Molecular Genetics Commons^™

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

Identification And Characterization Of Genes Involved In Metabolism Of N5 Monoene Precursors To N5 Anacardic Acids In The Trichomes Of Pelargonium X Hortorum., Richa A. Singhal

Electronic Theses and Dissertations

Unusual monoenoic fatty acids (UMFA’s) and specialized metabolites called anacardic acids (AnAc) are produced in glandular trichomes of Pelargonium ´ hortorum (geranium). The UMFA’s, 16:1^∆11 and 18:1^∆13 are precursors for the synthesis of unsaturated AnAc 22:1n5and 24:1n5 that contribute to pest resistance in geraniums. UMFAs and their derived AnAc metabolites not only provide a useful biological marker that differentiates the biosynthetic pathway for unusual mononenes from the common fatty acids (i.e. stearic, palmitic, oleic, linoleic and linolenic) but also have industrial, medical and agricultural applications. Fatty acid biosynthesis enzymes like acyl carrier proteins (ACPs); thioesterases (TEs) and β-ketoacyl-ACP …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold …

Is A Mitochondrial Plasmid Really A Virus?, Mackenzie Strehle

UCARE: Research Products

In addition to containing a large and complex mitochondrial genome, the mitochondria of several species of plants have been shown to contain an independent, self-replicating DNA molecule in the form of a plasmid. Plants in the Brassica genus contain a linear plasmid that is approximately 11.6 kilobases in length. The plasmid is characterized by the presence of terminal inverted repeats and covalently bonded proteins at its termini (Handa 2008). The plasmid also contains six ORFs that encode DNA and RNA polymerases and a number of unknown proteins (Figure 1). Currently, both the function of this plasmid and the mechanisms by …

Investigation Into The Cell Wall And Cellulose Biosynthesis In Model Species And In The C4 Model Plant Setaria Viridis, Mizuki Tateno

Theses and Dissertations--Plant and Soil Sciences

A uniform feature of all plant cells is the presence of a cell wall. The cell wall functions in facilitating directional expansion and is therefore important for cell shape and morphogenesis. All plant cell walls contain cellulose microfibrils embedded in a network of polysaccharides, lignin and protein. Cellulose is evolutionarily conserved and is made by all plants as well as other members of various taxonomic kingdoms. From a human perspective, the field of renewable energy has had an ever increasing interest in using the cell wall for production of renewable platform chemicals and fuels. However, the biosynthesis of these components …

Rna Sequencing Analysis Of The Msl2msl3, Crl, And Ggps1 Mutants Indicates That Diverse Sources Of Plastid Dysfunction Do Not Alter Leaf Morphology Through A Common Signaling Pathway, Darron R. Luesse, Margaret E. Wilson, Elizabeth S. Haswell

Biology Faculty Research

Determining whether individual genes function in the same or in different pathways is an important aspect of genetic analysis. As an alternative to the construction of higher-order mutants, we used contemporary expression profiling methods to perform pathway analysis on several Arabidopsis thaliana mutants, including the mscS-like (msl)2msl3 double mutant. MSL2 and MSL3 are implicated in plastid ion homeostasis, and msl2msl3 double mutants exhibit leaves with a lobed periphery, a rumpled surface, and disturbed mesophyll cell organization. Similar developmental phenotypes are also observed in other mutants with defects in a range of other chloroplast or mitochondrial functions, including …

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

Establishment Of Biotrophy By The Maize Anthracnose Pathogen Colletotrichum Graminicola: Use Of Bioinformatics And Transcriptomics To Address The Potential Roles Of Secretion, Stress Response, And Secreted Proteins, Ester Alvarenga Santos Buiate

Theses and Dissertations--Plant Pathology

Colletotrichum graminicola is a hemibiotrophic pathogen of maize that causes anthracnose leaf and stalk rot diseases. The pathogen penetrates the host and initially establishes an intracellular biotrophic infection, in which the hyphae are separated from the living host cell by a membrane that is elaborated by the host, apparently in response to pathogen signals. A nonpathogenic mutant (MT) of C. graminicola was generated that germinates and penetrates the host normally, but is incapable of establishing a normal biotrophic infection. The mutated gene is Cpr1, conserved in eukaryotes and predicted to encode a component of the signal peptidase complex. How …

Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos

Theses and Dissertations--Biosystems and Agricultural Engineering

Fabrication of effective algae cultivation systems adjacent to coal-fired power plants to fixate waste CO₂ would represent a sizable step towards achieving a carbon neutral energy cycle. However, emission gas would elevate the algal cultivation system temperature and decreases its pH without expensive preprocessing. Increased temperature and acidity constitutes a profound stress on the algae. Although stressed algae produce heat shock proteins (HSPs) that promote protein folding and protect against stress, the ordinary biological response is insufficient to protect against coal flue gas. Experimental upregulation of HSPs could make algae respond to the stress caused by high temperatures and …

Functional Genomics Of Maize Endosperm Maturation And Protein Quality, Lingling Yuan

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Maize is one of the most important cereal crops and widely cultivated throughout the world. The study on maize kernel development including protein quality improvement is essential for removing dietary protein deficiency because of the lack of essential amino acids, especially lysine and tryptophan, in maize kernel. Quality Protein Maize (QPM) is a hard kernel variant of the high-lysine mutant, opaque-2. We created opaque QPM variants to identify opaque-2 modifier genes and to investigate deletion mutagenesis combined with Illumina sequencing as a maize functional genomics tool. A K0326Y-QPM deletion mutant, line 107, was null for the 27- and 50-kD …

Soil Microbial Community Distributions And Disease Suppressiveness In The Coastal Plain Of Georgia, Michael J. Sabula

College of Graduate Studies: Theses & Dissertations

This study compared the soil microbial communities of three vegetation types in the coastal plain of Georgia: 1. crop land actively in use for agricultural production, 2. transitional grassland in early stages of secondary succession, and 3. pristine unmanaged forest land. Microbial species diversity and quantities of microbial DNA were determined from each of these vegetation types at three separate locations near Statesboro, Georgia. Length heterogeneity PCR(LH-PCR) methods and subsequent analysis of fungal, bacterial, and metazoan communities by analysis of similarity (ANOSIM) revealed high within-group similarity by vegetation type, indicating land management intensity and vegetation cover is a strong determining …

Overexpression/Silencing Of Selected Soybean Genes Alters Resistance To Pathogens, Mohamed H. El-Habbak

Theses and Dissertations--Plant Pathology

Plant diseases remain a major obstruction to meeting the world’s increased demand for soybean oil and protein. Reducing the losses caused by diseases in order to improve crop production is a high priority for agricultural research. The need for novel strategies for plant disease control cannot be overstated. In the present study, selected defense-related genes were silenced and/or overexpressed in soybean using a virus-based vector and the resultant plants were tested for their responses to pathogens. The first part of the study focused on Rps1k (Resistance to Phytophthora sojae) gene. The two conserved domains encoding ‘P-Loop NTPase’ and ‘PLN03210’ …

Dna-Binding Site Recognition By Bhlh And Mads-Domain Transcription Factors, Joshua R. Werkman

Theses and Dissertations--Plant and Soil Sciences

Herewithin, two transcription factor (TF) regulatory complexes were investigated. A bHLH–MYB–WDR (BMW) DNA-binding complex from maize was the first complex to be studied. R, a maize bHLH involved in the activation of genes in the anthocyanin pathway, had been characterized to indirectly bind DNA despite the presence of a functional DNA-binding domain. Findings presented here reveal that this is only partially correct. Direct DNA-binding by R was found to be dependent upon two distinct dimerization domains that function as a switch. This switch-like mechanism allows R to be repurposed for the activation of promoters of differing cis-element structure.

The …

Some Like It Hot, Some Like It Warm: Phenotyping To Explore Thermotolerance Diversity, C. H. Yeh, Nicholas J. Kaplinsky, C. Hu, Y. Y. Charng

Biology Faculty Works

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This ‘thermotolerance diversity’ means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables …

Mutation And Complementation Of A Cellulose Synthase (Cesa) Gene, Ahmed Y. El-Araby

Senior Honors Projects

Cellulose is a carbohydrate polymer that is composed of repeating glucose subunits. Being the most abundant organic compound in the biosphere and comprising a large percentage of all plant biomass, cellulose is extremely plentiful and has a significant role in nature. Cellulose is present in plant cell walls, in commercial products such as those made from wood or cotton, and is of interest to the biofuel industry as a potential alternative fuel source. Although indigestible by humans, cellulose is nutritionally valuable, serving as a dietary fiber. Because of its ubiquity and importance in many areas, studying cellulose will prove to …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

Determining The Fate Of Hybridized Genomes In The Allopolyploid Brassica Napus, Tina Y. Wang

Master's Theses

Polyploidy is widely acknowledged as a widespread mechanism in the evolution and speciation of the majority of flowering plants. Allopolyploid forms through interspecific hybridization and whole genome duplication. While allopolyploids may display increased vigor relative to their progenitors, they can also face challenges to fertility following hybridization. Genetic changes in allopolyploids result from recombination between the hybridized subgenomes, which can influence phenotype and ultimately determine fitness of future generations. To study dynamic changes that follow allopolyploid formation, Brassica napus lineages were derived by hybridizing Brassica oleracea and Brassica rapa. Two lineages of B. napus were analyzed for genetic and phenotypic …

Implications Of The Plastid Genome Sequence Of Typha (Typhaceae, Poales) For Understanding Genome Evolution In Poaceae, Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including …

Development Of Protocols For Tissue Culture And Mutagenesis In Two Variegated Sansevieria Sp., Irmawati Akma Abdul Hapiz

Student Works (2010-2019)

Studies were conducted to develop the tissue culture protocol and mutagenesis through Gamma ray irradiation for two variegated Sansevieria species known as Sansevieria trifasciata var. Laurentii (goldband Sansevieria) and Sansevieria trifasciata var. Hahnii (birdnest Sansevieria). Seven combinations of BAP and NAA were chosen which are represented by letter A= 1.00 mg/I BAP, B = 1.00 mg/I BAP + 0.25 mg/I NAA, C = 2.00 mg/I BAP + 0.50 mg/I NAA, D = 2.00 mg/I BAP + 1.00 mg/I NAA, E = 3.00 mg/I BAP + 1.00 mg/I NAA, F = 4.00 mg/I BAP + 1.00 mg/I NAA and G = …

Molecular Characterization And Expression Analysis Of Putative Rpk1 And Putative Clv1 In Malaysian Indica Rice (Oryza Sativa L.) Cv.Mr219 And Malaysian Wild Rice (Oryza Rufipogon) Irgc105491., Law Yee Song

Student Works (2010-2019)

Two candidate yield-related genes, putative Receptor-like Protein Kinase 1 (putative RPK1) and putative CLAVATA1 Receptor Kinase (putative CLV1), were selected for molecular characterization and expression analysis. This was carried out using in four rice lines comprising the parents and two BC₂F₇ lines from a local rice breeding program, with Malaysian rice variety, Oryza sativa ssp. indica cv. MR219 as recurrent parent, and Oryza rufipogon (IRGC105491) as donor parent. Approximately 2.8 kb and 2.6 kb putative RPK1 cDNA nucleotide sequences were obtained from Oryza rufipogon and Oryza sativa ssp. indica cv. MR219 respectively. However, only 402 …

Characterization Of Microrna172 And Its Potential Target In Oil Palm (Elaeis Guineensis Jaq.), Fatemeh Mehrpooyan

Student Works (2010-2019)

Oil palm (Elaeis guineensis) is the world’s major perennial monocot crop and contributes highly to the economies of South East Asia. As the oil palm fruit is the source of the main economic output for this crop, floral development is a critical process related to oil palm productivity. miR172 has been shown to be an important regulator of the AP2 family transcription factors involved in floral timing in a number of plants and belongs to a group of highly conserved miRNA that can be identified based on sequence homology. Six oil palm miR172 paralogs, representing two distinct mature miR172 sequences, …

Phylogeographical Patterns Of Neobalanocarpus Heimii (Dipterocarpaceae) For The Evolutionary History And Chain Of Custody Certification., Tnah Lee Hong

Student Works (2010-2019)

Tectonic movement and climatic oscillations during the Cenozoic have had dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber, Neobalanocarpus heimii (Dipterocarpaceae), based on chloroplast DNA (cpDNA) variation. Fifteen haplotypes were identified from 10 intraspecific variable sites of five non-coding cpDNA regions: trnL intron, trnS-trnG spacer, trnG intron, trnK intron and psbK-trnS spacer. Two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to survive in multiple refugia during climatic oscillation: …

Biolistic Transformation Of Oil Palm Using The Phosphomannose Isomerase (Pmi) Gene As The Positive Selectable Marker., Bahariah Bohari

Student Works (2010-2019)

The selectable marker system based on the Escherichia coli phosphomannose isomerase (pmi) gene was adapted for genetic transformation of oil palm. This system makes use of the pmi gene that encodes phosphomannose isomerase, which converts mannose-6-phosphate to fructose-6-phosphate and uses mannose as the selection agent. This is to anticipate the future requirement of using non-antibiotic resistance genes for the commercialization of transgenic oil palm. The use of antibiotic or herbicide-based selection systems has caused much public concern due to inadequate knowledge of the agents’ impact on the environment and on human health. In this study, four transformation vectors, namely pMI3, …

A Systematic Study Of Fagraea Sensu Lato And A Revision Of The Peninsular Malaysian Taxa., Sugumaran Manickam

Student Works (2010-2019)

systematic study of the Peninsular Malaysian species of Fagraea sensu lato was undertaken. This was done in the light of recent revisionary work done for Borneo that documented 20 new species and demonstrated that previous species concepts for Fagraea were too broad. Parallel to this the distinction of the subgeneric groups recognised as sections, i.e., Cyrtophyllum, Fagraea and Racemosae, were investigated with molecular phylogenetic methods. Representative taxa from the Malay Peninsula and Borneo augmented by sequences from other taxa in the same subtribe and tribe were used in the molecular analysis. Gene sequences from ITS, trnL–F (trnL intron + trnL–F …

Computational Identification Of Micro Rna In Musa Sp Est Sequences., Tan Yew Seong

Student Works (2010-2019)

MicroRNAs (miRNAs) are small single-stranded non-protein-coding RNAs of about 22 nucleotides that play an important role in post-transcriptional gene regulation in animals and plants by targeting mRNAs for direct cleavage of mRNAs or repression of mRNA translation. In this study, a homology search based approach has been used for identifying the novel miRNA genes of Musa sp. using the BLAST program with a total of 42,978 Musa sp. expressed sequence tags (EST) were compared to a total of 959 previously known plant miRNA sequences. Forty-seven candidate miRNA with homology to previously known miRNAs were identified. By using the mFold3.1 program, …

Temperature Compensation Of Auxin Dependent Developmental Patterning, Nicholas J. Kaplinsky

Biology Faculty Works

The establishment of localized auxin gradients plays a central role in developmental patterning in plants. Auxin levels and responses have been shown to increase with temperature although developmental patterning is not affected. This suggests the existence of a homeostatic mechanism that ensures that patterning occurs normally over a range of temperatures. We recently described the cloning and characterization of BOBBER1 (BOB1), an Arabidopsis gene which encodes a small heat shock protein. BOB1 is required for the establishment of auxin gradients and for normal developmental patterning. BOB1 is also required for organismal thermotolerance and localizes to heat shock granules at elevated …

Bobber1 Is A Noncanonical Arabidopsis Small Heat Shock Protein Required For Both Development And Thermotolerance, Dahlia Erin Perez , '08, J. S. Hoyer, Ayanna Iman Johnson , '09, Zachary Ray Moody , '07, J. Lopez, Nicholas J. Kaplinsky

Biology Faculty Works

Plants have evolved a range of cellular responses to maintain developmental homeostasis and to survive over a range of temperatures. Here, we describe the in vivo and in vitro functions of BOBBER1 (BOB1), a NudC domain containing Arabidopsis (Arabidopsis thaliana) small heat shock protein. BOB1 is an essential gene required for the normal partitioning and patterning of the apical domain of the Arabidopsis embryo. Because BOB1 loss-of-function mutants are embryo lethal, we used a partial loss-of-function allele (bob1-3) to demonstrate that BOB1 is required for organismal thermotolerance and postembryonic development. Recombinant BOB1 protein functions as a molecular chaperone and prevents …

Partitioning The Apical Domain Of The Arabidopsis Embryo Requires The Bobber1 Nudc Domain Protein, R. J. Jurkuta, Nicholas J. Kaplinsky, Jennifer Elizabeth Spindel , '10, M. K. Barton

Biology Faculty Works

The apical domain of the embryo is partitioned into distinct regions that will give rise to the cotyledons and the shoot apical meristem. In this article, we describe a novel screen to identify Arabidopsis thaliana embryo arrest mutants that are defective in this partitioning, and we describe the phenotype of one such mutant, bobber1. bobber1 mutants arrest at the globular stage of development, they express the meristem-specific SHOOTMERISTEMLESS gene throughout the top half of the embryo, and they fail to express the AINTEGUMENTA transcript normally found in cotyledons. Thus, BOBBER1 is required to limit the extent of the meristem domain …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.