1
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Bishop PJ, Pierce SE. The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part II-Hindlimb. Anat Rec (Hoboken) 2024; 307:1826-1896. [PMID: 37727023 DOI: 10.1002/ar.25310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023]
Abstract
This paper is the second in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the hindlimb. Although the hindlimb skeleton did not undergo as marked a transformation on the line to mammals as did the forelimb skeleton, the anatomy of extant tetrapods indicates that major changes to musculature have nonetheless occurred. To better understand these changes, this study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 80 character-state complexes covering all muscles crossing the hip, knee, and ankle joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. The evolutionary history of mammalian hindlimb musculature was complex, nonlinear, and protracted, with several instances of convergence and pulses of anatomical transformation that continued well into the crown group. Numerous traits typically regarded as characteristically "mammalian" have much greater antiquity than previously recognized, and for some traits, most synapsids are probably more reflective of the ancestral amniote condition than are extant saurians. More broadly, this study highlights the utility of the fossil record in interpreting the evolutionary appearance of distinctive anatomies.
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Affiliation(s)
- Peter J Bishop
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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2
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Ponce de León MA, Bailey BN. Quantifying water-use efficiency in plant canopies with varying leaf angle and density distribution. Ann Bot 2024; 133:605-620. [PMID: 38362930 PMCID: PMC11037486 DOI: 10.1093/aob/mcae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AND AIMS Variation in architectural traits related to the spatial and angular distribution of leaf area can have considerable impacts on canopy-scale fluxes contributing to water-use efficiency (WUE). These architectural traits are frequent targets for crop improvement and for improving the understanding and predictions of net ecosystem carbon and water fluxes. METHODS A three-dimensional, leaf-resolving model along with a range of virtually generated hypothetical canopies were used to quantify interactions between canopy structure and WUE by examining its response to variation of leaf inclination independent of leaf azimuth, canopy heterogeneity, vegetation density and physiological parameters. KEY RESULTS Overall, increasing leaf area index (LAI), increasing the daily-averaged fraction of leaf area projected in the sun direction (Gavg) via the leaf inclination or azimuth distribution and increasing homogeneity had a similar effect on canopy-scale daily fluxes contributing to WUE. Increasing any of these parameters tended to increase daily light interception, increase daily net photosynthesis at low LAI and decrease it at high LAI, increase daily transpiration and decrease WUE. Isolated spherical crowns could decrease photosynthesis by ~60 % but increase daily WUE ≤130 % relative to a homogeneous canopy with equivalent leaf area density. There was no observed optimum in daily canopy WUE as LAI, leaf angle distribution or heterogeneity was varied. However, when the canopy was dense, a more vertical leaf angle distribution could increase both photosynthesis and WUE simultaneously. CONCLUSIONS Variation in leaf angle and density distributions can have a substantial impact on canopy-level carbon and water fluxes, with potential trade-offs between the two. These traits might therefore be viable target traits for increasing or maintaining crop productivity while using less water, and for improvement of simplified models. Increasing canopy density or decreasing canopy heterogeneity increases the impact of leaf angle on WUE and its dependent processes.
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Affiliation(s)
| | - Brian N Bailey
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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3
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Bean NK, Edmunds PJ. The scaling of metabolic traits differs among larvae and juvenile colonies of scleractinian corals. J Exp Biol 2024:jeb.246362. [PMID: 38634316 DOI: 10.1242/jeb.246362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Body size profoundly affects organism fitness and ecosystem dynamics through the scaling of physiological traits. This study tests for variation in metabolic scaling and its potential drivers among corals differing in life history strategies and taxonomic identity. Data were compiled from published sources and augmented with empirical measurements of corals in Moorea, French Polynesia. The data compilation revealed metabolic isometry in broadcasted larvae, but size-independent metabolism in brooded larvae; empirical measures of Pocillopora acuta larvae also supported size-independent metabolism in brooded coral larvae. In contrast, for juvenile colonies (i.e., 1-4 cm diameter), metabolic scaling was isometric for Pocillopora spp., and negatively allometric for Porites spp. The scaling of biomass with surface area was isometric for Pocillopora spp., but positively allometric for Porites spp., suggesting the surface area:biomass ratio mediates metabolic scaling in these corals. The scaling of tissue biomass and metabolism were not affected by light treatment (i.e., either natural photoperiods or constant darkness) in both juvenile taxa. However, biomass was reduced by 9-15% in the juvenile corals from the light treatments and this coincided with higher metabolic scaling exponents, thus supporting the causal role of biomass in driving variation in scaling. This study shows that metabolic scaling is plastic in early life stages of corals, with intrinsic differences between life history strategy (i.e., brooded and broadcasted larvae) and taxa (i.e., Pocillopora spp. and Porites spp.), and acquired differences attributed to changes in area-normalized biomass.
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Affiliation(s)
- Nina K Bean
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA
- Department of Biology, Florida International University, 3000 NE 151st St, North Miami, FL 33181, USA
| | - Peter J Edmunds
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA
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4
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Bell MA, Lim G, Caldwell C, Emlen DJ, Swanson BO. Rhinoceros beetle (Trypoxylus dichotomus) cuticular hydrocarbons contain information about body size and sex. PLoS One 2024; 19:e0299796. [PMID: 38483942 PMCID: PMC10939270 DOI: 10.1371/journal.pone.0299796] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Japanese rhinoceros beetle (Trypoxylus dichotomus) males have exaggerated horns that are used to compete for territories. Larger males with larger horns tend to win these competitions, giving them access to females. Agonistic interactions include what appears to be assessment and often end without escalating to physical combat. However, it is unknown what information competitors use to assess each other. In many insect species chemical signals can carry a range of information, including social position, nutritional state, morphology, and sex. Specifically, cuticular hydrocarbons (CHCs), which are waxes excreted on the surface of insect exoskeletons, can communicate a variety of information. Here, we asked whether CHCs in rhinoceros beetles carry information about sex, body size, and condition that could be used by males during assessment behavior. Multivariate analysis of hydrocarbon composition revealed patterns associated with both sex and body size. We suggest that Rhinoceros beetles could be communicating information through CHCs that would explain behavioral decisions.
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Affiliation(s)
- Micah A. Bell
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Garrett Lim
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Chelsey Caldwell
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Douglas J. Emlen
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Brook O. Swanson
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
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5
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Saqib QM, Ahmad I, Mannan A, Mahmood J, Ameen S, Patil CS, Noman M, Kim J, Okyay MS, Patil SR, Ko Y, Noh HJ, Wong BM, Kim B, Bae J, Baek JB. Triboelectric Energy Harvesting from Highly Conjugated Fused Aromatic Ladder Structure Under Extreme Environmental Conditions. Adv Mater 2024:e2311029. [PMID: 38299366 DOI: 10.1002/adma.202311029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Practical application of triboelectric nanogenerators (TENGs) has been challenging, particularly, under harsh environmental conditions. This work proposes a novel 3D-fused aromatic ladder (FAL) structure as a tribo-positive material for TENGs, to address these challenges. The 3D-FAL offers a unique materials engineering platform for tailored properties, such as high specific surface area and porosity, good thermal and mechanical stability, and tunable electronic properties. The fabricated 3D-FAL-based TENG reaches a maximum peak power density of 451.2 µW cm-2 at 5 Hz frequency. More importantly, the 3D-FAL-based TENG maintains stable output performance under harsh operating environments, over wide temperature (-45-100 °C) and humidity ranges (8.3-96.7% RH), representing the development of novel FAL for sustainable energy generation under challenging environmental conditions. Furthermore, the 3D-FAL-based TENG proves to be a promising device for a speed monitoring system engaging reconstruction in virtual reality in a snowy environment.
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Affiliation(s)
- Qazi Muhammad Saqib
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Ishfaq Ahmad
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 Donostia-San, Sebastian, 20018, Spain
| | - Abdul Mannan
- Department of Physics, University of Management and Technology, Lahore, 54770, Pakistan
| | - Javeed Mahmood
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Oxide & Organic Nanomaterials for Energy & Environment (ONE) Laboratory, Chemistry Program; Advanced Membranes & Porous Materials (AMPM) Center; KAUST Catalysis Center (KCC); Physical Science & Engineering (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Shahid Ameen
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Chandrashekhar S Patil
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Muhammad Noman
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jungmin Kim
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Mahmut Sait Okyay
- Materials Science & Engineering Program, Department of Chemistry, University of California-Riverside, Riverside, CA, 92521, USA
| | - Swapnil R Patil
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Youngbin Ko
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Hyuk-Jun Noh
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Bryan M Wong
- Materials Science & Engineering Program, Department of Chemistry, University of California-Riverside, Riverside, CA, 92521, USA
| | - BongSoo Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jinho Bae
- Department of Ocean System Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jong-Beom Baek
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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Zwolak R, Clement D, Sih A, Schreiber SJ. Granivore abundance shapes mutualism quality in plant-scatterhoarder interactions. New Phytol 2024; 241:1840-1850. [PMID: 38044708 DOI: 10.1111/nph.19443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]
Abstract
Conditional mutualisms involve costs and benefits that vary with environmental factors, but mechanisms driving these dynamics remain poorly understood. Scatterhoarder-plant interactions are a prime example of this phenomenon, as scatterhoarders can either increase or reduce plant recruitment depending on the balance between seed dispersal and predation. We explored factors that drive the magnitude of net benefits for plants in this interaction using a mathematical model, with parameter values based on European beech (Fagus sylvatica) and yellow-necked mice (Apodemus flavicollis). We measured benefits as the percentage of germinating seeds, and examined how varying rodent survival (reflecting, e.g. changes in predation pressure), the rate of seed loss to other granivores, the abundance of alternative food resources, and changes in masting patterns affect the quality of mutualism. We found that increasing granivore abundance can degrade the quality of plant-scatterhoarder mutualism due to increased cache pilferage. Scatterhoarders are predicted to respond by increasing immediate consumption of gathered seeds, leading to higher costs and reduced benefits for plants. Thus, biotic changes that are detrimental to rodent populations can be beneficial for tree recruitment due to adaptive behavior of rodents. When scatterhoarder populations decline too drastically (< 5 individuals ha-1 ); however, tree recruitment may also suffer.
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Affiliation(s)
- Rafał Zwolak
- Department of Systematic Zoology, Institute of Environmental Biology, Adam Mickiewicz University, Umultowska 89, Poznań, 61-614, Poland
| | - Dale Clement
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Andrew Sih
- Center of Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Sebastian J Schreiber
- Center of Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
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7
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Latchney SE, Cadney MD, Hopkins A, Garland T. Maternal upbringing and selective breeding for voluntary exercise behavior modify patterns of DNA methylation and expression of genes in the mouse brain. Genes Brain Behav 2023; 22:e12858. [PMID: 37519068 PMCID: PMC10733581 DOI: 10.1111/gbb.12858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Selective breeding has been utilized to study the genetic basis of exercise behavior, but research suggests that epigenetic mechanisms, such as DNA methylation, also contribute to this behavior. In a previous study, we demonstrated that the brains of mice from a genetically selected high runner (HR) line have sex-specific changes in DNA methylation patterns in genes known to be genomically imprinted compared to those from a non-selected control (C) line. Through cross-fostering, we also found that maternal upbringing can modify the DNA methylation patterns of additional genes. Here, we identify an additional set of genes in which DNA methylation patterns and gene expression may be altered by selection for increased wheel-running activity and maternal upbringing. We performed bisulfite sequencing and gene expression assays of 14 genes in the brain and found alterations in DNA methylation and gene expression for Bdnf, Pde4d and Grin2b. Decreases in Bdnf methylation correlated with significant increases in Bdnf gene expression in the hippocampus of HR compared to C mice. Cross-fostering also influenced the DNA methylation patterns for Pde4d in the cortex and Grin2b in the hippocampus, with associated changes in gene expression. We also found that the DNA methylation patterns for Atrx and Oxtr in the cortex and Atrx and Bdnf in the hippocampus were further modified by sex. Together with our previous study, these results suggest that DNA methylation and the resulting change in gene expression may interact with early-life influences to shape adult exercise behavior.
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Affiliation(s)
- Sarah E. Latchney
- Department of BiologySt. Mary's College of MarylandSt. Mary's CityMarylandUSA
| | - Marcell D. Cadney
- Department of Evolution, Ecology, and Organismal BiologyUniversity of CaliforniaRiversideCaliforniaUSA
- Neuroscience Research Institute, University of CaliforniaSanta BarbaraCaliforniaUSA
| | | | - Theodore Garland
- Department of Evolution, Ecology, and Organismal BiologyUniversity of CaliforniaRiversideCaliforniaUSA
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8
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Le Meillour L, Zazzo A, Zirah S, Tombret O, Barriel V, Arthur KW, Arthur JW, Cauliez J, Chaix L, Curtis MC, Gifford-Gonzalez D, Gunn I, Gutherz X, Hildebrand E, Khalidi L, Millet M, Mitchell P, Studer J, Vila E, Welker F, Pleurdeau D, Lesur J. The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa. R Soc Open Sci 2023; 10:231002. [PMID: 38026023 PMCID: PMC10663795 DOI: 10.1098/rsos.231002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.
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Affiliation(s)
- Louise Le Meillour
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - Antoine Zazzo
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Olivier Tombret
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Véronique Barriel
- Centre de Recherche en Paléontologie – Paris (CR2P), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, CP 38, 8 rue Buffon, 75005 Paris, France
| | - Kathryn W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - John W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - Jessie Cauliez
- Unité Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (TRACES), CNRS, Université Toulouse Jean Jaurès, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Louis Chaix
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Matthew C. Curtis
- Anthropology Program, California State University Channel Islands, 1 University Drive, Camarillo, CA 93012, USA
| | - Diane Gifford-Gonzalez
- Department of Anthropology, University of California, Santa Cruz, Social Sciences 1 Faculty Svcs, 1156 High Street, Santa Cruz, CA 95064-1077, USA
| | - Imogen Gunn
- Museum of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Xavier Gutherz
- Unité Archéologie des Sociétés Méditerranéennes (ASM), CNRS, Université Montpellier III, Ministère de la Culture, INRAP, Montpellier, France
| | | | - Lamya Khalidi
- Unité Cultures et Environnements. Préhistoire, Antiquité, Moyen Age (CEPAM), Université Côte d'Azur, CNRS, 24 avenue des Diables Bleus, 06300 Nice, France
| | - Marie Millet
- Département des Antiquités Égyptiennes, Musée du Louvre, Paris, France
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, OX1 3TG, United Kingdom and Rock Art Research Institute, University of the Witwatersrand, PO Wits 2050, Johannesburg, South Africa
| | - Jacqueline Studer
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Emmanuelle Vila
- Unité Archéorient, Environnements et sociétés de l'Orient ancien, CNRS, Université de Lyon 2, Maison de l'Orient et de la Méditerranée, 7 rue Raulin, 69007 Lyon, France
| | - Frido Welker
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - David Pleurdeau
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Joséphine Lesur
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
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9
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Prall W, Sheikh AH, Bazin J, Bigeard J, Almeida-Trapp M, Crespi M, Hirt H, Gregory BD. Pathogen-induced m6A dynamics affect plant immunity. Plant Cell 2023; 35:4155-4172. [PMID: 37610247 PMCID: PMC10615206 DOI: 10.1093/plcell/koad224] [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] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023]
Abstract
Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104,USA
| | - Arsheed H Sheikh
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Jean Bigeard
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Marilia Almeida-Trapp
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Heribert Hirt
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna,Austria
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104,USA
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Foerster I, Seames W, Oleksik J, Kubatova A, Ross A. A Comprehensive Study of Techniques to Optimize the Extraction of Lipids from the Autotrophic Strain of the Microalgae Chlorella vulgaris. Life (Basel) 2023; 13:1997. [PMID: 37895378 PMCID: PMC10608289 DOI: 10.3390/life13101997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Microalgae represent a promising source of triglycerides and free fatty acids, synthesized in the form of lipids, for use in renewable fuels and chemicals. One challenge is the ability to efficiently recover the lipids from within the microalgae cell. Although various techniques have been studied individually, a comprehensive study of extraction techniques using consistent experimental and analytical methodology is missing. This study aims to provide this unifying comparison using the common microalgae strain Chlorella vulgaris. The factors that were surveyed and then optimized to achieve maximum extraction efficiency included the solvent type; mechanical pre-treatment using a ball mill at a variety of grinding speeds; microalgae-to-solvent ratio; extraction facilitated by microwave; extraction facilitated by sonication; extraction facilitated using increased temperature; and extraction facilitated by in situ transesterification to convert the lipids into esters prior to extraction. The optimum conditions determined during these studies were utilizing methanol as the solvent, with ball mill pretreatment at a grinding speed of 500 rpm, and a 1:9 microalgae to solvent ratio. When used in combination with microwave-assisted extraction at a temperature of 140 °C, approximately 24 wt% of the initial lipids were recovered. Recoveries of over 70 wt% were obtained without a microwave at extraction temperatures of over 200 °C.
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Affiliation(s)
- Ian Foerster
- Chemical Engineering Department, University of North Dakota, 243 Centennial Drive Stop 7101, Grand Forks, ND 58202, USA;
| | - Wayne Seames
- Chemical Engineering Department, University of North Dakota, 243 Centennial Drive Stop 7101, Grand Forks, ND 58202, USA;
| | - Jasmine Oleksik
- Energy & Environmental Research Center, University of North Dakota, 15 N. 23rd St., Grand Forks, ND 58202, USA;
| | - Alena Kubatova
- Chemistry Department, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, ND 58202, USA;
| | - Andrew Ross
- School of Chemical and Process Engineering, University of Leeds, 209 Clarendon Road, Leeds LS2 9JT, UK;
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11
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Miller EC. Historical biogeography supports Point Conception as the site of turnover between temperate East Pacific ichthyofaunas. PLoS One 2023; 18:e0291776. [PMID: 37725614 PMCID: PMC10508600 DOI: 10.1371/journal.pone.0291776] [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: 04/24/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
The cold temperate and subtropical marine faunas of the Northeastern Pacific meet within California as part of one of the few eastern boundary upwelling ecosystems in the world. Traditionally, it is believed that Point Conception is the precise site of turnover between these two faunas due to sharp changes in oceanographic conditions. However, evidence from intraspecific phylogeography and species range terminals do not support this view, finding stronger biogeographic breaks elsewhere along the coast. Here I develop a new application of historical biogeographic approaches to uncover sites of transition between faunas without needing an a priori hypothesis of where these occur. I used this approach to determine whether the point of transition between northern and southern temperate faunas occurs at Point Conception or elsewhere within California. I also examined expert-vetted latitudinal range data of California fish species from the 1970s and the 2020s to assess how biogeography could change with the backdrop of climate change. The site of turnover was found to occur near Point Conception, in concordance with the traditional view. I suggest that recent species- and population-level processes could be expected to give signals of different events from historical biogeography, possibly explaining the discrepancy across studies. Species richness of California has increased since the 1970s, mostly due to species's ranges expanding northward from Baja California (Mexico). Range shifts under warming conditions seem to be increasing the disparity between northern and southern faunas of California, creating a more divergent biogeography.
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Affiliation(s)
- Elizabeth Christina Miller
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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12
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Fu M, Solovey K, Salzman O, Alterovitz R. Toward certifiable optimal motion planning for medical steerable needles. Int J Rob Res 2023; 42:798-826. [PMID: 37905207 PMCID: PMC10613120 DOI: 10.1177/02783649231165818] [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] [Indexed: 11/02/2023]
Abstract
Medical steerable needles can follow 3D curvilinear trajectories to avoid anatomical obstacles and reach clinically significant targets inside the human body. Automating steerable needle procedures can enable physicians and patients to harness the full potential of steerable needles by maximally leveraging their steerability to safely and accurately reach targets for medical procedures such as biopsies. For the automation of medical procedures to be clinically accepted, it is critical from a patient care, safety, and regulatory perspective to certify the correctness and effectiveness of the planning algorithms involved in procedure automation. In this paper, we take an important step toward creating a certifiable optimal planner for steerable needles. We present an efficient, resolution-complete motion planner for steerable needles based on a novel adaptation of multi-resolution planning. This is the first motion planner for steerable needles that guarantees to compute in finite time an obstacle-avoiding plan (or notify the user that no such plan exists), under clinically appropriate assumptions. Based on this planner, we then develop the first resolution-optimal motion planner for steerable needles that further provides theoretical guarantees on the quality of the computed motion plan, that is, global optimality, in finite time. Compared to state-of-the-art steerable needle motion planners, we demonstrate with clinically realistic simulations that our planners not only provide theoretical guarantees but also have higher success rates, have lower computation times, and result in higher quality plans.
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Affiliation(s)
- Mengyu Fu
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kiril Solovey
- Department of Electrical and Computer Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Oren Salzman
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ron Alterovitz
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Zhao M, Kurtis SM, White ND, Moncrieff AE, Leite RN, Brumfield RT, Braun EL, Kimball RT. Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae). Syst Biol 2023; 72:161-178. [PMID: 36130303 PMCID: PMC10452962 DOI: 10.1093/sysbio/syac062] [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: 10/20/2021] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation].
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Affiliation(s)
- Min Zhao
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Sarah M Kurtis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Noor D White
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, Bethesda, MD 20892, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Andre E Moncrieff
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Rafael N Leite
- Graduate Program in Ecology, National Institute of Amazonian Research, Manaus, AM, Brazil
| | - Robb T Brumfield
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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14
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Tong J, Li X, Wang J, He H, Xu T, Zhu K. Bioinspired stability enhancement in deuterium-substituted organic-inorganic hybrid perovskite solar cells. PNAS Nexus 2023; 2:pgad160. [PMID: 37255848 PMCID: PMC10226519 DOI: 10.1093/pnasnexus/pgad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
In hybrid perovskite solar cells (PSCs), the reaction of hydrogens (H) located in the amino group of the organic A-site cations with their neighboring halides plays a central role in degradation. Inspired by the retarded biological activities of cells in heavy water, we replaced the light H atom with its abundant, twice-as-heavy, nonradioactive isotope, deuterium (D) to hamper the motion of H. This D substitution retarded the formation kinetics of the detrimental H halides in Pb-based PSCs, as well as the H bond-mediated oxidation of Sn2+ in Sn-Pb-based narrow-bandgap PSCs, evidenced by accelerated stability studies. A computational study indicated that the zero point energy of D-based formamidinium (FA) is lower than that of pristine FA. In addition, the smaller increase in entropy in D-based FA than in pristine FA accounts for the increased formation free energy of the Sn2+ vacancies, which leads to the retarded oxidation kinetics of Sn2+. In this study, we show that substituting active H with D in organic cations is an effective way to enhance the stability of PSCs without sacrificing photovoltaic (PV) performance. This approach is also adaptable to other stabilizing methods.
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Affiliation(s)
| | | | - Jianxin Wang
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Haiying He
- To whom correspondence should be addressed: (K.Z.); (T.X.); (H.H.)
| | - Tao Xu
- To whom correspondence should be addressed: (K.Z.); (T.X.); (H.H.)
| | - Kai Zhu
- To whom correspondence should be addressed: (K.Z.); (T.X.); (H.H.)
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15
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Saadi AJ, Bibermair J, Kocot KM, Roberts NG, Hirose M, Calcino A, Baranyi C, Chaichana R, Wood TS, Schwaha T. Phylogenomics reveals deep relationships and diversification within phylactolaemate bryozoans. Proc Biol Sci 2022; 289:20221504. [PMID: 36350215 PMCID: PMC9653232 DOI: 10.1098/rspb.2022.1504] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/12/2022] [Indexed: 11/02/2023] Open
Abstract
Bryozoans are mostly sessile colonial invertebrates that inhabit all kinds of aquatic ecosystems. Extant bryozoan species fall into two clades with one of them, Phylactolaemata, being the only exclusively freshwater clade. Phylogenetic relationships within the class Phylactolaemata have long been controversial owing to their limited distinguishable characteristics that reflect evolutionary relationships. Here, we present the first phylogenomic analysis of Phylactolaemata using transcriptomic data combined with dense taxon sampling of six families to better resolve the interrelationships and to estimate divergence time. Using maximum-likelihood and Bayesian inference approaches, we recovered a robust phylogeny for Phylactolaemata in which the interfamilial relationships are fully resolved. We show Stephanellidae is the sister taxon of all other phylactolaemates and confirm that Lophopodidae represents the second offshoot within the phylactolaemate tree. Plumatella fruticosa clearly falls outside Plumatellidae as previous investigations have suggested, and instead clusters with Pectinatellidae and Cristatellidae as the sister taxon of Fredericellidae. Our results demonstrate that cryptic speciation is very likely in F. sultana and in two species of Plumatella (P. repens and P. casmiana). Divergence time estimates show that Phylactolaemata appeared at the end of the Ediacaran and started to diverge in the Silurian, although confidence intervals were large for most nodes. The radiation of most extant phylactolaemate families occurred mainly in the Palaeogene and Neogene highlighting post-extinction diversification.
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Affiliation(s)
- Ahmed J. Saadi
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Julian Bibermair
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Kevin M. Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Nickellaus G. Roberts
- Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kitasato 1-15-1, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Andrew Calcino
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Christian Baranyi
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Ratcha Chaichana
- Department of Environmental Technology and Management, Faculty of Environment, Kasetsart University, Bangkok, Thailand
| | - Timothy S. Wood
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | - Thomas Schwaha
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
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16
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Levis NA, McKay DJ, Pfennig DW. Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression. Proc Biol Sci 2022; 289:20221764. [PMID: 36285495 PMCID: PMC9597403 DOI: 10.1098/rspb.2022.1764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is 'phenotypic accommodation', which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles (Spea multiplicata). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE.
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Affiliation(s)
- Nicholas A. Levis
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel J. McKay
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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17
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Kellom M, Pagliara S, Richards TA, Santoro A. Correction to 'Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments' (2022) by Kellom et al. Open Biol 2022; 12:220268. [PMID: 36167087 PMCID: PMC9514889 DOI: 10.1098/rsob.220268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Abstract
Host-induced gene silencing (HIGS) refers to the silencing of genes in pathogens and pests by expressing homologous double-stranded RNAs (dsRNA) or artificial microRNAs (amiRNAs) in the host plant. The discovery of such trans-kingdom RNA silencing has enabled the development of RNA interference-based approaches for controlling diverse crop pathogens and pests. Although HIGS is a promising strategy, the mechanisms by which these regulatory RNAs translocate from plants to pathogens, and how they induce gene silencing in pathogens, are poorly understood. This lack of understanding has led to large variability in the efficacy of various HIGS treatments. This variability is likely due to multiple factors, such as the ability of the target pathogen or pest to take up and/or process RNA from the host, the specific genes and target sequences selected in the pathogen or pest for silencing, and where, when, and how the dsRNAs or amiRNAs are produced and translocated. In this review, we summarize what is currently known about the molecular mechanisms underlying HIGS, identify key unanswered questions, and explore strategies for improving the efficacy and reproducibility of HIGS treatments in the control of crop diseases.
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Affiliation(s)
- Hana Zand Karimi
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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19
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Bai Y, Yang X, Yu H, Chen X. Substrate and Process Engineering for Biocatalytic Synthesis and Facile Purification of Human Milk Oligosaccharides. ChemSusChem 2022; 15:e202102539. [PMID: 35100486 PMCID: PMC9272545 DOI: 10.1002/cssc.202102539] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/30/2022] [Indexed: 05/08/2023]
Abstract
Innovation in process development is essential for applying biocatalysis in industrial and laboratory production of organic compounds, including beneficial carbohydrates such as human milk oligosaccharides (HMOs). HMOs have attracted increasing attention for their potential application as key ingredients in products that can improve human health. To efficiently access HMOs through biocatalysis, a combined substrate and process engineering strategy is developed, namely multistep one-pot multienzyme (MSOPME) design. The strategy allows access to a pure tagged HMO in a single reactor with a single C18-cartridge purification process, despite the length of the target. Its efficiency is demonstrated in the high-yielding (71-91 %) one-pot synthesis of twenty tagged HMOs (83-155 mg), including long-chain oligosaccharides with or without fucosylation or sialylation up to nonaoses from a lactoside without the isolation of the intermediate oligosaccharides. Gram-scale synthesis of an important HMO derivative - tagged lacto-N-fucopentaose-I (LNFP-I) - proceeds in 84 % yield. Tag removal is carried out in high efficiency (94-97 %) without the need for column purification to produce the desired natural HMOs with a free reducing end. The method can be readily adapted for large-scale synthesis and automation to allow quick access to HMOs, other glycans, and glycoconjugates.
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Affiliation(s)
- Yuanyuan Bai
- Department of Chemistry, University of California, Davis, One Shields Avenue, 95616, Davis, California, USA
| | - Xiaohong Yang
- Department of Chemistry, University of California, Davis, One Shields Avenue, 95616, Davis, California, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, One Shields Avenue, 95616, Davis, California, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, One Shields Avenue, 95616, Davis, California, USA
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20
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Lei M, Qu X, Wan H, Jin D, Wang S, Zhao Z, Yin M, Payne GF, Liu C. Electro-assembly of a dynamically adaptive molten fibril state for collagen. Sci Adv 2022; 8:eabl7506. [PMID: 35108048 PMCID: PMC8809537 DOI: 10.1126/sciadv.abl7506] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/08/2021] [Indexed: 05/25/2023]
Abstract
Collagen is a biological building block that is hierarchically assembled into diverse morphological structures that, in some cases, is dynamically adaptive in response to external cues and in other cases forms static terminal structures. Technically, there is limited capabilities to guide the emergence of collagen's hierarchical organization to recapitulate the richness of biological structure and function. Here, we report an electro-assembly pathway to create a dynamically adaptive intermediate molten fibril state for collagen. Structurally, this intermediate state is composed of partially aligned and reversibly associating fibrils with limited hierarchical structure. These molten fibrils can be reversibly reconfigured to offer dynamic properties such as stimuli-stiffening, stimuli-contracting, self-healing, and self-shaping. Also, molten fibrils can be guided to further assemble to recapitulate the characteristic hierarchical structural features of native collagen (e.g., aligned fibers with D-banding). We envision that the electro-assembly of collagen fibrils will provide previously unidentified opportunities for tailored collagen-based biomedical materials.
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Affiliation(s)
- Miao Lei
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Frontier Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai 200237, China
| | - Haoran Wan
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Dawei Jin
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Shijia Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiling Zhao
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Biomedical Device Institute, 5118 A. James Clark Hall, College Park, MD 20742, USA
| | - Meng Yin
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Biomedical Device Institute, 5118 A. James Clark Hall, College Park, MD 20742, USA
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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21
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Laugier EJ, Casana J, Cabanes D. Phytolith evidence for the pastoral origins of multi-cropping in Mesopotamia (ancient Iraq). Sci Rep 2022; 12:60. [PMID: 35013508 PMCID: PMC8748697 DOI: 10.1038/s41598-021-03552-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/06/2021] [Indexed: 01/16/2023] Open
Abstract
Multi-cropping was vital for provisioning large population centers across ancient Eurasia. In Southwest Asia, multi-cropping, in which grain, fodder, or forage could be reliably cultivated during dry summer months, only became possible with the translocation of summer grains, like millet, from Africa and East Asia. Despite some textual sources suggesting millet cultivation as early as the third millennium BCE, the absence of robust archaeobotanical evidence for millet in semi-arid Mesopotamia (ancient Iraq) has led most archaeologists to conclude that millet was only grown in the region after the mid-first millennium BCE introduction of massive, state-sponsored irrigation systems. Here, we present the earliest micro-botanical evidence of the summer grain broomcorn millet (Panicum miliaceum) in Mesopotamia, identified using phytoliths in dung-rich sediments from Khani Masi, a mid-second millennium BCE site located in northern Iraq. Taphonomic factors associated with the region's agro-pastoral systems have likely made millet challenging to recognize using conventional macrobotanical analyses, and millet may therefore have been more widespread and cultivated much earlier in Mesopotamia than is currently recognized. The evidence for pastoral-related multi-cropping in Bronze Age Mesopotamia provides an antecedent to first millennium BCE agricultural intensification and ties Mesopotamia into our rapidly evolving understanding of early Eurasian food globalization.
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Affiliation(s)
- Elise Jakoby Laugier
- Graduate Program in Ecology, Evolution, Environment, and Society (EEES), Dartmouth College, Hanover, NH, 03755, USA.
- Department of Anthropology, Dartmouth College, Hanover, NH, 03755, USA.
- Department of Anthropology, Rutgers University, New Brunswick, NJ, 08901, USA.
- Center for Human Evolutionary Studies (CHES), Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Jesse Casana
- Department of Anthropology, Dartmouth College, Hanover, NH, 03755, USA
| | - Dan Cabanes
- Department of Anthropology, Rutgers University, New Brunswick, NJ, 08901, USA
- Center for Human Evolutionary Studies (CHES), Rutgers University, New Brunswick, NJ, 08901, USA
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22
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Bilkey N, Li H, Borodinov N, Ievlev AV, Ovchinnikova OS, Dixit R, Foston M. Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy. Quant Plant Biol 2022; 3:e31. [PMID: 37077971 PMCID: PMC10095902 DOI: 10.1017/qpb.2022.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/11/2022] [Accepted: 10/07/2022] [Indexed: 05/03/2023]
Abstract
Spatial heterogeneity in composition and organisation of the primary cell wall affects the mechanics of cellular morphogenesis. However, directly correlating cell wall composition, organisation and mechanics has been challenging. To overcome this barrier, we applied atomic force microscopy coupled with infrared (AFM-IR) spectroscopy to generate spatially correlated maps of chemical and mechanical properties for paraformaldehyde-fixed, intact Arabidopsis thaliana epidermal cell walls. AFM-IR spectra were deconvoluted by non-negative matrix factorisation (NMF) into a linear combination of IR spectral factors representing sets of chemical groups comprising different cell wall components. This approach enables quantification of chemical composition from IR spectral signatures and visualisation of chemical heterogeneity at nanometer resolution. Cross-correlation analysis of the spatial distribution of NMFs and mechanical properties suggests that the carbohydrate composition of cell wall junctions correlates with increased local stiffness. Together, our work establishes new methodology to use AFM-IR for the mechanochemical analysis of intact plant primary cell walls.
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Affiliation(s)
- Natasha Bilkey
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Huiyong Li
- Department of Energy, Environmental and Chemical Engineering, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Nikolay Borodinov
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Anton V. Ievlev
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Olga S. Ovchinnikova
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Ram Dixit
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
- Author for correspondence: M. Foston, E-mail:
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Lively CM, Xu J, Ben-Ami F. Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence. Biol Lett 2021; 17:20210321. [PMID: 34932924 PMCID: PMC8692037 DOI: 10.1098/rsbl.2021.0321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here, we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.
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Affiliation(s)
- Curtis M. Lively
- Department of Biology, Indiana University, Bloomington, 1001 East Third Street, IN 47405, USA
| | - Julie Xu
- Department of Biology, Indiana University, Bloomington, 1001 East Third Street, IN 47405, USA
| | - Frida Ben-Ami
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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24
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Schultz DT, Francis WR, McBroome JD, Christianson LM, Haddock SHD, Green RE. A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 (Bethesda) 2021; 11:jkab302. [PMID: 34545398 PMCID: PMC8527503 DOI: 10.1093/g3journal/jkab302] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/18/2021] [Indexed: 11/12/2022]
Abstract
Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.
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Affiliation(s)
- Darrin T Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Jakob D McBroome
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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25
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Ke F, Dai Z, Pachman M, Yuan X. Exploring multiuser virtual teaching simulation as an alternative learning environment for student instructors. Instr Sci 2021; 49:831-854. [PMID: 34456363 PMCID: PMC8380300 DOI: 10.1007/s11251-021-09555-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
In this mixed-method study, we investigated the impact and design of a multiuser, virtual reality (VR) supported teaching simulation, in comparison with live classroom teaching simulation, on the participatory training of teaching and the teaching knowledge development of student instructors. A total of 40 university teaching assistants participated in a 4-h training session in which they were randomly assigned to a VR simulation or a live classroom simulation condition. The study indicated that the VR simulation better promoted the lab-teaching knowledge development than the live simulation, whereas the latter better fostered class-teaching knowledge development. All participants reported higher teaching self-efficacy after the training. The qualitative data indicated that domain-specific challenges and authentic environmental prompting in the VR simulation fostered both experiential and vicarious learning of teaching. However, VR participants lacked mutual engagement in collaborative role-playing. The study findings suggest that VR-based simulation can supplement and work as an alternative to the live classroom simulation to host participatory teaching development.
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Affiliation(s)
- Fengfeng Ke
- Department of Educational Psychology and Learning Systems, Florida State University, Tallahassee, FL 32306-4453 USA
| | - Zhaihuan Dai
- Department of Educational Psychology and Learning Systems, Florida State University, Tallahassee, FL 32306-4453 USA
| | - Mariya Pachman
- Distance Learning and Instructional Technology, Texas A&M University, Kingsville, TX 78363 USA
| | - Xin Yuan
- Department of Computer Science, Florida State University, Tallahassee, FL 32306 USA
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26
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Pan C, Yang D, Zhao X, Liu Y, Li M, Ye L, Ali M, Yu F, Lamin-Samu AT, Fei Z, Lu G. PIF4 negatively modulates cold tolerance in tomato anthers via temperature-dependent regulation of tapetal cell death. Plant Cell 2021; 33:2320-2339. [PMID: 34009394 PMCID: PMC8364245 DOI: 10.1093/plcell/koab120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 05/30/2023]
Abstract
Extreme temperature conditions seriously impair male reproductive development in plants; however, the molecular mechanisms underlying the response of anthers to extreme temperatures remain poorly described. The transcription factor phytochrome-interacting factor4 (PIF4) acts as a hub that integrates multiple signaling pathways to regulate thermosensory growth and architectural adaptation in plants. Here, we report that SlPIF4 in tomato (Solanum lycopersicum) plays a pivotal role in regulating cold tolerance in anthers. CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease Cas9-generated SlPIF4 knockout mutants showed enhanced cold tolerance in pollen due to reduced temperature sensitivity of the tapetum, while overexpressing SlPIF4 conferred pollen abortion by delaying tapetal programmed cell death (PCD). SlPIF4 directly interacts with SlDYT1, a direct upstream regulator of SlTDF1, both of which (SlDYT1 and SlTDF1) play important roles in regulating tapetum development and tapetal PCD. Moderately low temperature (MLT) promotes the transcriptional activation of SlTDF1 by the SlPIF4-SlDYT1 complex, resulting in pollen abortion, while knocking out SlPIF4 blocked the MLT-induced activation of SlTDF1. Furthermore, SlPIF4 directly binds to the canonical E-box sequence in the SlDYT1 promoter. Collectively, these findings suggest that SlPIF4 negatively regulates cold tolerance in anthers by directly interacting with the tapetal regulatory module in a temperature-dependent manner. Our results shed light on the molecular mechanisms underlying the adaptation of anthers to low temperatures.
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Affiliation(s)
- Changtian Pan
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Dandan Yang
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Xiaolin Zhao
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Yue Liu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Mengzhuo Li
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Lei Ye
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Ali
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Fangjie Yu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Gang Lu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
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27
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Li Z, Huang X, Ye X, Jiang Y, Martin Y, Ning H, Hodgson ME, Li X. Measuring global multi-scale place connectivity using geotagged social media data. Sci Rep 2021; 11:14694. [PMID: 34282241 PMCID: PMC8290042 DOI: 10.1038/s41598-021-94300-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Shaped by human movement, place connectivity is quantified by the strength of spatial interactions among locations. For decades, spatial scientists have researched place connectivity, applications, and metrics. The growing popularity of social media provides a new data stream where spatial social interaction measures are largely devoid of privacy issues, easily assessable, and harmonized. In this study, we introduced a global multi-scale place connectivity index (PCI) based on spatial interactions among places revealed by geotagged tweets as a spatiotemporal-continuous and easy-to-implement measurement. The multi-scale PCI, demonstrated at the US county level, exhibits a strong positive association with SafeGraph population movement records (10% penetration in the US population) and Facebook's social connectedness index (SCI), a popular connectivity index based on social networks. We found that PCI has a strong boundary effect and that it generally follows the distance decay, although this force is weaker in more urbanized counties with a denser population. Our investigation further suggests that PCI has great potential in addressing real-world problems that require place connectivity knowledge, exemplified with two applications: (1) modeling the spatial spread of COVID-19 during the early stage of the pandemic and (2) modeling hurricane evacuation destination choice. The methodological and contextual knowledge of PCI, together with the open-sourced PCI datasets at various geographic levels, are expected to support research fields requiring knowledge in human spatial interactions.
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Affiliation(s)
- Zhenlong Li
- Geoinformation and Big Data Research Laboratory, Department of Geography, University of South Carolina, Columbia, SC, USA.
| | - Xiao Huang
- Department of Geosciences, University of Arkansas, Fayetteville, AR, USA
| | - Xinyue Ye
- Department of Landscape Architecture and Urban Planning, Texas A&M University, College Station, TX, USA
| | - Yuqin Jiang
- Geoinformation and Big Data Research Laboratory, Department of Geography, University of South Carolina, Columbia, SC, USA
| | - Yago Martin
- School of Public Administration, University of Central Florida, Orlando, FL, USA
| | - Huan Ning
- Geoinformation and Big Data Research Laboratory, Department of Geography, University of South Carolina, Columbia, SC, USA
| | - Michael E Hodgson
- Geoinformation and Big Data Research Laboratory, Department of Geography, University of South Carolina, Columbia, SC, USA
| | - Xiaoming Li
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, USA
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28
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Zhang L, Steward RA, Wheat CW, Reed RD. High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. Genome Biol Evol 2021; 13:evab145. [PMID: 34282459 PMCID: PMC8290113 DOI: 10.1093/gbe/evab145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84× coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.
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Affiliation(s)
- Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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29
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Pyle R, Jovanovic N, Subramanian D, Palem KV, Patel AB. Domain-driven models yield better predictions at lower cost than reservoir computers in Lorenz systems. Philos Trans A Math Phys Eng Sci 2021; 379:20200246. [PMID: 33583272 PMCID: PMC7898131 DOI: 10.1098/rsta.2020.0246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Recent advances in computing algorithms and hardware have rekindled interest in developing high-accuracy, low-cost surrogate models for simulating physical systems. The idea is to replace expensive numerical integration of complex coupled partial differential equations at fine time scales performed on supercomputers, with machine-learned surrogates that efficiently and accurately forecast future system states using data sampled from the underlying system. One particularly popular technique being explored within the weather and climate modelling community is the echo state network (ESN), an attractive alternative to other well-known deep learning architectures. Using the classical Lorenz 63 system, and the three tier multi-scale Lorenz 96 system (Thornes T, Duben P, Palmer T. 2017 Q. J. R. Meteorol. Soc. 143, 897-908. (doi:10.1002/qj.2974)) as benchmarks, we realize that previously studied state-of-the-art ESNs operate in two distinct regimes, corresponding to low and high spectral radius (LSR/HSR) for the sparse, randomly generated, reservoir recurrence matrix. Using knowledge of the mathematical structure of the Lorenz systems along with systematic ablation and hyperparameter sensitivity analyses, we show that state-of-the-art LSR-ESNs reduce to a polynomial regression model which we call Domain-Driven Regularized Regression (D2R2). Interestingly, D2R2 is a generalization of the well-known SINDy algorithm (Brunton SL, Proctor JL, Kutz JN. 2016 Proc. Natl Acad. Sci. USA 113, 3932-3937. (doi:10.1073/pnas.1517384113)). We also show experimentally that LSR-ESNs (Chattopadhyay A, Hassanzadeh P, Subramanian D. 2019 (http://arxiv.org/abs/1906.08829)) outperform HSR ESNs (Pathak J, Hunt B, Girvan M, Lu Z, Ott E. 2018 Phys. Rev. Lett. 120, 024102. (doi:10.1103/PhysRevLett.120.024102)) while D2R2 dominates both approaches. A significant goal in constructing surrogates is to cope with barriers to scaling in weather prediction and simulation of dynamical systems that are imposed by time and energy consumption in supercomputers. Inexact computing has emerged as a novel approach to helping with scaling. In this paper, we evaluate the performance of three models (LSR-ESN, HSR-ESN and D2R2) by varying the precision or word size of the computation as our inexactness-controlling parameter. For precisions of 64, 32 and 16 bits, we show that, surprisingly, the least expensive D2R2 method yields the most robust results and the greatest savings compared to ESNs. Specifically, D2R2 achieves 68 × in computational savings, with an additional 2 × if precision reductions are also employed, outperforming ESN variants by a large margin. This article is part of the theme issue 'Machine learning for weather and climate modelling'.
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Affiliation(s)
| | | | | | | | - Ankit B. Patel
- Baylor College of Medicine, Rice UniversityHouston, TX, USA
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30
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Shaw AK, White LA, Michalska-Smith M, Borer ET, Craft ME, Seabloom EW, Snell-Rood EC, Travisano M. Lessons from movement ecology for the return to work: Modeling contacts and the spread of COVID-19. PLoS One 2021; 16:e0242955. [PMID: 33481803 PMCID: PMC7822505 DOI: 10.1371/journal.pone.0242955] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/12/2020] [Indexed: 01/16/2023] Open
Abstract
Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS-CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at a large research university, using approaches from movement ecology and contact network epidemiology. First, we develop a dynamical pathogen model describing movement between home and work; we show that limiting social contact, via reduced people or reduced time in the workplace are fairly equivalent strategies to slow pathogen spread. Second, we develop a model based on spatial contact patterns within a specific office and lab building on campus; we show that restricting on-campus activities to labs (rather than labs and offices) could dramatically alter (modularize) contact network structure and thus, potentially reduce pathogen spread by providing a workplace mechanism to reduce contact. Here we argue that explicitly accounting for human movement and contact behavior in the workplace can provide additional strategies to slow pathogen spread that can be used in conjunction with ongoing public health efforts.
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Affiliation(s)
- Allison K. Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Lauren A. White
- National Socio-Environmental Synthesis Center, Annapolis, Maryland, United States of America
| | - Matthew Michalska-Smith
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Meggan E. Craft
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Emilie C. Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michael Travisano
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
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31
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Reddy RB, Langergraber KE, Sandel AA, Vigilant L, Mitani JC. The development of affiliative and coercive reproductive tactics in male chimpanzees. Proc Biol Sci 2021; 288:20202679. [PMID: 33402074 PMCID: PMC7892417 DOI: 10.1098/rspb.2020.2679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Like many animals, adult male chimpanzees often compete for a limited number of mates. They fight other males as they strive for status that confers reproductive benefits and use aggression to coerce females to mate with them. Nevertheless, small-bodied, socially immature adolescent male chimpanzees, who cannot compete with older males for status nor intimidate females, father offspring. We investigated how they do so through a study of adolescent and young adult males at Ngogo in Kibale National Park, Uganda. Adolescent males mated with nulliparous females and reproduced primarily with these first-time mothers, who are not preferred as mating partners by older males. Two other factors, affiliation and aggression, also influenced mating success. Specifically, the strength of affiliative bonds that males formed with females and the amount of aggression males directed toward females predicted male mating success. The effect of male aggression toward females on mating success increased as males aged, especially when they directed it toward females with whom they shared affiliative bonds. These results mirror sexual coercion in humans, which occurs most often between males and females involved in close, affiliative relationships.
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Affiliation(s)
- Rachna B. Reddy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kevin E. Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Aaron A. Sandel
- Department of Anthropology, University of Texas at Austin, Austin, TX 78712, USA
| | - Linda Vigilant
- Max Planck Institute for Evolutionary AnthropologyLeipzig, Germany
| | - John C. Mitani
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
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Lambrecht G, Rodríguez de Vera C, Jambrina-Enríquez M, Crevecoeur I, Gonzalez-Urquijo J, Lazuen T, Monnier G, Pajović G, Tostevin G, Mallol C. Characterisation of charred organic matter in micromorphological thin sections by means of Raman spectroscopy. Archaeol Anthropol Sci 2021; 13:13. [PMID: 33456618 PMCID: PMC7788033 DOI: 10.1007/s12520-020-01263-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
UNLABELLED Burned or charred organic matter in anthropogenic combustion features may provide important clues about past human activities related to fire. To interpret archaeological hearths, a correct identification of the organic source material is key. In the present work, Raman spectroscopy is applied to characterise the structural properties of char produced in laboratory heating- and open-fire experiments. This reference data set is compared to analyses of three different archaeological sites with Middle Palaeolithic combustion contexts. The results show that it is possible to determine whether a charred fragment is the product of burning animal-derived matter (e.g. meat) or plant-derived matter (e.g. wood) by plotting a few Raman spectral parameters (i.e. position of G and D bands, and intensity ratios H D/H G and H V/H G) against one another. The most effective parameters for discriminating animal- from plant-derived matter are the position of the G band and the H V/H G intensity ratio. This method can be applied on raw sample material and on uncovered micromorphological thin sections. The latter greatly compliments micromorphology by providing information about char fragments without any clear morphological characteristics. This study is the first of its kind and may provide archaeologists with a robust new method to distinguish animal- from plant-derived char in thin sections. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12520-020-01263-3.
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Affiliation(s)
- Glenn Lambrecht
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Caterina Rodríguez de Vera
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Margarita Jambrina-Enríquez
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Jesus Gonzalez-Urquijo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria (IIIPC), Universidad de Cantabria, Santander, Spain
| | - Talía Lazuen
- Université de Bordeaux, CNRS, UMR 5199 - PACEA, Pessac, France
| | - Gilliane Monnier
- Department of Anthropology, University of Minnesota, Minneapolis, MN USA
| | | | - Gilbert Tostevin
- Department of Anthropology, University of Minnesota, Minneapolis, MN USA
| | - Carolina Mallol
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Departamento de Geografía e Historia, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Abstract
Recently, it has been found that Jackiw-Teitelboim (JT) gravity, which is a two-dimensional theory with bulk action - 1 / 2 ∫ d 2 x g ϕ ( R + 2 ) , is dual to a matrix model, that is, a random ensemble of quantum systems rather than a specific quantum mechanical system. In this article, we argue that a deformation of JT gravity with bulk action - 1 / 2 ∫ d 2 x g ( ϕ R + W ( ϕ ) ) is likewise dual to a matrix model. With a specific procedure for defining the path integral of the theory, we determine the density of eigenvalues of the dual matrix model. There is a simple answer if W(0) = 0, and otherwise a rather complicated answer.
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Affiliation(s)
- Edward Witten
- Institute for Advanced Study, Einstein Drive, Princeton, NJ 08540, USA
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Clark J, Dickinson DL. The effect of sleep on public good contributions and punishment: Experimental evidence. PLoS One 2020; 15:e0240324. [PMID: 33119643 PMCID: PMC7595432 DOI: 10.1371/journal.pone.0240324] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/23/2020] [Indexed: 12/03/2022] Open
Abstract
We investigate the effect of a full week of sleep restriction (SR) vs. well-restedness (WR) on contributions in a common public good experiment, the voluntary contributions mechanism (VCM). We examine the effect of sleep manipulation on decisions regarding both contributions and punishment of non-contributors. Actigraphy devices are used to confirm that our random assignment to sleep condition generates significant differences in objective nightly sleep duration and sleepiness. We find that when punishment is unavailable public good contributions do not differ by SR/WR assignment. When punishment is available, we find evidence that SR subjects contribute more than WR subjects, respond more to the availability of punishment than do WR subjects, and that the availability of punishment significantly increases the contributions of SR but not WR subjects. Yet SR subjects do not punish others more or less than WR subjects. Our main findings are robust when considering compliance and sample selection. However, some findings are not robust to an alternative but less objective sleep control measure that is based partly on participants' self-identified optimal sleep levels.
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Affiliation(s)
- Jeremy Clark
- Department of Economics and Finance, University of Canterbury, Christchurch, New Zealand
| | - David L. Dickinson
- Department of Economics and CERPA, Appalachian State University, Boone, North Carolina, United States of America
- IZA Institute of Labor Economics, Bonn, Germany
- Economic Science Institute, Chapman University, Orange, California, United States of America
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Abstract
Archaeologists use differences in metals from burial contexts to identify variation in social inequalities during the European Bronze Age. Many have argued that these social inequalities depended on access to, and control of, trade routes. In this paper, I model critical gateways in the Tisza river-a river system in the Carpathian Basin that might have enabled privileged access to metal in some areas but not others. I then evaluate the concentration of metal on different topological nodes of the river network in an attempt to understand what best explains the distribution of metals across this landscape. I do this by describing Bronze Age metal consumption and display in cemeteries from four micro-regions of the Tisza, and compare them with network 'betweenness centrality' values for locations along the river. I find support for the argument that favourably located river nodes had better access to metal in the earlier part of the Bronze Age.
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Affiliation(s)
- Paul R. Duffy
- The Italian Academy for Advanced Studies in America, Columbia University, New York, New York, United States of America
- The Archaeology Centre, University of Toronto, Toronto, Ontario, Canada
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36
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Goršič M, Dai B, Novak D. Load Position and Weight Classification during Carrying Gait Using Wearable Inertial and Electromyographic Sensors. Sensors (Basel) 2020; 20:E4963. [PMID: 32887309 PMCID: PMC7506954 DOI: 10.3390/s20174963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 11/17/2022]
Abstract
Lifting and carrying heavy objects is a major aspect of physically intensive jobs. Wearable sensors have previously been used to classify different ways of picking up an object, but have seen only limited use for automatic classification of load position and weight while a person is walking and carrying an object. In this proof-of-concept study, we thus used wearable inertial and electromyographic sensors for offline classification of different load positions (frontal vs. unilateral vs. bilateral side loads) and weights during gait. Ten participants performed 19 different carrying trials each while wearing the sensors, and data from these trials were used to train and evaluate classification algorithms based on supervised machine learning. The algorithms differentiated between frontal and other loads (side/none) with an accuracy of 100%, between frontal vs. unilateral side load vs. bilateral side load with an accuracy of 96.1%, and between different load asymmetry levels with accuracies of 75-79%. While the study is limited by a lack of electromyographic sensors on the arms and a limited number of load positions/weights, it shows that wearable sensors can differentiate between different load positions and weights during gait with high accuracy. In the future, such approaches could be used to control assistive devices or for long-term worker monitoring in physically demanding occupations.
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Affiliation(s)
- Maja Goršič
- Department of Electrical and Computer Engineering, University of Wyoming, Laramie, WY 82071, USA;
- Division of Kinesiology and Health, University of Wyoming, Laramie, WY 82071, USA;
| | - Boyi Dai
- Division of Kinesiology and Health, University of Wyoming, Laramie, WY 82071, USA;
| | - Domen Novak
- Department of Electrical and Computer Engineering, University of Wyoming, Laramie, WY 82071, USA;
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Shohel M, McAdams NEB, Cramer BD, Forbes TZ. Ontogenetic variability in crystallography and mosaicity of conodont apatite: implications for microstructure, palaeothermometry and geochemistry. R Soc Open Sci 2020; 7:200322. [PMID: 32874630 PMCID: PMC7428274 DOI: 10.1098/rsos.200322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
X-ray diffraction data from Silurian conodonts belonging to various developmental stages of the species Dapsilodus obliquicostatus demonstrate changes in crystallography and degree of nanocrystallite ordering (mosaicity) in both lamellar crown tissue and white matter. The exclusive use of a single species in this study, combined with systematic testing of each element type at multiple locations, provided insight into microstructural and crystallographic differentiation between element type (Sa , Sb -c , M) as well as between juveniles and adults. A relative increase in the unit cell dimensions a/c ratio of nanocrystallites during growth was apparent in areas demonstrating single-crystal behaviour, but no such relationship was seen in dominantly polycrystalline areas. Systematic variations in mosaicity were identified, with mosaicity (as a proxy for disorder) increasing during growth, as well as along elements from tip to base. These results provide potential insight into the integrity of conodont apatite as a recorder of palaeoseawater chemistry, as well as demonstrate the need to consider the influence of ontogeny and element type on the use of conodonts in palaeothermometry and geochemical investigations.
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Affiliation(s)
- Mohammad Shohel
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Neo E. B. McAdams
- Department of Geosciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Bradley D. Cramer
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Tori Z. Forbes
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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Talukder A, Li X, Hu H. Position-wise binding preference is important for miRNA target site prediction. Bioinformatics 2020; 36:3680-3686. [PMID: 32186709 PMCID: PMC8453239 DOI: 10.1093/bioinformatics/btaa195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/16/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION It is a fundamental task to identify microRNAs (miRNAs) targets and accurately locate their target sites. Genome-scale experiments for miRNA target site detection are still costly. The prediction accuracies of existing computational algorithms and tools are often not up to the expectation due to a large number of false positives. One major obstacle to achieve a higher accuracy is the lack of knowledge of the target binding features of miRNAs. The published high-throughput experimental data provide an opportunity to analyze position-wise preference of miRNAs in terms of target binding, which can be an important feature in miRNA target prediction algorithms. RESULTS We developed a Markov model to characterize position-wise pairing patterns of miRNA-target interactions. We further integrated this model as a scoring method and developed a dynamic programming (DP) algorithm, MDPS (Markov model-scored Dynamic Programming algorithm for miRNA target site Selection) that can screen putative target sites of miRNA-target binding. The MDPS algorithm thus can take into account both the dependency of neighboring pairing positions and the global pairing information. Based on the trained Markov models from both miRNA-specific and general datasets, we discovered that the position-wise binding information specific to a given miRNA would benefit its target prediction. We also found that miRNAs maintain region-wise similarity in their target binding patterns. Combining MDPS with existing methods significantly improves their precision while only slightly reduces their recall. Therefore, position-wise pairing patterns have the promise to improve target prediction if incorporated into existing software tools. AVAILABILITY AND IMPLEMENTATION The source code and tool to calculate MDPS score is available at http://hulab.ucf.edu/research/projects/MDPS/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Orlando, FL 32816, USA
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Monihan SM, Magness CA, Ryu CH, McMahon MM, Beilstein MA, Schumaker KS. Duplication and functional divergence of a calcium sensor in the Brassicaceae. J Exp Bot 2020; 71:2782-2795. [PMID: 31989164 PMCID: PMC7210777 DOI: 10.1093/jxb/eraa031] [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: 08/05/2019] [Accepted: 01/27/2020] [Indexed: 05/09/2023]
Abstract
The presence of varied numbers of CALCINEURIN B-LIKE10 (CBL10) calcium sensor genes in species across the Brassicaceae and the demonstrated role of CBL10 in salt tolerance in Arabidopsis thaliana and Eutrema salsugineum provided a unique opportunity to determine if CBL10 function is modified in different species and linked to salt tolerance. Salinity effects on species growth and cross-species complementation were used to determine the extent of conservation and divergence of CBL10 function in four species representing major lineages within the core Brassicaceae (A. thaliana, E. salsugineum, Schrenkiella parvula, and Sisymbrium irio) as well as the first diverging lineage (Aethionema arabicum). Evolutionary and functional analyses indicate that CBL10 duplicated within expanded lineage II of the Brassicaceae and that, while portions of CBL10 function are conserved across the family, there are species-specific variations in CBL10 function. Paralogous CBL10 genes within a species diverged in expression and function probably contributing to the maintenance of the duplicated gene pairs. Orthologous CBL10 genes diverged in function in a species-specific manner, suggesting that functions arose post-speciation. Multiple CBL10 genes and their functional divergence may have expanded calcium-mediated signaling responses and contributed to the ability of certain members of the Brassicaceae to maintain growth in salt-affected soils.
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Affiliation(s)
- Shea M Monihan
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Choong-Hwan Ryu
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Karen S Schumaker
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
- Correspondence:
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40
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Powers JS, Vargas G G, Brodribb TJ, Schwartz NB, Pérez-Aviles D, Smith-Martin CM, Becknell JM, Aureli F, Blanco R, Calderón-Morales E, Calvo-Alvarado JC, Calvo-Obando AJ, Chavarría MM, Carvajal-Vanegas D, Jiménez-Rodríguez CD, Murillo Chacon E, Schaffner CM, Werden LK, Xu X, Medvigy D. A catastrophic tropical drought kills hydraulically vulnerable tree species. Glob Chang Biol 2020; 26:3122-3133. [PMID: 32053250 DOI: 10.1111/gcb.15037] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/17/2020] [Accepted: 02/02/2020] [Indexed: 06/10/2023]
Abstract
Drought-related tree mortality is now a widespread phenomenon predicted to increase in magnitude with climate change. However, the patterns of which species and trees are most vulnerable to drought, and the underlying mechanisms have remained elusive, in part due to the lack of relevant data and difficulty of predicting the location of catastrophic drought years in advance. We used long-term demographic records and extensive databases of functional traits and distribution patterns to understand the responses of 20-53 species to an extreme drought in a seasonally dry tropical forest in Costa Rica, which occurred during the 2015 El Niño Southern Oscillation event. Overall, species-specific mortality rates during the drought ranged from 0% to 34%, and varied little as a function of tree size. By contrast, hydraulic safety margins correlated well with probability of mortality among species, while morphological or leaf economics spectrum traits did not. This firmly suggests hydraulic traits as targets for future research.
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Affiliation(s)
- Jennifer S Powers
- Department of Ecology, Evolution, & Behavior, University of Minnesota, St. Paul, MN, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - German Vargas G
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Naomi B Schwartz
- Department of Geography, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Pérez-Aviles
- Department of Ecology, Evolution, & Behavior, University of Minnesota, St. Paul, MN, USA
| | - Chris M Smith-Martin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | | | - Filippo Aureli
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
- Instituto de Neuroetologia, Universidad Veracruzana, Xalapa, Mexico
| | - Roger Blanco
- Programa de Investigación, Área de Conservación Guanacaste, Sistema Nacional de Areas de Conservación, Ministerio de Ambiente y Energía, Liberia, Costa Rica
| | - Erick Calderón-Morales
- Department of Ecology, Evolution, & Behavior, University of Minnesota, St. Paul, MN, USA
| | | | | | - María Marta Chavarría
- Programa de Investigación, Área de Conservación Guanacaste, Sistema Nacional de Areas de Conservación, Ministerio de Ambiente y Energía, Liberia, Costa Rica
| | | | - César D Jiménez-Rodríguez
- Escuela de Ingeniería Forestal, Tecnológico de Costa Rica, Cartago, Costa Rica
- Water Resources Section, Delft University of Technology, Delft, The Netherlands
| | - Evin Murillo Chacon
- Programa de Investigación, Área de Conservación Guanacaste, Sistema Nacional de Areas de Conservación, Ministerio de Ambiente y Energía, Liberia, Costa Rica
| | - Colleen M Schaffner
- Instituto de Neuroetologia, Universidad Veracruzana, Xalapa, Mexico
- Psychology Department, Adams State University, Alamosa, CO, USA
| | - Leland K Werden
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Xiangtao Xu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - David Medvigy
- Department of Biological Science, University of Notre Dame, Notre Dame, IN, USA
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Lee YK, Xi Z, Lee YJ, Kim YH, Hao Y, Choi H, Lee MG, Joo YC, Kim C, Lien JM, Choi IS. Computational wrapping: A universal method to wrap 3D-curved surfaces with nonstretchable materials for conformal devices. Sci Adv 2020; 6:eaax6212. [PMID: 32300643 PMCID: PMC7148111 DOI: 10.1126/sciadv.aax6212] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 01/14/2020] [Indexed: 05/19/2023]
Abstract
This study starts from the counterintuitive question of how we can render conventional stiff, nonstretchable, and even brittle materials sufficiently conformable to fully wrap curved surfaces, such as spheres, without failure. Here, we extend the geometrical design method of computational origami to wrapping. Our computational wrapping approach provides a robust and reliable method for fabricating conformal devices for arbitrary curved surfaces with a computationally designed nonpolyhedral developable net. This computer-aided design transforms two-dimensional (2D)-based materials, such as Si wafers and steel sheets, into various targeted conformal structures that can fully wrap desired 3D structures without fracture or severe plastic deformation. We further demonstrate that our computational wrapping approach enables a design platform that can transform conventional nonstretchable 2D-based devices, such as electroluminescent lighting and flexible batteries, into conformal 3D curved devices.
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Affiliation(s)
- Yu-Ki Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Zhonghua Xi
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
| | - Young-Joo Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun-Hyeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yue Hao
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
| | - Hongjin Choi
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoung-Gyu Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Young-Chang Joo
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Changsoon Kim
- Graduate School of Convergence Science and Technology, and Inter-University Semiconductor Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Jyh-Ming Lien
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
- Corresponding author. (J.-M.L.); (I.-S.C.)
| | - In-Suk Choi
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Corresponding author. (J.-M.L.); (I.-S.C.)
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Andrén H, Hobbs NT, Aronsson M, Brøseth H, Chapron G, Linnell JDC, Odden J, Persson J, Nilsen EB. Harvest models of small populations of a large carnivore using Bayesian forecasting. Ecol Appl 2020; 30:e02063. [PMID: 31868951 PMCID: PMC7187313 DOI: 10.1002/eap.2063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 05/27/2023]
Abstract
Harvesting large carnivores can be a management tool for meeting politically set goals for their desired abundance. However, harvesting carnivores creates its own set of conflicts in both society and among conservation professionals, where one consequence is a need to demonstrate that management is sustainable, evidence-based, and guided by science. Furthermore, because large carnivores often also have high degrees of legal protection, harvest quotas have to be carefully justified and constantly adjusted to avoid damaging their conservation status. We developed a Bayesian state-space model to support adaptive management of Eurasian lynx harvesting in Scandinavia. The model uses data from the annual monitoring of lynx abundance and results from long-term field research on lynx biology, which has provided detailed estimates of key demographic parameters. We used the model to predict the probability that the forecasted population size will be below or above the management objectives when subjected to different harvest quotas. The model presented here informs decision makers about the policy risks of alternative harvest levels. Earlier versions of the model have been available for wildlife managers in both Sweden and Norway to guide lynx harvest quotas and the model predictions showed good agreement with observations. We combined monitoring data with data on vital rates and were able to estimate unobserved additional mortality rates, which are most probably due to poaching. In both countries, the past quota setting strategy suggests that there has been a de facto threshold strategy with increasing proportion, which means that there is no harvest below a certain population size, but above this threshold there is an increasing proportion of the population harvested as the population size increases. The annual assessment of the monitoring results, the use of forecasting models, and a threshold harvest approach to quota setting will all reduce the risk of lynx population sizes moving outside the desired goals. The approach we illustrate could be adapted to other populations of mammals worldwide.
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Affiliation(s)
- Henrik Andrén
- Grimsö Wildlife Research StationDepartment of EcologySwedish University of Agricultural SciencesSE‐730 91RiddarhyttanSweden
| | - N. Thompson Hobbs
- Natural Resource Ecology LaboratoryDepartment of Ecosystem Science and Sustainability, and Graduate Degree Program in EcologyColorado State UniversityFort CollinsColorado80523USA
| | - Malin Aronsson
- Grimsö Wildlife Research StationDepartment of EcologySwedish University of Agricultural SciencesSE‐730 91RiddarhyttanSweden
- Department of ZoologyStockholm UniversitySE‐106 91StockholmSweden
| | - Henrik Brøseth
- Rovdata, Norwegian Institute for Nature ResearchP.O. Box 5685, TorgardNO‐7485TrondheimNorway
| | - Guillaume Chapron
- Grimsö Wildlife Research StationDepartment of EcologySwedish University of Agricultural SciencesSE‐730 91RiddarhyttanSweden
| | - John D. C. Linnell
- Norwegian Institute for Nature ResearchP.O. Box 5685, TorgardNO‐7485TrondheimNorway
| | - John Odden
- Norwegian Institute for Nature ResearchP.O. Box 5685, TorgardNO‐7485TrondheimNorway
| | - Jens Persson
- Grimsö Wildlife Research StationDepartment of EcologySwedish University of Agricultural SciencesSE‐730 91RiddarhyttanSweden
| | - Erlend B. Nilsen
- Norwegian Institute for Nature ResearchP.O. Box 5685, TorgardNO‐7485TrondheimNorway
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Shivaiah KK, Ding G, Upton B, Nikolau BJ. Non-Catalytic Subunits Facilitate Quaternary Organization of Plastidic Acetyl-CoA Carboxylase. Plant Physiol 2020; 182:756-775. [PMID: 31792149 PMCID: PMC6997691 DOI: 10.1104/pp.19.01246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/19/2019] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana), like most dicotyledonous plants, expresses a multicomponent, heteromeric acetyl-CoA carboxylase (htACCase), which catalyzes the generation of the malonyl-CoA precursor of de novo fatty acid biosynthesis. This enzyme consists of four catalytic subunits: biotin carboxylase (BC), carboxyltransferase (CT)-α, CT-β, and biotin carboxyl carrier protein (BCCP1 or BCCP2). By coexpressing combinations of components in a bacterial expression system, we demonstrate noncatalytic BADCs facilitate the assembly and activation of BCCP-BADC-BC subcomplexes catalyzing the bicarbonate-dependent hydrolysis of ATP, which is the first half-reaction catalyzed by the htACCase enzyme. Although BADC proteins do not directly impact formation of the CT-αβ subcomplex, the BADC-facilitated BCCP-BADC-BC subcomplex can more readily interact with the CT-αβ subcomplex to facilitate the generation of malonyl-CoA. The Arabidopsis genome encodes three BADC isoforms (BADC1, BADC2, and BADC3), and BADC2 and BADC3 (rather than BADC1), in combination with BCCP1, best support this quaternary-structural organization and catalytic activation of the htACCase enzyme. Physiological genetic studies validate these attributes as Arabidopsis double mutants singularly expressing BADC2, BADC3, or BADC1 present increasingly greater deleterious impacts on morphological and biochemical phenotypes. Specifically, plants expressing only BADC2 develop normally, plants only expressing BADC3 suffer a stunted root-growth phenotype, and plants expressing only BADC1 are embryo-lethal. The latter phenotype may also be associated with the distinct suborganelle localization of BADC1 in plastids as compared to the localization of the other two BADC homologs. These finding can inspire novel strategies to improve the biological sources of fats and oils for dietary and industrial applications.
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Affiliation(s)
- Kiran-Kumar Shivaiah
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Bryon Upton
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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Huang J, Wang C, Li X, Fang X, Huang N, Wang Y, Ma H, Wang Y, Copenhaver GP. Conservation and Divergence in the Meiocyte sRNAomes of Arabidopsis, Soybean, and Cucumber. Plant Physiol 2020; 182:301-317. [PMID: 31719152 PMCID: PMC6945826 DOI: 10.1104/pp.19.00807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/22/2019] [Indexed: 05/15/2023]
Abstract
Meiosis is a critical process for sexual reproduction. During meiosis, genetic information on homologous chromosomes is shuffled through meiotic recombination to produce gametes with novel allelic combinations. Meiosis and recombination are orchestrated by several mechanisms including regulation by small RNAs (sRNAs). Our previous work in Arabidopsis (Arabidopsis thaliana) meiocytes showed that meiocyte-specific sRNAs (ms-sRNAs) have distinct characteristics, including positive association with the coding region of genes that are transcriptionally upregulated during meiosis. Here, we characterized the ms-sRNAs in two important crops, soybean (Glycine max) and cucumber (Cucumis sativus). Ms-sRNAs in soybean have the same features as those in Arabidopsis, suggesting that they may play a conserved role in eudicots. We also investigated the profiles of microRNAs (miRNAs) and phased secondary small interfering RNAs in the meiocytes of all three species. Two conserved miRNAs, miR390 and miR167, are highly abundant in the meiocytes of all three species. In addition, we identified three novel cucumber miRNAs. Intriguingly, our data show that the previously identified phased secondary small interfering RNA pathway involving soybean-specific miR4392 is more abundant in meiocytes. These results showcase the conservation and divergence of ms-sRNAs in flowering plants, and broaden our understanding of sRNA function in crop species.
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Affiliation(s)
- Jiyue Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
| | - Cong Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiang Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaolong Fang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Gregory P Copenhaver
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
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Holder TRN, Gruen ME, Roberts DL, Somers T, Bozkurt A. A Systematic Literature Review of Animal-Assisted Interventions in Oncology (Part II): Theoretical Mechanisms and Frameworks. Integr Cancer Ther 2020; 19:1534735420943269. [PMID: 32698731 PMCID: PMC7378713 DOI: 10.1177/1534735420943269] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/29/2020] [Accepted: 05/20/2020] [Indexed: 11/16/2022] Open
Abstract
Animal-assisted interventions (AAIs) can improve patients' quality of life as complementary medical treatments. Part I of this 2-paper systematic review focused on the methods and results of cancer-related AAIs; Part II discusses the theories of the field's investigators. Researchers cite animal personality, physical touch, physical movement, distraction, and increased human interaction as sources of observed positive outcomes. These mechanisms then group under theoretical frameworks such as the social support hypothesis or the human-animal bond concept to fully explain AAI in oncology. The cognitive activation theory of stress, the science of unitary human beings, and the self-object hypothesis are additional frameworks mentioned by some researchers. We also discuss concepts of neurobiological transduction connecting mechanisms to AAI benefits. Future researchers should base study design on theories with testable hypotheses and use consistent terminology to report results. This review aids progress toward a unified theoretical framework and toward more holistic cancer treatments.
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Affiliation(s)
- Timothy R. N. Holder
- University of North Carolina, Chapel
Hill, NC, USA
- North Carolina State University,
Raleigh, NC, USA
| | | | | | | | - Alper Bozkurt
- University of North Carolina, Chapel
Hill, NC, USA
- North Carolina State University,
Raleigh, NC, USA
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Bateson M, Eisenberg DTA, Nettle D. Controlling for baseline telomere length biases estimates of the rate of telomere attrition. R Soc Open Sci 2019; 6:190937. [PMID: 31824705 PMCID: PMC6837209 DOI: 10.1098/rsos.190937] [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] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
Longitudinal studies have sought to establish whether environmental exposures such as smoking accelerate the attrition of individuals' telomeres over time. These studies typically control for baseline telomere length (TL) by including it as a covariate in statistical models. However, baseline TL also differs between smokers and non-smokers, and telomere attrition is spuriously linked to baseline TL via measurement error and regression to the mean. Using simulated datasets, we show that controlling for baseline TL overestimates the true effect of smoking on telomere attrition. This bias increases with increasing telomere measurement error and increasing difference in baseline TL between smokers and non-smokers. Using a meta-analysis of longitudinal datasets, we show that as predicted, the estimated difference in telomere attrition between smokers and non-smokers is greater when statistical models control for baseline TL than when they do not, and the size of the discrepancy is positively correlated with measurement error. The bias we describe is not specific to smoking and also applies to other exposures. We conclude that to avoid invalid inference, models of telomere attrition should not control for baseline TL by including it as a covariate. Many claims of accelerated telomere attrition in individuals exposed to adversity need to be re-assessed.
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Affiliation(s)
- Melissa Bateson
- Centre for Behaviour and Evolution and Institute of Neuroscience, Newcastle University, Henry Wellcome Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | - Daniel Nettle
- Centre for Behaviour and Evolution and Institute of Neuroscience, Newcastle University, Henry Wellcome Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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Nelson G, Ellis S. The history and impact of digitization and digital data mobilization on biodiversity research. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170391. [PMID: 30455209 PMCID: PMC6282090 DOI: 10.1098/rstb.2017.0391] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [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] [Accepted: 08/08/2018] [Indexed: 11/12/2022] Open
Abstract
The first two decades of the twenty-first century have seen a rapid rise in the mobilization of digital biodiversity data. This has thrust natural history museums into the forefront of biodiversity research, underscoring their central role in the modern scientific enterprise. The advent of mobilization initiatives such as the United States National Science Foundation's Advancing Digitization of Biodiversity Collections (ADBC), Australia's Atlas of Living Australia (ALA), Mexico's National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil's Centro de Referência em Informação (CRIA) and China's National Specimen Information Infrastructure (NSII) has led to a rapid rise in data aggregators and an exponential increase in digital data for scientific research and arguably provide the best evidence of where species live. The international Global Biodiversity Information Facility (GBIF) now serves about 131 million museum specimen records, and Integrated Digitized Biocollections (iDigBio) in the USA has amassed more than 115 million. These resources expose collections to a wider audience of researchers, provide the best biodiversity data in the modern era outside of nature itself and ensure the primacy of specimen-based research. Here, we provide a brief history of worldwide data mobilization, their impact on biodiversity research, challenges for ensuring data quality, their contribution to scientific publications and evidence of the rising profiles of natural history collections.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Gil Nelson
- iDigBio, Florida State University, 142 Collegiate Loop, Tallahassee, FL 32306, USA
| | - Shari Ellis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
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Singh J, Purohit PK. Allosteric interactions in a birod model of DNA. Proc Math Phys Eng Sci 2018; 474:20180136. [PMID: 34025206 PMCID: PMC6237492 DOI: 10.1098/rspa.2018.0136] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/05/2018] [Indexed: 06/12/2023] Open
Abstract
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory of DNA elasticity remains a challenge. Here, we quantify allosteric interactions between two entities bound to DNA by using the theory of birods. We recognize that molecules bound to DNA cause local deformations that can be captured in a birod model which consists of two elastic strands interacting via an elastic web representing the basepairs. We show that the displacement field caused by bound entities decays exponentially with distance from the binding site. We compute the interaction energy between two proteins on DNA as a function of distance between them and find that it decays exponentially while oscillating with the periodicity of the double helix, in excellent agreement with experiments. The decay length of the interaction energy can be determined in terms of the mechanical properties of the strands and the webbing in our birod model, and it varies with the GC content of the DNA. Our model provides a framework for viewing allosteric interactions in DNA within the ambit of configurational forces of continuum elasticity.
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Copley TR, Aliferis KA, Kliebenstein DJ, Jabaji SH. An integrated RNAseq- 1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease. BMC Plant Biol 2017; 17:84. [PMID: 28449662 PMCID: PMC5408482 DOI: 10.1186/s12870-017-1020-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 12/14/2016] [Accepted: 03/27/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Rhizoctonia solani AG1-IA is a devastating phytopathogen causing Rhizoctonia foliar blight (RFB) of soybean worldwide with yield losses reaching 60%. Plant defense mechanisms are complex and information from different metabolic pathways is required to thoroughly understand plant defense regulation and function. Combining information from different "omics" levels such as transcriptomics, metabolomics, and proteomics is required to gain insights into plant metabolism and its regulation. As such, we studied fluctuations in soybean metabolism in response to R. solani infection at early and late disease stages using an integrated transcriptomics-metabolomics approach, focusing on the regulation of soybean primary metabolism and oxidative stress tolerance. RESULTS Transcriptomics (RNAseq) and metabolomics (1H NMR) data were analyzed individually and by integration using bidirectional orthogonal projections to latent structures (O2PLS) to reveal possible links between the metabolome and transcriptome during early and late infection stages. O2PLS analysis detected 516 significant transcripts, double that reported in the univariate analysis, and more significant metabolites than detected in partial least squares discriminant analysis. Strong separation of treatments based on integration of the metabolomes and transcriptomes of the analyzed soybean leaves was revealed, similar trends as those seen in analyses done on individual datasets, validating the integration method being applied. Strong fluctuations of soybean primary metabolism occurred in glycolysis, the TCA cycle, photosynthesis and photosynthates in response to R. solani infection. Data were validated using quantitative real-time PCR on a set of specific markers as well as randomly selected genes. Significant increases in transcript and metabolite levels involved in redox reactions and ROS signaling, such as peroxidases, thiamine, tocopherol, proline, L-alanine and GABA were also recorded. Levels of ethanol increased 24 h post-infection in soybean leaves, and alcohol dehydrogenase (ADH) loss-of-function mutants of Arabidopsis thaliana had higher necrosis than wild type plants. CONCLUSIONS As a proof-of-concept, this study offers novel insights into the biological correlations and identification of candidate genes and metabolites that can be used in soybean breeding for resistance to R. solani AG1-IA infection. Additionally, these findings imply that alcohol and its associated gene product ADH may have important roles in plant resistance to R. solani AG1-IA causing foliar blight.
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Affiliation(s)
- Tanya R. Copley
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, H9X 3V9 Canada
| | - Konstantinos A. Aliferis
- Department of Plant Science, Laboratory of Pesticide Science, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | - Suha H. Jabaji
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, H9X 3V9 Canada
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