Cold-Shock Domains—Abundance, Structure, Properties, and Nucleic-Acid Binding
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Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R. -
NANOG and LIN28 Dramatically Improve Human Cell Reprogramming
© 2019. Published by The Company of Biologists Ltd | Biology Open (2019) 8, bio047225. doi:10.1242/bio.047225 RESEARCH ARTICLE NANOG and LIN28 dramatically improve human cell reprogramming by modulating LIN41 and canonical WNT activities Ling Wang, Yue Su, Chang Huang, Yexuan Yin, Alexander Chu, Alec Knupp and Young Tang* ABSTRACT (Hussein et al., 2014). The first transcriptional change occurs at the Human cell reprogramming remains extremely inefficient and the early reprogramming stage, with cells undergoing mesenchymal-to- underlying mechanisms by different reprogramming factors are epithelial transition (MET) for iPSC colony formation (Hussein elusive. We found that NANOG and LIN28 (NL) synergize to improve et al., 2014; Li et al., 2010; Samavarchi-Tehrani et al., 2010). This OCT4, SOX2, KLF4 and MYC (OSKM)-mediated reprogramming by stage is followed by the second wave that occurs during maturation ∼76-fold and shorten reprogramming latency by at least 1 week. This and stabilization, when the pluripotency regulatory network is synergy is inhibited by GLIS1 but reinforced by an inhibitor of the activated and stabilized in reprogrammed cells (Buganim et al., 2012; histone methyltransferase DOT1L (iDOT1L) to a ∼127-fold increase in Golipour et al., 2012; Hussein et al., 2014; Polo et al., 2012; TRA-1-60-positive (+) iPSC colonies. Mechanistically, NL serve as the Samavarchi-Tehrani et al., 2010). In human cells, the early-to-middle main drivers of reprogramming in cell epithelialization, the expression reprogramming stages are characterized by multiple waves of lineage- of Let-7 miRNA target LIN41, and the activation of canonical WNT/β- related gene activation in the order of developmental reversal, with CATENIN signaling, which can be further enhanced by iDOT1L MET occurring at the middle-to-late-reprogramming stage along with treatment. -
New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology
Cancer Research and Treatment 2003;35(4):304-313 New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology Yong-Wan Kim, Ph.D.1, Min-Je Suh, M.S.1, Jin-Sik Bae, M.S.1, Su Mi Bae, M.S.1, Joo Hee Yoon, M.D.2, Soo Young Hur, M.D.2, Jae Hoon Kim, M.D.2, Duck Young Ro, M.D.2, Joon Mo Lee, M.D.2, Sung Eun Namkoong, M.D.2, Chong Kook Kim, Ph.D.3 and Woong Shick Ahn, M.D.2 1Catholic Research Institutes of Medical Science, 2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul; 3College of Pharmacy, Seoul National University, Seoul, Korea Purpose: This study utilized both mRNA differential significant genes of unknown function affected by the display and the Gene Ontology (GO) analysis to char- HPV-16-derived pathway. The GO analysis suggested that acterize the multiple interactions of a number of genes the cervical cancer cells underwent repression of the with gene expression profiles involved in the HPV-16- cancer-specific cell adhesive properties. Also, genes induced cervical carcinogenesis. belonging to DNA metabolism, such as DNA repair and Materials and Methods: mRNA differential displays, replication, were strongly down-regulated, whereas sig- with HPV-16 positive cervical cancer cell line (SiHa), and nificant increases were shown in the protein degradation normal human keratinocyte cell line (HaCaT) as a con- and synthesis. trol, were used. Each human gene has several biological Conclusion: The GO analysis can overcome the com- functions in the Gene Ontology; therefore, several func- plexity of the gene expression profile of the HPV-16- tions of each gene were chosen to establish a powerful associated pathway, identify several cancer-specific cel- cervical carcinogenesis pathway. -
A Lncrna/Lin28/Mirlet7 Axis Coupled to DNA Methylation Fine Tunes the Dynamics of a Cell State Transition
bioRxiv preprint doi: https://doi.org/10.1101/131110; this version posted April 26, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Li, M.A. et al A lncRNA/Lin28/Mirlet7 axis coupled to DNA methylation fine tunes the dynamics of a cell state transition Meng Amy Li1*,2,#, Paulo P. Amaral3, Priscilla Cheung2, Jan H. Bergmann4,9, Masaki Kinoshita1, Tüzer Kalkan1, Meryem Ralser1, Sam Robson3, Ferdinand von Meyenn5, Maike Paramor1, Fengtang Yang6, Caifu Chen7, Jennifer Nichols1, David L. Spector4, Tony Kouzarides3, Lin He2,#, Austin Smith1,8,# 1. Wellcome Trust - Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, UK 2. Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California 94705, USA 3. The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK 4. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA 5. Babraham Institute, Babraham, Cambridge, CB22 3AT 6. Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1SA, UK 7. Integrated DNA Technologies, 200 Chesapeake Drive, Redwood City, CA 94063, USA. 8. Department of Biochemistry, University of Cambridge, CB2 1QW, UK 9. Current address: Agenus inc., Hochbergerstrasse 60C, 4057 Basel, Switzerland *. Current address. # . Correspondence: [email protected], [email protected] and [email protected] Lead contact: Austin Smith Summary Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a condition poised for lineage specification. -
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. -
Atnea1-Identification and Characterization of a Novel Plant Nuclear Envelope Associated Protein
Vol. 13(7), pp. 844-856, 12 February, 2014 DOI: 10.5897/AJB2013.13078 ISSN 1684-5315 ©2014 Academic Journals African Journal of Biotechnology http://www.academicjournals.org/AJB Full Length Research Paper AtNEA1-identification and characterization of a novel plant nuclear envelope associated protein Ting Lu Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK. Accepted 29 January, 2014 In animal and yeast cells, a cross nuclear envelope structure linker of nucleoskeleton and cytoskeleton (LINC) is formed by outer nuclear membrane SUN proteins and inner nuclear membrane KASH proteins. However, little information was acquired about plant SUN-KASH structure until they were found in plant SUN proteins in 2010 and KASH proteins in 2012. The SUN-KASH complex alongside with actin in the microfilament cytoskeleton and nucleaoskeleton together shape the main cell skeleton structure and involve in many important biological functions including cell structure stability, cell movement and cell division. In searching of other plant nuclear envelope associated proteins, arabidopsis nuclear envelop associated (AtNEA1) protein 1, a plant nucleoplasmic protein, was identified from biological studies. AtNEA1 was predicted to have a nuclear localisation signal (NLS), two coiled coil domains and one transmembrane (TM) domain. The mutants with the deletion of respective putative domains were observed under confocal microscopy. The subcellular localisation of mutants implied that putative NLS is not essential for AtNEA1 to diffuse through NPC but can strongly increase the efficiency, both coiled coil domains participate in the interaction of AtNEA1 with its unknown INM intrinsic interaction partner, and putative TM appeared to be non-functional. -
Identification of Plant SUN Domain-Interacting Tail Proteins and Analysis of Their Function in Nuclear Positioning
Identification of Plant SUN Domain-Interacting Tail Proteins and Analysis of Their Function in Nuclear Positioning DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of the Ohio State University By Xiao Zhou, M. S. Graduate Program in Plant Cellular and Molecular Biology The Ohio State University 2013 Dissertation Committee: Professor Iris Meier, Advisor Professor Biao Ding Professor Stephen Osmani Professor R. Keith Slotkin Copyright by Xiao Zhou 2013 Abstract The nuclear envelope (NE) is a double membrane system consisting of an inner nuclear membrane (INM) and an outer nuclear membrane (ONM). Studies in opisthokonts revealed that the two membranes are bridged by protein complexes formed by the INM Sad1/UNC-84 (SUN) proteins and the ONM Klarsicht/ANC-1/Syne-1 homology (KASH) proteins. These SUN-KASH NE bridges are usually linkers of the nucleoskeleton to the cytoskeleton (LINC) conserved across eukaryotes. LINC complexes are key players in multiple cellular processes, such as nuclear and chromosomal positioning and nuclear shape determination, which in turn influence the gametogenesis and several aspects of development. Although these cellular processes have long been also known in plants, no KASH proteins are encoded in the plant genomes. I identified WPP domain interacting proteins (WIPs) as the first plant KASH protein analogs. WIPs are plant-specific ONM proteins that redundantly anchor Ran GTPase activating protein (RanGAP) to the NE. Arabidopsis thaliana WIPs (AtWIPs) interact with Arabidopsis thaliana SUN proteins (AtSUNs), which is required for both AtWIP1 and AtRanGAP1 NE localization. In addition, AtWIPs and AtSUNs are necessary for maintaining the elongated nuclear shape of Arabidopsis epidermal cells. -
Entropy Based Analysis of Vertebrate Sperm Protamines Sequences: Evidence of Potential Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines Christian D
Powell et al. BMC Genomics (2020) 21:277 https://doi.org/10.1186/s12864-020-6681-2 RESEARCH ARTICLE Open Access Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines Christian D. Powell1,2,DanielC.Kirchoff1, Jason E. DeRouchey1 and Hunter N. B. Moseley2,3,4* Abstract Background: Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. Results: Protamine sequences from UniProt’s databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. Conclusions: High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. -
Datasheet: VMA00210 Product Details
Datasheet: VMA00210 Description: MOUSE ANTI NAB1 Specificity: NAB1 Format: Purified Product Type: PrecisionAb™ Monoclonal Clone: OTI1D2 Isotype: IgG1 Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Product Form Purified IgG - liquid Preparation Mouse monoclonal antibody purified by affinity chromatography from ascites Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers 1% Bovine Serum Albumin 50% Glycerol Immunogen Recombinant protein corresponding to amino acids 237-487 of human NAB1 (NP_005957) produced in E. coli External Database UniProt: Links Q13506 Related reagents Entrez Gene: 4664 NAB1 Related reagents Specificity Mouse anti Human NAB1 antibody recognizes the NGFI-A-binding protein 1, also known as Page 1 of 2 EGR-1-binding protein 1, EGR1 binding protein 1 and transcriptional regulatory protein p54. Mouse anti Human NAB1 antibody detects a band of 54 kDa. The antibody has been extensively validated for western blotting using whole cell lysates. Western Blotting Anti NAB1 detects a band of approximately 54 kDa in Jurkat cell lysates Instructions For Use Please refer to the PrecisionAb western blotting protocol. -
An Ontogenetic Switch Drives the Positive and Negative Selection of B Cells
An ontogenetic switch drives the positive and negative selection of B cells Xijin Xua, Mukta Deobagkar-Lelea, Katherine R. Bulla, Tanya L. Crockforda, Adam J. Meadb, Adam P. Cribbsc, David Simsc, Consuelo Anzilottia, and Richard J. Cornalla,1 aMedical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom; bMedical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom; and cMedical Research Council, Weatherall Institute of Molecular Medicine, Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom Edited by Michael Reth, University of Freiburg, Freiburg, Germany, and approved January 6, 2020 (received for review September 3, 2019) + Developing B cells can be positively or negatively selected by self- BM HSCs increased CD5 B-1a B cell development (15), while antigens, but the mechanisms that determine these outcomes are expression of let-7b in FL pro-B cells blocked the development of incompletely understood. Here, we show that a B cell intrinsic B-1 B cells (17). These findings support the notion of hard-wired switch between positive and negative selection during ontogeny differences during ontogeny, but possibly downstream of the HSC is determined by a change from Lin28b to let-7 gene expression. commitment stage. Ectopic expression of a Lin28b transgene in murine B cells restored Several lines of evidence also suggest that B-1 B cells can un- the positive selection of autoreactive B-1 B cells by self-antigen in dergo positive selection, which is linked to their B cell receptor adult bone marrow. -
The LIN28B-IMP1 Post-Transcriptional Regulon Has Opposing Effects On
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2018 The IN28BL -IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine Blair B. Madison et al Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Downloaded from genesdev.cshlp.org on August 7, 2018 - Published by Cold Spring Harbor Laboratory Press The LIN28B–IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine Priya Chatterji,1,2,14 Kathryn E. Hamilton,1,3,14 Shun Liang,4 Sarah F. Andres,1 H.R. Sagara Wijeratne,4 Rei Mizuno,1 Lauren A. Simon,1,3 Philip D. Hicks,1 Shawn W. Foley,5 Jason R. Pitarresi,1 Andres J. Klein-Szanto,6,7 Amanda T. Mah,8 Laurianne Van Landeghem,9 Brian D. Gregory,5 Christopher J. Lengner,10 Blair B. Madison,11 Premal Shah,4,12 and Anil K. Rustgi1,2,13 1Department of Medicine, Division of Gastroenterology, 2Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19014, USA; 3Department of Pediatrics, Division of Gastroenterology, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19014, USA; 4Department of Genetics, Rutgers University, New Brunswick, New Jersey 08901, USA; 5Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19014, USA; 6Department of Pathology, 7Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA; 8Department of Medicine, Hematology Division, Stanford University, Stanford, California 94305, USA; 9Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, USA; 10Department of Biomedical Sciences, School of Veterinary Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; 11Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, St. -
Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance
biomolecules Review Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance Catherine Gough and Ari Sadanandom * Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1913341263 Abstract: Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness. Keywords: post-translational modifications; plant immunity; phosphorylation; ubiquitination; SUMOylation; defence Citation: Gough, C.; Sadanandom, A. 1. Introduction Understanding and Exploiting Plant growth and survival are constantly threatened by biotic stress, including plant Post-Translational Modifications for pathogens consisting of viruses, bacteria, fungi, and chromista. In the context of agriculture, Plant Disease Resistance. Biomolecules crop yield losses due to pathogens are estimated to be around 20% worldwide in staple 2021, 11, 1122. https://doi.org/ crops [1]. The spread of pests and diseases into new environments is increasing: more 10.3390/biom11081122 extreme weather events associated with climate change create favourable environments for food- and water-borne pathogens [2,3]. Academic Editors: Giovanna Serino The significant estimates of crop losses from pathogens highlight the need to de- and Daisuke Todaka velop crops with disease-resistance traits against current and emerging pathogens.