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The Soybean Aphid Suction Trap Network: Sampling The Aerobiological “Soup”, Doris Lagos-Kutz, David J. Voegtlin, David Onstad, David Hogg, David Ragsdale, Kelley Tilmon, Erin Hodgson, Christina Difonzo, Russell Groves, Christian Krupke, Joseph Laforest, Nicholas J. Selter, Emily Duerr, Benjamin Bradford, Glen L. Hartman Apr 2020

The Soybean Aphid Suction Trap Network: Sampling The Aerobiological “Soup”, Doris Lagos-Kutz, David J. Voegtlin, David Onstad, David Hogg, David Ragsdale, Kelley Tilmon, Erin Hodgson, Christina Difonzo, Russell Groves, Christian Krupke, Joseph Laforest, Nicholas J. Selter, Emily Duerr, Benjamin Bradford, Glen L. Hartman

Entomology Publications

The initiation of the soybean aphid suction trap network (STN) in 2001 marked the beginning of a rich and fruitful collaborative effort that has produced a wealth of data about the soybean aphid, other insect species, and other organisms that make up the aerobiological “soup.” Collaboration among researchers, extension specialists, and agriculturalists has provided information about seasonal migration patterns of the soybean aphid and monitoring of other insect species. The physical collections of the “soup” have been stored and used for past research, and will serve as a foundation for future research.


Observations Show That Wind Farms Substantially Modify The Atmospheric Boundary Layer Thermal Stratification Transition In The Early Evening, Daniel A. Rajewski, Eugene S. Takle, Andy Vanloocke, Samantha L. Purdy Mar 2020

Observations Show That Wind Farms Substantially Modify The Atmospheric Boundary Layer Thermal Stratification Transition In The Early Evening, Daniel A. Rajewski, Eugene S. Takle, Andy Vanloocke, Samantha L. Purdy

Agronomy Publications

Single wind turbines and large wind farms modify local scales of atmospheric boundary layer (ABL) turbulence through different mechanisms dependent on location within the wind farm. These changes in turbulence scales would most likely have notable influence on surface fluxes and microclimate during the afternoon and early evening stability transition. Profiles of Richardson number and shear and buoyancy from 1‐Hz tall tower measurements in and near a wind farm in an agricultural landscape were used to quantify departures in stability characteristics during the fallow seasons. A single turbine wake decoupled turbulent connection between the surface and above the wind ...


Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt Mar 2020

Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt

Agronomy Publications

Doubled haploid (DH) technology has changed the maize-breeding landscape in recent years. Traditionally, DH production requires the use of chemical doubling agents to induce haploid genome doubling and, subsequently, male fertility. These chemicals can be harmful to humans and the plants themselves, and typically result in a doubling rate of 10%–30%. Spontaneous genome doubling and male fertility of maize haploids, without using chemical doubling agents, have been observed to a limited extent, for nearly 70 years. Rates of spontaneous haploid genome doubling (SHGD) have ranged from less than 5% to greater than 50%. Recently, there has been increased interest ...


Genetic And Genomic Characterization Of Vulva Size Traits In Yorkshire And Landrace Gilts, Flor-Anita Corredor, Leticia P. Sanglard, Richard J. Leach, Jason W. Ross, Aileen F. Keating, Nick V. L. Serão Mar 2020

Genetic And Genomic Characterization Of Vulva Size Traits In Yorkshire And Landrace Gilts, Flor-Anita Corredor, Leticia P. Sanglard, Richard J. Leach, Jason W. Ross, Aileen F. Keating, Nick V. L. Serão

Animal Science Publications

Background: Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits.

Results: Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0 ...


Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital Mar 2020

Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital

Office of Biotechnology Publications

Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a’s natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive ...


Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele Mar 2020

Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of workflows. Scripting is often used, but it has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides high level APIs to popular RNA-Seq tools. Pipelines can be customized by ...


Survival Of White-Tailed Deer Fawns In Central Iowa, Patrick G. Mcgovern, Stephen J. Dinsmore, Julie A. Blanchong Mar 2020

Survival Of White-Tailed Deer Fawns In Central Iowa, Patrick G. Mcgovern, Stephen J. Dinsmore, Julie A. Blanchong

Natural Resource Ecology and Management Publications

Understanding demographic parameters such as survival is important for scientifically sound wildlife management. Survival can vary by region, sex, age-class, habitat, and other factors. White-tailed deer fawn survival is highly variable across the species’ range. While recent studies have investigated fawn survival in several Midwestern states, there have been no published estimates from Iowa for 30 years. We radio-collared 48 fawns in central Iowa from 2015–2017 to estimate survival, home range size, and habitat composition and identity causes of mortality. Estimated fawn survival (± SE) was similar to other Midwest studies at 30 (0.78 ± 0.07)) and 60 days ...


Serum Vitamin B12, And Related Mtrr And Cubilin Genotypes, Predict Neural Outcomes Across The Ad Spectrum, K. E. Mcliman, A. D. Collazo Martinez, Jonathan P. Mochel, Karin D. Allenspach, Auriel A. Willette Mar 2020

Serum Vitamin B12, And Related Mtrr And Cubilin Genotypes, Predict Neural Outcomes Across The Ad Spectrum, K. E. Mcliman, A. D. Collazo Martinez, Jonathan P. Mochel, Karin D. Allenspach, Auriel A. Willette

Biomedical Sciences Publications

Epidemiological studies show mixed findings for serum vitamin B12 and both cognitive and regional volume outcomes. No studies to date have comprehensively examined, in non-supplemented individuals, serum B12 level associations with neurodegeneration, hypometabolism, and cognition across the Alzheimer's disease (AD) spectrum. Serum vitamin B12 was assayed from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL). Voxel-wise analyses regressed B12 levels against regional gray matter (GM) volume and glucose metabolism (p


An Environmental And Economic Analysis Of Flocculation Technology Applied To A Corn-Based Ethanol Plant, Maria C. T. B. Oliveira, Kurt A. Rosentrater Feb 2020

An Environmental And Economic Analysis Of Flocculation Technology Applied To A Corn-Based Ethanol Plant, Maria C. T. B. Oliveira, Kurt A. Rosentrater

Agricultural and Biosystems Engineering Publications

The stimulation of renewable fuel production is related to the environmental issues resulting from the extraction and utilization of fossil fuels. Although corn-based ethanol is one of the leading renewable fuels and promises to mitigate these environmental impacts, it generates large volumes of wastewater with high concentrations of organic material (CODcr > 30,000 mg/L) and low pH (3.5–4.5), which leads to serious environmental concerns. A common method of treatment of distillery wastewater is the Dry Distilled Grain Soluble (DDGS) process, which separates liquid and solid fractions; however, a disadvantage of this process is its high ...


Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau Feb 2020

Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

Plant epidermal cells express unique molecular machinery that juxtapose the assembly of intracellular lipid components and the unique extracellular cuticular lipids that are unidirectionally secreted to plant surfaces. In maize (Zea mays L.), mutations at the glossy2 (gl2) locus affect the deposition of extracellular cuticular lipids. Sequence-based genome scanning identified a novel gl2 homolog in the maize genome, Gl2-like. Sequence homology identifies that both the Gl2-like and Gl2 genes are members of the BAHD superfamily of acyltransferases, with close sequence homology to the Arabidopsis CER2 gene. Transgenic experiments demonstrate that Gl2-like and Gl2 functionally complement the Arabidopsis cer2 mutation, with ...


Population Modeling Of Tumor Growth Curves And The Reduced Gompertz Model Improve Prediction Of The Age Of Experimental Tumors, Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullin, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sebastien Benzekry Feb 2020

Population Modeling Of Tumor Growth Curves And The Reduced Gompertz Model Improve Prediction Of The Age Of Experimental Tumors, Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullin, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sebastien Benzekry

Biomedical Sciences Publications

Tumor growth curves are classically modeled by means of ordinary differential equations. In analyzing the Gompertz model several studies have reported a striking correlation between the two parameters of the model, which could be used to reduce the dimensionality and improve predictive power. We analyzed tumor growth kinetics within the statistical framework of nonlinear mixed-effects (population approach). This allowed the simultaneous modeling of tumor dynamics and inter-animal variability. Experimental data comprised three animal models of breast and lung cancers, with 833 measurements in 94 animals. Candidate models of tumor growth included the exponential, logistic and Gompertz models. The exponential and ...


Transcriptome And Parasitome Analysis Of Beet Cyst Nematode Heterodera Schachtii, Abdelnaser M. Elashry, Samer S. Habash, Paramasivan Vijayapalani, Nahal Brocke-Ahmadinejad, Roman Blümel, Arun Seetharam, Heiko Schoof, Florian M. W. Grundler Feb 2020

Transcriptome And Parasitome Analysis Of Beet Cyst Nematode Heterodera Schachtii, Abdelnaser M. Elashry, Samer S. Habash, Paramasivan Vijayapalani, Nahal Brocke-Ahmadinejad, Roman Blümel, Arun Seetharam, Heiko Schoof, Florian M. W. Grundler

Office of Biotechnology Publications

Beet cyst nematodes depend on a set of secretory proteins (effectors) for the induction and maintenance of their syncytial feeding sites in plant roots. In order to understand the relationship between the beet cyst nematode H. schachtii and its host, identification of H. schachtii effectors is crucial and to this end, we sequenced a whole animal pre-infective J2-stage transcriptome in addition to pre- and post-infective J2 gland cell transcriptome using Next Generation Sequencing (NGS) and identified a subset of sequences representing putative effectors. Comparison between the transcriptome of H. schachtii and previously reported related cyst nematodes and root-knot nematodes revealed ...


Effects Of Farrowing Stall Layout And Number Of Heat Lamps On Sow And Piglet Production Performance, Suzanne M. Leonard, Hongwei Xin, Tami M. Brown-Brandl, Brett C. Ramirez, Somak Dutta, Gary A. Rohrer Feb 2020

Effects Of Farrowing Stall Layout And Number Of Heat Lamps On Sow And Piglet Production Performance, Suzanne M. Leonard, Hongwei Xin, Tami M. Brown-Brandl, Brett C. Ramirez, Somak Dutta, Gary A. Rohrer

Agricultural and Biosystems Engineering Publications

Most farrowing facilities in the United States use stalls and heat lamps to improve sow and piglet productivity. This study investigated these factors by comparing production outcomes for three different farrowing stall layouts (traditional, expanded creep area, expanded sow area) and use of one or two heat lamps. Data were collected on 427 sows and their litters over one year. Results showed no statistical differences due to experimental treatment for any of the production metrics recorded, excluding percent stillborn. Parity one sows had fewer piglets born alive (p < 0.001), lower percent mortality (p = 0.001) and over-lay (p = 0.003), and a greater number of piglets weaned (p < 0.001) with lower average daily weight gain (ADG) (p < 0.001) and more uniform litters (p = 0.001) as compared to higher parity sows. Farrowing turn, associated with group/seasonal changes, had a significant impact on most of the production metrics measured. Number of piglets born influenced the percent stillborn (p < 0.001). Adjusted litter size had a significant impact on percent mortality (p < 0.001), percent over-lay (p < 0.001), and number of piglets weaned (p < 0.001). As the number of piglets weaned per litter increased, both piglet ADG and litter uniformity decreased (p < 0.001). This information can be used to guide producers in farrowing facility design.


Vaginal Microbiota Diverges In Sows With Low And High Reproductive Performance After Porcine Reproductive And Respiratory Syndrome Vaccination, L. P. Sanglard, S. Schmitz-Esser, K. A. Gray, D. C. L. Linhares, C. J. Yeoman, J. C. M. Dekkers, M. C. Niederwerder, N. V. L. Serão Feb 2020

Vaginal Microbiota Diverges In Sows With Low And High Reproductive Performance After Porcine Reproductive And Respiratory Syndrome Vaccination, L. P. Sanglard, S. Schmitz-Esser, K. A. Gray, D. C. L. Linhares, C. J. Yeoman, J. C. M. Dekkers, M. C. Niederwerder, N. V. L. Serão

Animal Science Publications

Previous studies have demonstrated evidence for a relationship between the vaginal microbiome and reproductive performance, suggesting the vaginal microbiota may serve as a tool to predict farrowing outcomes in commercial pigs. In this study, we compared the vaginal microbiome in sows with low and high farrowing performance and used it to classify animals with contrasting reproductive outcomes in commercial sows following immune challenge with porcine respiratory and reproductive syndrome (PRRS) vaccination. Eighteen microbes were differentially abundant (q-value < 0.05) between the Low and High farrowing performance groups. Among them, Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae unclassified, Prevotella, and Phascolarctobacterium were also selected in the discriminant and linear regression analyses, and could be used ...


Genome Of Tripterygium Wilfordii And Identification Of Cytochrome P450 Involved In Triptolide Biosynthesis, Lichan Tu, Ping Su, Zhongren Zhang, Linhui Gao, Jiadian Wang, Tianyuan Hu, Jiawei Zhou, Yifeng Zhang, Yujun Zhao, Yuan Liu, Yadi Song, Yuru Tong, Yun Lu, Jian Yang, Cao Xu, Meirong Jia, Reuben J. Peters, Luqi Huang, Wei Gao Feb 2020

Genome Of Tripterygium Wilfordii And Identification Of Cytochrome P450 Involved In Triptolide Biosynthesis, Lichan Tu, Ping Su, Zhongren Zhang, Linhui Gao, Jiadian Wang, Tianyuan Hu, Jiawei Zhou, Yifeng Zhang, Yujun Zhao, Yuan Liu, Yadi Song, Yuru Tong, Yun Lu, Jian Yang, Cao Xu, Meirong Jia, Reuben J. Peters, Luqi Huang, Wei Gao

Biochemistry, Biophysics and Molecular Biology Publications

Triptolide is a trace natural product of Tripterygium wilfordii. It has antitumor activities, particularly against pancreatic cancer cells. Identification of genes and elucidation of the biosynthetic pathway leading to triptolide are the prerequisite for heterologous bioproduction. Here, we report a reference-grade genome of T. wilfordii with a contig N50 of 4.36 Mb. We show that copy numbers of triptolide biosynthetic pathway genes are impacted by a recent whole-genome triplication event. We further integrate genomic, transcriptomic, and metabolomic data to map a gene-to-metabolite network. This leads to the identification of a cytochrome P450 (CYP728B70) that can catalyze oxidation of a ...


Beef Cattle That Respond Differently To Fescue Toxicosis Have Distinct Gastrointestinal Tract Microbiota, Lucas R. Koester, Daniel H. Poole, Nick V. L. Serão, Stephan Schmitz-Esser Feb 2020

Beef Cattle That Respond Differently To Fescue Toxicosis Have Distinct Gastrointestinal Tract Microbiota, Lucas R. Koester, Daniel H. Poole, Nick V. L. Serão, Stephan Schmitz-Esser

Animal Science Publications

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance ...


Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen Feb 2020

Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen

Agronomy Publications

Kernel abortion is common phenomenon in vivo haploid induction and closely linked with haploid induction rate, but little information of kernel abortion is available and its genetic basis still unclear. We used two mapping populations including 186 and 263 F2.3 family lines to analyze the different degree of kernel abortion and identify quantitative trait loci (QTL) responsible for kernel abortion during haploid induction. In total 62 putative QTL, accounting for 3.27–14.70% of the phenotypic variation in kernel abortion traits, were detected across all 10 chromosomes. Ten QTL with over 10% contribution to phenotypic variation were affecting ...


Utilization Of Mechanocatalytic Oligosaccharides By Ethanologenic Escherichia Coli As A Model Microbial Cell Factory, Tao Jin, Mats Käldström, Adriana Benavides, Marcelo D. Kaufman Rechulski, Laura R. Jarboe Feb 2020

Utilization Of Mechanocatalytic Oligosaccharides By Ethanologenic Escherichia Coli As A Model Microbial Cell Factory, Tao Jin, Mats Käldström, Adriana Benavides, Marcelo D. Kaufman Rechulski, Laura R. Jarboe

Chemical and Biological Engineering Publications

Mechanocatalysis is a promising method for depolymerization of lignocellulosic biomass. Microbial utilization of the resulting oligosaccharides is one potential route of adding value to the depolymerized biomass. However, it is unclear how readily these oligosaccharides are utilized by standard cell factories. Here, we investigate utilization of cellulose subjected to mechanocatalytic depolymerization, using ethanologenic Escherichia coli as a model fermentation organism. The mechanocatalytic oligosaccharides supported ethanol titers similar to those observed when glucose was provided at comparable concentrations. Tracking of the various oligomers, using maltose (alpha-1,4) and cellobiose (beta-1,4) oligomers as representative standards of the orientation, but not linkage ...


Lack Of Interactive Effects Between Diet Composition Or Acid Addition With Drying Method On Amino Acid Digestibility Values In Porcine Ileal Digesta, Brian Kerr, Shelby M. Curry, Brett C. Ramirez Jan 2020

Lack Of Interactive Effects Between Diet Composition Or Acid Addition With Drying Method On Amino Acid Digestibility Values In Porcine Ileal Digesta, Brian Kerr, Shelby M. Curry, Brett C. Ramirez

Agricultural and Biosystems Engineering Publications

Two experiments were conducted to determine the effect of oven drying (OD) or freeze drying (FD) on apparent ileal digestibility (AID) of amino acids (AA) in diets fed to pigs. In Exp. 1, 15 barrows (88.4 ± 6.4 kg) were allotted to either a corn starch-soybean meal (CST), potato starch-soybean meal (PST), or corn-soybean meal (CSBM) diet, over 2 collection periods. Following collection, samples were pooled within pig and subdivided into either OD or FD, resulting in 10 observations per diet by drying method combination. In Exp. 2, 11 barrows (63.3 ± 3.8 kg) were fed a CST ...


Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne Jan 2020

Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne

Plant Pathology and Microbiology Publications

Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA ...


Detection And Density Of Breeding Marsh Birds In Iowa Wetlands, Rachel A. Vanausdall, Stephen J. Dinsmore Jan 2020

Detection And Density Of Breeding Marsh Birds In Iowa Wetlands, Rachel A. Vanausdall, Stephen J. Dinsmore

Natural Resource Ecology and Management Publications

Accounting for imperfect detection is an important process when obtaining estimates of density or abundance for breeding birds, and this is particularly true when researchers are monitoring birds to assess the success of restored wetlands. Due to the dramatic decline in areal cover and habitat quality, wetland restoration in the Prairie Pothole Region (PPR) is critically important to breeding birds. The Shallow Lakes Restoration Project (SLRP), a partnership between the Iowa Department of Natural Resources and Ducks Unlimited, Inc., aims to restore degraded shallow lakes throughout the Iowa PPR. We conducted unlimited-radius point counts with call-broadcast surveys for breeding marsh ...


Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh Jan 2020

Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh

Mechanical Engineering Publications

Background Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and ...


Cost Assessment Of Five Different Maize Grain Handling Techniques To Reduce Postharvest Losses From Insect Contamination, Bernard Darfour, Kurt A. Rosentrater Jan 2020

Cost Assessment Of Five Different Maize Grain Handling Techniques To Reduce Postharvest Losses From Insect Contamination, Bernard Darfour, Kurt A. Rosentrater

Agricultural and Biosystems Engineering Publications

Farmers in developing nations encounter high postharvest losses mainly attributable to the lack of modern techniques for threshing, cleaning, grading, and grain storage. Mechanized handling of grain in developing countries is rare, although the technology is effective against insects and pest infestations. The objective was to evaluate the cost-effectiveness of five grain handling techniques that have the ability to reduce postharvest losses from insect infestation. The five methods were metal silo plus all accessories (m. silo + acc.), metal silo only (m. silo), woven polypropylene plus phosphine (w. PP. + Phos.), woven polypropylene only (w. PP.), and Purdue Improved Crop Storage bags ...


The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller Jan 2020

The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller

Plant Pathology and Microbiology Publications

Maize chlorotic mottle virus (MCMV) combines with a potyvirus in maize lethal necrosis disease (MLND), an emerging disease worldwide that often causes catastrophic yield loss. To inform resistance strategies, we characterized the translation initiation mechanism of MCMV. We report that, like other tombusvirids, MCMV RNA contains a cap-independent translation element (CITE) in its 3’ untranslated region (UTR). The MCMV 3’ CITE (MTE) was mapped to nucleotides 4164-4333 in the genomic RNA. SHAPE probing revealed that the MTE is a variant of the panicum mosaic virus-like 3’ CITE (PTE). Like the PTE, electrophoretic mobility shift assays (EMSAs) indicated that eukaryotic translation ...


The Gossypium Longicalyx Genome As A Resource For Cotton Breeding And Evolution, Corrinne E. Grover, Mengqiao Pan, Daojun Yuan, Mark A. Arick Ii, Guanjing Hu, Logan Brase, David M. Stelly, Zefu Lu, Robert J. Schmitz, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall Jan 2020

The Gossypium Longicalyx Genome As A Resource For Cotton Breeding And Evolution, Corrinne E. Grover, Mengqiao Pan, Daojun Yuan, Mark A. Arick Ii, Guanjing Hu, Logan Brase, David M. Stelly, Zefu Lu, Robert J. Schmitz, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall

Ecology, Evolution and Organismal Biology Publications

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby ...


A Systematic Review And Qualitative Synthesis Resulting In A Typology Of Elementary Classroom Movement Integration Interventions, Spyridoula Vazou, Collin A. Webster, Gregory Stewart, Priscila Candal, Cate A. Egan, Adam Pennell, Laura B. Russ Jan 2020

A Systematic Review And Qualitative Synthesis Resulting In A Typology Of Elementary Classroom Movement Integration Interventions, Spyridoula Vazou, Collin A. Webster, Gregory Stewart, Priscila Candal, Cate A. Egan, Adam Pennell, Laura B. Russ

Kinesiology Publications

Background/Objective: Movement integration (MI) involves infusing physical activity into normal classroom time. A wide range of MI interventions have succeeded in increasing children’s participation in physical activity. However, no previous research has attempted to unpack the various MI intervention approaches. Therefore, this study aimed to systematically review, qualitatively analyze, and develop a typology of MI interventions conducted in primary/ elementary school settings.

Subjects/Methods: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed to identify published MI interventions. Irrelevant records were removed first by title, then by abstract, and finally by full texts of articles ...


Epidemiology, Detection, And Intervention/Control Of Cyclospora Cayetanensis: A Scoping Review Protocol, Sarah C. Totton, Annette M. O'Connor, Mary E. Torrence, Jan M. Sargeant Jan 2020

Epidemiology, Detection, And Intervention/Control Of Cyclospora Cayetanensis: A Scoping Review Protocol, Sarah C. Totton, Annette M. O'Connor, Mary E. Torrence, Jan M. Sargeant

Veterinary Diagnostic and Production Animal Medicine Reports

Background: Cyclosporiasis is a food- and waterborne illness in humans caused by the consumption of contaminated food or water. As the causative agent, Cyclospora cayetanensis, has only been recently described, the published literature is limited and no scoping reviews on this topic have yet been conducted.

Objectives: Our objective is to conduct a scoping review of the epidemiology, detection in matrix, and intervention/control of C. cayetanensis worldwide in humans, plant-based food, and in the environment with the aim of identifying gaps in the literature, potential areas where there may be sufficient literature to warrant a systematic review, and prioritizing ...


De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham Jan 2020

De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham

Plant Pathology and Microbiology Publications

Phakopsora pachyrhizi, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of P. pachyrhizi candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial de novo assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts ...


Community-Driven Metadata Standards For Agricultural Microbiome Research, J. P. Dundore-Arias, E. A. Eloe-Fadrosh, L. M. Schriml, Gwyn A. Beattie, F. P. Brennan, P. E. Busby, R. B. Calderon, S. C. Castle, J. B. Emerson, S. E. Everhart, K. Eversole, K. E. Frost, J. R. Herr, A. I. Huerta, A. S. Iyer-Pascuzzi, A. K. Kalil, J. E. Leach, J. Leonard, J. E. Maul, B. Prithiviraj, M. Potrykus, N. R. Redekar, J. A. Rojas, K. A. T. Silverstein, D. J. Tomso, S. G. Tringe, B. A. Vinatzer, L. L. Kinkel Jan 2020

Community-Driven Metadata Standards For Agricultural Microbiome Research, J. P. Dundore-Arias, E. A. Eloe-Fadrosh, L. M. Schriml, Gwyn A. Beattie, F. P. Brennan, P. E. Busby, R. B. Calderon, S. C. Castle, J. B. Emerson, S. E. Everhart, K. Eversole, K. E. Frost, J. R. Herr, A. I. Huerta, A. S. Iyer-Pascuzzi, A. K. Kalil, J. E. Leach, J. Leonard, J. E. Maul, B. Prithiviraj, M. Potrykus, N. R. Redekar, J. A. Rojas, K. A. T. Silverstein, D. J. Tomso, S. G. Tringe, B. A. Vinatzer, L. L. Kinkel

Plant Pathology and Microbiology Publications

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for ...


Evaluation Of An Elk Detection Probability Model In The Black Hills, South Dakota, Evan C. Phillips, Chadwick P. Lehman, Robert W. Klaver, Angela R. Jarding, Susan P. Rupp, Jonathan A. Jenks, Christopher N. Jacques Jan 2020

Evaluation Of An Elk Detection Probability Model In The Black Hills, South Dakota, Evan C. Phillips, Chadwick P. Lehman, Robert W. Klaver, Angela R. Jarding, Susan P. Rupp, Jonathan A. Jenks, Christopher N. Jacques

Natural Resource Ecology and Management Publications

Since 1993, elk (Cervus canadensis nelsoni) abundance in the Black Hills of South Dakota has been estimated using a detection probability model previously developed in Idaho, though it is likely biased because of a failure to account for visibility biases under local conditions. To correct for this bias, we evaluated the current detection probability across the Black Hills during January and February 2009–2011 using radio-collared elk. We used logistic regression to evaluate topographic features, habitat characteristics, and group characteristics relative to their influence on detection probability of elk. Elk detection probability increased with less vegetation cover (%), increased group size ...