Physical Sciences and Mathematics Commons^™

Extensive Tissue-Specific Transcriptomic Plasticity In Maize Primary Roots Upon Water Deficit, Nina Opitz, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Ronny Brandt, Hans-Peter Piepho, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the …

Non-Syntenic Genes Drive Rtcs-Dependent Regulation Of The Embryo Transcriptome During Formation Of Seminal Root Primordia In Maize (Zea Mays L.), Huanhuan Tai, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo …

Post-Weaning Blood Transcriptomic Differences Between Yorkshire Pigs Divergently Selected For Residual Feed Intake, Haibo Liu, Yet T. Nguyen, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

Background: Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired. In this study, we aimed to explore whether differences exist in the global gene expression profiles of peripheral blood of 35 to 42 day-old …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Parallel Genome-Wide Expression Profiling Of Host And Pathogen During Soybean Cyst Nematode Infection Of Soybean, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Leonard Hearne, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course of infection in a compatible interaction was performed using the Affymetrix GeneChip soybean genome array. Among 35,611 soybean transcripts monitored, we identified 429 genes that showed statistically significant differential expression between uninfected and nematode-infected root tissues. These included genes encoding enzymes involved in primary metabolism; biosynthesis of phenolic compounds, lignin, and flavonoids; genes related to stress and defense responses; cell wall modification; cellular signaling; and transcriptional regulation. Among 7,431 SCN transcripts monitored, 1,850 genes showed statistically significant differential …

Sequence Mining And Transcript Profiling To Explore Cyst Nematode Parasitism, Axel A. Elling, Makedonka Mitreva, Xiaowu Gai, John Martin, Justin Recknor, Eric L. Davis, Richard S. Hussey, Dan Nettleton, James P. Mccarter, Thomas J. Baum

Dan Nettleton

Background: Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants.

Results: We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean …

Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of …

Flor Revisited (Again): Eqtl And Mutational Analysis Of Nb-Lrr Mediated Immunity To Powdery Mildew In Barley, Roger P. Wise, Priyanka Surana, Gregory S. Fuerst, Ruo Xu, Divya Mistry, Julie A. Dickerson, Dan Nettleton Dr.

Dan Nettleton

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rar1 (Required for Mla12-specified resistance1), and Rom1 (Restoration of Mla-specified resistance1). The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance, however, much remains to be discovered regarding the precise signaling underlying plant immunity. Genetic analyses of fast-neutron mutants derived from CI 16151 (Mla6) uncovered a novel locus, designated Rar3 (Required for Mla6-specified resistance3). Rar3 segregates independent of Mla6 and Rar1, and rar3 mutants are susceptible to Blumeria graminis f. sp. hordei …

Identification Of Differentially Expressed Gene Categories In Microarray Studies Using Nonparametric Multivariate Analysis, Dan Nettleton, Justin Recknor, James M. Reecy

Dan Nettleton

The field of microarray data analysis is shifting emphasis from methods for identifying differentially expressed genes to methods for identifying differentially expressed gene categories. The latter approaches utilize a priori information about genes to group genes into categories and enhance the interpretation of experiments aimed at identifying expression differences across treatments. While almost all of the existing approaches for identifying differentially expressed gene categories are practically useful, they suffer from a variety of drawbacks. Perhaps most notably, many popular tools are based exclusively on gene-specific statistics that cannot detect many types of multivariate expression change. We have developed a nonparametric …

Developmental Transcript Profiling Of Cyst Nematode Feeding Cells In Soybean Roots, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and …

Comparison Of Transcript Profiles In Wild-Type And O2 Maize Endosperm In Different Genetic Backgrounds, Hongwu Jia, Dan Nettleton, Joan M. Peterson, Gricelda Vasquez-Carrillo, Jean-Luc Jannink, M. Paul Scott

Dan Nettleton

Mutations in the Opaque2 (O2) gene of maize (Zea mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on genetic background. We propose two hypotheses to explain differences in phenotypic severity in different genetic backgrounds: (i) Specific genes are differentially (o2 vs. wild-type) expressed only in certain genotypes, and (ii) A set of genes are differentially expressed in all backgrounds, but the degree of differential expression differs in different backgrounds. To determine …

Arca Controls Metabolism, Chemotaxis, And Motility Contributing To The Pathogenicity Of Avian Pathogenic Escherichia Coli, Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, Robert L. Jernigan, Andrew Lithio, Dan Nettleton, Ling Li, Eve S. Wurtele, Lisa K. Nolan, Chengping Lu, Ganwu Li

Dan Nettleton

Avian pathogenic Escherichia coli (APEC) strains cause one of the three most significant infectious diseases in the poultry industry and are also potential food-borne pathogens threating human health. In this study, we showed that ArcA (aerobic respiratory control), a global regulator important for E. coli's adaptation from anaerobic to aerobic conditions and control of that bacterium's enzymatic defenses against reactive oxygen species (ROS), is involved in the virulence of APEC. Deletion of arcA significantly attenuates the virulence of APEC in the duck model. Transcriptome sequencing (RNA-Seq) analyses comparing the APEC wild type and the arcA mutant indicate that ArcA regulates …

A Diallel Analysis Of A Maize Donor Population Response To In Vivo Maternal Haploid Induction I: Inducibility, Gerald N. De La Fuente, Ursula K. Frei, Benjamin Trampe, Daniel Nettleton, Wei Zhang, Thomas Lubberstedt

Dan Nettleton

The maize in vivo maternal doubled haploid (DH) system is an important tool used by maize breeders and geneticists around the world. The ability to rapidly produce DH lines of maize for breeding allows breeders to quickly respond to new selection criteria based on the ever changing biotic and abiotic stresses that maize is subjected to across its growing area. There are two important steps in the generation of DH lines using the in vivo maternal DH system: 1) the production and identification of haploid progeny, and 2) the doubling of genomes to create fertile, diploid inbred lines that can …

Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of …

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism And Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, Ling Li

Dan Nettleton

Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; …

Draft Genome Sequences Of Three Monokaryotic Isolates Of The White-Rot Basidiomycete Fungus Dichomitus Squalens, Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, Steven Ahrendt, Vivian Ng, Kerrie W. Barry, Chris Daum, Igor V. Grigoriev, Kristiina S. Hildén, Miia R. Mäkelä, Ronald P. De Vries

William B. Andreopoulos

Introduction: Social-Ecological Resilience And Law, Ahjond S. Garmestani, Craig R. Allen, Craig Anthony Arnold, Lance H. Gunderson

Craig Anthony (Tony) Arnold

Environmental law is intimately connected to ecological concepts and understanding. The legal instruments, institutions, and administration of law in the United States are predicated on assumptions that nature is globally stable and that the inherent variability in ecological systems is bounded. This current legal framework is based upon an understanding of ecological systems operating near an equilibrium, or if disturbed, moving back toward an equilibrium. Such assumptions make much current environmental law ill-suited for many pressing environmental issues (Ruhl 1999; Garmestani et al. 2009; Craig 2010; Verchick 2010; Benson and Garmestani 2011). Emerging environmental challenges, such as cross-boundary water governance …

Quantifying Uncertainty And Trade-Offs In Resilience Assessments, Craig R. Allen, Hannah E. Birgé, David G. Angeler, Craig A. Arnold, Brian C. Chaffin, Daniel A. Decaro, Ahjond S. Garmestani, Lance Gunderson

Craig Anthony (Tony) Arnold

Several frameworks have been developed to assess the resilience of social-ecological systems, but most require substantial data inputs, time, and technical expertise. Stakeholders and practitioners often lack the resources for such intensive efforts. Furthermore, most end with problem framing and fail to explicitly address trade-offs and uncertainty. To remedy this gap, we developed a rapid survey assessment that compares the relative resilience of social-ecological systems with respect to a number of resilience properties. This approach generates large amounts of information relative to stakeholder inputs. We targeted four stakeholder categories: government (policy, regulation, management), end users (farmers, ranchers, landowners, industry), agency/public …

Barriers And Bridges To The Integration Of Social–Ecological Resilience And Law, Olivia Odom Green, Ahjond S. Garmestani, Craig R. Allen, Lance H. Gunderson, J.B. Ruhl, Craig A. Arnold, Nicholas A.J. Graham, Barbara Cosens, David G. Angeler, Brian C. Chaffin, C.S. Holling

Craig Anthony (Tony) Arnold

There is a fundamental difference between the ways in which ecologists and lawyers view uncertainty: in the study of ecology, uncertainty provides a catalyst for exploration, whereas uncertainty is antithetical to the rule of law. This issue is particularly troubling in environmental management, where the tensions between law and ecology become apparent. Rather than acknowledge uncertainties in management actions, legal frameworks often force a false sense of certainty in linking cause and effect. While adaptive management has been developed to deal with uncertainty, laws and legal wrangling can be obstacles to implementation. In this article, we recommend resilience-based governance – …

Combining Survey And Non-Survey Data For Improved Sub-Area Prediction Using A Multi-Level Model, Jae Kwang Kim, Zhonglei Wang, Zhengyuan Zhu, Nathan B. Cruze

Zhengyuan Zhu

Combining information from different sources is an important practical problem in survey sampling. Using a hierarchical area-level model, we establish a framework to integrate auxiliary information to improve state-level area estimates. The best predictors are obtained by the conditional expectations of latent variables given observations, and an estimate of the mean squared prediction error is discussed. Sponsored by the National Agricultural Statistics Service of the US Department of Agriculture, the proposed model is applied to the planted crop acreage estimation problem by combining information from three sources, including the June Area Survey obtained by a probability-based sampling of lands, administrative …

Recent Efforts To Elucidate The Scientific Validity Of Animal-Based Drug Tests By The Pharmaceutical Industry, Pro-Testing Lobby Groups, And Animal Welfare Organisations, Jarrod Bailey

Jarrod Bailey, PhD

Background: Even after several decades of human drug development, there remains an absence of published, substantial, comprehensive data to validate the use of animals in preclinical drug testing, and to point to their predictive nature with regard to human safety/toxicity and efficacy. Two recent papers, authored by pharmaceutical industry scientists, added to the few substantive publications that exist. In this brief article, we discuss both these papers, as well as our own series of three papers on the subject, and also various views and criticisms of lobby groups that advocate the animal testing of new drugs.

Main text: We argue …

Nitrogen Fertilizer Suppresses Mineralization Of Soil Organic Matter In Maize Agroecosystems, Navreet K. Mahal, William R. Osterholz, Fernando E. Miguez, Hanna J. Poffenbarger, John E. Sawyer, Daniel C. Olk, Sotirios V. Archontoulis, Michael J. Castellano

John E. Sawyer

The possibility that N fertilizer increases soil organic matter (SOM) mineralization and, as a result, reduces SOM stocks has led to a great debate about the long-term sustainability of maize-based agroecosystems as well as the best method to estimate fertilizer N use efficiency (FNUE). Much of this debate is because synthetic N fertilizer can positively or negatively affect SOM mineralization via several direct and indirect pathways. Here, we test a series of hypotheses to determine the direction, magnitude, and mechanism of N fertilizer effect on SOM mineralization and discuss the implications for methods to estimate FNUE.Wemeasured the effect of synthetic …

Modeling Spatial And Temporal Variation In Natural Background Specific Conductivity, John Olson, Susan M. Cormier

John Olson

Inferring Processes Of Coevolutionary Diversification In A Community Of Panamanian Strangler Figs And Associated Pollinating Wasps, Jordan D. Satler, Edward Allen Herre, K. Charlotte Jandér, Deren A. R. Eaton, Carlos A. Machado, Tracy A. Heath, John D. Nason

Tracy Heath

The fig and pollinator wasp obligate mutualism is diverse (~750 described species), ecologically important, and ancient (~80-90 Ma), providing model systems for generating and testing many questions in evolution and ecology. Once thought to be a prime example of strict one-to-one cospeciation, current thinking suggests that genera of pollinator wasps coevolve with corresponding subsections of figs, but the degree to which cospeciation or other processes contributes to the association at finer scales is unclear. Here we use genome-wide sequence data from a community of Panamanian strangler figs (Ficus subgenus Urostigma, section Americana) and associated fig wasp pollinators …

Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. Mcintosh, Eptisam Lambo, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson

Tyler Johnson

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. The Mu, Delta, and Kappa (MOP, DOP, KOP) opioid receptors are particularly intriguing members of this receptor family as they are the targets involved in many neurobiological diseases such as addiction, pain, stress, anxiety, and depression. Recently we discovered that the aaptamine class of marine sponge derived natural products exhibit selective agonist activity in vitro for the DOP versus MOP receptor. Our findings may explain …

Anp Chromatography-Coupled With Hdx-Ms | A Potential Approach To Reduce Proton Back-Exchange In Structural Proteomics Assay, Seiichiro Watanabe

Seiichiro Watanabe

No abstract provided.

Predicting Combined Effects Of Land Use And Climate Change On River And Stream Salinity, John Olson

John Olson

Generating High-Order Optical And Spin Harmonics From Ferromagnetic Monolayers, G.P. Zhang, M.S. Si, M. Murakami, Y.H. Bai, Thomas F. George

Thomas George

Intro To Command Line Coding (Fastqe & Fastp), Ray A. Enke

Ray Enke Ph.D.

Belowground Rhizomes In Paleosols: The Hidden Half Of An Early Devonian Vascular Plant, Jinzhuang Xue, Zhenzhen Deng, Pu Huang, Kangjun Huang, Michael J. Benton, Ying Cui

Ying Cui

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant−soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus. The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils …