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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 ................................................................................................. -
Minocycline, a Microglial Inhibitor, Blocks Spinal CCL2-Induced Heat
Huang et al. Journal of Neuroinflammation 2014, 11:7 JOURNAL OF http://www.jneuroinflammation.com/content/11/1/7 NEUROINFLAMMATION RESEARCH Open Access Minocycline, a microglial inhibitor, blocks spinal CCL2-induced heat hyperalgesia and augmentation of glutamatergic transmission in substantia gelatinosa neurons Chung-Yu Huang1†, Ying-Ling Chen2†, Allen H Li3, Juu-Chin Lu1 and Hung-Li Wang1,4,5* Abstract Background: Several lines of evidence suggest that CCL2 could initiate the hyperalgesia of neuropathic pain by causing central sensitization of spinal dorsal horn neurons and facilitating nociceptive transmission in the spinal dorsal horn. The cellular and molecular mechanisms by which CCL2 enhances spinal pain transmission and causes hyperalgesia remain unknown. The substantia gelatinosa (lamina II) of the spinal dorsal horn plays a critical role in nociceptive transmission. An activated spinal microglia, which is believed to release pro-inflammatory cytokines including TNF-α, plays an important role in the development of neuropathic pain, and CCL2 is a key mediator for spinal microglia activation. In the present study, we tested the hypothesis that spinal CCL2 causes the central sensitization of substantia gelatinosa neurons and enhances spinal nociceptive transmission by activating the spinal microglia and augmenting glutamatergic transmission in lamina II neurons. Methods: CCL2 was intrathecally administered to 2-month-old male rats. An intrathecal injection of CCL2 induced heat hyperalgesia, which was assessed using the hot plate test. Whole-cell voltage-clamp recordings substantia gelatinosa neurons in spinal cord slices were performed to record glutamatergic excitatory postsynaptic currents (EPSCs) and GABAergic inhibitory postsynaptic currents (IPSCs). Results: The hot plate test showed that 1 day after the intrathecal injection of CCL2 (1 μg), the latency of hind-paw withdrawal caused by a heat stimulus was significantly reduced in rats. -
Vulnerable Web Application Framework
University of Rhode Island DigitalCommons@URI Open Access Master's Theses 2015 Vulnerable Web Application Framework Nicholas J. Giannini University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/theses Recommended Citation Giannini, Nicholas J., "Vulnerable Web Application Framework" (2015). Open Access Master's Theses. Paper 629. https://digitalcommons.uri.edu/theses/629 This Thesis is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Master's Theses by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. VULNERABLE WEB APPLICATION FRAMEWORK BY NICHOLAS J. GIANNINI A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN COMPUTER SCIENCE AND STATISTICS UNIVERSITY OF RHODE ISLAND 2015 MASTER OF SCIENCE THESIS OF NICHOLAS GIANNINI APPROVED: Thesis Committee: Major Professor Victor Fay-Wolfe Lisa DiPippo Haibo He Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2015 ABSTRACT Utilizing intentionally vulnerable web applications to teach and practice cyber security principles and techniques provides a unique hands-on experience that is otherwise unobtainable without working in the real world. Creating such applications that emulate those of actual businesses and organizations without exposing actual businesses to inadvertent security risks can be a daunting task. To address these issues, this project has created Porous, an open source framework specifically for creating intentionally vulnerable web applications. The implementation of Porous offers a simplified approach to building realistic vulnerable web applications that may be tailored to the needs of specific cyber challenges or classroom exercises. -
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. -
Implementación De Framework De Desarrollo Web Durante Un Proyecto”
UNIVERSIDAD POLITÉCNICA DE SINALOA PROGRAMA ACADÉMICO DE INGENIERÍA EN INFORMÁTICA Tesina “Implementación de Framework de desarrollo web durante un proyecto” Para obtener la acreditación de las estadías profesionales y contar con los créditos para el grado de Ingeniero en Informática. Autor: Bernal Corral Daniel Asesor: M. C. Alejandro Pérez Pasten Borja Asesor OR: Ing. Omar Vidaña Peraza Mazatlán, Sinaloa 13 de Diciembre del 2019 Agradecimientos Agradezco a mis padres por brindarme todo su apoyo durante mis estudios, por darme las clases más importantes, por haber hecho posible que llegara a este momento, por enseñarme que no siempre todo sale perfecto y que debo esforzarme para obtener lo que quiero, por darme ánimos para seguir, por preocuparse por mí y esforzarse para que mi vida fuera mejor. A mi asesor por aconsejarme y corregir los errores que cometí durante el desarrollo de la tesina, por tomarse el tiempo para ver cada detalle y hacer recomendaciones, sugerir opciones, etc. A mi hermano por ayudarme a no rendirme, por asumir su rol de hermano mayor y tratar de guiar, por preocuparse por mí y ayudarme siempre que lo he necesitado. A los profesores que he tenido a lo largo de mis estudios y que me aportaron un poco de su conocimiento para enriquecer el mío. A todos mis compañeros que me ayudaron a hacer más amenas las clases. 6 ÍNDICE TEMÁTICO Índice de imágenes. 9 Resumen. ….. .11 Abstract. …. .11 Introducción. 11 Capítulo I. .. ... …12 1. Antecedentes. .. 13 1.1. Localización. .. ….. 13 1.2. Objetivos de la institución. …………….. 13 1.3. Visión. .14 1.4. -
User Manual for Ilearnplus
User Manual for iLearnPlus Zhen Chen1,†, Pei Zhao2,†, Chen Li3,†, Fuyi Li3,4,5, Dongxu Xiang3,4, Yong-Zi Chen6, Tatsuya Akutsu7, Roger J. Daly3, Geoffrey I. Webb4, Quanzhi Zhao1,8,*, Lukasz Kurgan9,* and Jiangning Song3,4,* 1Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China, 2State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China, 3Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, 4Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia, 5Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia, 6Laboratory of Tumor Cell Biology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China, 7Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan, 8Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450046, China, 9Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA †These authors contributed equally to this work. *To whom the correspondence should be addressed. Tel: +61-3-9902-9304; -
Jury Selection Kelburg
( Johnson v. California (2005) 125 S.Ct 2410 ., 2410 125 SUPREME COURT REPORTER . JOHNSON V; ,CALIFORNIA 2411 Ciie ..'t2!1 S.Ct. 2410 (2005') ," 'f~ o .' , ':':r;fi~#m~ii> l' Jay Shawn:JOHNSciN.Petltfoner. v. CAf;.IFORlIiIA. • No. O~96.4. '. Arl!lled.AprlI)8. !!Q05• .. \ .. ,; \,,,,' ~)I: CJ·:· ~ j. ,i 2412 125 SUPREME COURT REPORTER cr," JOHNSON ·v. CALIFORNIA, 2413 CUe.ull' S,C!. 2410 11005) U.S. 79. 106 S.Ot. 1712. 90 L.Ed.2d 69. proffered facts gives· urise to an inference BREYE;R. JJ.• joined. BREYER. J .• ,fiIed permits state 'courts to estsbllah the stan of discriminatory purpose." 476 U.S .• at a concurring opinio~, THOMAS, J., filed dards used to evaluate' the pnfficiency of 94. 106 S.Ot. 1712. The Court explained a dissenting opinion, prima facie cases of purposeful discrimina that to establlah a prima facie case. the tion in jury selection. Reviewing BatBon, defendaqt inust show that hill .membersljip Stephen B.' Bedrick. Oakland. CA. for Wheeler. and their progeny, the court con~ in a cognizable ~acial group, t11;e prosecu cluded that Wheele". "strong likelihood" tor's' exerciae of peremptory challenges to Petitioner. standard is entirely consistent with Bat remove members oC that group, the indis Seth K. SchaUt" San . J;i'rancisc~, CA, for Ban. Under Batson, the court held. a state putable 'fi~t that such challenges permit Respondent. court may require the' objector to present those inclined to discriminate to do so. and Stephen B. Bedrick. Oakland. CA. Elic not merely enough evidence to permit an any other rel~van~ circwnstnnces raise an . -
Headless Toolkit: 14 Essential Tools for the Future of Composable Commerce
Headless toolkit: 14 essential tools for the future of composable commerce Authors: Tom Karwatka, Piotr Karwatka, Bartosz Picho, Damian Kłaptocz, Bartłomiej Loc, Piotr Znamirowski, Kacper Cebo Introduction Headless toolkit: 14 essential tools for the future of composable commerce We see that the eCommerce software monoliths are starting to crumble. We’ve been working with eCommerce platforms for more than 12 years at Divante, and we see the competition getting fiercer with every year. The fast-paced eCommerce world is a ruthless test for any tech bottlenecks and weak spots. It can quickly push you to the wall where your old software gets stuck against your budget, just like the Ever Given container ship in the Suez Canal. The headless approach is an answer to those problems. It replaces a complex picture with puzzle pieces that you can quickly move around, plug them in and out, and seamlessly replace if necessary. It gives you the maneuverability to pursue constant optimization, ambitious business results, and new trends. This eBook will introduce you to new and prospective technologies for the upcoming years. It presents a set of proven headless tools that have been on Divante’s radar for some time and are steadily growing in popularity. Introduction We’ve tried them out so you don’t have to go through each solution one by one. It’s all in here. It consists of three chapters that start with the initiation of the project and follows through to the headless technology: ■ What comes next: Composable commerce An introduction by Tom Karwatka that presents our vision for the composable future. -
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. -
Lead PHP Developer (M/F) in Frankfurt Am Main and Seville
Lead PHP Developer (m/f) in Frankfurt am Main and Seville You have gained relevant experiences developing scalable online solutions, for instance a new airline booking platform, a global e- learning solution for a pharmaceutical company or a website of a consumer goods manufacturer’s international brands? As a true team player, you can always see the bigger picture? You are the perfect interface between Project Management and Dev Team? You are both encouraged and motivated by a tight schedule and complex requirements? Let’s talk business: About us: We, an agency for marketing, IT & Experience Design with 180 employees and offices in Frankfurt, Geneva, Cologne and Seville. For our team in Frankfurt, we are currently looking for a Lead PHP developer (m/f), who enjoys to actively co-develop and immerse into codes, whilst being able to take the technological project lead and therefore, function as the interface between Project Management and developers. You: Possess an excellent PHP developer know-how, ideally having good Drupal, Symfony, MySQL (or frameworks based on Symfony, such as Silex, Laravel, etc.) skills Are familiar with concepts of test-based development, BDD, Clean Code, Continuous Integration (Jenkins) and deployment processes Enjoy agile and dynamic processes, shorter release cycles and a close cooperation with the Project Management Are part of a creative team, being responsible for all Software Development aspects – from first requirement acquisition to development, testing and launch Have impressive communication skills, -
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).