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Behringer MG, Ho WC, Miller SF, Worthan SB, Cen Z, Stikeleather R, Lynch M. Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine. Curr Biol 2024; 34:1403-1413.e5. [PMID: 38460514 DOI: 10.1016/j.cub.2024.02.040] [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: 10/04/2023] [Revised: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.
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Affiliation(s)
- Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA; Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 21st Avenue S, Nashville, TN 37232, USA.
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA; Department of Biology, University of Texas at Tyler, University Blvd., Tyler, TX 75799, USA.
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Zeer Cen
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
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Doidge NP, Allen JL, Bushell R, Whittle KM, Zane-Todd L, Lynch M, Browning GF, Marenda MS. Detection and Differentiation of Entomopathogenic Serratia spp. to Inform Reintroduction of the Critically Endangered Lord Howe Island Stick Insect Dryococelus australis. J Wildl Dis 2024; 60:306-318. [PMID: 38243844 DOI: 10.7589/jwd-d-23-00125] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/09/2023] [Indexed: 01/22/2024]
Abstract
Once rodents have been successfully eradicated from Lord Howe Island, Australia, the critically endangered Lord Howe Island stick insect (Dryococelus australis (Montrouzier)) may be reintroduced, a century after it was thought to have become extinct. In captive populations of D. australis, elevated mortalities have been associated with bacterial pathogens. To better define the infectious risk posed by entomopathogens to the reintroduction program, we investigated the bacteria isolated from captive D. australis kept at Melbourne Zoo and on Lord Howe Island and from environmental samples and free-living invertebrates collected on various parts of the island. At Melbourne Zoo, Serratia and Pseudomonas spp. were the bacteria most frequently isolated between 2013 and 2019. Serratia spp. were also the organisms most frequently isolated from insects sampled in April 2019 from the captive population on Lord Howe Island. In addition, Serratia spp. were isolated from a range of environmental samples collected on Lord Howe Island during March-April 2019. These environmental isolates had a broader range of biochemical and molecular characteristics than those obtained from the captive insect populations. A large proportion of these isolates were urease positive and had biochemical profiles previously not described for Serratia spp. This study highlights the need for better surveillance for potential pathogens in understudied regions and sites. We conclude that infections caused by Serratia spp. might pose a problem to the captive breeding program for D. australis but that the risk of introducing novel pathogens to Lord Howe Island through infected insects is low. Our study explores some of the potential risks involved in captive breeding and provides a valuable example of using pathogen surveillance to better inform an invertebrate conservation program.
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Affiliation(s)
- Nicholas P Doidge
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
- Melbourne Zoo, Elliot Avenue, Parkville, Victoria, 3052, Australia
| | - Joanne L Allen
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Corner Park Drive and Flemington Road, Building 400, Parkville, Victoria, 3010, Australia
| | - Rhys Bushell
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - Katie-Marie Whittle
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
| | - Laura Zane-Todd
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
| | - Michael Lynch
- Melbourne Zoo, Elliot Avenue, Parkville, Victoria, 3052, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Corner Park Drive and Flemington Road, Building 400, Parkville, Victoria, 3010, Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
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Zhang MS, Nee T, Lynch M, Rose J, Morris A, Chandra D. Disproportionate Use of the ED by Patients 3-Years After e-Cigarette-Associated or Vaping-Associated Lung Injury. Chest 2024:S0012-3692(24)00258-7. [PMID: 38387649 DOI: 10.1016/j.chest.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024] Open
Affiliation(s)
- Michael S Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Taylor Nee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Michael Lynch
- Department of Emergency Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Jason Rose
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Divay Chandra
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA; Electronic Cigarette Research Initiative, University of Pittsburgh, Pittsburgh, PA.
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Zhang Y, Li H, Wang Y, Nie M, Zhang K, Pan J, Zhang Y, Ye Z, Zufall RA, Lynch M, Long H. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 2024; 9:e0116123. [PMID: 38259100 PMCID: PMC10878089 DOI: 10.1128/msystems.01161-23] [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: 11/01/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.
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Affiliation(s)
- Yuanyuan Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Haichao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yaohai Wang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Mu Nie
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Kexin Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Jiao Pan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yu Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province, China
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
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Heil JM, Lassiter JM, Salzman MS, Herring A, Hoppe J, Lynch M, Weiner SG, Roberts B, Haroz R. A qualitative assessment of emergency physicians' experiences with robust emergency department buprenorphine bridge programs. Acad Emerg Med 2024. [PMID: 38357749 DOI: 10.1111/acem.14880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
OBJECTIVES Emergency departments (EDs) are a critical point of entry into treatment for patients struggling with opioid use disorder (OUD). When initiated in the ED, buprenorphine is associated with increased addiction treatment engagement at 30 days when initiated. Despite this association, it has had slow adoption. The barriers to ED buprenorphine utilization are well documented; however, the benefits of prescribing buprenorphine for emergency physicians (EPs) have not been explored. This study utilized semistructured interviews to explore and understand how EPs perceive their experiences working in EDs that have successfully implemented ED bridge programs (EDBPs) for patients with OUD. METHODS Semistructured interviews were conducted with EPs from four geographically diverse academic hospitals with established EDBPs. Interviews were recorded and transcribed, and emergent themes were identified using codebook thematic analysis. Analysis credibility and transparency were confirmed with peer debriefing. RESULTS Twenty-two interviews were conducted across the four sites. Three key themes were constructed during the analyses: (1) provided EPs agency; (2) transformed EPs' emotions, attitudes, and behaviors related to treating patients with OUD; and (3) improved EPs' professional quality of life. CONCLUSIONS Participants in this study reported several common themes related to participation in their hospital's BP. Overall our results suggest that physicians who participate in EDBPs may feel a renewed sense of fulfillment and purpose in their personal and professional lives. These positive changes may lead to increased job satisfaction in hospitals that have successfully launched EDBP.
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Affiliation(s)
- Jessica Marie Heil
- Center for Healing, Division of Addiction Medicine, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Matthew S Salzman
- Center for Healing, Division of Addiction Medicine, Cooper University Health Care, Camden, New Jersey, USA
- Department of Emergency Medicine, Division of Addiction Medicine and Medical Toxicology, Cooper University Health Care, Camden, New Jersey, USA
- Cooper Medical School of Rowan University, Cooper University Healthcare, Camden, New Jersey, USA
| | - Andrew Herring
- Department of Emergency Medicine, Highland Hospital-Alameda Health System, University of California, San Francisco, California, USA
| | - Jason Hoppe
- Department of Emergency Medicine, University of Colorado School of Medicine, Colorado, Aurora, USA
| | - Michael Lynch
- University of Pittsburgh School of Medicine Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Scott G Weiner
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Brian Roberts
- Department of Emergency Medicine, Division of Addiction Medicine and Medical Toxicology, Cooper University Health Care, Camden, New Jersey, USA
- Cooper Medical School of Rowan University, Cooper University Healthcare, Camden, New Jersey, USA
| | - Rachel Haroz
- Center for Healing, Division of Addiction Medicine, Cooper University Health Care, Camden, New Jersey, USA
- Department of Emergency Medicine, Division of Addiction Medicine and Medical Toxicology, Cooper University Health Care, Camden, New Jersey, USA
- Cooper Medical School of Rowan University, Cooper University Healthcare, Camden, New Jersey, USA
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6
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Davila-Payan CS, Hill A, Kayembe L, Alexander JP, Lynch M, Pallas SW. Analysis of the yearly transition function in measles disease modeling. Stat Med 2024; 43:435-451. [PMID: 38100282 DOI: 10.1002/sim.9951] [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: 05/10/2022] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 12/17/2023]
Abstract
Globally, there were an estimated 9.8 million measles cases and 207 500 measles deaths in 2019. As the effort to eliminate measles around the world continues, modeling remains a valuable tool for public health decision-makers and program implementers. This study presents a novel approach to the use of a yearly transition function that formulates mathematically the vaccine schedules for different age groups while accounting for the effects of the age of vaccination, the timing of vaccination, and disease seasonality on the yearly number of measles cases in a country. The methodology presented adds to an existing modeling framework and expands its analysis, making its utilization more adjustable for the user and contributing to its conceptual clarity. This article also adjusts for the temporal interaction between vaccination and exposure to disease, applying adjustments to estimated yearly counts of cases and the number of vaccines administered that increase population immunity. These new model features provide the ability to forecast and compare the effects of different vaccination timing scenarios and seasonality of transmission on the expected disease incidence. Although the work presented is applied to the example of measles, it has potential relevance to modeling other vaccine-preventable diseases.
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Affiliation(s)
- C S Davila-Payan
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - A Hill
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L Kayembe
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J P Alexander
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Lynch
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S W Pallas
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Adriaanse K, Lynch M, Sutherland D, Traub R, Lowe J, Hufschmid J. Toxoplasma gondii Does Not Inhibit the Assisted Colonization of Eastern Barred Bandicoots (Perameles gunnii) to Phillip Island, Victoria, Australia. J Wildl Dis 2024; 60:116-125. [PMID: 37889935 DOI: 10.7589/jwd-d-23-00069] [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: 04/21/2023] [Accepted: 09/05/2023] [Indexed: 10/29/2023]
Abstract
Eastern barred bandicoots (Perameles gunnii) are thought to be highly susceptible to disease caused by infection with the protozoan parasite Toxoplasma gondii. This study followed a population of 67 P. gunnii introduced onto the Summerland Peninsula, Phillip Island, Australia, where the prevalence of T. gondii infection in the feral cat population was known to be very high. Prior to release, bandicoots were tested for serologic exposure to T. gondii using the modified agglutination test. A subset of bandicoots was tested on four occasions after release onto the peninsula. No seroconversion was detected at any time point. A subset of bandicoots was radiotracked after release and at two additional trapping sessions to help monitor survival. Toxoplasma gondii DNA was not detected by PCR in eight carcasses recovered for necropsy. Fourteen founder bandicoots (21% of founders) were known to be alive at 500 d post-release. A total of 29 unmarked bandicoots were trapped over the study period, confirming that the bandicoots were successfully reproducing on the island. Body weight, packed cell volume, and total plasma protein were used as measures of individual animal health; population health was inferred from these data. Body weight was significantly associated with trip number, with a general trend of increasing weight after release onto the island. This study showed that eastern barred bandicoots were able to establish a new population despite a probably high environmental load of T. gondii.
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Affiliation(s)
- Katherine Adriaanse
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Building 400, Corner Flemington Road and Park Drive, Parkville, Victoria 3052, Australia
- Zoos Victoria, Elliot Avenue, Parkville, Victoria 3052, Australia
| | - Michael Lynch
- Zoos Victoria, Elliot Avenue, Parkville, Victoria 3052, Australia
| | - Duncan Sutherland
- Phillip Island Nature Parks, PO Box 97, Cowes, Victoria 3922, Australia
| | - Rebecca Traub
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Building 400, Corner Flemington Road and Park Drive, Parkville, Victoria 3052, Australia
| | - Jasmine Lowe
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Building 400, Corner Flemington Road and Park Drive, Parkville, Victoria 3052, Australia
| | - Jasmin Hufschmid
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Building 400, Corner Flemington Road and Park Drive, Parkville, Victoria 3052, Australia
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Rafferty S, Byrne B, Goh A, Porter E, Lynch M, Ahmad K, O'Brien J, Field S. Radiological staging and surveillance imaging of high risk cutaneous malignant melanoma in the Mid-West of Ireland. Ir Med J 2023; 116:868. [PMID: 38258702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
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Long H, Johri P, Gout JF, Ni J, Hao Y, Licknack T, Wang Y, Pan J, Jiménez-Marín B, Lynch M. Paramecium Genetics, Genomics, and Evolution. Annu Rev Genet 2023; 57:391-410. [PMID: 38012024 DOI: 10.1146/annurev-genet-071819-104035] [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: 11/29/2023]
Abstract
The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.
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Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Timothy Licknack
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Berenice Jiménez-Marín
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
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Eakins J, Lynch M, Carolan JC, Rowan NJ. Studies on the novel effects of electron beam treated pollen on colony reproductive output in commercially-reared bumblebees (Bombus terrestris) for mass pollination applications. Sci Total Environ 2023; 899:165614. [PMID: 37478954 DOI: 10.1016/j.scitotenv.2023.165614] [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] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/23/2023]
Abstract
Commercially-reared bumblebees provide an important pollinator service that helps support food production and security. The deployment of an appropriate non-thermal disinfection technology for the bulk treatment of pollen collected from honeybees for the feeding of commercial bumblebees is important in order to mitigate against complex diseases and unwanted pathogen spillover to native bees. High level disinfection of pollen was achieved using an electron (e)-beam dose of 100 kGy that corresponded to 78 % loss of cellular viability of bee pathogens before feeding to bumblebees as measured by the novel in vitro use of flow cytometry (FCM). Novel findings showed that e-beam treated-pollen that was fed to bumblebees produced fewer females, gynes and exhibited an absence of males when compared to control bumblebee colonies that were fed untreated commercial pollen. A similar trend emerged in bumblebee colony reproductive outputs when using membrane filtered washed pollen. Proteomic analysis of bumblebees from individual colonies fed with treated-pollen revealed a differential abundance of proteins associated with stress, immunity and metabolism when compared to the untreated pollen control group. Microbiome analysis of the bumblebee gut content revealed differences in microbiota between treated and untreated pollen in bumblebee colony studies. This novel study evaluated the impact of industrial e-beam treated-pollen on complex bee disease mitigation where physically treated-pollen fed to bumblebees was shown to substantially affect colony reproductive outputs.
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Affiliation(s)
- J Eakins
- Centre for Disinfection and Sterilization, Faculty of Science and Health, Technological Institute of the Shannon, Midlands Campus, Ireland; Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - M Lynch
- Centre for Disinfection and Sterilization, Faculty of Science and Health, Technological Institute of the Shannon, Midlands Campus, Ireland
| | - J C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - N J Rowan
- Centre for Disinfection and Sterilization, Faculty of Science and Health, Technological Institute of the Shannon, Midlands Campus, Ireland.
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Ye Z, Wei W, Pfrender ME, Lynch M. Evolutionary Insights from a Large-Scale Survey of Population-Genomic Variation. Mol Biol Evol 2023; 40:msad233. [PMID: 37863047 PMCID: PMC10630549 DOI: 10.1093/molbev/msad233] [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: 05/03/2023] [Revised: 09/11/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
The field of genomics has ushered in new methods for studying molecular-genetic variation in natural populations. However, most population-genomic studies still rely on small sample sizes (typically, <100 individuals) from single time points, leaving considerable uncertainties with respect to the behavior of relatively young (and rare) alleles and, owing to the large sampling variance of measures of variation, to the specific gene targets of unusually strong selection. Genomic sequences of ∼1,700 haplotypes distributed over a 10-year period from a natural population of the microcrustacean Daphnia pulex reveal evolutionary-genomic features at a refined scale, including previously hidden information on the behavior of rare alleles predicted by recent theory. Background selection, resulting from the recurrent introduction of deleterious alleles, appears to strongly influence the dynamics of neutral alleles, inducing indirect negative selection on rare variants and positive selection on common variants. Temporally fluctuating selection increases the persistence of nonsynonymous alleles with intermediate frequencies, while reducing standing levels of variation at linked silent sites. Combined with the results from an equally large metapopulation survey of the study species, classes of genes that are under strong positive selection can now be confidently identified in this key model organism. Most notable among rapidly evolving Daphnia genes are those associated with ribosomes, mitochondrial functions, sensory systems, and lifespan determination.
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Affiliation(s)
- Zhiqiang Ye
- Hubei Key Laboratory of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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12
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Ye Z, Pfrender ME, Lynch M. Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates. Genome Biol Evol 2023; 15:evad202. [PMID: 37946625 PMCID: PMC10664402 DOI: 10.1093/gbe/evad202] [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: 05/31/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. In this study, we compared population-genomics data between Daphnia pulex and Daphnia pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. Daphnia pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, a higher incidence of private alleles, and a substantially more linkage disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended life span in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although approximately 160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.
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Affiliation(s)
- Zhiqiang Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
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13
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Ni J, Pan J, Wang Y, Chen T, Feng X, Li Y, Lin T, Lynch M, Long H, Li W. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Mar Life Sci Technol 2023; 5:564-572. [PMID: 38045552 PMCID: PMC10689312 DOI: 10.1007/s42995-023-00182-1] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/02/2023] [Indexed: 12/05/2023]
Abstract
High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures, greatly promoting biological studies involving large amounts of complex samples, especially those involving environmental and pathogen-monitoring ones. Commercial library preparation kits for amplicon sequencing, which generally require multiple steps, including adapter ligation and indexing, are expensive and time-consuming, especially for applications at a large scale. To overcome these limitations, a "one-step PCR approach" has been previously proposed for constructions of amplicon libraries using long fusion primers. However, efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed. To tackle these, we present an integrative protocol for one-step PCR amplicon library construction (OSPALC). High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples. With this protocol, the amplicon library is constructed through one regular PCR with long primers, and the total cost per DNA/cDNA sample decreases to just 7% of the typical cost via the multi-step PCR approach. Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study. Tools to design primers targeting at any genomic regions are also presented. In principle, OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples, and will facilitate research in numerous fields. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00182-1.
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Affiliation(s)
- Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tianhao Chen
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Xinshi Feng
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yichen Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47401 USA
- Present Address: SLAC National Accelerator Laboratory, Stanford University, Stanford, 94305 USA
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14
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Lin T, Pan J, Gregory C, Wang Y, Tincher C, Rivera C, Lynch M, Long H, Zhang Y. Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E. coli. Mar Life Sci Technol 2023; 5:538-550. [PMID: 38045542 PMCID: PMC10689325 DOI: 10.1007/s42995-023-00185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/27/2023] [Indexed: 12/05/2023]
Abstract
Antibiotic-resistant bacteria severely threaten human health. Besides spontaneous mutations generated by endogenous factors, the resistance might also originate from mutations induced by certain antibiotics, such as the fluoroquinolones. Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems. However, the relative contributions of these molecular mechanisms remain unclear, hindering understanding of the generation of resistant pathogens. Here, using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains, as well as those of the strains deficient for the mismatch repair (MMR) and the oxidative damage repair pathways, we find that the SOS response is the major mutagenesis contributor in mutation elevation, responsible for ~ 30-50% of the total base-pair substitution (BPS) mutation-rate elevation upon treatment with sublethal levels of norfloxacin (0 ~ 50 ng/mL). We further estimate the significance of the effects on other mutational features of these mechanisms (i.e., transversions, structural variations, and mutation spectrum) in E. coli using linear models. The SOS response plays a positive role in all three mutational features (mutation rates of BPSs, transversions, structural variations) and affects the mutational spectrum. The repair systems significantly reduce the BPS mutation rate and the transversion rate, regardless of whether antibiotics are present, while significantly increasing the structural variation rate in E. coli. Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00185-y.
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Affiliation(s)
- Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Caitlyn Rivera
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Yu Zhang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- School of Mathematics Science, Ocean University of China, Qingdao, 266000 China
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15
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Lynch M, Ali F, Lin T, Wang Y, Ni J, Long H. The divergence of mutation rates and spectra across the Tree of Life. EMBO Rep 2023; 24:e57561. [PMID: 37615267 PMCID: PMC10561183 DOI: 10.15252/embr.202357561] [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: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Farhan Ali
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeAZUSA
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMMEOcean University of ChinaQingdaoChina
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16
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Toles M, Kistler C, Lin FC, Lynch M, Wessell K, Mitchell SL, Hanson LC. Palliative care for persons with late-stage Alzheimer's and related dementias and their caregivers: protocol for a randomized clinical trial. Trials 2023; 24:606. [PMID: 37743478 PMCID: PMC10518941 DOI: 10.1186/s13063-023-07614-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Limited access to specialized palliative care exposes persons with late-stage Alzheimer's disease and related dementias (ADRD) to burdensome treatment and unnecessary hospitalization and their caregivers to avoidable strain and financial burden. Addressing this unmet need, the purpose of this study was to conduct a randomized clinical trial (RCT) of the ADRD-Palliative Care (ADRD-PC) program. METHODS The study will use a multisite, RCT design and will be set in five geographically diverse US hospitals. Lead investigators and outcome assessors will be masked. The study will use 1:1 randomization of patient-caregiver dyads, and sites will enroll N = 424 dyads of hospitalized patients with late-stage ADRD with their family caregivers. Intervention dyads will receive the ADRD-PC program of (1) dementia-specific palliative care, (2) standardized caregiver education, and (3) transitional care. Control dyads will receive publicly available educational material on dementia caregiving. Outcomes will be measured at 30 days (interim) and 60 days post-discharge. The primary outcome will be 60-day hospital transfers, defined as visits to an emergency department or hospitalization ascertained from health record reviews and caregiver interviews (aim 1). Secondary patient-centered outcomes, ascertained from 30- and 60-day health record reviews and caregiver telephone interviews, will be symptom treatment, symptom control, use of community palliative care or hospice, and new nursing home transitions (aim 2). Secondary caregiver-centered outcomes will be communication about prognosis and goals of care, shared decision-making about hospitalization and other treatments, and caregiver distress (aim 3). Analyses will use intention-to-treat, and pre-specified exploratory analyses will examine the effects of sex as a biologic variable and the GDS stage. DISCUSSION The study results will determine the efficacy of an intervention that addresses the extraordinary public health impact of late-stage ADRD and suffering due to symptom distress, burdensome treatments, and caregiver strain. While many caregivers prioritize comfort in late-stage ADRD, shared decision-making is rare. Hospitalization creates an opportunity for dementia-specific palliative care, and the study findings will inform care redesign to advance comprehensive dementia-specific palliative care plus transitional care. TRIAL REGISTRATION ClinicalTrials.gov NCT04948866. Registered on July 2, 2021.
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Affiliation(s)
- M Toles
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - C Kistler
- Department of Family Medicine and Palliative Care Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - F C Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Lynch
- Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K Wessell
- Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S L Mitchell
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA
| | - L C Hanson
- Division of Geriatrics and Palliative Care Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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17
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Hoelzel AR, Lynch M. The raw material of evolution. Science 2023; 381:942-943. [PMID: 37651506 DOI: 10.1126/science.adk0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Estimates of whale mutation rates contribute to understanding evolutionary processes.
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Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, Durham, UK
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
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18
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Lynch M. Masatoshi Nei (1931 to 2023): Founder of molecular evolutionary genetics. Proc Natl Acad Sci U S A 2023; 120:e2312259120. [PMID: 37590429 PMCID: PMC10465990 DOI: 10.1073/pnas.2312259120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ85281
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19
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Moger-Reischer RZ, Glass JI, Wise KS, Sun L, Bittencourt DMC, Lehmkuhl BK, Schoolmaster DR, Lynch M, Lennon JT. Evolution of a minimal cell. Nature 2023; 620:122-127. [PMID: 37407813 PMCID: PMC10396959 DOI: 10.1038/s41586-023-06288-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 09/15/2021] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life1,2. Here we report on how an engineered minimal cell3,4 contends with the forces of evolution compared with the Mycoplasma mycoides non-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria, but were not affected by genome minimization. Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution. Despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same. This pattern reflected epistatic effects of mutations in ftsZ, which encodes a tubulin-homologue protein that regulates cell division and morphology5,6. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides critical insights into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered cells2,7-9.
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Affiliation(s)
| | - J I Glass
- J. Craig Venter Institute, La Jolla, CA, USA
| | - K S Wise
- J. Craig Venter Institute, La Jolla, CA, USA
| | - L Sun
- J. Craig Venter Institute, La Jolla, CA, USA
- Novartis Gene Therapy, San Diego, CA, USA
| | - D M C Bittencourt
- J. Craig Venter Institute, La Jolla, CA, USA
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Brasília, Brazil
| | - B K Lehmkuhl
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - D R Schoolmaster
- US Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA, USA
| | - M Lynch
- Arizona State University, Tempe, AZ, USA
| | - J T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA.
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20
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Moger-Reischer RZ, Glass JI, Wise KS, Sun L, Bittencourt DMC, Lehmkuhl BK, Schoolmaster DR, Lynch M, Lennon JT. Publisher Correction: Evolution of a minimal cell. Nature 2023; 620:E18. [PMID: 37495703 PMCID: PMC10412442 DOI: 10.1038/s41586-023-06454-1] [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: 07/28/2023]
Affiliation(s)
| | - J I Glass
- J. Craig Venter Institute, La Jolla, CA, USA
| | - K S Wise
- J. Craig Venter Institute, La Jolla, CA, USA
| | - L Sun
- J. Craig Venter Institute, La Jolla, CA, USA
- Novartis Gene Therapy, San Diego, CA, USA
| | - D M C Bittencourt
- J. Craig Venter Institute, La Jolla, CA, USA
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Brasília, Brazil
| | - B K Lehmkuhl
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - D R Schoolmaster
- US Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA, USA
| | - M Lynch
- Arizona State University, Tempe, AZ, USA
| | - J T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA.
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21
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Devi A, Speyer G, Lynch M. The divergence of mean phenotypes under persistent directional selection. Genetics 2023; 224:iyad091. [PMID: 37200616 PMCID: PMC10552002 DOI: 10.1093/genetics/iyad091] [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: 02/26/2023] [Revised: 02/26/2023] [Accepted: 05/04/2023] [Indexed: 05/20/2023] Open
Abstract
Numerous organismal traits, particularly at the cellular level, are likely to be under persistent directional selection across phylogenetic lineages. Unless all mutations affecting such traits have large enough effects to be efficiently selected in all species, gradients in mean phenotypes are expected to arise as a consequence of differences in the power of random genetic drift, which varies by approximately five orders of magnitude across the Tree of Life. Prior theoretical work examining the conditions under which such gradients can arise focused on the simple situation in which all genomic sites affecting the trait have identical and constant mutational effects. Here, we extend this theory to incorporate the more biologically realistic situation in which mutational effects on a trait differ among nucleotide sites. Pursuit of such modifications leads to the development of semi-analytic expressions for the ways in which selective interference arises via linkage effects in single-effects models, which then extend to more complex scenarios. The theory developed clarifies the conditions under which mutations of different selective effects mutually interfere with each others' fixation and shows how variance in effects among sites can substantially modify and extend the expected scaling relationships between mean phenotypes and effective population sizes.
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Affiliation(s)
- Archana Devi
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Gil Speyer
- Knowledge Enterprise, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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Abstract
Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.
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Affiliation(s)
- Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ85287
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23
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Zhou X, Pan J, Wang Y, Lynch M, Long H, Zhang Y. de novo structural variations of Escherichia coli detected by Nanopore long-read sequencing. Genome Biol Evol 2023:7192464. [PMID: 37293824 DOI: 10.1093/gbe/evad106] [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: 01/02/2023] [Revised: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
Spontaneous mutations power evolution, while large-scale structural variations (SVs) remain poorly studied, primarily because of the lack of long-read sequencing techniques and powerful analytical tools. Here, we explore the SVs of Escherichia coli by running 67 wild-type (WT) and 37 MMR-deficient (ΔmutS) mutation accumulation lines, each experiencing more than 4000 cell divisions, by applying Nanopore long-read sequencing and Illumina PE150 sequencing, and verifying the results by Sanger sequencing. In addition to precisely repeating previous mutation rates of base-pair substitutions and indels mutation rates, we do find significant improvement in insertion and deletion detection using long-read sequencing. The long-read sequencing and corresponding softwares can particularly detect bacterial SVs in both simulated and real datasets with high accuracy. These lead to SV rates of 2.77 × 10-4 (WT) and 5.26 × 10-4 (MMR-deficient) per cell division per genome, which is comparable with previous reports. This study provides the SV rates of E. coli by applying long-read sequencing and SV-detection programs, revealing a broader and more accurate picture of spontaneous mutations in bacteria.
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Affiliation(s)
- Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China 266003
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China 266003
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China 266003
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA 85281
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China 266003
| | - Yu Zhang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China 266003
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province, China 266000
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24
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Gout JF, Hao Y, Johri P, Arnaiz O, Doak TG, Bhullar S, Couloux A, Guérin F, Malinsky S, Potekhin A, Sawka N, Sperling L, Labadie K, Meyer E, Duharcourt S, Lynch M. Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Mol Biol Evol 2023:7156828. [PMID: 37154524 DOI: 10.1093/molbev/msad107] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 12/19/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance is still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the P. aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and one additional outgroup, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene-dosage changes. This exceptional dataset of 13 species sharing an ancestral WGD and two closely related outgroup species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology.
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Affiliation(s)
- Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Parul Johri
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Simran Bhullar
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Fréderic Guérin
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Sophie Malinsky
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
| | - Natalia Sawka
- Institute of Systematic and Evolution of Animals, Polish Academy of Science, 31-016 Krakow, Poland
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Eric Meyer
- Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 75005 Paris, France
| | - Sandra Duharcourt
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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25
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Ye Z, Wei W, Pfrender M, Lynch M. Evolutionary Insights from a Large-scale Survey of Population-genomic Variation. bioRxiv 2023:2023.05.03.539276. [PMID: 37205430 PMCID: PMC10187179 DOI: 10.1101/2023.05.03.539276] [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: 05/21/2023]
Abstract
Results from data on > 1000 haplotypes distributed over a nine-year period from a natural population of the microcrustacean Daphnia pulex reveal evolutionary-genomic features at a refined scale, including key population-genetic properties that are obscured in studies with smaller sample sizes. Background selection, resulting from the recurrent introduction of deleterious alleles, appears to strongly influence the dynamics of neutral alleles, inducing indirect negative selection on rare variants and positive selection on common variants. Fluctuating selection increases the persistence of nonsynonymous alleles with intermediate frequencies, while reducing standing levels of variation at linked silent sites. Combined with the results from an equally large metapopulation survey of the study species, regions of gene structure that are under strong purifying selection and classes of genes that are under strong positive selection in this key species can be confidently identified. Most notable among rapidly evolving Daphnia genes are those associated with ribosomes, mitochondrial functions, sensory systems, and lifespan determination.
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Affiliation(s)
- Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Michael Pfrender
- Department of Biological Sciences, Notre Dame University, Notre Dame, IN 46556
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
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26
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Lynch M, Wei W, Ye Z, Pfrender M. The Genome-wide Signature of Short-term Temporal Selection. bioRxiv 2023:2023.04.28.538790. [PMID: 37162919 PMCID: PMC10168312 DOI: 10.1101/2023.04.28.538790] [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] [Indexed: 05/11/2023]
Abstract
Despite evolutionary biology's obsession with natural selection, few studies have evaluated multi-generational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a nine-year population-genomic survey of the microcrustacean Daphnia pulex. The genome-sequences of > 800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals), the preponderance of weak negative selection operating on minor alleles, and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the development of new theoretical expressions for the interpretation of population-genomic data.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Michael Pfrender
- Department of Biological Sciences, Notre Dame University, Notre Dame, IN 46556
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27
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Wang Y, Buck A, Kastrunes G, Abbas R, Lynch M, Zhong Z, Hoang SM, Miklosi A, Huang K, Cho JW, Grimaud M, Razimbaud C, Chang M, Fayed A, Apollon A, Murugan N, Li ZH, Thai T, Zerefa L, Piel B, Ivanova E, Cameron A, Nguyen QD, Zhu Z, Wei K, Laimon YN, Sheshdeh AB, Signoretti S, Braun DA, Wu CJ, Choueiri TK, Wee J, Paweletz CP, Hemberg M, Culhane AC, Barbie DA, Freeman GJ, Marasco WA. Abstract 886: Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Chimeric Antigen Receptor (CAR) T cell therapy is a new type of “living drug” that has proven to be a powerful immunotherapy for hematologic malignancies. To date, there are six CAR-T products approved by the FDA for hematologic malignancies, four targeting CD19, and two targeting B-cell maturation antigen (BCMA). However, this success has not yet been transferred to solid tumors. A major hurdle is the on-target off-tumor toxicities due to the shared expression of target antigen on normal tissues. Carbonic anhydrase IX (CAIX) is highly expressed in clear cell renal cell carcinoma (ccRCC); however, it is also expressed on bile duct at a lower physiological level leading to off-tumor toxicity of CAIX targeted therapies. The first anti-CAIX CAR-T studies, using the 1st generation G250 CAR-T cells plus IL-2 to treat patients with metastatic ccRCC, caused severe liver enzyme abnormalities in the treated patients after CAR-T cell infusions. To understand CAIX expression on tumor and normal tissues, we quantified CAIX expression on ccRCC patient samples and healthy bile duct tissues using direct stochastic optical reconstruction microscopy (dSTORM) which provides single-molecule resolution. Tet-On inducible CAIX expressing cell lines were established to mimic various CAIX densities on normal tissue and tumor samples. Using biolayer interferometry (BLI) and avidity analyzer, we identified a low-affinity, high-avidity anti-CAIX CAR G9. G9 CAR-T cells only kill CAIX high ccRCC tumor cells but not CAIX low normal cholangiocytes, and exhibited a CAIX density dependent response to Tet-On inducible CAIX expressing cell lines. Compared to high-affinity G250 CAR-T cells, G9 showed a better safety profile and a wider therapeutic window. G9 demonstrated a superior ex vivo efficacy on ccRCC patient derived organotypic tumor spheroids (PDOTS) 3D cultures which recapitulate ccRCC patient tumor microenvironment (TME), as well as low toxicity on cholangiocyte derived organotypic spheroids (CDOS). In summary, affinity/avidity fine-tuned CAIX targeted CAR-T cell therapy holds promise to achieve cures of ccRCC by efficaciously killing tumor cells and mitigating on-target off-tumor toxicity on normal tissues.
Citation Format: Yufei Wang, Alicia Buck, Gabriella Kastrunes, Rabia Abbas, Michael Lynch, Zhou Zhong, Song-My Hoang, Andras Miklosi, Kun Huang, Jae-Won Cho, Marion Grimaud, Cecile Razimbaud, Matthew Chang, Atef Fayed, Audrey Apollon, Nithyassree Murugan, Ze-Hua Li, Tran Thai, Luann Zerefa, Brandon Piel, Elena Ivanova, Amy Cameron, Quang-De Nguyen, Zhu Zhu, Kevin Wei, Yasmin Nabil Laimon, Aseman Bagheri Sheshdeh, Sabina Signoretti, David A. Braun, Catherine J. Wu, Toni K. Choueiri, Jon Wee, Cloud P. Paweletz, Martin Hemberg, Aedin C. Culhane, David A. Barbie, Gordon J. Freeman, Wayne A. Marasco. Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 886.
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Affiliation(s)
- Yufei Wang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Kun Huang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | - Atef Fayed
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Ze-Hua Li
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Tran Thai
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Zhu Zhu
- 5Brigham and Women's Hospital, Boston, MA
| | - Kevin Wei
- 5Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | | | - Jon Wee
- 5Brigham and Women's Hospital, Boston, MA
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28
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Wu K, Li H, Wang Y, Liu D, Li H, Zhang Y, Lynch M, Long H. Silver nanoparticles elevate mutagenesis of eukaryotic genomes. G3 (Bethesda) 2023; 13:6986423. [PMID: 36635051 PMCID: PMC9997555 DOI: 10.1093/g3journal/jkad008] [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: 11/28/2022] [Revised: 11/28/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023]
Abstract
Metal nanoparticles, especially silver, have been used in various medical scenarios, due to their excellent antimicrobial effects. Recent studies have shown that AgNPs do not exert mutagenic effects on target bacteria, but the degree to which they compromise eukaryotic genomes remains unclear. To study this, we evaluated the mutagenic effects of AgNPs on the fission yeast Schizosaccharomyces pombe ATCC-16979, of which ∼23% genes are homologous to human ones, at single-nucleotide resolution, and whole-genome scale by running 283 mutation accumulation lines for ∼260,000 cell divisions in total. We also explored the action and mutagenesis mechanisms using differential gene-expression analysis based on RNAseq. Upon AgNPs treatment, the genomic base-substitution mutation rate of S. pombe at four-fold degenerate sites increased by 3.46×, and small indels were prone to occur in genomic regions that are not simple sequence repeats. The G:C → T:A transversion rate was also significantly increased, likely mostly from oxidative damage. Thus, in addition to their antimicrobial potency, AgNPs might pose slight genotoxicity threats to eukaryotic and possibly human genomes, though at a low magnitude.
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Affiliation(s)
- Kun Wu
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province 266237, China
| | - Haichao Li
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Yaohai Wang
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Dan Liu
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Hui Li
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Yu Zhang
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province 266000, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province 266237, China
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Kucukyildirim S, Ozdemirel HO, Lynch M. Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea. G3 (Bethesda) 2023; 13:jkac303. [PMID: 36519377 PMCID: PMC9997560 DOI: 10.1093/g3journal/jkac303] [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: 06/02/2022] [Revised: 07/02/2021] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
Archaea are a major part of Earth's microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum. Although Hfx. volcanii and Hbt. salinarum have different salt requirements, both species have highly polyploid genomes and similar GC content. We accumulated mutations for an average of 1250 generations in 67 mutation accumulation lines of Hbt. salinarum, and revealed 84 single-base substitutions and 10 insertion-deletion mutations. The estimated base-substitution mutation rate of 3.99 × 10-10 per site per generation or 1.0 × 10-3 per genome per generation in Hbt. salinarum is similar to that reported for Hfx. volcanii (1.2 × 10-3 per genome per generation), but the genome-wide insertion-deletion rate and spectrum of mutations are somewhat dissimilar in these archaeal species. The spectra of spontaneous mutations were AT biased in both archaea, but they differed in significant ways that may be related to differences in the fidelity of DNA replication/repair mechanisms or a simple result of the different salt concentrations.
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Affiliation(s)
| | | | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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30
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Ye Z, Bishop T, Wang Y, Shahriari R, Lynch M. Evolution of sex determination in crustaceans. Mar Life Sci Technol 2023; 5:1-11. [PMID: 37073332 PMCID: PMC10077267 DOI: 10.1007/s42995-023-00163-4] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Sex determination (SD) involves mechanisms that determine whether an individual will develop into a male, female, or in rare cases, hermaphrodite. Crustaceans harbor extremely diverse SD systems, including hermaphroditism, environmental sex determination (ESD), genetic sex determination (GSD), and cytoplasmic sex determination (e.g., Wolbachia controlled SD systems). Such diversity lays the groundwork for researching the evolution of SD in crustaceans, i.e., transitions among different SD systems. However, most previous research has focused on understanding the mechanism of SD within a single lineage or species, overlooking the transition across different SD systems. To help bridge this gap, we summarize the understanding of SD in various clades of crustaceans, and discuss how different SD systems might evolve from one another. Furthermore, we review the genetic basis for transitions between different SD systems (i.e., Dmrt genes) and propose the microcrustacean Daphnia (clade Branchiopoda) as a model to study the transition from ESD to GSD.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Trent Bishop
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Ryan Shahriari
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
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31
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Nadarajah R, Ludman P, Appelman Y, Brugaletta S, Budaj A, Bueno H, Huber K, Kunadian V, Leonardi S, Lettino M, Milasinovic D, Gale CP, Budaj A, Dagres N, Danchin N, Delgado V, Emberson J, Friberg O, Gale CP, Heyndrickx G, Iung B, James S, Kappetein AP, Maggioni AP, Maniadakis N, Nagy KV, Parati G, Petronio AS, Pietila M, Prescott E, Ruschitzka F, Van de Werf F, Weidinger F, Zeymer U, Gale CP, Beleslin B, Budaj A, Chioncel O, Dagres N, Danchin N, Emberson J, Erlinge D, Glikson M, Gray A, Kayikcioglu M, Maggioni AP, Nagy KV, Nedoshivin A, Petronio AP, Roos-Hesselink JW, Wallentin L, Zeymer U, Popescu BA, Adlam D, Caforio ALP, Capodanno D, Dweck M, Erlinge D, Glikson M, Hausleiter J, Iung B, Kayikcioglu M, Ludman P, Lund L, Maggioni AP, Matskeplishvili S, Meder B, Nagy KV, Nedoshivin A, Neglia D, Pasquet AA, Roos-Hesselink JW, Rossello FJ, Shaheen SM, Torbica A, Gale CP, Ludman PF, Lettino M, Bueno H, Huber K, Leonardi S, Budaj A, Milasinovic (Serbia) D, Brugaletta S, Appelman Y, Kunadian V, Al Mahmeed WAR, Kzhdryan H, Dumont C, Geppert A, Bajramovic NS, Cader FA, Beauloye C, Quesada D, Hlinomaz O, Liebetrau C, Marandi T, Shokry K, Bueno H, Kovacevic M, Crnomarkovic B, Cankovic M, Dabovic D, Jarakovic M, Pantic T, Trajkovic M, Pupic L, Ruzicic D, Cvetanovic D, Mansourati J, Obradovic I, Stankovic M, Loh PH, Kong W, Poh KK, Sia CH, Saw K, Liška D, Brozmannová D, Gbur M, Gale CP, Maxian R, Kovacic D, Poznic NG, Keric T, Kotnik G, Cercek M, Steblovnik K, Sustersic M, Cercek AC, Djokic I, Maisuradze D, Drnovsek B, Lipar L, Mocilnik M, Pleskovic A, Lainscak M, Crncic D, Nikojajevic I, Tibaut M, Cigut M, Leskovar B, Sinanis T, Furlan T, Grilj V, Rezun M, Mateo VM, Anguita MJF, Bustinza ICM, Quintana RB, Cimadevilla OCF, Fuertes J, Lopez F, Dharma S, Martin MD, Martinez L, Barrabes JA, Bañeras J, Belahnech Y, Ferreira-Gonzalez I, Jordan P, Lidon RM, Mila L, Sambola A, Orvin K, Sionis A, Bragagnini W, Cambra AD, Simon C, Burdeus MV, Ariza-Solé A, Alegre O, Alsina M, Ferrando JIL, Bosch X, Sinha A, Vidal P, Izquierdo M, Marin F, Esteve-Pastor MA, Tello-Montoliu A, Lopez-Garcia C, Rivera-Caravaca JM, Gil-Pérez P, Nicolas-Franco S, Keituqwa I, Farhan HA, Silva L, Blasco A, Escudier JM, Ortega J, Zamorano JL, Sanmartin M, Pereda DC, Rincon LM, Gonzalez P, Casado T, Sadeghipour P, Lopez-Sendon JL, Manjavacas AMI, Marin LAM, Sotelo LR, Rodriguez SOR, Bueno H, Martin R, Maruri R, Moreno G, Moris C, Gudmundsdottir I, Avanzas P, Ayesta A, Junco-Vicente A, Cubero-Gallego H, Pascual I, Sola NB, Rodriguez OA, Malagon L, Martinez-Basterra J, Arizcuren AM, Indolfi C, Romero J, Calleja AG, Fuertes DG, Crespín Crespín M, Bernal FJC, Ojeda FB, Padron AL, Cabeza MM, Vargas CM, Yanes G, Kitai T, Gonzalez MJG, Gonzalez Gonzalez J, Jorge P, De La Fuente B, Bermúdez MG, Perez-Lopez CMB, Basiero AB, Ruiz AC, Pamias RF, Chamero PS, Mirrakhimov E, Hidalgo-Urbano R, Garcia-Rubira JC, Seoane-Garcia T, Arroyo-Monino DF, Ruiz AB, Sanz-Girgas E, Bonet G, Rodríguez-López J, Scardino C, De Sousa D, Gustiene O, Elbasheer E, Humida A, Mahmoud H, Mohamed A, Hamid E, Hussein S, Abdelhameed M, Ali T, Ali Y, Eltayeb M, Philippe F, Ali M, Almubarak E, Badri M, Altaher S, Alla MD, Dellborg M, Dellborg H, Hultsberg-Olsson G, Marjeh YB, Abdin A, Erglis A, Alhussein F, Mgazeel F, Hammami R, Abid L, Bahloul A, Charfeddine S, Ellouze T, Canpolat U, Oksul M, Muderrisoglu H, Popovici M, Karacaglar E, Akgun A, Ari H, Ari S, Can V, Tuncay B, Kaya H, Dursun L, Kalenderoglu K, Tasar O, Kalpak O, Kilic S, Kucukosmanoglu M, Aytekin V, Baydar O, Demirci Y, Gürsoy E, Kilic A, Yildiz Ö, Arat-Ozkan A, Sinan UY, Dagva M, Gungor B, Sekerci SS, Zeren G, Erturk M, Demir AR, Yildirim C, Can C, Kayikcioglu M, Yagmur B, Oney S, Xuereb RG, Sabanoglu C, Inanc IH, Ziyrek M, Sen T, Astarcioglu MA, Kahraman F, Utku O, Celik A, Surmeli AO, Basaran O, Ahmad WAW, Demirbag R, Besli F, Gungoren F, Ingabire P, Mondo C, Ssemanda S, Semu T, Mulla AA, Atos JS, Wajid I, Appelman Y, Al Mahmeed WAR, Atallah B, Bakr K, Garrod R, Makia F, Eldeeb F, Abdekader R, Gomaa A, Kandasamy S, Maruthanayagam R, Nadar SK, Nakad G, Nair R, Mota P, Prior P, Mcdonald S, Rand J, Schumacher N, Abraheem A, Clark M, Coulding M, Qamar N, Turner V, Negahban AQ, Crew A, Hope S, Howson J, Jones S, Lancaster N, Nicholson A, Wray G, Donnelly P, Gierlotka M, Hammond L, Hammond S, Regan S, Watkin R, Papadopoulos C, Ludman P, Hutton K, Macdonald S, Nilsson A, Roberts S, Monteiro S, Garg S, Balachandran K, Mcdonald J, Singh R, Marsden K, Davies K, Desai H, Goddard W, Iqbal N, Chalil S, Dan GA, Galasko G, Assaf O, Benham L, Brown J, Collins S, Fleming C, Glen J, Mitchell M, Preston S, Uttley A, Radovanovic M, Lindsay S, Akhtar N, Atkinson C, Vinod M, Wilson A, Clifford P, Firoozan S, Yashoman M, Bowers N, Chaplin J, Reznik EV, Harvey S, Kononen M, Lopesdesousa G, Saraiva F, Sharma S, Cruddas E, Law J, Young E, Hoye A, Harper P, Balghith M, Rowe K, Been M, Cummins H, French E, Gibson C, Abraham JA, Hobson S, Kay A, Kent M, Wilkinson A, Mohamed A, Clark S, Duncan L, Ahmed IM, Khatiwada D, Mccarrick A, Wanda I, Read P, Afsar A, Rivers V, Theobald T, Cercek M, Bell S, Buckman C, Francis R, Peters G, Stables R, Morgan M, Noorzadeh M, Taylor B, Twiss S, Widdows P, Brozmannová D, Wilkinson V, Black M, Clark A, Clarkson N, Currie J, George L, Mcgee C, Izzat L, Lewis T, Omar Z, Aytekin V, Phillips S, Ahmed F, Mackie S, Oommen A, Phillips H, Sherwood M, Aleti S, Charles T, Jose M, Kolakaluri L, Ingabire P, Karoudi RA, Deery J, Hazelton T, Knight A, Price C, Turney S, Kardos A, Williams F, Wren L, Bega G, Alyavi B, Scaletta D, Kunadian V, Cullen K, Jones S, Kirkup E, Ripley DP, Matthews IG, Mcleod A, Runnett C, Thomas HE, Cartasegna L, Gunarathne A, Burton J, King R, Quinn J, Sobolewska J, Munt S, Porter J, Christenssen V, Leng K, Peachey T, Gomez VN, Temple N, Wells K, Viswanathan G, Taneja A, Cann E, Eglinton C, Hyams B, Jones E, Reed F, Smith J, Beltrano C, Affleck DC, Turner A, Ward T, Wilmshurst N, Stirrup J, Brunton M, Whyte A, Smith S, Murray V, Walker R, Novas V, Weston C, Brown C, Collier D, Curtis K, Dixon K, Wells T, Trim F, Ghosh J, Mavuri M, Barman L, Dumont C, Elliott K, Harrison R, Mallinson J, Neale T, Smith J, Toohie J, Turnbull A, Parker E, Hossain R, Cheeseman M, Balparda H, Hill J, Hood M, Hutchinson D, Mellows K, Pendlebury C, Storey RF, Barker J, Birchall K, Denney H, Housley K, Cardona M, Middle J, Kukreja N, Gati S, Kirk P, Lynch M, Srinivasan M, Szygula J, Baker P, Cruz C, Derigay J, Cigalini C, Lamb K, Nembhard S, Price A, Mamas M, Massey I, Wain J, Delaney J, Junejo S, Martin K, Obaid D, Hoyle V, Brinkworth E, Davies C, Evans D, Richards S, Thomas C, Williams M, Dayer M, Mills H, Roberts K, Goodchild F, Dámaso ES, Greig N, Kundu S, Donaldson D, Tonks L, Beekes M, Button H, Hurford F, Motherwell N, Summers-Wall J, Felmeden D, Tapia V, Keeling P, Sheikh U, Yonis A, Felmeden L, Hughes D, Micklewright L, Summerhayes A, Sutton J, Panoulas V, Prendergast C, Poghosyan K, 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S, Popescu MI, Cozma A, Babes EE, Rus M, Ardelean A, Larisa R, Moisi M, Ban E, Buzle A, Filimon G, Dobreanu D, Lupu S, Mitre A, Rudzik R, Sus I, Opris D, Somkereki C, Mornos C, Petrescu L, Betiu A, Volcescu A, Ioan O, Luca C, Maximov D, Mosteoru S, Pascalau L, Roman C, Brie D, Crisan S, Erimescu C, Falnita L, Gaita D, Gheorghiu M, Levashov S, Redkina M, Novitskii N, Dementiev E, Baglikov A, Zateyshchikov D, Zubova E, Rogozhina A, Salikov A, Nikitin I, Reznik EV, Komissarova MS, Shebzukhova M, Shitaya K, Stolbova S, Larina V, Akhmatova F, Chuvarayan G, Arefyev MN, Averkov OV, Volkova AL, Sepkhanyan MS, Vecherko VI, Meray I, Babaeva L, Goreva L, Pisaryuk A, Potapov P, Teterina M, Ageev F, Silvestrova G, Fedulaev Y, Pinchuk T, Staroverov I, Kalimullin D, Sukhinina T, Zhukova N, Ryabov V, Kruchinkina E, Vorobeva D, Shevchenko I, Budyak V, Elistratova O, Fetisova E, Islamov R, Ponomareva E, Khalaf H, Shaimaa AA, Kamal W, Alrahimi J, Elshiekh A, Balghith M, Ahmed A, Attia N, Jamiel AA, Potpara T, Marinkovic M, Mihajlovic M, Mujovic N, Kocijancic A, Mijatovic Z, Radovanovic M, Matic D, Milosevic A, Savic L, Subotic I, Uscumlic A, Zlatic N, Antonijevic J, Vesic O, Vucic R, Martinovic SS, Kostic T, Atanaskovic V, Mitic V, Stanojevic D, Petrovic M. Cohort profile: the ESC EURObservational Research Programme Non-ST-segment elevation myocardial infraction (NSTEMI) Registry. Eur Heart J Qual Care Clin Outcomes 2022; 9:8-15. [PMID: 36259751 DOI: 10.1093/ehjqcco/qcac067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022]
Abstract
AIMS The European Society of Cardiology (ESC) EURObservational Research Programme (EORP) Non-ST-segment elevation myocardial infarction (NSTEMI) Registry aims to identify international patterns in NSTEMI management in clinical practice and outcomes against the 2015 ESC Guidelines for the management of acute coronary syndromes in patients presenting without ST-segment-elevation. METHODS AND RESULTS Consecutively hospitalised adult NSTEMI patients (n = 3620) were enrolled between 11 March 2019 and 6 March 2021, and individual patient data prospectively collected at 287 centres in 59 participating countries during a two-week enrolment period per centre. The registry collected data relating to baseline characteristics, major outcomes (in-hospital death, acute heart failure, cardiogenic shock, bleeding, stroke/transient ischaemic attack, and 30-day mortality) and guideline-recommended NSTEMI care interventions: electrocardiogram pre- or in-hospital, pre-hospitalization receipt of aspirin, echocardiography, coronary angiography, referral to cardiac rehabilitation, smoking cessation advice, dietary advice, and prescription on discharge of aspirin, P2Y12 inhibition, angiotensin converting enzyme inhibitor (ACEi)/angiotensin receptor blocker (ARB), beta-blocker, and statin. CONCLUSION The EORP NSTEMI Registry is an international, prospective registry of care and outcomes of patients treated for NSTEMI, which will provide unique insights into the contemporary management of hospitalised NSTEMI patients, compliance with ESC 2015 NSTEMI Guidelines, and identify potential barriers to optimal management of this common clinical presentation associated with significant morbidity and mortality.
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Affiliation(s)
- Ramesh Nadarajah
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, LS2 9JT Leeds, UK.,Leeds Institute of Data Analytics, University of Leeds, LS2 9JT Leeds, UK.,Department of Cardiology, Leeds Teaching Hospitals NHS Trust, LS1 3EX Leeds, UK
| | - Peter Ludman
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
| | - Yolande Appelman
- Department of Cardiology, Amsterdam UMC-Vrije Universiteit, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Salvatore Brugaletta
- Hospital Clinic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Andrzej Budaj
- Department of Cardiology, Center of Postgraduate Medical Education, Grochowski Hospital, Warsaw, Poland
| | - Hector Bueno
- Cardiology Department, Hospital Universitario 12 de Octubre and Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Kurt Huber
- 3rd Medical Department, Cardiology and Intensive Care Medicine, Clinic Ottakring (Wilhelminenhospital), Vienna, Austria.,Medical Faculty, Sigmund Freud University, Vienna, Austria
| | - Vijay Kunadian
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Cardiothoracic Centre, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sergio Leonardi
- University of Pavia, Pavia, Italy.,Fondazione IRCCS Policlinico S.Matteo, Pavia, Italy
| | - Maddalena Lettino
- Cardio-Thoracic and Vascular Department, San Gerardo Hospital, ASST-Monza, Monza, Italy
| | - Dejan Milasinovic
- Department of Cardiology, University Clinical Center of Serbia and Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Chris P Gale
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, LS2 9JT Leeds, UK.,Leeds Institute of Data Analytics, University of Leeds, LS2 9JT Leeds, UK.,Department of Cardiology, Leeds Teaching Hospitals NHS Trust, LS1 3EX Leeds, UK
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Choy S, Paolino A, Kim B, Lim S, Seo J, Tan S, Tan W, Corbett M, Barker J, Lynch M, Smith C, Mahil S. 100 Deep learning image analyses in dermatology, beyond skin lesions: a systematic review. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Du-Harpur X, Ganier C, Harun N, Rashidghamat E, Luscombe N, Watt F, Lynch M. 048 The transcriptional landscape of hidradenitis suppurativa at single-cell and spatial resolution. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Egan A, Farrell A, Byrne B, Lynch M. 12 VACCINATION UP-TAKE IN DERMATOLOGY PATIENTS OVER THE AGE OF 65 YEARS ON BIOLOGICAL TREATMENT. Age Ageing 2022. [DOI: 10.1093/ageing/afac218.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Biologic and immunosuppressive therapies play important roles in the management of a wide variety of dermatologic diseases. However, immunotherapies can negatively affect normal immune functioning, placing these patients at high risk of infection. The strength of the immune system also declines with increasing age. Thus, in accordance with the British Association of Dermatology guidelines (August 2021), patients taking biologic therapy can and should have their covid, influenza and pneumococcal vaccinations.
Methods
We conducted a retrospective audit of all patients over the age of 65 years on biological therapy in the dermatology clinic between March 2021 to March 2022. Data on patients covid, influenza and pneumococcal vaccination status was obtained from Dermatology database and patients medical records.
Results
A total of 18 patients over the age of 65 years, were on biological therapy in the Dermatology Department, between March 2021 to March 2022. The mean age was found to be 71 years with a standard deviation of 5.2 and there was equal gender distribution. 94% (n=17) of patients had psoriasis and 6% (n=1) had eczema. With regards to biological treatments, 17% (n=3) of patients were on Adalimumab,11% (n=2) on Etanercept and 28% (n=5) on Cosntyx. 100% (n=18) had all three of their covid-19 vaccines. 50% (n=8) are awaiting their 4th covid vaccination. 94% (n=17) of patients had their influenza vaccine. 66% (n=12) had their pneumococcal vaccination, the patients who had not had their pneumococcal vaccination were recommended and advised to have it.
Conclusion
This audit confirms dermatology patients over the age of sixty-five years, are compliant on receiving their covid vaccinations, as recommended by the BAD. However, only 66% of patients had their pneumococcal vaccination and 94% had their influenza vaccine, illustrating the need for educational intervention on the importance of vaccination. This will then be followed by a reaudit next year to complete the audit cycle.
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Affiliation(s)
- A Egan
- University Hospital Limerick Geriatrics Department, , Dooradoyle, Limerick, Ireland
| | - A Farrell
- University Hospital Limerick Dermatology Department, , Dooradoyle, Limerick, Ireland
| | - B Byrne
- University Hospital Limerick Dermatology Department, , Dooradoyle, Limerick, Ireland
| | - M Lynch
- University Hospital Limerick Dermatology Department, , Dooradoyle, Limerick, Ireland
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Kuo KH, Layton DM, Lal A, Al-Samkari H, Bhatia J, Kosinski PA, Tong B, Lynch M, Uhlig K, Vichinsky EP. LONG-TERM EFFICACY AND SAFETY OF THE ORAL PYRUVATE KINASE ACTIVATOR MITAPIVAT IN ADULTS WITH NON–TRANSFUSION-DEPENDENT ALPHA- OR BETA-THALASSEMIA. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Lynch M, Ye Z, Urbany L, Maruki T, Wei W. The Linkage-disequilibrium and Recombinational Landscape in Daphnia pulex. Genome Biol Evol 2022; 14:6726537. [PMID: 36170345 PMCID: PMC9642108 DOI: 10.1093/gbe/evac145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
By revealing the influence of recombinational activity beyond what can be achieved with controlled crosses, measures of linkage disequilibrium (LD) in natural populations provide a powerful means of defining the recombinational landscape within which genes evolve. In one of the most comprehensive studies of this sort ever performed, involving whole-genome analyses on nearly 1,000 individuals of the cyclically parthenogenetic microcrustacean Daphnia pulex, the data suggest a relatively uniform pattern of recombination across the genome. Patterns of LD are quite consistent among populations; average rates of recombination are quite similar for all chromosomes; and although some chromosomal regions have elevated recombination rates, the degree of inflation is not large, and the overall spatial pattern of recombination is close to the random expectation. Contrary to expectations for models in which crossing-over is the primary mechanism of recombination, and consistent with data for other species, the distance-dependent pattern of LD indicates excessively high levels at both short and long distances and unexpectedly low levels of decay at long distances, suggesting significant roles for factors such as nonindependent mutation, population subdivision, and recombination mechanisms unassociated with crossing over. These observations raise issues regarding the classical LD equilibrium model widely applied in population genetics to infer recombination rates across various length scales on chromosomes.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, Plön, Germany
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, Pllön, Germany
| | - Lina Urbany
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306, Plon, Germany
| | - Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, Plon, Germany
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, Plon, Germany
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McCarver V, Dreyfuss I, Segars K, Knopp E, Lynch M, Miller R. 34030 Primary cutaneous follicle center lymphoma mimicking alopecia areata: A case report. J Am Acad Dermatol 2022. [DOI: 10.1016/j.jaad.2022.06.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Reidy N, Coetzee H, Roche C, Brazil E, O'Sullivan L, Brady D, Lynch M. SARS-CoV-2 Testing and Patient Waiting Times in the Emergency Department. Ir Med J 2022; 115:633. [PMID: 36300733] [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] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aim Emergency Departments (EDs) were impacted early in the coronavirus disease 2019 (COVID-19) pandemic, with high attendance numbers. EDs relied upon SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) tests to triage patients and facilitate admission to appropriate wards, meaning positive patients were isolated as early as possible. In October 2020, we introduced a 24-hour SARS-CoV-2 testing service. We examined the impact of this on patient experience times (PETs) in the ED, and on healthcare-associated (HA) COVID-19 infections. Methods Data on PETs before and after the introduction of 24-hour testing were available from the ED. HA COVID-19 infections were reported weekly to the Health Services Executive as a key performance indicator. Results Mean PET prior to the pandemic was 20 hours and dropped to 10 and 13 hours respectively in the first and second wave. A surge in case numbers and ED attendances during the third wave was not reflected in a rise in PETs, with a mean PET of 11 hours, significantly below pre-pandemic levels. HA-COVID-19 infections remained stable between wave one and three (83 v 92). Conclusion The introduction of 24-hour SARS-CoV-2 testing in our ED contributed to a reduction in PETs, facilitated appropriate patient placement at ward level, and kept HA-COVID-19 infections at acceptably low levels.
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Affiliation(s)
- N Reidy
- Department of Clinical Microbiology, Mater Hospital, Dublin, Ireland
| | - H Coetzee
- Department of Emergency Medicine, Mater Hospital, Dublin, Ireland
| | - C Roche
- Department of Emergency Medicine, Mater Hospital, Dublin, Ireland
| | - E Brazil
- Department of Emergency Medicine, Mater Hospital, Dublin, Ireland
| | - L O'Sullivan
- Department of Clinical Microbiology, Mater Hospital, Dublin, Ireland
| | - D Brady
- Department of Clinical Microbiology, Mater Hospital, Dublin, Ireland
| | - M Lynch
- Department of Clinical Microbiology, Mater Hospital, Dublin, Ireland
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Harrison JF, Biewener A, Bernhardt JR, Burger JR, Brown JH, Coto ZN, Duell ME, Lynch M, Moffett ER, Norin T, Pettersen AK, Smith FA, Somjee U, Traniello JFA, Williams TM. White Paper: An Integrated Perspective on the Causes of Hypometric Metabolic Scaling in Animals. Integr Comp Biol 2022; 62:icac136. [PMID: 35933126 PMCID: PMC9724154 DOI: 10.1093/icb/icac136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/16/2022] [Accepted: 05/19/2022] [Indexed: 11/15/2022] Open
Abstract
Larger animals studied during ontogeny, across populations, or across species, usually have lower mass-specific metabolic rates than smaller animals (hypometric scaling). This pattern is usually observed regardless of physiological state (e.g. basal, resting, field, maximally-active). The scaling of metabolism is usually highly correlated with the scaling of many life history traits, behaviors, physiological variables, and cellular/molecular properties, making determination of the causation of this pattern challenging. For across-species comparisons of resting and locomoting animals (but less so for across populations or during ontogeny), the mechanisms at the physiological and cellular level are becoming clear. Lower mass-specific metabolic rates of larger species at rest are due to a) lower contents of expensive tissues (brains, liver, kidneys), and b) slower ion leak across membranes at least partially due to membrane composition, with lower ion pump ATPase activities. Lower mass-specific costs of larger species during locomotion are due to lower costs for lower-frequency muscle activity, with slower myosin and Ca++ ATPase activities, and likely more elastic energy storage. The evolutionary explanation(s) for hypometric scaling remain(s) highly controversial. One subset of evolutionary hypotheses relies on constraints on larger animals due to changes in geometry with size; for example, lower surface-to-volume ratios of exchange surfaces may constrain nutrient or heat exchange, or lower cross-sectional areas of muscles and tendons relative to body mass ratios would make larger animals more fragile without compensation. Another subset of hypotheses suggests that hypometric scaling arises from biotic interactions and correlated selection, with larger animals experiencing less selection for mass-specific growth or neurolocomotor performance. A additional third type of explanation comes from population genetics. Larger animals with their lower effective population sizes and subsequent less effective selection relative to drift may have more deleterious mutations, reducing maximal performance and metabolic rates. Resolving the evolutionary explanation for the hypometric scaling of metabolism and associated variables is a major challenge for organismal and evolutionary biology. To aid progress, we identify some variation in terminology use that has impeded cross-field conversations on scaling. We also suggest that promising directions for the field to move forward include: 1) studies examining the linkages between ontogenetic, population-level, and cross-species allometries, 2) studies linking scaling to ecological or phylogenetic context, 3) studies that consider multiple, possibly interacting hypotheses, and 4) obtaining better field data for metabolic rates and the life history correlates of metabolic rate such as lifespan, growth rate and reproduction.
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Affiliation(s)
- Jon F Harrison
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Andrew Biewener
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joanna R Bernhardt
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Yale Institute for Biospheric Studies, New Haven, CT 06520, USA
| | - Joseph R Burger
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - James H Brown
- Center for Evolutionary and Theoretical Immunology, The University of New Mexico, Albuquerque, NM 87131, USA
| | - Zach N Coto
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Meghan E Duell
- Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Emma R Moffett
- Department of Ecology and Evolution, University of California, Irvine, CA 92697, USA
| | - Tommy Norin
- DTU Aqua | National Institute of Aquatic Resources, Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs. Lyngby, Denmark
| | - Amanda K Pettersen
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ummat Somjee
- Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - Terrie M Williams
- Division of Physical and Biological Sciences, University of California, Santa Cruz, CA 95064, USA
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Maruki T, Ye Z, Lynch M. Evolutionary Genomics of a Subdivided Species. Mol Biol Evol 2022; 39:6650829. [PMID: 35895848 PMCID: PMC9372567 DOI: 10.1093/molbev/msac152] [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] [Indexed: 11/18/2022] Open
Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State Univ., Tempe, AZ 85287USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State Univ., Tempe, AZ 85287USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State Univ., Tempe, AZ 85287USA
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Abstract
Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum. Most creatures on Earth are single cell organisms. The tree of life comprises three domains, two of which – bacteria and archaea – are formed exclusively of creatures that spend their existence as independent cells. Yet even eukaryotes, the domain which include animals and plants, feature single cell species such as yeasts and algae. Regardless of which group they belong to, all single-celled organisms must find food in their environment. For this, many are equipped with flagella, whip-like structures that protrude from the cell and allow it to swim. In fact, archaea, bacteria and eukaryotes have all independently evolved these structures. However, flagella are also expensive for an organism to build, maintain and operate. They are only worth having if the advantages they bring to the cell compensate for their cost; many single-cell species do not carry flagella and obtain their food without having to swim. To explore this trade-off, Schavemaker and Lynch calculated the cost of building and using flagella for about 200 species across the tree of life. The analysis show that the amount of energy spent on flagella varied between 0.1% and 40% of the entire cell budget. This investment is only worthwhile if the cell is above a certain size. Smaller than this, and the organism is better off obtaining its food passively. The results also show that while eukaryotic flagella are much bigger and quite different than their bacterial counterpart, both appendages share the same patterns of cost effectiveness. However only eukaryotic cells, which are on average larger than bacteria, can afford to evolve such sizable and complex structures; making just one would cost more than the entire energy budget of a bacterial cell. Many single-cell species which are critical for the health of the planet are equipped with flagella, such as the microorganisms which recycle matter in the oceans and release carbon dioxide. Understanding the costs and benefits of flagella could explain more about this aspect of the carbon cycle, and therefore global warming.
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Affiliation(s)
- Paul E Schavemaker
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, United States
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, United States
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Lynch M, Schavemaker PE, Licknack TJ, Hao Y, Pezzano A. Evolutionary bioenergetics of ciliates. J Eukaryot Microbiol 2022; 69:e12934. [PMID: 35778890 DOI: 10.1111/jeu.12934] [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: 02/14/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Understanding why various organisms evolve alternative ways of living requires information on both the fitness advantages of phenotypic modifications and the costs of constructing and operating cellular features. Although the former has been the subject of a myriad of ecological studies, almost no attention has been given to how organisms allocate resources to alternative structures and functions. We address these matters by capitalizing on an array of observations on diverse ciliate species and from the emerging field of evolutionary bioenergetics. A relatively robust and general estimator for the total cost of a cell per cell cycle (in units of ATP equivalents) is provided, and this is then used to understand how the magnitudes of various investments scale with cell size. Among other things, we examine the costs associated with the large macronuclear genomes of ciliates, as well as ribosomes, various internal membranes, osmoregulation, cilia, and swimming activities. Although a number of uncertainties remain, the general approach taken may serve as blueprint for expanding this line of work to additional traits and phylogenetic lineages.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Paul E Schavemaker
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Timothy J Licknack
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Arianna Pezzano
- Ira A. Fulton Schools of Engineering, School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ
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43
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Abstract
Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, “marking” one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. PLoS Biol 2022; 20:e3001669. [PMID: 35639797 PMCID: PMC9154105 DOI: 10.1371/journal.pbio.3001669] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Peter D. Keightley
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susanne P. Pfeifer
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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45
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Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol 2022; 39:msac081. [PMID: 35446958 PMCID: PMC9040049 DOI: 10.1093/molbev/msac081] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Iain Konigsberg
- Division of Biomedical Informatics & Personalized Medicine, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Thomas G. Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Heewook Lee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, No. 72 Binhai Road, Qingdao, Shandong Province 266237, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Ye Z, Zhao C, Raborn RT, Lin M, Wei W, Hao Y, Lynch M. Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol Biol Evol 2022; 39:6553573. [PMID: 35325186 PMCID: PMC9004417 DOI: 10.1093/molbev/msac059] [Citation(s) in RCA: 4] [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] [Indexed: 11/13/2022] Open
Abstract
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Chaoxian Zhao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - R Taylor Raborn
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Man Lin
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Wen Wei
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Yue Hao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
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47
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Abstract
The current study investigated the neural correlates of non-suicidal self-injury (NSSI) and suicidal ideation across the dorsolateral prefrontal cortex. Two-hundred ninety-six undergraduates solved anagram tasks while being monitored by a functional near-infrared spectroscopy device, and completed a questionnaire assessing behaviors and symptoms. Repeated measures analysis of variance revealed location-specific changes in neural activity based on NSSI, suicidal ideation, task type, and cognitive demand. The presence of suicidal ideation was associated with specific patterns of neural activity, modified by sex and task type. Interestingly, participants who engaged in NSSI exhibited some deactivation of the dlPFC when faced with more difficult cognitive challenges. Future research on these processes may allow for noninvasive imaging techniques to help screen risk for suicidality and NSSI.
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Selwood KE, Antos M, Bramwell M, Lee A, Lynch M, Magrath MJL, Maute K, Melvin F, Mott R, Perri M, Whiteford C, Clarke RH. Emergency conservation interventions during times of crisis: A case study for a threatened bird species in the Australian Black Summer bushfires. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Katherine E. Selwood
- Zoos Victoria Parkville Victoria Australia
- School of Biosciences University of Melbourne Parkville Victoria Australia
| | - Mark Antos
- Science and Management Effectiveness Parks Victoria Melbourne Victoria Australia
| | - Mick Bramwell
- Forest, Fire and Regions Department of Environment, Land, Water and Planning Bairnsdale Victoria Australia
| | - Adam Lee
- Zoos Victoria Parkville Victoria Australia
| | | | - Michael J. L. Magrath
- Zoos Victoria Parkville Victoria Australia
- School of Biosciences University of Melbourne Parkville Victoria Australia
| | - Kimberly Maute
- Centre for Sustainable Ecosystem Solutions University of Wollongong Wollongong New South Wales Australia
| | | | - Rowan Mott
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Marc Perri
- Forest, Fire and Regions Department of Environment, Land, Water and Planning Orbost Victoria Australia
| | | | - Rohan H. Clarke
- School of Biological Sciences Monash University Clayton Victoria Australia
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Ho WC, Behringer MG, Miller SF, Gonzales J, Nguyen A, Allahwerdy M, Boyer GF, Lynch M. Evolutionary Dynamics of Asexual Hypermutators Adapting to a Novel Environment. Genome Biol Evol 2021; 13:evab257. [PMID: 34864972 PMCID: PMC8643662 DOI: 10.1093/gbe/evab257] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2021] [Indexed: 12/24/2022] Open
Abstract
How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments.
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Affiliation(s)
- Wei-Chin Ho
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Megan G Behringer
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Samuel F Miller
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jadon Gonzales
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Amber Nguyen
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Meriem Allahwerdy
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Gwyneth F Boyer
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Kucukyildirim S, Miller SF, Lynch M. Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium Acidobacterium capsulatum. Ecol Evol 2021; 11:17609-17614. [PMID: 35003627 PMCID: PMC8717266 DOI: 10.1002/ece3.8429] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/07/2022] Open
Abstract
Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base-substitution mutation rate of 1.22 × 10-10 per site per generation or 4 × 10-4 per genome per generation, which is significantly lower than the consensus value (2.5-4.6 × 10-3) of mesothermophilic (~15-40°C) and neutrophilic (pH 6-8) prokaryotic organisms. However, the insertion-deletion rate (0.43 × 10-10 per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.
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Affiliation(s)
- Sibel Kucukyildirim
- Department of BiologyHacettepe UniversityAnkaraTurkey
- Department of BiologyIndiana UniversityBloomingtonINUSA
| | - Samuel F. Miller
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeArizonaUSA
| | - Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeArizonaUSA
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