Curriculum Vita
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Nuclear DNA Content, Chromatin Organization and Chromosome Banding in Brown and Yellow Seeds of Dasypyrum Villosum (L.) P
Heredity 72 (1994) 365—373 Received 7 September 1993 Genetical Society of Great Britain Nuclear DNA content, chromatin organization and chromosome banding in brown and yellow seeds of Dasypyrum villosum (L.) P. Candargy R. CREMONINI*, N. COLONNAI-, A. STEFANIt, I. GALASSO4 & D. PIGNONE4 Dipartimento di Scienze Botaniche, Università di Pisa, Via L. Ghini 5, 56126 Pisa, tScuo/a Super/ore Studi Universitari e Perfezionamento 'S. Anna Via Carducci 40, 56127 Pisa, and Istituto del Germoplasma, CNR, Via Amendola 165, 70123 Ban, Italy Bandingpatterns of metaphase chromosomes and nuclear DNA content in root meristematic cells of yellow and brown seeds of Dasypyrum villosum were determined. Microdensitometric evaluation of nuclear absorptions at different thresholds of optical density after Feulgen reaction indicated the organization of the chromatin in interphase nuclei, and allowed an evaluation of the amount of heterochromatin. These results were compared with those obtained after the application of banding techniques. Keywords:chromatinorganization, chromosome banding, Dasypyrum villosum, fluorochromes, kernels. evident morphological differences; both of them are Introduction able to produce ears with yellow and brown caryopses Manyspecies closely related to Triticum are known to (Stefani & Onnis, 1983). have agronomic characters that make them interesting A different behaviour of seed germination and for wheat improvement, and many studies have been viability during ripening and ageing (Meletti & Onnis, carried out on the possibility of introducing alien genes 1961; Stefani & Onnis, 1983; De Gara et al., 1991) into cultivated wheats (Knott, 1987). and a different duration of the mitotic cycle (Innocenti The genus Dasypyrum includes two Mediterranean & Bitonti, 1983) have been reported for the two types wild species: an annual outcrossing diploid, Dasypyrum of caryopses. -
Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture
Genes 2015, 6, 790-811; doi:10.3390/genes6030790 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture Navneet K. Matharu 1,* and Sajad H. Ahanger 2,* 1 Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA 2 Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, Wagistrasse 14, Zurich 8952, Switzerland * Authors to whom correspondence should be addressed; E-Mails: [email protected] (N.K.M.); [email protected] (S.H.A.). Academic Editor: Jessica Tyler Received: 8 June 2015 / Accepted: 20 August 2015 / Published: 1 September 2015 Abstract: The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. -
Ultrastructure in Ochromonas Danica
EFFECTS OF CHLORAMPHENICOL ON CHLOROPLAST AND MITOCHONDRIAL ULTRASTRUCTURE IN OCHROMONAS DANICA HEIDI SMITH-JOHANNSEN and SARAH P . GIBBS From the Department of Biology, McGill University, Montreal 110, P. Q., Canada ABSTRACT The effect of chloramphenicol (CAP) on cell division and organelle ultrastructure was studied during light-induced chloroplast development in the Chrysophyte alga, Ochromonas danica . Since the growth rate of the CAP-treated cells is the same as that of the control cells for the first 12 hr in the light, CAP is presumed to be acting during that interval solely by inhibiting protein synthesis on chloroplast and mitochondrial ribosomes. CAP markedly inhibits chloroplast growth and differentiation . During the first 12 hr in the light, chloro- phyll synthesis is inhibited by 9317/c , the formation of new thylakoid membranes is reduced by 91 70, and the synthesis of chloroplast ribosomes is inhibited by 81 %. Other chloroplast- associated abnormalities which occur during the first 12 hr and become more pronounced with extended CAP treatment are the presence of prolamellar bodies and of abnormal stacks of thylakoids, the proliferation of the perinuclear reticulum, and the accumulation of dense granular material between the chloroplast envelope and the chloroplast endo- plasmic reticulum . CAP also causes a progressive loss of the mitochondrial cristae, which is paralleled by a decline in the growth rate of the cells, but it has no effect on the synthesis of mitochondrial ribosomes. We postulate that one or more chloroplast ribosomal proteins are synthesized on chloroplast ribosomes, whereas mitochondrial ribosomal pro- teins are synthesized on cytoplasmic ribosomes. INTRODUCTION Both chloroplasts and mitochondria are known insoluble inner membrane proteins, are believed to contain DNA and RNA and to have all the to be synthesized on mitochondrial ribosomes (3) . -
Repetitive Elements in Humans
International Journal of Molecular Sciences Review Repetitive Elements in Humans Thomas Liehr Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany; [email protected] Abstract: Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well. Keywords: variable numbers of tandem repeats (VNTRs); microsatellites; minisatellites; small-scale repetitive elements (SSREs); chromosomal heteromorphisms (CHs); higher-order repeat (HOR); retroviral DNA 1. Introduction Citation: Liehr, T. Repetitive In humans, like in other higher species, the genome of one individual never looks 100% Elements in Humans. Int. J. Mol. Sci. alike to another one [1], even among those of the same gender or between monozygotic 2021, 22, 2072. -
Reporterseq Reveals Genome-Wide Dynamic Modulators of the Heat
RESEARCH ARTICLE ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors Brian D Alford1†, Eduardo Tassoni-Tsuchida1,2†, Danish Khan1, Jeremy J Work1, Gregory Valiant3, Onn Brandman1* 1Department of Biochemistry, Stanford University, Stanford, United States; 2Department of Biology, Stanford University, Stanford, United States; 3Department of Computer Science, Stanford University, Stanford, United States Abstract Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time- resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time- specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway- specific readouts. *For correspondence: [email protected] †These authors contributed equally to this work Introduction Competing interests: The The heat shock response (HSR) is a conserved stress response that shields cells from cytoplasmic authors declare that no proteotoxicity by increasing the expression of protective proteins (Lindquist, 1986; Mori- competing interests exist. -
Live Cell Imaging of Meiosis in Arabidopsis Thaliana
TOOLS AND RESOURCES Live cell imaging of meiosis in Arabidopsis thaliana Maria A Prusicki1, Emma M Keizer2†, Rik P van Rosmalen2†, Shinichiro Komaki1‡, Felix Seifert1§, Katja Mu¨ ller1, Erik Wijnker3, Christian Fleck2#*, Arp Schnittger1* 1Department of Developmental Biology, University of Hamburg, Hamburg, Germany; 2Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands; 3Department of Plant Science, Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands Abstract To follow the dynamics of meiosis in the model plant Arabidopsis, we have established a live cell imaging setup to observe male meiocytes. Our method is based on the concomitant visualization of microtubules (MTs) and a meiotic cohesin subunit that allows following five cellular *For correspondence: parameters: cell shape, MT array, nucleus position, nucleolus position, and chromatin condensation. [email protected] (CF); [email protected] We find that the states of these parameters are not randomly associated and identify 11 cellular (AS) states, referred to as landmarks, which occur much more frequently than closely related ones, indicating that they are convergence points during meiotic progression. As a first application of our †These authors contributed system, we revisited a previously identified mutant in the meiotic A-type cyclin TARDY equally to this work ASYNCHRONOUS MEIOSIS (TAM). Our imaging system enabled us to reveal both qualitatively and Present address: ‡Plant Cell -
Communications Between Mitochondria and Endoplasmic Reticulum in the Regulation of Metabolic Homeostasis
cells Review Communications between Mitochondria and Endoplasmic Reticulum in the Regulation of Metabolic Homeostasis Pengcheng Zhang, Daniels Konja, Yiwei Zhang and Yu Wang * The State Key Laboratory of Pharmaceutical Biotechnology, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China; [email protected] (P.Z.); [email protected] (D.K.); [email protected] (Y.Z.) * Correspondence: [email protected] Abstract: Mitochondria associated membranes (MAM), which are the contact sites between en- doplasmic reticulum (ER) and mitochondria, have emerged as an important hub for signaling molecules to integrate the cellular and organelle homeostasis, thus facilitating the adaptation of energy metabolism to nutrient status. This review explores the dynamic structural and functional features of the MAM and summarizes the various abnormalities leading to the impaired insulin sensitivity and metabolic diseases. Keywords: mitochondria; endoplasmic reticulum; MAM; energy metabolism 1. Introduction Citation: Zhang, P.; Konja, D.; Zhang, In mammalian cells, the mitochondrion is the organelle specialized for energy produc- Y.; Wang, Y. Communications tion through the processes of oxidative phosphorylation, tricarboxylic acid (TCA) cycle between Mitochondria and and fatty acid β-oxidation [1]. Approximately 90% of cellular reactive oxygen species Endoplasmic Reticulum in the (ROS) are produced from mitochondria during the reactions of oxidative phosphorylation Regulation of Metabolic Homeostasis. (OXPHOS) -
Effects on Transcription and Nuclear Organization
30 Oct 2001 7:3 AR AR144-08.tex AR144-08.SGM ARv2(2001/05/10) P1: GJC Annu. Rev. Genet. 2001. 35:193–208 Copyright c 2001 by Annual Reviews. All rights reserved CHROMATIN INSULATORS AND BOUNDARIES: Effects on Transcription and Nuclear Organization Tatiana I. Gerasimova and Victor G. Corces Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218; e-mail: [email protected]; [email protected] Key Words DNA, chromatin, insulators, transcription, nucleus ■ Abstract Chromatin boundaries and insulators are transcriptional regulatory el- ements that modulate interactions between enhancers and promoters and protect genes from silencing effects by the adjacent chromatin. Originally discovered in Drosophila, insulators have now been found in a variety of organisms, ranging from yeast to hu- mans. They have been found interspersed with regulatory sequences in complex genes and at the boundaries between active and inactive chromatin. Insulators might mod- ulate transcription by organizing the chromatin fiber within the nucleus through the establishment of higher-order domains of chromatin structure. CONTENTS INTRODUCTION .....................................................193 SPECIFIC EXAMPLES OF INSULATOR ELEMENTS .......................194 Insulator Elements in Drosophila .......................................195 The Chicken -Globin Locus and Other Vertebrate Boundary Elements ........................................198 Yeast Boundary Elements .............................................199 MECHANISMS OF INSULATOR FUNCTION .............................200 OTHER FACTORS INVOLVED IN INSULATOR FUNCTION .................203 INTRODUCTION Insulators or chromatin boundaries are DNA sequences defined operationally by two characteristics: They interfere with enhancer-promoter interactions when present between them, and they buffer transgenes from chromosomal position effects (diagrammed in Figures 1 and 2) (30). These two properties must be mani- festations of the normal role these sequences play in the control of gene expression. -
Dynamics and Interplay of Nuclear Architecture, Genome Organization, and Gene Expression
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Dynamics and interplay of nuclear architecture, genome organization, and gene expression Robert Schneider and Rudolf Grosschedl1 Max Planck Institute of Immunobiology, 79108 Freiburg, Germany The organization of the genome in the nucleus of a eu- The nucleus is organized in specific compartments karyotic cell is fairly complex and dynamic. Various fea- that include proteinaceous nuclear bodies, eukaryotic tures of the nuclear architecture, including compart- and heterochromatic chromatin domains, compartmen- mentalization of molecular machines and the spatial talized multiprotein complexes, and nuclear pores that arrangement of genomic sequences, help to carry out and allow for nucleocytoplasmic transport. The dynamic, regulate nuclear processes, such as DNA replication, temporal, and spatial organization of the eukaryotic cell DNA repair, gene transcription, RNA processing, and nucleus emerges as a central determinant of genome mRNA transport. Compartmentalized multiprotein function, and it is important to understand the relation- complexes undergo extensive modifications or exchange ship between nuclear architecture, genome organization, of protein subunits, allowing for an exquisite dynamics and gene expression. Recently, high-resolution tech- of structural components and functional processes of the niques have permitted new insights into the nuclear ar- nucleus. The architecture of the interphase nucleus is chitecture and its relationship to gene expression. linked to the spatial arrangement of genes and gene clus- In this review, we focus on the dynamic organization ters, the structure of chromatin, and the accessibility of of the genome into chromosome territories and chroma- regulatory DNA elements. In this review, we discuss re- tin domains. -
Advanced Cellular Biochemistry
University of Montana ScholarWorks at University of Montana Syllabi Course Syllabi Spring 2-1-2007 BMED 600.01: Advanced Cellular Biochemistry Mark L. Grimes University of Montana - Missoula, [email protected] Scott Samuels University of Montana, Missoula, [email protected] Follow this and additional works at: https://scholarworks.umt.edu/syllabi Let us know how access to this document benefits ou.y Recommended Citation Grimes, Mark L. and Samuels, Scott, "BMED 600.01: Advanced Cellular Biochemistry" (2007). Syllabi. 11120. https://scholarworks.umt.edu/syllabi/11120 This Syllabus is brought to you for free and open access by the Course Syllabi at ScholarWorks at University of Montana. It has been accepted for inclusion in Syllabi by an authorized administrator of ScholarWorks at University of Montana. For more information, please contact [email protected]. Advanced Cellular Biochemistry Bioc/Phar 600 Spring 2007 Instructors M. Grimes Scott Samuels 243-4977; HS 112 243-6145; Clapp 207 [email protected] [email protected] Class 8:40 am - 10:00 am MF Skaggs Building 336 Jan 22, 2007 - May 4, 2007 Class 8:40 am - 10:00 am W Skaggs Building 114 Jan 22, 2007 - May 4, 2007 Catalog course description (4 cr.) Exploration on a molecular level the regulation of structure, function, and dynamics of eukaryotic cells. Topics include membranes, cytoskeleton, transcription, translation, signal transduction, cell motility, cell proliferation, and programmed cell death. Overview Cell Biology is vast and dense and encompasses biochemistry, biophysics, molecular biology, microscopy, genetics, physiology, computer science, and developmental biology. This course will use as a main text Alberts, et al., Molecular Biology of the Cell, 4th ed. -
Genetically Customized Generations—A Need for Increased Regulatory Control Over Gene Editing Technology in the United States
SMU Law Review Volume 73 Issue 3 Article 10 2020 Genetically Customized Generations—A Need for Increased Regulatory Control over Gene Editing Technology in the United States Morgan Mendicino Southern Methodist University, Dedman School of Law, [email protected] Follow this and additional works at: https://scholar.smu.edu/smulr Part of the Law Commons Recommended Citation Morgan Mendicino, Comment, Genetically Customized Generations—A Need for Increased Regulatory Control over Gene Editing Technology in the United States, 73 SMU L. REV. 585 (2020) https://scholar.smu.edu/smulr/vol73/iss3/10 This Comment is brought to you for free and open access by the Law Journals at SMU Scholar. It has been accepted for inclusion in SMU Law Review by an authorized administrator of SMU Scholar. For more information, please visit http://digitalrepository.smu.edu. GENETICALLY CUSTOMIZED GENERATIONS—A NEED FOR INCREASED REGULATORY CONTROL OVER GENE EDITING TECHNOLOGY IN THE UNITED STATES Morgan Mendicino* ABSTRACT Gene editing technology, once a far-fetched scientific fantasy, has be- come a tangible reality. One emerging form of gene editing in particular, human germline genome editing, possesses revolutionary capabilities that warrant cautious examination. Recent advancements in research have demonstrated that such biotechnology could be used to alter the genetic makeup of unborn children and the hereditary genes of future generations. This biotechnology may possess the ability to save countless human lives, but we must ask—What happens when the line between preventing disease and “playing God” becomes blurry? Human germline genome editing raises a multitude of widespread and deeply rooted questions surrounding the fate of humanity, all of which thwart justifying its present-day use. -
Keith Roberts Porter: 1912–1997
Keith Roberts Porter: 1912–1997 eith Roberts Porter died on May 2, 1997, just over a month short of his 85th birthday. He had the K perspicacity, good fortune, and patience to take advantage of the fast moving frontier of analytical biology after the Second World War to provide many of the tech- niques and experimental approaches that established the new field of biomedical research now known as cell biol- ogy. He was renowned for taking the first electron micro- graph of an intact cell, but his contributions went far be- yond that seminal instance. They ranged from technical developments, such as the roller flask for cell culture and the Porter-Blum ultramicrotome, to experimental and ob- servational achievements, such as studies on the synthesis and assembly of collagen, on the role of coated vesicles in endocytosis, on lipid digestion in the intestine, and on the universality of the 9 1 2 axoneme in cilia. The initial ultra- structure descriptions of the endoplasmic reticulum and the sarcoplasmic reticulum, identification of the role of T-tubules in excitation–contraction coupling in muscle and the role of the cytoskeleton in cell transformation and shape change, were his, as were many other contributions, described in some detail elsewhere (Peachey and Brinkley, 1983; Moberg, 1996). Absent from this list are his early pi- oneering work establishing the androgenetic haploid in frogs, an exercise in nuclear transplantation with conse- quences for the recent cloning of mammals, and his later ad- ventures with pigment migration in fish chromatophores. In addition to his specific scientific contributions, Keith Porter also made more important philosophical contribu- tions to the field that he helped to shape.