Biomedical subjects

Zhong Wang

Publications and source records attributed to Zhong Wang.

At least 19 recordsLinked to original sources

PubMed2026

Integrating multi-omics technologies to decipher microbiome functions.

Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science.

Multiomics↗

PubMed2026

Comparative transcriptomic and physiological analyses uncover key regulatory pathways associated with drought tolerance in wheat.

Drought severely limits wheat yield, yet its molecular basis remains incompletely understood. We compared a drought-tolerant line (A25) and a drought-sensitive line (A8) under water deficit across three developmental stages using physiological assays and transcriptomics. A25 exhibited stronger osmotic adjustment and antioxidant defense, with higher proline accumulation and enhanced activities of ascorbate peroxidase, catalase, and other ROS-scavenging enzymes. RNA-seq revealed distinct drought-responsive expression patterns, with differentially expressed genes enriched in MAPK signaling and ABA-dependent pathways. ABA-responsive genes were more abundant and strongly induced in A25, suggesting enhanced ABA signal transduction as a key mechanism. Weighted gene co-expression network analysis identified a drought-associated purple module positively correlated with physiological resistance, from which six hub genes (MAPKKK17, Avr9/Cf-9, RPPL1, RGA1, UBC28, AGPs5) were highlighted as potential regulators. Collectively, coordinated activation of ABA signaling and MAPK cascades, mediated by these hub genes, underlies the robust drought tolerance of A25, providing promising molecular targets for wheat breeding and improvement.

Triticum↗

PubMed2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings.

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Sequence Analysis, DNA↗

PubMed2024

DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings.

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 23 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. Model, codes, and data is publicly available at https://github.com/MAGlCS-LAB/DNABERT_S.

Journal Article↗

PubMed2006

A comparative study on the individual and combined effects of baicalin and jasminoidin on focal cerebral ischemia-reperfusion injury.

To compare the individual effects of baicalin and jasminoidin with the combined effect of them on cerebral ischemia-reperfusion injury, and test whether the combined administration of baicalin and jasminoidin can improve the therapeutic effect. Male Sprague-Dawley rats underwent focal cerebral ischemia for 1.5 h and reperfusion for 24 h. Just before reperfusion, tested drugs (baicalin, jasminoidin, a drug combination consisting of baicalin and jasminoidin, or nimodipine) were intravenously treated. Diffusion weighted imaging (DWI) of magnetic resonance imaging (MRI), behavior examination, 2,3,5-triphenyltetrazolium chloride (TTC) staining, histological examination, and real-time PCR for BDNF and caspase-3 were performed. All of the drug treatments could significantly ameliorate the results of TTC and histological examination, and the baicalin/jasminoidin combination did so most prominently. This combination could also significantly ameliorate DWI of MRI and behavior examination results, and promote the expression of BDNF and inhibit the expression of caspase-3. On the whole, both baicalin and jasminoidin have a preventive effect against ischemic stroke, although their effects are not very strong. However, the combination of baicalin and jasminoidin can significantly improve their effectiveness. This may be related to its better regulation on the BDNF and caspase-3.

Analysis of Variance↗

PubMed2006

Gastric lavage in acute organophosphorus pesticide poisoning (GLAOP)--a randomised controlled trial of multiple vs. single gastric lavage in unselected acute organophosphorus pesticide poisoning.

BACKGROUND: Organophosphorus (OP) pesticide poisoning is the most common form of pesticide poisoning in many Asian countries. Guidelines in western countries for management of poisoning indicate that gastric lavage should be performed only if two criteria are met: within one hour of poison ingestion and substantial ingested amount. But the evidence on which these guidelines are based is from medicine overdoses in developed countries and may be irrelevant to OP poisoning in Asia. Chinese clinical experience suggests that OP remains in the stomach for several hours or even days after ingestion. Thus, there may be reasons for doing single or multiple gastric lavages for OP poisoning. There have been no randomised controlled trials (RCTs) to assess this practice of multiple lavages. Since it is currently standard therapy in China, we cannot perform a RCT of no lavage vs. a single lavage vs. multiple lavages. We will compare a single gastric lavage with three gastric lavages as the first stage to assess the role of gastric lavage in OP poisoning. METHODS/DESIGN: We have designed an RCT assessing the effectiveness of multiple gastric lavages in adult OP self-poisoning patients admitted to three Chinese hospitals within 12 hrs of ingestion. Patients will be randomised to standard treatment plus either a single gastric lavage on admission or three gastric lavages at four hour intervals. The primary outcome is in-hospital mortality. Analysis will be on an intention-to-treat basis. On the basis of the historical incidence of OP at the study sites, we expect to enroll 908 patients over three years. This projected sample size provides sufficient power to evaluate the death rate; and a variety of other exposure and outcome variables, including particular OPs and ingestion time. Changes of OP level will be analyzed in order to provide some toxic kinetic data. DISCUSSION: the GLAOP study is a novel, prospective cohort study that will explore to the toxic kinetics of OP and effects of gastric lavage on it. Given the poor information about the impact of gastric lavage on clinical outcomes for OP patients, this study can provide important information to inform clinical practice.

Journal Article↗

PubMed2006

Increased hypothalamic protein tyrosine phosphatase 1B contributes to leptin resistance with age.

Animals at advanced ages exhibit a reduction in central leptin sensitivity. However, changes in growth, metabolism, and obesity risk occur much earlier in life, particularly during the transition from youth to middle age. To determine when initial decreases in central leptin sensitivity occur, leptin-dependent suppression of food intake was tested in 8-, 12-, and 20-wk-old male, chow-fed Sprague Dawley rats. Intracerebroventricular leptin injection (3 microg) suppressed 24-h food intake in 8- and 12-wk-old rats (P < 0.05) but not 20-wk-old rats. To identify potential cellular mediators of this resistance, we focused on protein tyrosine phosphatase 1B (PTP1B), a recently described inhibitor of leptin signaling. PTP1B protein levels, as determined by Western blot, were significantly higher in mediobasal hypothalamic punches collected from 20-wk-old rats, compared with 8-wk-old rats (P < 0.05). When 20-wk-old rats were fasted for 24 h, levels of hypothalamic PTP1B decreased (P < 0.05), coincident with a restoration of leptin sensitivity. To directly test whether inhibition of PTP1B restores leptin sensitivity, 20-wk-old chow-fed rats were pretreated with a pharmacological PTP1B inhibitor 1 h before leptin, and 24-h food intake was recorded. As expected, leptin alone produced a small but nonsignificant reduction in food intake. However, pretreatment with the PTP1B inhibitor resulted in a marked improvement in leptin-dependent suppression of food intake (P < 0.05). These data are consistent with the hypothesis that increases in PTP1B contribute to hypothalamic leptin resistance as rats transition into middle age.

Aging↗

PubMed2006

Sex-lethal is a target of Bruno-mediated translational repression in promoting the differentiation of stem cell progeny during Drosophila oogenesis.

The RNA Recognition Motif (RRM) type RNA binding protein Bruno is required for the differentiation of cystoblasts, the committed daughters of germline stem cells in the Drosophila ovary. To understand how Bruno controls cystoblast differentiation, we used a bioinformatics approach to identify potential mRNA targets of Bruno. One such target is the Sex-lethal (Sxl) transcript MS11, which contains four Bruno Response Elements (BREs) in its 3' untranslated region. Electrophoresis mobility shift assays demonstrated that Bruno specifically binds to the BREs of Sxl MS11 mRNA. Tagged transgenic Sxl MS11 cDNA constructs were used to show that Bruno represses the translation of the Sxl MS11 mRNA via the BRE-containing region in the 3'UTR. The lack of either Bruno or the BRE-containing region leads to overexpression of SXL, which in turn causes defects in cystoblast differentiation similar to the Bruno mutant phenotype. Therefore, Sxl MS11 represents a novel target of Bruno-mediated translational repression required for cystoblast differentiation.

3' Untranslated Regions↗

PubMed2006

Inactivation of PKCtheta leads to increased susceptibility to obesity and dietary insulin resistance in mice.

In this study, we investigated the metabolic phenotype of PKCtheta knockout mice (C57BL/6J) on chow diet and high-fat diet (HFD). The knockout (KO) mice are normal in growth and reproduction. On the chow diet, body weight and food intake were not changed in the KO mice; however, body fat content was increased with a corresponding decrease in body lean mass. Energy expenditure and spontaneous physical activity were decreased in the KO mice. On HFD, energy expenditure and physical activity remained low in the KO mice. The body weight and fat content were increased rapidly in the KO mice. At 8 wk on HFD, severe insulin resistance was detected in the KO mice with hyperinsulinemic euglycemic clamp and insulin tolerance test. Insulin action in both hepatic and peripheral tissues was reduced in the KO mice. Plamsa free fatty acid was increased, and expression of adiponectin in the adipose tissue was decreased, in the KO mice on HFD. This study suggests that loss of PKCtheta reduces energy expenditure and increases the risk of dietary obesity and insulin resistance in mice.

Adiponectin↗

PubMed2006

Evidence of influence of genomic DNA sequence on human X chromosome inactivation.

A significant number of human X-linked genes escape X chromosome inactivation and are thus expressed from both the active and inactive X chromosomes. The basis for escape from inactivation and the potential role of the X chromosome primary DNA sequence in determining a gene's X inactivation status is unclear. Using a combination of the X chromosome sequence and a comprehensive X inactivation profile of more than 600 genes, two independent yet complementary approaches were used to systematically investigate the relationship between X inactivation and DNA sequence features. First, statistical analyses revealed that a number of repeat features, including long interspersed nuclear element (LINE) and mammalian-wide interspersed repeat repetitive elements, are significantly enriched in regions surrounding transcription start sites of genes that are subject to inactivation, while Alu repetitive elements and short motifs containing ACG/CGT are significantly enriched in those that escape inactivation. Second, linear support vector machine classifiers constructed using primary DNA sequence features were used to correctly predict the X inactivation status for >80% of all X-linked genes. We further identified a small set of features that are important for accurate classification, among which LINE-1 and LINE-2 content show the greatest individual discriminatory power. Finally, as few as 12 features can be used for accurate support vector machine classification. Taken together, these results suggest that features of the underlying primary DNA sequence of the human X chromosome may influence the spreading and/or maintenance of X inactivation.

Base Sequence↗

PubMed2006

[Severe hypospadias repair: reconstructing penis, scrotum and urethra].

OBJECTIVE: To investigate the surgical technic of re-shape penis and scrotum, as well as construct urethra in severe hypospadias patients. METHODS: Twenty-two cases of perineal hypospadias with abnormal penis and scrotum were involved in operative repair. All the patients underwent two-stage of repair technic. The penis sponge were completely stretched out and uprighted in the first-stage. Foreskin and partial penis back skin was transferred into the ventral of penis and scrotum crack. At second-stage, urethroplasty was performed using bladder mucosa folded into half tube that sutured with urothra plate to reconstruct the urothra. The scrotum were re-shaped using foreskin and skinflap. RESULTS: The operation's successful rate was 68% (15/22). There were 7 cases (32%) suffered from urethrocutaneous fistula and recovered after repair. Five cases (23%) occurred stricture of urethra and were treated by urethra dilatation. The appearance of penis and scrotum in 22 cases were satisfied. CONCLUSIONS: The operative methods should be made according to the type of hypospadias and of scrotum. The technic were effective on severe hypospadias with abnormal scrotum, even for the patients who need more than 10 cm urethra construct. The appearance of penis and scrotum were satisfied after following up.

Adolescent↗

PubMed2006

A novel class of small RNAs in mouse spermatogenic cells.

Small noncoding RNAs, including small interfering RNAs (siRNAs) and micro RNAs (miRNAs) of approximately 21 nucleotides (nt) in length, have emerged as potent regulators of gene expression at both transcriptional and post-transcriptional levels in diverse organisms. Here we report the identification of a novel class of small RNAs in the mouse male germline termed piwi-interacting RNAs (piRNAs). piRNAs are approximately 30 nt in length. They are expressed during spermatogenesis, mostly in spermatids. piRNAs are associated with MIWI, a spermatogenesis-specific PIWI subfamily member of the Argonaute protein family, and depend on MIWI for their biogenesis and/or stability. Furthermore, a subpopulation of piRNAs are associated with polysomes, suggesting their potential role in translational regulation.

Animals↗

PubMed2006

Hot bands in jet-cooled and ambient temperature spectra of chloromethylene.

Rotationally resolved spectra of several bands lying to the red of the origin of the A(1)A" - X (1)A' band system of chloromethylene (HCCl), were recorded by laser absorption spectroscopy in ambient temperature and jet-cooled samples. The radical was made by excimer laser photolysis of dibromochloromethane, diluted in inert gas, at 193 nm. The jet-cooled sample showed efficient rotational but less vibrational cooling. Analysis showed that the observed bands originate in the (upsilon(1),upsilon(2),upsilon(3)) = (010), (001), and (011) vibrational levels of the ground electronic state of the radical, while the upper-state levels involved were (000), (010), (001), and (011). Vibrational energies and rotational constants describing the rotational levels in the lower-state vibrational levels were determined by fitting to combination differences. The analysis also resulted in a reevaluation of the C-Cl stretching frequency in the excited state and we find E(001)' = 13 206.57 or 926.17 cm(-1) above the A(1)A" (000) rotationless level for HC(35)Cl. Scaled ab initio potential energy surfaces for the A and X states were used to compute the transition moment surface and thereby the relative intensities of different vibronic transitions, providing additional support for the assignments and permitting the prediction of the shorter wavelength spectrum. All the observed upper state levels showed some degree of perturbation in their rotational energy levels, particularly in K(a) = 1, presumably due to coupling with near-resonant vibrationally excited levels of the ground electronic state. Transitions originating in the low-lying a(3)A" were also predicted to occur in the same wavelength region, but could not be identified in the spectra.

Journal Article↗

PubMed2006

New polyethyleneglycol-functionalized texaphyrins: synthesis and in vitro biological studies.

The synthesis of four new analogues of motexafin gadolinium (MGd), a gadolinium(III) texaphyrin complex in clinical trials for its anticancer properties, is described. These new derivatives contain either 1,2-diaminobenzene or 2,3-diaminonaphthalene subunits as the source of the imine nitrogens and bear multiple 2-[2-(2-methoxyethoxy)ethoxy]ethoxy (PEG) groups, on either meso aryl or beta-pyrrolic substituents, to increase their water solubility. All four analogues were found to be more active in vitro than the parent system MGd as judged from cell proliferation assays using the PC3 and A549 cell lines.

Antineoplastic Agents↗

PubMed2006

Inflammatory cytokine regulation of transgene expression in human fibroblast-like synoviocytes infected with adeno-associated virus.

OBJECTIVE: An ideal gene transfer vector for chronic inflammatory diseases such as rheumatoid arthritis (RA) would provide local transgene expression only when the disease is active. To determine whether adeno-associated virus (AAV) possesses this ability, the effects of inflammatory cytokines on transgene expression were evaluated in human RA fibroblast-like synoviocytes (FLS). METHODS: Human FLS were infected with AAV in the presence or absence of inflammatory cytokines or synovial fluid obtained from patients with RA. Transgene expression was monitored by either enzyme-linked immunosorbent assay or flow cytometry. Transgene messenger RNA (mRNA) was measured by real-time quantitative reverse transcription-polymerase chain reaction. RESULTS: Inflammatory cytokines increased transgene expression in FLS by up to 60-fold. Synovial fluid from patients with RA, but not from patients without arthritis, was also able to increase expression in synoviocytes. Protein expression correlated with transgene mRNA levels. The enhanced expression required the continued presence of cytokines because, upon removal, transgene expression returned to baseline levels. Expression could be repeatedly reinduced by reexposure to cytokines. The effect was not promoter specific and was demonstrated to be phosphatidylinositol 3-kinase-dependent. CONCLUSION: These results suggest that expression of a therapeutic transgene can be controlled by the presence of inflammation following AAV gene transfer, making it an attractive vector for chronic inflammatory diseases such as RA.

Arthritis, Rheumatoid↗

PubMed2006

Effects of tenotomy on patients with infantile nystagmus syndrome: foveation improvement over a broadened visual field.

PURPOSE: To investigate the effects of four-muscle tenotomy on visual function and gaze angle in patients with infantile nystagmus syndrome (INS). METHODS: Eye movements of nine patients with infantile nystagmus were recorded using infrared reflection or high-speed digital video techniques. Experimental protocols were designed to record the patients' eye-movement waveforms, pre- and post-tenotomy, at different gaze angles. We used the eXpanded Nystagmus Acuity Function (NAFX) to measure tenotomy-induced changes in the nystagmus at primary position and various gaze angles. The longest foveation domains (LFD) were measured from fitted curves. Peak-to-peak nystagmus amplitudes and foveation-period durations were also measured. All measurements were made unmasked. RESULTS: All seven patients with narrow, high-NAFX, gaze-angle regions showed broadening of these regions of higher visual function. Three patients showed moderate NAFX improvement (13.9-32.6%) at primary position, five showed large improvement (39.9-162.4%), and one showed no NAFX change (due to his high pretenotomy NAFX). Primary position measured acuities improved in six patients. All patients had reductions in nystagmus amplitudes ranging from 14.6 to 37%. The duration of the foveation period increased in all nine patients (11.2-200%). The percentage improvements in both the NAFX and the LFD decreased with higher pretenotomy values. CONCLUSIONS: In addition to elevating primary position NAFX, tenotomy also broadens the high-NAFX regions. This broadening effect is more prominent in patients who had sharp pretenotomy NAFX peaks. Four-muscle tenotomy produces higher primary position NAFX increases in infantile nystagmus patients whose pretenotomy values are relatively low, with the improvement decreasing at higher pretenotomy values. The tenotomy procedure improves visual function beyond primary position acuity. This extends the utility of surgical therapy to several different classes of patients with INS for whom other procedures are contraindicated. The pretenotomy NAFX can now be used to predict both primary position acuity improvements and broadening of a patient's high-NAFX range of gaze angles.

Adolescent↗

PubMed2006

Acetylated flavanone glycosides from the rhizomes of Cyclosorus acuminatus.

Six new flavanone glycosides (1-6) were isolated from the methanol extract of the rhizomes of Cyclosorus acuminatus, together with the parent flavanone glycoside 2a. Their structures were established on the basis of spectroscopic and chemical methods. All compounds showed moderate activity against Streptococcus pneumoniae and Haemophilus influenzae.

Anti-Infective Agents↗

PubMed2006

Fatty acids and coccidiosis: effects of dietary supplementation with different oils on coccidiosis in chickens.

This study was undertaken to investigate the effects of dietary oils on coccidiosis of chickens infected with Eimeria tenella. Five hundred and four 1-day-old male Arbor Acres chicks were randomly assigned to seven groups. Seven diets were supplemented with poultry oil at 25 and 45 g/kg, corn oil at 25 and 45 g/kg, fish oil at 25 and 45 g/kg, and without oils, respectively, from 1 to 42 days of age. Chickens were inoculated by gavage with 3 x 10(5) sporulated oocysts at 21 days of age. Diets supplemented with oils at 45 g/kg resulted in higher body weight gain than with oils at 25 g/kg or without oils. The packed cell volume in chicks fed with diets supplemented with poultry oil was lower than that in chicks fed with diets supplemented with fish oil, corn oil and without oil. Chickens fed with diets supplemented with poultry oil had higher mortality than that of chickens fed with diets without oil. At 7 days post infection, the chickens consuming fish or corn oil diets had lower levels of plasma carotenoids than those fed with poultry oil supplement or without oils. Fish oil supplementation increased serum interleukin-6 levels in chickens compared with poultry oil at 25 and 45 g/kg and corn oil at 25 g/kg. Fish oil or corn oil enhanced secretory IgA levels in the lumen of the caecum, and oil supplementation tended to decrease serum IgG levels. In conclusion, the diets supplemented with saturated fatty acids aggravated mortality in chickens infected with E. tenella. The deleterious effects on coccidiosis of the diets supplemented with poultry oils might be related to the decreased levels of caecal E. tenella antigen-binding-specific secretory IgA or serum IgG.

Animal Feed↗