Supplementary Table 1. All Differentially Expressed Genes from Microarray Screening Analysis
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Meta-Analysis and Inding from Seoul Breast Cancer Study (SEBCS)
The Pharmacogenomics Journal https://doi.org/10.1038/s41397-018-0016-6 ARTICLE Associations between genetic polymorphisms of membrane transporter genes and prognosis after chemotherapy: meta-analysis and finding from Seoul Breast Cancer Study (SEBCS) 1 1 1 1 2 3 4 Ji-Eun Kim ● Jaesung Choi ● JooYong Park ● Chulbum Park ● Se Mi Lee ● Seong Eun Park ● Nan Song ● 5 6 4,7 8 1,4,9 10 Seokang Chung ● Hyuna Sung ● Wonshik Han ● Jong Won Lee ● Sue K. Park ● Mi Kyung Kim ● 4,7 9,11 1,4,9,12 1,4,9 Dong-Young Noh ● Keun-Young Yoo ● Daehee Kang ● Ji-Yeob Choi Received: 7 June 2017 / Revised: 13 October 2017 / Accepted: 4 December 2017 © Macmillan Publishers Limited, part of Springer Nature 2018 Abstract Membrane transporters can be major determinants of the pharmacokinetic profiles of anticancer drugs. The associations between genetic variations of ATP-binding cassette (ABC) and solute carrier (SLC) genes and cancer survival were investigated through a meta-analysis and an association study in the Seoul Breast Cancer Study (SEBCS). Including the SEBCS, the meta-analysis was conducted among 38 studies of genetic variations of transporters on various cancer survivors. 1234567890();,: The population of SEBCS consisted of 1 338 breast cancer patients who had been treated with adjuvant chemotherapy. A total of 7 750 SNPs were selected from 453 ABC and/or SLC genes typed by an Affymetrix 6.0 chip. ABCB1 rs1045642 was associated with poor progression-free survival in a meta-analysis (HR = 1.33, 95% CI: 1.07–1.64). ABCB1, SLC8A1, and SLC12A8 were associated with breast cancer survival in SEBCS (Pgene < 0.05). -
Inhibition of Breast and Brain Cancer Cell Growth by Bccipα, An
Oncogene (2001) 20, 336 ± 345 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc Inhibition of breast and brain cancer cell growth by BCCIPa,an evolutionarily conserved nuclear protein that interacts with BRCA2 Jingmei Liu1, Yuan Yuan1,2, Juan Huan2 and Zhiyuan Shen*,1 1Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center; 915 Camino de Salud, NE. Albuquerque, New Mexico, NM 87131, USA; 2Graduate Program of Molecular Genetics, College of Medicine, University of Illinois at Chicago, 900 S. Ashland Ave. Chicago, Illinois, IL 60607, USA BRCA2 is a tumor suppressor gene involved in mammary mouse BRCA2. It is expected that important functions tumorigenesis. Although important functions have been of BRCA2 reside in these conserved domains. Based on assigned to a few conserved domains of BRCA2, little is the functional analysis of the conserved BRCA2 known about the longest internal conserved domain domains, several models have been proposed for the encoded by exons 14 ± 24. We identi®ed a novel protein, role of BRCA2 in tumor suppression. designated BCCIPa, that interacts with part of the An N-terminus conserved domain in exon 3 (amino internal conserved region of human BRCA2. Human acids 48 ± 105) has been implicated in transcriptional BCCIP represents a family of proteins that are regulation of gene expression (Milner et al., 1997; evolutionarily conserved, and contain three distinct Nordling et al., 1998). Deletion of this region has been domains: an N-terminus acidic domain (NAD) of 30 ± identi®ed in breast cancers (Nordling et al., 1998). -
New Products JULY 2013
R&D Systems Tools for Cell Biology Research™ New Products JULY 2013 GMP-grade Recombinant Proteins Contents R&D Systems now offers GMP-grade cytokines and growth factors for research and further manu- facturing applications where current Good Manufacturing Practices (GMP) are required. GMP-grade Recombinant Proteins 2 proteins are manufactured in our ISO-certified facility in compliance with relevant guidelines1 and are produced with extensive documentation at every stage of development from cell culture to final fill and Quantikine® ELISA Kits 3 formulation. GMP-grade Recombinant Human IL-6 and Recombinant Human TNF-a have recently been added to our line of GMP-grade proteins. Additional GMP-grade proteins will be available in the next several months. For an up-to-date product listing or additional information, please visit our website at Luminex® Screening Assays 4 www.RnDSystems.com/GMP. Luminex® Performance Assays 4-5 Features New GMP Proteins ✓ Extensive documentation at every stage of development ProtEin SOURCE Catalog # SIZE Polyclonal Antibodies 6-7 ✓ Documentation of lot-to-lot consistency and traceability Human IL-6 E. coli 206-GMP-010 10 µg Monoclonal Antibodies 7-8 of materials used 206-GMP-050 50 µg ✓ Rigorous quality control using stringent analytical 206-GMP-01M 1 mg processes Biotinylated Antibodies 8 Human TNF-a/ E. coli 210-GMP-010 10 µg ✓ Proven formulations to ensure consistent reconstitution TNFSF1A and results 210-GMP-050 50 µg Antibody Controls 8 210-GMP-01M 1 mg ELISpot Kits & Development Modules 8 30000 60 Fluorokine® Flow Cytometry Kits 8 25000 17348 ) 2 50 20000 Fluorochrome-labeled Antibodies 9 40 8673 DuoSet® ELISA and DuoSet IC ELISA 15000 Development Systems 10 30 Peak Intensity Peak 10000 20 Cell-Based ELISA Assay Kits 10 5000 17565 (Mean RFU x10 Viability Cell 8780 10 Parameter Assay Kits 10 0 0 6000 9000 12000 15000 18000 21000 24000 -3 -2 -1 0 1 10 10 10 10 10 Apoptosis Detection 10 Mass Charge Ratio Recombinant Human TNF-α GMP (ng/mL) MALDI-TOF Analysis of GMP-grade Recombinant Human TNF-a. -
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
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Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Aromatic side-chain flips orchestrate the conformational sampling of functional loops in Cite this: Chem. Sci.,2021,12,9318 † All publication charges for this article human histone deacetylase 8 have been paid for by the Royal Society a a bcd of Chemistry Vaibhav Kumar Shukla, ‡ Lucas Siemons, ‡ Francesco L. Gervasio and D. Flemming Hansen *a Human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and an important drug-target. High-resolution structures of HDAC8 in complex with substrates or inhibitors are available, which have provided insights into the bound state of HDAC8 and its function. Here, using long all-atom unbiased molecular dynamics simulations and Markov state modelling, we show a strong correlation between the conformation of aromatic side chains near the active site and opening and closing of the surrounding functional loops of HDAC8. We also investigated two mutants known to allosterically downregulate the enzymatic activity of HDAC8. Based on experimental data, we hypothesise that I19S-HDAC8 is unable to Received 6th April 2021 Creative Commons Attribution 3.0 Unported Licence. release the product, whereas both product release and substrate binding are impaired in the S39E- Accepted 27th May 2021 HDAC8 mutant. The presented results deliver detailed insights into the functional dynamics of HDAC8 DOI: 10.1039/d1sc01929e and provide a mechanism for the substantial downregulation caused by allosteric mutations, including rsc.li/chemical-science a disease causing one. Introduction II (HDAC-4, -5, -6, -7, -9, and HDAC10), and class III (SIRT1-7) have sequence similarity to yeast Rpd3, Hda1, and Sir2, Acetylation of lysine side chains occurs as a co-translation or respectively, whereas class IV (HDAC11) shares sequence simi- 2 This article is licensed under a post-translational modication of proteins and was rst iden- larity with both class I and II proteins. -
Statistical Methods for High-Dimensional Networked Data Analysis
Statistical Methods for High-Dimensional Networked Data Analysis by Yan Zhou A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biostatistics) in The University of Michigan 2015 Doctoral Committee: Professor Peter X. K. Song, Chair Professor Matthias Kretzler Assistant Professor Xiaoquan William Wen Professor Ji Zhu c Yan Zhou 2015 All Rights Reserved To my family ii ACKNOWLEDGEMENTS I would like to acknowledge many people for their help throughout my graduate study. I would first like to express my deepest gratitude to my advisor Dr. Peter X.- K. Song, for sharing his knowledge, encouraging me to work hard and constantly try to improve my work, and giving me the freedom to explore a diverse set of projects. He is the one who first sparked my interest in networked data analysis. I am not only respectful for his immense knowledge, motivation, and enthusiasm towards research, but also appreciate his invaluable guidance and enthusiastic encouragement during many difficult moments in my research. I could not have imagined having a better advisor and mentor for my Ph.D. study. I would also like to thank my other thesis committee members Dr. Ji Zhu, Dr. Xiaoquan Willian Wen and Dr. Matthias Kretzler for their help and advices that made me more productive than what I could achieve on my own. All enlightening discussions I had with them have lead to better contents of this dissertation. In addition, I would like to acknowledge my collaborators, Dr. Pei Wang, Dr. Betsy Lozoff and Dr. Fengji Geng, who offered me excellent opportunities and con- structive suggestions to apply my statistical knowledge to solve real-world problems, which greatly strengthened the scientific background of my dissertation research. -
Efficient Zygotic Genome Editing Via RAD51-Enhanced Interhomolog Repair 2 3 Jonathan J
bioRxiv preprint doi: https://doi.org/10.1101/263699; this version posted August 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair 2 3 Jonathan J. Wilde1,3, Tomomi Aida1,3, Martin Wienisch1, Qiangge Zhang1, Peimin Qi1, and 4 Guoping Feng1,2* 5 6 Affiliations: 7 1McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, 8 Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA 9 10 2Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, 11 Massachusetts 02142, USA 12 13 3These authors contributed equally to this work. 14 15 *E-mail: [email protected] 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 bioRxiv preprint doi: https://doi.org/10.1101/263699; this version posted August 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 47 Recent advances in genome editing have greatly improved knock-in (KI) efficiency1- 48 9. Searching for factors to further improve KI efficiency for therapeutic use and generation 49 of non-human primate (NHP) models, we found that the strand exchange protein RAD51 50 can significantly increase homozygous KI using CRISPR/Cas9 in mouse embryos through 51 an interhomolog repair (IHR) mechanism. -
Conservation of the BRCA1 Gene
Rochester Institute of Technology RIT Scholar Works Theses 1-2007 Conservation of the BRCA1 gene Matthew Gary Wronkowski Follow this and additional works at: https://scholarworks.rit.edu/theses Recommended Citation Wronkowski, Matthew Gary, "Conservation of the BRCA1 gene" (2007). Thesis. Rochester Institute of Technology. Accessed from This Thesis is brought to you for free and open access by RIT Scholar Works. It has been accepted for inclusion in Theses by an authorized administrator of RIT Scholar Works. For more information, please contact [email protected]. Conservation of the BRCAI Gene Approved: G.R.Skuse Gary R. Skuse, Ph.D. Director of Bioinformatics Richard L. Doolittle Richard L. Doolittle, Ph.D. Head, Department of Biological Sciences Submitted in partial fulfillment of the requirements for the Master of Science degree in Bioinformatics at the Rochester Institute of Technology. Matthew Wronkowski April 2007 Committee Members Anne Haake, Ph.D. is professor of information technology and bioinformatics courses at the Rochester Institute of Technology. Dina Newman, Ph.D. is a professor of human genomics and biology courses in the College of Science at the Rochester Institute of Technology. Maureen Ferran, Ph.D. is a professor of biology and virology in the College of Science at the Rochester Institute of Technology. Gary Skuse, Ph.D. is director of the Bioinformatics program at the Rochester Institute of Technology. Copyright Release Form Title of thesis: Conservation of the BRCAI Gene Name of author: Matthew Gary Wronkowski Degree: Masters of Science Program: Bioinformatics College: Science I understand that I must submit a print copy of my thesis to the RIT Archives, per current RIT guidelines for the completion of my degree. -
Downloaded the “Top Edge” Version
bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Drosophila models of pathogenic copy-number variant genes show global and 2 non-neuronal defects during development 3 Short title: Non-neuronal defects of fly homologs of CNV genes 4 Tanzeen Yusuff1,4, Matthew Jensen1,4, Sneha Yennawar1,4, Lucilla Pizzo1, Siddharth 5 Karthikeyan1, Dagny J. Gould1, Avik Sarker1, Yurika Matsui1,2, Janani Iyer1, Zhi-Chun Lai1,2, 6 and Santhosh Girirajan1,3* 7 8 1. Department of Biochemistry and Molecular Biology, Pennsylvania State University, 9 University Park, PA 16802 10 2. Department of Biology, Pennsylvania State University, University Park, PA 16802 11 3. Department of Anthropology, Pennsylvania State University, University Park, PA 16802 12 4 contributed equally to work 13 14 *Correspondence: 15 Santhosh Girirajan, MBBS, PhD 16 205A Life Sciences Building 17 Pennsylvania State University 18 University Park, PA 16802 19 E-mail: [email protected] 20 Phone: 814-865-0674 21 1 bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 22 ABSTRACT 23 While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non- 24 neuronal phenotypes, functional studies evaluating these regions have focused on the molecular 25 basis of neuronal defects. -
YY1/BCCIP Coordinately Regulates P53-Responsive Element (P53re)-Mediated Transactivation of P21waf1/Cip1
International Journal of Molecular Sciences Article YY1/BCCIP Coordinately Regulates P53-Responsive Element (p53RE)-Mediated Transactivation of p21Waf1/Cip1 Yi Sui 1, Tingting Wu 1, Fuqiang Li 2, Fei Wang 1, Yong Cai 1,3,4,* and Jingji Jin 1,3,4,* 1 Department of Biochemistry and Molecular Biology, School of Life Sciences, Jilin University, Changchun 130012, China; [email protected] (Y.S.); [email protected] (T.W.); [email protected] (F.W.) 2 School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; [email protected] 3 National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China 4 Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun 130012, China * Correspondence: [email protected] (Y.C.); [email protected] (J.J.); Tel.: +86-431-8515-5132 (Y.C.); +86-431-8515-5475 (J.J.) Received: 1 April 2019; Accepted: 26 April 2019; Published: 28 April 2019 Abstract: Transactivation of p21 (cyclin-dependent kinase inhibitor 1A, CDKN1A) is closely related to the recruitment of transcription cofactors at the p53 responsive elements (p53REs) in its promoter region. Human chromatin remodeling enzyme INO80 can be recruited to the p53REs of p21 promoter and negatively regulates p21. As one of the key subunits of the INO80 complex, YY1 has also been confirmed to bind to the p53RE sites of p21 promoter. Importantly, YY1 was recently reported to be bound and stabilized by BCCIP (BRCA2 and CDKN1A-interacting protein). Therefore, we hypothesized that the YY1/BCCIP complex plays an important role in regulating the transactivation of p21. -
Biochemical Characterization and Comparison of Aspartylglucosaminidases Secreted in Venom of the Parasitoid Wasps Asobara Tabida and Leptopilina Heterotoma
RESEARCH ARTICLE Biochemical characterization and comparison of aspartylglucosaminidases secreted in venom of the parasitoid wasps Asobara tabida and Leptopilina heterotoma Quentin Coulette1, SeÂverine Lemauf2, Dominique Colinet2, Geneviève PreÂvost1, Caroline Anselme1, Marylène Poirie 2, Jean-Luc Gatti2* a1111111111 1 Unite ªEcologie et Dynamique des Systèmes AnthropiseÂsº (EDYSAN, FRE 3498 CNRS-UPJV), Universite de Picardie Jules Verne, Amiens, France, 2 Universite CoÃte d'Azur, INRA, CNRS, ISA, Sophia Antipolis, a1111111111 France a1111111111 a1111111111 * [email protected] a1111111111 Abstract Aspartylglucosaminidase (AGA) is a low-abundance intracellular enzyme that plays a key OPEN ACCESS role in the last stage of glycoproteins degradation, and whose deficiency leads to human Citation: Coulette Q, Lemauf S, Colinet D, PreÂvost aspartylglucosaminuria, a lysosomal storage disease. Surprisingly, high amounts of AGA- G, Anselme C, Poirie M, et al. (2017) Biochemical characterization and comparison of like proteins are secreted in the venom of two phylogenetically distant hymenopteran para- aspartylglucosaminidases secreted in venom of the sitoid wasp species, Asobara tabida (Braconidae) and Leptopilina heterotoma (Cynipidae). parasitoid wasps Asobara tabida and Leptopilina These venom AGAs have a similar domain organization as mammalian AGAs. They share heterotoma. PLoS ONE 12(7): e0181940. https:// with them key residues for autocatalysis and activity, and the mature - and -subunits also doi.org/10.1371/journal.pone.0181940 α β form an (αβ)2 structure in solution. Interestingly, only one of these AGAs subunits (α for Editor: Erjun Ling, Institute of Plant Physiology and AtAGA and for LhAGA) is glycosylated instead of the two subunits for lysosomal human Ecology Shanghai Institutes for Biological β Sciences, CHINA AGA (hAGA), and these glycosylations are partially resistant to PGNase F treatment. -
Biosynthesis of Natural Products Containing Β-Amino Acids
Natural Product Reports Biosynthesis of natural products containing β -amino acids Journal: Natural Product Reports Manuscript ID: NP-REV-01-2014-000007.R1 Article Type: Review Article Date Submitted by the Author: 21-Apr-2014 Complete List of Authors: Kudo, Fumitaka; Tokyo Institute Of Technology, Department of Chemistry Miyanaga, Akimasa; Tokyo Institute Of Technology, Department of Chemistry Eguchi, T; Tokyo Institute Of Technology, Department of Chemistry and Materials Science Page 1 of 20 Natural Product Reports NPR RSC Publishing REVIEW Biosynthesis of natural products containing βββ- amino acids Cite this: DOI: 10.1039/x0xx00000x Fumitaka Kudo, a Akimasa Miyanaga, a and Tadashi Eguchi *b Received 00th January 2014, We focus here on β-amino acids as components of complex natural products because the presence of β-amino acids Accepted 00th January 2014 produces structural diversity in natural products and provides characteristic architectures beyond that of ordinary DOI: 10.1039/x0xx00000x α-L-amino acids, thus generating significant and unique biological functions in nature. In this review, we first survey the known bioactive β-amino acid-containing natural products including nonribosomal peptides, www.rsc.org/ macrolactam polyketides, and nucleoside-β-amino acid hybrids. Next, the biosynthetic enzymes that form β-amino acids from α-amino acids and de novo synthesis of β-amino acids are summarized. Then, the mechanisms of β- amino acid incorporation into natural products are reviewed. Because it is anticipated that the rational swapping of the β-amino acid moieties with various side chains and stereochemistries by biosynthetic engineering should lead to the creation of novel architectures and bioactive compounds, the accumulation of knowledge regarding β- amino acid-containing natural product biosynthetic machinery could have a significant impact in this field.