Characterizing the 3D Interactions of the Base-Pair Stems
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A Mutation in DNA Polymerase Α Rescues WEE1KO Sensitivity to HU
International Journal of Molecular Sciences Article A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU Thomas Eekhout 1,2 , José Antonio Pedroza-Garcia 1,2 , Pooneh Kalhorzadeh 1,2, Geert De Jaeger 1,2 and Lieven De Veylder 1,2,* 1 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; [email protected] (T.E.); [email protected] (J.A.P.-G.); [email protected] (P.K.); [email protected] (G.D.J.) 2 Center for Plant Systems Biology, VIB, 9052 Gent, Belgium * Correspondence: [email protected] Abstract: During DNA replication, the WEE1 kinase is responsible for safeguarding genomic integrity by phosphorylating and thus inhibiting cyclin-dependent kinases (CDKs), which are the driving force of the cell cycle. Consequentially, wee1 mutant plants fail to respond properly to problems arising during DNA replication and are hypersensitive to replication stress. Here, we report the identification of the pola-2 mutant, mutated in the catalytic subunit of DNA polymerase α, as a suppressor mutant of wee1. The mutated protein appears to be less stable, causing a loss of interaction with its subunits and resulting in a prolonged S-phase. Keywords: replication stress; DNA damage; cell cycle checkpoint Citation: Eekhout, T.; Pedroza- 1. Introduction Garcia, J.A.; Kalhorzadeh, P.; De Jaeger, G.; De Veylder, L. A Mutation DNA replication is a highly complex process that ensures the chromosomes are in DNA Polymerase α Rescues correctly replicated to be passed onto the daughter cells during mitosis. Replication starts WEE1KO Sensitivity to HU. Int. -
SUPPLEMENTARY TABLE 1 Non-Destructive Characterisation Of
Electronic Supplementary Material (ESI) for Analyst. This journal is © The Royal Society of Chemistry 2016 SUPPLEMENTARY TABLE 1 Non-destructive characterisation of mesenchymal stem cell differentiation using LC-MS-based metabolite footprinting Amal Surrati 1, Rob Linforth 2, Ian Fisk 2, VirginieSottile1*, Dong-Hyun Kim 3*. 1Wolfson Centre for Stem Cells, Tissue, Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, CBS Building - University Park, Nottingham NG7 2RD (U.K.) 2Division of Food Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD (U.K.) 3Centre for Analytical Bioscience, Division of Molecular and Cellular Sciences, School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD (U.K.) *Correspondence to: Email: [email protected] Tel: +44 1158231235 Email: [email protected] Tel: +44 1157484697 Supplementary Table 1: Metabolites changed in MSC-conditioned medium compared to fresh medium (blank). ↑ indicates the metabolites that increased in all MSC-conditioned medium (control and OS) compared to their corresponding blanks, and ↓ indicates decreased metabolites. ID confidence: Metabolite identification level according to the metabolomics standards initiative 29,30 ; L1 – Level 1, L2 – Level 2. Change RT ID Identifier compared Exact mass Formula Putative metabolite (min) confidence (PubChem) to blank medium 179.0946 5.30 C10H13NO2 (-)-Salsolinol L2 91588 ↑ 358.1410 10.12 C20H22O6 (+)-Pinoresinol L2 7741 ↑ 148.0371 -
Supporting Information
Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus. -
Exploring the Non-Canonical Functions of Metabolic Enzymes Peiwei Huangyang1,2 and M
© 2018. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2018) 11, dmm033365. doi:10.1242/dmm.033365 REVIEW SPECIAL COLLECTION: CANCER METABOLISM Hidden features: exploring the non-canonical functions of metabolic enzymes Peiwei Huangyang1,2 and M. Celeste Simon1,3,* ABSTRACT A key finding from studies of metabolic enzymes is the existence The study of cellular metabolism has been rigorously revisited over the of mechanistic links between their nuclear localization and the past decade, especially in the field of cancer research, revealing new regulation of transcription. By modulating gene expression, insights that expand our understanding of malignancy. Among these metabolic enzymes themselves facilitate adaptation to rapidly insights isthe discovery that various metabolic enzymes have surprising changing environments. Furthermore, they can directly shape a ’ activities outside of their established metabolic roles, including in cell s epigenetic landscape (Kaelin and McKnight, 2013). the regulation of gene expression, DNA damage repair, cell cycle Strikingly, several metabolic enzymes exert completely distinct progression and apoptosis. Many of these newly identified functions are functions in different cellular compartments. Nuclear fructose activated in response to growth factor signaling, nutrient and oxygen bisphosphate aldolase, for example, directly interacts with RNA ́ availability, and external stress. As such, multifaceted enzymes directly polymerase III to control transcription (Ciesla et al., 2014), -
Fall-2020-Print-Axia
INSIDE THIS SPECIAL FALL 2020 Contents EDITION OF ACS AXIAL axial.acs.org deeper ACS PUBLICATIONS SHANGHAITECH UNIVERSITY NEW ENVIRONMENTAL SCIENCE & WHAT CHEMISTS NEED LAUNCHESdive NEW JOURNALS PARTNERS WITH ACS PUBLICATIONS TO TECHNOLOGY JOURNALS TO KNOW ABOUT Explore the ResearchFOCUSED behind ON theFOOD 2020 AND Journal Citation Reports® LAUNCH ACCOUNTS OF MATERIALS NAME EDITORS AND MACHINE LEARNING AGRICULTURAL CHEMISTRY RESEARCH OPEN FOR SUBMISSIONS The 2020 Journal Citation Reports® (JCR) show the vital role ACS Publications journals play in publishing important, highly cited research. Thanks to the dedication and brilliance of our authors and reviewers, 89% of ACS journals have an Impact Factor greater than 3 this year. Browse this year’s JCR figures, which are based on citations from 2018 to 2019: EXPLORE THE RESEARCH HOW ACS IS SUPPORTING THE LEARN HOW ACS SUPPORTS SCIMEETINGS: PRESENT YOUR RESEARCH BEHIND THE 2020 JOURNAL CHEMISTRY COMMUNITY DURING THE OPEN SCIENCE BEYOND THE ACS FALL 2020 VIRTUAL CITATION REPORTS® COVID-19 PANDEMIC MEETING & EXPO Impact Factor 20.832 Impact Factor 4.473 Impact Factor Impact Factor 4.152 8.758 Impact Factor Impact Factor 4.486 Impact Factor 12.685 12.350 Impact Factor 4.434 Impact Factor Impact Factor 3.381 19.003 Impact Factor 3.418 Impact Factor Impact Factor 3.975 Impact Factor 4.614 6.042 Impact Factor Impact Factor Impact Factor 7.333 14.588 6.864 Impact Factor 2.870 Impact Factor Impact Factor 6.785 4.411 Impact Factor 7.632 Impact Factor 6.092 Impact Factor 2.865 Impact Factor 4.031 pubs.acs.org/acsagscitech ACS PUBLICATIONS LAUNCHES NEW JOURNALS FOCUSED ON FOOD AND AGRICULTURAL CHEMISTRY ournal of Agricultural and Food Chemistry Technical University of Munich and the chair of is growing into a family of journals with the Food Chemistry and Molecular Sensors. -
Marnix Medema Curriculum Vitae
Page 1 of 10 Curriculum vitae Personal Information FIRST NAME / SURNAME Marnix Medema ADDRESS (PRIVATE) Soetendaalseweg 16A, 6721XB Bennekom, NL ADDRESS (WORK) Droevendaalsesteeg 1, 6708PB Wageningen, NL TEL +31317484706 / +31654758321 (cell) EMAIL [email protected] WEB http://www.marnixmedema.nl NATIONALITY Dutch DATE OF BIRTH 24.01.1986 GENDER Male Work Experience & Education DATES March 2015 - present EMPLOYER Wageningen University, Wageningen, The Netherlands POSITION Assistant Professor DATES August 2013 - February 2015 EMPLOYER MPI for Marine Microbiology, Bremen, Germany POSITION Postdoctoral Researcher DATES September 2010 - March 2011 EMPLOYER University of California, San Francisco, USA POSITION Visiting Research Scholar DATES September 2009 - August 2013 EMPLOYER University of Groningen, The Netherlands POSITION PhD Student DATE / DISTINCTION 27.09.2013, cum laude ** DATES September 2006 - August 2008 QUALIFICATION AWARDED Master of Science Biomolecular Science, cum laude ** INSTITUTION University of Groningen, The Netherlands DATES September 2003 - August 2006 QUALIFICATION AWARDED Bachelor of Science Biology, cum laude ** INSTITUTION Radboud University Nijmegen, The Netherlands ** In the Netherlands, only two classes of honors are used: eervolle vermelding ("honorable mention") and cum laude, typically only to mark exceptional achievement. [...] Generally, less than 20% receive the "honorable mention" distinction, and "cum laude" is even harder to attain (less than 1%-5% depending on the university and study program). -
Mcm10 Has Potent Strand-Annealing Activity and Limits Translocase-Mediated Fork Regression
Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression Ryan Maylea, Lance Langstona,b, Kelly R. Molloyc, Dan Zhanga, Brian T. Chaitc,1,2, and Michael E. O’Donnella,b,1,2 aLaboratory of DNA Replication, The Rockefeller University, New York, NY 10065; bHoward Hughes Medical Institute, The Rockefeller University, New York, NY 10065; and cLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 Contributed by Michael E. O’Donnell, November 19, 2018 (sent for review November 8, 2018; reviewed by Zvi Kelman and R. Stephen Lloyd) The 11-subunit eukaryotic replicative helicase CMG (Cdc45, Mcm2-7, of function using genetics, cell biology, and cell extracts have GINS) tightly binds Mcm10, an essential replication protein in all identified Mcm10 functions in replisome stability, fork progres- eukaryotes. Here we show that Mcm10 has a potent strand- sion, and DNA repair (21–25). Despite significant advances in the annealing activity both alone and in complex with CMG. CMG- understanding of Mcm10’s functions, mechanistic in vitro studies Mcm10 unwinds and then reanneals single strands soon after they of Mcm10 in replisome and repair reactions are lacking. have been unwound in vitro. Given the DNA damage and replisome The present study demonstrates that Mcm10 on its own rap- instability associated with loss of Mcm10 function, we examined the idly anneals cDNA strands even in the presence of the single- effect of Mcm10 on fork regression. Fork regression requires the strand (ss) DNA-binding protein RPA, a property previously unwinding and pairing of newly synthesized strands, performed by associated with the recombination protein Rad52 (26). -
Is Glyceraldehyde-3-Phosphate Dehydrogenase a Central Redox Mediator?
1 Is glyceraldehyde-3-phosphate dehydrogenase a central redox mediator? 2 Grace Russell, David Veal, John T. Hancock* 3 Department of Applied Sciences, University of the West of England, Bristol, 4 UK. 5 *Correspondence: 6 Prof. John T. Hancock 7 Faculty of Health and Applied Sciences, 8 University of the West of England, Bristol, BS16 1QY, UK. 9 [email protected] 10 11 SHORT TITLE | Redox and GAPDH 12 13 ABSTRACT 14 D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an immensely important 15 enzyme carrying out a vital step in glycolysis and is found in all living organisms. 16 Although there are several isoforms identified in many species, it is now recognized 17 that cytosolic GAPDH has numerous moonlighting roles and is found in a variety of 18 intracellular locations, but also is associated with external membranes and the 19 extracellular environment. The switch of GAPDH function, from what would be 20 considered as its main metabolic role, to its alternate activities, is often under the 21 influence of redox active compounds. Reactive oxygen species (ROS), such as 22 hydrogen peroxide, along with reactive nitrogen species (RNS), such as nitric oxide, 23 are produced by a variety of mechanisms in cells, including from metabolic 24 processes, with their accumulation in cells being dramatically increased under stress 25 conditions. Overall, such reactive compounds contribute to the redox signaling of the 26 cell. Commonly redox signaling leads to post-translational modification of proteins, 27 often on the thiol groups of cysteine residues. In GAPDH the active site cysteine can 28 be modified in a variety of ways, but of pertinence, can be altered by both ROS and 29 RNS, as well as hydrogen sulfide and glutathione. -
Additional File 4. P. Vinckei Genes Ordered According to the Gene Expression of Their Orthologs in P
A fast and cost-effective microsampling protocol incorporating reduced animal usage for time- series transcriptomics in rodent malaria parasites Item Type Article Authors Ramaprasad, Abhinay; Subudhi, Amit; Culleton, Richard; Pain, Arnab Citation Ramaprasad A, Subudhi AK, Culleton R, Pain A (2019) A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites. Malaria Journal 18. Available: http:// dx.doi.org/10.1186/s12936-019-2659-4. Eprint version Publisher's Version/PDF DOI 10.1186/s12936-019-2659-4 Publisher Springer Nature Journal Malaria Journal Rights This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Download date 28/09/2021 01:24:39 Item License http://creativecommons.org/licenses/by/4.0/ Link to Item http://hdl.handle.net/10754/628424 Additional file 4. P. vinckei genes ordered according to the gene expression of their orthologs in P. falciparum. Pfalciparum ortholog gene_id 6h 12h 18h 24h Product PF3D7_1432500 PVVCY_1001720 6.742 -
Unveiling Structural and Functional Divergences Of
Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, Djemel Hamdane To cite this version: Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, et al.. Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: per- spectives on the evolution scenario. Nucleic Acids Research, Oxford University Press, 2018, 46 (3), pp.1386-1394. 10.1093/nar/gkx1294. hal-01727508 HAL Id: hal-01727508 https://hal.sorbonne-universite.fr/hal-01727508 Submitted on 9 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License 1386–1394 Nucleic Acids Research, 2018, Vol. 46, No. 3 Published online 27 December 2017 doi: 10.1093/nar/gkx1294 Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles -
N6-Methyladenosine (M6a) Is an Endogenous A3 Adenosine Receptor Ligand
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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. N6-methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand Akiko Ogawa,1, 2, 3 Chisae Nagiri,4, 13 Wataru Shihoya,4, 13 Asuka Inoue,5, 6, 7, 13 Kouki Kawakami,5 Suzune Hiratsuka,5 Junken Aoki,7, 8 Yasuhiro Ito,3 Takeo Suzuki,9 Tsutomu Suzuki,9 Toshihiro Inoue,3 Osamu Nureki,4 Hidenobu Tanihara,10 Kazuhito Tomizawa,2, 11 Fan-Yan Wei1, 2, 12, 14 1Department of Modomics Biology & Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai 980-8575, Japan. 2Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 3Department of Ophthalmology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 4Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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. 5Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan. -
2017 Catalog 2017 Catalog
2017CATALOG ABOUT ACS AMERICAN CHEMICAL SOCIETY With more than 157,000 members, the American Chemical Society (ACS) Table of Contents>>> is the world’s largest scientific society and one of the world’s leading sources of authoritative scientific information. A nonprofit organization chartered by Congress, ACS is at the forefront of the evolving About ACS Publications ................................................................................. 3 worldwide chemical enterprise and the premier professional home for chemists, chemical Editorial Excellence for 138 years ..............................................................................................................4 What Fuels ACS Publications’ Growth ......................................................................................................6 engineers, and related professionals around the globe. ACS Publications’ Unsurpassed Performance .........................................................................................8 ACS Publications’ Impact on Chemistry ................................................................................................ 10 Select Highlights from ACS Journals ...................................................................................................... 12 An Inspiring Online Platform ................................................................................................................... 14 ACS on Campus ..........................................................................................................................................