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Chi Zhang

Publications and source records attributed to Chi Zhang.

67 records · Page 4Linked to original sources
PubMed2003

Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G.

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Gō-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T(opt). The optimal folding temperature T(opt) is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T(opt) and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T(opt) and start to diverge when the temperature is lower than T(opt). The distribution of FPT is close to a log-normal-like distribution at T > or = T(opt). At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Computer Simulation↗
PubMed2003

A point mutation in bioactive RNA results in the failure of mutant heart correction in Mexican axolotls.

Ambystoma mexicanum is an intriguing animal model for studying heart development because it carries a mutation in gene c. Hearts of homozygous recessive (c/c) mutant embryos do not contain organized myofibrils and fail to beat. The defect can be corrected by organ-culturing the mutant heart in the presence of RNA from anterior endoderm or endoderm/mesoderm-conditioned medium. By screening a cDNA library made of total conditioned medium RNA from normal axolotl embryonic endoderm, we isolated a single clone (MIR), the synthetic RNA from which corrects the mutant heart defect by promoting myofibrillogenesis and thus was named MIR (myofibrillogenesis inducing RNA). In the present study, we have examined MIR gene expression in mutant axolotl hearts at early pre-heart-beat developmental stages and found its quantitative expression, as detected by RT-PCR, to be the same as in normal hearts. However, careful analysis of sequence data revealed a G-->U point mutation in the mutant MIR RNA. Further computational analyses, using GENEBEE software to compare normal and mutant MIR RNAs show a significant alteration in RNA secondary structure of the point-mutated MIR RNA. The results from bioassay and confocal microscopy immunofluorescent studies demonstrate that, unlike MIR RNA derived from normal embryos, the mutated MIR RNA does not promote myofibrillogenesis in mutant embryonic hearts and fails to rescue/correct the mutant heart defect.

Ambystoma mexicanum↗
PubMed2003

Sheep heart RNA stimulates myofibril formation and beating in cardiac mutant axolotl hearts in organ culture.

In the Mexican axolotl, Ambystoma mexicanum, recessive mutant gene c, when homozygous, results in a failure of the heart to form sarcomeric myofibrils and contract normally. Previous studies have shown that purified RNA from normal anterior endoderm or from medium conditioned with anterior endoderm/pre-cardiac mesoderm has the capacity to rescue mutant hearts in organ culture. In the present study, RNA extracted from adult sheep heart was tested for its capacity to promote differentiation in the mutant axolotl hearts. Mutant hearts cultured in the presence of the sheep heart RNA in Steinberg's solution for 48 h displayed rhythmic contractions. Ultrastructural studies showed that the rescued mutant axolotl ventricular myocardial cells contained myofibrils of normal morphology. Mutant hearts cultured in Steinberg's solution alone did not beat throughout their lengths and myofibrils were not observable in the ventricles. Confocal microscopy confirmed the increase of Tropomyosin expression and formation of myofibrils in mutant hearts treated by sheep heart RNA. Thus, sheep heart RNA promotes myofibrillogenesis and the development of contractile function in embryonic cardiac mutant axolotl hearts.

Ambystoma mexicanum↗
PubMed2003

The polymorphisms of intron1 sequences of HLA-A and -B.

Human leucocyte antigen (HLA) class I antigens are highly polymorphic membrane glycoproteins present on most nucleated cells. The polymorphism region is mainly located in exons 2 and 3 of HLA class I genes, which is flanked by introns 1 and 3. Thus, the sequence information of introns 1 and 3 is important for the genotyping of HLA. However, the information about them has not been extensively reported by now. In this work, the intron 1 sequences of HLA-A and -B of 51 standard genomic DNAs provided by the 13th International Histocompatibility Work Group (IHWG) were cloned and sequenced. The polymorphism of the intron sequences were also analyzed by the software Clustal W 1.82. Some sequences were chosen to compare with the standard sequences published in National Center for Biotechnology Information (NCBI). The comparison showed that all the sequences matched exactly with the standard sequences. The knowledge of intron 1 sequences could be very important not only for developing DNA-based typing strategies for the HLA-A and -B alleles but also for establishing an understanding of the evolutionary mechanisms involved in the polymorphism generation of HLA class I alleles.

HLA-A Antigens↗
PubMed2003

Hedgehog signal transduction via Smoothened association with a cytoplasmic complex scaffolded by the atypical kinesin, Costal-2.

The seven-transmembrane protein Smoothened (Smo) transduces extracellular activation of the Hedgehog (Hh) pathway by an unknown mechanism to increase transcriptional activity of the latent cytoplasmic transcription factor Ci (Cubitus interruptus). Here, we present evidence that Smo associates directly with a Ci-containing complex that is scaffolded and stabilized by the atypical kinesin, Costal-2 (Cos2). This complex constitutively suppresses pathway activity, but Hh signaling reverses its regulatory effect to promote Ci-mediated transcription. In response to Hh activation of Smo, Cos2 mediates accumulation and phosphorylation of Smo at the membrane as well as phosphorylation of the cytoplasmic components Fu and Su(fu). Positive response of Cos2 to Hh stimulation requires a portion of the Smo cytoplasmic tail and the Cos2 cargo domain, which interacts directly with Smo.

Amino Acid Sequence↗
PubMed2002

Vasopressin rapidly increases phosphorylation of UT-A1 urea transporter in rat IMCDs through PKA.

The UT-A1 urea transporter plays an important role in maintaining the hyperosmolar milieu of the inner medulla. Vasopressin increases urea permeability in rat terminal inner medullary collecting ducts (IMCDs) within 5-10 min. To elucidate the mechanism, IMCD suspensions were radiolabeled with [(32)P]orthophosphate. UT-A1 was immunoprecipitated and analyzed by autoradiogram and Western blot. Both the 97- and 117-kDa UT-A1 proteins were phosphorylated. Vasopressin treatment increased the phosphorylation of both UT-A1 proteins at 2 min, which peaked at 5-10 min and remained elevated for up to 30 min. There was a discernable increase in UT-A1 phosphorylation with 10 pM and a 50% increase with 10-100 nM vasopressin. 1-Desamino-8-D-arginine vasopressin (dDAVP) or 8-(4-chlorophenylthio)-cAMP (CPT-cAMP) also increased UT-A1 phosphorylation. The vasopressin-stimulated increase in UT-A1 phosphorylation was blocked by H-89 or a specific peptide inhibitor of protein kinase A. Phosphatase inhibitors (okadaic acid, calyculin) increased UT-A1 phosphorylation. We conclude that vasopressin increases UT-A1 phosphorylation via protein kinase A within 2-5 min in rat IMCDs. This suggests that phosphorylation of UT-A1 may be the mechanism by which vasopressin rapidly increases urea permeability in vivo.

Animals↗
PubMed2002

Protein kinase C-mediated desmin phosphorylation is related to myofibril disarray in cardiomyopathic hamster heart.

The cardiomyopathic (CM) Syrian golden hamster (strain UM-X7.1) exhibits a hereditary cardiomyopathy, which causes premature death resulting from congestive heart failure. The CM animals show extensive cardiac myofibril disarray and myocardial calcium overload. The present study has been undertaken to examine the role of desmin phosphorylation in myofibril disarray observed in CM hearts. The data from skinned myofibril protein phosphorylation assays have shown that desmin can be phosphorylated by protein kinase C (PKC). There is no significant difference in the content of desmin between CM and control hamster hearts. However, the desmin from CM hearts has a higher phosphorylation level than that of the normal hearts. Furthermore, we have examined the distribution of desmin and myofibril organization with immunofluorescent microscopy and immunogold electron microscopy in cultured cardiac myocytes after treatment with the PKC-activating phorbol ester, 12-O-tetradecanylphorbol-13-acetate (TPA). When the cultured normal hamster cardiac cells are treated with TPA, desmin filaments are disassembled and the myofibrils become disarrayed. The myofibril disarray closely mimics that observed in untreated CM cultures. These results suggest that disassembly of desmin filaments, which could be caused by PKC-mediated phosphorylation, may be a factor in myofibril disarray in cardiomyopathic cells and that the intermediate filament protein, desmin, plays an important role in maintaining myofibril alignment in cardiac cells.

Animals↗
PubMed2002

Hepatic cirrhosis increases sensitivity of kidney to endotoxin in rats.

BACKGROUND: Renal failure in cirrhotic patients is a severe complication and endotoxemia might be involved. We investigated the effect of endotoxin on renal function of cirrhotic rats and the potential protective role of N-acetylcysteine (NAC). MATERIAL/METHODS: Hepatic cirrhosis was generated in a rat model by carbon tetrachloride. Both cirrhotic and normal rats were insulted by endotoxin intravenously, while another cirrhotic group was pre-treated with NAC. Blood urea nitrogen (BUN) and creatinine were assayed eight hours later. The changes in serum tumor necrosis factor-a (TNF-a) were assayed by ELISA. The histological changes in the kidney were observed after hematoxylin and eosin staining. RESULTS: Endotoxin increased the BUN and creatinine levels in both normal and cirrhotic rats, with a much higher elevation in the latter group. TNF-a concentration was also increased by endotoxin; the changes are positively correlated with BUN and creatinine. NAC pretreatment significantly attenuates the effects of endotoxin on BUN, creatinine and TNF-a levels in cirrhotic rats with no improvement in systemic toxicity symptoms. There were no obvious histological changes in the kidney of these animals. CONCLUSIONS: Hepatic cirrhosis increased the sensitivity of renal function to endotoxemia, which may be protected by NAC.

Acetylcysteine↗
PubMed2002

[Construction of physical map and polymorphism analysis of mtDNA region R from Mo17CMS-J of maize].

Total DNA from twenty-six CMS lines of maize under Mo17, 77 and W23 nuclear background were used for PCR amplification, including N, T, C, S four groups of cytoplasms. The primers was prefabricated according the sequence of R region published by Zebala (1997). Through these amplifications, mitochondrial DNA fragments were obtained from maize total DNA. Generally the results in one group are identical. And they are different from the others. The amplified fragments were sequenced and also give us much more information about the structure of mitochondrial genes that may lead to CMS. In order to isolate and identify the CMS genes, we developed a new platform to construct physical map of chromosome DNA by means of restriction enzyme double-digestion. The elongation of contigs is based on Southern hybridization. Having retrieved DNA from agarose gel after electrophoresis by beta-agarase, we labelled it with 32P-dCTP as a probe. We detected the positive clones in the gene library. Two contigs were revealed. And a restriction map covering 40 kb was constructed, including R region.

Base Sequence↗
PubMed2002

[Effects of soy extract on lipid metabolism in ovariectomized rats].

OBJECTIVE: To study effects of soy extract on lipid metabolims in ovariectomized rats. METHOD: 90 Wistar rats were randomly divided into 9 groups: control group, sham group, model group, estrogen group, soy isoflavone group of high dose, soy isoflavone group of low dose, soy extract of high dose, soy extract of low dose, and soy polysaccharde group, 10 rats in each group. Except fer of control and sham groups, the test rats were ovariectomized. One week after operation, the rats were treated with different drugs. Six weeks after operation, the rats were killed, with serum and liver taken, and serumglycerol(sGT), cholesterol(sGC), LDL, HDL and liver homogenate hGT, hGC, measured. RESULT: The level of sGC, LDL in ovariectmized rats increased significantly, compared with that in control and sham groups. In liver both the level of hGT and hGC were higher than that in liver from control and sham groups. Administration of estrogen or soy extract or soy isoflavone could attenuate these in ovariectomized rats, but soy polysacchardes did not have any effects. CONCLUSION: Ovariectomized rats have an imbalance of lipid metabolism, the level of hGT and hGC were increased, and administration of estrogen, soy extracts or soy isoflavone could decrease these changes induced by ovariectomizing.

Animals↗
PubMed2002

[Effects of soy extract on energy balance in ovariectomized rats].

OBJECTIVE: In order to study on effects of soy extract on energy metabolims in ovariectomized rats. METHOD: 90 Wistar rats were randomly divided into 9 groups: control group, sham group, model group, estrogen group, soy isoflavone group of high dose, soy isoflavone of low dose, soy extract of high dose, soy extract of low dose, 10 rats each group. Beside of control and sham groups, the rest rats were ovariectomized. One week after operation, the rats were treatmented with different drugs, measument of body weigh and feed weigh each week. Six week after operation, the rats were killed, serum were taken, abdomen lipid were removed and weight. RESULT: The ovariectomized rats took more food and got weight gain significantly; Body mess index(BMI), Abdomen lipid weigh and food transform rate in Model group increased significantly than control and sham groups. Administration of estrogen or soy extract or soy isoflavone could block these changes in ovariectomized rats, but soy polysaccharides did not have the effects. CONCLUSION: Ovariectomized rats have imbalance of energy metabolism, weigh gain and accumulation of abdomen lipid; administration of estrogen, soy extracts or soy isoflavone could attenuate these changes induced by ovariectomizing.

Animals↗
PubMedDate not supplied

Domain graph of Arabidopsis proteome by comparative analysis.

The domain graph of domains and domain combinations of Arabidopsis thaliana is established based on pfam 14.0 database and analyzed via comparison with 10 eukaryotic, 30 bacterial, and 16 archaeal proteomes. The comparative analysis of the domain graphs provides a useful platform for revealing global insights on the evolution of plant kingdom. More importantly, it is a powerful tool for searching not only the possible new function of both plant-specific and nonspecific domains via specific domain combinations in Arabidopsis thaliana but also the functional role of unknown domains. As an example, we present the functional link between ubiquitin and Myb_DNA-binding domains via Bromodomain as the plant specific evidence for the association between transcription and ubiquitin. We further show that PentatricoPeptide Repeats (PPR) proteins have plant-specific links with a wide variety of domains responsible for RNA binding/metabolism, modulation of protein-protein interactions, ubiquitin-conjugation, cell growth/maintenance, catalysis, and others. This further supports the recently proposed association of PPR proteins with specific RNA transcripts and defined effector proteins. Moreover, the domain graph built from tissue-specific genes is frequently associated with DNA binding domains, suggesting that the differentiation of tissue cell types is contributed mostly by tissue-specific transcriptional process. DOGMA (DOmain Graph via coMparitive analysis for Arabidopsis thaliana) is available on-line with a variety of search tools at http://theory.med.buffalo.edu/DOGMA. The database, which allows user-specified search for plant specific domains and their combinations, will be useful as an additional tool for annotation of the proteins that play specific roles in plants and other organisms.

Arabidopsis↗