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Biomedical subjects

Y Shi

Publications and source records attributed to Y Shi.

At least 73 records · Page 4Linked to original sources
PubMed2001

Structure refinement of the layered composite crystal Sc2B1.1C3.2 in a five-dimensional formalism.

The crystal structure of a layered compound Sc(2)B(1.1)C(3.2), scandium boride carbide (M(r) = 140.43), has been re-refined as a commensurate composite crystal using 1795 single-crystal X-ray diffraction intensities with I > 2 sigma(I) collected by Shi, Leithe-Jasper, Bourgeois, Bando & Tanaka [(1999), J. Solid State Chem. 148, 442--449]. The crystal is composed of two layered subsystem structures, i.e. Sc--C--Sc sandwiches and graphite-like layers of the composition B(1/3)C(2/3). The structure refinement was performed in a five-dimensional formalism based on the trigonal superspace group P3m1(p00)(0p0)0m0. The unit cell and other crystal data are a = b = 3.387 (1), c = 6.703 (2) A, V = 66.59 (1) A(3), sigma(1) = (9/7 0 0), sigma(2) = (0 9/7 0), Z = 1, D(x) = 3.501 Mg m(-3). Two different three-dimensional sections through the superspace were analyzed, corresponding to two different superstructure models, one with P3m1 and the other with P3m1. A random distribution of B and C was assumed in the graphite-like layer and 41 structural parameters were introduced. R(F)/wR(F) were 0.0533/0.0482 and 0.0524/0.0476, respectively, for the first and second models. Although the difference between these R(F) or wR(F) values was too fine to exclude one of the models definitely, the advantages of using a superspace group were obvious. It not only brought about better convergence of refinement cycles by virtue of fewer parameters, but also gave an insight into the problem of symmetry of the superstructure.

Journal Article↗
PubMed2001

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signaling and adaptation.

Bacterial chemotaxis is controlled by the conformational changes of the receptors in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signaling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology an understanding of cooperation in ligand binding and receptor signaling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semiquantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.

Adaptation, Physiological↗
PubMed2001

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

BACKGROUND: The availability of complete genome sequences enables all the members of a gene family to be identified without limitations imposed by temporal, spatial or quantitative aspects of mRNA expression. Using the nearly completed human genome sequence, we combined in silico and experimental approaches to define the complete human nuclear receptor (NR) set. This information was used to carry out a comparative genomic study of the NR superfamily. RESULTS: Our analysis of the human genome identified two novel NR sequences. Both these contained stop codons within the coding regions, indicating that both are pseudogenes. One (HNF4 gamma-related) contained no introns and expressed no detectable mRNA, whereas the other (FXR-related) produced mRNA at relatively high levels in testis. If translated, the latter is predicted to encode a short, non-functional protein. Our analysis indicates that there are fewer than 50 functional human NRs, dramatically fewer than in Caenorhabditis elegans and about twice as many as in Drosophila. Using the complete human NR set we made comparisons with the NR sets of C. elegans and Drosophila. Searches for the >200 NRs unique to C. elegans revealed no human homologs. The comparative analysis also revealed a Drosophila member of NR subfamily NR3, confirming an ancient metazoan origin for this subfamily. CONCLUSIONS: This work provides the basis for new insights into the evolution and functional relationships of NR superfamily members.

Amino Acid Sequence↗
PubMed2001

Poly(ADP-ribosyl)ation of transcription factor Yin Yang 1 under conditions of DNA damage.

Under conditions of severe DNA damage the nuclear enzyme poly(ADP-ribose) polymerase 1 (PARP-1) is activated, catalyzing the modification of proteins by forming and attaching to them poly(ADP-ribose) chains. A specific physical interaction between PARP-1 and transcription factor Yin Yang 1 (YY1) in vitro was shown previously, which had important consequences for the activities of both proteins. It is demonstrated here that YY1 and PARP-1 form complexes in vivo. YY1 was transiently poly(ADP-ribosyl)ated immediately after genotoxic treatment of HeLa cells. The narrow time frame of the modification coincides with that known for the activation of PARP-1 under these conditions. This immediate modification correlated with a decreased affinity of YY1 to its cognate DNA binding sites.

Base Sequence↗
PubMed2001

Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1).

Pnn (PNN) is a nuclear and cell adhesion-related protein. Previous work has suggested that Pnn/DRS/memA is a potential tumor suppressor involved in the regulation of cell adhesion and cell migration. Using the ecdysone-inducible mammalian expression system, a stable inducible GFP-tagged human Pnn gene (PNNGFP) expressing 293 cell line was created (EcR293-PNNGFP). Cells induced to express PNNGFP not only exhibited increased cell-cell adhesion but also exhibited changes in cell growth and cell cycle progression. cDNA array analyses, together with real time PCR, revealed that the effects of exogenously expressed Pnn on cellular behavior may be linked to the regulation of the expression of specific subset genes. This subset includes cell cycle-related genes such as p21(cip1/waf1), CDK4, CPR2; cell migration and invasion regulatory genes such as RhoA, CDK5, TIMP-1, MMP-7, and EMMPRIN; and MIC-1. Concordant with previous observations of Pnn-induced phenotype changes, genes coding for epithelial associated processes and cell division controls were elevated, while those coding for increased cell motility and cellular reorganizations were downregulated. We utilized p21 promoter-luciferase reporter constructs and demonstrated that a marked stimulation of p21 promoter activity in 293 cells correlated with increased Pnn expression. Taken together, these data indicate that Pnn may participate in the regulation of gene expression, thereby, positively promoting cell-cell adhesion, and negatively affecting cell migration and cell proliferation.

Cell Adhesion↗
PubMed2001

Transcription factor Yin Yang 1 stimulates poly(ADP-ribosyl)ation and DNA repair.

Poly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme that catalyzes the synthesis of ADP-ribose polymers from NAD(+). The function of PARP-1 is related to important nuclear processes including DNA repair and transcription. Previous studies demonstrated a specific physical interaction between PARP-1 and the transcription factor Yin Yang 1 (YY1) in vitro. In this study, a functional relationship between both proteins in response to genotoxic treatment of cells is presented. The interaction of YY1 with PARP-1 greatly stimulates the enzymatic activity of PARP-1. Consistent with this, the overexpression of YY1 in HeLa cells resulted in an enhanced synthesis of poly(ADP-ribose) and an acceleration of DNA repair in response to a treatment with methyl-N'-nitro-N'-nitrosoguanidine.

Cell Cycle↗
PubMed2001

Oxidative stress and lipid retention in vascular grafts: comparison between venous and arterial conduits.

BACKGROUND: Because saphenous vein grafts (SVGs) exhibit greater cellular heterogeneity and worse clinical outcomes than arterial grafts (AGs), we examined oxidative stress and lipid retention in different vascular conduits. METHODS AND RESULTS: In a porcine model of graft interposition into carotid artery, superoxide anion (.O(2)(-)) was measured at 2 weeks after surgery. SVGs demonstrated increased.O(2)(-) production compared with AGs (SOD-inhibitable nitro blue tetrazolium reduction, P<0.01). The NAD(P)H oxidase inhibitor diphenyleneiodonium (P<0.01) abolished SVG-derived.O(2)(-), whereas the inhibitors of other pro-oxidant enzymes were ineffective. The change in oxidative stress was also reflected by lower activity of the endogenous antioxidant superoxide dismutase in SVGs than in AGs (P<0.001). SVG remodeling was associated with increased synthesis of sulfated glycosaminoglycans and augmented expression of a core protein, versican. These changes were accompanied by SVGs retaining significantly more (125)I-labeled LDL than AGs ex vivo (P<0.001). In hyperlipemic animals, lipid accumulation and oxidized epitopes were preferentially noted in the intima of SVGs at 1 month after surgery. CONCLUSIONS: This study demonstrated significant differences in the biology of SVGs and AGS: SVGs exhibited higher oxidative stress, LDL accumulation, and the presence of oxidized epitopes. These findings suggest that proatherogenic changes in SVGs may commence early after surgical revascularization.

Animals↗
PubMed2001

[Keratin 17 gene mutation in patients with steatocystoma multiplex].

OBJECTIVE: To study the relationship between steatocystoma multiplex (SCM) and keratin 17 gene mutation. METHODS: The keratin 17 gene mutation in the cDNA of cystic tissue of 5 patients of SCM and in the DNA in peripheral blood of 25 patients with SCM from a SCM family was studied by direct sequencing of the RT-PCR products, nested PCR, and restricted fraction length polymorphism (RFLP) analysis. Thirty-nine blood specimens from the unaffected members of that family were collected and tested too. Ten DNA pool specimens and other 2000 DNA pool specimens of normal individuals outside that SCM family were used as controls. RESULTS: In the base 428, 94(th) codon in keratin 17 gene in the cDNA of patients' cystic tissue, R94C mutation, a G-->A mutation, was detected Nested PCR, and restricted enzyme Acil polymorphism analysis showed that in the DNA specimens of peripheral blood of patients a mutated allele lacking enzyme cutting locus was detected, thus causing an uncut band with 200 bp while the corresponding allele was cut and caused two bands with 108 bp and 92 bp. In the DNA pool specimens of normal controls only these two bands with 108 bp and 92 bp were observed. CONCLUSION: The R94C mutation in keratin 17 gene is one of the genetic bases of SCM in Chinese. The results of this study provide scientific data for genetic diagnosis and counseling of SCM.

Adolescent↗
PubMed2001

Retrograde tracing of zinc-enriched (ZEN) neuronal somata in rat spinal cord.

The zinc selenide autometallographic (ZnSeAMG) technique for tracing the retrograde axonal transport of zinc ions in zinc-enriched (ZEN) neurons was used to map the distribution of ZEN neuronal somata in rat spinal cord. After a local injection of sodium selenide into the dorsal or ventral horn, ZnSeAMG-labeled ZEN neurons appeared in Rexed's laminae V, VII and X while laminae I and II were void. A few scattered ZEN somata were observed in the remaining laminae. The labeled neurons differed in shape and size, and the relatively high level of labeled somata around the injection site suggests that many ZEN neurons have relatively short axons or boutons en passage close to the neuronal origin. Ultrastructurally, the retrogradely transported zinc selenide clusters were found in the lysosomes of ZEN somata and proximal dendrites. Electron microscopic studies also revealed two different kinds of ZEN terminals: (1) terminals with flat synaptic vesicles making symmetric synaptic contacts; and (2) terminals with round vesicles making asymmetric synaptic contacts. The present study suggests the existence of propriospinal systems of ZEN neurons comprising both segmental and intersegmental ZEN connections and having either inhibitory or excitatory ZEN terminals. The ZEN neurons seem to form a vast network of terminals located primarily in the gray matter, but also contacting dendrites radiating into the white matter. Important functions of this rather massive system of ZEN terminals can not be deduced from our present knowledge, but the systems appear to be involved in both motor and sensory functions.

Animals↗
PubMed2001

Sharp, an inducible cofactor that integrates nuclear receptor repression and activation.

A yeast two-hybrid screen using the conserved carboxyl terminus of the nuclear receptor corepressor SMRT as a bait led to the isolation of a novel human gene termed SHARP (SMRT/HDAC1 Associated Repressor Protein). SHARP is a potent transcriptional repressor whose repression domain (RD) interacts directly with SMRT and at least five members of the NuRD complex including HDAC1 and HDAC2. In addition, SHARP binds to the steroid receptor RNA coactivator SRA via an intrinsic RNA binding domain and suppresses SRA-potentiated steroid receptor transcription activity. Accordingly, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. Surprisingly, the expression of SHARP is itself steroid inducible, suggesting a simple feedback mechanism for attenuation of the hormonal response.

Amino Acid Motifs↗
PubMed2001

PEA3 sites within the progression elevated gene-3 (PEG-3) promoter and mitogen-activated protein kinase contribute to differential PEG-3 expression in Ha-ras and v-raf oncogene transformed rat embryo cells.

Transformation of normal cloned rat embryo fibroblast (CREF) cells with cellular oncogenes results in acquisition of anchorage-independent growth and oncogenic potential in nude mice. These cellular changes correlate with an induction in the expression of a cancer progression-promoting gene, progression elevated gene-3 (PEG-3). To define the mechanism of activation of PEG-3 as a function of transformation by the Ha-ras and v-raf oncogenes, evaluations of the signaling and transcriptional regulation of the approximately 2.0 kb promoter region of the PEG-3 gene, PEG-Prom, was undertaken. The full-length and various mutated regions of the PEG-Prom were linked to a luciferase reporter construct and tested for promoter activity in CREF and oncogene-transformed CREF cells. An analysis was also performed using CREF cells doubly transformed with Ha-ras and the Ha-ras specific suppressor gene Krev-1, which inhibits the transformed phenotype in vitro. These assays document an association between expression of the transcription regulator PEA3 and PEG-3. The levels of PEA3 and PEG-3 RNA and proteins are elevated in the oncogenically transformed CREF cells, and reduced in transformation and tumorigenic suppressed Ha-ras/Krev-1 doubly transformed CREF cells. Enhanced tumorigenic behavior, PEG-3 promoter function and PEG-3 expression in Ha-ras transformed cells were all dependent upon increased activity within the mitogen-activated protein kinase (MAPK) pathway. Electrophoretic mobility shift assays and DNase I footprinting experiments indicate that PEA3 binds to sites within the PEG-Prom in transformed rodent cells in an area adjacent to the TATA box in a MAPK-dependent fashion. These findings demonstrate an association between Ha-ras and v-raf transformation of CREF cells with elevated PEA3 and PEG-3 expression, and they implicate MAPK signaling via PEA3 as a signaling cascade involved in activation of the PEG-Prom.

Animals↗
PubMed2001

Degree of antigen adsorption in the vaccine or interstitial fluid and its effect on the antibody response in rabbits.

The effect of the degree of adsorption of lysozyme by aluminium hydroxide adjuvant on the immune response in rabbits was studied. The surface charge of the adjuvant was modified by pretreatment with phosphate anion to produce five vaccines having degrees of adsorption ranging from 3 to 90%. The degree of adsorption of vaccines exhibiting 3, 35 or 85% adsorption changed to 40% within 1 h after each vaccine was mixed with sheep interstitial fluid to simulate subcutaneous administration. The mean anti-lysozyme antibody titers produced by the vaccines were the same and were four times greater than that produced by a lysozyme solution. Thus, the degree of adsorption of lysozyme in sheep interstitial fluid rather than the degree of adsorption in the vaccine correlated with the immune response.

Adjuvants, Immunologic↗
PubMed2001

Formation of a stable heterodimer between Smad2 and Smad4.

Smad proteins mediate transforming growth factor beta signaling from the cell membrane to the nucleus. Upon phosphorylation by the activated receptor kinases, the receptor-regulated Smad, such as Smad2, forms a heterocomplex with the co-mediator Smad, Smad4. This heterocomplex is then translocated into the nucleus, where it associates with other transcription factors and regulates expression of ligand-responsive genes. The stoichiometry between receptor-regulated Smad and co-mediator Smad is important for understanding the molecular mechanisms of the signaling process. Using purified recombinant proteins, we demonstrate that Smad2 and Smad4 form a stable heterodimer and that the Smad4 activation domain is important for the formation of this complex. Many tumor-derived missense mutations disrupt the formation of this heterocomplex in in vitro interaction assays. Mapping these mutations onto the structures of Smad4 and Smad2 identifies a symmetric interface between these two Smad proteins. Importantly, two previous models on the formation of a heterocomplex are incompatible with our observations and other reported evidence.

Chromatography, Gel↗
PubMed2001

[Alteration of subcellular distribution of protein kinase C isoforms in swelling-activated multi-drug-resistant gastric cancer cells and its significance].

OBJECTIVE: To study the alteration of expression and subcellular distribution of classical protein kinase (cPKC) isoforms in gastric cancer cells SGC7901 and their multidrug-resistant cell line SGC7901/VCR under condition of swelling activation and to study the significance of such alterations. METHODS: Immuno-fluorescence technique and Western Blotting were used to determine the expression and subcellular distribution of cPKC isoforms in gastric cancer cells SGC7901 and its multidrug-resistant cell line SGC7901/VCR under normal condition and during continuous hypotonic perfusion. The co-expression of p-glycoprotein (Pgp) and protein kinase C alpha (PKC alpha) was visualized by immunofluorescence double labeling and laser confocus microscopy. RESULTS: Under the normal condition, the four isoenzymes of cPKC were expressed in both the cell membrane and the nuclei of the gastric cancer cells SGC7901 and their multidrug-resistant cell line SGC7901/VCR; PKC alpha was strongly positively expressed in the multidrug-resistant cells and positively expressed in the drug-sensitive cells; PKC beta I and PKC beta II were positively expressed in both drug-resistant and drug-sensitive cells, and PKC gamma was strongly positively expressed in both cells. In drug-resistant cell line, cell-swelling and translocation of PKC alpha and PKC gamma were observed ten minutes after continuous hypotonic perfusion. Thirty minutes after the perfusion, almost all the PKCalpha was translocated into the cell membrane of SGC7901/VCR, part of the PKC gamma was translocated into the nucleus, and the cell volume increased to two to three times as much as before. Sixty minutes later, the subcellular distribution of PKCalpha and PKC gamma and the cell volume returned to normal. In drug-sensitive cells, 10 approximately 20 minutes after the continuous hypotonic perfusion nearly all the PKCalpha was translocated into the cell membrane, part of PKC gamma was translocated into the cell membrane, and the cell volume increased to two to three times as much as before. Forty minutes later, PKCalpha and PKCgamma had basically returned to normal. The subcellular distribution of PKCbeta I and PKC beta II remained unchanged in both SGC7901 and SGC7901/VCR. Co-expression of Pgy and PKCalpha was observed in both drug-sensitive and drug-resistant cells, especially in the former. CONCLUSION: Only PKCalpha and PKC gamma isoforms play an important role in the regulation of signal transduction of Pgy and cell volume under continuous perfusion and are related to the expression of PKC alpha and Pgy. PKC beta I and PKC beta II may have nothing to do with such processes.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2001

Heat shock protein 90 mediates the balance of nitric oxide and superoxide anion from endothelial nitric-oxide synthase.

The balance of nitric oxide (.NO) and superoxide anion (O(2)) plays an important role in vascular biology. The association of heat shock protein 90 (Hsp90) with endothelial nitric-oxide synthase (eNOS) is a critical step in the mechanisms by which eNOS generates.NO. As eNOS is capable of generating both.NO and O(2), we hypothesized that Hsp90 might also mediate eNOS-dependent O(2) production. To test this hypothesis, bovine coronary endothelial cells (BCEC) were pretreated with geldanamycin (GA, 10 microg/ml; 17.8 microm) and then stimulated with the calcium ionophore, (5 microm). GA significantly decreased -stimulated eNOS-dependent nitrite production (p < 0.001, n = 4) and significantly increased -stimulated eNOS-dependent O(2) production (p < 0.001, n = 8). increased phospho-eNOS(Ser-1179) levels by >1.6-fold over vehicle (V)-treated levels. Pretreatment with GA by itself or with increased phospho-eNOS levels. In unstimulated V-treated BCEC cultures low amounts of Hsp90 were found to associate with eNOS. Pretreatment with GA and/or increased the association of Hsp90 with eNOS. These data show that Hsp90 is essential for eNOS-dependent.NO production and that inhibition of ATP-dependent conformational changes in Hsp90 uncouples eNOS activity and increases eNOS-dependent O(2) production.

Animals↗
PubMed2001

An essential role for nuclear receptors SXR/PXR in detoxification of cholestatic bile acids.

Hepatic hydroxylation is an essential step in the metabolism and excretion of bile acids and is necessary to avoid pathologic conditions such as cholestasis and liver damage. In this report, we demonstrate that the human xenobiotic receptor SXR (steroid and xenobiotic receptor) and its rodent homolog PXR (pregnane X receptor) serve as functional bile acid receptors in both cultured cells and animals. In particular, the secondary bile acid derivative lithocholic acid (LCA) is highly hepatotoxic and, as we show here, a metabolic substrate for CYP3A hydroxylation. By using combinations of knockout and transgenic animals, we show that activation of SXR/PXR is necessary and sufficient to both induce CYP3A enzymes and confer resistance to toxicity by LCA, as well as other xenotoxicants such as tribromoethanol and zoxazolamine. Therefore, we establish SXR and PXR as bile acid receptors and a role for the xenobiotic response in the detoxification of bile acids.

Animals↗
PubMed2001

Structural basis of caspase-7 inhibition by XIAP.

The inhibitor of apoptosis (IAP) proteins suppress cell death by inhibiting the catalytic activity of caspases. Here we present the crystal structure of caspase-7 in complex with a potent inhibitory fragment from XIAP at 2.45 A resolution. An 18-residue XIAP peptide binds the catalytic groove of caspase-7, making extensive contacts to the residues that are essential for its catalytic activity. Strikingly, despite a reversal of relative orientation, a subset of interactions between caspase-7 and XIAP closely resemble those between caspase-7 and its tetrapeptide inhibitor DEVD-CHO. Our biochemical and structural analyses reveal that the BIR domains are dispensable for the inhibition of caspase-3 and -7. This study provides a structural basis for the design of the next-generation caspase inhibitors.

Apoptosis↗