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Omufwoko KS, Cronin AL, Nguyen TTH, Webb AE, Traniello IM, Kocher SD. Developmental transcriptomes predict adult social behaviours in the socially flexible sweat bee, Lasioglossum baleicum. Mol Ecol 2023:e17244. [PMID: 38108560 DOI: 10.1111/mec.17244] [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: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Natural variation can provide important insights into the genetic and environmental factors that shape social behaviour and its evolution. The sweat bee, Lasioglossum baleicum, is a socially flexible bee capable of producing both solitary and eusocial nests. We demonstrate that within a single nesting aggregation, soil temperatures are a strong predictor of the social structure of nests. Sites with warmer temperatures in the spring have a higher frequency of social nests than cooler sites, perhaps because warmer temperatures provide a longer reproductive window for those nests. To identify the molecular correlates of this behavioural variation, we generated a de novo genome assembly for L. baleicum, and we used transcriptomic profiling to compare adults and developing offspring from eusocial and solitary nests. We find that adult, reproductive females have similar expression profiles regardless of social structure in the nest, but that there are strong differences between reproductive females and workers from social nests. We also find substantial differences in the transcriptomic profiles of stage-matched pupae from warmer, social-biased sites compared to cooler, solitary-biased sites. These transcriptional differences are strongly predictive of adult reproductive state, suggesting that the developmental environment may set the stage for adult behaviours in L. baleicum. Together, our results help to characterize the molecular mechanisms shaping variation in social behaviour and highlight a potential role of environmental tuning during development as a factor shaping adult behaviour and physiology in this socially flexible bee.
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Affiliation(s)
- Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Adam L Cronin
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Thi Thu Ha Nguyen
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey, USA
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey, USA
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Wolf SW, Ruttenberg DM, Knapp DY, Webb AE, Traniello IM, McKenzie-Smith GC, Leheny SA, Shaevitz JW, Kocher SD. NAPS: Integrating pose estimation and tag-based tracking. Methods Ecol Evol 2023; 14:2541-2548. [PMID: 38681746 PMCID: PMC11052584 DOI: 10.1111/2041-210x.14201] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/02/2023] [Indexed: 05/01/2024]
Abstract
1. Significant advances in computational ethology have allowed the quantification of behaviour in unprecedented detail. Tracking animals in social groups, however, remains challenging as most existing methods can either capture pose or robustly retain individual identity over time but not both. 2. To capture finely resolved behaviours while maintaining individual identity, we built NAPS (NAPS is ArUco Plus SLEAP), a hybrid tracking framework that combines state-of-the-art, deep learning-based methods for pose estimation (SLEAP) with unique markers for identity persistence (ArUco). We show that this framework allows the exploration of the social dynamics of the common eastern bumblebee (Bombus impatiens). 3. We provide a stand-alone Python package for implementing this framework along with detailed documentation to allow for easy utilization and expansion. We show that NAPS can scale to long timescale experiments at a high frame rate and that it enables the investigation of detailed behavioural variation within individuals in a group. 4. Expanding the toolkit for capturing the constituent behaviours of social groups is essential for understanding the structure and dynamics of social networks. NAPS provides a key tool for capturing these behaviours and can provide critical data for understanding how individual variation influences collective dynamics.
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Affiliation(s)
- Scott W. Wolf
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Dee M. Ruttenberg
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Daniel Y. Knapp
- Department of Physics, Princeton University, Princeton, New Jersey, USA
| | - Andrew E. Webb
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Ian M. Traniello
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | | | - Sophie A. Leheny
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Joshua W. Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Physics, Princeton University, Princeton, New Jersey, USA
| | - Sarah D. Kocher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
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3
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McNamara LM, Scott KM, Boyd RN, Farmer EA, Webb AE, Novak IE. Constructing validity evidence from a pilot key-features assessment of clinical decision-making in cerebral palsy diagnosis: application of Kane's validity framework to implementation evaluations. BMC Med Educ 2023; 23:668. [PMID: 37710200 PMCID: PMC10503270 DOI: 10.1186/s12909-023-04631-4] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/29/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Physician decision-making skills training is a priority to improve adoption of the cerebral palsy (CP) clinical guideline and, through this, lower the age of CP diagnosis. Clinical guideline implementation aims to improve physician practice, but evaluating meaningful change is complex. Limitations in the validity evidence of evaluation instruments impact the evidence base. Validity frameworks, such as Kane's, enable a targeted process to gather evidence for instrument scores, congruent to context and purpose. Yet, application of argument-based methodology to implementation validation is rare. Key-features examination methodology has established validity evidence supporting its use to measure decision-making skills, with potential to predict performance. We aimed to apply Kane's framework to evaluate a pilot key-features examination on physician decision-making in early CP diagnosis. METHODS Following Kane's framework, we evaluated evidence across inferences of scoring, generalisation, extrapolation and implications in a study design describing the development and pilot of a CP diagnosis key-features examination for practising physicians. If found to be valid, we proposed to use the key-feature scores as an outcome measure of decision-making post education intervention to expedite CP diagnosis and to correlate with real-world performance data to predict physician practice. RESULTS Supporting evidence for acceptance of scoring inferences was achieved through examination development with an expert group (n = 10) and pilot results (n = 10): (1) high internal consistency (0.82); (2) acceptable mean item-discrimination (0.34); and (3) acceptable reliability of examination scorers (95.2% congruence). Decreased physician acceptance of examination time (70%) was identified as a threat and prioritised in case reduction processes. Partial acceptance of generalisation, extrapolation and implications inferences were defensible with: (1) accumulated development evidence following established key-features methodology; (2) high pilot acceptance for authenticity (90%); and (3) plausibility of assumptions of score correlation with population register data. CONCLUSIONS Kane's approach is beneficial for prioritising sources of validity evidence alongside the iterative development of a key-features examination in the CP field. The validity argument supports scoring assumptions and use of scores as an outcome measure of physician decision-making for CP guideline education implementation interventions. Scoring evidence provides the foundation to direct future studies exploring association of key-feature scores with real-world performance.
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Affiliation(s)
- L M McNamara
- Specialty of Child and Adolescent Health, Faculty of Medicine, The University of Sydney, Sydney, Australia.
| | - K M Scott
- Specialty of Child and Adolescent Health, Faculty of Medicine, The University of Sydney, Sydney, Australia
| | - R N Boyd
- The Faculty of Medicine, Queensland Cerebral Palsy and Rehabilitation Research Centre, The University of Queensland, Brisbane, Australia
| | - E A Farmer
- Graduate School of Medicine, University of Wollongong, Wollongong, Australia
| | - A E Webb
- Faculty of Medicine and Health, Cerebral Palsy Alliance Research Institute, The University of Sydney, Sydney, Australia
| | - I E Novak
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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4
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Omufwoko KS, Cronin AL, Nguyen TTH, Webb AE, Traniello IM, Kocher SD. Developmental transcriptomes predict adult social behaviors in the socially flexible sweat bee, Lasioglossum baleicum. bioRxiv 2023:2023.08.14.553238. [PMID: 37645955 PMCID: PMC10462039 DOI: 10.1101/2023.08.14.553238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Natural variation can provide important insights into the genetic and environmental factors that shape social behavior and its evolution. The sweat bee, Lasioglossum baleicum , is a socially flexible bee capable of producing both solitary and eusocial nests. We demonstrate that within a single nesting aggregation, soil temperatures are a strong predictor of the social structure of nests. Sites with warmer temperatures in the spring have a higher frequency of social nests than cooler sites, perhaps because warmer temperatures provide a longer reproductive window for those nests. To identify the molecular correlates of this behavioral variation, we generated a de novo genome assembly for L. baleicum , and we used transcriptomic profiling to compare adults and developing offspring from eusocial and solitary nests. We find that adult, reproductive females have similar expression profiles regardless of social structure in the nest, but that there are strong differences between reproductive females and workers from social nests. We also find substantial differences in the transcriptomic profiles of stage-matched pupae from warmer, social-biased sites compared to cooler, solitary-biased sites. These transcriptional differences are strongly predictive of adult reproductive state, suggesting that the developmental environment may set the stage for adult behaviors in L. baleicum . Together, our results help to characterize the molecular mechanisms shaping variation in social behavior and highlight a potential role of environmental tuning during development as a factor shaping adult behavior and physiology in this socially flexible bee.
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Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. Nat Ecol Evol 2023; 7:557-569. [PMID: 36941345 DOI: 10.1038/s41559-023-02001-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023]
Abstract
Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.
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Affiliation(s)
- Beryl M Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Benjamin E R Rubin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Callum J Kingwell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Z Yan Wang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Karen M Kapheim
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biology, Utah State University, Logan, UT, USA
| | - Eli S Wyman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Per A Adastra
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Liu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - S RaElle Jackson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shawn M Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Matthew J McBride
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Nikki Van Dorp
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mauricio Fernández Otárola
- Biodiversity and Tropical Ecology Research Center (CIBET) and School of Biology, University of Costa Rica, San José, Costa Rica
| | - Melanie Pham
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Schraiber
- Department of Biology, Temple University, Philadelphia, PA, USA
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Fernando Villanea
- Department of Biology, Temple University, Philadelphia, PA, USA
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Robert J Paxton
- Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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Hyland EM, Webb AE, Kennedy KF, Gerek Ince ZN, Loscher CE, O'Connell MJ. Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biol Evol 2021; 13:6454097. [PMID: 34893845 PMCID: PMC8691055 DOI: 10.1093/gbe/evab268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven distinct residues in mouse TRIF (mTRIF), as compared with human and other mammalian orthologs, thus predicting protein functional shift in mTRIF. We reconstructed TRIF for the most recent common ancestor of mouse and human, and mutated this at the seven sites to their extant mouse/human states. We overexpressed these TRIF mutants in immortalized human and mouse cell lines and monitored TRIF-dependent cytokine production and gene expression induction. We show that optimal TRIF function in human and mouse is dependent on the identity of the positively selected sites. These data provide us with molecular data relating observed differences in response between mouse and human MyD88-independent signaling in the innate immune system with protein functional change.
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Affiliation(s)
- Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Kathy F Kennedy
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Z Nevin Gerek Ince
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Christine E Loscher
- Immunomodulation Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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7
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McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biol Evol 2020; 11:2678-2690. [PMID: 31400206 PMCID: PMC6764479 DOI: 10.1093/gbe/evz163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.
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Affiliation(s)
- Ann M McCartney
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Institute for Global Food Security, Queens University Belfast, United Kingdom
| | - Paul Cormican
- Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Raymond J Moran
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland
| | - Kate D Lee
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,School of Biological Sciences, University of Auckland, New Zealand.,School of Fundamental Sciences, Massey University, New Zealand
| | | | - Javier Prado-Martinez
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queens University Belfast, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.,NAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
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8
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Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O’Connell MJ, Palsbøll PJ, Maley CC. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Mol Biol Evol 2019; 36:1746-1763. [PMID: 31070747 PMCID: PMC6657726 DOI: 10.1093/molbev/msz099] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans-an observation known as Peto's Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.
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Affiliation(s)
- Marc Tollis
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | | | - Andrew E Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | | | - Aleah F Caulin
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA
| | | | - Martine Bèrubè
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Nader Pourmand
- Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Tomas Marques-Bonet
- Instituto de Biologia Evolutiva (UPF-CSIC), PRBB, Barcelona, Spain
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Mary J O’Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Per J Palsbøll
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Carlo C Maley
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
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9
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Webb AE, Webster SC, Collingbourne S, Bretaud D, Lawrence AM, Weidt S, Mintert F, Hensinger WK. Resilient Entangling Gates for Trapped Ions. Phys Rev Lett 2018; 121:180501. [PMID: 30444422 DOI: 10.1103/physrevlett.121.180501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 06/09/2023]
Abstract
Constructing a large-scale ion trap quantum processor will require entangling gate operations that are robust in the presence of noise and experimental imperfection. We experimentally demonstrate how a new type of Mølmer-Sørensen gate protects against infidelity caused by heating of the motional mode used during the gate. Furthermore, we show how the same technique simultaneously provides significant protection against slow fluctuations and mis-sets in the secular frequency. Since this parameter sensitivity is worsened in cases where the ions are not ground-state cooled, our method provides a path towards relaxing ion cooling requirements in practical realizations of quantum computing and simulation.
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Affiliation(s)
- A E Webb
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
| | - S C Webster
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
| | - S Collingbourne
- QOLS, Blackett Laboratory, Imperial College London, London, SW7 2BW, United Kingdom
| | - D Bretaud
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
- QOLS, Blackett Laboratory, Imperial College London, London, SW7 2BW, United Kingdom
| | - A M Lawrence
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
- QOLS, Blackett Laboratory, Imperial College London, London, SW7 2BW, United Kingdom
| | - S Weidt
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
| | - F Mintert
- QOLS, Blackett Laboratory, Imperial College London, London, SW7 2BW, United Kingdom
| | - W K Hensinger
- Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, United Kingdom
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10
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Webb AE, Youngworth IA, Kaya M, Gitter CL, O'Hare EA, May B, Cheng HH, Delany ME. Narrowing the wingless-2 mutation to a 227 kb candidate region on chicken chromosome 12. Poult Sci 2018; 97:1872-1880. [PMID: 29562287 PMCID: PMC5951118 DOI: 10.3382/ps/pey073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/27/2018] [Indexed: 01/01/2023] Open
Abstract
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders.
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Affiliation(s)
- A E Webb
- Department of Animal Science, University of California, Davis 95616
| | - I A Youngworth
- Department of Animal Science, University of California, Davis 95616
| | - M Kaya
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
| | - C L Gitter
- Department of Animal Science, University of California, Davis 95616
| | - E A O'Hare
- Department of Animal Science, University of California, Davis 95616
| | - B May
- Department of Animal Science, University of California, Davis 95616
| | - H H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
| | - M E Delany
- Department of Animal Science, University of California, Davis 95616
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11
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Lynch M, Walsh TA, Marszalowska I, Webb AE, Mac Aogáin M, Rogers TR, Windle H, Kelleher D, O'Connell MJ, Loscher CE. Erratum to: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response. BMC Evol Biol 2017; 17:135. [PMID: 28606132 PMCID: PMC5469175 DOI: 10.1186/s12862-017-0990-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/01/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Mark Lynch
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Thomas A Walsh
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Izabela Marszalowska
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Micheál Mac Aogáin
- Department of Clinical Microbiology, Trinity College Dublin, St James Hospital Dublin, Dublin, Ireland
| | - Thomas R Rogers
- Department of Clinical Microbiology, Trinity College Dublin, St James Hospital Dublin, Dublin, Ireland
| | - Henry Windle
- Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - Dermot Kelleher
- Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. .,Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT, UK.
| | - Christine E Loscher
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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12
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Lynch M, Walsh TA, Marszalowska I, Webb AE, Mac Aogain M, Rogers TR, Windle H, Kelleher D, O'Connell MJ, Loscher CE. Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response. BMC Evol Biol 2017; 17:90. [PMID: 28335725 PMCID: PMC5364705 DOI: 10.1186/s12862-017-0937-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 11/01/2016] [Accepted: 03/15/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surface Layer Proteins (SLPs) from different C. difficile ribotypes (RT) however whether these differences influence severity of infection is still not clear. RESULTS We used a molecular evolutionary approach to analyse SLPs from twenty-six C. difficile RTs representing different slpA sequences. We demonstrate that SLPs from RT 027 and 078 exhibit evidence of positive selection (PS). We compared the effect of these SLPs to those purified from RT 001 and 014, which did not exhibit PS, and demonstrate that the presence of sites under positive selection correlates with ability to activate macrophages. SLPs from RTs 027 and 078 induced a more potent response in macrophages, with increased levels of IL-6, IL-12p40, IL-10, MIP-1α, MIP-2 production relative to RT 001 and 014. Furthermore, RTs 027 and 078 induced higher expression of CD40, CD80 and MHC II on macrophages with decreased ability to phagocytose relative to LPS. CONCLUSIONS These results tightly link sequence differences in C. difficile SLPs to disease susceptibility and severity, and suggest that positively selected sites in the SLPs may play a role in driving the emergence of hyper-virulent strains.
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Affiliation(s)
- Mark Lynch
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Thomas A Walsh
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Izabela Marszalowska
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Micheál Mac Aogain
- Department of Clinical Microbiology, Trinity College Dublin, St James Hospital Dublin, Dublin, Ireland
| | - Thomas R Rogers
- Department of Clinical Microbiology, Trinity College Dublin, St James Hospital Dublin, Dublin, Ireland
| | - Henry Windle
- Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - Dermot Kelleher
- Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. .,Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT, UK.
| | - Christine E Loscher
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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13
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Weidt S, Randall J, Webster SC, Lake K, Webb AE, Cohen I, Navickas T, Lekitsch B, Retzker A, Hensinger WK. Trapped-Ion Quantum Logic with Global Radiation Fields. Phys Rev Lett 2016; 117:220501. [PMID: 27925715 DOI: 10.1103/physrevlett.117.220501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Trapped ions are a promising tool for building a large-scale quantum computer. However, the number of required radiation fields for the realization of quantum gates in any proposed ion-based architecture scales with the number of ions within the quantum computer, posing a major obstacle when imagining a device with millions of ions. Here, we present a fundamentally different approach for trapped-ion quantum computing where this detrimental scaling vanishes. The method is based on individually controlled voltages applied to each logic gate location to facilitate the actual gate operation analogous to a traditional transistor architecture within a classical computer processor. To demonstrate the key principle of this approach we implement a versatile quantum gate method based on long-wavelength radiation and use this method to generate a maximally entangled state of two quantum engineered clock qubits with fidelity 0.985(12). This quantum gate also constitutes a simple-to-implement tool for quantum metrology, sensing, and simulation.
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Affiliation(s)
- S Weidt
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - J Randall
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
- QOLS, Blackett Laboratory, Imperial College London, London SW7 2BW, United Kingdom
| | - S C Webster
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - K Lake
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - A E Webb
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - I Cohen
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Givat Ram, Israel
| | - T Navickas
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - B Lekitsch
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - A Retzker
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Givat Ram, Israel
| | - W K Hensinger
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
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14
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Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep 2015; 10:112-22. [PMID: 25565328 PMCID: PMC4536333 DOI: 10.1016/j.celrep.2014.12.008] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.
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Affiliation(s)
- Michael Keane
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy Semeiks
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Yang I Li
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Thomas Craig
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Lone Bruhn Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Sipko van Dam
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David Brawand
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Patrícia I Marques
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyung-Soon Yim
- KIOST, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Nick V Grishin
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | | | | | - Elias M Oziolor
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Cole W Matson
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gary W Stuart
- The Center for Genomic Advocacy (TCGA) and Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - J Craig George
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Robert Suydam
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - John W Bickham
- Battelle Memorial Institute, Houston, TX 77079, USA; Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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15
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Weidt S, Randall J, Webster SC, Standing ED, Rodriguez A, Webb AE, Lekitsch B, Hensinger WK. Ground-State Cooling of a Trapped Ion Using Long-Wavelength Radiation. Phys Rev Lett 2015; 115:013002. [PMID: 26182094 DOI: 10.1103/physrevlett.115.013002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 06/04/2023]
Abstract
We demonstrate ground-state cooling of a trapped ion using radio-frequency (rf) radiation. This is a powerful tool for the implementation of quantum operations, where rf or microwave radiation instead of lasers is used for motional quantum state engineering. We measure a mean phonon number of n[over ¯]=0.13(4) after sideband cooling, corresponding to a ground-state occupation probability of 88(7)%. After preparing in the vibrational ground state, we demonstrate motional state engineering by driving Rabi oscillations between the |n=0⟩ and |n=1⟩ Fock states. We also use the ability to ground-state cool to accurately measure the motional heating rate and report a reduction by almost 2 orders of magnitude compared with our previously measured result, which we attribute to carefully eliminating sources of electrical noise in the system.
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Affiliation(s)
- S Weidt
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - J Randall
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
- QOLS, Blackett Laboratory, Imperial College London, London SW7 2BW, United Kingdom
| | - S C Webster
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - E D Standing
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - A Rodriguez
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - A E Webb
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - B Lekitsch
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
| | - W K Hensinger
- Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, United Kingdom
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16
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Webb AE, Gerek ZN, Morgan CC, Walsh TA, Loscher CE, Edwards SV, O'Connell MJ. Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response. Mol Biol Evol 2015; 32:1717-29. [PMID: 25758009 PMCID: PMC4476151 DOI: 10.1093/molbev/msv051] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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] [Indexed: 12/24/2022] Open
Abstract
It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes.
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Affiliation(s)
- Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Dublin 9, Ireland
| | - Z Nevin Gerek
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia
| | - Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Dublin 9, Ireland
| | - Thomas A Walsh
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Dublin 9, Ireland
| | - Christine E Loscher
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Dublin 9, Ireland Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University
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17
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Abstract
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
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Affiliation(s)
- Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
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18
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Abstract
Native folding and splicing by the Saccharomyces cerevisiae mitochondrial bI5 group I intron RNA is facilitated by both the S. cerevisiae CBP2 and Neurospora crassa CYT-18 protein cofactors. Both protein-bI5 RNA complexes splice at similar rates, suggesting that the RNA active site structure is similar in both ribonucleoproteins. In contrast, the two proteins assemble with the bI5 RNA by distinct mechanisms and bind opposing, but partially overlapping, sides of the group I intron catalytic core. Assembly with CBP2 is limited by a slow, unimolecular RNA folding step characterized by a negligible activation enthalpy. We show that assembly with CYT-18 shows four distinctive features. (1) CYT-18 binds stably to the bI5 RNA at the diffusion controlled limit, but assembly to a catalytically active RNA structure is still limited by RNA folding, as visualized directly using time-resolved footprinting. (2) This mechanism of rapid stable protein binding followed by subsequent assembly steps has a distinctive kinetic signature: the apparent ratio of k(off) to k(on), determined in a partitioning experiment, differs from the equilibrium K(d) by a large factor. (3) Assembly with CYT-18 is characterized by a large activation enthalpy, consistent with a rate limiting conformational rearrangement. (4) Because assembly from the kinetically trapped state is faster at elevated temperature, we can identify conditions where CYT-18 accelerates (catalyzes) bI5 RNA folding relative to assembly with CBP2.
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Affiliation(s)
- A E Webb
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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19
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Abstract
Most large RNAs achieve their active, native structures only as complexes with one or more cofactor proteins. By varying the Mg(2+) concentration, the catalytic core of the bI5 group I intron RNA can be manipulated into one of three states, expanded, collapsed or native, or into balanced equilibria between these states. Under near-physiological conditions, the bI5 RNA folds rapidly to a collapsed but non-native state. Hydroxyl radical footprinting demonstrates that assembly with the CBP2 protein cofactor chases the RNA from the collapsed state to the native state. In contrast, CBP2 also binds to the RNA in the expanded state to form many non-native interactions. This structural picture is reinforced by functional splicing experiments showing that RNA in an expanded state forms a non-productive, kinetically trapped complex with CBP2. Thus, rapid folding to the collapsed state functions to self-chaperone bI5 RNA folding by preventing premature interaction with its protein cofactor. This productive, self-chaperoning role for RNA collapsed states may be especially important to avert misassembly of large multi-component RNA-protein machines in the cell.
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Affiliation(s)
- A E Webb
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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20
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Abstract
At physiological Mg2+ concentrations, the catalytic core of the bI5 group I intron does not fold into its native structure. In contrast, as judged by the global size, this RNA undergoes structural collapse at Mg 2+ concentrations much lower than required to drive folding of the RNA completely to the native state. The bI5 RNA therefore exists in equilibrium between expanded and collapsed non-native states. The activation energy of RNA folding from the collapsed state to the native state is negligible and the reaction is not accelerated by the addition of urea. This collapsed state is thus distinct from the kinetic traps observed during folding of other large RNAs. The collapsed non-native state forms readily in the case of bI5 RNA and may exist generically prior to assembly of other ribonucleoprotein holoenzymes, such as the ribosome.
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MESH Headings
- Base Sequence
- Catalysis
- Chromatography, Gel
- Conserved Sequence/genetics
- Cytochrome b Group/genetics
- Dose-Response Relationship, Drug
- Introns/genetics
- Kinetics
- Magnesium/pharmacology
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation/drug effects
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing/genetics
- RNA Stability/drug effects
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Mitochondrial
- Solvents
- Thermodynamics
- Urea/pharmacology
- Yeasts/genetics
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Affiliation(s)
- K L Buchmueller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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21
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Heap RB, Fleet IR, Hamon M, Brown KD, Stanley CJ, Webb AE. Mechanisms of transfer of steroid hormones and growth factors into milk. Endocrinol Exp 1986; 20:101-18. [PMID: 3489593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper we examine the ability of the mammary gland to remove from circulating blood three compounds which differ in their physico-chemical and structural properties. Mammary extraction of progesterone, oestrone sulphate and epidermal growth factor (EGF) is similar at peak lactation in goats, but the proportion of labelled infusate that is transferred into milk is greater for oestrone sulphate and EGF than progesterone which is rapidly metabolised by mammary tissue. The kinetics of transfer of progesterone, oestrone sulphate and EGF from blood into milk show that transcellular processes are involved, and on the basis of earlier hypotheses and new information reported here the results indicate the probable importance of simple and facilitated diffusion pathways for progesterone and oestrone sulphate, and secretory mechanisms for oestrone sulphate and EGF. Although evidence is lacking for a direct effect of hormones in milk on mammary function, their concentration in milk may reflect changes in local regulation of mammary secretion. Considerable practical value is attached to the immunodiagnostic use of milk hormone concentrations to determine ovarian and placental endocrine activity during pregnancy in domestic ruminants.
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22
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Stanley CJ, Paris F, Webb AE, Heap RB, Ellis ST, Hamon M, Worsfold A, Booth JM. Use of a new and rapid milk progesterone assay to monitor reproductive activity in the cow. Vet Rec 1986; 118:664-7. [PMID: 3526700 DOI: 10.1136/vr.118.24.664] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A new and rapid enzyme-amplified immunoassay (AELIA) has been developed for the measurement of progesterone in milk. The AELIA system is a non-isotopic method that gives results within 35 minutes. Milk progesterone concentrations measured in 10 cows sampled daily at various stages of the reproductive cycle were very similar to those recorded by a validated radioimmunoassay. The results show that the speed and sensitivity of the AELIA system would make it possible to diagnose pregnancy rapidly at about 24 days after insemination, to predict the onset of behavioural oestrus from decreasing progesterone values during the third week after a preceding oestrus, and to obtain a daily record of milk progesterone levels in animals treated for infertility of ovarian origin.
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