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Biomedical subjects

Yan Zheng

Publications and source records attributed to Yan Zheng.

At least 19 recordsLinked to original sources
PubMed2025

A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.

UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem. IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.

Humans↗
PubMed2025

Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.

Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.

Humans↗
PubMed2006

Interleukin-22, a T(H)17 cytokine, mediates IL-23-induced dermal inflammation and acanthosis.

Psoriasis is a chronic inflammatory skin disease characterized by hyperplasia of the epidermis (acanthosis), infiltration of leukocytes into both the dermis and epidermis, and dilation and growth of blood vessels. The underlying cause of the epidermal acanthosis in psoriasis is still largely unknown. Recently, interleukin (IL)-23, a cytokine involved in the development of IL-17-producing T helper cells (T(H)17 cells), was found to have a potential function in the pathogenesis of psoriasis. Here we show that IL-22 is preferentially produced by T(H)17 cells and mediates the acanthosis induced by IL-23. We found that IL-23 or IL-6 can directly induce the production of IL-22 from both murine and human naive T cells. However, the production of IL-22 and IL-17 from T(H)17 cells is differentially regulated. Transforming growth factor-beta, although crucial for IL-17 production, actually inhibits IL-22 production. Furthermore, IL-22 mediates IL-23-induced acanthosis and dermal inflammation through the activation of Stat3 (signal transduction and activators of transcription 3) in vivo. Our results suggest that T(H)17 cells, through the production of both IL-22 and IL-17, might have essential functions in host defence and in the pathogenesis of autoimmune diseases such as psoriasis. IL-22, as an effector cytokine produced by T cells, mediates the crosstalk between the immune system and epithelial cells.

Animals↗
PubMed2006

A cooperative beads-on-a-string approach to exceptionally stable DNA triplexes.

A poly(dT) oligomer can serve as the string on which synthetic hairpins possessing poly(dA) and poly(dT) arms connected by a hydrophobic perylene diimide linker are assembled like beads on a string. The synthetic hairpins form head-to-head dimers and trimers, respectively, in the absence of the poly(dT) string and in the presence of a string with inverted polarity at mid-strand. However, they assemble in cooperative head-to-tail fashion on normal poly(dT) oligomers.

Circular Dichroism↗
PubMed2006

A magnetic biomimetic nanocatalyst for cleaving phosphoester and carboxylic ester bonds under mild conditions.

[Structure: see text] As a result of the unique surface structure of nanospheres, Asp and His residues supported on a 12 nm maghemite nanoparticle worked collaboratively as a biomimetic nanocatalyst for hydrolyzing paraoxon (phosphoester) and 4-nitrophenyl acetate (carboxylic ester) in Milli-Q water (pH 7.0) at 37 degrees C, without employing extremes of pH or heavy metals. Our nanocatalyst could be facilely recovered via magnetic concentration. The isolated catalyst exhibited long-term stability, showing no significant loss of its catalytic activity for repeated uses after 3 months.

Amino Acid Sequence↗
PubMed2006

Enhanced recovery of arsenite sorbed onto synthetic oxides by L-ascorbic acid addition to phosphate solution: calibrating a sequential leaching method for the speciation analysis of arsenic in natural samples.

Stripping voltammetry capable of detecting 0.3microg/L arsenate and arsenite was applied for speciation analysis of arsenic sorbed onto synthetic ferrihydrite, goethite at As/Fe ratio of approximately 1.5mg/g with or without birnessite after sequential extraction using 1M phosphate (24 and 16 h) and 1.2M HCl (1h). Precautions to avoid oxygen were undertaken by extracting under anaerobic conditions and by adding 0.1M l-ascorbic acid to 1M NaH(2)PO(4) (pH 5). Addition of l-ascorbic acid did not reduce As(V) to As(III). The recovery rate for As(III) using l-ascorbic acid for extraction (pH 5) but not for adsorption was 81% and 74% of total sorbed As, and was 99% and 97% of extracted As for ferrihydrite and goethite, respectively. Birnessite oxidized most As(III) during the adsorption procedure. l-ascorbic acid used both in adsorption and extraction procedures improved the recovery of As(III) to 79-94% for ferrihydrite-birnessite and 57-94% for goethite-birnessite systems with Fe/Mn ratios of 7, 70, 140 and 280g/g.

Adsorption↗
PubMed2006

Transplantation of endothelial progenitor cells transferred by vascular endothelial growth factor gene for vascular regeneration of ischemic flaps.

BACKGROUND: Neovascularization occurs through two mechanisms: angiogenesis and vasculogenesis. Therefore, there are two strategies to promote neovascularization: therapeutic angiogenesis and therapeutic vasculogenesis (endothelial progenitor cells therapy). MATERIALS AND METHODS: In this study, we examined whether or not endothelial progenitor cells combined with vascular endothelial growth factor (VEGF) gene therapy is useful for ischemia surgical flaps in vivo. At the same time, we quantitatively compared the neovascularization ability of transplanted endothelial progenitor cells (EPCs) transducted with VEGF165 gene and EPCs alone. EPCs were isolated from cord blood of healthy human volunteers, cultured in vitro for 7 days and identified by immunofluorescence. After transduced with VEGF165 gene in vitro, proliferative activity of EPCs was assessed using MTT assay. CM-DiI was used to trace EPCs in vivo 4 days after injection of 5 x 10(5) VEGF-transduced EPCs(VEGF-transduced EPCs group, n = 10), 5 x 10(5) EPCs (non-transduced EPCs group, n = 10) in 500 microL EBM-2 media, or 500 microL EBM-2 media (EBM-2 media group, n = 10) local, a cranially based flap was elevated on the back of nude mice. The percent flap survival, neovasculariztion and blood flow recovery of flaps was detected. RESULTS: EPCs expressed cell markers CD34, KDR, and CD133. A statistically significant increase in percent flap survival was observed in mice of VEGF-transduced EPCs group as compared with that of non-transduced EPCs group: 67.99 +/- 6.64% versus 59.43 +/- 4.69% (P < 0.01), and 41.24 +/- 2.44% in EBM-2 media group (P < 0.01). The capillary density and blood flow recovery of flaps in VEGF-transduced EPCs group were both improved. CM-DiI-labeled VEGF-transduced EPCs were observed in vivo and the numbers of cells increased. CONCLUSION: EPCs from human cord blood can increased neovascularization of ischemic flaps and augmented the survival areas, and VEGF-transduced EPCs have more powerful ability of promoting neovascularization in animal model of ischemic flaps.

Animals↗
PubMed2006

Magnetic nanoparticles as an orthogonal support of polymer resins: applications to solid-phase suzuki cross-coupling reactions.

[reaction: see text] Most of the reactants immobilized on conventional solid-phase resins are buried inside the interiors of lightly cross-linked polystyrene beads. An orthogonal support of solid-phase resins needs to be small enough to penetrate the interpolymeric chain spaces of a swollen resin to reach reaction sites. In this paper, we report the use of magnetic nanoparticles ( approximately 4 nm) as an orthogonal matrix to assist solid-phase reactions. A magnetic nanoparticle-supported homogeneous Pd catalyst was employed for promoting the Suzuki cross-coupling of an aryl halide on resins and an excessive arylboronic acid in solution. The workup separating three components (the catalyst, product, and remaining arylborate) is a chromatography-free process. The Pd catalyst was magnetically isolated and recycled from the reaction mixture by applying an external magnetic field. Then, a filtration process was followed to recover the excess borate reagent from the resins/product. Our work here presents the first example of an orthogonal matrix of solid-phase resins and shows the promise of employing nanomaterials in organic synthesis.

Borates↗
PubMed2006

Water manganese exposure and children's intellectual function in Araihazar, Bangladesh.

Exposure to manganese via inhalation has long been known to elicit neurotoxicity in adults, but little is known about possible consequences of exposure via drinking water. In this study, we report results of a cross-sectional investigation of intellectual function in 142 10-year-old children in Araihazar, Bangladesh, who had been consuming tube-well water with an average concentration of 793 microg Mn/L and 3 microg arsenic/L. Children and mothers came to our field clinic, where children received a medical examination in which weight, height, and head circumference were measured. Children's intellectual function was assessed on tests drawn from the Wechsler Intelligence Scale for Children, version III, by summing weighted items across domains to create Verbal, Performance, and Full-Scale raw scores. Children provided urine specimens for measuring urinary As and creatinine and were asked to provide blood samples for measuring blood lead, As, Mn, and hemoglobin concentrations. After adjustment for sociodemographic covariates, water Mn was associated with reduced Full-Scale, Performance, and Verbal raw scores, in a dose-response fashion; the low level of As in water had no effect. In the United States, roughly 6% of domestic household wells have Mn concentrations that exceed 300 microg Mn/L, the current U.S. Environmental Protection Agency lifetime health advisory level. We conclude that in both Bangladesh and the United States, some children are at risk for Mn-induced neurotoxicity.

Arsenic↗
PubMed2006

[Studies of methods and exploitation of computer software for mapping interactive genes].

There are six possible types of gene interaction in qualitative traits, namely, complementary, duplicate, cumulative, dominant epistasis, recessive epistasis and inhibiting. In genetic studies, the problem of mapping interactive genes may be met sometimes, but no systematic researches on the methodology and computer software for the mapping of interactive genes have been reported up to date. In this paper, methods for the mapping of interactive genes based on maximum-likelihood estimation and corresponding computer software (IGMapping 1.0) are presented. Computer simulations have shown that the methods proposed can unbiasedly estimate the recombination frequency or linkage distance between a codominant marker and an interactive gene.

Chromosome Mapping↗
PubMed2006

Dissecting the mechanism of T-cell anergy with immunophilin ligands.

T-cell receptor engagement in the absence of costimulation leads to T-cell anergy. The biochemical and molecular mechanisms responsible for this form of T-cell tolerance are becoming better defined. This review examines the intersection between T-cell receptor-induced anergy and the immunophilin ligands ciclosporin A, FK-506, rapamycin and sanglifehrin A, and focuses on how these compounds play an important role in dissecting the pathways leading to the induction and maintenance of anergy. Finally, the clinical role of these compounds as immunosuppressive agents will be discussed in the context of their effects on promoting or inhibiting T-cell anergy.

Animals↗
PubMed2005

Arsenic redistribution between sediments and water near a highly contaminated source.

Mechanisms controlling arsenic partitioning between sediment, groundwater, porewaters, and surface waters were investigated at the Vineland Chemical Company Superfund site in southern New Jersey. Extensive inorganic and organic arsenic contamination at this site (historical total arsenic > 10 000 microg L(-1) or > 130 microM in groundwater) has spread downstream to the Blackwater Branch, Maurice River, and Union Lake. Stream discharge was measured in the Blackwater Branch, and water samples and sediment cores were obtained from both the stream and the lake. Porewaters and sediments were analyzed for arsenic speciation as well as total arsenic, iron, manganese, and sulfur, and they indicate that geochemical processes controlling mobility of arsenic were different in these two locations. Arsenic partitioning in the Blackwater Branch was consistent with arsenic primarily being controlled by sulfur, whereas in Union Lake, the data were consistent with arsenic being controlled largely by iron. Stream discharge and arsenic concentrations indicate that despite large-scale groundwater extraction and treatment, > 99% of arsenic transport away from the site results from continued discharge of high arsenic groundwater to the stream, rather than remobilization of arsenic in stream sediments. Changing redox conditions would be expected to change arsenic retention on sediments. In sulfur-controlled stream sediments, more oxic conditions could oxidize arsenic-bearing sulfide minerals, thereby releasing arsenic to porewaters and streamwaters; in iron-controlled lake sediments, more reducing conditions could release arsenic from sediments via reductive dissolution of arsenic-bearing iron oxides.

Arsenic↗
PubMed2005

A role for B cell-activating factor of the TNF family in chemically induced autoimmunity.

After exposure to subtoxic doses of heavy metals such as mercury, H-2s mice develop an autoimmune syndrome consisting of the rapid production of IgG autoantibodies that are highly specific for nucleolar autoantigens and a polyclonal increase in serum IgG1 and IgE. In this study, we observe that HgCl2 administration in susceptible mice results in the elevated production of B cell-activating factor of the TNF family ((BAFF) also known as BLyS, TALL-1, zTNF-4, THANK, and TNSF13B), a B cell growth factor belonging to the TNF family. A transmembrane activator and calcium-modulating and cyclophilin ligand interactor (TACI)-Ig fusion protein (which neutralizes both BAFF and a proliferation-inducing ligand (APRIL), another TNF family member) inhibited Hg-induced autoantibody or serum IgE production. These results are discussed in the context of the inhibitory effect of TACI-Ig on B cell maturation at the transitional stage.

Animals↗
PubMed2005

ICOS-B7 homologous protein interactions are necessary for mercury-induced autoimmunity.

After exposure to subtoxic doses of heavy metals such as mercury, H-2(s) mice develop an autoimmune syndrome consisting of the rapid production of IgG autoantibodies that are highly specific for nucleolar autoantigens and a polyclonal increase in serum IgG1 and IgE. In this study, we explore the role of one of the members of the CD28-B7 costimulation families, ICOS-B7 homologous protein (B7h), in the regulation of mercury-induced autoimmunity. The expression of ICOS on T cells was more enhanced in susceptible A.SW mice than in non-responsive C57BL/6 and DBA/2 mice after HgCl(2) treatment. Furthermore, in A.SW mice treated with HgCl(2), administration of a blocking anti-ICOS Ab effectively inhibited anti-nucleolar autoantibodies and total serum IgE production. Taken together, these results indicate that the ICOS-B7h costimulation pathway is required for this autoimmune syndrome and suggest that targeting this pathway might have therapeutic benefits for human autoimmune diseases.

Animals↗
PubMed2005

Analysis of synonymous codon usage bias in Chlamydia.

Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexually transmitted diseases, and are associated with cardiovascular diseases. The analysis of codon usage may improve our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of target genes to improve their expression for gene therapy. Here, we analyzed the codon usage of C. muridarum, C. trachomatis (here indicating biovar trachoma and LGV), C. pneumoniae, and C. psittaci using the codon usage database and the CUSP (Create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). The results show that the four genomes have similar codon usage patterns, with a strong bias towards the codons with A and T at the third codon position. Compared with Homo sapiens, the four chlamydial species show discordant seven or eight preferred codons. The ENC (effective number of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained by the G+C content, while translational selection and gene length exert relatively weaker influences. Moreover, mutational pressure appears to be the major determinant of the codon usage variation among the chlamydial genes. In addition, we compared the codon preferences of C. trachomatis with those of E. coli, yeast, adenovirus and Homo sapiens. There are 23 codons showing distinct usage differences between C. trachomatis and E. coli, 24 between C. trachomatis and adenovirus, 21 between C. trachomatis and Homo sapiens, but only six codons between C. trachomatis and yeast. Therefore, the yeast system may be more suitable for the expression of chlamydial genes. Finally, we compared the codon preferences of C. trachomatis with those of six eukaryotes, eight prokaryotes and 23 viruses. There is a strong positive correlation between the differences in coding GC content and the variations in codon bias (r=0.905, P<0.001). We conclude that the variation of codon bias between C. trachomatis and other organisms is much less influenced by phylogenetic lineage and primarily determined by the extent of disparities in GC content.

Animals↗
PubMed2005

Genotype-phenotype correlation between the polymorphic UGT2B17 gene deletion and NNAL glucuronidation activities in human liver microsomes.

The nicotine-derived tobacco-specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), is one of the most potent and abundant procarcinogens found in tobacco and tobacco smoke, and glucuronidation of its major metabolite, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), is an important mechanism for NNK detoxification. In cigarette smokers and tobacco chewers, there is a wide variation in the urinary levels of the ratio of NNAL to NNAL glucuronide (NNAL-Gluc). To determine whether genetic variation plays a potential role in this inter-individual variability, NNAL-glucuronidating activities were analysed in a series of human liver microsomal specimens and compared with UGT2B17 deletion genotypes in the same subjects. Assays performed in vitro demonstrated that over-expressed UGT2B17 exhibits high O-glucuronidating activity against NNAL. When stratifying subjects by UGT2B17 genotype, a significant or near-significant decrease in NNAL-O-Gluc formation was observed in liver microsomes from individuals who were either heterozygous [(+/0), P=0.07] or homozygous [(0/0), P=0.016] for the UGT2B17 deletion compared to liver microsomes from individuals with intact UGT2B17 alleles [(+/+)]. There was a significant (P<0.01) association between the level of liver microsomal NNAL-O-glucuronide formation and increasing numbers of the UGT2B17 null alleles in the liver microsomal specimens examined in this study, and a significant decrease in NNAL-O-Gluc formation was observed when comparing liver microsomes from individuals who had at least one UGT2B17 allele deleted [(+/0)+(0/0)] versus microsomes from UGT2B17 (+/+) subjects (P=0.004). When stratifying by the median value of NNAL-O-Gluc formation activity, a significantly (P=0.015) higher number of subjects with liver microsomes having low NNAL-O-Gluc formation activity contained the UGT2B17 null genotype compared to subjects with liver microsomes exhibiting high NNAL-O-Gluc formation activity. When stratifying by UGT2B7/UGT2B17 haplotypes, the association between the level of liver microsomal NNAL-O-glucuronide formation and increasing numbers of the UGT2B17 null allele was at the level of statistical significance for subjects with the UGT2B7 (*1/*2) (P=0.05) or UGT2B7 (*2/*2) (P<0.02) genotypes. These data suggest that the UGT2B17 deletion polymorphism is associated with a reduced rate of NNAL detoxification in vivo and may increase individual susceptibility to tobacco-related cancers.

Base Sequence↗
PubMed2005

[Deep neck abscess: analysis of 50 cases].

OBJECTIVE: To identify the predisposing factors of deep neck abscess and review diagnosis and treatment experience. METHODS: A respective review was conducted in 50 cases who were diagnosed as having deep neck abscess in this hospital from Jan. 1997 to Dec. 2002. RESULTS: The causes of deep neck abscess were tooth diseases (3 cases), acute tonsillitis and laryngitis (8 cases), infection of upper respiratory tract (9 cases), foreign bodies in esophagus (14 cases), diabetes mellitus (5 cases), uncertain cause (11 cases). Among 21 cases of pus bacterial cultivation, 13 (64%) cases were positive. By different ways of drainage including neck-mediastinum incision, and use of large dosage of antibiotics, 46 six cases were cured and 4 cases died. Two died of massive hemorrhage of neck blood vessel burst, one massive hemorrhage of upper digestive tract, another infective shock. CONCLUSIONS: Once deep neck abscess is diagnosed, early surgical drainage, appropriate use of antibiotics and control of complications and accompanying diseases are very important to improve the cure rate.

Adolescent↗