Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold.
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Bacillus Phages↗
Biomedical subjects
R Zhang
Publications and source records attributed to R Zhang.
Anti-SARS drug screening by molecular docking.
Starting from a collection of 1386 druggable compounds obtained from the 3D pharmacophore search, we performed a similarity search to narrow down the scope of docking studies. The template molecule is KZ7088 (Chou et al., 2003, Biochem Biophys Res Commun 308: 148-151). The MDL MACCS keys were used to fingerprint the molecules. The Tanimoto coefficient is taken as the metric to compare fingerprints. If the similarity threshold was 0.8, a set of 50 unique hits and 103 conformers were retrieved as a result of similarity search. The AutoDock 3.011 was used to carry out molecular docking of 50 ligands to their macromolecular protein receptors. Three compounds, i.e., C(28)H(34)O(4)N(7)Cl, C(21)H(36)O(5)N(6), and C(21)H(36)O(5)N(6), were found that may be promising candidates for further investigation. The main feature shared by these three potential inhibitors as well as the information of the involved side chains of SARS Cov Mpro may provide useful insights for the development of potent inhibitors against SARS enzyme.
Antiviral Agents↗
Combination of MIG (CXCL9) chemokine gene therapy with low-dose cisplatin improves therapeutic efficacy against murine carcinoma.
MIG (monokine induced by interferon-gamma) is a CXC chemokine ligand (CXCL9) that can potently inhibit angiogenesis, and displays thymus-dependent antitumor effects. The effectiveness of a treatment combining gene therapy with plasmid-borne MIG (pORF-MIG) and low-dose cisplatin chemotherapy was determined using colon carcinoma (CT26) and Lewis lung carcinoma (LL/2c) murine models. The program was carried out via intramuscular delivery of pORF-MIG at 100 mug/mouse twice a week for 4 weeks, and/or intraperitoneal delivery of cisplatin at 0.6 mg/kg/mouse every 3 days for 48 days. Tumor volume and survival time were evaluated after treatment. CD31 immunohistochemical staining in tumor tissues and alginate capsule models in vivo was used to evaluate angiogenesis. Induction of apoptosis and cytotoxic T-lymphocyte (CTL) activity were also assessed. The combination of pORF-MIG and low-dose cisplatin produced significant antitumor activity, with complete tumor regression in 4/10 of CT26 colon carcinomas and 3/10 of LL/2c lung carcinomas, low vascularity, in alginate capsules, apparently degraded tumor microvessel density, and increased induction of apoptotic and CTL activities compared with either treatment alone. This study suggests that the combination of pORF-MIG plus cisplatin augments the inhibition of angiogenesis and the induction of apoptosis or CTL activity, all of which enhance antitumor activity. These findings may prove useful in further explorations of the application of combinatorial approaches to the treatment of solid tumors.
Animals↗
3-year study of donepezil therapy in Alzheimer's disease: effects of early and continuous therapy.
Delays in the diagnosis of Alzheimer's disease, and, therefore, delays in treatment, may have a detrimental effect on a patient's long-term well-being. This study assessed the effects of postponing donepezil treatment for 1 year by comparing patients treated continuously for 3 years with those who received placebo for 1 year followed by open-label donepezil for 2 years. Patients (n = 286) with possible or probable Alzheimer's disease (according to DSM-IV, NINCDS-ADRDA, and Mini-Mental State Examination criteria; see text) were randomized to receive donepezil (5 mg/day for 4 weeks, 10 mg/day thereafter) or placebo (delayed-start group) for 1 year. Of the 192 completers, 157 began a 2-year, open-label phase of donepezil treatment. Outcome measures were the Gottfries-Bråne-Steen scale, the Mini-Mental State Examination, the Global Deterioration Scale, the Progressive Deterioration Scale, the Neuropsychiatric Inventory, and safety (adverse events). Mixed regression analysis was used to compare changes between the groups over 3 years on the efficacy measures. There was a trend for patients receiving continuous therapy to have less global deterioration (Gottfries-Bråne-Steen scale) than those who had delayed treatment (p = 0.056). Small but statistically significant differences between the groups were observed for the secondary measures of cognitive function (Mini-Mental State Examination; p = 0.004) and cognitive and functional abilities (Global Deterioration Scale; p = 0.0231) in favor of continuous donepezil therapy. Over 90% of the patients in both cohorts experienced one treatment-emergent adverse event; most were considered mild or moderate. In conclusion, patients in whom the start of treatment is delayed may demonstrate slightly reduced benefits as compared with those seen in patients starting donepezil therapy early in the course of Alzheimer's disease. These data support the long-term efficacy and safety of donepezil.
Aged↗
The possible study of HuaXi-1 solution for all intra-abdominal organ preservation: a study in rats.
OBJECTIVE: University of Wisconsin (UW) solution continues to be the most commonly used solution for intra-abdominal organs. However, it is expensive. Therefore, we have formulated HuaXi-1 (HX-1) solution. The aim of this research was to assess the effect of HX-1 solution compared to UW, Collins 2, and hypertonic citrate solutions on intra-abdominal organs. METHODS: The effects of HX-1 solution for all intra-abdominal organ preservation were studied in a noncirculated, isolated, perfused rat liver model, in rat pancreas isografts in diabetic rats, and in a kidney autotransplant model. The effects were investigated by measuring hepatic tissue water content, sinusoidal lining cell mortality, Krebs-Henseleits perfusate, aspartate aminotransferase, the number of livers secreting bile during isolated perfusion, blood glucose, glucose tolerance tests, serum insulin of the rat pancreas-transplant recipients, the maximum serum creatinine levels, kidney graft survival rates, and observing the morphological changes in liver, pancreas, and kidneys. RESULTS: HX-1 solution preserved rat liver well for 24 hours as effectively as UW, rat pancreas as well for 48 hours, and dog kidney as well for 72 hours. CONCLUSION: The experimental findings indicated that HX-1 solution was effective to preserve all intra-abdominal organs; it may simplify cold storage of organs for transplantation.
Abdomen↗
NGF receptor TrkAd5: therapeutic agent and drug design target.
Biochemical studies have shown that domain 5 of the TrkA (tropomyosin receptor kinase A) receptor is involved in the binding of NGF (nerve growth factor). Crystallographic studies have confirmed this, demonstrating that one homodimer of NGF binds to two TrkAd5 molecules. TrkAd5 has been made recombinantly in Escherichia coli, purified and shown to bind NGF with picomolar affinity. We have used the co-ordinates of the crystal structure of the NGF-TrkAd5 complex to screen approximately two million compounds in silico for the identification of small molecule agonists/antagonists. Selected hits were shown to be active in an in vitro ligand-binding assay; structure-activity relationships are now being investigated. In addition, TrkAd5 has been shown to be efficacious in preclinical models of inflammatory pain and asthma by the sequestration of excess levels of endogenous NGF, and therefore represents a novel therapeutic agent.
Alzheimer Disease↗
Peroxisome proliferator-activated receptor (PPAR) delta genetic polymorphism and its association with insulin resistance index and fasting plasma glucose concentrations in Chinese subjects.
AIMS: Previous studies have shown that the peroxisome proliferator-activated receptor delta (PPARD) genetic polymorphism affects cholesterol metabolism in Whites. This association was not observed in a Korean population in a separate study, but this study showed a link between the PPARD polymorphism and body weight and fasting plasma glucose. The purpose of this study was to determine whether polymorphisms of PPARD influence glucose and cholesterol metabolism in Chinese subjects. We investigated the association between the polymorphism (-87T/C) of the human PPARD gene and phenotypes related to body weight, insulin sensitivity, glucose and lipid metabolism in Chinese subjects. METHODS: Unrelated Chinese subjects (n = 663) in Shanghai were studied; 287 had newly diagnosed Type 2 diabetes mellitus and 376 were non-diabetic control subjects over 40 years old. Clinical parameters were collected and genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: In normal glucose tolerant (NGT) subjects, the C allele carriers had higher fasting plasma glucose concentrations (P = 0.0078) and a lower insulin sensitivity index (ISI) (P = 0.0365). The C allele carriers also showed higher concentrations of low-density lipoprotein cholesterol (P = 0.0261) and percentage of body fat (P = 0.0357). There was a trend towards higher visceral adiposity in C allele carriers, but the difference was not significant (P = 0.0830). In diabetes patients, similar results were detected for plasma glucose concentrations (fasting plasma glucose P < 0.0001, 2-h plasma glucose P = 0.0052) and insulin sensitivity (homeostasis model assessment of insulin resistance P = 0.0094; ISI P = 0.0058). CONCLUSION: The PPARD-87T/C polymorphism is associated with higher fasting plasma glucose concentrations in both NGT and diabetic subjects, largely due to impaired insulin sensitivity.
Blood Glucose↗
Prevalence and correlates of hepatitis C infection among users of North America's first medically supervised safer injection facility.
BACKGROUND: North America's first medically supervised safer injection facility (SIF) for illicit drug users was opened in Vancouver, Canada on 22 September 2003. We examined the prevalence and correlates of hepatitis C (HCV) infection among a representative cohort of SIF users. METHODS: Users of the Vancouver SIF were selected at random and asked to enrol in the Scientific Evaluation of Supervised Injecting (SEOSI) cohort. At baseline, venous blood samples were collected and an interviewer-administered questionnaire was performed. Participants who were HCV-positive were compared with HCV-negative subjects using bivariate and logistic regression analyses. RESULTS: Between 1 December 2003 and 30 July 2004, 691 participants were enrolled into the SEOSI cohort, among whom 605 (87.6%) were HCV-positive at baseline. Factors independently associated with HCV infection in logistic regression analyses included: involvement with the sex trade [adjusted odds ratio (AOR) 3.7, 95% confidence interval (CI) 2.1-6.1], history of borrowing syringes (AOR 1.8, 95%CI 1.1-2.9), and history of incarceration (AOR 2.6, 95%CI 1.5-4.4). Daily heroin use was protective against HCV infection (AOR 0.6, 95%CI 0.3-0.9). CONCLUSION: The SIF has attracted injection drug users with a high burden of HCV infection and a substantial proportion of uninfected individuals. Although cross-sectional, this study provides some insight into historical risks for HCV infection among this population, and prospective follow-up of this cohort will be useful to determine if use of the SIF is associated with reduced risk behaviour and HCV incidence.
Canada↗
1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase.
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Amino Acid Sequence↗
An active region model for capturing fractal flow patterns in unsaturated soils: model development.
Preferential flow commonly observed in unsaturated soils allows rapid movement of solute from the soil surface or vadose zone to the groundwater, bypassing a significant volume of unsaturated soil and increasing the risk of groundwater contamination. A variety of evidence indicates that complex preferential patterns observed from fields are fractals. In this study, we developed a relatively simple active region model to incorporate the fractal flow pattern into the continuum approach. In the model, the flow domain is divided into active and inactive regions. Flow occurs preferentially in the active region (characterized by fractals), and inactive region is simply bypassed. A new constitutive relationship (the portion of the active region as a function of saturation) was derived. The validity of the proposed model is demonstrated by the consistency between field observations and the new constitutive relationship.
Fractals↗
Preparation and characterization of straight and zigzag AlN nanowires.
Hexagonal single-crystal AlN nanowires with straight or zigzag morphologies were successfully synthesized by the reaction of aluminum alloy in an ammonia/nitrogen atmosphere at 1100 degrees C. It is found that the crystal tropism of the nanowires is along [0001], whereas the growth directions of the zigzag nanowires shift between [2111] and [2111].
Letter↗
Characterisation of hydrogel gel swelling by molecular exclusion.
A facile method for the characterization of hydrogel swelling is described which is based on the determination of changes in the liquid phase concentration of an excluded tracer as gel swells in a constant volume system. The utility of this approach is demonstrated with two responsive hydrogel preparations, one where swelling is influenced by system pH, the other by changes in specific solute concentration.
Dextrans↗
Poly-L-proline type II peptide mimics as probes of the active site occupancy requirements of cGMP-dependent protein kinase.
Based on the X-ray crystal structure of cAMP-dependent protein kinase (PKA) with the endogenous inhibitor PKI and the X-ray crystal structure of cyclin-dependent kinase 2 (CDK2) with a substrate peptide, a proposal is put forth that some protein kinases bind peptide substrates in their active sites in the poly-L-proline type II (PPII) conformation. In this work, PPII peptide mimics are evaluated as pseudosubstrate inhibitors of cGMP-dependent protein kinase (PKG) to explore if PKG also binds peptide substrates in the PPII conformation. Inhibition data of our PPII mimetics provide evidence that the P-1, P-2, and P-3 residues of substrate peptides bind in the PPII conformation (phi approximately -75 degrees, psi approximately 145 degrees). In addition, the inhibition data also suggest that the P-1, P-2, and P-3 residues in substrate peptides bind with a gauche(-) chi1 angle.
Catalytic Domain↗
Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.
MOTIVATION: Although a great deal of research has been undertaken in the area of promoter prediction, prediction techniques are still not fully developed. Many algorithms tend to exhibit poor specificity, generating many false positives, or poor sensitivity. The neural network prediction program NNPP2.2 is one such example. RESULTS: To improve the NNPP2.2 prediction technique, the distance between the transcription start site (TSS) associated with the promoter and the translation start site (TLS) of the subsequent gene coding region has been studied for Escherichia coli K12 bacteria. An empirical probability distribution that is consistent for all E.coli promoters has been established. This information is combined with the results from NNPP2.2 to create a new technique called TLS-NNPP, which improves the specificity of promoter prediction. The technique is shown to be effective using E.coli DNA sequences, however, it is applicable to any organism for which a set of promoters has been experimentally defined. AVAILABILITY: The data used in this project and the prediction results for the tested sequences can be obtained from http://www.uow.edu.au/~yanxia/E_Coli_paper/SBurden_Results.xls CONTACT: alh98@uow.edu.au.
Algorithms↗
NAD-sensitive hydrogel for the release of macromolecules.
A hydrogel membrane containing immobilized ligands and receptors was synthesized and investigated for the controlled diffusion of test proteins (cytochrome C and hemoglobin). Both Cibacron blue (ligand) and lysozyme (receptor) were covalently linked to dextran molecules that were subsequently crosslinked to form a gel. The resulting stable hydrogels contained both covalent and affinity crosslinks such that their intrinsic porosities were sensitive to competitive displacers of the affinity interaction between lysozyme and Cibacron blue. Transport experiments in a twin chamber diffusion cell showed that as NAD was added to the donor side, the dissociation of the binding sites between the Cibacron blue and the lysozyme led to an increase in protein diffusion through the hydrogel. The results showed that addition of NAD caused a saturable concentration-dependent increase in the transport of both cytochrome C and hemoglobin. This effect was shown to be both specific and reversible.
Coated Materials, Biocompatible↗
Evidence of a myogenic response in vasomotor control of forearm and palm cutaneous microcirculations.
Previous investigations of autoregulatory mechanisms in the control of skin blood flow suffer from the possibility of interfering effects of the autonomic nervous system. To address this question, in 11 subjects cutaneous vascular responses were measured during acute changes in perfusion pressure (using Valsalva maneuver; VM) before and after ganglionic blockade via systemic trimethaphan infusion. Cutaneous vascular conductance at baseline (CVC(base)) and during the last 5 s of the VM (CVC(VM)) were measured from forearm (nonglabrous) and palm (glabrous) skin. During the VM without ganglionic blockade, compared with CVC(base), CVC(VM) decreased significantly at the palm [0.79 +/- 0.17 to 0.55 +/- 0.17 arbitrary units (AU)/mmHg; P = 0.002] but was unchanged at the forearm (0.13 +/- 0.02 to 0.16 +/- 0.02 AU/mmHg; P = 0.50). After ganglionic blockade, VM induced pronounced decreases in perfusion pressure, which resulted in significant increases in CVC(VM) at both forearm (0.19 +/- 0.03 to 0.31 +/- 0.07 AU/mmHg; P = 0.008) and palm (1.84 +/- 0.29 to 2.76 +/- 0.63 AU/mmHg; P = 0.003) sites. These results suggest that, devoid of autonomic control, both glabrous and nonglabrous skin are capable of exhibiting vasomotor autoregulation during pronounced reductions in perfusion pressure.
Adult↗
Electrochemical lithography: fabrication of nanoscale Si tips by porous anodization of Al/Si wafer.
Porous anodization of Al/Si wafer in sulfuric acid results in the formation of Si nanotips on the surface of Si substrate with ultrahigh packing density.
Journal Article↗
Phase diagram of aggregation of oppositely charged colloids in salty water.
Aggregation of two oppositely charged colloids in salty water is studied. We focus on the role of Coulomb interaction in strongly asymmetric systems in which the charge and size of one colloid is much larger than the other one. In the solution, each large colloid (macroion) attracts a certain number of oppositely charged small colloids (Z-ion) to form a complex. If the concentration ratio of the two colloids is such that complexes are not strongly charged, they condense in a macroscopic aggregate. As a result, the phase diagram in a plane of concentrations of two colloids consists of an aggregation domain sandwiched between two domains of stable solutions of complexes. The aggregation domain has a central part of total aggregation and two wings corresponding to partial aggregation. A quantitative theory of the phase diagram in the presence of monovalent salt is developed. It is shown that as the Debye-Hückel screening radius r(s) decreases, the aggregation domain grows, but the relative size of the partial aggregation domains becomes much smaller. As an important application of the theory, we consider solutions of long double-helix DNA with strongly charged positive spheres (artificial chromatin). We also consider implications of our theory for in vitro experiments with the natural chromatin. Finally, the effect of different shapes of macroions on the phase diagram is discussed.
Binding Sites↗