Thesis (M.S. in psychology)--Washington State University, December 2008. / Title from PDF title page (viewed on July 10, 2009). "Department of Psychology." Includes bibliographical references (p. 27-37).

Even under the best management strategies contemporary crops face yield losses from diverse threats such as, pathogens, pests, and environmental stress. Adding to this management challenge is that under current global climate projections these impacts are predicted to become even greater. Natural genetic variation, long used by traditional plant breeders, holds great promise for adapting high performing agronomic lines to these stressors. Yet, efforts to bolster crop plant resilience using wild relatives have been hindered by time consuming efforts to develop genomic tools and/or identify the genetic basis for agronomic traits. Thus, increasing crop plant resilience requires developing and deploying approaches that leverage current high-throughput sequencing technologies to more rapidly and robustly develop genomic tools in these systems. Here we report the integration of bioinformatic and statistical tools to leverage high-throughput sequencing to 1) develop a machine learning approach to determine factors impacting transcriptome assembly and quantitatively evaluate transcriptome completeness, 2) dissect complex physiological pathway interactions in Solanum pimpinellifolium under combined stresses—using comparative transcriptomics, and 3) develop a genome assembly pipeline that can be deployed to rapidly assemble a more contiguous genome, unraveling previously hidden complexity, using Phytopthora capsici as a model. As a result, we have generated strategic guidelines for transcriptome assembly and developed an orthologue and reference free, machine learning based tool "WWMT" to quantitatively score transcriptome completeness from short read data. Secondly, we identified "hub genes" and describe genes involved with "cross-talk" between drought and herbivore stress response pathways. Finally, we demonstrate a protocol for combining long-read sequencing from the Oxford Nanopore Technologies MinION, and short-read data, to rapidly assembly a cost-effective, contiguous and relatively complete genome. Here we uncovered hidden variation in a well-known plant pathogen finding that the genome was 92% bigger than previous estimates with more than 39% of duplicated regions, supporting a hypothesized recent whole genome duplication in this clade. This community resource will support new functional and evolutionary studies in this economically important pathogen. / Doctor of Philosophy / Meeting the food production demands of a burgeoning population in a changing environment, means adapting crop plants to become more resilient to environmental stress. One of the greatest barriers to understanding and predicting crop responses to future environmental change is our poor understanding of the functional and genomic basis of stress resistance traits for contemporary crops. This impediment presents a barrier for rapid crop improvement technologies, such as, gene editing or genomic selection, that is only partially overcome by generating large amounts of sequencing data. Here we need tools that allow us to process and evaluate huge amounts of data generated from next generation sequencing studies to help identify genomic regions associated with agronomic traits. We also need technical approaches that allow us to disentangle the complex genetic interactions that drive plant stress responses. Here we present work that used statistical analysis and recent advances of artificial intelligence to develop a bioinformatic approach to evaluate genomic sequencing data prior to downstream analyses. Secondly, we used a reductionist approach to filter thousands of genes to key genes associated with combined stress responses (herbivory and drought), in the most widely used vegetable in the world, tomato. Finally, we developed a method for generating whole genome sequences that is low-cost and time sensitive and tested it using a well-known plant pathogen genome, wherein we unraveled significant hidden complexity. Overall this work provides community-wide genomic tools and information to promote crop resilience.

>Magister Scientiae - MSc / Agricultural production is one of the most important sectors which provide food for the growing world population which is estimated to reach 9.7 billion by 2050, thus there is a need to produce more food. Climate change, on the other hand, is negatively affecting major global crops such as maize, sorghum, wheat and barley. Environmental factors such as salinity, drought, high temperatures and pathogens affect plant production by oxidatively damaging the physiological processes in plants, leading to plant death. Poor irrigation used to combat drought result in salinasation, which is estimated to affect 50% of arable land by 2050. Plants have developed several mechanisms that protect them against stress and these include overexpression of stress responsive genes and altered signal transduction to change the expression of stress responsive genes, among others. Cyclic 3’5’ guanosine monophosphate (cGMP), a second messenger that is synthesised by guanylyl cyclase (GC), transmit signals to various cellular functions in plants during plant development, growth and response to abiotic and biotic stresses. Arabidopsis thaliana nitric oxide guanylyl cyclase 1 (AtNOGC1) is a guanylyl cyclase which upon activation by nitric oxide (NO) leads to the production of more cGMP. Cyclic GMP further activates protein kinases, ion gated channels and phosphodiesterase which mediate response to various stresses. In this project the role of AtNOGC1 was investigated in response to abiotic and biotic stresses through analysis of its evolutionary relationships, promoter, gene expression and functional analysis via the viability assays in Escherichia coli (E.coli). Phylogenetic tree, exon-intron structure and conserved motifs were analysed using the Molecular Evolutionary Genetics Analysis (MEGA V.7), Gene Structure Display Server 2.0 (GSDS 2.0), and Multiple Expectation Maximisation for Motif Elicitation (MEME) tools respectively. AtNOGC1’s gene expression was analysed by the Real-Time Quantitative Reverse Transcription Polymerase Reaction (qRT-PCR), whereas functional analysis was carried out using the cell viability (liquid and spot) assays to determine its ability to confer stress tolerance to E. coli.

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains xii, 129 p.; also includes graphics Includes bibliographical references (p. 73-85). Available online via OhioLINK's ETD Center

Thesis (Ph.D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains ix, 129 p.; also includes graphics. Includes bibliographical references (p. 120-129). Available online via OhioLINK's ETD Center

Submitted by Programa de Pós-graduação em Biotecnologia (mebiotec.ufba@gmail.com) on 2017-04-04T13:35:47Z No. of bitstreams: 1 Dissertação_Paulo_Teixeira.pdf: 5196941 bytes, checksum: 5f169d111dd41c2034826870deb144a2 (MD5) / Approved for entry into archive by Delba Rosa (delba@ufba.br) on 2017-07-03T15:30:13Z (GMT) No. of bitstreams: 1 Dissertação_Paulo_Teixeira.pdf: 5196941 bytes, checksum: 5f169d111dd41c2034826870deb144a2 (MD5) / Made available in DSpace on 2017-07-03T15:30:13Z (GMT). No. of bitstreams: 1 Dissertação_Paulo_Teixeira.pdf: 5196941 bytes, checksum: 5f169d111dd41c2034826870deb144a2 (MD5) / CAPES / A mamoneira (Ricinus communis L.) é uma espécie que apresenta destaque no cenário das oleaginosas, principalmente pela composição química e qualidade do óleo extraído de suas sementes como fonte de matéria prima para a produção de biodiesel. Além das vantagens de ser uma cultura de fácil manejo, e com ampla faixa de adaptação e tolerância podendo ser cultivada em ambientes desfavoráveis e baixos custos de produção. Devido a estes fatores, criaram-se incentivos e perspectivas de expansão do seu cultivo pela agricultura familiar no semiárido nordestino, região caracterizada pela escassez de chuvas e frequentes secas. O objetivo deste trabalho consistiu em caracterizar o processo de formação da semente de Mamona da cultivar MPA 11 e analisar funcionalmente os eventos do ciclo celular e eventos fisiológicos durante o desenvolvimento e maturação das sementes, bem como durante a germinação das sementes embebidas sob condições de restrição hídrica por meio de osmocondicionamento. Como material biológico foi utilizado sementes do cultivar MPA11 produzida pela Empresa Baiana de Desenvolvimento Agrícola (EBDA) cultivadas na Fazenda Experimental da UFBA (São Gonçalo dos Campos-BA). Foram realizadas visitas semanais para colheita de frutos a cada sete dias até o 63° dia após a marcação (DAM), os quais passaram por análises biométricas, sendo medidos largura e comprimento de frutos; largura, comprimento e espessura de sementes, teor de umidade e conteúdo de matéria seca das sementes. As sementes colhidas aos 63 DAM foram submetidas à secagem e osmocondicionamento, e subsequente teste de germinação, conduzido em quatro repetições de 25 sementes por tratamento, sendo o delineamento experimental inteiramente casualizado em esquema fatorial de 2 x 2. Para o estudo do ciclo celular durante o desenvolvimento foram utilizados embriões de sementes com 28, 35, 42, 49, 56 e 63 DAM para análise de conteúdo de DNA por citometria de fluxo, tubulina por western blotting e microtúbulos por microscopia de imunofluorescência. Para estudo do ciclo celular durante a germinação, foram extraídos os eixos embrionários nos períodos de 0, 24, 48, 72 e 96 h das sementes embebidas em água, sendo realizadas análises de tubulina e microtúbulos. A cultivar MPA11 apresenta ciclo precoce, com suas sementes alcançando a maturidade fisiológica aos 35 DAM estando às mesmas maduras aos 56 DAM, sendo esta uma variedade promissora para o semiárido nordestino. Para os tratamentos de secagem aplicados às sementes maduras, não houve diferenças significativas. No entanto, o osmocondicionamento permitiu às sementes iniciar etapas do processo de germinação, o que melhorou a velocidade de germinação após embebição em água. Neste estudo, um modelo de desenvolvimento e germinação de sementes de mamona da cultivar MPA11 da EBDA é proposto, o que representa um avanço na compreensão do desenvolvimento e germinação de sementes de mamona. / The castor bean (Ricinus communis L.) is a species that has featured in the scenario of oilseeds, mainly by the chemical composition and quality of the oil extracted from its seeds as a source of raw material for the production of biodiesel. Besides the advantages of being a culture of easy handling and wide range of adaptation and tolerance can be grown on low costs and unfavorable production environments. Due to these factors, it created incentives and opportunities for expansion of its cultivation on family farms in the northeastern semi-arid region characterized by low rainfall and frequent droughts. The aim of this study was to characterize the process of formation of Castor seed cultivar MPA11 and functionally analyze the cell cycle events and physiological events during development and maturation of seeds and during germination of seeds soaked under constraint conditions water through priming. As biological material MPA11 seeds of cultivar produced by the Bahia Agricultural Development Company (EBDA) grown at the Experimental Farm UFBa (São Gonçalo dos Campos-BA) were used. Weekly visits to harvest fruit were taken every seven days until the 63 th day after (DAM) marking, which passed through biometric analysis, being measured width and fruit length; width, length and thickness of seed moisture content and dry matter content of the seeds. Seeds harvested at 63 DAM were dried and priming, and subsequent germination test conducted in four replicates of 25 seeds per treatment, the completely randomized design in a factorial 2 x 2 To study the cell cycle during developing embryos of seeds with 28, 35, 42, 49, 56 and 63 DMA analysis of DNA content by flow cytometry, western blotting for tubulin and microtubules by immunofluorescence microscopy. To study the cell cycle during germination the embryonic axes to periods of 0, 24, 48, 72 and 96 h of seeds soaked in water, the analysis being performed tubulin and microtubules were extracted. Cultivar MPA11 presents early cycle with its seeds reach physiological maturity at 35 to being mature same at 56 DAM, which is a promising variety for the semi-arid northeast. For the drying treatments applied to mature seeds, there were no significant differences. However, osmopriming allowed the seeds start germinating stages of the process, which improved the germination rate after soaking in water. In this study, a model of development and germination of castor bean cultivar MPA11 EBDA is proposed, representing a breakthrough in understanding the development and germination of castor seeds.

Philosophiae Doctor - PhD / This study explores the roles of exogenously applied nitric oxide, exogenously applied caffeic acid and salt stress on the antioxidant system in cereal (exemplified by maize) and legume (using soybean as an example) plants together with their influence on membrane integrity and cell death.This study investigates changes in H2O2 content, root lipid peroxidation, root cell death and antioxidant enzymatic activity in maize roots in response to exogenously applied nitric oxide (NO) and salt stress. This part of the study is based on the partially understood interaction between NO and reactive oxygen species (ROS) such as H2O2 and the role of antioxidant enzymes in plant salt stress responses. The results show that application of salt (NaCl) results in elevated levels of H2O2 and an increase in lipid peroxidation, consequently leading to increased cell death. The study also shows that by regulating the production and detoxification of ROS through modulation of antioxidant enzymatic activities, NO plays a pivotal role in maize responses to salt stress. The study argues for NO as a regulator of redox homeostasis that prevents excessive ROS accumulation during exposure of maize to salinity stress that would otherwise be deleterious to maize. This study extends the role of exogenously applied NO to improve salt stress tolerance in cereals crops (maize) further to its role in enhancing salt stress tolerance in legumes. The effect of long-term exposure of soybean to NO and salt stress on root nodule antioxidant activity was investigated to demonstrate the role of NO in salt stress tolerance. The results show that ROS scavenging antioxidative enzymes like SOD, GPX and GR are differentially regulated in response to exogenous application of NO and salt stress. It remains to be determined if the NOinduced changes in antioxidant enzyme activity under salt stress are sufficient to efficiently reduce ROS accumulation in soybean root nodules to levels close to those of unstressed soybean root nodules. Furthermore, this study investigates the effect of long-term exposure of soybean to exogenous caffeic acid (CA) and salt stress, on the basis of the established role of CA as an antioxidant and the involvement of antioxidant enzymes in plant salt stress responses. The effect of CA on soybean nodule number, biomass (determined on the basis of nodule dry weight, root dry weight and shoot dry weight), nodule NO content, and nodule cyclic guanosine monophosphate (cGMP) content in response to salt stress was investigated. Additionally, CA-induced changes in nodule ROS content, cell viability, lipid peroxidation and antioxidant enzyme activity as well as some genes that encode antioxidant enzymes were investigated in the presence or absence of salt stress. The study shows that long-term exposure of soybean to salt stress results in reduced biomass associated with accumulation of ROS, elevated levels of lipid peroxidation and elevated levels of cell death. However, exogenously applied CA reversed the negative effects of salt stress on soybean biomass, lipid peroxidation and cell death. CA reduced the salt stress-induced accumulation of ROS by mediating changes in root nodule antioxidant enzyme activity and gene expression. These CA-responsive antioxidant enzymes were found to be superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione peroxidase (GPX), and glutathione reductase (GR), which contributed to the scavenging of ROS in soybean nodules under salt stress. The work reported in Chapter 2 has been published in a peer-reviewed journal [Keyster M, Klein A, Ludidi N (2012) Caspase-like enzymatic activity and the ascorbate-glutathione cycle participate in salt stress tolerance of maize conferred by exogenously applied nitric oxide. Plant Signaling and Behavior 7: 349-360]. My contribution to the published paper was all the work that is presented in Chapter 2,whereas the rest of the work in the paper (which is not included in Chapter 2) was contributed by Dr Marshall Keyster.

Mosses are small avascular bryophytes with a haploid dominant gametophyte and a diploid sporophyte stage. The gametophyte cells are single layered and lack a protective cuticle, which is the first line of defense in vascular plants. These factors would render them highly susceptible to stress but on the contrary, mosses have flourished on land for the past 450 million years with tolerance to both abiotic and biotic stress. Occurrence of unique lipids in bryophytes was considered as an adaptive means to survive harsh terrestrial condition. A recent study identified a lipid metabolite, anandamide in the Physcomitrella patens. Anandamide (NAE 20:4) belongs to a group of fatty acid ethanolamides or N –acylethanolamines (NAEs). In eukaryotes, NAEs were shown to play an important role in mediating stress responses. In plants, NAE 14:0 has been implicated in biotic stress response; its levels increased up to 50-fold in elicitor-treated tobacco plants, along with induction of defense gene expression and inhibition of alkalization. In animals anandamide acts as an endocannabinoid ligand and mediates several physiological responses including stress. This study aims to use P. patens as the model system because of its available genomic database and prior studies on biotic stress, to examine if NAE 20:4 contributes to their ability to tolerate biotic stress. It is hypothesized that the occurrence of anandamide will play a role in mediating biotic stress tolerance in P. patens. To test this hypothesis, three specific aims are proposed. They are to determine the effect of 1) elicitor-treatment on NAE and fatty acid profile in the moss, 2) anandamide on elicitor-induced morphological and physiological changes in the moss and 3) anandamide on elicitor-induced defense gene expression in moss. Mosses utilize similar defense mechanisms as flowering plants and disease symptoms can easily be studied using microscopy because of their haploid dominant gametophyte stage with monolayer cells. The induction of defense gene expression will be studied by quantitative PCR and changes in lipid profile by selective lipidomics. This study is expected to provide novel insights into the role of anandamide in early land plants, specifically in response to biotic stress.

No description available.

Species vary phenotypically and genetically across their environmental range limits, and this variation can influence ecological processes. Ecologically meaningful intraspecific variation might be particularly important in the context of agricultural weeds and exotic invaders, because intraspecific variation in these species might allow them to rapidly adapt to their unusually dynamic and variable environments. In a greenhouse study, we explored intraspecific variation in the size, rhizome production, and competitive ability of the global invader, Johnsongrass (Sorghum halepense), representing populations from agricultural and non-agricultural habitats across its introduced North American range. We also used these populations to explore the relationship between phenotypic variation and genomic endoreduplication responses to the common stresses herbicides, competition, and clipping. Endoreduplication occurs when plants increase their genome size by increasing their nuclear chromosome number, with some evidence showing correlations with stress response. We found that Johnsongrass plants from agricultural habitats were larger than plants from non-agricultural habitats, but there was no difference between habitats in either rhizome production or competitive ability. Two of the five herbicides we tested, primisulfuron and imazethapyr, had the strongest suppressive effects on Johnsongrass, and also stimulated the greatest rates of endoreduplication. Furthermore, agricultural populations showed higher levels of endoreduplication. We found no overall effect of competition on endoreduplication, although endoreduplication was higher for non-agricultural populations than agricultural populations. When competing with corn, but not with conspecifics, Johnsongrass roots increased endoreduplication by 13%. Clipping induced substantial endoreduplication, but there was no difference between agricultural and non-agricultural populations. Our results suggest that endoreduplication may play a role in some, but not all, stress responses in Johnsongrass. Furthermore, our results indicate that Johnsongrass has adapted in some phenotypic and genomic ways to agricultural habitats in North America. Such adaptation may play a role in this species' success as both an agricultural weed and an exotic invader. / Master of Science in Life Sciences / Agricultural weeds and exotic invasive plant species cause substantial economic and ecological impacts. Exploring the ways in which these species thrive, spread, and cope with different forms of stress contributes to our understanding of why these plants can be so successful and cause such damage. We studied how one of the world’s worst weeds and invaders of natural systems, Johnsongrass (Sorghum halepense), responded via growth and by increases in the amount of DNA in its cells to different forms of stress. We also asked whether any Johnsongrass populations appeared to have adapted to agricultural habitats. We found that Johnsongrass plants grown from seed collected from agricultural fields produced larger plants than those from non-agricultural locations (e.g., roadsides), suggesting some degree of adaptation to agricultural environments by Johnsongrass. We also found that stress from sub-lethal doses of some herbicides suppressed the growth of Johnsongrass, simultaneously stimulating more cells with increased cell DNA content, a genomic process called endoreduplication. Interestingly, there were higher rates of endoreduplication in plants from agricultural populations in the herbicide experiment, suggesting that endoreduplication may help Johnsongrass cope with stress and that agricultural populations show adaptive increases in this genomic stress response. Competition from corn or other Johnsongrass plants suppressed target Johnsongrass plants, but did not stimulate more endoreduplication in the suppressed plants. Finally, clipping reduced the size of Johnsongrass substantially, and also stimulated increased rates of endoreduplication. In general, our results indicate that Johnsongrass has adapted in some ways to agricultural habitats in North America, and that this adaptation may play a role in this species’ success as both an agricultural weed and an exotic invader.