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A Reference Genome For Bluegill (Centrarchidae: Lepomis Macrochirus), William B. Ludt, Eamon C. Corbett, Jerry Kattawar, Prosanta Chakrabarty, Brant C. Faircloth Mar 2023

A Reference Genome For Bluegill (Centrarchidae: Lepomis Macrochirus), William B. Ludt, Eamon C. Corbett, Jerry Kattawar, Prosanta Chakrabarty, Brant C. Faircloth

Faculty Publications

North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including …

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Dna Assays For Genetic Discrimination Of Three Phragmites Australis Subspecies In The United States, Denise L. Lindsay, Xin Guan, Nathan E. Harms, James T. Cronin, Laura A. Meyerson, Richard F. Lance Mar 2023

Dna Assays For Genetic Discrimination Of Three Phragmites Australis Subspecies In The United States, Denise L. Lindsay, Xin Guan, Nathan E. Harms, James T. Cronin, Laura A. Meyerson, Richard F. Lance

Faculty Publications

Premise: To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real-time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. Methods and Results: Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available …

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Unhealthy Herds And The Predator–Spreader: Understanding When Predation Increases Disease Incidence And Prevalence, Robert L. Richards, Bret D. Elderd, Meghan A. Duffy Mar 2023

Unhealthy Herds And The Predator–Spreader: Understanding When Predation Increases Disease Incidence And Prevalence, Robert L. Richards, Bret D. Elderd, Meghan A. Duffy

Faculty Publications

Disease ecologists now recognize the limitation behind examining host–parasite interactions in isolation: community members—especially predators—dramatically affect host–parasite dynamics. Although the initial paradigm was that predation should reduce disease in prey populations (“healthy herds hypothesis”), researchers have realized that predators sometimes increase disease in their prey. These “predator–spreaders” are now recognized as critical to disease dynamics, but empirical research on the topic remains fragmented. In a narrow sense, a “predator–spreader” would be defined as a predator that mechanically spreads parasites via feeding. However, predators affect their prey and, subsequently, disease transmission in many other ways such as altering prey population structure, …

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Pseudomonas Aeruginosa Dps (Pa0962) Functions In H2o2 Mediated Oxidative Stress Defense And Exhibits In Vitro Dna Cleaving Activity, Nimesha Rajapaksha, Anabel Soldano, Huili Yao, Fabrizio Donnarumma, Maithri M. Kashipathy, Steve Seibold, Kevin P. Battaile, Scott Lovell, Mario Rivera Mar 2023

Pseudomonas Aeruginosa Dps (Pa0962) Functions In H2o2 Mediated Oxidative Stress Defense And Exhibits In Vitro Dna Cleaving Activity, Nimesha Rajapaksha, Anabel Soldano, Huili Yao, Fabrizio Donnarumma, Maithri M. Kashipathy, Steve Seibold, Kevin P. Battaile, Scott Lovell, Mario Rivera

Faculty Publications

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe2+ utilizing H2O2 (not O2) as an oxidant, suggesting Pa Dps functions to aid P. …

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The Interaction Of Rurality And Rare Cancers For Travel Time To Cancer Care, Tracy Onega, Jennifer Alford-Teaster, Chris Leggett, Andrew Loehrer, Julie E. Weiss, Erika L. Moen, Catherine C. Pollack, Fahui Wang Mar 2023

The Interaction Of Rurality And Rare Cancers For Travel Time To Cancer Care, Tracy Onega, Jennifer Alford-Teaster, Chris Leggett, Andrew Loehrer, Julie E. Weiss, Erika L. Moen, Catherine C. Pollack, Fahui Wang

Faculty Publications

Purpose: Geographic access to cancer care is known to significantly impact utilization and outcomes. Longer travel times have negative impacts for patients requiring highly specialized care, such as for rare cancers, and for those in rural areas. Scant population-based research informs geographic access to care for rare cancers and whether rurality impacts that access. Methods: Using Medicare data (2014-2015), we identified prevalent cancers and cancer-directed surgeries, chemotherapy, and radiation. We classified cancers as rare (incidence <6/100,000/year) or common (incidence ≥6/100,000/year) using previously published thresholds and categorized rurality from ZIP code of beneficiary residence. We estimated travel time between beneficiaries and providers for each service based on ZIP code. Descriptive statistics summarized travel time by rare versus common cancers, service type, and rurality. Findings: We included 1,169,761 Medicare beneficiaries (21.9% in nonmetropolitan areas), 87,399; 7.5% had rare cancers, with 9,133,003 cancer-directed services. Travel times for cancer services ranged from approximately 29 minutes (25th percentile) to 68 minutes (75th percentile). Travel times were similar for rare and common cancers overall (median: 45 vs 43 minutes) but differed by service type; 13.4% of surgeries were >2 hours away for rare cancers, compared to 8.3% for common cancers. Increasing rurality disproportionately increased travel time to surgical care for rare compared to …

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Surface Plasmon Resonance (Spr) Sensor For Cancer Biomarker Detection, Sreyashi Das, Ram Devireddy, Manas Ranjan Gartia Mar 2023

Surface Plasmon Resonance (Spr) Sensor For Cancer Biomarker Detection, Sreyashi Das, Ram Devireddy, Manas Ranjan Gartia

Faculty Publications

A biomarker is a physiological observable marker that acts as a stand-in and, in the best-case scenario, forecasts a clinically significant outcome. Diagnostic biomarkers are more convenient and cost-effective than directly measuring the ultimate clinical outcome. Cancer is among the most prominent global health problems and a major cause of morbidity and death globally. Therefore, cancer biomarker assays that are trustworthy, consistent, precise, and verified are desperately needed. Biomarker-based tumor detection holds a lot of promise for improving disease knowledge at the molecular scale and early detection and surveillance. In contrast to conventional approaches, surface plasmon resonance (SPR) allows for …

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Policy Comparison Of Lead Hunting Ammunition Bans And Voluntary Nonlead Programs For California Condors, Robin M. Rotman, John H. Schulz, Samantha Totoni, Sonja A. Wilhelm Stanis, Christine Jie Li, Mark Morgan, Damon M. Hall, Elisabeth B. Webb Mar 2023

Policy Comparison Of Lead Hunting Ammunition Bans And Voluntary Nonlead Programs For California Condors, Robin M. Rotman, John H. Schulz, Samantha Totoni, Sonja A. Wilhelm Stanis, Christine Jie Li, Mark Morgan, Damon M. Hall, Elisabeth B. Webb

Faculty Publications

The endangered California condor (Gymnogyps californianus) is negatively affected by lead poisoning from spent lead‐based hunting ammunition. Because lead poisoning is the primary mortality factor affecting condors, the California Fish and Game Commission banned lead hunting ammunition during 2008 in the southern California condor range followed by a statewide ban implemented in 2019. In contrast, the Arizona Game and Fish Department instituted an outreach and awareness program encouraging voluntary use of nonlead hunting ammunition in the northern portion of the state during 2005 and a similar program was launched in Utah during 2012. The juxtaposition of policy tools provided a …

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Sophisticated Vs. Rugged: Examining Gendered Brand Communication Styles And Social Media Engagement, Joanne T. Cao, Jamye Foster, Gallayanee S. Yaoyuneyong, Lacey K. Wallace Mar 2023

Sophisticated Vs. Rugged: Examining Gendered Brand Communication Styles And Social Media Engagement, Joanne T. Cao, Jamye Foster, Gallayanee S. Yaoyuneyong, Lacey K. Wallace

Faculty Publications

Advertising and marketing managers understand that not all brands need to be on social media, but what is not clearly understood is consumers’ engagement expectations for brands that are on social media. Therefore, this study investigates the impact of brand personality, specifically sophisticated and rugged brands, and gendered communication styles on consumers’ expectations of social media engagement. A scenario-based experiment is performed to test the hypotheses using a mock brand. The main study consisted of a Qualtrics consumer panel, and a MANOVA was utilized to examine three components of social media engagement (consumption, contribution, and creation) on the two brand …

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Meridional Survey Of The Central Pacific Reveals Iodide Accumulation In Equatorial Surface Waters And Benthic Sources In The Abyssal Plain, Rintaro Moriyasu, Kenneth M. Bolster, Dalton S. Hardisty, David C. Kadko, Mark P. Stephens, James W. Moffett Mar 2023

Meridional Survey Of The Central Pacific Reveals Iodide Accumulation In Equatorial Surface Waters And Benthic Sources In The Abyssal Plain, Rintaro Moriyasu, Kenneth M. Bolster, Dalton S. Hardisty, David C. Kadko, Mark P. Stephens, James W. Moffett

Faculty Publications

The distributions of iodate and iodide were measured along the GEOTRACES GP15 meridional transect at 152°W from the shelf of Alaska to Papeete, Tahiti. The transect included oxygenated waters near the shelf of Alaska, the full water column in the central basin in the North Pacific Basin, the upper water column spanning across seasonally mixed regimes in the north, oligotrophic regimes in the central gyre, and the equatorial upwelling. Iodide concentrations are highest in the permanently stratified tropical mixed layers, which reflect accumulation due to light-dependent biological processes, and decline rapidly below the euphotic zone. Vertical mixing coefficients (K …

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Evolution Of Coronal Magnetic Field Parameters During X5.4 Solar Flare, Seth H. Garland, Benjamin F. Akers, Vasyl B. Yurchyshyn, Robert D. Loper, Daniel J. Emmons Mar 2023

Evolution Of Coronal Magnetic Field Parameters During X5.4 Solar Flare, Seth H. Garland, Benjamin F. Akers, Vasyl B. Yurchyshyn, Robert D. Loper, Daniel J. Emmons

Faculty Publications

The coronal magnetic field over NOAA Active Region 11,429 during a X5.4 solar flare on 7 March 2012 is modeled using optimization based Non-Linear Force-Free Field extrapolation. Specifically, 3D magnetic fields were modeled for 11 timesteps using the 12-min cadence Solar Dynamics Observatory (SDO) Helioseismic and Magnetic Imager photospheric vector magnetic field data, spanning a time period of 1 hour before through 1 hour after the start of the flare. Using the modeled coronal magnetic field data, seven different magnetic field parameters were calculated for 3 separate regions: areas with surface |Bz| ≥ 300 G, areas of flare brightening seen …

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Florawear: Wearable Living Interface, Hye Yeon Nam, Janiece Campbell, Andrew M. Webb, Brendan Harmon Feb 2023

Florawear: Wearable Living Interface, Hye Yeon Nam, Janiece Campbell, Andrew M. Webb, Brendan Harmon

Faculty Publications

While nature can benefit people both mentally and physically, contemporary society has become increasingly disconnected from nature. To rebuild a stronger connection with nature in our everyday life, we introduce FloraWear, a do-it-yourself, wearable living interface, that enables people to easily and closely connect with plants. This pictorial introduces how knowledge is built and shared with others using hybrid craft and fabrication, illustrates the material experiments and design development for FloraWear, and discusses how it affects wearers. Then we summarize how FloraWear can help catalyze a shift in people's perspectives towards nature. By developing emotional ties to their wearable plants, …

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Simple Mathematical Equations For Calculating Oxidation Number Of Organic Carbons, Number Of Transferred Electrons, Oxidative Ratio, And Mole Of Oxygen Molecule In Combustion Reactions, Pong Yuen, Cheng Man Diana Lau Feb 2023

Simple Mathematical Equations For Calculating Oxidation Number Of Organic Carbons, Number Of Transferred Electrons, Oxidative Ratio, And Mole Of Oxygen Molecule In Combustion Reactions, Pong Yuen, Cheng Man Diana Lau

Faculty Publications

The oxidation number and number of transferred electrons are two paramount parameters in the study of redox reactions. Their calculations are both important and challenging. The oxidation number of organic carbons is used in organic chemistry, biochemistry, and applied chemistry. Combustion reaction is a classical type of redox reaction, in which the oxygen molecule (O2) is the oxidizing agent. In this article, the integration of three sets of relations is explored by using the method of balancing organic combustion: (i) number of transferred electrons and oxidation number of organic carbons, (ii) mole of oxygen molecule and number of transferred electrons, …

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Analysis And Technical Optimization Of Processing Condition For Better Quality Of Robusta Coffee Production, Usman Ahmad, Khalimatus Sa’Diyah, Sathivel Subramaniam Feb 2023

Analysis And Technical Optimization Of Processing Condition For Better Quality Of Robusta Coffee Production, Usman Ahmad, Khalimatus Sa’Diyah, Sathivel Subramaniam

Faculty Publications

The wet processing of robusta coffee starts with harvesting coffee cherries, followed by sorting the cherries, pulping, fermentation, washing, drying, hard skin hulling, bean sorting, and packaging. Soaking fruit before pulping is an alternative for coffee farmers to delay the pulping process if time does not al-low it. The fermentation process aims to remove mucus that is firmly attached to the hard skin. The addition of L. casei bacteria can accelerate the process but affect the final taste. This study aimed to optimize the duration of soaking and fermentation processes for obtaining coffee beans with a minimum number of unpeeled …

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Team Moms And Tiger Moms: Formal Sports Participation And Closeness To Mothers: Supplementary Materials, Tom R. Leppard, Mikaela J. Dufur Feb 2023

Team Moms And Tiger Moms: Formal Sports Participation And Closeness To Mothers: Supplementary Materials, Tom R. Leppard, Mikaela J. Dufur

Faculty Publications

Recent research highlights that relationships with parents are among those strengthened when youth play sports. This recent work, however, largely focuses on fathers, arguing that because of the persistent emphasis on masculinity in sporting spaces, youth sports might be especially effective at facilitating stronger relationships between fathers and children. This chapter asks how the mother-child dyad is influenced by youth formal participation in sports during their adolescence, including whether these patters differ for daughters and sons. The intense time investments the entire family unit incurs to support youth sport participation might be borne primarily by mothers; this in turn might …

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Antibody Development To Identify Components Of Iis And Mtor Signaling Pathways In Lepidopteran Species, A Set Of Non-Model Insects, Alissa R. Armstrong, Carol Boggs Feb 2023

Antibody Development To Identify Components Of Iis And Mtor Signaling Pathways In Lepidopteran Species, A Set Of Non-Model Insects, Alissa R. Armstrong, Carol Boggs

Faculty Publications

Nutritional stress impacts many insect species that have differing reproductive strategies and life histories, yet it is unclear how nutrient-sensing signaling pathways mediate tissue-specific responses to changes in dietary input. In Drosophila melanogaster , insulin/insulin-like growth factor (IIS) and mTOR-mediated signaling within adipocytes regulates oogenesis. To facilitate comparative study of nutrient-sensing pathway activity in the fat body, we developed antibodies to assess IIS (anti-FOXO) and mTOR signaling (anti-TOR) across three nymphalid species (Lepidoptera). By optimizing whole-mount fat body immunostaining, we find FOXO nuclear enrichment in adult adipocytes, like that observed in Drosophila . Additionally, we show a previously uncharacterized TOR …

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Enhanced Phase Sensitivity In A Mach-Zehnder Interferometer Via Photon Recycling, Dong Li, Chun Hua Yuan, Xiaoping Ma, Qingle Wang, Hwang Lee, Yao Yao, Weiping Zhang Feb 2023

Enhanced Phase Sensitivity In A Mach-Zehnder Interferometer Via Photon Recycling, Dong Li, Chun Hua Yuan, Xiaoping Ma, Qingle Wang, Hwang Lee, Yao Yao, Weiping Zhang

Faculty Publications

We propose an alternative scheme for phase estimation in a Mach-Zehnder interferometer (MZI) with photon recycling. It is demonstrated that with the same coherent-state input and homodyne detection, our proposal possesses a phase sensitivity beyond the traditional MZI. For instance, it can achieve an enhancement factor of ∼9.32 in the phase sensitivity compared with the conventional scheme even with a photon loss of 10% on the photon-recycled arm. From another point of view, the quantum Cramér-Rao bound (QCRB) is also investigated. It is found that our scheme is able to achieve a lower QCRB than the traditional one. Intriguingly, the …

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Acquisition Of New Function Through Gene Duplication In The Metallocarboxypeptidase Family, Daniel Fajardo, Ritchie Saint Jean, Peter J. Lyons Feb 2023

Acquisition Of New Function Through Gene Duplication In The Metallocarboxypeptidase Family, Daniel Fajardo, Ritchie Saint Jean, Peter J. Lyons

Faculty Publications

Gene duplication is a key frst step in the process of expanding the functionality of a multigene family. In order to better understand the process of gene duplication and its role in the formation of new enzymes, we investigated recent duplication events in the M14 family of proteolytic enzymes. Within vertebrates, four of 23 M14 genes were frequently found in duplicate form. While AEBP1, CPXM1, and CPZ genes were duplicated once through a large-scale, likely whole-genome duplication event, the CPO gene underwent many duplication events within fsh and Xenopus lineages. Bioinformatic analyses of enzyme specifcity and conservation suggested a greater …

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Active Control Of Equilibrium, Near-Equilibrium, And Far-From-Equilibrium Colloidal Systems, Mark N. Mcdonald, Qinyu Zhu, Walter F. Paxton, Cameron K. Peterson, Douglas R. Tree Feb 2023

Active Control Of Equilibrium, Near-Equilibrium, And Far-From-Equilibrium Colloidal Systems, Mark N. Mcdonald, Qinyu Zhu, Walter F. Paxton, Cameron K. Peterson, Douglas R. Tree

Faculty Publications

The development of top-down active control over bottom-up colloidal assembly processes has the potential to produce materials, surfaces, and objects with applications in a wide range of fields spanning from computing to materials science to biomedical engineering. In this review, we summarize recent progress in the field using a taxonomy based on how active control is used to guide assembly. We find there are three distinct scenarios: (1) navigating kinetic pathways to reach a desirable equilibrium state, (2) the creation of a desirable metastable, kinetically trapped, or kinetically arrested state, and (3) the creation of a desirable far-from-equilibrium state through …

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The Injured Sciatic Nerve Atlas (Isnaat), Insights Into The Cellular And Molecular Basis Of Neural Tissue Degeneration And Regeneration, Xiao-Feng Zhao, Lucas D. Huffman, Hannah Hafner, Mitre Athaiya, Matthew C. Finneran, Ashley L. Kalinski, Rafi Kohen, Corey Flynn, Ryan Passino, Craig N. Johnson, David Kohrman, Riki Kawaguchi, Lynda Js Yang, Jeffery L. Twiss, Daniel H. Geschwind, Gabriel Corfas, Roman J. Giger Feb 2023

The Injured Sciatic Nerve Atlas (Isnaat), Insights Into The Cellular And Molecular Basis Of Neural Tissue Degeneration And Regeneration, Xiao-Feng Zhao, Lucas D. Huffman, Hannah Hafner, Mitre Athaiya, Matthew C. Finneran, Ashley L. Kalinski, Rafi Kohen, Corey Flynn, Ryan Passino, Craig N. Johnson, David Kohrman, Riki Kawaguchi, Lynda Js Yang, Jeffery L. Twiss, Daniel H. Geschwind, Gabriel Corfas, Roman J. Giger

Faculty Publications

Upon trauma, the adult murine peripheral nervous system (PNS) displays a remarkable degree of spontaneous anatomical and functional regeneration. To explore extrinsic mechanisms of neural repair, we carried out single-cell analysis of naïve mouse sciatic nerve, peripheral blood mononuclear cells, and crushed sciatic nerves at 1 day, 3 days, and 7 days following injury. During the first week, monocytes and macrophages (Mo/Mac) rapidly accumulate in the injured nerve and undergo extensive metabolic reprogramming. Proinflammatory Mo/Mac with a high glycolytic flux dominate the early injury response and rapidly give way to inflammation resolving Mac, programmed toward oxidative phosphorylation. Nerve crush injury …

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Bioaugmentation With Tetrasphaera To Improve Biological Phosphorus Removal From Anaerobic Digestate Of Swine Wastewater, Jiaxin Wang, Chiqian Zhang, Ping Li, Hui Xu, Weiqu Wang, Weizhao Yin, Jinhua Wu, Zhiqiang Hu Feb 2023

Bioaugmentation With Tetrasphaera To Improve Biological Phosphorus Removal From Anaerobic Digestate Of Swine Wastewater, Jiaxin Wang, Chiqian Zhang, Ping Li, Hui Xu, Weiqu Wang, Weizhao Yin, Jinhua Wu, Zhiqiang Hu

Faculty Publications

Tetrasphaera-enhanced biological phosphorus removal (T-EBPR) was developed by augmenting conventional EBPR (C-EBPR) with Tetrasphaera to improve phosphorus removal from anaerobic digestate of swine wastewater. At influent total phosphorus (TP) concentrations of 45 to 55 mg/L, T-EBPR achieved effluent TP concentration of 4.17 ± 1.02 mg/L, 54% lower than that in C-EBPR (8.98 ± 0.76 mg/L). The enhanced phosphorous removal was presumably due to the synergistic effect of Candidatus Accumulibacter and Tetrasphaera occupying different ecological niches. Bioaugmentation with Tetrasphaera promoted the polyphosphate accumulation metabolism depending more on the glycolysis pathway, as evidenced by an increase in intracellular storage compounds of glycogen …

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Peat Decomposition And Erosion Contribute To Pond Deepening In A Temperate Salt Marsh, Sheron Luk, Meagan J. Eagle, Giulio Mariotti, Kelsey Gosselin, Jonathan Sanderman, Amanda C. Spivak Feb 2023

Peat Decomposition And Erosion Contribute To Pond Deepening In A Temperate Salt Marsh, Sheron Luk, Meagan J. Eagle, Giulio Mariotti, Kelsey Gosselin, Jonathan Sanderman, Amanda C. Spivak

Faculty Publications

Salt marsh ponds expand and deepen over time, potentially reducing ecosystem carbon storage and resilience. The water filled volumes of ponds represent missing carbon due to prevented soil accumulation and removal by erosion and decomposition. Removal mechanisms have different implications as eroded carbon can be redistributed while decomposition results in loss. We constrained ponding effects on carbon dynamics in a New England marsh and determined whether expansion and deepening impact nearby soils by conducting geochemical characterizations of cores from three ponds and surrounding high marshes and models of wind-driven erosion. Radioisotope profiles demonstrate that ponds are not depositional environments and …

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Assessing Impacts Of Climate Change On Selected Foundation Species And Ecosystem Services In The South-Central Usa, R. James Ansley, Victor H. Rivera-Monroy, Kerry Griffis-Kyle, Bruce Hoagland, Amanda Emert, Todd Fagin, Scott R. Loss, Heather R. Mccarthy, Nicholas G. Smith, Elizabeth F. Waring Feb 2023

Assessing Impacts Of Climate Change On Selected Foundation Species And Ecosystem Services In The South-Central Usa, R. James Ansley, Victor H. Rivera-Monroy, Kerry Griffis-Kyle, Bruce Hoagland, Amanda Emert, Todd Fagin, Scott R. Loss, Heather R. Mccarthy, Nicholas G. Smith, Elizabeth F. Waring

Faculty Publications

Climate change, interacting with and exacerbating anthropogenic modifications to the landscape, is altering ecosystem structure and function, biodiversity, and species distributions. Among the most visible short-term impacts are the altered ecological roles of foundation species—those species, native or non-native—that create locally stable environmental conditions and strongly influence ecosystem services. Understanding the future of these species is crucial for projecting impacts on ecosystem services at both local and regional scales. Here we present foundation species by ecoregion study cases across the US South-Central Region (Louisiana, New Mexico, Oklahoma, and Texas), including C4 grasses, mesquite, and northern bobwhite in the Southern Great …

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Metagenomics And Metatranscriptomics Reveal Broadly Distributed, Active, Novel Methanotrophs In The Gulf Of Mexico Hypoxic Zone And In The Marine Water Column, Kathryn L. Howe, Kiley W. Seitz, Lauren G. Campbell, Brett J. Baker, J. Cameron Thrash, Nancy N. Rabalais, Mary Kate Rogener, Samantha B. Joye, Olivia U. Mason Feb 2023

Metagenomics And Metatranscriptomics Reveal Broadly Distributed, Active, Novel Methanotrophs In The Gulf Of Mexico Hypoxic Zone And In The Marine Water Column, Kathryn L. Howe, Kiley W. Seitz, Lauren G. Campbell, Brett J. Baker, J. Cameron Thrash, Nancy N. Rabalais, Mary Kate Rogener, Samantha B. Joye, Olivia U. Mason

Faculty Publications

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role …

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Potential Repercussions Of Offshore Wind Energy Development In The Northeast United States For The Atlantic Surfclam Survey And Population Assessment, Sarah Borsetti, Daphne M. Munroe, Andrew M. Scheld, Eric N. Powell, John M. Klinck, Eileen E. Hofmann Feb 2023

Potential Repercussions Of Offshore Wind Energy Development In The Northeast United States For The Atlantic Surfclam Survey And Population Assessment, Sarah Borsetti, Daphne M. Munroe, Andrew M. Scheld, Eric N. Powell, John M. Klinck, Eileen E. Hofmann

Faculty Publications

The Atlantic surfclam Spisula solidissima fishery, which spans the U.S. Northeast continental shelf, is among the most exposed to offshore wind energy development impacts because of the overlap of fishing grounds with wind energy lease areas, the hydraulic dredges used by the fishing vessels, and the location of vessel home ports relative to the fishing grounds. The Atlantic surfclam federal assessment survey is conducted using a commercial fishing vessel in locations that overlap with the offshore wind energy development. Once wind energy turbines, cables, and scour protection are installed, survey operations within wind energy lease areas may be curtailed or …

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Influence Of Soldiers On Exploratory Foraging Behavior In The Formosan Subterranean Termite, Coptotermes Formosanus (Blattodea: Rhinotermitidae), Joseph Mccarthy, Arjun Khadka, Hasim Hakanoglu, Qian Sun Feb 2023

Influence Of Soldiers On Exploratory Foraging Behavior In The Formosan Subterranean Termite, Coptotermes Formosanus (Blattodea: Rhinotermitidae), Joseph Mccarthy, Arjun Khadka, Hasim Hakanoglu, Qian Sun

Faculty Publications

Termites are eusocial insects that live in organized colonies consisting of reproductives, workers, and soldiers. Soldiers are specialized for defense but are expensive to maintain, as they are incapable of husbandry and must be fed and groomed by workers. The soldiers of several species influence foraging behavior by acting as scouts that initiate foraging or by mediating worker behavioral plasticity during food exploration. These behaviors imply that soldiers may play a keystone role in termite colony function, apart from defense. Subterranean termite workers tunnel through soil in search of food while accompanied by varying proportions of soldiers, depending on the …

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Genetic Characterization Of The Partial Disease Resistance Of Rice To Bacterial Panicle Blight And Sheath Blight By Combined Qtl Linkage And Qtl-Seq Analyses, John Christian Ontoy, Bishnu Shrestha, Hari Sharan Karki, Inderjit Barphagha, Brijesh Angira, Adam Famoso, Jong Hyun Ham Feb 2023

Genetic Characterization Of The Partial Disease Resistance Of Rice To Bacterial Panicle Blight And Sheath Blight By Combined Qtl Linkage And Qtl-Seq Analyses, John Christian Ontoy, Bishnu Shrestha, Hari Sharan Karki, Inderjit Barphagha, Brijesh Angira, Adam Famoso, Jong Hyun Ham

Faculty Publications

Bacterial panicle blight (BPB) and sheath blight (SB) are major diseases of rice and few cultivars have shown a high level of resistance to these diseases. A recombinant inbred line (RIL) population developed from the U.S. cultivars Jupiter (moderately resistant) and Trenasse (susceptible) was investigated to identify loci associated with the partial disease resistance to BPB and SB. Disease phenotypes in BPB and SB, as well as the days-to-heading (DTH) trait, were evaluated in the field. DTH was correlated to BPB and SB diseases, while BPB was positively correlated to SB in the field trials with this RIL population. Genotyping …

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Wheat Long Noncoding Rnas From Organelle And Nuclear Genomes Carry Conserved Microrna Precursors Which May Together Comprise Intricate Networks In Insect Responses, Bala Ani Akpinar, Tugdem Muslu, Gadi V.P. Reddy, Munevver Dogramaci, Hikmet Budak Feb 2023

Wheat Long Noncoding Rnas From Organelle And Nuclear Genomes Carry Conserved Microrna Precursors Which May Together Comprise Intricate Networks In Insect Responses, Bala Ani Akpinar, Tugdem Muslu, Gadi V.P. Reddy, Munevver Dogramaci, Hikmet Budak

Faculty Publications

Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also …

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Wetland Occupancy By Duck Broods In Cropland-Dominated Landscapes Of The United States Prairie Pothole Region, Blake J. Mitchell, Catrina V. Terry, Kevin M. Ringelman, Kaylan M. Kemink, Michael J. Anteau, Adam K. Janke Feb 2023

Wetland Occupancy By Duck Broods In Cropland-Dominated Landscapes Of The United States Prairie Pothole Region, Blake J. Mitchell, Catrina V. Terry, Kevin M. Ringelman, Kaylan M. Kemink, Michael J. Anteau, Adam K. Janke

Faculty Publications

The Prairie Pothole Region (PPR) is globally important for breeding waterfowl but has been altered via wetland drainage and grassland conversion to accommodate agricultural land use. Thus, understanding the ecology of waterfowl in these highly modified landscapes is essential for their conservation. Brood occurrence is the cumulative outcome of key life-history events including pair formation and territory establishment, nest success, and early brood survival. We applied new technological advances in brood surveying methods to understand brood use of wetlands and how land use and wetland-specific factors influenced brood use of 413 wetlands in crop-dominated landscapes in the PPR of Iowa, …

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Framework Of The Alu Subfamily Evolution In The Platyrrhine Three-Family Clade Of Cebidae, Callithrichidae, And Aotidae, Jessica M. Storer, Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, Mark A. Batzer Feb 2023

Framework Of The Alu Subfamily Evolution In The Platyrrhine Three-Family Clade Of Cebidae, Callithrichidae, And Aotidae, Jessica M. Storer, Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, Mark A. Batzer

Faculty Publications

The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire …

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Identification Of Differential-Expressed Genes In Banana-Biostimulant Interaction Using Suppression Subtractive Hybridization, Tatiana Chavez-Navarrete, Luis Sanchez-Timm, Ricardo Pacheco-Coello, Niranjan Baisakh, Efrén Santos-Ordóñez Feb 2023

Identification Of Differential-Expressed Genes In Banana-Biostimulant Interaction Using Suppression Subtractive Hybridization, Tatiana Chavez-Navarrete, Luis Sanchez-Timm, Ricardo Pacheco-Coello, Niranjan Baisakh, Efrén Santos-Ordóñez

Faculty Publications

The use of environmental-friendly agricultural inputs to increase yield in crops could reduce environmental contamination and alleviate (a)biotic stress. In this study, we applied a foliar liquid biostimulant to banana plants, which was developed from the anaerobic fermentation of microorganisms with organic remains (manure and plant waste) and minerals to use as environmental-friendly product. To determine the effect of this biostimulant in the plants, a Suppression Subtractive Hybridization (SSH) library was developed from banana leaves in greenhouse conditions. Furthermore, salicylic and jasmonic pathways activation was evaluated by gene expression analysis. First, the application of the biostimulant to banana leaves increased …

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