Biomedical subjects

Haiyan Zhang

Publications and source records attributed to Haiyan Zhang.

15 recordsLinked to original sources

PubMed2026

Migraine is not a risk factor for glaucoma: Evidence from a bidirectional Mendelian randomization study.

Numerous compelling observational studies have indicated that migraine is a risk factor for the development of glaucoma. Nevertheless, some studies have observed entirely opposite results. The objective of our research is to evaluate the potential relationship between migraine and glaucoma by employing a bidirectional Mendelian Randomization (MR) approach. This method enables us to rigorously assess the causal links between these 2 conditions, thereby addressing the discrepancies in existing literature. Independent genetic variants associated with glaucoma and migraine at the genome-wide significance level were selected as instrumental variables. All summary data were obtained from the genome-wide association study database. The primary method employed in the bidirectional MR analysis was the inverse variance weighted method, while sensitivity analyses utilized the leave-one-out method, MR-Egger method, and MR-Pleiotropy RESidual Sum and Outlier‌ method. When migraine and its subtypes (specifically migraine with aura and migraine without aura) were evaluated as exposure factors, we found no evidence of a causal relationship with glaucoma and its subtypes (namely angle-closure glaucoma and open-angle glaucoma). Subsequently, in the reverse MR analysis, when glaucoma and its subtypes (angle-closure glaucoma and open-angle glaucoma) were assessed as exposure factors, there was no substantial evidence to support a causal relationship with migraine or its subtypes (migraine with aura and migraine without aura). Furthermore, sensitivity analyses also reinforced the robustness of our bidirectional MR findings. Our bidirectional MR analysis mitigates the biases associated with traditional observational studies, highlighting that there is no direct causal relationship between migraine and the risk of glaucoma.

Humans↗

PubMed2026

Near Full-Length Genome Characterization of a Novel Second-Generation HIV-1 CRF01_AE/CRF07_BC Recombinant Identified in an MSM Individual in Guizhou, China.

The cocirculation of CRF01_AE and CRF07_BC among men who have sex with men (MSM) in China may facilitate the emergence of genetically complex HIV-1 recombinants. Here, we identified and characterized a novel second-generation HIV-1 CRF01_AE/CRF07_BC recombinant, designated GY0192, from a 25-year-old MSM individual in Guiyang, Guizhou Province, southwest China, using near full-length genome (NFLG) analysis. Recombination analyses identified four breakpoints at HXB2 positions 3,125, 5,687, 6,375, and 9,176, generating a distinct five-segment mosaic genome. Subregion phylogenetic analyses showed that the two CRF01_AE-derived fragments clustered with the CRF01_AE cluster 5 lineage, while all three CRF07_BC-derived fragments grouped with CRF07_BC lineages frequently circulating among MSM in China, indicating that both parental components of GY0192 were phylogenetically related to lineages frequently reported among MSM populations in China. The virus was also predicted to be CCR5-tropic, adding epidemiological relevance because CCR5-tropic viruses are commonly involved in transmission and early infection. Together, these findings identify GY0192 as a distinct CRF01_AE/CRF07_BC mosaic and suggest that cocirculating MSM-associated HIV-1 lineages may provide opportunities for interlineage recombination. This case expands the known spectrum of CRF01_AE/CRF07_BC recombinants in Guizhou and underscores the value of NFLG-based surveillance for detecting underrecognized HIV-1 genetic complexity in southwest China.

Humans↗

PubMed2005

The coordinate regulation of the p53 and mTOR pathways in cells.

Cell growth and proliferation requires an intricate coordination between the stimulatory signals arising from nutrients and growth factors and the inhibitory signals arising from intracellular and extracellular stresses. Alteration of the coordination often causes cancer. In mammals, the mTOR (mammalian target of rapamycin) protein kinase is the central node in nutrient and growth factor signaling, and p53 plays a critical role in sensing genotoxic and other stresses. The results presented here demonstrate that activation of p53 inhibits mTOR activity and regulates its downstream targets, including autophagy, a tumor suppression process. Moreover, the mechanisms by which p53 regulates mTOR involves AMP kinase activation and requires the tuberous sclerosis (TSC) 1/TSC2 complex, both of which respond to energy deprivation in cells. In addition, glucose starvation not only signals to shut down mTOR, but also results in the transient phosphorylation of the p53 protein. Thus, p53 and mTOR signaling machineries can cross-talk and coordinately regulate cell growth, proliferation, and death.

AMP-Activated Protein Kinases↗

PubMed2005

Cadmium accumulation and oxidative burst in garlic (Allium sativum).

To investigate the temporal sequence of physiological reactions of garlic (Allium sativum) to cadmium (Cd) treatment, seedlings developed from cloves were grown in increasing concentrations of CdCl2, ranging from 1-10 mM, for up to 8 days in sand. Analysis of Cd uptake indicated that most Cd accumulated in roots, but some was also translocated and accumulated in leaves at longer exposure time (after 12h) and higher concentrations (5 and 10mM) of CdCl2. Changes in activities of antioxidative enzymes, including superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), were characterized in leaves of garlic seedlings. Cd (5 and 10 mM) initially inhibited the activities of SOD and CAT but thereafter recovered or even increased compared with control plants. POD activities at 5 and 10 mM of Cd increased more than 3-4 times over control plants within 12 h and then dropped, but were still higher than controls at the end of the experiment. Otherwise lipid peroxidation enhanced with the increasing of incubation time and concentrations of external Cd. Leaves exposed to 1 mM CdCl2 showed a less pronounced response and only a small reduction in shoot growth. These results suggested that in leaves of garlic seedlings challenged by CdCl2 at higher concentrations, induction of these various enzymes is part of a general defense strategy to cope with overproduction of reactive oxygen. The possible mechanism of antioxidative enzymes changing before Cd accumulation in leaves of garlic seedlings is discussed.

Cadmium Chloride↗

PubMed2005

Long-term expansion of human neural progenitor cells by epigenetic stimulation in vitro.

Human neural progenitor cells (hNPCs) are currently believed to have important potential for clinical application and basic neuroscience research. In the present study, we have developed a new technique for expansion of human neural progenitor cells in vitro. We showed that the cultures of hNPCs in monolayer could keep the same features with that growing in neurospheres. These cells expressed the typical protein of neural progenitors, nestin, and could form neurons and astrocytes upon differentiation. Using this method, we achieved an exponential increase in cells number over a period of 240 days in vitro. We also confirmed these cells expressed the orphan nuclear receptor-related factor 1 (Nurr1). Furthermore, we acquired the GFP-expressing human neural progenitor cells using retroviral-mediated transgenic system. The results of present study indicate the feasibility of long-term in vitro expansion of human neural progenitor cells using the monolayer culture technique, which may be of value as vehicles for ex vivo gene transfer to the CNS and as a potential source for basic research of dopaminergic (DA) neurons development.

Blotting, Western↗

PubMed2004

Dry matter, lipids, and proteins of canola seeds as affected by germination and seedling growth under illuminated and dark environments.

The effect of germination and growth under illuminated and dark environments on canola seed reserves was investigated. Depletion of proteins and lipids in whole seedlings and their top (leaf/cotyledons) and bottom parts (stem/roots/seed coat) was independent of light, whereas the protein solubility increased at a faster rate under an illuminated environment than in the dark. A rapid increase in free fatty acids but a net decrease of dry matter content in seedlings grown in the dark environment was observed. The dry matter content of seedlings grown in the illuminated environment increased due to photosynthetic biomass accumulation.

Brassica napus↗

PubMed2004

SuperPose: a simple server for sophisticated structural superposition.

The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments, PDB (Protein Data Bank) coordinates and RMSD statistics, as well as difference distance plots and images (both static and interactive) of the superimposed molecules. SuperPose employs a simple interface that requires only PDB files or accession numbers as input. All other superposition decisions are made by the program. SuperPose is uniquely able to superimpose structures that differ substantially in sequence, size or shape. It is also capable of handling a much larger range of superposition queries and situations than many standalone programs and yields results that are intuitively more in agreement with known biological or structural data. The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/.

Amino Acid Sequence↗

PubMed2004

Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring.

Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases. The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information. We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins. This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification. To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences. In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software. MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST. To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database. The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database. Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification. It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.

Algorithms↗

PubMed2004

Visceral perception thresholds after rectal thermal and pressure stimuli in irritable bowel syndrome patients.

BACKGROUND AND AIM: Visceral hypersensitivity has been shown to be present in irritable bowel syndrome (IBS). The current study sought to compare the characteristics of visceral perception thresholds after rectal thermal and pressure stimuli between IBS patients and healthy subjects. METHODS: A total of 46 patients with IBS were diagnosed using Rome II criteria. Thirteen healthy individuals participated in the study. Rectal visceral perception thresholds were examined in patients with IBS and in normal controls after thermal and pressure stimuli. Subjects were asked to report the sensation type, location, and spread. RESULTS: Compared with healthy subjects, IBS patients demonstrated significantly initially lower perception thresholds and defecation thresholds to rectal thermal and pressure stimuli, particularly in patients with diarrhea-predominant IBS. Ice stimuli on the abdominal wall had varied effects on symptoms in patients with IBS and did not affect perception thresholds. CONCLUSIONS: Visceral perception thresholds were decreased significantly after rectal thermal and pressure stimuli in patients with IBS. Visceral hypersensitivity may be one of the important pathogenic mechanisms in IBS.

Adult↗

PubMed2003

VADAR: a web server for quantitative evaluation of protein structure quality.

VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. These include excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality. These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar.

Algorithms↗

PubMed2003

RefDB: a database of uniformly referenced protein chemical shifts.

RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website.

Animals↗

PubMed2003

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http://redpoll.pharmacy.ualberta.ca.

Animals↗

PubMed2003

On the validity of Stokes-Einstein-Debye relations for rotational diffusion in colloidal suspensions.

According to the Stokes-Einstein-Debye (SED) relation, the rotational diffusion coefficient of a colloidal tracer sphere scales with the inverse of the solvent viscosity. Here we investigate the generalization of the SED relation to tracer diffusion in suspensions of neutral and charged colloidal host spheres. Rotational diffusion coefficients are measured with dynamic light scattering and phosphorescence spectroscopy, and calculated including two- and three-particle hydrodynamic interactions. We find that rotational tracer diffusion is always faster than predicted by the SED relation, except for large tracer/host size ratios lambda. In the case of neutral particles this observation is rationalized by introducing an apparent lambda-dependent slip boundary coefficient. For charged spheres at low ionic strength, large deviations from SED scaling are found due to the strongly hindered host sphere dynamics. Finally, we present some first experiments on tracer sphere diffusion in suspensions of host rods, showing that hydrodynamic hindrance by rods is much stronger than by spheres. We conclude by pointing to some interesting unresolved issues for future research.

Journal Article↗

PubMed2003

Synthesis and docking studies of alkylene-linked dimers of (-)-huperzine A.

(-)-Huperzine A (5, HupA), an alkaloid isolated from the herb Huperzia serrata, is a potent, selective and reversible acetylcholinesterase (AchE) inhibitor. Based on the hypothesis with respect to two binding sites in the active gorge of AChE and the good example of bis-tacrine, it was predicted from the docking studies of alkylene-linked dimers of HupA that dimers 6 (n = 5, 7, 9) might have good AChE inhibitory activity. Therefore, six dimers with 7-12 methylene units as tethers were thus prepared. It was found that these dimers were less potent than HupA in inhibition of AChE. The difference of the inhibitory potency between these dimers is coincident with the results of the docking studies.

Alkaloids↗

PubMed2003

Beta-carotene protects rats against bronchitis induced by cigarette smoking.

OBJECTIVE: To investigate the protective effects of beta-carotene in rats against the development of chronic bronchitis induced by cigarette smoking. METHODS: Forty-two Male Wistar rats were randomly divided into three study groups: (1) control (n = 15), animals underwent no treatment; (2) cigarette smoking (n = 15), animals developed chronic bronchitis through long-term cigarette smoking twice a day for 75 d; (3) beta-carotene plus cigarette smoking animals (n = 12) were given 1 ml or 15 mg/kg beta-carotene orally every day just before cigarette smoking. The levels of IL-6, IL-8, NO, superoxide dismutase (SOD) and lipoperoxide (LPO) in serum, bronchoalveolar lavage fluid (BALF) and lung tissue were measured and the pathological changes to lung tissue were analyzed using light microscopy. RESULTS: Long-term cigarette smoking caused an obvious increase in the amount of IL-6, IL-8 and LPO and a sharp decrease in the levels of NO and SOD in smoking animals compared to controls. beta-carotene intake reversed all the changes induced by smoking and alleviated the pathological changes caused by chronic bronchitis. CONCLUSIONS: Quantitative oral intake of beta-carotene had protective effects against chronic bronchitis induced by long-term cigarette smoking, which was associated with the increased production of NO, the clearance of some oxidative free radicals (OFR) and the alleviation of chronic inflammation.

Animals↗