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Kumar H, Qin X, Bhushan B, Dutt T, Panigrahi M. DeepGenomeScan of 15 Worldwide Bovine Populations Detects Spatially Varying Positive Selection Signals. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024. [PMID: 39315920 DOI: 10.1089/omi.2024.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Identifying genomic regions under selection is essential for understanding the genetic mechanisms driving species evolution and adaptation. Traditional methods often fall short in detecting complex, spatially varying selection signals. Recent advances in deep learning, however, present promising new approaches for uncovering subtle selection signals that traditional methods might miss. In this study, we utilized the deep learning framework DeepGenomeScan to detect spatially varying selection signatures across 15 bovine populations worldwide. Our analysis uncovered novel insights into selective sweep hotspots within the bovine genome, revealing key genes associated with physiological and adaptive traits that were previously undetected. We identified significant quantitative trait loci linked to milk protein and fat percentages. By comparing the selection signatures identified in this study with those reported in the Bovine Genome Variation Database, we discovered 38 novel genes under selection that were not identified through traditional methods. These genes are primarily associated with milk and meat yield and quality. Our findings enhance our understanding of spatially varying selection's impact on bovine genomic diversity, laying a foundation for future research in genetic improvement and conservation. This is the first deep learning-based study of selection signatures in cattle, offering new insights for evolutionary and livestock genomics research.
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Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
- ICAR-National Research Centre on Mithun, Medziphema, India
| | - Xinghu Qin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
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Alencar RM, Sepulveda CCP, Martinez-Villegas L, Bahia AC, Santana RA, de Souza IB, D'Elia GMA, Duarte APM, de Lacerda MVG, Monteiro WM, Secundino NFC, Pimenta PFP, Koerich LB. Unravelling the genome of the brackish water malaria vector Anopheles aquasalis. Sci Rep 2023; 13:20472. [PMID: 37993652 PMCID: PMC10665375 DOI: 10.1038/s41598-023-47830-1] [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: 02/09/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Malaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.
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Affiliation(s)
- Rodrigo Maciel Alencar
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Cesar Camilo Prado Sepulveda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Luis Martinez-Villegas
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Ana Cristina Bahia
- Laboratório de Bioquímica de Insetos e Parasitos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, CEP 21.941-170, Brazil
| | - Rosa Amélia Santana
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
| | - Igor Belém de Souza
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Gigliola Mayara Ayres D'Elia
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Ana Paula Marques Duarte
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Marcus Vinicius Guimarães de Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
- University of Texas Medical Branch, Galveston, United States of America
| | - Wuelton Marcelo Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Nágila Francinete Costa Secundino
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Paulo Filemon Paolucci Pimenta
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
| | - Leonardo Barbosa Koerich
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 31.270-901, Brazil.
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Orr SE, Collins LB, Jima DD, Buchwalter DB. Salinity-induced ionoregulatory changes in the gill proteome of the mayfly, Neocloeon triangulifer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120609. [PMID: 36368556 DOI: 10.1016/j.envpol.2022.120609] [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: 08/11/2022] [Revised: 10/06/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Ecologists have observed declines in the biodiversity of sensitive freshwater organisms in response to increasing concentrations of major ions (salinization). Yet, how changing salinities physiologically challenge aquatic organisms, such as mayflies, remains remarkably understudied. Moreover, it is not well understood the degree to which species respond and acclimate to salinity changes. Our lab is developing the Baetid mayfly, N. triangulifer, as a model organism for physiological research. We have previously described acclimatory changes in both ion flux rates and altered mRNA transcript levels in response to chronic exposures to elevated major ion concentrations at the whole animal level. In the present study, we use shotgun proteomics to identify the specific proteins associated with apical ion transport and how their abundance changes in response to chronic salinity exposures in gills. Gills were isolated from the penultimate nymphal stage of N. triangulifer reared under control culture conditions, elevated NaCl (157 mg L-1 Na), elevated CaCl2 (121 mg L-1 Ca), elevated Ca/MgSO4 (735 mg L-1 SO4). These conditions mirrored those from previously published physiological work. We also acutely exposed nymphs to dilute (50% dilution of culture water with deionized water) to explore proteomic changes in the gills in response to dilute conditions. We report 710 unique peptide sequences among treatment groups, including important apical ion transporters such as Ca-ATPase, Na/K ATPase, and V-ATPase. Treatment with elevated NaCl and Ca/MgSO4 appeared to cause more significant differential protein expression (452 and 345, respectively) compared to CaCl2 and dilute groups (134 and 17, respectively). Finally, we demonstrated the breadth of physiological functions in gills by exploring non-transport related pathways found in our dataset, including ATP synthesis, calcium signaling, and oxidative stress response. We discuss our results in the context of freshwater salinization and the challenges of working with non-model species without fully sequenced and annotated genomes.
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Affiliation(s)
- Sarah E Orr
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Leonard B Collins
- Molecular Education, Technology and Research Innovation Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - David B Buchwalter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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Singh A, Patel NF, Allam M, Chan WY, Mohale T, Ismail A, Oliver SV. Marked Effects of Larval Salt Exposure on the Life History and Gut Microbiota of the Malaria Vector Anopheles merus (Diptera: Culicidae). INSECTS 2022; 13:1165. [PMID: 36555074 PMCID: PMC9787035 DOI: 10.3390/insects13121165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Anopheles merus can breed in a range of saltwater concentrations. The consequences of this ability on the life history of adult An. merus are poorly understood. This study examined the effects of exposure to 0, 2.1875, 4.375, 8.75, and 17.5 g/L of sodium chloride on An. merus. The effects on larval development, adult longevity, fertility, and fecundity, as well as deltamethrin tolerance were examined. The effect of larval salt exposure on the expression of defensin-1 in adults was examined by quantitative Real-Time PCR. Finally, the effect of the larval salt concentration on microbial dynamics was assessed by 16S Next Generation Sequencing. High concentrations of saltwater increased larval development time and number of eggs laid, as well as deltamethrin tolerance. Larval exposure to salt also reduced the expression of defensin-1. The exposure also had a significant effect on microbial diversity in larvae and adults. The diversity of larvae decreased once adults emerged. Salt-tolerant bacterial genera predominated in larvae but were absent in adults. High salt concentrations resulted in greater abundance of Plasmodium-protective genera in adults. Although this study was conducted on a laboratory strain of An. merus, these data suggest that osmoregulation has a significant effect on the life history of the species with potential epidemiological consequences.
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Affiliation(s)
- Ashmika Singh
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Nashrin F. Patel
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi 15551, United Arab Emirates
| | - Wai-Yin Chan
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Thabo Mohale
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Shüné V. Oliver
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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5
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Orr SE, Negrão Watanabe TT, Buchwalter DB. Physiological plasticity and acclimatory responses to salinity stress are ion-specific in the mayfly, Neocloeon triangulifer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117221. [PMID: 33975217 DOI: 10.1016/j.envpol.2021.117221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/09/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Freshwater salinization is a rapidly emerging ecological issue and is correlated with significant declines in aquatic biodiversity. It remains unclear how changing salinity regimes affect the physiology of sensitive aquatic insects. We used the parthenogenetic mayfly, Neocloeon triangulifer, to ask how ionic exposure history alters physiological processes and responses to subsequent major ion exposures. Using radiotracers (22Na, 35SO4, and 45Ca), we observed that mayflies chronically reared in elevated sodium or sulfate (157 mg L-1 Na or 667 mg L-1 SO4) had 2-fold (p < 0.0001) and 8-fold (p < 0.0001) lower ion uptake rates than mayflies reared in dilute control water (16 mg L-1 Na and 23 mg L-1 SO4) and subsequently transferred to elevated salinities, respectively. These acclimatory ion transport changes provided protection in 96-h toxicity bioassays for sodium, but not sulfate. Interestingly, calcium uptake was uniformly much lower and minimally influenced by exposure history, but was poorly tolerated in the toxicity bioassays. With qRT-PCR, we observed that the expression of many ion transporter genes in mayflies was influenced by elevated salinity in an ion-specific manner (general upregulation in response to sulfate, downregulation in response to calcium). Elevated sodium exposure had minimal influence on the same genes. Finally, we provide novel light microscopic evidence of histomorphological changes within the epithelium of the Malpighian tubules (insect primary excretory system) that undergoes cellular degeneration and necrosis secondary to calcium toxicity. We conclude that physiological plasticity to salinity stress is ion-specific and provide evidence for ion-specific toxicity mechanisms in N. triangulifer.
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Affiliation(s)
- Sarah E Orr
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Tatiane Terumi Negrão Watanabe
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27607, USA
| | - David B Buchwalter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27607, USA.
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Ramasamy R, Thiruchenthooran V, Jayadas TTP, Eswaramohan T, Santhirasegaram S, Sivabalakrishnan K, Naguleswaran A, Uzest M, Cayrol B, Voisin SN, Bulet P, Surendran SN. Transcriptomic, proteomic and ultrastructural studies on salinity-tolerant Aedes aegypti in the context of rising sea levels and arboviral disease epidemiology. BMC Genomics 2021; 22:253. [PMID: 33836668 PMCID: PMC8034070 DOI: 10.1186/s12864-021-07564-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Aedes aegypti mosquito, the principal global vector of arboviral diseases, lays eggs and undergoes larval and pupal development to become adult mosquitoes in fresh water (FW). It has recently been observed to develop in coastal brackish water (BW) habitats of up to 50% sea water, and such salinity tolerance shown to be an inheritable trait. Genomics of salinity tolerance in Ae. aegypti has not been previously studied, but it is of fundamental biological interest and important for controlling arboviral diseases in the context of rising sea levels increasing coastal ground water salinity. RESULTS BW- and FW-Ae. aegypti were compared by RNA-seq analysis on the gut, anal papillae and rest of the carcass in fourth instar larvae (L4), proteomics of cuticles shed when L4 metamorphose into pupae, and transmission electron microscopy of cuticles in L4 and adults. Genes for specific cuticle proteins, signalling proteins, moulting hormone-related proteins, membrane transporters, enzymes involved in cuticle metabolism, and cytochrome P450 showed different mRNA levels in BW and FW L4 tissues. The salinity-tolerant Ae. aegypti were also characterized by altered L4 cuticle proteomics and changes in cuticle ultrastructure of L4 and adults. CONCLUSIONS The findings provide new information on molecular and ultrastructural changes associated with salinity adaptation in FW mosquitoes. Changes in cuticles of larvae and adults of salinity-tolerant Ae. aegypti are expected to reduce the efficacy of insecticides used for controlling arboviral diseases. Expansion of coastal BW habitats and their neglect for control measures facilitates the spread of salinity-tolerant Ae. aegypti and genes for salinity tolerance. The transmission of arboviral diseases can therefore be amplified in multiple ways by salinity-tolerant Ae. aegypti and requires appropriate mitigating measures. The findings in Ae. aegypti have attendant implications for the development of salinity tolerance in other fresh water mosquito vectors and the diseases they transmit.
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Affiliation(s)
- Ranjan Ramasamy
- ID-FISH Technology Inc., Milpitas, CA, 95035, USA. .,Department of Zoology, University of Jaffna, Jaffna, Sri Lanka.
| | | | | | | | | | | | | | - Marilyne Uzest
- UMR BGPI, University of Montpellier, INRAE, CIRAD, SupAgro, Montpellier, France
| | - Bastien Cayrol
- UMR BGPI, University of Montpellier, INRAE, CIRAD, SupAgro, Montpellier, France
| | | | - Philippe Bulet
- Platform BioPark Archamps, Archamps, France.,CR Université Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Grenoble, France
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Gallichotte EN, Dobos KM, Ebel GD, Hagedorn M, Rasgon JL, Richardson JH, Stedman TT, Barfield JP. Towards a method for cryopreservation of mosquito vectors of human pathogens. Cryobiology 2021; 99:1-10. [PMID: 33556359 DOI: 10.1016/j.cryobiol.2021.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
Mosquito-borne diseases are responsible for millions of human deaths every year, posing a massive burden on global public health. Mosquitoes transmit a variety of bacteria, parasites and viruses. Mosquito control efforts such as insecticide spraying can reduce mosquito populations, but they must be sustained in order to have long term impacts, can result in the evolution of insecticide resistance, are costly, and can have adverse human and environmental effects. Technological advances have allowed genetic manipulation of mosquitoes, including generation of those that are still susceptible to insecticides, which has greatly increased the number of mosquito strains and lines available to the scientific research community. This generates an associated challenge, because rearing and maintaining unique mosquito lines requires time, money and facilities, and long-term maintenance can lead to adaptation to specific laboratory conditions, resulting in mosquito lines that are distinct from their wild-type counterparts. Additionally, continuous rearing of transgenic lines can lead to loss of genetic markers, genes and/or phenotypes. Cryopreservation of valuable mosquito lines could help circumvent these limitations and allow researchers to reduce the cost of rearing multiple lines simultaneously, maintain low passage number transgenic mosquitoes, and bank lines not currently being used. Additionally, mosquito cryopreservation could allow researchers to access the same mosquito lines, limiting the impact of unique laboratory or field conditions. Successful cryopreservation of mosquitoes would expand the field of mosquito research and could ultimately lead to advances that would reduce the burden of mosquito-borne diseases, possibly through rear-and-release strategies to overcome mosquito insecticide resistance. Cryopreservation techniques have been developed for some insect groups, including but not limited to fruit flies, silkworms and other moth species, and honeybees. Recent advances within the cryopreservation field, along with success with other insects suggest that cryopreservation of mosquitoes may be a feasible method for preserving valuable scientific and public health resources. In this review, we will provide an overview of basic mosquito biology, the current state of and advances within insect cryopreservation, and a proposed approach toward cryopreservation of Anopheles stephensi mosquitoes.
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Affiliation(s)
- Emily N Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Karen M Dobos
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Mary Hagedorn
- Smithsonian Conservation Biology Institute, Smithsonian Institution, Front Royal, VA, USA; Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA
| | - Jason L Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Jennifer P Barfield
- Department of Biomedical Sciences, Animal Reproduction and Biotechnology Laboratory, Colorado State University, Fort Collins, CO, USA.
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8
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Botella-Cruz M, Pallarés S, Millán A, Velasco J. Role of cuticle hydrocarbons composition in the salinity tolerance of aquatic beetles. JOURNAL OF INSECT PHYSIOLOGY 2019; 117:103899. [PMID: 31202853 DOI: 10.1016/j.jinsphys.2019.103899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 06/09/2023]
Abstract
Salinity tolerance has enabled the colonization of inland saline waters and promoted species diversification in some lineages of aquatic insects. However, the mechanisms behind this tolerance, particularly the role of cuticle hydrocarbons (CHCs), are not well-known. We characterized the CHC profile of eight species of two water beetle genera (Nebrioporus, Adephaga: Dytiscidae and Enochrus, Polyphaga: Hydrophilidae), which span the fresh-hypersaline gradient, to: i) determine the interspecific variation of CHC composition in relation to species' salinity tolerance; ii) explore plastic adjustments in CHC profiles in response to salinity changes at the intraspecific level in saline-tolerant species. CHC profiles were highly species-specific, more complex and diverse in composition, and characterized by longer-chain-length compounds in the species with higher salinity tolerance within each genus. Higher salinity tolerance in the Enochrus species was also associated with an increase in the relative abundance of branched alkanes, and with a lower proportion of n-alkanes and unsaturated compounds. These CHC characteristics are related with improved waterproofing capacity and suggest that reducing cuticle permeability was one of the key mechanisms to adapt to saline waters. Similar CHC composition patterns were found at the intraspecific level between populations from lower and higher salinity sites within saline-tolerant species of each genus. These saline species also displayed an extraordinary ability to adjust CHC profiles to changing salinity conditions in the laboratory in a relatively short time, which reflects great plasticity and a high potential to deal with daily and seasonal environmental fluctuations in the highly dynamic saline habitats.
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Affiliation(s)
| | - Susana Pallarés
- Department of Zoology, University of Sevilla, Sevilla, Spain; Instituto de Ciencias Ambientales (ICAM), University of Castilla-La Mancha, Toledo, Spain
| | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, Spain
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9
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Ruzzante L, Reijnders MJ, Waterhouse RM. Of Genes and Genomes: Mosquito Evolution and Diversity. Trends Parasitol 2019; 35:32-51. [DOI: 10.1016/j.pt.2018.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
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10
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Arribas P, Gutiérrez-Cánovas C, Botella-Cruz M, Cañedo-Argüelles M, Antonio Carbonell J, Millán A, Pallarés S, Velasco J, Sánchez-Fernández D. Insect communities in saline waters consist of realized but not fundamental niche specialists. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2018.0008. [PMID: 30509910 DOI: 10.1098/rstb.2018.0008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 12/16/2022] Open
Abstract
Considering how organisms adapt to stress is essential if we are to anticipate biological responses to global change in ecosystems. Communities in stressful environments can potentially be assembled by specialists (i.e. species that only occur in a limited range of environmental conditions) and/or generalist species with wider environmental tolerances. We review the existing literature on the salinity tolerance of aquatic insects previously identified as saline specialists because they were exclusively found in saline habitats, and explore if these saline realized niche specialists are also specialists in their fundamental niches or on the contrary are fundamental niche generalist species confined to the highest salinities they can tolerate. The results suggest that species inhabiting saline waters are generalists in their fundamental niches, with a predominant pattern of high survival in freshwater-low salinity conditions, where their fitness tends to be similar or even higher than in saline waters. Additionally, their performance in freshwater tends to be similar to related strictly freshwater species, so no apparent trade-off of generalization is shown. These results are discussed in the framework of the ecological and evolutionary processes driving community assembly across the osmotic stress gradient, and their potential implications for predicting impacts from saline dilution and freshwater salinization.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 La Laguna, Canary Islands, Spain
| | - Cayetano Gutiérrez-Cánovas
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - María Botella-Cruz
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - Miguel Cañedo-Argüelles
- Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM-LAB), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | | | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - Susana Pallarés
- Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - David Sánchez-Fernández
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain .,Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
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11
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Velasco J, Gutiérrez-Cánovas C, Botella-Cruz M, Sánchez-Fernández D, Arribas P, Carbonell JA, Millán A, Pallarés S. Effects of salinity changes on aquatic organisms in a multiple stressor context. Philos Trans R Soc Lond B Biol Sci 2018; 374:20180011. [PMID: 30509913 PMCID: PMC6283958 DOI: 10.1098/rstb.2018.0011] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2018] [Indexed: 12/29/2022] Open
Abstract
Under global change, the ion concentration of aquatic ecosystems is changing worldwide. Many freshwater ecosystems are being salinized by anthropogenic salt inputs, whereas many naturally saline ones are being diluted by agricultural drainages. This occurs concomitantly with changes in other stressors, which can result in additive, antagonistic or synergistic effects on organisms. We reviewed experimental studies that manipulated salinity and other abiotic stressors, on inland and transitional aquatic habitats, to (i) synthesize their main effects on organisms' performance, (ii) quantify the frequency of joint effect types across studies and (iii) determine the overall individual and joint effects and their variation among salinity-stressor pairs and organism groups using meta-analyses. Additive effects were slightly more frequent (54%) than non-additive ones (46%) across all the studies (n = 105 responses). However, antagonistic effects were dominant for the stressor pair salinity and toxicants (44%, n = 43), transitional habitats (48%, n = 31) and vertebrates (71%, n = 21). Meta-analyses showed detrimental additive joint effects of salinity and other stressors on organism performance and a greater individual impact of salinity than the other stressors. These results were consistent across stressor pairs and organism types. These findings suggest that strategies to mitigate multiple stressor impacts on aquatic ecosystems should prioritize restoring natural salinity concentrations.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.
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Affiliation(s)
- Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Cayetano Gutiérrez-Cánovas
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - María Botella-Cruz
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - David Sánchez-Fernández
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
- Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), c/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Islas Canarias, Spain
| | | | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Susana Pallarés
- Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
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12
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Uyhelji HA, Kupfer DM, White VL, Jackson ML, Van Dongen HPA, Burian DM. Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation. BMC Genomics 2018; 19:341. [PMID: 29739334 PMCID: PMC5941663 DOI: 10.1186/s12864-018-4664-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairment from sleep loss in humans. This study employs microarrays and bioinformatics analyses to explore candidate gene expression biomarkers associated with total sleep deprivation (TSD), and more specifically, the phenotype of neurobehavioral impairment from TSD. Healthy adult volunteers were recruited to a sleep laboratory for seven consecutive days (six nights). After two Baseline nights of 10 h time in bed, 11 subjects underwent an Experimental phase of 62 h of continuous wakefulness, followed by two Recovery nights of 10 h time in bed. Another six subjects underwent a well-rested Control condition of 10 h time in bed for all six nights. Blood was drawn for measuring gene expression on days two, four, and six at 4 h intervals from 08:00 to 20:00 h, corresponding to 12 timepoints across one Baseline, one Experimental, and one Recovery day. Results Altogether 212 genes changed expression in response to the TSD Treatment, with most genes exhibiting down-regulation during TSD. Also, 28 genes were associated with neurobehavioral impairment as measured by the Psychomotor Vigilance Test. The results support previous findings associating TSD with the immune response and ion signaling, and reveal novel candidate biomarkers such as the Speedy/RINGO family of cell cycle regulators. Conclusions This study serves as an important step toward understanding gene expression changes during sleep deprivation. In addition to exploring potential biomarkers for TSD, this report presents novel candidate biomarkers associated with lapses of attention during TSD. Although further work is required for biomarker validation, analysis of these genes may aid fundamental understanding of the impact of TSD on neurobehavioral performance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4664-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hilary A Uyhelji
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA.
| | - Doris M Kupfer
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA.
| | - Vicky L White
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA
| | - Melinda L Jackson
- Sleep and Performance Research Center & Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, 99210, USA.,Present address: School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Hans P A Van Dongen
- Sleep and Performance Research Center & Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, 99210, USA
| | - Dennis M Burian
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA
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13
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Pallarés S, Arribas P, Bilton DT, Millán A, Velasco J, Ribera I. The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles. Mol Ecol 2017; 26:5614-5628. [PMID: 28833872 DOI: 10.1111/mec.14334] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats.
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Affiliation(s)
- Susana Pallarés
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, Santa Cruz de Tenerife, Spain
| | - David T Bilton
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, UK
| | - Andrés Millán
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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14
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Passow CN, Brown AP, Arias-Rodriguez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Mol Ecol 2017; 26:4211-4225. [PMID: 28598519 PMCID: PMC5731456 DOI: 10.1111/mec.14198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
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Affiliation(s)
| | - Anthony P. Brown
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
- Texas A&M Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Wesley C. Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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15
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Botella-Cruz M, Villastrigo A, Pallarés S, López-Gallego E, Millán A, Velasco J. Cuticle hydrocarbons in saline aquatic beetles. PeerJ 2017; 5:e3562. [PMID: 28717597 PMCID: PMC5511699 DOI: 10.7717/peerj.3562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/20/2017] [Indexed: 11/20/2022] Open
Abstract
Hydrocarbons are the principal component of insect cuticle and play an important role in maintaining water balance. Cuticular impermeability could be an adaptative response to salinity and desiccation in aquatic insects; however, cuticular hydrocarbons have been poorly explored in this group and there are no previous data on saline species. We characterized cuticular hydrocarbons of adults and larvae of two saline aquatic beetles, namely Nebrioporus baeticus (Dytiscidae) and Enochrus jesusarribasi (Hydrophilidae), using a gas chromatograph coupled to a mass spectrometer. The CHC profile of adults of both species, characterized by a high abundance of branched alkanes and low of unsaturated alkenes, seems to be more similar to that of some terrestrial beetles (e.g., desert Tenebrionidae) compared with other aquatic Coleoptera (freshwater Dytiscidae). Adults of E. jesusarribasi had longer chain compounds than N. baeticus, in agreement with their higher resistance to salinity and desiccation. The more permeable cuticle of larvae was characterized by a lower diversity in compounds, shorter carbon chain length and a higher proportion of unsaturated hydrocarbons compared with that of the adults. These results suggest that osmotic stress on aquatic insects could exert a selection pressure on CHC profile similar to aridity in terrestrial species.
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Affiliation(s)
| | - Adrián Villastrigo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Susana Pallarés
- Department of Ecology and Hydrology, University of Murcia, Spain
| | - Elena López-Gallego
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), Murcia, Spain
| | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, Spain
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