequence predicted by the nucleotide sequence indicates that L3T4 is a member of the Ig gene superfamily. It is most closely related to Ig and Tcr V regions. Although the amino-terminal domain of L3T4 is the portion of the molecule that is most similar to V-regions, L3T4 is one of the polydomain members of the Ig gene superfamily. Studies of the expression of L3T4 mRNA in various tissues led to the surprising finding that this gene is transcribed not only in T lymphoid cells, but also in brain. The predominant form of L3T4 mRNA expressed in brain is foreshortened as compared to that in T lineage cells, and it is most likely the product of a distinct transcriptional start site. If translated, the protein encoded by this brain transcript would be 217 amino acids in length and would lack the signal peptide and the amino-terminal 214 amino acids of the mature protein. It is not known whether a stable protein product is synthesized from this mRNA or what its function might be. However, these findings place L3T4 in an intriguing class of Ig gene superfamily members characterized by coexpression in the immune system and the nervous system.

Animals↗
PubMed1986

Isolation and sequence of L3T4 complementary DNA clones: expression in T cells and brain.

T lymphocytes express on their surface not only a specific receptor for antigen and major histocompatibility complex proteins, but also a number of additional glycoproteins that are thought to play accessory roles in the processes of recognition and signal transduction. L3T4 is one such T-cell surface protein that is expressed on most mouse thymocytes and on mature mouse T cells that recognize class II (Ia) major histocompatibility complex proteins. Such cells are predominantly of the helper/inducer phenotype. In this study, complementary DNA clones encoding L3T4 were isolated and sequenced. The predicted protein sequence shows that L3T4 is a member of the immunoglobulin gene superfamily. It is encoded by a single gene that does not require rearrangement prior to expression. Although the protein has not previously been demonstrated on nonhematopoietic cells, two messenger RNA species specific for L3T4 are found in brain. The minor species comigrates with the L3T4 transcript in T cells, whereas the major species is 1 kilobase smaller.

Amino Acid Sequence↗
PubMed1985

The T cell differentiation antigen Leu-2/T8 is homologous to immunoglobulin and T cell receptor variable regions.

Leu-2/T8 is a cell surface glycoprotein expressed by most cytotoxic and suppressor T lymphocytes. Its expression on T cells correlates best with recognition of class I major histocompatibility complex antigens, and it has been postulated to be a receptor for these proteins. We have determined the complete primary structure of Leu-2/T8 from the nucleotide sequence of its cDNA. The protein contains a classical signal peptide, two external domains, a hydrophobic transmembrane region, and a cytoplasmic tail. The N-terminal domain of the protein has striking homology to variable regions of immunoglobulins and the T cell receptor. The membrane-proximal domain appears to be a hinge-like region similar to that of immunoglobulin heavy chains. The superfamily of immunologically important surface molecules can now be extended to include Leu-2/T8.

Amino Acid Sequence↗
PubMed1985

Rearranged beta T cell receptor genes in a helper T cell clone specific for lysozyme: no correlation between V beta and MHC restriction.

The helper T cell clone 3H.25 is specific for hen egg white lysozyme and the class II MHC molecule I-Ab. This TH cell has three rearrangements in the beta-chain gene family-a V beta-D beta-J beta 1 and a D beta 2-J beta 2 rearrangement on one homolog and a D beta 1-J beta 2 rearrangement on the other. These observations demonstrate that this functional T lymphocyte expresses only a single V beta gene segment and, accordingly, exhibits allelic exclusion of beta-chain gene expression. The rearranged 3H.25 V beta gene segment is the same as that expressed in a T helper cell specific for cytochrome c and an I-Ek MHC molecule. Thus, there is no simple correlation between the V beta gene segment and antigen specificity or MHC restriction.

Animals↗