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Duvane JA, Dupont S. Drivers of biological response to fluctuating seawater ph conditions in sea urchin echinus esculentus larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173383. [PMID: 38777045 DOI: 10.1016/j.scitotenv.2024.173383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
A large body of evidence is documenting the impact of reduced pH on marine species and ecosystems. This information is used to infer the present and future impacts of ocean acidification. However, a vast majority of the studies were performed using constant pH and the high level of pH variability experienced by marine organisms on the coastal zone was often overlooked. Recent studies highlight the key role of this variability in driving biological response to pH as well as species sensitivity to ocean acidification. For example, it was hypothesized that because of local adaptation, the extreme of the present range of pH variability is a good predictor for local biological thresholds. Using a complex experimental design, we investigated what part of the pH variability is driving the biological response of the sea urchin Echinus esculentus larvae. Comparing stable (pH 8.13, 7.82, 7.53) and fluctuating treatments (12 h at pH 8.13 and 12 h at pH 7.53) following natural or inverted diurnal cycles, we were able to show that (i) under constant conditions, low pH deviating from the present range of natural variability had a negative effect on larval growth rate and calcification; (ii) under fluctuating conditions, a desynchronization of the pH variation with the photoperiod led to decreased larval growth rate and calcification; (iii) overall, larval fitness (survival, growth and calcification) was higher under fluctuating conditions as compared to constant. While these data do not support the hypothesis that the minimum pH is the main driver of the biological response, they provide evidence of adaptation to variability in a coastal species with associated a cost of plasticity but not a cost of canalization.
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Affiliation(s)
- Jossias Alberto Duvane
- Department of Biological and Environmental Sciences, University of Gothenburg, Fiskebäckskil 45178, Sweden; Department of Biological Sciences, Eduardo Mondlane University, Maputo CP257, Mozambique.
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, Fiskebäckskil 45178, Sweden; IAEA Marine Environment Laboratories, Radioecology Laboratory, 4 Quai Antoine 1er, 98000, Monaco
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2
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Michel M, Skourtanioti E, Pierini F, Guevara EK, Mötsch A, Kocher A, Barquera R, Bianco RA, Carlhoff S, Coppola Bove L, Freilich S, Giffin K, Hermes T, Hiß A, Knolle F, Nelson EA, Neumann GU, Papac L, Penske S, Rohrlach AB, Salem N, Semerau L, Villalba-Mouco V, Abadie I, Aldenderfer M, Beckett JF, Brown M, Campus FGR, Chenghwa T, Cruz Berrocal M, Damašek L, Duffett Carlson KS, Durand R, Ernée M, Fântăneanu C, Frenzel H, García Atiénzar G, Guillén S, Hsieh E, Karwowski M, Kelvin D, Kelvin N, Khokhlov A, Kinaston RL, Korolev A, Krettek KL, Küßner M, Lai L, Look C, Majander K, Mandl K, Mazzarello V, McCormick M, de Miguel Ibáñez P, Murphy R, Németh RE, Nordqvist K, Novotny F, Obenaus M, Olmo-Enciso L, Onkamo P, Orschiedt J, Patrushev V, Peltola S, Romero A, Rubino S, Sajantila A, Salazar-García DC, Serrano E, Shaydullaev S, Sias E, Šlaus M, Stančo L, Swanston T, Teschler-Nicola M, Valentin F, Van de Vijver K, Varney TL, Vigil-Escalera Guirado A, Waters CK, Weiss-Krejci E, Winter E, Lamnidis TC, Prüfer K, Nägele K, Spyrou M, Schiffels S, Stockhammer PW, Haak W, Posth C, Warinner C, Bos KI, Herbig A, Krause J. Ancient Plasmodium genomes shed light on the history of human malaria. Nature 2024; 631:125-133. [PMID: 38867050 PMCID: PMC11222158 DOI: 10.1038/s41586-024-07546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.
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MESH Headings
- Female
- Humans
- Male
- Altitude
- Americas/epidemiology
- Asia/epidemiology
- Biological Evolution
- Disease Resistance/genetics
- DNA, Ancient/analysis
- Europe/epidemiology
- Genome, Mitochondrial/genetics
- Genome, Protozoan/genetics
- History, Ancient
- Malaria/parasitology
- Malaria/history
- Malaria/transmission
- Malaria/epidemiology
- Malaria, Falciparum/epidemiology
- Malaria, Falciparum/history
- Malaria, Falciparum/parasitology
- Malaria, Falciparum/transmission
- Malaria, Vivax/epidemiology
- Malaria, Vivax/history
- Malaria, Vivax/parasitology
- Malaria, Vivax/transmission
- Plasmodium/genetics
- Plasmodium/classification
- Plasmodium falciparum/genetics
- Plasmodium falciparum/isolation & purification
- Plasmodium malariae/genetics
- Plasmodium malariae/isolation & purification
- Plasmodium vivax/genetics
- Plasmodium vivax/isolation & purification
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Affiliation(s)
- Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, .
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Federica Pierini
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Angela Mötsch
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raffaela A Bianco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Selina Carlhoff
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lorenza Coppola Bove
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
| | - Suzanne Freilich
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Taylor Hermes
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - Alina Hiß
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian Knolle
- Department of Medical Engineering and Biotechnology, University of Applied Sciences Jena, Jena, Germany
| | - Elizabeth A Nelson
- Microbial Palaeogenomics Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, Australia
- Adelaide Data Science Centre, University of Adelaide, Adelaide, Australia
| | - Nada Salem
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, IUCA-Aragosaurus, Universitity of Zaragoza, Zaragoza, Spain
| | - Isabelle Abadie
- Inrap - Institut national de recherches archéologiques préventives, Paris, France
- Centre Michel de Boüard, Centre de recherches archéologiques et historiques anciennes et médiévales, Université de Caen Normandie, Caen, France
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA, USA
| | | | - Matthew Brown
- Sociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USA
| | - Franco G R Campus
- Department of History, Human Sciences, and Education, University of Sassari, Sassari, Italy
| | - Tsang Chenghwa
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - María Cruz Berrocal
- Institute of Heritage Sciences (INCIPIT), Spanish National Research Council (CSIC), Santiago de Compostela, Spain
| | - Ladislav Damašek
- Institute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech Republic
| | | | - Raphaël Durand
- Service d'archéologie préventive Bourges plus, Bourges, France
- UMR 5199 PACEA, Université de Bordeaux, Pessac Cedex, France
| | - Michal Ernée
- Department of Prehistoric Archaeology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Hannah Frenzel
- Anatomy Institute, University of Leipzig, Leipzig, Germany
| | - Gabriel García Atiénzar
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
| | | | - Ellen Hsieh
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - Maciej Karwowski
- Institut für Urgeschichte und Historische Archäologie, University of Vienna, Vienna, Austria
| | - David Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nikki Kelvin
- Division of Ancient Pathogens, BioForge Canada Limited, Halifax, Nove Scotia, Canada
| | - Alexander Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Rebecca L Kinaston
- BioArch South, Waitati, New Zealand
- Griffith Centre for Social and Cultural Studies, Griffith University, Nathan, Queensland, Australia
| | - Arkadii Korolev
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Kim-Louise Krettek
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, Weimar, Germany
| | - Luca Lai
- Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Cory Look
- Sociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USA
| | - Kerttu Majander
- Department of Environmental Science, Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Michael McCormick
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Initiative for the Science of the Human Past at Harvard, Department of History, Harvard University, Cambridge, MA, USA
| | - Patxuka de Miguel Ibáñez
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
- Servicio de Obstetricia, Hospital Virgen de los Lirios-Fisabio, Alcoi, Spain
- Sección de Antropología, Sociedad de Ciencias Aranzadi, Donostia - San Sebastián, Spain
| | - Reg Murphy
- University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Kerkko Nordqvist
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Friederike Novotny
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Martin Obenaus
- Silva Nortica Archäologische Dienstleistungen, Thunau am Kamp, Austria
| | - Lauro Olmo-Enciso
- Department of History, University of Alcalá, Alcalá de Henares, Spain
| | - Päivi Onkamo
- Department of Biology, University of Turku, Turku, Finland
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt, Halle, Germany
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Valerii Patrushev
- Centre of Archaeological and Ethnographical Investigation, Mari State University, Yoshkar-Ola, Russia
| | - Sanni Peltola
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Romero
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
- Departamento de Biotecnología, Universidad de Alicante, San Vicente del Raspeig, Spain
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Elena Serrano
- Instituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, Santander, Spain
- TAR Arqueología, Madrid, Spain
| | | | - Emanuela Sias
- Centro Studi sulla Civiltà del Mare, Stintino, Italy
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Ladislav Stančo
- Institute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech Republic
| | - Treena Swanston
- Department of Anthropology, Economics and Political Science, MacEwan University, Edmonton, Alberta, Canada
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | | | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Center for Archaeological Sciences, University of Leuven, Leuven, Belgium
- Dienst Archeologie - Stad Mechelen, Mechelen, Belgium
| | - Tamara L Varney
- Department of Anthropology, Lakehead University, Thunder Bay, Ontario, Canada
| | | | - Christopher K Waters
- Heritage Department, National Parks of Antigua and Barbuda, St. Paul's Parish, Antigua and Barbuda
| | - Estella Weiss-Krejci
- Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
- Institut für Ur- und Frühgeschichte, Heidelberg University, Heidelberg, Germany
- Department of Social and Cultural Anthropology, University of Vienna, Vienna, Austria
| | - Eduard Winter
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria Spyrou
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, .
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3
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Soni V, Jensen JD. Temporal challenges in detecting balancing selection from population genomic data. G3 (BETHESDA, MD.) 2024; 14:jkae069. [PMID: 38551137 DOI: 10.1093/g3journal/jkae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024]
Abstract
The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding inference, and the expected signatures of balancing selection additionally change in a temporal fashion. Here we use forward-in-time simulations to quantify expected statistical power to detect balancing selection using both site frequency spectrum- and linkage disequilibrium-based methods under a variety of evolutionarily realistic null models. We find that whilst site frequency spectrum-based methods have little power immediately after a balanced mutation begins segregating, power increases with time since the introduction of the balanced allele. Conversely, linkage disequilibrium-based methods have considerable power whilst the allele is young, and power dissipates rapidly as the time since introduction increases. Taken together, this suggests that site frequency spectrum-based methods are most effective at detecting long-term balancing selection (>25N generations since the introduction of the balanced allele) whilst linkage disequilibrium-based methods are effective over much shorter timescales (<1N generations), thereby leaving a large time frame over which current methods have little power to detect the action of balancing selection. Finally, we investigate the extent to which alternative evolutionary processes may mimic these patterns, and demonstrate the need for caution in attempting to distinguish the signatures of balancing selection from those of both neutral processes (e.g. population structure and admixture) as well as of alternative selective processes (e.g. partial selective sweeps).
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Affiliation(s)
- Vivak Soni
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA
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4
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Mortazavi SMJ, Zare O, Ghasemi L, Taghizadeh P, Faghani P, Arshadi M, Mortazavi SAR, Sihver L. A Reexamination of Peto's Paradox: Insights Gained from Human Adaptation to Varied Levels of Ionizing and Non-ionizing Radiation. J Biomed Phys Eng 2024; 14:309-314. [PMID: 39027707 PMCID: PMC11252545 DOI: 10.31661/jbpe.v0i0.2402-1729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/27/2024] [Indexed: 07/20/2024]
Abstract
Humans have generally evolved some adaptations to protect against UV and different levels of background ionizing radiation. Similarly, elephants and whales have evolved adaptations to protect against cancer, such as multiple copies of the tumor suppressor gene p53, due to their large size and long lifespan. The difference in cancer protection strategies between humans and elephants/whales depends on genetics, lifestyle, environmental exposures, and evolutionary pressures. In this paper, we discuss how the differences in evolutionary adaptations between humans and elephants could explain why elephants have evolved a protective mechanism against cancer, whereas humans have not. Humans living in regions with high levels of background radiation, e.g. in Ramsar, Iran where exposure rates exceed those on the surface of Mars, seem to have developed some kind of protection against the ionizing radiation. However, humans in general have not developed cancer-fighting adaptations, so they instead rely on medical technologies and interventions. The difference in cancer protection strategies between humans and elephants/whales depends on genetics, lifestyle, environmental exposures, and evolutionary pressures. In this paper, we discuss how the differences in evolutionary adaptations between humans and elephants could explain why elephants have evolved a protective mechanism against cancer, whereas humans have not. Studying elephant adaptations may provide insights into new cancer prevention and treatment strategies for humans, but further research is required to fully understand the evolutionary disparities.
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Affiliation(s)
- Seyed Mohammad Javad Mortazavi
- Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Zare
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leyla Ghasemi
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parmis Taghizadeh
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parsa Faghani
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Arshadi
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Lembit Sihver
- Department of Physics, East Carolina University, Greenville, USA
- Royal Military College of Canada, Kingston, ON, Canada
- Department of Radiation Physics, Technische Universität Wien, Atominstitut, Vienna, Austria
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5
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Shen Q, Song G, Lin H, Bai H, Huang Y, Lv F, Wang S. Sensing, Imaging, and Therapeutic Strategies Endowing by Conjugate Polymers for Precision Medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310032. [PMID: 38316396 DOI: 10.1002/adma.202310032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Conjugated polymers (CPs) have promising applications in biomedical fields, such as disease monitoring, real-time imaging diagnosis, and disease treatment. As a promising luminescent material with tunable emission, high brightness and excellent stability, CPs are widely used as fluorescent probes in biological detection and imaging. Rational molecular design and structural optimization have broadened absorption/emission range of CPs, which are more conductive for disease diagnosis and precision therapy. This review provides a comprehensive overview of recent advances in the application of CPs, aiming to elucidate their structural and functional relationships. The fluorescence properties of CPs and the mechanism of detection signal amplification are first discussed, followed by an elucidation of their emerging applications in biological detection. Subsequently, CPs-based imaging systems and therapeutic strategies are illustrated systematically. Finally, recent advancements in utilizing CPs as electroactive materials for bioelectronic devices are also investigated. Moreover, the challenges and outlooks of CPs for precision medicine are discussed. Through this systematic review, it is hoped to highlight the frontier progress of CPs and promote new breakthroughs in fundamental research and clinical transformation.
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Affiliation(s)
- Qi Shen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Gang Song
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongrui Lin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Haotian Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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6
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Glaser-Schmitt A, Ramnarine TJS, Parsch J. Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster. Mol Ecol 2024; 33:e17024. [PMID: 37222070 DOI: 10.1111/mec.17024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
Allele frequencies can shift rapidly within natural populations. Under certain conditions, repeated rapid allele frequency shifts can lead to the long-term maintenance of polymorphism. In recent years, studies of the model insect Drosophila melanogaster have suggested that this phenomenon is more common than previously believed and is often driven by some form of balancing selection, such as temporally fluctuating or sexually antagonistic selection. Here we discuss some of the general insights into rapid evolutionary change revealed by large-scale population genomic studies, as well as the functional and mechanistic causes of rapid adaptation uncovered by single-gene studies. As an example of the latter, we consider a regulatory polymorphism of the D. melanogaster fezzik gene. Polymorphism at this site has been maintained at intermediate frequency over an extended period of time. Regular observations from a single population over a period of 7 years revealed significant differences in the frequency of the derived allele and its variance across collections between the sexes. These patterns are highly unlikely to arise from genetic drift alone or from the action of sexually antagonistic or temporally fluctuating selection individually. Instead, the joint action of sexually antagonistic and temporally fluctuating selection can best explain the observed rapid and repeated allele frequency shifts. Temporal studies such as those reviewed here further our understanding of how rapid changes in selection can lead to the long-term maintenance of polymorphism as well as improve our knowledge of the forces driving and limiting adaptation in nature.
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Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timothy J S Ramnarine
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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7
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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
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Rao E, Kumar Chandraker S, Misha Singh M, Kumar R. Global distribution of β-thalassemia mutations: An update. Gene 2024; 896:148022. [PMID: 38007159 DOI: 10.1016/j.gene.2023.148022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/29/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
One excellent illustration of how a single gene abnormality may result in a spectrum of disease incidence is the incredible phenotypic variety of β-thalassemia, which spans from severe anemia and transfusion needs to an utterly asymptomatic sickness. However, genetic causes of β-thalassemia and how the anemia's severity might be altered at various stages in its pathophysiology have been well investigated. There are currently known to be more than 350 mutations that cause genetic disease. However only 20 β thalassemia mutations account for more than 80% of the β thalassemia mutation across the globe due to phenomenon of geographical clustering where each population has a few common mutations together with a varying number of rare ones. Due to migration of the population, the spectrum of thalassemia mutation in changing from time to time. In this review, efforts are made to collate β globin gene mutations in different countries and populations.
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Affiliation(s)
- Ekta Rao
- ICMR-National Institute of Research in Tribal Health, Jabalpur, M.P, India
| | | | - Mable Misha Singh
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Ravindra Kumar
- ICMR-National Institute of Research in Tribal Health, Jabalpur, M.P, India.
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Ito S, Chiba S, Konuma J. Overcoming the congenitally disadvantageous mutation through adaptation to environmental UV exposure in land snails. Biol Lett 2023; 19:20230356. [PMID: 37990565 PMCID: PMC10663782 DOI: 10.1098/rsbl.2023.0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/02/2023] [Indexed: 11/23/2023] Open
Abstract
Congenital fitness-disadvantageous mutations are not maintained in the population; they are purged from the population through processes such as purifying selection. However, these mutations could persist in the population as polymorphisms when it is advantageous for the individuals carrying them in adapting to a specific external environment. We tested this hypothesis using the dimorphic land snail Euhadra peliomphala simodae in Japan; these snails have dark or bright coloured shells. The survival rate of dark snails at hatching was lower than that of the bright ones, as observed in the F1 progenies produced through crossing. Dark snails have a congenital fitness-disadvantageous mutation; however, they also have protection against ultraviolet radiation. They have a higher survival rate than the bright snails in a UV environment, as observed using the UV exposure experiments and UV transmittance measurements. This is a good example of a congenitally disadvantageous mutation that is advantageous for adapting to the external environment. These results explain the maintenance of polymorphism and highlight the genotypic and phenotypic diversity in the wild population.
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Affiliation(s)
- Shun Ito
- Izu Oshima Geopark Promotion Committee Office, Tokyo, Japan
- Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
- Graduate School of Life Science, Tohoku University, Miyagi, Japan
| | - Junji Konuma
- Department of Biology, Faculty of Science, Toho University, Chiba, Japan
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10
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Ariff A, Song Y, Aguilar R, Nhabomba A, Manaca MN, Khoo SK, Wiertsema S, Bassat Q, Barbosa A, Quintó L, Laing IA, Guinovart C, Alonso PL, Dobaño C, Le Souëf P, Zhang G. Genetic variants of TLR4, including the novel variant, rs5030719, and related genes are associated with susceptibility to clinical malaria in African children. Malar J 2023; 22:177. [PMID: 37287037 DOI: 10.1186/s12936-023-04549-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/31/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Malaria is a deadly disease caused by Plasmodium spp. Several blood phenotypes have been associated with malarial resistance, which suggests a genetic component to immune protection. METHODS One hundred and eighty-seven single nucleotide polymorphisms (SNPs) in 37 candidate genes were genotyped and investigated for associations with clinical malaria in a longitudinal cohort of 349 infants from Manhiça, Mozambique, in a randomized controlled clinical trial (RCT) (AgeMal, NCT00231452). Malaria candidate genes were selected according to involvement in known malarial haemoglobinopathies, immune, and pathogenesis pathways. RESULTS Statistically significant evidence was found for the association of TLR4 and related genes with the incidence of clinical malaria (p = 0.0005). These additional genes include ABO, CAT, CD14, CD36, CR1, G6PD, GCLM, HP, IFNG, IFNGR1, IL13, IL1A, IL1B, IL4R, IL4, IL6, IL13, MBL, MNSOD, and TLR2. Of specific interest, the previously identified TLR4 SNP rs4986790 and the novel finding of TRL4 SNP rs5030719 were associated with primary cases of clinical malaria. CONCLUSIONS These findings highlight a potential central role of TLR4 in clinical malarial pathogenesis. This supports the current literature and suggests that further research into the role of TLR4, as well as associated genes, in clinical malaria may provide insight into treatment and drug development.
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Affiliation(s)
- Amir Ariff
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Yong Song
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia
- School of Public Health, Curtin University, Perth, WA, 6102, Australia
| | - Ruth Aguilar
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Augusto Nhabomba
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Maria Nelia Manaca
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Siew-Kim Khoo
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
| | - Selma Wiertsema
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
| | - Quique Bassat
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Arnoldo Barbosa
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Llorenç Quintó
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Ingrid A Laing
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
- School of Medicine, The University of Western Australia, Perth, WA, 6008, Australia
| | - Caterina Guinovart
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Pedro L Alonso
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Peter Le Souëf
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia.
- School of Medicine, The University of Western Australia, Perth, WA, 6008, Australia.
| | - Guicheng Zhang
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia.
- School of Public Health, Curtin University, Perth, WA, 6102, Australia.
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6102, Australia.
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11
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Akoth M, Odhiambo J, Omolo B. Genome-wide association testing in malaria studies in the presence of overdominance. Malar J 2023; 22:119. [PMID: 37038187 PMCID: PMC10084622 DOI: 10.1186/s12936-023-04533-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/15/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND In human genetics, heterozygote advantage (heterosis) has been detected in studies that focused on specific genes but not in genome-wide association studies (GWAS). For example, heterosis is believed to confer resistance to certain strains of malaria in patients heterozygous for the sickle-cell gene, haemoglobin S (HbS). Yet the power of allelic tests can be substantially diminished by heterosis. Since GWAS (and haplotype-associations) also utilize allelic tests, it is unclear to what degree GWAS could underachieve because heterosis is ignored. METHODS In this study, a two-step approach to genetic association testing in malaria studies in a GWAS setting that may enhance the power of the tests was proposed, by identifying the underlying genetic model first before applying the association tests. Generalized linear models for dominant, recessive, additive, and heterotic effects were fitted and model selection was performed. This was achieved via tests of significance using the MAX and allelic tests, noting the minimum p-values across all the models and the proportion of tests that a given genetic model was deemed the best. An example dataset, based on 17 SNPs, from a robust genetic association study and simulated genotype datasets, were used to illustrate the method. Case-control genotype data on malaria from Kenya and Gambia were used for validation. RESULTS AND CONCLUSION Results showed that the allelic test returned some false negatives under the heterosis model, suggesting reduced power in testing genetic association. Disparities were observed for some chromosomes in the Kenyan and Gambian datasets, including the sex chromosomes. Thus, GWAS and haplotype associations should be treated with caution, unless the underlying genetic model had been determined.
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Affiliation(s)
- Morine Akoth
- Strathmore Institute of Mathematical Sciences, Strathmore University, Ole Sangale Road, Nairobi, Kenya.
| | - John Odhiambo
- Strathmore Institute of Mathematical Sciences, Strathmore University, Ole Sangale Road, Nairobi, Kenya
| | - Bernard Omolo
- Strathmore Institute of Mathematical Sciences, Strathmore University, Ole Sangale Road, Nairobi, Kenya
- Division of Mathematics & Computer Science, University of South Carolina-Upstate, 800 University Way, Spartanburg, USA
- School of Public Health, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
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12
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Gu H, Wang L, Lv X, Yang W, Zhang L, Zhang Z, Zhu T, Jia Y, Chen Y, Qu L. Domestication affects sex-biased gene expression evolution in the duck. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221313. [PMID: 37035296 PMCID: PMC10073915 DOI: 10.1098/rsos.221313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Genes with sex-biased expression are thought to underlie sexually dimorphic phenotypes and are therefore subject to different selection pressures in males and females. Many authors have proposed that sexual conflict leads to the evolution of sex-biased expression, which allows males and females to reach separate phenotypic and fitness optima. The selection pressures associated with domestication may cause changes in population architectures and mating systems, which in turn can alter their direction and strength. We compared sex-biased expression and genetic signatures in wild and domestic ducks (Anas platyrhynchos), and observed changes of sexual selection and identified the genomic divergence affected by selection forces. The extent of sex-biased expression in both sexes is positively correlated with the level of both d N /d S and nucleotide diversity. This observed changing pattern may mainly be owing to relaxed genetic constraints. We also demonstrate a clear link between domestication and sex-biased evolutionary rate in a comparative framework. Decreased polymorphism and evolutionary rate in domesticated populations generally matched life-history phenotypes known to experience artificial selection. Taken together, our work suggests the important implications of domestication in sex-biased evolution and the roles of artificial selection and sexual selection for shaping the diversity and evolutionary rate of the genome.
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Affiliation(s)
- Hongchang Gu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Li Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Zebin Zhang
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
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Prabhu SR, Ware AP, Umakanth S, Hande M, Mahabala C, Saadi AV, Satyamoorthy K. Erythrocyte miRNA-92a-3p interactions with PfEMP1 as determinants of clinical malaria. Funct Integr Genomics 2023; 23:93. [PMID: 36941394 PMCID: PMC10027640 DOI: 10.1007/s10142-023-01028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023]
Abstract
Based on the recently added high throughput analysis data on small noncoding RNAs in modulating disease pathophysiology of malaria, we performed an integrative computational analysis for exploring the role of human-host erythrocytic microRNAs (miRNAs) and their influence on parasite survival and host homeostasis. An in silico analysis was performed on transcriptomic datasets accessed from PlasmoDB and Gene Expression Omnibus (GEO) repositories analyzed using miRanda, miRTarBase, mirDIP, and miRDB to identify the candidate miRNAs that were further subjected to network analysis using MCODE and DAVID. This was followed by immune infiltration analysis and screening for RNA degradation mechanisms. Seven erythrocytic miRNAs, miR-451a, miR-92a-3p, miR-16-5p, miR-142-3p, miR-15b-5p, miR-19b-3p, and miR-223-3p showed favourable interactions with parasite genes expressed during blood stage infection. The miR-92a-3p that targeted the virulence gene PfEMP1 showed drastic reduction during infection. Performing pathway analysis for the human-host gene targets for the miRNA identified TOB1, TOB2, CNOT4, and XRN1 genes that are associated to RNA degradation processes, with the exoribonuclease XRN1, highly enriched in the malarial samples. On evaluating the role of exoribonucleases in miRNA degradation further, the pattern of Plasmodium falciparum_XRN1 showed increased levels during infection thus suggesting a defensive role for parasite survival. This study identifies miR-92a-3p, a member of C13orf25/ miR-17-92 cluster, as a novel miRNA inhibitor of the crucial parasite genes responsible for symptomatic malaria. Evidence for a plausible link to chromosome 13q31.3 loci controlling the epigenetic disease regulation is also suggested.
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Affiliation(s)
- Sowmya R Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shashikiran Umakanth
- Department of Medicine, Dr. TMA Pai Hospital, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Manjunath Hande
- Department of Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chakrapani Mahabala
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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14
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Qin Z, Li J, Tam B, Sinha S, Zhao B, Bhaskaran SP, Huang T, Wu X, Chian JS, Guo M, Kou SH, Lei H, Zhang L, Wang X, Lagniton PNP, Xiao F, Jiang X, Wang SM. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population. Int J Cancer 2023; 152:1159-1173. [PMID: 36385461 PMCID: PMC10098510 DOI: 10.1002/ijc.34359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.
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Affiliation(s)
- Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Shanmuga Priya Bhaskaran
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Teng Huang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaobing Wu
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jia Sheng Chian
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Maoni Guo
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Li Zhang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaoyu Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Philip Naderev P Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xinyang Jiang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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15
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Muppidi P, Wright E, Wassmer SC, Gupta H. Diagnosis of cerebral malaria: Tools to reduce Plasmodium falciparum associated mortality. Front Cell Infect Microbiol 2023; 13:1090013. [PMID: 36844403 PMCID: PMC9947298 DOI: 10.3389/fcimb.2023.1090013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Cerebral malaria (CM) is a major cause of mortality in Plasmodium falciparum (Pf) infection and is associated with the sequestration of parasitised erythrocytes in the microvasculature of the host's vital organs. Prompt diagnosis and treatment are key to a positive outcome in CM. However, current diagnostic tools remain inadequate to assess the degree of brain dysfunction associated with CM before the window for effective treatment closes. Several host and parasite factor-based biomarkers have been suggested as rapid diagnostic tools with potential for early CM diagnosis, however, no specific biomarker signature has been validated. Here, we provide an updated review on promising CM biomarker candidates and evaluate their applicability as point-of-care tools in malaria-endemic areas.
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Affiliation(s)
- Pranavi Muppidi
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emily Wright
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Samuel C. Wassmer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Himanshu Gupta
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, UP, India
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16
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Divya M, Prabhu SR, Satyamoorthy K, Saadi AV. Therapeutics through glycobiology: an approach for targeted elimination of malaria. Biologia (Bratisl) 2023; 78:1-5. [PMID: 36643690 PMCID: PMC9830602 DOI: 10.1007/s11756-023-01312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
The emergence of drug resistance in Plasmodium jeopardises worldwide malaria eradication efforts necessitating novel therapeutic approaches and therefore the identification of key metabolic pathways of parasite and human host for drug development garners importance. Enzymopathies like glucose-6-phosphate-dehydrogenase (G6PD) and pyruvate kinase (PK) deficiencies have been shown to protect against the severe consequences of malaria. Glycome profiles and the regulatory mechanisms involving the microRNAs or transcription factors' expression related to the histo-blood group glycogenes may add up to resolve the underlying pathogenesis. The glycan derivatives viz. heparin-like molecules (HLMs) interrupt parasite proliferation that can be exploited as leads for alternative therapies. The Plasmodium invasion of erythrocytes involve events of receptor recognition, adhesion, and ligand interactions. Since post translational modifications like N-glycosylation of merozoite surface proteins and several erythrocyte cluster of differentiation (CD) antigens and complement receptor, among others, are crucial to parasite invasion, understanding of post translational modification of proteins involved in the parasite-host interactions should identify viable antimalarial strategies.
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Affiliation(s)
- Mallya Divya
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Sowmya R. Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
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17
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Aqil A, Speidel L, Pavlidis P, Gokcumen O. Balancing selection on genomic deletion polymorphisms in humans. eLife 2023; 12:79111. [PMID: 36625544 PMCID: PMC9943071 DOI: 10.7554/elife.79111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains an imperative exercise. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS (genome-wide association studies) associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, University at BuffaloBuffaloUnited States
| | - Leo Speidel
- University College London, Genetics InstituteLondonUnited Kingdom
- The Francis Crick InstituteLondonUnited Kingdom
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation of Research and Technology-HellasHeraklionGreece
| | - Omer Gokcumen
- Department of Biological Sciences, University at BuffaloBuffaloUnited States
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18
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Malinowska JK, Żuradzki T. Towards the multileveled and processual conceptualisation of racialised individuals in biomedical research. SYNTHESE 2022; 201:11. [PMID: 36591336 PMCID: PMC9795162 DOI: 10.1007/s11229-022-04004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
In this paper, we discuss the processes of racialisation on the example of biomedical research. We argue that applying the concept of racialisation in biomedical research can be much more precise, informative and suitable than currently used categories, such as race and ethnicity. For this purpose, we construct a model of the different processes affecting and co-shaping the racialisation of an individual, and consider these in relation to biomedical research, particularly to studies on hypertension. We finish with a discussion on the potential application of our proposition to institutional guidelines on the use of racial categories in biomedical research.
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Affiliation(s)
| | - Tomasz Żuradzki
- Institute of Philosophy & Interdisciplinary Centre for Ethics, Jagiellonian University, ul. Grodzka 52, 31-044 Kraków, Poland
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19
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Nortey LN, Anning AS, Nakotey GK, Ussif AM, Opoku YK, Osei SA, Aboagye B, Ghartey-Kwansah G. Genetics of cerebral malaria: pathogenesis, biomarkers and emerging therapeutic interventions. Cell Biosci 2022; 12:91. [PMID: 35715862 PMCID: PMC9204375 DOI: 10.1186/s13578-022-00830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Cerebral malaria (CM) is a preeminent cause of severe disease and premature deaths in Sub-Saharan Africa, where an estimated 90% of cases occur. The key features of CM are a deep, unarousable coma that persists for longer than 1 h in patients with peripheral Plasmodium falciparum and no other explanation for encephalopathy. Significant research efforts on CM in the last few decades have focused on unravelling the molecular underpinnings of the disease pathogenesis and the identification of potential targets for therapeutic or pharmacologic intervention. These efforts have been greatly aided by the generation and study of mouse models of CM, which have provided great insights into key events of CM pathogenesis, revealed an interesting interplay of host versus parasite factors that determine the progression of malaria to severe disease and exposed possible targets for therapeutic intervention in severe disease.
Main Body
This paper reviews our current understanding of the pathogenic and immunologic factors involved in CM. We present the current view of the roles of certain gene products e.g., the var gene, ABCA-1, ICAM-1, TNF-alpha, CD-36, PfEMP-1 and G6PD, in CM pathogenesis. We also present alterations in the blood–brain barrier as a consequence of disease proliferation as well as complicated host and parasite interactions, including the T-cell immune reaction, reduced deformation of erythrocytes and cytoadherence. We further looked at recent advances in cerebral malaria treatment interventions by emphasizing on biomarkers, new diagnostic tools and emerging therapeutic options.
Conclusion
Finally, we discuss how the current understanding of some of these pathogenic and immunologic factors could inform the development of novel therapeutic interventions to fight CM.
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Balentine CM, Bolnick DA. Parallel evolution in human populations: A biocultural perspective. Evol Anthropol 2022; 31:302-316. [PMID: 36059181 DOI: 10.1002/evan.21956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/09/2022] [Accepted: 07/30/2022] [Indexed: 12/27/2022]
Abstract
Parallel evolution-where different populations evolve similar traits in response to similar environments-has been a topic of growing interest to biologists and biological anthropologists for decades. Parallel evolution occurs in human populations thanks to myriad biological and cultural mechanisms that permit humans to survive and thrive in diverse environments worldwide. Because humans shape and are shaped by their environments, biocultural approaches that emphasize the interconnections between biology and culture are key to understanding parallel evolution in human populations as well as the nuances of human biological variation and adaptation. In this review, we discuss how biocultural theory has been and can be applied to studies of parallel evolution and adaptation more broadly. We illustrate this through four examples of parallel evolution in humans: malaria resistance, lactase persistence, cold tolerance, and high-altitude adaptation.
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Affiliation(s)
- Christina M Balentine
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.,Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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21
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Schneider KA, Salas CJ. Evolutionary genetics of malaria. Front Genet 2022; 13:1030463. [DOI: 10.3389/fgene.2022.1030463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Many standard-textbook population-genetic results apply to a wide range of species. Sometimes, however, population-genetic models and principles need to be tailored to a particular species. This is particularly true for malaria, which next to tuberculosis and HIV/AIDS ranks among the economically most relevant infectious diseases. Importantly, malaria is not one disease—five human-pathogenic species of Plasmodium exist. P. falciparum is not only the most severe form of human malaria, but it also causes the majority of infections. The second most relevant species, P. vivax, is already considered a neglected disease in several endemic areas. All human-pathogenic species have distinct characteristics that are not only crucial for control and eradication efforts, but also for the population-genetics of the disease. This is particularly true in the context of selection. Namely, fitness is determined by so-called fitness components, which are determined by the parasites live-history, which differs between malaria species. The presence of hypnozoites, i.e., dormant liver-stage parasites, which can cause disease relapses, is a distinct feature of P. vivax and P. ovale sp. In P. malariae inactivated blood-stage parasites can cause a recrudescence years after the infection was clinically cured. To properly describe population-genetic processes, such as the spread of anti-malarial drug resistance, these features must be accounted for appropriately. Here, we introduce and extend a population-genetic framework for the evolutionary dynamics of malaria, which applies to all human-pathogenic malaria species. The model focuses on, but is not limited to, the spread of drug resistance. The framework elucidates how the presence of dormant liver stage or inactivated blood stage parasites that act like seed banks delay evolutionary processes. It is shown that, contrary to standard population-genetic theory, the process of selection and recombination cannot be decoupled in malaria. Furthermore, we discuss the connection between haplotype frequencies, haplotype prevalence, transmission dynamics, and relapses or recrudescence in malaria.
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22
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Evolutionary consequences of vector-borne transmission: how using vectors shapes host, vector and pathogen evolution. Parasitology 2022; 149:1667-1678. [PMID: 36200511 PMCID: PMC10090782 DOI: 10.1017/s0031182022001378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transmission mode is a key factor that influences host–parasite coevolution. Vector-borne pathogens are among the most important disease agents for humans and wildlife due to their broad distribution, high diversity, prevalence and lethality. They comprise some of the most important and widespread human pathogens, such as yellow fever, leishmania and malaria. Vector-borne parasites (in this review, those transmitted by blood-feeding Diptera) follow unique transmission routes towards their vertebrate hosts. Consequently, each part of this tri-partite (i.e. parasite, vector and host) interaction can influence co- and counter-evolutionary pressures among antagonists. This mode of transmission may favour the evolution of greater virulence to the vertebrate host; however, pathogen–vector interactions can also have a broad spectrum of fitness costs to the insect vector. To complete their life cycle, vector-borne pathogens must overcome immune responses from 2 unrelated organisms, since they can activate responses in both vertebrate and invertebrate hosts, possibly creating a trade-off between investments against both types of immunity. Here, we assess how dipteran vector-borne transmission shapes the evolution of hosts, vectors and the pathogens themselves. Hosts, vectors and pathogens co-evolve together in a constant antagonistic arms race with each participant's primary goal being to maximize its performance and fitness.
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Olatunde AC, Cornwall DH, Roedel M, Lamb TJ. Mouse Models for Unravelling Immunology of Blood Stage Malaria. Vaccines (Basel) 2022; 10:1525. [PMID: 36146602 PMCID: PMC9501382 DOI: 10.3390/vaccines10091525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria comprises a spectrum of disease syndromes and the immune system is a major participant in malarial disease. This is particularly true in relation to the immune responses elicited against blood stages of Plasmodium-parasites that are responsible for the pathogenesis of infection. Mouse models of malaria are commonly used to dissect the immune mechanisms underlying disease. While no single mouse model of Plasmodium infection completely recapitulates all the features of malaria in humans, collectively the existing models are invaluable for defining the events that lead to the immunopathogenesis of malaria. Here we review the different mouse models of Plasmodium infection that are available, and highlight some of the main contributions these models have made with regards to identifying immune mechanisms of parasite control and the immunopathogenesis of malaria.
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Affiliation(s)
| | | | | | - Tracey J. Lamb
- Department of Pathology, University of Utah, Emma Eccles Jones Medical Research Building, 15 N Medical Drive E, Room 1420A, Salt Lake City, UT 84112, USA
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Never-homozygous genetic variants in healthy populations are potential recessive disease candidates. NPJ Genom Med 2022; 7:54. [PMID: 36075934 PMCID: PMC9458638 DOI: 10.1038/s41525-022-00322-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
The rapid pace with which genetic variants are now being determined means there is a pressing need to understand how they affect biological systems. Variants from healthy individuals have previously been used to study blood groups or HLA diversity and to identify genes that can apparently be nonfunctional in healthy people. These studies and others have observed a lower than expected frequency of homozygous individuals for potentially deleterious alleles, which would suggest that several of these alleles can lead to recessive disorders. Here we exploited this principle to hunt for potential disease variants in genomes from healthy people. We identified at least 108 exclusively heterozygous variants with evidence for an impact on biological function. We discuss several examples of candidate variants/genes including CCDC8, PANK3, RHD and NLRP12. Overall, the results suggest there are many, comparatively frequent, potentially lethal or disease-causing variants lurking in healthy human populations.
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25
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Konozy EHE, Osman MEFM, Ghartey-Kwansah G, Abushama HM. The striking mimics between COVID-19 and malaria: A review. Front Immunol 2022; 13:957913. [PMID: 36081516 PMCID: PMC9445119 DOI: 10.3389/fimmu.2022.957913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives COVID-19 is a transmissible illness triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since its onset in late 2019 in Wuhan city of China, it continues to spread universally, leading to an ongoing pandemic that shattered all efforts to restrain it. On the other hand, in Africa, the COVID-19 infection may be influenced by malaria coinfection. Hence, in this review article, we aimed to give a comprehensive account of the similarities between COVID-19 and malaria in terms of symptoms, clinical, immunological, and molecular perspectives. Methodology In this article, we reviewed over 50 research papers to highlight the multilayered similarities between COVID-19 and malaria infections that might influence the ontology of COVID-19. Results Despite the poor health and fragile medical system of many sub-Saharan African countries, they persisted with a statistically significantly low number of COVID-19 cases. This was attributed to many factors such as the young population age, the warm weather, the lack of proper diagnosis, previous infection with malaria, the use of antimalarial drugs, etc. Additionally, population genetics appears to play a significant role in shaping the COVID-19 dynamics. This is evident as recent genomic screening analyses of the angiotensin-converting enzyme 2 (ACE2) and malaria-associated-variants identified 6 candidate genes that might play a role in malaria and COVID-19 incidence and severity. Moreover, the clinical and pathological resemblances between the two diseases have made considerable confusion in the diagnosis and thereafter curb the disease in Africa. Therefore, possible similarities between the diseases in regards to the clinical, pathological, immunological, and genetical ascription were discussed. Conclusion Understanding the dynamics of COVID-19 infection in Sub-Saharan Africa and how it is shaped by another endemic disease like malaria can provide insights into how to tailor a successful diagnostic, intervention, and control plans that lower both disease morbidity and mortality.
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Affiliation(s)
| | | | - George Ghartey-Kwansah
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
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Thiam F, Diop G, Coulonges C, Derbois C, Mbengue B, Thiam A, Nguer CM, Zagury JF, Deleuze JF, Dieye A. G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria. PeerJ 2022; 10:e13487. [PMID: 35811813 PMCID: PMC9266585 DOI: 10.7717/peerj.13487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/03/2022] [Indexed: 01/24/2023] Open
Abstract
Background Host genetic factors contribute to the variability of malaria phenotypes and can allow a better understanding of mechanisms involved in susceptibility and/or resistance to Plasmodium falciparum infection outcomes. Several genetic polymorphisms were reported to be prevalent among populations living in tropical malaria-endemic regions and induce protection against malaria. The present study aims to investigate the prevalence of HBB (chr11) and G6PD (chrX) deficiencies polymorphisms among Senegalese populations and their associations with the risk for severe Plasmodium falciparum malaria occurrence. Methods We performed a retrospective study with 437 samples, 323 patients recruited in hospitals located in three different endemic areas where malaria episodes were confirmed and 114 free malaria controls. The patients enrolled were classified into two groups: severe malaria (SM) (153 patients) and uncomplicated malaria (UM) (170 patients). PCR and DNA sequencing assessed host genetic polymorphisms in HBB and G6PD. Using a multivariate regression and additive model, estimates of the impact of human HBB and G6PD polymorphisms on malaria incidence were performed. Results Six frequent SNPs with minor allele frequencies (MAF) > 3% were detected in the HBB gene (rs7946748, rs7480526, rs10768683, rs35209591, HbS (rs334) and rs713040) and two in the G6PD gene (rs762515 and rs1050828 (G6PD-202 G > A). Analysis of selected HbS polymorphism showed significant association with protective effect against severe malaria with a significant p-value = 0.033 (OR 0.38, 95% CI [0.16-0.91]) for SM vs. UM comparison. Surprisingly, our study did not identify the protective effect of variant HbC polymorphism against severe malaria. Finally, we found some of the polymorphisms, like HbS (rs334), are associated with age and biological parameters like eosinophils, basophils, lymphocytes etc. Conclusion Our data report HBB and G6PD polymorphisms in the Senegalese population and their correlation with severe/mild malaria and outcome. The G6PD and HBB deficiencies are widespread in West Africa endemic malaria regions such as The Gambia, Mali, and Burkina Faso. The study shows the critical role of genetic factors in malaria outcomes. Indeed, genetic markers could be good tools for malaria endemicity prognosis.
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Affiliation(s)
- Fatou Thiam
- Groupe de Recherche Biotechnologie Appliquée et Bioprocédés Environnementaux (GRBA-BE), Laboratoire Eau, Energie, Environnement et Procédés Industriels (LE3PI), Département de Génie Chimique et Biologie Appliquée, Ecole Supérieure Polytechnique, Université Cheikh Anta DIOP de Dakar, Dakar Fann, Dakar, Sénégal
| | - Gora Diop
- Unité Postulante de Biologie Génétique, Génomique et Bio-informatique (G2B), Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar Fann, Dakar, Sénégal,Pole d’Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, Dakar, Sénégal
| | - Cedric Coulonges
- Equipe GBA «Génomique, Bioinformatique & Applications », Conservatoire National des Arts et Métiers, Paris, France
| | - Céline Derbois
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Babacar Mbengue
- Service d’Immunologie, Faculté de Médecine, de Pharmacie et d’Odontostomatologie, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Alassane Thiam
- Pole d’Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, Dakar, Sénégal
| | - Cheikh Momar Nguer
- Groupe de Recherche Biotechnologie Appliquée et Bioprocédés Environnementaux (GRBA-BE), Laboratoire Eau, Energie, Environnement et Procédés Industriels (LE3PI), Département de Génie Chimique et Biologie Appliquée, Ecole Supérieure Polytechnique, Université Cheikh Anta DIOP de Dakar, Dakar Fann, Dakar, Sénégal
| | - Jean Francois Zagury
- Equipe GBA «Génomique, Bioinformatique & Applications », Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-Francois Deleuze
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Alioune Dieye
- Service d’Immunologie, Faculté de Médecine, de Pharmacie et d’Odontostomatologie, Université Cheikh Anta DIOP, Dakar, Sénégal
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Garg P, Jadhav B, Lee W, Rodriguez OL, Martin-Trujillo A, Sharp AJ. A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits. Am J Hum Genet 2022; 109:1065-1076. [PMID: 35609568 PMCID: PMC9247821 DOI: 10.1016/j.ajhg.2022.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/28/2022] [Indexed: 01/04/2023] Open
Abstract
The human genome contains tens of thousands of large tandem repeats and hundreds of genes that show common and highly variable copy-number changes. Due to their large size and repetitive nature, these variable number tandem repeats (VNTRs) and multicopy genes are generally recalcitrant to standard genotyping approaches and, as a result, this class of variation is poorly characterized. However, several recent studies have demonstrated that copy-number variation of VNTRs can modify local gene expression, epigenetics, and human traits, indicating that many have a functional role. Here, using read depth from whole-genome sequencing to profile copy number, we report results of a phenome-wide association study (PheWAS) of VNTRs and multicopy genes in a discovery cohort of ∼35,000 samples, identifying 32 traits associated with copy number of 38 VNTRs and multicopy genes at 1% FDR. We replicated many of these signals in an independent cohort and observed that VNTRs showing trait associations were significantly enriched for expression QTLs with nearby genes, providing strong support for our results. Fine-mapping studies indicated that in the majority (∼90%) of cases, the VNTRs and multicopy genes we identified represent the causal variants underlying the observed associations. Furthermore, several lie in regions where prior SNV-based GWASs have failed to identify any significant associations with these traits. Our study indicates that copy number of VNTRs and multicopy genes contributes to diverse human traits and suggests that complex structural variants potentially explain some of the so-called "missing heritability" of SNV-based GWASs.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - William Lee
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, Room 8-116, Box 1498, New York, NY 10029, USA.
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28
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Introini V, Marin-Menendez A, Nettesheim G, Lin YC, Kariuki SN, Smith AL, Jean L, Brewin JN, Rees DC, Cicuta P, Rayner JC, Penman BS. The erythrocyte membrane properties of beta thalassaemia heterozygotes and their consequences for Plasmodium falciparum invasion. Sci Rep 2022; 12:8934. [PMID: 35624125 PMCID: PMC9142571 DOI: 10.1038/s41598-022-12060-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Malaria parasites such as Plasmodium falciparum have exerted formidable selective pressures on the human genome. Of the human genetic variants associated with malaria protection, beta thalassaemia (a haemoglobinopathy) was the earliest to be associated with malaria prevalence. However, the malaria protective properties of beta thalassaemic erythrocytes remain unclear. Here we studied the mechanics and surface protein expression of beta thalassaemia heterozygous erythrocytes, measured their susceptibility to P. falciparum invasion, and calculated the energy required for merozoites to invade them. We found invasion-relevant differences in beta thalassaemic cells versus matched controls, specifically: elevated membrane tension, reduced bending modulus, and higher levels of expression of the major invasion receptor basigin. However, these differences acted in opposition to each other with respect to their likely impact on invasion, and overall we did not observe beta thalassaemic cells to have lower P. falciparum invasion efficiency for any of the strains tested.
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Affiliation(s)
- Viola Introini
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge, UK
| | | | | | - Yen-Chun Lin
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Silvia N Kariuki
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Letitia Jean
- University of Oxford, Sir William Dunn School of Pathology, Oxford, UK
| | - John N Brewin
- King's College London and King's College Hospital, London, UK
| | - David C Rees
- King's College London and King's College Hospital, London, UK
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Bridget S Penman
- University of Warwick, Zeeman Institute, School of Life Sciences, Coventry, UK.
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29
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Ferreira NS, Mathias JLS, Albuquerque SRL, Almeida ACG, Dantas AC, Anselmo FC, Lima ES, Lacerda MVG, Nogueira PA, Ramasawmy R, Gonçalves MS, Moura Neto JP. Duffy blood system and G6PD genetic variants in vivax malaria patients from Manaus, Amazonas, Brazil. Malar J 2022; 21:144. [PMID: 35527254 PMCID: PMC9080172 DOI: 10.1186/s12936-022-04165-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
Background Over a third of the world’s population is at risk of Plasmodium vivax-induced malaria. The unique aspect of the parasite’s biology and interactions with the human host make it harder to control and eliminate the disease. Glucose-6-phosphate dehydrogenase (G6PD) deficiency and Duffy-negative blood groups are two red blood cell (RBC) variations that can confer protection against malaria. Methods Molecular genotyping of G6PD and Duffy variants was performed in 225 unrelated patients (97 with uncomplicated and 128 with severe vivax malaria) recruited at a Reference Centre for Infectious Diseases in Manaus. G6PD and Duffy variants characterizations were performed using Real Time PCR (qPCR) and PCR–RFLP, respectively. Results The Duffy blood group system showed a phenotypic distribution Fy(a + b−) of 70 (31.1%), Fy(a + b +) 96 (42.7%), Fy(a−b +) 56 (24.9%) and Fy(a−b−) 1 (0.44%.) The genotype FY*A/FY*B was predominant in both uncomplicated (45.3%) and severe malaria (39.2%). Only one Duffy phenotype Fy(a-b) was found and this involved uncomplicated vivax malaria. The G6PD c.202G > A variant was found in 11 (4.88%) females and 18 (8.0%) males, while c.376A > G was found in 20 females (8.88%) and 23 (10.22%) male patients. When combined GATA mutated and c.202G > A and c.376A > G mutated, was observed at a lower frequency in uncomplicated (3.7%) in comparison to severe malaria (37.9%). The phenotype Fy(a−b +) (p = 0.022) with FY*B/FY*B (p = 0.015) genotype correlated with higher parasitaemia. Conclusions A high prevalence of G6PD c202G > A and c.376A > G and Duffy variants is observed in Manaus, an endemic area for vivax malaria. In addition, this study reports for the first time the Duffy null phenotype Fy(a-b-) in the population of the Amazonas state. Moreover, it is understood that the relationship between G6PD and Duffy variants can modify clinical symptoms in malaria caused by P. vivax and this deserves to be further investigated and explored among this population. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04165-y.
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30
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Muralidhar P, Veller C. Dominance shifts increase the likelihood of soft selective sweeps. Evolution 2022; 76:966-984. [PMID: 35213740 PMCID: PMC9928167 DOI: 10.1111/evo.14459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/04/2022] [Indexed: 01/21/2023]
Abstract
Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.
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Affiliation(s)
- Pavitra Muralidhar
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616,corresponding author:
| | - Carl Veller
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616
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31
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Albrecht-Schgoer K, Lackner P, Schmutzhard E, Baier G. Cerebral Malaria: Current Clinical and Immunological Aspects. Front Immunol 2022; 13:863568. [PMID: 35514965 PMCID: PMC9067128 DOI: 10.3389/fimmu.2022.863568] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
This review focuses on current clinical and immunological aspects of cerebral malaria induced by Plasmodium falciparum infection. Albeit many issues concerning the inflammatory responses remain unresolved and need further investigations, current knowledge of the underlying molecular mechanisms is highlighted. Furthermore, and in the light of significant limitations in preventative diagnosis and treatment of cerebral malaria, this review mainly discusses our understanding of immune mechanisms in the light of the most recent research findings. Remarkably, the newly proposed CD8+ T cell-driven pathophysiological aspects within the central nervous system are summarized, giving first rational insights into encouraging studies with immune-modulating adjunctive therapies that protect from symptomatic cerebral participation of Plasmodium falciparum infection.
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Affiliation(s)
- Karin Albrecht-Schgoer
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Lackner
- Department of Neurology, Klinik Floridsdorf, Wien, Austria
| | - Erich Schmutzhard
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
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32
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Tandoh KZ, Quaye O. Genetic associations in chronic hepatitis B infection: toward developing polygenic risk scores. Future Microbiol 2022; 17:541-549. [PMID: 35332782 DOI: 10.2217/fmb-2021-0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chronic hepatitis B (CHB) infection results in multiple clinical phenotypes of varying severity. One of the critical gaps in CHB management is the lack of a genetic-based tool to aid existing hepatocellular carcinoma and cirrhosis risk stratification models for patients with active CHB. Such individual predictive models for CHB are plagued by an inherent limitation of discriminatory power that clearly indicates the need for their improvement. In this article, we highlight genetic association studies in CHB that identified HLA and cytokine genetic susceptibility loci to CHB. We advance the position that translating CHB genetic susceptibility loci into polygenic risk scores will be a welcome addendum to the current arsenal of CHB outcome predictive models. We conclude with comments on hurdles that future research efforts should address within the research enclave of CHB and advocate for increased genetic data representation from sub-Saharan Africa.
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Affiliation(s)
- Kwesi Z Tandoh
- Department of Biochemistry, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
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33
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Schmidt A, M. Groh A, S. Frick J, Vehreschild MJGT, U. Ludwig K. Genetic Predisposition and the Variable Course of Infectious Diseases. DEUTSCHES ARZTEBLATT INTERNATIONAL 2022; 119:117-123. [PMID: 35101171 PMCID: PMC9160423 DOI: 10.3238/arztebl.m2022.0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 08/31/2021] [Accepted: 01/11/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Contact with a pathogen is followed by variable courses of infectious disease, which are only partly explicable by classical risk factors. The susceptibility to infection is variable, as is the course of disease after infection. In this review, we discuss the extent to which this variation is due to genetic factors of the affected individual (the host). METHODS Selective review of the literature on host genetics in infectious disease, with special attention to the pathogens SARSCoV- 2, influenza viruses, Mycobacterium tuberculosis, and human immunodeficiency virus (HIV). RESULTS Genetic variants of the host contribute to the pathogenesis of infectious diseases. For example, in HIV infection, a relatively common variant leading to a loss of function of the HIV co-receptor CCR5 affects the course of the disease, as do variants in genes of the major histocompatibility complex (MHC) region. Rare monogenic variants of the interferon immune response system contribute to severe disease courses in COVID-19 and influenza (type I interferon in these two cases) and in tuberculosis (type II interferon). An estimated 1.8% of life-threatening courses of COVID-19 in men under age 60 are caused by a deficiency of toll-like receptor 7. The scientific understanding of host genetic factors has already been beneficial to the development of effective drugs. In a small number of cases, genetic information has also been used for individual therapeutic decision-making and for the identification of persons at elevated risk. CONCLUSION A comprehensive understanding of host genetics can improve the care of patients with infectious diseases. Until the present, the clinical utility of host genetics has been limited to rare cases; in the future, polygenic risk scores summarizing the relevant genetic variants in each patient will enable a wider benefit. To make this possible, multicenter studies are needed that will systematically integrate clinical and genetic data.
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Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, Medical Faculty of the University of Bonn & Bonn University Hospital
| | - Ana M. Groh
- Medical Department II, Infectiology, University HospitalFrankfurt, Goethe University Frankfurt
| | - Julia S. Frick
- Interfaculty Institute for Microbiology and Infection Medicine, University Hospital and Faculty of Medicine Tübingen
- MVZ Laboratory Ludwigsburg GbR
| | | | - Kerstin U. Ludwig
- Institute of Human Genetics, Medical Faculty of the University of Bonn & Bonn University Hospital
- * Institut für Humangenetik, Department of Genomics Universitätsklinikum Bonn Venusberg-Campus 1, Gebäude 76 53127 Bonn, Germany
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34
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The Myth of the Genetically Sick African. GENEALOGY 2022. [DOI: 10.3390/genealogy6010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Western medicine has an unfortunate history where it has been applied to address the health of African Americans. At its origins, it was aligned with the objectives of colonialism and chattel slavery. The degree to which medical “science” concerned itself with persons of African descent was to keep them alive for sale on the auction block, or to keep them healthy as they toiled to generate wealth for their European owners. Medicine in early America relied upon both dead and live African bodies to test its ideas to benefit Europeans. As medicine moved from quackery to a discipline based in science, its understanding of human biological variation was flawed. This was not a problem confined to medicine alone, but to the biological sciences in general. Biology had no solid theoretical basis until after 1859. As medicine further developed in the 20th century, it never doubted the difference between Europeans and Africans, and also asserted the innate inferiority of the latter. The genomic revolution in the latter 20th century produced tools that were deployed in a biomedical culture still mired in “racial” medicine. This lack of theoretical perspective still misdirects research associated with health disparity. In contrast to this is evolutionary medicine, which relies on a sound unification of evolutionary (ultimate) and physiological, cellular, and molecular (proximate) mechanisms. Utilizing the perspectives of evolutionary medicine is a prerequisite for an effective intervention in health disparity and finally dispelling the myth of the genetically sick African.
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35
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Damena D, Agamah FE, Kimathi PO, Kabongo NE, Girma H, Choga WT, Golassa L, Chimusa ER. Insilico Functional Analysis of Genome-Wide Dataset From 17,000 Individuals Identifies Candidate Malaria Resistance Genes Enriched in Malaria Pathogenic Pathways. Front Genet 2021; 12:676960. [PMID: 34868193 PMCID: PMC8639191 DOI: 10.3389/fgene.2021.676960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Recent genome-wide association studies (GWASs) of severe malaria have identified several association variants. However, much about the underlying biological functions are yet to be discovered. Here, we systematically predicted plausible candidate genes and pathways from functional analysis of severe malaria resistance GWAS summary statistics (N = 17,000) meta-analysed across 11 populations in malaria endemic regions. We applied positional mapping, expression quantitative trait locus (eQTL), chromatin interaction mapping, and gene-based association analyses to identify candidate severe malaria resistance genes. We further applied rare variant analysis to raw GWAS datasets (N = 11,000) of three malaria endemic populations including Kenya, Malawi, and Gambia and performed various population genetic structures of the identified genes in the three populations and global populations. We performed network and pathway analyses to investigate their shared biological functions. Our functional mapping analysis identified 57 genes located in the known malaria genomic loci, while our gene-based GWAS analysis identified additional 125 genes across the genome. The identified genes were significantly enriched in malaria pathogenic pathways including multiple overlapping pathways in erythrocyte-related functions, blood coagulations, ion channels, adhesion molecules, membrane signalling elements, and neuronal systems. Our population genetic analysis revealed that the minor allele frequencies (MAF) of the single nucleotide polymorphisms (SNPs) residing in the identified genes are generally higher in the three malaria endemic populations compared to global populations. Overall, our results suggest that severe malaria resistance trait is attributed to multiple genes, highlighting the possibility of harnessing new malaria therapeutics that can simultaneously target multiple malaria protective host molecular pathways.
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Affiliation(s)
- Delesa Damena
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Peter O Kimathi
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ntumba E Kabongo
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Hundaol Girma
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wonderful T Choga
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lemu Golassa
- Aklilu Lema Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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36
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Kamiya T, Davis NM, Greischar MA, Schneider D, Mideo N. Linking functional and molecular mechanisms of host resilience to malaria infection. eLife 2021; 10:e65846. [PMID: 34636723 PMCID: PMC8510579 DOI: 10.7554/elife.65846] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
It remains challenging to understand why some hosts suffer severe illnesses, while others are unscathed by the same infection. We fitted a mathematical model to longitudinal measurements of parasite and red blood cell density in murine hosts from diverse genetic backgrounds to identify aspects of within-host interactions that explain variation in host resilience and survival during acute malaria infection. Among eight mouse strains that collectively span 90% of the common genetic diversity of laboratory mice, we found that high host mortality was associated with either weak parasite clearance, or a strong, yet imprecise response that inadvertently removes uninfected cells in excess. Subsequent cross-sectional cytokine assays revealed that the two distinct functional mechanisms of poor survival were underpinned by low expression of either pro- or anti-inflammatory cytokines, respectively. By combining mathematical modelling and molecular immunology assays, our study uncovered proximate mechanisms of diverse infection outcomes across multiple host strains and biological scales.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology and Evolutionary Biology, University of TorontoTorontoCanada
| | - Nicole M Davis
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Megan A Greischar
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthacaUnited States
| | - David Schneider
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of TorontoTorontoCanada
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37
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Jezewski AJ, Lin YH, Reisz JA, Culp-Hill R, Barekatain Y, Yan VC, D'Alessandro A, Muller FL, Odom John AR. Targeting Host Glycolysis as a Strategy for Antimalarial Development. Front Cell Infect Microbiol 2021; 11:730413. [PMID: 34604112 PMCID: PMC8482815 DOI: 10.3389/fcimb.2021.730413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Glycolysis controls cellular energy, redox balance, and biosynthesis. Antiglycolytic therapies are under investigation for treatment of obesity, cancer, aging, autoimmunity, and microbial diseases. Interrupting glycolysis is highly valued as a therapeutic strategy, because glycolytic disruption is generally tolerated in mammals. Unfortunately, anemia is a known dose-limiting side effect of these inhibitors and presents a major caveat to development of antiglycolytic therapies. We developed specific inhibitors of enolase – a critical enzyme in glycolysis – and validated their metabolic and cellular effects on human erythrocytes. Enolase inhibition increases erythrocyte susceptibility to oxidative damage and induces rapid and premature erythrocyte senescence, rather than direct hemolysis. We apply our model of red cell toxicity to address questions regarding erythrocyte glycolytic disruption in the context of Plasmodium falciparum malaria pathogenesis. Our study provides a framework for understanding red blood cell homeostasis under normal and disease states and clarifies the importance of erythrocyte reductive capacity in malaria parasite growth.
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Affiliation(s)
- Andrew J Jezewski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Yu-Hsi Lin
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, Aurora, CO, United States
| | - Rachel Culp-Hill
- Department of Biochemistry and Molecular Genetics, Aurora, CO, United States
| | - Yasaman Barekatain
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Victoria C Yan
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, Aurora, CO, United States
| | - Florian L Muller
- Department of Cancer Systems Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Neuro-Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
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38
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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39
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Oncologic Anthropology: An Interdisciplinary Approach to Understanding the Association Between Genetically Defined African Ancestry and Susceptibility for Triple Negative Breast Cancer. CURRENT BREAST CANCER REPORTS 2021. [DOI: 10.1007/s12609-021-00426-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Azizzadeh-Roodpish S, Garzon MH, Mainali S. Classifying single nucleotide polymorphisms in humans. Mol Genet Genomics 2021; 296:1161-1173. [PMID: 34259913 DOI: 10.1007/s00438-021-01805-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation amongst the human population and are key to personalized medicine. New tests are presented to distinguish pathogenic/malign (i.e., likely to contribute to or cause a disease) from nonpathogenic/benign SNPs, regardless of whether they occur in coding (exon) or noncoding (intron) regions in the human genome. The tests are based on the nearest neighbor (NN) model of Gibbs free energy landscapes of DNA hybridization and on deep structural properties of DNA revealed by an approximating metric (the h-distance) in DNA spaces of oligonucleotides of a common size. The quality assessments show that the newly defined PNPG test can classify a SNP with an accuracy about 73% for the required parameters. The best performance among machine learning models is a feed-forward neural network with fivefold cross-validation accuracy of at least 73%. These results may provide valuable tools to solve the SNP classification problem, where tools are lacking, to assess the likelihood of disease causing in unclassified SNPs. These tests highlight the significance of hybridization chemistry in SNPs. They can be applied to further the effectiveness of research in the areas of genomics and metabolomics.
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Affiliation(s)
| | - Max H Garzon
- Computer Science, The University of Memphis, Memphis, TN, 38152, USA.
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41
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Zeng K, Charlesworth B, Hobolth A. Studying models of balancing selection using phase-type theory. Genetics 2021; 218:6237896. [PMID: 33871627 DOI: 10.1093/genetics/iyab055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 11/15/2022] Open
Abstract
Balancing selection (BLS) is the evolutionary force that maintains high levels of genetic variability in many important genes. To further our understanding of its evolutionary significance, we analyze models with BLS acting on a biallelic locus: an equilibrium model with long-term BLS, a model with long-term BLS and recent changes in population size, and a model of recent BLS. Using phase-type theory, a mathematical tool for analyzing continuous time Markov chains with an absorbing state, we examine how BLS affects polymorphism patterns in linked neutral regions, as summarized by nucleotide diversity, the expected number of segregating sites, the site frequency spectrum, and the level of linkage disequilibrium (LD). Long-term BLS affects polymorphism patterns in a relatively small genomic neighborhood, and such selection targets are easier to detect when the equilibrium frequencies of the selected variants are close to 50%, or when there has been a population size reduction. For a new mutation subject to BLS, its initial increase in frequency in the population causes linked neutral regions to have reduced diversity, an excess of both high and low frequency derived variants, and elevated LD with the selected locus. These patterns are similar to those produced by selective sweeps, but the effects of recent BLS are weaker. Nonetheless, compared to selective sweeps, nonequilibrium polymorphism and LD patterns persist for a much longer period under recent BLS, which may increase the chance of detecting such selection targets. An R package for analyzing these models, among others (e.g., isolation with migration), is available.
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Affiliation(s)
- Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Asger Hobolth
- Department of Mathematics, Aarhus University, Aarhus DK-8000, Denmark
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42
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Tukwasibwe S, Traherne JA, Chazara O, Jayaraman J, Trowsdale J, Moffett A, Jiang W, Nankabirwa JI, Rek J, Arinaitwe E, Nsobya SL, Atuheirwe M, Frank M, Godwin A, Jagannathan P, Cose S, Kamya MR, Dorsey G, Rosenthal PJ, Colucci F, Nakimuli A. Diversity of KIR genes and their HLA-C ligands in Ugandan populations with historically varied malaria transmission intensity. Malar J 2021; 20:111. [PMID: 33632228 PMCID: PMC7908804 DOI: 10.1186/s12936-021-03652-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/16/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Malaria is one of the most serious infectious diseases in the world. The malaria burden is greatly affected by human immunity, and immune responses vary between populations. Genetic diversity in KIR and HLA-C genes, which are important in immunity to infectious diseases, is likely to play a role in this heterogeneity. Several studies have shown that KIR and HLA-C genes influence the immune response to viral infections, but few studies have examined the role of KIR and HLA-C in malaria infection, and these have used low-resolution genotyping. The aim of this study was to determine whether genetic variation in KIR and their HLA-C ligands differ in Ugandan populations with historically varied malaria transmission intensity using more comprehensive genotyping approaches. METHODS High throughput multiplex quantitative real-time PCR method was used to genotype KIR genetic variants and copy number variation and a high-throughput real-time PCR method was developed to genotype HLA-C1 and C2 allotypes for 1344 participants, aged 6 months to 10 years, enrolled from Ugandan populations with historically high (Tororo District), medium (Jinja District) and low (Kanungu District) malaria transmission intensity. RESULTS The prevalence of KIR3DS1, KIR2DL5, KIR2DS5, and KIR2DS1 genes was significantly lower in populations from Kanungu compared to Tororo (7.6 vs 13.2%: p = 0.006, 57.2 vs 66.4%: p = 0.005, 33.2 vs 46.6%: p < 0.001, and 19.7 vs 26.7%: p = 0.014, respectively) or Jinja (7.6 vs 18.1%: p < 0.001, 57.2 vs 63.8%: p = 0.048, 33.2 vs 43.5%: p = 0.002, and 19.7 vs 30.4%: p < 0.001, respectively). The prevalence of homozygous HLA-C2 was significantly higher in populations from Kanungu (31.6%) compared to Jinja (21.4%), p = 0.043, with no significant difference between Kanungu and Tororo (26.7%), p = 0.296. CONCLUSIONS The KIR3DS1, KIR2DL5, KIR2DS5 and KIR2DS1 genes may partly explain differences in transmission intensity of malaria since these genes have been positively selected for in places with historically high malaria transmission intensity. The high-throughput, multiplex, real-time HLA-C genotyping PCR method developed will be useful in disease-association studies involving large cohorts.
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Affiliation(s)
- Stephen Tukwasibwe
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | | | - Olympe Chazara
- Department of Pathology, University of Cambridge, Cambridge, UK
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - Jyothi Jayaraman
- Department of Pathology, University of Cambridge, Cambridge, UK
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - Wei Jiang
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Joaniter I. Nankabirwa
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | - John Rek
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | - Emmanuel Arinaitwe
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | - Samuel L. Nsobya
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | - Maxine Atuheirwe
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
| | - Mubiru Frank
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
| | - Anguzu Godwin
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
| | | | - Stephen Cose
- MRC/UVRI and LSHTM Uganda Research Unit, Kampala, Uganda
| | - Moses R. Kamya
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, 2C Nakasero Hill Road, Kampala, Uganda
| | | | | | - Francesco Colucci
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, CB2 0SW UK
| | - Annettee Nakimuli
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, P.O BOX 7072, Kampala, Uganda
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43
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Abstract
Males and females of the same species share the majority of their genomes, yet they are frequently exposed to conflicting selection pressures. Gene regulation is widely assumed to resolve these conflicting sex-specific selection pressures, and although there has been considerable focus on elucidating the role of gene expression level in sex-specific adaptation, other regulatory mechanisms have been overlooked. Alternative splicing enables different transcripts to be generated from the same gene, meaning that exons which have sex-specific beneficial effects can in theory be retained in the gene product, whereas exons with detrimental effects can be skipped. However, at present, little is known about how sex-specific selection acts on broad patterns of alternative splicing. Here, we investigate alternative splicing across males and females of multiple bird species. We identify hundreds of genes that have sex-specific patterns of splicing and establish that sex differences in splicing are correlated with phenotypic sex differences. Additionally, we find that alternatively spliced genes have evolved rapidly as a result of sex-specific selection and suggest that sex differences in splicing offer another route to sex-specific adaptation when gene expression level changes are limited by functional constraints. Overall, our results shed light on how a diverse transcriptional framework can give rise to the evolution of phenotypic sexual dimorphism.
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Affiliation(s)
- Thea F Rogers
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Daniela H Palmer
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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44
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Sato S. Plasmodium-a brief introduction to the parasites causing human malaria and their basic biology. J Physiol Anthropol 2021; 40:1. [PMID: 33413683 PMCID: PMC7792015 DOI: 10.1186/s40101-020-00251-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
Malaria is one of the most devastating infectious diseases of humans. It is problematic clinically and economically as it prevails in poorer countries and regions, strongly hindering socioeconomic development. The causative agents of malaria are unicellular protozoan parasites belonging to the genus Plasmodium. These parasites infect not only humans but also other vertebrates, from reptiles and birds to mammals. To date, over 200 species of Plasmodium have been formally described, and each species infects a certain range of hosts. Plasmodium species that naturally infect humans and cause malaria in large areas of the world are limited to five-P. falciparum, P. vivax, P. malariae, P. ovale and P. knowlesi. The first four are specific for humans, while P. knowlesi is naturally maintained in macaque monkeys and causes zoonotic malaria widely in South East Asia. Transmission of Plasmodium species between vertebrate hosts depends on an insect vector, which is usually the mosquito. The vector is not just a carrier but the definitive host, where sexual reproduction of Plasmodium species occurs, and the parasite's development in the insect is essential for transmission to the next vertebrate host. The range of insect species that can support the critical development of Plasmodium depends on the individual parasite species, but all five Plasmodium species causing malaria in humans are transmitted exclusively by anopheline mosquitoes. Plasmodium species have remarkable genetic flexibility which lets them adapt to alterations in the environment, giving them the potential to quickly develop resistance to therapeutics such as antimalarials and to change host specificity. In this article, selected topics involving the Plasmodium species that cause malaria in humans are reviewed.
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Affiliation(s)
- Shigeharu Sato
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
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45
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Abstract
Spurred into action by the COVID-19 pandemic, the global scientific community has, in a short of period of time, made astonishing progress in understanding and combating COVID-19. Given the known human protein machinery for (a) SARS-CoV-2 entry, (b) the host innate immune response, and (c) virus-host interactions (protein-protein and RNA-protein), the potential effects of human genetic variation in this machinery, which may contribute to clinical differences in SARS-CoV-2 pathogenesis and help determine individual risk for COVID-19 infection, are explored. The Genome Aggregation Database (gnomAD) was used to show that several rare germline exome variants of proteins in these pathways occur in the human population, suggesting that carriers of these rare variants (especially for proteins of innate immunity pathways) are at risk for severe symptoms (like the severe symptoms in patients who are known to be rare variant carriers), whereas carriers of other variants could have a protective advantage against infection. The occurrence of genetic variation is thus expected to motivate the experimental probing of natural variants to understand the mechanistic differences in SARS-CoV-2 pathogenesis from one individual to another.
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Affiliation(s)
- Suvobrata Chakravarty
- Chemistry & Biochemistry, South
Dakota State University, Brookings, South Dakota 57007, United
States
- BioSNTR, Brookings, South
Dakota 57007, United States
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46
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Anguita-Ruiz A, Aguilera CM, Gil Á. Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies. Nutrients 2020; 12:nu12092689. [PMID: 32899182 PMCID: PMC7551416 DOI: 10.3390/nu12092689] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/15/2023] Open
Abstract
In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.
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Affiliation(s)
- Augusto Anguita-Ruiz
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n. Armilla, 18016 Granada, Spain; (A.A.-R.); (C.M.A.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
- CIBEROBN (Physiopathology of Obesity and Nutrition Network CB12/03/30038), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Concepción M. Aguilera
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n. Armilla, 18016 Granada, Spain; (A.A.-R.); (C.M.A.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
- CIBEROBN (Physiopathology of Obesity and Nutrition Network CB12/03/30038), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n. Armilla, 18016 Granada, Spain; (A.A.-R.); (C.M.A.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
- CIBEROBN (Physiopathology of Obesity and Nutrition Network CB12/03/30038), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-958241000 (ext. 20307)
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47
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Vankadari N. Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence. J Phys Chem Lett 2020; 11:6655-6663. [PMID: 32787225 PMCID: PMC7409919 DOI: 10.1021/acs.jpclett.0c01698] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/28/2020] [Indexed: 05/08/2023]
Abstract
The COVID-19 pandemic is an urgent global health emergency, and the presence of Furin site in the SARS-CoV-2 spike glycoprotein alters virulence and warrants further molecular, structural, and biophysical studies. Here we report the structure of Furin in complex with SARS-CoV-2 spike glycoprotein, demonstrating how Furin binds to the S1/S2 region of spike glycoprotein and eventually cleaves the viral protein using experimental functional studies, molecular dynamics, and docking. The structural studies underline the mechanism and mode of action of Furin, which is a key process in host cell entry and a hallmark of enhanced virulence. Our whole-exome sequencing analysis shows the genetic variants/alleles in Furin were found to alter the binding affinity for viral spike glycoprotein and could vary in infectivity in humans. Unravelling the mechanisms of Furin action, binding dynamics, and the genetic variants opens the growing arena of bona fide antibodies and development of potential therapeutics targeting the blockage of Furin cleavage.
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Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of
Biochemistry and Molecular Biology, Monash
University, Victoria 3800,
Australia
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48
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Jasti N, Sebagh D, Riaz M, Wang X, Koripella B, Palanisamy V, Mohammad N, Chen Q, Friedrich M. Towards reconstructing the dipteran demise of an ancient essential gene: E3 ubiquitin ligase Murine double minute. Dev Genes Evol 2020; 230:279-294. [PMID: 32623522 DOI: 10.1007/s00427-020-00663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Genome studies have uncovered many examples of essential gene loss, raising the question of how ancient genes transition from essentiality to dispensability. We explored this process for the deeply conserved E3 ubiquitin ligase Murine double minute (Mdm), which is lacking in Drosophila despite the conservation of its main regulatory target, the cellular stress response gene p53. Conducting gene expression and knockdown experiments in the red flour beetle Tribolium castaneum, we found evidence that Mdm has remained essential in insects where it is present. Using bioinformatics approaches, we confirm the absence of the Mdm gene family in Drosophila, mapping its loss to the stem lineage of schizophoran Diptera and Pipunculidae (big-headed flies), about 95-85 million years ago. Intriguingly, this gene loss event was preceded by the de novo origin of the gene Companion of reaper (Corp), a novel p53 regulatory factor that is characterized by functional similarities to vertebrate Mdm2 despite lacking E3 ubiquitin ligase protein domains. Speaking against a 1:1 compensatory gene gain/loss scenario, however, we found that hoverflies (Syrphidae) and pointed-wing flies (Lonchopteridae) possess both Mdm and Corp. This implies that the two p53 regulators have been coexisting for ~ 150 million years in select dipteran clades and for at least 50 million years in the lineage to Schizophora and Pipunculidae. Given these extensive time spans of Mdm/Corp coexistence, we speculate that the loss of Mdm in the lineage to Drosophila involved further acquisitions of compensatory gene activities besides the emergence of Corp. Combined with the previously noted reduction of an ancestral P53 contact domain in the Mdm homologs of crustaceans and insects, we conclude that the loss of the ancient Mdm gene family in flies was the outcome of incremental functional regression over long macroevolutionary time scales.
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Affiliation(s)
- Naveen Jasti
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.,Institute for Protein Design, Washington University, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Dylan Sebagh
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Mohammed Riaz
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Xin Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Bharat Koripella
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Vasanth Palanisamy
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Nabeel Mohammad
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Qing Chen
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA. .,Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA.
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49
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Lavorgna G, Vago R, Montorsi F, Salonia A. Surnames in Y-Chromosome–related Diseases: A New Tool for the Urologist? Eur Urol 2020; 77:767-768. [DOI: 10.1016/j.eururo.2020.02.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
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50
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Old and Recent Advances in Life Cycle, Pathogenesis, Diagnosis, Prevention, and Treatment of Malaria Including Perspectives in Ethiopia. ScientificWorldJournal 2020. [DOI: 10.1155/2020/1295381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Malaria, caused by apicomplexan parasite, is an old disease and continues to be a major public health threat in many countries. This article aims to present different aspects of malaria including causes, pathogenesis, prevention, and treatment in an articulate and comprehensive manner. Six Plasmodium species are recognized as the etiology of human malaria, of which Plasmodium falciparum is popular in East and Southern Africa. Malaria is transmitted mainly through Anopheles gambiae and Anopheles funestus, the two most effective malaria vectors in the world. Half of the world’s population is at risk for malaria infection. Globally, the morbidity and mortality rates of malaria have become decreased even though few reports in Ethiopia showed high prevalence of malaria. The malaria parasite has a complex life cycle that takes place both inside the mosquito and human beings. Generally, diagnosis of malaria is classified into clinical and parasitological diagnoses. Lack of clear understanding on the overall biology of Plasmodium has created a challenge in an effort to develop new drugs, vaccines, and preventive methods against malaria. However, three types of vaccines and a lot of novel compounds are under perclinical and clinical studies that are triggered by the occurrence of resistance among commonly used drugs and insecticides. Antiadhesion adjunctive therapies are also under investigation in the laboratory. In addition to previously known targets for diagnostic tool, vaccine and drug discovery scientists from all corner of the world are in search of new targets and chemical entities.
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