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Trindade FJ, Rodrigues MR, Figueiró HV, Li G, Murphy WJ, Eizirik E. Genome-wide SNPs clarify a complex radiation and support recognition of an additional cat species. Mol Biol Evol 2021; 38:4987-4991. [PMID: 34320647 PMCID: PMC8557425 DOI: 10.1093/molbev/msab222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus, the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the “tigrina” morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species.
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Affiliation(s)
- Fernanda J Trindade
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil
| | - Maíra R Rodrigues
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,USP, Department of Genetics and Evolutionary Biology, Institute of Biosciences, São Paulo, Brazil
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.,College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
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2
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Gouveia MH, Borda V, Leal TP, Moreira RG, Bergen AW, Kehdy FSG, Alvim I, Aquino MM, Araujo GS, Araujo NM, Furlan V, Liboredo R, Machado M, Magalhaes WCS, Michelin LA, Rodrigues MR, Rodrigues-Soares F, Sant Anna HP, Santolalla ML, Scliar MO, Soares-Souza G, Zamudio R, Zolini C, Bortolini MC, Dean M, Gilman RH, Guio H, Rocha J, Pereira AC, Barreto ML, Horta BL, Lima-Costa MF, Mbulaiteye SM, Chanock SJ, Tishkoff SA, Yeager M, Tarazona-Santos E. Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas. Mol Biol Evol 2021; 37:1647-1656. [PMID: 32128591 DOI: 10.1093/molbev/msaa033] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.
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Affiliation(s)
- Mateus H Gouveia
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil.,Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD
| | - Victor Borda
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thiago P Leal
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Estatística, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rennan G Moreira
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genômica, Centro de Laboratórios Multiusuário (CELAM), ICB, UFMG, Belo Horizonte, MG, Brazil
| | - Andrew W Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Fernanda S G Kehdy
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Isabela Alvim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marla M Aquino
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gilderlanio S Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará - Campus Guamá, Belém, PA, Brazil
| | - Nathalia M Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vinicius Furlan
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, Campus UFV-Florestal, Florestal, MG, Brazil
| | - Raquel Liboredo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Moara Machado
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Wagner C S Magalhaes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Núcleo de Ensino e Pesquisas do Instituto Mário Penna - NEP-IMP, Bairro Luxemburgo, Belo Horizonte, MG, Brazil
| | - Lucas A Michelin
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maíra R Rodrigues
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Hanaisa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Meddly L Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marília O Scliar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Giordano Soares-Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Roxana Zamudio
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Camila Zolini
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Beagle, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Catira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Michael Dean
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert H Gilman
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Maria F Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Sarah A Tishkoff
- Department of Genetics and Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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3
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Lam ECS, Li R, Rodrigues MR, Vires L, Adams RL, Sherrill JD, Oblong JE. Enhanced retinoid response by a combination of the vitamin A ester retinyl propionate with niacinamide and a flavonoid containing Ceratonia siliqua extract in retinoid responsive in vitro models. Int J Cosmet Sci 2020; 43:102-106. [PMID: 33048363 DOI: 10.1111/ics.12669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Retinoids have been used for decades as efficacious topical agents to treat photoaged skin. The purpose of our present research is to evaluate whether the activity of the vitamin A ester retinyl propionate (RP) can be enhanced by niacinamide (Nam) and a flavonoid containing Ceratonia siliqua (CS) fruit extract in retinoid responsive in vitro models. METHODS Retinyl propionate was tested alone and in combination with Nam and CS in an RARα reporter cell line for promoter activation and compared to trans-retinoic acid (tRA) activation. These treatments were also tested in keratinocytes for gene expression profiling by qPCR using a panel of 40 retinoid responsive genes. RESULTS tRA or RP elicited RARα reporter activation in a dose-dependent manner. The combination of 0.5 μM or 2 μM RP with 10 mM Nam had a 56% and 95% signal increase compared to RP, respectively. The addition of 1% CS to 0.5 μM or 2 μM RP with 10 mM Nam elicited a further increase of 114% and 156%, respectively, over RP and Nam combinations. All retinoids elicited an increase in expression of 40 retinoid sensitive genes over control levels. Of the 40 genes, 27 were enhanced by either 0.1 μM RP or 0.5 μM RP with 10 mM Nam and 1% CS. Nam or CS had very modest activity in both models. CONCLUSION The combination of RP with Nam and CS showed a higher retinoid response than RP in two separate retinoid responsive in vitro models. We hypothesize Nam and CS enhances RP activity by modulating metabolism to tRA via increasing NAD+ pools and inhibiting reduction of retinal (RAL) back to retinol, respectively. The findings provide evidence that this combination may have enhanced efficacy for treating the appearance of photoaged skin.
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Affiliation(s)
- E C S Lam
- Procter and Gamble International Operations SA SG Branch, Singapore, Singapore
| | - R Li
- Procter and Gamble International Operations SA SG Branch, Singapore, Singapore
| | - M R Rodrigues
- Procter and Gamble International Operations SA SG Branch, Singapore, Singapore
| | - L Vires
- The Procter and Gamble Company, Cincinnati, OH, USA
| | - R L Adams
- The Procter and Gamble Company, Cincinnati, OH, USA
| | - J D Sherrill
- The Procter and Gamble Company, Cincinnati, OH, USA
| | - J E Oblong
- The Procter and Gamble Company, Cincinnati, OH, USA
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4
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Bauer AE, Hewitt LM, Parrott JL, Bartlett AJ, Gillis PL, Deeth LE, Rudy MD, Vanderveen R, Brown L, Campbell SD, Rodrigues MR, Farwell AJ, Dixon DG, Frank RA. The toxicity of organic fractions from aged oil sands process-affected water to aquatic species. Sci Total Environ 2019; 669:702-710. [PMID: 30893625 DOI: 10.1016/j.scitotenv.2019.03.107] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The process of surface mining and extracting bitumen from oil sand produces large quantities of tailings and oil sands process-affected water (OSPW). The industry is currently storing OSPW on-site while investigating strategies for their detoxification. One such strategy relies on the biodegradation of organic compounds by indigenous microbes, resulting in aged tailings waters with reduced toxicity. This study assessed the toxicity of OSPW aged statically for approximately 18 years. Dissolved organics in aged OSPW were fractionated using a preparative solid-phase extraction method that generated three organic fractions (F1-F3) of increasing polarity. Eight aquatic species from different trophic levels were exposed to whole OSPW (WW) and the derived OSPW organic fractions to assess toxicity: Pimephales promelas, Oryzias latipes, Vibrio fischeri, Daphnia magna, Lampsilis cardium, Hyalella azteca, Ceriodaphnia dubia, and Hexagenia spp. Broad comparisons revealed that P. promelas and H. azteca were most sensitive to dissolved organics within aged OSPW, while WW was most toxic to L. cardium and H. azteca. Three cases of possible contaminant interactions occurred within whole OSPW treatments, as toxicity was higher than organic fractions for H. azteca and L. cardium, and lower for P. promelas. As such, the drivers of toxicity appeared to be dependent on the species exposed. Of the organic fractions assessed, F3 (most polar) was the most toxic overall while F2 (intermediate polarity) displayed little toxicity to all species evaluated. This presents strong evidence that classical mono-carboxylic naphthenic acids, mostly present in F1 (least polar), are not primarily responsible for the toxicity in aged tailings. The current study indicates that although the aged tailings source (≥18 years) did not display acute toxicity to the majority of organisms assessed, inorganic components and polyoxygenated organics may pose a persistent concern to some aquatic organisms.
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Affiliation(s)
- Anthony E Bauer
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, ON, Canada
| | - L M Hewitt
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada.
| | - J L Parrott
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - A J Bartlett
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - P L Gillis
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - L E Deeth
- Department of Mathematics and Statistics, University of Guelph, Guelph N1G 2W1, ON, Canada
| | - M D Rudy
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - R Vanderveen
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - L Brown
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - S D Campbell
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - M R Rodrigues
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
| | - A J Farwell
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, ON, Canada
| | - D G Dixon
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, ON, Canada
| | - R A Frank
- Water Science and Technology Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington L7S 1A1, ON, Canada
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5
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Magalhães WCS, Araujo NM, Leal TP, Araujo GS, Viriato PJS, Kehdy FS, Costa GN, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Tarazona-Santos E, Rodrigues MR. EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow. Genome Res 2018; 28:1090-1095. [PMID: 29903722 PMCID: PMC6028131 DOI: 10.1101/gr.225458.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 05/24/2018] [Indexed: 12/24/2022]
Abstract
EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel—the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs (info score ≥ 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources.
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Affiliation(s)
- Wagner C S Magalhães
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Instituto Mario Penna, Núcleo de Ensino e Pesquisa, Belo Horizonte, Minas Gerais, 30380-472, Brazil
| | - Nathalia M Araujo
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Thiago P Leal
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Gilderlanio S Araujo
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Paula J S Viriato
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Fernanda S Kehdy
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, 21040-900, Brazil
| | - Gustavo N Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, 40110-040, Brazil
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, 40110-040, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, 40296-710, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, 96020-220, Brazil
| | - Maria Fernanda Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, 30190-009, Brazil
| | - Alexandre C Pereira
- Instituto do Coração, Universidade de São Paulo, São Paulo, São Paulo, 05403-900, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Maíra R Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Faculdade de Ciências Médicas e Instituto de Matemática, Estatística e Ciência da Computação, Universidade de Campinas, São Paulo, 13083-894, Brazil
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6
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Zuccherato LW, Schneider S, Tarazona-Santos E, Hardwick RJ, Berg DE, Bogle H, Gouveia MH, Machado LR, Machado M, Rodrigues-Soares F, Soares-Souza GB, Togni DL, Zamudio R, Gilman RH, Duarte D, Hollox EJ, Rodrigues MR. Population genetics of immune-related multilocus copy number variation in Native Americans. J R Soc Interface 2017; 14:rsif.2017.0057. [PMID: 28356540 DOI: 10.1098/rsif.2017.0057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/02/2017] [Indexed: 12/22/2022] Open
Abstract
While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy-Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f, which quantifies the departure of homozygosity from the Hardy-Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1, FCGR3A, FCGR3B and FCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.
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Affiliation(s)
- Luciana W Zuccherato
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Silvana Schneider
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Douglas E Berg
- Department of Molecular Microbiology, Washington University in Saint Louis School of Medicine, St Louis, MO, USA.,Department of Medicine, University of California San Diego, CA, USA
| | - Helen Bogle
- Department of Genetics, University of Leicester, Leicester, UK
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lee R Machado
- Department of Genetics, University of Leicester, Leicester, UK.,School of Health, University of Northampton, Northampton, UK
| | - Moara Machado
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giordano B Soares-Souza
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diego L Togni
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roxana Zamudio
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Asociación Benéfica PRISMA, Lima, Peru.,Universidade Peruana Cayetano Heredia, Lima, Peru
| | - Denise Duarte
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Maíra R Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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7
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Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, Trinca CS, Rodrigues MR, Linderoth T, Bi K, Silveira L, Azevedo FCC, Kantek D, Ramalho E, Brassaloti RA, Villela PMS, Nunes ALV, Teixeira RHF, Morato RG, Loska D, Saragüeta P, Gabaldón T, Teeling EC, O’Brien SJ, Nielsen R, Coutinho LL, Oliveira G, Murphy WJ, Eizirik E. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Sci Adv 2017; 3:e1700299. [PMID: 28776029 PMCID: PMC5517113 DOI: 10.1126/sciadv.1700299] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/19/2017] [Indexed: 05/05/2023]
Abstract
The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.
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Affiliation(s)
- Henrique V. Figueiró
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Fernanda J. Trindade
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Juliana Assis
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Fabiano Pais
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Fernandes
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Sarah H. D. Santos
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Agostinho Antunes
- Departamento de Biologia, Faculdade de Ciências and CIIMAR/CIMAR, Universidade do Porto, Porto, Portugal
| | - Cristine S. Trinca
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Maíra R. Rodrigues
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Fernando C. C. Azevedo
- Universidade Federal de São João Del Rey, São João Del Rey, Minas Gerais, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
| | - Daniel Kantek
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Emiliano Ramalho
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Ricardo A. Brassaloti
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | | | - Rodrigo H. F. Teixeira
- Zoológico Municipal de Sorocaba, Sorocaba, São Paulo, Brazil
- Programa de Pós-Graduação em Animais Selvagens, Universidade Estadual Paulista–Botucatu, São Paulo, Brazil
| | - Ronaldo G. Morato
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Damian Loska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Luiz L. Coutinho
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | - Guilherme Oliveira
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
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8
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Araújo GS, Lima LHC, Schneider S, Leal TP, da Silva APC, Vaz de Melo POS, Tarazona-Santos E, Scliar MO, Rodrigues MR. Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks). Bioinformatics 2016; 32:1247-9. [PMID: 26673785 DOI: 10.1093/bioinformatics/btv708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/29/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The 1000 Genomes Project (1KGP) and thousands of Genome-Wide Association Studies (GWAS) performed during the last years have generated an enormous amount of information that needs to be integrated to better understand the genetic architecture of complex diseases in different populations. This integration is important in areas such as genetics, epidemiology, anthropology, as well as admixture mapping design and GWAS-replications. Network-based approaches that explore the genetic bases of human diseases and traits have not yet incorporated information on genetic diversity among human populations. RESULTS We propose Disease-ANCEstry networks (DANCE), a graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. DANCE provides an interactive way to explore the human SNP-Disease Network and its projection, a Disease-Disease Network. With these functionalities, DANCE fills a gap in our ability to handle and understand the knowledge generated by GWAS and 1KGP. We provide a number of case studies that show how DANCE can be used to explore the relationships between human complex diseases, their genetic bases and variability in different human populations. AVAILABILITY AND IMPLEMENTATION DANCE is freely available at http://ldgh.com.br/dance/ We recommend using DANCE with Mozilla Firefox, Safari, Chrome or Internet Explorer (v9 or v10). CONTACT gilderlanio@gmail.com or maira.r.rodrigues@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Silvana Schneider
- Department of Statistics, Federal University of Minas Gerais, Belo Horizonte, Brazil
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9
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Abstract
Today there is an increase in the number of cooperative initiatives in different domains to make tools and data available to global communities free or charge. Such cooperative systems are open, heterogeneous, dynamic, and lack a formal payment system. Incentivising cooperation in these scenarios is essential to maintain their effectiveness. Therefore, there is a recognised need to move away from an ad hoc approach to one in which cooperation is supported and encouraged. The agent-oriented paradigm has been advocated as a natural way to design and implement systems that are distributed and heterogeneous. However, developing an agent-oriented system for today's cooperative systems is challenging. It requires a means not only to provide non-monetary incentives for service providers, but also to consider the level of quality of cooperations, in terms of the quality of provided and received services. In this context, the key contribution of this paper is a framework for non-monetary interactions among self-interested agents, in which the motivation to cooperate and the bases for analysing cooperations come from Piaget's theory of exchange values. Our framework includes a computational model of these values, which defines how exchange values are accumulated and spent by interacting agents. We illustrate how our framework can be used by agents to analyze cooperations and to take decisions about them, and provide an empirical evaluation.
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Affiliation(s)
- Maíra R. Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte, MG CEP 31270-910, Brazil
| | - Michael Luck
- Department of Informatics, King's College London, Strand, London, WC2R 2LS, UK
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10
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Rodrigues MR, Magalhães WCS, Machado M, Tarazona-Santos E. A graph-based approach for designing extensible pipelines. BMC Bioinformatics 2012; 13:163. [PMID: 22788675 PMCID: PMC3496580 DOI: 10.1186/1471-2105-13-163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 06/22/2012] [Indexed: 11/10/2022] Open
Abstract
Background In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest implementation of pipelines involves hardcoding the execution steps into programs or scripts. This approach can lead to problems when a pipeline is expanding because the incorporation of new tools is often error prone and time consuming. Current approaches to pipeline development such as workflow management systems focus on analysis tasks that are systematically repeated without significant changes in their course of execution, such as genome annotation. However, more dynamism on the pipeline composition is necessary when each execution requires a different combination of steps. Results We propose a graph-based approach to implement extensible and low-maintenance pipelines that is suitable for pipeline applications with multiple functionalities that require different combinations of steps in each execution. Here pipelines are composed automatically by compiling a specialised set of tools on demand, depending on the functionality required, instead of specifying every sequence of tools in advance. We represent the connectivity of pipeline components with a directed graph in which components are the graph edges, their inputs and outputs are the graph nodes, and the paths through the graph are pipelines. To that end, we developed special data structures and a pipeline system algorithm. We demonstrate the applicability of our approach by implementing a format conversion pipeline for the fields of population genetics and genetic epidemiology, but our approach is also helpful in other fields where the use of multiple software is necessary to perform comprehensive analyses, such as gene expression and proteomics analyses. The project code, documentation and the Java executables are available under an open source license at
http://code.google.com/p/dynamic-pipeline. The system has been tested on Linux and Windows platforms. Conclusions Our graph-based approach enables the automatic creation of pipelines by compiling a specialised set of tools on demand, depending on the functionality required. It also allows the implementation of extensible and low-maintenance pipelines and contributes towards consolidating openness and collaboration in bioinformatics systems. It is targeted at pipeline developers and is suited for implementing applications with sequential execution steps and combined functionalities. In the format conversion application, the automatic combination of conversion tools increased both the number of possible conversions available to the user and the extensibility of the system to allow for future updates with new file formats.
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Affiliation(s)
- Maíra R Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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11
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Lobo FP, Rodrigues MR, Rodrigues GOL, Hilário HO, Souza RA, Tauch A, Miyoshi A, Franco GC, Azevedo V, Franco GR. KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. Nucleic Acids Res 2012; 40:W491-7. [PMID: 22675073 PMCID: PMC3394310 DOI: 10.1093/nar/gks490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The enrichment analysis is a standard procedure to interpret ‘omics’ experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org.
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Affiliation(s)
- Francisco P Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Campinas, São Paulo 13083 886, Brazil.
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12
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Magalhães WCS, Rodrigues MR, Silva D, Soares-Souza G, Iannini ML, Cerqueira GC, Faria-Campos AC, Tarazona-Santos E. DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies. Genet Epidemiol 2012; 36:360-7. [PMID: 22508222 DOI: 10.1002/gepi.21629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/08/2012] [Accepted: 02/08/2012] [Indexed: 11/07/2022]
Abstract
Large-scale genomics initiatives such as the HapMap project and the 1000-genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from different sources, as well as to assist these scientists to perform their analyses efficiently. We developed such a bioinformatics platform, DIVERGENOME, to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups. The platform is composed of two integrated components, a relational database (DIVERGENOMEdb), and a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology (DIVERGENOMEtools). In DIVERGENOMEdb, information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in projects. These can be queried according to permissions. Here, we validated DIVERGENOME through a use case regarding the analysis of SLC2A4 genetic diversity in human populations. DIVERGENOME, with its intuitive Web interface and automatic data loading capability, facilitates its use by individuals without bioinformatics background, allowing complex queries to be easily interrogated and straightforward data format conversions (not available in similar platforms). DIVERGENOME is open source, freely available, and can be accessed online (pggenetica.icb.ufmg.br/divergenome) or hosted locally.
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Affiliation(s)
- Wagner C S Magalhães
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Brazil.
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13
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Scott DJ, Devonshire AS, Adeleye YA, Schutte ME, Rodrigues MR, Wilkes TM, Sacco MG, Gribaldo L, Fabbri M, Coecke S, Whelan M, Skinner N, Bennett A, White A, Foy CA. Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets. Toxicology 2011; 290:50-8. [PMID: 21871943 DOI: 10.1016/j.tox.2011.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 08/09/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n=400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment.
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Affiliation(s)
- D J Scott
- LGC, Queens Rd, Teddington, TW11 0LY, UK.
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14
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Rodrigues MR, Sá Miranda MC, Amaral O. Allelic frequency determination of the 24-bp chitotriosidase duplication in the Portuguese population by real-time PCR. Blood Cells Mol Dis 2005; 33:362-4. [PMID: 15528158 DOI: 10.1016/j.bcmd.2004.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2004] [Indexed: 10/26/2022]
Abstract
Chitotriosidase is a human chitinase produced by macrophages. Its enzymatic activity is markedly elevated in serum of patients suffering from lysosomal storage disorders, as well as other diseases in which macrophages are activated. Therefore, it is a useful tool as a secondary marker in the diagnosis of several disorders including Gaucher disease type 1 and Niemann-Pick disease. The determination of chitotriosidase levels as a diagnosis complement in some lysosomal storage disorders and in enzyme replacement therapy follow-up of Gaucher disease patients is of great importance. However, the fact that a mutation caused by a 24-bp duplication in the CHIT1 gene resulting in deficiency of plasma chitotriosidase activity is very frequent makes the establishment of the frequency of this mutation in different population groups necessary. Furthermore, in order to validate the use of chitotriosidase activity as a marker, it is indispensable to screen individuals for this particular mutation. In this work, we present the results of a study where the allelic frequency of the above mentioned CHIT1 gene mutation was determined in the Portuguese population by real-time PCR. The frequency of carriers encountered in this sample of Portuguese individuals was of 37%.
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Affiliation(s)
- M R Rodrigues
- Instituto de Genética Medica Jacinto de Magalhaes, Unidade de Enzimologia, Porto, Portugal
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15
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Silva SO, Rodrigues MR, Ximenes VF, Bueno-da-Silva AEB, Amarante-Mendes GP, Campa A. Neutrophils as a specific target for melatonin and kynuramines: effects on cytokine release. J Neuroimmunol 2004; 156:146-52. [PMID: 15465605 DOI: 10.1016/j.jneuroim.2004.07.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 07/19/2004] [Accepted: 07/28/2004] [Indexed: 10/26/2022]
Abstract
A growing body of evidence suggests that the pineal hormone, melatonin, has immunomodulatory properties, although very little is known about its effect on leukocytes. Therefore, we aimed to investigate the effect of melatonin and its oxidation product N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK) on cytokine production by neutrophils and peripheral blood mononuclear cells (PBMCs). AFMK (0.001-1 mM) inhibits the lipopolysaccharide (LPS)-mediated production of tumor necrosis factor-alpha (TNF-alpha) and interleukin-8 (IL-8) more efficiently in neutrophils than PBMCs. Moreover, the inhibitory activity of AFMK is stronger than that of melatonin. Interestingly, monocytes efficiently oxidize melatonin to AFMK. We conclude that neutrophils are one of the main targets for melatonin and that at least part of the effects described for melatonin on immune cells may be due to its oxidation product, AFMK. We also consider that the oxidation of melatonin may be an important event in the cross-talking between neutrophils and monocytes.
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Affiliation(s)
- S O Silva
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo CEP 05508-900, SP, Brazil
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16
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Cardoso ML, Rodrigues MR, Leão E, Martins E, Diogo L, Rodrigues E, Garcia P, Rolland MO, Vilarinho L. The E37X is a common HMGCL mutation in Portuguese patients with 3-hydroxy-3-methylglutaric CoA lyase deficiency. Mol Genet Metab 2004; 82:334-8. [PMID: 15308132 DOI: 10.1016/j.ymgme.2004.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Revised: 05/28/2004] [Accepted: 06/02/2004] [Indexed: 11/18/2022]
Abstract
3-Hydroxy-3-methylglutaric aciduria (OMIM 246450) is an autosomal recessive inborn error of the final step of leucine catabolic and ketogenic pathways, caused by deficiency of the enzyme 3-hydroxy-3-methylglutaryl CoA lyase (HL, HMGCL, EC 4.1.3.4). Clinically, deficiency of the enzyme results in metabolic acidosis, hyperammonemia, and infantile hypoketotic hypoglycaemia usually presenting during the first year of life with vomiting, lethargy, hypotonia, and sometimes with respiratory distress and coma. HL deficiency is relatively common in Arabic populations but seems to be rare in Europe. Our recent experience suggests that HL deficiency is the most frequent organic aciduria in the Portuguese population. We herein report on the molecular study of the HMGCL gene in 11 cases originated from the Northern area of Portugal. We detected the E37X (c.109G > T) mutation, in 84.1% of the alleles, one allele carried the V168fs(-2) (504_505delCT) and other allele the novel D204N (c.610G > A) mutation. The mutation of the last allele remained unidentified. The relatively high frequency of the "common" HMGCL Portuguese mutation makes useful the development of a rapid and specific molecular confirmation of new cases with HL deficiency in our country.
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Affiliation(s)
- M L Cardoso
- Instituto de Genética Médica Jacinto de Magalhães, Porto, Portugal
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17
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da Costa VV, Saraiva RA, de Almeida AC, Rodrigues MR, Nunes LG, Ferreira JC. The effect of nitrous oxide on the inhibition of somatosensory evoked potentials by sevoflurane in children. Anaesthesia 2001; 56:202-7. [PMID: 11251424 DOI: 10.1046/j.1365-2044.2001.01543.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Inhalational anaesthetics inhibit somatosensory evoked potentials. The present study examined the effect of nitrous oxide in anaesthetic mixture with sevoflurane on the somatosensory evoked potential in children. Forty-five patients aged between 6 months and 6 years undergoing club foot surgery were studied to verify the influence of sevoflurane alone (21 patients) and sevoflurane with nitrous oxide (24 patients) on the somatosensory evoked potential. Fractional inspired concentration of nitrous oxide and fractional end-tidal (alveolar) sevoflurane were measured to estimate the multiples and submultiples of the minimal alveolar concentration (age corrected). The somatosensory evoked potential signals were obtained by stimulation of the median nerve. Nitrous oxide (FI = 0.63 +/- 2.5) with sevoflurane caused more reduction in the amplitude of somatosensory evoked potential waves and a greater increase in the latency of somatosensory evoked potential waves in comparison with sevoflurane alone. The results show that it is possible to obtain the inhibition of somatosensory evoked potential with smaller concentrations of sevoflurane, when it is used with nitrous oxide.
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Affiliation(s)
- V V da Costa
- Department of Clinical Neurophysiology, SARAH Hospital of Brasilia, SMHS Quadra 501 Conjunto: A, 70330-150 Brasilia DF, Brazil
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Funderburgh JL, Hevelone ND, Roth MR, Funderburgh ML, Rodrigues MR, Nirankari VS, Conrad GW. Decorin and biglycan of normal and pathologic human corneas. Invest Ophthalmol Vis Sci 1998; 39:1957-64. [PMID: 9727420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
PURPOSE Corneas with scars and certain chronic pathologic conditions contain highly sulfated dermatan sulfate, but little is known of the core proteins that carry these atypical glycosaminoglycans. In this study the proteoglycan proteins attached to dermatan sulfate in normal and pathologic human corneas were examined to identify primary genes involved in the pathobiology of corneal scarring. METHODS Proteoglycans from human corneas with chronic edema, bullous keratopathy, and keratoconus and from normal corneas were analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative immunoblotting, and immunohistology with peptide antibodies to decorin and biglycan. RESULTS Proteoglycans from pathologic corneas exhibit increased size heterogeneity and binding of the cationic dye alcian blue compared with those in normal corneas. Decorin and biglycan extracted from normal and diseased corneas exhibited similar molecular size distribution patterns. In approximately half of the pathologic corneas, the level of biglycan was elevated an average of seven times above normal, and decorin was elevated approximately three times above normal. The increases were associated with highly charged molecular forms of decorin and biglycan, indicating modification of the proteins with dermatan sulfate chains of increased sulfation. Immunostaining of corneal sections showed an abnormal stromal localization of biglycan in pathologic corneas. CONCLUSIONS The increased dermatan sulfate associated with chronic corneal pathologic conditions results from stromal accumulation of decorin and particularly of biglycan in the affected corneas. These proteins bear dermatan sulfate chains with increased sulfation compared with normal stromal proteoglycans.
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Affiliation(s)
- J L Funderburgh
- Division of Biology, Kansas State University, Manhattan 66506-4901, USA
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Abstract
Recent methods for detection of viruses in clinical specimens include immunofluorescence, immunoperoxidase, immune adherence hemagglutination, radioimmunoassay, enzyme-linked immunosorbent assay (ELISA), and immunoelectron microscopy. Some are useful for the detection of traces of viral antigens but are more complicated and time-consuming than others. Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections.
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Heersink B, Rodrigues MR, Flanagan JC. Inflammatory pseudotumor of the orbit. Ann Ophthalmol 1977; 9:17-22, 25-9. [PMID: 576377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The history and confusing terminology regarding reports of inflammatory pseudotumor of the orbit are reviewed. The wide clinical spectrum and variety of associated conditions is emphasized. Twenty-seven patients from the Wills Eye Hospital with clinical records and histopathologic material consistent with orbital pseudotumor were reviewed and an attempt was made to correlate the histopathologic findings with clinical presentation, response to steroids, and final outcome. Adequate follow-up averaging 3.6 years was obtained in 17 cases. Most cases in the series had a favorable outcome, and patients demonstrating the acute and subacute stages of Type II patterns responded to systemic steroids. Repeated and extensive surgical intervention appear to be harmful.
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