SUPPLEMENTARY TEXT. Systems Analysis with the Gaggle Mrna
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Chemical Transformations Encoded by a Gene Cluster in Streptomyces Coelicolor Containing an Unusual Gtp Cyclohydrolase
Chemical Transformations Encoded by a Streptomyces coelicolor Gene Cluster with an Unusual GTP Cyclohydrolase Item Type text; Electronic Dissertation Authors Spoonamore, James Edward Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 11/10/2021 06:44:52 Link to Item http://hdl.handle.net/10150/194825 CHEMICAL TRANSFORMATIONS ENCODED BY A GENE CLUSTER IN STREPTOMYCES COELICOLOR CONTAINING AN UNUSUAL GTP CYCLOHYDROLASE by James Edward Spoonamore ______________________________ A Dissertation Submitted to the Faculty of the DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOPHYSICS In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2008 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by James Edward Spoonamore entitled Chemical Transformations Encoded by a Gene Cluster in Streptomyces coelicolor Containing an Unusual GTP Cyclohydrolase and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy _______________________________________________________________________ Date: April 16, 2008 Vahe Bandarian _______________________________________________________________________ -
Systems Biology Approaches to Mining High Throughput Biological Data
BioMed Research International Systems Biology Approaches to Mining High Throughput Biological Data Guest Editors: Fang-Xiang Wu, Min Li, Jishou Ruan, and Feng Luo Systems Biology Approaches to Mining High Throughput Biological Data BioMed Research International Systems Biology Approaches to Mining High Throughput Biological Data Guest Editors: Fang-Xiang Wu, Min Li, Jishou Ruan, and Feng Luo Copyright © 2015 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Systems Biology Approaches to Mining High Throughput Biological Data, Fang-Xiang Wu, Min Li, Jishou Ruan, and Feng Luo Volume 2015, Article ID 504362, 2 pages ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity, Gamage Upeksha Ganegoda, Yu Sheng, and Jianxin Wang Volume 2015, Article ID 213750, 11 pages Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization, YongchaoDou,XiaomeiGuo,LinglingYuan,DavidR.Holding,andChiZhang Volume 2015, Article ID 789516, 9 pages ?? -Profiles: A Nonlinear Clustering Method for Pattern Detection in High Dimensional, Data Kai Wang, Qing Zhao, Jianwei Lu, and Tianwei Yu Volume 2015, Article ID 918954, 10 pages Screening Ingredients from Herbs against Pregnane X Receptor in -
The Role of Peptidyl Arginine Deiminase, Type IV (PAD4) in the Pathology of Shock/Sepsis
The Role of Peptidyl arginine deiminase, type IV (PAD4) in the Pathology of Shock/Sepsis By Bethany Marie Biron B.A., Worcester State College M.S., Johns Hopkins University Dissertation Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Division of Biology and Medicine at Brown University Providence RI May 2017 © Copyright 2017 by Bethany M. Biron This dissertation by Bethany Marie Biron is accepted in its present form by the Department of Pathobiology as satisfying the dissertation requirement for the degree of Doctor of Philosophy. Date_____________ _________________________________ Alfred Ayala, Co-Advisor Date_____________ _________________________________ Jonathan Reichner, Co-Advisor Advisor Recommended to the Graduate Council Date_____________ _________________________________ Craig Lefort, Reader Date_____________ _________________________________ Daithi Heffernan, Reader Date_____________ _________________________________ Bruce Levy, Outside Reader Approved by the Graduate Council Date_____________ _________________________________ Andrew Campbell, Dean of the Graduate School i Bethany M. Biron Girard, BA, MS Pathobiology Graduate Program-Pre-doctoral Student Co-Mentored by Alfred Ayala/Jonathan Reichner Division of Surgical Research Rhode Island Hospital Brown Medical School Aldrich 239, 593 Eddy Street Providence, RI 02903 Email: [email protected] Primary Research Field My current research involves studying the citrullination of histones via Protein Arginine Deiminase 4 (PAD4) and its involvement in Neutrophil Extracellular trap formation in disease states. Acute lung injury (ALI) is a common sequela of shock/trauma and is associated with significant mortality. Trauma patients exposed to a secondary infectious challenge are considered at significant risk for inflammatory lung injury. Neutrophil extracellular traps (NETs) are capable of microbial killing essential for combating systemic infection, but are also associated with detrimental inflammation in the host. -
Cat# CRE-02 Creatininase Size: 50 Mu Life Technologies (India) Pvt. Ltd
Product Specification Sheet Cat# CRE-02 Creatininase Size: 50 mU General Information creatininase (EC 3.5.2.10; Creatinine amidohydrolase; CAS# 90285-13-2; EINECS# 232-768-8; ~275 aa depending upon the species; ) is an enzyme that catalyzes the chemical reaction creatinine + H2O creatine Thus, the two substrates of this enzyme are creatinine and H2O, whereas its product is creatine. This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in cyclic amides. The systematic name of this enzyme class is creatinine amidohydrolase. This enzyme is also called creatinine hydrolase. This enzyme participates in arginine and proline metabolism. Source: Creatininase is an enzyme that is produced in E. Coli using recombinant DNA technology. It is supplied in powder form with no additives or preservatives. The product is supplied on enzyme activity (KU; The amount of enzyme which produces 1 umol of creatine per min at 37oC and pH 6.5. The final enzyme preparation contains minimal amounts of the relevant contaminants (<1.0 of catalase). The activity is >~500 U/mg material. Storage and Usage Store powder at -20oC or below under dry conditions. Allow the product to reach room temp before opening the vial and dissolve in appropriate buffers for usage. Before returning to storage, re-dessicate under vaccumn over silica gel for a minimum of 4 hours to provide best conditions for long term preservation of enzyme activity. References Starkenburg SR (2006) Appl Environ. Microbiol. 72, 2050 CRE-02 90603A Alpha Diagnostic Intl Inc., 6203 Woodlake Center Dr, San Antonio, TX 78244, USA; India Contact: Life Technologies (India) Pvt. -
Ammecr1 CRISPR/Cas9 KO Plasmid (M): Sc-424992
SANTA CRUZ BIOTECHNOLOGY, INC. Ammecr1 CRISPR/Cas9 KO Plasmid (m): sc-424992 BACKGROUND APPLICATIONS The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Ammecr1 CRISPR/Cas9 KO Plasmid (m) is recommended for the disruption CRISPR-associated protein (Cas9) system is an adaptive immune response of gene expression in mouse cells. defense mechanism used by archea and bacteria for the degradation of foreign genetic material (4,6). This mechanism can be repurposed for other 20 nt non-coding RNA sequence: guides Cas9 to a specific target location in the genomic DNA functions, including genomic engineering for mammalian systems, such as gene knockout (KO) (1,2,3,5). CRISPR/Cas9 KO Plasmid products enable the U6 promoter: drives gRNA scaffold: helps Cas9 expression of gRNA bind to target DNA identification and cleavage of specific genes by utilizing guide RNA (gRNA) sequences derived from the Genome-scale CRISPR Knock-Out (GeCKO) v2 Termination signal library developed in the Zhang Laboratory at the Broad Institute (3,5). Green Fluorescent Protein: to visually verify transfection CRISPR/Cas9 REFERENCES Knockout Plasmid CBh (chicken β-Actin hybrid) promoter: drives 1. Cong, L., et al. 2013. Multiplex genome engineering using CRISPR/Cas 2A peptide: expression of Cas9 systems. Science 339: 819-823. allows production of both Cas9 and GFP from the 2. Mali, P., et al. 2013. RNA-guided human genome engineering via Cas9. same CBh promoter Science 339: 823-826. Nuclear localization signal 3. Ran, F.A., et al. 2013. Genome engineering using the CRISPR-Cas9 system. Nuclear localization signal SpCas9 ribonuclease Nat. Protoc. 8: 2281-2308. -
A Korarchael Genome Reveals Insights Into the Evolution of The
A korarchaeal genome reveals insights into the evolution of the Archaea James G. Elkins*†, Mircea Podar‡, David E. Graham§, Kira S. Makarova¶, Yuri Wolf¶, Lennart Randau||, Brian P. Hedlund**, Céline Brochier-Armanet††, Victor Kunin‡‡, Iain Anderson‡‡, Alla Lapidus‡‡, Eugene Goltsman‡‡, Kerrie Barry‡‡, Eugene V. Koonin¶, Phil Hugenholtz‡‡, Nikos Kyrpides‡‡, Gerhard Wanner§§, Paul Richardson‡‡, Martin Keller‡, and Karl O. Stetter*¶¶|||| *Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, D-93053, Regensburg, Germany; ‡Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; §Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712; ¶National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; ||Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; **School of Life Sciences, University of Nevada, Las Vegas, NV, 89154; **Université de Provence - Aix-Marseille I, Laboratoire de chimie bactérienne, UPR CNRS 9043, Marseille, France; ‡‡DOE Joint Genome Institute, Walnut Creek, CA 94598; §§Institute of Botany, LM University of Munich, D-80638, Munich, Germany; ¶¶Institute of Geophysics and Planetary Science, University of California, Los Angeles, CA 90095 †Present address: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 ||||To whom correspondence should be addressed: Karl O. Stetter Universität Regensburg Lehrstuhl für Mikrobiologie Universitätstraße 31 93343 Regensburg Phone: +49-941 943-1821, -3161 Fax: +49-941 943-3243 E-Mail: [email protected] Manuscript info: 13 pages, 2 figures, 2 tables. Abbreviations: SSU, small subunit; LSU, large subunit; arCOGs, archaeal clusters of orthologous groups; RNAP, RNA polymerase; EF, elongation factor; HGT, horizontal gene transfer. -
Chandran Et Al. Supporting Info.Pdf
Supporting Information (SI) Appendix Part 1. Impact of tissue preparation, LMD, and RNA amplification on array output. p. 2 Text S1: Detailed Experimental Design and Methods Figure S1A: Correlation analysis indicates tissue preparation has minimal impact on ATH1 array output. Figure S1B: Correlation analysis indicates RNA degradation does not significantly impact array output. Figure S1C: Correlation analysis indicates two-round amplification does not significantly impact array output. Figure S1D: Independent biological replicates of LMD samples are highly correlated. Figure S1E: Validation of LMD array expression by qPCR. Table S1: Tissue preparation-associated genes Part 2. Analysis of LMD and parallel whole leaf array data. p. 13 Table S2A: Known PM-impacted genes enriched in LMD dataset Table S2B: Dataset of LMD and whole leaf genes with PM-altered expression Table S2C: LMD PM MapMan Results and Bins Table S2D: ics1 vs. WT LMD PM MapMan Results and Bins Table S2E: Infection site-specific changes for redox and calcium categories Table S2F: cis-acting regulatory element motif analysis Part 3. Process network construction p. 149 3A. Photosynthesis 3B. Cold/dehydration response Part 4. Powdery mildew infection of WT and myb3r4 mutants p. 173 Text S4: Detailed Experimental Design and Methods (supplement to manuscript) Figure S4A. Uninfected 4 week old WT and myb3r4 plants Figure S4B. myb3r4 mutants exhibit reduced visible PM growth and reproduction Figure S4C. PM-infected WT and myb3r4 mutants do not exhibit cell death Figure S4D. Endoreduplication occurs at site of PM infection not distal to infection Figure S4E. Ploidy correlates with nuclear size. Part 1. Impact of tissue preparation, LMD, and RNA amplification on array output. -
O O2 Enzymes Available from Sigma Enzymes Available from Sigma
COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc. -
Evolutionary Conserved Networks of Human Height Identify Multiple Mendelian Causes of Short Stature
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2019 Evolutionary conserved networks of human height identify multiple Mendelian causes of short stature Hauer, Nadine N ; Popp, Bernt ; Taher, Leila ; Vogl, Carina ; et al ; Rauch, Anita Abstract: Height is a heritable and highly heterogeneous trait. Short stature affects 3% of the population and in most cases is genetic in origin. After excluding known causes, 67% of affected individuals remain without diagnosis. To identify novel candidate genes for short stature, we performed exome sequencing in 254 unrelated families with short stature of unknown cause and identified variants in 63 candidate genes in 92 (36%) independent families. Based on systematic characterization of variants and functional analysis including expression in chondrocytes, we classified 13 genes as strong candidates. Whereas variants in at least two families were detected for all 13 candidates, two genes had variants in 6 (UBR4) and 8 (LAMA5) families, respectively. To facilitate their characterization, we established a clustered network of 1025 known growth and short stature genes, which yielded 29 significantly enriched clusters, including skeletal system development, appendage development, metabolic processes, and ciliopathy. Eleven of the candidate genes mapped to 21 of these clusters, including CPZ, EDEM3, FBRS, IFT81, KCND1, PLXNA3, RASA3, SLC7A8, UBR4, USP45, and ZFHX3. Fifty additional growth-related candidates we identified await confirmation in other affected families. Our study identifies Mendelian forms ofgrowth retardation as an important component of idiopathic short stature. DOI: https://doi.org/10.1038/s41431-019-0362-0 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-179378 Journal Article Published Version The following work is licensed under a Creative Commons: Attribution 4.0 International (CC BY 4.0) License. -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.