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Biomedical subjects

Yong Zhang

Publications and source records attributed to Yong Zhang.

At least 163 records · Page 9Linked to original sources

Construction of polymeric and oligomeric lanthanide(III) thiolates from preformed complexes [(TMS)2N]3Ln(mu-Cl)Li(THF)3 (Ln = Pr, Nd, Sm; (TMS)2N = Bis(trimethylsilyl)amide).

The complex [{(TMS)2N}4(mu4-Cl)Sm4(mu-SPh)4(mu3-Cl)Li(THF)] has been formed by protonolysis of [(Me3Si)2N]3Sm(mu-Cl)Li(THF)3 with 1 equiv of HSPh, which contains a square array of Sm(III) ions connected by a central mu4-Cl ligand. The edges of the square Sm4 array are bridged by four mu3-Cl and four mu-SPh ligands. The four Sm atoms and Li atom are connected by four mu3-Cl ligands.

Journal Article↗

The Genomes of Oryza sativa: a history of duplications.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Base Sequence↗

Effects of the plant-derived hallucinogen salvinorin A on basal dopamine levels in the caudate putamen and in a conditioned place aversion assay in mice: agonist actions at kappa opioid receptors.

RATIONALE: Salvinorin A is a naturally occurring hallucinogen derived from the plant Salvia divinorum. Salvinorin A is also a potent and selective kappa opioid receptor agonist in vitro. It has been shown that kappa agonists decrease dopamine levels in the caudate putamen and nucleus accumbens and cause conditioned place aversion in rodents. OBJECTIVES: To study the effects of salvinorin A on basal dopamine levels in the caudate putamen and nucleus accumbens, and to determine whether salvinorin A induces conditioned place preference or aversion and changes in locomotor activity in the mouse. METHODS: In the first experiment, changes in dopamine levels in these brain regions after administration of salvinorin A were measured with in vivo microdialysis. In the second experiment, we examined whether salvinorin A led to conditioned place preference or aversion, and changes in locomotor activity during conditioning sessions. RESULTS: The higher doses of salvinorin A studied (1.0 mg/kg and 3.2 mg/kg, i.p.) significantly decreased dopamine levels in the caudate putamen, but not in the nucleus accumbens, and this effect was completely blocked by pre-injection with 10 mg/kg of the kappa opioid receptor antagonist nor-binaltorphimine. The same doses of salvinorin A caused conditioned place aversion and decreased locomotor activity. CONCLUSIONS: The inhibitory effect of salvinorin A on striatal dopamine levels may contribute to its induction of conditioned place aversion and decreases in locomotion in mice. These findings are consistent with the in vitro characterization of salvinorin A as a kappa opioid receptor agonist. It is of interest that a compound such as salvinorin A, that lowers striatal dopamine levels and leads to conditioned place aversion in rodents, is self-administered by humans under certain conditions.

Animals↗

Excitatory purinergic neurotransmission in smooth muscle of guinea-pig [corrected] taenia caeci.

Non-adrenergic, non-cholinergic (NANC) inhibitory neurotransmission has been an area of intense interest in gut motor physiology, whereas excitatory NANC neurotransmission has received less attention. In order to further explore excitatory NANC neurotransmission, we performed conventional intracellular recordings from guinea-pig taenia caeci smooth muscle. Tissue was perfused with oxygenated Krebs solution at 35 degrees C and nerve responses evoked by either oral or aboral nerve stimulation (NS) (4 square wave pulses, 0.3 ms duration, 20 Hz). Electrical activity was characterized by slow waves upon which one to three action potentials were superimposed. Oral NS evoked an inhibitory junction potential (IJP) at either the valley or peak of the slow wave. Application of nifedipine (1 microM) abolished slow waves and action potentials, but membrane potential flunctuations (1-3 mV) and IJPs remained unaffected. Concomitant application of apamin (300 nM), a small-conductance Ca(2+)-activated K(+) channel blocker, converted the IJP to an EJP that was followed by slow IJP. Further administration of N(G)-nitro-l-arginine methyl ester (l-NAME, 200 microM), a nitric oxide synthase inhibitor, abolished the slow IJP without affecting the EJP, implying that the slow IJP is due to nitrergic innervation. The EJP was abolished by tetrodotoxin (1 microM), but was not significantly affected by atropine (3 microM) and guanethidine (3 microM) or hexamethonium (500 microM). Substance P (SP, 1 microM) desensitization caused slight attenuation of the EJP, but the EJP was abolished by desensitization with alpha,beta-methylene ATP (50 microM), a P2 purinoceptor agonist that is more potent than ATP at the P2X receptor subtype, suramin (100 microM), a non-selective P2 purinoceptor antagonist, and pyridoxal-phosphate-6-azophenyl-2',4'-disulphonic acid (PPADS, 100 microM) , a selective P2X purinoceptor antagonist. In contrast, the EJP was unaffected by MRS-2179 (2 microM), a selective P2Y(1) receptor antagonist. Aboral NS evoked an apamin- and l-NAME-sensitive IJP, but virtually no NANC EJP. These data suggest the presence of polarized excitatory purinergic neurotransmission in guinea-pig taenia caeci, which appears to be mediated by P2X purinoceptors, most likely the P2X(1) subtype.

Action Potentials↗

Identification of gene expression modifications in myostatin-stimulated myoblasts.

Myostatin belongs to the transforming growth factor beta superfamily and has been shown to function as an inhibitor of skeletal muscle proliferation and differentiation. To gain insight into the molecular mechanisms of myostatin function during myogenesis, differential display reverse transcription PCR was employed to identify altered gene expressions associated with myostatin inhibitory function in chicken fetal myoblasts (CFMs). In this work, we have identified seven up-regulated and 12 down-regulated genes in myostatin stimulated CFMs. Those genes are involved in myogenic differentiation, cell architecture, energy metabolism, signal transduction, and apoptosis. The down-regulation of muscle creatine kinase B, troponin C, and myosin regulatory light chain is in agreement with the myostatin negative role in myocyte differentiation. In addition, the expression alteration of skeletal muscle-specific cardiac ankyrin repeat protein and the bcl-2 related anti-apoptotic protein Nr-13 suggests possible unique roles for myostatin in regulating myogenesis by controlling cofactors participated transcriptional regulation and apoptosis.

Animals↗

Dynamics of solitary wave scattering in the Fermi-Pasta-Ulam model.

In this Letter, we study the scattering dynamics of a pair of solitary waves in the Fermi-Pasta-Ulam model with interaction potential V(x)=alphax(2)/2+x(4)/4 and establish a quantitative connection between the scattering property and the energy transport behavior. The energy and momentum conservation laws are obtained and the scattering rates of solitary waves are calculated. Our studies suggest that the anharmonic limit model with alpha=0 can be taken as a paradigm model for studying lattice solitary waves.

Journal Article↗

NONCODE: an integrated knowledge database of non-coding RNAs.

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.

Base Sequence↗

ChickVD: a sequence variation database for the chicken genome.

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the 'Chicken Variation Database' (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn.

Animals↗

SPD--a web-based secreted protein database.

With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They were further annotated via a proteome annotation pipeline that we developed. We also set up a secreted protein classification pipeline and classified our predicted secreted proteins into different functional categories. To make the dataset more convincing and comprehensive, nine reference datasets are also integrated, such as the secreted proteins from the Gene Ontology Annotation (GOA) system at the European Bioinformatics Institute, and the vertebrate secreted proteins from Swiss-Prot. All these entries were grouped via a TribeMCL based clustering pipeline. We have constructed a web-based secreted protein database, which has been publicly available at http://spd.cbi.pku.edu.cn. Users can browse the database via a GO assignment or chromosomal-location-based interface. Moreover, text query and sequence similarity search are also provided, and the sequence and annotation data can be downloaded freely from the SPD website.

Animals↗

Expression of RECK gene and MMP-9 in hilar cholangiocarcinoma and its clinical significance.

In order to study the expression of transformation suppressor gene RECK and MMP-9 in hilar cholangiocarcinomas and its clinical significance, and explore the roles of RECK gene in metastasis and invasion of hilar cholangiocarcinoma, the expression levels of RECK, and MMP-9 mRNA were detected by using reverse transcription-polymerase reaction in 42 paraffin-embedded samples of hilar cholangiocarcinomas and 10 samples of benign bile duct diseases. The results showed that in hilar cholangiocarcinoma tissues, the expression of RECK gene was 0.235 +/- 0.062, significantly lower than in normal bile duct tissues (0.533 +/- 0.024, P < 0.05). In hilar cholangiocarcinoma tissues, the expression of MMP-9 (0.528 +/- 0.039) was significantly higher than in the normal tissues (0.311 +/- 0.032, P < 0.05). The expression of RECK gene was closely related to the intrahepatic and surrounding organs invasion (P < 0.05). It was concluded that RECK gene could inhibit the expression of MMP-9 in hilar cholangiocarcinomas and closely correlated with the biological behaviors. The abnormal expression of RECK gene might be one of the molecular mechanisms of hilar cholangiocarcinoma metastasis.

Adult↗

Effect of growth factors on in vitro development of caprine preantral follicle oocytes.

The objective of this work was to examine the effect of various growth factors including epidermal growth factor (EGF) and insulin-like growth factor-I (IGF-I), either individually or in association, in the presence of follicle stimulating hormone (FSH) on the in vitro growth and viability of caprine preantral follicle oocytes. Preantral follicles were disassociated enzymatically and mechanically from prepuberal caprine ovaries after the animals were anesthetically ovariectomized. In experiment, caprine preantral follicles in groups 1-4 were cultured in growth culture medium, growth culture medium+EGF, growth culture medium+IGF-I and growth culture medium+IGF-I+EGF, respectively, for 9 days. The results indicated that EGF (50 mg/l) increased the survival rate of oocytes, but decreased the growth rate of oocytes; IGF-I (100 mg/l) effectively maintained the survival of oocytes and stimulated their growth; IGF-I (100 mg/l) and EGF (50mg/l) in combination produced a higher effect on both of the survival and the growth rate of oocytes than IGF-I or EGF alone. Conclusively, the growth factors can effectively maintain the survival of caprine preantral follicle oocytes and regulated their growth in culture. EGF and IGF-I in association could synergically meliorate the culture system of caprine preantral follicle oocytes.

Animals↗

Intrathecal morphine and ketorolac analgesia after surgery: comparison of spontaneous and elicited responses in rats.

Pain after surgery results in significant morbidity, and systemic opioids often fail to provide adequate analgesia without marked sedation and respiratory depression. Intrathecal morphine provides better analgesia, but is limited by delayed respiratory depression. Intrathecal injection of the cyclooxygenase inhibitor, ketorolac, has recently entered clinical trials, and the current study examined the interaction between intrathecal morphine and ketorolac to treat postoperative pain. We also sought to compare these treatments on a commonly used assessment of withdrawal threshold and a new assessment of spontaneous behavior after surgery. Male Sprague Dawley rats and underwent hind paw incision or subcostal laparotomy surgery. Intrathecal morphine, ketorolac, or their combination were injected on the first postoperative day, with outcome measure being return to pre-surgery withdrawal threshold with von Frey filament testing of the paw after paw incision, or return to pre-surgery exploratory activity after laparotomy. Intrathecal morphine completely reversed the effects of surgery in both models, but intrathecal ketorolac only partially reversed them. Ketorolac enhanced the potency of morphine several fold in both models, and did so synergistically after paw incision. In all cases drug potency was greater for spontaneous than elicited responses. These data confirm that spinal opioid receptor and cyclooxygenase enzyme inhibition diminish elicited tactile hypersensitivity after surgery, and that they similarly return spontaneous behavior to normal. Differences in drug potency could reflect fundamental differences in outcome measures or in the surgical procedures themselves. These data support combination study of intrathecal morphine and ketorolac for postoperative pain.

Analgesics, Opioid↗

Medium and large injured dorsal root ganglion cells increase TRPV-1, accompanied by increased alpha2C-adrenoceptor co-expression and functional inhibition by clonidine.

Some electrophysiologic studies demonstrate new, excitatory alpha2-adrenoceptors on peripheral nociceptors and their dorsal root ganglion (DRG) cell bodies after nerve injury, yet administration of alpha2-adrenoceptor agonists at these sites reduces hypersensitivity rather than worsens it. Since TRPV-1 expressing nociceptor afferents are important in many pain states, we examined the expression of this channel and its co-expression with alpha2C-adrenoceptors in injured DRG cell bodies and the ability of alpha2-adrenoceptors to inhibit responses to stimulation. Rats underwent tight ligation of the left L5 and L6 spinal nerves, followed by behavioral testing, removal of L5 and L6 DRGs, and either immunostaining for TRPV-1 channels and alpha2C-adrenoceptors or intracellular calcium videomicroscopy in response to electrical field stimulation before and after perfusion with clonidine and capsaicin. Spinal nerve ligation produced tactile allodynia. In normal and sham controls, about one-third of DRG neurons were TRPV-1-immunoreactive (IR), one half were alpha2C-adrenoceptor-IR and one-fourth co-expressed both. After nerve ligation there was a reduction in the number of small, strongly TRPV-1-IR or alpha2C-adrenoceptor-IR neurons, but an increase in medium and large, lightly stained cells and in their co-expression. The proportion of clonidine inhibited cells which responded to capsaicin increased 5 fold after injury. We conclude that TRPV-1 and alpha2C-adrenoceptors are up-regulated in some injured medium and large size neurons after nerve ligation. Increased co-expression by immunocytochemistry, and increased proportion of cells inhibited by clonidine and expressing functional TRPV-1 channels suggest that these cells may play an important role in the analgesic effects of alpha2-adrenoceptor agonists in neuropathic pain.

Adrenergic alpha-Agonists↗

Luminescence behavior of Eu3+ doped LaF3 nanoparticles.

Europium-doped LaF3 nanoparticles have been prepared by the ionic reaction in the ethanol at 60 degrees C. From the XRD pattern of nanoparticles and the emission spectra of Eu3+ ions, it has been concluded that the Eu3+ ions could easily substitute the La3+ sites and the solid solution La(1-x)Eu(x)F3 can be synthesized. Due to very low phonon energies of LaF3 matrix, the 5D1 emission of Eu3+ ions in La(1-x)Eu(x)F3 nanoparticles can be observed at room temperature when doping concentration of Eu3+ ions is lower than 30 mol%. The quenching process of 5D1 emission can be attributed to cross-relaxation. Since clusters of Eu3+ ions and resonance energy transfer only occurs within one particle due to the hindrance by the particle boundary, the concentration quenching resulted from resonance energy transfer between neighboring Eu3+ ions occurs at higher Eu3+ concentrations in the Eu3+ doped LaF3 nanoparticles.

Europium↗

Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays.

As the data generated by microarray technology continue to amass, it is necessary to compare and combine gene expression data from different platforms. To evaluate the performance of cDNA and long oligonucleotide (60-mer) arrays, we generated gene expression profiles for two cancer cell lines and compared the data between the two platforms. All 6182 unique genes represented on both platforms were included in the analysis. A limited correlation (r = 0.4708) was obtained and the difference in measurement of low-expression genes was considered to contribute to the limited correlation. Further restriction of the data set to differentially expressed genes detected in cDNA microarrays (1205 genes) and oligonucleotide arrays (1325 genes) showed modest correlations of 0.7076 and 0.6441 between the two platforms. Quantitative real-time PCR measurements of a set of 10 genes showed better correlation with oligonucleotide arrays. Our results demonstrate that there is substantial variation in the data generated from cDNA and 60-mer oligonucleotide arrays. Although general agreement was observed in measurements of differentially expressed genes, we suggest that data from different platforms could not be directly amassed.

Cell Line, Tumor↗

Serial analysis of gene expression in the silkworm, Bombyx mori.

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Animals↗

Effects of enhanced ultraviolet-B radiation on algae and cyanobacteria.

This article provides an overview of existing literature on the ultraviolet-B (UV-B) radiation effects on algae and cyanobacteria. We report on the effects of UV-B radiation to the growth and development, biomass, sensitivity, photosynthetic pigments, UV-B absorbing compounds, photosynthesis, protein and DNA damage, enzyme activity, nitrogen fixation and assimilation of nitrogen, protective mechanisms of algae and cyanobacteria, the accommodation of algae and cyanobacteria to environmental stress, and the effects to ecology system. Many of the studies show the dramatic effects of UV-B radiation; but typically these studies were conducted under conditions with supplemental UV-B irradiance that was higher than would ever occur outside experimental conditions or natural condition. A few of the studies reviewed used experimental conditions and supplemental UV-B irradiance that approached realism. Enhanced UV-B generally decreased chlorophyll content, whereas it increased UV-B absorbing compounds in many algae. Decrease in photosynthesis, particularly at higher UV-B doses, was due to both direct (effect on photosystem) and indirect (decrease in pigments) effects. The decreases in chlorophyll pigments and photosynthesis resulted in lower biomass. However, algae and cyanobacteria have evolved various avoidance and repair mechanisms to protect themselves against the damaging effects of UV radiation to acclimate to enhanced UV-B radiation. The review points to areas where further studies on the relationships among nitrogenase, Rubisco, antioxidase activity, signal, antioxidants, and free radicals under enhanced UV-B are needed to quantify the effects of UV-B radiation on algae and cyanobacteria. These studies are needed in order to develop dose response functions that can facilitate development of dynamic simulation models for use in UV-B and other environmental impact assessments.

Cyanobacteria↗

Intrathecal morphine reduces allodynia after peripheral nerve injury in rats via activation of a spinal A1 adenosine receptor.

BACKGROUND: The degree to which intrathecally administered morphine can alleviate hypersensitivity in animals after peripheral nerve injury is controversial, and the mechanisms by which morphine works in these circumstances are uncertain. In normal animals, morphine induces adenosine release, and in vitro data suggest that this link is disrupted after peripheral nerve injury. Therefore, using a controlled, blinded study design, the authors tested intrathecal morphine efficacy in rats with peripheral nerve injury and the role of spinal A1 adenosine receptors in the action of morphine. METHODS: Male rats underwent intrathecal catheter implantation and lumbar spinal nerve ligation, resulting in hypersensitivity to tactile stimulation of the paw. Intrathecal morphine alone or with naloxone or the specific A1 adenosine receptor antagonist, 1,3-dipropyl-8-cyclopentyxanthine (DPCPX), was administered, and withdrawal threshold to von Frey filament application to the hind paw was determined. RESULTS: Intrathecal morphine (0.25-30 microg) dose-dependently reversed mechanical hypersensitivity after spinal nerve ligation, with an ED50 of 0.79 microg. The effect of morphine was blocked by intrathecal naloxone. Intrathecal DPCPX alone had no effect on withdrawal threshold after spinal nerve ligation but completely reversed the effect of morphine, with an ID50 of 5.6 microg. CONCLUSIONS: This study is in accord with two recent reports that support short-term efficacy of intrathecal morphine to reverse hypersensitivity to mechanical stimuli in animal models of neuropathic pain. Despite previous studies demonstrating that morphine releases less adenosine after peripheral nerve injury, the current study suggests that the antihypersensitivity effect of morphine in these conditions is totally reliant on A1 adenosine receptor activation.

Animals↗