Three New Species of Tursiocola (Bacillariophyta) from the Skin of the West Indian Manatee (Trichechus manatus)

Three new species of Tursiocola are described from the skin of the West Indian manatee bringing the total number of known species in the genus to seven. The range of morphological diversity within the genus is greatly expanded. The number of poroid rows on the copulae is no longer a valid characteristic for the separation of Tursiocola from the ceticolous genus Epiphalaina. The presence of a butterfly-like structure in the central area of the former is at present the best criterion for separating the 2 genera. The 3 new Tursiocola species accounted for nearly 90% of all diatom valves on the manatee skin. No other diatom taxa previously described as new from the skin of cetaceans were present on the manatee

Tursiocola denysii sp. nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta)

Tursiocola denysii sp. nov. is described from the dorsal neck skin of loggerhead sea turtles (Caretta caretta), bringing the total number of known species in the genus Tursiocola to eight. A gradient of striae density on the valve face, the low length: width ratio of the valves, radiate striae at mid-valve, and a second partial row of pores on the valvocopulae are characteristics that expand the range of morphological diversity within the genus. The different morphology of the pars interior and the pars exterior of the valvocopula is described for the first time in the genus. T. denysii accounted for up to ca. 40% of all diatom valves on the skin of loggerhead turtles. This is the first report of a new epizoic diatom species from the skin of loggerhead sea turtles

Medlinella amphoroidea gen. et sp. nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta)

Medlinella amphoroidea gen. et sp. nov. is described from the dorsal neck skin of loggerhead sea turtles (Caretta caretta). The presence of girdle septa, multiple copulae, and the marine epizoic habitat of Medlinella amphoroidea are characteristic features shared with many species in the similar Tripterion, Chelonicola, and Poulinea genera. The semi-lanceolate valve shape, the asymmetric valve face with distinct dorsal and ventral striae, and the volate pore occlusions distinguish Medlinella from these genera. Medlinella amphoroidea accounted for up to 50% of all diatom valves on the skin of examined loggerhead turtles. Examination of the type slides of Tripterion kalamensis and T. philoderma for comparative purposes revealed morphological features that were either insufficiently or incorrectly described in the original publications. Our observations confirm that T. philoderma lacks septa and therefore does not conform to the genus description of Tripterion. The description of cingulum structure in Tripterion kalamensis is amended to identify multiple porose copulae that are open at one end. While the description of Medlinella creates another monotypic genus within a group of similar marine epizoic genera, we feel the novel character state (volate occlusions) present in this taxon is significant. Clearly, however, further phylogenetic analysis of morphological, or the development of molecular characters in the group of similar genera is required

Hematology, plasma biochemistry, and hormonal analysis of captive Louisiana pine snakes (Pituophis ruthveni): effects of intrinsic factors and analytical methodology

Blood analyte data are useful in health assessments and management of reptiles. There is a knowledge gap for blood analyte data of the endangered Louisiana pine snake (LPS; Pituophis ruthveni). The objectives of this study were to provide baseline hematology, plasma biochemical, and hormone data of captive LPS, to compare the data in juvenile and adult snakes and in adult snakes by sex, and to investigate methodological differences in hormone (serum vs. plasma) and protein analyses (total solids versus total protein). Blood samples from apparently healthy captive LPS were analyzed for hematology and plasma biochemistry (n = 11) and plasma and serum hormone analyses (n = 9). Packed cell volume (PCV) and absolute heterophils were significantly higher in adult compared with juvenile LPS, while PCV, white blood cell count, and absolute lymphocytes were higher in adult males compared with adult females. Significantly higher plasma concentrations were found in adults compared with juveniles for calcium, total protein, total solids, albumin, globulins, and bile acids. No significant differences were observed in 17β-estradiol measured in serum and plasma when comparing adults and juveniles and for 17β-estradiol in adult males and females. Plasma concentrations of 17β-estradiol were significantly lower than in serum. Serum testosterone in two adult males was 8.33 and 35.53 nmol/L, respectively, while it was undetectable in females and juveniles (n = 5). This study is the first to provide baseline information on blood analytes in endangered LPS, which will be useful for individual animals in managed care and as baseline for future population-level assessments

Diagnostic Performance of Clinicopathological Analytes in Otostrongylus circumlitis-Infected Rehabilitating Juvenile Northern Elephant Seals (Mirounga angustirostris)

The nematode lungworm, Otostrongylus circumlitis (OC), is a significant cause of northern elephant seal (NES; Mirounga angustirostris) mortality at The Marine Mammal Center (TMMC, Sausalito, CA). The current lack of specific antemortem diagnostic tests for pre-patent OC infection in NES makes diagnosis, proper treatment, and assessment of efficacy of medications challenging. Severe inflammation and disseminated intravascular coagulation (DIC) develop rapidly and are difficult to treat once clinical signs develop. Certain blood inflammatory and hemostasis biomarkers for early diagnosis have recently been investigated. The objective of this study was to investigate the diagnostic performance of complete blood count, serum chemistry, acute phase proteins, protein electrophoresis, and coagulation parameters for diagnosis of OC clinical infection in NES. Samples from NES with OC infection confirmed by gross pathology with blood collected antemortem during clinical disease (n = 9) and NES initially admitted for malnutrition and sampled shortly before release after successful rehabilitation (n = 20) were included in the study. Using Receiver operator characteristic (ROC) curve analysis, the diagnostic performances (area under the curve [AUC]) of albumin (0.994), albumin:globulin ratio (0.983), serum amyloid A (0.972), activated partial thromboplastin time (0.936), total bilirubin (0.975), and gamma-glutamyl transferase (0.939) were high (AUC > 0.9). These results confirm systemic inflammation and DIC, and support previously reported clinical and gross pathological findings in NES infected with OC. In addition to AUC values, this study produced cut-off points, sensitivity, specificity, confidence intervals, and predictive values for analytes with high diagnostic performance. This data will be useful in the diagnosis and clinical management of OC-infected NES and will aid in assessment of treatment efficacy

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

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.

This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.3448Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.We thank all participants of all the studies included for enabling this research by their participation in these studies. Computer resources for this project have been provided by the high-performance computing centers of the University of Michigan and the University of Regensburg. Group-specific acknowledgments can be found in the Supplementary Note. The Center for Inherited Diseases Research (CIDR) Program contract number is HHSN268201200008I. This and the main consortium work were predominantly funded by 1X01HG006934-01 to G.R.A. and R01 EY022310 to J.L.H

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival