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1 Supplementary Information in Vivo Mrna Display Enables
Supplementary Information In vivo mRNA display enables Large-scale Proteomics by Next Generation Sequencing P. Oikonomou1,2,3, R. Salatino2, S. Tavazoie1,2,3* 1Department of Biological Sciences, Columbia University, New York City, New York, United States 2Department of Systems Biology, Columbia University, New York City, New York, United States 3Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York, United States * Correspondence: P.O.: [email protected]; S.T.: [email protected] Table of Contents Methods ..................................................................................................................................... 4 Plasmid Construction .............................................................................................................. 4 Yeast Strains .......................................................................................................................... 4 In vivo mRNA display Library Generation ............................................................................... 5 Yeast cell culture .................................................................................................................... 5 Excess Coat Protein ............................................................................................................... 6 Non-Specific Functional Controls for in vivo mRNA display .................................................... 6 Whole cell lysate preparation ................................................................................................. -
Sage Creations Organic Farm
Sage Creations Organic Farm TOMATOES, VEGETABLES, HERBS & FLOWERS 2020 CERTIFIED ORGANIC PLANT STARTS: 4" TOMATOES & VEGETABLES $4.75 EACH OR 5 FOR $21.00 - 4" HERBS $5.50 OR 5 FOR $25.00; 6" HERBS(INCLUDES MEDICINALS) $8.00; 2 1/2" Certified Organic FLOWERS & HERBS 2 1/2" FOR $3.25; or 6 FOR $16; LAVENDER PLANTS 3 1/2" POT $8.00 & GALLON POT$13.95; Full Lavender flat $7.25 each(18 per flat); 2.5" VEGGIE $2.25 Veggie Six by CDA Pack $12 OR 6 OR MORE individual plants $2.00/each. No sales tax on plants. We grow from seed or our own cuttings. NOT EVERYTHING IS LISTED. LAVENDER CULTIVARS ON SEPARATE LIST. Order Qty VARIETY Description Heirloom and Open Polinated Tomatoes Bred by the University of Arkansas and will produce fruit in hot weather. Pink tomatoes that are 6 to 8 oz. and very Arkansas Traveler flavorful. Azoychka Heirloom from Russia. Small lemon yellow beefsteak. Matures early -70 days. 8 oz fruit. Sweet with a hint of citrus. Ananas Noir Dark purple and green, beautiful large beefsteak 1 to 1 1/2 lb fruit Aunt Gerties Gold 1 lb fruit best tasting yellow. Heirloom from Virginia Aunt Ginny's Deep pink beefsteak. Potato leafed. Black PearFrom Tula DarkDeep brown,reddish shaped brown mediumlike minature size; pears,sweet flavor;flavored very with productive an excellent, even rich during taste. hot Perfect weather for salads. Brandywine Sudduth's Strainpink classic Brandywine Red - Landis ValleyLarger Strain and ribbed compared to regular Brandwine Red. Is not potato leaved. -
Table of Contents Fair Schedule
Table of Contents Fair Schedule ................................................................................................................................................................. 3 Fair Board ...................................................................................................................................................................... 8 Announcements ............................................................................................................................................................. 5 Premium Payment Categories ....................................................................................................................................... 9 General Rules & Regulations ......................................................................................................................................... 7 Health Regulations ......................................................................................................................................................................... 9 Junior Fair ................................................................................................................................................................... 10 Youth Livestock Auction Rules ................................................................................................................................... 10 Livestock Judging Contest ............................................................................................................................ -
Identification of Five Upregulated Genes in Transplanted
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 6463-6467, July 1994 Medical Sciences Chronic cardiac rejection: Identification of five upregulated genes in transplanted hearts by differential mRNA display (gene expreson/traplant arterlosclerosl/cardlac tnsplatatlon/polymerase chain reaction) ULRIKE UTANS*, PENG LIANG*, LAURI R. WYNERt, MoRRis J. KARNOVSKYt, AND MARY E. RUSSELL*tt§ *Cardiovascular Biology Laboratory, Harvard School of Public Health, tHarvard Medical School, and tCardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115 Communicated by Arthur B. Pardee, March 25, 1994 (receivedfor review November 18, 1993) ABSTRACT Tran t arteriosclerosis, the major man- planted heart that limits transplant survival (3, 4). Studies of festation of chronic rejection, develops after alogeneic (Lewis the process in humans have been restricted by the limited to F344) but not syngeneic (Lewis to Lewis) rat cardiac availability of tissue for analysis. Clinical specimens are transplantation. To identify transcriptionaly regulated medi- heterogeneous in their degree of chronic rejection, their ators asiated with chronic cardiac rejection, we adapted the extent of superimposed disease processes, and the period differential mRNA display technique for in vvo a nt between the time they are obtained and the time of trans- specimens. Gene tanscript patterns In four allogenec hearts plantation. Also, transplanted hearts obtained at autopsy are showing early signs of chronic rejection were compared with not suitable for analysis (which requires viable tissue), and those in two syngeneic hearts exposed to the same surgical the utility of endomyocardial biopsy specimens is limited by procedure but histologically normal. Twelve differentially ex- their small size. Moreover, the restricted extent of arterio- pressed cDNA bands were Identied. -
Short De-Etiolation Increases the Rooting of VC801 Avocado Rootstock
plants Article Short De-Etiolation Increases the Rooting of VC801 Avocado Rootstock Zvi Duman 1,2, Gal Hadas-Brandwein 1,2, Avi Eliyahu 1,2, Eduard Belausov 1, Mohamad Abu-Abied 1, Yelena Yeselson 1, Adi Faigenboim 1, Amnon Lichter 3, Vered Irihimovitch 1 and Einat Sadot 1,* 1 The Institute of Plant Sciences, The Volcani Center, ARO, 68 HaMaccabim Road, Rishon LeZion 7528809, Israel; [email protected] (Z.D.); [email protected] (G.H.-B.); [email protected] (A.E.); [email protected] (E.B.); [email protected] (M.A.-A.); [email protected] (Y.Y.); [email protected] (A.F.); [email protected] (V.I.) 2 The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel 3 The Institute of Post Harvest and Food Sciences, The Volcani Center, ARO, 68 HaMaccabim Road, Rishon LeZion 7528809, Israel; [email protected] * Correspondence: [email protected] Received: 5 August 2020; Accepted: 2 November 2020; Published: 3 November 2020 Abstract: Dark-grown (etiolated) branches of many recalcitrant plant species root better than their green counterparts. Here it was hypothesized that changes in cell-wall properties and hormones occurring during etiolation contribute to rooting efficiency. Measurements of chlorophyll, carbohydrate and auxin contents, as well as tissue compression, histological analysis and gene-expression profiles were determined in etiolated and de-etiolated branches of the avocado rootstock VC801. Differences in chlorophyll content and tissue rigidity, and changes in xyloglucan and pectin in cambium and parenchyma cells were found. -
In Vivo Mrna Display Enables Large-Scale Proteomics by Next Generation Sequencing
In vivo mRNA display enables large-scale proteomics by next generation sequencing Panos Oikonomoua,b,c,1, Roberto Salatinob, and Saeed Tavazoiea,b,c,1 aDepartment of Biological Sciences, Columbia University, New York, NY 10027; bDepartment of Systems Biology, Columbia University, New York, NY 10032; and cDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY10032 Edited by Jack W. Szostak, Massachusetts General Hospital, Boston, MA, and approved August 25, 2020 (received for review February 11, 2020) Large-scale proteomic methods are essential for the functional between genotype and phenotype, whereby a protein or peptide characterization of proteins in their native cellular context. How- is linked to its encoding nucleic acid. For example, in phage ever, proteomics has lagged far behind genomic approaches in display, the nucleic acid encoding the capsid displayed peptide is scalability, standardization, and cost. Here, we introduce in vivo contained within the phage (33). The resulting collection of mRNA display, a technology that converts a variety of proteomics displayed peptides can be used for the in vitro characterization of applications into a DNA sequencing problem. In vivo-expressed protein interactions, protein engineering, and selection of human proteins are coupled with their encoding messenger RNAs antibody fragment libraries (34–36). Alternative in vitro methods (mRNAs) via a high-affinity stem-loop RNA binding domain inter- linking nucleotide information to phenotype include mRNA action, enabling high-throughput identification of proteins with display (37, 38), ribosome display (39), and yeast display (40). In high sensitivity and specificity by next generation DNA sequenc- the past decade, many of these technologies have been coupled ing. -
Growing Herbs in Laramie County
Catherine Wissner UW Extension Service Laramie County Cheyenne, Wyoming What they offer: planting information, ancient history and lore, poetry, musings, photography, illustrations, recipes, chemical constituents and medicinal virtues of herbs. From the botanical viewpoint, an herb is a seed plant that does not produce a woody stem like a tree. But an herb will live long enough to develop flowers and seeds. Richters catalog out of Canada, list over 200 herbs, 43 different types of Basil, 40 mints, 15 Rosemary’s, 35 Sages, and 10 Beebalms. Seed Savers Exchange lists over 350 herbs. So many choices so little time….. Known as the mint family. Comprising about 210 genera and some 3,500 species. The plants are frequently aromatic in all parts include many widely used culinary, such as: Basil, Mint, Rosemary, Sage, Savory, Marjoram, Oregano, Thyme, Lavender. Mostly with opposite leaves, when crushed the foliage usually emitting various, mostly pleasant odors. Stems usually square. Flowers usually abundant and quite attractive, the sepals and corollas variously united. Calyx 2-lipped or not. Corollas strongly 2-lipped (labiate, hence the family name). Herbs fit into one or more classifications according to use - - culinary, aromatic, ornamental, and medicinal. Culinary herbs are probably the most useful to herb gardeners, having a wide range of uses in cooking. Strong herbs -- winter savory, rosemary, sage. Herbs for accent -- sweet basil, dill, mint, sweet marjoram, tarragon, thyme. Herbs for blending -- chives, parsley, summer savory.. Aromatic herbs Most have pleasant smelling flowers or foliage. Oils from aromatic herbs can also be used to produce perfumes and various scents. -
In Vivo Mrna Display Enables Large-Scale Proteomics by Next Generation Sequencing
In vivo mRNA display enables large-scale proteomics by next generation sequencing Panos Oikonomoua,b,c,1, Roberto Salatinob, and Saeed Tavazoiea,b,c,1 aDepartment of Biological Sciences, Columbia University, New York, NY 10027; bDepartment of Systems Biology, Columbia University, New York, NY 10032; and cDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY10032 Edited by Jack W. Szostak, Massachusetts General Hospital, Boston, MA, and approved August 25, 2020 (received for review February 11, 2020) Large-scale proteomic methods are essential for the functional between genotype and phenotype, whereby a protein or peptide characterization of proteins in their native cellular context. How- is linked to its encoding nucleic acid. For example, in phage ever, proteomics has lagged far behind genomic approaches in display, the nucleic acid encoding the capsid displayed peptide is scalability, standardization, and cost. Here, we introduce in vivo contained within the phage (33). The resulting collection of mRNA display, a technology that converts a variety of proteomics displayed peptides can be used for the in vitro characterization of applications into a DNA sequencing problem. In vivo-expressed protein interactions, protein engineering, and selection of human proteins are coupled with their encoding messenger RNAs antibody fragment libraries (34–36). Alternative in vitro methods (mRNAs) via a high-affinity stem-loop RNA binding domain inter- linking nucleotide information to phenotype include mRNA action, enabling high-throughput identification of proteins with display (37, 38), ribosome display (39), and yeast display (40). In high sensitivity and specificity by next generation DNA sequenc- the past decade, many of these technologies have been coupled ing. -
Mrna Display Is a Versatile Selection Method for the Generation of Novel
Chapter 1: Introduction and overview 2 Diverse combinatorial protein libraries have the potential to generate molecules which can bind virtually any desirable target. The number of potential protein targets is enormous; including post translational modifications and alternative splicing, the human proteome contains millions of proteins (1). Including microbial proteins, the number of useful targets is even greater. The natural diversity represented by the mammalian immune system has long been exploited for the generation of novel affinity reagents (2). In vitro selection techniques such as phage display, ribosome display, and mRNA display have been developed for generation of novel protein affinity reagents as an alternative to animal immunization (3). With the advent of these techniques, synthetic and semi- synthetic immunoglobulin libraries have been developed (4-6). One drawback of using antibodies as affinity reagents, however, is that antibody immunoglobulin domains require intrachain disulfide bonds for stability (7). This requirement makes antibodies difficult to express in large quantities and also limits their utility for intracellular applications. In conjunction with the development of in vitro selection techniques, there has been interest in the generation of alternative protein scaffolds which, like antibodies, are able to tolerate sizable sequence diversity but, unlike antibodies, also express well in the intracellular environment (3, 8, 9). There are many applications for the molecular recognition of natural proteins by novel protein affinity reagents (10). Recombinant antibodies are becoming increasingly common as therapeutics (11). Other applications include standard laboratory techniques such as immunoprecipitation, ELISA, western blot, and immunofluorescence microscopy. Applications for protein detection are expanding with the development of 3 ultra-sensitive nano-electonic devices (12) and the use of engineered antibodies in nuclear medicine (13). -
Plant Damage from Air Pollution
report on RPD No. 1005 PLANT July 2002 DEPARTMENT OF CROP SCIENCES DISEASE UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN PLANT DAMAGE FROM AIR POLLUTION Air pollution damage to vegetation has been recognized for more than 125 years. Air pollutants are a fact of modern life. The best guess is that between 100 and 200 million tons of man-made air pollutants are released each year into the atmosphere in the United States. According to U.S. EPA’s “Latest Findings on National Air Quality: 2000 Status and Trends”, over 160 million tons of pollution are emitted into the air each year in the United States. As society has become more industrialized, laws regulating air pollution have become more intense. Before 1955 only smoke laws existed. The U.S. Figure 1. Ozone injury to petunia plants. Clean Air Amendments of 1967 and 1970 established maximum limits, or standards, for several major air pollutants. Two standards are applied to each pollutant: The primary standard, which protects human health, and the secondary standard, which protects human welfare–principally plants and human structures. The clean air legislation also established federal and state environmental protection agencies (EPAs) and pollution control boards to monitor pollutant concentrations and enforce the air quality standards. For example, the Illinois EPA operates monitors for ozone (Figure 1) and sulfur dioxide, the two most common plant-damaging pollutants, in 23 of the state’s 102 counties. As a result, aggregate emissions of six principal pollutants tracked nationally have been cut 29 percent since 1970. Despite this progress, ground-level ozone levels in the southern and north central states have actually worsened in the past 10 years. -
Dictionary of Cultivated Plants and Their Regions of Diversity Second Edition Revised Of: A.C
Dictionary of cultivated plants and their regions of diversity Second edition revised of: A.C. Zeven and P.M. Zhukovsky, 1975, Dictionary of cultivated plants and their centres of diversity 'N -'\:K 1~ Li Dictionary of cultivated plants and their regions of diversity Excluding most ornamentals, forest trees and lower plants A.C. Zeven andJ.M.J, de Wet K pudoc Centre for Agricultural Publishing and Documentation Wageningen - 1982 ~T—^/-/- /+<>?- •/ CIP-GEGEVENS Zeven, A.C. Dictionary ofcultivate d plants andthei rregion so f diversity: excluding mostornamentals ,fores t treesan d lowerplant s/ A.C .Zeve n andJ.M.J ,d eWet .- Wageninge n : Pudoc. -11 1 Herz,uitg . van:Dictionar y of cultivatedplant s andthei r centreso fdiversit y /A.C .Zeve n andP.M . Zhukovsky, 1975.- Me t index,lit .opg . ISBN 90-220-0785-5 SISO63 2UD C63 3 Trefw.:plantenteelt . ISBN 90-220-0785-5 ©Centre forAgricultura l Publishing and Documentation, Wageningen,1982 . Nopar t of thisboo k mayb e reproduced andpublishe d in any form,b y print, photoprint,microfil m or any othermean swithou t written permission from thepublisher . Contents Preface 7 History of thewor k 8 Origins of agriculture anddomesticatio n ofplant s Cradles of agriculture and regions of diversity 21 1 Chinese-Japanese Region 32 2 Indochinese-IndonesianRegio n 48 3 Australian Region 65 4 Hindustani Region 70 5 Central AsianRegio n 81 6 NearEaster n Region 87 7 Mediterranean Region 103 8 African Region 121 9 European-Siberian Region 148 10 South American Region 164 11 CentralAmerica n andMexica n Region 185 12 NorthAmerica n Region 199 Specieswithou t an identified region 207 References 209 Indexo fbotanica l names 228 Preface The aimo f thiswor k ist ogiv e thereade r quick reference toth e regionso f diversity ofcultivate d plants.Fo r important crops,region so fdiversit y of related wild species areals opresented .Wil d species areofte nusefu l sources of genes to improve thevalu eo fcrops . -
The DIMINUTO Gene of Arabidopsis Is Involved in Regulating Cell Elongation
Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press The DIMINUTO gene of Arabidopsis is involved in regulating cell elongation Taku Takahashi, Alexander Gasch, Naoko Nishizawa, 1 and Nam-Hai Chua 2 Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10021-6399 USA; 1Faculty of Agriculture, University of Tokyo, Bunkyo-ku, Tokyo 113, Japan We have isolated a recessive mutation named diminuto (dim) from T-DNA transformed lines of Arabidopsis thaliana. Under normal growth conditions, the dim mutant has very short hypocotyls, petioles, stems, and roots because of the reduced size of cells along the longitudinal axes of these organs. In addition, dim results in the development of open cotyledons and primary leaves in dark-grown seedlings. The gene for DIM was cloned by T-DNA tagging. DIM encodes a novel protein of 561 amino acids that possesses bipartite sequence domains characteristic of nuclear localization signals. Molecular and physiological studies indicate that the loss-of-function mutant allele does not abolish the response of seedlings to light or phytohormones, although the inhibitory effect of light on hypocotyl elongation is greater in the mutant than in wild type. Moreover, the dim mutation affects the expression of a ~-tubulin gene, TUB1, which is thought to be important for plant cell growth. Our results suggest that the DIM gene product plays a critical role in the general process of plant cell elongation. [Key Words: Arabidopsis mutant; T-DNA tagging; cell elongation; tubulin genes; nuclear localization signals] Received October 13, 1994; revised version accepted November 29, 1994.