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Shurba JA, Whitehead KJ, Schley HL, Bauer BA, Barrett RK, Yarrow GK, Anderson JT. Does Nesting Material Affect Wood Duck (Aix sponsa) Nest Box Selection, Reproduction, and Eggshell Bacteria? J Wildl Dis 2024:500799. [PMID: 38755118 DOI: 10.7589/jwd-d-23-00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
Wood Ducks (Aix sponsa) are secondary cavity nesters that use natural cavities and artificial nest boxes, the latter of which has been attributed to the recovery of populations across the southeastern US. Continual use of these boxes results in a buildup of bacteria, parasites, and other pathogens. To avoid the accumulation of these deleterious organisms, best management practices include the occasional removal of old nesting material (i.e., wood shavings) and replacement with fresh wood shavings. No studies have been performed on the effects of shaving material on nest box selection, nest success, and bacterial growth. We monitored 142 and 111 nest boxes in Florida and Georgia, USA, respectively, and filled a random sample with aspen or cedar shavings. We then swabbed the surface of 144 and 150 eggs during 2020 and 2021, respectively, to screen for culturable bacteria. We detected no effect of shaving type on nest box selection, nest success, or egg surface bacterial growth. We found 3-8 bacterial colony types (1-123 colony-forming units [CFU]/box) and 1-8 bacterial colony types (3-382 CFU/box) among the Georgia and Florida samples, respectively. We detected no effect from shaving type on Wood Duck reproduction or bacterial growth in the sampled nest boxes. We concluded that both shaving types are suitable nesting materials for box-nesting Wood Duck populations and the continued use of either would be a reasonable decision for managers.
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Affiliation(s)
- Jacob A Shurba
- James C. Kennedy Waterfowl and Wetlands Conservation Center, Belle W. Baruch Institute of Coastal Ecology and Forest Science, Clemson University, PO Box 596, Georgetown, South Carolina 29442, USA
- Current address: Southeastern Cooperative Wildlife Disease Study, University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Kristi J Whitehead
- Department of Biological Sciences, Clemson University, 130 Delta Epsilon Court, Clemson, South Carolina 29634, USA
| | - Hannah L Schley
- Department of Entomology and Wildlife Ecology, University of Delaware, 531 South College Avenue, Newark, Delaware 19716, USA
| | - Beau A Bauer
- Nemours Wildlife Foundation, 161 Nemours Plantation Drive, Yemassee, South Carolina 29945, USA
| | - Russell K Barrett
- Department of Forestry and Environmental Conservation, Clemson University, 231 Lehotsky Hall, Clemson, South Carolina 29634, USA
| | - Greg K Yarrow
- Department of Forestry and Environmental Conservation, Clemson University, 231 Lehotsky Hall, Clemson, South Carolina 29634, USA
| | - James T Anderson
- James C. Kennedy Waterfowl and Wetlands Conservation Center, Belle W. Baruch Institute of Coastal Ecology and Forest Science, Clemson University, PO Box 596, Georgetown, South Carolina 29442, USA
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2
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Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JT, Ramakrishnan G, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow SC, Irizarry RA, Bulyk ML. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun 2024; 15:3110. [PMID: 38600112 PMCID: PMC11006913 DOI: 10.1038/s41467-024-47396-0] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.
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Affiliation(s)
- Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Patrick K Kimes
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Gayatri Ramakrishnan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Boston Bangalore Biosciences Beginnings Program, Harvard University, Cambridge, MA, USA
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dongyuan Song
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA
| | - Stephen C Blacklow
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Ferrell M, Wang Z, Anderson JT, Li XS, Witkowski M, DiDonato JA, Hilser JR, Hartiala JA, Haghikia A, Cajka T, Fiehn O, Sangwan N, Demuth I, König M, Steinhagen-Thiessen E, Landmesser U, Tang WHW, Allayee H, Hazen SL. Publisher Correction: A terminal metabolite of niacin promotes vascular inflammation and contributes to cardiovascular disease risk. Nat Med 2024:10.1038/s41591-024-02899-7. [PMID: 38448791 DOI: 10.1038/s41591-024-02899-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Affiliation(s)
- Marc Ferrell
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Program, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James T Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marco Witkowski
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
| | - Joseph A DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Hilser
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaana A Hartiala
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Arash Haghikia
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tomas Cajka
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ilja Demuth
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Maximilian König
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Ulf Landmesser
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - W H Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hooman Allayee
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA.
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4
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Ferrell M, Wang Z, Anderson JT, Li XS, Witkowski M, DiDonato JA, Hilser JR, Hartiala JA, Haghikia A, Cajka T, Fiehn O, Sangwan N, Demuth I, König M, Steinhagen-Thiessen E, Landmesser U, Tang WHW, Allayee H, Hazen SL. A terminal metabolite of niacin promotes vascular inflammation and contributes to cardiovascular disease risk. Nat Med 2024; 30:424-434. [PMID: 38374343 DOI: 10.1038/s41591-023-02793-8] [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: 03/16/2023] [Accepted: 12/22/2023] [Indexed: 02/21/2024]
Abstract
Despite intensive preventive cardiovascular disease (CVD) efforts, substantial residual CVD risk remains even for individuals receiving all guideline-recommended interventions. Niacin is an essential micronutrient fortified in food staples, but its role in CVD is not well understood. In this study, untargeted metabolomics analysis of fasting plasma from stable cardiac patients in a prospective discovery cohort (n = 1,162 total, n = 422 females) suggested that niacin metabolism was associated with incident major adverse cardiovascular events (MACE). Serum levels of the terminal metabolites of excess niacin, N1-methyl-2-pyridone-5-carboxamide (2PY) and N1-methyl-4-pyridone-3-carboxamide (4PY), were associated with increased 3-year MACE risk in two validation cohorts (US n = 2,331 total, n = 774 females; European n = 832 total, n = 249 females) (adjusted hazard ratio (HR) (95% confidence interval) for 2PY: 1.64 (1.10-2.42) and 2.02 (1.29-3.18), respectively; for 4PY: 1.89 (1.26-2.84) and 1.99 (1.26-3.14), respectively). Phenome-wide association analysis of the genetic variant rs10496731, which was significantly associated with both 2PY and 4PY levels, revealed an association of this variant with levels of soluble vascular adhesion molecule 1 (sVCAM-1). Further meta-analysis confirmed association of rs10496731 with sVCAM-1 (n = 106,000 total, n = 53,075 females, P = 3.6 × 10-18). Moreover, sVCAM-1 levels were significantly correlated with both 2PY and 4PY in a validation cohort (n = 974 total, n = 333 females) (2PY: rho = 0.13, P = 7.7 × 10-5; 4PY: rho = 0.18, P = 1.1 × 10-8). Lastly, treatment with physiological levels of 4PY, but not its structural isomer 2PY, induced expression of VCAM-1 and leukocyte adherence to vascular endothelium in mice. Collectively, these results indicate that the terminal breakdown products of excess niacin, 2PY and 4PY, are both associated with residual CVD risk. They also suggest an inflammation-dependent mechanism underlying the clinical association between 4PY and MACE.
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Affiliation(s)
- Marc Ferrell
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Program, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James T Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marco Witkowski
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
| | - Joseph A DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Hilser
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaana A Hartiala
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Arash Haghikia
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tomas Cajka
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ilja Demuth
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Maximilian König
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Ulf Landmesser
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - W H Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hooman Allayee
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA.
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Abstract
Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.
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Affiliation(s)
- James T Anderson
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
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Attaye I, Lassen PB, Adriouch S, Steinbach E, Patiño-Navarrete R, Davids M, Alili R, Jacques F, Benzeguir S, Belda E, Nemet I, Anderson JT, Alexandre-Heymann L, Greyling A, Larger E, Hazen SL, van Oppenraaij SL, Tremaroli V, Beck K, Bergh PO, Bäckhed F, ten Brincke SP, Herrema H, Groen AK, Pinto-Sietsma SJ, Clément K, Nieuwdorp M. Protein supplementation changes gut microbial diversity and derived metabolites in subjects with type 2 diabetes. iScience 2023; 26:107471. [PMID: 37599833 PMCID: PMC10432813 DOI: 10.1016/j.isci.2023.107471] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/05/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
High-protein diets are promoted for individuals with type 2 diabetes (T2D). However, effects of dietary protein interventions on (gut-derived) metabolites in T2D remains understudied. We therefore performed a multi-center, randomized-controlled, isocaloric protein intervention with 151 participants following either 12-week high-protein (HP; 30Energy %, N = 78) vs. low-protein (LP; 10 Energy%, N = 73) diet. Primary objectives were dietary effects on glycemic control which were determined via glycemic excursions, continuous glucose monitors and HbA1c. Secondary objectives were impact of diet on gut microbiota composition and -derived metabolites which were determined by shotgun-metagenomics and mass spectrometry. Analyses were performed using delta changes adjusting for center, baseline, and kidney function when appropriate. This study found that a short-term 12-week isocaloric protein modulation does not affect glycemic parameters or weight in metformin-treated T2D. However, the HP diet slightly worsened kidney function, increased alpha-diversity, and production of potentially harmful microbiota-dependent metabolites, which may affect host metabolism upon prolonged exposure.
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Affiliation(s)
- Ilias Attaye
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Pierre Bel Lassen
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition Department, Paris, France
| | - Solia Adriouch
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Emilie Steinbach
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Rafael Patiño-Navarrete
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Mark Davids
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Rohia Alili
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Flavien Jacques
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Sara Benzeguir
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Eugeni Belda
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - James T. Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH, USA
| | | | - Arno Greyling
- Unilever Foods Innovation Centre, Wageningen, the Netherlands
| | - Etienne Larger
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition Department, Paris, France
| | - Stanley L. Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland, OH, USA
| | - Sophie L. van Oppenraaij
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Katharina Beck
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Per-Olof Bergh
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45 Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Suzan P.M. ten Brincke
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Albert K. Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Karine Clément
- Sorbonne Université, INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Paris, France
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition Department, Paris, France
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
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7
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Skelly BP, Clipp HL, Landry SM, Rogers R, Phelps Q, Anderson JT, Rota CT. A flexible Bayesian approach for estimating survival probabilities from age‐at‐harvest data. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Brett P. Skelly
- Division of Forestry and Natural Resources West Virginia University Morgantown West Virginia USA
- West Virginia Division of Natural Resources Elkins West Virginia USA
| | - Hannah L. Clipp
- Division of Forestry and Natural Resources West Virginia University Morgantown West Virginia USA
| | - Stephanie M. Landry
- Division of Forestry and Natural Resources West Virginia University Morgantown West Virginia USA
- Department of Wildland Resources Utah State University Logan Utah USA
| | - Rich Rogers
- West Virginia Division of Natural Resources Romney West Virginia USA
| | - Quinton Phelps
- Department of Biology Missouri State University Springfield Missouri USA
| | - James T. Anderson
- James C. Kennedy Waterfowl and Wetlands Conservation Center Belle W. Baruch Institute of Coastal Ecology and Forest Science Georgetown South Carolina USA
| | - Christopher T. Rota
- Division of Forestry and Natural Resources West Virginia University Morgantown West Virginia USA
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8
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Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL. Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease. Cell Host Microbe 2023; 31:18-32.e9. [PMID: 36549300 PMCID: PMC9839529 DOI: 10.1016/j.chom.2022.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [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: 05/17/2022] [Revised: 09/22/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Recent studies show gut microbiota-dependent metabolism of dietary phenylalanine into phenylacetic acid (PAA) is critical in phenylacetylglutamine (PAGln) production, a metabolite linked to atherosclerotic cardiovascular disease (ASCVD). Accordingly, microbial enzymes involved in this transformation are of interest. Using genetic manipulation in selected microbes and monocolonization experiments in gnotobiotic mice, we identify two distinct gut microbial pathways for PAA formation; one is catalyzed by phenylpyruvate:ferredoxin oxidoreductase (PPFOR) and the other by phenylpyruvate decarboxylase (PPDC). PPFOR and PPDC play key roles in gut bacterial PAA production via oxidative and non-oxidative phenylpyruvate decarboxylation, respectively. Metagenomic analyses revealed a significantly higher abundance of both pathways in gut microbiomes of ASCVD patients compared with controls. The present studies show a role for these two divergent microbial catalytic strategies in the meta-organismal production of PAGln. Given the numerous links between PAGln and ASCVD, these findings will assist future efforts to therapeutically target PAGln formation in vivo.
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Affiliation(s)
- Yijun Zhu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Mohammed Dwidar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer A Buffa
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - James T Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Kymberleigh A Romano
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoming Fu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Masanori Funabashi
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Pooja Keranahalli
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Case Western Reserve University, College of Arts and Sciences, Cleveland, OH, USA
| | - Shawna Battle
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron N Tittle
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Adeline M Hajjar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA; Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA.
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9
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Xia W, Zhu B, Zhang S, Liu H, Qu X, Liu Y, Rudstam LG, Anderson JT, Ni L, Chen Y. Climate, hydrology, and human disturbance drive long-term (1988-2018) macrophyte patterns in water diversion lakes. J Environ Manage 2022; 319:115726. [PMID: 35849931 DOI: 10.1016/j.jenvman.2022.115726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/20/2022] [Revised: 06/24/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Macrophytes are affected by many natural and human stressors globally but their long-term responses to these multiple stressors are not often quantified. We employed remote sensing and statistical tools to analyze datasets from both short-term (2017-2018) field investigations to explore seasonal patterns, and long-term (1988-2018) Landsat remote-sensing images to detect annual patterns of macrophyte distributions and study their responses to changes in climate, hydrology, and anthropogenic activities in a chain of water diversion lakes in eastern China. We found: 1) biomass and species richness of macrophytes peaked in summer with dominant species of submerged macrophytes Ceratophyllum demersum, Potamogeton pectinatus, and Potamogeton maackianus and floating macrophytes Trapa bispinosa, and non-native species Cabomba caroliniana spread in midstream Luoma Lake and Nansi Lake in summer, while Potamogeton crispus was dominant in all the lakes in spring; 2) water physicochemical parameters (chloride and water depth), lake characteristics (area and water storage), climate factors (air temperature and precipitation), and anthropogenic activities (commercial fishery and urban development) were significantly correlated to the seasonal distribution of macrophytes; 3) long-term data showed a significantly negative correlation between coverage of floating macrophytes and precipitation where the wettest year of 2003 had the lowest coverage of floating macrophytes; and 4) climate (air temperature) and hydrology (water level) were positively correlated with total macrophyte coverage, but human disturbance indexed by the gross domestic product was negatively driving long-term coverage of macrophytes. Our study has important implications for understanding the long-term succession of macrophytes under both natural and human stressors, and for future environmental management and ecological restoration of freshwater lakes.
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Affiliation(s)
- Wentong Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China
| | - Bin Zhu
- Department of Biology, University of Hartford, West Hartford, CT, 06117, USA
| | - Shuanghu Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Han Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Qu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an, Jiangsu, 223002, China
| | - Yinglong Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China
| | - Lars G Rudstam
- Cornell Biological Field Station and Department of Natural Resources, Cornell University, 900 Shackelton Point Road, Bridgeport, NY, 13030, USA
| | - James T Anderson
- James C. Kennedy Waterfowl and Wetlands Conservation Center, Belle W. Baruch Institute of Coastal Ecology and Forest Science, Clemson University, P.O. Box 596, Georgetown, SC, 29442, USA
| | - Leyi Ni
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yushun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an, Jiangsu, 223002, China.
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10
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Slabe VA, Anderson JT, Millsap BA, Cooper JL, Harmata AR, Restani M, Crandall RH, Bodenstein B, Bloom PH, Booms T, Buchweitz J, Culver R, Dickerson K, Domenech R, Dominguez-Villegas E, Driscoll D, Smith BW, Lockhart MJ, McRuer D, Miller TA, Ortiz PA, Rogers K, Schwarz M, Turley N, Woodbridge B, Finkelstein ME, Triana CA, DeSorbo CR, Katzner TE. Demographic implications of lead poisoning for eagles across North America. Science 2022; 375:779-782. [PMID: 35175813 DOI: 10.1126/science.abj3068] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Lead poisoning occurs worldwide in populations of predatory birds, but exposure rates and population impacts are known only from regional studies. We evaluated the lead exposure of 1210 bald and golden eagles from 38 US states across North America, including 620 live eagles. We detected unexpectedly high frequencies of lead poisoning of eagles, both chronic (46 to 47% of bald and golden eagles, as measured in bone) and acute (27 to 33% of bald eagles and 7 to 35% of golden eagles, as measured in liver, blood, and feathers). Frequency of lead poisoning was influenced by age and, for bald eagles, by region and season. Continent-wide demographic modeling suggests that poisoning at this level suppresses population growth rates for bald eagles by 3.8% (95% confidence interval: 2.5%, 5.4%) and for golden eagles by 0.8% (0.7%, 0.9%). Lead poisoning is an underappreciated but important constraint on continent-wide populations of these iconic protected species.
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Affiliation(s)
- Vincent A Slabe
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.,Conservation Science Global, Bozeman, MT, USA
| | - James T Anderson
- James C. Kennedy Waterfowl and Wetlands Conservation Center, Clemson University, Georgetown, SC, USA
| | - Brian A Millsap
- Division of Migratory Bird Management, US Fish & Wildlife Service, Washington, DC, USA
| | | | - Alan R Harmata
- Ecology Department, Montana State University, Bozeman, MT, USA
| | | | | | | | | | - Travis Booms
- Alaska Department of Fish and Game, Fairbanks, AK, USA
| | - John Buchweitz
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | | | | | | | | | | | | | | | - David McRuer
- Wildlife Center of Virginia, Waynesboro, VA, USA.,Parks Canada, Gatineau, Quebec, Canada
| | | | - Patricia A Ortiz
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - Krysta Rogers
- Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | | | | | | | - Myra E Finkelstein
- Microbiology and Environmental Toxicology Department, University of California, Santa Cruz, CA, USA
| | - Christian A Triana
- Microbiology and Environmental Toxicology Department, University of California, Santa Cruz, CA, USA
| | | | - Todd E Katzner
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
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11
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Helsley RN, Miyata T, Kadam A, Varadharajan V, Sangwan N, Huang EC, Banerjee R, Brown AL, Fung KK, Massey WJ, Neumann C, Orabi D, Osborn LJ, Schugar RC, McMullen MR, Bellar A, Poulsen KL, Kim A, Pathak V, Mrdjen M, Anderson JT, Willard B, McClain CJ, Mitchell M, McCullough AJ, Radaeva S, Barton B, Szabo G, Dasarathy S, Garcia-Garcia JC, Rotroff DM, Allende DS, Wang Z, Hazen SL, Nagy LE, Brown JM. Gut microbial trimethylamine is elevated in alcohol-associated hepatitis and contributes to ethanol-induced liver injury in mice. eLife 2022; 11:76554. [PMID: 35084335 PMCID: PMC8853661 DOI: 10.7554/elife.76554] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
There is mounting evidence that microbes residing in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcohol-associated hepatitis (AH). However, mechanisms by which gut microbes synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. We used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, finding elevated levels of the microbial metabolite trimethylamine (TMA) in AH. In subsequent studies, we treated mice with non-lethal bacterial choline TMA lyase (CutC/D) inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. We show the gut microbial choline metabolite TMA is elevated in AH patients and correlates with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial CutC/D activity protects mice from ethanol-induced liver injury. CutC/D inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome and host liver transcriptome. The microbial metabolite TMA is elevated in patients with AH, and inhibition of TMA production from gut microbes can protect mice from ethanol-induced liver injury.
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Affiliation(s)
- Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, College of Medicine, University of Kentucky, Lexington, United States
| | - Tatsunori Miyata
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Anagha Kadam
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Emily C Huang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Kevin K Fung
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - William J Massey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Chase Neumann
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Danny Orabi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Rebecca C Schugar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Megan R McMullen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Annette Bellar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Kyle L Poulsen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Adam Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Vai Pathak
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Marko Mrdjen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - James T Anderson
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Belinda Willard
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Craig J McClain
- Department of Medicine, University of Louisville, Louisville, United States
| | - Mack Mitchell
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Arthur J McCullough
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Svetlana Radaeva
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, United States
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, United States
| | - Gyongyi Szabo
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, United States
| | - Srinivasan Dasarathy
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | | | - Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Daniela S Allende
- Department of Anatomical Pathology, Cleveland Clinic, Cleveland, United States
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Stanley L Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Cardiovascular Medicine, Heart and Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, United States
| | - Laura E Nagy
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Jonathan Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, United States.,Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
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12
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Schugar RC, Gliniak CM, Osborn LJ, Massey W, Sangwan N, Horak A, Banerjee R, Orabi D, Helsley RN, Brown AL, Burrows A, Finney C, Fung KK, Allen FM, Ferguson D, Gromovsky AD, Neumann C, Cook K, McMillan A, Buffa JA, Anderson JT, Mehrabian M, Goudarzi M, Willard B, Mak TD, Armstrong AR, Swanson G, Keshavarzian A, Garcia-Garcia JC, Wang Z, Lusis AJ, Hazen SL, Brown JM. Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms. eLife 2022; 11:63998. [PMID: 35072627 PMCID: PMC8813054 DOI: 10.7554/elife.63998] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 10/13/2020] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here, we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (Lepob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake but is instead associated with alterations in the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that gut microbial CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have potential as anti-obesity therapeutics.
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Affiliation(s)
- Rebecca C Schugar
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - William Massey
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony Horak
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Danny Orabi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy Burrows
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chelsea Finney
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kevin K Fung
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Frederick M Allen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Daniel Ferguson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony D Gromovsky
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chase Neumann
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kendall Cook
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy McMillan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Jennifer A Buffa
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - James T Anderson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Maryam Goudarzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Belinda Willard
- Research Core Services, Cleveland Clinic Lerner College of Medicine
| | - Tytus D Mak
- Mass Spectromety Data Center, National Institute of Standards and Technology (NIST)
| | | | - Garth Swanson
- Department of Internal Medicine, Rush University Medical Center
| | | | | | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles
| | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner College of Medicine
| | - Jonathan Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
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13
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Rounsville TF, Rogers RE, Welsh AB, Ryan CW, Anderson JT. Novel hair snare and genetic methods for non-invasive bobcat detection. Ecol Evol 2022; 12:e8435. [PMID: 35127004 PMCID: PMC8796956 DOI: 10.1002/ece3.8435] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 11/10/2022] Open
Abstract
Over the past 20 years, the use of non-invasive hair snare surveys in wildlife research and management has become more prevalent. While these tools have been used to answer important research questions, these techniques often fail to gather information on elusive carnivores, such as bobcats (Lynx rufus). Due to the limited success of previous bobcat studies using hair snares which required active rubbing, this technique has largely fallen out of use, in favor of camera trapping. The goal of our study was to construct a novel, passive bobcat hair snare that could be deployed regardless of terrain or vegetation features, which would be effective for use in capture-recapture population estimation at a large spatial scale. This new hair snare was deployed in 1500 10-km2 cells across West Virginia (USA) between two sampling seasons (2015-2016). Collected hair samples were analyzed with newly developed mitochondrial DNA primers specifically for felids and qPCR to determine species of origin, with enough sensitivity to identify samples as small as two bobcat hairs. Over the two years of the study, a total of 378 bobcat detections were recorded from 42,000 trap nights of sampling, for an overall rate of 0.9 detections/100 trap nights-nearly 2-6 times greater than any previous bobcat hair snare study. While the overall number of recaptured animals was low (n = 9), continued development of this platform should increase its usefulness in capture-recapture studies.
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Affiliation(s)
| | | | - Amy B. Welsh
- School of Natural ResourcesWest Virginia UniversityMorgantownWest VirginiaUSA
| | | | - James T. Anderson
- School of Natural ResourcesWest Virginia UniversityMorgantownWest VirginiaUSA
- Present address:
James C. Kennedy Waterfowl and Wetlands Conservation CenterBelle W. Baruch Institute of Coastal Ecology and Forest ScienceClemson UniversityP.O. Box 596GeorgetownSouth Carolina29442USA
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14
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Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res 2021; 31:1663-1679. [PMID: 34426512 PMCID: PMC8415381 DOI: 10.1101/gr.275472.121] [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: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. Eight hundred eighty-seven unique antibodies against 681 unique human transcription factors (TFs) were assayed by ultra-high-resolution ChIP-exo/seq, generating approximately 1200 ChIP-exo data sets, primarily in a single pass in one cell type (K562). Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed high-confidence target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that were distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We show and discuss the metrics and challenges to antibody validation in chromatin-based assays.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Luca Mariani
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Thomas R Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Prashant K Kuntala
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kylie Bocklund
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua Mairose
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah N Dweikat
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Katelyn Mistretta
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Daniela James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Zibo Zhao
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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15
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Mota JL, Brown DJ, Canning DM, Crayton SM, Lozon DN, Gulette AL, Anderson JT, Mali I, Dickerson BE, Forstner MRJ, Watson MB, Pauley TK. Influence of landscape condition on relative abundance and body condition of two generalist freshwater turtle species. Ecol Evol 2021; 11:5511-5521. [PMID: 34026025 PMCID: PMC8131803 DOI: 10.1002/ece3.7450] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 11/11/2022] Open
Abstract
Anthropogenic land use changes have broad impacts on biological diversity, often resulting in shifts in community composition. While many studies have documented negative impacts on occurrence and abundance of species, less attention has been given to native species that potentially benefit from anthropogenic land use changes. For many species reaching high densities in human-dominated landscapes, it is unclear whether these environments represent higher quality habitat than more natural environments. We examined the influence of landscape ecological integrity on relative abundance and body condition of two native generalist freshwater turtle species that are prevalent in anthropogenic systems, the painted turtle (Chrysemys picta) and red-eared slider (Trachemys scripta elegans). Relative abundance was negatively associated with ecological integrity for both species, but the relationship was not strongly supported for painted turtles. Body condition was positively associated with ecological integrity for painted turtles, with no strong association for red-eared sliders. Our study suggests that both species benefitted at the population level from reduced ecological integrity, but individual-level habitat quality was reduced for painted turtles. The differing responses between these two habitat generalists could partially explain why red-eared sliders have become a widespread exotic invasive species, while painted turtles have not.
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Affiliation(s)
- Joel L. Mota
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Donald J. Brown
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
- Northern Research StationU.S.D.A. Forest ServiceParsonsWVUSA
| | - Danielle M. Canning
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Sara M. Crayton
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Darien N. Lozon
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | | | - James T. Anderson
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Ivana Mali
- Department of BiologyEastern New Mexico UniversityPortalesNMUSA
| | | | | | - Mark B. Watson
- Department of Natural Sciences and MathematicsUniversity of CharlestonCharlestonWVUSA
| | - Thomas K. Pauley
- Department of Biological SciencesMarshall UniversityHuntingtonWVUSA
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16
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Boucher M, Tellez M, Anderson JT. Differences in distress: Variance and production of American Crocodile ( Crocodylus acutus) distress calls in Belize. Ecol Evol 2020; 10:9624-9634. [PMID: 33005335 PMCID: PMC7520206 DOI: 10.1002/ece3.6556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022] Open
Abstract
Acoustic communication of American Crocodiles (Crocodylus acutus) is relatively understudied. Our overall aim was to determine the acoustic structure of wild American Crocodile distress calls, distinguish call differences among size classes (hatchling, juvenile, sub-adult, and adult), and investigate call production on a gradient of human disturbance. American Crocodile distress calls have strong frequency modulation and are comprised of multiple harmonics in a downsweeping pattern. Measured parameters (total duration, first quartile duration, maximal frequency, first quartile frequency, end frequency, slope of first quartile, slope of last quartiles) differed significantly among size classes (p < .05). Hatchling distress calls are higher in frequency and strongly modulated, whereas calls produced by sub-adults and adults showed little modulation, are lower in frequency, and have greater overall duration. Proportion of crocodiles that produced distress calls during capture differed by size class and sampling location, particularly adult distress calls which are reported here to be produced with undocumented frequency. We determined that American Crocodiles of all size classes produce distress calls at varying rates among study sites. Our results demonstrate that American crocodiles produce distress call more frequently at sites with higher anthropogenic activity. Measured call parameters of juveniles and hatchling American crocodiles also varied among sites in relation to human disturbance. Calls recorded at sites of high anthropogenic impact have increased duration and less modulation which may adversely affect response to emitted distress calls. Proportional and call parameter variances suggest anthropogenic activity as a driver for increased call production and alteration of call parameters at high human-impacted sites.
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Affiliation(s)
- Miriam Boucher
- School of Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Marisa Tellez
- Crocodile Research CoalitionStann CreekBelize
- Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
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17
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Slabe VA, Anderson JT, Cooper J, Miller TA, Brown B, Wrona A, Ortiz P, Buchweitz J, McRuer D, Dominguez-Villegas E, Behmke S, Katzner T. Feeding Ecology Drives Lead Exposure of Facultative and Obligate Avian Scavengers in the Eastern United States. Environ Toxicol Chem 2020; 39:882-892. [PMID: 32022303 DOI: 10.1002/etc.4680] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/19/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
Lead poisoning of scavenging birds is a global issue. However, the drivers of lead exposure of avian scavengers have been understood from the perspective of individual species, not cross-taxa assemblages. We analyzed blood (n = 285) and liver (n = 226) lead concentrations of 5 facultative (American crows [Corvus brachyrhynchos], bald eagles [Haliaeetus leucocephalus], golden eagles [Aquila chrysaetos], red-shouldered hawks [Buteo lineatus], and red-tailed hawks [Buteo jamaicensis]) and 2 obligate (black vultures [Coragyps atratus] and turkey vultures [Cathartes aura] avian scavenger species to identify lead exposure patterns. Species and age were significant (α < 0.05) predictors of blood lead exposure of facultative scavengers; species, but not age, was a significant predictor of their liver lead exposure. We detected temporal variations in lead concentrations of facultative scavengers (blood: median = 4.41 µg/dL in spring and summer vs 13.08 µg/dL in autumn and winter; p = <0.001; liver: 0.32 ppm in spring and summer vs median = 4.25 ppm in autumn and winter; p = <0.001). At the species level, we detected between-period differences in blood lead concentrations of bald eagles (p = 0.01) and red-shouldered hawks during the winter (p = 0.001). During summer, obligate scavengers had higher liver lead concentrations than did facultative scavengers (median = 1.76 ppm vs 0.22 ppm; p = <0.001). These data suggest that the feeding ecology of avian scavengers is a determinant of the degree to which they are lead exposed, and they highlight the importance of dietary and behavioral variation in determining lead exposure. Environ Toxicol Chem 2020;39:882-892. © 2020 SETAC.
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Affiliation(s)
- Vincent A Slabe
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - James T Anderson
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Jeff Cooper
- Virginia Department of Game and Inland Fisheries, Richmond, Virginia, USA
| | | | - Bracken Brown
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Anna Wrona
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Patricia Ortiz
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, USA
| | - John Buchweitz
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, USA
| | - Dave McRuer
- Wildlife Center of Virginia, Waynesboro, Virginia, USA
| | | | - Shannon Behmke
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Todd Katzner
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, USA
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18
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Affiliation(s)
- Akif Keten
- Department of Wildlife Ecology and Management, Faculty of Forestry, Düzce University, Düzce 81620, Turkey
| | - Erdinc Sarcan
- IX. Region Directorate, Ministry of Agriculture and Forestry, Düzce 81620, Turkey
| | - James T. Anderson
- School of Natural Resources, West Virginia University, 1145 Evansdale Drive, Morgantown, WV 26506, USA
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19
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Lewis KE, Rota CT, Anderson JT. A comparison of wetland characteristics between Agricultural Conservation Easement Program and public lands wetlands in West Virginia, USA. Ecol Evol 2020; 10:3017-3031. [PMID: 32211173 PMCID: PMC7083671 DOI: 10.1002/ece3.6118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/09/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/06/2022] Open
Abstract
In West Virginia, USA, there are 24 conservation easement program wetlands enrolled in the Agricultural Conservation Easement Program (ACEP). These wetlands are located on private agricultural land and are passively managed. Due to their location within fragmented agricultural areas, wetlands enrolled in ACEP in West Virginia have the potential to add wetland ecosystem services in areas that are lacking these features. We evaluated ACEP wetlands compared to reference wetlands on public land in West Virginia by using surrounding land cover, vegetative cover, and wetland features and stressors such as the presence or absence of erosion, upland inclusion, algal mats, and evidence of impacts from the surrounding landscape as surrogate measurements of wetland function on 13 ACEP wetlands and 10 reference wetlands. ACEP wetlands had higher percentages of tree coverage and a higher proportion of agricultural land in the areas immediately surrounding the wetland. Reference wetlands had higher percent coverage of emergent vegetation and had a higher proportion of forest in the immediate landscape. Our findings suggest that ACEP wetlands provide valuable early successional and forested wetland cover in a state that is largely forested. Because of this, it is important to maintain and even expand ACEP in West Virginia to continue providing a valuable source of early successional wetland habitat.
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Affiliation(s)
- Katharine E Lewis
- Davis College of Agriculture, Natural Resources, and Design West Virginia University Morgantown WV USA
| | - Christopher T Rota
- Davis College of Agriculture, Natural Resources, and Design West Virginia University Morgantown WV USA
| | - James T Anderson
- Davis College of Agriculture, Natural Resources, and Design West Virginia University Morgantown WV USA
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20
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Anderson JT, Rogers JM, Barrera LA, Bulyk ML. Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting. Protein Sci 2019; 29:606-616. [PMID: 31833142 DOI: 10.1002/pro.3801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
Transcription activator-like effector (TALE) proteins have been used extensively for targeted binding of fusion proteins to loci of interest in (epi)genome engineering. Such approaches typically utilize four canonical TALE repeat variable diresidue (RVD) types, corresponding to the identities of two key amino acids, to target each nucleotide. Alternate RVDs with improved specificity are desired. Here, we focused on seven noncanonical RVDs that have been suggested to have improved specificity for their target nucleotides. We used custom protein binding microarrays to characterize the DNA-binding activity of 65 TALEs containing these alternate or corresponding canonical RVDs at multiple positions to ~5,000 unique DNA sequences per protein. We found that none of the noncanonical thymine-targeting RVDs displayed stronger preference for thymine than did the canonical RVD. Of the noncanonical RVDs with putatively improved specificity for guanine, only EN and NH showed greater discrimination of guanine over adenine. This improved specificity, however, comes at a cost: more substitutions of a noncanonical RVD for a canonical RVD generally decreased the protein's DNA-binding activity. Our results highlight the need to investigate RVD-nucleotide specificities in multiple protein contexts and suggest that a balance between canonical and noncanonical RVDs is needed to build TALEs with improved specificity.
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Affiliation(s)
- James T Anderson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts
| | - Luis A Barrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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21
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Slabe VA, Anderson JT, Cooper J, Ortiz P, Wrona A, Jensen MK, Buchweitz J, Katzner T. Lead Exposure of Red-Shouldered Hawks During the Breeding Season in the Central Appalachians, USA. Bull Environ Contam Toxicol 2019; 103:783-788. [PMID: 31646347 DOI: 10.1007/s00128-019-02732-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
Lead is toxic to humans and wildlife. Most studies of lead exposure of raptors focus on the winter, non-breeding season when they scavenge heavily. We evaluated blood lead concentrations (BLCs) of red-shouldered hawks (Buteo lineatus) during the non-scavenging season in the eastern United States. BLCs of 53 of 70 hawks were above the limit of detection ([Formula: see text] = 9.25 µg/dL ± 19.81; ± SD). Adult hawks had higher BLCs ([Formula: see text] = 12.86 µg/dL ± 24.72) than did nestlings ([Formula: see text] = 3.25 µg/dL ± 2.62; p ≤ 0.001, χ2 = 13.2). There was no difference in BLCs of adult hawks among physiographic provinces but there were differences between urban and non-urban settings (p = 0.04, χ2 = 4.2). Soils and invertebrate hawk prey also had quantifiable lead concentrations. Our work shows that red-shouldered hawks are exposed to lead when not scavenging, and suggests pathways by which these birds may be exposed.
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Affiliation(s)
- Vincent A Slabe
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - James T Anderson
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Jeff Cooper
- Virginia Department of Game and Inland Fisheries, Richmond, VA, USA
| | - Patricia Ortiz
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - Anna Wrona
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Meghan K Jensen
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - John Buchweitz
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Todd Katzner
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
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22
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Millikin AR, Woodley SK, Davis DR, Moore IT, Anderson JT. Water-borne and plasma corticosterone are not correlated in spotted salamanders. Ecol Evol 2019; 9:13942-13953. [PMID: 31938493 PMCID: PMC6953692 DOI: 10.1002/ece3.5831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/20/2019] [Accepted: 10/22/2019] [Indexed: 01/27/2023] Open
Abstract
Water-borne hormone measurement is a noninvasive method suitable for amphibians of all sizes that are otherwise difficult to sample. For this method, containment-water is assayed for hormones released by the animal. Originally developed in fish, the method has expanded to amphibians, but requires additional species-specific validations. We wanted to determine physiological relevance of water-borne corticosterone in spotted salamanders (Ambystoma maculatum) by comparing concentrations to those taken using established corticosterone sampling methods, such as plasma. Using a mixture of field and laboratory studies, we compared water-borne corticosterone levels to other traditional methods of sampling corticosterone for spotted salamander larvae, metamorphs, and adults. Despite multiple attempts, and detecting differences between age groups, we found no correlations between water-borne and plasma corticosterone levels in any age group. Water-borne sampling measures a rate of release; whereas plasma is the concentration circulating in the blood. The unique units of measurement may inherently prevent correlations between the two. These two methods may also require different interpretations of the data and the physiological meaning. We also note caveats with the method, including how to account for differences in body size and life history stages. Collectively, our results illustrate the importance of careful validation of water-borne hormone levels in each species in order to understand its physiological significance.
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Affiliation(s)
| | - Sarah K. Woodley
- Department of Biological SciencesDuquesne UniversityPittsburghPAUSA
| | - Drew R. Davis
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleySouth Padre IslandTXUSA
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23
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Goodman NS, Eitniear JC, Anderson JT. Time-activity budgets of stiff-tailed ducks in Puerto Rico. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00676] [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: 10/26/2022] Open
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24
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Slabe VA, Anderson JT, Cooper J, Brown B, Ortiz P, Buchweitz J, McRuer D, Katzner T. Lead in piscivorous raptors during breeding season in the Chesapeake Bay region of Maryland and Virginia, USA. Environ Toxicol Chem 2019; 38:862-871. [PMID: 30698866 DOI: 10.1002/etc.4376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Sources of lead exposure of many bird species are poorly understood. We analyzed blood lead concentrations from osprey (n = 244; Pandion haliaetus) and bald eagles (n = 68; Haliaeetus leucocephalus) and documented potential sources of lead they may encounter. Adult bald eagles had higher blood lead concentrations than did adult osprey. However, blood lead concentrations of nestlings were similar for both species. Although 62% of osprey had detectable lead concentrations ( x¯ = 1.99 ± 4.02 μg/dL, mean ± standard deviation [SD]), there was no difference in the detection frequency or lead concentrations between osprey adults and nestlings. Likewise, we found no differences in the detection frequency or lead concentrations in osprey adults and nestlings from high- and low-salinity areas. Of the bald eagle samples tested, 55% had detectable lead levels ( x¯ = 6.23 ± 10.74 μg/dL). Adult bald eagles had more detectable and higher lead concentrations than did nestlings or pre-adults. Among environmental samples, paint had the highest lead concentrations, followed by sediment, blue catfish (Ictalurus furcatus), and gizzard shad (Dorosoma cepedianum). There was no correlation between blood lead concentrations of osprey adults and their offspring. Our results indicate that, in the Chesapeake Bay region of Maryland and Virginia (USA), there are multiple sources by which piscivorous raptors may be exposed to lead. Environ Toxicol Chem 2019;38:862-871. © Published 2019 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
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Affiliation(s)
- Vincent A Slabe
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - James T Anderson
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Jeff Cooper
- Virginia Department of Game and Inland Fisheries, Richmond, Virginia, USA
| | - Bracken Brown
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Patricia Ortiz
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, USA
| | - John Buchweitz
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, USA
| | - Dave McRuer
- Wildlife Center of Virginia, Waynesboro, Virginia, USA
| | - Todd Katzner
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, USA
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25
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Affiliation(s)
- Tricia A. Miller
- Division of Forestry and Natural ResourcesWest Virginia University, PO Box 6125MorgantownWV26506USA
| | - Jeff L. Cooper
- Virginia Department of Game and Inland Fisheries1320 Belman RoadFredericksburgVA23230USA
| | - Adam E. Duerr
- Division of Forestry and Natural ResourcesWest Virginia University, PO Box 6125MorgantownWV26506USA
| | - Melissa A. Braham
- Division of Forestry and Natural ResourcesWest Virginia University, PO Box 6125MorgantownWV26506USA
| | - James T. Anderson
- Division of Forestry and Natural ResourcesWest Virginia University, PO Box 6125MorgantownWV26506USA
| | - Todd E. Katzner
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center970 Lusk StreetBoiseID83706USA
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26
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Gulette AL, Anderson JT, Brown DJ. Influence of Hoop-Net Trap Diameter on Capture Success and Size Distribution of Comparatively Large and Small Freshwater Turtles. Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.026.0111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Alissa L. Gulette
- School of Natural Resources, West Virginia University, Morgantown, WV 26506
| | - James T. Anderson
- School of Natural Resources, West Virginia University, Morgantown, WV 26506
| | - Donald J. Brown
- School of Natural Resources, West Virginia University, Morgantown, WV 26506
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Hall MR, Bardayan DW, Baugher T, Lepailleur A, Pain SD, Ratkiewicz A, Ahn S, Allen JM, Anderson JT, Ayangeakaa AD, Blackmon JC, Burcher S, Carpenter MP, Cha SM, Chae KY, Chipps KA, Cizewski JA, Febbraro M, Hall O, Hu J, Jiang CL, Jones KL, Lee EJ, O'Malley PD, Ota S, Rasco BC, Santiago-Gonzalez D, Seweryniak D, Sims H, Smith K, Tan WP, Thompson P, Thornsberry C, Varner RL, Walter D, Wilson GL, Zhu S. Key ^{19}Ne States Identified Affecting γ-Ray Emission from ^{18}F in Novae. Phys Rev Lett 2019; 122:052701. [PMID: 30822026 DOI: 10.1103/physrevlett.122.052701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Detection of nuclear-decay γ rays provides a sensitive thermometer of nova nucleosynthesis. The most intense γ-ray flux is thought to be annihilation radiation from the β^{+} decay of ^{18}F, which is destroyed prior to decay by the ^{18}F(p,α)^{15}O reaction. Estimates of ^{18}F production had been uncertain, however, because key near-threshold levels in the compound nucleus, ^{19}Ne, had yet to be identified. We report the first measurement of the ^{19}F(^{3}He,tγ)^{19}Ne reaction, in which the placement of two long-sought 3/2^{+} levels is suggested via triton-γ-γ coincidences. The precise determination of their resonance energies reduces the upper limit of the rate by a factor of 1.5-17 at nova temperatures and reduces the average uncertainty on the nova detection probability by a factor of 2.1.
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Affiliation(s)
- M R Hall
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - D W Bardayan
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - T Baugher
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - A Lepailleur
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - S D Pain
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - A Ratkiewicz
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - S Ahn
- National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - J M Allen
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - J T Anderson
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - A D Ayangeakaa
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - J C Blackmon
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - S Burcher
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - M P Carpenter
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - S M Cha
- Department of Physics, Sungkyunkwan University, Suwon 16419, South Korea
| | - K Y Chae
- Department of Physics, Sungkyunkwan University, Suwon 16419, South Korea
| | - K A Chipps
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J A Cizewski
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - M Febbraro
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - O Hall
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Physics, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - J Hu
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - C L Jiang
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - K L Jones
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - E J Lee
- Department of Physics, Sungkyunkwan University, Suwon 16419, South Korea
| | - P D O'Malley
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - S Ota
- Physics Division, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - B C Rasco
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - D Santiago-Gonzalez
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - D Seweryniak
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - H Sims
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
- Department of Physics, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - K Smith
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - W P Tan
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - P Thompson
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - C Thornsberry
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D Walter
- Department of Physics and Astronomy, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - G L Wilson
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Department of Physics and Applied Physics, University of Massachusetts Lowell, Lowell, Massachusetts 01854, USA
| | - S Zhu
- Physics Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Lewis KE, Rota CT, Lituma CM, Anderson JT. Influence of the Agricultural Conservation Easement Program wetland practices on winter occupancy of Passerellidae sparrows and avian species richness. PLoS One 2019; 14:e0210878. [PMID: 30677050 PMCID: PMC6345491 DOI: 10.1371/journal.pone.0210878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/03/2019] [Indexed: 11/19/2022] Open
Abstract
Wetlands enrolled in the Agricultural Conservation Easement Program (ACEP) are established as a means of restoring wetland ecosystems and wildlife habitat on private, agricultural land. In West Virginia, USA, ACEP wetlands have never been evaluated to determine how they function as wildlife habitat in comparison to other available wetland habitat in the state. We measured the wintering occupancy of Passerellidae species and apparent avian species richness on ACEP wetlands and a set of reference wetlands located on public land in West Virginia to evaluate if ACEP wetlands are being used similarly by avian species to other available wetland habitat in the state. Apparent avian species richness and the occupancy probability of four Passerellidae species—song sparrows (Melospiza melodia), dark-eyed juncos (Junco hyemalis), swamp sparrows (Melospiza georgiana), and white-throated sparrows (Zonotrichia albicollis)—did not differ between ACEP and reference sites. In addition to other vegetative and habitat associations for each species, dark-eyed junco occupancy was negatively correlated with wetland size while swamp sparrow occupancy and apparent avian species richness were positively associated with wetland size. These results indicate that ACEP wetlands are providing winter avian habitat as well as another source of wetland habitat in the state. Maintaining and expanding ACEP wetlands in West Virginia would continue to provide wetland systems in areas that are otherwise lacking these habitats.
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Affiliation(s)
- Katharine E. Lewis
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, United States of America
| | - Christopher T. Rota
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
| | - Christopher M. Lituma
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, United States of America
| | - James T. Anderson
- Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, United States of America
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Flaherty KL, Turk PJ, Anderson JT. Comparing stakeholder attitudes toward white-tailed deer and rare plant management in Canaan Valley, West Virginia. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Stiffler LL, Schroeder KM, Anderson JT, McRae SB, Katzner TE. Quantitative acoustic differentiation of cryptic species illustrated with King and Clapper rails. Ecol Evol 2018; 8:12821-12831. [PMID: 30619585 PMCID: PMC6309001 DOI: 10.1002/ece3.4711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/01/2018] [Accepted: 10/14/2018] [Indexed: 11/12/2022] Open
Abstract
Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quantitative tools that exist for species differentiation are still being refined. Using vocalizations recorded in the course of ecological studies of a King Rail (Rallus elegans) and a Clapper Rail (Rallus crepitans) population, we assessed the accuracy and effectiveness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k-nearest neighbor, weighted k-nearest neighbor, and neural networks) statistical classification methods for differentiating these species by their kek mating call. We identified 480 kek notes of each species and quantitatively characterized them with five standardized acoustic parameters. Overall, nonparametric classification methods outperformed parametric classification methods for species differentiation (nonparametric tools were between 57% and 81% accurate, parametric tools were between 57% and 60% accurate). Of the nine classification methods, Random Forest was the most accurate and precise, resulting in 81.1% correct classification of kek notes to species. This suggests that the mating calls of these sister species are likely difficult for human observers to tell apart. However, it also implies that appropriate statistical tools may allow reasonable species-level classification accuracy of recorded calls and provide an alternative to species classification where other capture- or genotype-based survey techniques are not possible.
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Affiliation(s)
- Lydia L. Stiffler
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWest Virginia
- Present address:
Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | - Katie M. Schroeder
- Department of BiologyEast Carolina UniversityGreenvilleNorth Carolina
- Present address:
Department of BiologyUniversity of Massachusetts AmherstAmherstMassachusetts
| | - James T. Anderson
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWest Virginia
| | - Susan B. McRae
- Department of BiologyEast Carolina UniversityGreenvilleNorth Carolina
| | - Todd E. Katzner
- U.S. Geological SurveyForest & Rangeland Ecosystem Science CenterBoiseIdaho
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McCoard KR, McCoard NS, Anderson JT. Observations of Wood Turtle Activity, Diet, Movements, and Morphometrics in the Central Appalachians. Northeast Nat (Steuben) 2018. [DOI: 10.1656/045.025.0401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kathryn R.P. McCoard
- West Virginia University, School of Natural Resources, PO Box 6125, Morgantown, WV 26506
| | - Noah S. McCoard
- West Virginia University, School of Natural Resources, PO Box 6125, Morgantown, WV 26506
| | - James T. Anderson
- West Virginia University, School of Natural Resources, PO Box 6125, Morgantown, WV 26506
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Coster SS, Welsh AB, Costanzo G, Harding SR, Anderson JT, McRae SB, Katzner TE. Genetic analyses reveal cryptic introgression in secretive marsh bird populations. Ecol Evol 2018; 8:9870-9879. [PMID: 30386582 PMCID: PMC6202719 DOI: 10.1002/ece3.4472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 04/05/2018] [Revised: 07/06/2018] [Accepted: 07/20/2018] [Indexed: 11/10/2022] Open
Abstract
Hybridization is common in bird populations but can be challenging for management, especially if one of the two parent species is of greater conservation concern than the other. King rails (Rallus elegans) and clapper rails (R. crepitans) are two marsh bird species with similar morphologies, behaviors, and overlapping distributions. The two species are found along a salinity gradient with the king rail in freshwater marshes and the clapper in estuarine marshes. However, this separation is not absolute; they are occasionally sympatric, and there are reports of interbreeding. In Virginia, USA, both king and clapper rails are identified by the state as Species of Greater Conservation Need, although clappers are thought to be more abundant and king rails have a higher priority ranking. We used a mitochondrial DNA marker and 13 diagnostic nuclear single nucleotide polymorphisms (SNPs) to identify species, classify the degree of introgression, and explore the evolutionary history of introgression in two putative clapper rail focal populations along a salinity gradient in coastal Virginia. Genetic analyses revealed cryptic introgression with site-specific rates of admixture. We identified a pattern of introgression where clapper rail alleles predominate in brackish marshes. These results suggest clapper rails may be displacing king rails in Virginia coastal waterways, most likely as a result of ecological selection. As introgression can result in various outcomes from outbreeding depression to local adaptation, continued monitoring of these populations would allow further exploration of hybrid fitness and inform conservation management.
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Affiliation(s)
- Stephanie S. Coster
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWest Virginia
| | - Amy B. Welsh
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWest Virginia
| | - Gary Costanzo
- Virginia Department of Game and Inland FisheriesCharles CityVirginia
| | | | - James T. Anderson
- Division of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWest Virginia
| | - Susan B. McRae
- Department of BiologyEast Carolina UniversityGreenvilleNorth Carolina
| | - Todd E. Katzner
- U.S. Geological SurveyForest and Rangeland Ecosystem Science CenterBoiseIdaho
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Affiliation(s)
- Lydia L. Stiffler
- Division of Forestry and Natural Resources; P.O. Box 6125, West Virginia University Morgantown WV 26506 USA
| | - James T. Anderson
- Division of Forestry and Natural Resources; P.O. Box 6125, West Virginia University Morgantown WV 26506 USA
| | - Todd E. Katzner
- U.S. Geological Survey, Forest & Rangeland Ecosystem Science Center; 970 Lusk Street Boise ID 83706 USA
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Flaherty KL, Rentch JS, Anderson JT. Wetland seed dispersal by white-tailed deer in a large freshwater wetland complex. AoB Plants 2018; 10:plx074. [PMID: 29383233 PMCID: PMC5777486 DOI: 10.1093/aobpla/plx074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Mechanisms of long-distance dispersal are important in establishing and maintaining plant populations in isolated wetland habitats. White-tailed deer (Odocoileus virginianus) have been cited as long-distance dispersers of both native and exotic plant species in North America; however, knowledge regarding their influence in wetlands is limited. Given traditional classification methods for seed dispersal, white-tailed deer are not likely viewed as important dispersal mechanism for wetland plants. We collected naturally deposited white-tailed deer faecal pellet piles from wetlands in Canaan Valley, West Virginia, USA. Pellet piles were cold-stratified and germinated seedlings over a layer of sterile potting mix. The percentage of germinated seedlings with a facultative wetland (FACW) or obligate wetland (OBL) plant indicator status were compared to the frequency of occurrence to those of germinated plants with facultative upland (FACU) or upland (UPL) indicator status. We identified 38 species. Of these, 1 % were UPL, 38 % were FACU, 18 % were FACW and 21 % were OBL. Graminoid species accounted for 42 %; forbs and woody species accounted for 29 % each. Our research has suggested that endozoochory by herbivores contributes to long-distance dispersal of wetland plants.
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Affiliation(s)
- Kelley L Flaherty
- College of Science, Technology and Math, Alderson Broaddus University, Philippi, WV, USA
| | - James S Rentch
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - James T Anderson
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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Onderak AM, Anderson JT. Loss of the RNA helicase SKIV2L2 impairs mitotic progression and replication-dependent histone mRNA turnover in murine cell lines. RNA 2017; 23:910-926. [PMID: 28351885 PMCID: PMC5435864 DOI: 10.1261/rna.060640.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 01/03/2017] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by 30%. Propidium iodide-based cell-cycle analysis of Skiv2l2 knockdown cells revealed defective progression through the G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression. Since SKIV2L2 targets RNAs to the nuclear exosome for processing and degradation, we identified RNA targets elevated in cells depleted of SKIV2L2 that could account for the observed twofold increase in mitotic cells. Skiv2l2 knockdown cells accumulated replication-dependent histone mRNAs, among other RNAs, that could impede mitotic progression and indirectly trigger differentiation.
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Affiliation(s)
- Alexis M Onderak
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
| | - James T Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
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Clipp HL, Peters ML, Anderson JT. Winter Waterbird Community Composition and Use at Created Wetlands in West Virginia, USA. Scientifica (Cairo) 2017; 2017:1730130. [PMID: 28386513 PMCID: PMC5366207 DOI: 10.1155/2017/1730130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/14/2017] [Accepted: 02/19/2017] [Indexed: 06/07/2023]
Abstract
Information on nonbreeding waterbirds using created wetlands in the Central Appalachian region of the United States is limited. We compared waterbird communities of two managed wetlands, created in 2013 and 2001, in West Virginia. We observed 27 species of waterbirds. Species richness and diversity were generally similar between the wetlands, but species composition and use differed. Branta canadensis (Canada Geese), Anas strepera (Gadwall), Bucephala albeola (Buffleheads), Aythya affinis (Lesser Scaup), and Aythya collaris (Ring-Necked Ducks) used the older wetland most frequently. Disparities in species use were the highest in March. The older wetland differed from the younger in supporting species such as diving ducks, possibly due to differences in size, vegetation, water depth, and microtopography. However, the ability to provide habitat for waterbirds during the winter was determined to be comparable between wetlands, despite their age difference.
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Affiliation(s)
- Hannah L. Clipp
- School of Natural Resources, West Virginia University, P.O. Box 6125, Morgantown, WV 26505, USA
| | - Michael L. Peters
- West Virginia Division of Natural Resources, P.O. Box 99, Farmington, WV 26571, USA
| | - James T. Anderson
- School of Natural Resources, West Virginia University, P.O. Box 6125, Morgantown, WV 26505, USA
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Abstract
Epigenetics, defined as inheritable and reversible phenomena that affect gene expression without altering the underlying base pair sequence has been shown to play an important role in the etiopathogenesis of obesity. Obesity is associated with extensive gene expression changes in tissues throughout the body. Epigenetics is emerging as perhaps the most important mechanism through which the lifestyle-choices we make can directly influence the genome. Considerable epidemiological, experimental and clinical data have been amassed showing that the risk of developing disease in later life is dependent on early life conditions, mainly operating within the normative range of developmental exposures. In addition to the 'maternal' interactions, there has been increasing interest in the epigenetic mechanisms through which 'paternal' influences on offspring development can be achieved. Nutrition, among many other environmental factors, is a key player that can induce epigenetic changes not only in the directly exposed organisms but also in subsequent generations through the transgenerational inheritance of epigenetic traits. Overall, significant progress has been made in the field of epigenetics and obesity and the first potential epigenetic markers for obesity that could be detected at birth have been identified. Fortunately, epigenetic phenomena are dynamic and rather quickly reversible with intensive lifestyle changes. This is a very promising and sustainable resolution to the obesity pandemic.
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Strain GF, Turk PJ, Helmick J, Anderson JT. Amphibian reproductive success as a gauge of functional equivalency of created wetlands in the Central Appalachians. Wildl Res 2017. [DOI: 10.1071/wr15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Evaluating the adequacy of created wetlands to replace the functions of lost natural wetlands is important because wetland mitigation is a major tool used to offset wetland losses. However, measurements such as vegetative cover and presence of wildlife may not provide sufficient evidence that created wetlands are functioning properly. Thus, examining the ecology of wetland biota such as that of amphibians may be a more useful surrogate for function. Aims The objectives of this study were to compare the abundance of amphibian metamorphs and survival and growth of larval amphibians in created wetlands, relative to natural wetlands. Methods Amphibian metamorphs were trapped in created and natural wetlands during the spring (April–May) and summer (June–August) of 2009 and 2010, and 165 green frog (Lithobates clamitans) larvae were raised during the spring of 2010 in laboratory aquaria containing water from created or natural wetlands. Key results Abundance of spring peeper (Pseudacris crucifer) metamorphs decreased significantly from 2009 to 2010 and abundance of green frog metamorphs increased with habitat complexity, but both were unaffected by wetland type. Detection probability of metamorphs of both species was low, increased with water temperature and declined with month of observation. Survival, growth curves and mass were similar among green frog larvae raised in created and natural wetland aquaria. Conclusions Our results suggest that the created and natural wetlands we examined function similarly with respect to providing adequate breeding habitat for green frogs and spring peepers. Implications Wetlands created to offset the loss of natural wetlands, although generally not designed for the purpose of wildlife habitat, can function as adequate breeding habitat for generalist amphibians such as green frogs and spring peepers.
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McCoard KR, Billings AA, Anderson JT. Wood Turtle Home Range and Habitat Use in the Central Appalachians. Chelonian Conservation and Biology 2016. [DOI: 10.2744/ccb-1215.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Correa SB, Anderson JT. A non-destructive sampling protocol for field studies of seed dispersal by fishes. J Fish Biol 2016; 88:1989-2003. [PMID: 27097831 DOI: 10.1111/jfb.12963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 09/10/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
This paper presents a standardized protocol for the non-lethal capture of fishes, sampling of stomach contents and quantification of seed dispersal efficiency by frugivorous fishes. Neotropical pacu Piaractus mesopotamicus individuals were collected with fruit-baited hooks. The diets of 110 fish were sampled using a lavage method, which retrieved >90% of stomach contents of both juveniles and adults and allowed individuals to recover within 5 min of treatment. The proportional volume of six food categories was similar for stomachs and whole digestive tracts retrieved by dissection. Fruit pulp was proportionally lower in the stomach. The abundance and species richness of intact seeds increased with fish size independent of whether only stomachs or whole digestive tracts were analysed. The analysis of stomach contents accounted for 62·5% of the total species richness of seeds dispersed by P. mesopotamicus and 96% of common seeds (seed species retrieved from more than one fish). Germination trials revealed that seed viability was similar for seeds collected from the stomach via lavage and seeds that passed through the entire digestive tract. Therefore, stomach contents provide an unbiased representation of the dietary patterns and seed dispersal of frugivorous fishes.
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Affiliation(s)
- S B Correa
- Department of Genetics and Odum School of Ecology, University of Georgia, 120 Green St, Athens, GA 30602-7223, U.S.A
| | - J T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, 120 Green St, Athens, GA 30602-7223, U.S.A
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Li Y, Burclaff J, Anderson JT. Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNAiMet Turnover in Saccharomyces cerevisiae and Mtr4p Enzymatic Activities In Vitro. PLoS One 2016; 11:e0148090. [PMID: 26820724 PMCID: PMC4731217 DOI: 10.1371/journal.pone.0148090] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/12/2016] [Indexed: 12/24/2022] Open
Abstract
RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Joseph Burclaff
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO, 63110, United States of America
| | - James T. Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53233, United States of America
- * E-mail:
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Cherefko C, Fridley C, Medsger J, Woody M, Anderson JT. White-Tailed Deer and Balsam Woolly Adelgid Effects on Balsam Fir in Canaan Valley. SOUTHEAST NAT 2015. [DOI: 10.1656/058.014.sp719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rentch JS, Fortney RH, Anderson JT, Grafton WN. Plant Communities of Abes Run Wetland, Canaan Valley State Park, West Virginia. SOUTHEAST NAT 2015. [DOI: 10.1656/058.014.sp714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kaushik P, Solomon DH, Greenberg JD, Anderson JT, Reed G, Pala O, Sumbul-Yuksel B, Kadam P, Kremer JM. Subcutaneous nodules are associated with cardiovascular events in patients with rheumatoid arthritis: results from a large US registry. Clin Rheumatol 2015; 34:1697-704. [PMID: 26242470 DOI: 10.1007/s10067-015-3032-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 05/05/2015] [Revised: 06/24/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Subcutaneous nodules are the most common conspicuous extra-articular manifestation of rheumatoid arthritis (RA). Cardiovascular disease (CVD) is the leading cause of death in patients with RA. The objective of this study is to examine the possibility of a relationship between subcutaneous nodules and "first ever" cardiovascular disease event, i.e., myocardial infarction (MI), stroke, or cardiovascular death in a large registry-cohort of patients with RA. Patient information was collected from the CORRONA registry from October 2001 to September 2011. A total of 26,042 patients with RA were studied for the presence or absence of subcutaneous nodules. Cox proportional hazards regression models were constructed to estimate the hazard ratios (HR) for CVD events in relation to subcutaneous nodules at baseline. Three statistical models were used to examine the association between subcutaneous nodules and CVD: Model A adjusted for age and sex associated risk, model B adjusted for traditional CV risk factors, and model C adjusted for factors in models A and B plus underlying RA-specific measures. The definition of primary exposure was "subcutaneous nodules at baseline." A total of 3908 patients had subcutaneous nodules at baseline. Of the 566 total composite CVD events, 138 occurred in the group that had SCN at baseline. Incidence rate-ratio values (patients with subcutaneous nodules at baseline vs. no subcutaneous nodules at baseline) for composite CVD events, MI, stroke, and cardiovascular death were 1.55, 1.65, 1.37, and 1.68, respectively. Adjusted HR values (95 % CI) for composite CVD events based on "subcutaneous nodules-status at baseline" (primary exposure) were as follows: 1.35 (1.11-1.63) for model A, 1.25 (1.03-1.52) for model B, and 1.03 (0.831-1.277) for model C. Subcutaneous nodules were associated with increased CVD events in RA. This association persisted after adjusting for age, sex, and traditional CV risk factors.
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Affiliation(s)
- Prashant Kaushik
- Division of Rheumatology Stratton VAMC, Albany, NY, USA. .,Department of Internal Medicine Albany Medical College, Albany, NY, USA.
| | - Daniel H Solomon
- Divisions of Rheumatology & Pharmacoepidemiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | | | | | - George Reed
- University of Massachusetts Medical School, Worcester, MA, USA.
| | - Ozlem Pala
- University of Miami Miller School of Medicine, Miami, FL, USA.
| | - Bahar Sumbul-Yuksel
- Division of Rheumatology, University of Nevada School of Medicine, Reno, NV, USA.
| | | | - Joel M Kremer
- Albany Medical College and Director of Research, The Center for Rheumatology, Albany, NY, USA.
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Kaushik P, Stone JH, Anderson JT, Dugar S, Mathew R, Nikolic B, Patel R. Medical mirroring: granulomatosis with polyangiitis (formerly Wegener's) mimicking immunoglobulin-G4 related disease. Int J Rheum Dis 2015; 21:885-889. [DOI: 10.1111/1756-185x.12687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Prashant Kaushik
- Albany Stratton Veterans Affairs Medical Center (VAMC); Albany New York USA
- Albany Medical College; Albany New York USA
| | - John H. Stone
- Harvard Medical School; Massachusetts General Hospital; Boston Massachusetts USA
- Clinical Rheumatology; Massachusetts General Hospital; Boston Massachusetts USA
| | | | | | - Roy Mathew
- Albany Stratton Veterans Affairs Medical Center (VAMC); Albany New York USA
- Albany Medical College; Albany New York USA
| | - Boris Nikolic
- Albany Stratton Veterans Affairs Medical Center (VAMC); Albany New York USA
| | - Raina Patel
- Albany Stratton Veterans Affairs Medical Center (VAMC); Albany New York USA
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