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The Treasure Vault Can Be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material Inger Greve Alsos, Sebastien Lavergne, Marie Kristine Føreid Merkel, Marti Boleda, Youri Lammers, Adriana Alberti, Charles Pouchon, France Denoeud, Iva Pitelkova, Mihai Pușcaș, et al. To cite this version: Inger Greve Alsos, Sebastien Lavergne, Marie Kristine Føreid Merkel, Marti Boleda, Youri Lammers, et al.. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. Plants, MDPI, 2020, 9 (4), pp.432. 10.3390/plants9040432. hal- 02612289 HAL Id: hal-02612289 https://hal.archives-ouvertes.fr/hal-02612289 Submitted on 12 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License plants Article The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material Inger Greve Alsos 1,* , Sebastien Lavergne 2, Marie Kristine Føreid Merkel 1, Marti Boleda 2, Youri Lammers 1, Adriana Alberti 3 , Charles Pouchon 2, France Denoeud 3, Iva Pitelkova 1, 4 2,5 6 2 Mihai Pus, cas, , Cristina Roquet , Bogdan-Iuliu Hurdu , Wilfried Thuiller , Niklaus E. -
The Mystery of the Missing Centriole Solved!
Downloaded from Carmichael’s Concise Review The Mystery of the Missing Centriole https://www.cambridge.org/core Coming Events Solved! 2018 European Microbiology Research Stephen W. Carmichael* and Jeffery L. Salisbury Conference December 3–5, 2018 Mayo Clinic, Rochester, MN 55905 Valencia, Spain http://europeanmicrobiology.madridge.com *[email protected] From Images to Knowledge with . IP address: ImageJ & Friends December 6–8, 2018 Heidelberg, Germany www.embl.de/training/events/2018/IMJ18-01 Most mammalian cells contain two centrioles that duplicate during cell division. One 170.106.33.19 American Society for Cell Biology would expect the human zygote to have two centrioles during interphase and four centrioles (ASCB) 2018 Annual Meeting during mitosis. However, four centrioles have never been shown in any mammalian zygote, December 8–12, 2018 only three. Since the human oocyte lacks centrioles, it seems the centrioles of the embryo are San Diego, CA paternally inherited. The paternal centrioles reside in the sperm neck, a region at the junction , on http://ascb.org/future-ascb-annual-meetings of the nucleus and flagellum. The neck also contains the striated columns and capitulum, 28 Sep 2021 at 15:40:20 2D Materials and Technologies which surround a relatively clear region called the vault. December 10–13, 2018 Melbourne, Australia The current dogma is that the centrioles in the sperm undergo reduction so that a www.fleet.org.au/icon2dmat sperm cell then contains one typical centriole, called the proximal centriole (PC), while the Smart NanoMaterials 2018: distal centriole (DC) disintegrates and the protein surrounding it is eliminated and replaced Advances, Innovation and Application by the vault. -
Phylogeny Recapitulates Learning: Self-Optimization of Genetic Code
bioRxiv preprint doi: https://doi.org/10.1101/260877; this version posted February 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Phylogeny Recapitulates Learning: Self-Optimization of Genetic Code Oliver Attie1, Brian Sulkow1, Chong Di1, and Wei-Gang Qiu1,2,3,* 1Department of Biological Sciences, Hunter College & 2Graduate Center, City University of New York; 3Department of Physiology and Biophysics & Institute for Computational Biomedicine, Weil Cornell Medical College, New York, New York, USA Emails: Oliver Attie [email protected]; Brian Sulkow [email protected]; Chong Di [email protected]; *Correspondence: [email protected] Abstract Learning algorithms have been proposed as a non-selective mechanism capable of creating complex adaptive systems in life. Evolutionary learning however has not been demonstrated to be a plausible cause for the origin of a specific molecular system. Here we show that genetic codes as optimal as the Standard Genetic Code (SGC) emerge readily by following a molecular analog of the Hebb’s rule (“neurons fire together, wire together”). Specifically, error-minimizing genetic codes are obtained by maximizing the number of physio-chemically similar amino acids assigned to evolutionarily similar codons. Formulating genetic code as a Traveling Salesman Problem (TSP) with amino acids as “cities” and codons as “tour positions” and implemented with a Hopfield neural network, the unsupervised learning algorithm efficiently finds an abundance of genetic codes that are more error- minimizing than SGC. -
Regulation, Evolution and Consequences of Cotranslational
Available online at www.sciencedirect.com ScienceDirect Regulation, evolution and consequences of cotranslational protein complex assembly 1 2 3 Eviatar Natan , Jonathan N Wells , Sarah A Teichmann and 2 Joseph A Marsh Most proteins assemble into complexes, which are involved in evolution, most prokaryotic complexes are homomers, almost all cellular processes. Thus it is crucial for cell viability while most eukaryotic complexes are heteromers [5–7]. that mechanisms for correct assembly exist. The timing of assembly plays a key role in determining the fate of the protein: Protein complexes are crucial for a large number of biolog- if the protein is allowed to diffuse into the crowded cellular ical functions, and different types of protein quaternary milieu, it runs the risk of forming non-specific interactions, structures have been shown to facilitate different biological potentially leading to aggregation or other deleterious functions and allosteric regulation [8 ,9–12]. A large num- outcomes. It is therefore expected that strong regulatory ber of other benefits have been proposed [4 ,13]. For mechanisms should exist to ensure efficient assembly. In this example, considering the possibility of acquiring mutations review we discuss the cotranslational assembly of protein during transcription and translation, it is more efficient to complexes and discuss how it occurs, ways in which it is synthesize a larger structure in modules of subunits. Im- regulated, potential disadvantages of cotranslational portantly, it also allows fine spatial and temporal regulation, interactions between proteins and the implications for the and reduces folding complexity in forming unique shapes inheritance of dominant-negative genetic disorders. such rings or filaments. -
Identification of DNAH6 Mutations in Infertile Men with Multiple
www.nature.com/scientificreports OPEN Identifcation of DNAH6 mutations in infertile men with multiple morphological abnormalities of the sperm fagella Chaofeng Tu1,2,3,4, Hongchuan Nie1,2,3,4, Lanlan Meng2, Shimin Yuan2, Wenbin He1,2,3, Aixiang Luo1, Haiyu Li1, Wen Li1,2,3, Juan Du1,2,3, Guangxiu Lu1,2,3, Ge Lin1,2,3 & Yue-Qiu Tan1,2,3* Male infertility due to spermatogenesis defects afects millions of men worldwide. However, the genetic etiology of the vast majority remains unclear. Here we describe three men with primary infertility due to multiple morphological abnormalities of the sperm fagella (MMAF) from two unrelated Han Chinese families. We performed whole-exome sequencing (WES) and Sanger sequencing on the proband of family 1, and found that he carried novel compound heterozygous missense mutations in dynein axonemal heavy chain 6 (DNAH6) that resulted in the substitution of a conserved amino acid residue and co-segregated with the MMAF phenotype in this family. Papanicolaou staining and transmission electron microscopy analysis revealed morphological and ultrastructural abnormalities in the sperm fagella in carriers of these genetic variants. Immunostaining experiments showed that DNAH6 was localized in the sperm tail. This is the frst report identifying novel recessive mutations in DNAH6 as a cause of MMAF. These fndings expand the spectrum of known MMAF mutations and phenotypes and provide information that can be useful for genetic and reproductive counseling of MMAF patients. Infertility is a major health concern that afects more than 20 million men worldwide1. Factors contributing to male infertility include genetic disorders, urogenital infections, and immunological or hormonal abnormalities. -
The Transformation of the Centrosome Into the Basal Body: Similarities and Dissimilarities Between Somatic and Male Germ Cells and Their Relevance for Male Fertility
cells Review The Transformation of the Centrosome into the Basal Body: Similarities and Dissimilarities between Somatic and Male Germ Cells and Their Relevance for Male Fertility Constanza Tapia Contreras and Sigrid Hoyer-Fender * Göttingen Center of Molecular Biosciences, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology-Developmental Biology, Faculty of Biology and Psychology, Georg-August University of Göttingen, 37077 Göttingen, Germany; [email protected] * Correspondence: [email protected] Abstract: The sperm flagellum is essential for the transport of the genetic material toward the oocyte and thus the transmission of the genetic information to the next generation. During the haploid phase of spermatogenesis, i.e., spermiogenesis, a morphological and molecular restructuring of the male germ cell, the round spermatid, takes place that includes the silencing and compaction of the nucleus, the formation of the acrosomal vesicle from the Golgi apparatus, the formation of the sperm tail, and, finally, the shedding of excessive cytoplasm. Sperm tail formation starts in the round spermatid stage when the pair of centrioles moves toward the posterior pole of the nucleus. The sperm tail, eventually, becomes located opposed to the acrosomal vesicle, which develops at the anterior pole of the nucleus. The centriole pair tightly attaches to the nucleus, forming a nuclear membrane indentation. An Citation: Tapia Contreras, C.; articular structure is formed around the centriole pair known as the connecting piece, situated in the Hoyer-Fender, S. The Transformation neck region and linking the sperm head to the tail, also named the head-to-tail coupling apparatus or, of the Centrosome into the Basal in short, HTCA. -
Effect of Correlated TRAN Abundances on Translation Errors and Evolution of Codon Usage Bias
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Faculty Publications and Other Works -- Ecology and Evolutionary Biology Ecology and Evolutionary Biology 9-2010 Effect of Correlated TRAN Abundances on Translation Errors and Evolution of Codon Usage Bias Premal Shah University of Tennessee - Knoxville Michael A. Gilchrist Follow this and additional works at: https://trace.tennessee.edu/utk_ecolpubs Part of the Ecology and Evolutionary Biology Commons Recommended Citation Shah, Premal and Gilchrist, Michael A., "Effect of Correlated TRAN Abundances on Translation Errors and Evolution of Codon Usage Bias" (2010). Faculty Publications and Other Works -- Ecology and Evolutionary Biology. https://trace.tennessee.edu/utk_ecolpubs/37 This Article is brought to you for free and open access by the Ecology and Evolutionary Biology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Faculty Publications and Other Works -- Ecology and Evolutionary Biology by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias Premal Shah1,2*, Michael A. Gilchrist1,2 1 Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America, 2 National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee, United States of America Abstract Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. -
The RNA Code and Protein Synthesis
Downloaded from symposium.cshlp.org on January 18, 2014 - Published by Cold Spring Harbor Laboratory Press The RNA Code and Protein Synthesis M. Nirenberg, T. Caskey, R. Marshall, et al. Cold Spring Harb Symp Quant Biol 1966 31: 11-24 Access the most recent version at doi:10.1101/SQB.1966.031.01.008 References This article cites 37 articles, 24 of which can be accessed free at: http://symposium.cshlp.org/content/31/11.refs.html Article cited in: http://symposium.cshlp.org/content/31/11#related-urls Email alerting Receive free email alerts when new articles cite this article - sign up in service the box at the top right corner of the article or click here To subscribe to Cold Spring Harbor Symposia on Quantitative Biology go to: http://symposium.cshlp.org/subscriptions Copyright © 1966 Cold Spring Harbor Laboratory Press Downloaded from symposium.cshlp.org on January 18, 2014 - Published by Cold Spring Harbor Laboratory Press The RNA Code and Protein Synthesis M. NIRENBERG, T. CASKEY, R. MARSHALL, R. BRIMACOMBE, D. KELLOGG, B. DOCTOIr D. HATFIELD, J. LEVIN, F. ROTTMAN, S. PESTKA, M. WILCOX, AND F. ANDERSON Laboratory of Biochemical Genetics, National Heart Institute, National Institutes of Health, Bethesda, Maryland and t Division of Biochemistry, Walter Reed Army Institute of Research, Walter Reed Army Medical Center, Washington, D.C. Many properties of the RNA code which were TABLE 1. CHARACTERISTICS OF AA-sRI~A BINDING TO RIBOSOMES discussed at the 1963 Cold Spring Harbor meeting were based on information obtained with randomly C14-Phe-sRNA bound to ribo- ordered synthetic polynucleotides. -
AP Biology Life’S Beginning on Earth According to Scientific Findings (Associated Learning Objectives: 1.9, 1.10, 1.11, 1.12, 1.27, 1.28, 1.29, 1.30, 1.31, and 1.32)
AP Auburn University AP Summer Institute BIOLOGYJuly 11-14, 2016 AP Biology Life’s beginning on Earth according to scientific findings (Associated Learning Objectives: 1.9, 1.10, 1.11, 1.12, 1.27, 1.28, 1.29, 1.30, 1.31, and 1.32) I. The four steps necessary for life to emerge on Earth. (This is according to accepted scientific evidence.) A. First: An abiotic (non-living) synthesis of Amino Acids and Nucleic Acids must occur. 1. The RNA molecule is believed to have evolved first. It is not as molecularly stable as DNA though. 2. The Nucleic Acids (DNA or RNA) are essential for storing, retrieving, or conveying by inheritance molecular information on constructing the components of living cells.. 3. The Amino Acids, the building blocks of proteins, are needed to construct the “work horse” molecules of a cell. a. The majority of a cell or organism, in biomass (dry weight of an organism), is mostly protein. B. Second: Monomers must be able to join together to form more complex polymers using energy that is obtained from the surrounding environment. 1. Seen in monosaccharides (simple sugars) making polysaccharides (For energy storage or cell walls of plants.) 2. Seen in the making of phospholipids for cell membranes. 3. Seen in the making of messenger RNA used in making proteins using Amino Acids. 4. Seen in making chromosomes out of strings of DNA molecules. (For information storage.) C. Third: The RNA/DNA molecules form and gain the ability to reproduce and stabilize by using chemical bonds and complimentary bonding. -
A Numerical Representation and Classification of Codons To
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.02.971036; this version posted March 3, 2020. 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. A Numerical Representation and Classication of Codons to Investigate Codon Alternation Patterns during Genetic Mutations on Disease Pathogenesis Antara Senguptaa, Pabitra Pal Choudhuryd, Subhadip Chakrabortyb,e, Swarup Royc,∗∗, Jayanta Kumar Dasd,∗, Ditipriya Mallicke, Siddhartha S Janae aDepartment of Master of Computer Applications, MCKV Institute of Engineering, Liluah, India bDepartment of Botany, Nabadwip Vidyasagar College, Nabadwip, India cDepartment of Computer Applications,Sikkim University, Gangtok, Sikkim, India dApplied Statistical Unit, Indian Statistical Institute, Kolkata, India eSchool of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India 1. Introduction Genes are the functional units of heredity [4]. It is mainly responsible for the structural and functional changes and for the variation in organisms which could be good or bad. DNA (Deoxyribose Nucleic Acid) sequences build the genes of organisms which in turn encode for particular protein us- ing codon. Any uctuation in this sequence (codons), for example, mishaps during DNA transcription, might lead to a change in the genetic code which alter the protein synthesis. This change is called mutation. Mutation diers from Single Nucleotide Polymorphism(SNP) in many ways [23]. For instance, occurrence of mutation in a population should be less than 1% whereas SNP occurs with greater than 1%. Mutation always occurs in diseased group whereas SNP is occurs in both diseased and control population. Mutation is responsible for some disease phenotype but SNP may or may not be as- sociated with disease phenotype. -
Identification and Functional Activation of Peroxisome Proliferator-Activated Receptor in Human Upper Aerodigestive Cancer
Identification and Functional Activation of Peroxisome Proliferator-Activated Receptor in Human Upper Aerodigestive Cancer A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Simon K. Wright, MD IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Frank G. Ondrey, MD., Ph.D November 2012 © Simon K. Wright, MD, 2012 Acknowledgements Supported by NCI/NIH P30 CA77598-07 Cancer Center Support Grant (FGO), The Translational Biomarkers Initiative and other funding from the Lions 5M Foundation (FGO), Iowa Health Systems Research Grant (SKW) and American Cancer Society Institutional Research Grant IRG-58-001-40IRG44 (PMG). i Abstract Squamous cell carcinoma of the head and neck (SCCHN) is an aggressive malignancy whose carcinogenesis occurs in multiple stages years to decades after carcinogen exposure. In spite of continued advances in the understanding of molecular biology of SCCHN and the introduction of a multitude of multi-modality treatment protocols, the 20-50% survival of stage III and IV disease has not changed appreciably in over twenty years. Efforts to treat or prevent recurrence have predominantly involved the use of cytotoxic chemotherapy, however the use of retinoids as a chemoprevention agent has been clinically assessed. Success has been limited by toxicity of retinoids and reversal of differentiation changes upon cessation of treatment. Peroxisome proliferator-activated receptors (PPARs) are lipid-activated transcription factors belonging to the steroid/thyroid/retinoic acid nuclear receptor superfamily. PPARs primarily target genes involved in lipid homeostasis; one isoform, PPARγ, directs the differentiation of precursor cells into adipocytes. PPARγ heterodimerizes with RXRα to form a functional transcription factor. -
Characterization of the Sea Urchin Major Vault Protein (SU-MVP)
DEVELOPMENTAL BIOLOGY 190, 117±128 (1997) ARTICLE NO. DB978676 Characterization of the Sea Urchin ViewMajor metadata, citation Vault and similar Protein: papers at core.ac.uk A Possible Role brought to you by CORE for Vault Ribonucleoprotein Particles provided by Elsevier - Publisher Connector in Nucleocytoplasmic Transport Danielle R. Hamill and Kathy A. Suprenant Department of Biochemistry, Cell and Molecular Biology, University of Kansas, Lawrence, Kansas 66045 Vaults are large ribonucleoprotein particles that have been identi®ed in a wide range of eukaryotic organisms. Although present in thousands of copies per cell, their function remains unknown. In this report, we identify the major vault protein in sea urchins as a 107-kDa polypeptide that copuri®es with microtubules and ribosomes. Although initially identi®ed in microtubule preparations, the sea urchin major vault protein is not predominantly microtubule-associated in vivo. Rather, the sea urchin major vault protein is present throughout the cytoplasm in eggs and embryos and in the nucleus in adult somatic cells. Within the nucleus, the sea urchin major vault protein is concentrated in the region of the nucleolus and to punctate regions of the nuclear envelope. In addition, the vault protein localizes to short linear strings juxtaposed to the exterior of the nucleus and extending outward into the cytoplasm. Based on their copuri®cation and intracellular distribution, vaults may be involved in the nucleocytoplasmic transport of ribosomes and/or mRNA. q 1997 Academic Press INTRODUCTION coincident with, and clustered at, the distal ends of actin stress ®bers (Kedersha and Rome, 1990). Vault immunoreac- A vault is a large ribonucleoprotein (RNP) particle nearly tivity appears to be excluded from the nucleus (Kedersha three times the size of a ribosome and 10-fold larger than and Rome, 1990).