Genetic Engineering in Nonhuman Primates for Human Disease Modeling
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Research Article Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis
Hindawi Publishing Corporation BioMed Research International Volume 2015, Article ID 124537, 10 pages http://dx.doi.org/10.1155/2015/124537 Research Article Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis Yee Wen Choon,1 Mohd Saberi Mohamad,1 Safaai Deris,1 Chuii Khim Chong,1 Sigeru Omatu,2 and Juan Manuel Corchado3 1 Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia 2 Department of Electronics, Information and Communication Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan 3 Biomedical Research Institute of Salamanca/BISITE Research Group, University of Salamanca, 37008 Salamanca, Spain Correspondence should be addressed to Mohd Saberi Mohamad; [email protected] Received 21 August 2014; Revised 22 October 2014; Accepted 31 October 2014 Academic Editor: Juan F. De Paz Copyright © 2015 Yee Wen Choon 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. Microbial strain optimisation for the overproduction of a desired phenotype has been a popular topic in recent years. Gene knockout is a genetic engineering technique that can modify the metabolism of microbial cells to obtain desirable phenotypes. Optimisation algorithms have been developed to identify the effects of gene knockout. However, the complexities of metabolic networks have made the process of identifying the effects of genetic modification on desirable phenotypes challenging. Furthermore, a vast number of reactions in cellular metabolism often lead to a combinatorial problem in obtaining optimal gene knockout. -
Gene Editing of Microalgae: Scientific Progress and Regulatory
biology Review Gene Editing of Microalgae: Scientific Progress and Regulatory Challenges in Europe Andrew Spicer 1,* and Attila Molnar 2 ID 1 Algenuity, Eden Laboratory, Bedfordshire MK43 9ND, UK 2 Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1234-765773 Received: 22 December 2017; Accepted: 1 March 2018; Published: 6 March 2018 Abstract: It is abundantly clear that the development of gene editing technologies, represents a potentially powerful force for good with regard to human and animal health and addressing the challenges we continue to face in a growing global population. This now includes the development of approaches to modify microalgal strains for potential improvements in productivity, robustness, harvestability, processability, nutritional composition, and application. The rapid emergence and ongoing developments in this area demand a timely review and revision of the current definitions and regulations around genetically modified organisms (GMOs), particularly within Europe. Current practices within the EU provide exemptions from the GMO directives for organisms, including crop plants and micro-organisms that are produced through chemical or UV/radiation mutagenesis. However, organisms generated through gene editing, including microalgae, where only genetic changes in native genes are made, remain currently under the GMO umbrella; they are, as such, excluded from practical and commercial opportunities in the EU. In this review, we will review the advances that are being made in the area of gene editing in microalgae and the impact of regulation on commercial advances in this area with consideration to the current regulatory framework as it relates to GMOs including GM microalgae in Europe. -
What Are Knockout Mice?
Lecture 37 Knockout mice Lecture 29 Cloning and Expression vectors Lecture 30 Eukaryotic Protein Expression Systems –I Lecture 31 Eukaryotic Protein Expression Systems –II Lecture 32 Eukaryotic Protein Expression Systems –III Lecture 33 Human Gene Therapy Lecture 34 DNA Vaccines Lecture 35 Transgenic Animals Lecture 36 Transgenic Plants Lecture 37 Knockout Mice What are knockout mice? A knockout mouse is a mouse in which a specific gene has been inactivated or “knocked out” by replacing it or disrupting it with an artificial piece of DNA. The loss of gene activity often causes changes in a mouse's phenotype and thus provides valuable information on the function of the gene. Researchers who developed the technology for the creation of knockout mice won Nobel Prize in the year 2007 The Nobel Prize in Physiology or Medicine 2007 was awarded jointly to Mario R. Capecchi, Sir Martin J. Evans and Oliver Smithies "for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells". Mario R. Capecchi Sir Martin J. Evans Oliver Smithies The ability to delete or mutate any gene of interest in mice has transformed the landscape of mammalian biology research. Cultivation of embryonic stem (ES) cells – Martin Evans • Gene targeting – Oliver Smithies • Gene knockout – Mario Capecchi Gene correction by Oliver Smithies Targeted correction of a mutant HPRT gene in mouse ES cells. Nature 330:576-8, 1987 This modification of a chosen gene in pluripotent ES cells demonstrates the feasibility of this route to manipulating mammalian genomes in predetermined ways. -------------------------------------------------------------------------------------- Nature. 1985 Sep 19-25;317(6034):230-4. -
DNA Repair and Synthetic Lethality
Int J Oral Sci (2011) 3:176-179. www.ijos.org.cn REVIEW DNA repair and synthetic lethality Gong-she Guo1, Feng-mei Zhang1, Rui-jie Gao2, Robert Delsite4, Zhi-hui Feng1,3*, Simon N. Powell4* 1School of Public Health, Shandong University, Jinan 250012, China; 2Second People’s Hospital of Weifang, Weifang 261041, China; 3Department of Radiation Oncology, Washington University in St Louis, St Louis MO 63108, USA; 4Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA Tumors often have DNA repair defects, suggesting additional inhibition of other DNA repair pathways in tumors may lead to synthetic lethality. Accumulating data demonstrate that DNA repair-defective tumors, in particular homologous recombination (HR), are highly sensitive to DNA-damaging agents. Thus, HR-defective tumors exhibit potential vulnerability to the synthetic lethality approach, which may lead to new therapeutic strategies. It is well known that poly (adenosine diphosphate (ADP)-ribose) polymerase (PARP) inhibitors show the synthetically lethal effect in tumors defective in BRCA1 or BRCA2 genes encoded proteins that are required for efficient HR. In this review, we summarize the strategies of targeting DNA repair pathways and other DNA metabolic functions to cause synthetic lethality in HR-defective tumor cells. Keywords: DNA repair; homologous recombination; synthetic lethality; BRCA; Rad52 International Journal of Oral Science (2011) 3: 176-179. doi: 10.4248/IJOS11064 Introduction polymerase (PARP) inhibitors are specifically toxic to homologous recombination (HR)-defective cells [3-4]. Synthetic lethality is defined as a genetic combination Playing a key role in maintaining genetic stability, HR is of mutations in two or more genes that leads to cell a major repair pathway for double-strand breaks (DSBs) death, whereas a mutation in any one of the genes does utilizing undamaged homologous DNA sequence [5-6]. -
Step-By-Step Knockout (Dsdna) Protocol.Pdf
Court Lab Protocol 3/21/11 Recombineering: Using Drug Cassettes to Knock out Genes in vivo James A. Sawitzke1, Lynn C. Thomason2, Mikhail Bubunenko1,2, Xintian Li1, Nina Costantino1, and Donald L. Court1 1Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702 2Gene Regulation and Chromosome Biology Laboratory, Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702 Purpose A “gene knockout” or “knockout” is a mutation that inactivates a gene function. These mutations are very useful for classical genetic studies as well as for modern techniques including functional genomics. In the past, knockouts of bacterial genes were often made by transposon mutagenesis. In this case, laborious screens are required to find a knockout in the gene of interest. Knockouts of other organisms have traditionally been made by first using in vitro genetic engineering to modify genes contained on plasmids or Bacterial Artificial Chromosomes (BACs) and later moving these modified constructs to the organism of interest by cell culture techniques. Other methods utilizing a combination of genetic engineering and in vivo homologous recombination were inefficient at best. Recombineering provides a new way to generate knockout mutations directly on the bacterial chromosome or to modify any plasmid or BAC in vivo as a prelude to making knockouts in other organisms. The constructs are designed to the base pair and are not dependent on suitable restriction sites. A drug cassette can be placed anywhere within a gene or the open reading of the gene can be replaced with the drug cassette. -
Generation of Mouse Conditional Knockout Alleles in One Step Using the I-GONAD Method
Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Method Generation of mouse conditional knockout alleles in one step using the i-GONAD method Renjie Shang,1,2 Haifeng Zhang,1 and Pengpeng Bi1,2 1Center for Molecular Medicine, University of Georgia, Athens, Georgia 30602, USA; 2Department of Genetics, University of Georgia, Athens, Georgia 30602, USA The Cre/loxP system is a powerful tool for gene function study in vivo. Regulated expression of Cre recombinase mediates precise deletion of genetic elements in a spatially– and temporally–controlled manner. Despite the robustness of this system, it requires a great amount of effort to create a conditional knockout model for each individual gene of interest where two loxP sites must be simultaneously inserted in cis. The current undertaking involves labor-intensive embryonic stem (ES) cell– based gene targeting and tedious micromanipulations of mouse embryos. The complexity of this workflow poses formida- ble technical challenges, thus limiting wider applications of conditional genetics. Here, we report an alternative approach to generate mouse loxP alleles by integrating a unique design of CRISPR donor with the new oviduct electroporation technique i-GONAD. Showing the potential and simplicity of this method, we created floxed alleles for five genes in one attempt with relatively low costs and a minimal equipment setup. In addition to the conditional alleles, constitutive knockout alleles were also obtained as byproducts of these experiments. Therefore, the wider applications of i-GONAD may promote gene func- tion studies using novel murine models. [Supplemental material is available for this article.] Our understanding of the genetic mechanisms of human diseases strains are readily available, generation of the loxP-flanked (floxed) has been largely expanded by loss-of-function studies using engi- alleles is challenging and labor-intensive due to the lack of an effi- neered mouse models. -
A Gain-Of-Function P53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia Through the Pluripotency Factor FOXH1
Published OnlineFirst May 8, 2019; DOI: 10.1158/2159-8290.CD-18-1391 RESEARCH ARTICLE A Gain-of-Function p53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia through the Pluripotency Factor FOXH1 Evangelia Loizou1,2, Ana Banito1, Geulah Livshits1, Yu-Jui Ho1, Richard P. Koche3, Francisco J. Sánchez-Rivera1, Allison Mayle1, Chi-Chao Chen1, Savvas Kinalis4, Frederik O. Bagger4,5, Edward R. Kastenhuber1,6, Benjamin H. Durham7, and Scott W. Lowe1,8 Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst May 8, 2019; DOI: 10.1158/2159-8290.CD-18-1391 ABSTRACT Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype AML (CK-AML). Here, we identify a gain-of-function (GOF) Trp53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The Trp53 R172H muta- tion (TP53 R175H in humans) exhibits a neomorphic function by promoting aberrant self-renewal in leu- kemic cells, a phenotype that is present in hematopoietic stem and progenitor cells (HSPC) even prior to their transformation. We identify FOXH1 as a critical mediator of mutant p53 function that binds to and regulates stem cell–associated genes and transcriptional programs. Our results identify a context where mutant p53 acts as a bona fi de oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 GOF in cancer. SIGNIFICANCE: Our study demonstrates how a GOF p53 mutant can hijack an embryonic transcrip- tion factor to promote aberrant self-renewal. -
Prospects of Gene Knockouts in the Functional Study of MAMP-Triggered Immunity: a Review
International Journal of Molecular Sciences Review Prospects of Gene Knockouts in the Functional Study of MAMP-Triggered Immunity: A Review Benedict C. Offor , Ian A. Dubery and Lizelle A. Piater * Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa; benedictoff[email protected] (B.C.O.); [email protected] (I.A.D.) * Correspondence: [email protected]; Tel.: +27-11-559-2403 Received: 5 March 2020; Accepted: 1 April 2020; Published: 6 April 2020 Abstract: Plants depend on both preformed and inducible defence responses to defend themselves against biotic stresses stemming from pathogen attacks. In this regard, plants perceive pathogenic threats from the environment through pattern recognition receptors (PRRs) that recognise microbe-associated molecular patterns (MAMPs), and so induce plant defence responses against invading pathogens. Close to thirty PRR proteins have been identified in plants, however, the molecular mechanisms underlying MAMP perception by these receptors/receptor complexes are not fully understood. As such, knockout (KO) of genes that code for PRRs and co-receptors/defence-associated proteins is a valuable tool to study plant immunity. The loss of gene activity often causes changes in the phenotype of the model plant, allowing in vivo studies of gene function and associated biological mechanisms. Here, we review the functions of selected PRRs, brassinosteroid insensitive 1 (BRI1) associated receptor kinase 1 (BAK1) and other associated defence proteins that have been identified in plants, and also outline KO lines generated by T-DNA insertional mutagenesis as well as the effect on MAMP perception—and triggered immunity (MTI). In addition, we further review the role of membrane raft domains in flg22-induced MTI in Arabidopsis, due to the vital role in the activation of several proteins that are part of the membrane raft domain theory in this regard. -
701.Full.Pdf
THE AVERAGE NUMBER OF GENERATIONS UNTIL EXTINCTION OF AN INDIVIDUAL MUTANT GENE IN A FINITE POPULATION MOT00 KIMURA' AND TOMOKO OHTA Department of Biology, Princeton University and National Institute of Genetics, Mishima, Japan Received June 13, 1969 AS pointed out by FISHER(1930), a majority of mutant genes which appear in natural populations are lost by chance within a small number of genera- tions. For example, if the mutant gene is selectively neutral, the probability is about 0.79 that it is lost from the population during the first 7 generations. With one percent selective advantage, this probability becomes about 0.78, namely, it changes very little. In general, the probability of loss in early generations due to random sampling of gametes is very high. The question which naturally follows is how long does it take, on the average, for a single mutant gene to become lost from the population, if we exclude the cases in which it is eventually fixed (established) in the population. In the present paper, we will derive some approximation formulas which are useful to answer this question, based on the theory of KIMURAand OHTA(1969). Also, we will report the results of Monte Carlo experiments performed to check the validity of the approximation formulas. APPROXIMATION FORMULAS BASED ON DIFFUSION MODELS Let us consider a diploid population, and denote by N and Ne, respectively, its actual and effective sizes. The following treatment is based on the diffusion models of population genetics (cf. KIMURA1964). As shown by KIMURAand OHTA (1969), if p is the initial frequency of the mutant gene, the average number of generations until loss of the mutant gene (excluding the cases of its eventual fixation) is - In this formula, 1 On leave from the National Institute of Genetics, Mishima, Japan. -
Statement by the Group of Chief Scientific Advisors
Statement by the Group of Chief Scientific Advisors A Scientific Perspective on the Regulatory Status of Products Derived from Gene Editing and the Implications for the GMO Directive On 25 July 2018, the Court of Justice of the European Biotechnology’ (SAM, 2017a), we have examined the Union ('the Court') decided that organisms obtained GMO Directive taking into account current by the new techniques of directed mutagenesis are knowledge and scientific evidence. genetically modified organisms (GMOs), within the meaning of the Directive 2001/18/EC on the release 1. The Ruling of the Court of Justice of genetically modified organisms into the On request by the French Conseil d'État, the Court environment ('GMO Directive')1,2, and that they are was asked to determine whether organisms subject to the obligations laid down by the GMO obtained by mutagenesis4 should be considered Directive. GMOs and which of those organisms are exempt New techniques of directed mutagenesis include according to the provisions of the GMO Directive. In gene editing such as CRISPR/Cas9 methodologies. particular, the Court was asked to determine The legal status of the products of such techniques whether organisms obtained by new directed was uncertain, because it was unclear whether they mutagenesis techniques are exempt from the fell within the scope of the GMO Directive. obligations imposed by the GMO Directive, as are those obtained by conventional, random These techniques enable the development of a wide mutagenesis techniques that existed before the range of agricultural applications and the ethical, adoption of the Directive, or are regulated like those legal, social and economic issues of their use are obtained by established techniques of genetic discussed intensively. -
An Activated Rac Mutant Functions As a Dominant Negative for Membrane RuIng
Oncogene (1998) 17, 625 ± 629 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc An activated Rac mutant functions as a dominant negative for membrane ruing Martin Alexander Schwartz, Jere E Meredith and William B Kiosses Department of Vascular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA Previous studies have shown that point mutations in the terminal eector domains (Westwick et al., 1997; eector domain of Rac1 block speci®c downstream Lamarche et al., 1996). Point mutants were con- pathways such as PAK, JNK/SAPK kinases and structed in V12 or Q61L backgrounds to give membrane ruing. Speci®cally, the F37A mutation, constitutively activated proteins that would show made in a constitutively activated Q61L background, dominant positive eects. These studies of Rac point activates PAK but fails to induce membrane rues. We mutations revealed that induction of membrane ruing now show that Q61L/F37A Rac not only fails to induce and cell cycle progression were independent of ruing but potently blocks membrane ruing induced by activation of PAK and other CRIB domain proteins, serum or PDGF. In the presence of serum, cells do and activation of the JNK/SAPK pathway (Westwick extend ®lopodia, suggesting that this mutant only blocks et al., 1997; Lamarche et al., 1996). a subset of the eectors that induce cytoskeletal One of these mutations, Q61L/F37A, was found to reorganization. At later times, this rac mutant induces abolish induction of membrane ruing and DNA membrane blebbing, but not apoptosis. These results synthesis but did not aect PAK or JNK/SAPK show that Q61L/F37A Rac, is constitutively activated activation (Lamarche et al., 1996). -
CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells
Review CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells Mateusz Kotowski and Sumana Sharma * MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; [email protected] * Correspondence: [email protected] Received: 15 October 2020; Accepted: 14 November 2020; Published: 18 November 2020 Abstract: While clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing techniques have been widely adapted for use in immortalised immune cells, efficient manipulation of primary T cells has proved to be more challenging. Nonetheless, the rapid expansion of the CRISPR toolbox accompanied by the development of techniques for delivery of CRISPR components into primary T cells now affords the possibility to genetically manipulate primary T cells both with precision and at scale. Here, we review the key features of the techniques for primary T cell editing and discuss how the new generation of CRISPR-based tools may advance genetic engineering of these immune cells. This improved ability to genetically manipulate primary T cells will further enhance our fundamental understanding of cellular signalling and transcriptional networks in T cells and more importantly has the potential to revolutionise T cell-based therapies. Keywords: primary T cells; CRISPR/Cas9; genome-editing; CAR-T cells 1. Introduction In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated protein 9 (Cas9)-based techniques have transformed our ability to genetically manipulate mammalian genomes. Among the many fields within biomedical research to benefit from the ease of genetic manipulation using the CRISPR/Cas9 system is the study of the immune system and especially T cells.