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Li SY, Tong MM, Li L, Hui F, Meng FZ, Zhao YL, Guo YM, Guo XY, Shi BL, Yan SM. Rectal microbiomes and serum metabolomics reveal the improved effect of Artemisia ordosica crude polysaccharides on the lactation performance, antioxidant and immune responses of lactating donkeys. J Dairy Sci 2024:S0022-0302(24)00741-0. [PMID: 38608958 DOI: 10.3168/jds.2023-24570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/02/2024] [Indexed: 04/14/2024]
Abstract
This study is aimed at investigating the effects of dietary supplementation with Artemisia ordosica crude polysaccharides (AOCP) on lactation performance, antioxidant status, and immune status of lactating donkeys and analyzing rectal microbiomes and serum metabolomes. Fourteen lactating Dezhou donkeys with similar age (6.16 ± 0.67 years of BW ± SD), weight (250.06 ± 25.18 kg), days in milk (39.11 ± 7.42 d), and averaged parity of 3 were randomly allocated into 2 treatments: a control group (CON, basal diet) and an AOCP group (AOCP, basal diet with 1.0 g/kg DM AOCP). Ten weeks were allotted for the experiment, 2 weeks for adaptation, and 8 weeks for collecting data and samples. The results showed that supplementation of donkey diets with AOCP increased lactation performance, including dry matter intake, milking yield, estimated milk yield, solids-corrected milk, energy-corrected milk, milk fat yield, milk protein yield, milk lactose yield, milk total solids yield, and milk solid not fat yield. The digestibility of dry matter, crude protein, acid detergent fiber, and neutral detergent fiber was increased in the AOCP group compared with the CON group. The AOCP group increased the concentrations of immunoglobulin A, immunoglobulin G, and immunoglobulin M, the activities of the superoxide dismutase, catalase and total antioxidant capacity in the serum. AOCP decreased the concentrations of tumor necrosis factor-α, nitric oxide, reactive oxygen species, and malondialdehyde in the serum. Compared with the CON group, AOCP increased propionate, butyrate, isovalerate, and total VFA concentrations in rectal feces (P < 0.05). The addition of AOCP to increased diversity (Shannon index) and altered structure of the rectal microflora. As a result of AOCP supplementation, there has been a significant improvement in the colonization of beneficial bacteria, including Lactobacillus, Unclassified_f_Prevotellacea, Ruminococcus, and Fibrobacter genera. In contrast, a decrease in the colonization of the Clostridium_sensu_stricto_1 bacterial genus and other pathogenic bacteria was observed. Meanwhile, metabolomics analysis found that AOCP supplementation upregulated metabolites L-tyrosine content while downregulating 9(S)-HODE, choline, sucrose, LysoPC (18:0), LysoPC (18:1(9Z), and LysoPC (20:2(11Z,14Z)) concentrations. These altered metabolites were involved in the PPAR signaling pathway, prolactin signaling pathway, glycerophospholipid metabolism, carbohydrate digestion and absorption, and tyrosine metabolism pathways, which were mainly related to antioxidant capacity, immune responses, and protein metabolism in the lactating donkeys. As a consequence of feeding AOCP diets, beneficial bacteria were abundant, and antioxidant and protein metabolism-related pathways were enriched, which may enhance lactation performance in donkeys. Therefore, supplementing AOCP diets is a desirable dietary strategy to improve donkey health and lactation performance.
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Affiliation(s)
- S Y Li
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - M M Tong
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - L Li
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - F Hui
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - F Z Meng
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - Y L Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - Y M Guo
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - X Y Guo
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - B L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Key Laboratory of Animal Nutrition and Feed Science at Universities of Inner Mongolia Autonomous Region, Hohhot, 010018, China
| | - S M Yan
- Contribution number: Basic Research Fund for Universities in Inner Mongolia Autonomous Region (Project No.BR22-13-13).
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DeGorter MK, Goddard PC, Karakoc E, Kundu S, Yan SM, Nachun D, Abell N, Aguirre M, Carstensen T, Chen Z, Durrant M, Dwaracherla VR, Feng K, Gloudemans MJ, Hunter N, Moorthy MPS, Pomilla C, Rodrigues KB, Smith CJ, Smith KS, Ungar RA, Balliu B, Fellay J, Flicek P, McLaren PJ, Henn B, McCoy RC, Sugden L, Kundaje A, Sandhu MS, Gurdasani D, Montgomery SB. Transcriptomics and chromatin accessibility in multiple African population samples. bioRxiv 2023:2023.11.04.564839. [PMID: 37986808 PMCID: PMC10659267 DOI: 10.1101/2023.11.04.564839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.
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Affiliation(s)
| | - Page C Goddard
- Department of Genetics, Stanford University, Stanford, CA
| | - Emre Karakoc
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Soumya Kundu
- Department of Computer Science, Stanford University, Stanford CA
| | | | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA
| | - Nathan Abell
- Department of Genetics, Stanford University, Stanford, CA
| | - Matthew Aguirre
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Tommy Carstensen
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Ziwei Chen
- Department of Computer Science, Stanford University, Stanford CA
| | | | | | - Karen Feng
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | | | - Naiomi Hunter
- Department of Genetics, Stanford University, Stanford, CA
| | | | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Kevin S Smith
- Department of Pathology, Stanford University, Stanford, CA
| | - Rachel A Ungar
- Department of Genetics, Stanford University, Stanford, CA
| | - Brunilda Balliu
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA and Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland and Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Paul Flicek
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Canada and Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Brenna Henn
- Department of Anthropology, University of California Davis, Davis CA and Genome Center, University of California Davis, Davis CA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore
| | - Lauren Sugden
- Department of Mathematics and Computer Science, Dusquesne University, Pittsburgh, PA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA
- Department of Computer Science, Stanford University, Stanford CA
| | | | - Deepti Gurdasani
- William Harvey Research Institute, Queen Mary University of London, London, UK; Kirby Institute, University of New South Wales, Australia; School of Medicine, University of Western Australia, Australia
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DeBoy EA, Tassia MG, Schratz KE, Yan SM, Cosner ZL, McNally EJ, Gable DL, Xiang Z, Lombard DB, Antonarakis ES, Gocke CD, McCoy RC, Armanios M. Familial Clonal Hematopoiesis in a Long Telomere Syndrome. N Engl J Med 2023; 388:2422-2433. [PMID: 37140166 PMCID: PMC10501156 DOI: 10.1056/nejmoa2300503] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Telomere shortening is a well-characterized cellular aging mechanism, and short telomere syndromes cause age-related disease. However, whether long telomere length is advantageous is poorly understood. METHODS We examined the clinical and molecular features of aging and cancer in persons carrying heterozygous loss-of-function mutations in the telomere-related gene POT1 and noncarrier relatives. RESULTS A total of 17 POT1 mutation carriers and 21 noncarrier relatives were initially included in the study, and a validation cohort of 6 additional mutation carriers was subsequently recruited. A majority of the POT1 mutation carriers with telomere length evaluated (9 of 13) had long telomeres (>99th percentile). POT1 mutation carriers had a range of benign and malignant neoplasms involving epithelial, mesenchymal, and neuronal tissues in addition to B- and T-cell lymphoma and myeloid cancers. Five of 18 POT1 mutation carriers (28%) had T-cell clonality, and 8 of 12 (67%) had clonal hematopoiesis of indeterminate potential. A predisposition to clonal hematopoiesis had an autosomal dominant pattern of inheritance, as well as penetrance that increased with age; somatic DNMT3A and JAK2 hotspot mutations were common. These and other somatic driver mutations probably arose in the first decades of life, and their lineages secondarily accumulated a higher mutation burden characterized by a clocklike signature. Successive generations showed genetic anticipation (i.e., an increasingly early onset of disease). In contrast to noncarrier relatives, who had the typical telomere shortening with age, POT1 mutation carriers maintained telomere length over the course of 2 years. CONCLUSIONS POT1 mutations associated with long telomere length conferred a predisposition to a familial clonal hematopoiesis syndrome that was associated with a range of benign and malignant solid neoplasms. The risk of these phenotypes was mediated by extended cellular longevity and by the capacity to maintain telomeres over time. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Emily A DeBoy
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Michael G Tassia
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Kristen E Schratz
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Stephanie M Yan
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Zoe L Cosner
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Emily J McNally
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Dustin L Gable
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Zhimin Xiang
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - David B Lombard
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Emmanuel S Antonarakis
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Christopher D Gocke
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Rajiv C McCoy
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Mary Armanios
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
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Yan SM, Huang YF, Xu L, Dong XY, Wang S, Jiao X, Yuan M, Wang GY. Escherichia coli inhibits endometriosis by inducing M1 polarity of peritoneal macrophages and the IL-1 signaling pathway. Mol Hum Reprod 2023:7133754. [PMID: 37079746 DOI: 10.1093/molehr/gaad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/28/2023] [Indexed: 04/22/2023] Open
Abstract
The development of endometriosis is closely linked to macrophages, and the type M1 macrophage has been hypothesized to play an inhibitory role in its progression. Escherichia coli induces macrophage polarization toward M1 in numerous diseases and differs in the reproductive tract of patients with and without endometriosis; however, its specific role in endometriosis development remains unknown. Therefore, in this study, E. coli was selected as a stimulator to induce macrophages, and its effects on the growth of endometriosis lesions in vitro and in vivo were investigated using C57BL/6N female mice and endometrial cells. It was revealed that E. coli inhibited the migration and proliferation of co-cultured endometrial cells by IL-1 in vitro and prevented the growth of lesions and induced macrophage polarization toward M1 in vivo. However, this change was counteracted by C-C motif chemokine receptor 2 inhibitors, suggesting that it was associated with bone marrow-derived macrophages. Overall, the presence of E. coli in the abdominal cavity may be a protective factor for endometriosis.
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Affiliation(s)
- S M Yan
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - Y F Huang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - L Xu
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - X Y Dong
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - S Wang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - X Jiao
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - M Yuan
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
| | - G Y Wang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250014, China
- Gynecology Laboratory, Shandong Provincial Hospital, Jinan, Shandong, 250021, China
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5
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Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. A complete reference genome improves analysis of human genetic variation. Science 2022; 376:eabl3533. [PMID: 35357935 DOI: 10.1126/science.abl3533] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.
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Affiliation(s)
- Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Stephanie M Yan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela C Soto
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Avdeyev
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Justin Wagner
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jennifer McDaniel
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nathan D Olson
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Melissa Meredith
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Skylar Martin
- Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Sergey Koren
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ryan Layer
- Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, National Human Genome Research Institute, Rockville, MD, USA
| | - Danny E Miller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Megan Y Dennis
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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6
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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022; 376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 894] [Impact Index Per Article: 447.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
| | - Lev Uralsky
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | | | | | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Shelise Y. Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | | | | | | | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Richard Durbin
- Wellcome Sanger Institute; Cambridge, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | | | - Giulio Formenti
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Robert S. Fulton
- Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
| | | | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- University of Tennessee Health Science Center; Memphis, TN, USA
| | - Patrick G.S. Grady
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | | | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
| | - Nancy F. Hansen
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | | | - Chirag Jain
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
- Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | - Valerie V. Maduro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Danny E. Miller
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
| | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Eugene W. Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
| | - Nathan D. Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research; Kansas City, MO, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
| | | | - Steven L. Salzberg
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Ying Sims
- Wellcome Sanger Institute; Cambridge, UK
| | | | - Daniela C. Soto
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan Sović
- Pacific Biosciences; Menlo Park, CA, USA
- Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
| | | | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | | | - Justin Wagner
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | | | | | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Stephanie M. Yan
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Alice C. Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan A. Alexandrov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research; Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
| | - Rachel J. O’Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
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7
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Xing YY, Zheng YK, Yang S, Zhang LH, Guo SW, Shi LL, Xu YQ, Jin X, Yan SM, Shi BL. Artemisia ordosica Polysaccharide Alleviated Lipopolysaccharide-induced Oxidative Stress of Broilers via Nrf2/Keap1 and TLR4/NF-κB Pathway. Ecotoxicol Environ Saf 2021; 223:112566. [PMID: 34340153 DOI: 10.1016/j.ecoenv.2021.112566] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/08/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Artemisia ordosica is one of the main shrubby perennials belonging to Artemisia species of Asteraceae and could be used in folk Chinese/Mongolian medicine to treat symptoms of various inflammatory ailments. The present study was conducted to investigate the protective effects of dietary Artemisia ordosica polysaccharide (AOP) against lipopolysaccharide (LPS) induced oxidative stress in broilers via Nrf2/Keap1 and TLR4/NF-κB pathway. A total of 192 1-day-old Arbor Acres male broilers were randomly allotted to four treatments with 6 replicates (n = 8): (1) CON group, non-challenged broilers fed basal diet; (2) LPS group, LPS-challenged broilers fed basal diet; (3) AOP group, non-challenged broilers fed basal diet supplemented with 750 mg/kg AOP; (4) LPS+AOP group, LPS-challenged broilers fed basal diet supplemented with 750 mg/kg AOP. The trial included starter phase (d 1-14), stress period Ⅰ (d 15-21), convalescence Ⅰ (d 22-28), stress period Ⅱ (d 29-35) and convalescence Ⅱ (d 36-42). During stress period Ⅰ (on d 15, 17, 19 and 21) and stress period Ⅱ (on d 29, 31, 33 and 35), broilers were injected intra-abdominally either with LPS solution or with an equal amount of sterile saline. The results showed that dietary AOP supplementation alleviated LPS-induced reduction in antioxidant enzyme activity and excessive production of ROS, 8-OHdG and PC in serum of broilers challenged with LPS. Moreover, dietary AOP supplementation alleviated the decrease of T-AOC and activities of SOD, CAT and GPx in liver of broilers challenged with LPS by increasing expression of Nrf2, and inhibiting over-expression of Keap1 both at gene and protein level. Additionally, dietary AOP supplementation decreased the over-production of IL-1β and IL-6 in liver of broilers challenged by LPS through decreasing mRNA expression of TLR4, MyD88, NF-κB P65, IL-1β and IL-6, and alleviating the increase of protein expression of TLR4, IKKβ, NF-κB P65, IL-1β, IL-6, and the decrease of protein expression of IkBα. In conclusion, dietary AOP supplementation could alleviate LPS-induced oxidative stress through Nrf2/Keap1 and TLR4/NF-κB pathway.
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Affiliation(s)
- Y Y Xing
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Y K Zheng
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - S Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - L H Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - S W Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - L L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Y Q Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - X Jin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - S M Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - B L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China.
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8
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Yan SM, Sherman RM, Taylor DJ, Nair DR, Bortvin AN, Schatz MC, McCoy RC. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife 2021; 10:e67615. [PMID: 34528508 PMCID: PMC8492059 DOI: 10.7554/elife.67615] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.
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Affiliation(s)
- Stephanie M Yan
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Rachel M Sherman
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Divya R Nair
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Andrew N Bortvin
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
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9
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Liu KF, Xue Y, Lu CY, Zhang XF, Yan SM, Kang J, Zhao J. [A dose-response meta-analysis on the relationship between daily tea intake and cardiovascular mortality based on the GRADE system]. Zhonghua Xin Xue Guan Bing Za Zhi 2021; 49:496-502. [PMID: 34034384 DOI: 10.3760/cma.j.cn112148-20200726-00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the relationship between daily tea intake and cardiovascular disease (CVD) mortality. Methods: PubMed, EMbase, The Cochrane, Chinese Biomedical Literature Database, CNKI, and Wanfang Database were searched to collect research on tea intake and CVD mortality. The search period was from the establishment of the database to June 2020. Two researchers independently screened and extracted literature. The risk of bias was evaluated in the included studies, a dose-response meta-analysis was conducted, sensitivity analysis and publication bias analysis of the research results, and quality evaluation of the included literature and GRADE classification of the evidence body were performed. Results: A total of 21 cohort or case-control studies were included, including 1 304 978 subjects. Among them, 38 222 deaths from CVD were reported. The quality scores of the included studies were all ≥ 6 points. The dose-response meta-analysis showed that for every additional cup of tea intake per day, the mortality rate of CVD decreased by about 3% (95%CI 0.95-0.98, P<0.05), and there was a non-linear dose-response relationship (P<0.05). Compared with people who do not drink tea, people who drink 1 to 8 cups of tea a day have 8% lower CVD mortality (RR=0.92, 95%CI 0.89-0.95), 13% (RR=0.87, 95 %CI 0.84-0.91), 15% (RR=0.85, 95%CI 0.82-0.89), 15% (RR=0.85, 95%CI 0.81-0.89), 16% (RR=0.84, 95%CI 0.80-0.89), 16% (RR=0.84, 95%CI 0.81-0.88), 16% (RR=0.84, 95%CI 0.81-0.87), 16% (RR=0.84, 95%CI 0.80-0.88), respectively. The results of traditional meta-analysis showed that compared with people who do not drink tea, people who drink more than 1 cup of tea a day are associated with 14% lower CVD mortality rate (RR=0.86, 95%CI 0.81-0.91, I2=73.2%, P<0.05). The results of subgroup analysis showed that compared with the corresponding people who did not drink tea, men who drank more than 1 cup of tea a day reduced the CVD mortality rate by 24%, women by 14%, European and American populations by 12%, and Asian populations by 15%. The population who consumed green tea decreased CVD mortality by 15%, and the population of non-smokers decreased CVD mortality by 20% (all P<0.05). The population who consumed black tea decreased CVD mortality by 8%, and the smoking population who consumed black tea decreased CVD mortality by 3%, and the difference was not statistically significant (all P>0.05). The results of the bias analysis showed that Begg=0.42 and Egger=0.62, indicating that the distribution on both sides of the funnel chart is symmetrical, suggesting that there is no publication bias. The results of sensitivity analysis showed that the effect size of the outcome index did not change significantly after excluding any article, indicating that the results are robust and credible. The GRADE evaluation showed that the evidence grades of the outcome indicators were all low grade. Conclusions: Daily tea consumption is related to reduced CVD mortality. It is therefore recommended to drink an appropriate amount of tea daily.
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Affiliation(s)
- K F Liu
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y Xue
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - C Y Lu
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - X F Zhang
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - S M Yan
- Department of Cardiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - J Kang
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - J Zhao
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Yan SM, McCoy RC. Archaic hominin genomics provides a window into gene expression evolution. Curr Opin Genet Dev 2020; 62:44-49. [PMID: 32615344 PMCID: PMC7483639 DOI: 10.1016/j.gde.2020.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/08/2023]
Abstract
Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.
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Affiliation(s)
- Stephanie M Yan
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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11
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Zhao YL, Yan SM, Beauchemin KA, Yang WZ. Feeding diets varying in forage proportion and particle length to lactating dairy cows: II. Effects on duodenal flows and intestinal digestibility of amino acids. J Dairy Sci 2020; 103:4355-4366. [PMID: 32113766 DOI: 10.3168/jds.2019-17607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022]
Abstract
A study was conducted to evaluate the effects of forage-to-concentrate (F:C) ratio and forage particle length (FPL) on intake, duodenal flow, and digestibility of individual AA in the intestine of lactating dairy cows. The experiment was designed as a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments using 4 lactating dairy cows (parity 2) with ruminal and duodenal cannulas. Low (35:65) and high (60:40) F:C ratios (dry matter basis) were combined with 2 FPL of alfalfa silage (short vs. long; 7.9 vs. 19.1 mm). Few interactions between F:C and FPL for duodenal flow and intestinal digestibility of AA occurred, but interactions were detected for intakes of several AA. Intake of essential AA and nonessential AA decreased with increasing F:C, and the intake of several individual AA increased or decreased with increasing FPL. Increasing F:C decreased duodenal flows of essential AA, nonessential AA, and microbial AA due to consistent decreased flows of most individual AA (except Glu). Degradability of most individual AA in the rumen was not affected by F:C ratio or FPL except that the degradability of His was greater with high than low F:C diets, and the degradability of Ser was greater with long versus short FPL diets. However, the degradability of individual AA within diet varied considerably. Overall, F:C ratio and FPL did not affect intestinal digestibility of AA and rumen undegradable protein AA, whereas the digestibility of individual AA in the intestine varied considerably regardless of dietary treatment. These results indicate that increasing F:C ratio decreased AA supply due to decreased flow of AA to the duodenum but altering FPL did not affect AA supply. The results also revealed the necessity to consider both the flows and digestibility of individual AA when optimizing ration formulation to meet AA requirements of dairy cows.
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Affiliation(s)
- Y L Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China; Agriculture and Agri-Food Canada, Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - S M Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - K A Beauchemin
- Agriculture and Agri-Food Canada, Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - W Z Yang
- Agriculture and Agri-Food Canada, Research Centre, Lethbridge, AB, T1J 4B1, Canada.
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12
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Shi HY, Yan SM, Guo YM, Zhang BQ, Guo XY, Shi BL. Vitamin A pretreatment protects NO-induced bovine mammary epithelial cells from oxidative stress by modulating Nrf2 and NF-κB signaling pathways. J Anim Sci 2018; 96:1305-1316. [PMID: 29669072 DOI: 10.1093/jas/sky037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/09/2018] [Indexed: 12/16/2022] Open
Abstract
It is known that physiological overproduction of nitric oxide (NO) contributes to oxidative stress and inflammation. Our published studies indicated that vitamin A (VA) reduces NO-induced oxidative stress in bovine mammary epithelial cells (BMECs) by increasing antioxidant enzyme activities. However, the precise mechanism is unclear. The present study was conducted to examine the protective effects of VA on NO-induced damage to BMECs in vitro using diethylenetriamine nitric oxide (DETA-NO) as the NO donor and to explore the intracellular signaling mechanisms of VA that involve nuclear factor erythroid 2-related factor (Nrf2) and nuclear factor kappa-B (NF-κB). Subconfluent BMECs were divided into 10 treatment groups with 6 replicates per treatment and were cultured with dimethyl sulfoxide (DMSO, vehicle negative control) or 0, 0.05, 0.1, 0.2, 0.5, 1, 2, 3, or 4 μg/mL of VA for 24 h and then incubated in the absence or presence of DETA-NO (1,000 μmol/liter) and VA for an additional 6 h. The results showed that exposure to DETA alone decreased cell proliferation compared with the negative control. Pretreatment with VA promoted the proliferation of BMECs, increased the activities of antioxidative enzymes including selenoprotein glutathione peroxidase (GPx) and thioredoxin reductase (TrxR) and their gene and protein expression but decreased NO and interleukin 1 (IL-1) contents in a quadratic manner (P < 0.05). In addition, the expression of mRNA and protein of factors that are related to NF-κB or Nrf2 signaling pathways in BMECs were regulated by VA in a quadratic dose-dependent manner; VA at a concentration of 1 μg/mL exhibited the strongest effect. Together, these results suggest that VA promotes antioxidant functions of BMECs by regulating the synthesis of selenoproteins including GPx and TrxR and by reducing concentrations of IL-1 and NO in vitro by modulating Nrf2 and NF-κB signaling pathways.
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Affiliation(s)
- H Y Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - S M Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Y M Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - B Q Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - X Y Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - B L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, P.R. China
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13
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Xu YQ, Xing YY, Wang ZQ, Yan SM, Shi BL. Pre-protective effects of dietary chitosan supplementation against oxidative stress induced by diquat in weaned piglets. Cell Stress Chaperones 2018; 23:703-710. [PMID: 29455342 PMCID: PMC6045548 DOI: 10.1007/s12192-018-0882-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/20/2018] [Accepted: 01/26/2018] [Indexed: 02/06/2023] Open
Abstract
The protective effects of chitosan (CS) supplementations on oxidative stress induced by diquat in weaned piglets were investigated. A total of 36 crossbreed piglets with an average live body weight (BW) of 8.80 ± 0.53 kg were weaned at 28 ± 2 days and randomly divided into six dietary treatments (n = 6): control (basal diet), negative control (10 mg diquat/kg BW injected to piglets fed with basal diet), and basal diet treatments containing either 250, 500, 1000, or 2000 mg/kg of CS administered to piglets injected with 10 mg diquat/kg BW. The experiment conducted for 21 days which consisted of pre-starter period (14 days) and starter period (7 days). BW, feed intake, and fecal consistency were monitored. Blood samples were collected to determine antioxidative and immune parameters. CS supplementation improved the growth performance and decreased fecal score of piglets from days 1 to 14. Diquat also induced oxidative stress and inflammatory responses by decreasing the activities of antioxidant and regulating cytokines. But dietary CS alleviated these negative effects induced by diquat that showed decreasing serum concentrations of pro-inflammatory cytokines but increasing activities of antioxidant enzymes and anti-inflammatory cytokines. Results indicated that CS attenuated the oxidative stress of piglets caused by diquat injection.
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Affiliation(s)
- Y Q Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Y Y Xing
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Z Q Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - S M Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - B L Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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14
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Zheng HL, Yan SM, Hu DH, Zhang X, Zhang YT, Guan QH, Ding QL. Extracellular redox state regulates catecholamine biosynthesis in PC12 cells with insulin resistance. Horm Metab Res 2014; 46:412-8. [PMID: 24806749 DOI: 10.1055/s-0034-1374613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Extracellular cysteine (Cys)/cystine (CySS) redox potential (Eh) plays a crucial role in maintaining redox homeostasis and an alteration of redox state occurs in various physiological conditions, including diabetes, cancer, and aging. This study was designed to determine whether a variation in extracellular redox state would alter the function of insulin-resistant PC12 cells. Various redox states were established by providing different extracellular Cys/CySS Eh to insulin-resistant PC12 cells. We intensively investigated the relationship between redox state and catecholamine biosynthesis in PC12 cells, and evaluated the changes in cellular reactive oxygen species (ROS), catecholamine (CA) synthesis, tyrosine hydroxylase (TH) expressions, and the activity of rate-limiting enzyme in CA synthesis by using DCF-fluorescence, HPLC, and the real-time PCR, respectively. We also determined the protein levels of NF-E2-related factor 2 (Nrf2), a redox sensitive transcription factor, using an ELISA assay. We found that the oxidized Cys/CySS Eh (0 mV) pretreatment decreased CA, TH, and Nrf2 levels, but induced ROS overproduction. Insulin induced a significant increase in CA synthesis and ROS production, blocked by more reducing redox conditions. The paradox of CA and TH alterations between insulin and 0 mV groups may be attributed to degree of redox imbalance as evidenced by different ROS levels in 2 groups, which is further confirmed by CA alterations in different concentrations of hydrogen peroxide. Additionally, dithiole-3-thione (D3T, an inducer of Nrf2) corrected 0 mV-induced TH inhibition. In conclusion, CA biosynthesis in insulin-resistant PC12 cells could be influenced by extracellular Cys/CySS redox effects on cellular redox sensitive transcription factors.
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Affiliation(s)
- H L Zheng
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - S M Yan
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - D H Hu
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - X Zhang
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - Y T Zhang
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - Q H Guan
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
| | - Q L Ding
- Experimental and Teaching Center of Medical Basis for Pharmacy, China, Pharmaceutical University, Nanjing, Jiangsu, China
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15
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Zhang X, Yan SM, Zheng HL, Hu DH, Zhang YT, Guan QH, Ding QL. A mechanism underlying hypertensive occurrence in the metabolic syndrome: cooperative effect of oxidative stress and calcium accumulation in vascular smooth muscle cells. Horm Metab Res 2014; 46:126-32. [PMID: 24108391 DOI: 10.1055/s-0033-1355398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several lines of evidence indicate that reactive oxygen species (ROS) overproduction under the metabolic syndrome condition is the leading cause of cardiovascular events. Calcium is an important stimulus for vasoconstriction and plays a pivotal role in the development of hypertension. Here, we investigate whether a relationship exists between metabolic syndrome-induced mitochondrial ROS overproduction and Ang II-mediated Ca2+ release in vascular smooth muscle cells (VSMC). The effect of mitochondrial ROS on AT1 expression, and Ca2+ and IP3 generation was studied in 2 VSMC models of metabolic syndrome using fura-2/AM probes and ELISA-based assay. Ang II-mediated aortic ring contraction in SD rats fed with high-fat diet (HFD) was measured using a force transducer connected to chart recorder. In the metabolic syndrome, almost 2-fold increased mitochondrial O2 - significantly upregulated AT1 expressions by ~60%, companied by elevated Ca2+ and IP3 levels in VSMC and enhanced aortic rings contraction. All these increments were blocked by rotenone (inhibitor of mitochondrial respiratory chain complex I), ruthenium red (inhibitor of calcium uniporter), cyclosporin A (inhibitor of mitochondrial permeability pore), and N-acetylcysteine. Therefore, in the states of metabolic syndrome, ROS overproduction in mitochondrial complex I enhances Ang II-mediated vascular contraction via an AT1-dependent pathway. In addition, the import of Ca2+ from endoplasmic reticulum to mitochondria via calcium uniporter and mitochondrial permeability pore seems to serve as a mechanism to further aggravate mitochondrial damage and vascular dysfunction that may contribute to the occurrence of hypertension.
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Affiliation(s)
- X Zhang
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - S M Yan
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - H L Zheng
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - D H Hu
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Y T Zhang
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Q H Guan
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Q L Ding
- Experimental and Teaching Center of Medical Basis for Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
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Abstract
1. Two experiments were conducted to investigate the effects of dietary chitosan on growth performance, energy availability and protein retention in broilers. 2. Experiment 1 was a 42-d growth assay, in which 294 1-d-old male broilers were given one of 7 dietary treatments. A control feed was supplemented with 5 levels of chitosan (0.2, 0.5, 1.0, 3.0 and 5.0 g/kg) or 50 mg/kg chlortetracycline (CTC). 3. Increasing chitosan inclusion gave a nonlinear increase (P< 0.001) in feed conversion efficiency (FCE). Optimal growth and feed conversion were obtained with 0.5-1.0 g/kg chitosan. 4. In experiment 2, 42 1-d-old male broilers (6/treatment) were individually housed but fed on the same diets as in experiment 1. Excreta were collected from d 19-21 and d 40-42. 5. The addition of 0.5-1.0 g/kg chitosan increased nitrogen retention compared with the control group (P< 0.01), while apparent metabolisable energy in the diets was not altered.
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Affiliation(s)
- B L Shi
- China Agricultural University, National Feed Engineering Technology Research Center, Beijing, China
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Beltrami AP, Urbanek K, Kajstura J, Yan SM, Finato N, Bussani R, Nadal-Ginard B, Silvestri F, Leri A, Beltrami CA, Anversa P. Evidence that human cardiac myocytes divide after myocardial infarction. N Engl J Med 2001; 344:1750-7. [PMID: 11396441 DOI: 10.1056/nejm200106073442303] [Citation(s) in RCA: 1073] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The scarring of the heart that results from myocardial infarction has been interpreted as evidence that the heart is composed of myocytes that are unable to divide. However, recent observations have provided evidence of proliferation of myocytes in the adult heart. Therefore, we studied the extent of mitosis among myocytes after myocardial infarction in humans. METHODS Samples from the border of the infarct and from areas of the myocardium distant from the infarct were obtained from 13 patients who had died 4 to 12 days after infarction. Ten normal hearts were used as controls. Myocytes that had entered the cell cycle in preparation for cell division were measured by labeling of the nuclear antigen Ki-67, which is associated with cell division. The fraction of myocyte nuclei that were undergoing mitosis was determined, and the mitotic index (the ratio of the number of nuclei undergoing mitosis to the number not undergoing mitosis) was calculated. The presence of mitotic spindles, contractile rings, karyokinesis, and cytokinesis was also recorded. RESULTS In the infarcted hearts, Ki-67 expression was detected in 4 percent of myocyte nuclei in the regions adjacent to the infarcts and in 1 percent of those in regions distant from the infarcts. The reentry of myocytes into the cell cycle resulted in mitotic indexes of 0.08 percent and 0.03 percent, respectively, in the zones adjacent to and distant from the infarcts. Events characteristic of cell division--the formation of the mitotic spindles, the formation of contractile rings, karyokinesis, and cytokinesis--were identified; these features demonstrated that there was myocyte proliferation after myocardial infarction. CONCLUSIONS Our results challenge the dogma that the adult heart is a postmitotic organ and indicate that the regeneration of myocytes may be a critical component of the increase in muscle mass of the myocardium.
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Affiliation(s)
- A P Beltrami
- Department of Medicine, New York Medical College, Valhalla 10595, USA
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You J, Zhuang L, Tang BZ, Yang WB, Ding SY, Li W, Wu RX, Zhang HL, Zhang YM, Yan SM, Zhang L. A randomized controlled clinical trial on the treatment of Thymosin a1 versus interferon-alpha in patients with hepatitis B. World J Gastroenterol 2001; 7:411-4. [PMID: 11819801 PMCID: PMC4688733 DOI: 10.3748/wjg.v7.i3.411] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2000] [Revised: 06/23/2000] [Accepted: 07/29/2000] [Indexed: 02/06/2023] Open
Affiliation(s)
- J You
- Department of Infectious Diseases, The First Affiliated Hospital of Kunming Medical College, 153# Xi Chang Road, Kunming 650032, Yunnan Province, China
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Abstract
Different cyclosporine concentration zones can exist in plasma due to the temperature dependency in distribution and association, therefore cyclosporine therapeutic and toxic effects may partially be related to these concentration zones.
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Affiliation(s)
- G Wu
- Faculty of Pharmacy, University of Mediterranean, 27 Jean Moulin, Marseilles, Cedex 05, 13385, France
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Wu G, Yan SM. Prediction of two- and three-amino-acid sequences of Citrobacter Freundii beta-lactamase from its amino acid composition. J Mol Microbiol Biotechnol 2000; 2:277-81. [PMID: 10937436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The repeated amino-acid sequences in Citrobacter Freundii beta-lactamase may be indispensable for its function, because such repetitions cannot be simply attributed to a chance. In order to fully explore the functional units in Citrobacter Freundii beta-lactamase, it may need to analyse all the amino acid pairs, triplets, etc. along Citrobacter Freundii beta-lactamase from one terminal to the other terminal, to count their frequencies and calculate their probabilities. The amino-acid sequence of Citrobacter Freundii beta-lactamase was counted according to two-, three- and four-amino-acid sequences. The counted frequency and probability were compared with the predicted frequency and probability. The amino acid sequences, which appear in Citrobacter Freundii beta-lactamase and can be predicted from its amino acid composition according to a purely random mechanism, should not be deliberately evolved and conserved. By contrast, the amino acid sequences, which appear in Citrobacter Freundii beta-lactamase but cannot be predicted from its amino acid composition according to a purely random mechanism, should be deliberately evolved and conversed. Accordingly 99 (26.053%) and 33 (8.684%) of 380 two-amino-acid sequences can be predicted by the frequency and probability according to a purely random mechanism. Some kinds of amino acid sequences, which absent in Citrobacter Freundii beta-lactamase and can be predicted from its amino acid composition according to a purely random mechanism, should not be deliberately excluded from Citrobacter Freundii beta-lactamase. By contrast, some kinds of amino acid sequences, which absent in Citrobacter Freundii beta-lactamase and cannot be predicted from its amino acid composition according to a purely random mechanism, should be deliberately excluded from Citrobacter Freundii beta-lactamase. Accordingly 89 (48.370%) and 41 (22.283%) of 184 kinds of absent two-amino-acid sequences can be predicted by the frequency and probability according to a purely random mechanism, and 7236 (99.848%) of 7247 kinds of absent three-amino-acid sequences can be predicted by the frequency according to a purely random mechanism. The amino acids, whose probabilities in following certain preceding amino acids can be predicted from Citrobacter Freundii beta-lactamase amino acid composition according to a purely random mechanism, should not be deliberately evolved and conversed, accordingly 2 (0.526%) of 380 counted first order Markov transition probabilities for the second amino acid in two-amino-acid sequences match the predicted conditional probabilities.
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Affiliation(s)
- G Wu
- Laboratoire de Toxicocinétique et Pharmacocinétique, Faculté de Pharmacie, Université de la Méditerranée Aix-Marseille II, France.
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Yan SM, Finato N, Di Loreto C, Beltrami CA. Nuclear size of myocardial cells in end-stage cardiomyopathies. Anal Quant Cytol Histol 1999; 21:174-80. [PMID: 10560488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
OBJECTIVE To determine the alteration of nuclear size in myocardial cells and the relationship between nuclear size and DNA ploidy classes in normal and cardiomyopathic human hearts. STUDY DESIGN The study group consisted of 46 hearts obtained at biopsy. These patients had undergone cardiac transplantation for intractable congestive heart failure (18 cases with ischemic cardiomyopathy and 28 cases with idiopathic dilated cardiomyopathy). Another 10 hearts were collected at autopsy and used as control hearts according to preautopsy, autopsy and histology criteria. One hundred fibroblasts and 200 myocytes were evaluated in each ventricle. The nuclear area and DNA content were estimated using image cytometry. RESULTS End-stage ischemic and dilated cardiomyopathies were characterized by an increase in nuclear size of both the myocyte and nonmyocyte population. The nuclear area of interstitial cells increased about 30% in cardiomyopathic hearts. Augmentation of average nuclear area of myocytes was 1.2-fold in the ischemic group and about 1.5-fold in the dilated group as compared with the control group. Also, a tendency was found for the coefficient of variation of average nuclear area to decrease in the interstitial cell population and increased in the myocyte population in cardiomyopathic situations. Furthermore, the nuclear area of myocytes enlarged as augmentation of nuclear DNA content. The relative nuclear areas of myocytes can be presented as: 2c:4c:8c:16c :32c:64c = 1:1.65:2.75:4.60:7.25:9.18. CONCLUSION The increase in nuclear size follows either one of two different processes: the first does not involve an increase in DNA content, whereas the second is concomitant with an incremental increase in DNA content. In the first instance, the enlargement of nuclear size is limited. In the second, augmentation of nuclear size can become very impressive. In end-stage ischemic and dilated cardiomyopathies, the nuclear growth of myocytes and interstitial cells may be due to different mechanisms. Enlargement of the nuclear area of myocytes represents a complex process, including simple nuclear hypertrophy, polyploidization and multinucleation. The main pattern of nuclear growth of interstitial cells is nuclear hypertrophy without an increase in DNA content.
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Affiliation(s)
- S M Yan
- Department of Pathology, University of Udine, Italy
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Yan SM, Guerra S, Finato N, Di Loreto C, Beltrami CA. Changes in DNA content of myocardial cells after cardiac explantation. Adv Clin Path 1999; 3:23-7. [PMID: 10655570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
To evaluate the changes in DNA content of myocardial cells, image cytometric measurement was performed on a series of specimens obtained from 7 explanted hearts with respect to different fixation times after cardiac explantation. Prior to fixation, the tissue samples were stored at 4 degrees C or at room temperature. When the tissue samples were stored at room temperature, the integrated optical density decreased after 48 hours from cardiac explantation. Meanwhile, the coefficient of variation of integrated optical density and the sum of intermediate ploidies of myocyte nuclei increased. However, no significant changes were found when tissue samples were kept at 4 degrees C. This study indicates that no significant changes in DNA content are found within two days from cardiac explantation.
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Affiliation(s)
- S M Yan
- Department of Anatomical Pathology, University of Udine, Udine, 33100, Italy
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Yan SM, Zhang YP, Liu DC. [Survey of heterophoria of 1500 normal male youth]. Zhonghua Hu Li Za Zhi 1995; 30:663-4. [PMID: 8715948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Liu AN, Yan SM. [Study and application of "binocular aniseikonia test chart"]. Zhonghua Yan Ke Za Zhi 1994; 30:348-50. [PMID: 7805536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the help of this chart, the image incongruity of simultaneous perception, fusion and stereoscopic vision can be precisely determined. It can objectively evaluate the binocular visual function and possesses important significance for the diagnosis and treatment of anisometropia, amblyopia, strabismus and visual fatigue.
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Affiliation(s)
- A N Liu
- Department of Ophthalmology, Navy General Hospital, Beijing
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Yan SM, Li LL, Yu SR, Xiao PG. [Effect of tabellae Polygoni cuspidati on blood lipids and rheological property in rats]. Zhongguo Zhong Yao Za Zhi 1993; 18:617-9, 640. [PMID: 8003218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- S M Yan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing
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Yan SM, Pan GF, Zou ZY. [Clinical analysis of CT image in 112 adult patients with tuberculous meningitis]. Zhonghua Jie He He Hu Xi Za Zhi 1993; 16:267-9, 318. [PMID: 7923427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Analysis of CT image in 112 patients with tuberculous meningitis, abnormal findings were shown in 80.4% cases. They were tuberculoma, hydrocephalus, basal cistern exudation, cerebral embolism, brain atrophy, miliary nodules, tuberculous abscesses and etc. Tuberculoma, hydrocephalus and basal cistern exudation are common changes in patients of cerebromeningitis type. Basal cistern exudation is the main image in early stage patients. Hydrocephalus occurred in patients of chronic stage. Manifold lesions occurred in late stage patients. The longer the disease course, the more is the abnormal finding rate by CT image. The prognosis of patients with normal CT image is good, the patients with manifold lesions are worse than those patients with single lesion by CT image, and sequelae developed more frequently in those patients with manifold lesions.
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Affiliation(s)
- S M Yan
- Changchun Tuberculosis Hospital
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Yan SM. [Clinical study on thyroid hormone levels in tuberculous patients]. Zhonghua Jie He He Hu Xi Za Zhi 1991; 14:298-300, 320. [PMID: 1819384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The article reported the results of serum total thyroxine (TT4), triiodothyronine (TT3), reverse triiodothyronine (rT3), triiodothyronine resin uptake ratio (T3RU) thyroid stimulating hormone (TSH), free thyroxine index (FT4I), and ratio of T3/rT3 in 103 tuberculous patients. The results showed the levels of serum TT4, TT3 and ratio T3/rT3 in tuberculous patients were lower than those of 50 healthy subjects (total P less than 0.01), rT3, T3RU and TSH were higher than those (total P less than 0.01). FT4I has no significant difference between the two groups (P greater than 0.05).
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Affiliation(s)
- S M Yan
- Changchun Tuberculosis Hospital
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Yan SM. [The clinical observation on ceruloplasmin in cerebrospinal fluid and serum of tuberculous meningitis patients]. Zhonghua Jie He He Hu Xi Za Zhi 1988; 11:228-30, 255-6. [PMID: 3228903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Yan SM, Flor-Henry P, Chen DY, Li TG, Qi SG, Ma ZX. Imbalance of hemispheric functions in the major psychoses: a study of handedness in the People's Republic of China. Biol Psychiatry 1985; 20:906-17. [PMID: 4040777 DOI: 10.1016/0006-3223(85)90216-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A study of hand preference and eye dominance in schizophrenia, manic-depressive psychosis, and normal controls was carried out in the People's Republic of China. An excess of sinistrality was found in both men and women schizophrenics, but not in manic-depressive patients. Both the manic-depressive and schizophrenic psychoses are characterized by a significant excess of left eye dominance and by an increasing divergence between eye and hand dominance when compared to the controls. The major published studies investigating hand preference in psychopathology are reviewed, and possible interpretations of the conflicting findings are suggested.
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Yan SM. [Hysteria and Briquet syndrome]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1985; 18:57-9. [PMID: 3886331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Yan SM. [The validation of diagnosis of manic-depressive disorder and reestimation of its admission rate]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1985; 18:50-2. [PMID: 3987460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
The authors applied DSM-III criteria to 268 consecutive Chinese inpatients. Nearly a quarter had affective disorder, a third had schizophrenia, and, except for one patient, none had alcoholism or drug abuse. The authors discuss the factors influencing hospitalization in China.
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