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Ze Zhang

Publications and source records attributed to Ze Zhang.

At least 19 recordsLinked to original sources
PubMed2026

Genome-wide identification of the peanut HD-Zip gene family and AhHDZ15 positively regulating salt and drought stress in heterologously overexpressed Arabidopsis.

Homeodomain-leucine zipper (HD-Zip) transcription factors play important roles in plant growth, development, and abiotic stress responses. However, bioinformatic analyses and functional studies of HD-Zip family in peanut are scarce. In this study, 128 AhHDZ genes were identified and classified into four subfamilies in the phylogenetic analysis. Transcriptomic data and RT-qPCR analysis indicated the expression levels of AhHDZ4 and AhHDZ15 were significantly elevated in response to 12 h of salt stress, while AhHDZ4/15/60/69/126 all showed a progressive increase over time in response to drought stress. AhHDZ15 protein was localized in the nucleus. Under salt and drought stress, the germination rates of AhHDZ15-overexpressing in Arabidopsis were significantly higher than wild-type (WT), and root lengths were also significantly longer than WT. In addition, the SOD, CAT, chlorophyll content, and Relative Leaf Water Content (RLWC) value of leaves in AhHDZ15-overexpressing lines were significantly higher than WT, while the MDA content was significantly lower than WT. The above results indicate that heterologous overexpression of AhHDZ15 enhanced salt and drought tolerance in Arabidopsis. Furthermore, AhHDZ15 could bind to the L1-box element of the AhVNI2 promoter, thereby activating AhVNI2 transcription and enhancing the expression of downstream salt stress-responsive genes. These findings implies a potential function of AhHDZ15 in peanut that requires further validation.

Arabidopsis↗
PubMed2026

Endothelial cell-specific DNA methylation alterations in breast cancer.

DNA methylation alterations are well-established contributors to carcinogenesis, yet, in the tumor microenvironment (TME), patterns of lineage and cell-specific methylation alterations are not well understood. Single-cell DNA methylation profiling in the TME is limited by technical challenges and high costs. Here, we use bulk DNA methylation, cell type deconvolution (HiTIMED), and an interaction testing framework (CellDMC) to identify reproducible, computationally inferred lineage-specific epigenetic alterations in the TME supported by orthogonal data sources. Tumor endothelial cells (TECs), critical regulators of angiogenesis, vascular permeability, and immune cell trafficking, acquire structural and functional abnormalities that promote tumor growth. We hypothesize that TECs have altered DNA methylation compared with endothelial cells in non-tumor tissues. In genome-scale methylation data from discovery and validation datasets (tumor n = 1071; non-tumor n = 415), we identify and validate >4500 TEC-specific CpGs with altered methylation, many mapping to genes involved in angiogenesis and endothelial function. Integration with gene expression data indicates that TEC-specific methylation alterations may reprogram transcriptional networks controlling angiogenesis. High-resolution, cell lineage-specific epigenetic landscapes can be inferred from bulk methylation data, implicating TEC-specific DNA methylation alterations as potential drivers of cancer angiogenesis and vascular dysfunction and providing a framework for future mechanistic and translational studies of the tumor vasculature.

DNA Methylation↗
PubMed2025

Phosphoproteomics delineates hepatocellular carcinoma subtypes and pinpoints therapeutic targets.

BACKGROUND AND AIMS: Only a minority of patients could benefit from systemic therapy owing to the high heterogeneity of HCC. Therefore, a deeper understanding of the pathogenesis of HCC is essential for precision therapy. Genomic and proteomic studies of HCC have enhanced our understanding of HCC. However, the phosphoproteomic characterization of HCC remains poorly understood. APPROACH AND RESULTS: We conducted an in-depth analysis of a clinical cohort of HCC using high-coverage phosphoproteomic. Effective therapeutic targets were validated using liver cancer cell lines and HCC patient-derived xenograft mouse models that correspond to the phosphoproteomic subtypes of HCC. Phosphoproteomic analysis classified HCC into 3 subtypes, A, B, and C, with increasing malignancy and correlation with clinical features, including patient prognosis, tumor staging, serum alpha-fetoprotein levels, tumor thrombus, and tumor size. Phosphoproteomic subtyping deeply reflected the biological characteristics and clinical features of patients with HCC​​​​​​. The profiles of HCC-dysregulated kinase activities inferred from the different phosphoproteomic subtypes consistently identify increased kinase activity related to cell proliferation. Subtype-C HCC patients showed the most significant dysregulation, indicating a potential therapeutic target. The corresponding drug, bosutinib, demonstrated efficacy in inhibiting the growth of subtype C tumors in liver cancer cell lines and HCC patient-derived xenograft mouse models representative of the phosphoproteomic HCC subtypes. CONCLUSIONS: Our study provides a comprehensive exploration of the phosphoproteomic landscape of HCC, establishing new subtypes that match clinical features and identifying potential therapeutic targets for the most malignant C subtype.

Carcinoma, Hepatocellular↗
PubMed2007

Electrically conductive biodegradable polymer composite for nerve regeneration: electricity-stimulated neurite outgrowth and axon regeneration.

Normal and electrically stimulated PC12 cell cultures and the implantation of nerve guidance channels were performed to evaluate newly developed electrically conductive biodegradable polymer composites. Polypyrrole (PPy) doped by butane sulfonic acid showed a significantly higher number of viable cells compared with PPy doped by polystyrenesulfonate after a 6-day culture. The PC12 cells were left to proliferate for 6 days, and the PPy-coated membranes, showing less initial cell adherence, recorded the same proliferation rate as did the noncoated membranes. Direct current electricity at various intensities was applied to the PC12 cell-cultured conductive membranes. After 7 days, the greatest number of neurites appeared on the membranes with a current intensity approximating 1.7-8.4 microA/cm. Nerve guidance channels made of conductive biodegradable composite were implanted into rats to replace 8 mm of sciatic nerve. The implants were harvested after 2 months and analyzed with immunohistochemistry and transmission electron microscopy. The regenerated nerve tissue displayed myelinated axons and Schwann cells that were similar to those in the native nerve. Electrical stimulation applied through the electrically conductive biodegradable polymers therefore enhanced neurite outgrowth in a current-dependent fashion. The conductive polymers also supported sciatic nerve regeneration in rats.

Absorbable Implants↗
PubMed2006

Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms.

The average length of genes in a eukaryote is larger than in a prokaryote, implying that evolution of complexity is related to change of gene lengths. Here, we show that although the average lengths of genes in prokaryotes and eukaryotes are much different, the average lengths of genes are highly conserved within either of the two kingdoms. This suggests that natural selection has clearly set a strong limitation on gene elongation within the kingdom. Furthermore, the average gene size adds another distinct characteristic for the discrimination between the two kingdoms of organisms.

Eukaryotic Cells↗
PubMed2006

Constructing genetic linkage maps under a tetrasomic model.

An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.

Chromosome Mapping↗
PubMed2006

In vitro homogeneous and heterogeneous degradation of poly(epsilon-caprolactone/polyethylene glycol/L-lactide): The absence of autocatalysis and the role of enzymes.

This study investigated the in vitro degradation behavior of poly(epsilon-caprolactone/polyethylene glycol/L-lactide) (PCEL) in comparison with that of three other biodegradable polymers. Polymer membranes were incubated in pancreatin solution, Ringer's solution, and distilled water at 37 degrees C for up to 20 weeks. Characterization involved measuring weight loss, observing the morphological changes by scanning electron microscopy (SEM), analyzing molecular weight using size exclusion chromatography (SEC), and studying the crystalline structure using differential scanning calorimetry (DSC). The hydrolysis in a simple aqueous solution experienced no autocatalysis, which was attributed to the high permeability of PCEL to water-soluble degradation products. Similar degradation rates were recorded for the PCEL and poly(L,L-lactide) (PLLA) test membranes. In the presence of pancreatin, the PCEL membrane experienced rapid heterogeneous surface erosion likely caused by the selective loss of its surface PEG components under enzymatic action. Pancreatin also substantially increased the even physical resorption of the other test polymers by eliminating autocatalysis. This study demonstrated that autocatalysis commonly experienced by poly(alpha-hydroxyl acid) can be reduced through chemical formulation or high enzyme activity.

Biocompatible Materials↗
PubMed2005

Rapid and efficient synthesis of poly-substituted quinolines assisted by p-toluene sulphonic acid under solvent-free conditions: comparative study of microwave irradiation versus conventional heating.

A rapid and efficient method for the preparation of various poly-substituted quinolines has been developed through the Friedländer condensation of 2-aminoarylketone or 2-aminoarylaldehyde with carbonyl compounds in the presence of p-toluene sulphonic acid, which was achieved by both microwave irradiation and conventional heating under solvent-free conditions.

Aldehydes↗
PubMed2005

Modeling population genetic data in autotetraploid species.

Allozyme and PCR-based molecular markers have been widely used to investigate genetic diversity and population genetic structure in autotetraploid species. However, an empirical but inaccurate approach was often used to infer marker genotype from the pattern and intensity of gel bands. Obviously, this introduces serious errors in prediction of the marker genotypes and severely biases the data analysis. This article developed a theoretical model to characterize genetic segregation of alleles at genetic marker loci in autotetraploid populations and a novel likelihood-based method to estimate the model parameters. The model properly accounts for segregation complexities due to multiple alleles and double reduction at autotetrasomic loci in natural populations, and the method takes appropriate account of incomplete marker phenotype information with respect to genotype due to multiple-dosage allele segregation at marker loci in tetraploids. The theoretical analyses were validated by making use of a computer simulation study and their utility is demonstrated by analyzing microsatellite marker data collected from two populations of sycamore maple (Acer pseudoplatanus L.), an economically important autotetraploid tree species. Numerical analyses based on simulation data indicate that the model parameters can be adequately estimated and double reduction is detected with good power using reasonable sample size.

Alleles↗
PubMed2005

Degenerative mineralization in the fibrous capsule of silicone breast implants.

The formation of a fibrous capsule made of long collagen fibers surrounding breast implants represents an unavoidable phenomenon as the patient's reaction to the presence of a foreign body. Depending upon the size and shape of the implants and the chemicals percolating through the shell, this fibrous capsule is continuously remodeled. The compaction of the foreign debris in the vicinity of the silicone shell is followed by the loss of cellular activity, shrinkage and necrosis. Calcification is the ultimate step. These phenomena were illustrated in the analysis of 18 explanted breast prostheses after 20 or more years of implantation. The degenerative mineralization was shown in scanning electron microscopy and light microscopy. The minerals proved to be bone-like hydroxyapatite by X-ray diffraction and Solid State NMR analysis. Whatever the characteristics of any sophisticated new model of breast implant, phenomenon of mineralization might be minimized but it is very unlikely that it would be totally eliminated.

Biocompatible Materials↗
PubMed2005

Evaluation of biodegradable synthetic scaffold coated on arterial prostheses implanted in rat subcutaneous tissue.

Polyester arterial prostheses impregnated with various synthetic biodegradable materials and with gelatin were implanted subcutaneously in rats for 3-180 days. The inflammation was assessed by quantifying the activity of alkaline phosphatase and by histology. The degradation of the scaffold materials was determined by scanning electron microscopy (SEM), size exclusion chromatography (SEC), and differential scanning calorimetry (DSC). The alkaline phosphatase activity induced by the polymer-impregnated grafts was similar to that induced by the non-impregnated controls during most of the post-implantation periods. Histological studies revealed that the acute inflammatory response was moderate to mild and was similar for all types of specimens, except for the gelatin-impregnated grafts that induced a severe acute inflammation during the first 2 weeks post-implantation. At 4 and 6 months, significant disintegration of the scaffold was observed, accompanied by enhanced tissue infiltration and a reactivation of the acute inflammatory phase. Linear and exponential degradation rates of the synthetic polymers were described. The relative degradation rates of the biodegradable polymers were ranked as following: PLLACL > PDLLA > PLLA > PCEL. In conclusion, biodegradable polymers may provide an option as sealant/scaffolding materials for vascular prosthesis. It is suggested that the degradation rate of the polymer scaffolding materials should be higher to achieve early healing while without inducing strong inflammation.

Absorbable Implants↗
PubMed2005

A simple method to detect the heterogeneity of nucleotide substitution processes by measuring asymmetry in paired comparison.

A simple method is presented, which uses a chi2 statistic to measure asymmetry of the substitution matrix between two DNA sequences in order to test a homogeneity hypothesis of the substitution processes. In theory, this chi2 test holds irrespective of whether there is among-site (i) heterogeneity in substitution rates, (ii) correlation in evolutionary rates/models, and (iii) variation in substitution models. Computer simulations showed that the chi2 test is powerful under a variety of models of sequence evolution. Comparison of the eleven sequenced arthropod mtDNAs by using this test revealed that most of the observed evolutionary models were homogeneous between the two mosquitoes but not between Daphnia pulex or Artemia franciscan and the other arthropods, probably due to shifts to a high AT content. A comparison to Kumar and Gadagkar's test by computer simulation as well as empirical data analysis is also given.

Animals↗
PubMed2004

Divergence pattern of duplicate genes in protein-protein interactions follows the power law.

The impact of the biological network structures on the divergence between the two copies of one duplicate gene pair involved in the networks has not been documented on a genome scale. Having analyzed the most recently updated Database of Interacting Proteins (DIP) by incorporating the information for duplicate genes of the same age in yeast, we find that there was a highly significantly positive correlation between the level of connectivity of ancient genes and the number of shared partners of their duplicates in the protein-protein interaction networks. This suggests that duplicate genes with a low ancestral connectivity tend to provide raw materials for functional novelty, whereas those duplicate genes with a high ancestral connectivity tend to create functional redundancy for a genome during the same evolutionary period. Moreover, the difference in the number of partners between two copies of a duplicate pair was found to follow a power-law distribution. This suggests that loss and gain of interacting partners for most duplicate genes with a lower level of ancestral connectivity is largely symmetrical, whereas the "hub duplicate genes" with a higher level of ancient connectivity display an asymmetrical divergence pattern in protein-protein interactions. Thus, it is clear that the protein-protein interaction network structures affect the divergence pattern of duplicate genes. Our findings also provide insights into the origin and development of biological networks.

Databases, Protein↗
PubMed2004

In vivo evaluation of a novel electrically conductive polypyrrole/poly(D,L-lactide) composite and polypyrrole-coated poly(D,L-lactide-co-glycolide) membranes.

This study evaluated the in vivo biocompatibility and biodegradation behavior of a novel polypyrrole (PPy)/poly(D,L-lactide) (PDLLA) composite and PPy-coated poly(D,L-lactide-co-glycolide) membranes. Test membranes were implanted subcutaneously in rats for 3-120 days. The biocompatibility was assessed by quantifying the alkaline and acid phosphatase secretion, the immunohistochemical staining of the ED-2-positive macrophages, and the histology at the tissue/material interface. The degradation was investigated using scanning electron microscopy. Pure PDLLA and poly(D,L-lactide-co-glycolide) membranes were used as references, whereas expanded polytetrafluoroethylene and a commercial styrene-butadiene rubber were used as controls. The enzyme activity of the PPy-containing specimens was shown to be similar to that of the references. The histological findings were consistent with the enzymatic results, showing a mild-to-moderate acute inflammation followed by a resolution of the inflammatory response with a decrease in inflammatory cells for each biodegradable membrane. The tissue reactions to the PPy, which was either in the form of nanoparticles or surface coating, were comparable to the response to the neighboring biodegradable materials. Elevated ED-2-positive macrophage populations appeared as early as day 3 in the loose connective tissue surrounding the implants. The density of these populations was related to the degree of inflammation. Scanning electron microscopy showed that the degradation of the PPy/PDLLA composite was not affected by the presence of PPy.

Acid Phosphatase↗