Structural genomics: a new era for pharmaceutical research.
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Computational Biology↗
Biomedical subjects
Yang Liu
Publications and source records attributed to Yang Liu.
The TRIPLES database: a community resource for yeast molecular biology.
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae-a relational database housing nearly half a million data points generated from an ongoing study using large-scale transposon mutagenesis to characterize gene function in yeast. At present, TRIPLES contains three principal data sets (i.e. phenotypic data, protein localization data and expression data) for over 3500 annotated yeast genes as well as several hundred non-annotated open reading frames. In addition, the TRIPLES web site provides online order forms linked to each data set so that users may request any strain or reagent generated from this project free of charge. In response to user requests, the TRIPLES web site has undergone several recent modifications. Our localization data have been supplemented with approximately 500 fluorescent micrographs depicting actual staining patterns observed upon indirect immunofluorescence analysis of indicated epitope-tagged proteins. These localization data, as well as all other data sets within TRIPLES, are now available in full as tab-delimited text. To accommodate increased reagent requests, all orders are now cataloged in a separate database, and users are notified immediately of order receipt and shipment. Also, TRIPLES is one of five sites incorporated into the new functional analysis tool Function Junction provided by the Saccharomyces Genome Database. TRIPLES may be accessed from the Yale Genome Analysis Center (YGAC) homepage at http://ygac.med.yale.edu.
Computer Graphics↗
Therapeutic ultrasound: its application in drug delivery.
Ultrasound is best known for its imaging capability in diagnostic medicine. However, there have been considerable efforts recently to develop therapeutic uses for it. The purpose of this review is to summarize some of the recent advances made in the area of therapeutic ultrasound as they relate to drug delivery. In particular, this review will focus on the applications of ultrasound to enhance the delivery and effect of three distinctive therapeutic drug classes: chemotherapeutic, thrombolytic, and gene-based drugs. In addition, ultrasound contrast agents have been recently developed for diagnostic ultrasound. New experimental evidence suggests that these contrast agents can be used as exogenous cavitation nuclei for enhancement of drug and gene delivery. Thus, brief review of this new class of agents and their roles in drug delivery will also be provided. By comparison to diagnostic ultrasound, progress in therapeutic use of ultrasound has been somewhat limited. The recent successes in ultrasound-related drug delivery research positions ultrasound as therapeutic tool for drug delivery in the future.
Animals↗
Glycosylation processing inhibition by castanospermine prevents experimental autoimmune encephalomyelitis by interference with IL-2 receptor signal transduction.
In this study, we explored the therapeutic targets of the glycosylation processing inhibitor, castanospermine (CAST), in murine passive transfer experimental autoimmune encephalomyelitis (EAE), a model disease of multiple sclerosis. By using lymphocytic-endothelial adhesion and transmigration assays, FACScan and Western blotting, we defined the effects of CAST on expression, function and signal transduction of glycoproteins crucial in the pathophysiology of this disease. CAST prevented clinical signs of EAE and completely inhibited inflammatory CNS infiltrates associated with this disease. Here, we showed that CAST blocks antigen-induced lymphocytic activation and clonal expansion in a dose-dependent manner. Importantly, we observed that CAST strongly impairs IL-2-induced signal transduction of the IL-2 receptor. In contrast, neither expression nor binding ability of the IL-2 receptor was affected by this drug. In addition, we were able to exclude major effects of CAST on expression and function of different glycoproteins important in antigen presentation as well as lymphocytic-endothelial adhesion and transmigration. In conclusion, CAST strongly interferes in the signal transduction of the IL-2 receptor. This could explain both inhibitory effects of CAST in clonal T cell expansion and development of transfer EAE. This relatively selective pharmacological effect of CAST highlights its potential as a novel immunomodulatory approach in multiple sclerosis.
Animals↗
An in vitro model of neurotrauma in organotypic spinal cord cultures from adult mice.
Cellular degeneration after spinal cord injury (SCI) involves numerous pathways. It is essential to use appropriate experimental models in order to understand the complex processes, which evolve after the initial trauma. The purpose of this study was to develop and assess an in vitro model of neurotrauma using organotypic slice culture of adult mice spinal cord. This model will facilitate the investigation of primary and secondary mechanisms of cell death that occurs after SCI. We modified previously described methods for generating organotypic cultures of murine spinal cord. The viability of organotypic cultures was assessed by observing the outgrowth of neurites and by using a mitochondria dependent dye for live cells (tetrazolium dye; MTT). The morphological integrity of cultures was examined histologically by hematoxylin and eosin (H&E) staining for general morphology and with luxol fast blue (LFB) for myelin. Neuronal and glial (GFAP; CNPase) markers were used to identify neurons, astrocytes and oligodendroglia, respectively. Primary injury was achieved by using a weight drop (0.2 g) model of injury. Cell death after primary injury was attenuated by pre-treatment with two known neuroprotective agents: the AMPA/KA blocker CNQX and methylprednisolone. The nuclear markers Propidium iodide and Sytox-green, as well as the TUNEL (in situ terminal deoxytransferase-mediated dUTP nick end labeling) technique, were used as a quantitative indicators of cell death at 24, 48 and 72 h post-injury using a confocal microscope and image analysis software. This novel in vitro model of SCI is easy to reproduce, will facilitate the examination of post-trauma cell death mechanisms and the neuroprotective effects of pharmacological agents and aid in the study of transgenic murine models.
Animals↗
Ultrasound-induced mild hyperthermia as a novel approach to increase drug uptake in brain microvessel endothelial cells.
PURPOSE: Drug delivery to the central nervous system (CNS) is limited by the blood-brain barrier (BBB). Thus, a noninvasive and reversible method to enhance BBB permeation of drugs is highly desirable. In the present work, we studied if ultrasound-induced mild hyperthermia (USHT, 0.4 watts (W)/cm2 at 41 degrees C) can enhance drug absorption in BBB endothelial cells, and we elucidated the mechanism of USHT on cellular accumulation. METHODS: To accomplish these aims, we studied the effects of hyperthermia (41 degrees C), USHT, P-glycoprotein (P-gp) modulator (PSC 833), and combination of USHT and PSC 833 on accumulation of P-gp substrate (R123) and non-P-gp substrates (sucrose, 2-deoxyglucose, and antipyrine) in monolayers of primary bovine brain microvessel endothelial cells (BBMEC). RESULTS: USHT, through its thermal effect, produces a significant (relative to controls; no USHT) and comparable increase in R123 accumulation with PSC 833. We also demonstrate that USHT increases permeability of hydrophobic (R123 and [14C]-antipyrine) and not hydrophilic molecules ([14C]-sucrose and 2-[3H]-deoxy-D-glucose). The enhanced permeability is reversible and size dependent, as USHT produces a much larger effect on cellular accumulation of [14C]-antitpyrine (molecular weight of 188 D) than that of R123 (molecular weight of 380.8 D). Although USHT increases membrane permeability, it did not affect P-gp activity or the activity of glucose transporters. CONCLUSIONS: Our results point to the potential use of USHT as a reversible and noninvasive approach to increase BBB permeation of hydrophobic drugs, including P-gp-recognized substrates.
Animals↗
ErbB2 is essential in the prevention of dilated cardiomyopathy.
Amplification of the gene encoding the ErbB2 (Her2/neu) receptor tyrosine kinase is critical for the progression of several forms of breast cancer. In a large-scale clinical trial, treatment with Herceptin (trastuzumab), a humanized blocking antibody against ErbB2, led to marked improvement in survival. However, cardiomyopathy was uncovered as a mitigating side effect, thereby suggesting an important role for ErbB2 signaling as a modifier of human heart failure. To investigate the physiological role of ErbB2 signaling in the adult heart, we generated mice with a ventricular-restricted deletion of Erbb2. These ErbB2-deficient conditional mutant mice were viable and displayed no overt phenotype. However, physiological analysis revealed the onset of multiple independent parameters of dilated cardiomyopathy, including chamber dilation, wall thinning and decreased contractility. Additionally, cardiomyocytes isolated from these conditional mutants were more susceptible to anthracycline toxicity. ErbB2 signaling in cardiomyocytes is therefore essential for the prevention of dilated cardiomyopathy.
Adult↗
Cis elements for transporter associated with antigen-processing-2 transcription: two new promoters and an essential role of the IFN response factor binding element in IFN-gamma-mediated activation of the transcription initiator.
Expression of cell surface MHC class I:peptide complex requires coordinated expression of multiple genes such as MHC class I heavy chain, beta(2)-microglobulin (beta(2)m), transporters associated with antigen-processing (TAP)-1 and TAP-2, and proteosomal components low-molecular weight polypeptide (LMP)-2 and LMP-7. All of these genes are expressed at defined and distinct levels in normal tissues, and are inducible by IFN-gamma. While the cis elements involved in transcription of the MHC class I heavy chain, beta(2)m, TAP-1 and LMP-2 have been analyzed extensively, those for TAP-2 and LMP-7 have not been well studied. Here we systematically analyzed the cis elements for TAP-2 transcription. We found at least two independent elements that are sufficient to activate transcription of a reporter gene. One (hereby called TAP-2 P1) is located 5' to the TAP-2 exon 1, while the other (hereby called TAP-2 P2) is a transcription initiator residing in intron 1. Analysis of the 5' sequence of TAP-2 mRNA indicates that both promoters are active. Moreover, while the TAP-2 promoter region contains cis elements that can mediate TAP-2 induction by IFN-gamma, such as gamma-activation site and IFN response factor binding element (IRFE), only the IRFE is required for IFN-gamma induction of TAP-2 promoter in vitro. The IRFE appears to work as an enhancer for the initiator (P2). Together with another promoter recently identified by others, TAP-2 therefore has three independent promoters that can be differentially regulated.
ATP-Binding Cassette Transporters↗
beta-fibrinogen gene -455A/G polymorphism and plasma fibrinogen level in Chinese stroke patients.
OBJECTIVES: To investigate the relationship between the beta-fibrinogen gene -455A/G polymorphism and plasma fibrinogen level and to determine the influence of the mutation on ischemic stroke. METHODS: Ninety-one patients (63.5 +/- 10.1 years) with ischemic stroke and 74 elderly control subjects (60.6 +/- 10.8 years) without any thromboembolic events and 98 healthy blood donators as young control (37.5 +/- 13.3 years) were enrolled in this trial. The beta-fibrinogen gene -455A/G polymorphism was analyzed for all subjects by PCR-RFLP with the restrictive enzyme Hae III, while plasma fibrinogen levels were obtained from the prothrombin time (PT) assay. For statistical analysis, the parameters were compared between any two different groups by the unpaired Student's t test and the Chi-square test. Before analysis, log transformations for concentrations of fibrinogen were carried out. RESULTS: H2 allele frequency was higher in male ischemic stroke patients than in the elderly control (22.7% vs 7.1%, chi(2) = 5.56, P < 0.02). There was no significant difference between the female groups. In those patients without any thromboembolic events (both elderly and young control groups), the frequency of H2 decreased with age (< or = 40, 21.3%; 41 - 59, 15.4%; and > or = 60, 10.2%). In the male elderly and young control groups, the level of plasma fibrinogen was lower in the H1H1 genotype (287 +/- 96 mg/dl and 234 +/- 58 mg/dl) than in H1H2 and H2H2 (331 +/- 44 mg/dl and 307 +/- 55 mg/dl; t = 2.53 and 9.67, P < 0.05). In the female elderly groups, this tendency was not found. CONCLUSION: Plasma fibrinogen expression is affected by the beta-fibrinogen gene -455A/G polymorphism, and the H2 allele may be a risk factor for ischemic stroke in Chinese males.
Aged↗
[The mechanism and application of posttranscriptional gene silencing].
The purpose of this review is to confirm the reason resulted the gene silence and explore the countermeasure avoiding the gene silence in transgene plant. The method is to divide the gene silencing into transcriptional gene silencing(TGS) and posttranscriptional gene silencing(PTGS). Several models resulted PTGS were analyzed by RNA threshold model, ectopic pairing and aberrant RNA model and ds-RNA model. The results showed that it was important to decide the phenomena of restraining transgene silencing and the mechanism of PTGS. The strategies of identification of gene function and prevention of virus were presented by RNAi and gene silencing respectively, etc.
Animals↗
[Determination of sodium phenytoin in plasma by high performance capillary zone electrophoresis].
A method to determine sodium phenytoin in plasma by high performance capillary zone electrophoresis (CZE) has been established. CZE was performed in 25 mmol/L phosphate buffer solution (pH 12) at 20 degrees C. The capillary column size was 75 microns i.d. x 30 cm (effective length). Sodium phenytoin was quantified with UV detector at 200 nm. The plasma was extracted by ether after plasma was processed with proteinase K for 3 h at 55 degrees C. Then the extract was evaporated to dryness. The residue was reconstituted in 1 mL of running buffer. The average recovery was higher than 95%. The precisions of intra-day and inter-day were 3.1% and 4.7% respectively. The detection limit of sodium phenytoin was 0.6 mg/L.
Electrophoresis, Capillary↗
[Analysis of a novel platinum anticancer compound HJ5 by high performance liquid chromatography].
Cis-dichloroamine (4-amino-2, 2, 6, 6-tetramethylpiperidine-1-oxyl) platinum (II) (abbreviated to HJ5) is a novel platinum anticancer compound which has prospects for research and application. In order to establish a conventional analytical method, an HPLC has been studied. Under the conditions of acetonitrile-water (10:90, volume ratio) as mobile phase, detection wavelength of 210 nm, a Phenomenex column C18(150 mm x 3.9 mm i.d., 10 microns). The linear equation, recovery and accuracy of the method were determined with external standard method. The HPLC has satisfactory resolution between the peaks of HJ5 and impurities. The peak areas of HJ5 were linear to its amounts detected and the detection limit was 0.07 microgram. The hydration of HJ5 can be inhibited effectively by NaCl solution. In a 9 g/L NaCl solution, the stability can be kept for more than 2 hours which is enough for analysis.
Antineoplastic Agents↗
[Preliminary clinical study of application of cyntridini triphosphatis and dexamethasone in treatment of sudden deafness].
OBJECTIVE: To investigate the effect of application of cytridini triphosphatis (CTP) combined with dexamethasone on sudden deafness. METHODS: Two-hundred and seven patients (312 ears) with sudden deafness were randomly divided into CTP group (n = 159 ears) and control group (n = 153 ears). Besides intravenous administration of CTP, another treatments in CTP group were the same as that in control group including hyperbaric oxygen, vasodilator, energy preparation such as ATP, CoA and dexamethasone (DXM). RESULTS: The hearing threshold was (75.56 +/- 30.24) dB HL in CTP group and (72.50 +/- 40.50)dB HL in control group (P > 0.05) before treatment. The average value of the hearing threshold after treatment was decreased by (50.08 +/- 21.47) dB HL in CTP group and (19.45 +/- 19.12) dB in control group(P < 0.05), respectively. CONCLUSION: The application of CTP combined with DXM can significantly improve the effect of treatment on sudden deafness and CTP may enhance the recovery rate in the patients with sudden deafness, which was much higher than that treated by the traditional methods. However, the mechanism of the effect of CTP coupled with DXM is still unknown and further study is necessary.
Adolescent↗
Detection of circulating hepatocellular carcinoma cells in peripheral venous blood by reverse transcription-polymerase chain reaction.
OBJECTIVE: To detect circulating hepatocellular carcinoma by demonstrating hepatocellular carcinoma cells or hepatocyte-associated mRNA in the nuclear cell component of peripheral blood (PBL). METHODS: Peripheral blood (5 ml samples were obtained from 93 patients with hepatocellular carcinoma (HCC) and from 33 control subjects (9 with liver cirrhosis after hepatitis B, 14 with chronic hepatitis B, 10 with normal liver function). To identify HCC cells in peripheral blood, liver-specific human alpha-fetoprotein (AFP) mRNA was amplified from total RNA extracted from whole blood by reverse transcription-polymerase chain reaction. RESULTS: AFPmRNA was detected in 50 blood samples from the HCC patients (50/93, 53.8%). In contrast, there were no clinical control patients whose samples showed detectable AFPmRNA in PBL. The presence of AFPmRNA in blood seemed to be correlated with the stage (by TNM classification) of HCC, the serum AFP value, and the presence of intrahepatic metastasis, portal vein thrombosis, tumor diameter and/or distant metastasis. In addition, AFPmRNA was detected in the blood of 21 patients with metastasis at extrahepatic organs (100%) in contrast to 29 (40.3%) of 72 patients without metastasis. CONCLUSION: The presence of AFPmRNA in peripheral blood may be an indicator of malignant hepatocytes, which might predict hematogenous spreading metastasis of tumor cells in patients with HCC.
Adult↗
Changes of AFPmRNA in blood after percutaneous ethanol injection treatment of hepatocellular carcinoma.
OBJECTIVE: To study the effects of percutaneous ethanol injection (PEI) in treatment of hepatocellular carcinoma (HCC). METHODS: Blood samples were taken from 9 HCC patients and detected by nested RT-PCR to find out AFPmRNA after PEI treatment 3-5 times within 2 weeks. RESULTS: Three (44.44%) of 4 patients with AFPmRNA positive turned to be negative after PEI treatment and 1 with AFPmRNA positive (11.11%) lasted within 2 weeks. CONCLUSION: PEI may diminish the possibility of distant metastasis of HCC.
Administration, Cutaneous↗
Detection of blood AFPmRNA in nude mice bearing human HCC using nested RT-PCR and its significance.
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Journal Article↗
Activation of the Erwinia carotovora subsp. carotovora pectin lyase structural gene pnlA: a role for RdgB.
The activation of pectin lyase (Pnl) production in Erwinia carotovora subsp. carotovora strain 71 occurs upon DNA damage via a unique regulatory circuit involving recA, rdgA and rdgB. In a similar Pnl-inducible system reconstituted in Escherichia coli, the rdgB product was found to activate the expression of pnlA, the structural gene for pectin lyase. The kinetic data presented here also show that transcription of pnlA followed that of rdgB in Er. carotovora subsp. carotovora, indicating a temporal order of gene expression. By deletion analysis we have localized the promoter/regulatory region within a 66 bp DNA segment upstream of the pnlA transcriptional start site. This region contains the -10 consensus sequence but not the sequences corresponding to the E. coli -35 region. For DNA-binding studies, rdgB was overexpressed in E. coli and a 14 kDa polypeptide was identified as the gene product. RdgB from crude extracts or a purified preparation caused an identical gel mobility shift of a 164 bp DNA segment containing the pnlA promoter/regulatory region. Utilizing DNase I protection assay the RdgB-binding site was localized between nucleotides -29 and -56, i.e. overlapping the position of the putative -35 box. The findings reported here, taken along with our previous observation that the rdgE product is required for pnlA expression, establishes that rdgB encodes a transcriptional factor which specifically interacts with the pnlA promoter/regulatory region.
Bacterial Proteins↗
Global regulation in Erwinia species by Erwinia carotovora rsmA, a homologue of Escherichia coli csrA: repression of secondary metabolites, pathogenicity and hypersensitive reaction.
Our previous studies revealed that rsmA of Erwinia carotovora subsp. carotovora strain 71 suppressed the synthesis of the cell density (quorum) sensing signal N-(3-oxohexanoyl)-L-homoserine lactone, the production of extracellular enzymes and tissue macerating ability in soft-rotting Erwinia species and that homologues of this negative regulator gene were present in other Erwinia species. Northern blot data presented here demonstrate that rsmA and rsmA-like genes are also expressed in soft-rotting and non-soft-rotting Erwinia spp. such as E. amylovora, E. carotovora subsp. atroseptica, E. carotovora subsp. betavasculorum, E. carotovora subsp. carotovora, E. chrysanthemi, E. herbicola and E. stewartii. A low-copy plasmid carrying rsmA of E. carotovora subsp. carotovora strain 71 caused suppression of antibiotic production in E. carotovora subsp. betavasculorum, flagellum formation in E. carotovora subsp. carotovora, carotenoid production in E. herbicola and E. stewartii, and indigoidine production in E. chrysanthemi. In E. amylovora, rsmA of E. carotovora subsp. carotovora suppressed the elicitation of the hypersensitive reaction in tobacco leaves and the production of disease symptoms in apple shoots, in addition to repressing motility and extracellular polysaccharide production. We conclude that rsmA homologues function as global regulators of secondary metabolic pathways as well as factors controlling host interaction of Erwinia species.
Anti-Bacterial Agents↗