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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. J Integr Plant Biol 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [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: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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2
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Casasanta MA, Jonaid GM, Kaylor L, Luqiu WY, Solares MJ, Schroen ML, Dearnaley WJ, Wilson J, Dukes MJ, Kelly DF. Expression of concern: Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy. Nanoscale 2024; 16:4919. [PMID: 38353946 PMCID: PMC10903400 DOI: 10.1039/d4nr90037e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024]
Abstract
Expression of concern for 'Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy' by Michael A. Casasanta et al., Nanoscale, 2021, 13, 7285-7293, https://doi.org/10.1039/D1NR00388G.
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Affiliation(s)
- Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - G M Jonaid
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - William Y Luqiu
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Maria J Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Mariah L Schroen
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Jarad Wilson
- RayBiotech Life, Peachtree Corners, GA 30092, USA
| | - Madeline J Dukes
- Applications Science, Protochips, Inc., Morrisville, NC 27560, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
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Terradas G, Manzano-Alvarez J, Vanalli C, Werling K, Cattadori IM, Rasgon JL. Temperature affects viral kinetics and vectorial capacity of Aedes aegypti mosquitoes co-infected with Mayaro and Dengue viruses. Parasit Vectors 2024; 17:73. [PMID: 38374048 PMCID: PMC10877814 DOI: 10.1186/s13071-023-06109-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Increasing global temperatures and unpredictable climatic extremes have contributed to the spread of vector-borne diseases. The mosquito Aedes aegypti is the main vector of multiple arboviruses that negatively impact human health, mostly in low socioeconomic areas of the world. Co-circulation and co-infection of these viruses in humans have been increasingly reported; however, how vectors contribute to this alarming trend remains unclear. METHODS Here, we examine single and co-infection of Mayaro virus (D strain, Alphavirus) and dengue virus (serotype 2, Flavivirus) in Ae. aegypti adults and cell lines at two constant temperatures, moderate (27 °C) and hot (32 °C), to quantify vector competence and the effect of temperature on infection, dissemination and transmission, including on the degree of interaction between the two viruses. RESULTS Both viruses were primarily affected by temperature but there was a partial interaction with co-infection. Dengue virus quickly replicates in adult mosquitoes with a tendency for higher titers in co-infected mosquitoes at both temperatures, and mosquito mortality was more severe at higher temperatures in all conditions. For dengue, and to a lesser extent Mayaro, vector competence and vectorial capacity were higher at hotter temperature in co- vs. single infections and was more evident at earlier time points (7 vs. 14 days post infection) for Mayaro. The temperature-dependent phenotype was confirmed in vitro by faster cellular infection and initial replication at higher temperatures for dengue but not for Mayaro virus. CONCLUSIONS Our study suggests that contrasting kinetics of the two viruses could be related to their intrinsic thermal requirements, where alphaviruses thrive better at lower temperatures compared to flaviviruses. However, more studies are necessary to clarify the role of co-infection at different temperature regimes, including under more natural temperature settings.
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Affiliation(s)
- Gerard Terradas
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jaime Manzano-Alvarez
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Chiara Vanalli
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Kristine Werling
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Isabella M Cattadori
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
| | - Jason L Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA.
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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Zavala-Paez M, Holliday J, Hamilton JA. Leveraging whole-genome sequencing to estimate telomere length in plants. Mol Ecol Resour 2024; 24:e13899. [PMID: 37966130 DOI: 10.1111/1755-0998.13899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/02/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
Changes in telomere length are increasingly used to indicate species' response to environmental stress across diverse taxa. Despite this broad use, few studies have explored telomere length in plants. Thus, evaluation of new approaches for measuring telomeres in plants is needed. Rapid advances in sequencing approaches and bioinformatic tools now allow estimation of telomere content from whole-genome sequencing (WGS) data, a proxy for telomere length. While telomere content has been quantified extensively using quantitative polymerase chain reaction (qPCR) and WGS in humans, no study to date has compared the effectiveness of WGS in estimating telomere length in plants relative to qPCR approaches. In this study, we use 100 Populus clones re-sequenced using short-read Illumina sequencing to quantify telomere length comparing three different bioinformatic approaches (Computel, K-seek and TRIP) in addition to qPCR. Overall, telomere length estimates varied across different bioinformatic approaches, but were highly correlated across methods for individual genotypes. A positive correlation was observed between WGS estimates and qPCR, however, Computel estimates exhibited the greatest correlation. Computel incorporates genome coverage into telomere length calculations, suggesting that genome coverage is likely important to telomere length quantification when using WGS data. Overall, telomere estimates from WGS provided greater precision and accuracy of telomere length estimates relative to qPCR. The findings suggest WGS is a promising approach for assessing telomere length and, as the field of telomere ecology evolves, may provide added value to assaying response to biotic and abiotic environments for plants needed to accelerate plant breeding and conservation management.
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Affiliation(s)
- Michelle Zavala-Paez
- Department of Ecosystem Science and Management, Pennsylvania State University, State College, Pennsylvania, USA
| | - Jason Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, State College, Pennsylvania, USA
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Ginnan N, Bordenstein SR. It is time to authenticate the Microbiome Sciences with accredited educational programs and departments. PLoS Biol 2023; 21:e3002420. [PMID: 38060452 PMCID: PMC10703218 DOI: 10.1371/journal.pbio.3002420] [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] [Indexed: 12/18/2023] Open
Abstract
The Microbiome Sciences are at a crucial maturation stage. Scientists and educators should now view the Microbiome Sciences as a flourishing and autonomous discipline, creating degree programs and departments that are conducive to cohesive growth.
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Affiliation(s)
- Nichole Ginnan
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Seth R. Bordenstein
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Vieira P, Kantor MR, Jansen A, Handoo ZA, Eisenback JD. Cellular insights of beech leaf disease reveal abnormal ectopic cell division of symptomatic interveinal leaf areas. PLoS One 2023; 18:e0292588. [PMID: 37797062 PMCID: PMC10553357 DOI: 10.1371/journal.pone.0292588] [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: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
The beech leaf disease nematode, Litylenchus crenatae subsp. mccannii, is recognized as a newly emergent nematode species that causes beech leaf disease (BLD) in beech trees (Fagus spp.) in North America. Changes of leaf morphology before emergence from the bud induced by BLD can provoke dramatic effects on the leaf architecture and consequently to tree performance and development. The initial symptoms of BLD appear as dark green, interveinal banding patterns of the leaf. Despite the fast progression of this disease, the cellular mechanisms leading to the formation of such aberrant leaf phenotype remains totally unknown. To understand the cellular basis of BLD, we employed several types of microscopy to provide an exhaustive characterization of nematode-infected buds and leaves. Histological sections revealed a dramatic cell change composition of these nematode-infected tissues. Diseased bud scale cells were typically hypertrophied and showed a high variability of size. Moreover, while altered cell division had no influence on leaf organogenesis, induction of cell proliferation on young leaf primordia led to a dramatic change in cell layer architecture. Hyperplasia and hypertrophy of the different leaf cell layers, coupled with an abnormal proliferation of chloroplasts especially in the mesophyll cell layers, resulted in the typical interveinal leaf banding. These discrepancies in leaf cell structure were depicted by an abnormal rate of cellular division of the leaf interveinal areas infected by the nematode, promoting significant increase of cell size and leaf thickness. The formation of symptomatic BLD leaves is therefore orchestrated by distinct cellular processes, to enhance the value of these feeding sites and to improve their nutrition status for the nematode. Our findings thus uncover relevant cellular events and provide a structural framework to understand this important disease.
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Affiliation(s)
- Paulo Vieira
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture—Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Mihail R. Kantor
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Andrew Jansen
- Electron and Confocal Microscopy Unit, United States Department of Agriculture–Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Zafar A. Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture—Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, Virginia, United States of America
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Xu S, Momin M, Ahmed S, Hossain A, Veeramuthu L, Pandiyan A, Kuo CC, Zhou T. Illuminating the Brain: Advances and Perspectives in Optoelectronics for Neural Activity Monitoring and Modulation. Adv Mater 2023; 35:e2303267. [PMID: 37726261 DOI: 10.1002/adma.202303267] [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: 04/07/2023] [Revised: 05/30/2023] [Indexed: 09/21/2023]
Abstract
Optogenetic modulation of brain neural activity that combines optical and electrical modes in a unitary neural system has recently gained robust momentum. Controlling illumination spatial coverage, designing light-activated modulators, and developing wireless light delivery and data transmission are crucial for maximizing the use of optical neuromodulation. To this end, biocompatible electrodes with enhanced optoelectrical performance, device integration for multiplexed addressing, wireless transmission, and multimodal operation in soft systems have been developed. This review provides an outlook for uniformly illuminating large brain areas while spatiotemporally imaging the neural responses upon optoelectrical stimulation with little artifacts. Representative concepts and important breakthroughs, such as head-mounted illumination, multiple implanted optical fibers, and micro-light-delivery devices, are discussed. Examples of techniques that incorporate electrophysiological monitoring and optoelectrical stimulation are presented. Challenges and perspectives are posed for further research efforts toward high-density optoelectrical neural interface modulation, with the potential for nonpharmacological neurological disease treatments and wireless optoelectrical stimulation.
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Affiliation(s)
- Shumao Xu
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Marzia Momin
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Salahuddin Ahmed
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Arafat Hossain
- Department of Electrical Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Loganathan Veeramuthu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Archana Pandiyan
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Chi-Ching Kuo
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Tao Zhou
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. Plant Cell 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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9
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Le V, Cellini B, Schilder R, Mongeau JM. Hawkmoths regulate flight torques with their abdomen for yaw control. J Exp Biol 2023; 226:309347. [PMID: 36995279 DOI: 10.1242/jeb.245063] [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: 09/15/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023]
Abstract
Many animals use body parts such as tails to stabilize posture while moving at high speed. In flying insects, leg or abdominal inertia can influence flight posture. In the hawkmoth Manduca sexta the abdomen contributes ∼50% of the total body weight and it can therefore serve to inertially redirect flight forces. How do torques generated by the wings and abdomen interact for flight control? We studied the yaw optomotor response of M. sexta by using a torque sensor attached to the thorax of moths. In response to yaw visual motion, the abdomen moved antiphase with the stimulus, head, and total torque. By studying moths with ablated wings and a fixed abdomen, we resolved abdomen and wing torques and revealed their individual contribution to total yaw torque production. Frequency domain analysis revealed that the abdomen torque is overall smaller than wing torque, although the abdomen torque is ∼80% of the wing torque at higher visual stimulus temporal frequency. Experimental data and modeling revealed that the wing and abdomen torque are transmitted linearly to the thorax. By modeling the thorax and abdomen as a two-link system, we show that abdomen flexion can inertially redirect the thorax to add constructively to wing steering efforts. Our work argues for considering the role of the abdomen in tethered insect flight experiments that use force/torque sensors. Taken together, the hawkmoth abdomen can regulate wing torques in free flight, which could modulate flight trajectories and increase maneuverability.
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Affiliation(s)
- Viet Le
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Benjamin Cellini
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Rudolf Schilder
- Department of Biology and Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Jean-Michel Mongeau
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, USA
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10
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Truelove S, Smith CP, Qin M, Mullany LC, Borchering RK, Lessler J, Shea K, Howerton E, Contamin L, Levander J, Kerr J, Hochheiser H, Kinsey M, Tallaksen K, Wilson S, Shin L, Rainwater-Lovett K, Lemairtre JC, Dent J, Kaminsky J, Lee EC, Perez-Saez J, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore y Piontti A, Vespignani A, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Orr M, Harrison G, Hurt B, Chen J, Vullikanti A, Marathe M, Hoops S, Bhattacharya P, Machi D, Chen S, Paul R, Janies D, Thill JC, Galanti M, Yamana TK, Pei S, Shaman JL, Healy JM, Slayton RB, Biggerstaff M, Johansson MA, Runge MC, Viboud C. Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination. eLife 2022; 11:e73584. [PMID: 35726851 PMCID: PMC9232215 DOI: 10.7554/elife.73584] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/03/2022] [Indexed: 01/01/2023] Open
Abstract
In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-19 Scenario Modeling Hub, an ensemble of nine mechanistic models produced 6-month scenario projections for July-December 2021 for the United States. These projections estimated substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant, projected to occur across most of the US, coinciding with school and business reopening. The scenarios revealed that reaching higher vaccine coverage in July-December 2021 reduced the size and duration of the projected resurgence substantially, with the expected impacts was largely concentrated in a subset of states with lower vaccination coverage. Despite accurate projection of COVID-19 surges occurring and timing, the magnitude was substantially underestimated 2021 by the models compared with the of the reported cases, hospitalizations, and deaths occurring during July-December, highlighting the continued challenges to predict the evolving COVID-19 pandemic. Vaccination uptake remains critical to limiting transmission and disease, particularly in states with lower vaccination coverage. Higher vaccination goals at the onset of the surge of the new variant were estimated to avert over 1.5 million cases and 21,000 deaths, although may have had even greater impacts, considering the underestimated resurgence magnitude from the model.
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Affiliation(s)
- Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Claire P Smith
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Michelle Qin
- Harvard UniversityCambridge, MassachusettsUnited States
| | - Luke C Mullany
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | | | - Justin Lessler
- University of North Carolina at Chapel HillChapel HillUnited States
| | - Katriona Shea
- Pennsylvania State UniversityUniversity ParkUnited States
| | - Emily Howerton
- Pennsylvania State UniversityUniversity ParkUnited States
| | | | | | | | | | - Matt Kinsey
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Kate Tallaksen
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Shelby Wilson
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Lauren Shin
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | | | | | - Juan Dent
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Joshua Kaminsky
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Elizabeth C Lee
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Javier Perez-Saez
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison Hill
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | | | | | | | - Kunpeng Mu
- Northeastern UniversityBostonUnited States
| | | | | | | | | | | | | | | | - Bryan Lewis
- University of VirginiaCharlottesvilleUnited States
| | - Brian Klahn
- University of VirginiaCharlottesvilleUnited States
| | | | - Mark Orr
- University of VirginiaCharlottesvilleUnited States
| | | | | | | | | | | | - Stefan Hoops
- University of VirginiaCharlottesvilleUnited States
| | | | - Dustin Machi
- University of VirginiaCharlottesvilleUnited States
| | - Shi Chen
- University of North Carolina at CharlotteCharlotteUnited States
| | - Rajib Paul
- University of North Carolina at CharlotteCharlotteUnited States
| | - Daniel Janies
- University of North Carolina at CharlotteCharlotteUnited States
| | | | | | | | - Sen Pei
- Columbia UniversityNew YorkUnited States
| | | | | | | | | | | | | | - Cecile Viboud
- Fogarty International Center, National Institutes of HealthBethesdaUnited States
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11
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Arnold CRK, Srinivasan S, Rodriguez S, Rydzak N, Herzog CM, Gontu A, Bharti N, Small M, Rogers CJ, Schade MM, Kuchipudi SV, Kapur V, Read AF, Ferrari MJ. A longitudinal study of the impact of university student return to campus on the SARS-CoV-2 seroprevalence among the community members. Sci Rep 2022; 12:8586. [PMID: 35597780 PMCID: PMC9124192 DOI: 10.1038/s41598-022-12499-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
Returning university students represent large-scale, transient demographic shifts and a potential source of transmission to adjacent communities during the COVID-19 pandemic. In this prospective longitudinal cohort study, we tested for IgG antibodies against SARS-CoV-2 in a non-random cohort of residents living in Centre County prior to the Fall 2020 term at the Pennsylvania State University and following the conclusion of the Fall 2020 term. We also report the seroprevalence in a non-random cohort of students collected at the end of the Fall 2020 term. Of 1313 community participants, 42 (3.2%) were positive for SARS-CoV-2 IgG antibodies at their first visit between 07 August and 02 October 2020. Of 684 student participants who returned to campus for fall instruction, 208 (30.4%) were positive for SARS-CoV-2 antibodies between 26 October and 21 December. 96 (7.3%) community participants returned a positive IgG antibody result by 19 February. Only contact with known SARS-CoV-2-positive individuals and attendance at small gatherings (20-50 individuals) were significant predictors of detecting IgG antibodies among returning students (aOR, 95% CI 3.1, 2.07-4.64; 1.52, 1.03-2.24; respectively). Despite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents was low and stable from before student arrival for the Fall 2020 term to after student departure. The study implies that heterogeneity in SARS-CoV-2 transmission can occur in geographically coincident populations.
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Affiliation(s)
- Callum R K Arnold
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Sreenidhi Srinivasan
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sophie Rodriguez
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Natalie Rydzak
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Catherine M Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nita Bharti
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Meg Small
- College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
- Social Science Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Connie J Rogers
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Margeaux M Schade
- College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V Kuchipudi
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Animal Science, Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew F Read
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew J Ferrari
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
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12
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Fosco GM, LoBraico EJ, Sloan CJ, Fang S, Feinberg ME. Family vulnerability, disruption, and chaos predict parent and child COVID-19 health-protective behavior adherence. Fam Syst Health 2022; 40:10-20. [PMID: 34694836 PMCID: PMC9289943 DOI: 10.1037/fsh0000649] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION This study examined the role of family functioning in predicting family adherence to health-protective behaviors (HPBs) aimed at reducing COVID-19 spread. Pre-COVID-19 family functioning, disruptions to family functioning (cohesion, conflict, routines), and family chaos during the COVID-19 pandemic were tested as pathways to HPB adherence. METHOD We utilized a sample of N = 204 families, comprising parents who had children (MAge = 4.17). Parents (MAge = 27.43) completed one survey prior to COVID-19 onset in the United States, and twice during COVID-19, at a 2-week interval. Structural equation modeling was used to test three potential pathways between prepandemic family-level functioning and HPB adherence during the COVID-19 pandemic. RESULTS Findings indicated that families with higher levels of chaos during COVID-19 demonstrated consistently lower HPB adherence across all three models. Additionally, disruptions in family cohesion from pre-COVID was associated with lower levels of parent and child HPB adherence. Family conflict was indirectly associated with HPB adherence via family chaos during COVID-19; whereas family routines were not associated with HPB adherence at all. DISCUSSION These findings suggest that family functioning is a meaningful predictor of HPB adherence. Family-based support may be effective in improving HPB adherence by focusing on promoting cohesion and reducing conflict and chaos for families coping with reduced community support and resources. Strategies for family-based supports are discussed. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
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Affiliation(s)
- Gregory M Fosco
- Department of Human Development and Family Studies, Pennsylvania State University
| | - Emily J LoBraico
- Department of Human Development and Family Studies, Pennsylvania State University
| | - Carlie J Sloan
- Department of Human Development and Family Studies, Pennsylvania State University
| | - Shichen Fang
- Edna Bennett Pierce Prevention Research Center, Pennsylvania State University
| | - Mark E Feinberg
- Edna Bennett Pierce Prevention Research Center, Pennsylvania State University
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13
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Ketumile D, Yang X, Sanchez R, Kundariya H, Rajewski J, Dweikat IM, Mackenzie SA. Implementation of Epigenetic Variation in Sorghum Selection and Implications for Crop Resilience Breeding. Front Plant Sci 2022; 12:798243. [PMID: 35154188 PMCID: PMC8828589 DOI: 10.3389/fpls.2021.798243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation, and have used these materials to evaluate changes in plant growth vigor. Plant crossing and selection in two distinct environments revealed features of phenotypic plasticity derived from MSH1 manipulation. Introduction of an epigenetic variation to an isogenic sorghum population, in the absence of selection, resulted in 10% yield increase under ideal field conditions and 20% increase under extreme low nitrogen conditions. However, incorporation of early-stage selection amplified these outcomes to 36% yield increase under ideal conditions and 64% increase under marginal field conditions. Interestingly, the best outcomes were derived by selecting mid-range performance early-generation lines rather than highest performing. Data also suggested that phenotypic plasticity derived from the epigenetic variation was non-uniform in its response to environmental variability but served to reduce genotype × environment interaction. The MSH1-derived growth vigor appeared to be associated with enhanced seedling root growth and altered expression of auxin response pathways, and plants showed evidence of cold tolerance, features consistent with observations made previously in Arabidopsis. These data imply that the MSH1 system is conserved across plant species, pointing to the value of parallel model plant studies to help devise effective plant selection strategies for epigenetic breeding in multiple crops.
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Affiliation(s)
- Dikungwa Ketumile
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Xiaodong Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Robersy Sanchez
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Hardik Kundariya
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - John Rajewski
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Ismail M. Dweikat
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Sally A. Mackenzie
- Department of Biology and Plant Science, The Pennsylvania State University, University Park, PA, United States
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Conway JM, Abel zur Wiesch P. Mathematical Modeling of Remdesivir to Treat COVID-19: Can Dosing Be Optimized? Pharmaceutics 2021; 13:1181. [PMID: 34452142 PMCID: PMC8400702 DOI: 10.3390/pharmaceutics13081181] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
The antiviral remdesivir has been approved by regulatory bodies such as the European Medicines Agency (EMA) and the US Food and Drug administration (FDA) for the treatment of COVID-19. However, its efficacy is debated and toxicity concerns might limit the therapeutic range of this drug. Computational models that aid in balancing efficacy and toxicity would be of great help. Parametrizing models is difficult because the prodrug remdesivir is metabolized to its active form (RDV-TP) upon cell entry, which complicates dose-activity relationships. Here, we employ a computational model that allows drug efficacy predictions based on the binding affinity of RDV-TP for its target polymerase in SARS-CoV-2. We identify an optimal infusion rate to maximize remdesivir efficacy. We also assess drug efficacy in suppressing both wild-type and resistant strains, and thereby describe a drug regimen that may select for resistance. Our results differ from predictions using prodrug dose-response curves (pseudo-EC50s). We expect that reaching 90% inhibition (EC90) is insufficient to suppress SARS-CoV-2 in the lungs. While standard dosing mildly inhibits viral polymerase and therefore likely reduces morbidity, we also expect selection for resistant mutants for most realistic parameter ranges. To increase efficacy and safeguard against resistance, we recommend more clinical trials with dosing regimens that substantially increase the levels of RDV-TP and/or pair remdesivir with companion antivirals.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16801, USA
| | - Pia Abel zur Wiesch
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16801, USA
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15
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Abstract
Analyses of transient dynamics are critical to understanding infectious disease transmission and persistence. Identifying and predicting transients across scales, from within-host to community-level patterns, plays an important role in combating ongoing epidemics and mitigating the risk of future outbreaks. Moreover, greater emphases on non-asymptotic processes will enable timely evaluations of wildlife and human diseases and lead to improved surveillance efforts, preventive responses, and intervention strategies. Here, we explore the contributions of transient analyses in recent models spanning the fields of epidemiology, movement ecology, and parasitology. In addition to their roles in predicting epidemic patterns and endemic outbreaks, we explore transients in the contexts of pathogen transmission, resistance, and avoidance at various scales of the ecological hierarchy. Examples illustrate how (i) transient movement dynamics at the individual host level can modify opportunities for transmission events over time; (ii) within-host energetic processes often lead to transient dynamics in immunity, pathogen load, and transmission potential; (iii) transient connectivity between discrete populations in response to environmental factors and outbreak dynamics can affect disease spread across spatial networks; and (iv) increasing species richness in a community can provide transient protection to individuals against infection. Ultimately, we suggest that transient analyses offer deeper insights and raise new, interdisciplinary questions for disease research, consequently broadening the applications of dynamical models for outbreak preparedness and management. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12080-021-00514-w.
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Affiliation(s)
- Yun Tao
- Intelligence Community Postdoctoral Research Fellowship Program, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106 USA
| | - Jessica L. Hite
- School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin, Madison, WI 53706 USA
| | - Kevin D. Lafferty
- Western Ecological Research Center at UCSB Marine Science Institute, U.S. Geological Survey, CA 93106 Santa Barbara, USA
| | - David J. D. Earn
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Nita Bharti
- Department of Biology Center for Infectious Disease Dynamics, Penn State University, University Park, PA 16802 USA
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16
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Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res 2021; 49:1497-1516. [PMID: 33450015 PMCID: PMC7897504 DOI: 10.1093/nar/gkaa1269] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [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: 06/05/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, UniversityPark, PA 16802, USA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Operations and Decision Systems, Université Laval, Canada
- CHU de Québec – Université Laval Research Center, Canada
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Di Chen
- Intercollege Graduate Degree Program in Genetics, Huck Institutes of the Life Sciences, Penn State University, UniversityPark, PA 16802, USA
| | - Kristin A Eckert
- Department of Pathology, Penn State University, College of Medicine, Hershey, PA 17033, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
- EMbeDS, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, PA, USA
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17
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Kinnear CL, Hansen E, Morley VJ, Tracy KC, Forstchen M, Read AF, Woods RJ. Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium. PLoS Biol 2020; 18:e3000987. [PMID: 33332354 PMCID: PMC7775125 DOI: 10.1371/journal.pbio.3000987] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 12/31/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
The antimicrobial resistance crisis has persisted despite broad attempts at intervention. It has been proposed that an important driver of resistance is selection imposed on bacterial populations that are not the intended target of antimicrobial therapy. But to date, there has been limited quantitative measure of the mean and variance of resistance following antibiotic exposure. Here we focus on the important nosocomial pathogen Enterococcus faecium in a hospital system where resistance to daptomycin is evolving despite standard interventions. We hypothesized that the intravenous use of daptomycin generates off-target selection for resistance in transmissible gastrointestinal (carriage) populations of E. faecium. We performed a cohort study in which the daptomycin resistance of E. faecium isolated from rectal swabs from daptomycin-exposed patients was compared to a control group of patients exposed to linezolid, a drug with similar indications. In the daptomycin-exposed group, daptomycin resistance of E. faecium from the off-target population was on average 50% higher than resistance in the control group (n = 428 clones from 22 patients). There was also greater phenotypic diversity in daptomycin resistance within daptomycin-exposed patients. In patients where multiple samples over time were available, a wide variability in temporal dynamics were observed, from long-term maintenance of resistance to rapid return to sensitivity after daptomycin treatment stopped. Sequencing of isolates from a subset of patients supports the argument that selection occurs within patients. Our results demonstrate that off-target gastrointestinal populations rapidly respond to intravenous antibiotic exposure. Focusing on the off-target evolutionary dynamics may offer novel avenues to slow the spread of antibiotic resistance.
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Affiliation(s)
- Clare L. Kinnear
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elsa Hansen
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Valerie J. Morley
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kevin C. Tracy
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Meghan Forstchen
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Institutes of the Life Sciences and Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Robert J. Woods
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
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18
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Yusuff T, Jensen M, Yennawar S, Pizzo L, Karthikeyan S, Gould DJ, Sarker A, Gedvilaite E, Matsui Y, Iyer J, Lai ZC, Girirajan S. Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PLoS Genet 2020; 16:e1008792. [PMID: 32579612 PMCID: PMC7313740 DOI: 10.1371/journal.pgen.1008792] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non-neuronal phenotypes, functional studies evaluating these regions have focused on the molecular basis of neuronal defects. We report a systematic functional analysis of non-neuronal defects for homologs of 59 genes within ten pathogenic CNVs and 20 neurodevelopmental genes in Drosophila melanogaster. Using wing-specific knockdown of 136 RNA interference lines, we identified qualitative and quantitative phenotypes in 72/79 homologs, including 21 lines with severe wing defects and six lines with lethality. In fact, we found that 10/31 homologs of CNV genes also showed complete or partial lethality at larval or pupal stages with ubiquitous knockdown. Comparisons between eye and wing-specific knockdown of 37/45 homologs showed both neuronal and non-neuronal defects, but with no correlation in the severity of defects. We further observed disruptions in cell proliferation and apoptosis in larval wing discs for 23/27 homologs, and altered Wnt, Hedgehog and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and KIF11/Klp61F. These findings were further supported by tissue-specific differences in expression patterns of human CNV genes, as well as connectivity of CNV genes to signaling pathway genes in brain, heart and kidney-specific networks. Our findings suggest that multiple genes within each CNV differentially affect both global and tissue-specific developmental processes within conserved pathways, and that their roles are not restricted to neuronal functions. Rare copy-number variants (CNVs), or large deletions and duplications in the genome, are associated with both neuronal and non-neuronal clinical features. Previous functional studies for these disorders have primarily focused on understanding the cellular mechanisms for neurological and behavioral phenotypes. To understand how genes within these CNVs contribute to developmental defects in non-neuronal tissues, we assessed 79 homologs of CNV and known neurodevelopmental genes in Drosophila models. We found that most homologs showed developmental defects when knocked down in the adult fly wing, ranging from mild size changes to severe wrinkled wings or lethality. Although a majority of tested homologs showed defects when knocked down specifically in wings or eyes, we found no correlation in the severity of the observed defects in these two tissues. A subset of the homologs showed disruptions in cellular processes in the developing fly wing, including alterations in cell proliferation, apoptosis, and cellular signaling pathways. Furthermore, human CNV genes also showed differences in gene expression patterns and interactions with signaling pathway genes across multiple human tissues. Our findings suggest that genes within CNV disorders affect global developmental processes in both neuronal and non-neuronal tissues.
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Affiliation(s)
- Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Siddharth Karthikeyan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dagny J. Gould
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Avik Sarker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Erika Gedvilaite
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yurika Matsui
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zhi-Chun Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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19
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Zhao B, Pritchard JR. Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration. PLoS Comput Biol 2019; 15:e1007467. [PMID: 31658270 PMCID: PMC6837539 DOI: 10.1371/journal.pcbi.1007467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/21/2019] [Revised: 11/07/2019] [Accepted: 10/08/2019] [Indexed: 01/05/2023] Open
Abstract
The somatic co-evolution of tumors and the cellular immune responses that combat them drives the diversity of immune-tumor interactions. This includes tumor mutations that generate neo-antigenic epitopes that elicit cytotoxic T-cell activity and subsequent pressure to select for genetic loss of antigen presentation. Most studies have focused on how tumor missense mutations can drive tumor immunity, but frameshift mutations have the potential to create far greater antigenic diversity. However, expression of this antigenic diversity is potentially regulated by Nonsense Mediated Decay (NMD) and NMD has been shown to be of variable efficiency in cancers. Here we studied how mutational changes influence global NMD and cytolytic immune responses. Using TCGA datasets, we derived novel patient-level metrics of 'NMD burden' and interrogated how different mutation and most importantly NMD burdens influence cytolytic activity using machine learning models and survival outcomes. We find that NMD is a significant and independent predictor of immune cytolytic activity. Different indications exhibited varying dependence on NMD and mutation burden features. We also observed significant co-alteration of genes in the NMD pathway, with a global increase in NMD efficiency in patients with NMD co-alterations. Finally, NMD burden also stratified patient survival in multivariate regression models in subset of cancer types. Our work suggests that beyond selecting for mutations that elicit NMD in tumor suppressors, tumor evolution may react to the selective pressure generated by inflammation to globally enhance NMD through coordinated amplification and/or mutation.
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Affiliation(s)
- Boyang Zhao
- Department of Biomedical Engineering, College of Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Quantalarity Research Group LLC, Houston, Texas, United States of America
- * E-mail: (BZ); (JRP)
| | - Justin R. Pritchard
- Department of Biomedical Engineering, College of Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (BZ); (JRP)
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