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Tenório BG, Kollath DR, Gade L, Litvintseva AP, Chiller T, Jenness JS, Stajich JE, Matute DR, Hanzlicek AS, Barker BM, Teixeira MDM. Tracing histoplasmosis genomic epidemiology and species occurrence across the USA. Emerg Microbes Infect 2024; 13:2315960. [PMID: 38465644 DOI: 10.1080/22221751.2024.2315960] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/04/2024] [Indexed: 03/12/2024]
Abstract
ABSTRACTHistoplasmosis is an endemic mycosis in North America frequently reported along the Ohio and Mississippi River Valleys, although autochthonous cases occur in non-endemic areas. In the United States, the disease is provoked by two genetically distinct clades of Histoplasma capsulatum sensu lato, Histoplasma mississippiense (Nam1) and H. ohiense (Nam2). To bridge the molecular epidemiological gap, we genotyped 93 Histoplasma isolates (62 novel genomes) including clinical, environmental, and veterinarian samples from a broader geographical range by whole-genome sequencing, followed by evolutionary and species niche modelling analyses. We show that histoplasmosis is caused by two major lineages, H. ohiense and H. mississippiense; with sporadic cases caused by H. suramericanum in California and Texas. While H. ohiense is prevalent in eastern states, H. mississipiense was found to be prevalent in the central and western portions of the United States, but also geographically overlapping in some areas suggesting that these species might co-occur. Species Niche Modelling revealed that H. ohiense thrives in places with warmer and drier conditions, while H. mississippiense is endemic to areas with cooler temperatures and more precipitation. In addition, we predicted multiple areas of secondary contact zones where the two species co-occur, potentially facilitating gene exchange and hybridization. This study provides the most comprehensive understanding of the genomic epidemiology of histoplasmosis in the USA and lays a blueprint for the study of invasive fungal diseases.
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Affiliation(s)
| | - Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jeff S Jenness
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew S Hanzlicek
- MiraVista Diagnostics, Indianapolis, IN, USA
- Department of Veterinary Clinical Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília, Brazil
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Wang SS, Hall ML, Lee E, Kim SC, Ramesh N, Lee SH, Jang JY, Bold RJ, Ku JL, Hwang CI. Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer. iScience 2024; 27:109414. [PMID: 38532888 PMCID: PMC10963232 DOI: 10.1016/j.isci.2024.109414] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/03/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
In pancreatic ductal adenocarcinoma (PDAC), no recurrent metastasis-specific mutation has been found, suggesting that epigenetic mechanisms, such as DNA methylation, are the major contributors of late-stage disease progression. Here, we performed the first whole-genome bisulfite sequencing (WGBS) on mouse and human PDAC organoid models to identify stage-specific and molecular subtype-specific DNA methylation signatures. With this approach, we identified thousands of differentially methylated regions (DMRs) that can distinguish between the stages and molecular subtypes of PDAC. Stage-specific DMRs are associated with genes related to nervous system development and cell-cell adhesions, and are enriched in promoters and bivalent enhancers. Subtype-specific DMRs showed hypermethylation of GATA6 foregut endoderm transcriptional networks in the squamous subtype and hypermethylation of EMT transcriptional networks in the progenitor subtype. These results indicate that aberrant DNA methylation contributes to both PDAC progression and subtype differentiation, resulting in significant and reoccurring DNA methylation patterns with diagnostic and prognostic potential.
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Affiliation(s)
- Sarah S. Wang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
| | - Madison L. Hall
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
| | - EunJung Lee
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
| | - Soon-Chan Kim
- Department of Biomedical Sciences, Korean Cell Line Bank, Laboratory of Cell Biology and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Neha Ramesh
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
| | - Sang Hyub Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jin-Young Jang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Richard J. Bold
- Division of Surgical Oncology, Department of Surgery, University of California, Davis, Sacramento, CA, USA
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Ja-Lok Ku
- Department of Biomedical Sciences, Korean Cell Line Bank, Laboratory of Cell Biology and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Chang-Il Hwang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
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Tzankov A, Tatarczuch M. Time to Be Launched 1 auXiliary Risk strat1fier in marginal zone lymphoma transformation: TBL1XR1. Cancer 2024; 130:1204-1207. [PMID: 38353491 DOI: 10.1002/cncr.35246] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The genetic profile of lymphomas has an increasing role in diagnosis, prognostication, and therapeutic decision making. In this issue of Cancer, Li and colleagues provide insights into the genomic landscape of high‐grade transformation of marginal zone lymphoma compared with both indolent marginal zone lymphoma and de novo diffuse large B‐cell lymphoma.
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Affiliation(s)
- Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Maciej Tatarczuch
- Monash Hematology and Blood Cancer Therapeutics Laboratory, Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 DOI: 10.1073/pnas.2310859121] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ON M5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Hendrik N Poinar
- Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Megan B Brickley
- Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
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Fenton S, Jacobs A, Bean CW, Adams CE, Elmer KR. Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs. Mol Ecol 2024; 33:e17305. [PMID: 38421099 DOI: 10.1111/mec.17305] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.
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Affiliation(s)
- Sam Fenton
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- NatureScot, Clydebank, UK
| | - Colin E Adams
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
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Falcone GJ, Woo D. Challenging Antiplatelet Therapy for Small Vessel Stroke Through Genetics. Stroke 2024; 55:943-945. [PMID: 38527142 DOI: 10.1161/strokeaha.124.046111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Affiliation(s)
- Guido J Falcone
- Department of Neurology (G.J.F.), Yale School of Medicine, New Haven, CT
- Center for Brain and Mind Health (G.J.F.), Yale School of Medicine, New Haven, CT
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, OH (D.W.)
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Wang X, Jiang Y, Sun Y. Revealing genomic heterogeneity and commonality: A penalized integrative analysis approach accounting for the adjacency structure of measurements. Genet Epidemiol 2024; 48:114-140. [PMID: 38317326 DOI: 10.1002/gepi.22549] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Advancements in high-throughput genomic technologies have revolutionized the field of disease biomarker identification by providing large-scale genomic data. There is an increasing focus on understanding the relationships among diverse patient groups with distinct disease subtypes and characteristics. Complex diseases exhibit both heterogeneity and shared genomic factors, making it essential to investigate these patterns to accurately detect markers and comprehensively understand the diseases. Integrative analysis has emerged as a promising approach to address this challenge. However, existing studies have been limited by ignoring the adjacency structure of genomic measurements, such as single nucleotide polymorphisms (SNPs) and DNA methylations. In this study, we propose a structured integrative analysis method that incorporates a spline type penalty to accommodate this adjacency structure. We utilize a fused lasso type penalty to identify both heterogeneity and commonality across the groups. Extensive simulations demonstrate its superiority compared to several direct competing methods. The analysis of The Cancer Genome Atlas melanoma data with DNA methylation measurements and GENEVA diabetes data with SNP measurements exhibit that the proposed analysis lead to meaningful findings with better prediction performance and higher selection stability.
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Affiliation(s)
- Xindi Wang
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Yu Jiang
- School of Public Health, The University of Memphis, Memphis, Tennessee, USA
| | - Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
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Velazquez-Miranda E, He M. More than just a simple barrier. eLife 2024; 13:e97247. [PMID: 38533842 DOI: 10.7554/elife.97247] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Endothelial cell subpopulations are characterized by unique gene expression profiles, epigenetic landscapes and functional properties.
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Affiliation(s)
- Erandi Velazquez-Miranda
- Department of Pathology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, United States
| | - Ming He
- Division of Molecular and Cellular Pathology, Department of Pathology, The University of Alabama, Birmingham, United States
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Sachdeva H, Shahin R, Ota S, Isabel S, Mangat CS, Stuart R, Padhi S, Chris A, Mishra S, Tan DHS, Braukmann TW, Eshaghi A, Mejia EM, Hizon NA, Finkelstein M. Preparing for Mpox Resurgence: Surveillance Lessons From Outbreaks in Toronto, Canada. J Infect Dis 2024; 229:S305-S312. [PMID: 38035826 DOI: 10.1093/infdis/jiad533] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND With many global jurisdictions, Toronto, Canada, experienced an mpox outbreak in spring/summer 2022. Cases declined following implementation of a large vaccination campaign. A surge in early 2023 led to speculation that asymptomatic and/or undetected local transmission was occurring in the city. METHODS Mpox cases and positive laboratory results are reported to Toronto Public Health. Epidemic curves and descriptive risk factor summaries for the 2022 and 2023 outbreaks were generated. First- and second-dose vaccination was monitored. Mpox virus wastewater surveillance and whole genome sequencing were conducted to generate hypotheses about the source of the 2023 resurgence. RESULTS An overall 515 cases were reported in spring/summer 2022 and 17 in the 2022-2023 resurgence. Wastewater data correlated with the timing of cases. Whole genome sequencing showed that 2022-2023 cases were distinct from 2022 cases and closer to sequences from another country, suggesting a new importation as a source. At the start of the resurgence, approximately 16% of first-dose vaccine recipients had completed their second dose. CONCLUSIONS This investigation demonstrates the importance of ongoing surveillance and preparedness for mpox outbreaks. Undetected local transmission was not a likely source of the 2022-2023 resurgence. Ongoing preexposure vaccine promotion remains important to mitigate disease burden.
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Affiliation(s)
- Herveen Sachdeva
- Toronto Public Health
- Dalla Lana School of Public Health, University of Toronto
| | - Rita Shahin
- Toronto Public Health
- Dalla Lana School of Public Health, University of Toronto
| | | | - Sandra Isabel
- Public Health Ontario, Toronto
- Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval
| | - Chand S Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | | | - Shovita Padhi
- Toronto Public Health
- Dalla Lana School of Public Health, University of Toronto
| | - Allison Chris
- Toronto Public Health
- Dalla Lana School of Public Health, University of Toronto
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto
- Department of Medicine, Temerty Faculty of Medicine
- Institute of Health Policy, Management and Evaluation and Institute of Medical Science, University of Toronto
- Institute for Clinical Evaluative Sciences (ICES)
- Division of Infectious Diseases, St Michael's Hospital, Toronto, Ontario, Canada
| | - Darrell H S Tan
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto
- Department of Medicine, Temerty Faculty of Medicine
- Institute of Health Policy, Management and Evaluation and Institute of Medical Science, University of Toronto
- Division of Infectious Diseases, St Michael's Hospital, Toronto, Ontario, Canada
| | | | | | - Edgard M Mejia
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | - Nikho A Hizon
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | - Michael Finkelstein
- Toronto Public Health
- Dalla Lana School of Public Health, University of Toronto
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Ryngajłło M, Cielecka I, Daroch M. Complete genome sequence and transcriptome response to vitamin C supplementation of Novacetimonas hansenii SI1 - producer of highly-stretchable cellulose. N Biotechnol 2024:S1871-6784(24)00011-6. [PMID: 38531507 DOI: 10.1016/j.nbt.2024.03.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/28/2024] [Accepted: 03/23/2024] [Indexed: 03/28/2024]
Abstract
Novacetimonas hansenii SI1, previously known as Komagataeibacter hansenii, produces bacterial nanocellulose (BNC) with unique ability to stretch. The addition of vitamin C in the culture medium increases the porosity of the membranes and their stretchability making them highly moldable. To better understand the genetic background of this strain, we obtained its complete genome sequence using a hybrid sequencing and assembly strategy. We described the functional regions in the genome which are important for the synthesis of BNC and acetan-like II polymer. We next investigated the effect of 1% vitamin C supplementation on the global gene expression profile using RNA sequencing. Our transcriptomic readouts imply that vitamin C functions mainly as a reducing agent. We found that the changes in cellular redox status are balanced by strong repression of the sulfur assimilation pathway. Moreover, in the reduced conditions, glucose oxidation is decreased and alternative pathways for energy generation, such as acetate accumulation, are activated. The presence of vitamin C negatively influences acetan-like II polymer biosynthesis, which may explain the lowered yield and changed mechanical properties of BNC. The results of this study enrich the functional characteristics of the genomes of the efficient producers of the N. hansenii species. Improved understanding of the adaptation to the presence of vitamin C at the molecular level has important guiding significance for influencing the biosynthesis of BNC and its morphology.
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Affiliation(s)
- Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, B. Stefanowskiego 2/22, 90-537 Lodz, Poland.
| | - Izabela Cielecka
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, B. Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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11
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lang You
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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Shorthouse D, Lister H, Freeman GS, Hall BA. Understanding large scale sequencing datasets through changes to protein folding. Brief Funct Genomics 2024:elae007. [PMID: 38521964 DOI: 10.1093/bfgp/elae007] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/25/2024] Open
Abstract
The expansion of high-quality, low-cost sequencing has created an enormous opportunity to understand how genetic variants alter cellular behaviour in disease. The high diversity of mutations observed has however drawn a spotlight onto the need for predictive modelling of mutational effects on phenotype from variants of uncertain significance. This is particularly important in the clinic due to the potential value in guiding clinical diagnosis and patient treatment. Recent computational modelling has highlighted the importance of mutation induced protein misfolding as a common mechanism for loss of protein or domain function, aided by developments in methods that make large computational screens tractable. Here we review recent applications of this approach to different genes, and how they have enabled and supported subsequent studies. We further discuss developments in the approach and the role for the approach in light of increasingly high throughput experimental approaches.
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Affiliation(s)
- David Shorthouse
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Harris Lister
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Gemma S Freeman
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
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Tabor JK, Dincer A, O'Brien J, Lei H, Vetsa S, Vasandani S, Jalal MI, Yalcin K, Morales-Valero SF, Marianayagam N, Alanya H, Elsamadicy AA, Millares Chavez MA, Aguilera SM, Mishra-Gorur K, McGuone D, Fulbright RK, Jin L, Erson-Omay EZ, Günel M, Moliterno J. Variations in the genomic profiles and clinical behavior of meningioma by racial and ethnic group. J Neurosurg 2024:1-9. [PMID: 38518289 DOI: 10.3171/2024.1.jns231633] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/09/2024] [Indexed: 03/24/2024]
Abstract
OBJECTIVE The influence of socioeconomic factors on racial disparities among patients with sporadic meningiomas is well established, yet other potential causative factors warrant further exploration. The authors of this study aimed to determine whether there is significant variation in the genomic profile of meningiomas among patients of different races and ethnicities and its correlation with clinical outcomes. METHODS The demographic, genomic, and clinical data of patients aged 18 years and older who had undergone surgery for sporadic meningioma between September 2008 and November 2021 were analyzed. Statistical analyses were performed to detect differences across all racial/ethnic groups, as were direct comparisons between Black and non-Black groups plus Hispanic and non-Hispanic groups. RESULTS This study included 460 patients with intracranial meningioma. Hispanic patients were significantly younger at surgery (53.9 vs 60.2 years, p = 0.0006) and more likely to show symptoms. Black patients had a higher incidence of anterior skull base tumors (OR 3.2, 95% CI 1.7-6.3, p = 0.0008) and somatic hedgehog mutations (OR 5.3, 95% CI 1.6-16.6, p = 0.003). Hispanics were less likely to exhibit the aggressive genomic characteristic of chromosome 1p deletion (OR 0.28, 95% CI 0.07-1.2, p = 0.06) and displayed higher rates of TRAF7 somatic driver mutations (OR 2.96 95% CI 1.1-7.8, p = 0.036). Black patients had higher rates of recurrence (OR 2.6, 95% CI 1.3-5.2, p = 0.009) and shorter progression-free survival (PFS; HR 2.9, 95% CI 1.6-5.4, p = 0.002) despite extents of resection (EORs) similar to those of non-Black patients (p = 0.745). No significant differences in overall survival were observed among groups. CONCLUSIONS Despite similar EORs, Black patients had worse clinical outcomes following meningioma resection, characterized by a higher prevalence of somatic hedgehog mutations, increased recurrence rates, and shorter PFS. Meanwhile, Hispanic patients had less aggressive meningiomas, a predisposition for TRAF7 mutations, and no difference in PFS. These findings could inform the care and treatment strategies for meningiomas, and they establish the foundation for future studies focusing on the genomic origins of these observed differences.
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Affiliation(s)
- Joanna K Tabor
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Alper Dincer
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
- 3Department of Neurosurgery, Tufts Medical Center, Boston, Massachusetts
| | - Joseph O'Brien
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Haoyi Lei
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Shaurey Vetsa
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Sagar Vasandani
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Muhammad I Jalal
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Kanat Yalcin
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Saul F Morales-Valero
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Neelan Marianayagam
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Hasan Alanya
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | | | | | - Stephanie M Aguilera
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Ketu Mishra-Gorur
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Declan McGuone
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
- 4Pathology
| | - Robert K Fulbright
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
- 6Radiology and Biomedical Imaging, Neuroradiology Section, Yale School of Medicine, New Haven, Connecticut
| | - Lan Jin
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - E Zeynep Erson-Omay
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
| | - Murat Günel
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
- 5Genetics, and
| | - Jennifer Moliterno
- Departments of1Neurosurgery
- 2The Chênevert Family Brain Tumor Center, Smilow Cancer Hospital, New Haven, Connecticut; and
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14
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Ohyama H, Hirotsu Y, Amemiya K, Amano H, Hirose S, Oyama T, Iimuro Y, Kojima Y, Mikata R, Mochizuki H, Kato N, Omata M. Liquid biopsy of wash samples obtained via endoscopic ultrasound-guided fine-needle biopsy: Comparison with liquid biopsy of plasma in pancreatic cancer. Diagn Cytopathol 2024. [PMID: 38516904 DOI: 10.1002/dc.25306] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
OBJECTIVES Pancreatic cancer (PC) has a poor prognosis and limited treatment options. Liquid biopsy, which analyzes circulating tumor DNA (ctDNA) in blood, holds promise for precision medicine; however, low ctDNA detection rates pose challenges. This study aimed to investigate the utility of wash samples obtained via endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) as a liquid biopsy for PC. METHODS A total of 166 samples (42 formalin-fixed paraffin-embedded [FFPE] tissues, 80 wash samples, and 44 plasma samples) were collected from 48 patients with PC for genomic analysis. DNA was extracted and quantified, and 60 significantly mutated genes were sequenced. The genomic profiles of FFPE tissues, wash samples, and plasma samples were compared. Finally, the ability to detect druggable mutations in 80 wash samples and 44 plasma samples was investigated. RESULTS The amount of DNA was significantly lower in plasma samples than in wash samples. Genomic analysis revealed a higher detection rate of oncogenic mutations in FFPE tissues (98%) and wash samples (96%) than in plasma samples (18%) and a comparable detection rate in FFPE tissues and wash samples. Tumor-derived oncogenic mutations were detected more frequently in wash samples than in plasma samples. Furthermore, the oncogenic mutations detection rate remained high in wash samples at all PC stages but low in plasma samples even at advanced PC stages. Using wash samples was more sensitive than plasma samples for identifying oncogenic and druggable mutations. CONCLUSIONS The wash sample obtained via EUS-FNB is an ideal specimen for use as a liquid biopsy for PC.
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Affiliation(s)
- Hiroshi Ohyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hiroyuki Amano
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Sumio Hirose
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuji Iimuro
- Department of Surgery, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuichiro Kojima
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Rintaro Mikata
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
- University of Tokyo, Tokyo, Japan
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15
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Chiu P, Limoges J, Pike A, Calzone K, Tonkin E, Puddester R, Gretchev A, Dewell S, Newton L, Leslie K. Integrating genomics into Canadian oncology nursing policy: Insights from a comparative policy analysis. J Adv Nurs 2024. [PMID: 38509799 DOI: 10.1111/jan.16099] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
AIM To learn from two jurisdictions with mature genomics-informed nursing policy infrastructure-the United States (US) and the United Kingdom (UK)-to inform policy development for genomics-informed oncology nursing practice and education in Canada. DESIGN Comparative document and policy analysis drawing on the 3i + E framework. METHODS We drew on the principles of a rapid review and identified academic literature, grey literature and nursing policy documents through a systematic search of two databases, a website search of national genomics nursing and oncology nursing organizations in the US and UK, and recommendations from subject matter experts on an international advisory committee. A total of 94 documents informed our analysis. RESULTS We found several types of policy documents guiding genomics-informed nursing practice and education in the US and UK. These included position statements, policy advocacy briefs, competencies, scope and standards of practice and education and curriculum frameworks. Examples of drivers that influenced policy development included nurses' values in aligning with evidence and meeting public expectations, strong nurse leaders, policy networks and shifting healthcare and policy landscapes. CONCLUSION Our analysis of nursing policy infrastructure in the US and UK provides a framework to guide policy recommendations to accelerate the integration of genomics into Canadian oncology nursing practice and education. IMPLICATIONS FOR THE PROFESSION Findings can assist Canadian oncology nurses in developing nursing policy infrastructure that supports full participation in safe and equitable genomics-informed oncology nursing practice and education within an interprofessional context. IMPACT This study informs Canadian policy development for genomics-informed oncology nursing education and practice. The experiences of other countries demonstrate that change is incremental, and investment from strong advocates and collaborators can accelerate the integration of genomics into nursing. Though this research focuses on oncology nursing, it may also inform other nursing practice contexts influenced by genomics.
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Affiliation(s)
- Patrick Chiu
- Faculty of Nursing, University of Alberta, Edmonton, Alberta, Canada
| | - Jacqueline Limoges
- Faculty of Health Disciplines, Athabasca University, Athabasca, Alberta, Canada
| | - April Pike
- Faculty of Nursing, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Kathleen Calzone
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Emma Tonkin
- Faculty of Life Sciences and Education, University of South Wales, Wales, UK
| | - Rebecca Puddester
- Faculty of Nursing, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Andrea Gretchev
- Faculty of Health Disciplines, Athabasca University, Athabasca, Alberta, Canada
| | - Sarah Dewell
- School of Nursing, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Lorelei Newton
- School of Nursing, University of Victoria, Victoria, British Columbia, Canada
| | - Kathleen Leslie
- Faculty of Health Disciplines, Athabasca University, Athabasca, Alberta, Canada
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16
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Redman MG, Horton RH, Carley H, Lucassen A. Ancestry, race and ethnicity: the role and relevance of language in clinical genetics practice. J Med Genet 2024; 61:313-318. [PMID: 38050060 DOI: 10.1136/jmg-2023-109370] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/28/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND The terms ancestry, race and ethnicity are used variably within the medical literature and within society and clinical care. Biological lineage can provide an important context for the interpretation of genomic data, but the language used, and practices around when to ascertain this, vary. METHODS Using a fictional case scenario we explore the relevance of questions around ancestry, race and ethnicity in clinical genetic practice. RESULTS In the UK, data on 'ethnicity' are routinely collected by those using genomic medicine, as well as within the wider UK National Health Service, although the reasons for this are not always clear to practitioners and patients. Sometimes it is requested as a proxy for biological lineage to aid variant interpretation, refine estimations of carrier frequency and guide decisions around the need for pharmacogenetic testing. CONCLUSION There are many challenges around the use and utility of these terms. Currently, genomic databases are populated primarily with data from people of European descent, and this can lead to health disparities and poorer service for minoritised or underserved populations. Sensitivity and consideration are needed when communicating with patients around these areas. We explore the role and relevance of language around biological lineage in clinical genetics practice.
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Affiliation(s)
- Melody Grace Redman
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel Helen Horton
- Centre for Personalised Medicine, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, UK
| | - Helena Carley
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Anneke Lucassen
- Centre for Personalised Medicine, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, UK
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17
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Perrin A, Métay C, Savarese M, Ben Yaou R, Demidov G, Nelson I, Solé G, Péréon Y, Bertini ES, Fattori F, D'Amico A, Ricci F, Ginsberg M, Seferian A, Boespflug-Tanguy O, Servais L, Chapon F, Lagrange E, Gaudon K, Bloch A, Ghanem R, Guyant-Maréchal L, Johari M, Van Goethem C, Fardeau M, Morales RJ, Genetti CA, Marttila M, Koenig M, Beggs AH, Udd B, Bonne G, Cossée M. Titin copy number variations associated with dominant inherited phenotypes. J Med Genet 2024; 61:369-377. [PMID: 37935568 PMCID: PMC10957311 DOI: 10.1136/jmg-2023-109473] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Titinopathies are caused by mutations in the titin gene (TTN). Titin is the largest known human protein; its gene has the longest coding phase with 364 exons. Titinopathies are very complex neuromuscular pathologies due to the variable age of onset of symptoms, the great diversity of pathological and muscular impairment patterns (cardiac, skeletal muscle or mixed) and both autosomal dominant and recessive modes of transmission. Until now, only few CNVs in TTN have been reported without clear genotype-phenotype associations. METHODS Our study includes eight families with dominant titinopathies. We performed next-generation sequencing or comparative genomic hybridisation array analyses and found CNVs in the TTN gene. We characterised these CNVs by RNA sequencing (RNAseq) analyses in six patients' muscles and performed genotype-phenotype inheritance association study by combining the clinical and biological data of these eight families. RESULTS Seven deletion-type CNVs in the TTN gene were identified among these families. Genotype and RNAseq results showed that five deletions do not alter the reading frame and one is out-of-reading frame. The main phenotype identified was distal myopathy associated with contractures. The analysis of morphological, clinical and genetic data and imaging let us draw new genotype-phenotype associations of titinopathies. CONCLUSION Identifying TTN CNVs will further increase diagnostic sensitivity in these complex neuromuscular pathologies. Our cohort of patients enabled us to identify new deletion-type CNVs in the TTN gene, with unexpected autosomal dominant transmission. This is valuable in establishing new genotype-phenotype associations of titinopathies, mainly distal myopathy in most of the patients.
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Affiliation(s)
- Aurélien Perrin
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Corinne Métay
- Unité Fonctionnelle de Cardiogénétique et Myogénétique moléculaire et cellulaire, Centre de Génétique Moléculaire et Chromosomique, Groupe Hospitalier La Pitié-Salpêtrière-Charles Foix, Paris, France
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Marco Savarese
- Tampere Neuromuscular Center, Folkhälsan Research Center, Helsinki, Finland
| | - Rabah Ben Yaou
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tubingen, Germany
| | - Isabelle Nelson
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Guilhem Solé
- CHU de Bordeaux, AOC National Reference Center for Neuromuscular Disorders, Bordeaux, France
| | - Yann Péréon
- Department of Clinical Neurophysiology, Reference Centre for Neuromuscular Diseases AOC, Filnemus, Euro-NMD, CHU Nantes, Nantes Université, Place Alexis-Ricordeau, Nantes, France
| | - Enrico Silvio Bertini
- Unit of Muscular and Neurodegenerative Disorders, Bambino Gesù Children Research Hospital, IRCCS, Rome, Italy
| | - Fabiana Fattori
- Unit of Muscular and Neurodegenerative Disorders, Bambino Gesù Children Research Hospital, IRCCS, Rome, Italy
| | - Adele D'Amico
- Unit of Muscular and Neurodegenerative Disorders, Bambino Gesù Children Research Hospital, IRCCS, Rome, Italy
| | - Federica Ricci
- Division of Child and Adolescent Neuropsychiatry, University of Turin, Turin, Italy
| | - Mira Ginsberg
- Department of Pediatric Neurology, Wolfson Medical Center, Holon, Israel
| | | | - Odile Boespflug-Tanguy
- Institut I-MOTION, Hôpital Armand Trousseau, Paris, France
- UMR 1141, INSERM, NeuroDiderot Université Paris Cité and APHP, Neuropédiatrie, French Reference Center for Leukodystrophies, LEUKOFRANCE, Hôpital Robert Debré, Paris, France
| | - Laurent Servais
- Institut I-MOTION, Hôpital Armand Trousseau, Paris, France
- MDUK Oxford Neuromuscular Centre & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Neuromuscular Reference Center, Division of Paediatrics, University and Hospital University of Liège, Liège, Belgium
| | - Françoise Chapon
- Département de pathologie, Centre de Compétence des Maladies Neuromusculaires, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Emmeline Lagrange
- Centre de Compétences des Maladies Neuro Musculaires, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Karen Gaudon
- Unité Fonctionnelle de Cardiogénétique et Myogénétique moléculaire et cellulaire, Centre de Génétique Moléculaire et Chromosomique, Groupe Hospitalier La Pitié-Salpêtrière-Charles Foix, Paris, France
| | - Adrien Bloch
- Unité Fonctionnelle de Cardiogénétique et Myogénétique moléculaire et cellulaire, Centre de Génétique Moléculaire et Chromosomique, Groupe Hospitalier La Pitié-Salpêtrière-Charles Foix, Paris, France
| | - Robin Ghanem
- Unité Fonctionnelle de Cardiogénétique et Myogénétique moléculaire et cellulaire, Centre de Génétique Moléculaire et Chromosomique, Groupe Hospitalier La Pitié-Salpêtrière-Charles Foix, Paris, France
| | | | - Mridul Johari
- Tampere Neuromuscular Center, Folkhälsan Research Center, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- Montpellier BioInformatique pour le Diagnostic Clinique (MOBIDIC), Plateau de Médecine Moléculaire et Génomique (PMMG), CHU Montpellier, Montpellier, France
| | - Michel Fardeau
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Raul Juntas Morales
- Department of Neurology, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Minttu Marttila
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- HiLIFE Helsinki Institute of Life Science, Tukholmankatu 8, FI-00014, University of Helsinki, Helsinki, Finland
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bjarne Udd
- Tampere Neuromuscular Center, Folkhälsan Research Center, Helsinki, Finland
| | - Gisèle Bonne
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France
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18
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Debette S, Paré G. Stroke Genetics, Genomics, and Precision Medicine. Stroke 2024. [PMID: 38511336 DOI: 10.1161/strokeaha.123.044212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Affiliation(s)
- Stéphanie Debette
- University of Bordeaux, INSERM, Bordeaux Population Health, France (S.D.)
- Department of Neurology, Institute for Neurodegenerative Diseases, Bordeaux University Hospital, France (S.D.)
| | - Guillaume Paré
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada (G.P.)
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19
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Belman S, Pesonen H, Croucher NJ, Bentley SD, Corander J. Estimating Between Country Migration in Pneumococcal Populations. G3 (Bethesda) 2024:jkae058. [PMID: 38507601 DOI: 10.1093/g3journal/jkae058] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing (GPS) project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (Fst) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic data were additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK, CB10 1SA
| | - Henri Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway, 0372
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London, UK, W12 0BZ
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK, CB10 1SA
| | - Jukka Corander
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK, CB10 1SA
- Department of Biostatistics, University of Oslo, Oslo, Norway, 0371
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, 02150
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20
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Audoor S, Bilcke G, Pargana K, Belišová D, Thierens S, Van Bel M, Sterck L, Rijsdijk N, Annunziata R, Ferrante MI, Vandepoele K, Vyverman W. Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction. Mol Ecol 2024:e17320. [PMID: 38506152 DOI: 10.1111/mec.17320] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/23/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.
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Affiliation(s)
- Sien Audoor
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Gust Bilcke
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Katerina Pargana
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Darja Belišová
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sander Thierens
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nadine Rijsdijk
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Associate to the National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for AI & Computational Biology, VIB, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
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21
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Mounsey O, Marchetti L, Parada J, Alarcón LV, Aliverti F, Avison MB, Ayala CS, Ballesteros C, Best CM, Bettridge J, Buchamer A, Buldain D, Carranza A, Corti Isgro M, Demeritt D, Escobar MP, Gortari Castillo L, Jaureguiberry M, Lucas MF, Madoz LV, Marconi MJ, Moiso N, Nievas HD, Ramirez Montes De Oca MA, Reding C, Reyher KK, Vass L, Williams S, Giraudo J, De La Sota RL, Mestorino N, Moredo FA, Pellegrino M. Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms. Appl Environ Microbiol 2024; 90:e0179123. [PMID: 38334306 PMCID: PMC10952494 DOI: 10.1128/aem.01791-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the β-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region. IMPORTANCE Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.
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Affiliation(s)
- Oliver Mounsey
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Laura Marchetti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Julián Parada
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura V. Alarcón
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Florencia Aliverti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matthew B. Avison
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Carlos S. Ayala
- University of Bristol Veterinary School, Langford, United Kingdom
| | | | - Caroline M. Best
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Judy Bettridge
- University of Bristol Veterinary School, Langford, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham, United Kingdom
| | - Andrea Buchamer
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Daniel Buldain
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alicia Carranza
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Maite Corti Isgro
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - David Demeritt
- Department of Geography, King’s College London, London, United Kingdom
| | | | - Lihuel Gortari Castillo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Jaureguiberry
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mariana F. Lucas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Universidad del Salvador, Facultad de Ciencias Agrarias y Veterinarias, Pilar, Argentina
| | - L. Vanina Madoz
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María José Marconi
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolás Moiso
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Hernán D. Nievas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | | | - Carlos Reding
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | | | - Lucy Vass
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Sara Williams
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - José Giraudo
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - R. Luzbel De La Sota
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nora Mestorino
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Fabiana A. Moredo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matías Pellegrino
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Cuarto, Facultad de Ciencias Exactas, Físico Químicas y Naturales, Río Cuarto, Argentina
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22
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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23
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Gallinson DG, Kozakiewicz CP, Rautsaw RM, Beer MA, Ruiz-Aravena M, Comte S, Hamilton DG, Kerlin DH, McCallum HI, Hamede R, Jones ME, Storfer A, McMinds R, Margres MJ. Intergenomic signatures of coevolution between Tasmanian devils and an infectious cancer. Proc Natl Acad Sci U S A 2024; 121:e2307780121. [PMID: 38466855 PMCID: PMC10962979 DOI: 10.1073/pnas.2307780121] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
Coevolution is common and frequently governs host-pathogen interaction outcomes. Phenotypes underlying these interactions often manifest as the combined products of the genomes of interacting species, yet traditional quantitative trait mapping approaches ignore these intergenomic interactions. Devil facial tumor disease (DFTD), an infectious cancer afflicting Tasmanian devils (Sarcophilus harrisii), has decimated devil populations due to universal host susceptibility and a fatality rate approaching 100%. Here, we used a recently developed joint genome-wide association study (i.e., co-GWAS) approach, 15 y of mark-recapture data, and 960 genomes to identify intergenomic signatures of coevolution between devils and DFTD. Using a traditional GWA approach, we found that both devil and DFTD genomes explained a substantial proportion of variance in how quickly susceptible devils became infected, although genomic architectures differed across devils and DFTD; the devil genome had fewer loci of large effect whereas the DFTD genome had a more polygenic architecture. Using a co-GWA approach, devil-DFTD intergenomic interactions explained ~3× more variation in how quickly susceptible devils became infected than either genome alone, and the top genotype-by-genotype interactions were significantly enriched for cancer genes and signatures of selection. A devil regulatory mutation was associated with differential expression of a candidate cancer gene and showed putative allele matching effects with two DFTD coding sequence variants. Our results highlight the need to account for intergenomic interactions when investigating host-pathogen (co)evolution and emphasize the importance of such interactions when considering devil management strategies.
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Affiliation(s)
- Dylan G. Gallinson
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Christopher P. Kozakiewicz
- School of Biological Sciences, Washington State University, Pullman, WA99163
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI49060
| | - Rhett M. Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Marc A. Beer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY14853
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- New South Wales Department of Primary Industries, Vertebrate Pest Research Unit, Orange, NSW2800, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Douglas H. Kerlin
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Hamish I. McCallum
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- CANECEV Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier34394, France
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Ryan McMinds
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Mark J. Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
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24
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Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024; 5:101443. [PMID: 38428430 DOI: 10.1016/j.xcrm.2024.101443] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin, which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies, combined with machine-learning approaches, we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed, proliferative, and chromatin-modifying states, with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling, we find that each state was associated with a combination of mutations in chromatin modifiers, copy-number alterations to TNFAIP3, and T follicular helper cells (Tfh) cell interactions, or primarily by a microenvironment rich in activated T cells. Altogether, these data define FL B cell transcriptional states across a large cohort of patients, contribute to our understanding of FL heterogeneity at the tumor cell level, and provide a foundation for guiding therapeutic intervention.
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Matthew J Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - ZhiZhang Yang
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Brian K Link
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Rebecca L King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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25
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Dufault-Thompson K, Jiang X. Annotating microbial functions with ProkFunFind. mSystems 2024; 9:e0003624. [PMID: 38364094 PMCID: PMC10949468 DOI: 10.1128/msystems.00036-24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
Analyzing microbial genomes has become an essential part of microbiology research, giving valuable insights into the functions and evolution of microbial species. Identifying genes of interest and assigning putative annotations to those genes is a central task in genome analysis, and a plethora of tools and approaches have been developed for this task. The ProkFunFind tool was developed to bridge the gap between these various annotation approaches, providing a flexible and customizable search approach to annotate microbial functions. ProkFunFind is designed around hierarchical definitions of biological functions, where individual genes can be identified using heterogeneous search terms consisting of sequences, profile hidden Markov models, protein domains, and orthology groups. This flexible and customizable search approach allows for searches to be tailored to specific biological functions, and the search results are output in multiple formats to facilitate downstream analyses. The utility of the ProkFunFind search tool was demonstrated through its application in searching for bacterial flagella, which are complex organelles composed of multiple genes. Overall, ProkFunFind provides an accessible and flexible way to integrate multiple types of annotation and sequence data while annotating biological functions in microbial genomes.IMPORTANCEGenome sequencing and analysis are increasingly important parts of microbiology, providing a way to predict metabolic functions, identify virulence factors, and understand the evolution of microbes. The expanded use of genome sequencing has also brought an abundance of search and annotation methods, but integrating the information from these different methods can be challenging and is often done through ad hoc approaches. To bridge the gap between different types of annotations, we developed ProkFunFind, a flexible and customizable search tool incorporating multiple search approaches and annotation types to annotate microbial functions. We demonstrated the utility of ProkFunFind by searching for gene clusters encoding flagellar genes using a combination of different annotation types and searches. Overall, ProkFunFind provides a reproducible and flexible way to identify gene clusters of interest, facilitating the meaningful analysis of new and existing microbial genomes.
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Affiliation(s)
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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26
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Oury N, Magalon H. Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics. Sci Rep 2024; 14:6437. [PMID: 38499737 PMCID: PMC10948807 DOI: 10.1038/s41598-024-57136-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France.
- Laboratoire Cogitamus, Paris, France.
- KAUST Red Sea Research Center and Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France
- Laboratoire Cogitamus, Paris, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
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27
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Mota LFM, Arikawa LM, Santos SWB, Fernandes Júnior GA, Alves AAC, Rosa GJM, Mercadante MEZ, Cyrillo JNSG, Carvalheiro R, Albuquerque LG. Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle. Sci Rep 2024; 14:6404. [PMID: 38493207 PMCID: PMC10944497 DOI: 10.1038/s41598-024-57234-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control. Prediction accuracy (Acc) was evaluated using a forward validation splitting the dataset based on birth year, considering the phenotypes adjusted for the fixed effects and covariates as pseudo-phenotypes. The MLNN and SVR approaches were trained by randomly splitting the training population into fivefold to select the best hyperparameters. The results show that the machine learning methods (MLNN and SVR) and MTGBLUP outperformed STGBLUP and the Bayesian regression approaches, increasing the Acc by approximately 8.9%, 14.6%, and 13.7% using MLNN, SVR, and MTGBLUP, respectively. Acc for SVR and MTGBLUP were slightly different, ranging from 0.62 to 0.69 and 0.62 to 0.68, respectively, with empirically unbiased for both models (0.97 and 1.09). Our results indicated that SVR and MTGBLUBP approaches were more accurate in predicting FE-related traits than Bayesian regression and STGBLUP and seemed competitive for GS of complex phenotypes with various degrees of inheritance.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Leonardo M Arikawa
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Anderson A C Alves
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil.
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Seeber PA, Batke L, Dvornikov Y, Schmidt A, Wang Y, Stoof-Leichsenring K, Moon K, Vohr SH, Shapiro B, Epp LS. Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes. eLife 2024; 12:RP89992. [PMID: 38488477 PMCID: PMC10942779 DOI: 10.7554/elife.89992] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.
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Affiliation(s)
| | - Laura Batke
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yury Dvornikov
- Agroengineering Department/Department of Landscape Design and Sustainable Ecosystems, Agrarian and Technological Institute, RUDN University, Moscow, Russian Federation
- Laboratory of Carbon Monitoring in Terrestrial Ecosystems, Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences, Pushchino, Russian Federation
| | | | - Yi Wang
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Katie Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | - Laura S Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
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29
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Dickman E, Schmitt ML, Marty K, Mahon SM. Oncology Nursing Society's Genomics and Precision Oncology Learning Library Resources for Nursing Practice. Clin J Oncol Nurs 2024; 28:133-141. [PMID: 38511921 DOI: 10.1188/24.cjon.133-141] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Oncology nurses need an understanding of genomic science to provide optimal care, yet they may have limited background in how this science guides treatment. The Oncology Nursing Society (ONS) responded to this identified need.
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30
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Baev V, Iliev I, Stefanov Y, Tsankova M, Marhova M, Apostolova E, Gozmanova M, Yahubyan G, Kostadinova S. Exploring the Genomic Landscape of Bacillus paranthracis PUMB_17 as a Proficient Phosphatidylcholine-Specific Phospholipase C Producer. Curr Issues Mol Biol 2024; 46:2497-2513. [PMID: 38534774 DOI: 10.3390/cimb46030158] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Phospholipases find versatile applications across industries, including detergent production, food modification, pharmaceuticals (especially in drug delivery systems), and cell signaling research. In this study, we present a strain of Bacillus paranthracis for the first time, demonstrating significant potential in the production of phosphatidylcholine-specific phospholipase C (PC-PLC). The investigation thoroughly examines the B. paranthracis PUMB_17 strain, focusing on the activity of PC-PLC and its purification process. Notably, the PUMB_17 strain displays extracellular PC-PLC production with high specific activity during the late exponential growth phase. To unravel the genetic makeup of PUMB_17, we employed nanopore-based whole-genome sequencing and subsequently conducted a detailed genome annotation. The genome comprises a solitary circular chromosome spanning 5,250,970 bp, featuring a guanine-cytosine ratio of 35.49. Additionally, two plasmids of sizes 64,250 bp and 5845 bp were identified. The annotation analysis reveals the presence of 5328 genes, encompassing 5186 protein-coding sequences, and 142 RNA genes, including 39 rRNAs, 103 tRNAs, and 5 ncRNAs. The aim of this study was to make a comprehensive genomic exploration that promises to enhance our understanding of the previously understudied and recently documented capabilities of Bacillus paranthracis and to shed light on a potential use of the strain in the industrial production of PC-PLC.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Ivan Iliev
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | | | - Marinela Tsankova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariana Marhova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
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31
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. Cell Genom 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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32
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She H, Hao Y, Song G, Luo X, Lei F, Zhai W, Qu Y. Gene expression plasticity followed by genetic change during colonization in a high-elevation environment. eLife 2024; 12:RP86687. [PMID: 38470231 DOI: 10.7554/elife.86687] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called 'plasticity first.' Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage), and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscles, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associated with decreased hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increased hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e. 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.
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Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xu Luo
- Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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33
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Sheriff EK, Andersen SE, Chatterjee A, Duerkop BA. Complete genome sequence of enterococcal phage G01. Microbiol Resour Announc 2024; 13:e0121723. [PMID: 38294211 DOI: 10.1128/mra.01217-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Here, we report the annotated genome of enterococcal phage G01. The G01 genome is 41,189 bp in length and contains 67 predicted open reading frames. Host range analysis revealed G01 can infect 28.6% (6/21) of Enterococcus faecalis strains tested and appears to not require the enterococcal phage infection protein PIPEF.
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Affiliation(s)
- Emma K Sheriff
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shelby E Andersen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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34
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Kridler MR, Viney IA, Custer JM, Schlottman B, Bartelme R, Carini P. Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona. Microbiol Resour Announc 2024; 13:e0108923. [PMID: 38376218 DOI: 10.1128/mra.01089-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Here, we present the genomes of two soil actinobacteria: Arthrobacter sp. strain AZCC_0090 and Mycobacterium sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.
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Affiliation(s)
- Melanie R Kridler
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Isabella A Viney
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Joy M Custer
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Bradley Schlottman
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Ryan Bartelme
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Paul Carini
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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35
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early-life adversity are exposure-dependent in wild baboons. Proc Natl Acad Sci U S A 2024; 121:e2309469121. [PMID: 38442181 PMCID: PMC10945818 DOI: 10.1073/pnas.2309469121] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
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Affiliation(s)
- Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Amanda J. Lea
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | | | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Mercy Y. Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi00502, Kenya
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig04103, Germany
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36
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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Allen CG, Bouchie G, Judge DP, Coen E, English S, Norman S, Kirchoff K, Ramos PS, Hirschhorn J, Lenert L, McMahon LL. Establishing an infrastructure to optimize the integration of genomics into research: Results from a precision health needs assessment. Transl Behav Med 2024:ibae008. [PMID: 38470971 DOI: 10.1093/tbm/ibae008] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Researchers across the translational research continuum have emphasized the importance of integrating genomics into their research program. To date capacity and resources for genomics research have been limited; however, a recent population-wide genomic screening initiative launched at the Medical University of South Carolina in partnership with Helix has rapidly advanced the need to develop appropriate infrastructure for genomics research at our institution. We conducted a survey with researchers from across our institution (n = 36) to assess current knowledge about genomics health, barriers, and facilitators to uptake, and next steps to support translational research using genomics. We also completed 30-minute qualitative interviews with providers and researchers from diverse specialties (n = 8). Quantitative data were analyzed using descriptive analyses. A rapid assessment process was used to develop a preliminary understanding of each interviewee's perspective. These interviews were transcribed and coded to extract themes. The codes included types of research, alignment with precision health, opportunities to incorporate precision health, examples of researchers in the field, barriers, and facilitators to uptake, educational activity suggestions, questions to be answered, and other observations. Themes from the surveys and interviews inform implementation strategies that are applicable not only to our institution, but also to other organizations interested in making genomic data available to researchers to support genomics-informed translational research.
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Affiliation(s)
| | | | | | - Emma Coen
- Medical University of South Carolina, Charleston, SC
| | - Sarah English
- Medical University of South Carolina, Charleston, SC
| | | | | | - Paula S Ramos
- Medical University of South Carolina, Charleston, SC
| | | | - Leslie Lenert
- Medical University of South Carolina, Charleston, SC
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. bioRxiv 2024:2023.09.13.557621. [PMID: 37745330 PMCID: PMC10515909 DOI: 10.1101/2023.09.13.557621] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA United States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY, United States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Angie M. Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Ann E. Hajek
- Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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Asbury K, Toseeb U, Barrow N. What do parents of nonverbal and minimally verbal autistic children think about genomic autism research? Autism 2024:13623613231213431. [PMID: 38459822 DOI: 10.1177/13623613231213431] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
LAY ABSTRACT In Summer 2021, a genomic study of autism, Spectrum 10 K, was paused due to backlash from the autistic and autism communities. This raised important questions about how these communities perceive genomic research. The Personal Experiences of Autism and Perceptions of DNA-based research study was established to address this issue among a range of sub-groups within these communities. Twenty parents of nonverbal or minimally verbal autistic children took part in the current study. Data were provided in diverse formats including online interviews, telephone interviews, and writing. This approach was co-produced with autistic experts by experience and involved a parent of a minimally verbal autistic child. Data were analysed using reflexive Thematic Analysis. We found that participants were supportive of autism research, including some genomic research, as long as it is designed to support autistic people and is ethical and transparent. However, while some believed that polygenic scores, genomic predictors of the statistical probability of being autistic, would be helpful, others argued that this would only be true in an ideal world and that the world is too far from ideal. Participants felt excluded from the autistic and autism communities and that the dominant voices in those communities do not represent them or their children. We concluded that genomic researchers need to work with the autistic and autism communities to design future work, and that it is important to ensure a representative range of voices are heard.
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40
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Song W, Wang JX, Cao LJ, Chen JC, Bao WX, Chen M, Wei SJ. A chromosome-level genome for the flower thrips Frankliniella intonsa. Sci Data 2024; 11:280. [PMID: 38459039 PMCID: PMC10923943 DOI: 10.1038/s41597-024-03113-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
The flower thrips Frankliniella intonsa (Thysanoptera: Thripidae) is a common insect found in flowers of many plants. Sometimes, F. intonsa causes damage to crops through direct feeding and transmission of plant viruses. Here, we assembled a chromosomal level genome of F. intonsa using the Illumina, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome had a size of 209.09 Mb, with a contig N50 of 997 bp, scaffold N50 of 13.415 Mb, and BUSCO completeness of 92.5%. The assembled contigs were anchored on 15 chromosomes. A set of 14,109 protein-coding genes were annotated in the genome with a BUSCO completeness of 95.0%. The genome contained 491 non-coding RNA and 0.57% of interspersed repeats. This high-quality genome provides a valuable resource for understanding the ecology, genetics, and evolution of F. intonsa, as well as for controlling thrips pests.
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Affiliation(s)
- Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jia-Xu Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, 100083, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wen-Xue Bao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, 100083, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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41
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Valentin Caban K, Kalesnik E, Green KA, Negro CJ, Nunez Rodriguez U, Peele MC, Nguyen CT, Cahill S, Dougherty K, Logue M, Hargraves S, Radziak H, Willette L, Ogunyinka E, Campbell DC, Adebamiro O, Schmeltzer C, Onimus J, Asaka HA, Bangura W, Shimp CM, Alade A, Sequira DM, Jimenez T, Swerdlow SJ, Harrison MK, Fallest-Strobl PC, Mastropaolo MD. Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker. Microbiol Resour Announc 2024:e0125123. [PMID: 38451225 DOI: 10.1128/mra.01251-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the host Microbacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK.
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Affiliation(s)
| | | | | | | | | | - Milan C Peele
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Sydney Cahill
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Melissa Logue
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | - Luke Willette
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | | | | | | | | | | | | | - Ameera Alade
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Tommy Jimenez
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | - Sarah J Swerdlow
- Biological Sciences, University of Pittsburgh Greensburg, Greensburg, Pennsylvania, USA
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42
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Wang S, Zhang W, Nie J. Editorial: Advances in genomics, genetics, and breeding of the cucurbit plant. Front Plant Sci 2024; 15:1378952. [PMID: 38516659 PMCID: PMC10956511 DOI: 10.3389/fpls.2024.1378952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Shenglin Wang
- College of Horticulture Science, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang, China
| | - Weiwei Zhang
- Department of Plant Science and Technology, Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Jingtao Nie
- College of Horticulture Science, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, Zhejiang, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang, China
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43
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Bursch KL, Goetz CJ, Jiao G, Nuñez R, Olp MD, Dhiman A, Khurana M, Zimmermann MT, Urrutia RA, Dykhuizen EC, Smith BC. Cancer-associated Polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. J Biol Chem 2024:107146. [PMID: 38460939 DOI: 10.1016/j.jbc.2024.107146] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
The Polybromo, BRG1-associated factors (PBAF) chromatin remodeling complex subunit Polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic post-translational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Mallika Khurana
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raul A Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Wilson CG, Pieszko T, Nowell RW, Barraclough TG. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet 2024:S0168-9525(24)00028-3. [PMID: 38458877 DOI: 10.1016/j.tig.2024.02.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.
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Affiliation(s)
- Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Tymoteusz Pieszko
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Reuben W Nowell
- Institute of Ecology and Evolution, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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45
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Gudi S, M P, Alagappan P, Raigar OP, Halladakeri P, Gowda RSR, Kumar P, Singh G, Tamta M, Susmitha P, Amandeep, Saini DK. Fashion meets science: how advanced breeding approaches could revolutionize the textile industry. Crit Rev Biotechnol 2024:1-27. [PMID: 38453184 DOI: 10.1080/07388551.2024.2314309] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Natural fibers have garnered considerable attention owing to their desirable textile properties and advantageous effects on human health. Nevertheless, natural fibers lag behind synthetic fibers in terms of both quality and yield, as these attributes are largely genetically determined. In this article, a comprehensive overview of the natural and synthetic fiber production landscape over the last 10 years is presented, with a particular focus on the role of scientific breeding techniques in improving fiber quality traits in key crops like cotton, hemp, ramie, and flax. Additionally, the article delves into cutting-edge genomics-assisted breeding techniques, including QTL mapping, genome-wide association studies, transgenesis, and genome editing, and their potential role in enhancing fiber quality traits in these crops. A user-friendly compendium of 11226 available QTLs and significant marker-trait associations derived from 136 studies, associated with diverse fiber quality traits in these crops is furnished. Furthermore, the potential applications of transcriptomics in these pivotal crops, elucidating the distinct genes implicated in augmenting fiber quality attributes are investigated. Additionally, information on 11257 candidate/characterized or cloned genes sourced from various studies, emphasizing their key role in the development of high-quality fiber crops is collated. Additionally, the review sheds light on the current progress of marker-assisted selection for fiber quality traits in each crop, providing detailed insights into improved cultivars released for different fiber crops. In conclusion, it is asserted that the application of modern breeding tools holds tremendous potential in catalyzing a transformative shift in the textile industry.
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Affiliation(s)
- Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Plant Pathology, ND State University, Fargo, ND, USA
| | - Pavan M
- Department of Apparel and Textile Science, Punjab Agricultural University, Ludhiana, India
| | - Praveenkumar Alagappan
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Om Prakash Raigar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, India
- VNR Seeds, Pvt. Ltd, Raipur, India
| | - Rakshith S R Gowda
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Centre for Crop and Food Innovation, Murdoch University, Perth, Australia
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Agronomy, Horticulture, and Plant Science, SD State University, Brookings, SD, USA
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- AgriLife Research Center at Beaumont, TX A&M University, College Station, TX, USA
| | - Meenakshi Tamta
- Department of Apparel and Textile Science, Punjab Agricultural University, Ludhiana, India
| | - Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Anakapalle, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Plant and Soil Science, TX Tech University, Lubbock, TX, USA
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46
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Bladen J, Cooper JC, Ridges JT, Guo P, Phadnis N. A new hybrid incompatibility locus between Drosophila melanogaster and Drosophila sechellia. Genetics 2024; 226:iyae001. [PMID: 38184848 PMCID: PMC10917521 DOI: 10.1093/genetics/iyae001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 11/11/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
Despite the fundamental importance of hybrid incompatibilities to the process of speciation, there are few cases where the evolution and genetic architecture of hybrid incompatibilities are understood. One of the longest studied hybrid incompatibilities causes F1 hybrid male inviability in crosses between Drosophila melanogaster females and males from the Drosophila simulans clade of species-Drosophila simulans, Drosophila mauritiana, and Drosophila sechellia. Here, we discover dramatic differences in the manifestation of this lethal hybrid incompatibility among the D. simulans clade of species. In particular, F1 hybrid males between D. melanogaster and D. sechellia are resistant to hybrid rescue through RNAi knockdown of an essential hybrid incompatibility gene. To understand the genetic basis of this inter-species difference in hybrid rescue, we developed a triple-hybrid mapping method. Our results show that 2 discrete large effect loci and many dispersed small effect changes across the genome underlie D. sechellia aversion to hybrid rescue. The large effect loci encompass a known incompatibility gene Lethal hybrid rescue (Lhr) and previously unknown factor, Sechellia aversion to hybrid rescue (Satyr). These results show that the genetic architecture of F1 hybrid male inviability is overlapping but not identical in the 3 inter-species crosses. Our results raise questions about whether new hybrid incompatibility genes can integrate into an existing hybrid incompatibility thus increasing in complexity over time, or if the continued evolution of genes can gradually strengthen an existing hybrid incompatibility.
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Affiliation(s)
- Jackson Bladen
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jacob C Cooper
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jackson T Ridges
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ping Guo
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nitin Phadnis
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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47
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Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylo genomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiol Spectr 2024:e0398023. [PMID: 38445873 DOI: 10.1128/spectrum.03980-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
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Affiliation(s)
- Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ningxiao Li
- Department of Plant Pathology, University of California, Davis, California, USA
- USDA-ARS, Salinas, California, USA
| | | | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - John G Gibbons
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, Pennsylvania, USA
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - David S Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, Heidelberg, Germany
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48
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Alakunle E, Kolawole D, Diaz-Cánova D, Alele F, Adegboye O, Moens U, Okeke MI. A comprehensive review of monkeypox virus and mpox characteristics. Front Cell Infect Microbiol 2024; 14:1360586. [PMID: 38510963 PMCID: PMC10952103 DOI: 10.3389/fcimb.2024.1360586] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Monkeypox virus (MPXV) is the etiological agent of monkeypox (mpox), a zoonotic disease. MPXV is endemic in the forested regions of West and Central Africa, but the virus has recently spread globally, causing outbreaks in multiple non-endemic countries. In this paper, we review the characteristics of the virus, including its ecology, genomics, infection biology, and evolution. We estimate by phylogenomic molecular clock that the B.1 lineage responsible for the 2022 mpox outbreaks has been in circulation since 2016. We interrogate the host-virus interactions that modulate the virus infection biology, signal transduction, pathogenesis, and host immune responses. We highlight the changing pathophysiology and epidemiology of MPXV and summarize recent advances in the prevention and treatment of mpox. In addition, this review identifies knowledge gaps with respect to the virus and the disease, suggests future research directions to address the knowledge gaps, and proposes a One Health approach as an effective strategy to prevent current and future epidemics of mpox.
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Affiliation(s)
- Emmanuel Alakunle
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
| | - Daniel Kolawole
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
| | - Diana Diaz-Cánova
- Department of Medical Biology, UIT – The Arctic University of Norway, Tromsø, Norway
| | - Faith Alele
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Oyelola Adegboye
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Ugo Moens
- Department of Medical Biology, UIT – The Arctic University of Norway, Tromsø, Norway
| | - Malachy Ifeanyi Okeke
- Department of Natural and Environmental Sciences, American University of Nigeria, Yola, Nigeria
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49
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Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ. Systematic profiling of ale yeast protein dynamics across fermentation and repitching. G3 (Bethesda) 2024; 14:jkad293. [PMID: 38135291 PMCID: PMC10917522 DOI: 10.1093/g3journal/jkad293] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is among the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout 2 fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.
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Affiliation(s)
- Riddhiman K Garge
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph O Armstrong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Barbara Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich 8049, Switzerland
| | - Vy Dang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyao Jiang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Haase MAB, Steenwyk JL, Boeke JD. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics 2024; 226:iyae008. [PMID: 38271560 PMCID: PMC10917516 DOI: 10.1093/genetics/iyae008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here, we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation-mediated by the trans-regulator Spt10-is ancient, likely emerging between 320 and 380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage, which coincided with the loss of 1 copy of its paralogous core histone genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora fast-evolving lineage.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
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