Biochemistry, Biophysics, and Structural Biology Commons^™

Detection And Capture Of Nitrogen Fixing Bacteria From Soil And Roots Using Plant Specific Lectins, Alana Horton

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Diazotrophs increase plant productivity by providing ammonia directly to plants in the rhizosphere or through association with the roots (Sun et al., 2021). Leveraging diazotrophs can aid in the reduction or application of harmful synthetic nitrogen fertilizers. This thesis aims to use plant root proteins, or lectins, to more rapidly recover viable diazotrophs that are likely to associate with crops. In this study, lectins, are used to recover bacteria from bulk soil by taking advantage of the binding relationship between lectins and bacterial cell surface polysaccharides. When commercially-available lectins were used with a magnetic pulldown to separate the lectin, bacterial …

Molecular Regulation Of The Salicylic Acid Hormone Pathway In Plants Under Changing Environmental Conditions, Christina A. M. Rossi, Eric J. R. Marchetta, Jong Hum Kim, Christian Castroverde

Biology Faculty Publications

Salicylic acid (SA) is a central plant hormone mediating immunity, growth, and development. Recently, studies have highlighted the sensitivity of the SA pathway to changing climatic factors and the plant microbiome. Here we summarize organizing principles and themes in the regulation of SA biosynthesis, signaling, and metabolism by changing abiotic/biotic environments, focusing on molecular nodes governing SA pathway vulnerability or resilience. We especially highlight advances in the thermosensitive mechanisms underpinning SA-mediated immunity, including differential regulation of key transcription factors (e.g., CAMTAs, CBP60g, SARD1, bHLH059), selective protein–protein interactions of the SA receptor NPR1, and dynamic phase separation of the recently identified …

Alterations In C:N Ratio To Understand Plant Metabolic Pathways In Response To Pressure From Goat Grazing In The Invasive Species: Rhamnus Cathartica, Vivian Marchan

Ignite the Spark Outstanding Undergraduate Research and Scholarship

The high fecundity and high germination rates of Rhamus cathartica serves the species to out-compete regional plant native species. Its high abundance in deciduous forest ecosystems forces species that are unable to utilize R. cathartica as a food source to migrate to areas of lower density, further contributing to the decline in regional biodiversity. Bare soil conditions left as the result of the high concentration of Nitrogen in senesced leaves and leaf litter, cause further amplification of the migration of non-plant species to areas of lower R. cathartica density. Nitrogen is essential to primary and secondary metabolism, thus minimizing the …

Structural Files For The Etr1 Ethylene-Receptor Dimer Based On Computational Modeling, Beenish J. Azhar, Safdar Abbas, Sitwat Aman, Maria V. Yamburenko, Wei Chen, Lena Muller, Buket Uzun, David A. Jewell, Jian Dong, Samina N. Shakeel, Georg Groth, Brad M. Binder, Gevorg Grigoryan, G. Eric Schaller

Dartmouth Scholarship

Structural models for the ETR1 homodimer were generated with AlphaFold-Multimer. Coppers were modeled under two potential coordinations involving Cys65 and His69 of the ETR1 homodimer, one in which the two coppers are bound independently and do not share an interaction with each other, and another where they are closely bonded.

See the following publication for details: Azhar, B.J., Abbas, S., Aman, S., Yamburenko, M.V., Chen, W., Müller, L., Uzun, B., Jewell, D.A., Dong, J., Shakeel, S.N., Groth, G., Binder, B.M., Grigoryan, G., Schaller, G.E. (2023) Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proc. Natl. Acad. …

Recent Insights On The Conformational Changes, Functionality, And Physiological Properties Of Plant-Based Protein–Polyphenol Conjugates, Mehnaza Manzoor, Zaria Fozonne Ngabou Tchameni, Zuhaib F. Bhat, Amit K. Jaiswal, Sundeep Jaglan

Articles

Plant proteins are promising sources of nutrition with enhanced health benefits due to their interaction with bioactive compounds like polyphenols. These interactions can form protein–polyphenol complexes with diverse properties and applications in the food, nutraceutical, and pharmaceutical industries. To exploit the potential of these conjugates, it is essential to understand how they are formed, characterized, and delivered. Various techniques such as spectroscopy, thermodynamics, and molecular docking simulations can reveal the mechanism and outcomes of protein–polyphenol binding. Moreover, the surface modification of protein–polyphenol conjugation can enhance the pharmacological effects of different drug molecules and enable their targeted delivery to specific tissues …

Of Transcription Factor And Transformation: Elucidating Gene Function In The Common Ice Plant, Mesembryanthemum Crystallinum, Chinenye Lilian Izuegbunam

Dissertations and Theses

Abiotic stresses negatively affect plant growth and development across the globe, which also affect the production of food, feed, biofuel, and fiber to meet the demands of a growing population. Thus, developing novel strategies to increase abiotic stress tolerance in crops is necessary. One of these strategies is exploring transcription factors (TFs) in Crassulacean Acid Metabolism (CAM) plants to improve plant abiotic stress tolerances. Therefore, the first objective of this dissertation determine the abiotic stress tolerance function of a CAM TF, McHB7opt in Arabidopsis. This study found that McHB7opt increased stress-responsive pathways related to seed germination and early seedling development. …

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

Theses and Dissertations

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 …

Plant Cell Wall Composition And In Vitro Fermentation Characteristics Of Cool-Season Forage Grasses From Two Growing Seasons In Central Kentucky, Sophia Danielle Newhuis

Theses and Dissertations--Animal and Food Sciences

Grass cell walls are rich in cellulose, hemicellulosic arabinoxylan (AX) polysaccharides, and lignin. AX structural differences such as degree and pattern of branching and the ester-linked phenolic acid content could affect plants’ digestibility when used as forage for livestock. However, there is little information about how these structural elements change over the growing season in the vegetative tissue of cool-season perennial grasses. Enhanced information about the cell wall composition and carbohydrate structure of forage material will provide a foundation for expanding our knowledge of how forage cell wall carbohydrate structures are utilized by ruminants. The objectives of this study were …

Novel Mechanistic Insight Into Ciliary Regulation: Old Pathways Yield New Mechanisms, Larissa L. Dougherty

Dartmouth College Ph.D Dissertations

Cilia are structures present on most eukaryotic cells which provide important signaling and motile components to cells from early development to fully differentiated and matured cells. Regulation of these structures is critical to proper functioning of the cell and is known to be tied to the cell cycle. Preparation for ciliary assembly following cell cycle exit and ciliary disassembly following cell cycle reentry requires components throughout the cell body and within the cilium to facilitate this process. Here I identify how the cell adapts to ensure modifications to cilia occur for assembly or disassembly using the model organism Chlamydomonas reinhardtii. …

Natural Variation In Temperature-Modulated Immunity To Pseudomonas Syringae Pv. Tomato (Pst Dc3000) In Arabidopsis Thaliana Plants, Christina A. M. Rossi

Theses and Dissertations (Comprehensive)

Studies conducted on the model plant-pathogen system Arabidopsis thaliana-Pseudomonas syringae pv. tomato (Pst) showed that elevated temperature suppresses the pathogen-induced production of salicylic acid (SA), which is a key plant defence hormone. This increased host vulnerability at higher temperatures is due to downregulated expression of CALMODULIN BINDING PROTEIN 60-LIKE G (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1), which encode master regulators of SA production. Collectively, these previous studies only focused on one natural accession of Arabidopsis called Columbia-0 (Col-0). However, the intraspecific variation in Arabidopsis immunity phenotypes under elevated temperature remains unknown. To fill this critical knowledge gap, my …

Phytochemical Constituents, Haematological Activities And Gc-Ms Analysis Of Isolated Oil Of Rosary Pea (Abrus Precatorius) In Wistar Rat Fed With High Lipid Diet, Osaro Iyekowa, Opara V Ndubuisi

Tanzania Journal of Science

The study is aimed at investigating the phytochemical constituents and haematological activities of the isolated oil in Wistar rat fed with high lipid diet. Powdered leaves of Abrus precatorious were extracted and phytochemical screening was done according to prescribed standard methods, while vacuum liquid chromatography (VLC) was adopted for oil isolation of the crude extract and characterized by gas chromatography-mass spectrometry (GC-MS). Thirty adult Wistar rats were randomly arranged into six groups (A, B, C, D, E and F) and treated under certain conditions. Haematological analyses were performed according to standard procedures. Saponins, alkaloids, terpenoids, flavonoids and glycosides were present. …

Dynamics Of Redox-Driven Molecular Processes In Local And Systemic Plant Immunity, Philip Berg

Theses and Dissertations

The work here presents two main parts. In the first part, chapters 1 – 3 focus on dynamical systems modeling in plant immunity, whereas chapters 4 – 6 describe contributions to computational modeling and analysis of proteomics and genomics data. Chapter 1 investigates dynamical and biochemical patterns of reversibly oxidized cysteines (RevOxCys) during effector-triggered immunity (ETI) in Arabidopsis, examines the regulatory patterns associated with Arabidopsis thimet oligopeptidase 1 and 2’s (TOP1 and TOP2), roles in the RevOxCys events during ETI, and analyzes the redox phenotype of the top1top2 mutant. The second chapter investigates the peptidome dynamics during ETI …

Wrack Lines Volume 22, Number 2, Fall-Winter 2022-2023, Nancy C. Balcom, Juliana Barrett, Judy Benson, Ben Crnic, Sto Len

Wrack Lines

With the theme, "Looking Ahead: People and Projects Shaping the Future," the Fall-Winter 2022-2023 leads with the first in what will be a series of articles about offshore wind development impacting Connecticut. That is followed by the inspiring story of how a dying forest was replanted for climate resilience. Next, a profile of longtime marine educator Tim Visel tells about his lasting impact on Connecticut schools and students. Lastly, the complex challenge of dealing with Contaminants of Emerging Concern is examined, with descriptions of how Sea Grant is involved and the particularly troublesome group of substances called PFAS.

Physicochemical Analysis Of Cold Brew And Hot Brew Peaberry Coffee, Evan T. Schwarzmann, Marlena P. Washington, Niny Z. Rao

College of Life Sciences Faculty Papers

Peaberry coffee is the result of a natural mutation of coffee beans, and they make up only about 5–7% of coffee crops. A typical coffee cherry contains two seeds that are developed against each other, resulting in the distinctive half-rounded shape of coffee beans. However, failing to fertilize both ovules of one of the seeds or failure in endosperm development can cause only one of the seeds to develop, resulting in smaller, denser beans with a more domed shape. Peaberry coffees are said to be sweeter, lighter, and more flavorful since the peaberry beans receive all nutrients from the coffee …

Anxiolytic Effects, Antioxidant And Anti-Inflammatory Activities Of The Methanol Extract Of Jatropha Tanjorensis Leaf, Anthony E. Aiwonegbe, Uwaila Omoruyi, Osahon K. Ogbeide, Blessing O. Imoukhuede, Benjamin O. Gabrielsson

Tanzania Journal of Science

The methanol leaf extract of Jatropha tanjorensis was analyzed for its bioactive components, in-vitro antioxidant, antidepressant, anxiolytic and anti-inflammatory activities using established methods. The phytochemicals detected were saponins, tannins, terpenoids, phenolic compounds, alkaloids, flavonoids and eugenols. The total phenolic content (TPC) was 36.48 mgGAE/g, while the total flavonoid content (TFC) was 145.92 mgQE/g of the extract. 1, 1-diphenyl-2-picrylhydrazyl radical scavenging activity gave an IC50 of 185.02 and 5.15 µg/mL for the extract and ascorbic acid (standard), respectively. The 50% lethal dose (LD50) was greater than 5000 mg/kg, while graded doses of 50, 100 and 200 mg/kg of the plant extract …

Arabidopsis Shoot Gravitropism Requires The Mediator Coactivator Complex, Gabriella Newton

Honors Theses

Gravitropism is a plant response to gravity in directing the growth of its organs, such as the root and the stem. Gravity is sensed by statocytes, unique cells that contain starch-filled amyloplasts, which trigger gravitropic growth response by modulating the distribution of growth hormone auxin in the elongation zone of the stem and root. Despite the fact that multiple factors have been identified as key regulators of shoot negative gravitropism, how these factors are regulated at the transcriptional level is largely unknown. In this study, we explore the role of transcriptional machinery in regulating shoot gravity sensing and responses by …

Comparative Genomics And Virulence Studies Of Streptomyces Soil Rot And Scab Pathogen Species, Natasha Soares

LSU Doctoral Dissertations

Comparative genomic analyses were performed to gain insights into the organization and content of the genome of Streptomyces ipomoeae, the soil rot pathogen that infects sweetpotatoes. Unlike Streptomyces scab pathogens, the thaxtomin phytotoxin gene cluster (txt) in S. ipomoeae does not appear to reside within a genomic island and has diverged from its scab pathogen counterparts. Increased usage of the rare TTA codon, particularly for the txt cluster, suggests greater translational control by the bldA tRNA in S. ipomoeae. Orthologous gene searches and secondary metabolite profiling yielded ortholog groups and metabolite gene clusters that were exclusive …

Classification Models For 2,4-D Formulations In Damaged Enlist Crops Through The Application Of Ftir Spectroscopy And Machine Learning Algorithms, Benjamin Blackburn

Theses and Dissertations

With new 2,4-Dichlorophenoxyacetic acid (2,4-D) tolerant crops, increases in off-target movement events are expected. New formulations may mitigate these events, but standard lab techniques are ineffective in identifying these 2,4-D formulations. Using Fourier-transform infrared spectroscopy and machine learning algorithms, research was conducted to classify 2,4-D formulations in treated herbicide-tolerant soybeans and cotton and observe the influence of leaf treatment status and collection timing on classification accuracy. Pooled Classification models using k-nearest neighbor classified 2,4-D formulations with over 65% accuracy in cotton and soybean. Tissue collected 14 DAT and 21 DAT for cotton and soybean respectively produced higher accuracies than the …

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 …

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

Investigation Of The Direct Effect Of A Precision Ascophyllum Nodosum Biostimulant On Nitrogen Use Efficiency In Wheat Seedlings, Łukasz Łangowski, Oscar Goñi, Elomofe Ikuyinminu, Ewan Feeney, Shane O'Connell

Publications

Reduction in the greenhouse gas (GHG) emissions and nitrogen (N) pollution of ground water by improving nitrogen use efficiency (NUE) in crops has become an intensively investigated research topic in pursuit of a more sustainable future. Although, distinct solutions have been proposed there are only a few reports documenting the detailed interplay between observed plant growth dynamics and changes in plant N related transcriptional and biochemical changes. It was previously demonstrated that the application of a formulated biostimulant (PSI-362) derived from Ascophyllum nodosum (ANE) improves N uptake in Arabidopsis thaliana and in barley. In this study, the effect of PSI-362 …

Investigation Of The Binding Domain Interfaces Of The C-Terminus Of The Albino3 Insertase And The 43kda Chloroplast Signal Recognition Particle Subunit Via Single Molecule Förster Resonance Energy Transfer, Amanda Tomanek

Chemistry & Biochemistry Undergraduate Honors Theses

Fluorescent labeling is a technique used for visualizing functional groups contained in biomolecules by fluorescence imaging. This technique was used in this project to analyze post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCP), which are the core complexes that harvest sunlight to drive photosynthetic electron transfer. This protein is synthesized in the cytosol and post-translationally targeted to the stroma of chloroplasts. CpSRP43 is a signal recognition particle (SRP) subunit unique to chloroplasts, which has been shown to interact with the stroma-soluble C-terminus of the thylakoid-bound Albino3 insertase (Alb3-Cterm). In the chloroplast stroma, targeting to thylakoids is performed via the cpSRP pathway …

Floating Treatment Wetlands For Brackish Waters: Plant Selection And Nutrient Uptake Potential., Andrea Landaverde

All Theses

Brackish water bodies in coastal regions provide critical ecosystem services that support human and environmental health. Anthropogenic activities such as agricultural and industrial activities, construction, urban settlements, and tourism contribute to increased inputs of nitrogen (N) and phosphorus (P) in brackish coastal ecosystems. Excess nutrients can lead to impaired water quality and affect marine organisms. Floating treatment wetlands (FTWs) are a vegetated-base technology used to remove contaminants from water column, that has been mainly studied and applied in freshwater systems. Application of FTWs in brackish systems requires further investigation, as high salinity in brackish waters could result in toxicity to …

Evaluating Alternative Ebullition Models For Predicting Peatland Methane Emission And Its Pathways Via Data–Model Fusion, Shuang Ma, Lifen Jiang, Rachel M. Wilson, Jeff P. Chanton, Scott Bridgham, Shuli Niu, Colleen M. Iversen, Avni Malhotra, Jiang Jiang, Xingjie Lu, Jason Keller, Xiaofeng Xu, Daniel M. Ricciuto, Paul J. Hanson, Yiqi Luo

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding the dynamics of peatland methane (CH₄) emissions and quantifying sources of uncertainty in estimating peatland CH₄ emissions are critical for mitigating climate change. The relative contributions of CH₄ emission pathways through ebullition, plant-mediated transport, and diffusion, together with their different transport rates and vulnerability to oxidation, determine the quantity of CH₄ to be oxidized before leaving the soil. Notwithstanding their importance, the relative contributions of the emission pathways are highly uncertain. In particular, the ebullition process is more uncertain and can lead to large uncertainties in modeled CH₄ emissions. To improve model simulations …

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

Plants Used By Nyamwezi Traditional Health Practitioners To Remedy Sexually Transmitted Infections In Sikonge, Tanzania, David S. Kacholi, Halima Amir

Journal of Humanities and Social Sciences

This study aims to document medicinal plants used by Nyamwezi traditional health practitioners (NTHPs) in managing sexually transmitted infections (STIs) in Sikonge District. The data on medicinal plants were collected using a semi-structured questionnaire. A total of 23 NTHPs were interviewed. The findings revealed that 28 medicinal plants, belonging to 16 families and 25 genera, are used for the management of STIs in Sikonge. Most species belonged to family Fabaceae (17.9%), Apocynaceae, Combretaceae and Euphorbiaceae (10.7% each), and Olacaceae and Rutaceae (7.1% each). Out of the recorded plants, 45.7% are used to manage gonorrhoea, 25.7% syphilis, 17.1% vaginal candidiasis, 8.6% …

Salicylic Acid And N-Hydroxypipecolic Acid At The Fulcrum Of The Plant Immunity-Growth Equilibrium, Alyssa Shields, Vanessa Shivnauth, Christian Danve M. Castroverde

Biology Faculty Publications

Salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are two central plant immune signals involved in both resistance at local sites of pathogen infection (basal resistance) and at distal uninfected sites after primary infection (systemic acquired resistance). Major discoveries and advances have led to deeper understanding of their biosynthesis and signaling during plant defense responses. In addition to their well-defined roles in immunity, recent research is emerging on their direct mechanistic impacts on plant growth and development. In this review, we will first provide an overview of how SA and NHP regulate local and systemic immune responses in plants. We …

Investigation Of The Methylome Pattern Changes In Phytophthora Sojae Infected Soybean (Glycine Max), Shyaron Poudel

Student Theses and Dissertations

Phytophthora stem and root rot (PSR), a soybean disease causes annual losses of up to $250 million in the United States alone. Using the Rps (resistant to Phytophthora sojae) gene in soybean is the main management technique. However, Rps genes are only effective until 8-15 years in the field. Therefore, further understanding of the Rps gene regulation and immune response in soybean is desperately needed. In this study, first, three commercial DNA methylation detection kits were examined on soybean (cultivar Williams 82,which carries Rps1k) DNA samples. All three kits provided libraries with excellent quality and coverage. Secondly, the differential DNA …

Unraveling The Anti-Inflammatory And Cardioprotective Mechanism Of Prenylated Stilbenoids From Peanut Hairy Root Cultures In Vitro And In Vivo, Md Rokib Hasan

Student Theses and Dissertations

Stilbenoids are a non-flavonoid class of polyphenols that are important for their potential medicinal applications. Resveratrol, ione of the most well-studied compounds of this group, has various medicinal properties including anti-inflammatory, antioxidant, anti-cancer and many other properties. Prenylated stilbenoids which include arachidin-1 and arachidin-3 are produced as a defense response to biotic and abiotic stresses in peanut (Arachis hypogaea). Prenylation has been shown to enhance the biological activities of polyphenolic compounds and thus arachidins may have higher anti-inflammatory activity than resveratrol in addition to many other potential health applications. However, the molecular mechanism of the arachidins as an anti-inflammatory and …