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Ying Li

Publications and source records attributed to Ying Li.

At least 181 records · Page 10Linked to original sources
PubMed2005

Incorporating structure to predict microRNA targets.

MicroRNAs (miRNAs) are a recently discovered set of regulatory genes that constitute up to an estimated 1% of the total number of genes in animal genomes, including Caenorhabditis elegans, Drosophila, mouse, and humans [Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. (2001) Science 294, 853-858; Lai, E. C., Tomancak, P., Williams, R. W. & Rubin, G.M. (2003) Genome Biol. 4, R42; Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. (2001) Science 294, 858-862; Lee, R. C. & Ambros, V. (2001) Science 294, 862-8644; and Lee, R. C., Feinbaum, R. L. & Ambros, V. (1993) Cell 115, 787-798]. In animals, miRNAs regulate genes by attenuating protein translation through imperfect base pair binding to 3' UTR sequences of target genes. A major challenge in understanding the regulatory role of miRNAs is to accurately predict regulated targets. We have developed an algorithm for predicting targets that does not rely on evolutionary conservation. As one of the features of this algorithm, we incorporate the folded structure of mRNA. By using Drosophila miRNAs as a test case, we have validated our predictions in 10 of 15 genes tested. One of these validated genes is mad as a target for bantam. Furthermore, our computational and experimental data suggest that miRNAs have fewer targets than previously reported.

3' Untranslated Regions↗
PubMed2005

[Construction of monovalent and compound nucleic acid vaccines against Toxoplasma gondii with gene encoding p30].

OBJECTIVE: To construct a monovalent gene vaccine pcDNA3.1-p30 and a compound gene vaccine pcDNA3.1-p30-ROP2 and assess the protective effect of the two vaccines against Toxoplasma gondii. METHODS: The sequences encoding p30 and ROP2 were amplified from the genomic DNA of T. gondii RH strain by polymerase chain reaction (PCR) and inserted into eukaryotic vector pcDNA3.1 to construct pcDNA3.1-p30 and pcDNA3.1-p30-ROP2. Mice were injected with the recombinant plasmid to observe the immunoprotectivity of the nucleic acid vaccine by using ELISA for detection of total IgG and observing the survival time after tachyzoites challenge. RESULTS: The recombinant plasmids pcDNA3.1-p30 and pcDNA3.1-p30-ROP2 were constructed. Mice in pcDNA3.1-p30-ROP2 group showed higher IgG (P < 0.05) and survived longer than those in pcDNA3.1-p30 group (P < 0.01) after challenged with T. gondii. CONCLUSION: Compound vaccine of genes from different stages of T. gondii elicits stronger immunoprotectivity in mice than a single gene vaccine.

Animals↗
PubMed2005

Simultaneous measurements of the flow velocities in a microchannel by wide/evanescent field illuminations with particle/single molecules.

A laser-induced fluorescence imaging method was developed to simultaneously measure flow velocities in the middle and near wall of a channel with particles or single molecules, by selectively switching from the wide field excitation mode to the evanescent wave excitation mode. Fluorescent microbeads with a diameter of 175 nm were used to calibrate the system, and the collisions of microbeads with channel walls were directly observed. The 175 nm microbeads velocities in the main flow and at 275 nm from the bottom of the channel were measured. The measured velocities of particles or single molecules in two positions in a microchannel were consistent with the calculated value based on Poiseuille flow theory when the diameter of a microbead was considered. The errors caused by Brownian diffusion in our measurement were negligible compared to the flow velocity. Single lambda DNA molecules were then used as a flowing tracer to measure the velocities. The velocity can be obtained at a distance of 309.0 +/- 82.6 nm away from bottom surface of the channel. The technique may be potentially useful for studying molecular transportation both in the center and at the bottom of the channel, and interactions between molecules and microchannel surfaces. It is especially important that the technique can be permitted to measure both velocities in the same experiment to eliminate possible experimental inconsistencies.

Bacteriophage lambda↗
PubMed2005

Detection of paternally inherited fetal point mutations for beta-thalassemia using size-fractionated cell-free DNA in maternal plasma.

CONTEXT: Currently, fetal point mutations cannot be reliably analyzed from circulatory fetal DNA in maternal plasma, due to the predominance of maternal DNA sequences. However, analysis of circulatory fetal DNA sequences in maternal plasma have been shown to selectively enrich for fetal DNA molecules on the basis of a smaller molecular size than maternal DNA. OBJECTIVE: To examine the prenatal analysis of 4 common beta-thalassemia point mutations: IVSI-1, IVSI-6, IVSI-110, and codon 39. DESIGN, SETTING, AND PATIENTS: A total of 32 maternal blood samples were collected at 10 to 12 weeks of gestation (mean, 10.7 weeks) between February 15, 2003, and February 25, 2004, in Bari, Italy, from women with risk for beta-thalassemia in their newborns immediately prior to chorionic villous sampling. Samples in which the father and mother did not carry the same mutation were examined. Circulatory DNA was size-fractionated by gel electrophoresis and polymerase chain reaction (PCR) amplified with a peptide-nucleic-acid clamp, which suppresses amplification of the normal maternal allele. Presence of the paternal mutant allele was detected by allele-specific real-time PCR. MAIN OUTCOME MEASURE: Detection of paternally inherited beta-globin gene point mutations. RESULTS: Presence or absence of the paternal mutant allele was correctly determined in 6 (86%) of 7 cases with the IVSI-1 mutation, 4 (100%) of 4 with the IVSI-6 mutation, 5 (100%) of 5 with the IVSI-110 mutation, and 13 (81%) of 16 with the codon 39 mutation. One false-positive test result was scored for the IVSI-1 mutation. Two cases with the codon 39 mutation were classified as uncertain and 1 case was excluded due to lack of a diagnostic test result at the time of analysis. These results yielded an overall sensitivity of 100% and specificity of 93.8%, with classified cases removed. CONCLUSION: Our recently described technique of the size-fractionation of circulatory DNA in maternal plasma may be potentially useful for the noninvasive prenatal determination of fetal point mutations.

Chorionic Villi Sampling↗
PubMed2005

Proton transfer of NH3-HCl catalyzed by only one molecule.

The proton transfer in NH(3)-HCl by only one molecule of catalyst was studied by using the MP2 method with the large 6-311++G(2d,2p) basis set. The 18 structures are obtained for the smallest units, NH(3)-HCl-A trimers, for which the proton transfer maybe occurred. The final results show that the proton transfers have occurred in the 15 cyclic shape structures for A = H(2)SO(4), H(2)SO(3), HCOOH (a), HF, H(2)O(2), HNO(3), HNO(2) (a), CH(3)OH, HCl, HNC, H(2)O, HNO(2) (b), NH(3), HCOOH (b), and HCHO, and not occurred in another 3 trimer structures for A = HCN, H(2)S, and PH(3). These results show that the proton transfer occurs from HCl to NH(3) when catalyst molecule A (acidic, neutral, or basic) not only as a proton donor strongly donates the proton to the Cl atom but as an acceptor strongly accepts the proton from the NH(3) molecule in the cyclic H-bond structure. In this work, a proton circumfluence model is proposed to explain the mechanism of the proton transfer. We find that, for the trimer, when the sum of two hydrogen bond lengths (R = R(1) + R(2)) is shorter than 5.0 A, molecule A has the ability to catalyze the proton transfer. In addition, we also find that the interaction energy E(int) between NH(3)-HCl and A is nearly related to the extent (R(H1)(-)(Cl)) of proton transfer, that is, the interaction energy E(int) increases with the proton transfer.

Ammonia↗
PubMed2005

Synthesis and antiviral activity of helioxanthin analogues.

A series of natural product analogues based on helioxanthin (2), with particular attention to modification of the lactone ring and methylenedioxy group, were synthesized and evaluated for their antiviral activities. Among them, lactam derivative 18 and helioxanthin cyclic hydrazide 28 exhibited significant in vitro antiviral activity against hepatitis B virus (EC(50) = 0.08 and 0.03 microM, respectively). Compound 18 showed the most potent antiviral activity against hepatitis C virus (55% inhibition at 1.0 microM). Compound 12, an acid-hydrolyzed product of helioxanthin cyclic imide derivative 9, was found to exhibit broad-spectrum antiviral activity against hepatitis B virus (EC(50) = 0.8 microM), herpes simplex virus type 1 (EC(50) = 0.15 microM) and type 2 (EC(50) < 0.1 microM), Epstein-Barr virus (EC(50) = 9.0 microM), and cytomegalovirus (EC(50) = 0.45 microM). Helioxanthin lactam derivative 18 also showed marked inhibition of herpes simplex virus type 1 (EC(50) = 0.29 microM) and type 2 (EC(50) = 0.16 microM). The cyclic hydrazide derivative of helioxanthin 28 and its brominated product 42 exhibited moderately potent activities against human immunodeficiency virus (EC(50) = 2.7 and 2.5 microM, respectively). Collectively, these molecules represent a novel set of antiviral compounds with unique structural features.

Antiviral Agents↗
PubMed2005

Comparison of para-aminophenol cytotoxicity in rat renal epithelial cells and hepatocytes.

Several chemicals, including para-aminophenol (PAP), produce kidney damage in the absence of hepatic damage. Selective nephrotoxicity may be related to the ability of the kidney to reabsorb filtered water, thereby raising the intraluminal concentration of toxicants and exposing tubular epithelial cells to higher concentrations than would be present in other tissues. The present experiments tested the hypothesis that hepatocytes and renal epithelial cells exposed to equivalent concentrations of PAP would be equally susceptible to toxicity. Hepatocytes and renal epithelial cells were prepared by collagenase digestion of tissues obtained from female Sprague-Dawley rats. Toxicity was monitored using trypan blue exclusion, oxygen consumption and ATP content. We measured the rate of PAP clearance and formation of PAP-glutathione conjugate by HPLC. We found that renal epithelial cells accumulated trypan blue and showed declines in oxygen consumption and ATP content at significantly lower concentrations of PAP and at earlier time points than hepatocytes. The half-life of PAP in hepatocyte incubations was significantly shorter (0.71+/-0.07 h) than in renal epithelial cell incubations (1.33+/-0.23 h), suggesting that renal epithelial cells were exposed to PAP for longer time periods than hepatocytes. Renal epithelial cells formed significantly less glutathione conjugates of PAP (PAP-SG) than did hepatocytes, consistent with less efficient detoxification of reactive PAP intermediates by renal epithelial cells. Finally, hepatocytes contained significant more reduced glutathione (NPSH) than did renal epithelial cells, possibly explaining the enhanced formation of PAP-SG by this cell population. In conclusion, our data indicates that renal epithelial cells are intrinsically more susceptible to PAP cytotoxicity than are hepatocytes. This enhanced cytotoxicity may be due to longer exposure to PAP and/or reduced detoxification of reactive intermediates due to lower concentrations of reduced NPSH in renal epithelial cells than in hepatocytes.

Aminophenols↗
PubMed2005

A neurotrophin axis in myeloma: TrkB and BDNF promote tumor-cell survival.

Multiple myeloma (MM) is a B-cell neoplasm that is characterized by the clonal expansion of malignant plasma cells and is frequently associated with chromosomal translocations placing an oncogene under the control of the immunoglobulin heavy chain enhancer. Despite these pathogenic translocations, MM cells remain dependent on external cues for survival. We present evidence that brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family of growth factors, and its high-affinity receptor, tropomyosin receptor kinase B (TrkB), contribute to these survival cues. MM cells express TrkB, and respond to BDNF by activating mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3 kinase-a PI3K target (PI3K/Akt) signaling cascades. Addition of BDNF protects human MM cell lines (HMCLs) from apoptosis induced by dexamethasone or bortezomib and prolongs the survival of primary MM cells cultured alone or with human bone marrow (BM) stroma. As BDNF and TrkB are expressed by osteoblasts, stromal cells, and endothelial cells within the BM microenvironment, a BDNF-TrkB axis may be critical to the interactions of MM with bone and stroma that contribute to MM tumor progression. Finally, BDNF is expressed by malignant plasma cells isolated from a subset of patients with MM, as well as by most HMCLs, suggesting a potential role for this neurotrophin axis in autocrine as well as paracrine support of MM.

Autocrine Communication↗
PubMed2005

Direct and indirect inhibition by catecholamines of hypocretin/orexin neurons.

Hypothalamic hypocretin enhances arousal, similar to the actions of norepinephrine (NE). The physiological actions of NE were examined in hypocretin neurons identified by selective green fluorescent protein expression in transgenic mouse hypothalamic slices using whole-cell recording. NE induced an outward current, inhibited spike frequency, and hyperpolarized hypocretin neurons dose dependently. Similar actions were evoked by the selective alpha2 adrenergic agonist clonidine. The alpha2 antagonist idazoxan increased spike frequency, suggesting tonic NE-mediated inhibition. The NE-induced current was inwardly rectified, and the reversal potential was dependent on external potassium concentration; it was blocked by barium in the bath and by GTP-gamma-S in the pipette, suggesting activation of a G-protein inward rectifying K+ (GIRK) current. NE and clonidine decreased calcium currents evoked by depolarizing voltage steps. The selective alpha1 adrenergic agonist phenylephrine had no effect on membrane potential but did increase IPSC frequency; miniature IPSC frequency was also increased, in some cells without any effect on amplitude, suggesting a facilitative presynaptic action at alpha1 receptors on GABAergic axons that innervate hypocretin neurons. NE therefore inhibits hypocretin neurons directly through two mechanisms: activation of a GIRK current, depression of calcium currents, and indirectly through increased inhibitory GABA input. Similar to NE, dopamine and epinephrine reduced or blocked spikes and, in the presence of TTX, showed direct hyperpolarizing actions. The action of dopamine was blocked by the D2 receptor antagonist eticlopride, whereas a D1/5 antagonist had no effect. These data suggest that catecholamines evoke strong inhibitory actions on hypocretin neurons and suggest negative feedback from catecholamine cells that may be excited by hypocretin.

Action Potentials↗
PubMed2005

Specific interaction of chalcone-protein: cardamonin binding site II on the human serum albumin molecule.

Cardamonin (2',4'-dihydroxy-6'-methoxychalcone), one of the main constituents from the seeds of Alpinia katsumadai Hayata, belongs to chalcone with its antibacterial, antiinflammatory and other important therapeutic activities of significant potency and low systemic toxicity. In this article, the interaction of cardamonin to human serum albumin (HSA) has been studied for the first time by spectroscopic methods including Fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD), and UV-absorption spectroscopy in combination with fluorescence quenching under physiological conditions with drug concentrations of 0.67-4.0 microM. The results of the spectroscopic measurements and the thermodynamic parameters obtained (the enthalpy change DeltaH(0) and the entropy change DeltaS(0) were calculated to be -25.312 and 7.040 J.mol(-1).K(-1) according to the van't Hoff equation) suggest that hydrophobic interaction is the predominant intermolecular forces stabilizing the complex, which is also in good agreement with the results of the molecule modeling study. The alterations of protein secondary structure in the presence of cardamonin in aqueous solution were quantitatively calculated by the evidence from CD and FTIR spectroscopes with reductions of alpha-helices of about 20%, decreases of beta-sheet structures of about 14%, and increases of beta-turn structures of about 15%. The quenching mechanism and the number of binding sites (n approximately 1) were obtained by fluorescence titration data. Fluorescent displacement measurements confirmed that cardamonin binds HSA on site II. In addition, the effects of common ions on the constants of the cardamonin-HSA complex were also discussed.

Binding Sites↗
PubMed2005

Serine protease HtrA1 is developmentally regulated in trophoblast and uterine decidual cells during placental formation in the mouse.

Development of a hemochorial placenta involves trophoblast proliferation, differentiation, and invasion into the uterus to promote blood flow to the embryo. Trophoblast invasion is tightly controlled by expression of specific proteases in the trophoblast and highly coordinated activities in the uterus. One uterine event essential for placentation is the developmentally regulated formation and regression of the decidua. In mice, decidual regression takes place in a temporal- and spatial-specific manner that is coordinated with placental development. In this study, we identified that the serine protease HtrA1 (high temperature requirement factor A1) was specifically expressed in differentiated trophoblast cells, especially the giant cells, during the early stages of placental development. A high level of HtrA1 expression was also detected in decidua capsularis specifically at the decidual-trophoblast interface where active involution occurs. Thus, we have identified a previously unknown role for HtrA1 as a protease potentially important for trophoblast differentiation/invasion and uterine decidual regression during placental development.

Animals↗
PubMed2005

Delayed repair of corticospinal tract lesions as an assay for the effectiveness of transplantation of Schwann cells.

We have previously shown that cultured adult olfactory ensheathing cells injected after 8 weeks into functionally complete unilateral lesions of the rat corticospinal tract induce restoration of paw reaching function to about 50% of normal, starting at around 10 days after transplantation. This provides an assay for determining the effectiveness of different methods of cell preparation or different cell types. We report that transplantation of cultured adult peripheral nerve Schwann cells also restores function, but the effect is delayed until around 30 days after transplantation and reaches only around 5-10% of normal. The presence of fibroblasts in the Schwann cell cultures neither improves, nor impairs the reparative effect, but fibroblasts alone (without Schwann cells) have no reparative effect. Without transplantation of exogenous Schwann cells, the ingrowth of endogenous Schwann cells which occurs spontaneously into these lesions does not restore function.

Animals↗
PubMed2005

Study of the tolerance of Hippochaete ramosissimum to Cu stress.

We investigated the tolerance of Hippochaete ramosissimum and the changes in physiological metabolism following exposure to copper using pot experiments and analyzing plant physiology and biochemistry. The results showed that Cu tolerance in Hippochaete ramosissimum varied significantly between different populations; the tolerance of plants living in Cu polluted areas for extended periods of time exceeded that of plants living in unpolluted areas. SOD and POD activities in highly Cu tolerant plants increased noticeably following exposure to Cu. This indicates that maintaining and increasing the two kinds of protective enzyme activities are the primary foundations of plant tolerance. However, no change in CAT activity was demonstrated following Cu exposure. In summary, there existed considerable differences in physiological metabolism between different populationsof Hippochaete ramosissimum following exposure to Cu.

Adaptation, Physiological↗
PubMed2005

Reduction of RF-induced sample heating with a scroll coil resonator structure for solid-state NMR probes.

Heating due to high power 1H decoupling limits the experimental lifetime of protein samples for solid-state NMR (SSNMR). Sample deterioration can be minimized by lowering the experimental salt concentration, temperature or decoupling fields; however, these approaches may compromise biological relevance and/or spectroscopic resolution and sensitivity. The desire to apply sophisticated multiple pulse experiments to proteins therefore motivates the development of probes that utilize the RF power more efficiently to generate a high ratio of magnetic to electric field in the sample. Here a novel scroll coil resonator structure is presented and compared to a traditional solenoid. The scroll coil is demonstrated to be more tolerant of high sample salt concentrations and cause less RF-induced sample heating. With it, the viable experimental lifetime of a microcrystalline ubiquitin sample has been extended by more than an order of magnitude. The higher B1 homogeneity and permissible decoupling fields enhance polarization transfer efficiency in 15N-13C correlation experiments employed for protein chemical shift assignments and structure determination.

Carbon Isotopes↗
PubMed2005

Retroviral transduction with SOX9 enhances re-expression of the chondrocyte phenotype in passaged osteoarthritic human articular chondrocytes.

OBJECTIVES: Articular chondrocytes proliferate in monolayer culture, but the expression of the transcription factor SOX9 falls and the ability of the cells to reform cartilage tissue declines. We have investigated whether retroviral SOX9 expression in extensively passaged human articular chondrocytes from osteoarthritic (OA) joints enables the cells to regain a cartilage matrix forming phenotype in pellet culture. DESIGN: Chondrocytes from normal and OA joints were retrovirally transduced with SOX9 and grown to passages 7-10 before being cultured as pellets of 500,000 cells for 14 days. Pellets were analysed by real time polymerase chain reaction, histology, immunohistochemistry and 1,9-dimethylmethylene blue assay. RESULTS: Chondrocytes from OA joints displayed higher expression of COL2A1 gene when transduced with SOX9 and cultured as pellets with 10% serum, but glycosaminoglycan (GAG) synthesis was low. Addition of transforming growth factor beta-3 and insulin like growth factor-1 increased collagen II expression and GAG synthesis in these SOX9 transduced cell pellets. The cells adopted a rounded morphology and there was increased deposition of collagen II protein compared to control green fluorescent protein transduced cell pellets. Similar results were seen with transduced chondrocytes from OA or healthy cartilage. SOX9 transduced human dermal fibroblasts did not show any chondrogenic response. DISCUSSION: Transduction with SOX9 primed the passaged articular chondrocytes to regain a chondrocytic phenotype in pellet culture and to form a cartilaginous matrix, which was enhanced by growth factors. Following transduction, chondrocytes from OA joints showed a similar capacity for chondrogenic recovery as those from healthy joints, which suggested that OA does not permanently compromise the chondrocyte phenotype.

Cartilage, Articular↗
PubMed2005

Positron annihilation spectroscopy for surface and interface studies in nanoscale polymeric films.

Positron annihilation spectroscopy (PAS), coupled with a variable mono-energetic positron beam, has been used to investigate surface and interfacial properties in thin polymeric films. Free-volume properties have been measured from ortho-Positronium (o-Ps) lifetime and the S parameter of Doppler broadening of energy spectra from annihilation radiation as a function of the depth and of the temperature in thin polymeric films. Depth profiles of glass transition temperature and nanoscale layered structures in polystyrene (PS) thin films on the Si substrate are presented.

Electrons↗
PubMed2005

New targets and inhibitors of HBV replication to combat drug resistance.

All the approved chemotherapeutic drugs for the treatment of HBV hepatitis are nucleoside analogs targeting on HBV DNA polymerase. Drugs targeting on other viral unique targets are needed. A new class of chemicals with novel action against HBV replication was discovered. A brief description of their mode of action is given.

Antiviral Agents↗