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Singh S, Sutkus L, Li Z, Baker S, Bear J, Dilger RN, Miller DJ. Standardization of a silver stain to reveal mesoscale myelin in histological preparations of the mammalian brain. J Neurosci Methods 2024; 407:110139. [PMID: 38626852 DOI: 10.1016/j.jneumeth.2024.110139] [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: 01/18/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND The brain is built of neurons supported by myelin, a fatty substance that improves cellular communication. Noninvasive magnetic resonance imaging (MRI) is now able to measure brain structure like myelin and requires histological validation. NEW METHOD Here we present work in small and large biomedical model mammals to standardize a silver impregnation method as a high-throughput histological myelin visualization procedure. Specifically, we built a new staining well plate to increase batch size, and then systematically varied the staining and clearing cycles to describe the staining response curve across taxa and conditions. We compared tissues fixed by immersion or perfusion, mounted versus free-floating, and cut as thicker or thinner slices, with two-weeks of post-fixation. RESULTS The staining response curves show optimal staining with a single exposure across taxa when incubation and clearing epochs are held to within 3-9 min. We show that clearing was slower in mounted vs free-floating tissue, and that staining was faster and caused fracturing earlier in thinner sliced and smaller volumes of tissue. COMPARISON WITH EXISTING METHODS We developed a batch processing approach to increase throughput while ensuring reproducibility and demonstrate the optimal conditions for fine myelinated fiber morphology visualization with short cycles (<9 minutes). CONCLUSIONS We present our optimized protocol to reveal mesoscale neuroanatomical myelin content in histology across mammals. This standard staining procedure will facilitate multiscale analyses of myelin content across development as well as in the presence of injury or disease.
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Affiliation(s)
- S Singh
- Department of Evolution, Ecology, and Behavior, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - L Sutkus
- Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - Z Li
- Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - S Baker
- Machine Shop, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - J Bear
- Machine Shop, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - R N Dilger
- Department of Animal Sciences, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America
| | - D J Miller
- Department of Evolution, Ecology, and Behavior, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Neuroscience Program, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, at the University of Illinois at Urbana-Champaign, 505 South Goodwin Ave, Urbana, IL 61801, United States of America.
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2
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Gewirtz-Meydan A, Koós M, Nagy L, Kraus SW, Demetrovics Z, Potenza MN, Ballester-Arnal R, Batthyány D, Bergeron S, Billieux J, Burkauskas J, Cárdenas-López G, Carvalho J, Castro-Calvo J, Chen L, Ciocca G, Corazza O, Csako R, Fernandez DP, Fujiwara H, Fernandez EF, Fuss J, Gabrhelík R, Gjoneska B, Gola M, Grubbs JB, Hashim HT, Islam MS, Ismail M, Jiménez-Martínez MC, Jurin T, Kalina O, Klein V, Költő A, Lee SK, Lewczuk K, Lin CY, Lochner C, López-Alvarado S, Lukavská K, Mayta-Tristán P, Miller DJ, Orosová O, Orosz G, Ponce FP, Quintana GR, Quintero Garzola GC, Ramos-Diaz J, Rigaud K, Rousseau A, De Tubino Scanavino M, Schulmeyer MK, Sharan P, Shibata M, Shoib S, Sigre-Leirós V, Sniewski L, Spasovski O, Steibliene V, Stein DJ, Strong C, Ünsal BC, Vaillancourt-Morel MP, Van Hout MC, Bőthe B. Global cross-cultural validation of a brief measure for identifying potential suicide risk in 42 countries. Public Health 2024; 229:13-23. [PMID: 38382177 DOI: 10.1016/j.puhe.2023.12.031] [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: 08/22/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 02/23/2024]
Abstract
OBJECTIVES This study aimed to examine the psychometric properties of the P4 suicide screener in a multinational sample. The primary goal was to evaluate the reliability and validity of the scale and investigate its convergent validity by analyzing its correlation with depression, anxiety, and substance use. STUDY DESIGN The study design is a cross-sectional self-report study conducted across 42 countries. METHODS A cross-sectional, self-report study was conducted in 42 countries, with a total of 82,243 participants included in the final data set. RESULTS The study provides an overview of suicide ideation rates across 42 countries and confirms the structural validity of the P4 screener. The findings indicated that sexual and gender minority individuals exhibited higher rates of suicidal ideation. The P4 screener showed adequate reliability, convergence, and discriminant validity, and a cutoff score of 1 is recommended to identify individuals at risk of suicidal behavior. CONCLUSIONS The study supports the reliability and validity of the P4 suicide screener across 42 diverse countries, highlighting the importance of using a cross-cultural suicide risk assessment to standardize the identification of high-risk individuals and tailoring culturally sensitive suicide prevention strategies.
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Affiliation(s)
- A Gewirtz-Meydan
- School of Social Work, Faculty of Social Welfare and Health Sciences, University of Haifa, Israel. Agewirtz-@univ.haifa.ac.il
| | - M Koós
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Forensic Psychiatry and Sex Research, University of Duisburg-Essen, Essen, Germany
| | - L Nagy
- Doctoral School of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - S W Kraus
- Department of Psychology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Z Demetrovics
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Centre of Excellence in Responsible Gaming, University of Gibraltar, Gibraltar, Gibraltar
| | - M N Potenza
- Yale University School of Medicine, New Haven, CT, USA; Connecticut Council on Problem Gambling, Wethersfield, CT, USA
| | - R Ballester-Arnal
- Departmento de Psicología Básica, Clínica y Psicobiología, University Jaume I of Castellón, Spain
| | - D Batthyány
- Institute for Behavioural Addictions, Sigmund Freud University Vienna, Austria
| | - S Bergeron
- Département de Psychologie, Université de Montréal, Montréal, Canada
| | - J Billieux
- Institute of Psychology, University of Lausanne, Lausanne, Switzerland; Center for Excessive Gambling, Addiction Medicine, Lausanne University Hospitals (CHUV), Lausanne, Switzerland
| | - J Burkauskas
- Laboratory of Behavioral Medicine, Neuroscience Institute, Lithuanian University of Health Sciences, Lithuania
| | - G Cárdenas-López
- Virtual Teaching and Cyberpsychology Laboratory, School of Psychology, National Autonomous University of Mexico, Mexico
| | - J Carvalho
- William James Center for Research, Departamento de Educação e Psicologia, Universidade de Aveiro, Aveiro, Portugal
| | - J Castro-Calvo
- Department of Personality, Assessment, and Psychological Treatments, University of Valencia, Spain
| | - L Chen
- Department of Psychology, College of Humanity and Social Science, Fuzhou University, China
| | - G Ciocca
- Section of Sexual Psychopathology, Department of Dynamic and Clinical Psychology, and Health Studies, Sapienza University of Rome, Rome, Italy
| | - O Corazza
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, UK; Department of Psychology and Cognitive Science, University of Trento, Italy
| | - R Csako
- Department of Psychology and Neuroscience, Auckland University of Technology, Auckland, New Zealand
| | | | - H Fujiwara
- Department of Neuropsychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Decentralized Big Data Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | | | - J Fuss
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Essen, Germany
| | - R Gabrhelík
- Charles University, First Faculty of Medicine, Department of Addictology, Prague, Czech Republic; General University Hospital in Prague, Department of Addictology, Czech Republic
| | - B Gjoneska
- Macedonian Academy of Sciences and Arts, Macedonia
| | - M Gola
- Institute of Psychlogy, Polish Academy of Sciences, Poland; Institute for Neural Computations, University of California San Diego, USA
| | - J B Grubbs
- University of New Mexico, Albuquerque, USA; Center for Alcohol, Substance Use, And Addiction (CASAA), University of New Mexico, Albuquerque, USA
| | - H T Hashim
- University of Baghdad, College of Medicine, Iraq
| | - M S Islam
- Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Centre for Advanced Research Excellence in Public Health, Savar, Dhaka 1342, Bangladesh
| | - M Ismail
- University of Baghdad, College of Medicine, Iraq
| | - M C Jiménez-Martínez
- Universidad Pedagógca y Tecnológica de Colombia, Colombia; Grupo de Investigación Biomédica y de Patología, Colombia
| | - T Jurin
- Department of Psychology, Humanities and Social Sciences, University of Zagreb, Croatia
| | - O Kalina
- Department of Educational Psychology and Psychology of Health, Pavol Jozef Safarik University in Kosice, Slovakia
| | - V Klein
- School of Psychology, University of Southampton, UK
| | - A Költő
- Health Promotion Research Centre, University of Galway, Ireland, UK
| | - S-K Lee
- Department of Psychiatry, Hallym University Chuncheon Sacred Heart Hospital, South Korea; Chuncheon Addiction Management Center, South Korea
| | - K Lewczuk
- Institute of Psychology, Cardinal Stefan Wyszynski University, Warsaw, Poland
| | - C-Y Lin
- Institute of Allied Health Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - C Lochner
- SAMRC Unit on Risk & Resilience in Mental Disorders, Stellenbosch University, South Africa
| | | | - K Lukavská
- Charles University, First Faculty of Medicine, Department of Addictology, Prague, Czech Republic; Charles University, Faculty of Education, Department of Psychology, Prague, Czech Republic
| | - P Mayta-Tristán
- Facultad de Medicina, Universidad Científica del Sur, Lima, Peru
| | - D J Miller
- College of Healthcare Sciences, James Cook University, Australia
| | - O Orosová
- Pavol Jozef Safarik University in Kosice, Department of Educational Psychology and Psychology of Health, Slovakia
| | | | - F P Ponce
- Facultad de Psicología, Universidad de Talca, Chile
| | - G R Quintana
- Departamento de Psicología y Filosofía, Facultad de Ciencias Sociales, Universidad de Tarapacá, Arica, Arica y Parinacota, Chile
| | - G C Quintero Garzola
- Florida State University, Panama; Sistema Nacional de Investigación (SNI), SENACYT, Panama
| | - J Ramos-Diaz
- Facultad de Ciencias de la Salud, Universidad Privada del Norte, Lima, Perú
| | | | - A Rousseau
- Leuven School for Mass Communication, KU Leuven, Leuven, Belgium
| | - M De Tubino Scanavino
- Department of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, Brazil; Experimental Pathophisiology Post Graduation Program, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | | | - P Sharan
- Department of Psychiatry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - M Shibata
- Department of Neuropsychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - S Shoib
- Department of Psychology, Shardha University, India; Department of Health Kashmir, India
| | - V Sigre-Leirós
- Institute of Psychology, University of Lausanne, Lausanne, Switzerland; Institute of Legal Psychiatry, Lausanne University Hospitals (CHUV), Lausanne, Switzerland
| | - L Sniewski
- Auckland University of Technology, New Zealand
| | - O Spasovski
- Faculty of Philosophy, Ss. Cyril and Methodius University in Skopje, Macedonia; Faculty of Philosophy, University of Ss. Cyril and Methodius in Trnava, Slovakia
| | - V Steibliene
- Laboratory of Behavioral Medicine, Neuroscience Institute, Lithuanian University of Health Sciences, Lithuania
| | - D J Stein
- SAMRC Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, South Africa
| | - C Strong
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - B C Ünsal
- Doctoral School of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary; Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - M-P Vaillancourt-Morel
- Département de Psychologie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - M C Van Hout
- Public Health Institute, Faculty of Health, Liverpool John Moores University, UK
| | - B Bőthe
- Département de Psychologie, Université de Montréal, Montréal, Canada; Département de Psychologie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
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Glen A, Bürli RW, Livermore D, Buffham W, Merison S, Rowland AE, Newman R, Fieldhouse C, Miller DJ, Dawson LA, Matthews K, Carlton MB, Brice NL. Discovery and first-time disclosure of CVN766, an exquisitely selective orexin 1 receptor antagonist. Bioorg Med Chem Lett 2024; 100:129629. [PMID: 38295907 DOI: 10.1016/j.bmcl.2024.129629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Modulators of orexin receptors are being developed for neurological illnesses such as sleep disorders, addictive behaviours and other psychiatric diseases. We herein describe the discovery of CVN766, a potent orexin 1 receptor antagonist that has greater than 1000-fold selectivity for the orexin 1 receptor over the orexin 2 receptor and demonstrates low off target hits in a diversity screen. In agreement with its in vitro ADME data, CVN766 demonstrated moderate in vivo clearance in rodents and displayed good brain permeability and target occupancy. This drug candidate is currently being investigated in clinical trials for schizophrenia and related psychiatric conditions.
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Affiliation(s)
- Angela Glen
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Roland W Bürli
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - David Livermore
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - William Buffham
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Stephanie Merison
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Anna E Rowland
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Robert Newman
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Charlotte Fieldhouse
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - David J Miller
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Lee A Dawson
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Kim Matthews
- Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Mark B Carlton
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK
| | - Nicola L Brice
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK; Cerevance Ltd, 418 Cambridge Science Park, Milton Road, Cambridge CB4 0PZ, UK.
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4
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Miller DJ. Sperm in the Mammalian Female Reproductive Tract: Surfing Through the Tract to Try to Beat the Odds. Annu Rev Anim Biosci 2024; 12:301-319. [PMID: 37906840 DOI: 10.1146/annurev-animal-021022-040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Mammalian sperm are deposited in the vagina or the cervix/uterus at coitus or at artificial insemination, and the fertilizing sperm move through the female reproductive tract to the ampulla of the oviduct, the site of fertilization. But the destination of most sperm is not the oviduct. Most sperm are carried by retrograde fluid flow to the vagina, are phagocytosed, and/or do not pass barriers on the pathway to the oviduct. The sperm that reach the site of fertilization are the exceptions and winners of one of the most stringent selection processes in nature. This review discusses the challenges sperm encounter and how the few sperm that reach the site of fertilization overcome them. The sperm that reach the goal must navigate viscoelastic fluid, swim vigorously and cooperatively along the walls of the female tract, avoid the innate immune system, and respond to potential cues to direct their movement.
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Affiliation(s)
- David J Miller
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
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5
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O'Brien PA, Tan S, Frade PR, Robbins SJ, Engelberts JP, Bell SC, Vanwonterghem I, Miller DJ, Webster NS, Zhang G, Bourne DG. Validation of key sponge symbiont pathways using genome-centric metatranscriptomics. Environ Microbiol 2023; 25:3207-3224. [PMID: 37732569 DOI: 10.1111/1462-2920.16509] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Microbiome Research, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, Tasmania, Australia
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology and Women's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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Carter B, Hernandez UF, Miller DJ, Blaikie A, Horowitz VR, Alemán BJ. Coupled Nanomechanical Graphene Resonators: A Promising Platform for Scalable NEMS Networks. Micromachines (Basel) 2023; 14:2103. [PMID: 38004960 PMCID: PMC10672897 DOI: 10.3390/mi14112103] [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] [Received: 10/19/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Arrays of coupled nanoelectromechanical resonators are a promising foundation for implementing large-scale network applications, such as mechanical-based information processing and computing, but their practical realization remains an outstanding challenge. In this work, we demonstrate a scalable platform of suspended graphene resonators, such that neighboring resonators are persistently coupled mechanically. We provide evidence of strong coupling between neighboring resonators using two different tuning methods. Additionally, we provide evidence of inter-resonator coupling of higher-order modes, demonstrating the rich dynamics that can be accessed with this platform. Our results establish this platform as a viable option for realizing large-scale programmable networks, enabling applications such as phononic circuits, tunable waveguides, and reconfigurable metamaterials.
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Affiliation(s)
- Brittany Carter
- Department of Physics, University of Oregon, Eugene, OR 97403, USA (A.B.)
| | - Uriel F. Hernandez
- Department of Physics, University of Oregon, Eugene, OR 97403, USA (A.B.)
| | - David J. Miller
- Department of Physics, University of Oregon, Eugene, OR 97403, USA (A.B.)
| | - Andrew Blaikie
- Department of Physics, University of Oregon, Eugene, OR 97403, USA (A.B.)
| | | | - Benjamín J. Alemán
- Department of Physics, University of Oregon, Eugene, OR 97403, USA (A.B.)
- Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
- Center for Optical, Molecular, and Quantum Science, University of Oregon, Eugene, OR 97403, USA
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403, USA
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7
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Srivastava P, Johns ST, Walters R, Miller DJ, Van der Kamp MW, Allemann RK. Active Site Loop Engineering Abolishes Water Capture in Hydroxylating Sesquiterpene Synthases. ACS Catal 2023; 13:14199-14204. [PMID: 37942265 PMCID: PMC10629212 DOI: 10.1021/acscatal.3c03920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Terpene synthases (TS) catalyze complex reactions to produce a diverse array of terpene skeletons from linear isoprenyl diphosphates. Patchoulol synthase (PTS) from Pogostemon cablin converts farnesyl diphosphate into patchoulol. Using simulation-guided engineering, we obtained PTS variants that eliminate water capture. Further, we demonstrate that modifying the structurally conserved Hα-1 loop also reduces hydroxylation in PTS, as well as in germacradiene-11-ol synthase (Gd11olS), leading to cyclic neutral intermediates as products, including α-bulnesene (PTS) and isolepidozene (Gd11olS). Hα-1 loop modification could be a general strategy for engineering sesquiterpene synthases to produce complex cyclic hydrocarbons without the need for structure determination or modeling.
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Affiliation(s)
- Prabhakar
L. Srivastava
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Sam T. Johns
- School
of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Rebecca Walters
- School
of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
| | - David J. Miller
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Marc W. Van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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8
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Horowitz J, Quattrini AM, Brugler MR, Miller DJ, Pahang K, Bridge TCL, Cowman PF. Bathymetric evolution of black corals through deep time. Proc Biol Sci 2023; 290:20231107. [PMID: 37788705 PMCID: PMC10547549 DOI: 10.1098/rspb.2023.1107] [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: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023] Open
Abstract
Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.
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Affiliation(s)
- Jeremy Horowitz
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
| | - Andrea M. Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
| | - Mercer R. Brugler
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary Street, Beaufort, SC 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Molecular and Cell Biology, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
| | - Kristina Pahang
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
| | - Tom C. L. Bridge
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- College of Science and Engineering, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
| | - Peter F. Cowman
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Molecular and Cell Biology, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- College of Science and Engineering, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
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9
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Hughes JR, McMorrow KJ, Bovin N, Miller DJ. An oviduct glycan increases sperm lifespan by diminishing the production of ubiquinone and reactive oxygen species†. Biol Reprod 2023; 109:356-366. [PMID: 37427962 PMCID: PMC10502565 DOI: 10.1093/biolre/ioad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Sperm storage by females after mating for species-dependent periods is used widely among animals with internal fertilization to allow asynchrony between mating and ovulation. Many mammals store sperm in the lower oviduct where specific glycans on oviduct epithelial cells retain sperm to form a reservoir. Binding to oviduct cells suppresses sperm intracellular Ca2+ and increases sperm longevity. We investigated the mechanisms by which a specific oviduct glycan, 3-O-sulfated Lewis X trisaccharide (suLeX), prolongs the lifespan of porcine sperm. Using targeted metabolomics, we found that binding to suLeX diminishes the abundance of 4-hydroxybenzoic acid, the precursor to ubiquinone (also known as Coenzyme Q), 30 min after addition. Ubiquinone functions as an electron acceptor in the electron transport chain (ETC). 3-O-sulfated Lewis X trisaccharide also suppressed the formation of fumarate. A component of the citric acid cycle, fumarate is synthesized by succinate-coenzyme Q reductase, which employs ubiquinone and is also known as Complex II in the ETC. Consistent with the reduced activity of the ETC, the production of harmful reactive oxygen species (ROS) was diminished. The enhanced sperm lifespan in the oviduct may be because of suppressed ROS production because high ROS concentrations have toxic effects on sperm.
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Affiliation(s)
- Jennifer R Hughes
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Katie J McMorrow
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolai Bovin
- Department of Chemical Biology of Glycans and Lipids, Shemyakin Institute of Bioorganic Chemistry, Moscow, Russia
| | - David J Miller
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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10
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Brown MA, Zappitelli KM, Singh L, Yuan RC, Bemrose M, Brogden V, Miller DJ, Smear MC, Cogan SF, Gardner TJ. Direct laser writing of 3D electrodes on flexible substrates. Nat Commun 2023; 14:3610. [PMID: 37330565 PMCID: PMC10276853 DOI: 10.1038/s41467-023-39152-7] [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: 12/20/2022] [Accepted: 05/31/2023] [Indexed: 06/19/2023] Open
Abstract
This report describes a 3D microelectrode array integrated on a thin-film flexible cable for neural recording in small animals. The fabrication process combines traditional silicon thin-film processing techniques and direct laser writing of 3D structures at micron resolution via two-photon lithography. Direct laser-writing of 3D-printed electrodes has been described before, but this report is the first to provide a method for producing high-aspect-ratio structures. One prototype, a 16-channel array with 300 µm pitch, demonstrates successful electrophysiological signal capture from bird and mouse brains. Additional devices include 90 µm pitch arrays, biomimetic mosquito needles that penetrate through the dura of birds, and porous electrodes with enhanced surface area. The rapid 3D printing and wafer-scale methods described here will enable efficient device fabrication and new studies examining the relationship between electrode geometry and electrode performance. Applications include small animal models, nerve interfaces, retinal implants, and other devices requiring compact, high-density 3D electrodes.
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Affiliation(s)
- Morgan A Brown
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Kara M Zappitelli
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Loveprit Singh
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Rachel C Yuan
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Melissa Bemrose
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Valerie Brogden
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - David J Miller
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Matthew C Smear
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
| | - Stuart F Cogan
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Timothy J Gardner
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA.
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11
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Soto-Heras S, Sakkas D, Miller DJ. Sperm selection by the oviduct: perspectives for male fertility and assisted reproductive technologies†. Biol Reprod 2023; 108:538-552. [PMID: 36625382 PMCID: PMC10106845 DOI: 10.1093/biolre/ioac224] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
The contribution of sperm to embryogenesis is gaining attention with up to 50% of infertility cases being attributed to a paternal factor. The traditional methods used in assisted reproductive technologies for selecting and assessing sperm quality are mainly based on motility and viability parameters. However, other sperm characteristics, including deoxyribonucleic acid integrity, have major consequences for successful live birth. In natural reproduction, sperm navigate the male and female reproductive tract to reach and fertilize the egg. During transport, sperm encounter many obstacles that dramatically reduce the number arriving at the fertilization site. In humans, the number of sperm is reduced from tens of millions in the ejaculate to hundreds in the Fallopian tube (oviduct). Whether this sperm population has higher fertilization potential is not fully understood, but several studies in animals indicate that many defective sperm do not advance to the site of fertilization. Moreover, the oviduct plays a key role in fertility by modulating sperm transport, viability, and maturation, providing sperm that are ready to fertilize at the appropriate time. Here we present evidence of sperm selection by the oviduct with emphasis on the mechanisms of selection and the sperm characteristics selected. Considering the sperm parameters that are essential for healthy embryonic development, we discuss the use of novel in vitro sperm selection methods that mimic physiological conditions. We propose that insight gained from understanding how the oviduct selects sperm can be translated to assisted reproductive technologies to yield high fertilization, embryonic development, and pregnancy rates.
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Affiliation(s)
- Sandra Soto-Heras
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - David J Miller
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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12
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Ketzer M, Praeg D, Augustin AH, Rodrigues LF, Steiger AK, Rahmati-Abkenar M, Viana AR, Miller DJ, Malinverno A, Dickens GR, Cupertino JA. Gravity complexes as a focus of seafloor fluid seepage: the Rio Grande Cone, SE Brazil. Sci Rep 2023; 13:4590. [PMID: 36944652 PMCID: PMC10030975 DOI: 10.1038/s41598-023-31815-1] [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: 10/24/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Seafloor methane emissions can affect Earth's climate and ocean chemistry. Vast quantities of methane formed by microbial decomposition of organic matter are locked within gas hydrate and free gas on continental slopes, particularly in large areas with high sediment accumulations such as deep-sea fans. The release of methane in slope environments has frequently been associated with dissociation of gas hydrates near the edge of the gas hydrate stability zone on the upper slope, with discharges in greater water depths less understood. Here we show, using data from the Rio Grande Cone (western South Atlantic), that the intrinsic, gravity-induced downslope collapse of thick slope sediment accumulations creates structures that serve as pathways for gas migration, unlocking methane and causing seafloor emissions via giant gas flares in the water column. The observed emissions in the study region (up to 310 Mg year-1) are three times greater than estimates for the entire US North Atlantic margin and reveal the importance of collapsing sediment accumulations for ocean carbon cycling. Similar outgassing systems on the Amazon and Niger fans suggest that gravity tectonics on passive margins is a common yet overlooked mechanism driving massive seafloor methane emissions in sediment-laden continental slopes.
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Affiliation(s)
- M Ketzer
- Department of Biology and Environmental Science, Linnaeus University, 391 81, Kalmar, Sweden.
| | - D Praeg
- Géoazur, 250 Rue Albert Einstein, 06560, Valbonne, France
| | - A H Augustin
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
| | - L F Rodrigues
- Universidade Federal do Rio Grande, Rio Grande, 96203-900, Brazil
| | - A K Steiger
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
| | - M Rahmati-Abkenar
- Department of Biology and Environmental Science, Linnaeus University, 391 81, Kalmar, Sweden
| | - A R Viana
- Petrobras Petroleo Brasileiro SA, Rio de Janeiro, 20031-170, Brazil
| | - D J Miller
- Petrobras Petroleo Brasileiro SA, Rio de Janeiro, 20031-170, Brazil
| | - A Malinverno
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY, 10964, USA
| | | | - J A Cupertino
- Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, 91619-900, Brazil
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13
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Xu J, Mead O, Moya A, Caglar C, Miller DJ, Adamski M, Adamska M. Wound healing and regeneration in the reef building coral Acropora millepora. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.979278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Branching scleractinian corals are niche-constructing organisms, providing continuously-growing, structural foundation for spectacularly biodiverse coral reef ecosystems. A large part of their success lies in the ability to quickly regenerate following mechanical damage. Even now, when the corals undergo great decline due to anthropogenic weather and storm extremes, it is surprising how little is known about molecular mechanisms governing regeneration in these iconic organisms. In this study, we used RNA-seq to identify genes involved in the regeneration of Acropora millepora, starting with the initial wound closure up to complete rebuilding of lost structures. Many of the differentially expressed genes we found in the wound healing steps are homologues of genes known to be involved in wound healing and regeneration of bilaterian and other cnidarian species, prominently including multiple components of FGF and Wnt signalling pathways. Comparison between genes involved in wound healing and continuous growth of the colony demonstrates both similarity and distinctiveness of the genetic programmes controlling these processes. A striking example is specific expression of c-Fos, a transcription factor with conserved role in early injury response, during the earliest stages of wound healing of A. millepora. By comparing results obtained in diverse experimental conditions including a closed-loop, recirculating aquarium and a flow-through system of marine station, we have demonstrated feasibility of using zooxanthellate scleractinian corals as experimental models in fundamental biology research, including studies of regeneration.
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14
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Mason BM, Koyanagi M, Sugihara T, Iwasaki M, Slepak V, Miller DJ, Sakai Y, Terakita A. Multiple opsins in a reef-building coral, Acropora millepora. Sci Rep 2023; 13:1628. [PMID: 36710295 PMCID: PMC9884665 DOI: 10.1038/s41598-023-28476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/19/2023] [Indexed: 01/30/2023] Open
Abstract
Opsins, light-sensitive G protein-coupled receptors, have been identified in corals but their properties are largely unknown. Here, we identified six opsin genes (acropsins 1-6) from a coral species Acropora millepora, including three novel opsins (acropsins 4-6), and successfully characterized the properties of four out of the six acropsins. Acropsins 1 and 6 exhibited light-dependent cAMP increases in cultured cells, suggesting that the acropsins could light-dependently activate Gs-type G protein like the box jellyfish opsin from the same opsin group. Spectral sensitivity curves having the maximum sensitivities at ~ 472 nm and ~ 476 nm were estimated for acropsins 1 and 6, respectively, based on the light wavelength-dependent cAMP increases in these opsins-expressing cells (heterologous action spectroscopy). Acropsin 2 belonging to the same group as acropsins 1 and 6 did not induce light-dependent cAMP or Ca2+ changes. We then successfully estimated the acropsin 2 spectral sensitivity curve having its maximum value at ~ 471 nm with its chimera mutant which possessed the third cytoplasmic loop of the Gs-coupled jellyfish opsin. Acropsin 4 categorized as another group light-dependently induced intracellular Ca2+ increases but not cAMP changes. Our results uncovered that the Acropora coral possesses multiple opsins coupling two distinct cascades, cyclic nucleotide and Ca2+signaling light-dependently.
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Affiliation(s)
- Benjamin M Mason
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.,Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Mitsumasa Koyanagi
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan.,Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Tomohiro Sugihara
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan.,Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Makoto Iwasaki
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Vladlen Slepak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.,Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yusuke Sakai
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Akihisa Terakita
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan. .,Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan.
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15
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Hughes JR, McMorrow KJ, Bovin N, Miller DJ. An oviduct glycan increases sperm lifespan by diminishing ubiquinone and production of reactive oxygen species. bioRxiv 2023:2023.01.08.523174. [PMID: 36712093 PMCID: PMC9881936 DOI: 10.1101/2023.01.08.523174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sperm storage by females after mating for species-dependent periods is used widely among animals with internal fertilization to allow asynchrony between mating and ovulation. Many mammals store sperm in the lower oviduct where specific glycans on epithelial cells retain sperm to form a reservoir. Binding to oviduct cells suppresses sperm intracellular Ca 2+ and increases sperm longevity. We investigated the mechanisms by which a specific oviduct glycan, 3-O-sulfated Lewis X trisaccharide (suLe X ), prolongs the lifespan of porcine sperm. Using targeted metabolomics, we report that binding to suLe X diminishes the abundance of the precursor to ubiquinone and suppresses formation of fumarate, a specific citric acid cycle component, diminishing the activity of the electron transport chain and reducing the production of harmful reactive oxygen species (ROS). The enhanced sperm lifespan in the oviduct may be due to suppressed ROS production as many reports have demonstrated toxic effects of high ROS concentrations on sperm.
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16
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Cumming GS, Adamska M, Barnes ML, Barnett J, Bellwood DR, Cinner JE, Cohen PJ, Donelson JM, Fabricius K, Grafton RQ, Grech A, Gurney GG, Hoegh-Guldberg O, Hoey AS, Hoogenboom MO, Lau J, Lovelock CE, Lowe R, Miller DJ, Morrison TH, Mumby PJ, Nakata M, Pandolfi JM, Peterson GD, Pratchett MS, Ravasi T, Riginos C, Rummer JL, Schaffelke B, Wernberg T, Wilson SK. Research priorities for the sustainability of coral-rich western Pacific seascapes. Reg Environ Change 2023; 23:66. [PMID: 37125023 PMCID: PMC10119535 DOI: 10.1007/s10113-023-02051-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/25/2023] [Indexed: 05/03/2023]
Abstract
Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 ('Life below Water') of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia-Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation; elucidating drivers and mechanisms of change; understanding how seascape functions and services are produced, and how people depend on them; costs, benefits, and trade-offs to people in changing seascapes; improving seascape technologies and practices; learning to govern and manage seascapes for all; sustainable use, justice, and human well-being; bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions; and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.
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Affiliation(s)
- Graeme S. Cumming
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Maja Adamska
- Australian Research Council Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, Australia
- Research School of Biology, Australian National University, Canberra, Australia
| | - Michele L. Barnes
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Jon Barnett
- School of Geography, Earth, and Atmospheric Sciences, University of Melbourne, Melbourne, Australia
| | - David R. Bellwood
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - Joshua E. Cinner
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | | | - Jennifer M. Donelson
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | | | - R. Quentin Grafton
- Crawford School of Public Policy, Australian National University, Canberra, Australia
| | - Alana Grech
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Georgina G. Gurney
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Ove Hoegh-Guldberg
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, Brisbane, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Andrew S. Hoey
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Mia O. Hoogenboom
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - Jacqueline Lau
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- WorldFish, Penang, Malaysia
| | | | - Ryan Lowe
- Australian Research Council Centre of Excellence for Coral Reef Studies, University of Western Australia, Perth, Australia
- Oceans Institute, University of Western Australia, Perth, Australia
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, 4811 Australia
| | - Tiffany H. Morrison
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Peter J. Mumby
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, Brisbane, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Martin Nakata
- Indigenous Education and Research Centre, James Cook University, Townsville, 4811 Australia
| | - John M. Pandolfi
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, Brisbane, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Garry D. Peterson
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Morgan S. Pratchett
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-Son, Okinawa Japan
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Jodie L. Rummer
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
- College of Science and Engineering, James Cook University, Townsville, Australia
| | | | - Thomas Wernberg
- Oceans Institute, University of Western Australia, Perth, Australia
- Institute of Marine Research, Floedevigen Research Station, Nis, Norway
| | - Shaun K. Wilson
- Oceans Institute, University of Western Australia, Perth, Australia
- Western Australia Government Department of Biodiversity, Conservation and Attractions, Perth, Australia
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17
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Wang H, Miller DJ, Kesidis G. Anomaly detection of adversarial examples using class-conditional generative adversarial networks. Comput Secur 2023. [DOI: 10.1016/j.cose.2022.102956] [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: 12/05/2022]
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18
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Déglin SE, Burstyn I, Chen CL, Miller DJ, Gribble MO, Hamade AK, Chang ET, Avanasi R, Boon D, Reed J. Considerations towards the better integration of epidemiology into quantitative risk assessment. Glob Epidemiol 2022; 4:100084. [PMID: 37637021 PMCID: PMC10445996 DOI: 10.1016/j.gloepi.2022.100084] [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] [Received: 08/23/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental epidemiology has proven critical to study various associations between environmental exposures and adverse human health effects. However, there is a perception that it often does not sufficiently inform quantitative risk assessment. To help address this concern, in 2017, the Health and Environmental Sciences Institute initiated a project engaging the epidemiology, exposure science, and risk assessment communities with tripartite representation from government agencies, industry, and academia, in a dialogue on the use of environmental epidemiology for quantitative risk assessment and public health decision making. As part of this project, four meetings attended by experts in epidemiology, exposure science, toxicology, statistics, and risk assessment, as well as one additional meeting engaging funding agencies, were organized to explore incentives and barriers to realizing the full potential of epidemiological data in quantitative risk assessment. A set of questions was shared with workshop participants prior to the meetings, and two case studies were used to support the discussion. Five key ideas emerged from these meetings as areas of desired improvement to ensure that human data can more consistently become an integral part of quantitative risk assessment: 1) reducing confirmation and publication bias, 2) increasing communication with funding agencies to raise awareness of research needs, 3) developing alternative funding channels targeted to support quantitative risk assessment, 4) making data available for reuse and analysis, and 5) developing cross-disciplinary and cross-sectoral interactions, collaborations, and training. We explored and integrated these themes into a roadmap illustrating the need for a multi-stakeholder effort to ensure that epidemiological data can fully contribute to the quantitative evaluation of human health risks, and to build confidence in a reliable decision-making process that leverages the totality of scientific evidence.
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Affiliation(s)
- Sandrine E. Déglin
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Igor Burstyn
- Department of Environmental and Occupational Health, Drexel University, Philadelphia, PA, United States of America
| | - Connie L. Chen
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - David J. Miller
- U.S. Environmental Protection Agency, Washington, DC, United States of America
| | - Matthew O. Gribble
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, United States of America
| | - Ali K. Hamade
- Oregon Health Authority, Portland, OR, United States of America
| | - Ellen T. Chang
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, United States of America
| | | | - Denali Boon
- Corteva Agriscience, Indianapolis, IN, United States of America
| | - Jennifer Reed
- Bayer Crop Science, Chesterfield, MO, United States of America
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19
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Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
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Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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20
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Miller DJ. 294 Awardee Talk: Porcine Sperm Storage in the Oviduct Before Fertilization: A Sweet Spot. J Anim Sci 2022. [DOI: 10.1093/jas/skac247.260] [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: 11/13/2022] Open
Abstract
Abstract
Sperm storage in the female reproductive tract from sperm deposition until ovulation is conserved among a wide variety of animals allowing some asynchrony between mating and ovulation. Mammals, reptiles, birds, amphibians, and insects are among those that store sperm from a day or two to as long as a decade. We have studied the molecular basis of how sperm are retained and then released from the reservoirs in the female tract to fertilize oocytes, primarily in swine. Previous research by others implicated various oviduct glycans as receptors to retain sperm in the lower oviduct, the isthmus, but the complete structures of the glycans that bound sperm had not been identified. We used an array of hundreds of glycans to identify those that bound sperm and identified several glycans with sperm binding ability. Further inspection revealed that all sperm binding glycans contained at least one of two motifs, either a branched 6-sialylated structure or a Lewis X trisaccharide. Profiling all glycans produced by the isthmus showed that these motifs were abundant among the complex N-linked glycans of the isthmus. Further, they were found on the apical surface of the isthmic epithelium where they are available to bind sperm. These glycans suppressed the normal increase in intracellular free Ca2+ in sperm during capacitation and, when immobilized on beads, lengthened sperm lifespan, mimicking the effect of sperm of binding to the oviduct. Binding to oviduct glycans alters sperm metabolism in specific ways to prolong sperm viability. Sperm are released from immobilized glycans by progesterone, which induces hyperactivated motility, and by capacitation, which reduces the binding affinity of capacitated sperm for oviduct glycans. This information may be used to improve sperm lifespan in vivo or enhance sperm storage outside of the female tract.
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21
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Schmidt CA, Cooke I, Wilson DT, Miller DJ, Peigneur S, Tytgat J, Field M, Takjoo R, Smout MJ, Loukas A, Daly NL. Newly Discovered Peptides from the Coral Heliofungia actiniformis Show Structural and Functional Diversity. J Nat Prod 2022; 85:1789-1798. [PMID: 35829679 DOI: 10.1021/acs.jnatprod.2c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Scleractinian corals are crucially important to the health of some of the world's most biodiverse, productive, and economically important marine habitats. Despite this importance, analysis of coral peptidomes is still in its infancy. Here we show that the tentacle extract from the stony coral Heliofungia actiniformis is rich in peptides with diverse and novel structures. We have characterized the sequences and three-dimensional structures of four new peptides, three of which have no known homologues. We show that a 2 kDa peptide, Hact-2, promotes significant cell proliferation on human cells and speculate this peptide may be involved in the remarkable regenerative capacity of corals. We found a 3 kDa peptide, Hact-3, encoded within a fascin-like domain, and homologues of Hact-3 are present in the genomes of other coral species. Two additional peptides, Hact-4 and Hact-SCRiP1, with limited sequence similarity, both contain a beta-defensin-like fold and highlight a structural link with the small cysteine-rich proteins (SCRiP) family of proteins found predominantly in corals. Our results provide a first glimpse into the remarkable and unexplored structural diversity of coral peptides, providing insight into their diversity and putative functions and, given the ancient lineage of corals, potential insight into the evolution of structural motifs.
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Affiliation(s)
- Casey A Schmidt
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
| | - David T Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Steve Peigneur
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, 3000, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, 3000, Belgium
| | - Matthew Field
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Rozita Takjoo
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Michael J Smout
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Norelle L Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
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22
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Rosenberg Y, Simon‐Blecher N, Lalzar M, Yam R, Shemesh A, Alon S, Perna G, Cárdenas A, Voolstra CR, Miller DJ, Levy O. Urbanization comprehensively impairs biological rhythms in coral holobionts. Glob Chang Biol 2022; 28:3349-3364. [PMID: 35218086 PMCID: PMC9311646 DOI: 10.1111/gcb.16144] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/28/2023]
Abstract
Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology & Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.
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Affiliation(s)
- Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Noa Simon‐Blecher
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Maya Lalzar
- Bioinformatics Service UnitUniversity of HaifaHaifaIsrael
| | - Ruth Yam
- Department of Earth and Planetary SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Aldo Shemesh
- Department of Earth and Planetary SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Shahar Alon
- Faculty of EngineeringBar‐Ilan UniversityRamat GanIsrael
| | - Gabriela Perna
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Anny Cárdenas
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | | | - David J. Miller
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular SciencesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
- The H. Steinitz Marine Biology LaboratoryThe Interuniversity Institute for Marine Sciences of EilatEilatIsrael
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23
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Xiang Z, Miller DJ, Kesidis G. Detection of Backdoors in Trained Classifiers Without Access to the Training Set. IEEE Trans Neural Netw Learn Syst 2022; 33:1177-1191. [PMID: 33326384 DOI: 10.1109/tnnls.2020.3041202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With wide deployment of deep neural network (DNN) classifiers, there is great potential for harm from adversarial learning attacks. Recently, a special type of data poisoning (DP) attack, known as a backdoor (or Trojan), was proposed. These attacks do not seek to degrade classification accuracy, but rather to have the classifier learn to classify to a target class t∗ whenever the backdoor pattern is present in a test example originally from a source class s∗ . Launching backdoor attacks does not require knowledge of the classifier or its training process-only the ability to poison the training set with exemplars containing a backdoor pattern (labeled with the target class). Defenses against backdoors can be deployed before/during training, post-training, or at test time. Here, we address post-training detection in DNN image classifiers, seldom considered in existing works, wherein the defender does not have access to the poisoned training set, but only to the trained classifier itself, as well as to clean (unpoisoned) examples from the classification domain. This scenario is of great interest because e.g., a classifier may be the basis of a phone app that will be shared with many users. Detection may thus reveal a widespread attack. We propose a purely unsupervised anomaly detection (AD) defense against imperceptible backdoor attacks that: 1) detects whether the trained DNN has been backdoor-attacked; 2) infers the source and target classes in a detected attack; 3) estimates the backdoor pattern itself. Our AD approach involves learning (via suitable cost function minimization) the minimum size/norm perturbation (putative backdoor) required to induce the classifier to misclassify (most) examples from class s to class t , for all (s,t) pairs. Our hypothesis is that nonattacked pairs require large perturbations, while the attacked pair (s∗, t∗) requires much smaller ones. This is convincingly borne out experimentally. We identify a variety of plausible cost functions and devise a novel, robust hypothesis testing approach to perform detection inference. We test our approach, in comparison with the state-of-the-art methods, for several backdoor patterns, attack settings and mechanisms, and data sets and demonstrate its favorability. Our defense essentially requires setting a single hyperparameter (the detection threshold), which can e.g., be chosen to fix the system's false positive rate.
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24
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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25
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Miller DJ, Niziol LM, Elam AR, Heisler M, Lee PP, Resnicow K, Musch DC, Darnley-Fisch D, Mitchell J, Newman-Casey PA. Demographic, Clinical, and Psychosocial Predictors of Change in Medication Adherence in the Support, Educate, Empower Program. Ophthalmol Glaucoma 2022; 5:47-57. [PMID: 34098169 PMCID: PMC8716681 DOI: 10.1016/j.ogla.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/13/2021] [Accepted: 06/01/2021] [Indexed: 01/03/2023]
Abstract
PURPOSE To investigate whether demographic, clinical, or psychosocial factors act as moderators of change in medication adherence in the Support, Educate, Empower (SEE) program. DESIGN Prospective, single-arm pilot study with a pre-post design. PARTICIPANTS Patients with glaucoma aged ≥ 40 years and taking ≥ 1 glaucoma medication were recruited from the University of Michigan Kellogg Eye Center. Those who had electronically measured adherence ≤ 80% in the 3-month eligibility monitoring period were enrolled in the SEE program. METHODS Medication adherence was monitored electronically during the 7-month intervention and calculated as the percentage of doses taken correctly. Change in adherence at different points in the SEE program and cumulative change in adherence were modeled with linear regression, and baseline demographic, clinical, and psychosocial factors were investigated for significant associations. MAIN OUTCOME MEASURES Demographic, clinical, and psychosocial variables associated with change in medication adherence in the SEE program. RESULTS Thirty-nine participants completed the SEE program. These participants were on average 63.9 years old (standard deviation [SD], 10.7 years), 56% (n = 22) were male, 44% (n = 17) were White, and 49% (n = 19) were Black. Medication adherence improved from an average of 59.9% (SD, 18.5%) at baseline to 83.6% (SD, 17.5%) after the final SEE session, for an increase of 23.7% (SD, 17.5%). Although participants with lower income (< $25 000 and $25 000-50 000 vs. >$50 000) had lower baseline adherence (48.4% and 64.1% vs. 70.4%), these individuals had greater increases in adherence during the first month of medication reminders (19.6% and 21.6% vs. 10.2%; P = 0.05 and P = 0.007, respectively). Participants taking fewer glaucoma medications also had significantly greater increases in adherence with medication reminders (P < 0.001). Those with higher levels of glaucoma-related distress (GD) had lower baseline adherence and greater increases in adherence with glaucoma coaching (P = 0.06). CONCLUSIONS Patient-level factors associated with relatively greater improvements in medication adherence through the SEE Program included lower income, fewer glaucoma medications, and increased GD. These findings demonstrate that the SEE program can improve glaucoma self-management even among participants with social and psychological barriers to medication adherence.
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Affiliation(s)
- David J. Miller
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan,Department of Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, Michigan
| | - Leslie M. Niziol
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Angela R. Elam
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michele Heisler
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Paul P. Lee
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kenneth Resnicow
- Department of Health Behavior and Health Education, University of Michigan Medical School, Ann Arbor, Michigan
| | - David C. Musch
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan,Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | | | - Jamie Mitchell
- School of Social Work, University of Michigan, Ann Arbor, MI
| | - Paula Anne Newman-Casey
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan
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26
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Déglin SE, Chen CL, Miller DJ, Lewis RJ, Chang ET, Hamade AK, Erickson HS. Environmental epidemiology and risk assessment: Exploring a path to increased confidence in public health decision-making. Glob Epidemiol 2021; 3:100048. [PMID: 37635726 PMCID: PMC10445995 DOI: 10.1016/j.gloepi.2021.100048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/25/2023] Open
Abstract
Throughout history, environmental epidemiology has proven crucial to identify certain threats to human health and to provide a basis for the development of life-saving public health policies. However, epidemiologists are facing challenges when studying tenuous threats such as environmental exposure to chemicals, whose association with adverse health effects may be difficult to characterize. As a result, epidemiological data can seldom be fully leveraged for quantitative risk assessment and decision-making. Despite two decades of efforts to improve a more systematic integration of human data to evaluate human health risks, assessors still heavily rely on animal data to do so, while epidemiology plays more of a secondary role. Although the need for more and better collaboration between risk assessors and epidemiologists is widely recognized, both fields tend to remain siloed. In 2017, the Health and Environmental Sciences Institute initiated a project engaging the epidemiology, exposure science, and regulatory communities with tripartite representation from regulators, industry, and academia in a dialogue on the use of environmental epidemiology for regulatory decision-making. Several focus groups attended by epidemiology, exposure science, and risk assessment experts were organized to explore incentives and barriers to collaboration, to ultimately bridge the gap between the various disciplines, and to realize the full potential of epidemiological data in risk assessment. Various ideas that have emerged from these meetings could help ensure the better integration of epidemiological data in quantitative risk assessment and contribute to building confidence in a robust and science-based regulatory decision-making process.
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Affiliation(s)
- Sandrine E. Déglin
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Connie L. Chen
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - David J. Miller
- U.S. Environmental Protection Agency, Washington, DC, United States of America
| | - R. Jeffrey Lewis
- ExxonMobil Biomedical Sciences, Inc., Annandale, NJ, United States of America
| | - Ellen T. Chang
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, United States of America
| | - Ali K. Hamade
- Oregon Health Authority, Portland, OR, United States of America
| | - Heidi S. Erickson
- Health & Medical, Chevron Services Company (a division of Chevron USA Inc.), Houston, TX, United States of America
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27
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Barraza SJ, Sindac JA, Dobry CJ, Delekta PC, Lee PH, Miller DJ, Larsen SD. Synthesis and biological activity of conformationally restricted indole-based inhibitors of neurotropic alphavirus replication: Generation of a three-dimensional pharmacophore. Bioorg Med Chem Lett 2021; 46:128171. [PMID: 34098081 PMCID: PMC8272561 DOI: 10.1016/j.bmcl.2021.128171] [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: 02/15/2021] [Revised: 05/26/2021] [Accepted: 05/30/2021] [Indexed: 11/29/2022]
Abstract
We have previously reported the development of indole-based CNS-active antivirals for the treatment of neurotropic alphavirus infection, but further optimization is impeded by a lack of knowledge of the molecular target and binding site. Herein we describe the design, synthesis and evaluation of a series of conformationally restricted analogues with the dual objectives of improving potency/selectivity and identifying the most bioactive conformation. Although this campaign was only modestly successful at improving potency, the sharply defined SAR of the rigid analogs enabled the definition of a three-dimensional pharmacophore, which we believe will be of value in further analog design and virtual screening for alternative antiviral leads.
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Affiliation(s)
- Scott J Barraza
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
| | - Janice A Sindac
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
| | - Craig J Dobry
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Philip C Delekta
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Pil H Lee
- Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
| | - David J Miller
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States.
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28
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Fingerhut LCHW, Miller DJ, Strugnell JM, Daly NL, Cooke IR. ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics 2021; 36:5262-5263. [PMID: 32683445 DOI: 10.1093/bioinformatics/btaa653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/28/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
SUMMARY Antimicrobial peptides (AMPs) are the key components of the innate immune system that protect against pathogens, regulate the microbiome and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. AVAILABILITY AND IMPLEMENTATION ampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://github.com/legana/ampir. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Legana C H W Fingerhut
- Department of Molecular and Cell Biology, Centre for Tropical Bioinformatics and Molecular Biology, Townsville, Qld, 4811, Australia.,Department of Molecular and Cell Biology, Townsville, Qld, 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, Centre for Tropical Bioinformatics and Molecular Biology, Townsville, Qld, 4811, Australia.,Department of Molecular and Cell Biology, Townsville, Qld, 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Norelle L Daly
- Department of Molecular and Cell Biology, Centre for Tropical Bioinformatics and Molecular Biology, Townsville, Qld, 4811, Australia.,Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4870, Australia
| | - Ira R Cooke
- Department of Molecular and Cell Biology, Centre for Tropical Bioinformatics and Molecular Biology, Townsville, Qld, 4811, Australia.,Department of Molecular and Cell Biology, Townsville, Qld, 4811, Australia
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29
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Pospiech M, Owens SE, Miller DJ, Austin-Muttitt K, Mullins JGL, Cronin JG, Allemann RK, Sheldon IM. Bisphosphonate inhibitors of squalene synthase protect cells against cholesterol-dependent cytolysins. FASEB J 2021; 35:e21640. [PMID: 33991130 DOI: 10.1096/fj.202100164r] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 01/29/2023]
Abstract
Certain species of pathogenic bacteria damage tissues by secreting cholesterol-dependent cytolysins, which form pores in the plasma membranes of animal cells. However, reducing cholesterol protects cells against these cytolysins. As the first committed step of cholesterol biosynthesis is catalyzed by squalene synthase, we explored whether inhibiting this enzyme protected cells against cholesterol-dependent cytolysins. We first synthesized 22 different nitrogen-containing bisphosphonate molecules that were designed to inhibit squalene synthase. Squalene synthase inhibition was quantified using a cell-free enzyme assay, and validated by computer modeling of bisphosphonate molecules binding to squalene synthase. The bisphosphonates were then screened for their ability to protect HeLa cells against the damage caused by the cholesterol-dependent cytolysin, pyolysin. The most effective bisphosphonate reduced pyolysin-induced leakage of lactate dehydrogenase into cell supernatants by >80%, and reduced pyolysin-induced cytolysis from >75% to <25%. In addition, this bisphosphonate reduced pyolysin-induced leakage of potassium from cells, limited changes in the cytoskeleton, prevented mitogen-activated protein kinases cell stress responses, and reduced cellular cholesterol. The bisphosphonate also protected cells against another cholesterol-dependent cytolysin, streptolysin O, and protected lung epithelial cells and primary dermal fibroblasts against cytolysis. Our findings imply that treatment with bisphosphonates that inhibit squalene synthase might help protect tissues against pathogenic bacteria that secrete cholesterol-dependent cytolysins.
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Affiliation(s)
- Mateusz Pospiech
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Siân E Owens
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | | | | | - James G Cronin
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | - I Martin Sheldon
- Swansea University Medical School, Swansea University, Swansea, UK
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30
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Grinblat M, Cooke I, Shlesinger T, Ben-Zvi O, Loya Y, Miller DJ, Cowman PF. Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals). Mol Phylogenet Evol 2021; 164:107265. [PMID: 34274488 DOI: 10.1016/j.ympev.2021.107265] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/15/2022]
Abstract
While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the coral community level, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy based largely on skeletal macromorphology has underestimated the diversity of many coral families. Here, we use targeted enrichment methods to sequence 2476 ultraconserved elements (UCEs) and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). Moreover, we analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both F. fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally for H. limax in the Red Sea. By combining UCE/exon data and mitochondrial sequences captured in off-target reads, we reinforce earlier findings that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for taxonomic and systematic re-evaluations of some species and genera within the family Fungiidae. This work demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which we can test phylogenetic hypotheses based on morphological and/or life history traits.
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Affiliation(s)
- Mila Grinblat
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Tom Shlesinger
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL, USA
| | - Or Ben-Zvi
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel; The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Yossi Loya
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland, Australia.
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31
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Xiang Z, Miller DJ, Kesidis G. Reverse engineering imperceptible backdoor attacks on deep neural networks for detection and training set cleansing. Comput Secur 2021. [DOI: 10.1016/j.cose.2021.102280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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33
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Daigneault BW, Miller DJ. Transient receptor potential polycystin-2 (TRPP2) regulates motility and intracellular calcium of porcine sperm. Andrologia 2021; 53:e14124. [PMID: 34042198 DOI: 10.1111/and.14124] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Polycystin-2, also known as transient receptor potential polycystin-2 (TRPP2), is a membrane protein that regulates calcium homeostasis in renal epithelial cells. Mutations in PKD2, the gene encoding human TRPP2, cause enlarged cystic kidneys and contribute to polycystic kidney disease (PKD). Male Drosophila melanogaster with mutations in amo, the homolog of PKD2, display a mild decrease in sperm motility but have a drastic reduction in fertility due to failed sperm migration and storage within the female tract. Although TRPP2 has critical roles for Drosophila sperm function, the protein has not been described in mammalian sperm. Herein, we report the localization of TRPP2 in porcine sperm and identify functions of TRPP2 in regulating intracellular Ca2+ and motility. Porcine sperm treated with an antibody to TRPP2 in capacitating medium had reduced average path velocity and curvilinear velocity (p < .05). Blocking TRPP2 also increased sperm tail beat-cross frequency (p < .05). After 90 min of capacitation, sperm incubated with TRPP2 antibody had decreased intracellular Ca2+ concentration compared to controls (p < .05), consistent with TRPP2 function as a plasma membrane cation channel. This is the first report that mammalian sperm contain TRPP2, which appears to regulate intracellular Ca2+ and motility patterns in porcine sperm.
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Affiliation(s)
- Bradford W Daigneault
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.,Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - David J Miller
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA
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34
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Miller DJ. 208 Sperm Retention, Storage and Release from the Oviduct: A Story of Sugars, Steroids, and Channels. J Anim Sci 2021. [DOI: 10.1093/jas/skab054.187] [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
Because mating is not always synchronized with ovulation, females from many species store sperm in the female reproductive tract until ovulation and fertilization. This may be done for short periods, a day or two for swine and cattle, or longer periods. Other mammals, such as some species of bats, store sperm for several months. Chickens and turkeys store sperm for 2–4 weeks and queens of some species of insects store sperm for over a decade in specialized structures. How sperm are retained, kept fertile for varying times and released is unclear. We have identified two specific carbohydrate motifs that are abundant in the porcine oviduct that bind and retain sperm in the isthmus. When immobilized, these two glycans lengthen sperm lifespan and suppress the normal increase in intracellular Ca2+ that normally accompanies capacitation. Porcine sperm can be released from oviduct cells and immobilized glycans by progesterone, perhaps of ovarian or cumulus-oocyte complex origin, which activates CatSper, a sperm-specific Ca2+ channel. Progesterone, as well as other compounds that stimulate hyperactivated motility, trigger sperm release, suggesting that hyperactivated motility is sufficient to release porcine sperm from oviduct glycans. We also have found that blocking proteasome-induced sperm protein lysis diminishes the number of sperm released from oviduct glycans. Finally, a transcriptomic approach has identified several groups of genes that are differentially regulated in both bovine and porcine oviducts from estrus animals that are storing sperm compared to oviducts from diestrus animals. This provides clues about how sperm lifespan is extended during storage.
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35
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Xiang Z, Miller DJ, Wang H, Kesidis G. Detecting Scene-Plausible Perceptible Backdoors in Trained DNNs Without Access to the Training Set. Neural Comput 2021; 33:1329-1371. [PMID: 33617746 DOI: 10.1162/neco_a_01376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/07/2020] [Indexed: 11/04/2022]
Abstract
Backdoor data poisoning attacks add mislabeled examples to the training set, with an embedded backdoor pattern, so that the classifier learns to classify to a target class whenever the backdoor pattern is present in a test sample. Here, we address posttraining detection of scene-plausible perceptible backdoors, a type of backdoor attack that can be relatively easily fashioned, particularly against DNN image classifiers. A post-training defender does not have access to the potentially poisoned training set, only to the trained classifier, as well as some unpoisoned examples that need not be training samples. Without the poisoned training set, the only information about a backdoor pattern is encoded in the DNN's trained weights. This detection scenario is of great import considering legacy and proprietary systems, cell phone apps, as well as training outsourcing, where the user of the classifier will not have access to the entire training set. We identify two important properties of scene-plausible perceptible backdoor patterns, spatial invariance and robustness, based on which we propose a novel detector using the maximum achievable misclassification fraction (MAMF) statistic. We detect whether the trained DNN has been backdoor-attacked and infer the source and target classes. Our detector outperforms existing detectors and, coupled with an imperceptible backdoor detector, helps achieve posttraining detection of most evasive backdoors of interest.
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Affiliation(s)
- Zhen Xiang
- School of Electrical Engineering and Computer Science, College of Engineering, The Pennsylvania State University, University Park, PA 16802, U.S.A.
| | - David J Miller
- School of Electrical Engineering and Computer Science, College of Engineering, The Pennsylvania State University, University Park, PA 16802, U.S.A.
| | - Hang Wang
- School of Electrical Engineering and Computer Science, College of Engineering, The Pennsylvania State University, University Park, PA 16802, U.S.A.
| | - George Kesidis
- School of Electrical Engineering and Computer Science, College of Engineering, The Pennsylvania State University, University Park, PA 16802, U.S.A.
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36
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Sharif M, Kerns K, Sutovsky P, Bovin N, Miller DJ. Progesterone induces porcine sperm release from oviduct glycans in a proteasome-dependent manner. Reproduction 2021; 161:449-457. [PMID: 33589564 DOI: 10.1530/rep-20-0474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/15/2021] [Indexed: 12/30/2022]
Abstract
In mammals, the oviduct retains sperm, forming a reservoir from which they are released in synchrony with ovulation. However, the mechanisms underlying sperm release are unclear. Herein, we first examined in greater detail the release of sperm from the oviduct reservoir by sex steroids, and secondly, if the ubiquitin-proteasome system (UPS) mediates this release in vitro. Sperm were allowed to bind to oviductal cells or immobilized oviduct glycans, either bi-SiaLN or a suLeX, and channeled with steroids in the presence or absence of proteasome inhibitors. Previously, we have demonstrated progesterone-induced sperm release from oviduct cells and immobilized glycans in a steroid-specific manner. Herein, we found that the release of sperm from an immobilized oviduct glycan, a six-sialylated branched structure, and from immobilized fibronectin was inhibited by the CatSper blocker NNC 055-0396, akin to the previously reported ability of NNC 055-0396 to inhibit sperm release from another oviduct glycan, sulfated Lewis-X trisaccharide. Thus, CatSper may be required for release of sperm from a variety of adhesion systems. One possible mechanism for sperm release is that glycan receptors on sperm are degraded by proteasomes or shed from the sperm surface by proteasomal degradation. Accordingly, the inhibition of proteasomal degradation blocked sperm release from oviduct cell aggregates both immobilized oviduct glycans as well as fibronectin. In summary, progesterone-induced sperm release requires both active CatSper channels and proteasomal degradation, suggesting that hyperactivation and proteolysis are vital parts of the mechanism by which sperm move from the oviduct reservoir to the site of fertilization.
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Affiliation(s)
- Momal Sharif
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karl Kerns
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Peter Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Nicolai Bovin
- Shemyakin Institute of Bioorganic Chemistry, Moscow, Russia
| | - David J Miller
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Abstract
Albumin, a vital protein in cell culture systems, is derived from whole blood or blood products. The culture of human gametes and developing embryos for assisted reproduction (ART) uses albumin of human origin. Human serum albumin (HSA) is derived from expired blood obtained from blood banks. This blood has been stored in polyvinyl chloride bags made clear and flexible with di-2-ethylhexyl phthalate (DEHP). But DEHP can leach from the bags into stored blood and co-fractionate with HSA during albumin isolation. DEHP and its metabolite mono-ethylhexyl phthalate (MEHP), are known endocrine disruptors that are reported to have negative effects when directly supplemented in media for IVF using gametes from a variety of animals. Therefore, the contamination of ART media with DEHP and MEHP through HSA supplementation may have effects on the outcomes of ART procedures. While the embryology laboratory is strictly monitored to prevent a wide variety of contamination, phthalate contamination of HSA has not been broadly examined. This review outlines the function of HSA in ART procedures and the production of HSA from whole blood. Finally, the review highlights the effects of acute phthalate exposures on gametes during in vitro procedures.
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Affiliation(s)
- Jennifer R. Hughes
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL 61801, Phone 217-333-3408
| | - Sandra Soto-Heras
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL 61801, Phone 217-333-3408
| | | | - David J. Miller
- Department of Animal Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL 61801, Phone 217-333-3408
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Praher D, Zimmermann B, Dnyansagar R, Miller DJ, Moya A, Modepalli V, Fridrich A, Sher D, Friis-Møller L, Sundberg P, Fôret S, Ashby R, Moran Y, Technau U. Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proc Biol Sci 2021; 288:20203169. [PMID: 33622129 PMCID: PMC7935066 DOI: 10.1098/rspb.2020.3169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.
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Affiliation(s)
- Daniela Praher
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - David J. Miller
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, UK
| | - Arie Fridrich
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Lene Friis-Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Lyngby, Denmark
| | - Per Sundberg
- Department of Zoology, University of Gothenburg, Gothenburg, Sweden
| | - Sylvain Fôret
- Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia
| | - Regan Ashby
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
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Srivastava PL, Escorcia AM, Huynh F, Miller DJ, Allemann RK, van der Kamp MW. Redesigning the Molecular Choreography to Prevent Hydroxylation in Germacradien-11-ol Synthase Catalysis. ACS Catal 2021; 11:1033-1041. [PMID: 33614194 PMCID: PMC7886051 DOI: 10.1021/acscatal.0c04647] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/26/2020] [Indexed: 12/04/2022]
Abstract
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Natural sesquiterpene synthases have evolved to make complex terpenoids by quenching
reactive carbocations either by proton transfer or by hydroxylation (water capture),
depending on their active site. Germacradien-11-ol synthase (Gd11olS) from
Streptomyces coelicolor catalyzes the cyclization of farnesyl
diphosphate (FDP) into the hydroxylated sesquiterpene germacradien-11-ol. Here, we
combine experiment and simulation to guide the redesign of its active site pocket to
avoid hydroxylation of the product. Molecular dynamics simulations indicate two regions
between which water molecules can flow that are responsible for hydroxylation. Point
mutations of selected residues result in variants that predominantly form a complex
nonhydroxylated product, which we identify as isolepidozene. Our results indicate how
these mutations subtly change the molecular choreography in the Gd11olS active site and
thereby pave the way for the engineering of terpene synthases to make complex terpenoid
products.
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Affiliation(s)
- Prabhakar L. Srivastava
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Andrés M. Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Florence Huynh
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - David J. Miller
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
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40
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Mason B, Cooke I, Moya A, Augustin R, Lin MF, Satoh N, Bosch TCG, Bourne DG, Hayward DC, Andrade N, Forêt S, Ying H, Ball EE, Miller DJ. AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones. Dev Comp Immunol 2021; 114:103866. [PMID: 32937163 DOI: 10.1016/j.dci.2020.103866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/02/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
A candidate antimicrobial peptide (AmAMP1) was identified by searching the whole genome sequence of Acropora millepora for short (<125AA) cysteine-rich predicted proteins with an N-terminal signal peptide but lacking clear homologs in the SwissProt database. It resembled but was not closely related to damicornin, the only other known AMP from a coral, and was shown to be active against both Gram-negative and Gram-positive bacteria. These proteins define a family of AMPs present in corals and their close relatives, the Corallimorpharia, and are synthesised as preproproteins in which the C-terminal mature peptide contains a conserved arrangement of six cysteine residues. Consistent with the idea of a common origin for AMPs and toxins, this Cys motif is shared between the coral AMPs and the Shk neurotoxins of sea anemones. AmAMP1 is expressed at late stages of coral development, in ectodermal cells that resemble the "ganglion neurons" of Hydra, in which it has recently been demonstrated that a distinct AMP known as NDA-1 is expressed.
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Affiliation(s)
- B Mason
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia
| | - I Cooke
- Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - A Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia
| | - R Augustin
- Zoological Institute, Kiel University, Kiel, Germany
| | - M-F Lin
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan
| | - N Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan
| | - T C G Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - D G Bourne
- Department of Marine Ecosystems and Impacts, James Cook University, Townsville, 4811, Queensland, Australia
| | - D C Hayward
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - N Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia
| | - S Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - H Ying
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - E E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - D J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia; Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia; Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495, Onna, Okinawa, Japan.
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41
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Cowman PF, Quattrini AM, Bridge TC, Watkins-Colwell GJ, Fadli N, Grinblat M, Roberts TE, McFadden CS, Miller DJ, Baird AH. An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Mol Phylogenet Evol 2020; 153:106944. [DOI: 10.1016/j.ympev.2020.106944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
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Abstract
Abstract
After semen deposition, a fraction of sperm is transported through the female reproductive tract to the lower oviduct, the isthmus, where sperm are retained to form a reservoir. Some of these sperm are released to move to the upper oviduct, the site of fertilization. For sperm to make this journey, they must overcome challenges including possible phagocytosis, high fluid viscosity, and peristaltic contractions of the tract. The study of sperm transport is complex because so few sperm reach the site of fertilization. We have focused our studies on how sperm are retained in the reservoir, how storage prolongs sperm lifespan, and how sperm are released to fertilize oocytes. Sperm storage is particularly important in situations in which ovulation is not tightly synchronized with semen deposition. This occurs in domestic animals, but is especially notable in some species of bats, birds, and insects. Using porcine sperm and an array of 400 common glycans, we identified two specific glycan motifs found in all structures that bound sperm, a Lewis X trisaccharide and a branched 6-sialylated oligosaccharide. Tandem MS profiling indicated that both motifs were abundant in the asparagine-linked glycans of the oviduct epithelium and several larger oligosaccharides were identified that contained both motifs. When these motifs were immobilized, each could retain sperm, suppress Ca2+ influx and lengthen sperm lifespan. Secretions from the cumulus-oocyte complex (COC) and progesterone released sperm from immobilized oviduct glycans, suggesting that COCs can themselves signal sperm release. Progesterone-induced release required CatSper channels, sperm hyperactivation and was dependent on sperm protein degradation. These studies support a model in which sperm are retained in the isthmus by specific glycans on the epithelium, which extends sperm lifespan until COCs produce releasing factors that promote sperm liberation from the isthmus and movement to the ampulla to fertilize the COCs.
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43
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Schmidt CA, Wilson DT, Cooke I, Potriquet J, Tungatt K, Muruganandah V, Boote C, Kuek F, Miles JJ, Kupz A, Ryan S, Loukas A, Bansal PS, Takjoo R, Miller DJ, Peigneur S, Tytgat J, Daly NL. Identification and Characterization of a Peptide from the Stony Coral Heliofungia actiniformis. J Nat Prod 2020; 83:3454-3463. [PMID: 33166137 DOI: 10.1021/acs.jnatprod.0c00981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Marine organisms produce a diverse range of toxins and bioactive peptides to support predation, competition, and defense. The peptide repertoires of stony corals (order Scleractinia) remain relatively understudied despite the presence of tentacles used for predation and defense that are likely to contain a range of bioactive compounds. Here, we show that a tentacle extract from the mushroom coral, Heliofungia actiniformis, contains numerous peptides with a range of molecular weights analogous to venom profiles from species such as cone snails. Using NMR spectroscopy and mass spectrometry we characterized a 12-residue peptide (Hact-1) with a new sequence (GCHYTPFGLICF) and well-defined β-hairpin structure stabilized by a single disulfide bond. The sequence is encoded within the genome of the coral and expressed in the polyp body tissue. The structure present is common among toxins and venom peptides, but Hact-1 does not show activity against select examples of Gram-positive and Gram-negative bacteria or a range of ion channels, common properties of such peptides. Instead, it appears to have a limited effect on human peripheral blood mononuclear cells, but the ecological function of the peptide remains unknown. The discovery of this peptide from H. actiniformis is likely to be the first of many from this and related species.
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Affiliation(s)
- Casey A Schmidt
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David T Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Jeremy Potriquet
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
- AB Sciex, Brisbane, Queensland, Australia
| | - Katie Tungatt
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Visai Muruganandah
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Chloë Boote
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Felicity Kuek
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - John J Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Andreas Kupz
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Stephanie Ryan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Paramjit S Bansal
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Rozita Takjoo
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Steve Peigneur
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, 3000, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, 3000, Belgium
| | - Norelle L Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
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Cooke I, Ying H, Forêt S, Bongaerts P, Strugnell JM, Simakov O, Zhang J, Field MA, Rodriguez-Lanetty M, Bell SC, Bourne DG, van Oppen MJ, Ragan MA, Miller DJ. Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. Sci Adv 2020; 6:6/48/eabc6318. [PMID: 33246955 PMCID: PMC7695477 DOI: 10.1126/sciadv.abc6318] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/15/2020] [Indexed: 05/24/2023]
Abstract
Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.
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Affiliation(s)
- Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Pim Bongaerts
- California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Mauricio Rodriguez-Lanetty
- Institute of Environment and Department of Biological Sciences, Florida International University, Miami, Fl 33199, USA
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - David G Bourne
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Madeleine Jh van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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45
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Mohamed AR, Andrade N, Moya A, Chan CX, Negri AP, Bourne DG, Ying H, Ball EE, Miller DJ. Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Mol Ecol 2020; 29:3921-3937. [PMID: 32853430 DOI: 10.1111/mec.15612] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Despite the ecological significance of the mutualistic relationship between Symbiodiniaceae and reef-building corals, the molecular interactions during establishment of this relationship are not well understood. This is particularly true of the transcriptional changes that occur in the symbiont. In the current study, a dual RNA-sequencing approach was used to better understand transcriptional changes on both sides of the coral-symbiont interaction during the colonization of Acropora tenuis by a compatible Symbiodiniaceae strain (Cladocopium goreaui; ITS2 type C1). Comparison of transcript levels of the in hospite symbiont 3, 12, 48 and 72 hr after exposure to those of the same strain in culture revealed that extensive and generalized down-regulation of symbiont gene expression occurred during the infection process. Included in this "symbiosis-derived transcriptional repression" were a range of stress response and immune-related genes. In contrast, a suite of symbiont genes implicated in metabolism was upregulated in the symbiotic state. The coral data support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses, and additionally imply the involvement of some SCRiP family members in the colonization process. Consistent with previous ecological studies, the transcriptomic data suggest that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship can be established at the larval stage. This dual RNA-sequencing study provides insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle and the novel coral genes implicated in symbiosis.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Qld, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, Egypt.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, Australia
| | - Natalia Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Qld, Australia.,Department of Marine Ecosystems and Impacts, James Cook University, Townsville, Qld, Australia
| | - Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
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Da Pan, Tao L, Sun K, Golston LM, Miller DJ, Zhu T, Qin Y, Zhang Y, Mauzerall DL, Zondlo MA. Methane emissions from natural gas vehicles in China. Nat Commun 2020; 11:4588. [PMID: 32917876 PMCID: PMC7486943 DOI: 10.1038/s41467-020-18141-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Natural gas vehicles (NGVs) have been promoted in China to mitigate air pollution, yet our measurements and analyses show that NGV growth in China may have significant negative impacts on climate change. We conducted real-world vehicle emission measurements in China and found high methane emissions from heavy-duty NGVs (90% higher than current emission limits). These emissions have been ignored in previous emission estimates, leading to biased results. Applying our observations to life-cycle analyses, we found that switching to NGVs from conventional vehicles in China has led to a net increase in greenhouse gas (GHG) emissions since 2000. With scenario analyses, we also show that the next decade will be critical for China to reverse the trend with the upcoming China VI standard for heavy-duty vehicles. Implementing and enforcing the China VI standard is challenging, and the method demonstrated here can provide critical information regarding the fleet-level CH4 emissions from NGVs.
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Affiliation(s)
- Da Pan
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA. .,Center for Mid-Infrared Technologies for Health and The Environmental, NSF-ERC, Princeton, NJ, 08544, USA.
| | - Lei Tao
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA.,Center for Mid-Infrared Technologies for Health and The Environmental, NSF-ERC, Princeton, NJ, 08544, USA
| | - Kang Sun
- Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, NY, 14260, USA.,Research and Education in eNergy, Environment and Water (RENEW) Institute, University at Buffalo, Buffalo, NY, 14260, USA
| | - Levi M Golston
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA.,Center for Mid-Infrared Technologies for Health and The Environmental, NSF-ERC, Princeton, NJ, 08544, USA
| | - David J Miller
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA.,Center for Mid-Infrared Technologies for Health and The Environmental, NSF-ERC, Princeton, NJ, 08544, USA.,Currently at Environmental Defense Fund, New York, NY, 10010, USA
| | - Tong Zhu
- State Key Joint Laboratory for Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Yue Qin
- Department of Geography, The Ohio State University, Columbus, OH, 43210, USA.,Sustainability Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Yan Zhang
- Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Denise L Mauzerall
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA.,Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, 08544, USA
| | - Mark A Zondlo
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA. .,Center for Mid-Infrared Technologies for Health and The Environmental, NSF-ERC, Princeton, NJ, 08544, USA.
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47
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O'Brien PA, Tan S, Yang C, Frade PR, Andreakis N, Smith HA, Miller DJ, Webster NS, Zhang G, Bourne DG. Diverse coral reef invertebrates exhibit patterns of phylosymbiosis. ISME J 2020; 14:2211-2222. [PMID: 32444811 PMCID: PMC7608455 DOI: 10.1038/s41396-020-0671-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
Microbiome assemblages of plants and animals often show a degree of correlation with host phylogeny; an eco-evolutionary pattern known as phylosymbiosis. Using 16S rRNA gene sequencing to profile the microbiome, paired with COI, 18S rRNA and ITS1 host phylogenies, phylosymbiosis was investigated in four groups of coral reef invertebrates (scleractinian corals, octocorals, sponges and ascidians). We tested three commonly used metrics to evaluate the extent of phylosymbiosis: (a) intraspecific versus interspecific microbiome variation, (b) topological comparisons between host phylogeny and hierarchical clustering (dendrogram) of host-associated microbial communities, and (c) correlation of host phylogenetic distance with microbial community dissimilarity. In all instances, intraspecific variation in microbiome composition was significantly lower than interspecific variation. Similarly, topological congruency between host phylogeny and the associated microbial dendrogram was more significant than would be expected by chance across all groups, except when using unweighted UniFrac distance (compared with weighted UniFrac and Bray-Curtis dissimilarity). Interestingly, all but the ascidians showed a significant positive correlation between host phylogenetic distance and associated microbial dissimilarity. Our findings provide new perspectives on the diverse nature of marine phylosymbioses and the complex roles of the microbiome in the evolution of marine invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Chentao Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Pedro R Frade
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Hillary A Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
- AIMS@JCU, Townsville, QLD, Australia.
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Machado SA, Sharif M, Kadirvel G, Bovin N, Miller DJ. Adhesion to oviduct glycans regulates porcine sperm Ca2+ influx and viability. PLoS One 2020; 15:e0237666. [PMID: 32822385 PMCID: PMC7442259 DOI: 10.1371/journal.pone.0237666] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Received: 04/17/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
Before fertilization, sperm bind to epithelial cells of the oviduct isthmus to form a reservoir that regulates sperm viability and capacitation. The sperm reservoir maintains optimum fertility in species, like swine, in which semen deposition and ovulation may not be well synchronized. We demonstrated previously that porcine sperm bind to two oviductal glycan motifs, a biantennary 6-sialylated N-acetyllactosamine (bi-SiaLN) oligosaccharide and 3-O-sulfated Lewis X trisaccharide (suLeX). Here, we assessed the ability of these glycans to regulate sperm Ca2+ influx, capacitation and affect sperm lifespan. After 24 h, the viability of sperm bound to immobilized bi-SiaLN and suLeX was higher (46% and 41% respectively) compared to viability of free-swimming sperm (10–12%). Ca2+ is a central regulator of sperm function so we assessed whether oviduct glycans could affect the Ca2+ influx that occurs during capacitation. Using a fluorescent intracellular Ca2+ probe, we observed that both oviduct glycans suppressed the Ca2+ increase that occurs during capacitation. Thus, specific oviduct glycans can regulate intracellular Ca2+. Because the increase in intracellular Ca2+ was suppressed by oviduct glycans, we examined whether glycans affected capacitation, as determined by protein tyrosine phosphorylation and the ability to undergo a Ca2+ ionophore-induced acrosome reaction. We found no discernable suppression of capacitation in sperm bound to oviduct glycans. We also detected no effect of oviduct glycans on sperm motility during capacitation. In summary, LeX and bi-SiaLN glycan motifs found on oviduct oligosaccharides suppress the Ca2+ influx that occurs during capacitation and extend sperm lifespan but do not affect sperm capacitation or motility.
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Affiliation(s)
- Sergio A. Machado
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Momal Sharif
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Govindasamy Kadirvel
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Nicolai Bovin
- Shemyakin Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - David J. Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail:
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Mohamed AR, Chan CX, Ragan MA, Zhang J, Cooke I, Ball EE, Miller DJ. Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environ Microbiol Rep 2020; 12:435-443. [PMID: 32452166 DOI: 10.1111/1758-2229.12859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leads to the collapse of the association. This sensitivity has led to an interest in the potential of more stress-tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ('GBR Chromera') and compared with those of the reference strain of Chromera ('Sydney Chromera'), and to those of Symbiodiniaceae (Fugacium kawagutii, Cladocopium goreaui and Breviolum minutum), as well as the apicomplexan parasite, Plasmodium falciparum. In contrast to the high sequence divergence amongst representatives of different genera within the family Symbiodiniaceae, the two Chromera strains featured low sequence divergence at orthologous genes, implying that they are likely to be conspecifics. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization that explains the ecological dominance of Cladocopium spp. amongst Indo-Pacific reef corals. The presence of HSP20 genes may contribute to the high thermal tolerance of Chromera.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, Qld, 4067, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
- Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, 4811, Australia
- Zoology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Jia Zhang
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
| | - Ira Cooke
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton ACT, 2601, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
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50
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Hehenberger E, Eitel M, Fortunato SAV, Miller DJ, Keeling PJ, Cahill MA. Early eukaryotic origins and metazoan elaboration of MAPR family proteins. Mol Phylogenet Evol 2020; 148:106814. [PMID: 32278076 DOI: 10.1016/j.ympev.2020.106814] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 01/01/2023]
Abstract
The membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR genes (PGRMC-like, Neuferricin and Neudesin). Here we show that all three animal MAPR genes were already present in the common ancestor of the opisthokonts (comprising animals and fungi as well as related single-celled taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of cnidarians and bilaterians, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilaterian animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by animals (Metazoa). This study provides a conceptual framework for future studies, against which especially PGRMC1's multiple functions can perhaps be stratified and functionally dissected.
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Affiliation(s)
- Elisabeth Hehenberger
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sofia A V Fortunato
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael A Cahill
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Canberra, ACT 2601, Australia.
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