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Garg AD. The dynamic interface of genetics and immunity: toward future horizons in health & disease. Genes Immun 2023; 24:155-158. [PMID: 37464025 DOI: 10.1038/s41435-023-00213-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Abhishek D Garg
- Cell Stress & Immunity (CSI) Lab, Department for Cellular & Molecular Medicine (CMM), KU Leuven, Leuven, Belgium.
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Chambers EA, Tarvin RD, Santos JC, Ron SR, Betancourth-Cundar M, Hillis DM, Matz MV, Cannatella DC. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics. Ecol Evol 2023; 13:e9842. [PMID: 36911313 PMCID: PMC9994478 DOI: 10.1002/ece3.9842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 03/10/2023] Open
Abstract
Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Environmental Science, Policy, and Management and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Integrative Biology and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Juan C Santos
- Department of Biological Sciences St John's University New York New York USA
| | - Santiago R Ron
- Museo de Zoología, Escuela de Ciencias Biológicas Pontificia Universidad Católica del Ecuador Quito Ecuador
| | | | - David M Hillis
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
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3
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de Andrade STQ, Guidugli TI, Borrego A, Rodrigues BLC, Fernandes NCCDA, Guerra JM, de Sousa JG, Starobinas N, Jensen JR, Cabrera WHK, De Franco M, Ibañez OM, Massa S, Ribeiro OG. Slc11a1 gene polymorphism influences dextran sulfate sodium (DSS)-induced colitis in a murine model of acute inflammation. Genes Immun 2023; 24:71-80. [PMID: 36792680 PMCID: PMC10110460 DOI: 10.1038/s41435-023-00199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Ulcerative Colitis (UC) is an inflammatory disease characterized by colonic mucosal lesions associated with an increased risk of carcinogenesis. UC pathogenesis involves environmental and genetic factors. Genetic studies have indicated the association of gene variants coding for the divalent metal ion transporter SLC11A1 protein (formerly NRAMP1) with UC susceptibility in several animal species. Two mouse lines were genetically selected for high (AIRmax) or low (AIRmin) acute inflammatory responses (AIR). AIRmax is susceptible, and AIRmin is resistant to DSS-induced colitis and colon carcinogenesis. Furthermore, AIRmin mice present polymorphism of the Slc11a1 gene. Here we investigated the possible modulating effect of the Slc11a1 R and S variants in DSS-induced colitis by using AIRmin mice homozygous for Slc11a1 R (AIRminRR) or S (AIRminSS) alleles. We evaluated UC by the disease activity index (DAI), considering weight loss, diarrhea, blood in the anus or feces, cytokines, histopathology, and cell populations in the distal colon epithelium. AIRminSS mice have become susceptible to DSS effects, with higher DAI, IL6, G-CSF, and MCP-1 production and morphological and colon histopathological alterations than AIRminRR mice. The results point to a role of the Slc11a1 S allele in DSS colitis induction in the genetic background of AIRmin mice.
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Affiliation(s)
| | | | - Andrea Borrego
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | | | | | | | | | - Nancy Starobinas
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | | | | | | | | | - Solange Massa
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
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