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Biomedical subjects

Chi Zhang

Publications and source records attributed to Chi Zhang.

At least 19 recordsLinked to original sources
PubMed2026

Transcription factor NtELF3 promotes the polyphenol accumulation by targeting NtFLS-1 and NtCHIL-2 genes in tobacco.

Tobacco (Nicotiana tabacum L.) is an important economic crop, from which polyphenols are crucial for regulating its growth and development as well as shaping its quality. However, few genes associated with polyphenol accumulation have been cloned from tobacco, and the molecular mechanisms underlying this process remain poorly understood. Here, we found that the tobacco transcription factor EARLY FLOWERING 3 (NtELF3), which is highly expressed in tobacco leaves, positively regulates the accumulation of chlorogenic acid, neochlorogenic acid, cryptochlorogenic acid, rutin, scopoletin, and total polyphenols in tobacco middle leaves. The metabolomic and transcriptomic analyses of middle leaves showed that a total of 177 differentially accumulated metabolites and 7409 differentially expressed genes (DEGs) were identified in ntelf3-1 mutant versus wild type, respectively. Further investigation identified that 17 DEGs were involved in phenylpropanoid metabolic and flavonoid metabolic processes. Combined analysis indicated that the phenylpropanoid and flavonoid biosynthesis pathways were also co-enriched in kyoto encyclopedia of genes and genomes enrichment analysis. Molecular biology experiment demonstrated that NtELF3 directly binds to the promoters of NtFLS-1 and NtCHIL-2 that are both associated with phenylpropanoid and flavonoid biosynthesis, and promotes their expression. Taken together, our results not only provide new theoretical support for in-depth understanding of the regulatory mechanisms underlying polyphenol accumulation in tobacco, but also offer excellent genes and germplasm resources for tobacco quality breeding.

NtCHIL↗
PubMed2026

Single-cell transcriptomic atlas of Alzheimer's disease middle temporal gyrus reveals region, cell type, and sex specificity of gene expression with novel genetic risk for MERTK in female.

BackgroundAlzheimer's disease (AD), the most common age-related neurodegenerative disease, is closely associated with both amyloid-β plaque and neuroinflammation. Two thirds of AD patients are female, and they have a higher disease risk; women with AD have more extensive brain histological changes than men along with more severe cognitive symptoms and neurodegeneration.ObjectiveThis study aimed to determine how sex difference induces structural brain changes and molecular cell vulnerabilities in AD, with a focus on identifying sex-specific transcriptional alterations and genetic risk factors.MethodsWe performed single nucleus RNA sequencing on postmortem brains from individuals with AD and age- and sex-matched controls, focusing on the middle temporal gyrus, a cortical brain region strongly affected by the disease, and integrated single nucleus RNA sequencing results with genome-wide association study (GWAS) data using cell type-specific enrichment and generalized gene-set analysis approaches. The analysis pipeline is provided with threshold information.ResultsWe identified a selectively vulnerable subpopulation of layer 2/3 excitatory neurons that were RORB-negative and CDH9-expressing in both males and females. Disease-associated, but sex-independent, reactive astrocyte signatures were also present. In clear contrast, the microglia signatures of AD brains differed between males and females. Integrating single cell transcriptomic data with results from GWAS, we identified MERTK genetic variation as a candidate novel risk factor for AD selectively in females.ConclusionsTaken together, our single cell atlas of middle temporal gyrus revealed a unique cellular-level view of sex-specific transcriptional changes in AD, illuminating GWAS identification of sex-specific AD genes. These data serve as a rich resource for interrogation of the molecular and cellular basis of AD.

Alzheimer's disease↗
PubMed2026

Application efficacy evaluation of the STRSeqTyper122 kit and the FASTASeq 300 second generation sequencer in kinship identification.

Forensic DNA technology is the method of choice for kinship identification. However, existing standard methods still have certain limitations in accurately determining the range of kinship relationships. China's independently developed second generation sequencing technology and equipment are expected to enhance the capability of forensic DNA kinship identification. In this study, we utilized the STRSeqTyper122 second generation sequencing STR typing kit and the FASTASeq 300 second generation sequencer to analyze 107 real kinship samples. The analysis included 63 autosomal STR loci, 42 Y-STR loci, 16 X-STR loci, and one gender-determining locus, Amel. The samples covered various kinship relationships, including 113 parent-child pairs, 48 full-sibling pairs, 76 uncle-nephew pairs, 66 grandparent-grandchild pairs, and 4 half-sibling pairs. Combined with simulated data, the ITO method was applied to calculate the cumulative likelihood ratio (CLR) for different levels of kinship based on the length polymorphism and sequence polymorphism of autosomal STR loci, systematically evaluating the practical application performance of this system in kinship identification. The results showed that, using log10CLR values of 4 and -4 as thresholds, the system achieved 100% efficiency in identifying real parent-child and full-sibling relationships. For second degree kinship identification, the system efficiency based on simulated length polymorphism data was 55.2%, while sequence polymorphism improved it to 75.11%. For real sample data, length polymorphism based efficiency was 54.45%, and sequence polymorphism based efficiency reached 76.71%. The findings indicate that the STRSeqTyper122 kit holds significant value in first degree kinship identification. Sequence polymorphism can improve second degree kinship identification efficiency to over 75%.

Humans↗
PubMed2025

Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk.

BACKGROUND: Polygenic risk score (PRS) have proved to offer robust risk prediction for coronary artery disease (CAD). However, the global CAD PRS summarizes the joint effects of all the markers in the genome, masking potential genetic heterogeneity that may be important for disease interpretation and targeted interventions. METHODS: Using summary-level data, we identified 43 significant CAD-related traits based on genetic correlations, and further classified them into eight pleiotropy clusters based on their biological functions. We then partitioned the genome into 2,353 near-independent regions. Variants in each region were assigned to the trait most genetically similar to CAD, and then were labeled with the corresponding pleiotropy cluster. We grouped variants without labels into a ninth, non-specific cluster. The Pleiotropy Decomposed (PD) PRSs for each of the nine clusters were calculated using variants assigned to each cluster for 407,903 samples of European ancestry from the UK Biobank (UKBB). RESULTS: We decomposed the CAD PRS into nine PD-PRSs and further stratified individuals with high CAD-PRS into nine subgroups. Each PD-PRS accounted for a higher proportion of the global CAD-PRS within its corresponding subgroup than in the remaining subjects with high CAD-PRS (e.g., 25.2% (0.07) vs. 10.06% (0.07) for lipids-PD-PRS). Additionally, these subgroups showed distinct clinical features. For example, in the lipids-related subgroup, lipoprotein(a) and LDL-cholesterol levels were 67.5% and 18.3% higher, respectively, compared to the remaining high-risk individuals. Furthermore, significant interactions were observed between blood pressure and BP PD-PRS, and between current smoking and respiratory system PD-PRS. CONCLUSION: Our findings suggest that PD-PRSs may reveal substantial genetic and phenotypic heterogeneity among individuals with high CAD-PRS. The unique PD-PRS compositions of each individual can highlight the relative importance of different pleiotropic regions.

Humans↗
PubMed2023

Single-cell transcriptomic atlas of Alzheimer's disease middle temporal gyrus reveals region, cell type and sex specificity of gene expression with novel genetic risk for MERTK in female.

Alzheimer's disease, the most common age-related neurodegenerative disease, is closely associated with both amyloid-ß plaque and neuroinflammation. Two thirds of Alzheimer's disease patients are females and they have a higher disease risk. Moreover, women with Alzheimer's disease have more extensive brain histological changes than men along with more severe cognitive symptoms and neurodegeneration. To identify how sex difference induces structural brain changes, we performed unbiased massively parallel single nucleus RNA sequencing on Alzheimer's disease and control brains focusing on the middle temporal gyrus, a brain region strongly affected by the disease but not previously studied with these methods. We identified a subpopulation of selectively vulnerable layer 2/3 excitatory neurons that that were RORB-negative and CDH9-expressing. This vulnerability differs from that reported for other brain regions, but there was no detectable difference between male and female patterns in middle temporal gyrus samples. Disease-associated, but sex-independent, reactive astrocyte signatures were also present. In clear contrast, the microglia signatures of diseased brains differed between males and females. Combining single cell transcriptomic data with results from genome-wide association studies (GWAS), we identified MERTK genetic variation as a risk factor for Alzheimer's disease selectively in females. Taken together, our single cell dataset revealed a unique cellular-level view of sex-specific transcriptional changes in Alzheimer's disease, illuminating GWAS identification of sex-specific Alzheimer's risk genes. These data serve as a rich resource for interrogation of the molecular and cellular basis of Alzheimer's disease.

Journal Article↗
PubMed2006

An NF-kappaB and slug regulatory loop active in early vertebrate mesoderm.

BACKGROUND: In both Drosophila and the mouse, the zinc finger transcription factor Snail is required for mesoderm formation; its vertebrate paralog Slug (Snai2) appears to be required for neural crest formation in the chick and the clawed frog Xenopus laevis. Both Slug and Snail act to induce epithelial to mesenchymal transition (EMT) and to suppress apoptosis. METHODOLOGY & PRINCIPLE FINDINGS: Morpholino-based loss of function studies indicate that Slug is required for the normal expression of both mesodermal and neural crest markers in X. laevis. Both phenotypes are rescued by injection of RNA encoding the anti-apoptotic protein Bcl-xL; Bcl-xL's effects are dependent upon IkappaB kinase-mediated activation of the bipartite transcription factor NF-kappaB. NF-kappaB, in turn, directly up-regulates levels of Slug and Snail RNAs. Slug indirectly up-regulates levels of RNAs encoding the NF-kappaB subunit proteins RelA, Rel2, and Rel3, and directly down-regulates levels of the pro-apopotic Caspase-9 RNA. CONCLUSIONS/SIGNIFICANCE: These studies reveal a Slug/Snail-NF-kappaB regulatory circuit, analogous to that present in the early Drosophila embryo, active during mesodermal formation in Xenopus. This is a regulatory interaction of significance both in development and in the course of inflammatory and metastatic disease.

Animals↗
PubMed2006

Expression, refolding, and characterization of recombinant thrombopoietin/stem cell factor fusion protein in Escherichia coli.

Thrombopoietin/stem cell factor (TPO/SCF) is a novel fusion protein that combines the complementary biological effects of TPO and SCF into a single molecule. In this study, TPO/SCF gene was cloned into pET32a and expressed as a thioredoxin (Trx) fusion protein with a C-terminal 6His-tag in Escherichia coli BL21(DE3) under the control of T7 promoter. Trx-TPO/SCF protein approximately accounted for 20% of the total bacterial proteins and was found to accumulate in inclusion bodies. Inclusion bodies were separated from cellular debris, washed with buffer containing 2 M urea, and solubilized with 8 M urea. The refolding of Trx-TPO/SCF was then carried out by an on-column method. Soluble Trx-TPO/SCF was characterized for its dose-dependent effects on promoting cells proliferation in both TF1 and Mo7e cell lines. rhTPO/SCF was released by thrombin digestion and further purified by Ni(2+) affinity chromatography. Western blot analysis confirmed the identities of Trx-TPO/SCF and rhTPO/SCF.

Blotting, Western↗
PubMed2006

Protein binding site prediction using an empirical scoring function.

Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method called PINUP for binding site prediction of monomeric proteins. With only two weight parameters to optimize, PINUP produces not only 42.2% coverage of actual interfaces (percentage of correctly predicted interface residues in actual interface residues) but also 44.5% accuracy in predicted interfaces (percentage of correctly predicted interface residues in the predicted interface residues) in a cross validation using a 57-protein dataset. By comparison, the expected accuracy via random prediction (percentage of actual interface residues in surface residues) is only 15%. The binding sites of the 57-protein set are found to be easier to predict than that of an independent test set of 68 proteins. The average coverage and accuracy for this independent test set are 30.5 and 29.4%, respectively. The significant gain of PINUP over expected random prediction is attributed to (i) effective residue-energy score and accessible-surface-area-dependent interface-propensity, (ii) isolation of functional constraints contained in the conservation score from the structural constraints through the combination of residue-energy score (for structural constraints) and conservation score and (iii) a consensus region built on top-ranked initial patches.

Algorithms↗
PubMed2006

Effects of Ca2+ channel blockers on store-operated Ca2+ channel currents of Kupffer cells after hepatic ischemia/reperfusion injury in rats.

AIM: To study the effects of hepatic ischemia/reperfusion (I/R) injury on store-operated calcium channel (SOC) currents (I(SOC)) in freshly isolated rat Kupffer cells, and the effects of Ca(2+) channel blockers, 2-aminoethoxydiphenyl borate (2-APB), SK and F96365, econazole and miconazole, on I(SOC) in isolated rat Kupffer cells after hepatic I/R injury. METHODS: The model of rat hepatic I/R injury was established. Whole-cell patch-clamp techniques were performed to investigate the effects of 2-APB, SK and F96365, econazole and miconazole on I(SOC) in isolated rat Kupffer cells after hepatic I /R injury. RESULTS: I/R injury significantly increased I(SOC) from -80.4 +/- 25.2pA to -159.5 +/- 34.5pA ((b)P < 0.01, n = 30). 2-APB (20, 40, 60, 80, 100 micromol/L), SK and F96365 (5, 10, 20, 40, 50 micromol/L), econazole (0.1, 0.3, 1, 3, 10 micromol/L) and miconazole (0.1, 0.3, 1, 3, 10 micromol/L) inhibited I(SOC) in a concentration-dependent manner with IC50 of 37.41 micromol/L (n = 8), 5.89 micromol/L (n = 11), 0.21 micromol/L (n = 13), and 0.28 micromol/L (n = 10). The peak value of I(SOC) in the I-V relationship was decreased by the blockers in different concentrations, but the reverse potential of I(SOC) was not transformed. CONCLUSION: SOC is the main channel for the influx of Ca(2+) during hepatic I/R injuries. Calcium channel blockers, 2-APB, SK and F96365, econazole and miconazole, have obviously protective effects on I/R injury, probably by inhibiting I(SOC) in Kupffer cells and preventing the activation of Kupffer cells.

Animals↗
PubMed2006

Kinetics of decolorization of azo dye by bipolar pulsed barrier discharge in a three-phase discharge plasma reactor.

Removal of amaranth, a commercial synthetic azo dye widely used in the dye and food industry, was examined as a possible remediation technology for treating dye-contaminated water. Effects of various parameters such as gas flow rate, solution conductivity, pulse repetition frequency, etc., on decolorization kinetics were investigated. Experimental results show that an aqueous solution of 24 mg/l dye is 81.24% decolorized following 30 min plasma treatment for a 50 kV voltage and 0.75 m(3)/h gas flow rate. Decolorization reaction of amaranth in the plasma reactor is a pseudo first order reaction. Rate constant (k) of decolorization increases quickly with increasing the applied voltage, pulse repetition frequency and the gas flow rate. However, when the applied voltage is beyond 50 kV and increases further, increase rate of k decreases. In addition, k decreases quickly when the solution conductivity increases from 200 to 1481 microS/cm. The decolorization reaction has a high rate constant (k=0.0269 min(-1)) when the solution pH is beyond 10. Rate constant k decreases with the decrease of pH and reaches minimum at a pH of about 5 (k(min)=0.01603 min(-1)), then increases to 0.02105 min(-1) when pH decreases to 3.07. About 15% of the initial TOC can be degraded only in about 120 min non-thermal plasma treatment.

Azo Compounds↗
PubMed2006

Effect of land-cover change on terrestrial carbon dynamics in the southern United States.

Land-cover change has significant influence on carbon storage and fluxes in terrestrial ecosystems. The southern United States is thought to be the largest carbon sink across the conterminous United States. However, the spatial and temporary variability of carbon storage and fluxes due to land-cover change in the southern United States remains unclear. In this study, we first reconstructed the annual data set of land-cover of the southern United States from 1860 to 2003 with a spatial resolution of 8 km. Then we used a spatially explicit process-based biogeochemical model (Terrestrial Ecosystem Model [TEM] 4.3) to simulate the effects of cropland expansion and forest regrowth on the carbon dynamics in this region. The pattern of land-cover change in the southern United States was primarily driven by the change of cropland, including cropland expansion and forest regrowth on abandoned cropland. The TEM simulation estimated that total carbon storage in the southern United States in 1860 was 36.8 Pg C, which likely was overestimated, including 10.8 Pg C in the southeast and 26 Pg C in the south-central. During 1860-2003, a total of 9.4 Pg C, including 6.5 Pg C of vegetation and 2.9 Pg C of soil C pool, was released to the atmosphere in the southern United States. The net carbon flux due to cropland expansion and forest regrowth on abandoned cropland was approximately zero in the entire southern region between 1980 and 2003. The temporal and spatial variability of regional net carbon exchange was influenced by land-cover pattern, especially the distribution of cropland. The land-use analysis in this study is incomplete and preliminary. Finally, the limitations, improvements, and future research needs of this study were discussed.

Carbon↗
PubMed2006

NO-1886 upregulates ATP binding cassette transporter A1 and inhibits diet-induced atherosclerosis in Chinese Bama minipigs.

It is widely believed that high density lipoprotein-cholesterol (HDL-C) functions to transport cholesterol from peripheral cells to the liver by reverse cholesterol transport (RCT), a pathway that may protect against atherosclerosis by clearing excess cholesterol from arterial cells. A cellular ATP binding cassette transporter called ABCA1 mediates the first step of RCT. NO-1886 has been proven to be highly effective at increasing HDL-C and reducing atherosclerosis. However, the mechanism of atherosclerosis inhibition for NO-1886 is not fully understood. In this study, the effects of NO-1886 on ABCA1 were investigated in high-fat/high-sucrose/high-cholesterol-fed Chinese Bama minipigs. Administration of NO-1886 (0.1 g/kg body weight/day) in the diet for 5 months significantly reduced atherosclerosis lesions and significantly increased plasma HDL-C and apolipoprotein A-I levels. The mRNA and protein levels of ABCA1 in the liver, retroperitoneal adipose tissue, and aorta were increased by NO-1886 as well. Multivariate linear regression analysis showed that the levels of LPL in plasma and the levels of ABCA1 in aorta were independently associated with the atherosclerotic lesion area. In addition, NO-1886 upregulated liver X receptor alpha and affected the expression of scavenger receptor class B type I in the liver. These results demonstrate that the mechanism of atherosclerosis inhibition for NO-1886 is associated with its effect on ABCA1.

ATP Binding Cassette Transporter 1↗
PubMed2006

Investigation of horizontal gene transfer in poplar/Amanita muscaria ectomycorrhizas.

Fine roots of forest trees form together with certain soil fungi symbiotic structures (ectomycorrhizas), where fungal hyphae are in intimate contact with plant cells. Due to root cell degeneration, plant DNA is released and could be taken up by the fungus. The possibility that horizontal gene transfer might result in a risk for the environment should be evaluated before a massive release of genetically engineered trees into nature occurs, even though only a few convincing examples of horizontal gene transfer are known. Transgenic poplars containing a construct of the Streptomyces hygroscopicus bar gene under the control of the Cochliobolus heterostrophus GPD (glyceraldehyde-3-phosphate dehydrogenase) promoter were generated by Agrobacterium-mediated transformation. The functionality of this construct in the ectomycorrhizal model fungus Amanita muscaria was previously verified by protoplast-based fungal transformation. 35,000 ectomycorrhizas, formed between transgenic poplars and non-transgenic A. muscaria hyphae, were isolated and transferred to selective agar plates. Putative herbicide-resistant fungal colonies were obtained after the first round of selection. However, none of these colonies survived a transfer onto fresh selection medium, nor did they contain the bar gene, indicating that no horizontal gene transfer from poplar to A. muscaria occurred during symbiosis under axenic conditions. However, since ectomycorrhizas are associated under natural conditions with viruses, bacteria and other fungi, these additional associations should be evaluated in future.

Amanita↗
PubMed2006

QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization.

Solvent accessibility, one of the key properties of amino acid residues in proteins, can be used to assist protein structure prediction. Various approaches such as neural network, support vector machines, probability profiles, information theory, Bayesian theory, logistic function, and multiple linear regression have been developed for solvent accessibility prediction. In this article, a much simpler quadratic programming method based on the buriability parameter set of amino acid residues is developed. The new method, called QBES (Quadratic programming and Buriability Energy function for Solvent accessibility prediction), is reasonably accurate for predicting the real value of solvent accessibility. By using a dataset of 30 proteins to optimize three parameters, the average correlation coefficients between the predicted and actual solvent accessibility are about 0.5 for all four independent test sets ranging from 126 to 513 proteins. The method is efficient. It takes only 20 min for a regular PC to obtain results of 30 proteins with an average length of 263 amino acids. Although the proposed method is less accurate than a few more sophisticated methods based on neural network or support vector machines, this is the first attempt to predict solvent accessibility by energy optimization with constraints. Possible improvements and other applications of the method are discussed.

Protein Conformation↗
PubMed2006

Diode-pumped continuous-wave Nd:LuVO4 laser operating at 916 nm.

We realized an efficient diode-pumped Nd:LuVO4 continuous-wave (CW) laser operating at 916 nm. Laser experiments with 0.5 at. % Nd-doped Nd:LuVO4 crystals of various lengths and cutting directions were also investigated. The maximum output power of 930 mW was obtained with a slope efficiency of 27.2% and an optical conversion efficiency of 20.8% at the absorbed pump power of 4.5 W. The laser experiment shows that Nd:LuVO4 crystal can be used for an efficient diode-pumped laser system.

Journal Article↗
PubMed2006

Effects of NO-1886 on inflammation-associated cytokines in high-fat/high-sucrose/high-cholesterol diet-fed miniature pigs.

Inflammation, closely associated with obesity, is emerging as an important risk factor for the pathophysiological development of atherosclerosis and diabetes mellitus. Fat balance is critical in the aetiology of obesity. Lipoprotein lipase is an important enzyme in lipid metabolism. The aim of this study was to investigate the long-term effect of the lipoprotein lipase activator, NO-1886, on inflammation cytokines, adiposity and related diseases in miniature pigs fed a high-fat/high-sucrose/high-cholesterol diet (HFSC diet). Chinese Bama-miniature pigs were fed a control diet or HFSC diet with or without NO-1886 for 5 months. The levels of inflammation-associated cytokines were determined using the antibody arrays. Feeding of the HFSC diet to miniature pigs markedly increased the expression of inflammatory cytokines. On the other hand, supplementation of NO-1886 to HFSC diet decreased the expression of inflammatory cytokines significantly, protecting against the development of atherosclerosis and diabetes mellitus. NO-1886 may have a beneficial effect on the most inflammation-associated cytokines, and this effect may contribute to improving atherosclerosis and diabetes mellitus.

Animals↗
PubMed2006

Identification and characterization of collagen-binding activity in Streptococcus mutans wall-associated protein: a possible implication in dental root caries and endocarditis.

Streptococcus mutans is implicated in coronal and dental root decay, and in endocarditis. Comparative study of the amino acid sequence of S. mutans 47 kDa wall-associated protein A (WapA) revealed a collagen-binding domain (CBD) at the N-terminal region. Recombinant AgA (WapA truncated at the carboxyterminal end) was isolated, biotin-labeled, and analyzed by Solid Phase Binding Assay. The results showed that biotin-labeled AgA bound significantly and in a dose-dependent manner to immobilized collagen type I, and to a lesser extent to fibronectin, but not to collagen type IV or laminin. Binding of biotin-labeled S. mutans cells to collagen-coated surfaces was significantly inhibited by antibody to WapA or AgA (P<0.001). The results obtained confirmed the collagen-binding activity of CBD in AgA and WapA, and suggested that WapA may be used, not only as a vaccine against coronal and dental root caries, but also against S. mutans-mediated endocarditis.

Amino Acid Sequence↗