Coralsnake venomics: Analyses of venom gland transcriptomes and proteomes of six Brazilian taxa

Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2–6 toxin classes that account for 91–99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A2 (PLA2s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA2s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1–2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6–9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A2s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15–35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated

History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

Retrovirus infections in a sample of injecting drug users in Rio de Janeiro City, Brazil: prevalence of HIV-1 subtypes, and co-infection with HTLV-I/II

Made available in DSpace on 2010-08-23T16:58:34Z (GMT). No. of bitstreams: 3 license.txt: 1841 bytes, checksum: 6215bc047e32efa6f76c1618e2d3c4d8 (MD5) Bastos_Retroviruses infections in a Sample_2001.pdf: 100575 bytes, checksum: e444a5d51c55d26fa663e306de9d716a (MD5) Bastos_Retroviruses infections in a Sample_2001.pdf.txt: 35187 bytes, checksum: ea44fb3f7d3a35f8c95cfdbfc828036d (MD5) Previous issue date: 2001Made available in DSpace on 2010-11-04T14:20:07Z (GMT). No. of bitstreams: 3 Bastos_Retroviruses infections in a Sample_2001.pdf.txt: 35187 bytes, checksum: ea44fb3f7d3a35f8c95cfdbfc828036d (MD5) Bastos_Retroviruses infections in a Sample_2001.pdf: 100575 bytes, checksum: e444a5d51c55d26fa663e306de9d716a (MD5) license.txt: 1841 bytes, checksum: 6215bc047e32efa6f76c1618e2d3c4d8 (MD5) Previous issue date: 2001The HIV-1 en Subtyping Kit was kindly provided by the NIH AIDS Research and Reference Reagent Program and UNAIDS. M.L.G., F.I.B. and P.T. are personally supported by grants from CNPq and FAPERJ. This project was supported by the National Coordination of STD and AIDS/ UNDCP/World Bank; World Health Organization –Global Programme on AIDS/United Nations Programme on AIDS (UNAIDS), the FIOCRUZ Integrated AIDS Program/Brazilian Ministry of Health, the Brazilian Research Council (CNPq), and Rio de Janeiro State Council (FAPERJ).Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Department of Immunology. Laboratory of AIDS and Molecular Immunology. Rio de Janeiro, RJ, Brasil.Department of Health Information, Center for Information on Science and Technology, FIOCRUZ (UNAIDS Collaborative Centre), Rio de Janeiro, BrazilCenter for Drug Abuse Treatment and Research (NEPAD), State University of Rio de Janeiro, Rio de Janeiro, BrazilAdvanced Public Health Laboratory, Gonçalo Moniz Research Center, FIOCRUZ (UNAIDS Collaborative Centre), Bahia, BrazilLaboratory of Retrovirology, Federal University of São Paulo, São Paulo, BrazilOswaldo Cruz Foundation. Oswaldo Cruz Institute. Department of Immunology. Laboratory of AIDS and Molecular Immunology. Rio de Janeiro, RJ, Brasil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Department of Immunology. Laboratory of AIDS and Molecular Immunology. Rio de Janeiro, RJ, Brasil.Background :Retrovirus infections among injecting drug users (IDUs), a core at-risk population for both HIV-1 and HTLV-I/II infections in Brazil, were assessed within an ongoing cooperative research. Objecti e : The study assessed the seroprevalences of HIV-1 and HTLV-I/II infections, as well as the prevalence of HIV-1 subtypes in a sample of IDUs from Rio de Janeiro, Brazil. An attempt to evaluate HIV incidence was carried out using a dual ‘sensitive/less sensitive’ testing strategy. Study design : Cross-sectional evaluation of 175 IDUs. Serostatus for HIV-1 and HTLV-I/II were established by enzyme-linked immunosorbent assays, and confirmed by western blot. The dual testing strategy aimed to estimate HIV-1 incidence rates. Differentiation between HTLV-I and -II was performed by western blot. DNA samples were polymerase chain reaction amplified by a nested protocol, and HIV-1 subtyping was determined by heteroduplex mobility assay. Results : Forty-six and 29 samples were found to be, respectively, positive for HIV-1 and HTLV-I/II, 15 of them co-infected by both viruses. Among HTLV-I/II-infected patients, 75.9% were infected by HTLV-I. Thirty-one HIV samples were identified as B subtype, with seven of them showing the typical ‘Brazilian B’ pattern in the gp120 V3 loop, and ten were identified as F subtype. The use of less sensitive assays for HIV infection wrongly identified a deeply immunocompromised patient as an incident case. Conclusion :Moderately high seroprevalences were found for both HIV-1 and HTLV-I/II infections, HIV-1/HTLV-I co-infections being of special concern. A non-statistically significant higher prevalence of F subtype was observed, when compared with the distribution of F/B subtypes among Brazilian patients from other exposure categories. No recent HIV-1 infections were detected, but a limitation of the ‘sensitive/less-sensitive’ testing strategy was made evident

Addendum: Aird, S.D. et al. Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa. Toxins 2017, 9(6), 187

Following publication of this paper, Dr. Daniel Dashevsky discovered to our chagrin, that the transcriptomic datasets uploaded to the DNA Databank of Japan (DDBJ) contained numerous complete 3FTx sequences that were not included in our paper.[...