Biomedical subjects

H L Chen

Publications and source records attributed to H L Chen.

At least 127 records · Page 7Linked to original sources

PubMed1996

A protein class database organized with ProSite protein groups and PIR superfamilies.

A protein class (ProClass) database is developed as a "value-added" "second-generation" database organized according to family relationships. The database collects non-redundant protein sequence entries from SwissProt and PIR databases, and classifies them in families defined collectively by the ProSite protein groups and PIR superfamilies. The major objectives of the database are to maximize family information retrieval, to provide speedy family identification, and to help organizing existing protein sequence databases. The database has two sub-databases: PCFam (ProClass Family) to define protein families and provide links to ProSite patterns and PIR superfamilies, and PCSeq (ProClass Sequence) to describe sequence entries and provide links to PCFam, SwissProt, PIR, and ProSite databases. The current ProClass release has a total of 85,165 sequence entries, about half of which are classified in 3072 ProClass families; it also contains 10,431 newly established SwissProt-PIR links. The database can help reveal domain structures of related families, define new ProSite and PIR families, and provide family assignments for unclassified sequence entries. New ProSite and PIR family members are readily identified via database cross-reference, including 9437 SwissProt entries and 8522 PIR entries. False negative family members missed by both ProSite and PIR are detected using a neural network family identification system. The newly identified superfamily memberships are being incorporated into the current PIR database releases in a collaborative effort with the PIR. The ProClass database is accessible through anonymous FTP and on-line search on the World Wide Web.

Amino Acid Sequence↗

PubMed1996

Motif identification neural design for rapid and sensitive protein family search.

A new method, the motif identification neural design (MOTIFIND), has been developed for rapid and sensitive protein family identification. The method is an extension of our previous gene classification artificial neural system and employs new designs to enhance the detection of distant relationships. The new designs include an n-gram term weighting algorithm for extracting local motif patterns, an enhanced n-gram method for extracting residues of long-range correlation, and integrated neural networks for combining global and motif sequence information. The system has been tested and compared with several existing methods using three protein families, the cytochrome c, cytochrome b and flavodoxin. Overall it achieves 100% sensitivity and > 99.6% specificity, an accuracy comparable to BLAST, but at a speed of approximately 20 times faster. The system is much more robust than the PROSITE search which is based on simple signature patterns. MOTIFIND also compares favorably with BLIMPS, the Hidden Markov Model and PROFILESEARCH in detecting fragmentary sequences lacking complete motif regions and in detecting distant relationships, especially for members of under-represented subgroups within a family. MOTIFIND may be generally applicable to other proteins and has the potential to become a full-scale database search and sequence analysis tool.

Algorithms↗

PubMed1996

Tumor necrosis factors: pivotal components of pregnancy?

Tumor necrosis factor alpha is a major component of the infection-stimulated cytokine milieux associated with preterm labor and pregnancy termination. As a consequence, this potent factor is thought by some to have exclusively negative effects on the course of pregnancy. Yet in humans and other mammals, messenger RNA hybridizing with tumor necrosis factor alpha cRNA probes and protein detected by anti-tumor necrosis factor alpha have been identified in normal cycling and pregnant uteri, placentas, and embryos, consistent with an important role for tumor necrosis factor in female reproduction and embryonic development. Here, evidence for this intriguing dichotomy is presented, unresolved aspects are discussed, and potential roles for uteroplacental and embryonic tumor necrosis factor are proposed.

Embryo, Mammalian↗

PubMed1996

Tissue distribution of Epstein-Barr virus genotypes.

The genome of naturally occurring Epstein-Barr virus contains either two or three copies of a 29-bp tandem repeat sequence in the first intron of the BZLF gene. These genotypes differ markedly in their distribution between blood and epithelial tissues, presumably because they have adapted to separate life cycles in these sites. The genotype prevalent in the blood also appears to be better able to transform B lymphocytes.

Genome, Viral↗

PubMed1996

Dexamethasone rapidly increases hypothalamic neuropeptide Y secretion in adrenalectomized ob/ob mice.

A single intracerebroventricular injection of dexamethasone (DEX) rapidly (within 30 min) suppresses brown adipose tissue thermogenesis and increases plasma insulin concentrations in adrenal-ectomized (ADX) ob/ob mice but not in ADX lean mice. Intracerebroventricular neuropeptide Y (NPY) administered intracerebroventricularly causes these same metabolic changes within 30 min in both ob/ob and lean ADX mice. We therefore hypothesized that DEX exerts these rapid-onset metabolic actions in ob/ob mice via a phenotype-specific enhancement of NPY secretion within the central nervous system. In support of this hypothesis, DEX (a type II glucocorticoid receptor agonist) administered intracerebroventricularly selectively lowered NPY concentrations in the whole hypothalamus of ADX ob/ob mice by 35% and in the arcuate nucleus region by approximately 70% within 30 min but not in the brain stem or hippocampus or in any of these regions of lean mice. DEX also functioned in vitro to enhance depolarization-dependent release of NPY from hypothalamic blocks of ADX ob/ob mice but not of ADX lean mice. Thus DEX acts in the hypothalamus of ob/ob mice in a phenotype-specific manner to evoke rapid transport of NPY from cell bodies within the arcuate nucleus to terminal regions including the dorsomedial and ventromedial hypothalamic regions for release.

Adrenal Glands↗

PubMed1996

Identification of serotypes of Rickettsia tsutsugamushi by nested polymerase chain reaction.

Nested polymerase chain reaction (PCR) was applied to identify the serotypes of Rickettsia tsutsugamushi isolated from patients. The primers used for PCR were based on the nucleotide sequences encoding a 56 kDa antigen of rickettsiae. Comparing to the conventional immunofluorescence assay (IFA), which displays a considerable degree of cross-reactivity among different species, the result obtained suggests that the polymerase chain reaction method is much more reliable than IFA.

Animals↗

PubMed1996

IgE and monoclonal antibody binding by the mite allergen Der p 7.

BACKGROUND: The recently characterized group 7 house dust mite allergens give positive skin-test reactions in 53% of allergic patients. OBJECTIVE: This study was performed to compare the IgE binding activity of natural and recombinant Der p 7, to measure the binding in allergic sera in comparison to major allergen Der p 2 and characterize the response by competitive inhibition with monoclonal antibodies. METHODS: IgE anti Der p 2 and Der p 7 antibodies against the recombinant allergens and monoclonal binding activities were measured by a solid phase radioimmune assay. RESULTS: A competitive binding assay showed that rDer p 7 inhibited 91% of IgE-binding to natural Der p 7 in 2 sera and 73% in a further two. The IgE binding of rDer p 2 and Der p 7 from 41 sera was then compared. Of the sera 88% and 46% respectively showed positive binding. All of the 19 sera which bound Der p 7 also bound Der p 2 but 11 (58%) had bound IgE to Der p 7 as high or higher than the binding to Der p 2. These sera were mostly high responders to both allergens. A panel of six monoclonal antibodies produced against either rDer p 7 or rDer f7 was used for epitope analysis. All of these reacted with each allergen by enzyme linked immunosorbent assay (ELISA) and immunoblotting. Two patterns of cross inhibition of monoclonal antibody binding were observed and of five monoclonal antibodies tested, four could inhibit the binding of IgE (WH9, WH22, WP8 and HD19) while one (WH14) could not. CONCLUSIONS: Although Der p 7 only reacts with 50% of allergic sera it often has a high IgE binding activity and may be more important than the major Der p 2 allergen in a high percentage of subjects. The combined competitive inhibition experiments show the IgE response is directed at several specificities.

Antibodies, Monoclonal↗

PubMed1996

[In situ detection of Epstein-Barr virus in the non-neoplastic gastric glands and infiltrated lymphocytes].

Recently, clonal EBV-DNA and/or EBV-encoded small RNA(EBER1) have been detected in some gastric carcinomas. We reported the first observation of EBV infection in gastric glands with intestinal metaplasia, and characterized the EBV-infected lymphocytes which infiltrated in gastric mucosa. To determine the cellular location of EBV, EBER1 in situ hybridization(ISH) with an EBER1 oligonucleotide probe was applied to paraffin sections of the non-neoplastic gastric mucosa in 80 cases of gastric carcinoma and 49 cases of gastric ulcer. Not only was EBER1 expression detected in the nucleus of gastric cancer cells(5 cases) but also in non-neoplastic gastric epithelial cells(3 cases) and in infiltrated lymphocytes(40 cases). A single or a few shedding non-neoplastic epithelial cells in 2 cases of EBV-associated gastric cancer showed EBER1 expression. In one case, EBER1 was observed in all of the epithelial cells of a few gastric glands with intestinal metaplasia, suggesting that the stem cells of the metaplastic gastric glands were infected with EBV. EBV DNA was also detected in the EBER1-positive metaplastic glands scratched from the paraffin section by a single cell PCR method with a BamHI W primer pair. However, immunohistochemical examination showed that these metaplastic glands lacked expression of EBNA2 and LMP-1. The observation of these rare EBV-infected metaplastic glands reinforces the pre-transformation EBV infection hypothesis for EBV-associated gastric carcinoma. The double staining using ISH and immunohistochemistry revealed that EBER1 positive lymphocytes showed a B cell marker of L26(< 50%) but not T cell markers of UCHL1 and OPD4.

B-Lymphocytes↗

PubMed1996

ELISA-based colorimetric detection of Rickettsia tsutsugamushi DNA from patient sera by nested polymerase chain reaction.

A rapid diagnostic system for scrub typhus was established using colorimetric detection of nested polymerase chain reaction (PCR). This system relied on binding the amplified DNA via a sequence in one of oligodeoxyribonucleotide to the DNA-binding protein GCN4 coated on the well of a micotiter dish. The primer pairs used for the nested PCR were designed on the basis of the homologous nucleotide sequence of the gene that encodes the 56 kDa antigen of serovariants. With this colorimetric PCR, diagnosis can be performed easily from serum samples of patients before the antibody titer increases or in the early stage of the disease. Furthermore, these positive results are able to be confirmed by pathogenic isolation.

Base Sequence↗

PubMed1996

Motif identification neural design for rapid and sensitive protein family search.

The accelerated growth of the molecular sequencing data has generated a pressing need for advanced sequence annotation tools. This paper reports a new method, termed MOTIFIND (Motif Identification Neural Design), for rapid and sensitive protein family identification. The method is extended from our previous gene classification artificial neural system and employs two new designs to enhance the detection of distant relationships. These include an n-gram term weighting algorithm for extracting local motif patterns, and integrated neural networks for combining global and local sequence information. The system has been tested with three protein families of electron transferases, namely cytochrome c, cytochrome b and flavodoxin, with a 100% sensitivity and more than 99.6% specificity. The accuracy of MOTIFIND is comparable to the BLAST database search method, but its speed is more than 20 times faster. The system is much more robust than the PROSITE search which is based on simple signature patterns. MOTIFIND also compares favorably with the BLIMPS search of BLOCKS in detecting fragmentary sequences lacking complete motif regions. The method has the potential to become a full-scale database search and sequence analysis tool.

Algorithms↗

PubMed1995

Malignant lymphoma induction in rabbits by intravenous inoculation of Epstein-Barr-virus-related herpesvirus from HTLV-II-transformed cynomolgus leukocyte cell line (Si-IIA).

Malignant lymphomas, which were usually of T-cell type, were induced in 10 of 13 (77%) male rabbits (Japanese white, 8/10; New Zealand white, 2/3) inoculated i.v. with HTLV-II-transformed simian (Cynomolgus) leukocyte cell line (Si-IIA) cells. Of 7 rabbits injected with cell-free pellets from Si-IIA cultures, 5 also developed malignant lymphoma (15-28 days). Lymphoma development was completely inhibited by inactivation of cell-free pellets from Si-IIA culture with ethyl ether and was almost suppressed by neutralization of the cell-free pellets with anti-Si-IIA sera. Herpesvirus particles were discovered very rarely in Si-IIA cells, in addition to C-type virus particles, by electron microscopy. Si-IIA cells were positive for Epstein-Barr-virus (EBV)-associated nuclear antigen (EBNA) by immunofluorescence (IF) test. Antibody response to viral capsid antigen of EBV was also detected in sera from rabbits inoculated with Si-IIA. EBV-encoded RNA-1 (EBER-1) was demonstrated in Si-IIA, the tumor tissues and all rabbit tumor cell lines by in situ hybridization. EBV DNA was also detected in Si-IIA and rabbit lymphoma cell lines by polymerase chain reaction (PCR) and Southern blotting. However, EBV DNA was amplified only by some primers complementary to human EBV sequence (B95-8), but not by other primers. Integration of HTLV-II provirus genome could not be detected in Si-IIA-induced rabbit tumor cells. Moreover, no lymphoma was induced by inoculation of HTLV-IIC and MOT (other HTLV-II-producing human cell lines), B95-8(EBV-producing cell line) or TALL-1 and peripheral leukocytes from normal Cynomolgus (controls). Neither Herpesvirus saimiri nor H. ateles (simian oncogenic viruses) were detected in Si-IIA cells by IF test. These data suggest that the high rate of lymphoma induction in rabbits may not be caused by HTLV-II, human EBV (B95-8) or well-known simian oncogenic viruses, but by EBV-related herpesvirus derived from Si-IIA cells or HTLV-IIA cells, with which Si-IIA was established. The availability of this animal model promises to clarify the role of EBV in human lymphoma and provides a means of studying prophylactic and therapeutic regimens.

Animals↗

PubMed1995

Temporal and spatial expression of HLA-G messenger RNA in extraembryonic tissues of transgenic mice.

HLA-G, a nonclassical class I molecule, is expressed by trophoblasts, the only fetal cells in direct contact with maternal tissue. Results of previous experiments suggested that a 244-bp region located over 1 kb 5' from exon 1 is critical for extraembryonic expression of HLA-G in transgenic mice. We report here the production of HLA-G transgenic lines with a 6.0-kb HLA-G transgene that includes the 244-bp region. These lines exhibit copy number-dependent and developmentally appropriate transgene expression. One HLA-G transgenic line, G.3.2, exhibits extraembryonic HLA-G mRNA expression levels similar to those seen in human extraembryonic tissues. Studies of the cell-type-specific localization of HLA-G mRNA in placentas from the G.3.2 HLA-G transgenic mouse line show predominant localization of the HLA-G message in the spongiotrophoblast layer. This layer is in a similar anatomic location to the HLA-G-expressing human cytotrophoblast shell. The G.3.2 HLA-G transgenic mouse line should serve as an appropriate model for the study of HLA-G function at the maternal-fetal interface.

Animals↗

PubMed1995

Regulation of N-acetylglucosaminyltransferase V by protein kinases.

When 7721 human hepatocarcinoma cells were treated with 100 nM phorbol-12-myristate-13-acetate (PMA), the activity of N-acetylglucosaminyltransferase V(GnT-V) in the cells varied in accordance with the activity of membranous protein kinase C (PKC), but not with that of cytosolic PKC. Quercetin, a non-specific inhibitor of Ser/Thr protein kinase, and D-sphingosine and staurosporine, two specific inhibitors of PKC, blocked the activation of membranous PKC and GnT-V by PMA. Among the three inhibitors, quercetin was least effective. The inhibitory rates of quercetin and staurosporine toward membranous PKC and GnTV were proportional to the concentrations of the two inhibitors. The activities of GnTV and membranous protein kinase A (PKA) were also induced in parallel by dibutyryl cAMP (db-cAMP) and this induction was blocked by a specific PKA inhibitor. When cell free preparations of 7721 cells and human kidney were treated with alkaline phosphatase (ALP) to remove the phosphate groups, the GnTV activities were decreased. These results suggest that GnTV may be activated by membranous PKC or PKA, indirectly or directly, via phosphorylation of Ser/Thr residues.

Amino Acid Sequence↗

PubMed1995

Effect of retinoic acid on the structure of N-glycans on the surface of human hepatocarcinoma cells and its enzymatic mechanism.

In order to study the effect of retinoic acid on the structure of N-glycans on the cell surface, the N-glycans of glycoproteins on the surface of 7721 human hepatocarcinoma cells were labelled with [3H] mannose, added to the culture medium. The 3H-labelled N-glycans were prepared from cell-surface glycoproteins, desialylated, and subjected to sequential chromatography on concanavalin A and Datura stranonium agglutinin affinity columns to separate the glycans into four fractions of different type and different antennary number. It was found that the percentage of C2C2 biantennary complex type N-glycans was increased, but the high-mannose type as well as the tri- and tetraantennary complex types, especially that with a C2.6 branched structure, were decreased after the cells had been treated with retinoic acid for 3-5 days. Using a Lens culinaris agglutinin affinity column, it was discovered that the core fucose in the biantennary glycan was also decreased. The enzymatic mechanisms of the above changes were revealed in further study to involve the decrease of N-acetylglucosaminyl-transferase V and core alpha-1,6-fucosyltransferase by retinoic acid.

Asparagine↗

PubMed1995

Synthesis and granular localization of tumor necrosis factor-alpha in activated NK cells in the pregnant mouse uterus.

The synthesis and cellular localization of tumor necrosis factor-alpha (TNF-alpha) were studied in mouse GMG cells, which are activated NK cells in uterine decidual tissue during pregnancy. Synthesis of the protein was demonstrated in GMG cells on days 10 and 14 of pregnancy by in situ hybridization of TNF-alpha message. Immunostaining demonstrated that TNF-alpha protein was localized in the cytoplasmic granules of GMG cells at these times. The results suggest that the cytolytic activity of uterine NK cells may be due in part to TNF-alpha, and that this cytokine may be delivered to target cells intracellularly via transmembrane pores formed by perforin, which is also localized in uterine NK cell granules.

Animals↗

PubMed1995

Failed fertilization in vitro: second day micromanipulation of oocytes versus reinsemination.

OBJECTIVE: To compare routine reinsemination with 2nd day micromanipulation in patients with poor day 1 fertilization. DESIGN: A retrospective review of patient records. SETTING: The Mount Sinai Medical Center Assisted Reproductive Technologies Program. PARTICIPANTS: Patients undergoing IVF-ET who had poor fertilization (< 35%) with standard insemination and underwent second day reinsemination of oocytes (group I, n = 84) compared with patients who underwent 2nd day micromanipulation with subzonal insemination (group II, n = 12). MAIN OUTCOME MEASURES: Fertilization rate, cleavage rate, number of embryo transfers, and pregnancy rate. RESULTS: Fertilization rate and cleavage rate were significantly higher in group II patients. Pregnancies per transfer were similar between groups I (3/21, 14.3%) and II (0/9, 0%). Second day fertilization was possible in 9 of 12 group II patients, and fertilization rate was higher than day 1 in all nine, however, only 50% achieved cleavage, and none achieved pregnancy. CONCLUSIONS: Although micromanipulating oocytes that fail to fertilize may identify occult male factor infertility, may help the clinician plan future cycles, and may result in fertilization and even transfer of embryos in some cycles, there were no pregnancies in our series, and, for now, the clinical efficacy of this procedure remains in question.

Cleavage Stage, Ovum↗

PubMed1995

Penetration of hamster oocytes by human sperm in an in vitro fertilization microchamber after insemination with unprocessed semen.

OBJECTIVE: To determine if unprocessed human spermatozoa could capacitate in an IVF microchamber. DESIGN: Semen was loaded into an IVF microchamber with zona-free hamster oocytes, and a hamster penetration test was performed. SETTING: Medical School basic research laboratory. PATIENTS: Men who provided sperm for other laboratory tests. INTERVENTIONS: None. MAIN OUTCOME MEASURES: Penetration of zona-free hamster oocytes by human sperm. RESULTS: In 12 of 19 sperm samples, hamster egg penetration was detected. In most negative cases other measures of sperm function suggested that the SPA might be compromised. CONCLUSIONS: Positive hamster oocyte penetration after loading of unprocessed semen into an IVF microchamber indicates that the chamber supports sperm capacitation. Use of such microchambers thus might reduce or eliminate many steps in sperm processing.

Animals↗

PubMed1995

Gene therapy for lung cancer.

Lung cancer is a leading cause of cancer death and standard chemotherapies are resulting in only marginal improvements in outcome. Experimental approaches involving gene therapy are attractive in this clinical setting. There are two basic types of genes utilized, either those intended to induce immunity or those that are directly tumoricidal. Immunity-inducing genes that have been used in model (and some human) systems include MHC molecules, costimulatory molecules, and cytokines such as IL-2, IL-4, IL-6, GM-CSF. These are intended to induce effective systemic immune responses against tumor antigens which would not otherwise develop. Direct toxic approaches include the reintroduction of tumor suppressor genes or enzymes which convert non-toxic drugs to toxic ones, such as herpes thymidine kinase. As a means for gene delivery, retroviruses are the most common vehicle, although Adenovirus vectors and direct DNA delivery have specific advantages.

Antibody Formation↗