The Short‐Term Effects of Low‐Dose‐Rate Radiation on El4 Lymphoma Cell
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Elio™ Plasma Complete
™ elio plasma complete About PGDx elioTM plasma complete PGDx elio™ plasma complete is an end-to-end kitted liquid biopsy solution that analyzes circulating tumor DNA for genetic alterations in cancer, eliminating the need for an invasive biopsy or tumor tissue. Designed to be used across the globe on the PGDx elio™ testing platform, PGDx elio plasma complete also includes automated bioinformatics ensuring consistent, high-quality results. What does PGDx elioTM mean? Assay Specifications Empowering Local PARAMETER DETAILS Insight for Oncology Panel Size 2.1MB 521 genes for SNV & Indels 38 genes for amplifications 21 genes for translocations Panel Content and Variant Type bMSI bTMB (Muts/Mb) LOH status Sample requirement plasma ctDNA DNA input requirement 25ng recommended, 10ng minimum End-to-end Kitted 521 Genes From a Single Solution Sample Pass Rate 97.4% overall pass rate (227/233) Sample Sequencing platform/flowcell NovaSeq 6000/S2 flow cell Sequence run 2 x 150 bp Cases per sequencing run 16 (no external control required) Turn-key Developed Under Workflow Manual and Automated Available Bioinformatics Design Control Pipeline Average total coverage ~20,000x Performance Specifications PRODUCT FEATURES Variant Reportable Analytical Analytical Range Sensitivity Specificity (LOD95) Actionable • Plasma analysis for pan-cancer solid ≥ 0.1% VAF 0.40% VAF 100% SNVs/Indels tumor biomarker testing and discovery • 500+ gene kitted assay developed under Non-actionable ≥ 0.5% VAF 1.16% VAF 99.9% Design Control SNVs/Indels • Comprehensive coverage of biomarkers, All clinically relevant targets, cancer ≥ 3 fusion reads 0.33% VAF 100% Translocations signaling pathways and DNA damage repair pathways All ≥ 1.15-fold 1.32-fold 100% • Large panel size supports TMB and LOH Amplifications For Research Use Only. -
Use of Mathematical Modeling and Other Biophysical Methods For
USE OF MATHEMATICAL MODELING AND OTHER BIOPHYSICAL METHODS FOR INSIGHTS INTO IRON-RELATED PHENOMENA OF BIOLOGICAL SYSTEMS A Dissertation by JOSHUA D. WOFFORD Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Paul A. Lindahl Committee Members, David P. Barondeau Simon W. North Vishal M. Gohil Head of Department, Simon W. North December 2018 Major Subject: Chemistry Copyright 2018 Joshua D. Wofford ABSTRACT Iron is a crucial nutrient in most living systems. It forms the active centers of many proteins that are critical for many cellular functions, either by themselves or as Fe-S clusters and hemes. However, Fe is potentially toxic to the cell in high concentrations and must be tightly regulated. There has been much work into understanding various pieces of Fe trafficking and regulation, but integrating all of this information into a coherent model has proven difficult. Past research has focused on different Fe species, including cytosolic labile Fe or mitochondrial Fe-S clusters, as being the main regulator of Fe trafficking in yeast. Our initial modeling efforts demonstrate that both cytosolic Fe and mitochondrial ISC assembly are required for proper regulation. More recent modeling efforts involved a more rigorous multi- tiered approach. Model simulations were optimized against experimental results involving respiring wild-type and Mrs3/4-deleted yeast. Simulations from both modeling studies suggest that mitochondria possess a “respiratory shield” that prevents a vicious cycle of nanoparticle formation, ISC loss, and subsequent loading of mitochondria with iron. -
Large XPF-Dependent Deletions Following Misrepair of a DNA Double Strand Break Are Prevented by the RNA:DNA Helicase Senataxin
www.nature.com/scientificreports OPEN Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented Received: 26 October 2017 Accepted: 9 February 2018 by the RNA:DNA helicase Published: xx xx xxxx Senataxin Julien Brustel1, Zuzanna Kozik1, Natalia Gromak2, Velibor Savic3,4 & Steve M. M. Sweet1,5 Deletions and chromosome re-arrangements are common features of cancer cells. We have established a new two-component system reporting on epigenetic silencing or deletion of an actively transcribed gene adjacent to a double-strand break (DSB). Unexpectedly, we fnd that a targeted DSB results in a minority (<10%) misrepair event of kilobase deletions encompassing the DSB site and transcribed gene. Deletions are reduced upon RNaseH1 over-expression and increased after knockdown of the DNA:RNA helicase Senataxin, implicating a role for DNA:RNA hybrids. We further demonstrate that the majority of these large deletions are dependent on the 3′ fap endonuclease XPF. DNA:RNA hybrids were detected by DNA:RNA immunoprecipitation in our system after DSB generation. These hybrids were reduced by RNaseH1 over-expression and increased by Senataxin knock-down, consistent with a role in deletions. Overall, these data are consistent with DNA:RNA hybrid generation at the site of a DSB, mis-processing of which results in genome instability in the form of large deletions. DNA is the target of numerous genotoxic attacks that result in diferent types of damage. DNA double-strand breaks (DSBs) occur at low frequency, compared with single-strand breaks and other forms of DNA damage1, however DSBs pose the risk of translocations and deletions and their repair is therefore essential to cell integrity. -
Studies of Iron Sulfur Cluster Maturation and Transport DISSERTATION Presented in Partial Fulfillment of the Requirements for Th
Studies of Iron Sulfur Cluster Maturation and Transport DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jingwei Li Graduate Program in Chemistry The Ohio State University 2015 Dissertation Committee: Professor James A. Cowan, Advisor Professor Ross E. Dalbey Professor Claudia Turro Copyright by Jingwei Li 2015 Abstract Cellular iron homeostasis is critically dependent on sensory and regulatory mechanisms that maintain a balance of intracellular iron concentrations. Divergence from a healthy iron concentration can result in common disease states such as anemia and ataxia. With the goal of understanding the molecular basis for such health problems, and advancing the knowledge based toward potential remedies, an understanding of the molecular details of cellular iron transport and the biological chemistry of iron species is an essential prerequisite. In that regard, iron-sulfur clusters are ubiquitous iron-containing centers in a variety of proteins and serve a multitude of roles that include electron transfer, catalysis of reactions, and sensors of cellular oxygen and iron levels. Recently, a substantial body of evidence has suggested an essential role for cellular glutathione (a molecule normally implicated with eliminating reactive oxygen species from cells) in the regulation, stabilization and biosynthesis of cellular iron-sulfur clusters in humans and other complex organisms. We have demonstrated that glutathione can naturally bind to iron-sulfur cluster precursors and have isolated and characterized this species and shown it to be stable under physiological conditions. More importantly, we have demonstrated that the glutathione-bound iron-sulfur cluster can be transported by a ii critical export protein from the cellular mitochondrion. -
MECHANISMS in ENDOCRINOLOGY: Novel Genetic Causes of Short Stature
J M Wit and others Genetics of short stature 174:4 R145–R173 Review MECHANISMS IN ENDOCRINOLOGY Novel genetic causes of short stature 1 1 2 2 Jan M Wit , Wilma Oostdijk , Monique Losekoot , Hermine A van Duyvenvoorde , Correspondence Claudia A L Ruivenkamp2 and Sarina G Kant2 should be addressed to J M Wit Departments of 1Paediatrics and 2Clinical Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, Email The Netherlands [email protected] Abstract The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFkB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. -
Neurodegeneration in Accelerated Aging
DOCTOR OF MEDICAL SCIENCE DANISH MEDICAL JOURNAL Neurodegeneration in Accelerated Aging Morten Scheibye-Knudsen This review has been accepted as a thesis together with 7 previously published pa- pers by the University of Copenhagen, October 16, 2014 and defended on January 14, 2016 Official opponents: Alexander Bürkle, University of Konstanz Lars Eide, University of Oslo Correspondence: Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen E-mail: [email protected] Dan Med J 2016;63(11):B5308 INTRODUCTION The global elderly population has been progressively increasing throughout the 20th century and this growth is projected to per- sist into the late 21st century resulting in 20% of the total world population being aged 65 or more by the year 2100 (Figure 1). 80% of the total cost of health care is accrued after 40 years of Figure 2. The phenotype of human aging. age where chronic diseases become prevalent [1, 2]. With an ex- that appear to regulate the aging process [4,5]. These include the ponential increase in health care costs, it follows that the chronic insulin and IGF-1 signaling cascades [4], protein synthesis and diseases that accumulate in an aging population poses a serious quality control [6], regulation of cell proliferation through factors socioeconomic problem. Finding treatments to age related dis- such as mTOR [7], stem cell maintenance 8 as well as mitochon- eases, therefore becomes increasingly more pertinent as the pop- drial preservation [9]. Most of these pathways are conserved ulation ages. Even more so since there appears to be a continu- through evolution and appear to regulate aging in many lower or- ous increase in the prevalence of chronic diseases in the aging ganisms. -
Role of Rim101p in the Ph Response in Candida Albicans Michael Weyler
Role of Rim101p in the pH response in Candida albicans Michael Weyler To cite this version: Michael Weyler. Role of Rim101p in the pH response in Candida albicans. Biomolecules [q-bio.BM]. Université Paris Sud - Paris XI, 2007. English. tel-00165802 HAL Id: tel-00165802 https://tel.archives-ouvertes.fr/tel-00165802 Submitted on 27 Jul 2007 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. UNIVERSITE PARISXI UFR SCIENTIFIQUE D’ORSAY THESE présentée par Michael Weyler pour obtenir le grade de DOCTEUR EN SCIENCES DE L’UNIVERSITE PARISXI-ORSAY LE RÔLE DE RIM101p DANS LA RÉPONSE AU pH CHEZ CANDIDA ALBICANS Soutenance prévue le 6 juillet 2007 devant le jury composé de: Pr. Dr. H. Delacroix Président Dr. J-M. Camadro Rapporteur Pr. Dr. F. M. Klis Rapporteur Dr. G. Janbon Examinateur Dr. M. Lavie-Richard Examinateur Pr. Dr. C. Gaillardin Examinateur Remerciements Tout d’abord je voudrais remercier vivement mon directeur de thèse, Prof. Claude Gaillardin, pour m’avoir permis d’effectuer ce travail au sein de son laboratoire, pour ses conseils et sa disponibilité malgré son calendrier bien remplis. Je lui remercie également pour m’avoir laissé beaucoup de liberté dans mon travail, et pour la possibilité de participer aux différents congrès au cours de ma formation de thèse. -
Programmed Cell-Death by Ferroptosis: Antioxidants As Mitigators
International Journal of Molecular Sciences Review Programmed Cell-Death by Ferroptosis: Antioxidants as Mitigators Naroa Kajarabille 1 and Gladys O. Latunde-Dada 2,* 1 Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of the Basque Country (UPV/EHU), 01006 Vitoria, Spain; [email protected] 2 King’s College London, Department of Nutritional Sciences, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK * Correspondence: [email protected] Received: 9 September 2019; Accepted: 2 October 2019; Published: 8 October 2019 Abstract: Iron, the fourth most abundant element in the Earth’s crust, is vital in living organisms because of its diverse ligand-binding and electron-transfer properties. This ability of iron in the redox cycle as a ferrous ion enables it to react with H2O2, in the Fenton reaction, to produce a hydroxyl radical ( OH)—one of the reactive oxygen species (ROS) that cause deleterious oxidative damage • to DNA, proteins, and membrane lipids. Ferroptosis is a non-apoptotic regulated cell death that is dependent on iron and reactive oxygen species (ROS) and is characterized by lipid peroxidation. It is triggered when the endogenous antioxidant status of the cell is compromised, leading to lipid ROS accumulation that is toxic and damaging to the membrane structure. Consequently, oxidative stress and the antioxidant levels of the cells are important modulators of lipid peroxidation that induce this novel form of cell death. Remedies capable of averting iron-dependent lipid peroxidation, therefore, are lipophilic antioxidants, including vitamin E, ferrostatin-1 (Fer-1), liproxstatin-1 (Lip-1) and possibly potent bioactive polyphenols. -
Single-Cell RNA-Seq Analysis of the Brainstem of Mutant SOD1 Mice Reveals Perturbed Cell Types and Pathways of Amyotrophic Lateral Sclerosis
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Neurobiol Manuscript Author Dis. Author manuscript; Manuscript Author available in PMC 2020 September 26. Published in final edited form as: Neurobiol Dis. 2020 July ; 141: 104877. doi:10.1016/j.nbd.2020.104877. Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis Wenting Liua, Sharmila Venugopala, Sana Majida, In Sook Ahna, Graciel Diamantea, Jason Honga, Xia Yanga,b,c,*, Scott H. Chandlera,b,* aDepartment of Integrative Biology & Physiology, University of California, 2024 Terasaki Bld, 610 Charles E. Young Dr. East, Los Angeles, USA bBrain Research Institute, University of California, Los Angeles, USA cInstitute for Quantitative and Computational Biosciences, University of California, Los Angeles, USA Abstract Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease in which motor neurons throughout the brain and spinal cord progressively degenerate resulting in muscle atrophy, paralysis and death. Recent studies using animal models of ALS implicate multiple cell-types (e.g., astrocytes and microglia) in ALS pathogenesis in the spinal motor systems. To ascertain cellular vulnerability and cell-type specific mechanisms of ALS in the brainstem that orchestrates oral-motor functions, we conducted parallel single cell RNA sequencing (scRNA-seq) analysis using the high-throughput Drop-seq method. We isolated 1894 and 3199 cells from the brainstem of wildtype and mutant SOD1 symptomatic mice respectively, at postnatal day 100. We recovered major known cell types and neuronal subpopulations, such as interneurons and motor neurons, and trigeminal ganglion (TG) peripheral sensory neurons, as well as, previously uncharacterized interneuron subtypes. -
Regulation of the Intranuclear Distribution of the Cockayne Syndrome Proteins Received: 26 July 2017 Teruaki Iyama, Mustafa N
www.nature.com/scientificreports OPEN Regulation of the Intranuclear Distribution of the Cockayne Syndrome Proteins Received: 26 July 2017 Teruaki Iyama, Mustafa N. Okur, Tyler Golato, Daniel R. McNeill, Huiming Lu , Accepted: 1 November 2018 Royce Hamilton, Aishwarya Raja, Vilhelm A. Bohr & David M. Wilson III Published: xx xx xxxx Cockayne syndrome (CS) is an inherited disorder that involves photosensitivity, developmental defects, progressive degeneration and characteristics of premature aging. Evidence indicates primarily nuclear roles for the major CS proteins, CSA and CSB, specifcally in DNA repair and RNA transcription. We reveal herein a complex regulation of CSB targeting that involves three major consensus signals: NLS1 (aa467-481), which directs nuclear and nucleolar localization in cooperation with NoLS1 (aa302-341), and NLS2 (aa1038-1055), which seemingly optimizes nuclear enrichment. CSB localization to the nucleolus was also found to be important for full UVC resistance. CSA, which does not contain any obvious targeting sequences, was adversely afected (i.e. presumably destabilized) by any form of truncation. No inter-coordination between the subnuclear localization of CSA and CSB was observed, implying that this aspect does not underlie the clinical features of CS. The E3 ubiquitin ligase binding partner of CSA, DDB1, played an important role in CSA stability (as well as DDB2), and facilitated CSA association with chromatin following UV irradiation; yet did not afect CSB chromatin binding. We also observed that initial recruitment of CSB to DNA interstrand crosslinks is similar in the nucleoplasm and nucleolus, although fnal accumulation is greater in the former. Whereas assembly of CSB at sites of DNA damage in the nucleolus was not afected by RNA polymerase I inhibition, stable retention at these sites of presumed repair was abrogated. -
Understanding Nucleotide Excision Repair and Its Roles in Cancer and Ageing
REVIEWS DNA DAMAGE Understanding nucleotide excision repair and its roles in cancer and ageing Jurgen A. Marteijn*, Hannes Lans*, Wim Vermeulen, Jan H. J. Hoeijmakers Abstract | Nucleotide excision repair (NER) eliminates various structurally unrelated DNA lesions by a multiwise ‘cut and patch’-type reaction. The global genome NER (GG‑NER) subpathway prevents mutagenesis by probing the genome for helix-distorting lesions, whereas transcription-coupled NER (TC‑NER) removes transcription-blocking lesions to permit unperturbed gene expression, thereby preventing cell death. Consequently, defects in GG‑NER result in cancer predisposition, whereas defects in TC‑NER cause a variety of diseases ranging from ultraviolet radiation‑sensitive syndrome to severe premature ageing conditions such as Cockayne syndrome. Recent studies have uncovered new aspects of DNA-damage detection by NER, how NER is regulated by extensive post-translational modifications, and the dynamic chromatin interactions that control its efficiency. Based on these findings, a mechanistic model is proposed that explains the complex genotype–phenotype correlations of transcription-coupled repair disorders. The integrity of DNA is constantly threatened by endo of an intricate DNA-damage response (DDR), which genously formed metabolic products and by-products, comprises sophisticated repair and damage signalling such as reactive oxygen species (ROS) and alkylating processes. The DDR involves DNA-damage sensors and agents, and by its intrinsic chemical instability (for exam signalling kinases that regulate a range of downstream ple, by its ability to spontaneously undergo hydrolytic mediator and effector molecules that control repair, cell deamination and depurination). Environmental chemi cycle progression and cell fate4. The core of this DDR is cals and radiation also affect the physical constitution of formed by a network of complementary DNA repair sys DNA1. -
Diallyl Disulfide Inhibits the Proliferation of HT-29 Human Colon Cancer Cells by Inducing Differentially Expressed Genes
MOLECULAR MEDICINE REPORTS 4: 553-559, 2011 Diallyl disulfide inhibits the proliferation of HT-29 human colon cancer cells by inducing differentially expressed genes YOU-SHENG HUANG1,2, NA XIE1,2, QI SU1, JIAN SU1, CHEN HUANG1 and QIAN-JIN LIAO1 1Cancer Research Institute, University of South China, Hengyang, Hunan 421001; 2Department of Pathology, Hainan Medical University, Haikou, Hainan 571101, P.R. China Received November 22, 2010; Accepted February 28, 2011 DOI: 10.3892/mmr.2011.453 Abstract. Diallyl disulfide (DADS), a sulfur compound Introduction derived from garlic, has been shown to have protective effects against colon carcinogenesis in several studies performed in Colon cancer is one of the major causes of cancer death rodent models. However, its molecular mechanism of action worldwide (1). An understanding of the mechanisms involved remains unclear. This study was designed to confirm the anti- in the occurrence and development of colon cancer would aid proliferative activity of DADS and to screen for differentially in its therapy. Epidemiological investigations have provided expressed genes induced by DADS in human colon cancer cells compelling evidence that environmental factors are modifiers with the aim of exploring its possible anticancer mechanisms. in colon cancer (1-3); diet has also been shown to be an impor- The anti-proliferative capability of DADS in the HT-29 human tant determinant of cancer risk and tumor behavior (3-5). colon cancer cells was analyzed by MTT assays and flow Garlic consumption is very popular all over the world. cytometry. The differences in gene expression between DADS- Epidemiological studies have shown an inverse correlation treated (experimental group) and untreated (control group) between the consumption of garlic and colon cancer in certain HT-29 cells were identified using two-directional suppression areas (6).