Qingxin Kaiqiao Fang Inhibits Aβ25-35-Induced Apoptosis In
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Nucleotide Sequence and Analysis of the 58.3 to 65.5-Kb Early Region of Bacteriophage T4
Volume 14 Number 21 1986 Nucleic Acids Research Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4 Kristoffer Valerie 13.4, John Stevens', Mark Lynch'5, Earl E.Henderson12 and Jon K.de Riel1 'Fels Research Institute, and 2Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140, USA and 3Department of Biochemistry and Biotechnology, Royal Institute of Technology, S-100 44 Stockholm, Sweden Received 21 July 1986; Revised and Accepted 30 September 1986 ABSTRACT The complete 7.2-kb nucleotide sequence from the 58.3 to 65.5-kb early region of bacteriophage T4 has been determined by Maxam and Gilbert sequencing. Computer analysis revealed at least 20 open reading frames (ORFs) within this sequence. All major ORFs are transcribed from the left strand, suggesting that they are expressed early during infection. Among the ORFs, we have identified the pIIII, II, denV and tk genes. The ORFs are very tightly spaced, even over Lapping in some instances, and when ORF interspacing occurs, promoter-like sequences can be implicated. Several of the sequences preceding the ORFs, in particular those at ipIII, ipII, denV, and orf6l.9, can potentially form stable stem-loop structures. INTRODUCTION Recently, considerable progress has been made studying the bacteriophage T4 genome at the molecular level due to the development of T4 strains with unmod- ified DNA suitable for digestion with restriction endonucleases (1). Many T4 genes have since been cloned, sequenced, and their gene products overproduced in Escherichia coli (for review see ref. 2). A majority of the T4 genes studied so far have been essential and non-essential genes with well-characterized pheno- types. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Zbtb16 Regulates Social Cognitive Behaviors and Neocortical
Usui et al. Translational Psychiatry (2021) 11:242 https://doi.org/10.1038/s41398-021-01358-y Translational Psychiatry ARTICLE Open Access Zbtb16 regulates social cognitive behaviors and neocortical development Noriyoshi Usui 1,2,3,4, Stefano Berto5,AmiKonishi1, Makoto Kondo1,4, Genevieve Konopka5,HideoMatsuzaki 2,6,7 and Shoichi Shimada1,2,4 Abstract Zinc finger and BTB domain containing 16 (ZBTB16) play the roles in the neural progenitor cell proliferation and neuronal differentiation during development, however, how the function of ZBTB16 is involved in brain function and behaviors unknown. Here we show the deletion of Zbtb16 in mice leads to social impairment, repetitive behaviors, risk- taking behaviors, and cognitive impairment. To elucidate the mechanism underlying the behavioral phenotypes, we conducted histological analyses and observed impairments in thinning of neocortical layer 6 (L6) and a reduction of TBR1+ neurons in Zbtb16 KO mice. Furthermore, we found increased dendritic spines and microglia, as well as developmental defects in oligodendrocytes and neocortical myelination in the prefrontal cortex (PFC) of Zbtb16 KO mice. Using genomics approaches, we identified the Zbtb16 transcriptome that includes genes involved in neocortical maturation such as neurogenesis and myelination, and both autism spectrum disorder (ASD) and schizophrenia (SCZ) pathobiology. Co-expression networks further identified Zbtb16-correlated modules that are unique to ASD or SCZ, respectively. Our study provides insight into the novel roles of ZBTB16 in behaviors and neocortical development related to the disorders. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction identified as a causative mutation for skeletal defects, ZBTB16 (PLZF) encodes a transcription factor, which genital hypoplasia, and mental retardation (SGYMR)6,7. -
Transcriptional Regulation Differs in Affected Facioscapulohumeral Muscular Dystrophy Patients Compared to Asymptomatic Related Carriers
University of Massachusetts Medical School eScholarship@UMMS Wellstone Center for FSHD Publications Wellstone Center for FSHD 2009-04-14 Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers Patricia Arashiro University of Sao Paulo Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/wellstone_pubs Part of the Cell Biology Commons, Developmental Biology Commons, Molecular Biology Commons, Molecular Genetics Commons, Musculoskeletal Diseases Commons, and the Nervous System Diseases Commons Repository Citation Arashiro P, Eisenberg I, Kho AT, Cerqueira AM, Canovas M, Silva HC, Pavanello RC, Verjovski-Almeida S, Kunkel LM, Zatz M. (2009). Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers. Wellstone Center for FSHD Publications. https://doi.org/10.1073/pnas.0901573106. Retrieved from https://escholarship.umassmed.edu/ wellstone_pubs/18 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in Wellstone Center for FSHD Publications by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers Patricia Arashiroa, Iris Eisenbergb, Alvin T. Khoc, Antonia M. P. Cerqueiraa, Marta -
Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line
Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line Mahnaz Nezamivand-Chegini Shiraz University Hamed Kharrati-Koopaee Shiraz University https://orcid.org/0000-0003-2345-6919 seyed taghi Heydari ( [email protected] ) Shiraz University of Medical Sciences https://orcid.org/0000-0001-7711-1137 Hasan Giahi Shiraz University Ali Dehshahri Shiraz University of Medical Sciences Mehdi Dianatpour Shiraz University of Medical Sciences Kamran Bagheri Lankarani Shiraz University of Medical Sciences Research Keywords: Tamoxifen, breast cancer, genetic variants, RNA-seq. Posted Date: August 17th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-783422/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/33 Abstract Background Breast cancer is one of the most important causes of mortality in the world, and Tamoxifen therapy is known as a medication strategy for estrogen receptor-positive breast cancer. In current study, two hypotheses of Tamoxifen consumption in breast cancer cell line (MCF7) were investigated. First, the effect of Tamoxifen on genes expression prole at transcriptome level was evaluated between the control and treated samples. Second, due to the fact that Tamoxifen is known as a mutagenic factor, there may be an association between the alterations of genetic variants and Tamoxifen treatment, which can impact on the drug response. Methods In current study, the whole-transcriptome (RNA-seq) dataset of four investigations (19 samples) were derived from European Bioinformatics Institute (EBI). At transcriptome level, the effect of Tamoxifen was investigated on gene expression prole between control and treatment samples. -
Identification of Novel Nasopharyngeal Carcinoma
Imaging, Diagnosis, Prognosis Identification of Novel Nasopharyngeal Carcinoma Biomarkers by Laser Capture Microdissection and Proteomic Analysis Ai-Lan Cheng,1, 3 Wei-Guo Huang,1, 3 Zhu-Chu Chen,1, 2 Fang Peng,1Peng-Fei Zhang,1Mao-Yu Li,1 Feng Li,1, 2 Jian-Ling Li,1Cui Li,1Hong Yi,1Bin Yi,1and Zhi-Qiang Xiao1 Abstract Purpose: To identify novel nasopharyngeal carcinoma (NPC) biomarkers by laser capture microdissection and a proteomic approach. Experimental Design: Proteins from pooled microdissected NPC and normal nasopharyngeal epithelial tissues (NNET) were separated by two-dimensional gel electrophoresis, and differential proteins were identified by mass spectrometry. Expression of three differential proteins (stathmin, 14 -3 -3j, and annexin I) in the above two tissues as well as four NPC cell lines was determined by Western blotting. Immunohistochemistry was also done to detect the expression ofthree differential proteins in 98 cases of primary NPC, 30 cases of NNET, and 20 cases of cervical lymph node metastases, and the correlation oftheir expression levels with clinicopathologic features and clinical outcomes were evaluated. Results: Thirty-six differential proteins between the NPC and NNET were identified. The expression levels ofstathmin, 14-3-3 j, and annexin I in the two types oftissues were confirmed and related to differentiation degree and/or metastatic potential of the NPC cell lines. Significant stathmin up-regulation and down-regulation of14-3-3 j and annexin I were observed in NPC versus NNET, and significant down-regulation of 14-3-3j and annexin I was also observed in lymph node metastasis versus primary NPC. In addition, stathmin up-regulation and down- regulation of14-3-3 j and annexin I were significantly correlated with poor histologic differentiation, advanced clinical stage, and recurrence, whereas down-regulation of 14-3-3j and annexin I was also significantly correlated with lymph node and distant metastasis. -
Salty Taste Deficits in CALHM1 Knockout Mice M
Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2014 Salty Taste Deficits in CALHM1 Knockout Mice M. G. Tordoff H. T. Ellis T. R. Aleman A. Downing P. Marambaud Northwell Health See next page for additional authors Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Medical Molecular Biology Commons Recommended Citation Tordoff M, Ellis H, Aleman T, Downing A, Marambaud P, Foskett ,J Dana R, McCaughey S. Salty Taste Deficits in CALHM1 Knockout Mice. 2014 Jan 01; 39(6):Article 2870 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/2870. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. For more information, please contact [email protected]. Authors M. G. Tordoff, H. T. Ellis, T. R. Aleman, A. Downing, P. Marambaud, J. K. Foskett, R. M. Dana, and S. A. McCaughey This article is available at Donald and Barbara Zucker School of Medicine Academic Works: https://academicworks.medicine.hofstra.edu/articles/2870 Chem. Senses 39: 515–528, 2014 doi:10.1093/chemse/bju020 Advance Access publication May 20, 2014 Salty Taste Deficits in CALHM1 Knockout Mice Michael G. Tordoff1, Hillary T. Ellis1, Tiffany R. Aleman1, Arnelle Downing1, Philippe Marambaud2, J. Kevin Foskett3, Rachel M. Dana4 and Stuart -
1.3 the CRAC Channel
CRAC channel related proteins in the pathogenesis of inborn errors of immunity Laura Jane Rice Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Medicine and Health Under the supervision of Rashida Anwar PhD and Sinisa Savic MD, PhD June 2021 Publication statement The candidate confirms that the work submitted is her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Laura Jane Rice to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. © 2021 The University of Leeds and Laura Jane Rice ii Acknowledgements This work was funded by University of Leeds and CSL Behring (West Sussex, UK). I would like to thank my supervisors for their continued support. Rashida Anwar for her scientific knowledge, detail driven questions and help during the writing of this thesis. Sinisa Savic for his encouragement and clinical and immunology expertise. The Anwar group and Level 9 WTBB PhD students made this experience enjoyable with coffee and gin. I was fortunate to have collaborators with experience in CRAC channel research. -
Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles Or Functional Redundancy?
GBE Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? Rafael Mina Piergiorge1, Antonio Basılio de Miranda2, Ana Carolina Guimaraes~ 1,*, and Marcos Catanho1 1Laboratorio de Genoˆ mica Funcional e Bioinformatica, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil 2Laboratorio de Biologia Computacional e Sistemas, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil *Corresponding author: E-mail: carolg@fiocruz.br. Accepted: July 4, 2017 Abstract Since enzymes catalyze almost all chemical reactions that occur in living organisms, it is crucial that genes encoding such activities are correctly identified and functionally characterized. Several studies suggest that the fraction of enzymatic activities in which multiple events of independent origin have taken place during evolution is substantial. However, this topic is still poorly explored, and a comprehensive investigation of the occurrence, distribution, and implications of these events has not been done so far. Fundamental questions, such as how analogous enzymes originate, why so many events of independent origin have apparently occurred during evolution, and what are the reasons for the coexistence in the same organism of distinct enzymatic forms catalyzing the same reaction, remain unanswered. Also, several isofunctional enzymes are still not recognized as nonhomologous, even with substantial evidence indicating different evolutionary histories. In this work, we begin to investigate the biological significance of the cooccur- rence of nonhomologous isofunctional enzymes in human metabolism, characterizing functional analogous enzymes identified in metabolic pathways annotated in the human genome. Our hypothesis is that the coexistence of multiple enzymatic forms might not be interpreted as functional redundancy. Instead, these enzymatic forms may be implicated in distinct (and probably relevant) biological roles. -
Anti-CALHM1 Antibody (ARG56385)
Product datasheet [email protected] ARG56385 Package: 100 μl anti-CALHM1 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes CALHM1 Tested Reactivity Hu, Rat Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name CALHM1 Antigen Species Human Immunogen Recombinant protein of Human CALHM1 Conjugation Un-conjugated Alternate Names FAM26C; Calcium homeostasis modulator protein 1; Protein FAM26C Application Instructions Application table Application Dilution IHC-P 1:50 - 1:200 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control SH-SY5Y Calculated Mw 38 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. www.arigobio.com 1/2 Bioinformation Database links GeneID: 255022 Human Swiss-port # Q8IU99 Human Gene Symbol CALHM1 Gene Full Name calcium homeostasis modulator 1 Background This gene encodes a calcium channel that plays a role in processing of amyloid-beta precursor protein. A polymorphism at this locus has been reported to be associated with susceptibility to late-onset Alzheimer's disease in some populations, but the pathogenicity of this polymorphism is unclear.[provided by RefSeq, Mar 2010] Function Pore-forming subunit of a voltage-gated ion channel required for sensory perception of sweet, bitter and umami tastes. -
Identification of Isobutyryl-Coa Dehydrogenase and Its Deficiency
Molecular Genetics and Metabolism 77 (2002) 68–79 www.academicpress.com Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans Tien V. Nguyen,a Brage S. Andresen,b,c Thomas J. Corydon,b Sandro Ghisla,d Nasser Abd-El Razik,d Al-Walid A. Mohsen,a Stephen D. Cederbaum,e Diane S. Roe,f Charles R. Roe,f Nicolas J. Lench,g and Jerry Vockleya,* a Department of Medical Genetics, Mayo Clinic, Rochester, MN 55905, USA b Institute for Human Genetics, Aarhus University, Aarhus, Denmark c Research Unit for Molecular Medicine, Skejby Sygehus and Aarhus University, Aarhus, Denmark d Faculty of Biology, University of Konstanz, Konstanz, Germany e Department of Pediatrics, UCLA Medical Center, Los Angeles, CA, USA f Institute of Metabolic Disease, Baylor University, Dallas, TX, USA g Molecular Medicine Unit, University of Leeds, St. JamesÕ University Hospital, Leeds, UK Received 19 July 2002; received in revised form 31 July 2002; accepted 1 August 2002 Abstract The acyl-CoA dehydrogenases (ACDs) are a family of related enzymes that catalyze the a,b-dehydrogenation of acyl-CoA esters. Two homologues active in branched chain amino acid metabolism have previously been identified. We have used expression in Escherichia coli to produce a previously uncharacterized ACD-like sequence (ACAD8) and define its substrate specificity. Purified À1 À1 recombinant enzyme had a kcat=Km of 0.8, 0.23, and 0.04 (lM s ) with isobutyryl-CoA, (S) 2-methylbutyryl-CoA, and n-propionyl- CoA, respectively, as substrates. Thus, this enzyme is an isobutyryl-CoA dehydrogenase. A single patient has previously been described whose fibroblasts exhibit a specific deficit in the oxidation of valine.