151
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Parker CT, Villafuerte DA, Miller WG, Huynh S, Chapman MH, Hanafy Z, Jackson JH, Miller MA, Kathariou S. Genomic Analysis Points to Multiple Genetic Mechanisms for Non-Transformable Campylobacter jejuni ST-50. Microorganisms 2024; 12:327. [PMID: 38399730 PMCID: PMC10893306 DOI: 10.3390/microorganisms12020327] [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: 01/15/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Campylobacter jejuni and Campylobacter coli are well known for their natural competence, i.e., their capacity for the uptake of naked DNA with subsequent transformation. This study identifies non-transformable C. jejuni and C. coli strains from domestic animals and employs genomic analysis to investigate the strain genotypes and their associated genetic mechanisms. The results reveal genetic associations leading to a non-transformable state, including functional DNase genes from bacteriophages and mutations within the cts-encoded DNA-uptake system, which impact the initial steps of the DNA uptake during natural transformation. Interestingly, all 38 tested C. jejuni ST-50 strains from the United States exhibit a high prevalence of non-transformability, and the strains harbor a variety of these genetic markers. This research emphasizes the role of these genetic markers in hindering the transfer of antimicrobial resistance (AMR) determinants, providing valuable insights into the genetic diversity of Campylobacter. As ST-50 is a major clone of C. jejuni globally, we additionally determined the prevalence of the genetic markers for non-transformability among C. jejuni ST-50 from different regions of the world, revealing distinct patterns of evolution and a strong selective pressure on the loss of competence in ST-50 strains, particularly in the agricultural environment in the United States. Our findings contribute to a comprehensive understanding of genetic exchange mechanisms within Campylobacter strains, and their implications for antimicrobial resistance dissemination and evolutionary pathways within specific lineages.
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Affiliation(s)
- Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - David A. Villafuerte
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Mary H. Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Zahra Hanafy
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - James H. Jackson
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - Morgan A. Miller
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - Sophia Kathariou
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
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152
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Sowders JM, Jewell JB, Tanaka K. CPK28 is a modulator of purinergic signaling in plant growth and defense. Plant J 2024. [PMID: 38308597 DOI: 10.1111/tpj.16656] [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: 07/20/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/05/2024]
Abstract
Extracellular ATP (eATP) is a key signaling molecule that plays a pivotal role in plant growth and defense responses. The receptor P2K1 is responsible for perceiving eATP and initiating its signaling cascade. However, the signal transduction mechanisms downstream of P2K1 activation remain incompletely understood. We conducted a comprehensive analysis of the P2K1 interactome using co-immunoprecipitation-coupled tandem mass spectrometry, leading to the identification of 121 candidate proteins interacting with P2K1. In silico analysis narrowed down the candidates to 47 proteins, including Ca2+ -binding proteins, ion transport-related proteins, and receptor kinases. To investigate their involvement in eATP signaling, we employed a screening strategy based on changes in gene expression in response to eATP in mutants of the identified interactors. This screening revealed several Ca2+ -dependent protein kinases (CPKs) that significantly affected the expression of eATP-responsive genes, suggesting their potential roles in eATP signaling. Notably, CPK28 and CPK6 showed physical interactions with P2K1 both in yeast and plant systems. Calcium influx and gene expression studies demonstrated that CPK28 perturbed eATP-induced Ca2+ mobilization and some early transcriptional responses. Overexpression of CPK28 resulted in an antagonistic physiological response to P2K1-mediated eATP signaling during both plant growth and defense responses to the necrotrophic pathogen Botrytis cinerea. Our findings highlight CPK28, among other CPKs, as a modulator of P2K1-mediated eATP signaling, providing valuable insights into the coordination of eATP signaling in plant growth and immunity.
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Affiliation(s)
- Joel M Sowders
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, Washington, 99164, USA
| | - Jeremy B Jewell
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, 99164, USA
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, Washington, 99164, USA
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153
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Thesma V, Rains GC, Mohammadpour Velni J. Development of a Low-Cost Distributed Computing Pipeline for High-Throughput Cotton Phenotyping. Sensors (Basel) 2024; 24:970. [PMID: 38339687 PMCID: PMC10857260 DOI: 10.3390/s24030970] [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: 12/21/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
In this paper, we present the development of a low-cost distributed computing pipeline for cotton plant phenotyping using Raspberry Pi, Hadoop, and deep learning. Specifically, we use a cluster of several Raspberry Pis in a primary-replica distributed architecture using the Apache Hadoop ecosystem and a pre-trained Tiny-YOLOv4 model for cotton bloom detection from our past work. We feed cotton image data collected from a research field in Tifton, GA, into our cluster's distributed file system for robust file access and distributed, parallel processing. We then submit job requests to our cluster from our client to process cotton image data in a distributed and parallel fashion, from pre-processing to bloom detection and spatio-temporal map creation. Additionally, we present a comparison of our four-node cluster performance with centralized, one-, two-, and three-node clusters. This work is the first to develop a distributed computing pipeline for high-throughput cotton phenotyping in field-based agriculture.
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Affiliation(s)
- Vaishnavi Thesma
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA;
| | - Glen C. Rains
- Department of Entomology, University of Georgia Tifton Campus, Tifton, GA 31793, USA;
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154
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Patrick RM, Huang XQ, Dudareva N, Li Y. Rhythmic histone acetylation acts in concert with day-night oscillation of the floral volatile metabolic network. New Phytol 2024; 241:1829-1839. [PMID: 38058220 DOI: 10.1111/nph.19447] [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: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
The biosynthesis of specialized metabolites is strictly regulated by environmental inputs such as the day-night cycle, but the underlying mechanisms remain elusive. In Petunia hybrida cv. Mitchell flowers, the biosynthesis and emission of volatile compounds display a diurnal pattern with a peak in the evening to attract nocturnal pollinators. Using petunia flowers as a model system, we found that chromatin level regulation, especially histone acetylation, plays an essential role in mediating the day-night oscillation of the biosynthetic gene network of specialized metabolites. By performing time-course chromatin immunoprecipitation assays for histone modifications, we uncovered that a specific group of genes involved in the regulation, biosynthesis, and emission of floral volatile compounds, which displays the greatest magnitude in day-night oscillating gene expression, is associated with highly dynamic histone acetylation marks H3K9ac and H3K27ac. Specifically, the strongest oscillating genes featured a drastic removal of histone acetylation marks at night, potentially to shut down the biosynthesis of floral volatile compounds during the morning when they are not needed. Inhibiting daytime histone acetylation led to a compromised evening induction of these genes. Overall, our study suggested an active role of chromatin modification in the diurnal oscillation of specialized metabolic network.
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Affiliation(s)
- Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xing-Qi Huang
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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155
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Liu L, Ashraf MA, Morrow T, Facette M. Stomatal closure in maize is mediated by subsidiary cells and the PAN2 receptor. New Phytol 2024; 241:1130-1143. [PMID: 37936339 DOI: 10.1111/nph.19379] [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: 05/02/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
Stomata are epidermal pores that facilitate plant gas exchange. Grasses have fast stomatal movements, likely due to their dumbbell-shaped guard cells and lateral subsidiary cells. Subsidiary cells reciprocally exchange water and ions with guard cells. However, the relative contribution of subsidiary cells during stomatal closure is unresolved. We compared stomatal gas exchange and stomatal aperture dynamics in wild-type and pan1, pan2, and pan1;pan2 Zea mays (L.) (maize) mutants, which have varying percentages of aberrantly formed subsidiary cells. Stomata with 1 or 2 defective subsidiary cells cannot close properly, indicating that subsidiary cells are essential for stomatal function. Even though the percentage of aberrant stomata is similar in pan1 and pan2, pan2 showed a more severe defect in stomatal closure. In pan1, only stomata with abnormal subsidiary cells fail to close normally. In pan2, all stomata have stomatal closure defects, indicating that PAN2 has an additional role in stomatal closure. Maize Pan2 is orthologous to Arabidopsis GUARD CELL HYDROGEN PEROXIDE-RESISANT1 (GHR1), which is also required for stomatal closure. PAN2 acts downstream of Ca2+ in maize to promote stomatal closure. This is in contrast to GHR1, which acts upstream of Ca2+ , and suggests the pathways could be differently wired.
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Affiliation(s)
- Le Liu
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - M Arif Ashraf
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Taylor Morrow
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Michelle Facette
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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156
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Pollock HS, Rutt CL, Cooper WJ, Brawn JD, Cheviron ZA, Luther DA. Equivocal support for the climate variability hypothesis within a Neotropical bird assemblage. Ecology 2024; 105:e4206. [PMID: 37950619 DOI: 10.1002/ecy.4206] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/03/2023] [Accepted: 10/05/2023] [Indexed: 11/13/2023]
Abstract
The climate variability hypothesis posits that an organism's exposure to temperature variability determines the breadth of its thermal tolerance and has become an important framework for understanding variation in species' susceptibilities to climate change. For example, ectotherms from more thermally stable environments tend to have narrower thermal tolerances and greater sensitivity to projected climate warming. Among endotherms, however, the relationship between climate variability and thermal physiology is less clear, particularly with regard to microclimate variation-small-scale differences within or between habitats. To address this gap, we explored associations between two sources of temperature variation (habitat type and vertical forest stratum) and (1) thermal physiological traits and (2) temperature sensitivity metrics within a diverse assemblage of Neotropical birds (n = 89 species). We used long-term temperature data to establish that daily temperature regimes in open habitats and forest canopy were both hotter and more variable than those in the forest interior and forest understory, respectively. Despite these differences in temperature regime, however, we found little evidence that species' thermal physiological traits or temperature sensitivity varied in association with either habitat type or vertical stratum. Our findings provide two novel and important insights. First, and in contrast to the supporting empirical evidence from ectotherms, the thermal physiology of birds at our study site appears to be largely decoupled from local temperature variation, providing equivocal support for the climate variability hypothesis in endotherms. Second, we found no evidence that the thermal physiology of understory forest birds differed from that of canopy or open-habitat species-an oft-invoked, yet previously untested, mechanism for why these species are so vulnerable to environmental change.
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Affiliation(s)
- Henry S Pollock
- Department of Natural Resources and Environmental Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Cameron L Rutt
- Department of Biology, George Mason University, Fairfax, Virginia, USA
- American Bird Conservancy, The Plains, Virginia, USA
| | | | - Jeffrey D Brawn
- Department of Natural Resources and Environmental Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - David A Luther
- Department of Biology, George Mason University, Fairfax, Virginia, USA
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157
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Niles MT, McCarthy AC, Malacarne J, Bliss S, Belarmino EH, Laurent J, Merrill SC, Nowak SA, Schattman RE. Home and wild food procurement were associated with improved food security during the COVID-19 pandemic in two rural US states. Sci Rep 2024; 14:2682. [PMID: 38302511 PMCID: PMC10834469 DOI: 10.1038/s41598-024-52320-z] [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: 07/29/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Both food insecurity and home and wild food procurement (HWFP), including gardening, increased in many countries during the COVID-19 pandemic; yet little evidence has demonstrated what impact HWFP had on food security. Using data from a representative sample of nearly 1000 residents in the two most rural US states (Vermont and Maine) conducted via an online survey in Spring/Summer 2021, as well as matching techniques, we compare food security outcomes among households who did and did not participate in HWFP in the first year of the pandemic. Nearly 60% of respondents engaged in HWFP in some way during the first year of the pandemic, with food insecure households more likely to do HWFP. Furthermore, HWFP early in the COVID-19 pandemic is associated with improved food security in the 9-12 months later, though these improvements were primarily associated with newly, not chronically, food insecure households. Newly and chronically food insecure households were more likely to want to continue these activities in the future, but also exhibited greater barriers to land access and costs associated with these activities. These results suggest that HWFP may provide food security improvements for certain households that utilize them, especially during crisis situations. Future research about HWFP should continue to explore multiple HWFP strategies, their barriers, and their potentially myriad relationships to food security, diet, and health outcomes, especially with longitudinal data.
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Affiliation(s)
- Meredith T Niles
- Department of Nutrition and Food Sciences, University of Vermont, 355 Carrigan Wing, 109 Carrigan Drive, Burlington, VT, 05405, USA.
- Gund Institute for Environment, University of Vermont, Burlington, VT, USA.
| | - Ashley C McCarthy
- Department of Nutrition and Food Sciences, University of Vermont, 355 Carrigan Wing, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | | | - Sam Bliss
- Gund Institute for Environment, University of Vermont, Burlington, VT, USA
- Rubenstein School of Natural Resources, University of Vermont, Burlington, VT, USA
| | - Emily H Belarmino
- Department of Nutrition and Food Sciences, University of Vermont, 355 Carrigan Wing, 109 Carrigan Drive, Burlington, VT, 05405, USA
- Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | - Jennifer Laurent
- Department of Nursing, University of Vermont, Burlington, VT, USA
| | - Scott C Merrill
- Gund Institute for Environment, University of Vermont, Burlington, VT, USA
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Sarah A Nowak
- Department of Pathology & Laboratory Medicine, University of Vermont, Burlington, VT, USA
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158
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Kari ZA, Téllez-Isaías G, Khoo MI, Wee W, Kabir MA, Cheadoloh R, Wei LS. Resveratrol impacts on aquatic animals: a review. Fish Physiol Biochem 2024; 50:307-318. [PMID: 38376668 DOI: 10.1007/s10695-024-01319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 02/10/2024] [Indexed: 02/21/2024]
Abstract
Aquaculture has intensified tremendously with the increasing demand for protein sources as the global population grows. However, this industry is plagued with major challenges such as poor growth performance, the lack of a proper environment, and immune system impairment, thus creating stress for the aquaculture species and risking disease outbreaks. Currently, prophylactics such as antibiotics, vaccines, prebiotics, probiotics, and phytobiotics are utilized to minimize the negative impacts of high-density farming. One of the promising prophylactic agents incorporated in fish feed is resveratrol, a commercial phytophenol derived via the methanol extraction method. Recent studies have revealed many beneficial effects of resveratrol in aquatic animals. Therefore, this review discusses and summarizes the roles of resveratrol in improving growth performance, flesh quality, immune system, antioxidant capacity, disease resistance, stress mitigation, and potential combination with other prophylactic agents for aquatic animals.
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Affiliation(s)
- Zulhisyam Abdul Kari
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600, Jeli, Kelantan, Malaysia.
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600, Jeli, Kelantan, Malaysia.
| | | | - Martina Irwan Khoo
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Malaysia
| | - Wendy Wee
- Center of Fundamental and Continuing Education, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | | | - Romalee Cheadoloh
- Faculty of Science Technology and Agriculture, Yala Rajabhat University, 133 Thetsaban 3 Rd, Sateng, Mueang, 95000, Yala Province, Thailand
| | - Lee Seong Wei
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600, Jeli, Kelantan, Malaysia.
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600, Jeli, Kelantan, Malaysia.
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159
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Faske TM, Agneray AC, Jahner JP, Osuna-Mascaró C, Sheta LM, Richardson BA, Leger EA, Parchman TL. Environment predicts the maintenance of reproductive isolation in a mosaic hybrid zone of rubber rabbitbrush. Evolution 2024; 78:300-314. [PMID: 37962379 DOI: 10.1093/evolut/qpad207] [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: 07/31/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Widely distributed plants of western North America experience divergent selection across environmental gradients, have complex histories shaped by biogeographic barriers and distributional shifts and often illustrate continuums of reproductive isolation. Rubber rabbitbrush (Ericameria nauseosa) is a foundational shrub species that occurs across diverse environments of western North America. Its remarkable phenotypic diversity is currently ascribed to two subspecies-Ericameria nauseosa nauseosa and Ericameria nauseosa consimilis-and 22 named varieties. To understand how genetic variation is partitioned across subspecies, varieties, and environments, we used high throughput sequencing of reduced representation libraries. We found clear evidence for divergence between the two subspecies, despite largely sympatric distributions. Numerous locations exhibiting admixed ancestry were not geographically localized but were widely distributed across a mosaic hybrid zone. The occurrence of hybrid and subspecific ancestries was strongly predicted by environmental variables as well as the proximity to major ecotones between ecoregions. Although this repeatability illustrates the importance of environmental factors in shaping reproductive isolation, variability in the prevalence of hybridization also indicates these factors likely differ across ecological contexts. There was mixed evidence for the evolutionary cohesiveness of varieties, but several genetically distinct and narrow endemic varieties exhibited admixed subspecific ancestries, hinting at the possibility for transgressive hybridization to contribute to phenotypic novelty and the colonization of new environments in E. nauseosa.
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Affiliation(s)
- Trevor M Faske
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Alison C Agneray
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
- Bureau of Land Management, Nevada State Office, Reno, NV 89502, United States
| | - Joshua P Jahner
- Department of Botany, University of Wyoming, Laramie, WY, 82071, United States
| | | | - Lana M Sheta
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Bryce A Richardson
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID 83843, United States
| | - Elizabeth A Leger
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
- Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, United States
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160
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Liu S, Lin G, Ramachandran SR, Daza LC, Cruppe G, Tembo B, Singh PK, Cook D, Pedley KF, Valent B. Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. New Phytol 2024; 241:1266-1276. [PMID: 37984076 DOI: 10.1111/nph.19402] [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: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole-genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini-chromosome. Genome assembly of a Zambian strain revealed that its mini-chromosome was similar to the B71 mini-chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome and rapid genomic changes suggest the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Sowmya R Ramachandran
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Lidia Calderon Daza
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Giovana Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Batiseba Tembo
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, 10101, Zambia
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, 56237, Mexico
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Kerry F Pedley
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
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161
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Brehm AM, Mortelliti A. Environmental heterogeneity modifies the link between personality and survival in fluctuating small mammal populations. J Anim Ecol 2024; 93:196-207. [PMID: 38102795 DOI: 10.1111/1365-2656.14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
Despite numerous studies examining the fitness consequences of animal personalities, predictions concerning the relationship between personality and survival are not consistent with empirical observations. Theory predicts that individuals who are risky (i.e. bold, active and aggressive) should have higher rates of mortality; however, empirical evidence shows high levels of variation in behaviour-survival relationships in wild populations. We suggest that this mismatch between predictions under theory and empirical observations results from environmental contingencies that drive heterogeneity in selection. This uncertainty may constrain any universal directional relationships between personality traits and survival. Specifically, we hypothesize that spatiotemporal fluctuations in perceived risk that arise from variability in refuge abundance and competitor density alter the relationship between personality traits and survival. In a large-scale manipulative experiment, we trapped four small mammal species in five subsequent years across six forest stands treated with different management practices in Maine, United States. Stands all occur within the same experimental forest but contain varying amounts of refuge and small mammal densities fluctuate over time and space. We quantified the effects of habitat structure and competitor density on the relationship between personality traits and survival to assess whether directional relationships differed depending on environmental contingencies. In the two most abundant species, deer mice and southern red-backed voles, risky behaviours (i.e. higher aggression and boldness) predicted apparent monthly survival probability. Mice that were more aggressive (less docile) had higher survival. Voles that were bolder (less timid) had higher survival, but in the risky forest stands only. Additionally, traits associated with stress coping and de-arousal increased survival probability in both species at high small mammal density but decreased survival at low density. In the two less abundant study species, there was no evidence for an effect of personality traits on survival. Our field experiment provides partial support for our hypothesis: that spatiotemporal fluctuations in refuge abundance and competitor density alter the relationship between personality traits and survival. Our findings also suggest that behaviours associated with stress coping and de-arousal may be subject to density-dependent selection and should be further assessed and incorporated into theory.
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Affiliation(s)
- Allison M Brehm
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, Maine, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alessio Mortelliti
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, Maine, USA
- Department of Life Sciences, University of Trieste, Trieste, Italy
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162
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Yeh DA, Dai B, Gómez MI, Walton VM. Does monitoring pests pay off? a bioeconomic assessment of Drosophila suzukii controls. Pest Manag Sci 2024; 80:708-723. [PMID: 37770414 DOI: 10.1002/ps.7801] [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: 05/16/2023] [Revised: 08/26/2023] [Accepted: 09/29/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Drosophila suzukii is a significant invasive pest that has caused high management costs and economic losses for blueberry growers in the United States. The status quo control strategy commonly used by growers is to apply pesticides proactively and frequently to reduce infestation. Recent studies have shown that the calendar-based spraying strategy might be unsustainable in the long term, making the reduction of pesticide reliance a top priority for the berry industry. Incorporating pest monitoring into the control strategy could be an option to improve efficiency while reducing pesticide usage. This study assesses the economic implications of monitoring-based control strategies compared to calendar-based spraying control strategies for organic blueberry production in Oregon. We combine a D. suzukii population model into the economic simulation framework, evaluate two monitoring methods (adult trapping and fruit sampling), and identify the profit-maximizing control strategy under different scenarios. RESULTS In the baseline scenario, control strategies that incorporate fruit sampling exhibit the highest average profits. Although the status quo control strategy (spraying every 3 days) generates higher average revenue than monitoring-based strategies, the cost from the higher number of pesticide application offsets the returns. CONCLUSION This study uses a novel bioeconomic simulation framework to show that incorporating fruit sampling can be a promising tool to reduce pesticide reliance while controlling D. suzukii infestation. These findings provide clearer information on the economic viability of using monitoring-based pest control strategies in organic berry production, and the assessment framework sheds light on the economics of pest management. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- D Adeline Yeh
- U.S. Department of Agriculture, Economic Research Service, Kansas City, Missouri, USA
| | - Bingyan Dai
- Charles H. Dyson School of Applied Economics and Management, Cornell University, Ithaca, New York, USA
| | - Miguel I Gómez
- Charles H. Dyson School of Applied Economics and Management, Cornell University, Ithaca, New York, USA
| | - Vaughn M Walton
- Department of Horticulture, Oregon State University, Corvallis, Oregon, USA
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163
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Mishra S, Moar W, Jurat-Fuentes JL. Larvae of Colorado potato beetle (Leptinotarsa decemlineata Say) resistant to double-stranded RNA (dsRNA) remain susceptible to small-molecule pesticides. Pest Manag Sci 2024; 80:905-909. [PMID: 37822012 DOI: 10.1002/ps.7825] [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: 08/22/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Implementation of resistance management tools is crucial for the continued efficacy of insect control technologies. An important aspect of insect resistance management (IRM) is the combined or sequential use of different modes-of-action to reduce selection pressure and delay evolution of resistance. This is especially important for insect pests with established ability to develop resistance to insecticides, such as the Colorado potato beetle (Leptinotarsa decemlineata, CPB). A new class of insecticides, based on double-stranded RNA (dsRNA) activating the gene silencing RNA-interference (RNAi) pathway, are currently under review for regulatory approval and commercial use in the USA against CPB. However, there is no information available on the potential for cross-resistance between RNAi insecticides and other classes of insecticides used against CPB. Herein, we aim to fill this knowledge gap by capitalizing on the availability of a CPB strain highly resistant to dsRNAs and test its susceptibility to diverse small-molecule insecticide classes compared to reference dsRNA-susceptible CPB strains. RESULTS Differences in activity were observed among the four insecticides tested, with abamectin demonstrating highest activity against all three strains of CPB. However, no differences were observed among the dsRNA-resistant and susceptible CPB strains for any of the tested compounds. Overall, these results demonstrate lack of cross-resistance to commonly used chemical insecticides in the dsRNA-resistant strain of CPB. CONCLUSION These data support the use of these different insecticide classes along with RNAi-based insecticides as part of an effective insect resistance management framework aimed at delaying resistance in CPB. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Swati Mishra
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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164
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Gerber BD, Devarajan K, Farris ZJ, Fidino M. A model-based hypothesis framework to define and estimate the diel niche via the 'Diel.Niche' R package. J Anim Ecol 2024; 93:132-146. [PMID: 38213300 DOI: 10.1111/1365-2656.14035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024]
Abstract
How animals use the diel period (24-h light-dark cycle) is of fundamental importance to understand their niche. While ecological and evolutionary literature abound with discussion of diel phenotypes (e.g. diurnal, nocturnal, crepuscular, cathemeral), they lack clear and explicit quantitative definitions. As such, inference can be confounded when evaluating hypotheses of animal diel niche switching or plasticity across studies because researchers may be operating under different definitions of diel phenotypes. We propose quantitative definitions of diel phenotypes using four alternative hypothesis sets (maximizing, traditional, general and selection) aimed at achieving different objectives. Each hypothesis set is composed of mutually exclusive hypotheses defined based on the activity probabilities in the three fundamental periods of light availability (twilight, daytime and night-time). We develop a Bayesian modelling framework that compares diel phenotype hypotheses using Bayes factors and estimates model parameters using a multinomial model with linear inequality constraints. Model comparison, parameter estimation and visualizing results can be done in the Diel.Niche R package. A simplified R Shiny web application is also available. We provide extensive simulation results to guide researchers on the power to discriminate among hypotheses for a range of sample sizes (10-1280). We also work through several examples of using data to make inferences on diel activity, and include online vignettes on how to use the Diel.Niche package. We demonstrate how our modelling framework complements other analyses, such as circular kernel density estimators and animal movement modelling. Our aim is to encourage standardization of the language of diel activity and bridge conceptual frameworks and hypotheses in diel research with data and models. Lastly, we hope more research focuses on the ecological and conservation importance of understanding how animals use diel time.
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Affiliation(s)
- Brian D Gerber
- Department of Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
| | - Kadambari Devarajan
- Department of Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
| | - Zach J Farris
- Department of Public Health and Exercise Science, Appalachian State University, Boone, North Carolina, USA
| | - Mason Fidino
- Conservation & Science Department, Lincoln Park Zoo, Chicago, Illinois, USA
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165
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Smith BL, Fernando S, King MD. Escherichia coli resistance mechanism AcrAB-TolC efflux pump interactions with commonly used antibiotics: a molecular dynamics study. Sci Rep 2024; 14:2742. [PMID: 38302495 PMCID: PMC10834472 DOI: 10.1038/s41598-024-52536-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
While antibiotic resistance poses a threat from both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB), GNB pose a more imminent public health hazard globally. GNB are a threat to growing antibiotic resistance because of the complex makeup of the membrane. The AcrAB-TolC efflux pump is a known resistance mechanism of Escherichia coli (E. coli) cells. This study utilized molecular dynamics modeling to visualize some of the changes occurring at a molecular level when airborne bacteria are exposed to stress and antibiotics. This study was conducted to build upon previous experimental research showing that there is an increase in antibiotic resistance and efflux pump activity when exposed to aerosolization. AcrB and AcrAB-TolC proteins were simulated under standard and increased pressure to compare the effect of aerosolization on the binding to the three different antibiotics (puromycin (PUY), ampicillin (AMP) and sulfamethoxazole-trimethoprim (SXT)) to the AcrB binding site. Analysis such as root-mean-square deviation of atomic positions and root-mean-square fluctuation, the opening of TolC, and the significant molecular mechanics with generalized Born and surface area solvation (MM-GBSA) scores associated with specific ligands were recorded. Resistance in experimental data indicated a relationship between the docking scores and some ligand-protein interactions. Results showed that there was more flexibility in the proteins within simulations conducted under standard pressure for the AcrB protein and the full tripartite complex AcrAB-TolC, showing that increased pressure causes more rigidity. MM-GBSA scores, used to calculate the free energy of ligand-protein binding, did not show a significant change, but interestingly, the strongest MM-GBSA scores were for ligands that moved to another binding pocket and did not result in resistance or opening of the efflux pump. However, the ligand moved from the binding site and did not cause the opening of TolC to increase significantly, whereas PUY and AMP were bound to the binding site for the duration of all simulations. AMP ligands under increased pressure showed the largest change in opening of the TolC efflux pump and aligns with experimental data showing E. coli cells had the most resistance to AMP after aerosolization. These results, in addition to other real-time changes such as OM proteins and mutations of targets within the cell, could be used to delineate and mitigate antibiotic resistance mechanisms.
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Affiliation(s)
- Brooke L Smith
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA
| | - Sandun Fernando
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA
| | - Maria D King
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA.
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166
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Cardenas M, Seibert B, Cowan B, Fraiha ALS, Carnaccini S, Gay LC, Faccin FC, Caceres CJ, Anderson TK, Vincent Baker AL, Perez DR, Rajao DS. Amino acid 138 in the HA of a H3N2 subtype influenza A virus increases affinity for the lower respiratory tract and alveolar macrophages in pigs. PLoS Pathog 2024; 20:e1012026. [PMID: 38377132 PMCID: PMC10906893 DOI: 10.1371/journal.ppat.1012026] [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: 10/31/2023] [Revised: 03/01/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Influenza A virus (FLUAV) infects a wide range of hosts and human-to-swine spillover events are frequently reported. However, only a few of these human viruses have become established in pigs and the host barriers and molecular mechanisms driving adaptation to the swine host remain poorly understood. We previously found that infection of pigs with a 2:6 reassortant virus (hVIC/11) containing the hemagglutinin (HA) and neuraminidase (NA) gene segments from the human strain A/Victoria/361/2011 (H3N2) and internal gene segments of an endemic swine strain (sOH/04) resulted in a fixed amino acid substitution in the HA (A138S, mature H3 HA numbering). In silico analysis revealed that S138 became predominant among swine H3N2 virus sequences deposited in public databases, while 138A predominates in human isolates. To understand the role of the HA A138S substitution in the adaptation of a human-origin FLUAV HA to swine, we infected pigs with the hVIC/11A138S mutant and analyzed pathogenesis and transmission compared to hVIC/11 and sOH/04. Our results showed that the hVIC/11A138S virus had an intermediary pathogenesis between hVIC/11 and sOH/04. The hVIC/11A138S infected the upper respiratory tract, right caudal, and both cranial lobes while hVIC/11 was only detected in nose and trachea samples. Viruses induced a distinct expression pattern of various pro-inflammatory cytokines such as IL-8, TNF-α, and IFN-β. Flow cytometric analysis of lung samples revealed a significant reduction of porcine alveolar macrophages (PAMs) in hVIC/11A138S-infected pigs compared to hVIC/11 while a MHCIIlowCD163neg population was increased. The hVIC/11A138S showed a higher affinity for PAMs than hVIC/11, noted as an increase of infected PAMs in bronchoalveolar lavage fluid (BALF), and showed no differences in the percentage of HA-positive PAMs compared to sOH/04. This increased infection of PAMs led to an increase of granulocyte-monocyte colony-stimulating factor (GM-CSF) stimulation but a reduced expression of peroxisome proliferator-activated receptor gamma (PPARγ) in the sOH/04-infected group. Analysis using the PAM cell line 3D4/21 revealed that the A138S substitution improved replication and apoptosis induction in this cell type compared to hVIC/11 but at lower levels than sOH/04. Overall, our study indicates that adaptation of human viruses to the swine host involves an increased affinity for the lower respiratory tract and alveolar macrophages.
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Affiliation(s)
- Matias Cardenas
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Brianna Cowan
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Ana Luiza S. Fraiha
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Flavio Cargnin Faccin
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - C. Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Amy L. Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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167
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Mercado-Reyes JA, Pereira TS, Manandhar A, Rimer IM, McAdam SAM. Extreme drought can deactivate ABA biosynthesis in embolism-resistant species. Plant Cell Environ 2024; 47:497-510. [PMID: 37905689 DOI: 10.1111/pce.14754] [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: 03/25/2022] [Revised: 08/24/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
The phytohormone abscisic acid (ABA) is synthesised by plants during drought to close stomata and regulate desiccation tolerance pathways. Conifers and some angiosperms with embolism-resistant xylem show a peaking-type (p-type) response in ABA levels, in which ABA levels increase early in drought then decrease as drought progresses, declining to pre-stressed levels. The mechanism behind this dynamic remains unknown. Here, we sought to characterise the mechanism driving p-type ABA dynamics in the conifer Callitris rhomboidea and the highly drought-resistant angiosperm Umbellularia californica. We measured leaf water potentials (Ψl ), stomatal conductance, ABA, conjugates and phaseic acid (PA) levels in potted plants during a prolonged but non-fatal drought. Both species displayed a p-type ABA dynamic during prolonged drought. In branches collected before and after the peak in endogenous ABA levels in planta, that were rehydrated overnight and then bench dried, ABA biosynthesis was deactivated beyond leaf turgor loss point. Considerable conversion of ABA to conjugates was found to occur during drought, but not catabolism to PA. The mechanism driving the decline in ABA levels in p-type species may be conserved across embolism-resistant seed plants and is mediated by sustained conjugation of ABA and the deactivation of ABA accumulation as Ψl becomes more negative than turgor loss.
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Affiliation(s)
- Joel A Mercado-Reyes
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Talitha Soares Pereira
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Anju Manandhar
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Ian M Rimer
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
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168
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Davis E, Caparco AA, Steinmetz NF, Pokorski JK. Poly(Oxanorbornene)-Protein Conjugates Prepared by Grafting-to ROMP as Alternatives for PEG. Macromol Biosci 2024; 24:e2300255. [PMID: 37688508 DOI: 10.1002/mabi.202300255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/14/2023] [Indexed: 09/11/2023]
Abstract
PEGylation is the gold standard in protein-polymer conjugation, improving circulation half-life of biologics while mitigating the immune response to a foreign substance. However, preexisting anti-PEG antibodies in healthy humans are becoming increasingly prevalent and elicitation of anti-PEG antibodies when patients are administered with PEGylated therapeutics challenges their safety profile. In the current study, two distinct amine-reactive poly(oxanorbornene) (PONB) imide-based water-soluble block co-polymers are synthesized using ring-opening metathesis polymerization (ROMP). The synthesized block-copolymers include PEG-based PONB-PEG and sulfobetaine-based PONB-Zwit. The polymers are then covalently conjugated to amine residues of lysozyme (Lyz) and urate oxidase (UO) using a grafting-to bioconjugation technique. Both Lyz-PONB and UO-PONB conjugates retained significant bioactivities after bioconjugation. Immune recognition studies of UO-PONB conjugates indicated a comparable lowering of protein immunogenicity when compared to PEGylated UO. PEG-specific immune recognition is negligible for UO-PONB-Zwit conjugates, as expected. These polymers provide a new alternative for PEG-based systems that retain high levels of activity for the biologic while showing improved immune recognition profiles.
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Affiliation(s)
- Elizabathe Davis
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, 92093, USA
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169
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Khan M, Chen XXL, Dias M, Santos JR, Kour S, You J, van Bruggen R, Youssef MMM, Wan YW, Liu Z, Rosenfeld JA, Tan Q, Pandey UB, Yalamanchili HK, Park J. MATR3 pathogenic variants differentially impair its cryptic splicing repression function. FEBS Lett 2024; 598:415-436. [PMID: 38320753 DOI: 10.1002/1873-3468.14806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated variants impact this function. We show that loss of MATR3 leads to cryptic exon inclusion in many transcripts. We reveal that ALS-linked S85C pathogenic variant reduces MATR3 solubility but does not impair RNA binding. In parallel, we report a novel neurodevelopmental disease-associated M548T variant, located in the RRM2 domain, which reduces protein solubility and impairs RNA binding and cryptic splicing repression functions of MATR3. Altogether, our research identifies cryptic events within functional genes and demonstrates how disease-associated variants impact MATR3 cryptic splicing repression function.
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Affiliation(s)
- Mashiat Khan
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Xiao Xiao Lily Chen
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Michelle Dias
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jhune Rizsan Santos
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Justin You
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Rebekah van Bruggen
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Mohieldin M M Youssef
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Qiumin Tan
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeehye Park
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
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170
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Avidor-Reiss T. Renaissance in sperm cytoplasmic contribution to infertility. J Assist Reprod Genet 2024; 41:293-296. [PMID: 37955781 PMCID: PMC10894777 DOI: 10.1007/s10815-023-02987-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Tomer Avidor-Reiss
- Department of Biological Sciences, College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH, 43607, USA.
- Department of Urology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, 43607, USA.
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171
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Cox RB, Lin H, Larzelere RE, Bao J. Fear of Deportation and Hispanic Early Adolescent Substance Use: a Moderated Mediation Model of Stress and Hope. Prev Sci 2024; 25:318-329. [PMID: 37976009 PMCID: PMC10891215 DOI: 10.1007/s11121-023-01593-3] [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] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
Reports of deportation can create a state of chronic fear in children living in mixed-status immigrant families over their own or a loved one's potential deportation. One indicator of health disparities among youth is elevated rates of alcohol, tobacco, and other drug use (ATOD). Yet little is known about the effects of fear of deportation (FOD) on ATOD or what might promote resilience. We explore the associations between FOD and ATOD use, how stress mediates this relationship, and whether hope moderates the mediated pathway from FOD to ATOD. Participants were 200 first- and second-generation 7th grade Hispanic youth (49% female) assessed across three waves of data. A moderated mediation model tested the indirect effect of FOD on ATOD through stress and whether hope moderated these associations. FOD was measured by the Family Fear of Deportation Scale. Snyder's Children's Hope Scale measured hope. Stress was measured by a short version of Pediatric Psychological Stress Measure. ATOD was adapted from the Monitoring the Future project. FOD was not directly associated with ATOD use. However, this path was fully mediated by stress. Hope significantly moderated the path from FOD to stress such that a one unit increase in hope completely offset the effects of FOD on stress. Hope did not moderate the path from stress to ATOD use. Interventions that increase awareness of deportation trauma, alleviate stress, and promote hope may help prevent, delay initiation into, and/or decrease ATOD among Hispanic first- and second-generation youth.
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Affiliation(s)
- Ronald B Cox
- Institute for Public Health Practice, Research and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA.
| | - Hua Lin
- Institute for Public Health Practice, Research and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Robert E Larzelere
- Institute for Public Health Practice, Research and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Juan Bao
- Public Policy Center, University of Iowa, Iowa City, USA
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172
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Brainard SH, Sanders DM, Bruna T, Shu S, Dawson JC. The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus. Plant Biotechnol J 2024; 22:472-483. [PMID: 37870930 PMCID: PMC10826982 DOI: 10.1111/pbi.14199] [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: 05/08/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions 'Rush' and 'Winkler'. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for 'Rush' and 'Winkler', respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. 'Rush' has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.
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Affiliation(s)
- Scott H. Brainard
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Dean M. Sanders
- University of Wisconsin Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Tomas Bruna
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Julie C. Dawson
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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173
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Dzakovich MP, Goggans ML, Thomas-Ahner JM, Moran NE, Clinton SK, Francis DM, Cooperstone JL. Transcriptomics and Metabolomics Reveal Tomato Consumption Alters Hepatic Xenobiotic Metabolism and Induces Steroidal Alkaloid Metabolite Accumulation in Mice. Mol Nutr Food Res 2024; 68:e2300239. [PMID: 38212250 DOI: 10.1002/mnfr.202300239] [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: 04/18/2023] [Revised: 10/18/2023] [Indexed: 01/13/2024]
Abstract
SCOPE Tomato consumption is associated with many health benefits including lowered risk for developing certain cancers. It is hypothesized that tomato phytochemicals are transported to the liver and other tissues where they alter gene expression in ways that lead to favorable health outcomes. However, the effects of tomato consumption on mammalian liver gene expression and chemical profile are not well defined. METHODS AND RESULTS The study hypothesizes that tomato consumption would alter mouse liver transcriptomes and metabolomes compared to a control diet. C57BL/6J mice (n = 11-12/group) are fed a macronutrient matched diet containing either 10% red tomato, 10% tangerine tomato, or no tomato powder for 6 weeks after weaning. RNA-Seq followed by gene set enrichment analyses indicates that tomato type and consumption, in general, altered expression of phase I and II xenobiotic metabolism genes. Untargeted metabolomics experiments reveal distinct clustering between control and tomato fed animals. Nineteen molecular formulas (representing 75 chemical features) are identified or tentatively identified as steroidal alkaloids and isomers of their phase I and II metabolites; many of which are reported for the first time in mammals. CONCLUSION These data together suggest tomato consumption may impart benefits partly through enhancing detoxification potential.
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Affiliation(s)
- Michael P Dzakovich
- Department of Horticulture and Crop Science, The Ohio State University, 2001 Fyffe Court, Columbus, OH, 43210, USA
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Ave., Houston, TX, 77030, USA
| | - Mallory L Goggans
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Court, Columbus, OH, 43210, USA
| | - Jennifer M Thomas-Ahner
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Nancy E Moran
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Ave., Houston, TX, 77030, USA
| | - Steven K Clinton
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - David M Francis
- Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Ave, Wooster, OH, 44691, USA
| | - Jessica L Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, 2001 Fyffe Court, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Court, Columbus, OH, 43210, USA
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174
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Chapagain S, Pruthi R, Singh L, Subudhi PK. Comparison of the genetic basis of salt tolerance at germination, seedling, and reproductive stages in an introgression line population of rice. Mol Biol Rep 2024; 51:252. [PMID: 38302786 DOI: 10.1007/s11033-023-09049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/02/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Salinity is a major limitation for rice farming due to climate change. Since salt stress adversely impact rice plants at germination, seedling, and reproductive stages resulting in poor crop establishment and reduced grain yield, enhancing salt tolerance at these vulnerable growth stages will enhance rice productivity in salinity prone areas. METHODS AND RESULTS An introgression line (ILs) population from a cross between a high yielding cultivar 'Cheniere' and a salt tolerant donor 'TCCP' was evaluated to map quantitative trait loci (QTLs) for traits associated with salt tolerance at germination, seedling, and reproductive stages. Using a genotyping-by-sequencing based high density SNP linkage map, a total of 7, 16, and 30 QTLs were identified for five germination traits, seven seedling traits, and ten reproductive traits, respectively. There was overlapping of QTLs for some traits at different stages indicating the pleiotropic effects of these QTLs or clustering of linked genes. Candidate genes identified for salt tolerance were OsSDIR1 and SERF for the seedling stage, WRKY55 and OsUBC for the reproductive stage, and MYB family transcription factors for all three stages. Gene ontology analysis revealed significant GO terms related to nucleotide binding, protein binding, protein kinase activity, antiporter activity, active transmembrane transporter activity, calcium-binding protein, and F- box protein interaction domain containing protein. CONCLUSIONS The colocalized QTLs for traits at different growth stages would be helpful to improve multiple traits simultaneously using marker-assisted selection. The salt tolerant ILs have the potential to be released as varieties or as pre-breeding lines for developing salt tolerant rice varieties.
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Affiliation(s)
- Sandeep Chapagain
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Lovepreet Singh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Prasant K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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175
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Hooe SL, Smith AD, Dean SN, Breger JC, Ellis GA, Medintz IL. Multienzymatic Cascades and Nanomaterial Scaffolding-A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products. Adv Mater 2024; 36:e2309963. [PMID: 37944537 DOI: 10.1002/adma.202309963] [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: 09/25/2023] [Revised: 10/25/2023] [Indexed: 11/12/2023]
Abstract
Synthetic biology is touted as the next industrial revolution as it promises access to greener biocatalytic syntheses to replace many industrial organic chemistries. Here, it is shown to what synthetic biology can offer in the form of multienzyme cascades for the synthesis of the most basic of new materials-chemicals, including especially designer chemical products and their analogs. Since achieving this is predicated on dramatically expanding the chemical space that enzymes access, such chemistry will probably be undertaken in cell-free or minimalist formats to overcome the inherent toxicity of non-natural substrates to living cells. Laying out relevant aspects that need to be considered in the design of multi-enzymatic cascades for these purposes is begun. Representative multienzymatic cascades are critically reviewed, which have been specifically developed for the synthesis of compounds that have either been made only by traditional organic synthesis along with those cascades utilized for novel compound syntheses. Lastly, an overview of strategies that look toward exploiting bio/nanomaterials for accessing channeling and other nanoscale materials phenomena in vitro to direct novel enzymatic biosynthesis and improve catalytic efficiency is provided. Finally, a perspective on what is needed for this field to develop in the short and long term is presented.
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Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, Washington, DC, 20001, USA
| | - Aaron D Smith
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Scott N Dean
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
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176
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Chicowski AS, Bredow M, Utiyama AS, Marcelino‐Guimarães FC, Whitham SA. Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. Plant Biotechnol J 2024; 22:296-315. [PMID: 37883664 PMCID: PMC10826999 DOI: 10.1111/pbi.14206] [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: 07/06/2023] [Revised: 09/19/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023]
Abstract
Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.
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Affiliation(s)
- Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Alice Satiko Utiyama
- Brazilian Agricultural Research Corporation – National Soybean Research Center (Embrapa Soja)LondrinaParanáBrazil
- Department of AgronomyFederal University of ViçosaViçosaMinas GeraisBrazil
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
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177
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Chen LD, Caprio MA, Chen DM, Kouba AJ, Kouba CK. Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians. PLoS Comput Biol 2024; 20:e1011876. [PMID: 38354202 PMCID: PMC10898777 DOI: 10.1371/journal.pcbi.1011876] [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: 04/11/2023] [Revised: 02/27/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Near infrared spectroscopy coupled with predictive modeling is a growing field of study for addressing questions in wildlife science aimed at improving management strategies and conservation outcomes for managed and threatened fauna. To date, the majority of spectroscopic studies in wildlife and fisheries applied chemometrics and predictive modeling with a single-algorithm approach. By contrast, multi-model approaches are used routinely for analyzing spectroscopic datasets across many major industries (e.g., medicine, agriculture) to maximize predictive outcomes for real-world applications. In this study, we conducted a benchmark modeling exercise to compare the performance of several machine learning algorithms in a multi-class problem utilizing a multivariate spectroscopic dataset obtained from live animals. Spectra obtained from live individuals representing eleven amphibian species were classified according to taxonomic designation. Seven modeling techniques were applied to generate prediction models, which varied significantly (p < 0.05) with regard to mean classification accuracy (e.g., support vector machine: 95.8 ± 0.8% vs. K-nearest neighbors: 89.3 ± 1.0%). Through the use of a multi-algorithm approach, candidate algorithms can be identified and applied to more effectively model complex spectroscopic data collected for wildlife sciences. Other key considerations in the predictive modeling workflow that serve to optimize spectroscopic model performance (e.g., variable selection and cross-validation procedures) are also discussed.
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Affiliation(s)
- Li-Dunn Chen
- Department of Biochemistry, Molecular Biology, Entomology, & Plant Pathology, Mississippi State University, Mississippi, United States of America
| | - Michael A. Caprio
- Department of Biochemistry, Molecular Biology, Entomology, & Plant Pathology, Mississippi State University, Mississippi, United States of America
| | - Devin M. Chen
- Department of Wildlife, Fisheries, & Aquaculture, Mississippi State University, Mississippi, United States of America
| | - Andrew J. Kouba
- Department of Wildlife, Fisheries, & Aquaculture, Mississippi State University, Mississippi, United States of America
| | - Carrie K. Kouba
- Department of Biochemistry, Molecular Biology, Entomology, & Plant Pathology, Mississippi State University, Mississippi, United States of America
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178
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Shanahan M, Simone-Finstrom M, Tokarz P, Rinkevich F, Read QD, Spivak M. Thinking inside the box: Restoring the propolis envelope facilitates honey bee social immunity. PLoS One 2024; 19:e0291744. [PMID: 38295039 PMCID: PMC10830010 DOI: 10.1371/journal.pone.0291744] [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: 04/06/2023] [Accepted: 09/05/2023] [Indexed: 02/02/2024] Open
Abstract
When wild honey bee colonies (Apis mellifera) nest in hollow tree cavities, they coat the rough cavity walls with a continuous layer of propolis, a substance comprised primarily of plant resins. Studies have shown that the resulting "propolis envelope" leads to both individual- and colony-level health benefits. Unfortunately, the smooth wooden boxes most commonly used in beekeeping do little to stimulate propolis collection. As a result, most managed bees live in hives that are propolis-poor. In this study, we assessed different surface texture treatments (rough wood boxes, boxes outfitted with propolis traps, and standard, smooth wood boxes) in terms of their ability to stimulate propolis collection, and we examined the effect of propolis on colony health, pathogen loads, immune gene expression, bacterial gene expression, survivorship, and honey production in both stationary and migratory beekeeping contexts. We found that rough wood boxes are the most effective box type for stimulating propolis deposition. Although the use of rough wood boxes did not improve colony survivorship overall, Melissococcus plutonius detections via gene expression were significantly lower in rough wood boxes, and viral loads for multiple viruses tended to decrease as propolis deposition increased. By the end of year one, honey bee populations in migratory rough box colonies were also significantly larger than those in migratory control colonies. The use of rough wood boxes did correspond with decreased honey production in year one migratory colonies but had no effect during year two. Finally, in both stationary and migratory operations, propolis deposition was correlated with a seasonal decrease and/or stabilization in the expression of multiple immune and bacterial genes, suggesting that propolis-rich environments contribute to hive homeostasis. These findings provide support for the practical implementation of rough box hives as a means to enhance propolis collection and colony health in multiple beekeeping contexts.
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Affiliation(s)
- Maggie Shanahan
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael Simone-Finstrom
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Baton Rouge, Louisiana, United States of America
| | - Philip Tokarz
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Baton Rouge, Louisiana, United States of America
| | - Frank Rinkevich
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Baton Rouge, Louisiana, United States of America
| | - Quentin D. Read
- United States Department of Agriculture—Agricultural Research Service Southeast Area, Raleigh, North Carolina, United States of America
| | - Marla Spivak
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
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179
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Keremane M, Singh K, Ramadugu C, Krueger RR, Skaggs TH. Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange. Plants (Basel) 2024; 13:411. [PMID: 38337944 PMCID: PMC10856814 DOI: 10.3390/plants13030411] [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: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the "fatal yellows" disease.
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Affiliation(s)
- Manjunath Keremane
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Khushwant Singh
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Robert R. Krueger
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Todd H. Skaggs
- USDA ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA;
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180
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Allen PE, Miller CW. Inbreeding depression in a sexually selected weapon and the homologue in females. J Evol Biol 2024; 37:28-36. [PMID: 38285664 DOI: 10.1093/jeb/voad011] [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: 04/21/2021] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/31/2024]
Abstract
Theory predicts that traits with heightened condition dependence, such as sexually selected traits, should be affected by inbreeding to a greater degree than other traits. The presence of environmental stress may compound the negative consequences of inbreeding depression. In this study, we examined inbreeding depression across multiple traits and whether it increased with a known form of environmental stress. We conducted our experiment using both sexes of the sexually dimorphic leaf-footed cactus bug, Narnia femorata (Hemiptera: Coreidae). Adult male cactus bugs have enlarged hind legs used as weapons in male-male contests; these traits, and their homologue in females, have been previously found to exhibit high condition dependence. In this study, we employed a small developmental group size as an environmental stress challenge. Nymph N. femorata aggregate throughout their juvenile stages, and previous work has shown the negative effects of small group size on survivorship and body size. We found evidence of inbreeding depression for survival and seven of the eight morphological traits measured in both sexes. Inbreeding depression was higher for the size of the male weapon and the female homolog. Additionally, small developmental group size negatively affected survival to adulthood. However, small group size did not magnify the effects of inbreeding on morphological traits. These findings support the hypothesis that traits with heightened condition dependence exhibit higher levels of inbreeding depression.
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Affiliation(s)
- Pablo E Allen
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States
| | - Christine W Miller
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States
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181
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Zaccaron AZ, Stergiopoulos I. Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes. BMC Biol 2024; 22:25. [PMID: 38281938 PMCID: PMC10823647 DOI: 10.1186/s12915-024-01818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes. RESULTS Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum. CONCLUSIONS Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA.
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Gallagher K, Bernstein I, Collings C, Main D, Ahmad G, Naughton S, Daddam J, Mavangira V, Vandehaar M, Zhou Z. Abomasal infusion of branched-chain amino acids or branched-chain keto-acids alter lactation performance and liver triglycerides in fresh cows. J Anim Sci Biotechnol 2024; 15:13. [PMID: 38281954 PMCID: PMC10823655 DOI: 10.1186/s40104-023-00973-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Dairy cows are at high risk of fatty liver disease in early lactation, but current preventative measures are not always effective. Cows with fatty liver have lower circulating branched-chain amino acid (BCAA) concentrations whereas cows with high circulating BCAA levels have low liver triglyceride (TG). Our objective was to determine the impact of BCAA and their corresponding ketoacids (branched-chain ketoacids, BCKA) on production performance and liver TG accumulation in Holstein cows in the first 3 weeks postpartum. METHODS Thirty-six multiparous Holstein cows were used in a randomized block design experiment. Cows were abomasally infused for the first 21 d postpartum with solutions of 1) saline (CON, n = 12); 2) BCA (67 g valine, 50 g leucine, and 34 g isoleucine, n = 12); and 3) BCK (77 g 2-ketovaline calcium salt, 57 g 2-ketoleucine calcium salt, and 39 g 2-ketoisoleucine calcium salt, n = 12). All cows received the same diet. Treatment effects were determined using PROC GLIMMIX in SAS. RESULTS No differences were detected for body weight, body condition score, or dry matter intake averaged over the first 21 d postpartum. Cows receiving BCK had significantly lower liver TG concentrations compared to CON (6.60% vs. 4.77%, standard error of the mean (SEM) 0.49) during the first 3 weeks of lactation. Infusion of BCA increased milk yield (39.5 vs. 35.3 kg/d, SEM 1.8), milk fat yield (2.10 vs. 1.69 kg/d, SEM 0.08), and lactose yield (2.11 vs. 1.67 kg/d, SEM 0.07) compared with CON. Compared to CON, cows receiving BCA had lower plasma glucose (55.0 vs. 59.2 mg/dL, SEM 0.86) but higher β-hydroxybutyrate (9.17 vs. 6.00 mg/dL, SEM 0.80). CONCLUSIONS Overall, BCAA supplementation in this study improved milk production, whereas BCKA supplementation reduced TG accumulation in the liver of fresh cows.
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Affiliation(s)
- Kristen Gallagher
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Isabelle Bernstein
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Cynthia Collings
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - David Main
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Ghayyoor Ahmad
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Sarah Naughton
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Jayasimha Daddam
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Vengai Mavangira
- Department of Veterinary Diagnostic and Production Animal Medicine, Ames, 50011, USA
| | - Mike Vandehaar
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA
| | - Zheng Zhou
- Department of Animal Science, Michigan State University, East Lansing, 48824, USA.
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183
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Raffeld AM, Bradford MA, Jackson RD, Rath D, Sanford GR, Tautges N, Oldfield EE. The importance of accounting method and sampling depth to estimate changes in soil carbon stocks. Carbon Balance Manag 2024; 19:2. [PMID: 38277090 PMCID: PMC10811869 DOI: 10.1186/s13021-024-00249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND As interest in the voluntary soil carbon market surges, carbon registries have been developing new soil carbon measurement, reporting, and verification (MRV) protocols. These protocols are inconsistent in their approaches to measuring soil organic carbon (SOC). Two areas of concern include the type of SOC stock accounting method (fixed-depth (FD) vs. equivalent soil mass (ESM)) and sampling depth requirement. Despite evidence that fixed-depth measurements can result in error because of changes in soil bulk density and that sampling to 30 cm neglects a significant portion of the soil profile's SOC stock, most MRV protocols do not specify which sampling method to use and only require sampling to 30 cm. Using data from UC Davis's Century Experiment ("Century") and UW Madison's Wisconsin Integrated Cropping Systems Trial (WICST), we quantify differences in SOC stock changes estimated by FD and ESM over 20 years, investigate how sampling at-depth (> 30 cm) affects SOC stock change estimates, and estimate how crediting outcomes taking an empirical sampling-only crediting approach differ when stocks are calculated using ESM or FD at different depths. RESULTS We find that FD and ESM estimates of stock change can differ by over 100 percent and that, as expected, much of this difference is associated with changes in bulk density in surface soils (e.g., r = 0.90 for Century maize treatments). This led to substantial differences in crediting outcomes between ESM and FD-based stocks, although many treatments did not receive credits due to declines in SOC stocks over time. While increased variability of soils at depth makes it challenging to accurately quantify stocks across the profile, sampling to 60 cm can capture changes in bulk density, potential SOC redistribution, and a larger proportion of the overall SOC stock. CONCLUSIONS ESM accounting and sampling to 60 cm (using multiple depth increments) should be considered best practice when quantifying change in SOC stocks in annual, row crop agroecosystems. For carbon markets, the cost of achieving an accurate estimate of SOC stocks that reflect management impacts on soils at-depth should be reflected in the price of carbon credits.
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Affiliation(s)
- Anna M Raffeld
- Environmental Defense Fund, 555 12th Street, Suite 400, Washington, DC, 20004 , USA.
| | - Mark A Bradford
- The Forest School, Yale School of the Environment, Yale University, 360 Prospect St., New Haven, CT, 06511, USA
| | - Randall D Jackson
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Daniel Rath
- Natural Resources Defense Council, 1152 15th St NW, Washington, DC, 20005, USA
| | - Gregg R Sanford
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Nicole Tautges
- Michael Fields Agricultural Institute, East Troy, WI, PO Box 990, 53120, USA
| | - Emily E Oldfield
- Environmental Defense Fund, 555 12th Street, Suite 400, Washington, DC, 20004 , USA
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184
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Raymo G, Ali A, Ahmed RO, Salem M. Early-Life Fecal Transplantation from High Muscle Yield Rainbow Trout to Low Muscle Yield Recipients Accelerates Somatic Growth through Respiratory and Mitochondrial Efficiency Modulation. Microorganisms 2024; 12:261. [PMID: 38399665 PMCID: PMC10893187 DOI: 10.3390/microorganisms12020261] [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: 01/04/2024] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Previous studies conducted in our lab revealed microbial assemblages to vary significantly between high (ARS-FY-H) and low fillet yield (ARS-FY-L) genetic lines in adult rainbow trout. We hypothesized that a high ARS-FY-H donor microbiome can accelerate somatic growth in microbiome-depleted rainbow trout larvae of the ARS-FY-L line. Germ-depleted larvae of low ARS-FY-L line trout reared in sterile environments were exposed to high- or low-fillet yield-derived microbiomes starting at first feeding for 27 weeks. Despite weight-normalized diets, somatic mass was significantly increased in larvae receiving high fillet yield microbiome cocktails at 27 weeks post-hatch. RNA-seq from fish tails reveals enrichment in NADH dehydrogenase activity, oxygen carrier, hemoglobin complex, gas transport, and respiratory pathways in high fillet yield recolonized larvae. Transcriptome interrogation suggests a relationship between electron transport chain inputs and body weight assimilation, mediated by the gut microbiome. These findings suggest that microbiome payload originating from high fillet yield adult donors primarily accelerates juvenile somatic mass assimilation through respiratory and mitochondrial input modulation. Further microbiome studies are warranted to assess how increasing beneficial microbial taxa could be a basis for formulating appropriate pre-, pro-, or post-biotics in the form of feed additives and lead to fecal transplantation protocols for accelerated feed conversion and fillet yield in aquaculture.
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Affiliation(s)
| | | | | | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742-231, USA; (G.R.); (A.A.); (R.O.A.)
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Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, Sharakhova MV. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes. BMC Biol 2024; 22:16. [PMID: 38273363 PMCID: PMC10809549 DOI: 10.1186/s12915-024-01825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. METHODS In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. RESULTS We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. CONCLUSION The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
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Affiliation(s)
- Sergei S Ryazansky
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Molecular Genetics of Cell, NRC "Kurchatov Institute", Moscow, Russia
| | - Chujia Chen
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Group of Genomic Mechanisms of Development, Institute of Cytology and Genetics, Novosibirsk, Russia
- Laboratory of Structural and Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Vitor L Dos Anjos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Rong Guo
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Theresa Menna
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily Ferrill
- County of San Diego Vector Control Program, San Diego, CA, USA
| | - Karen E Schultz
- Mosquito and Vector Management District of Santa Barbara County, Santa Barbara, CA, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | | | | | - Chunhong Mao
- Biocomplexity Institute & Initiative University of Virginia, Charlottesville, VA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, the University of Tennessee, Knoxville, TN, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Zhijian Tu
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia.
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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186
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Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS Omega 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
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Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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187
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Handler AM, Furlong RB. The hAT family hopper transposon exists as highly similar yet discontinuous elements in the Bactrocera tephritid fly genus. Insect Mol Biol 2024. [PMID: 38251981 DOI: 10.1111/imb.12891] [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: 07/26/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
The hAT family transposable element, hopper, was originally discovered as a defective 3120-bp full-length element in a wild-type strain of the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), and subsequently a functional 3131-bp element, hopperBdwe , was isolated from a white eye mutant strain. The latter study showed that closely related elements exist in melonfly, Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae), a closely related subgenus, suggesting that hopper could have a widespread presence in the Bactrocera genus. To further understand the distribution of hopper within and beyond the B. dorsalis species complex, primer pairs from hopperBdwe and its adjacent genomic insertion site were used to survey the presence and relatedness of hopper in five species within the complex and four species beyond the complex. Based on sequence identity of a 1.94 kb internal nucleotide sequence, the closest relationships were with mutated elements from B. dorsalis s.s. and species synonymized with B. dorsalis including B. papayae, B. philippinensis and B. invadens, ranging in identity between 88.4% and 99.5%. Notably, Bactrocera carambolae (Drew & Hancock) (Diptera: Tephritidae), which is most closely related to B. dorsalis beyond the synonymized species, shared hopper identities of 97.3%-99.5%. Beyond the B. dorsalis complex, Z. cucurbitae, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) and Bactrocera zonata (Saunders) (Diptera: Tephritidae) shared identities of 83.1%-97.1%, while hopper was absent from the Bactrocera oleae (Gmelin) (Diptera: Tephritidae) strain tested. While the functional autonomous hopperBdwe element was not detected in these species, another closely related hopper element isolated from a B. dorsalis genetic sexing strain has an uninterrupted transposase open reading frame. The discontinuous presence of hopper in the Bactrocera genus has implications for its use for genomic manipulation and understanding the phylogenetic relationship of these species.
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Affiliation(s)
- Alfred M Handler
- Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, Florida, USA
| | - Richard B Furlong
- Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, Florida, USA
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Lee H, Diaz R, Cronin JT. Dieback and dredge soils of Phragmites australis in the Mississippi River Delta negatively impact plant biomass. Sci Rep 2024; 14:1935. [PMID: 38253645 PMCID: PMC10803353 DOI: 10.1038/s41598-024-52488-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
Phragmites australis is exhibiting extensive dieback in the Lower Mississippi River Delta (MRD). We explored the potential for restoration of these marshes by (1) characterizing the chemical profiles of soils collected from healthy and dieback stands of P. australis and from sites recently created from dredge-disposal soils that were expected to be colonized by P. australis and (2) experimentally testing the effects of these soil types on the growth of three common P. australis lineages, Delta, Gulf and European. Soil chemical properties included Al, Ca, Cu, Fe, K, Mg, Mn, Na, P, S, Zn, % organic matter, % carbon, % nitrogen, and pH. Dieback soils were characterized by higher % organic matter, % carbon, % nitrogen, and higher S and Fe concentrations, whereas healthy soils had higher Cu, Al, P and Zn. In comparison, dredge sites were low in nutrients and organic matter compared to healthy soils. Rhizomes of each P. australis lineage were planted in each soil type in a common garden and greenhouse and allowed to grow for five months. Aboveground biomass was 16% lower in dieback and 44% lower in dredge soils than in healthy soils. However, we could detect no significant differences in response to soil types among lineages. Although dredge and dieback sites are not optimal for P. australis growth, plants can thrive on these soils, and we recommend restorative measures be initiated as soon as possible to minimize soil erosion.
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Affiliation(s)
- Herie Lee
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Rodrigo Diaz
- Department of Entomology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - James T Cronin
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA.
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189
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Zimowska GJ, Xavier N, Qadri M, Handler AM. A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex. Sci Rep 2024; 14:1924. [PMID: 38253542 PMCID: PMC10803768 DOI: 10.1038/s41598-023-51068-2] [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: 06/05/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472 bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420 bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.
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Affiliation(s)
- Grazyna J Zimowska
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Nirmala Xavier
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masroor Qadri
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Alfred M Handler
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA.
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Keane JA, Ealy AD. An Overview of Reactive Oxygen Species Damage Occurring during In Vitro Bovine Oocyte and Embryo Development and the Efficacy of Antioxidant Use to Limit These Adverse Effects. Animals (Basel) 2024; 14:330. [PMID: 38275789 PMCID: PMC10812430 DOI: 10.3390/ani14020330] [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: 12/16/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The in vitro production (IVP) of bovine embryos has gained popularity worldwide and in recent years and its use for producing embryos from genetically elite heifers and cows has surpassed the use of conventional superovulation-based embryo production schemes. There are, however, several issues with the IVP of embryos that remain unresolved. One limitation of special concern is the low efficiency of the IVP of embryos. Exposure to reactive oxygen species (ROS) is one reason why the production of embryos with IVP is diminished. These highly reactive molecules are generated in small amounts through normal cellular metabolism, but their abundances increase in embryo culture because of oocyte and embryo exposure to temperature fluctuations, light exposure, pH changes, atmospheric oxygen tension, suboptimal culture media formulations, and cryopreservation. When uncontrolled, ROS produce detrimental effects on the structure and function of genomic and mitochondrial DNA, alter DNA methylation, increase lipid membrane damage, and modify protein activity. Several intrinsic enzymatic pathways control ROS abundance and damage, and antioxidants react with and reduce the reactive potential of ROS. This review will focus on exploring the efficiency of supplementing several of these antioxidant molecules on oocyte maturation, sperm viability, fertilization, and embryo culture.
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Affiliation(s)
| | - Alan D. Ealy
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA;
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191
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Nguyen AV, Yaghoobi M, Zhang S, Li P, Li Q, Dogan B, Ahnrud GP, Flock G, Marek P, Simpson KW, Abbaspourrad A. Adaptive Laboratory Evolution of Probiotics toward Oxidative Stress Using a Microfluidic-Based Platform. Small 2024:e2306974. [PMID: 38247174 DOI: 10.1002/smll.202306974] [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: 08/14/2023] [Revised: 11/28/2023] [Indexed: 01/23/2024]
Abstract
Adaptive laboratory evolution (ALE) can be used to make bacteria less susceptible to oxidative stress. An alternative to large batch scale ALE cultures is to use microfluidic platforms, which are often more economical and more efficient. Microfluidic ALE platforms have shown promise, but many have suffered from subpar cell passaging mechanisms and poor spatial definition. A new approach is presented using a microfluidic Evolution on a Chip (EVoc) design which progressively drives microbial cells from areas of lower H2 O2 concentration to areas of higher concentration. Prolonged exposure, up to 72 h, revealed the survival of adaptive strains of Lacticaseibacillus rhamnosus GG, a beneficial probiotic often included in food products. After performing ALE on this microfluidic platform, the bacteria persisted under high H2 O2 concentrations in repeated trials. After two progressive exposures, the ability of L. rhamnosus to grow in the presence of H2 O2 increased from 1 mm H2 O2 after a lag time of 31 h to 1 mm after 21 h, 2 mm after 28 h, and 3 mm after 42 h. The adaptive strains have different morphology, and gene expression compared to wild type, and genome sequencing revealed a potentially meaningful single nucleotide mutation in the protein omega-amidase.
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Affiliation(s)
- Ann V Nguyen
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Mohammad Yaghoobi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Peilong Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Qike Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Gianna P Ahnrud
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Genevieve Flock
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Patrick Marek
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
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192
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Lee HJ, Kim HD, Ryu D. Practical Strategies to Reduce Ochratoxin A in Foods. Toxins (Basel) 2024; 16:58. [PMID: 38276534 PMCID: PMC10819544 DOI: 10.3390/toxins16010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Ochratoxin A (OTA), a potent nephrotoxin, is one of the most deleterious mycotoxins, with its prevalence in agricultural crops and their processed foods around the world. OTA is a major concern to food safety, as OTA exposure through dietary intake may lead to a significant level of accumulation in the body as a result of its long half-life (about 35 days). Its potent renal toxicity and high risk of exposure as well as the difficulty in controlling environmental factors OTA production has prompted the need for timely information on practical strategies for the food industry to effectively manage OTA contamination during food processing. The effects of various food processes, including both nonthermal and thermal methods, on the reduction in OTA were summarized in this review, with emphasis on the toxicity of residual OTA as well as its known and unknown degradation products. Since complete removal of OTA from foodstuffs is not feasible, additional strategies that may facilitate the reduction in OTA in food, such as adding baking soda and sugars, was also discussed, so that the industry may understand and apply practical measures to ensure the safety of its products destined for human consumption.
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Affiliation(s)
- Hyun Jung Lee
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - Hae Dun Kim
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA;
| | - Dojin Ryu
- Division of Food, Nutrition and Exercise Sciences, University of Missouri, Columbia, MO 65211, USA;
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193
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Stinson I, Li HH, Tsui MTK, Ku P, Ulus Y, Cheng Z, Lam HM. Tree foliage as a net accumulator of highly toxic methylmercury. Sci Rep 2024; 14:1757. [PMID: 38242950 PMCID: PMC10799008 DOI: 10.1038/s41598-024-51469-x] [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: 07/26/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
Tree canopies are known to elevate atmospheric inputs of both mercury (Hg) and methylmercury (MeHg). While foliar uptake of gaseous Hg is well documented, little is known regarding the temporal dynamics and origins of MeHg in tree foliage, which represents typically less than 1% of total Hg in foliage. In this work, we examined the foliar total Hg and MeHg content by following the growth of five individual trees of American Beech (Fagus grandifolia) for one growing season (April-November, 2017) in North Carolina, USA. We show that similar to other studies foliar Hg content increased almost linearly over time, with daily accumulation rates ranging from 0.123 to 0.161 ng/g/day. However, not all trees showed linear increases of foliar MeHg content along the growing season; we found that 2 out of 5 trees showed elevated foliar MeHg content at the initial phase of the growing season but their MeHg content declined through early summer. However, foliar MeHg content among all 5 trees showed eventual increases through the end of the growing season, proving that foliage is a net accumulator of MeHg while foliar gain of biomass did not "dilute" MeHg content.
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Affiliation(s)
- Idus Stinson
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Han-Han Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
| | - Martin Tsz-Ki Tsui
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| | - Peijia Ku
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Yener Ulus
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
- Department of Environmental Studies, Davidson College, Davidson, NC, 28035, USA
| | - Zhang Cheng
- College of Environment, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hon-Ming Lam
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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194
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Waite JM, Dardick C. IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle. BMC Biol 2024; 22:8. [PMID: 38233837 PMCID: PMC10795295 DOI: 10.1186/s12915-024-01813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene clades LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC). RESULTS Here, we investigated the influence of light on different aspects of GSA phenotypes in LAZY and DRO mutants, as well as the influence of known light signaling pathways on IGT gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for changes in the angle of shoot branch tip and root growth in response to light. Single lazy1 mutant branch tips turn upward in the absence of light and in low light, similar to wild-type, and mimic triple and quadruple IGT mutants in constant light and high-light conditions, while triple and quadruple IGT/LAZY mutants show little to no response to changing light regimes. Further, the expression of IGT/LAZY genes is differentially influenced by daylength, circadian clock, and light signaling. CONCLUSIONS Collectively, the data show that differential expression of LAZY and DRO genes are required to enable plants to alter organ angles in response to light-mediated signals.
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Affiliation(s)
- Jessica Marie Waite
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA.
- Present Address: USDA Tree Fruit Research Laboratory, 1104 N Western Avenue, Wenatchee, WA, USA.
| | - Christopher Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA
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195
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Stella SL, Guadagnin AR, Velasco-Acosta DA, Ferreira CR, Rubessa M, Wheeler MB, Luchini D, Cardoso FC. Rumen-protected methionine supplementation alters lipid profile of preimplantation embryo and endometrial tissue of Holstein cows. Front Vet Sci 2024; 10:1301986. [PMID: 38298457 PMCID: PMC10827937 DOI: 10.3389/fvets.2023.1301986] [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: 09/25/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
Our objective is to evaluate the effects of feeding rumen-protected Met (RPM) throughout the transition period and early lactation on the lipid profile of the preimplantation embryos and the endometrial tissue of Holstein cows. Treatments consisted of feeding a total mixed ration with top-dressed RPM (Smartamine® M, Adisseo, Alpharetta, GA, United States; MET; n = 11; RPM at a rate of 0.08% of DM: Lys:Met = 2.8:1) or not (CON; n = 9, Lys:Met = 3.5:1). Endometrial biopsies were performed at 15, 30, and 73 days in milk (DIM). Prior to the endometrial biopsy at 73 DIM, preimplantation embryos were harvested via flushing. Endometrial lipid profiles were analyzed using multiple reaction monitoring-profiling and lipid profiles of embryos were acquired using matrix assisted laser desorption/ionization mass spectrometry. Relative intensities levels were used for principal component analysis. Embryos from cows in MET had greater concentration of polyunsaturated lipids than embryos from cows in CON. The endometrial tissue samples from cows in MET had lesser concentrations of unsaturated and monounsaturated lipids at 15 DIM, and greater concentration of saturated, unsaturated (specifically diacylglycerol), and monounsaturated (primarily ceramides) lipids at 30 DIM than the endometrial tissue samples from cows in CON. In conclusion, feeding RPM during the transition period and early lactation altered specific lipid classes and lipid unsaturation level of preimplantation embryos and endometrial tissue.
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Affiliation(s)
- Stephanie L. Stella
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Anne R. Guadagnin
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Schothorst Feed Research, Lelystad, Netherlands
| | - Diego A. Velasco-Acosta
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- The Colombian Corporation for Agricultural Research (CORPOICA), Bogotá, Colombia
| | - Christina R. Ferreira
- Metabolite Profiling Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
| | - Marcello Rubessa
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Matthew B. Wheeler
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | | | - Felipe C. Cardoso
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
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196
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Bakner NW, Ulrey EE, Collier BA, Chamberlain MJ. Prospecting during egg laying informs incubation recess movements of eastern wild turkeys. Mov Ecol 2024; 12:4. [PMID: 38229127 DOI: 10.1186/s40462-024-00451-3] [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: 08/03/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Central place foragers must acquire resources and return to a central location after foraging bouts. During the egg laying (hereafter laying) period, females are constrained to a nest location, thus they must familiarize themselves with resources available within their incubation ranges after nest site selection. Use of prospecting behaviors by individuals to obtain knowledge and identify profitable (e.g., resource rich) locations on the landscape can impact demographic outcomes. As such, prospecting has been used to evaluate nest site quality both before and during the reproductive period for a variety of species. METHODS Using GPS data collected from female eastern wild turkeys (Meleagris gallopavo silvestris) across the southeastern United States, we evaluated if prospecting behaviors were occurring during laying and what landcover factors influenced prospecting. Specifically, we quantified areas prospected during the laying period using a cluster analysis and the return frequency (e.g., recess movements) to clustered laying patches (150-m diameter buffer around a clustered laying period location) during the incubation period. RESULTS The average proportion of recess movements to prospected locations was 56.9%. Nest fate was positively influenced (μ of posterior distribution with 95% credible 0.19, 0.06-0.37, probability of direction = 99.8%) by the number of patches (90-m diameter buffer around a clustered laying period location) a female visited during incubation recesses. Females selected for areas closer to the nest site, secondary roads, hardwood forest, mixed pine-hardwood forest, water, and shrub/scrub, whereas they avoided pine forest and open-treeless areas. CONCLUSIONS Our findings suggest that having a diverse suite of clustered laying patches to support incubation recesses is impactful to nest fate. As such, local conditions within prospected locations during incubation may be key to successful reproductive output by wild turkeys. We suggest that prospecting could be important to other phenological periods. Furthermore, future research should evaluate how prospecting for brood-rearing locations may occur before or during the incubation period.
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Affiliation(s)
- Nicholas W Bakner
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA.
| | - Erin E Ulrey
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
| | - Bret A Collier
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Michael J Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
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197
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Yerebakan MO, Hu B. Wearable Sensors Assess the Effects of Human-Robot Collaboration in Simulated Pollination. Sensors (Basel) 2024; 24:577. [PMID: 38257670 PMCID: PMC10821395 DOI: 10.3390/s24020577] [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: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Pollination for indoor agriculture is hampered by environmental conditions, requiring farmers to pollinate manually. This increases the musculoskeletal illness risk of workers. A potential solution involves Human-Robot Collaboration (HRC) using wearable sensor-based human motion tracking. However, the physical and biomechanical aspects of human interaction with an advanced and intelligent collaborative robot (cobot) during pollination remain unknown. This study explores the impact of HRC on upper body joint angles during pollination tasks and plant height. HRC generally resulted in a significant reduction in joint angles with flexion decreasing by an average of 32.6 degrees (p ≤ 0.001) for both shoulders and 30.5 degrees (p ≤ 0.001) for the elbows. In addition, shoulder rotation decreased by an average of 19.1 (p ≤ 0.001) degrees. However, HRC increased the left elbow supination by 28.3 degrees (p ≤ 0.001). The positive effects of HRC were reversed when the robot was unreliable (i.e., missed its target), but this effect was not applicable for the left elbow. The effect of plant height was limited with higher plant height increasing right shoulder rotation but decreasing right elbow pronation. These findings aim to shed light on both the benefits and challenges of HRC in agriculture, providing valuable insights before deploying cobots in indoor agricultural settings.
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Affiliation(s)
| | - Boyi Hu
- Department of Industrial and Systems Engineering, University of Florida, Gainesville, FL 32611, USA;
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198
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Holtsclaw RE, Mahmud S, Koo AJ. Identification and characterization of GLYCEROLIPASE A1 for wound-triggered JA biosynthesis in Nicotiana benthamiana leaves. Plant Mol Biol 2024; 114:4. [PMID: 38227103 DOI: 10.1007/s11103-023-01408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/03/2023] [Indexed: 01/17/2024]
Abstract
Although many important discoveries have been made regarding the jasmonate signaling pathway, how jasmonate biosynthesis is initiated is still a major unanswered question in the field. Previous evidences suggest that jasmonate biosynthesis is limited by the availability of fatty acid precursor, such as ⍺-linolenic acid (⍺-LA). This indicates that the lipase responsible for releasing α-LA in the chloroplast, where early steps of jasmonate biosynthesis take place, is the key initial step in the jasmonate biosynthetic pathway. Nicotiana benthamiana glycerol lipase A1 (NbGLA1) is homologous to N. attenuata GLA1 (NaGLA1) which has been reported to be a major lipase in leaves for jasmonate biosynthesis. NbGLA1 was studied for its potential usefulness in a species that is more common in laboratories. Virus-induced gene silencing of both NbGLA1 and NbGLA2, another homolog, resulted in more than 80% reduction in jasmonic acid (JA) biosynthesis in wounded leaves. Overexpression of NbGLA1 utilizing an inducible vector system failed to increase JA, indicating that transcriptional induction of NbGLA1 is insufficient to trigger JA biosynthesis. However, co-treatment with wounding in addition to NbGLA1 induction increased JA accumulation several fold higher than the gene expression or wounding alone, indicating an enhancement of the enzyme activity by wounding. Domain-deletion of a 126-bp C-terminal region hypothesized to have regulatory roles increased NbGLA1-induced JA level. Together, the data show NbGLA1 to be a major lipase for wound-induced JA biosynthesis in N. benthamiana leaves and demonstrate the use of inducible promoter-driven construct of NbGLA1 in conjunction with its transient expression in N. benthamiana as a useful system to study its protein function.
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Affiliation(s)
- Rebekah E Holtsclaw
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA
- Rubi Laboratories, 94577, San Leandro, CA, USA
| | - Sakil Mahmud
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA
| | - Abraham J Koo
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA.
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199
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Subramani M, Urrea CA, Tamatamu SR, Sripathi VR, Williams K, Chintapenta LK, Todd A, Ozbay G. Comprehensive Proteomic Analysis of Common Bean ( Phaseolus vulgaris L.) Seeds Reveal Shared and Unique Proteins Involved in Terminal Drought Stress Response in Tolerant and Sensitive Genotypes. Biomolecules 2024; 14:109. [PMID: 38254709 PMCID: PMC10813106 DOI: 10.3390/biom14010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein-chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant-pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Carlos A. Urrea
- Panhandle Research Extension and Education Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA;
| | - Sowjanya R. Tamatamu
- Center for Molecular Biology, Alabama A&M University, Normal, AL 35762, USA; (S.R.T.); (V.R.S.)
| | | | - Krystal Williams
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Lathadevi K. Chintapenta
- Biology Department, College of Arts and Sciences (CAS), University of Wisconsin-River Falls, River Falls, WI 54022, USA;
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Gulnihal Ozbay
- Department of Agriculture and Natural Resources, Delaware State University, 1200 North DuPont Highway, Dover, DE 19901, USA
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200
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Han L, Tian Z, Wojan TR, Goetz SJ. Testing biasedness of self-reported microbusiness innovation in the annual business survey. PLoS One 2024; 19:e0296667. [PMID: 38215177 PMCID: PMC10786406 DOI: 10.1371/journal.pone.0296667] [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: 07/20/2023] [Accepted: 12/16/2023] [Indexed: 01/14/2024] Open
Abstract
This study tests for potential bias in self-reported innovation due to the inclusion of a research and development (R&D) module that only microbusinesses (less than 10 employees) receive in the Annual Business Survey (ABS). Previous research found that respondents to combined innovation/R&D surveys reported innovation at lower rates than respondents to innovation-only surveys. A regression discontinuity design is used to test whether microbusinesses, which constitute a significant portion of U.S. firms with employees, are less likely to report innovation compared to other small businesses. In the vicinity of the 10-employee threshold, the study does not detect statistically significant biases for new-to-market and new-to-business product innovation. Statistical power analysis confirms the nonexistence of biases with a high power. Comparing the survey design of ABS to earlier combined innovation/R&D surveys provides valuable insights for the proposed integration of multiple Federal surveys into a single enterprise platform survey. The findings also have important implications for the accuracy and reliability of innovation data used as an input to policymaking and business development strategies in the United States.
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Affiliation(s)
- Luyi Han
- Northeast Regional Center for Rural Development, Penn State University, State College, Pennsylvania, United States of America
| | - Zheng Tian
- Northeast Regional Center for Rural Development, Penn State University, State College, Pennsylvania, United States of America
| | - Timothy R. Wojan
- Oak Ridge Institute for Science and Education Research Ambassadors Program, National Center for Science and Engineering Statistics, National Science Foundation, Oak Ridge, Tennessee, United States of America
| | - Stephan J. Goetz
- Northeast Regional Center for Rural Development, Department of Agricultural Economics, Sociology, and Education, Penn State University, State College, Pennsylvania, United States of America
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