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Biomedical subjects

Yue Zhang

Publications and source records attributed to Yue Zhang.

At least 91 records · Page 5Linked to original sources

BMP-1/Tolloid-like metalloproteases process endorepellin, the angiostatic C-terminal fragment of perlecan.

Endorepellin, the C-terminal domain of the heparan sulfate proteoglycan perlecan, possesses angiostatic activity. The terminal laminin-like globular (LG3) domain of endorepellin appears to possess most of the biological activity on endothelial cells. LG3 protein has been detected in the urine of patients with end-stage renal disease and in the amniotic fluid of pregnant women with premature rupture of fetal membranes. These findings suggest that proteolytic processing of endorepellin and the generation of LG3 might have biological significance. In this study, we have identified specific enzymes of the bone morphogenetic protein-1 (BMP-1)/Tolloid family of metalloproteases that cleave LG3 from recombinant endorepellin at the physiologically relevant site and that cleave LG3 from endogenous perlecan in cultured mouse and human cells. The BMP-1/Tolloid family of metalloproteases is thereby implicated in the processing of a major basement membrane proteoglycan and in the liberation of an anti-angiogenic factor. Using molecular modeling, site-directed mutagenesis and angiogenic assays, we further demonstrate that LG3 activity requires specific amino acids involved in Ca(2+) coordination.

Angiostatic Proteins↗

Direct ab initio dynamics study on the rate constants and kinetics isotope effects of CH(3)O+H-->CH(2)O+H(2) reaction.

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH(3)O+H-->CH(2)O+H(2). The unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set, the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set, and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set methods were employed to optimize the structures and to calculate frequencies for all stationary points. Minimum energy paths were obtained by the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional and the unrestricted quadratic configuration interaction calculation including single and double substitutions with the same Dunning's correlation consistent polarized valence double-zeta basis set levels of theory. No barrier is found at the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set level of theory in contrast to a small barrier of 1.43 kcal mol(-1) at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory. In particular, the barrier vanishes as the energies along the minimum energy path MEP are refined at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set level of theory. Smaller barriers of 0.47 and 0.17 kcal mol(-1) were obtained at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence triple-zeta basis set levels of theory, respectively. The forward rate constants are evaluated with the canonical variational transition state theory in the temperature range of 300-2500 K. The calculated forward rate constants at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory are in good agreement with the available experimental data. The kinetic isotope effects are estimated.

Journal Article↗

Residue depletion of tilmicosin in chicken tissues.

A high-performance liquid chromatography (HPLC) method with detection at 290 nm was modified and validated for the determination of tilmicosin residues in broiler chicken tissues. The limits of detection (LOD) of the method were 0.01 microg/g for muscle and 0.025 microg/g for liver and kidney. Average recoveries ranged from 80.4 to 88.3%. Relative standard deviation values ranged from 5.2 to 12.1%. Residue depletion of tilmicosin in broiler chickens was examined after dosing over a 5-day period by incorporation of the drug into drinking water at 37.5 and 75.0 mg/L. Tilmicosin concentrations in liver and kidney were highest on day 3 of medication and on day 5 in muscle, in both low- and high-dose groups. The residue levels in both groups were significantly higher in liver than in kidney or muscle. A minimum withdrawal time of 9 days was indicated for residue levels in muscle, liver, and kidney tissues below the maximum residue level (MRL).

Animals↗

Cloning, expression and subcellular localization of HN1 and HN1L genes, as well as characterization of their orthologs, defining an evolutionarily conserved gene family.

The present work reported the cloning and characterization of two novel human genes--HN1 (hematopoietic- and neurologic-expressed sequence 1) and HN1L (HN1-like gene) which are proposed to be involved in embryo development. HN1 is mapped on chromosome 17q25.2, with two transcripts (1.0 and 1.6 kb in length, respectively) due to alternative splicing. HN1 is expressed abundantly in testis and skeletal muscle among 16 human tissues, and it is localized in the nucleus indicated by GFP fusion expression. Western blot confirmed that HN1 encodes a 16.5-kDa protein. HN1L is on chromosome 16p13.3, with three splicing in the length of 2.0, 4.0 and 4.2 kb, respectively. HN1L is expressed in a variety of tissues such as liver, kidney, prostate, testis and uterus at varying levels. HN1L gene encodes a 20-kDa protein, which is localized in both the nucleus and cytoplasm. Fourteen of HN1 and sixteen of HN1L homologous genes in different species were determined and analyzed by BLAST searches. Silicon analyses of the 14 orthologous proteins of HN1 and 16 orthologous proteins of HN1L revealed that they share great conservation in vertebrate. Additionally, we identified nine pseudogenes of HN1 (six) and HN1L (three) in the genomes of the human, mouse and rat. Based on sequence alignments and phylogenetic analysis, all these homologous genes and pseudogenes were defined as a HN1 gene family.

Amino Acid Motifs↗

Smurf1: a link between cell polarity and ubiquitination.

Members of the Rho family of small guanosine triphosphatases are well known for their important functions in the dynamic regulation of actin cytoskeleton. We recently found that a HECT domain E3 ubiquitin ligase, called Smurf1, regulates cell polarity and protrusion formation by targeting RhoA for degradation at cellular protrusions. Smurf1 regulates these functions as a partner of protein kinase Cxi, a component of the polarity complex. Furthermore, using siRNA-mediated knockdown, we demonstrated this pathway is required to maintain the transformed morphology and motility of a tumor cell. Smurf1 thus provides a link between the control of cell polarity and ubiquitin-mediated RhoA degradation during directional cell movements. Here we further discuss the mechanism by which the spatial control of Smurf1 activity is accomplished and the potential implications of these findings in cancer and development.

Animals↗

A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O-->CH2O + CH3.

We present a direct ab initio and hybrid density functional theory dynamics study of the thermal rate constants of the unimolecular decomposition reaction of C2H5O-->CH2O + CH3 at a high-pressure limit. MPW1K/6-31+G(d,p), MP2/6-31+G(d,p), and MP2(full)/6-31G(d) methods were employed to optimize the geometries of all stationary points and to calculate the minimum energy path (MEP). The energies of all the stationary points were refined at a series of multicoefficient and multilevel methods. Among all methods, the QCISD(T)/aug-cc-pVTZ energies are in good agreement with the available experimental data. The rate constants were evaluated based on the energetics from the QCISD(T)/aug-cc-pVTZ//MPW1K/6-31+G(d,p) level of theory using both microcanonical variational transition state theory (microVT) and RRKM theory with the Eckart tunneling correction in the temperature range of 300-2500 K. The calculated rate constants at the QCISD(T)/aug-cc-pVTZ/MPW1K/6-31+G(d,p) level of theory are in good consistent with experimental data. The fitted three-parameter Arrhenius expression from the microVT/Eckart rate constants in the temperature range 200-2500 K is k = 2.52 x 10(12)T(0.41)e(-8894.0/T) s(-1). The falloff curves of pressure-dependent rate constants are performed using master-equation method within the temperature range of 391-471 K. The calculated results are in good agreement with the available experimental data.

Journal Article↗

FGDP: functional genomics data pipeline for automated, multiple microarray data analyses.

UNLABELLED: Gene expression microarrays and oligonucleotide GeneChips have provided biologists with a means of measuring, in a single experiment, the expression levels of entire genomes under a variety of conditions. As with any nascent field, there is no single accepted method for analyzing the new data types, with new methods appearing monthly. Investigators using the new technology must constantly seek access to the latest tools and explore their data in multiple ways. The functional genomics data pipeline provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed and provides a web server and interface for presenting results. AVAILABILITY: Source code and executables are available under the GNU public license at http://bioinformatics.fccc.edu/

Computing Methodologies↗

First-principles pair potentials across the metal-ceramic interface.

Systematic approaches are presented to invert the first-principle binding energy to obtain the pair potentials across the metal/ceramic interfaces. The conformation characteristics of two virtual interface models suitable for the inversion are summarized: (1) the positions of one kind of ceramic ions stay unchanged, but those of the other change; or, (2) there is no change in the relative positions of the ceramic ions to the metal atoms but the positions of two kinds of ceramic ions are all exchanged each other. As an example, we derive the pair potentials of Ni-Zr(4+) and Ni-O(2-) across the Ni/ZrO(2) interface with this method, which exhibit comparable accuracy to the first-principle results. This provides direct evidence that the interfacial potentials obtained from this method can reasonably describe the general features of bondings across the metal-ceramic interface. The limitation of this method is also discussed.

Journal Article↗

High-level production of soluble tumor necrosis factor-related apoptosis-inducing ligand (Apo2L/TRAIL) in high-density cultivation of recombinant Escherichia coli using a combined feeding strategy.

Recombinant Escherichia coli strain C600/pBV-TRAIL (encoding for 114-281 amino acids of TRAIL's soluble fragment) produced a recombinant human tumor necrosis factor-related apoptosis-inducing ligand (Apo2L/TRAIL). Using a combined strategy of exponential feeding and pH-stat feeding, high concentrations of biomass (65 g dry wt l(-1)) and active soluble TRAIL (1.4 g l(-1)) were obtained within 30 h. The accumulation of acetate, which usually occurs during the process of high-density culture of Escherichia coli and especially in the induction stage of protein synthesis, was avoided.

Apoptosis Regulatory Proteins↗

Cloning and characterization of a novel human RNA binding protein gene PNO1.

Present work reported the cloning and characterization of a human novel RNA binding gene Partner of NOB1 (PNO1), with a length of 1637bp and a putative open reading frame of 759 bp, isolated from human kidney. It is composed of seven exons and is localized on chromosome 2p14. Western blot showed that the molecular weight of PNO1 is about 35kDa. RT-PCR results in 16 human tissues indicated that PNO1 is expressed mainly in liver, lung, spleen and kidney, slightly in thymus, testis, ovary, respectively, but not in heart, brain, skeletal muscle, placenta, pancreas, prostate, small intestine, colon and peripheral blood leukocytes. GFP fusion expression in mammalian cells exhibited its localization in the nucleus, especially in nucleoli. Subcellular localization of thirteen GFP fusion PNO1 deletion proteins showed that the region of 92-230 aa is solely responsible for its nucleolar retention, and KH domain alone is not sufficient for nucleolar retention. The PNO1 family shows significant conservation in both eukaryotes and prokaryotes.

Amino Acid Sequence↗

[Transport of proteins and peptides across human cultured alveolar A549 cell monolayers].

AIM: An in vitro cultured monolayer system of alveolar epithelial cells was used as a model to investigate the transport pathway peptides or proteins, salmon calcitonin (sCT), insulin (INS), recombinant hirudin (rHAV2), and recombinant human growth hormone (rhGH), in pulmonary epithelium in vivo. METHODS: Human lung adenocarcinoma A549 cells formed continuous monolayers with growing polycarbonate filters of Transwell plate. Transport studies of macromolecules in the monolayer system were carried out after 6 days in culture. The transport of peptides or proteins with MW 3,400 - 22,000 was studied in cultured human lung adenocarcinoma A549 cell monolayers at different conditions. RESULTS: The results showed that the apparent permeability coefficients (Papp) of these macromolecules across A549 cell monolayers ranged from 2 x 10(-6) to 5 x 10(-6) cm x s(-1) and exhibited good inverse correlation with molecule weight. No concentration, direction and temperature dependence were observed in the permeation of sCT, INS and rHAV2. While the Papp of rhGH in the BA direction (2.25 x 10(-6) cm x s(-1)) was significantly less than that in the reverse direction. The Papp values of rhGH were concentration and temperature independent in the AB direction. CONCLUSION: These findings suggest that the hydrophilic peptides and proteins, salmon calcitonin, insulin, recombinant hirudin, and recombinant human growth hormone used in this study, appeared to penetrate the A549 cell monolayers via a paracellular pathway by passive diffusion mechanism.

Adenocarcinoma↗

[Value of measurements of blood flow velocity in central retinal artery in thyroid-associated ophthalmopathy].

OBJECTIVE: To study the clinical values of measurement of blood flow velocity in central retinal artery in thyroid-associated ophthalmopathy (TAO). METHODS: Thirty normal subjects without any thyroid disorders or any eye abnormalities were assigned into the control group, and 30 TAO patients were assigned into the TAO group. Color Doppler ultrasonography was done to measure the blood flow velocity in central retinal artery. Measurement results were compared between these two groups. RESULTS: The peak systolic velocity and end diastolic velocity of blood flow were significantly lower in TAO group (P < 0.001), while the resistance index significantly increased (P < 0.001). CONCLUSION: Measurement of blood flow velocity in central retinal artery with Color Doppler ultrasonography is an easy and useful way to appraise the hemodynamics of the central retinal artery in TAO patients.

Adult↗

[High-cell density cultivation of recombinant Escherichia coli for production of TRAIL by using a 2-stage feeding strategy].

Escherichia coli was genetically engineered to produce recombinant tumor necrosis factor-related apoptosis inducing ligand (Apo2L/TRAIL) using a temperature-inducible expression system. To create a fed-batch culture condition that allows efficient production of TRAIL, different feeding strategy including discontinuous, DO-stat and pH-stat feeding strategies were compared. Then, a special 2-stage feeding strategy was developed. High concentration of biomass (300g wet cell weight per liter of culture broth) and active soluble TRAIL protein (1.1g/L) was obtained by applying a high-cell-density cultivation procedure with the 2-stage feeding strategy. Cultivation of recombinant E. coli was started as a batch process at 30 degrees C and then followed by fed-batch culture when the dissolved oxygen concentration presented a steep increase resulted from the exhaustion of glucose in the medium. At the first phase of fermentation (batch phase), agitation rate was enhanced to control dissolved oxygen at 30 percent. When glucose in the medium was used up, indicated by a sudden rise in pH value and dissolved oxygen, the second phase (fed-batch phase) was started with glucose and nitrogen resource being supplied automatically. At the beginning of fed-batch operation, stirrer rate was cascaded with dissolved oxygen signals to keep it at 20 percent (DO-stat). During the fed-batch phase, glucose was limited to control the specific growth rate under the critical value microcrit, to avoid acetic acid excretion. When the stirrer speed arrived at its up-limit, the flow rate of feed was kept constant. In the inducing phase(42 degrees C for 4h) glucose was fed as a pH regulating agent (pH-stat) and the specific growth rate and dissolved oxygen decreased sharply. Aqueous ammonia was used for maintaining pH value at 7.0 throughout the first two phases. In the whole fermentation, acetic acid concentration didn't exceed 2.9 g/L. At the end of the high-cell-density cultivation process, no acetic acid could be detected in the medium. These results indicated that our fed-batch strategy was able to prevent acetate accumulation significantly. Although high cell density has been achieved, the induction process was not optimized satisfactorily and much work should be done further. Furthermore, since no special ways, like pure oxygen, pressure, has been used in our experiments, this efficient approaches would be useful not only in a pilot scale but also in an industry scale. Finally, simple purification procedure based on immobilized metal affinity column (IMAC) and CM-Sepharose column was implemented to isolate the TRAIL. Yields of more than 800mg TRAIL per liter of culture broth were obtained, the final purity reaching more than 95%. The purified TRAIL showed strong cytotoxity activity against human pancreatic 1990 tumor cells, with ED50 about 1.6 microg/mL.

Escherichia coli↗

Regulation of cell polarity and protrusion formation by targeting RhoA for degradation.

The Rho family of small guanosine triphosphatases regulates actin cytoskeleton dynamics that underlie cellular functions such as cell shape changes, migration, and polarity. We found that Smurf1, a HECT domain E3 ubiquitin ligase, regulated cell polarity and protrusive activity and was required to maintain the transformed morphology and motility of a tumor cell. Atypical protein kinase C zeta (PKCzeta), an effector of the Cdc42/Rac1-PAR6 polarity complex, recruited Smurf1 to cellular protrusions, where it controlled the local level of RhoA. Smurf1 thus links the polarity complex to degradation of RhoA in lamellipodia and filopodia to prevent RhoA signaling during dynamic membrane movements.

Animals↗

SVA elements are nonautonomous retrotransposons that cause disease in humans.

L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements.

Base Sequence↗

CUL-4A stimulates ubiquitylation and degradation of the HOXA9 homeodomain protein.

The HOXA9 homeodomain protein is a key regulator of hematopoiesis and embryonic development. HOXA9 is expressed in primitive hematopoietic cells, and its prompt downregulation is associated with myelocytic maturation. Although transcriptional inactivation of HOXA9 during hematopoietic differentiation has been established, little is known about the biochemical mechanisms underlying the subsequent removal of HOXA9 protein. Here we report that the CUL-4A ubiquitylation machinery controls the stability of HOXA9 by promoting its ubiquitylation and proteasome-dependent degradation. The homeodomain of HOXA9 is responsible for CUL-4A-mediated degradation. Interfering CUL-4A biosynthesis by ectopic expression or by RNA-mediated interference resulted in alterations of the steady-state levels of HOXA9, mirrored by impairment of the ability of 32D myeloid progenitor cells to undergo proper terminal differentiation into granulocytes. These results revealed a novel regulatory mechanism of hematopoiesis by ubiquitin-dependent proteolysis.

Cell Differentiation↗

Intracellular membrane localization of pseudomonas ExoS and Yersinia YopE in mammalian cells.

ExoS (453 amino acids) is a bi-functional type-III cytotoxin of Pseudomonas aeruginosa. Residues 96-233 comprise the Rho GTPase-activating protein (Rho GAP) domain, while residues 234-453 comprise the 14-3-3-dependent ADP-ribosyltransferase domain. Residues 51-72 represent a membrane localization domain (MLD), which targets ExoS to perinuclear vesicles within mammalian cells. YopE (219 amino acids) is a type-III cytotoxin of Yersinia that is also a Rho GAP. Residues 96-219 comprise the YopE Rho GAP domain. While the Rho GAP domains of ExoS and YopE share structural homology, unlike ExoS, the intracellular localization of YopE within mammalian cells has not been resolved and is the subject of this investigation. Deletion mapping showed that the N terminus of YopE was required for intracellular membrane localization of YopE in CHO cells. A fusion protein containing the N-terminal 84 amino acids of YopE localized to a punctate-perinuclear region in mammalian cells and co-localized with a fusion protein containing the MLD of ExoS. Residues 54-75 of YopE (termed YopE-MLD) were necessary and sufficient for intracellular localization in mammalian cells. The YopE-MLD localized ExoS to intracellular membranes and targeted ExoS to ADP-ribosylate small molecular weight membrane proteins as observed for native type-III delivered ExoS. These data indicate that the YopE MLD functionally complements the ExoS MLD for intracellular targeting in mammalian cells.

ADP Ribose Transferases↗