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Predicting Market Squid (Doryteuthis Opalescens) Landings From Pre-Recruit Abundance, Stephen Ralston, Emmanis Dorval, Laura Ryley, Keith M. Sakuma, John C. Field Jan 2018

Predicting Market Squid (Doryteuthis Opalescens) Landings From Pre-Recruit Abundance, Stephen Ralston, Emmanis Dorval, Laura Ryley, Keith M. Sakuma, John C. Field

United States Department of Commerce: Staff Publications

The fishery for market squid (Doryteuthis opalescens) in California is typical of many of the world’s cephalopod fisheries, in that a very short life span and the effect of environmental forcing on recruitment result in enormous interannual variability in catches and population size. We evaluate the utility of a pre-recruit index of squid abundance that is based on midwater trawl sampling in the 3–5 months preceding the onset of the fishery as a basis for predicting landings. Catches in the survey largely represent squid in the 30–50 mm dorsal mantle length size range, representing individuals 30–90 day old. …

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Simulated Computational Model Lesson Improves Foundational Systems Thinking Skills And Conceptual Knowledge In Biology Students, H. E. Bergan-Roller, N. J. Galt, Christopher J. Chizinski, T. Helikar, J. T. Dauer Jan 2018

Simulated Computational Model Lesson Improves Foundational Systems Thinking Skills And Conceptual Knowledge In Biology Students, H. E. Bergan-Roller, N. J. Galt, Christopher J. Chizinski, T. Helikar, J. T. Dauer

School of Natural Resources: Faculty Publications

No abstract provided.

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Imaging Spectrometry And Fluorometry In Support Of Flex: What Can We Learn From Multi-Scale Experiments, John A. Gamon, G. Y. Hmimina, G. Miao, K. Guan, K. Springer, R. Wang, R. Yu, H. Gholizadeh, R. Moore, E. Walter-Shea, T. Arkebauer, A. Suyker, T. Franz, B. Wardlow Jan 2018

Imaging Spectrometry And Fluorometry In Support Of Flex: What Can We Learn From Multi-Scale Experiments, John A. Gamon, G. Y. Hmimina, G. Miao, K. Guan, K. Springer, R. Wang, R. Yu, H. Gholizadeh, R. Moore, E. Walter-Shea, T. Arkebauer, A. Suyker, T. Franz, B. Wardlow

School of Natural Resources: Faculty Publications

No abstract provided.

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Flexible Robotic Actuators, Stephen A. Morin, Robert F. Shepherd, Adam Stokes, Filip Ilievski, Ramses V. Martinez, Jamie L. Branch, Carina R. Fish, Lihua Jin, Rui M. D. Nunes, Zhigang Suo, George M. Whitesides Jan 2018

Flexible Robotic Actuators, Stephen A. Morin, Robert F. Shepherd, Adam Stokes, Filip Ilievski, Ramses V. Martinez, Jamie L. Branch, Carina R. Fish, Lihua Jin, Rui M. D. Nunes, Zhigang Suo, George M. Whitesides

Department of Chemistry: Faculty Publications

Systems and methods for providing flexible robotic actuators are disclosed. Some embodiments of the disclosed subject matter include a soft robot capable of providing a radial deflection motions; a soft tentacle actuator capable of providing a variety of motions and providing transportation means for various types of materials; and a hybrid robotic system that retains desirable characteristics of both soft robots and hard robots. Some embodiments of the disclosed subject matter also include methods for operating the dis closed robotic systems.

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The Signature Of Undetected Change: An Exploratory Electrotomographic Investigation Of Gradual Change Blindness, John E. Kiat, Michael D. Dodd, Robert F. Belli, Jacob E. Cheadle Jan 2018

The Signature Of Undetected Change: An Exploratory Electrotomographic Investigation Of Gradual Change Blindness, John E. Kiat, Michael D. Dodd, Robert F. Belli, Jacob E. Cheadle

Department of Psychology: Faculty Publications

Neuroimaging-based investigations of change blindness, a phenomenon in which seemingly obvious changes in visual scenes fail to be detected, have significantly advanced our understanding of visual awareness. The vast majority of prior investigations, however, utilize paradigms involving visual disruptions (e.g., intervening blank screens, saccadic movements, “mudsplashes”), making it difficult to isolate neural responses toward visual changes cleanly. To address this issue in this present study, high-density EEG data (256 channel) were collected from 25 participants using a paradigm in which visual changes were progressively introduced into detailed real-world scenes without the use of visual disruption. Oscillatory activity associated with undetected …

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A Generative Model Of Cognitive State From Task And Eye Movements, W. Joseph Macinnes, Amelia R. Hunt, Alasdair D. F. Clarke, Michael D. Dodd Jan 2018

A Generative Model Of Cognitive State From Task And Eye Movements, W. Joseph Macinnes, Amelia R. Hunt, Alasdair D. F. Clarke, Michael D. Dodd

Department of Psychology: Faculty Publications

The early eye tracking studies of Yarbus provided descriptive evidence that an observer’s task influences patterns of eye movements, leading to the tantalizing prospect that an observer’s intentions could be inferred from their saccade behavior. We investigate the predictive value of task and eye movement properties by creating a computational cognitive model of saccade selection based on instructed task and internal cognitive state using a Dynamic Bayesian Network (DBN). Understanding how humans generate saccades under different conditions and cognitive sets links recent work on salience models of low-level vision with higher level cognitive goals. This model provides a Bayesian, cognitive …

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Factor Structure And Gender Invariance Testing For The Sport Anxiety Scale-2 (Sas-2), Leilani Madrigal, Vincenzo Roma, Todd Caze, Arthur C. Maerlender, Debra Hope Jan 2018

Factor Structure And Gender Invariance Testing For The Sport Anxiety Scale-2 (Sas-2), Leilani Madrigal, Vincenzo Roma, Todd Caze, Arthur C. Maerlender, Debra Hope

Center for Brain, Biology, and Behavior: Faculty Publications

This study aimed to provide further psychometric validation of the Sport Anxiety Scale-2 (SAS-2) by assessing the factor structure, invariance across gender, and convergent and divergent validity of the SAS-2 by correlating both related (i.e., anxiety sensitivity, brief fear of negative evaluation, intolerance of uncertainty, and negative affect) and unrelated constructs (i.e., positive affect, self-confidence). A total of 542 current and former competitive athletes completed a questionnaire through Amazon’s Mechanical Turk system. All data were collected via online survey. Participants were randomly assigned to an exploratory factor analysis (n = 271) and confirmatory factor analysis group (n = 271). Results …

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Accumulating Data To Optimally Predict Obesity Treatment (Adopt): Recommendations From The Biological Domain, Michael Rosenbaum, Tanya Agurs-Collins, Molly S. Bray, Kevin D. Hall, Mark Hopkins, Maren Laughlin, Paul S. Maclean, Padma Maruvada, Cary R. Savage, Dana M. Small, Luke Stoeckel Jan 2018

Accumulating Data To Optimally Predict Obesity Treatment (Adopt): Recommendations From The Biological Domain, Michael Rosenbaum, Tanya Agurs-Collins, Molly S. Bray, Kevin D. Hall, Mark Hopkins, Maren Laughlin, Paul S. Maclean, Padma Maruvada, Cary R. Savage, Dana M. Small, Luke Stoeckel

Center for Brain, Biology, and Behavior: Faculty Publications

Background: The responses to behavioral, pharmacological, or surgical obesity treatments are highly individualized. The Accumulating Data to Optimally Predict obesity Treatment (ADOPT) project provides a framework for how obesity researchers, working collectively, can generate the evidence base needed to guide the development of tailored, and potentially more effective, strategies for obesity treatment. Objectives: The objective of the ADOPT biological domain subgroup is to create a list of high-priority biological measures for weight-loss studies that will advance the understanding of individual variability in response to adult obesity treatments. This list includes measures of body composition, energy homeostasis (energy intake and output), …

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Left Lateralized Cerebral Glucose Metabolism Declines In Amyloid-Β Positive Persons With Mild Cognitive Impairment, Christopher M. Weise, Kewei Chen, Yinghua Chen, Xiaoying Kuang, Cary R. Savage, Eric M. Reiman Jan 2018

Left Lateralized Cerebral Glucose Metabolism Declines In Amyloid-Β Positive Persons With Mild Cognitive Impairment, Christopher M. Weise, Kewei Chen, Yinghua Chen, Xiaoying Kuang, Cary R. Savage, Eric M. Reiman

Center for Brain, Biology, and Behavior: Faculty Publications

Background: Previous publications indicate that Alzheimer's Disease (AD) related cortical atrophy may develop in asymmetric patterns, with accentuation of the left hemisphere. Since fluorodeoxyglucose positron emission tomography (FDG PET) measurements of the regional cerebral metabolic rate of glucose (rCMRgl) provide a sensitive and specific marker of neurodegenerative disease progression, we sought to investigate the longitudinal pattern of rCMRgl in amyloid-positive persons with mild cognitive impairment (MCI) and dementia, hypothesizing asymmetric declines of cerebral glucose metabolism. Methods: Using florbetapir PET and cerebrospinal fluid (CSF) measures to define amyloid-β (Aβ) positivity, 40 Aβ negative (Aβ-) cognitively unimpaired controls (CU; 76 ± 5y), …

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Novel Biomarkers Of Physical Activity Maintenance In Midlife Women: Preliminary Investigation, Kelly A. Bosak, Vlad B. Papa, Morgan G. Brucks, Cary R. Savage, Joseph E. Donnelly, Laura E. Martin Jan 2018

Novel Biomarkers Of Physical Activity Maintenance In Midlife Women: Preliminary Investigation, Kelly A. Bosak, Vlad B. Papa, Morgan G. Brucks, Cary R. Savage, Joseph E. Donnelly, Laura E. Martin

Center for Brain, Biology, and Behavior: Faculty Publications

The precision health initiative is leading the discovery of novel biomarkers as important indicators of biological processes or responses to behavior, such as physical activity. Neural biomarkers identified by magnetic resonance imaging (MRI) hold promise to inform future research, and ultimately, for transfer to the clinical setting to optimize health outcomes. This study investigated resting-state and functional brain biomarkers between midlife women who were maintaining physical activity in accordance with the current national guidelines and previously acquired age-matched sedentary controls. Approval was obtained from the Human Subjects Committee. Participants included nondiabetic, healthy weight to overweight (body mass index 19–29.9 kg/m …

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Development Of Ifox-Hunting As A Functional Genomic Tool And Demonstration Of Its Use To Identify Early Senescence-Related Genes In The Polyploid Brassica Napus, Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xi, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang Jan 2018

Development Of Ifox-Hunting As A Functional Genomic Tool And Demonstration Of Its Use To Identify Early Senescence-Related Genes In The Polyploid Brassica Napus, Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xi, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang

Center for Plant Science Innovation: Faculty Publications

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and …

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Conventional And Hyperspectral Time-Series Imaging Of Maize Lines Widely Used In Field Trials, Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C. Schnable Jan 2018

Conventional And Hyperspectral Time-Series Imaging Of Maize Lines Widely Used In Field Trials, Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Background: Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer …

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Single-Molecule Sequencing And Optical Mapping Yields An Improved Genome Of Woodland Strawberry (Fragaria Vesca) With Chromosome-Scale Contiguity, Patrick P. Edger, Robert Vanburen, Marivi Colle, Thomas J. Poorten, Ching Man Wai, Chad E. Niederhuth, Elizabeth I. Alger, Shujun Ou, Charlotte B. Acharya, Jie Wang, Pete Callow, Michael R. Mckain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P. Mower, Janet P. Slovin, Timo Hytonen, Ning Jiang, Kevin L. Childs, Steven J. Knapp Jan 2018

Single-Molecule Sequencing And Optical Mapping Yields An Improved Genome Of Woodland Strawberry (Fragaria Vesca) With Chromosome-Scale Contiguity, Patrick P. Edger, Robert Vanburen, Marivi Colle, Thomas J. Poorten, Ching Man Wai, Chad E. Niederhuth, Elizabeth I. Alger, Shujun Ou, Charlotte B. Acharya, Jie Wang, Pete Callow, Michael R. Mckain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P. Mower, Janet P. Slovin, Timo Hytonen, Ning Jiang, Kevin L. Childs, Steven J. Knapp

Center for Plant Science Innovation: Faculty Publications

Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes.We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ~7.9 million base pairs (Mb), representing a ~300-fold improvement of the previous version. The vast majority (>99.8%) …

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Identification Of Bottlenecks In The Accumulation Of Cyclic Fatty Acids In Camelina Seed Oil, Xiao-Hong Yu, Rebecca E. Cahoon, Patrick J. Horn, Hai Shi, Richa R. Prakash, Yuanheng Cai, Maegan Hearney, Kent D. Chapman, Edgar B. Cahoon, Jorg Schwender, John Shanklin Jan 2018

Identification Of Bottlenecks In The Accumulation Of Cyclic Fatty Acids In Camelina Seed Oil, Xiao-Hong Yu, Rebecca E. Cahoon, Patrick J. Horn, Hai Shi, Richa R. Prakash, Yuanheng Cai, Maegan Hearney, Kent D. Chapman, Edgar B. Cahoon, Jorg Schwender, John Shanklin

Center for Plant Science Innovation: Faculty Publications

Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. Thus, to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation and seedling …

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Integrating Phylogenetic And Network Approaches To Study Gene Family Evolution: The Case Of The Agamous Family Of Floral Genes, Daniel Santana De Carvalho, James C. Schnable, Ana Maria R. Almeida Jan 2018

Integrating Phylogenetic And Network Approaches To Study Gene Family Evolution: The Case Of The Agamous Family Of Floral Genes, Daniel Santana De Carvalho, James C. Schnable, Ana Maria R. Almeida

Center for Plant Science Innovation: Faculty Publications

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations …

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Functional Modeling Of Plant Growth Dynamics, Y. Xu, Y. Qiu, James C. Schnable Jan 2018

Functional Modeling Of Plant Growth Dynamics, Y. Xu, Y. Qiu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Recent advances in automated plant phenotyping have enabled the collection of time series measurements from the same plants of a wide range of traits at different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change among different plant genotypes and different treatment conditions. Two widely used methods of modeling growth with time are pointwise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Pointwise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to …

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Gipc Glcnac Glycosyltransferase, Toshiki Ishikawa, Lin Fang, Emilie A. Rennie, Julien Sechet, Jingwei Yan, Beibei Jing, William Moore, Edgar B. Cahoon, Henrik V. Scheller, Maki Kawai-Yamada, Jenny C. Mortimer Jan 2018

Gipc Glcnac Glycosyltransferase, Toshiki Ishikawa, Lin Fang, Emilie A. Rennie, Julien Sechet, Jingwei Yan, Beibei Jing, William Moore, Edgar B. Cahoon, Henrik V. Scheller, Maki Kawai-Yamada, Jenny C. Mortimer

Center for Plant Science Innovation: Faculty Publications

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structure, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis thaliana, and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain N-acetylglucosamine (GlcNAc) and glucosamine …

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Sma1, A Homolog Of The Splicing Factor Prp28, Has A Multifaceted Role In Mirna Biogenesis In Arabidopsis, Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu Jan 2018

Sma1, A Homolog Of The Splicing Factor Prp28, Has A Multifaceted Role In Mirna Biogenesis In Arabidopsis, Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEADbox pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences primiRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also …

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Generation And Evaluation Of Modified Opaque-2 Popcorn Suggests A Route To Quality Protein Popcorn, Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, David R. Holding Jan 2018

Generation And Evaluation Of Modified Opaque-2 Popcorn Suggests A Route To Quality Protein Popcorn, Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Center for Plant Science Innovation: Faculty Publications

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC2F4 individuals with vitreous kernels were confirmed to be o2 mutants by …

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Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook Jan 2018

Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook

Center for Plant Science Innovation: Faculty Publications

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, …

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Lycophyte Plastid Genomics: Extreme Variation In Gc, Gene And Intron Content And Multiple Inversions Between A Direct And Inverted Orientation Of The Rrna Repeat, Jeffrey P. Mower, Peng-Fei Ma, Felix Grewe, Alex Taylor, Todd P. Michael, Robert Vanburen, Yin-Long Qiu Jan 2018

Lycophyte Plastid Genomics: Extreme Variation In Gc, Gene And Intron Content And Multiple Inversions Between A Direct And Inverted Orientation Of The Rrna Repeat, Jeffrey P. Mower, Peng-Fei Ma, Felix Grewe, Alex Taylor, Todd P. Michael, Robert Vanburen, Yin-Long Qiu

Center for Plant Science Innovation: Faculty Publications

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) …

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The Role Of Type Iii Effectors From Xanthomonas Axonopodis Pv. Manihotis In Virulence And Suppression Of Plant Immunity, Cesar Augusto Medina, Paola Andrea Reyes, Cesar Augusto Trujillo, Juan Luis Gonzalez, David Alejandro Bejarano, Nathaly Andrea Montenegro, Jonathan M. Jacobs, Anna Joe, Silvia Restrepo, James R. Alfano, Adriana Bernal Jan 2018

The Role Of Type Iii Effectors From Xanthomonas Axonopodis Pv. Manihotis In Virulence And Suppression Of Plant Immunity, Cesar Augusto Medina, Paola Andrea Reyes, Cesar Augusto Trujillo, Juan Luis Gonzalez, David Alejandro Bejarano, Nathaly Andrea Montenegro, Jonathan M. Jacobs, Anna Joe, Silvia Restrepo, James R. Alfano, Adriana Bernal

Center for Plant Science Innovation: Faculty Publications

Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role …

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Xanthomonas Oryzae Pv. Oryzae Tale Proteins Recruit Ostfiiaγ1 To Compensate For The Absence Of Ostfiiaγ5 In Bacterial Blight In Rice, Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R. Alfano Jan 2018

Xanthomonas Oryzae Pv. Oryzae Tale Proteins Recruit Ostfiiaγ1 To Compensate For The Absence Of Ostfiiaγ5 In Bacterial Blight In Rice, Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R. Alfano

Center for Plant Science Innovation: Faculty Publications

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted …

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From Icon Of Empire To National Emblem: New Evidence For The Fallow Deer Of Barbuda, Sophia Perdikaris, Allison Bain, Sandrine Grouard, Karis Baker, Edith Gonzalez, A. Rus Hoelzel, Holly Miller, Reaksha Persaud, Naomi Sykes Jan 2018

From Icon Of Empire To National Emblem: New Evidence For The Fallow Deer Of Barbuda, Sophia Perdikaris, Allison Bain, Sandrine Grouard, Karis Baker, Edith Gonzalez, A. Rus Hoelzel, Holly Miller, Reaksha Persaud, Naomi Sykes

School of Global Integrative Studies: Faculty Publications

Barbuda and Antigua’s national animal is the fallow deer, Dama dama dama, a species native to the eastern Mediterranean that has been transported around the world by people during the last 8000 years. The timing and circumstances by which fallow deer came to be established on Barbuda are currently uncertain but, by examining documentary, osteological and genetic evidence, this paper will consider the validity of existing theories. It will review the dynamics of human–Dama relationships from the 1500s AD to the present day and consider how the meaning attached to this species has changed through time: from a …

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Altered Ratio Of T Follicular Helper Cells To T Follicular Regulatory Cells Correlates With Autoreactive Antibody Response In Simian Immunodeficiency Virus–Infected Rhesus Macaques, Wenjin Fan, Andrew James Demers, Yanmin Wan, Qingsheng Li Jan 2018

Altered Ratio Of T Follicular Helper Cells To T Follicular Regulatory Cells Correlates With Autoreactive Antibody Response In Simian Immunodeficiency Virus–Infected Rhesus Macaques, Wenjin Fan, Andrew James Demers, Yanmin Wan, Qingsheng Li

Nebraska Center for Virology: Faculty Publications

Individuals with chronic HIV-1 infection have an increased prevalence of autoreactive Abs. Many of the isolated HIV broadly neutralizing Abs from these individuals are also autoreactive. However, the underlying mechanism(s) that produce these autoreactive broadly neutralizing Abs remains largely unknown. The highly regulated coordination among B cells, T follicular helper (TFH) cells, and T follicular regulatory (TFR) cells in germinal centers (GCs) of peripheral lymphatic tissues (LTs) is essential for defense against pathogens while also restricting autoreactive responses. We hypothesized that an altered ratio of TFH/TFR cells in the GC contributes to the …

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Applying Eye-Tracking Research In Education And Communication To Agricultural Education And Communication: A Review Of Literature, Holli R. Leggette, Amber H. Rice, Candis Carraway, Marshall A. Baker, Nathan W. Conner Jan 2018

Applying Eye-Tracking Research In Education And Communication To Agricultural Education And Communication: A Review Of Literature, Holli R. Leggette, Amber H. Rice, Candis Carraway, Marshall A. Baker, Nathan W. Conner

Department of Agricultural Leadership, Education, and Communication: Faculty Publications

The purpose of this integrative literature review was to synthesize the eye-tracking literature related to education and communication in the Social Sciences Citation Index (SSCI) to formulate a conceptual model and develop a research agenda that guides eye-tracking research in agricultural education and communication. To do so, we reviewed the literature to identify basic elements of eye-tracking research, examined specific variables related to eye-tracking research, and synthesized the findings into a conceptual model. We found and reviewed 77 articles published between 2010 and 2016 within education (56) and communication (21). Research implications for agricultural education included an examination of classroom …

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On-Road Emissions Of Ammonia: An Underappreciated Source Of Atmospheric Nitrogen Deposition, Mark E. Fenn, Andrzej Bytnerowicz, Susan L. Schilling, Dena M. Vallano, Erika S. Zavaleta, Stuart B. Weiss, Connor Morozumi, Linda H. Geiser, Kenneth Hanks Jan 2018

On-Road Emissions Of Ammonia: An Underappreciated Source Of Atmospheric Nitrogen Deposition, Mark E. Fenn, Andrzej Bytnerowicz, Susan L. Schilling, Dena M. Vallano, Erika S. Zavaleta, Stuart B. Weiss, Connor Morozumi, Linda H. Geiser, Kenneth Hanks

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

We provide updated spatial distribution and inventory data for on-road NH3 emissions for the continental United States (U.S.) On-road NH3 emissions were determined from on-road CO2 emissions data and empirical NH3:CO2 vehicle emissions ratios. Emissions of NH3 from on-road sources in urbanized regions are typically 0.1– 1.3 t km−2 yr−1 while NH3 emissions in agricultural regions generally range from 0.4–5.5 t km−2 yr−1, with a few hot spots as high as 5.5–11.2 t km−2 yr−1. Counties with higher vehicle NH3 emissions than from agriculture …

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Ecological-Economic Assessment Of The Effects Of Freshwater Flow In The Florida Everglades On Recreational Fisheries, Christina Estela Brown, Mahadev G. Bhat, Jennifer S. Rehage, Ali Mirchi, Ross Boucek, Victor Engel, Jerald S. Ault, Pallab Mozumder, David Watkins, Michael Sukop Jan 2018

Ecological-Economic Assessment Of The Effects Of Freshwater Flow In The Florida Everglades On Recreational Fisheries, Christina Estela Brown, Mahadev G. Bhat, Jennifer S. Rehage, Ali Mirchi, Ross Boucek, Victor Engel, Jerald S. Ault, Pallab Mozumder, David Watkins, Michael Sukop

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

This research develops an integrated methodology to determine the economic value to anglers of recreational fishery ecosystem services in Everglades National Park that could result from different water management scenarios. The study first used bio-hydrological models to link managed freshwater inflows to indicators of fishery productivity and ecosystem health, then link those models to anglers' willingness-to-pay for various attributes of the recreational fishing experience and monthly fishing effort. This approach allowed us to estimate the foregone economic benefits of failing to meet monthly freshwater delivery targets. The study found that the managed freshwater delivery to the Park had declined substantially …

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Mixing Of Two Greater Sandhill Crane Populations In Northeast Oregon, M. Cathy Nowak, Krista J. Mougey, Daniel P. Collins, Blake A. Grisham Jan 2018

Mixing Of Two Greater Sandhill Crane Populations In Northeast Oregon, M. Cathy Nowak, Krista J. Mougey, Daniel P. Collins, Blake A. Grisham

Proceedings of the North American Crane Workshop

The Oregon Department of Fish and Wildlife (ODFW) Ladd Marsh Wildlife Area in northeast Oregon hosts a small group of nesting greater sandhill cranes (Grus canadensis tabida). There were no data on where these birds wintered, and we had no understanding of how these birds fit into the larger picture of western sandhill crane population delineation. ODFW began color-banding pre-fledging colts in 2007 and added satellite tracking with platform transmitter terminals (PTTs) in 2015. To date, we have captured 15 colts and 13 adults and marked them with color bands. We also fitted 1 colt and 8 adult …

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An Updated Distribution Map For The Lower Colorado River Valley Population Of Greater Sandhill Cranes, Blake A. Grisham, Daniel P. Collins, Kammie L. Kruse, Courtenay M. Conring, Jeffrey M. Knetter, Warren C. Conway Jan 2018

An Updated Distribution Map For The Lower Colorado River Valley Population Of Greater Sandhill Cranes, Blake A. Grisham, Daniel P. Collins, Kammie L. Kruse, Courtenay M. Conring, Jeffrey M. Knetter, Warren C. Conway

Proceedings of the North American Crane Workshop

The U.S. Fish and Wildlife Service (USFWS) recognizes 6 migratory populations of sandhill cranes (Grus canadensis) in the United States, 4 of which occur in or west of the Rocky Mountains. Traditionally the Lower Colorado River Valley Population (LCRVP; greater sandhill crane [G. c. tabida]) was thought to be distributed across the Imperial (California) and Lower Colorado River (Arizona) Valleys, southward into Mexico via the Colorado River delta in winter and northeastern Nevada (Elko and White Pine Counties) during summer. Conservation and management concern exists over known distribution based on winter and summer surveys because discrepancies …

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