Determinants of Genome-Wide Distribution and Evolution of Uorfs in Eukaryotes ✉ Hong Zhang 1, Yirong Wang1,2, Xinkai Wu 1, Xiaolu Tang 1, Changcheng Wu 1 & Jian Lu 1
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Case Report Clinical Report of a 17Q12 Microdeletion with Additionally Unreported Clinical Features
Hindawi Publishing Corporation Case Reports in Genetics Volume 2014, Article ID 264947, 6 pages http://dx.doi.org/10.1155/2014/264947 Case Report Clinical Report of a 17q12 Microdeletion with Additionally Unreported Clinical Features Jennifer L. Roberts,1 Stephanie K. Gandomi,2 Melissa Parra,2 Ira Lu,2 Chia-Ling Gau,2 Majed Dasouki,1,3 and Merlin G. Butler1 1 The University of Kansas Medical Center, Kansas City, KS 66160, USA 2 Ambry Genetics, Aliso Viejo, CA 92656, USA 3 King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia Correspondence should be addressed to Stephanie K. Gandomi; [email protected] Received 18 March 2014; Revised 13 May 2014; Accepted 14 May 2014; Published 2 June 2014 Academic Editor: Philip D. Cotter Copyright © 2014 Jennifer L. Roberts et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copy number variations involving the 17q12 region have been associated with developmental and speech delay, autism, aggression, self-injury, biting and hitting, oppositional defiance, inappropriate language, and auditory hallucinations. We present a tall- appearing 17-year-old boy with marfanoid habitus, hypermobile joints, mild scoliosis, pectus deformity, widely spaced nipples, pes cavus, autism spectrum disorder, intellectual disability, and psychiatric manifestations including physical and verbal aggression, obsessive-compulsive behaviors, and oppositional defiance. An echocardiogram showed borderline increased aortic root size. An abdominal ultrasound revealed a small pancreas, mild splenomegaly with a 1.3 cm accessory splenule, and normal kidneys and liver. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
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. -
Insights Into Comparative Genomics, Codon Usage Bias, And
plants Article Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes Xiaofeng Chi 1,2 , Faqi Zhang 1,2 , Qi Dong 1,* and Shilong Chen 1,2,* 1 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; [email protected] (X.C.); [email protected] (F.Z.) 2 Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China * Correspondence: [email protected] (Q.D.); [email protected] (S.C.) Received: 29 October 2020; Accepted: 17 November 2020; Published: 18 November 2020 Abstract: Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast genomes of five species (Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, and Nitraria tangutorum) from Biebersteiniaceae and Nitrariaceae. High similarity was detected in the gene order, content and orientation of the five chloroplast genomes; 13 highly variable regions were identified among the five species. An accelerated substitution rate was found in the protein-coding genes, especially clpP. The effective number of codons (ENC), parity rule 2 (PR2), and neutrality plots together revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported (Nitrariaceae (Biebersteiniaceae + The Rest)) relationships in Sapindales. Our findings can provide useful information for analyzing phylogeny and molecular evolution within Biebersteiniaceae and Nitrariaceae. -
1. a 6-Frame Translation Map of a Segment of DNA Is Shown, with Three Open Reading Frames (A, B, and C). Orfs a and B Are Known to Be in Separate Genes
1. A 6-frame translation map of a segment of DNA is shown, with three open reading frames (A, B, and C). ORFs A and B are known to be in separate genes. 1a. Two transcription bubbles are shown, one in ORF A and one in ORF B. In the transcription bubble diagram, mark the following: • the location of RNA polymerase on the appropriate strand in each bubble • the RNA transcripts to show the relative lengths of RNA made by those two polymerases 1b. Are the promoters for ORFs A and/or B present in the DNA region shown in this diagram? Promoter for A: Present? Yes No (circle one) If present, mark its location and label it. Promoter for B: Present? Yes No (circle one) If present, mark its location and label it. 1c. Electron microscopy experiments failed to show RNA polymerases over the ORF "C" region of DNA. State whether each of the three explanations listed below is valid or not, explaining as necessary: Explanation If valid, just write “Valid.” If invalid, BRIEFLY explain why. _______________________________________________________________________ ORFs B and C are exons of the same gene and a splicing error causes ORF C to be left out. Splicing occurs after transcription. Incorrect splicing doesn't explain why transcription didn't happen. ORF C has a mutation in its start (ATG) codon, preventing transcription. The start codon is used for translation, not transcription... whether or not the start codon is intact, transcription could still happen. ORF C has a promoter mutation preventing transcription. VALID. (A promoter mutation is consistent with failure to transcribe the gene.) 2. -
Metagenomic Characterization of Unicellular Eukaryotes in the Urban Thessaloniki Bay
Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay George Tsipas SCHOOL OF ECONOMICS, BUSINESS ADMINISTRATION & LEGAL STUDIES A thesis submitted for the degree of Master of Science (MSc) in Bioeconomy Law, Regulation and Management May, 2019 Thessaloniki – Greece George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ Student Name: George Tsipas SID: 268186037282 Supervisor: Prof. Dr. Savvas Genitsaris I hereby declare that the work submitted is mine and that where I have made use of another’s work, I have attributed the source(s) according to the Regulations set in the Student’s Handbook. May, 2019 Thessaloniki - Greece Page 2 of 63 George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ 1. Abstract The present research investigates through metagenomics sequencing the unicellular protistan communities in Thermaikos Gulf. This research analyzes the diversity, composition and abundance in this marine environment. Water samples were collected monthly from April 2017 to February 2018 in the port of Thessaloniki (Harbor site, 40o 37’ 55 N, 22o 56’ 09 E). The extraction of DNA was completed as well as the sequencing was performed, before the downstream read processing and the taxonomic classification that was assigned using PR2 database. A total of 1248 Operational Taxonomic Units (OTUs) were detected but only 700 unicellular eukaryotes were analyzed, excluding unclassified OTUs, Metazoa and Streptophyta. In this research-based study the most abundant and diverse taxonomic groups were Dinoflagellata and Protalveolata. Specifically, the most abundant groups of all samples are Dinoflagellata with 190 OTUs (27.70%), Protalveolata with 139 OTUs (20.26%) Ochrophyta with 73 OTUs (10.64%), Cercozoa with 67 OTUs (9.77%) and Ciliophora with 64 OTUs (9.33%). -
Mutation Bias Shapes Gene Evolution in Arabidopsis Thaliana
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.17.156752; this version posted June 18, 2020. 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 4.0 International license. Mutation bias shapes gene evolution in Arabidopsis thaliana 1,2† 1 1 3,4 Monroe, J. Grey , Srikant, Thanvi , Carbonell-Bejerano, Pablo , Exposito-Alonso, Moises , 5 6 7 1† Weng, Mao-Lun , Rutter, Matthew T. , Fenster, Charles B. , Weigel, Detlef 1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany 2 Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA 3 Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA 4 Department of Biology, Stanford University, Stanford, CA 94305, USA 5 Department of Biology, Westfield State University, Westfield, MA 01086, USA 6 Department of Biology, College of Charleston, SC 29401, USA 7 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA † corresponding authors: [email protected], [email protected] Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1–4 and evolutionary optimization of genic 3,5 mutation rates remains controversial . However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6 , which is predicted by more recent theory to be a prerequisite for beneficial mutation 7 rates between different classes of genes to readily evolve . To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. -
Redefining the Specificity of Phosphoinositide-Binding by Human
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 2020. 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. Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins Nilmani Singh1†, Adriana Reyes-Ordoñez1†, Michael A. Compagnone1, Jesus F. Moreno Castillo1, Benjamin J. Leslie2, Taekjip Ha2,3,4,5, Jie Chen1* 1Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; 2Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205; 3Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; 4Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205; 5Howard Hughes Medical Institute, Baltimore, MD 21205, USA †These authors contributed equally to this work. *Correspondence: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 2020. 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. ABSTRACT Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employed a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. -
Phylogenomic Analysis of Balantidium Ctenopharyngodoni (Ciliophora, Litostomatea) Based on Single-Cell Transcriptome Sequencing
Parasite 24, 43 (2017) © Z. Sun et al., published by EDP Sciences, 2017 https://doi.org/10.1051/parasite/2017043 Available online at: www.parasite-journal.org RESEARCH ARTICLE Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single-cell transcriptome sequencing Zongyi Sun1, Chuanqi Jiang2, Jinmei Feng3, Wentao Yang2, Ming Li1,2,*, and Wei Miao2,* 1 Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, PR China 2 Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, PR China 3 Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, PR China Received 22 April 2017, Accepted 12 October 2017, Published online 14 November 2017 Abstract- - In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Hetero- trichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. -
Congenital Disorders of Glycosylation from a Neurological Perspective
brain sciences Review Congenital Disorders of Glycosylation from a Neurological Perspective Justyna Paprocka 1,* , Aleksandra Jezela-Stanek 2 , Anna Tylki-Szyma´nska 3 and Stephanie Grunewald 4 1 Department of Pediatric Neurology, Faculty of Medical Science in Katowice, Medical University of Silesia, 40-752 Katowice, Poland 2 Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; [email protected] 3 Department of Pediatrics, Nutrition and Metabolic Diseases, The Children’s Memorial Health Institute, W 04-730 Warsaw, Poland; [email protected] 4 NIHR Biomedical Research Center (BRC), Metabolic Unit, Great Ormond Street Hospital and Institute of Child Health, University College London, London SE1 9RT, UK; [email protected] * Correspondence: [email protected]; Tel.: +48-606-415-888 Abstract: Most plasma proteins, cell membrane proteins and other proteins are glycoproteins with sugar chains attached to the polypeptide-glycans. Glycosylation is the main element of the post- translational transformation of most human proteins. Since glycosylation processes are necessary for many different biological processes, patients present a diverse spectrum of phenotypes and severity of symptoms. The most frequently observed neurological symptoms in congenital disorders of glycosylation (CDG) are: epilepsy, intellectual disability, myopathies, neuropathies and stroke-like episodes. Epilepsy is seen in many CDG subtypes and particularly present in the case of mutations