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  • 1
    Publication Date: 2015-01-16
    Description: The Plasmodium Genetic Modification ( Plasmo GEM) database ( http://plasmogem.sanger.ac.uk ) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. Plasmo GEM currently consists of 〉2000 plasmids designed to modify the genome of Plasmodium berghei , a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. Plasmo GEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The Plasmo GEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2010-09-25
    Description: Plasmodium falciparum is the most prevalent and lethal of the malaria parasites infecting humans, yet the origin and evolutionary history of this important pathogen remain controversial. Here we develop a single-genome amplification strategy to identify and characterize Plasmodium spp. DNA sequences in faecal samples from wild-living apes. Among nearly 3,000 specimens collected from field sites throughout central Africa, we found Plasmodium infection in chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla), but not in eastern gorillas (Gorilla beringei) or bonobos (Pan paniscus). Ape plasmodial infections were highly prevalent, widely distributed and almost always made up of mixed parasite species. Analysis of more than 1,100 mitochondrial, apicoplast and nuclear gene sequences from chimpanzees and gorillas revealed that 99% grouped within one of six host-specific lineages representing distinct Plasmodium species within the subgenus Laverania. One of these from western gorillas comprised parasites that were nearly identical to P. falciparum. In phylogenetic analyses of full-length mitochondrial sequences, human P. falciparum formed a monophyletic lineage within the gorilla parasite radiation. These findings indicate that P. falciparum is of gorilla origin and not of chimpanzee, bonobo or ancient human origin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997044/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997044/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Weimin -- Li, Yingying -- Learn, Gerald H -- Rudicell, Rebecca S -- Robertson, Joel D -- Keele, Brandon F -- Ndjango, Jean-Bosco N -- Sanz, Crickette M -- Morgan, David B -- Locatelli, Sabrina -- Gonder, Mary K -- Kranzusch, Philip J -- Walsh, Peter D -- Delaporte, Eric -- Mpoudi-Ngole, Eitel -- Georgiev, Alexander V -- Muller, Martin N -- Shaw, George M -- Peeters, Martine -- Sharp, Paul M -- Rayner, Julian C -- Hahn, Beatrice H -- P30 AI 7767/AI/NIAID NIH HHS/ -- P30 AI027767/AI/NIAID NIH HHS/ -- P30 AI027767-21A1/AI/NIAID NIH HHS/ -- R01 AI058715/AI/NIAID NIH HHS/ -- R01 AI058715-06A1/AI/NIAID NIH HHS/ -- R01 AI058715-07/AI/NIAID NIH HHS/ -- R01 AI50529/AI/NIAID NIH HHS/ -- R01 I58715/PHS HHS/ -- R03 AI074778/AI/NIAID NIH HHS/ -- R03 AI074778-02/AI/NIAID NIH HHS/ -- R37 AI050529/AI/NIAID NIH HHS/ -- R37 AI050529-07/AI/NIAID NIH HHS/ -- R37 AI050529-08/AI/NIAID NIH HHS/ -- T32 AI007245/AI/NIAID NIH HHS/ -- T32 AI007245-26/AI/NIAID NIH HHS/ -- T32 GM008111/GM/NIGMS NIH HHS/ -- T32 GM008111-13/GM/NIGMS NIH HHS/ -- U19 AI 067854/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-06/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Sep 23;467(7314):420-5. doi: 10.1038/nature09442.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864995" target="_blank"〉PubMed〈/a〉
    Keywords: Africa/epidemiology ; Animals ; Animals, Wild/classification/parasitology ; Ape Diseases/epidemiology/*parasitology/transmission ; DNA, Mitochondrial/analysis/genetics ; Evolution, Molecular ; Feces/parasitology ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome, Protozoan/genetics ; Gorilla gorilla/classification/*parasitology ; Humans ; Malaria, Falciparum/epidemiology/*parasitology/transmission/*veterinary ; Molecular Sequence Data ; Pan paniscus/parasitology ; Pan troglodytes/parasitology ; Phylogeny ; Plasmodium/classification/genetics/isolation & purification ; Plasmodium falciparum/genetics/*isolation & purification ; Prevalence ; Zoonoses/parasitology/transmission
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-11-15
    Description: Erythrocyte invasion by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion requires a series of extracellular recognition events between erythrocyte receptors and ligands on the merozoite, the invasive form of the parasite. None of the few known receptor-ligand interactions involved are required in all parasite strains, indicating that the parasite is able to access multiple redundant invasion pathways. Here, we show that we have identified a receptor-ligand pair that is essential for erythrocyte invasion in all tested P. falciparum strains. By systematically screening a library of erythrocyte proteins, we have found that the Ok blood group antigen, basigin, is a receptor for PfRh5, a parasite ligand that is essential for blood stage growth. Erythrocyte invasion was potently inhibited by soluble basigin or by basigin knockdown, and invasion could be completely blocked using low concentrations of anti-basigin antibodies; importantly, these effects were observed across all laboratory-adapted and field strains tested. Furthermore, Ok(a-) erythrocytes, which express a basigin variant that has a weaker binding affinity for PfRh5, had reduced invasion efficiencies. Our discovery of a cross-strain dependency on a single extracellular receptor-ligand pair for erythrocyte invasion by P. falciparum provides a focus for new anti-malarial therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245779/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245779/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crosnier, Cecile -- Bustamante, Leyla Y -- Bartholdson, S Josefin -- Bei, Amy K -- Theron, Michel -- Uchikawa, Makoto -- Mboup, Souleymane -- Ndir, Omar -- Kwiatkowski, Dominic P -- Duraisingh, Manoj T -- Rayner, Julian C -- Wright, Gavin J -- 077108/Wellcome Trust/United Kingdom -- 089084/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 2T32 AI007535-12/AI/NIAID NIH HHS/ -- G19/9/Medical Research Council/United Kingdom -- R01 AI057919/AI/NIAID NIH HHS/ -- R01 AI057919-05/AI/NIAID NIH HHS/ -- R01AI057919/AI/NIAID NIH HHS/ -- R36 CK000119-01/CK/NCEZID CDC HHS/ -- England -- Nature. 2011 Nov 9;480(7378):534-7. doi: 10.1038/nature10606.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22080952" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD147/chemistry/genetics/*metabolism ; Erythrocytes/metabolism/*parasitology ; Gene Knockdown Techniques ; *Host-Parasite Interactions ; Humans ; Models, Molecular ; Plasmodium falciparum/*physiology ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-06-23
    Description: Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Manske, Magnus -- Miotto, Olivo -- Campino, Susana -- Auburn, Sarah -- Almagro-Garcia, Jacob -- Maslen, Gareth -- O'Brien, Jack -- Djimde, Abdoulaye -- Doumbo, Ogobara -- Zongo, Issaka -- Ouedraogo, Jean-Bosco -- Michon, Pascal -- Mueller, Ivo -- Siba, Peter -- Nzila, Alexis -- Borrmann, Steffen -- Kiara, Steven M -- Marsh, Kevin -- Jiang, Hongying -- Su, Xin-Zhuan -- Amaratunga, Chanaki -- Fairhurst, Rick -- Socheat, Duong -- Nosten, Francois -- Imwong, Mallika -- White, Nicholas J -- Sanders, Mandy -- Anastasi, Elisa -- Alcock, Dan -- Drury, Eleanor -- Oyola, Samuel -- Quail, Michael A -- Turner, Daniel J -- Ruano-Rubio, Valentin -- Jyothi, Dushyanth -- Amenga-Etego, Lucas -- Hubbart, Christina -- Jeffreys, Anna -- Rowlands, Kate -- Sutherland, Colin -- Roper, Cally -- Mangano, Valentina -- Modiano, David -- Tan, John C -- Ferdig, Michael T -- Amambua-Ngwa, Alfred -- Conway, David J -- Takala-Harrison, Shannon -- Plowe, Christopher V -- Rayner, Julian C -- Rockett, Kirk A -- Clark, Taane G -- Newbold, Chris I -- Berriman, Matthew -- MacInnis, Bronwyn -- Kwiatkowski, Dominic P -- 075491/Z/04/Wellcome Trust/United Kingdom -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 082370/Wellcome Trust/United Kingdom -- 089275/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 090770/Wellcome Trust/United Kingdom -- 090770/Z/09/Z/Wellcome Trust/United Kingdom -- 092654/Wellcome Trust/United Kingdom -- 093956/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 55005502/Howard Hughes Medical Institute/ -- G0600718/Medical Research Council/United Kingdom -- G19/9/Medical Research Council/United Kingdom -- Intramural NIH HHS/ -- England -- Nature. 2012 Jul 19;487(7407):375-9. doi: 10.1038/nature11174.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722859" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Biodiversity ; Genome, Protozoan ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Falciparum/*parasitology ; Phylogeny ; Plasmodium falciparum/classification/*genetics ; Polymorphism, Single Nucleotide ; Principal Component Analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2015-06-19
    Description: There is an urgent need for new drugs to treat malaria, with broad therapeutic potential and novel modes of action, to widen the scope of treatment and to overcome emerging drug resistance. Here we describe the discovery of DDD107498, a compound with a potent and novel spectrum of antimalarial activity against multiple life-cycle stages of the Plasmodium parasite, with good pharmacokinetic properties and an acceptable safety profile. DDD107498 demonstrates potential to address a variety of clinical needs, including single-dose treatment, transmission blocking and chemoprotection. DDD107498 was developed from a screening programme against blood-stage malaria parasites; its molecular target has been identified as translation elongation factor 2 (eEF2), which is responsible for the GTP-dependent translocation of the ribosome along messenger RNA, and is essential for protein synthesis. This discovery of eEF2 as a viable antimalarial drug target opens up new possibilities for drug discovery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700930/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700930/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baragana, Beatriz -- Hallyburton, Irene -- Lee, Marcus C S -- Norcross, Neil R -- Grimaldi, Raffaella -- Otto, Thomas D -- Proto, William R -- Blagborough, Andrew M -- Meister, Stephan -- Wirjanata, Grennady -- Ruecker, Andrea -- Upton, Leanna M -- Abraham, Tara S -- Almeida, Mariana J -- Pradhan, Anupam -- Porzelle, Achim -- Martinez, Maria Santos -- Bolscher, Judith M -- Woodland, Andrew -- Norval, Suzanne -- Zuccotto, Fabio -- Thomas, John -- Simeons, Frederick -- Stojanovski, Laste -- Osuna-Cabello, Maria -- Brock, Paddy M -- Churcher, Tom S -- Sala, Katarzyna A -- Zakutansky, Sara E -- Jimenez-Diaz, Maria Belen -- Sanz, Laura Maria -- Riley, Jennifer -- Basak, Rajshekhar -- Campbell, Michael -- Avery, Vicky M -- Sauerwein, Robert W -- Dechering, Koen J -- Noviyanti, Rintis -- Campo, Brice -- Frearson, Julie A -- Angulo-Barturen, Inigo -- Ferrer-Bazaga, Santiago -- Gamo, Francisco Javier -- Wyatt, Paul G -- Leroy, Didier -- Siegl, Peter -- Delves, Michael J -- Kyle, Dennis E -- Wittlin, Sergio -- Marfurt, Jutta -- Price, Ric N -- Sinden, Robert E -- Winzeler, Elizabeth A -- Charman, Susan A -- Bebrevska, Lidiya -- Gray, David W -- Campbell, Simon -- Fairlamb, Alan H -- Willis, Paul A -- Rayner, Julian C -- Fidock, David A -- Read, Kevin D -- Gilbert, Ian H -- 079838/Wellcome Trust/United Kingdom -- 091625/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 100476/Wellcome Trust/United Kingdom -- R01 AI090141/AI/NIAID NIH HHS/ -- R01 AI103058/AI/NIAID NIH HHS/ -- England -- Nature. 2015 Jun 18;522(7556):315-20. doi: 10.1038/nature14451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. ; Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA. ; Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK. ; Department of Life Sciences, Imperial College, London SW7 2AZ, UK. ; University of California, San Diego, School of Medicine, 9500 Gilman Drive 0760, La Jolla, California 92093, USA. ; Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia. ; Department of Global Health, College of Public Health University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, USA. ; GlaxoSmithKline, Tres Cantos Medicines Development Campus-Diseases of the Developing World, Severo Ochoa 2, Tres Cantos 28760, Madrid, Spain. ; TropIQ Health Sciences, Geert Grooteplein 28, Huispost 268, 6525 GA Nijmegen, The Netherlands. ; Centre for Drug Candidate Optimisation, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia. ; Eskitis Institute, Brisbane Innovation Park, Nathan Campus, Griffith University, Queensland 4111, Australia. ; Malaria Pathogenesis Laboratory, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, 10430 Jakarta, Indonesia. ; Medicines for Malaria Venture, PO Box 1826, 20 route de Pre-Bois, 1215 Geneva 15, Switzerland. ; Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland. ; 1] Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK. ; 1] Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA [2] Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26085270" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimalarials/administration & dosage/adverse ; effects/pharmacokinetics/*pharmacology ; Drug Discovery ; Female ; Gene Expression Regulation/*drug effects ; Life Cycle Stages/drug effects ; Liver/drug effects/parasitology ; Malaria/drug therapy/*parasitology ; Male ; Models, Molecular ; Peptide Elongation Factor 2/antagonists & inhibitors/metabolism ; Plasmodium/*drug effects/genetics/growth & development/*metabolism ; Plasmodium berghei/drug effects/physiology ; Plasmodium falciparum/drug effects/metabolism ; Plasmodium vivax/drug effects/metabolism ; Protein Biosynthesis/*drug effects ; Quinolines/administration & dosage/chemistry/pharmacokinetics/*pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-04-20
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752651/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752651/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharp, Paul M -- Rayner, Julian C -- Hahn, Beatrice H -- 095831/Wellcome Trust/United Kingdom -- R01 AI091595/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 19;340(6130):284-6. doi: 10.1126/science.1236958.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23599472" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*transmission/virology ; Animals ; *Biological Evolution ; Genetic Predisposition to Disease ; HIV-1/physiology ; Hominidae/*parasitology/*virology ; Host-Parasite Interactions/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Malaria, Falciparum/genetics/parasitology/*transmission ; Mutation ; N-Acetylneuraminic Acid/biosynthesis/genetics ; Plasmodium falciparum/physiology ; Zoonoses/parasitology/*transmission/virology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Teaching statistics 13 (1991), S. 0 
    ISSN: 1467-9639
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Mathematics
    Notes: Simulation is used to show why the divisor in the sample variance is n, - 1. Choice of the divisor for the sample standard deviation is also discussed.
    Type of Medium: Electronic Resource
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  • 8
    Publication Date: 2011-09-08
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
  • 10
    Publication Date: 2013-12-02
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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