The Pseudogene Problem and RT-Qpcr Data Normalization; SYMPK
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Nuclear and Mitochondrial Genome Defects in Autisms
UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome. -
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. -
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments Stephen A
Clinical Chemistry 55:4 611–622 (2009) Special Report The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments Stephen A. Bustin,1* Vladimir Benes,2 Jeremy A. Garson,3,4 Jan Hellemans,5 Jim Huggett,6 Mikael Kubista,7,8 Reinhold Mueller,9 Tania Nolan,10 Michael W. Pfaffl,11 Gregory L. Shipley,12 Jo Vandesompele,5 and Carl T. Wittwer13,14 BACKGROUND: Currently, a lack of consensus exists on SUMMARY: Following these guidelines will encourage how best to perform and interpret quantitative real- better experimental practice, allowing more reliable time PCR (qPCR) experiments. The problem is exac- and unequivocal interpretation of qPCR results. erbated by a lack of sufficient experimental detail in © 2009 American Association for Clinical Chemistry many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments. The fluorescence-based quantitative real-time PCR (qPCR)15 (1–3), with its capacity to detect and mea- CONTENT: The Minimum Information for Publication sure minute amounts of nucleic acids in a wide range of of Quantitative Real-Time PCR Experiments (MIQE) samples from numerous sources, is the enabling tech- guidelines target the reliability of results to help ensure nology par excellence of molecular diagnostics, life sci- the integrity of the scientific literature, promote con- ences, agriculture, and medicine (4, 5). Its conceptual sistency between laboratories, and increase experimen- and practical simplicity, together with its combination tal transparency. MIQE is a set of guidelines that de- of speed, sensitivity, and specificity in a homogeneous scribe the minimum information necessary for assay, have made it the touchstone for nucleic acid evaluating qPCR experiments. -
HSF1 Polyclonal Antibody Catalog # AP70419
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 HSF1 Polyclonal Antibody Catalog # AP70419 Specification HSF1 Polyclonal Antibody - Product Information Application WB Primary Accession Q00613 Reactivity Human, Mouse Host Rabbit Clonality Polyclonal HSF1 Polyclonal Antibody - Additional Information Gene ID 3297 Other Names HSF1; HSTF1; Heat shock factor protein 1; HSF 1; Heat shock transcription factor 1; HSTF 1 Dilution WB~~Western Blot: 1/500 - 1/2000. Immunohistochemistry: 1/100 - 1/300. HSF1 Polyclonal Antibody - Background Immunofluorescence: 1/200 - 1/1000. ELISA: 1/10000. Not yet tested in other Function as a stress-inducible and applications. DNA-binding transcription factor that plays a central role in the transcriptional activation of Format the heat shock response (HSR), leading to the Liquid in PBS containing 50% glycerol, 0.5% expression of a large class of molecular BSA and 0.02% sodium azide. chaperones heat shock proteins (HSPs) that protect cells from cellular insults' damage Storage Conditions -20℃ (PubMed:1871105, PubMed:11447121, PubMed:1986252, PubMed:7760831, PubMed:7623826, PubMed:8946918, PubMed:8940068, PubMed:9341107, HSF1 Polyclonal Antibody - Protein Information PubMed:9121459, PubMed:9727490, PubMed:9499401, PubMed:9535852, Name HSF1 (HGNC:5224) PubMed:12659875, PubMed:12917326, PubMed:15016915, PubMed:25963659, Synonyms HSTF1 PubMed:26754925). In unstressed cells, is present in a HSP90-containing multichaperone Function complex that maintains it in a non-DNA-binding Functions -
Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle
SYMPLEKIN AND TRANSFORMING ACIDIC COILED-COIL CONTAINING PROTEIN 3 SUPPORT THE CANCER CELL MITOTIC SPINDLE Kathryn M. Cappell A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in the Department of Pharmacology, School of Medicine. Chapel Hill 2011 Approved by: Advisor: Dr. Angelique Whitehurst Reader: Dr. David Siderovski Reader: Dr. Channing Der Reader: Dr. Pilar Blancafort Reader: Dr. Mohanish Deshmukh ABSTRACT KATHRYN CAPPELL: Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle (Under the direction of Dr. Angelique Whitehurst) An increased rate of proliferation in cancer cells, combined with abnormalities in spindle architecture, places tumors under increased mitotic stress. Previously, our laboratory performed a genome-wide paclitaxel chemosensitizer screen to identify genes whose depletion sensitizes non- small cell lung cancer (NSCLC) cells to mitotic stress induced by paclitaxel treatment. This screen uncovered a cohort of genes that are required for viability only in the presence of paclitaxel. Two genes uncovered in this screen were the polyadenylation scaffold symplekin and the gametogenic protein transforming acidic coiled-coil containing protein 3 (TACC3). Herein, we examine the impact of polyadenylation and gametogenesis on the tumor cell mitotic spindle. First, we demonstrate that depletion of SYMPK and other polyadenylation components sensitizes many NSCLC cells, but not normal immortalized lines, to paclitaxel by inducing mitotic errors and leading to abnormal mitotic progression. Second, we demonstrate that multiple gametogenic genes are required for normal microtubule dynamics and mitotic spindle formation in the presence of paclitaxel. -
Phospho-HSF1 (Ser326) Rabbit Pab 产品说明书
正能生物 Phospho-HSF1 (Ser326) Rabbit pAb 货号:384621 Size 100ul 50ul Antibody type Primary antibody Conjugation Unconjugated Modification Phosphoralated Isotype Rabbit IgG Host Rabbit Application WB , IHC-P , IHC-F , ICC/IF , FC , IP Purification Affinity purified Cross reactivity Human Gene name HSF1 Alternative names HSTF1 Gene symbol HSTF1 Description Swiss-Prot Acc.Q00613.Function as a stress-inducible and DNA-binding transcription factor that plays a central role in the transcriptional activation of the heat shock response (HSR), leading to the expression of a large class of molecular chaperones heat shock proteins (HSPs) that protect cells from cellular insults' damage (PubMed:1871105, PubMed:11447121, PubMed:1986252, PubMed:7760831, PubMed:7623826, PubMed:8946918, PubMed:8940068, PubMed:9341107, PubMed:9121459, PubMed:9727490, PubMed:9499401, PubMed:9535852, PubMed:12659875, PubMed:12917326, PubMed:15016915, PubMed:25963659, PubMed:26754925). In unstressed cells, is present in a HSP90-containing multichaperone complex that maintains it in a non-DNA-binding inactivated monomeric form (PubMed:9727490, PubMed:11583998, PubMed:16278218). Upon exposure to heat and other stress stimuli, undergoes homotrimerization and activates HSP gene transcription through binding to site-specific heat shock elements (HSEs) present in the promoter regions of HSP genes (PubMed:1871105, PubMed:1986252, PubMed:8455624, PubMed:7935471, PubMed:7623826, PubMed:8940068, PubMed:9727490, PubMed:9499401, PubMed:10359787, PubMed:11583998, PubMed:12659875, PubMed:16278218, PubMed:25963659, PubMed:26754925). Activation is reversible, and during the attenuation and recovery phase period of the HSR, returns to its unactivated form (PubMed:11583998, PubMed:16278218). Binds to inverted 5'-NGAAN-3' pentamer DNA sequences (PubMed:1986252, PubMed:26727489). Binds to chromatin at heat shock gene promoters (PubMed:25963659). -
Quantitative SUMO Proteomics Reveals the Modulation of Several
www.nature.com/scientificreports OPEN Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated Received: 10 October 2017 Accepted: 28 March 2018 proteins and an anti-senescence Published: xx xx xxxx function of UBC9 Francis P. McManus1, Véronique Bourdeau2, Mariana Acevedo2, Stéphane Lopes-Paciencia2, Lian Mignacca2, Frédéric Lamoliatte1,3, John W. Rojas Pino2, Gerardo Ferbeyre2 & Pierre Thibault1,3 Several regulators of SUMOylation have been previously linked to senescence but most targets of this modifcation in senescent cells remain unidentifed. Using a two-step purifcation of a modifed SUMO3, we profled the SUMO proteome of senescent cells in a site-specifc manner. We identifed 25 SUMO sites on 23 proteins that were signifcantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation. Many cellular mechanisms of defense have evolved to reduce the onset of tumors and potential cancer develop- ment. One such mechanism is cellular senescence where cells undergo cell cycle arrest in response to various stressors1,2. Multiple triggers for the onset of senescence have been documented. While replicative senescence is primarily caused in response to telomere shortening3,4, senescence can also be triggered early by a number of exogenous factors including DNA damage, elevated levels of reactive oxygen species (ROS), high cytokine signa- ling, and constitutively-active oncogenes (such as H-RAS-G12V)5,6. -
Related Regulators of 3′ UTR Processing with KAPAC Andreas J
Gruber et al. Genome Biology (2018) 19:44 https://doi.org/10.1186/s13059-018-1415-3 METHOD Open Access Discovery of physiological and cancer- related regulators of 3′ UTR processing with KAPAC Andreas J. Gruber† , Ralf Schmidt†, Souvik Ghosh, Georges Martin, Andreas R. Gruber, Erik van Nimwegen and Mihaela Zavolan* Abstract 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. Keywords: Cleavage and polyadenylation, APA, CFIm, KAPAC, PAQR, HNRNPC, PTBP1, Prostate adenocarcinoma, Glioblastoma, Colon adenocarcinoma Background signal, consisting of the CPSF1, CPSF4, FIP1L1, and The 3′ ends of most eukaryotic mRNAs are generated WDR33 proteins, has been identified [6, 7]. through endonucleolytic cleavage and polyadenylation Most genes have multiple poly(A) sites (PAS), which (CPA) [1–3]. These steps are carried out in mammalian are differentially processed across cell types [8], likely cells by a 3′ end processing complex composed of the due to cell type-specific interactions with RNA-binding cleavage and polyadenylation specificity factor (which in- proteins (RBPs). The length of 3′ UTRs is most strongly cludes the proteins CPSF1 (also known as CPSF160), dependent on the mammalian cleavage factor I (CFIm), CPSF2 (CPSF100), CPSF3 (CPSF73), CPSF4 (CPSF30), which promotes the use of distal poly(A) sites [5, 9–12]. -
Technical Aspects and Recommendations for Single-Cell Qpcr
Molecular Aspects of Medicine xxx (2017) 1e8 Contents lists available at ScienceDirect Molecular Aspects of Medicine journal homepage: www.elsevier.com/locate/mam Technical aspects and recommendations for single-cell qPCR * Anders Ståhlberg a, , Mikael Kubista b, c a Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Box 425, 40530 Gothenburg, Sweden b TATAA Biocenter, Odinsgatan 28, 41103 Gothenburg, Sweden c Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Prague, Czech Republic article info abstract Article history: Single cells are basic physiological and biological units that can function individually as well as in groups Received 17 May 2017 in tissues and organs. It is central to identify, characterize and profile single cells at molecular level to be Received in revised form able to distinguish different kinds, to understand their functions and determine how they interact with 16 July 2017 each other. During the last decade several technologies for single-cell profiling have been developed and Accepted 24 July 2017 used in various applications, revealing many novel findings. Quantitative PCR (qPCR) is one of the most Available online xxx developed methods for single-cell profiling that can be used to interrogate several analytes, including DNA, RNA and protein. Single-cell qPCR has the potential to become routine methodology but the Keywords: Single-cell analysis technique is still challenging, as it involves several experimental steps and few molecules are handled. qPCR Here, we discuss technical aspects and provide recommendation for single-cell qPCR analysis. The Single-cell qPCR workflow includes experimental design, sample preparation, single-cell collection, direct lysis, reverse Single-cell workflow transcription, preamplification, qPCR and data analysis. -
Antisense Oligonucleotide-Based Therapeutic Against Menin for Triple-Negative Breast Cancer Treatment
biomedicines Article Antisense Oligonucleotide-Based Therapeutic against Menin for Triple-Negative Breast Cancer Treatment Dang Tan Nguyen 1,†, Thi Khanh Le 1,2,† , Clément Paris 1,†, Chaïma Cherif 1 , Stéphane Audebert 3 , Sandra Oluchi Udu-Ituma 1,Sébastien Benizri 4 , Philippe Barthélémy 4 , François Bertucci 1, David Taïeb 1,5 and Palma Rocchi 1,* 1 Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, 13273 Marseille, France; [email protected] (D.T.N.); [email protected] (T.K.L.); [email protected] (C.P.); [email protected] (C.C.); [email protected] (S.O.U.-I.); [email protected] (F.B.); [email protected] (D.T.) 2 Department of Life Science, University of Science and Technology of Hanoi (USTH), Hanoi 000084, Vietnam 3 Marseille Protéomique, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France; [email protected] 4 ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, 33076 Bordeaux, France; [email protected] (S.B.); [email protected] (P.B.) 5 Biophysics and Nuclear Medicine Department, La Timone University Hospital, European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France * Correspondence: [email protected]; Tel.: +33-626-941-287 † These authors contributed equally. Citation: Nguyen, D.T.; Le, T.K.; Paris, C.; Cherif, C.; Audebert, S.; Abstract: The tumor suppressor menin has dual functions, acting either as a tumor suppressor or Oluchi Udu-Ituma, S.; Benizri, S.; as an oncogene/oncoprotein, depending on the oncological context. -
NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment. -
Cov2-ID, a MIQE-Compliant Sub-20-Min 5-Plex RT-PCR Assay
www.nature.com/scientificreports OPEN CoV2‑ID, a MIQE‑compliant sub‑20‑min 5‑plex RT‑PCR assay targeting SARS‑CoV‑2 for the diagnosis of COVID‑19 Stephen Bustin1*, Amy Coward2, Garry Sadler2, Louise Teare2 & Tania Nolan1 Accurate, reliable and rapid detection of SARS‑CoV‑2 is essential not only for correct diagnosis of individual COVID‑19 disease but also for the development of a rational strategy aimed at lifting confnement restrictions and preparing for possible recurrent waves of viral infections. We have used the MIQE guidelines to develop two versions of a unique fve plex RT‑qPCR test, termed CoV2‑ID, that allows the detection of three viral target genes, a human internal control for confrming the presence of human cells in a sample and a control artifcial RNA for quality assessment and potential quantifcation. Viral targets can be detected either individually with separate fuorophores or jointly using the same fuorophore, thus increasing the test’s reliability and sensitivity. It is robust, can consistently detect two copies of viral RNA, with a limit of detection of a single copy and can be completed in around 15 min. It was 100% sensitive and 100% specifc when tested on 23 RNA samples extracted from COVID‑19 positive patients and fve COVID‑19 negative patients. We also propose using multiple cycle fuorescence detection, rather than real‑time PCR to reduce signifcantly the time taken to complete the assay as well as assuage the misunderstandings underlying the use of quantifcation cycles (Cq). Finally, we have designed an assay for the detection of the D614G mutation and show that all of the samples isolated in the Chelmsford, Essex area between mid‑April and June 2020, have the mutant genotype whereas a sample originating in Australia was infected with the wild type genotype.