Biomedical subjects

Yanling Zhang

Publications and source records attributed to Yanling Zhang.

At least 19 recordsLinked to original sources

PubMed2026

Chromosome-level de novo assembly of the nuclear and mitochondrial genomes of Arcopilus aureus, a filamentous fungus with multifaceted ecological and economic roles.

The filamentous fungus Arcopilus aureus (Sordariale: Chaetomiaceae) is notable for its multi-domain significance across agriculture, medicine, and industry. In this study, we generated a chromosome-level nuclear genome and a complete circular mitogenome for A. aureus by integrating data from next-generation sequencing, PacBio HiFi, and Hi-C technologies. The final nuclear genome assembly spans 33.77 Mb (GC content: 57.67%), and was organized into seven chromosomal-sized scaffolds (only one gap) with an N50 size of 5.09 Mb and BUSCO completeness of 95.91%. A total of 10,282 protein-coding genes, 228 non-coding RNAs, and ~1.77 Mb of repetitive elements were predicted in the nuclear genome. By contrast, the mitogenome of A. aureus is 33,820 bp in length, with a GC content of 25.96%. It harbors 15 typical mitochondrial protein-coding genes, one unidentified ORF, two rRNAs (small subunit rns and large subunit rnl), and 28 tRNAs. This high-quality genome assembly provides a valuable resource for understanding the ecology, genetics, and evolution of A. aureus, which facilitates elucidating its mechanisms of biocontrol, infection, and metabolite synthesis.

Genome, Mitochondrial↗

PubMed2007

A novel OPA1 mutation responsible for autosomal dominant optic atrophy with high frequency hearing loss in a Chinese family.

PURPOSE: To investigate the genetic findings and phenotypic characters of autosomal dominant optic atrophy (ADOA). DESIGN: Case report and experimental study. METHODS: Molecular genetic analysis and clinical examinations were performed in a Chinese family with ADOA. Mutations in OPA1 were detected by direct sequencing. Haplotypes were constructed and compared with the phenotypes in the family. RESULTS: Nine family members were diagnosed with ADOA and some of them were accompanied with hearing loss and/or high myopia. A novel heterozygous mutation, c.2848_2849delGA(p.Asp950CysfsX4), was detected in all ADOA patients. The mutation and the mutation bearing haplotype cosegregated with the nine affected members. One family member had high myopia without vision or hearing loss. This patient along with unaffected ones did not harbor the mutation. CONCLUSIONS: A novel mutation, c.2848_2849delGA in OPA1, was identified in a Chinese family with ADOA. This mutation is associated with hearing loss, but likely not high myopia.

Adolescent↗

PubMed2006

Acrosome reaction induced by recombinant human zona pellucida 3 peptides rhuZP3a22 approximately 176 and rhuZP3b177 approximately 348 and their mechanism.

To explore the biological characteristics of the recombinant zona pellucida 3 (ZP3) peptides of rhuZP3a22 approximately 176 and rhuZP3b177 approximately 348, we examined whether rhuZP3a22 approximately 176 or rhuZP3b177 approximately 348 trigger the acrosome reaction (AR) of human spermatozoa and we investigated the underlying mechanism. The assessment of AR was performed using chlortetracycline staining. The intracellular free calcium concentration ([Ca2+]i) in Fura-2/AM-loaded human sperm was monitored with a spectrofluorophotometer. We found that rhuZP3a22 approximately 176 and rhuZP3b177 approximately 348 were capable of eliciting AR at different concentrations. With the addition of either peptide, the [Ca2+]i level was raised to a peak with or without a plateau. The AR could be inhibited by pertussis toxin (PTX), EGTA, and pimozide (a T-type calcium channel blocker), whereas verapamil was less effective in this regard. The results of the present study suggest that peptides rhuZP3a22 approximately 176 and rhuZP3b177 approximately 348 have a role similar to human ZP3, and that the mechanism of the response to the peptides involves influx of calcium, the G protein pathway, and a T-type calcium channel.

Acrosome Reaction↗

PubMed2006

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

Animals↗

PubMed2006

Design, synthesis, and evaluation of efflux substrate-metal chelator conjugates as potential antimicrobial agents.

Maintaining a proper balance of metal concentrations is critical to the survival of bacteria. We have designed and synthesized a series of conjugates of metal chelators and efflux transporter substrates aimed at disrupting bacterial metal homeostasis to achieve bacterial killing. Biological studies showed that two of the compounds had very significant antimicrobial effect with an MIC value of 7.8 microg/mL against Gram-positive Bacillus subtilis.

Anti-Bacterial Agents↗

PubMed2006

Production and characterization of clinical grade Escherichia coli derived Plasmodium falciparum 42 kDa merozoite surface protein 1 (MSP1(42)) in the absence of an affinity tag.

The 42 kDa cleavage product from the carboxyl end of the Plasmodium falciparum merozoite surface protein 1 (MSP1(42)) is an important blood-stage malaria vaccine target. Several recombinant protein expression systems have been used for production of MSP1(42) including yeast (Saccharomyces cerevisiae and Pichia pastoris), Escherichia coli, baculovirus and transgenic animals. To date, all of the reported recombinant proteins include a 6 x His affinity tag to facilitate purification, including three MSP1(42) clinical grade proteins currently in human trials. Under some circumstances, the presence of the 6 x His tag may not be desirable. Therefore, we were interested to produce clinical grade MSP1(42) without a 6 x His affinity tag from E. coli inclusion bodies. We produced a recombinant MSP1(42) with a P. falciparum FUP (Uganda-Palo Alto) phenotype which accounts for a substantial proportion of the MSP1(42) protein observed in African isolates. EcMSP1(42)-FUP was produced in E. coli inclusion bodies by high cell mass induction with IPTG using 5 L and 60 L bioreactors. Isolated inclusion bodies were solubilized in 8M guanidine-HCl and the EcMSP1(42)-FUP protein refolded by rapid dilution. Refolded EcMSP1(42)-FUP was purified using hydrophobic interaction chromatography, anion exchange chromatography, and size exclusion chromatography, and subject to biochemical characterization for integrity, identity, and purity. Endotoxin and host cell protein levels were within acceptable limits for human use. The process was successfully transferred to pilot-scale production in a cGMP environment. A final recovery of 87.8 mg of clinical-grade material per liter of fermentation broth was achieved. The EcMSP1(42)-FUP clinical antigen is available for preclinical evaluation and human studies.

Animals↗

PubMed2006

Polymorphic amino acids at codons 9 and 37 of HLA-DQB1 alleles may confer susceptibility to cervical cancer among Chinese women.

Cervical cancer is strongly associated with the infection by oncogenic forms of human papillomavirus (HPV). Although most women are able to clear HPV infection, some develop persistent infections that may lead to cancer, implying genetic susceptibility factors for malignant progression. To verify whether HLA class II DQB1 polymorphism is related to cervical cancer in Chinese population, HLA-DQB typing was carried out by PCR-SBT for 258 patients with cervical cancer and 284 healthy controls, and the allele frequencies were calculated. In this study, HLA-DQB1*060101 and DQB1*0602 alleles were significantly higher in the HPV16 infected patients with cervical cancer compared with healthy controls (chi(2) = 31.7452, p < 0.0001; chi(2) = 12.7838, p(c) = 0.0066), but DQB1*050201 allele was significantly lower (chi(2) = 26.2187, p < 0.0001). This result indicates that HLA-DQB1*060101 and DQB1*0602 may confer susceptibility to cervical cancer, and DQB1*050201 may contribute to the resistance to the development of cervical cancer among Chinese women. Sequence analysis reveals that DQB1*060101 allele encodes Leu at position 9 and Asp at position 37, unique to the susceptibility to cervical cancer, whereas the other DQB1 alleles encode Phe or Tyr and Ile or Tyr at the same two positions, respectively. This finding implies that polymorphic amino acids at the putative antigen binding residues 9 and 37 of HLA-DQB1 alleles may play an important role in the development of cervical cancer.

Amino Acid Sequence↗

PubMed2006

A mammalian organelle map by protein correlation profiling.

Protein localization to membrane-enclosed organelles is a central feature of cellular organization. Using protein correlation profiling, we have mapped 1,404 proteins to ten subcellular locations in mouse liver, and these correspond with enzymatic assays, marker protein profiles, and confocal microscopy. These localizations allowed assessment of the specificity in published organellar proteomic inventories and demonstrate multiple locations for 39% of all organellar proteins. Integration of proteomic and genomic data enabled us to identify networks of coexpressed genes, cis-regulatory motifs, and putative transcriptional regulators involved in organelle biogenesis. Our analysis ties biochemistry, cell biology, and genomics into a common framework for organelle analysis.

Animals↗

PubMed2006

Therapeutic approach for diabetic nephropathy using gene delivery of translocase of inner mitochondrial membrane 44 by reducing mitochondrial superoxide production.

Hyperglycemia-induced overproduction of mitochondrial reactive oxygen species has emerged as a major player in diabetic vascular complications. Mammalian translocase of inner mitochondrial membrane 44 (TIM44) was identified by upregulation in diabetic mouse kidneys. TIM44 functions as a membrane anchor of mitochondrial heat-shock protein 70 (mtHsp70) to TIM23 complex and is involved in the import of mitochondria-targeted preproteins into mitochondrial matrix. The process is dependent on inner membrane potential and ATP hydrolysis on ATPase domain of mitochondrial heat-shock protein 70. Hemagglutination virus of Japan-envelope vector that carries pcDNA3.1 plasmid that contains the full-length cDNA of TIM44 and control plasmid were injected weekly into the tail vein of uninephrectomized streptozotocin-induced diabetic CD-1 mice. The gene delivery alleviated proteinuria and renal hypertrophy at 8 wk after the injection, inhibited renal cell proliferation and apoptosis, and suppressed superoxide production. In vitro experiments, using human proximal tubular (HK2) cells, revealed that the gene delivery of TIM44 reversed high glucose-induced metabolic and cellular abnormalities such as enhanced reactive oxygen species production, increased ATP contents, alterations in inner membrane potential, increased cell proliferation, and apoptosis. Transfection with siRNA and expressing vector of TIM44 revealed that TIM44 facilitates import of antioxidative enzymes such as superoxide dismutase and glutathione peroxidase into mitochondria. The gene delivery of TIM44 therefore seems to be beneficial for the maintenance of mitochondrial function and is a novel therapeutic approach for diabetic nephropathy.

Adenosine Triphosphate↗

PubMed2006

Water-soluble fluorescent boronic acid compounds for saccharide sensing: substituent effects on their fluorescence properties.

Four new naphthalene-based boronic acid compounds (1-4) were synthesized. The effect of various carbohydrates on their fluorescence properties has been studied in aqueous phosphate buffer at pH 7.4. Different substitutions on the aniline group of the naphthalene ring resulted in significant differences in fluorescence properties for these four compounds. Compound 1 shows ratiometric fluorescence changes upon addition of a sugar. Compounds 2 and 3 do not show ratiometric fluorescence changes but show very large fluorescence intensity changes (about 70-fold fluorescence intensity increase). In addition to the quantifiable fluorescence property changes upon sugar addition, the fluorescence color changes of 1-3 are also visible to the naked eye. However, amidation of the aniline nitrogen atom significantly diminishes the fluorescence intensity of compound 4. The crystal structure of one boronic acid provided some insight into the structural features that are important for the fluorescence properties of these compounds.

Biosensing Techniques↗

PubMed2006

Analysis of mutations in the E6/E7 oncogenes and L1 gene of human papillomavirus 16 cervical cancer isolates from China.

Human papillomavirus type 16 (HPV16) has a number of intratypic variants; each has a different geographical distribution and some are associated with enhanced oncogenic potential. Cervical samples were collected from 223 cervical cancer patients and from 196 age-matched control subjects in China. DNA samples were amplified by using primers specific for the E6, E7 and partial L1 regions. Products were sequenced and analysed. It was found by using a PCR-sequence-based typing method that HPV infection rates in China were 92.8 % in cervical cancer patients and 15.8 % in healthy controls. HPV16 was detected in 70.4 % of cervical cancer patients and in 6.1 % of controls. In HPV16-positive cervical cancers, 23.6 % belonged to the prototype, 65.5 % were of the Asian variant, 5.5 % were of African type 1 and 3.6 % were European variants, whilst only one was a new variant that differed from any variant published so far. Prevalences of HPV16 E6 D25E and E113D variants were 67.3 and 9 %, respectively. In addition to D25E and E113D, the following E6 variations were found in this study: R129K, E89Q, S138C, H78Y, L83V and F69L. The results also showed that the prevalences of three hot spots of E7 nucleotide variation, N29S, S63F and a silent variation, nt T846C, were 70.2 % (33/47), 51.1 % (24/47) and 61.7 % (29/47), respectively. The following L1 variations were found in this study: S377A, K387E, E378D, K382E and T379P. It was also found that the average age of Asian variant-positive cervical cancer patients (42.98+/-10.43 years) was 7.56 years lower than that of prototype-positive patients (50.54+/-10.91). It is suggested that the high frequency of HPV16 Asian variants might contribute to the high incidence of cervical cancer in China.

Capsid Proteins↗

PubMed2006

The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

BACKGROUND: Urine is a desirable material for the diagnosis and classification of diseases because of the convenience of its collection in large amounts; however, all of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our laboratory has developed methods for the in-depth characterization of body fluids; these involve a linear ion trap-Fourier transform (LTQ-FT) and a linear ion trap-orbitrap (LTQ-Orbitrap) mass spectrometer. Here we applied these methods to the analysis of the human urinary proteome. RESULTS: We employed one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis and reverse phase high-performance liquid chromatography for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution, and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at parts per million accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in urine obtained from ten healthy donors, while essentially eliminating false-positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene Ontology (GO) analysis. Furthermore, extracellular, lysosomal, and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are probably present in urine by secretion in exosomes. CONCLUSION: Our analysis provides a high-confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained using different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future.

Chromatography, High Pressure Liquid↗

PubMed2006

[Analysis of curvature distribution on corneal surface].

PURPOSE: To detect the characters of the curvature distribution from a mathematical point of view. METHODS: Subjects were measured with Orbscan II corneal topography system. Anterior and posterior corneal radius of curvature and thickness of the points located 1.5 mm, 2.5 mm, 3.5 mm and 4.5 mm away from the corneal apex on certain meridians, including 0 degrees, 30 degrees, 60 degrees, 90 degrees, 120 degrees, 150 degrees, 180 degrees, 210 degrees, 240 degrees, 270 degrees, 300 degrees and 330 degrees meridians, were collected. Distributions of corneal curvature between the two principal meridians were discussed. RESULTS: The curvature of oblique meridian might be described with the formula F' = Fa+(Fb-Fa) xSin2alpha. CONCLUSIONS: Anterior and posterior corneal surfaces are similar to toric surface. The distributions of corneal curvature between the two principal meridians have something to do with the law of sine.

Adult↗

PubMed2005

Effects of cooking and storage on residues of cyadox in chicken muscle.

The aim of this study was to investigate the depletion of residues of cyadox in chicken muscle over time. The heat stabilities of cyadox (CYX) and its two metabolites, 1,4-bisdesoxycyadox (BDCYX) and quinoxaline-2-carboxylic acid (QCA), in water, cooking oil, and as incurred residues in chicken muscle were investigated. CYX was shown to be unstable with a half-life of about 37.7 min in 100 degrees C water. In hot cooking oil at 180 degrees C, all three compounds were unstable. CYX decreased quickly and was not able to be detected after heating for 2 min. Diode-array analysis of CYX standard solution in cooking oil indicated that a portion of BDCYX was formed. The residues of CYX and BDCYX deteriorated rapidly in frozen storage, while that of QCA changed slowly. Muscles containing CYX residues were boiled, microwaved, or fried for the specified times. During boiling, CYX and BDCYX were reduced 94% and 81% in 10 min, respectively. During microwave cooking, CYX and BDCYX were reduced 54% and 47% in 2.5 min, respectively. During frying, CYX and BDCYX were reduced 86% and 76%, respectively. No significant reduction of QCA was found for the three cooking methods. The half-lives of CYX residues in cooked chicken muscles were estimated as follows: 2.22 min for CYX and 4.44 min for BDCYX by boiling; 6.66 min for CYX and 9.36 min for BDCYX by microwaving.

Animals↗

PubMed2005

MicroTom--a high-throughput model transformation system for functional genomics.

We have developed a high-throughput Agrobacterium-mediated transformation model system using both nptII and the 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens strain CP4 (cp4) based selections in MicroTom, a miniature rapid-cycling cherry tomato variety. With the NPTII selection system, transformation frequency calculated as independent transgenic events per inoculated explant ranged from 24 to 80% with an average of 56%, in industrial production scale transformation experiments. For CP4, with glyphosate selection, the average transformation frequency was 57%. Stable transformation frequency was positively correlated with transient expression (R=0.85), and variable with the genes of interest. DNA integration and germline transformation were confirmed by biological assay, Southern Blot analysis, and R(1) phenotype segregation. Transgene expression was observed in leaf, root, stem, flower, and fruit tissues of the transgenic plants. Ninety-five percent of transgenic events coexpressed two introduced genes based on beta-glucuronidase (GUS) and neonmycin phosphotransferase II (NPTII) expression. Seventy-five percent of transgenic events contained one to two copies of the introduced uidA (GUS) gene based on Southern analysis. Transgenic plants from the cotyledon explants to the transgenic plants transferred to soil were produced within about 2-3 months depending on the genes of interest. The utility of this MicroTom model transformation system for functional genomic studies, such as identification of genes related to important agricultural traits and gene function, is discussed.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

PubMed2005

Microparticle-based lung delivery of INH decreases INH metabolism and targets alveolar macrophages.

Microparticles prepared by the precipitation with a compressed antisolvent (PCA) process were evaluated for their potential in targeting an ionizable prodrug of isoniazid (INH), isoniazid methanesulfonate (INHMS), for sustained delivery of INH to alveolar macrophages (AMs). The charged prodrug was ion-paired with two different hydrophobic cations (tetrapentylammonium (TPA)- and tetraheptylammonium (THA)-bromide), and loaded separately into the poly(l-lactide) (PLA) microparticles. The drug/polymer particles were spherical in shape and between 1 and 3 mum in diameter. The choice of hydrophobic cations did not affect drug incorporation efficiencies or the release kinetics of INH from the microparticles. Using a sensitive liquid chromatographic tandem mass spectrometric (LC-MS/MS) assay developed for INH, high level of INH was detected in NR8383, a rat AM cell line, following exposure of these cells to drug-loaded microparticles. To confirm the microparticles can target AMs in vivo, we compared the INH levels in lavaged bronchoalveolar macrophages by LC-MS/MS after the Sprague-Dawley rats were administered either INHMS in PLA microparticles by intra-tracheal instillation or INH solution by gavage or intra-tracheal instillation. As expected, only microparticles provided sustained and targeted delivery of INH to AMs. Most importantly, this method of delivery led to substantial reduction in the blood levels of acetylisoniazid (AcINH), a major and potential toxic metabolite of INH.

Animals↗

PubMed2005

Associations of high-risk HPV types and viral load with cervical cancer in China.

BACKGROUND: Cervical cancer is the second most common cancer in women worldwide. Infection with some genotypes of human papillomavirus is the most important risk factor associated with cervical cancer. OBJECTIVE: The aim of this study was to determine the prevalence and genotypes of HPV in China, and to evaluate the correlation between viral load of high risk HPV and cervical cancer and its precursors. STUDY DESIGN: A cross-sectional study was carried out, wherein cervical samples were collected from 541 patients with cervical cancer, 262 with CIN, 139 with cervicitis and 68 age-matched healthy controls. Hybrid Capture 2 was employed to detect HPV DNA. Specimens from HPV DNA positive cervical cancer were tested for HPV types by using type specific PCR and general primer PCR with sequence-based typing (GP PCR-SBT). RESULTS: Overall high risk HPV prevalence was 68.8% in CIN1, 80.3% in CIN2, 90.2% in CIN3, 90.9% in cervical cancer in situ, 89.9% in invasive cervical cancer and 25% in healthy controls from China. The most common HPV DNA type found in patients with cervical cancer was HPV16 (79.6%), followed by HPV58 (5.92%), HPV33 (3.29%), HPV18 (1.97%), HPV6 (1.97%), HPV31 (1.31%), HPV39 (1.31%), HPV68 (1.31%) and other HPV types (3.3%). It was found that there was a significantly increased risk of increasing CIN stage with high viral load. Frequency of low viral load found in the controls was 13.2% and 22.9% of CIN1, obtaining an OR of 4.2 (1.5-12.0). Associations (OR) among low viral load and CIN2/3, CIS, and CC were 6.7 (2.9-15.6), 9.4 (2.7-32.3) and 8.3 (3.7-18.4), respectively. While high viral loads were found in 5.9% of controls, 27.1% of CIN1, 42.1% of CIN2/3 and 48.5% of CIS, demonstrating increasing odds ratios with severity of disease (OR for CIS=68.0, 95% CI=17.8-259.7). CONCLUSIONS: HPV16 was the most common genotype in central China. The developing cervical cancer precursors were associated with elevated high-risk HPV viral load.

Adolescent↗

PubMed2005

Subchronic oral toxicity study with cyadox in Wistar rats.

To investigate the potential subchronic toxicity of cyadox, groups of 15 male and 15 female Wistar rats were fed with diets containing cyadox (0, 50, 150 or 2500 mg/kg) or olaquindox (150 mg/kg), approximately equivalent to cyadox 5, 15, 250 or olaquindox 15 mg/kg b.w./day, for 13 weeks. Five rats/sex/group were sacrificed on days 30, 60 and 90. No test-material-related changes were seen in mortality, clinical signs, hematology, clinical chemistry, organ weight data and macroscopic examinations. Except that body weights of both sexes of the 2500 mg/kg cyadox group were significantly lower than controls beginning after the second week of treatment. Body weights of females of 150 mg/kg olaquindox group were significantly lower than those of the control group at weeks 3 and 4. Other groups were unaffected by treatments. Histopathological observations revealed that 2500 mg/kg cyadox or 150 mg/kg olaquindox induced swelling and fatty degeneration of the hepatocytes and proximal renal tubular epithelial cells. It was for the first time that changes were found in the liver and kidneys of rats fed 2500 mg/kg cyadox. The no-observed-adverse-effect level (NOAEL) of cyadox for rats was estimated to be 150 mg/kg dietary dose level.

Administration, Oral↗