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Ghosh G, Neely BA, Bland AM, Whitmer ER, Field CL, Duignan PJ, Janech MG. Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions ( Zalophus californianus). J Proteome Res 2024. [PMID: 38807289 DOI: 10.1021/acs.jproteome.4c00103] [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: 05/30/2024]
Abstract
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis (DAT) have consistently increased. Outside of direct measurement of domoic acid in bodily fluids at the time of stranding, there are no practical nonlethal clinical tests for the diagnosis of DAT that can be utilized in a rehabilitation facility. Proteomics analysis was conducted to discover candidate protein markers of DAT using cerebrospinal fluid from stranded California sea lions with acute DAT (n = 8), chronic DAT (n = 19), or without DAT (n = 13). A total of 2005 protein families were identified experiment-wide. A total of 83 proteins were significantly different in abundance across the three groups (adj. p < 0.05). MDH1, PLD3, ADAM22, YWHAG, VGF, and CLSTN1 could discriminate California sea lions with or without DAT (AuROC > 0.75). IGKV2D-28, PTRPF, KNG1, F2, and SNCB were able to discriminate acute DAT from chronic DAT (AuROC > 0.75). Proteins involved in alpha synuclein deposition were over-represented as classifiers of DAT, and many of these proteins have been implicated in a variety of neurodegenerative diseases. These proteins should be considered potential markers for DAT in California sea lions and should be prioritized for future validation studies as biomarkers.
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Affiliation(s)
- Gautam Ghosh
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Benjamin A Neely
- National Institute of Standards and Technology (NIST) Charleston, Charleston, South Carolina 29412, United States
| | - Alison M Bland
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Emily R Whitmer
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Cara L Field
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Pádraig J Duignan
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Michael G Janech
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
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Solosky AM, Claudio IM, Chappel JR, Kirkwood-Donelson KI, Janech MG, Bland AM, Gulland FMD, Neely BA, Baker ES. Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592757. [PMID: 38766156 PMCID: PMC11100735 DOI: 10.1101/2024.05.06.592757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Domoic acid is a neurotoxin secreted by the marine diatom genus, Pseudo-nitzschia, during toxic algal bloom events. California sea lions ( Zalophus californianus ) are exposed to domoic acid through ingestion of fish that feed on toxic diatoms, resulting in a domoic acid toxicosis (DAT), which can vary from mild to fatal. Sea lions with mild disease can be treated if toxicosis is detected early after exposure, therefore, rapid diagnosis of DAT is essential but also challenging. In this work, we performed multi-omics analyses, specifically proteomic and lipidomic, on blood samples from 31 California sea lions. Fourteen sea lions were diagnosed with DAT based on clinical signs and postmortem histological examination of brain tissue, and 17 had no evidence of DAT. Proteomic analyses revealed three apolipoproteins with statistically significant lower abundance in the DAT individuals compared to the non-DAT individuals. These proteins are known to transport lipids in the blood. Lipidomic analyses highlighted 29 lipid levels that were statistically different in the DAT versus non-DAT comparison, 28 of which were downregulated while only one was upregulated. Furthermore, of the 28 downregulated lipids, 15 were triglycerides, illustrating their connection with the perturbed apolipoproteins and showing their potential for use in rapid DAT diagnoses. SYNOPSIS Multi-omics evaluations reveal blood apolipoproteins and triglycerides are altered in domoic acid toxicosis in California sea lions.
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Mohr DW, Gaughran SJ, Paschall J, Naguib A, Pang AWC, Dudchenko O, Aiden EL, Church DM, Scott AF. A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability. Genes (Basel) 2022; 13:genes13071270. [PMID: 35886053 PMCID: PMC9323584 DOI: 10.3390/genes13071270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
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Affiliation(s)
- David W. Mohr
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
| | - Stephen J. Gaughran
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA;
| | - Justin Paschall
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
| | - Ahmed Naguib
- Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego, CA 92121, USA; (A.N.); (A.W.C.P.)
| | - Andy Wing Chun Pang
- Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego, CA 92121, USA; (A.N.); (A.W.C.P.)
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (O.D.); (E.L.A.)
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (O.D.); (E.L.A.)
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | | | - Alan F. Scott
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
- Correspondence:
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Liu L, Megens HJ, Crooijmans RP, Bosse M, Huang Q, Sonsbeek GBV, Groenen MA, Madsen O. The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. Mol Biol Evol 2022; 39:6596366. [PMID: 35642310 PMCID: PMC9178973 DOI: 10.1093/molbev/msac110] [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] [Indexed: 11/13/2022] Open
Abstract
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
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Affiliation(s)
- Langqing Liu
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Qitong Huang
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Martien Am Groenen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
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Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis. Genes (Basel) 2022; 13:genes13030541. [PMID: 35328094 PMCID: PMC8954904 DOI: 10.3390/genes13030541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the ‘krill surplus hypothesis’. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology.
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Noh HJ, Turner-Maier J, Schulberg SA, Fitzgerald ML, Johnson J, Allen KN, Hückstädt LA, Batten AJ, Alfoldi J, Costa DP, Karlsson EK, Zapol WM, Buys ES, Lindblad-Toh K, Hindle AG. The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling. Commun Biol 2022; 5:140. [PMID: 35177770 PMCID: PMC8854659 DOI: 10.1038/s42003-022-03089-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractThe Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal.
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