Plasma proteomics of green turtles (\u3cem\u3eChelonia mydas\u3c/em\u3e) reveals pathway shifts and potential biomarker candidates associated with health and disease

Evaluating sea turtle health can be challenging due to an incomplete understanding of pathophysiologic responses in these species. Proteome characterization of clinical plasma samples can provide insights into disease progression and prospective biomarker targets. A TMT-10-plex-LC–MS/MS platform was used to characterize the plasma proteome of five, juvenile, green turtles (Chelonia mydas) and compare qualitative and quantitative protein changes during moribund and recovered states. The 10 plasma samples yielded a total of 670 unique proteins. Using ≥1.2-fold change in protein abundance as a benchmark for physiologic upregulation or downregulation, 233 (34.8%) were differentially regulated in at least one turtle between moribund and recovered states. Forty-six proteins (6.9%) were differentially regulated in all five turtles with two proteins (0.3%) demonstrating a statistically significant change. A principle component analysis showed protein abundance loosely clustered between moribund samples or recovered samples and for turtles that presented with trauma (n = 3) or as intestinal floaters (n = 2). Gene Ontology terms demonstrated that moribund samples were represented by a higher number of proteins associated with blood coagulation, adaptive immune responses and acute phase response, while recovered turtle samples included a relatively higher number of proteins associated with metabolic processes and response to nutrients. Abundance levels of 48 proteins (7.2%) in moribund samples significantly correlated with total protein, albumin and/or globulin levels quantified by biochemical analysis. Differentially regulated proteins identified with immunologic and physiologic functions are discussed for their possible role in the green turtle pathophysiologic response and for their potential use as diagnostic biomarkers. These findings enhance our ability to interpret sea turtle health and further progress conservation, research and rehabilitation programs for these ecologically important species

Reflections from the Workshop on AI-Assisted Decision Making for Conservation

In this white paper, we synthesize key points made during presentations and discussions from the AI-Assisted Decision Making for Conservation workshop, hosted by the Center for Research on Computation and Society at Harvard University on October 20-21, 2022. We identify key open research questions in resource allocation, planning, and interventions for biodiversity conservation, highlighting conservation challenges that not only require AI solutions, but also require novel methodological advances. In addition to providing a summary of the workshop talks and discussions, we hope this document serves as a call-to-action to orient the expansion of algorithmic decision-making approaches to prioritize real-world conservation challenges, through collaborative efforts of ecologists, conservation decision-makers, and AI researchers.Comment: Co-authored by participants from the October 2022 workshop: https://crcs.seas.harvard.edu/conservation-worksho

Cultivating epizoic diatoms provides insights into the evolution and ecology of both epibionts and hosts

11 pages, 3 figures, 1 table, supplementary information https://doi.org/10.1038/s41598-022-19064-0.-- Data availability: DNA sequence data generated for this study are published on the NCBI GenBank online sequence depository under the accession numbers listed in Table S1. Additional micrographs and cleaned voucher material from the sequenced cultures are available from lead author MPAOur understanding of the importance of microbiomes on large aquatic animals—such as whales, sea turtles and manatees—has advanced considerably in recent years. The latest observations indicate that epibiotic diatom communities constitute diverse, polyphyletic, and compositionally stable assemblages that include both putatively obligate epizoic and generalist species. Here, we outline a successful approach to culture putatively obligate epizoic diatoms without their hosts. That some taxa can be cultured independently from their epizoic habitat raises several questions about the nature of the interaction between these animals and their epibionts. This insight allows us to propose further applications and research avenues in this growing area of study. Analyzing the DNA sequences of these cultured strains, we found that several unique diatom taxa have evolved independently to occupy epibiotic habitats. We created a library of reference sequence data for use in metabarcoding surveys of sea turtle and manatee microbiomes that will further facilitate the use of environmental DNA for studying host specificity in epizoic diatoms and the utility of diatoms as indicators of host ecology and health. We encourage the interdisciplinary community working with marine megafauna to consider including diatom sampling and diatom analysis into their routine practicesFinancial support for sequencing and SEM comes from the Jane and the Roland Blumberg Centennial Professorship in Molecular Evolution at UT Austin and the US Department of Defense (grant number W911NF-17-2-0091). Sampling in South Africa was done with partial financial support from The Systematics Association (UK) through the Systematics Research Fund Award granted to RM (2017 and 2020). Work in the Adriatic Sea was supported by Croatian Science Foundation, project UIP-05-2017-5635 (TurtleBIOME). KF has been fully supported by the “Young researchers' career development project – training of doctoral students” of the CSF funded by the EU from the European Social Fund. NJR was funded by the Spanish government (AEI) through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

COMPARISON OF AGAROSE GEL AND CAPILLARY ZONE ELECTROPHORESIS METHODS USING PLASMA FROM GREEN TURTLES ( CHELONIA MYDAS )

Agarose gel electrophoresis (AGE) has been widely implemented throughout veterinary medicine and for analysis of plasma proteins of avian and reptile species. Capillary zone electrophoresis (CZE) is becoming a standard method in human clinical pathology laboratories but has not widely been used for the analysis of animal samples. The objective of the present study was to compare protein fractions derived from AGE and CZE methods using plasma from the green turtle ( ). Plasma samples were analyzed by AGE and CZE per manufacturer guidelines. The methods were assessed by CV analysis, Spearman's correlation, Passing-Bablok regression, and Bland Altman plots. CZE consistently resolved more fractions than AGE with three fractions observed in the prealbumin migrating region versus one for AGE and two fractions in the γ globulin region versus one for AGE. Compared with AGE, CZE showed a lower CV in intra-assay tests (1.0-4.9% vs 2.0-28.3%) and a lower or overlapping CV in interassay tests (1.0-10.6 vs 2.3-22.0). The prealbumin, α2 globulin, and β globulin fractions correlated the least between the methods (for all three fractions: ≤ 0.28, > 0.21). Moderate, significant correlations between AGE and CZE methods were observed for albumin ( = 0.78, < 0.0001) and γ globulins ( = 0.78, < 0.0001). CZE has a higher precision and ease of use over AGE and offers the opportunity to resolve additional protein fractions. This will necessitate the development of new conventions in placement of fraction delimits, definition of species-specific reference intervals, and evaluation of clinical utility in abnormal turtles

Morphological variation in leatherback (Dermochelys coriacea) hatchlings at Sandy Point National Wildlife Refuge, US Virgin Islands

Understanding species’ mating systems provides important information about their ecology, life history, and behavior. Direct observations of mating behaviors can be challenging, but molecular techniques can reveal information about mating systems and paternal identity in difficult-to-observe species such as sea turtles. Genetic markers can be used to assess the paternity of a clutch and to assign hatchlings to a father. Leatherback turtles Dermochelys coriacea sometimes mate with multiple individuals, resulting in clutches with mixed paternity; however, the effects of multiple paternity on hatchling quality are unclear. Leatherback hatchlings at Sandy Point National Wildlife Refuge, St. Croix, US Virgin Islands, exhibit visible variation in individual body size, sometimes within the same clutch. We collected morphometrics and tissue samples from hatchlings across multiple nesting seasons (2009, 2012, 2013, 2015, and 2016) and found that hatchlings exhibited small but statistically significant differences in morphometrics between years. We used maternal and hatchling microsatellite genotypes to reconstruct paternal genotypes, assigning fathers to each hatchling. We found multiple paternity in 5 of 17 clutches analyzed and compared differences in morphometrics between full-siblings with differences between half-siblings. We found no significant differences between morphometrics of hatchlings from the same mother but different fathers. We compared within-clutch variances in morphometrics for clutches with and without multiple paternity and found no significant difference in morphological variation between them. Therefore, we could not attribute differences in hatchling size within a clutch to paternal contribution. Understanding other factors affecting hatchling morphology, and other possible fitness metrics, may reveal insights into the benefits, or lack thereof, of polyandry in sea turtles

The Iconic Atlantic Goliath Grouper (Epinephelus itajara): A Comprehensive Assessment of Health Indices in the Southeastern United States Population

The Atlantic Goliath Grouper ( Epinephelus itajara ) population has rebounded from near extinction to an international status as vulnerable due in part to regional species recovery efforts. The southeastern US population has been recovering with the main spawning locations off the coasts of Florida. Despite their economic importance to the catch-and-release fishery and the dive industry, and their ecological importance as ecosystem engineers resulting in positive impacts on reefs and species richness, baseline health assessment information is very limited in this species to date. The objectives of this study were to: (1) establish reference intervals for hematological and plasma biochemical analytes, and report immune function, oxidative stress, and vitellogenin in mature males and females; (2) evaluate total length, age, and sex in relation to blood analytes in juvenile and mature fish; (3) assess analytes across sampled months in mature male and female fish; and (4) describe the typical light microscopy findings in liver and gill biopsies, including quantitative assessment of pigmented macrophage aggregates. Health indices are reported as reference intervals when applicable, or otherwise descriptively. Blood analyte correlations with length and age, sex differences, and comparisons across months provided relevant physiological considerations, including differences in protein/energy metabolism, tissue growth, sexual maturation, active reproduction, and antigenic stimulation. Liver histology identified changes associated with life stage, active reproduction, or of subclinically to clinically insignificant infectious and/or inflammatory processes. Hepatocellular vacuolation and pigmented macrophage aggregates were prominent. Pigmented macrophage aggregates correlated with total length, presumably from continuous antigenic stimulation and/or metabolic changes as fish grow. Gill histological findings were subtle. The data presented herein provide an essential baseline assessment of a suite of health variables in an iconic marine teleost species, serves as a springboard for future studies relevant to conservation physiology, and allows for population-level applications for conservation management and policy

Nontargeted lipidomics in nesting females of three sea turtle species in Florida by ultra-high-pressure liquid chromatography–high-resolution tandem mass spectrometry (UHPLC–HRMS/MS) reveals distinct species-specific lipid signatures

In recent years, the utility of lipidomics has been recognized in environmental toxicology and biomonitoring efforts due to the ubiquitous nature and importance of lipids in many cellular processes including signal transduction, energy storage, and cellular compartmentalization. Additionally, technological advances in high-resolution mass spectrometry have enabled the rapid expansion of the field, creating a surge in interest in comparative studies of lipid metabolism from a Systems Biology standpoint. Here, we adapted a nontargeted lipidomic approach for the study of plasma samples from nesting female leatherback (Dermochelys coriacea), loggerhead (Caretta caretta), and green (Chelonia mydas) sea turtles in Florida using ultra-high-performance liquid chromatography/high-resolution tandem mass spectrometry. We identified 877 lipids in common between the three species, of which the concentrations for 467 lipids were statistically different between two or more group comparisons. Principal component analysis revealed unique lipidomic signatures associated with each species of turtle, including various glycerophosphatidylcholines, glycerophosphatidylethanolamines, triacylglycerols, and oxidized triacylglycerols that were higher in leatherback sea turtles, diacylglycerols and select glycerophosphatidylinositols which were higher in loggerhead sea turtles, and specific plasmanyl-phosphatidylcholines that were higher in green sea turtles. Our results indicate that lipidomic profiling can be a useful tool for studying lipid metabolism and physiology of different species of sea turtles, while establishing baseline data that may be used as reference in future studies for observation of differences in life stages, for following spatial and temporal trends in nesting turtles, and for investigating population dynamics in response to various stressors.Partial funding for sample collection and nightly surveys was provided by The Albert E. and Birdie W. Einstein Fund. The corresponding author would like to acknowledge funding support from the University of Florida College of Veterinary Medicine startup package.Peer reviewe

Heat, health and hatchlings: associations of in situ nest temperatures with morphological and physiological characteristics of loggerhead sea turtle hatchlings from Florida

Incubation temperatures, in addition to an embryo’s genetic makeup, are critical in many aspects of adequate sea turtle embryonic development. The effects of high and low incubation temperatures on hatchling quality have been previously examined; however, many of these studies were conducted on relocated or laboratory-reared nests, which do not accurately reflect natural nest temperature fluctuations. To observe the impacts of varying in situ incubation temperatures on loggerhead sea turtle (Caretta caretta) hatchling morphology, various health variables and locomotor performance, temperature data loggers were deployed in 15 loggerhead nests on Juno Beach, Florida, between May and July 2018. Over the course of the study period, 10 morphological traits were measured, blood analytes and heart rate were assessed for the establishment of reference intervals and the self-righting response in seawater was evaluated. Warmer months were associated with smaller body size and higher body condition index, larger umbilical scar size, slower righting time, lower heart rates and higher packed cell volume, hemoglobin, total solids, total white blood cell count, absolute heterophils and absolute basophils. These findings provide evidence that higher in situ incubation temperatures have the potential to adversely affect hatchlings from warmer nests due to increased risk of predation from smaller body sizes, decreased physical responses and overall fitness, altered hemodynamic balance (e.g. dehydration) and potential inflammation and/or stress. With rising temperatures, we predict sea turtle hatchlings may have increasing risks of developing suboptimal physiological features affecting overall fitness and ultimately survival. These results demonstrate that rising environmental temperatures can negatively impact sea turtle hatchlings, thus representing additional stress on sea turtle populations and contributing to our understanding of potential pathophysiological effects of climate change on the delicate life-stage class of the sea turtle hatchling. This information will be useful for formulating effective future sea turtle management plans