Biomedical subjects

K N Potter

Publications and source records attributed to K N Potter.

25 records · Page 2Linked to original sources

PubMed1986

Methylation blockage and other improvements to a comprehensive DNA analysis program.

A comprehensive DNA analysis computer program was described in the second special issue of Nucleic Acids Research on the applications of computers to research on nucleic acids by Stone and Potter (1). Criteria used in designing the program were user friendliness, ability to handle large DNA sequences, low storage requirement, migratability to other computers and comprehensive analysis capability. The program has been used extensively in an industrial-research environment. This paper talks about improvements to that program. These improvements include testing for methylation blockage of restriction enzyme recognition sites, homology analysis, RNA folding analysis, integration of a large DNA database (GenBank), a site specific mutagenesis analysis, a protein database and protein searching programs. The original design of the DNA analysis program using a command executive from which any analytical programs can be called, has proven to be extremely versatile in integrating both developed and outside programs to the file management system employed.

Base Sequence↗

PubMed1984

A DNA analysis program designed for computer novices working in an industrial-research environment.

A program designed for DNA sequence analysis by people with no computer background or experience is described. The criteria used in the program design were (i) user friendliness, (ii) ability to handle large DNA files (greater than 10 kilobases), (iii) low storage requirements so that it could be put on a personal computer (IBM), (iv) written in a widely used language (FORTRAN 77) and (v) ability to handle all of the needed tasks for DNA analysis. The program consists of an executive that controls a set of modular subprograms. A file management system using 'SEQ' and 'SITE' files is also in place. SEQ files contain long DNA nucleotide sequences (e.g. restriction enzyme sites). Related SEQ and SITE files are grouped into categories. A SITE category can include related sequences a user wishes to search for in a longer SEQ sequence from a designated category. For example, all of the restriction enzyme recognition sites can group into a single category called 'Enzymes' and can be searched for in a SEQ sequence which has been placed in the SEQ file category 'Plasmids'. Colour graphics is also used as a visual aid.

Base Sequence↗

PubMed1978

Modification of Trichoplusia ni nuclear polyhedrosis virus passaged in vivo.

A designated strain of plaque-purified Trichoplusia ni nuclear polyhedrosis virus (NPV) was used to initiate a serial passage series in vivo. The virulence of polyhedra inclusion bodies (PIB) and the distribution of MP (many PIB) and FP (few PIB) strains in hemolymph were monitored. When virus was passaged per os as PIB, there was no major change in virulence after 15 passes in insects. Plaque analysis of hemolymph from the infected insects indicated that there was no selection for the FP strain of virus. There was little overall change in the infectivity of nonoccluded virus (NOV) after 16 passes by injection into T. ni larvae; however, plaque analysis of the hemolymph from the infected insects indicated progressive selection of FP virus. It is postulated that when PIB are the vehicles of virus transmission, there is no progressive accumulation of noninfectious FP PIB; however, when NOV are the vehicles of virus transmission, FP NOV production displaces MP virus synthesis. This may result from a growth advantage of the FP NOV over the MP NOV as shown in vitro and from the noninfectious nature of FP PIB.

Animals↗

PubMed1976

Strain selection during serial passage of Trichoplusia in nuclear polyhedrosis virus.

Two strains of a nuclear polyhedrosis virus (NPV) of Trichoplusia ni were isolated on the basis of plaque morphology. They are designated as MP (having greater than 30 polyhedra per nucleus) and FP (having fewer than 10 polyhedra per nucleus). Serial, undiluted passage of plaque, purified MP nonoccluded. Virus (NOV) in tissue culture led to the production of the FP phenotype detectable at passage 9. With continued serial, undiluted passage, FP became the predominant strain. Comparative growth curves showed that FP NOV are released faster than MP NOV. MP morphology was not observed after 14 serial, undiluted passages of plaque-purified FP. By the plaque neutralization assay, NOV from both strains of virus was neutralized by the homologus and heterologous antisera. The FP phenotype was observed when FP virus was grown in culture at 17, 22, and 27 C. Hence, the FP phenotype was not considered to be the result of temperature-inhibited crystallization of polyhedrin under standard tissue culture conditions. The NOV of both strains killed insects when injected directly into the hemocoele of T. ni larvae. Only MP inclusion bodies were virulent per os. The FP inclusion bodies fed to cabbage looper larvae did not kill, and no infectious agent could be detected in the hemolymph. Electron micrographs of MP polyhedra showed bundles of nucleocapsids of normal length within the polyhedra, whereas FP polyhedra contained heterogeneous, electron-dense material, which could account for their lack of pathogenicity.

Animals↗

PubMed1976

Comparison of vesicular stomatitis virus defective interfering particle synthesis in chick embryo and L cells.

A comparison of the ability of vesicular stomatitis virus (VSV) to generate and replicate defective interfering (DI) particles in primary chick embryo (CE) and mouse L cells was investigated as a means of analyzing host control over DI-particle synthesis and interfering capacity. Serial undiluted passage of VSV in CE and L cells indicate that VSV-DI particles are generated and (or) replicate with greater efficiency in CE than in L cells. When DI particles accumulate in L cells, they are able to interfere with infectious particle replication. The DI particles from CE cells interfered to the same extent with infectious particle replication in both CE and L cells. L cells, therefore, are not considered 'low-interference' hosts in which DI particles are produced and do not interfere with infectious virus replication, but rather hosts which restrict the production of DI particles.

Animals↗

PubMedDate not supplied

The molecular specificity of insulin autoantibodies.

Insulin autoantibodies (IAA) are one of several markers for Type I (autoimmune) diabetes, but alone deserve special attention. Unlike the other markers, their ligand is unique to the beta cell. IAA are the first markers to appear during the symptomless period which precedes diabetes and they are present in the vast majority of young children destined to develop diabetes. The primary and tertiary structures of insulin have been known for decades. Binding studies with insulin variants have shown epitope restriction that can distinguish Type 1 diabetes-predictive from non-predictive IAA-positive sera, thereby improving specificity for the test. With two major international Type 1 diabetes prevention trials underway, there is a pressing need to refine markers that reliably indicate the presence of, and remission from, autoimmune insulitis. The binding regions of antibodies are assembled from three multi-gene families, and some of their diversity derives from random mutation during their antigen-driven maturation. There is evidence that mature IAA derive from germline-encoded 'natural' antibodies, and that the gene segments utilised by IAA may be influenced by clinical context. Monoclonal anti-idiotypic (anti-Id) antibodies can serve as probes for antibody variable region determinants, and antibodies to the different epitopes of beef and porcine insulins have already been analysed with monoclonal reagents. Used as antibodies in a radioimmunoassay format, monoclonal anti-Ids will identify and measure autoantibody idiotopes as if they were ligands. The challenge now is to replace the conventional radiobinding assays for IAA, which only detect and titrate, with radioimmunoassays that can be standardised in absolute units. There is sufficient evidence for the existence of Type 1 diabetes-predictive IAA idiotopes to justify the development of idiotope-specific radioimmunoassays which ignore Type 1 diabetes-unrelated IAA.

Amino Acid Sequence↗

PubMedDate not supplied

Molecular characterization of cold agglutinins.

An unusual bias involving the exclusive usage of the V4-34 gene segment by pathogenic antibodies with I/i antigen specificity has been documented in the literature. In addition, all unmutated and several mutated V4-34 encoded antibodies have been shown to be reactive with the anti-idiotypic monoclonal antibody 9G4. The 9G4 Id, therefore, is a marker for V4-34 gene segment expression. Based on these two correlations, it became vital to localize and characterize the nature of the 9G4 Id and to determine the relationship between the Id and I binding. Mutational analysis indicated that the 9G4 Id is located in framework region 1 (FR1) of V4-34 encoded antibodies. Two distinct sections of FR1, encompassing amino acid residues 6-12 and 23-25, form the 9G4 Id. Mutational analysis demonstrated that both FR1 and CDRH3 were required for I binding. When either one was disrupted, the mutant antibody could not bind I. This indicates that I binds through a framework region, and not exclusively through CDRH3. This renders the I interaction with the V4-34 encoded portion of immunoglobulins unconventional, with characteristics similar to superantigen binding to immunoglobulin through FR. When the FR1 DNA sequence of V4-34 was exchanged for FR1 sequences from other VH families I binding was lost, providing a structural explanation for this restricted VH usage. An understanding of the localization and structure of the 9G4 Id and the requirements of V4-34 encoded antibodies for I binding provide insights into the structure of pathogenic antibodies and their requirements for binding antigen. This information should be useful in analyzing new interactions such as the lytic activity of some V4-34 encoded antibodies for B cells.

Agglutinins↗