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Full-Text Articles in Life Sciences

What Have Long-Term Field Studies Taught Us About Population Dynamics?, Beth A. Reinke, David A. W. Miller, Fredric J. Janzen Nov 2019

What Have Long-Term Field Studies Taught Us About Population Dynamics?, Beth A. Reinke, David A. W. Miller, Fredric J. Janzen

Ecology, Evolution and Organismal Biology Publications

Long-term studies have been crucial to the advancement of population biology, especially our understanding of population dynamics. We argue that this progress arises from three key characteristics of long-term research. First, long-term data are necessary to observe the heterogeneity that drives most population processes. Second, long-term studies often inherently lead to novel insights. Finally, long-term field studies can serve as model systems for population biology, allowing for theory and methods to be tested under well-characterized conditions. We illustrate these ideas in three long-term field systems that have made outsized contributions to our understanding of population ecology, evolution, and conservation biology ...


Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan Sep 2019

Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan

Agronomy Publications

Nitrogen (N) fertilizer recommendation tools could be improved for estimating corn (Zea mays L.) N needs by incorporating site-specific soil and weather information. However, an evaluation of analytical methods is needed to determine the success of incorporating this information. The objectives of this research were to evaluate statistical and machine learning (ML) algorithms for utilizing soil and weather information for improving corn N recommendation tools. Eight algorithms [stepwise, ridge regression, least absolute shrinkage and selection operator (Lasso), elastic net regression, principal component regression (PCR), partial least squares regression (PLSR), decision tree, and random forest] were evaluated using a dataset containing ...


Declining Liquidity In Iowa Farms: 2014–2017, Alejandro Plastina Aug 2019

Declining Liquidity In Iowa Farms: 2014–2017, Alejandro Plastina

Alejandro Plastina

The goal of the present study is to describe the evolution of financial liquidity in Iowa farms for 2014–2017, using a unique panel of 220 mid-scale commercial farms. Farms with vulnerable liquidity ratings increased from 33.2 percent in December 2014 to 45.0 percent in December 2017. On average, farms lost $244 of working capital per acre over that period, but farms with vulnerable liquidity ratings in December 2017 lost almost 60 percent more than that, or $388. Average farm size, machinery investment per acre, farm net worth per acre, debt-to-asset ratio, and age of operator were not ...


Avoiding Unnecessary Liver Transplantation: Recognizing Increased Prevalence In Alcohol-Associated Liver Disease (Ald), Andrew T. Shen, Rangaswamy Nagarajan, Nicole T. Shen M.D. Aug 2019

Avoiding Unnecessary Liver Transplantation: Recognizing Increased Prevalence In Alcohol-Associated Liver Disease (Ald), Andrew T. Shen, Rangaswamy Nagarajan, Nicole T. Shen M.D.

SMU Data Science Review

In recent years there has been an increase in liver transplantation for alcohol-associated liver disease (ALD). Unlike other etiologies of liver disease, patients with ALD that meet transplant criteria may improve with abstinence, negating the need for transplant. ALD patients on the transplant waitlist that will improve with abstinence, are not only placed at risk for harm by receiving an unnecessary transplant, but also prevent other transplant candidates from receiving a liver. This paper addresses the issue of ALD patients who were at risk for harm from receiving an unnecessary transplant by evaluating the feature importance of machine learning models ...


Age Structure Of Horn Fly (Diptera: Muscidae) Populations Estimated By Pterin Concentrations, E. S. Krafsur, A. L. Rosales, J. F. Robison-Cox, J. P. Turner Aug 2019

Age Structure Of Horn Fly (Diptera: Muscidae) Populations Estimated By Pterin Concentrations, E. S. Krafsur, A. L. Rosales, J. F. Robison-Cox, J. P. Turner

Elliot Krafsur

Pterins accumulate in the head capsules of horn flies, Haematobia irritans irritans (L.), as a linear function of time and temperature. Pterin concentrations were used to estimate chronological ages and to establish correlations between chronological age and ovarian development and reproductive success in 12 horn fly populations in 1988 and 1989. Male ages were estimated spectrofluorometrically. There were statistically significant differences between years in population age structure measured by pterins. Survival rates estimated from pterin concentration distributions were consistent with a one-parameter exponential model with constant survival rate. Mean daily survival rates were 0.81 for females and 0.84 ...


Population Genetics Of Glossina Morsitans Submorsitans (Diptera: Glossinidae), E. S. Krafsur, M. Madsen, D. L. Wohlford, S. Mihok, N. T. Griffiths Aug 2019

Population Genetics Of Glossina Morsitans Submorsitans (Diptera: Glossinidae), E. S. Krafsur, M. Madsen, D. L. Wohlford, S. Mihok, N. T. Griffiths

Elliot Krafsur

Breeding structure of Glossina morsitans submorsitans Newstead was evaluated by using genetic markers in mitochondrial DNA where diversity was scored at two loci in five natural populations from The Gambia and two populations in Ethiopia (form ugandensis Vanderplank), countries separated by c. 5450 km. Twenty six haplotype combinations were found, of which 17 were shared among two or more populations. Nine haplotypes were found in The Gambia and 23 haplotypes in Ethiopia. There were 12 unique haplotypes. Only six haplotypes were shared between the two countries. Populations in The Gambia (he = 0.26 ± 0.04) showed less than a third ...


Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan Aug 2019

Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan

John E. Sawyer

Nitrogen (N) fertilizer recommendation tools could be improved for estimating corn (Zea mays L.) N needs by incorporating site-specific soil and weather information. However, an evaluation of analytical methods is needed to determine the success of incorporating this information. The objectives of this research were to evaluate statistical and machine learning (ML) algorithms for utilizing soil and weather information for improving corn N recommendation tools. Eight algorithms [stepwise, ridge regression, least absolute shrinkage and selection operator (Lasso), elastic net regression, principal component regression (PCR), partial least squares regression (PLSR), decision tree, and random forest] were evaluated using a dataset containing ...


Factors That Influence New Students’ Decision To Attend Two Midwestern Land-Grant Universities, Elizabeth A. Foreman, Scott W. Smalley, Michael S. Retallick Aug 2019

Factors That Influence New Students’ Decision To Attend Two Midwestern Land-Grant Universities, Elizabeth A. Foreman, Scott W. Smalley, Michael S. Retallick

Scott Smalley

The purpose of this quantitative study was to describe the people and factors that influenced new students’ decisions to attend the colleges of agriculture at two Midwestern land grant universities. Athletics was identified as the most common pre-collegiate activity. Students identified their parent as the most influential person in selecting their college. The top factor which influenced students' college decision was pursuing a career that interested them. The findings from this study can guide recruitment efforts at land-grant universities by allowing institutions to be more intentional with their recruitment efforts. Future research needs to be conducted to determine the timing ...


State Wide Self-Assessment Of General Program Standards For Agricultural Education, Kelsey R. Sands, Adam D. Sacquitne, Scott W. Smalley, Michael S. Retallick Aug 2019

State Wide Self-Assessment Of General Program Standards For Agricultural Education, Kelsey R. Sands, Adam D. Sacquitne, Scott W. Smalley, Michael S. Retallick

Scott Smalley

A quality program is the ultimate goal for many secondary agricultural education programs. To ensure quality agricultural education programs, standards were established to measure the extent agricultural education programs in Iowa were implementing standards. Utilizing Ajzen’s Theory of Planned Behavior, researchers incorporated the Iowa Council on Agricultural Education standards as an evaluation tool. A census study was conducted in Iowa with high school agricultural education teachers (N = 255) to better understand the extent that standards outlined by the Iowa Council on Agricultural Education were being met in agricultural education programs. In the general program standard area, improvement is needed ...


Factors That Influence New Students’ Decision To Attend Two Midwestern Land-Grant Universities, Elizabeth A. Foreman, Scott W. Smalley, Michael S. Retallick Aug 2019

Factors That Influence New Students’ Decision To Attend Two Midwestern Land-Grant Universities, Elizabeth A. Foreman, Scott W. Smalley, Michael S. Retallick

Michael Retallick

The purpose of this quantitative study was to describe the people and factors that influenced new students’ decisions to attend the colleges of agriculture at two Midwestern land grant universities. Athletics was identified as the most common pre-collegiate activity. Students identified their parent as the most influential person in selecting their college. The top factor which influenced students' college decision was pursuing a career that interested them. The findings from this study can guide recruitment efforts at land-grant universities by allowing institutions to be more intentional with their recruitment efforts. Future research needs to be conducted to determine the timing ...


State Wide Self-Assessment Of General Program Standards For Agricultural Education, Kelsey R. Sands, Adam D. Sacquitne, Scott W. Smalley, Michael S. Retallick Aug 2019

State Wide Self-Assessment Of General Program Standards For Agricultural Education, Kelsey R. Sands, Adam D. Sacquitne, Scott W. Smalley, Michael S. Retallick

Michael Retallick

A quality program is the ultimate goal for many secondary agricultural education programs. To ensure quality agricultural education programs, standards were established to measure the extent agricultural education programs in Iowa were implementing standards. Utilizing Ajzen’s Theory of Planned Behavior, researchers incorporated the Iowa Council on Agricultural Education standards as an evaluation tool. A census study was conducted in Iowa with high school agricultural education teachers (N = 255) to better understand the extent that standards outlined by the Iowa Council on Agricultural Education were being met in agricultural education programs. In the general program standard area, improvement is needed ...


Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton Aug 2019

Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton

Dan Nettleton

This paper investigates the problem of adjusting for spatial effects in genomic prediction. Despite being seldomly considered in genome-wide association studies (GWAS), spatial effects often affect phenotypic measurements of plants. We consider a Gaussian random field (GRF) model with an additive covariance structure that incorporates genotype effects, spatial effects and subpopulation effects. An empirical study shows the existence of spatial effects and heterogeneity across different subpopulation families while simulations illustrate the improvement in selecting genotypically superior plants by adjusting for spatial effects in genomic prediction.


Qqs Orphan Gene And Its Interactor Nf‐Yc4 Reduce Susceptibility To Pathogens And Pests, Mingsheng Qi, Wenguang Zheng, Xuefeng Zhao, Jessica D. Hohenstein, Yuba Kandel, Seth O’Conner, Yifan Wang, Chuanlong Du, Dan Nettleton, Gustavo C. Macintosh, Gregory L. Tylka, Eve Syrkin Wurtele, Steven A. Whitham, Ling Li Aug 2019

Qqs Orphan Gene And Its Interactor Nf‐Yc4 Reduce Susceptibility To Pathogens And Pests, Mingsheng Qi, Wenguang Zheng, Xuefeng Zhao, Jessica D. Hohenstein, Yuba Kandel, Seth O’Conner, Yifan Wang, Chuanlong Du, Dan Nettleton, Gustavo C. Macintosh, Gregory L. Tylka, Eve Syrkin Wurtele, Steven A. Whitham, Ling Li

Ling Li

Enhancing the nutritional quality and disease resistance of crops without sacrificing productivity is a key issue for developing varieties that are valuable to farmers and for simultaneously improving food security and sustainability. Expression of the Arabidopsis thaliana species‐specific AtQQS (Qua‐Quine Starch) orphan gene or its interactor, NF‐YC4 (Nuclear Factor Y, subunit C4), has been shown to increase levels of leaf/seed protein without affecting the growth and yield of agronomic species. Here, we demonstrate that overexpression of AtQQS and NF‐YC4 in Arabidopsis and soybean enhances resistance/reduces susceptibility to viruses, bacteria, fungi, aphids, and soybean cyst ...


Conditional Causal Mediation Analysis Of Factors Associated With Cover Crop Adoption In Iowa, Usa, Danhyang Lee, J. Gordon Arbuckle, Zhengyuan Zhu, Laurie Nowatzke Aug 2019

Conditional Causal Mediation Analysis Of Factors Associated With Cover Crop Adoption In Iowa, Usa, Danhyang Lee, J. Gordon Arbuckle, Zhengyuan Zhu, Laurie Nowatzke

J. Gordon Arbuckle

The Iowa Nutrient Reduction Strategy is a statewide effort that aims to encourage voluntary adoption of conservation practices by farmers to reduce the loss of nitrogen and phosphorus that contribute to water quality impairments in the Upper Midwest and drive hypoxic conditions in the Gulf of Mexico. This work is an analysis of the first 2 years (2015–2016) of a 5‐year survey of Iowa farmers. We employ causal mediation analysis to examine the direct and indirect effects of key explanatory variables (e.g., information sources, nutrient management influences, involvement in watershed management activities, and conservation technical assistance) and ...


Small Rna Discovery In The Interaction Between Barley And The Powdery Mildew Pathogen, Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra Mathioni, Blake C. Meyers, Dan Nettleton, Roger P. Wise Jul 2019

Small Rna Discovery In The Interaction Between Barley And The Powdery Mildew Pathogen, Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra Mathioni, Blake C. Meyers, Dan Nettleton, Roger P. Wise

Dan Nettleton

Background: Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells.

Results: RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding ...


Heat Stress Alters Ovarian Insulin-Mediated Phosphatidylinositol-3 Kinase And Steroidogenic Signaling In Gilt Ovaries, Jackson Nteeba, M. Victoria Sanz-Fernandez, Robert P. Rhoads, Lance H. Baumgard, Jason W. Ross, Aileen F. Keating Jul 2019

Heat Stress Alters Ovarian Insulin-Mediated Phosphatidylinositol-3 Kinase And Steroidogenic Signaling In Gilt Ovaries, Jackson Nteeba, M. Victoria Sanz-Fernandez, Robert P. Rhoads, Lance H. Baumgard, Jason W. Ross, Aileen F. Keating

Aileen Keating

Heat Stress (HS) compromises a variety of reproductive functions in several mammalian species. Inexplicably, HS animals are frequently hyperinsulinemic despite marked hyperthermia-induced hypophagia. Our objectives were to determine the effects of HS on insulin signaling and components essential to steroid biosynthesis in the pig ovary. Female pigs (35±4 kg) were exposed to constant thermal neutral (TN; 20°C; 35-50% humidity; n = 6) or HS conditions (35°C; 20-35% humidity; n = 6) for either 7 (n = 10) or 35 d (n = 12). After 7d, HS increased (P < 0.05) ovarian mRNA abundance of the insulin receptor (INSR), insulin receptor substrate 1 (IRS1), protein kinase B subunit 1 (AKT1), low density lipoprotein receptor (LDLR), luteinizing hormone receptor (LHCGR), and aromatase (CYP19a). After 35d, HS increased INSR, IRS1, AKT1, LDLR, LHCGR, CYP19a, and steroidogenic acute regulatory protein (STAR) ovarian mRNA abundance. In addition, after 35d, HS increased ovarian phosphorylated IRS1 (pIRS1), phosphorylated AKT (pAKT), STAR and CYP19a protein abundance. Immunostaining analysis revealed similar localization of INSR and pAKT1 in the cytoplasmic membrane and oocyte cytoplasm, respectively, of all stage follicles, and in theca and granulosa cells. Collectively, these results demonstrate that HS alters ovarian insulin mediated-PI3K signaling pathway members which likely impacts follicle activation and viability. In summary, environmentally-induced HS is an endocrine disrupting exposure that modifies ovarian physiology and potentially compromises production of ovarian hormones essential for fertility and pregnancy maintenance.


Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton Jul 2019

Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton

Statistics Publications

This paper investigates the problem of adjusting for spatial effects in genomic prediction. Despite being seldomly considered in genome-wide association studies (GWAS), spatial effects often affect phenotypic measurements of plants. We consider a Gaussian random field (GRF) model with an additive covariance structure that incorporates genotype effects, spatial effects and subpopulation effects. An empirical study shows the existence of spatial effects and heterogeneity across different subpopulation families while simulations illustrate the improvement in selecting genotypically superior plants by adjusting for spatial effects in genomic prediction.


Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe Jul 2019

Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe

Michael J Weber

The Topeka shiner Notropis topeka is native to Iowa, Kansas, Minnesota, Missouri, Nebraska, and South Dakota and has been federally listed as endangered since 1998. Our goals were to determine the present distribution and qualitative status of Topeka shiners throughout its current range in Iowa and characterize the extent of decline in relation to its historic distribution. We compared the current (2016–2017) distribution to distributions portrayed in three earlier time periods. In 2016–2017 Topeka shiners were found in 12 of 20 HUC10 watersheds where they occurred historically. Their status was classified as stable in 21% of the HUC10 ...


Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe Jul 2019

Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe

Kevin J. Roe

The Topeka shiner Notropis topeka is native to Iowa, Kansas, Minnesota, Missouri, Nebraska, and South Dakota and has been federally listed as endangered since 1998. Our goals were to determine the present distribution and qualitative status of Topeka shiners throughout its current range in Iowa and characterize the extent of decline in relation to its historic distribution. We compared the current (2016–2017) distribution to distributions portrayed in three earlier time periods. In 2016–2017 Topeka shiners were found in 12 of 20 HUC10 watersheds where they occurred historically. Their status was classified as stable in 21% of the HUC10 ...


Transcript-Based Cloning Of Rrp46, A Regulator Of Rrna Processing And R Gene–Independent Cell Death In Barley–Powdery Mildew Interactions, Liu Xi, Matthew J. Moscou, Yan Meng, Weihui Xu, Rico A. Caldo, Miranda Shaver, Dan Nettleton, Roger P. Wise Jul 2019

Transcript-Based Cloning Of Rrp46, A Regulator Of Rrna Processing And R Gene–Independent Cell Death In Barley–Powdery Mildew Interactions, Liu Xi, Matthew J. Moscou, Yan Meng, Weihui Xu, Rico A. Caldo, Miranda Shaver, Dan Nettleton, Roger P. Wise

Dan Nettleton

Programmed cell death (PCD) plays a pivotal role in plant development and defense. To investigate the interaction between PCD and R gene–mediated defense, we used the 22K Barley1 GeneChip to compare and contrast time-course expression profiles of Blumeria graminis f. sp hordei (Bgh) challenged barley (Hordeum vulgare) cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast neutron–derived Bgh-induced tip cell death1 mutant, bcd1. Mixed linear model analysis identified genes associated with the cell death phenotype as opposed to Rgene–mediated resistance. One-hundred fifty genes were found at the threshold P value < 0.0001 and a false discovery rate bcd1mutant. Gene Ontology and rice (Oryza ...


Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton Jul 2019

Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton

Dan Nettleton

The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental ...


Nested Hierarchical Functional Data Modeling And Inference For The Analysis Of Functional Plant Phenotypes, Yuhang Xu, Yehua Li, Dan Nettleton Jul 2019

Nested Hierarchical Functional Data Modeling And Inference For The Analysis Of Functional Plant Phenotypes, Yuhang Xu, Yehua Li, Dan Nettleton

Dan Nettleton

In a plant science Root Image Study, the process of seedling roots bending in response to gravity is recorded using digital cameras, and the bending rates are modeled as functional plant phenotype data. The functional phenotypes are collected from seeds representing a large variety of genotypes and have a three-level nested hierarchical structure, with seeds nested in groups nested in genotypes. The seeds are imaged on different days of the lunar cycle, and an important scientific question is whether there are lunar effects on root bending. We allow the mean function of the bending rate to depend on the lunar ...


Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger Jul 2019

Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger

Dan Nettleton

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching patterns of ...


Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger Jul 2019

Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger

Dan Nettleton

Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed ...


Genomic Neighborhoods For Arabidopsisretrotransposons: A Role For Targeted Integration In The Distribution Of The Metaviridae, Brooke D. Peterson-Burch, Dan Nettleton, Daniel F. Voytas Jul 2019

Genomic Neighborhoods For Arabidopsisretrotransposons: A Role For Targeted Integration In The Distribution Of The Metaviridae, Brooke D. Peterson-Burch, Dan Nettleton, Daniel F. Voytas

Dan Nettleton

Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.

Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution ...


Is Animal-Based Biomedical Research Being Used In Its Original Context?, Constança Carvalho, Daniel Alves, Andrew Knight, Luís Vicente Jul 2019

Is Animal-Based Biomedical Research Being Used In Its Original Context?, Constança Carvalho, Daniel Alves, Andrew Knight, Luís Vicente

Andrew Knight, Ph.D.

No abstract provided.


Critically Evaluating Animal Research, Andrew Knight Jul 2019

Critically Evaluating Animal Research, Andrew Knight

Andrew Knight, Ph.D.

No abstract provided.


Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe Jul 2019

Status Of The Topeka Shiner In Iowa, Clay L. Pierce, Nicholas T. Simpson, Alexander P. Bybel, Courtney L. Zambory, Michael J. Weber, Kevin J. Roe

Natural Resource Ecology and Management Publications

The Topeka shiner Notropis topeka is native to Iowa, Kansas, Minnesota, Missouri, Nebraska, and South Dakota and has been federally listed as endangered since 1998. Our goals were to determine the present distribution and qualitative status of Topeka shiners throughout its current range in Iowa and characterize the extent of decline in relation to its historic distribution. We compared the current (2016–2017) distribution to distributions portrayed in three earlier time periods. In 2016–2017 Topeka shiners were found in 12 of 20 HUC10 watersheds where they occurred historically. Their status was classified as stable in 21% of the HUC10 ...


Barleybase—An Expression Profiling Database For Plant Genomics, Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson Jul 2019

Barleybase—An Expression Profiling Database For Plant Genomics, Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson

Dan Nettleton

BarleyBase (BB) ( www.barleybase.org ) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or ...


Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger Jul 2019

Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Maize (Zea mays) displays an exceptional level of structural genomic diversity, which is likely unique among higher eukaryotes. In this study, we surveyed how the genetic divergence of two maize inbred lines affects the transcriptomic landscape in four different primary root tissues of their F1-hybrid progeny. An extreme instance of complementation was frequently observed: genes that were expressed in only one parent but in both reciprocal hybrids. This single-parent expression (SPE) pattern was detected for 2341 genes with up to 1287 SPE patterns per tissue. As a consequence, the number of active genes in hybrids exceeded that of their parents ...