Exploring the Loci Responsible for Awn Development in Rice Through Comparative Analysis of All AA Genome Species
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UNIVERSITY of CALIFORNIA, SAN DIEGO Functional Analysis of Sall4
UNIVERSITY OF CALIFORNIA, SAN DIEGO Functional analysis of Sall4 in modulating embryonic stem cell fate A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular Pathology by Pei Jen A. Lee Committee in charge: Professor Steven Briggs, Chair Professor Geoff Rosenfeld, Co-Chair Professor Alexander Hoffmann Professor Randall Johnson Professor Mark Mercola 2009 Copyright Pei Jen A. Lee, 2009 All rights reserved. The dissertation of Pei Jen A. Lee is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ Co-Chair ______________________________________________________________ Chair University of California, San Diego 2009 iii Dedicated to my parents, my brother ,and my husband for their love and support iv Table of Contents Signature Page……………………………………………………………………….…iii Dedication…...…………………………………………………………………………..iv Table of Contents……………………………………………………………………….v List of Figures…………………………………………………………………………...vi List of Tables………………………………………………….………………………...ix Curriculum vitae…………………………………………………………………………x Acknowledgement………………………………………………….……….……..…...xi Abstract………………………………………………………………..…………….....xiii Chapter 1 Introduction ..…………………………………………………………………………….1 Chapter 2 Materials and Methods……………………………………………………………..…12 -
Viral Strategies to Arrest Host Mrna Nuclear Export
Viruses 2013, 5, 1824-1849; doi:10.3390/v5071824 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export Sharon K. Kuss *, Miguel A. Mata, Liang Zhang and Beatriz M. A. Fontoura Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; E-Mails: [email protected] (M.A.M.); [email protected] (L.Z.); [email protected] (B.M.A.F) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-214-633-2001; Fax: +1-214-648-5814. Received: 10 June 2013; in revised form: 27 June 2013 / Accepted: 11 July 2013 / Published: 18 July 2013 Abstract: Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses. Keywords: virus; influenza virus; vesicular stomatitis virus; VSV; NS1; matrix protein; nuclear export; nucleo-cytoplasmic trafficking; mRNA export; NXF1; TAP; CRM1; Rae1 1. Introduction Nucleo-cytoplasmic trafficking of proteins and RNA is critical for proper cellular functions and survival. -
Morphological and Molecular Dissection of Wild Rices from Eastern India Suggests Distinct Speciation Received: 8 May 2017 Accepted: 22 January 2018 Between O
www.nature.com/scientificreports OPEN Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation Received: 8 May 2017 Accepted: 22 January 2018 between O. rufpogon and O. nivara Published: xx xx xxxx populations Rashmita Samal, Pritesh Sundar Roy, Auromira Sahoo, Meera Kumari Kar, Bhaskar Chandra Patra, Bishnu Charan Marndi & Jwala Narasimha Rao Gundimeda The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufpogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplifcation of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classifed these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear diferentiation into two distinct groups indicates that O. rufpogon and O. nivara could be treated as two diferent species. -
Loss of Function at RAE2, a Previously Unidentified EPFL, Is Required for Awnlessness in Cultivated Asian Rice
Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice Kanako Bessho-Ueharaa,1, Diane R. Wangb,1, Tomoyuki Furutaa, Anzu Minamia, Keisuke Nagaia, Rico Gamuyaoa, Kenji Asanoa, Rosalyn B. Angeles-Shima, Yoshihiro Shimizua, Madoka Ayanoa, Norio Komedaa, Kazuyuki Doic, Kotaro Miurad, Yosuke Todae, Toshinori Kinoshitae, Satohiro Okudae, Tetsuya Higashiyamae, Mika Nomotof, Yasuomi Tadaf, Hidefumi Shinoharaf, Yoshikatsu Matsubayashif, Anthony Greenbergb, Jianzhong Wug, Hideshi Yasuih, Atsushi Yoshimurah, Hitoshi Moric,2, Susan R. McCouchb,2, and Motoyuki Ashikaria,2 aBioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; bSection of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901; cGraduate School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; dFaculty of Biotechnology, Fukui Prefectural University, 4-1-1 Eiheiji-Town, Fukui 910-1195, Japan; eInstitute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan; fDivision of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan; gNational Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan; and hFaculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Edited by Maarten Koornneef, Max Planck Institute for Plant Breeding Research, Cologne, Germany, and approved June 22, 2016 (received for review March 24, 2016) Domestication of crops based on artificial selection has contributed important for habitat expansion and survival of wild rice. Under numerous beneficial traits for agriculture. Wild characteristics such domestication, the awnless phenotype has been selected to facilitate as red pericarp and seed shattering were lost in both Asian (Oryza planting, harvesting, and storage of seeds (17). -
F-Box Protein RAE1 Regulates the Stability of the Aluminum-Resistance Transcription Factor STOP1 in Arabidopsis
F-box protein RAE1 regulates the stability of the aluminum-resistance transcription factor STOP1 in Arabidopsis Yang Zhanga,b,1, Jie Zhanga,1, Jinliang Guoa,b,1, Fanglin Zhoua, Somesh Singha, Xuan Xub, Qi Xiec, Zhongbao Yangd, and Chao-Feng Huanga,b,2 aNational Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, 200032 Shanghai, China; bCollege of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; cState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; and dKey Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, College of Life Science, Shandong University, 250100 Jinan, China Edited by Luis Herrera-Estrella, Center for Research and Advanced Studies, Irapuato, Mexico, and approved November 19, 2018 (received for review August 21, 2018) Aluminum (Al) toxicity is a major factor limiting crop production expression of STOP1-downstream Al-resistance genes, including on acid soils, which represent over 30% of the world’s arable land. AtALMT1, AtMATE, and ALS3, is induced by Al (8, 12). These Some plants have evolved mechanisms to detoxify Al. Arabidopsis, results suggest the possibility that STOP1 might be regulated by for example, secretes malate via the AtALMT1 transporter to che- Al at posttranscriptional or posttranslational levels. late and detoxify Al. The C2H2-type transcription factor STOP1 plays a Ubiquitin-mediated protein degradation is an important post- crucial role in Al resistance by inducing the expression of a set of translational mechanism that regulates numerous biological processes genes, including AtALMT1. -
BUB3 That Dissociates from BUB1 Activates Caspase-Independent Mitotic Death (CIMD)
Cell Death and Differentiation (2010) 17, 1011–1024 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd BUB3 that dissociates from BUB1 activates caspase-independent mitotic death (CIMD) Y Niikura1, H Ogi1, K Kikuchi1 and K Kitagawa*,1 The cell death mechanism that prevents aneuploidy caused by a failure of the spindle checkpoint has recently emerged as an important regulatory paradigm. We previously identified a new type of mitotic cell death, termed caspase-independent mitotic death (CIMD), which is induced during early mitosis by partial BUB1 (a spindle checkpoint protein) depletion and defects in kinetochore–microtubule attachment. In this study, we have shown that survived cells that escape CIMD have abnormal nuclei, and we have determined the molecular mechanism by which BUB1 depletion activates CIMD. The BUB3 protein (a BUB1 interactor and a spindle checkpoint protein) interacts with p73 (a homolog of p53), specifically in cells wherein CIMD occurs. The BUB3 protein that is freed from BUB1 associates with p73 on which Y99 is phosphorylated by c-Abl tyrosine kinase, resulting in the activation of CIMD. These results strongly support the hypothesis that CIMD is the cell death mechanism protecting cells from aneuploidy by inducing the death of cells prone to substantial chromosome missegregation. Cell Death and Differentiation (2010) 17, 1011–1024; doi:10.1038/cdd.2009.207; published online 8 January 2010 Aneuploidy – the presence of an abnormal number of of spindle checkpoint activity.20,21 -
The Molecular Genetic Study About Awnedness of Rice
The molecular genetic study about awnedness of rice (イネの芒に関する分子遺伝学的研究) Laboratory of Molecular Biosystem, Division of Molecular Cell Function, Department of Bioengineering Sciences, Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan Kanako UEHARA March 2017 Contents Chapter 1: General introduction 2 References 7 Chapter 2: Evaluation of awn phenotype in chromosome segment substitution lines (CSSL). Introduction 12 Results 15 Discussion 23 Materials and methods 27 References 29 Tables and Figures 34 Chapter 3: Identification of Regulator of Awn Elongation 2 which is responsible for awn elongation. Introduction 60 Results 62 Discussion 78 Materials and methods 82 References 99 Tables and Figures 106 Acknowledgements 147 List of publications 148 1 Chapter 1 General introduction 2 Through the long domestication history, cultivated plants contribute to human health and prosperity. It is because human selected the species that have beneficial traits for agriculture from wild species over a long time period. In other words, human took an effort to improve wild species to be more manageable, to a higher yield and better taste. For example, the fruit of tomato (Solanum lycopersicum) has been selected larger and larger than its ancestor (Lin et al. 2014), and Brassica oleracea has been selected to represent the extraordinary diversity such as cabbage, kale, broccoli and so on (Maggioni et al. 2010). Among the agricultural products, cereals are the most important foods for human. Not only fruits or vegetables but also cereals have been domesticated. The wild progenitors of the major cereals, wheat (Triticum aestivum), maize (Zea mays) and rice (Oryza sativa), show weed like structure and physiological traits (Doebley et al. -
Oryza Glaberrima Steud)
plants Review Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud) Peterson W. Wambugu 1, Marie-Noelle Ndjiondjop 2 and Robert Henry 3,* 1 Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148 – 00100, Nairobi, Kenya; [email protected] 2 M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Ivory Coast; [email protected] 3 Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia * Correspondence: [email protected]; +61-7-661733460551 Received: 23 August 2019; Accepted: 25 September 2019; Published: 26 September 2019 Abstract: African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. -
Invasive Plants of West Africa: Concepts, Overviews and Sustainable Management
& ling Wa yc s c te e M Noba et al., Adv Recycling Waste Manag 2017, 2:1 R a n n i a Advances in Recycling & Waste s g DOI: 10.4172/2475-7675.1000121 e e c m n e a n v t d A Management: Open Access Research Article Open Access Invasive Plants of West Africa: Concepts, Overviews and Sustainable Management Noba K1*, Bassene C1,2, Ngom A1, Gueye M1, Camara AA1, Kane M1, Ndoye F1,3, Dieng B1, Rmballo R1, Ba N1, Bodian M Y1, Sane S1, Diop D1,4, Gueye M1,5, Konta I S1,6, Kane A1,3, Mbaye MS1, and Ba AT1 1Laboratory of Botany and Biodiversity, Plant Biology Department, Faculty of Sciences and Technics, University Cheikh Anta Diop, Dakar-Fann, PB 5005, Senegal 2Section of Plant Production and Agriculture, Faculty of Science and Agriculture, Aquaculture and Food Technology, University Gaston Berger of Saint Louis, PB 234 Saint Louis, Senegal 3Common Microbiology Laboratory, Institute of Research for Development, Hann Bel Air Dakar, Senegal 4Laboratory of Botany, Fundamental Institute of Black Africa (IFAN), PB 5005 Dakar-Fann, Senegal 5Direction of National Parks of Senegal, PB 5135, Dakar-Fann, Senegal 6National Agency of Insertion and Agricultural Development (NAIAD), Ministry of Agriculture, Dakar, Senegal Abstract Invasive species are considered as one of the most environmental challenges of the 21st century. They constitute the second cause of biodiversity loss and lead to high economic disruption and public health. Despite significant, financial and human investments made by countries and world conservation of biodiversity agencies, there are not strategies that lead to appropriate measures for sustainable management and control. -
Slavery on South Carolina Rice Plantations
Slavery on South Carolina Rice Plantations The Migration of People and Knowledge in Early Colonial America Between 1505 and 1888 around 12 million Africans were enslaved and brought to the New World. The issues that arise from slavery are complex and vast. It is impossible to understand slavery from one lesson because it has existed throughout time and across different populations, in fact slavery still exists to this day. In this lesson you will learn about slavery on South Carolina rice plantations during Colonial America by reading this handout, reviewing charts and figures, and reading personal accounts. The “door of no return” at Elmina Castle. It leads from the dungeons of Elmina Castle in Ghana, West Africa to a harbor where slave ships docked. Elmina Castle was built on an island by the Dutch and African empires that controlled this area of West Africa in the 1700- 1800s. Both the Dutch and West African empires accumulated great power and wealth as thousands of enslaved Africans passed through the Door of No Return onto slave ships that took them to the New World. South Carolina Along the coastal lands of South Carolina are rice fields, they are now abandoned; the land has been reclaimed by wild grass and a few river alligators. The Gullah, African Americans who were originally from the West Coast of Africa, still populate the barrier islands along the coast today. During the 1700’s enslaved people worked tirelessly under deadly conditions to grow a crop that was as profitable as gold. Over 40,000 acres of land was cleared and 780 miles of canals were dug by the beginning of the 1800s.1 Disease, heat-stroke, and injuries killed many who worked the rice fields, but the rice was so valuable that the demand for enslaved people grew. -
Rice Scientific Classification Kingdom: Plantae Division: Magnoliophyta
Rice From Wikipedia, the free encyclopedia Rice Oryza sativa Scientific classification Kingdom: Plantae Division: Magnoliophyta Class: Liliopsida Order: Poales Family: Poaceae Genus: Oryza Species • Oryza glaberrima • Oryza sativa Rice refers to two species ( Oryza sativa and Oryza glaberrima ) of grass , native to tropical and subtropical southern & southeastern Asia and to Africa , which together provide more than one fifth of the calories consumed by humans [1]. (The term "wild rice" can refer to wild species of Oryza, but conventionally refers to species of the related genus Zizania , both wild and domesticated.) Rice is an annual plant , growing to 1–1.8 m tall, occasionally more, with long slender leaves 50–100 cm long and 2–2.5 cm broad. The small wind-pollinated flowers are produced in a branched arching to pendulous inflorescence 30–50 cm long. The seed is a grain (caryopsis) 5–12 mm long and 2–3 mm thick. Contents • 1 Cultivation • 2 Preparation as food o 2.1 Cooking • 3 History o 3.1 Etymology o 3.2 History of cultivation • 4 World production and trade • 5 Rice Pests • 6 Cultivars Cultivation The planting of rice is often a labour intensive process Rice is a dietary staple for a large part of the world's human population , making it the most consumed cereal grain . Rice is the world's third largest crop, behind maize ("corn") and wheat . Rice cultivation is well suited to countries and regions with low labour costs and high rainfall , as it is very labour-intensive to cultivate and requires plenty of water for irrigation , much like the licorice crops found in Eastern Europe. -
A Comparative Study of Genetic Relationships Among the AA-Genome Oryza Species Using RAPD and SSR Markers
____________________________________________________________________________www.paper.edu.cn Theor Appl Genet (2003) 108:113–120 DOI 10.1007/s00122-003-1414-x ORIGINAL PAPER Fugang Ren · Bao-Rong Lu · Shaoqing Li · Jingyu Huang · Yingguo Zhu A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers Received: 14 February 2003 / Accepted: 31 May 2003 / Published online: 19 September 2003 Springer-Verlag 2003 Abstract In order to estimate genetic relationships of the nome Oryza accessions. However, the RAPD analysis AA-genome Oryza species, RAPD and SSR analyses provides a more-informative result in terms of the overall were performed with 45 accessions, including 13 culti- genetic relationships at the species level compared to the vated varieties (eight Oryza sativa and five Oryza SSR analysis. The SSR analysis effectively reveals glaberrima) and 32 wild accessions (nine Oryza rufi- diminutive variation among accessions or individuals pogon, seven Oryza nivara, three Oryza glumaepatula, within the same species, given approximately the same four Oryza longistaminata, six Oryza barthii, and three number of primers or primer-pairs used in the studies. Oryza meridionalis). A total of 181 clear and repeatable bands were amplified from 27 selected RAPD primers, and 101 alleles were detected from 29 SSR primer pairs. Introduction The dendrogram constructed using UPGMA from a genetic-similarity matrix based on the RAPD data The genus Oryza L. is an economically valuable plant supported the clustering of distinct five groups with a group in the grass family (Poaceae), because it includes few exceptions: O. rufipogon/O. nivara/O. meridionalis, the world’s single most-important food crop, rice, that is a O.