Biomedical subjects

Yu Zhang

Publications and source records attributed to Yu Zhang.

At least 73 records · Page 4Linked to original sources

PubMed2006

Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma.

PURPOSE: The most common genitourinary malignancy in China is bladder transitional cell carcinoma (TCC). Early diagnosis of new and recurrent bladder cancers, followed by timely treatment, will help decrease mortality. There are currently no satisfactory markers for bladder cancer available in clinics. Better diagnostic methods are highly demanded. EXPERIMENTAL DESIGN: In this research, we have used comprehensive expressed sequence tag analysis, serial analysis of gene expression, and microarray analysis and quickly discovered a candidate marker, urothelial carcinoma associated 1 (UCA1). The UCA1 gene was characterized and its performance as a urine marker was analyzed by reverse transcription-PCR with urine sediments. A total of 212 individuals were included in this study, 94 having bladder cancers, 33 ureter/pelvic cancers, and 85 normal and other urinary tract disease controls. RESULTS: UCA1 was identified as a novel noncoding RNA gene dramatically up-regulated in TCC and it is the most TCC-specific gene yet identified. The full-length cDNA was 1,439 bp, and sequence analysis showed that it belonged to the human endogenous retrovirus H family. Clinical tests showed that UCA1 assay was highly specific (91.8%, 78 of 85) and very sensitive (80.9%, 76 of 94) in the diagnosis of bladder cancer and was especially valuable for superficial G2-G3 patients (sensitivity 91.1%, 41 of 45). It showed excellent differential diagnostic performance in various urinary tract diseases without TCC. CONCLUSIONS: UCA1 is a very sensitive and specific unique marker for bladder cancer. It could have important implications in postoperative noninvasive follow-up. This research also highlights a shortcut to new cancer diagnostic assays through integration of in silico isolation methods with translational clinical tests based on RNA detection protocols.

Biomarkers, Tumor↗

PubMed2006

An ultrathin self-humidifying membrane for PEM fuel cell application: fabrication, characterization, and experimental analysis.

An ultrathin poly(tetrafluoroethylene) (PTFE)-reinforced multilayer self-humidifying composite membrane (20 microm, thick) is developed. The membrane is composed of Nafion-impregnated porous PTFE composite as the central layer, and SiO2 supported nanosized Pt particles (Pt-SiO2) imbedded into the Nafion as the two side layers. The proton exchange membrane (PEM) fuel cell employing the self-humidifying membrane (Pt-SiO2/NP) turns out a peak power density of 1.40 W cm(-2) and an open circuit voltage (OCV) of 1.032 V under dry H2/O2 condition. The excellent performance is attributed to the combined result of both the accelerated water back-diffusion in the thin membrane and the adsorbing/releasing water properties of the Pt-SiO2 catalyst in the side layers. Moreover, the inclusion of the hygroscopic Pt-SiO2 catalyst inside the membrane results in an enhanced anode self-humidification capability and also the decreased cathode polarization (accordingly an improved cell OCV). Several techniques, such as transmission electronic microscopy, scanning electronic microscopy, energy dispersive spectroscopy, thermal analysis and electrochemical impedance spectroscopy etc., are employed to characterize the Pt-SiO2/NP membrane. The results are discussed in comparison with the plain Nafion/PTFE membrane (NP). It is established that the reverse net water drag (from the cathode to the anode) across the Pt-SiO2/NP membrane reaches 0.16 H2O/H+. This implies a good hydration of the Pt-SiO2/NP membrane and thus ensures an excellent PEM fuel cell performance under self-humidification operation.

Electric Power Supplies↗

PubMed2006

Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development.

Repression of photomorphogenesis in Arabidopsis thaliana requires activity of the COP9 signalosome (CSN), CDD, and COP1 complexes, but how these three complexes work in concert to accomplish this important developmental switch has remained unknown. Here, we demonstrate that Arabidopsis CULLIN4 (CUL4) associates with the CDD complex and a common catalytic subunit to form an active E3 ubiquitin ligase both in vivo and in vitro. The partial loss of function of CUL4 resulted in a constitutive photomorphogenic phenotype with respect to morphogenesis and light-regulated gene expression. Furthermore, CUL4 exhibits a synergistic genetic interaction with COP10 and DET1. Therefore, this CUL4-based E3 ligase is essential for the repression of photomorphogenesis. This CUL4-based E3 ligase appears to associate physically with COP1 E3 ligase and positively regulates the COP1-dependent degradation of photomorphogenesis-promoting transcription factors, whereas the CSN controls the biochemical modification of CUL4 essential for E3 activity. Thus, this study suggests a biochemical activity connection between CSN and CDD complexes in their cooperation with COP1 in orchestrating the repression of photomorphogenesis.

Arabidopsis↗

PubMed2006

Function of aquaporins in female and male reproductive systems.

The flow of water and some other small molecules across cell membranes is important in many of the processes underlying reproduction. The fluid movement is strongly associated with the presence of aquaporins (AQPs) in the female and male reproductive systems. It has been suggested that AQPs mediate water movement into the antral follicle and play important roles in follicle development. AQPs are known to be involved in the early stage of spermatogenesis, in the secretion of tubule liquid and in the concentration and storage of spermatozoa. Fluid reabsorption in some regions of the male reproductive tract is under steroid hormone control and could be mediated by various AQPs. Also AQPs take part in the processes of fertilization, blastocyst formation (as the pathway for transtrophoectodermal water movement during cavitation) and implantation. Alterations in the expression and function or regulation of AQPs have already been demonstrated in disorders of the male reproductive system, such as abnormal sperm motility, the abnormal epididymis and infertility seen in cystic fibrosis, and varicocele. This article extensively reviews the distribution of AQPs in mammalian reproductive tissues and discusses their possible physiological and pathophysiological roles.

Amniotic Fluid↗

PubMed2006

HDAC6-p97/VCP controlled polyubiquitin chain turnover.

HDAC6 is a unique cytoplasmic deacetylase capable of interacting with ubiquitin. Using a combination of biophysical, biochemical and biological approaches, we have characterized the ubiquitin-binding domain of HDAC6, named ZnF-UBP, and investigated its biological functions. These studies show that the three Zn ion-containing HDAC6 ZnF-UBP domain presents the highest known affinity for ubiquitin monomers and mediates the ability of HDAC6 to negatively control the cellular polyubiquitin chain turnover. We further show that HDAC6-interacting chaperone, p97/VCP, dissociates the HDAC6-ubiquitin complexes and counteracts the ability of HDAC6 to promote the accumulation of polyubiquitinated proteins. We propose that a finely tuned balance of HDAC6 and p97/VCP concentrations determines the fate of ubiquitinated misfolded proteins: p97/VCP would promote protein degradation and ubiquitin turnover, whereas HDAC6 would favour the accumulation of ubiquitinated protein aggregates and inclusion body formation.

3T3 Cells↗

PubMed2006

A coalescence-guided hierarchical Bayesian method for haplotype inference.

Haplotype inference from phase-ambiguous multilocus genotype data is an important task for both disease-gene mapping and studies of human evolution. We report a novel haplotype-inference method based on a coalescence-guided hierarchical Bayes model. In this model, a hierarchical structure is imposed on the prior haplotype frequency distributions to capture the similarities among modern-day haplotypes attributable to their common ancestry. As a consequence, the model both allows distinct haplotypes to have different a priori probabilities according to the inferred hierarchical ancestral structure and results in a proper joint posterior distribution for all the parameters of interest. A Markov chain-Monte Carlo scheme is designed to draw from this posterior distribution. By using coalescence-based simulation and empirically generated data sets (Whitehead Institute's inflammatory bowel disease data sets and HapMap data sets), we demonstrate the merits of the new method in comparison with HAPLOTYPER and PHASE, with or without the presence of recombination hotspots and missing genotypes.

Algorithms↗

PubMed2006

Double minute chromosomes in mouse methotrexate-resistant cells studied by atomic force microscopy.

Double minute chromosomes (DMs) are acentric, autonomously replicating extra-chromosomes and frequently mediate gene amplification in tumor and drug resistant cells. Atomic force microscopy (AFM) is a powerful tool in microbiology. We used AFM to explore the ultrastructure of DMs in mouse fibroblasts 3T3R500. DMs in various phases of cell cycle were also studied in order to elucidate the mechanisms of their duplication and separation. Metaphase spread and induced premature condensed chromosomes (PCCs) were observed under the AFM. DMs were detected to be composed of two compact spheres linked by fibers. The fibers of DMs directly connected with metaphase chromosomes were observed. Many single-minutes and few DMs were detected in G1 PCCs, while more DMs were detected in S PCCs than in G1 PCCs. Besides, all of the DMs in G2 PCCs were coupled. Our present results suggested that DMs might divide into single-minutes during or before G1-phase, followed by duplication of the single-minutes in S-phase. Moreover, we introduced a new powerful tool to study DMs and got some ideal results.

Animals↗

PubMed2006

Sorption of palladium(II), rhodium(III), and platinum(IV) on Fe(3)O(4) nanoparticles.

The adsorption of palladium(II), rhodium(III), and platinum(IV) from diluted hydrochloric acid solutions onto Fe(3)O(4) nanoparticles has been investigated. The parameters studied include the contact time and the concentrations of metals and other solutes such as H(+) and chloride. The equilibrium time was reached in less than 20 min for all metals. The maximum loading capacity of Fe(3)O(4) nanoparticles for Pd(II), Rh(III), and Pt(IV) was determined to be 0.103, 0.149, and 0.068 mmol g(-1), respectively. A sorption mechanism for Pd(II), Rh(III), and Pt(IV) has been proposed and their conditional adsorption equilibrium constants have been determined to be logK=1.72, 1.69, and 1.84, respectively. Different compositions of eluting solution were tested for the recovery of Pt(IV), Pd(II), and Rh(III) from Fe(3)O(4) nanoparticles. It was found that 0.5 mol L(-1) HNO(3) can elute all of the metal ions simultaneously, while 1 mol L(-1) NaHSO(3) was an effective eluting solution for Rh(III), and 0.5 mol L(-1) NaClO(4) for Pt(IV). In competitive adsorption, the nanoparticles showed stronger affinity for Rh(III) than for Pd(II) and Pt(IV).

Journal Article↗

PubMed2006

Controllable size, shape and morphology of molybdic acid self-aggregated with rhodamine B to construct functional material.

Controllable size, shape and morphology of rhodamine B/molybdic acid (RBMA) aggregates were prepared from a self-aggregation reaction in a molybdic acid and rhodamine B (RhB) coexisting solution. Nanodisks, as well as microcrystal rods and polyhexagonal microcrystal rods, have been obtained in conventional bulk solutions at different temperatures. Large-sized network microcrystal rods and branched fractal aggregates constructed with nanosubunits after the nucleation duration of an ice-water-cooled process have also been achieved under the evaporation-enhanced conditions on glass substrates. The factors affecting the size, shape and morphology of RBMA aggregates including temperature, nucleation and growth, and processing conditions are discussed. The results show that photofunctional molecules (RhB) modified the surface of the molybdic acid particles and influenced their self-aggregation. The temperature and nucleation play key roles in the formation of RBMA aggregates. The structures of RBMA aggregates were characterized by X-ray diffraction, infrared spectra and elemental dispersive spectroscopy. The results indicate that the aggregates show the characteristics of RhB-mediated hydrated ammonium molybdenum bronze with the metastable hexagonal phase. Visible-light-induced electrons transfer reactions in the RBMA aggregates from rhodamine B molecules to MoO3 matrixes were measured by UV-vis spectra and X-ray photoelectron spectra, and the fluorescent image was observed by laser scanning confocal microscopy.

Microscopy, Electron, Scanning↗

PubMed2006

XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice.

Inactivation of the XRCC4 nonhomologous end-joining factor in the mouse germ line leads to embryonic lethality, in association with apoptosis of newly generated, postmitotic neurons. We now show that conditional inactivation of the XRCC4 in nestin-expressing neuronal progenitor cells, although leading to no obvious phenotype in a WT background, leads to early onset of neuronally differentiated medulloblastomas (MBs) in a p53-deficient background. A substantial proportion of the XRCC4/p53-deficient MBs have high-level N-myc gene amplification, often intrachromosomally in the context of complex translocations or other alterations of chromosome 12, on which N-myc resides, or extrachromosomally within double minutes. In addition, most XRCC4/p53-deficient MBs harbor clonal translocations of chromosome 13, which frequently involve chromosome 6 as a partner. One copy of the patched gene (Ptc), which lies on chromosome 13, was deleted in all tested XRCC4/p53-deficient MBs in the context of translocations or interstitial deletions. In addition, Cyclin D2, a chromosome 6 gene, was amplified in a subset of tumors. Notably, amplification of Myc-family or Cyclin D2 genes and deletion of Ptc also have been observed in human MBs. We therefore conclude that, in neuronal cells of mice, the nonhomologous end-joining pathway plays a critical role in suppressing genomic instability that, in a p53-deficient background, routinely contributes to genesis of MBs with recurrent chromosomal alterations.

Alleles↗

PubMed2006

Stereoselective cascade reactions that incorporate a 7-exo acyl radical cyclization.

[reaction: see text] Radical cascades that feature a 7-exo acyl radical cyclization followed by a 6-exo or 5-exo alkyl radical cyclization proceed with very good yields and diastereoselectivities. Two stereocenters are created by the reaction, and a single isomeric product was obtained from each of the five substrates examined. The relative configurations of the products are consistent with cyclizations occurring via chairlike or pseudochairlike transition states.

Alkaloids↗

PubMed2006

[PLAC1/CP1 gene expression and autologous humoral immunity in gastric cancer patients].

OBJECTIVE: To investigate PLAC1/CP1 as a potential candidate gene in gastric cancer therapy. METHODS: Reverse transcription-polymerase chain reaction (RT-PCR) method was used to detect the expression of PLAC1/CP1 mRNA in gastric cancer tissues and paired adjacent non-cancerous tissues resected from 28 patients with gastric cancer. Specific antibodies against PLAC1/CP1 were also detected by ELISA method in gastric cancer patients. RESULTS: Fourteen (50%,14/28) out of the 28 gastric cancer samples were PLAC1/CP1 mRNA positive. Of the 28 serum samples tested,eight (29%,8/28) displayed positive seroreactivity against PLAC1/CP1 antigen, accounting for 57% (8/14) of PLAC1/CP1 mRNA positive samples. CONCLUSION: PLAC1/CP1 mRNA was expressed in high frequency and induced spontaneous antibody responses in gastric cancer patients. PLAC1/CP1 may be a valuable candidate antigen in gastric cancer immunotherapy.

Antibodies, Neoplasm↗

PubMed2006

Modulation of protein aggregation by polyethylene glycol conjugation: GCSF as a case study.

Polyethylene glycol (PEG) conjugation to proteins has emerged as an important technology to produce drug molecules with sustained duration in the body. However, the implications of PEG conjugation to protein aggregation have not been well understood. In this study, conducted under physiological pH and temperature, N-terminal attachment of a 20 kDa PEG moiety to GCSF had the ability to (1) prevent protein precipitation by rendering the aggregates soluble, and (2) slow the rate of aggregation relative to GCSF. Our data suggest that PEG-GCSF solubility was mediated by favorable solvation of water molecules around the PEG group. PEG-GCSF appeared to aggregate on the same pathway as that of GCSF, as evidenced by (a) almost identical secondary structural transitions accompanying aggregation, (b) almost identical covalent character in the aggregates, and (c) the ability of PEG-GCSF to rescue GCSF precipitation. To understand the role of PEG length, the aggregation properties of free GCSF were compared to 5kPEG-GCSF and 20kPEG-GCSF. It was observed that even 5kPEG-GCSF avoided precipitation by forming soluble aggregates, and the stability toward aggregation was vastly improved compared to GCSF, but only marginally less stable than the 20kPEG-GCSF. Biological activity measurements demonstrated that both 5kPEG-GCSF and 20kPEG-GCSF retained greater activity after incubation at physiological conditions than free GCSF, consistent with the stability measurements. The data is most compatible with a model where PEG conjugation preserves the mechanism underlying protein aggregation in GCSF, steric hindrance by PEG influences aggregation rate, while aqueous solubility is mediated by polar PEG groups on the aggregate surface.

Chemical Precipitation↗

PubMed2006

Rapid determination of acrylamide contaminant in conventional fried foods by gas chromatography with electron capture detector.

Gas chromatography coupled with electron capture detector (GC-ECD) was successfully developed and applied for the rapid determination of acrylamide in conventional fried foods, such as potato crisps, potato chips, and fried chicken wings. The method included defatting with n-hexane, extraction with aqueous solution of sodium chloride (NaCl), derivatization with potassium bromate (KBrO3) and potassium bromide (KBr), and liquid-liquid extraction with ethyl acetate. The final acrylamide extract was analyzed by GC-ECD for quantification and by GC-MS for confirmation. The chromatographic analysis was performed on the HP-INNOWax capillary column, and good retention and peak response of acrylamide were achieved under the optimal conditions (numbers of theoretical plates N = 83,815). The limit of detection (LOD) was estimated to be 0.1 microg kg(-1) on the basis of ECD technique. Recoveries of acrylamide from conventional samples spiked at levels of 150, 500 and 1000 microg kg(-1) (n = 4 for each level) ranged between 87 and 97% with relative standard deviations (RSD) of less than 4%. Furthermore, the GC-ECD method showed that no clean-up steps of acrylamide derivative would be performed prior to injection and was slightly more sensitive than the MS/MS-based methods. Validation and quantification results demonstrated that this method should be regarded as a new, low-cost, and robust alternative for conventional investigation of acrylamide.

Acrylamide↗

PubMed2006

Identification and functional perspective of a novel HLA-A allele: A*0279.

A novel HLA-A allele, HLA-A*0279, was identified using PCR-SSP and PCR-SBT methods. It is inheritable. HLA-A*0279 differs from HLA-A*020601 by a single nucleotide at position 497 in exon 3, leading to an amino acid change from Threonine to Isoleucine at the alpha2 helix of HLA molecule. To investigate whether the altered amino acid residue could affect its peptide-binding repertoire, we compared the predicted crystal structure of HLA-A*020601 and HLA-A*0279 by Swiss-PdbViewer software analysis. We found that the crystal structure of the two molecules is very similar except for a difference in the number of hydrogen bonds they can possibly form, which in turn could affect their structural stability. To test whether HLA-A*0279 has the ability to cross-present A*0201 - restricted peptides to T cells, the full lenght cDNA of HLA-A*0201, -A* 020601 and -A*0279 were respectively transfected into COS-7 cells, which were then used as targets in IFN-gamma release Elispot assay. A*2079 was found to be able to present A*0201- restricted peptides to and induce the response of CTL, thus it can be classified as member of the HLA-A2 functional supertype family. This finding would benefit the design of peptide vaccines to be applied in broader populations.

Adult↗

PubMed2006

[Non-infectious pulmonary complications after allogeneic hematopoietic stem cell transplantation: analysis of 17 cases].

OBJECTIVE: To analyze the clinical feature, cause, treatment and outcome of late onset non-infectious pulmonary complications (LONIPC) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS: The clinical data of 17 patients with malignant hematological diseases who survived for at least 3 months and suffered from LONIPC after allo-HSCT were retrospectively analyzed. RESULTS: The incidence of LONIPC was 17.7% in allo-HSCT recipients. The median of onset of respiratory symptoms was 6.5 months (3-13.5 months). Seven patients came down with LONIPC during fast tapering of cyclosporine A prophylaxis and 15 patients had already chronic graft versus host disease (cGVHD) before the occurrence of respiratory symptoms. The initial symptoms were non-productive cough and dyspnoea in all patients; five of them had low grade or moderate fever. CT scans revealed patchy ground-glass opacities, irregular patchy consolidation, band-like opacities, and micronodular densities. Histological examination of transbronchial biopsy showed infiltration of lymphocyte and monocytes in interstitium, peribronchiolar fibrosis and alveoli pulmonis obliteration. The response rate of corticosteroids in addition to cyclosporine therapy was 70.6%. Treatment beginning at the early stage was more effective than that beginning late. The mortality rate of LONIPC was 35.3%. Chest CT scanning showed lung fibrosis in the patients with protracted LONIPC. CONCLUSION: The clinical manifestations and radiological changes of LONIPC are non-specific. The diagnosis is made by combination of functional and histological examinations and exclusion of pathogen infection. Examination of transbronchial biopsy is of significance for the diagnosis. LONIPC may be considered as pathognomonic of cGVHD in the lung of patients after allo-HSCT; and cGVHD should be regarded as a useful diagnostic proof for LONIPC. Earlier treatment with corticosteroids and maintenance treatment may result in improved survival and decrease of the fibrotic residue.

Adolescent↗

PubMed2006

[Effects of RNAi on hypoxia inducible factor-1alpha activity and proliferation of hypoxic pulmonary artery smooth muscle cells in rat].

Pulmonary vascular remodeling is one of the major characteristics of hypoxia-induced pulmonary hypertension, mainly represented by over-proliferation of pulmonary artery smooth muscle cells (PASMCs). Hypoxia inducible factor-1alpha (HIF-1alpha) is a transcription factor which is produced by the cells exposed to hypoxia. HIF-1alpha up-regulates the expression of many hypoxia response genes (HRGs) for the body to adapt to hypoxia and maintain homeostasis. The expression of HIF-1alpha in the PASMCs is remarkably elevated under hypoxic condition and it stimulates the proliferation of PASMCs. In this experiment, we used gene clone technology to design and synthesize two siRNAs based on the sequence of HIF-1alpha mRNA. They were separately subcloned into the plasmid of pGenesil-1 containing U6 promoter. The pGenesil-1 vector of the RNA interference eukaryotic expression vector specific to HIF-1alpha gene was constructed. DNA sequencing of the plasmid verified the successful construction of the HIF-1alpha RNAi. We isolated and cultured the PASMCs of rat. The pGenesil-1 vector was transferred into the PASMCs with METAFECTENE in vitro. The positive cell clones transfected with pGenesil-1 were obtained after being screened with 400 mug/ml G418. These PASMCs were cultured in normoxia and hypoxia. After 48 h, the effects of RNAi on the expression of HIF-1alpha mRNA were detected by RT-PCR. The cellular growth activities were assayed by MTT colorimetry and flow cytometry in vitro. The results showed that for the PASMCs cultured in hypoxia for 48 h, the cell proliferation of blank group and control group were remarkably increased and the HIF-1alpha mRNA expressions were up-regulated, while the cell proliferation of the treatment groups did not increase and the HIF-1alpha mRNA expressions were not up-regulated. In conclusion, we successfully constructed the recombinant plasmid of RNAi and transfected them into the PASMCs in vitro. The RNAi inhibited the expression of HIF-1alpha mRNA in the PASMCs, and subsequently it remarkably suppressed the proliferation of PASMCs in hypoxia. These results indicate that HIF-1alpha plays a pivotal role in PASMC proliferation.

Animals↗

PubMed2006

Refinement of optical map assemblies.

MOTIVATION: Genomic mutations and variations provide insightful information about the functionality of sequence elements and their association with human diseases. Traditionally, variations are identified through analysis of short DNA sequences, usually shorter than 1000 bp per fragment. Optical maps provide both faster and more cost-efficient means for detecting such differences, because a single map can span over 1 million bp. Optical maps are assembled to cover the whole genome, and the accuracy of assembly is critical. RESULTS: We present a computationally efficient model-based method for improving quality of such assemblies. Our method provides very high accuracy even with moderate coverage (<20 x). We utilize a hidden Markov model to represent the consensus map and use the expectation-Maximization algorithm to drive the refinement process. We also provide quality scores to assess the quality of the finished map. AVAILABILITY: Code is available from www.cmb.usc.edu/people/valouev/

Algorithms↗