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Biomedical subjects

J C Shepherd

Publications and source records attributed to J C Shepherd.

At least 19 recordsLinked to original sources
PubMed1995

Preventing cervical cancer: the role of the Bethesda system.

The Papanicolaou smear is a well-established component of preventive health protocols for women. The purpose of this screening tool is to detect precursor lesions of invasive cervical carcinoma; however, the natural progression of these lesions is unclear, and it currently is not possible to determine which of the many dysplastic findings have carcinogenic potential. Furthermore, disagreement exists concerning the time frame for the malignant transformation of dysplastic cervical lesions. Despite these concerns, cervical screening has been credited with reducing morbidity and mortality from invasive cervical carcinoma in certain populations, and almost all family physicians provide this service to their female patients. The Bethesda system of cytopathologic reporting (introduced in 1988 and revised in 1991) is designed to improve communication between pathologists and clinicians. Compared with other taxonomies, the Bethesda system allows for distinction between changes associated with inflammation and infection and those reflecting squamous cell atypia and dysplasia.

Algorithms↗
PubMed1994

Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator.

The transporter associated with antigen processing (TAP) delivers peptides to the lumen of the endoplasmic reticulum in an adenosine triphosphate (ATP) dependent fashion for presentation by major histocompatibility complex class I molecules. We show that the mouse TAP translocator (H-2b haplotype) selects peptides based on a minimal size of nine residues, and on the presence of a hydrophobic COOH-terminal amino acid. The preponderance of COOH-terminal hydrophobic amino acids in peptides capable of binding to mouse class I molecules thus fits remarkably well with the specificity of the TAP translocator. In addition to transport in the lumenal direction, efflux of peptide in the cytosolic direction is observed in an ATP- and temperature-dependent manner. By maintaining a low peptide concentration at the site of class I assembly, this efflux mechanism may ensure that class I molecules are loaded preferentially with high affinity peptides.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1993

TAP1-dependent peptide translocation in vitro is ATP dependent and peptide selective.

T cells detect infection of cells by recognizing peptide fragments of foreign proteins bound to class I molecules of the major histocompatibility complex (MHC) on the surface of the infected cell. MHC class I molecules bind peptide in the endoplasmic reticulum, and analysis of mutant cells has demonstrated that an adequate supply of peptides requires the presence of two genes in the MHC class II locus that encode proteins called transporters associated with antigen processing (TAP) 1 and 2. TAP1 and TAP2 are members of the ATP-binding cassette family of membrane translocators. In this study, we demonstrate in a cell-free system that TAP1 is part of an ATP-dependent, sequence-specific, peptide translocator.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1991

A protein secreted in vivo by Echinococcus granulosus inhibits elastase activity and neutrophil chemotaxis.

A cDNA encoding the carboxy-terminal of the 12-kDa subunit of antigen B of Echinococcus granulosus has been cloned and sequenced. In addition, an amino acid sequence has been generated for the amino-terminal which is tentatively contiguous with the open reading frame of the DNA-derived sequence. Comparison of the inferred sequence of the 12-kDa antigen with other known sequences indicated a limited similarity to alpha-1 antitrypsin. In functional assays, gel-purified native 12-kDa antigen from natural infections inhibited elastase but not trypsin or chymotrypsin, providing further evidence that this antigen is a parasite protease inhibitor. Possibly unrelated to its anti-protease activity but a potentially important function of the 12-kDa antigen was its ability to inhibit recruitment of neutrophils. These functions may be important to the viability of the parasite in the face of the host immune response. In addition, the match between the DNA-derived sequence and the protein sequence was imperfect, with some residues having, according to the amino acid sequencing, two alternatives in approximately equal concentrations, and four DNA-derived residues failing to match with the protein sequence at all. The 12-kDa antigen may be expressed as isoforms from a polymorphic gene and, as far as aware, this observed sequence polymorphism has not, to date, been described for any other flatworm antigen.

Amino Acid Sequence↗
PubMed1989

Purification of a novel class of coated vesicles mediating biosynthetic protein transport through the Golgi stack.

We describe a scheme for the purification of the nonclathrin-coated vesicles that mediate transport of proteins between Golgi cisternae and probably from ER to Golgi. These "Golgi-derived coated vesicles" accumulate when Golgi membranes are incubated with ATP and cytosol in the presence of GTP gamma S, a compound that blocks vesicle fusion. The coated vesicles dissociate from the Golgi cisternae in high salt and can then be purified by employing differential and density gradient centrifugation. Golgi-derived coated vesicles have a putative polypeptide composition that is distinct from both cytosol and Golgi membranes, as well as from that of clathrin-coated vesicles.

Animals↗
PubMed1989

Fruit flies with additional expression of the elongation factor EF-1 alpha live longer.

In Drosophila melanogaster, the decrease in protein synthesis that accompanies aging is preceded by a decrease in elongation factor EF-1 alpha protein and mRNA. Here we show that Drosophila transformed with a P-element vector containing an EF-1 alpha gene under control of hsp70 regulatory sequences have a longer life-span than control flies.

Animals↗
PubMed1987

DNA recognition by a new family of type I restriction enzymes: a unique relationship between two different DNA specificities.

The DNA sequences recognized by the allelic type I restriction enzymes EcoR124 and EcoR124/3 were determined. EcoR124 recognizes 5'-GAA(N6)RTCG-3' and EcoR124/3 recognizes 5'-GAA(N7)RTCG-3'. These are typical of sequences recognized by type I recognition enzymes in that they consist of two specific domains separated by a non-specific spacer sequence. For these two enzymes, the specific sequences are identical but the length of the non-specific spacer is different. The specific domains of EcoR124/3 are thus 3.4 A further apart than those of EcoR124 and rotated with respect to each other through a further 36 degrees.

Base Sequence↗
PubMed1987

Specific and cross-reactive antigens of Echinococcus granulosus hydatid cyst fluid.

The parasite antigens of Echinococcus granulosus hydatid cyst fluid have been characterised using the techniques of radioiodination, immunoprecipitation, SDS-PAGE, and immunoblotting. Five major subunit antigens of the parasite have been identified of relative molecular mass (Mr) 12,000, 16,000, two at 20,000, and 38,000 when reduced. The 12 and 16 kDa molecules are specific to E. granulosus and are excreted/secreted by both U.K. strains of the parasite and all human isolates examined, although not all hydatid disease patients produce antibodies to them. These molecules may be suitable for detection in specific immunodiagnosis. The 38 kDa molecule associates, via a disulphide linkage, with one of the 20 kDa molecules to form a single molecule of 60 kDa. This antigen is cross-reactive with human antibody to other cestode, trematode, and nematode parasites. Part of this cross-reactivity is associated with the presence of phosphorylcholine bound to the 38 kDa subunit.

Animals↗
PubMed1985

Two type I restriction enzymes from Salmonella species. Purification and DNA recognition sequences.

We have purified the type I restriction enzymes SB and SP from Salmonella typhimurium and S. potsdam, respectively, and determined the DNA sequences that they recognize. These sequences resemble those previously determined for the type I enzymes, EcoB, EcoK and EcoA, in that the specific part of the sequence is divided into two domains by a spacer of non-specific sequence that has a fixed length for each enzyme. Two main differences from the previously determined sequences are seen. Both of the new sequences are degenerate and one of them, SB, has one trinucleotide and one pentanucleotide-specific domain rather than the trinucleotide and tetranucleotide domains seen for all of the other enzymes. The only conserved features of the recognition sequences are the adenosyl residues that are methylated in the modification reaction. For all of the enzymes these are situated ten or 11 base-pairs apart, one on each strand of the DNA. This suggests that the enzymes bind to DNA along one face of the double helix making protein-DNA interaction in two successive major grooves with most of the non-specific spacer sequence in the intervening minor groove.

Adenosine Triphosphatases↗
PubMed1984

The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.

The EcoA restriction enzyme from Escherichia coli 15T- has been isolated. It proves to be an unusual enzyme, clearly related functionally to the classical type I restriction enzymes. The basic enzyme is a two subunit modification methylase. Another protein species can be purified which by itself has no enzymatic activities but which converts the modification methylase to an ATP and S-adenosylmethionine-dependent restriction endonuclease. The DNA recognition sequence of EcoA has an overall structure that is very similar to previously determined type I sequences. It is: 5'-GAGNNNNNNNGTCA-3' 3'-CTCNNNNNNNCAGT-5' where N can be any nucleotide. Modification methylates the adenosyl residue in the specific trinucleotide and the adenosyl residue in the lower strand of the specific tetranucleotide.

Base Sequence↗
PubMed1983

The sequence of the bacteriophage P1 genome region serving as hot target for IS2 insertion.

A restriction fragment of the bacteriophage P1 genome known to serve as a hot target for IS2 insertion in its host, Escherichia coli K12, was entirely sequenced. It is 1756 bp long and it contains four long open reading frames, all in the same orientation. The two middle frames overlap partially. Eight of the nine studied IS2 insertions affecting phage reproduction map within three of these reading frames. No common feature was found between the nine target sites which have served for IS2 integration. However, there are two structural elements which might possibly contribute to rendering the studied DNA segment a hot region for IS2 insertion. The first is formed by two neighbouring, 30 and 40 bp regions of homology with an internal segment of IS2. The second is the pentanucleotide 5' GGTAT3', which is carried nine times in the sequenced fragment and which is found always in at least one copy within a variable distance of less than 100 bp of each inserted IS2 element.

Base Sequence↗
PubMed1981

The DNA sequence of the phage lambda genome between PL and the gene bet.

We have determined 3,400 base pairs of DNA sequence from the phage gamma genome which starts to the right of PL and runs to the left into the gene bet. The sequence thus includes the genes, N, ral, Ea10, cIII, kil and gam, as well as the transcription terminators TL1 and TL2. One surprising feature of the sequence is the presence in the region expected to be occupied by ral of a long open reading frame that, if it is expressed, would have to be transcribed from left to right, or counter to transcription from PL.

Bacteriophage lambda↗
PubMed1981

Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code.

Strong rhythms with a period of three bases have been seen while correlating the relative positions of purines and pyrimidines and of the four individual bases in the complete DNA sequence of the viruses phi X174, G4 and fd. Generally weaker variations of the same type have been found in the DNA virus SV40, the plasmid pBR322, the RNA virus MS2, and elsewhere in procaryotes and eucaryotes (e.g. in a ribosomal protein gene cluster of E. coli and the sea urchin histone genes). From the interrelation of four-base with purine-pyrimidine rhythms it seems that the purine-pyrimidine relationships have a basic significance. An explanation is proposed in terms of the former use of a comma-less genetic code (i.e. readable only in one frame) of the general form RNY (R = purine, Y = pyrimidine and N = purine or pyrimidine). In spite of subsequent mutation, there appears to be still enough of the primitive messages remaining to produce these periodic variations with their characteristic properties in phase and amplitude. Particularly good evidence for this hypothesis is provided by the fact that the phases for the stronger rhythms are the same in all the genomes tested and can be successfully predicted by a simple consideration of the original RNY pattern. With regard to amplitude it can be similarly foreseen which variations will be more clearly marked than others. The observed behaviour of the amplitude as the separation between correlated bases increases is also explained by the insertions, deletions and point mutations which have occurred. Additionally it is possible to account for some notable features of the non-random use of codons for the same amino acid by this theory.

Base Sequence↗