Biochemistry Commons^™

Methanogen Metabolic Flexibility, Sean R. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …

Water-Soluble Porphyrin Complexes For The Biological Inactivation Of Fentanyl, Anneli Nina

Theses and Dissertations

This work aimed to investigate the degradation of fentanyl in aqueous solutions using unsupported water-soluble cobalt(III) porphyrins (55 and 56), AuNP supported water-soluble cobalt(III) porphyrins (67 and 68), and liposome supported water-soluble cobalt(III) porphyrins (69 and 70). Complexes 55, 56, 68, and 69 have been shown to remove fentanyl from aqueous solutions at 37 ºC. The degradation of fentanyl, and the identification of breakdown products were analyzed with the use of time-of-flight mass spectrometry (TOFMS). Complex 55 has been shown to completely degrade fentanyl at 37 ºC in as little as two hours with a 400 mol% catalyst loading. Complex …

Effect Of A Commonly Used Veterinary Antibiotic On Oxidative Stress And Root Transporters Of Edible Legumes And Leafy Crops, Safaa Nassar, Jamilah Borjac

BAU Journal - Science and Technology

Antibiotic accumulation in soil and plants is a rising problem in agriculture creating a serious threat to living organisms in the environment, hence needing huge attention. To this end, glasshouse pot experiments were conducted to simulate contamination by veterinary antibiotic at 150 mg kg^-1 and 4800 mg kg^-1 in a virgin soil in which lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), arugula (Eruca sativa Mill.) and cress (Lepidium sativum L.) were grown, aiming at evaluating the potential toxicity of antibiotic in plants roots during their growth period. Biomarkers of toxicity such as malondialdehyde and proline …

Mechanism Of Sila- And Germafluorenes For Biological Applications, Shelby Jarrett

Dissertations

2,7-disubstituted silafluorenes and germafluorenes, originally designed for OLED applications, are a class of fluorescent dyes that have gained recent interest as probes for bioimaging and as biosensors to monitor cellular dynamics and interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Here, their spectral properties are investigated under aqueous conditions for relevant biological applications. These molecules display intense blue fluorescence in the solid state and in solution, have high extinction coefficients, and exhibit appreciable solubility in aqueous solution. To better understand potential applications, the mechanism of fluorescence was investigated. It …

New Simple And Robust Method For Determination Of Polarity Of Deep Eutectic Solvents (Dess) By Means Of Contact Angle Measurement, Łukasz Cichocki, Dorota Warmińska, Justyna Łuczak, Grzegorz Boczkaj, Andrzej Przyjazny

Natural Sciences Publications

The paper presents a new method for evaluating the polarity and hydrophobicity of deep eutectic solvents (DESs) based on the measurement of the DES contact angle on glass. DESs consisting of benzoic acid derivatives and quaternary ammonium chlorides–tetrabutylammonium chloride (TBAC) and benzyldimethylhexadecylammonium chloride (16-BAC)—in selected molar ratios were chosen for the study. To investigate the DESs polarity, an optical goniometer and an ET(30)" role="presentation" style="box-sizing: border-box; max-height: none; display: inline; line-height: normal; font-size: 13.2px; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; color: rgb(34, 34, 34); font-family: Arial, …

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) …

Deciphering Phosphoprotein Phosphatase Signaling Networks Using Proteomics Approaches, Brooke Brauer

Dartmouth College Ph.D Dissertations

Protein phosphorylation is a highly regulated mechanism of cell signaling control and its deregulation is implicated in disease. The kinases that catalyze the addition of phosphate groups onto their substrate proteins have been well studied, their signaling pathways mapped, and their effects on cell and organismal health observed. Knowledge of the phosphatases that reverse the reaction only recently began to come into focus. Phosphoprotein phosphatases (PPPs), long thought to be housekeeping enzymes, are now known to be exquisitely specific towards their substrates, but the exact nature of phosphatase regulation—both upstream and downstream of the phosphatase—is unclear.

PPPs recognize substrates through …

Ten Steps To Organize A Virtual Scientific Symposium And Engage Your Global Audience, Jiye Son, Jasmine Sabio, Ankit Jain, Rein V. Ulijn

Publications and Research

The paper describes guidelines for the planning, organization, and successful execution of virtual, global scientific conferences for global audiences. The guidelines are based on experience and lessons learned during the organization of the 3-day 2020 Virtual Systems Chemistry Symposium hosted on Zoom webinar and Twitter, held on May 2020 with over 1000 registered participants from 46 different countries.

Variation On A Theme: The Structures And Biosynthesis Of Specialized Fatty Acid Natural Products In Plants, Samuel Scott, Edgar B. Cahoon, Lucas Busta

Department of Biochemistry: Faculty Publications

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly …

Luminescence And Scintillation In The Niobium Doped Oxyfluoride Rb4Ge5O9F6:Nb, Darren Carone, Vladislav V. Klepov, Scott T. Misture, Joseph C. Schaeperkoetter, Luiz G. Jacobsohn, Mina Aziziha, Juliano Schorne-Pinto, Stuart A. J. Thomson, Adrian T. Hines, Theodore M. Besmann, Hans Conrad Zur Loye

Faculty Publications

A new niobium-doped inorganic scintillating oxyfluoride, Rb₄Ge₅O₉F₆:Nb, was synthesized in single crystal form by high-temperature flux growth. The host structure, Rb₄Ge₅O₉F₆, crystallizes in the orthorhombic space group Pbcn with lattice parameters a = 6.98430(10) Å, b = 11.7265(2) Å, and c = 19.2732(3) Å, consisting of germanium oxyfluoride layers made up of Ge₃O₉ units connected by GeO₃F₃ octahedra. In its pure form, Rb₄Ge₅O₉F₆ shows neither luminescence nor scintillation but when doped …

Expression And Purification Of E. Coli Yoaa, A Putative Helicase, Mark Gregory, Vincent Sutera Mr., Susan Lovett Dr.

Medical Student Research Symposium

All cells must maintain their genomic integrity to survive, which they achieve through several repair mechanisms that necessitate unwinding the damaged DNA by helicases. In Escherichia coli (E. coli), YoaA has been genetically shown to be involved in DNA repair and shares conserved sequences with helicase DinG. The goal of our study was to purify YoaA for further biochemical characterization. For expression, YoaA was fused to a His tag and overexpressed in MG1655 E.coli under the lacZ or T7 promoters for 2 hours, 4 hours, or overnight at 24oC, 30oC or 37oC. For purification, crude lysate was applied to a …

Dj-1 Is Not A Deglycase And Makes A Modest Contribution To Cellular Defense Against Methylglyoxal Damage In Neurons, Melissa Conti Mazza, Sarah C. Shuck, Jiusheng Lin, Michael Moxley, John Termini, Mark R. Cookson, Mark A. Wilson

Department of Biochemistry: Faculty Publications

Human DJ-1 is a cytoprotective protein whose absence causes Parkinson's disease and is also associated with other diseases. DJ-1 has an established role as a redox-regulated protein that defends against oxidative stress and mitochondrial dysfunction. Multiple studies have suggested that DJ-1 is also a protein/nucleic acid deglycase that plays a key role in the repair of glycation damage caused by methylglyoxal (MG), a reactive α-keto aldehyde formed by central metabolism. Contradictory reports suggest that DJ-1 is a glyoxalase but not a deglycase and does not play a major role in glycation defense. Resolving this issue is important for understanding how …

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

Collaborative Research: Surface-Specific Aerosol Chemistry: Direct Observations, Kinetics, And Environmental Impact, Yi Rao

Funded Research Records

No abstract provided.

Expression And Purification Of The Bacterial Protein Curli Csga And Its Cross-Interactions With Amyloid-B, Leah Grace Cantrell

Honors Theses

One of the main causes of neurodegenerative diseases is aggregation of amyloid proteins that are toxic to the neurons. Proteins like amyloid-β (Aβ) and α-syneuclein (α-syn) form hallmark aggregate lesions that contribute to pathological processes in the brain in Alzheimer and Parkinson’s patients, respectively. Recent ground-breaking studies have suggested a link between the microbiota of the gut and neurodegenerative diseases, called the “gut-brain axis.” It has been long known that the protein, CsgA found in many enteric bacteria, forms amyloid fibers of its own called Curli. Curli fibrils are a structural component of bacterial colonies and maintain the integrity of …

Altered Collective Mitochondrial Dynamics In The Arabidopsis Msh1 Mutant Compromising Organelle Dna Maintenance, Joanna M. Chustecki, Ross D. Etherington, Daniel J. Gibbs, Iain G. Johnston

Department of Biochemistry: Faculty Publications

Mitochondria form highly dynamic populations in the cells of plants (and almost all eukaryotes). The characteristics and benefits of this collective behaviour, and how it is influenced by nuclear features, remain to be fully elucidated. Here, we use a recently developed quantitative approach to reveal and analyse the physical and collective ‘social’ dynamics of mitochondria in an Arabidopsis msh1 mutant where the organelle DNA maintenance machinery is compromised. We use a newly created line combining the msh1 mutant with mitochondrially targeted green fluorescent protein (GFP), and characterize mitochondrial dynamics with a combination of single-cell time-lapse microscopy, computational tracking, and network …

Highly Swellable Hydrogels Prepared From Extensively Oxidized Lignin, Jihyeon Hwang, Daniella V. Martinez, Estevan J. Martinez, Gift Metavarayuth, Dustin Goodlett, Qi Wang, Mitra Ganewatta, Michael S. Kent, Chuanbing Tang

Faculty Publications

Biopolymers such as lignin are gaining renewed appeal due to the need for sustainable materials. Herein, we used chelator-mediated Fenton (CMF) chemistry to oxidize Kraft lignin to develop sustainable super absorbent materials. The CMF chemistry adds oxygen, opens aromatic rings and increases COOH content, producing hydrophilic lignin without depolymerization. UV absorption, molecular weight, elemental analysis, and titration were used to study the chemical compositions of CMF-processed lignin. Then the chemically modified hydrophilic lignin was used to produce lignin-based hydrogels utilizing an aqueous polymerization and cross-linking reaction that enabled tunable properties. The resulting lignin hydrogels absorbed water up to 96% and …

Understanding Rapid Intercalation Materials One Parameter At A Time, Wessel Van Den Bergh, Morgan Stefik

Faculty Publications

Demand for fast, energy-dense storage drives the research into nanoscale intercalation materials. Nanomaterials accelerate kinetics and can modify reaction path thermodynamics, intercalant solubility, and reversibility. The discovery of intercalation pseudocapacitance has opened questions about their fundamental operating principles. For example, are their capacitor-like current responses caused by storing energy in special near-surface regions or rather is this response due to normal intercalation limited by a slower faradaic surface-reaction? This review highlights emerging methods combining tailored nanomaterials with the process of elimination to disambiguate cause-and-effect at the nanoscale. This method is applied to multiple intercalation pseudocapacitive materials showing that the timescales …

Oligomerization Of Amyloid-Β Peptide In The Presence Of Gangliosides–Implications For Alzheimer Disease, Sydney Boyd

Honors Theses

Alzheimer disease (AD) is a neurodegenerative disorder that leads to memory impairment and cognitive dysfunction in elderly populations worldwide. A key characteristic of AD is the formation of neuritic plaques composed of extracellularly deposited aggregates of amyloid-β (Aβ), an intrinsically disordered protein. Although Aβ fibrils were once thought to be the prime initiators of the disease, research has since been shifted to consider soluble, low molecular weight Aβ oligomers as the driving force behind AD toxicity. Due to its origin as a cleavage product of amyloid precursor protein (APP), an integral membrane protein, Aβ is known to perpetually interact with …

Molecular Mechanism Of Rapamycin Resistance In Cancer Cells, Sohag Chakraborty

Dissertations, Theses, and Capstone Projects

The mammalian target of rapamycin (mTOR) acts as the central regulator of multiple cellular processes including cell growth, proliferation, and survival by integrating signals via nutrients, growth factors, hormones, and energy sensing. In cancer cells, the mTOR pathway is highly dysregulated providing survival signals to the cells for their uncontrolled growth. Hence, mTOR has evolved to be a potential therapeutic target for cancer treatment for the past two decades. Application of micro-molar doses of Rapamycin in vitro has been found to successfully inhibit mTOR complex 1 (mTORC1) by blocking the phosphorylation of its downstream substrates- a) ribosomal protein p70 S6 …