Molecular Biology Commons^™

Exploring The Dark Matter Of Proteomics, Armin G. Geiger

Doctoral Dissertations

Proteomics, particularly mass spectrometry (MS)-based proteomics, has become an essential tool in understanding biological complexity and function at the molecular level. However, a significant fraction of spectral data generated in these studies, often referred to as the "Dark Matter of Proteomics'', remains unexplored and unidentified, concealing potentially vital biological insights. This dissertation addresses the challenge of uncovering this dark matter through the innovative use of computational techniques to enhance peptide identification and quantification in Kalanchoë fedtschenkoi, a model organism for Crassulacean Acid Metabolism (CAM).

The research employs a quantification-centered approach to MS data analysis, leveraging both MS1 and MS2 …

Practical Challenges In Delivering Dsrna For Woody Plant Protection, Zachary Bragg

Theses and Dissertations--Entomology

Unprecedented weather events associated with climate change, coupled with extensive anthropogenic stresses, have reduced the effectiveness of traditional forest pest management approaches, which can no longer keep pace with invasive species overwhelming naïve landscapes and native pests experiencing eruptive and expansive outbreaks. Double-stranded RNA-(dsRNA) mediated gene silencing, a type of RNA interference (RNAi), has been coopted for use as a biopesticide against a multitude of agricultural and horticultural pests and could serve as a powerful tool for woody plant protection. While effective initiation of gene silencing and subsequent mortality have been demonstrated in multiple tree pests, effective and efficient methods …

Csi Botany: Dna Barcode “Fingerprints” Identify Cryptic Urban Flora, Luis R. Vega

Theses

As short genomic markers, DNA barcodes can play a role in conservation by identifying cryptic species and hybrids when morphological approaches fall short. Here we present our application of barcodes to the identities of two wetland taxa as part of an ongoing floristic inventory of Van Cortlandt Park (VCP), Bronx, NY. Previous barcode data by Marriott et al. (2018) identified the VCP lake water lily as the exotic Nymphaea alba, rather than the native N. odorata as historically described. In addition, cattails in the park were historically identified as the native Typha latifolia and the exotic T. angustifolia …

Determination Of The Functional Role Of Rab-Ggt In Physcomitrium Patens., Hyun Jin Jung

Electronic Theses and Dissertations

Protein prenylation, a common lipid post-translational modification, is required for growth and development in eukaryotes. Rab geranylgeranylation involves the addition of one or two 20-carbon geranylgeranyl moieties to Rab-GTPase target proteins, which regulate intracellular vesicle trafficking. The reaction is carried out by heterodimeric Rab geranylgeranyltransferase (Rab-GGT), which is composed of two associated α- and β-subunits, with the assistance of an additional protein called Rab escort protein (REP). Loss of function of the Rab-GGT α subunit RGTA1 has not been reported in any plant. While knockout of either of the two β subunits RGTB1 or RGTB2 results in …

The Importance Of Co2 Recapture In The Co2 Concentrating Mechanism Of Chlamydomonas Reinhardtii, Ashwani Rai

LSU Doctoral Dissertations

The aim of this thesis is to investigate the CO₂ concentrating mechanism (CCM) of Chlamydomonas reinhardtii and to develop a quick method for estimating the activity of carbonic anhydrases (CAs). The first project demonstrates that there are two almost identical mitochondrial CAs in C. reinhardtii, CAH4 and CAH5, that help to maintain photosynthesis and minimize the leak of CO₂ generated by respiration and photorespiration. We used an RNAi approach to reduce the expression of CAH4 and CAH5 so that their physiological functions could be studied. RNAi mutants with low expression of CAH4 and CAH5 have impaired rates …

Nodulin 26 Like Intrinsic Proteins: Structurally Similar Membrane Channels With Diverse Functions In Plant Hypoxia Stress, Metalloid Nutrition & Toxicity, Zachary Beamer

Doctoral Dissertations

Plant nodulin 26 intrinsic proteins are categorized into three groups (NIP I, II, and III) based on pore architecture. NIP II and III participate in metalloid nutrition, whilst the function of a third (NIP I) is less understood. Here we investigate the physiological function of one NIP I protein (Arabidopsis thaliana NIP2;1) as a lactic acid channel, and also explore the structural basis for metalloid and water permeability of NIP I and NIP II proteins in general. In addition, a strategy was developed for the purification and crystallization of soybean nodulin 26 as a step towards structure determination of a …

The Impact Of Plant Secondary Metabolites On Auxin And Cytokinin Signaling, Timothy E. Shull

Theses and Dissertations--Plant and Soil Sciences

Secondary metabolites are a broad class of specialized compounds that mediate plant-environment interactions and mitigate stress. It is increasingly clear that many phenylalanine-derived secondary metabolites are nearly indispensable for plant survival and that plants adjust their growth according to their secondary metabolic outputs. Consequently, many phenylalanine-derived secondary metabolites have influence over hormone activity. For instance, multiple phenylpropanoid intermediates and catecholamines alter the sensitivity of plants to the central hormone auxin, which in concert with cytokinin directs most aspects of plant growth and development. This dissertation reviews previous research on the influence of phenylpropanoid intermediates and catecholamines on plants, with a …

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …

Calmodulin Like 38 Is Required For Autophagy Of Hypoxia-Induced Cytoplasmic Rna Granules In Arabidopsis Thaliana, Sterling Field

Doctoral Dissertations

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

Analysis Of Symptom Expressions And Transmission Rates Caused By The Plant Pathogen Phytophthora Ramorum On Native Chaparral Plants From The Genus Arctostaphylos, Bharati Gaonker

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora ramorum is the causal agent of Sudden Oak death (SOD), ramorum dieback and ramorum leaf blight which affect both forest environments and nurseries. This oomycete pathogen has had a huge economic impact on the nursery and lumber industry. Forests in California have experienced substantial mortality of oaks affecting the forest dynamics and diversity. Our research investigates four native species and two ornamental cultivars of plants, which belong to the genus Arctostaphylos (manzanita) and are considered to be new hosts for P. ramorum in the chaparral ecosystem of California. Symptom expression and transmission rates were analyzed on Arctostaphylos glauca, …

Regulation Of Plasmodesmata By Specialized Metabolites Glucosinolates In Arabidopsis Thaliana, Jessica C. Fernandez

Doctoral Dissertations

Communication is an essential component to all living organisms. In

plants, the additional cell wall surrounding each cell adds a layer of complexity

not observed in animals. To overcome the literal wall separating cells, plants

have evolved specialized pores to connect adjacent cells. Plasmodesmata (PD)

allow plants to have a continuous cytoplasm between cells. Although

plasmodesmata may appear simple and lack regulation, their structural

components and their regulatory machinery is complex and not well understood.

Organelle-to-nucleus-to-plasmodesmata signaling (ONPS) have been worked as

a leading model for a possible regulatory mechanism. Many of the details of

organelle-to-nucleus retrograde signaling pathways have …

Root Phosphomonoesterase As A Vital Component Of Increasing Phosphorus Availability In Tropical Forests, Kristine Grace Manno Cabugao

Doctoral Dissertations

Tropical forests, relative to other terrestrial ecosystems, exchange the largest amount of carbon with the atmosphere and also constitute a significant carbon sink. However, nutrient limitation, particularly of phosphorus (P), could limit growth of tropical forests and their function with the global carbon cycle. Thus, understanding root mechanisms to acquire P is necessary to representing the P cycle and corresponding interactions with plant growth. A large portion of total soil P in tropical forests occurs in organic forms, only accessible through root and microbial production of phosphatase enzymes. These phosphatase enzymes mineralize organic P into orthophosphate, the form of P …

Molecular Identification And Characterization Of Viral Pathogens Infecting Sweet Cherry, Aaron J. Simkovich

Electronic Thesis and Dissertation Repository

Stone fruits are a valuable crop grown worldwide, however pathogens such as viruses threaten fruit production by reducing tree health and fruit yield. In an orchard within the Niagara region of Ontario, symptoms typical of viral infection such as chlorosis and leaf deformation were seen on sweet cherry (Prunus avium L.) trees. Next generation sequencing was performed on symptomatic and asymptomatic leaves and four viruses were identified. On the tree displaying the most severe symptoms, Prune dwarf virus (PDV), was the only virus detected. A survey conducted during this work showed 42% of cherry trees on a single …

Subcellular Localization Of Tobacco Sabp2 Under Normal And Stress Conditions, Sanjeev Das

Undergraduate Honors Theses

Subcellular Localization of Tobacco SABP2 under Normal and Stress Conditions

Salicylic acid (SA), a phytohormone, plays an important role in plant physiology. SA mediated innate immune pathway is an important pathway for plant immunity against pathogens. Plants resisting pathogen infection synthesize higher levels of Methyl Salicylate (MeSA), which is then converted to SA by the esterase activity of Salicylic Acid Binding Protein 2 (SABP2). The high level of the converted SA leads to enhanced pathogen resistance. The study of subcellular localization of a protein is critical in explaining its potential biochemical functions. SABP2 tagged with eGFP was expressed transiently in …

Functions Of Cdk/Cyclin Complexes In Endoreplication Regulation By The Cdk Inhibitor Siamese, Kai Wang

LSU Doctoral Dissertations

Arabidopsis trichome (leaf hair) is a specialized single cell extended from epidermal cell on the leaves, which is a typical endoreplication and is also known as endoreduplication. Several D-type cyclins were tested to check the cell division in trichome, and the trichome expressing either CYCB1;2 or CDKB2;2 cannot trigger cell division, even if simultaneous expression of CYCB1;2 and CDKB2;2 failed to produce mitosis in trichome. Only CYCD3;1 specifically promotes multicellular trichome. cdkb1;1cdbk1;2 double mutants and sim cdkb1;1cdkb1;2 triple mutants exhibit the phenotype similar to the wild type and very limited cell division respectively. Overexpression of a CDKB1;1 dominant-negative construct that …

The Balancing Act Of Cytokinin In Environmental Stress Tolerance, Sumudu Sandeepani Karunadasa

Theses and Dissertations--Plant and Soil Sciences

Cytokinin, long known as a phytohormone that regulates plant growth and development, has been recently recognized as an important regulator of stress responses. However, our current knowledge about the mechanisms by which cytokinin regulates stress responses is fragmentary, as many of the studies in this field yielded conflicting results. Most of the work described here has focused on analyses of the molecular mechanisms of cytokinin-dependent regulation of growth and development under stress conditions, with an emphasis on the role of cytokinin-dependent regulation of protein synthesis in development and stress tolerance.

One of the important contributions of this study is the …

Analyzing Multigene Stacking And Genome Editing Strategies In Rice, Bhuvan Pathak

Graduate Theses and Dissertations

Crop improvement through biotechnology is an integrated effort, incorporating multiple approaches like integration of genes, editing of native genes, and removal of selection marker genes. Before streamlining the protocols, the efficiency and feasibility of the individual approach and their components must be tested. This study evaluated following approaches: 1) stacking an array of genes into a single locus by site-specific integration via Cre-lox recombination in rice, 2) determining the efficiency of I-SceI and the CCR5-ZFN in the targeted excisions of gene fragments in rice and Arabidopsis, and 3) determining the efficiency of CRISPR/Cas9 in generating targeted mutations for genome editing …

Systematics Of Carex Section Laxiflorae (Cyperaceae), Jenna Dorey

Dissertations, Theses, and Capstone Projects

Carex, with more than 2100 species, is the most species-rich genus of flowering plants in temperate regions of the world. Members of the family Cyperaceae are colloquially known as sedges, and members of the genus Carex are called “true sedges.” Carex occur on every continent except for Antarctica, they thrive in a panoply of habitats, and are ecologically important as a forage source for wildlife, carbon sequestration, prevention of soil erosion, and providing habitat for fresh water invertebrates. Despite their importance many sedges are still poorly known, such as the woodland sedges in Carex section Laxiflorae, which is …

A Seed Dormancy Gene-Mediated Biotechnology To Mitigate Transgene Flow Into Weedy Rice, Luai Nahar Muhammad

Electronic Theses and Dissertations

Transgene flows into wild/weedy relatives may cause ecological and economic problems. Seed dormancy is an adaptive trait that distributes germination over time and promotes persistence of weeds in agroecosystems. Silencing natural genes controlling seed dormancy (SD) could promote germination and reduce weed adaptability. The goal of this project was to develop a transgenic mitigation (TM) technology by linking to a primary transgene with an SD gene-silencing structure, as a tandem construct for transformation, to reduce the risk of gene flow into weed populations. In this research, the Bar (Bialaphos) gene for resistance to the glufosinate herbicide was used as a …

Disease Resistance In Wheat And Its Relatives, Ethan James Andersen

Electronic Theses and Dissertations

Plants have evolved a complex defense system against pests and pathogens utilizing many types of receptors, signaling factors, and defense compounds to detect pathogen presence and respond effectively. Since many pathogens have evolved immunesuppressing effectors used to reduce plant resistance, plants have evolved a family of receptors that detect pathogenic effectors as a result of an evolutionary arms race. These receptors contain Nucleotide-Binding Site and Leucine-Rich Repeat domains and are called NBS-LRR or NLR proteins. Many grasses possess huge genomes with hundreds of NLR-encoding genes, often found in clusters at the extra-pericentromeric regions of chromosomes, where unequal crossing over causes …

Defective Aba-Mediated Sugar Signalling Pathway In An Established Arabidopsis Thaliana Cell Suspension Culture Explains Its Stay-Green Phenotype At High Sugar Concentrations, Avery Mccarthy

Electronic Thesis and Dissertation Repository

An unusual sugar insensitive phenotype was identified in an established cell suspension culture of Arabidopsis thaliana. We characterized the physiology, biochemistry and genetics of the sugar insensitive cell culture, in order to identify factors contributing to the phenotype. Chlorophyll levels of the cell suspension culture were insensitive to high sucrose (6-15% w/v) and maintained a green phenotype. Immunoblotting indicated that levels of key photosynthetic proteins (PsaA, Lhcb2 and Rubisco) increased as a function of external sucrose concentration. The green cell culture was photosynthetically competent based on light-dependent, CO₂-saturated rates of O₂ evolution as well as Fv/Fm …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

Roles Of Phospholipases And Ribosomal S6 Kinase In Lipid Remodeling And Growth In Arabidopsis Response To Phosphate Deprivation, Yuan Su

Dissertations

Phosphate (Pi) is one of three macronutrients for plants, which is vital for plant growth and development. Understanding the mechanism by which plants respond and adapt to Pi deficiency not only unveils functions of genes and pathways involved, but also provides potential tools to manipulate crops to better stand Pi stress in low Pi-containing lands. One of the significant metabolic changes in plants under Pi starvation is the membrane lipid remodeling that converts Pi-containing lipids such as phospholipids to Pi-free lipids, such as glycolipids. To elucidate the metabolism and regulation of lipid remodeling, this dissertation characterizes the role of two …

Investigating Phosphorylation Patterns And Their Effect On The Activity Of Transcription Factor Taabf1 In Imbibing Cereal Grains, Grace Uwase

Honors Theses

The wheat transcription factor TaABF1 plays an important role in hormone-mediated regulation of seed dormancy and germination of cereal grains. Evidence shows that TaABF1 activity is regulated by phosphorylation, and previous work in our lab showed that when serine residues in its conserved regions; S36, S37, S113, S115 were altered to phosphomimetic aspartate, the 4xD TaABF1 mutant had increased activity as a transcription factor. However, when only S113 was altered, TaABF1’s activity was greatly reduced. The work presented here explored whether the S36D/S37D/S115D mutant would have stronger activity than the 4xD mutant. Using the particle bombardment technique to introduce the …

Gmmyb176 Interactome And Regulation Of Isoflavonoid Biosynthesis In Soybean, Arun Kumaran Anguraj Vadivel

Electronic Thesis and Dissertation Repository

MYB transcription factors are one of the largest transcription factor families characterized in plants. They are classified into four types: R1 MYB, R2R3 MYB, R3 MYB and R4 MYB. GmMYB176 is an R1MYB transcription factor that regulates Chalcone synthase (CHS8) gene expression and isoflavonoid biosynthesis in soybean. Silencing of GmMYB176 suppressed the expression of the GmCHS8 gene and reduced the accumulation of isoflavonoids in soybean hairy roots. However, overexpression of GmMYB176 does not alter either GmCHS8 gene expression or isoflavonoid levels suggesting that GmMYB176 alone is not sufficient for GmCHS8 gene regulation. I hypothesized that GmMYB176 acts cooperatively with another …

Myosin Xi-I Works In Tandem With A Microtubule-Associated Mechanism To Position The Nucleus In Arabidopsis Root Hairs, Ian Andrew Windham

Chancellor’s Honors Program Projects

No abstract provided.

Cytosolic Acetyl-Coa Promotes Histone H3 Lysine 27 Acetylation In Arabidopsis, Chen Chen

Electronic Thesis and Dissertation Repository

Acetyl-coenzyme A (acetyl-CoA) serves as a central metabolite in energy metabolism and biosynthesis. High level of acetyl-CoA can fuel the tricarboxylic acid (TCA) cycle to generate energy and store excess energy in fatty acids. Meanwhile, it also provides acetyl groups for protein acetylation, which normally occurs at the lysine or arginine residues. Acetylation regulates protein functions largely due to the change of total charges. Acetylation of histones, for example, can lead to loss of the interaction between histone and DNA, thus relaxing chromatin structure and potentially promoting gene expression. However, whether and how acetyl-CoA regulates plant chromatin remains unexplored. Here, …

Examining The Role Of Grp And Lik1 In Wall Associated Kinase (Wak) Perception Of Pectin In The Plant Cell Wall, Jack Ryan Mitchell

Honors Projects

Wall associated kinases (WAKs) are cell membrane bound receptor kinases that bind pectin and pectin fragments (OGs).The binding of WAKs to pectin sends a growth signal required for cell elongation and plant development. WAKs bind OGs with higher affinity than native pectin and instead activate a stress response. Glycine rich proteins (GRPs) are secreted cell wall proteins of unknown function. Seven GRPs with 65% sequence similarity are coded on a 90kb locus of Arabidopsis chromosome 2. GRP3 and WAK1 have been shown to bind in vitro, but single null mutations have no discernible phenotype, suggesting that the GRPs are redundant. …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …