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Neely BA, Ellisor DL, Davis WC. Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin ( Tursiops truncatus). Genes (Basel) 2023; 14:1696. [PMID: 37761836 PMCID: PMC10531373 DOI: 10.3390/genes14091696] [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: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins. Since the identification of larger proteins with more identified peptides implies reduced database fragmentation and improved gene annotation accuracy, we propose the metric NP10, which attempts to capture this quality improvement. The NP10 metric is calculated by first stratifying proteomic results by identifying the top decile (or 10th 10-quantile) of identified proteins based on the number of peptides per protein and then returns the median molecular weight of the resulting proteins. When using the 2016 versus 2012 Tursiops truncatus genome annotation to search this proteomic data set, there was a 21% improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which showed a 33% improvement in NP10. These results demonstrate that proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets across species to facilitate the evaluation of new de novo and existing genome.
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Affiliation(s)
- Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, 331 Fort Johnson Road, Charleston, SC 29412, USA; (D.L.E.); (W.C.D.)
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Neely BA, Becker DJ, Janech MG, Fenton MB, Simmons NB, Bland AM. Surveying the Vampire Bat ( Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res 2021; 20:2547-2559. [PMID: 33840197 PMCID: PMC9812275 DOI: 10.1021/acs.jproteome.0c00995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.
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Affiliation(s)
- Benjamin A. Neely
- Chemical Sciences Division, National, Institute of Standards and Technology, Charleston, South, Carolina 29412, United States
| | - Daniel J. Becker
- Department of Biology, University of, Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
| | - M. Brock Fenton
- Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of, Vertebrate Zoology, American Museum of Natural History, New York 10024, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
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Abstract
For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.
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Affiliation(s)
- Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY, USA
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Benjamin A. Neely
- Chemical Sciences Division, National Institute of Standards and Technology, Charleston, SC, USA
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Proteomic Analysis of Non-depleted Serum Proteins from Bottlenose Dolphins Uncovers a High Vanin-1 Phenotype. Sci Rep 2016; 6:33879. [PMID: 27667588 PMCID: PMC5036180 DOI: 10.1038/srep33879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/05/2016] [Indexed: 12/22/2022] Open
Abstract
Targeted approaches have been widely used to help explain physiological adaptations, but few studies have used non-targeted omics approaches to explore differences between diving marine mammals and terrestrial mammals. A rank comparison of undepleted serum proteins from common bottlenose dolphins (Tursiops truncatus) and pooled normal human serum led to the discovery of 11 proteins that appeared exclusive to dolphin serum. Compared to the comprehensive human plasma proteome, 5 of 11 serum proteins had a differential rank greater than 200. One of these proteins, Vanin-1, was quantified using parallel reaction monitoring in dolphins under human care and free-ranging dolphins. Dolphin serum Vanin-1 ranged between 31–106 μg/ml, which is 20–1000 times higher than concentrations reported for healthy humans. Serum Vanin-1 was also higher in dolphins under human care compared to free-ranging dolphins (64 ± 16 vs. 47 ± 12 μg/ml P < 0.05). Vanin-1 levels positively correlated with liver enzymes AST and ALT, and negatively correlated with white blood cell counts and fibrinogen in free-ranging dolphins. Major differences exist in the circulating blood proteome of the bottlenose dolphin compared to terrestrial mammals and exploration of these differences in bottlenose dolphins and other marine mammals may identify veiled protective strategies to counter physiological stress.
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Sobolesky PM, Harrell TS, Parry C, Venn-Watson S, Janech MG. Feeding a Modified Fish Diet to Bottlenose Dolphins Leads to an Increase in Serum Adiponectin and Sphingolipids. Front Endocrinol (Lausanne) 2016; 7:33. [PMID: 27148164 PMCID: PMC4838613 DOI: 10.3389/fendo.2016.00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/08/2016] [Indexed: 01/16/2023] Open
Abstract
Feeding a modified fish diet has been suggested to improve insulin sensitivity in bottlenose dolphins; however, insulin sensitivity was not directly measured. Since demonstrating an improvement in insulin sensitivity is technically difficult in dolphins, we postulated that directional changes in the hormone axis: fibroblast growth factor 21 (FGF21)/Adiponectin/Ceramide (Cer), could provide further support to this hypothesis. We measured 2-h post-prandial serum FGF21, total adiponectin, percent unmodified adiponectin, ceramide, and sphingosine levels from dolphins fed a diet rich in heptadecanoic acid (C17:0) over 24 weeks. Serum FGF21 was quantified by ELISA with an observed range of 129-1599 pg/ml, but did not significantly change over the 24-week study period. Total adiponectin levels (mean ± SD) significantly increased from 776 ± 400 pmol/ml at week 0 to 1196 ± 467 pmol/ml at week 24. The percent unmodified adiponectin levels (mean ± SD) decreased from 23.8 ± 6.0% at week 0 to 15.2 ± 5.2% at week 24. Interestingly, although FGF21 levels did not change, there was a good correlation between FGF21 and total adiponectin (ρ = 0.788, P < 0.001). We quantified the abundances of serum ceramides and sphingosines (SPH) because adiponectin has a defined role in sphingolipid metabolism through adiponectin receptor-mediated activation of ceramidases. The most abundant ceramide in dolphin sera was Cer 24:1 comprising 49% of the ceramides measured. Significant reductions were observed in the unsaturated Cer 18:1, Cer 20:1, and Cer 24:1, whereas significant increases were observed in saturated Cer 22:0, Cer 24:0, and Cer 26:0. However, total serum ceramides did not change. Significant elevations were detected for total sphingosine, dihydrosphingosine, sphingosine-1-phosphate, and dihydrosphingosine-1-phosphate. Proteomic analysis of the serum proteins revealed few changes in serum proteins over the study period. In conclusion, shifting the dolphin diet to fishes rich in odd chain saturated fatty acids, such as C17:0, resulted in increased serum levels of the insulin sensitizing hormone adiponectin and serum SPH consistent with an insulin-sensitizing phenotype. It is still unclear whether FGF21 plays a role in the regulation of adiponectin in dolphins, similar to that shown in laboratory animal models.
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Affiliation(s)
- Philip M. Sobolesky
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC, USA
| | - Tyler S. Harrell
- Grice Marine Laboratory, Department of Biology, College of Charleston, Charleston, SC, USA
| | - Celeste Parry
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Michael G. Janech
- Department of Medicine, Division of Nephrology, Medical University of South Carolina, Charleston, SC, USA
- Grice Marine Laboratory, Department of Biology, College of Charleston, Charleston, SC, USA
- *Correspondence: Michael G. Janech,
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Neely BA, Soper JL, Gulland FMD, Bell PD, Kindy M, Arthur JM, Janech MG. Proteomic analysis of cerebrospinal fluid in California sea lions (Zalophus californianus) with domoic acid toxicosis identifies proteins associated with neurodegeneration. Proteomics 2015; 15:4051-63. [DOI: 10.1002/pmic.201500167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/10/2015] [Accepted: 09/09/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Benjamin A. Neely
- Department of Medicine; Division of Nephrology; Medical University of South Carolina; Charleston SC USA
| | | | | | - P. Darwin Bell
- Department of Medicine; Division of Nephrology; Medical University of South Carolina; Charleston SC USA
| | - Mark Kindy
- Marine Biomedicine and Environmental Sciences Center; Medical University of South Carolina; Charleston SC USA
- Department of Regenerative Medicine and Cell Biology; Medical University of South Carolina; Charleston SC USA
- Department of Veterans’ Affairs; Research Service; Charleston SC USA
| | - John M. Arthur
- Department of Internal Medicine; Division of Nephrology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Michael G. Janech
- Department of Medicine; Division of Nephrology; Medical University of South Carolina; Charleston SC USA
- Marine Biomedicine and Environmental Sciences Center; Medical University of South Carolina; Charleston SC USA
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Venn-Watson S. Dolphins and diabetes: applying one health for breakthrough discoveries. Front Endocrinol (Lausanne) 2014; 5:227. [PMID: 25566195 PMCID: PMC4273662 DOI: 10.3389/fendo.2014.00227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/09/2014] [Indexed: 11/23/2022] Open
Affiliation(s)
- Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
- *Correspondence:
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Venn-Watson S, Smith CR, Stevenson S, Parry C, Daniels R, Jensen E, Cendejas V, Balmer B, Janech M, Neely BA, Wells R. Blood-Based Indicators of Insulin Resistance and Metabolic Syndrome in Bottlenose Dolphins (Tursiops truncatus). Front Endocrinol (Lausanne) 2013; 4:136. [PMID: 24130551 PMCID: PMC3793200 DOI: 10.3389/fendo.2013.00136] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/13/2013] [Indexed: 01/01/2023] Open
Abstract
Similar to people with metabolic syndrome, bottlenose dolphins (Tursiops truncatus) can have a sustained postprandial hyperglycemia and hyperinsulinemia, dyslipidemia, and fatty liver disease. A panel of potential postprandial blood-based indicators of insulin resistance and metabolic syndrome were compared among 34 managed collection dolphins in San Diego Bay, CA, USA (Group A) and 16 wild, free-ranging dolphins in Sarasota Bay, FL, USA (Group B). Compared to Group B, Group A had higher insulin (2.1 ± 2.5 and 13 ± 13 μIU/ml), glucose (87 ± 19 and 108 ± 12 mg/dl), and triglycerides (75 ± 28 and 128 ± 45 mg/dl) as well as higher cholesterol (total, high-density lipoprotein cholesterol, and very low density lipoprotein cholesterol), iron, transferrin saturation, gamma-glutamyl transpeptidase (GGT), alanine transaminase, and uric acid. Group A had higher percent unmodified adiponectin. While Group A dolphins were older, the same blood-based differences remained when controlling for age. There were no differences in body mass index (BMI) between the groups, and comparisons between Group B and Group A dolphins have consistently demonstrated lower stress hormones levels in Group A. Group A dolphins with high insulin (greater than 14 μIU/ml) had higher glucose, iron, GGT, and BMI compared to Group A dolphins with lower insulin. These findings support that some dolphin groups may be more susceptible to insulin resistance compared to others, and primary risk factors are not likely age, BMI, or stress. Lower high-molecular weight adiponectin has been identified as an independent risk factor for type 2 diabetes in humans and may be a target for preventing insulin resistance in dolphins. Future investigations with these two dolphin populations, including dietary and feeding differences, may provide valuable insight for preventing and treating insulin resistance in humans.
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Affiliation(s)
- Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
- *Correspondence: Stephanie Venn-Watson, National Marine Mammal Foundation, Translational Medicine and Research Program, 2240 Shelter Island Drive Ste 200, San Diego, CA 92106, USA e-mail:
| | - Cynthia Rowe Smith
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Sacha Stevenson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Celeste Parry
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Risa Daniels
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Eric Jensen
- Navy Marine Mammal Program, Space and Naval Warfare Systems Center Pacific, San Diego, CA, USA
| | - Veronica Cendejas
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Brian Balmer
- Sarasota Dolphin Research Program, Chicago Zoological Society c/o Mote Marine Laboratory, Sarastota, FL, USA
| | - Michael Janech
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Benjamin A. Neely
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Randall Wells
- Sarasota Dolphin Research Program, Chicago Zoological Society c/o Mote Marine Laboratory, Sarastota, FL, USA
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