PharmGED: pharmacogenetic effect database.
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Databases, Genetic↗
Biomedical subjects
H L Zhang
Publications and source records attributed to H L Zhang.
PharmGED: Pharmacogenetic Effect Database.
Prediction and elucidation of pharmacogenetic effects is important for facilitating the development of personalized medicines. Knowledge of polymorphism-induced and other types of drug-response variations is needed for facilitating such studies. Although databases of pharmacogenetic knowledge, polymorphism and toxicogenomic information have appeared, some of the relevant data are provided in separate web-pages and in terms of relatively long descriptions quoted from literatures. To facilitate easy and quick assessment of the relevant information, it is helpful to develop databases that provide all of the information related to a pharmacogenetic effect in the same web-page and in brief descriptions. We developed a database, Pharmacogenetic Effect Database (PharmGED), for providing sequence, function, polymorphism, affected drugs and pharmacogenetic effects. PharmGED can be accessed at http://bidd.cz3.nus.edu.sg/phg/ free of charge for academic use. It currently contains 1825 entries covering 108 disease conditions, 266 distinct proteins, 693 polymorphisms, 414 drugs/ligands cited from 856 references.
Animals↗
Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties.
Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational methods have been developed for predicting MHC-binding peptides, which achieve impressive prediction accuracies of 70-90% for binders and 40-80% for non-binders. These methods have been developed for peptides of fixed lengths, for a limited number of alleles, trained from small number of non-binders, and in some cases based straightforwardly on sequence. These limit prediction coverage and accuracy particularly for non-binders. It is desirable to explore methods that predict binders of flexible lengths from sequence-derived physicochemical properties and trained from diverse sets of non-binders. This work explores support vector machines (SVM) as such a method for developing prediction systems of 18 MHC class I and 12 class II alleles by using 4208-3252 binders and 234,333-168,793 non-binders, and evaluated by an independent set of 545-476 binders and 110,564-84,430 non-binders. Binder accuracies are 86-99% for 25 and 70-80% for 5 alleles, non-binder accuracies are 96-99% for 30 alleles. Binder accuracies are comparable and non-binder accuracies substantially improved against other results. Our method correctly predicts 73.3% of the 15 newly-published epitopes in the last 4 months of 2005. Of the 251 recently-published HLA-A*0201 non-epitopes predicted as binders by other methods, 63 are predicted as binders by our method. Screening of HIV-1 genome shows that, compared to other methods, a comparable percentage (75-100%) of its known epitopes is correctly predicted, while a lower percentage (0.01-5% for 24 and 5-8% for 6 alleles) of its constituent peptides are predicted as binders. Our software can be accessed at .
Alleles↗
Prediction of the functional class of lipid binding proteins from sequence-derived properties irrespective of sequence similarity.
Lipid binding proteins play important roles in signaling, regulation, membrane trafficking, immune response, lipid metabolism, and transport. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting lipid binding proteins irrespective of sequence similarity. This work explores the use of support vector machines (SVMs) as such a method. SVM prediction systems are developed using 14,776 lipid binding and 133,441 nonlipid binding proteins and are evaluated by an independent set of 6,768 lipid binding and 64,761 nonlipid binding proteins. The computed prediction accuracy is 78.9, 79.5, 82.2, 79.5, 84.4, 76.6, 90.6, 79.0, and 89.9% for lipid degradation, lipid metabolism, lipid synthesis, lipid transport, lipid binding, lipopolysaccharide biosynthesis, lipoprotein, lipoyl, and all lipid binding proteins, respectively. The accuracy for the nonmember proteins of each class is 99.9, 99.2, 99.6, 99.8, 99.9, 99.8, 98.5, 99.9, and 97.0%, respectively. Comparable accuracies are obtained when homologous proteins are considered as one, or by using a different SVM kernel function. Our method predicts 86.8% of the 76 lipid binding proteins nonhomologous to any protein in the Swiss-Prot database and 89.0% of the 73 known lipid binding domains as lipid binding. These findings suggest the usefulness of SVMs for facilitating the prediction of lipid binding proteins. Our software can be accessed at the SVMProt server (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi).
Algorithms↗
The IA-2 interactome.
AIMS/HYPOTHESIS: Islet antigen-2 (IA-2), a major autoantigen in type 1 diabetes, is an enzymatically inactive member of the transmembrane protein tyrosine phosphatase (PTP) family. IA-2 is located in dense-core secretory vesicles and is involved in the regulation of insulin secretion. The present experiments were initiated to identify those proteins that interact with IA-2 (i.e. the IA-2 interactome) as a first step towards elucidating the mechanism(s) by which IA-2 influences insulin secretion and serves as an autoantigen. MATERIALS AND METHODS: To determine the proteins with which IA-2 interacts, a yeast two-hybrid system was used to screen a human foetal library, and deletion mutants were used to determine the binding sites. Positive interactions were confirmed by immunoprecipitation pull-down experiments using cell lysate from transfected mammalian cell lines. RESULTS: Six new interacting proteins were identified by this approach: mitogen-activated protein kinase-activating death domain (MADD), the MADD isoform IG20, PTPrho, PTPsigma, sorting nexin 19 (SNX19) and cyclophilin A. Using a series of IA-2 deletion mutants, we identified the regions on the IA-2 molecule to which five of the interacting proteins bound. Amino acids 744-979 of IA-2 were required for the maximum binding of MADD, IG20 and SNX19, whereas amino acids 602-907 of IA-2 were required for the maximum binding of PTPrho and PTPsigma. Pull-down experiments with cell lysate from transfected mammalian cells confirmed the binding of the interacting proteins to IA-2. CONCLUSIONS/INTERPRETATION: The IA-2 interactome based on, pull-down experiments, currently consists of 12 proteins. The identification of these interacting proteins provides clues as to how IA-2 exerts its biological functions.
Animals↗
Prediction of functional class of novel plant proteins by a statistical learning method.
In plant genomes, the function of a substantial percentage of the putative protein-coding open reading frames (ORFs) is unknown. These ORFs have no significant sequence similarity to known proteins, which complicates the task of functional study of these proteins. Efforts are being made to explore methods that are complementary to, or may be used in combination with, sequence alignment and clustering methods. A web-based protein functional class prediction software, SVMProt, has shown some capability for predicting functional class of distantly related proteins. Here the usefulness of SVMProt for functional study of novel plant proteins is evaluated. To test SVMProt, 49 plant proteins (without a sequence homolog in the Swiss-Prot protein database, not in the SVMProt training set, and with functional indications provided in the literature) were selected from a comprehensive search of MEDLINE abstracts and Swiss-Prot databases in 1999-2004. These represent unique proteins the function of which, at present, cannot be confidently predicted by sequence alignment and clustering methods. The predicted functional class of 31 proteins was consistent, and that of four other proteins was weakly consistent, with published functions. Overall, the functional class of 71.4% of these proteins was consistent, or weakly consistent, with functional indications described in the literature. SVMProt shows a certain level of ability to provide useful hints about the functions of novel plant proteins with no similarity to known proteins.
Artificial Intelligence↗
Adult neural stem cell therapy: expansion in vitro, tracking in vivo and clinical transplantation.
Neural stem cells (NSCs) are present not only in the developing nervous systems, but also in the adult human central nervous system (CNS). It is long thought that the subventricular zone of the lateral ventricles and the dentate gyrus of the hippocampus are the main sources of human adult NSCs, which are considered to be a reservoir of new neural cells. Recently adult NSCs with potential neural capacity have been isolated from white matter and inferior prefrontal subcortex in the human brain. Rapid advances in the stem cell biology have raised appealing possibilities of replacing damaged or lost neural cells by transplantation of in vitro-expanded stem cells and/or their neuronal progeny. However, sources of stem cells, large scale expansion, control of the differentiations, and tracking in vivo represent formidable challenges. In this paper we review the characteristics of the adult human NSCs, their potentiality in terms of proliferation and differentiation capabilities, as well as their large scale expansion for clinical needs. This review focuses on the major advances in brain stem cell-based therapy from the clinical perspective, and summarizes our work in clinical phase I-II trials with autologuous transplantation of adult NSCs for patients with open brain trauma. It also describes multiple approaches to monitor adult human NSCs labeled superparamagnetic nanoparticles after transplantation and explores the intriguing possibility of stem cell transplantation.
Animals↗
A novel locus (DSAP2) for disseminated superficial actinic porokeratosis maps to chromosome 15q25.1-26.1.
BACKGROUND: Disseminated superficial actinic porokeratosis (DSAP) is a chronic cutaneous disorder characterized by multiple superficial keratotic lesions surrounded by a slightly raised keratotic border. It develops in teenagers in sun-exposed areas of skin and usually follows an autosomal dominant inheritance pattern. The first locus for DSAP was localized to chromosome 12q23.2-24.1, but no gene responsible for porokeratosis has been identified to date. OBJECTIVES: To determine whether DSAP is a genetically heterogeneous disorder and to identify the disease gene locus in a three-generation Chinese family with DSAP. METHODS: Genetic linkage analysis was carried out in this family using 15 microsatellite markers between D12S1671 and D12S369 on chromosome 12q, followed by a genome-wide scan with 382 microsatellite markers from the autosomes. RESULTS: Genetic linkage analysis with chromosome 12q markers suggested that the locus in this family is not linked to chromosome 12q. A genome-wide scan and fine mapping finally localized the locus for DSAP in this family to a 6.4-cM region between markers D15S1023 and D15S1030 at chromosome 15q25.1-26.1. This DSAP locus was named DSAP2. CONCLUSIONS: The previous results and this study have shown that DSAP is a genetically heterogeneous disorder; a novel locus for DSAP, termed DSAP2, was mapped to a 6.4-cM region between markers D15S1023 and D15S1030.
Adolescent↗
Structure of an acidic phospholipase A(2) from the venom of Deinagkistrodon acutus in a new crystal form.
The three-dimensional structure of an acidic phospholipase A(2) purified from the venom of Deinagkistrodon acutus (Agkistrodon acutus) was determined in a new crystal form by molecular replacement at 0.28 nm resolution with a crystallographic R factor of 21.9% (R-free=25.7%) and reasonable stereochemistry. Being similar to the previous reported crystal form, a significant conformational adaptation of segment 14-23 at the dimer interface was observed. This segment was related to the "interface recognition site" (IRS). It was found that a positively charged residue at position 34 seems to be a common feature for most of hemolytic PLA(2)s belonging to group II. Structural comparison between the two crystal forms showed that NaCl had significant effects on the crystal packing, thus leading to dramatic changes of the unit cell parameters. In the new crystal form, MPD (2-methyl-2, 4-pentanediol) molecules exist in the hydrophobic channel of the enzyme.
Agkistrodon↗
Evidence that a burst of DNA depurination in SENCAR mouse skin induces error-prone repair and forms mutations in the H-ras gene.
Treatment of SENCAR mouse skin with dibenzo[a,l]pyrene results in abundant formation of abasic sites that undergo error-prone excision repair, forming oncogenic H-ras mutations in the early preneoplastic period. To examine whether the abundance of abasic sites causes repair infidelity, we treated SENCAR mouse skin with estradiol-3,4-quinone (E(2)-3,4-Q) and determined adduct levels 1 h after treatment, as well as mutation spectra in the H-ras gene between 6 h and 3 days after treatment. E(2)-3,4-Q formed predominantly (> or =99%) the rapidly-depurinating 4-hydroxy estradiol (4-OHE(2))-1-N3Ade adduct and the slower-depurinating 4-OHE(2)-1-N7Gua adduct. Between 6 h and 3 days, E(2)-3,4-Q induced abundant A to G mutations in H-ras DNA, frequently in the context of a 3'-G residue. Using a T.G-DNA glycosylase (TDG)-PCR assay, we determined that the early A to G mutations (6 and 12 h) were in the form of G.T heteroduplexes, suggesting misrepair at A-specific depurination sites. Since G-specific mutations were infrequent in the spectra, it appears that the slow rate of depurination of the N7Gua adducts during active repair may not generate a threshold level of G-specific abasic sites to affect repair fidelity. These results also suggest that E(2)-3,4-Q, a suspected endogenous carcinogen, is a genotoxic compound and could cause mutations.
Animals↗
Neurotrophin-induced transport of a beta-actin mRNP complex increases beta-actin levels and stimulates growth cone motility.
Neurotrophin regulation of actin-dependent changes in growth cone motility may depend on the signaling of beta-actin mRNA transport. Formation of an RNP complex between the beta-actin mRNA zipcode sequence and Zipcode Binding Protein 1 (ZBP1) was required for its localization to growth cones. Antisense oligonucleotides to the zipcode inhibited formation of this RNP complex in vitro and the neurotrophin-induced localization of beta-actin mRNA and ZBP1 granules. Live cell imaging of neurons transfected with EGFP-ZBP1 revealed fast, bidirectional movements of granules in neurites that were inhibited by antisense treatment, as visualized by FRAP analysis. NT-3 stimulation of beta-actin protein localization was dependent on the 3'UTR and inhibited by antisense treatment. Growth cones exhibited impaired motility in the presense of antisense. These results suggest a novel mechanism to influence growth cone dynamics involving the regulated transport of mRNA.
3' Untranslated Regions↗
A randomized controlled clinical trial on the treatment of Thymosin a1 versus interferon-alpha in patients with hepatitis B.
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Adjuvants, Immunologic↗
Serum antioxidant status of civil aircrew.
Objective. To study the serum antioxidant status in civil aircrew members who had more than 4000 h of cumulative flight hours, therefore exposed to a higher dose of cosmic radiation comparing to the dose received by ground residents. Method. Differences in the serum levels of total antioxidant capacity (TAOC), superoxide dismutase (SOD) and malondialdehyde (MDA) were investigated in 230 crew members, 37 local ground residents in Xinjiang, and 37 ground residents in Tianjin. Result. Significantly higher levels of all the three serum indexes were found in civil aircrew members. Serum levels of TAOC and SOD were higher in Xinjiang than in Tianjin ground residents, although no difference was found for MDA. Positive correlations were observed among the three serum indexes in this study. Conclusion. The elevated serum level of MDA in civil aircrew members deserves a proper attention by health care policy makers.
Adult↗
Potentiation of ethanol-induced loss of the righting reflex by ascorbic acid in mice: interaction with dopamine antagonists.
The present investigation was carried out to determine the effect of ascorbic acid on ethanol-induced loss of the righting reflex (LORR) and the interactions between ascorbic acid and dopamine receptor antagonists in affecting this action of ethanol in mice. To test the effect of each drug on ethanol-induced LORR, ascorbic acid (31.25, 62.5, 125, 250, 500, 1000 mg/kg intraperitoneally [IP]) and dopamine receptor antagonists (haloperidol 0.5, 1.0 mg/kg; L-sulpiride 20, 40, 80 mg/kg; clozapine 0.625, 1.25, 2.5 mg/kg; SCH 23390 0.5, 1.0, 2.0 mg/kg subcutaneously [SC]) were administered, respectively, 30 min before ethanol (4.0 g/kg IP) administration. Ascorbic acid, at the dose of 1000 mg/kg, significantly potentiated ethanol-induced LORR in mice. Dopamine D(2) antagonists haloperidol (0.5, 1.0 mg/kg SC), and L-sulpiride (80 mg/kg SC) also significantly prolonged the duration of LORR induced by ethanol. Clozapine and SCH 23390, at the doses used, did not affect ethanol-induced LORR. In the interaction study, the synergistic effect of ascorbic acid (1000 mg/kg IP) on ethanol-induced LORR was significantly enhanced by dopamine D(2) antagonists haloperidol, L-sulpiride, and clozapine, and the highest dose of dopamine D(1) antagonist SCH 23390. These results suggest that ascorbic acid may potentiate ethanol-induced LORR partially via a mechanism mainly linked to blockade of dopamine D(2) receptors.
Animals↗
[Cloning and tissue expressive pattern analysis of the human ribosomal S6 kinase-RPS6KA5 cDNA].
Human ribosomal protein S6 kinase includes two protein families: P90RSK and P70S6K, they participate in two different signaling pathways. When the two kinases were inhibited by their antibodies or rapamycin, the proliferation of cells was arrested. However, their analog, the immunosupressant FK-506, can inhibit the proliferation of fibroblast PBL1 without interfering with the activities of P90RSK, P70S6K and MAPK. We take the tactics of "homolog screening" to demonstrate whether there are some novel proteins which can substitute for the known P90RSK and P70S6K or other pathways without interfering with the known P90RSK and P70S6K. With the conserved sequence of mouse p90RSK as a probe, we screened the homologous sequence in NCBI EST database and got three human EST fragments. With the assembled contig as a probe to screen human brain cDNA library, a full-length cDNA of 3833 bp was attained. It contains a completed open reading frame from 165 bp to 2570 bp encoding 802 amino acids. The putative protein has higher homology with other members of p90RSK family. The gene was named RPS6KA5, the accession number in GenBank is AF090421. Northern hybridization showed the gene expressed in 16 human tissues tested, and the gene was localized in 14q31-32.1 by RH mapping. Another novel P70S6K gene has also been cloned. Thus, our initial presumption that there is an analog of known P90RSK and P70S6K in human beings was proved.
Amino Acid Sequence↗
Neurotrophin regulation of beta-actin mRNA and protein localization within growth cones.
Neurotrophins play an essential role in the regulation of actin-dependent changes in growth cone shape and motility. We have studied whether neurotrophin signaling can promote the localization of beta-actin mRNA and protein within growth cones. The regulated localization of specific mRNAs within neuronal processes and growth cones could provide a mechanism to modulate cytoskeletal composition and growth cone dynamics during neuronal development. We have previously shown that beta-actin mRNA is localized in granules that were distributed throughout processes and growth cones of cultured neurons. In this study, we demonstrate that the localization of beta-actin mRNA and protein to growth cones of forebrain neurons is stimulated by neurotrophin-3 (NT-3). A similar response was observed when neurons were exposed to forskolin or db-cAMP, suggesting an involvement of a cAMP signaling pathway. NT-3 treatment resulted in a rapid and transient stimulation of PKA activity that preceded the localization of beta-actin mRNA. Localization of beta-actin mRNA was blocked by prior treatment of cells with Rp-cAMP, an inhibitor of cAMP-dependent protein kinase A. Depolymerization of microtubules, but not microfilaments, inhibited the NT-3-induced localization of beta-actin mRNA. These results suggest that NT-3 activates a cAMP-dependent signaling mechanism to promote the microtubule-dependent localization of beta-actin mRNA within growth cones.
Actin Cytoskeleton↗
Serotonin derivative, N-(p-Coumaroyl)serotonin, isolated from safflower (Carthamus tinctorius L.) oil cake augments the proliferation of normal human and mouse fibroblasts in synergy with basic fibroblast growth factor (bFGF) or epidermal growth factor (EGF).
N-(p-Coumaroyl)serotonin (CS) with antioxidative activity is present in safflower oil. We have reported that CS inhibits proinflammatory cytokine generation from human monocytes in vitro. As reactive oxygen species (ROS) affect cell proliferation, in this study the effect of CS on the proliferation of various cell types was examined. CS augments the proliferation of normal human and mouse fibroblast cells. The cells continue to proliferate in the presence of CS and form a transformed cell-like focus without transformation. CS, however, does not augment the proliferation of other cell types, either normal or tumor cells. CS augments the proliferation of fibroblasts in synergy with basic fibroblast growth factor (bFGF) or epidermal growth factor (EGF), but not with acidic FGF(aFGF) or platelet-derived growth factor (PDGF). This study using synthesized derivatives of CS reveals that the growth-promoting activity is not due to antioxidative activity. These findings indicate that CS is a natural compound with unique growth-promoting activity for fibroblasts.
Animals↗
Serotonin derivative, N-(p-coumaroyl) serotonin, inhibits the production of TNF-alpha, IL-1alpha, IL-1beta, and IL-6 by endotoxin-stimulated human blood monocytes.
We have reported that N-(p-coumaroyl) serotonin (CS) and its derivatives with antioxidative activity are present in safflower seeds. As reactive oxygen species (ROS) are implicated in the signaling of lipopolysaccharide (LPS), we examined whether CS has a suppressive effect on inflammatory cytokine generation from human monocytes in vitro. CS at 50-200 microM reduced tumor necrosis factor (TNF), interleukin-1 (IL-1), and IL-6 activities in the culture supernatants from LPS-stimulated human blood monocytes without cytotoxicity. ELISA assay revealed that the production of TNF-alpha, IL-1alpha, IL-1beta, and IL-6 was inhibited by CS. Northern blot analysis showed that LPS-induced expression of these cytokine mRNA in monocytes was suppressed by CS. NF-kappaB activation was also inhibited by CS. These findings indicate that CS has a suppressive effect on proinflammatory cytokine production from monocytes, and this effect is based in part on the suppression of cytokine mRNA expression through inhibition of NF-kappaB activation.
Cells, Cultured↗