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D Seto

Publications and source records attributed to D Seto.

At least 37 records · Page 2Linked to original sources
PubMed1993

An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms.

A data set consisting of DNA sequences from a large-scale shotgun DNA cloning and sequencing project has been collected and posted for public release. The purpose is to propose a standard genomic DNA sequencing data set by which various algorithms and implementations can be tested. This set of data is divided into two subsets, one containing raw DNA sequence data (1023 clones) and the other consisting of the corresponding partially refined or edited DNA sequence data (820 clones). Suggested criteria or guidelines for this data refinement are presented so that algorithms for preprocessing and screening raw sequences may be developed. Development of such preprocessing, screening, aligning, and assembling algorithms will expedite large-scale DNA sequencing projects so that the complete unambiguous consensus DNA sequences will be made available to the general research community in a quicker manner. Smaller scale routine DNA sequencing projects will also be greatly aided by such computational efforts.

Algorithms↗
PubMed1993

Modulation of hippocampal acetylcholine release: a potent central action of interleukin-2.

The potential of the T-cell growth factor interleukin-2 (IL-2) to modulate the release of ACh from rat hippocampus was studied in vitro, as a means to investigate the possible functional significance of this cytokine in the CNS. Hippocampal slices were superfused with Krebs' buffer medium, and endogenous ACh released into the superfusate was measured using a radioenzymatic assay. Recombinant human IL-2 present during a stimulation with 25 mM KCl altered, in a concentration-dependent manner, the evoked transmitter release. At a concentration of 15 U/ml (< or = 1 nM), IL-2 inhibited ACh release by more than 50% of the control level (evoked ACh release from the untreated contralateral hemispheres). Inhibition was observed within 20 min of tissue exposure to IL-2 and lasted for up to 1 hr. The inhibitory effect of IL-2 was reversible since transient tissue exposure to IL-2 did not affect subsequent evoked ACh release. IL-2 at this concentration also significantly decreased evoked ACh in frontal cortical slices, but was ineffective in the parietal cortex and striatum, revealing that IL-2 selectively modulates the release of ACh from certain, but not all, cholinergic nerve terminals in the CNS. At very low concentrations (1.5 mU/ml, < or = 0.1 pM), IL-2 transiently increased hippocampal evoked ACh release, resulting in a biphasic dose-response profile with no significant effect observed at 0.015 mU/ml (< or = 1 fM). Other cytokines (IL-1 alpha, IL-3, IL-5, IL-6, interferon alpha), tested in hippocampal slice incubations, failed to modulate ACh release.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetylcholine↗
PubMed1992

Organization, structure, and function of 95 kb of DNA spanning the murine T-cell receptor C alpha/C delta region.

We have analyzed the organization, structure, and function of the murine T-cell receptor C alpha/C delta region. This region spans 94.6 kb of DNA and contains the C alpha and C delta genes, as well as the V delta 5, J delta 2, and 50 different J alpha gene segments. Within this sequence we have identified 15 new J alpha gene segments, 40 new 5' RNA splice signals, and 40 new DNA rearrangement signals for the J alpha gene segments. The murine C alpha/C delta sequence contains an exceptionally high level of coding sequence with over 5.7% of the total sequence found in the exons. This is much more than that found in the beta-globin locus and the HPRT locus. Using the sequence data obtained from the C alpha/C delta region, we have designed simple assays to test for J alpha gene segment transcription and to determine the level of polymorphism for simple repeat sequences among different inbred strains of mice using the polymerase chain reaction. Furthermore, comparisons of this 95 kb of sequence with the available sequence from homologous regions of other species have led to the identification of a highly conserved sequence that is present throughout vertebrates and in the mouse binds lymphocyte-specific nuclear proteins. Comparisons of a 10-kb region, which includes the C alpha gene in human and mouse, average 66% sequence similarity. These studies support the contention that large-scale DNA sequencing projects of homologous regions of mouse and human will provide powerful new tools for studying the biology and evolution of loci such as the T-cell receptor and for identifying and posing new questions about the functions of conserved sequences.

Amino Acid Sequence↗
PubMed1992

Race, ethnicity and birth-weight: Hawaii 1983 to 1986.

A study of racial/ethnic-specific mean infant birth-weights reported on 1968 to 1972 live birth-weight certificates for Oahu, Hawaii is reviewed here. The 1983 to 1986 data confirm those earlier results: (a) The Hawaiian group is significantly heavier in mean birth-weights than other cohorts during the preterm period (33 to 36 weeks gestational age); (b) statistically significant differences also were present in mean birth-weights for the term and post-term periods (37 to 45 weeks gestational age); and (c) the ranking of cohorts from heaviest to lightest in mean birth-weights is Caucasian, Hawaiian, Japanese and Filipino respectively. The data raises 2 questions: (1) Which birth-weight standards are most applicable for Asian and Pacific Islanders; and (2) what are the implications of the race/ethnic-specific mean birth-weight differences relative to mortality, morbidity and developmental outcome?

Birth Weight↗
PubMed1991

Altered host range of HIV-1 after passage through various human cell types.

HIV-1 strains, including a molecularly cloned isolate, that had been passaged through different cell types adapted to faster growth in the same cell type and displayed a different host cell tropism. The only change in viral proteins revealed by immunoblot analyses was the molecular size of the envelope glycoprotein gp120 that varied for viruses recovered from the different infected cells. The alteration in size was most likely the result of modification of gp120. Host range differences were also observed for a molecularly cloned HIV-1 strain when passed through the peripheral white blood cells from different individuals. Thus, this phenomenon could have clinical relevance in HIV pathogenesis.

Blotting, Southern↗
PubMed1991

Growth factors and lymphokines: modulators of cholinergic neuronal activity.

It is well known that various markers of the cholinergic synapse are altered in Alzheimer's Disease. Much interest is currently focussing on the evaluation of the possible efficacy of certain growth factors, especially nerve growth factor (NGF), to reduce or reverse cholinergic neuronal losses. Here we report that other growth factors (epidermal growth factor and insulin-like growth factor I) and a lymphokine, interleukin-2, are able to block acetylcholine release in the rat hippocampus. This suggests that while certain growth factors like NGF may have positive effects on the cholinergic neuron, others may act as "negative" factors on this neuronal population.

Acetylcholine↗
PubMed1991

Development and application of a nonradioactive phosphorescent autoradiograph marker.

A simple and rapid method for permanently marking autoradiographs is described. This procedure is based on the phosphorescence of light-activated zinc sulfide and the subsequent exposure of x-ray films by this light emission. A lacquer-based carrier allows the zinc sulfide to remain in suspension and permits permanent marking onto diverse laboratory substrates such as x-ray films, paper, plastic wraps and nitrocellulose- and nylon-based membranes. An analogous wax-based carrier allows marking onto paper and dried acrylamide gels, which is useful for processing large numbers of radioactive DNA sequencing gels on a high-throughput scale. These inexpensive and nonhazardous markers will be useful in protocols that use x-ray films, regardless of whether radioactive or nonradioactive detection systems are used.

Autoradiography↗
PubMed1990

Phosphorescent zinc sulfide is a nonradioactive alternative for marking autoradiograms.

Phosphorescent zinc sulfide is a nonradioactive alternative for making orientation and identification markings on autoradiograms. Measurements with a luminometer show that light emission is linear with respect to ZnS concentration. A minimum activation time of 5 s has been determined, using an incandescent lamp as a light source. Emission decay kinetics show light emissions reached background levels within minutes, depending on the ZnS concentration. This time period is sufficient for X-ray films to be permanently marked. Because of its efficiency and nontoxicity, this autoradiogram marker could be extremely useful in many protocols, including high-throughput radioactive DNA sequencing. This nonradioactive marker will also be useful in protocols utilizing nonradioactive detection systems, such as those calling for biotinylated and chemiluminescent probes.

Autoradiography↗
PubMed1989

Isolates of human immunodeficiency virus type 1 from the brain may constitute a special group of the AIDS virus.

The biologic, serologic, and molecular properties of isolates of human immunodeficiency virus type 1 (HIV-1) from the central nervous system (CNS) were determined and compared to those of isolates from peripheral blood and lymph nodes. Among these were pairs of CNS and blood isolates obtained from six infected individuals. The data show that HIV-1 isolates from the CNS can be distinguished from peripheral blood isolates by their (i) relative inability to infect established T-cell lines, (ii) reduced cytopathogenicity, (iii) inability to modulate CD4 antigen expression on infected cells, (iv) efficient replication in peripheral blood macrophages, and (v) insensitivity to serum neutralization. Paired CNS and peripheral blood isolates from the same individual also display some differences in cellular tropism. The blood isolates replicate better in T-cell lines and glioma cell lines, whereas the paired CNS isolates replicate more efficiently in primary macrophages. These results suggest that viruses isolated from the CNS of infected individuals may represent a specific HIV-1 subgroup.

Acquired Immunodeficiency Syndrome↗
PubMed1989

Location and molecular cloning of the structural gene for the deoxyguanosine triphosphate triphosphohydrolase of Escherichia coli.

The structural gene for deoxyguanosine triphosphate triphosphohydrolase (dGTPase) (EC 3.1.5.1) and its regulator, optA, have been located on a lambda phage carrying a 17.5kb Escherichia coli DNA insert. The DNA fragment has been excised and ligated into pBR325 and also transferred to another lambda vector. From the results of transduction and transformation experiments, we find that the structural gene for dGTPase is very closely linked to optA and dapD, which locates it at approximately 3.6 minutes on the genetic map of E. coli K12. We propose the mnemonic dgt as the designation for the structural gene for this enzyme.

Bacteriophage lambda↗
PubMed1988

Simultaneous isolation of HIV-1 and HIV-2 from an AIDS patient.

Two distinct human immunodeficiency viruses, HIV-1SF480 and HIV-2UC2 were isolated simultaneously from the blood of an Ivory Coast patient with AIDS. The HIV subtypes were segregated by their differential ability to infect established human cell lines and by the cell surface expression of type-specific viral antigens. The viruses could be distinguished by both immunoblot and Southern blot analyses. The results indicate that an individual can be infected by both HIV subtypes.

Acquired Immunodeficiency Syndrome↗
PubMed1988

Isolation of the gene encoding the S. cerevisiae heat shock transcription factor.

The yeast heat shock transcription factor gene, HSF1, has been isolated from an S. cerevisiae genomic expression library (in lambda gt11). The sequenced gene encodes an 833 amino acid protein having a mass of 93,218 daltons. Expression of specific DNA-binding activity in E. coli and of transcriptional activity in yeast confirmed the identity of the cloned gene. Southern analysis and gene-disruption experiments indicate that the heat shock transcription factor is encoded by a single-copy, essential gene. The DNA-binding domain was localized to a 118 amino acid region in the amino-terminal third of the protein. Inspection of the DNA-binding domain reveals no resemblance to any currently known secondary structural motifs implicated in DNA recognition and binding.

Amino Acid Sequence↗
PubMed1988

Biologic features of HIV-1 that correlate with virulence in the host.

Individuals infected with the human immunodeficiency virus type 1 (HIV-1) may be asymptomatic or have AIDS-related complex or the acquired immuno deficiency syndrome (AIDS). Little is known about the factors that influence progression of infection to AIDS. In this study of isolates of HIV-1 obtained at intervals during the infection of four individuals, the development of disease was found to be correlated with the emergence of HIV-1 variants that were more cytopathic in vitro as the disease progressed and that replicated more efficiently in a wide variety of different human cells. The biologic properties of HIV-1 in vitro thus appear to reflect its virulence in the host. Further studies of such sequentially isolated viruses may lead to the identification of viral genes that govern pathogenesis.

AIDS-Related Complex↗
PubMed1988

The purification and properties of deoxyguanosine triphosphate triphosphohydrolase from Escherichia coli.

Deoxyguanosine triphosphate (dGTP) triphosphohydrolase (EC 3.1.5.1) has been purified approximately 16,000-fold to apparent homogeneity from extracts of Escherichia coli. The enzyme has a native molecular weight of 230,000 and a sedimentation coefficient of 9.3 S. Its subunit molecular weight derived from electrophoresis in denaturing polyacrylamide gels is 58,900, and it has a unique N-terminal sequence for the first 25 amino acids, which indicate that the native enzyme is composed of 4 homologous subunits. It is insensitive to sulfhydryl reagents and EDTA and can be heated to 60 degrees C for 60 min without loss of activity. The enzyme requires Mg2+ for activity, is highly specific for dGTP among the canonical deoxynucleoside triphosphates, and has a unique activity among nucleoside triphosphatases in that the products of the reaction are deoxyguanosine and inorganic tripolyphosphate. Preliminary evidence suggest that this enzyme is responsible for the optA mutant phenotype first described by Saito and Richardson (Saito, H., and Richardson, C.C. (1981) J. Virol. 37, 343-351).

Amino Acids↗