Life Sciences Commons^™

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell

Dan Nettleton

Shoots can be regenerated from Arabidopsis (Arabidopsis thaliana) root explants in tissue culture through a two-step process requiring preincubation on an auxin-rich callus induction medium. Regenerating tissues can be directed along different developmental pathways leading to the formation of shoots, new roots, or callus by transferring to the appropriate organ induction medium. Using gene-profiling methods, we identified groups of genes that serve as molecular signatures of the different developmental processes, i.e. genes that were specifically up- or down-regulated on one developmental pathway, but not on others. One transcription factor gene that was up-regulated during early shoot development was …

Loss Of Rna–Dependent Rna Polymerase 2 (Rdr2) Function Causes Widespread And Unexpected Changes In The Expression Of Transposons, Genes, And 24-Nt Small Rnas, Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially …

Comparative Gene Expression Profiles Between Heterotic And Non-Heterotic Hybrids Of Tetraploid Medicago Sativa, Xuehui Li, Yanling Wei, Dan Nettleton, E. Charles Brummer

Dan Nettleton

Background: Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.

Results: We tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% …

Interchromosomal Transfer Of Immune Regulation During Infection Of Barley With The Powdery Mildew Pathogen, Priyanka Surana, Ruo Xu, Gregory Fuerst, Antony V. E. Chapman, Dan Nettleton, Roger P. Wise

Dan Nettleton

Powdery mildew pathogens colonize over 9500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh. Two highly significant regions possessing trans eQTL were identified near …

Crowdsourcing Image Analysis For Plant Phenomics To Generate Ground Truth Data For Machine Learning, Naihui Zhou, Zachary D. Siegel, Scott Zarecor, Nigel Lee, Darwin A. Campbell, Carson M. Andorf, Dan Nettleton, Carolyn J. Lawrence-Dill, Baskar Ganapathysubramanian, Jonathan W. Kelly, Iddo Friedberg

Dan Nettleton

The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good quality. We explore an image analysis task involving the segmentation of corn tassels from images taken in a field setting. We investigate the accuracy, speed and other quality metrics when this task is performed by students for academic credit, Amazon MTurk workers, and Master Amazon MTurk …

Using Drones For Precision Agriculture, Jiyul Chang, Madhav P. Nepal

Madhav Nepal

In this teaching module, students will learn what Precision Agriculture is and how to apply drone into Precision Agriculture practices. To use data (images) taken by drone, students will learn the basic theory of Remote Sensing. Using images, students learn how to make NDVI (Normalized Difference Vegetation Index) maps and how to apply drone (remote sensing technique) in agriculture.

Medicago Sativa Has Reduced Biomass And Nodulation When Grown With Soil Microbiomes Conditioned To High Phosphorus Inputs, Laura M. Kaminsky, Grant L. Thompson, Ryan V. Trexler, Terrence H. Bell, Jenny Kao-Kniffin

Grant Thompson

Lethal Effects Of Leaf Leachate From The Non-Native Invasive Shrub Amur Honeysuckle (Lonicera Maackii) On A Model Aquatic Organism (Hyalella Azteca), Eric B. Borth, Kevin W. Custer, Ryan W. Mcewan

Ryan McEwan

The invasive shrub Lonicera maackii (Amur honeysuckle) is a problematic species in the eastern United States and there is growing evidence that materials from this species have toxic effects on some organisms. We used a sequence of microcosm bioassays to assess the influence of L. maackii leaf leachate on the macroinvertebrate Hyalella azteca, which is a standard aquatic organism for toxicity assessment. In a laboratory setting, H. azteca were exposed to a leaf leachate dilution series (6.25%, 12.5%, 25%, 50%, 100%) in 48-h toxicity tests. This was repeated throughout the growing season to assess the potential for changes in …

The Role Of Environmental Filtering In Structuring Appalachian Tree Communities: Topographic Influences On Functional Diversity Are Mediated Through Soil Characteristics, Julia I. Chapman, Ryan W. Mcewan

Ryan McEwan

Identifying the drivers of community assembly has long been a central goal in ecology, and the development of functional diversity indices has provided a new way of detecting the influence of environmental gradients on biotic communities. For an old-growth Appalachian forest, we used path analysis to understand how patterns of tree functional diversity relate to topography and soil gradients and to determine whether topographic effects are mediated through soil chemistry. All of our path models supported the idea of environmental filtering: stressful areas (high elevation, low soil moisture, low soil nutrients) were occupied by communities of low functional diversity, which …

Floristic Response To Urbanization: Filtering Of The Bioregional Flora In Indianapolis, Indiana, Usa, Rebecca W. Dolan, Myla F.J. Aronson, Andrew L. Hipp

Rebecca W. Dolan

PREMISE OF THE STUDY: Globally, urban plant populations are becoming increasingly important, as these plants play a vital role in ameliorating effects of ecosystem disturbance and climate change. Urban environments act as filters to bioregional flora, presenting survival challenges to spontaneous plants. Yet, because of the paucity of inventory data on plants in landscapes both before and after urbanization, few studies have directly investigated this effect of urbanization. METHODS: We used historical, contemporary, and regional plant species inventories for Indianapolis, Indiana USA to evaluate how urbanization filters the bioregional flora based on species diversity, functional traits, and phylogenetic community structure. …

Surface-Soil Properties Of Alder Balds With Respect To Grassy And Rhododendron Balds On Roan Mountain, North Carolina—Tennessee, James T. Donaldson, Zachary C. Dinkins, Foster Levy, Arpita Nandi

Foster Levy

We analyzed soils in Alder Bald, Grassy Bald, and Rhododendron Bald communities on Roan Mountain to infer the influence of vegetation on soil and to help guide management strategies. In all vegetation types, soils were acid (pH = 4–5) sandy loams. We found vegetation-associated differences for organic content, cation exchange capacity, acidity, two plant macronutrients (K, Mg), and three cations (Fe, Na, Zn). We predicted that nitrogen compounds would be highest in the Alder Bald because Alnus viridis ssp. crispa (Green Alder) can harbor nitrogen-fixing bacteria. Organic content was highest at the alder-bald sites, ammonium was similar among vegetation types, …

Pattern And Rate Of Decline Of A Population Of Carolina Hemlock (Tsuga Caroliniana Engelm.) In North Carolina, Foster Levy, Elaine S. Walker

Foster Levy

We monitored a population of Carolina Hemlocks in northwestern North Carolina for four years to examine the rate and pattern of decline in response to infestation by Adelges tsugae (Hemlock Woolly Adelgid). Our yearly census of hemlock condition and severity of the adelgid infestation included trees of all sizes. We estimated declines in condition as the portions of the leaf canopy that were lost. Initially, infestation occurred throughout the population but was severe in only a small cluster of individuals. Within 1 year, the area of severe infestation increased in size to encompass 48% of the population. In another region …

Supplemental Data, Russell J. Ingram, Foster Levy, Cindy L. Barrett, James T. Donaldson

Foster Levy

No abstract provided.

Deidamia Inscriptum (Lettered Sphinx Moth) Caterpillars Feeding On Oxydendrum Arboreum (Sourwood) And Their Predation By Black Bears In Northeast Tennessee, Foster Levy, David L. Wagner, Elaine S. Walker

Foster Levy

An outbreak of Deidamia inscriptum (Lettered Sphinx Moth) caterpillars was noted in northeast Tennessee where Oxydendrum arboreum (Sourwood) trees were defoliated. Nearly all published literature and online resources list only plants in the grape family (Vitaceae) as larval food plants. Food-plant preference trials using fresh leaves of 3 woody plant species showed that Deidamiacaterpillars from this region had a preference for Sourwood over Parthenocissus quinquefolia(Virginia Creeper), and rejected Acer rubrum (Red Maple), a non-host species. Ursus americanus(Black Bear) were feeding on the caterpillars as evidenced by bent and broken Sourwood saplings bearing claw marks and by abundant …

Developmental Functions Of Mir156-Regulated Squamosa Promoter Binding Protein-Like (Spl) Genes In Arabidopsis Thaliana, Mingli Xu, Tieqiang Hu, Jianfei Zhao, Mee-Yeon Park, Keith W. Earley, Gang Wu, Li Yang, Scott Poethig

Jianfei Zhao

Suppressor Of Phytochrome B4-#3 Represses Genes Associated With Auxin Signaling To Modulate Hypocotyl Growth, David Favero, Caitlin Jacques, Akira Iwase, Kimberly Le, Jianfei Zhao, Keiko Sugimoto, Michael Neff

Jianfei Zhao

Microclimate Moderates Plant Responses To Macroclimate Warming, Pieter De Frenne, Francisco Rodríguez-Sánchez, David Anthony Coomes, Lander Baeten, Gorik Verstraeten, Mark Vellend, Markus Bernhardt-Römermann, Carissa D. Brownd, Jörg Brunet, Johnny Cornelis, Guillaume M. Decocq, Hartmut Dierschke, Ove Eriksson, Frank S. Gilliam, Radim Hédl, Thilo Heinken, Martin Hermy, Patrick Hommel, Michael A. Jenkins, Daniel L. Kelly, Keith J. Kirby, Fraser J. G. Mitchell, Tobias Naaf, Miles Newman, George Peterken, Petr Petrík, Jan Schultz, Grégory Sonnier, Hans Van Calster, Donald M. Waller, Gian-Reto Walther, Peter S. White, Kerry D. Woods, Monika Wulf, Bente Jessen Graae, Kris Verheyen

Frank S. Gilliam

Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., “thermophilization” of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that “climatic lags” may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of …

Microclimate Moderates Plant Responses To Macroclimate Warming, Pieter De Frenne, Francisco Rodríguez-Sánchez, David Anthony Coomes, Lander Baeten, Gorik Verstraeten, Mark Vellend, Markus Bernhardt-Römermann, Carissa D. Brownd, Jörg Brunet, Johnny Cornelis, Guillaume M. Decocq, Hartmut Dierschke, Ove Eriksson, Frank S. Gilliam, Radim Hédl, Thilo Heinken, Martin Hermy, Patrick Hommel, Michael A. Jenkins, Daniel L. Kelly, Keith J. Kirby, Fraser J. G. Mitchell, Tobias Naaf, Miles Newman, George Peterken, Petr Petrík, Jan Schultz, Grégory Sonnier, Hans Van Calster, Donald M. Waller, Gian-Reto Walther, Peter S. White, Kerry D. Woods, Monika Wulf, Bente Jessen Graae, Kris Verheyen

Frank S. Gilliam

Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., “thermophilization” of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that “climatic lags” may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of …

Ataf2 Integrates Arabidopsis Brassinosteroid Inactivation And Seedling Photomorphogenesis, Hao Peng, Jianfei Zhao, Michael Neff

Jianfei Zhao

A Contribution To The Vascular Flora Of The Sequatchie Valley Within Sequatchie County, Tennessee, John Richard Evans

John Evans

The vascular flora of the Sequatchie Valley within Sequatchie County, Tennessee was studied for three growing seasons from 2008 through 2010. The Sequatchie Valley is located within the southeastern portion of the Cumberland Plateau and is generally considered to be part of the Cumberland Plateau Physiographic Province. Nevertheless, a number of geological and ecological factors distinguish the Sequatchie Valley from the elevated Cumberland Plateau, suggesting that the floristic composition of the valley may be different from the surrounding region. Although several previous floristic studies have been conducted on the plateau surface, very little attention has been given to the Sequatchie …

Documenting Effects Of Urbanization On Flora Using Herbarium Records, Rebecca W. Dolan, Marcia E. Moore, Jessica Stephens

Rebecca W. Dolan

As human populations increasingly live in cities, urban floras and the ecosystem services they provide are under increasing threat. Understanding the effects of urbanization on plants can help to predict future changes and identify ways to preserve biological diversity. Relatively few studies document changes through time in the flora of a focal region and those that do primarily address European floras. They often rely on contemporary spatial gradient studies as surrogates for changes with time. We compare historical species records (prior to 1940) with the current flora for Marion County, Indiana, USA, home to Indianapolis, the 13th largest city in …

Demographic Viability Of Populations Of Silene Regis In Midwestern Prairies: Relationships With Fire Management, Genetic Variation, Geographic Location, Population Size And Isolation, Eric S. Menges, Rebecca W. Dolan

Rebecca W. Dolan

We studied the demographic viability of populations of a long-lived iteroparous prairie perennial, Silene regia, in relation to management regimes, population sizes, geographical region (Ohio and Indiana vs. Missouri and Arkansas), degree of isolation and amount of genetic variation. Demographic data were collected from 16 populations for up to 7 years. This species has high survivorship, slow growth, frequent flowering and episodic seedling recruitment. Matrix projection methods were used to summarize population performance with and without recruitment. Median finite rates of increase by population varied from 0.57 to 1.82 and from 0.44 to 0.99, respectively. Populations with the highest rates …

Population Dynamics Of Ludwigia Leptocarpa (Onagraceae) And Some Factors Affecting Size Hierarchies In A Natural Population, Rebecca W. Dolan, Rebecca R. Sharitz

Rebecca W. Dolan

Germination cohorts of Ludwigia leptocarpa, a semi-aquatic annual plant were marked in the field at time of establishment and followed through the 1981 and 1982 growing seasons at a site in southern South Carolina. Data from each cohort were pooled to determine demographic characteristics of the population as a whole, then analyzed separately to determine the effect of time on germination on survivorship, relative growth rate, and adult size. Changes in numbers of L. leptocarpa fit a Deevey Type II survivorship curve. This and other characteristics of the species classify it as ‘r-selected’. Aspects of the life history may reflect …

Seaweed Beyond Sushi, Catherine V. Schmitt

Catherine Schmitt

No abstract provided.

Lichens Of Six Vernal Pools In Acadia National Park, Maine, Usa, Jason Barton, Brett Ciccotelli, Jillian E. Gall, Fred C. Olday, Bruce Connery, Tanner B. Harris, Alan M. Fryday, Nishanta Rajakaruna

Nishanta Rajakaruna

Whereas lichen-habitat relations have been well-documented globally, literature on lichens of vernal pools is scant. We surveyed six vernal pools at Acadia National Park on Mount Desert Island, Maine, USA for their lichen diversity. Sixty-seven species were identified, including seven species that are new reports for Acadia National Park: Fuscidea arboricola, Hypogymnia incurvoides, Lepraria finkii, Phaeographis inusta, Ropalospora viridis, Usnea flammea, and Violella fucata. Five species are considered uncommon or only locally common in New England: Everniastrum catawbiense, Hypogymnia krogiae, Pseudevernia cladonia, Usnea flammea, and Usnea merrillii. This …

Wheat Streak Mosaic Virus Infects Systemically Despite Extensive Coat Protein Deletions: Identification Of Virion Assembly And Cell-To-Cell Movement Determinants, Satyanarayana Tatineni, Frank A. Kovacs, Roy C. French

Satyanarayana Tatineni

Viral coat proteins function in virion assembly and virus biology in a tightly coordinated manner with a role for virtually every amino acid. In this study, we demonstrated that the coat protein (CP) of Wheat streak mosaic virus (WSMV) (genus Tritimovirus; family Potyviridae) is unusually tolerant of extensive deletions with continued virion assembly and/or systemic infection. A series of deletion and point mutations were created in the CP cistron of wild-type and/or GFP-tagged WSMV and examined the effects of these mutations on cell-to-cell and systemic transport and virion assembly of WSMV. Mutants with overlapping deletions comprising N-terminal amino acids 6 …

Insights Into The Evolution And Diversification Of The At-Hook Motif Nuclear Localized Gene Family In Land Plants, Jianfei Zhao, David Favero, Jiwen Qiu, Eric Roalson, Michael Neff

Jianfei Zhao

Insect Visitation Of Peduncular And Petiolar Extrafloral Nectar Glands On Castor Bean (Ricinus Communis L.) Plants In Southern California, Victor D. Carmona

Victor D. Carmona-Galindo

Castor bean (Ricinus communis L.) is a myrmecophytic plant species with specialized extrafloral nectar (EFN) glands that serve to attract predatory insects, which in return defend plant-tissues against herbivores. The EFN glands on castor bean plants are located along the leaf petioles as well as on the peduncles of its imperfect (unisexual) flowers. This field-project evaluates the richness, diversity, and species assemblage of insects visiting EFN glands located on (female and male) flower peduncles and leaf petioles on castor bean plants growing in a Southern California coastal landscape. We detected that EFN glands on female-flower peduncles were visited by an …

Arabidopsis Thaliana Ahl Family Modulates Hypocotyl Growth Redundantly By Interacting With Each Other Via The Ppc/Duf296 Domain, Jianfei Zhao, David Favero, Hao Peng, Michael Neff

Jianfei Zhao