Other Biochemistry, Biophysics, and Structural Biology Commons^™

Fishing For A Sustainable Future: Aquaponics As A Method Of Food Production, Richard Ramsundar

Student Theses 2015-Present

This thesis compares and explains the advantages aquaponics farming has over modern industrial intensive farming. Through a comparison natural capital usage, conservation, recycling and cost, the thesis advocates for the expansion of aquaponics usage in urban settings. The thesis also explains the history of intensive farming and aquaponics in America, the science of how aquaponics operates, the economic and environmental costs of modern intensive farming versus aquaponics farming, and the social implications of aquaponics. Lastly, I propose a policy that reallocates farm subsidies by modifying the Farm Bill. Then I propose policies that support creating a new standard of farm …

A Multilaboratory Comparison Of Calibration Accuracy And The Performance Of External References In Analytical Ultracentrifugation, Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Et Al. ..., Donald F. Becker, Peter Schuck

Department of Biochemistry: Faculty Publications

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy …

Proline Metabolism Increases Katg Expression And Oxidative Stress Resistance In Escherichia Coli, Lu Zhang, James R. Alfano, Donald F. Becker

Department of Biochemistry: Faculty Publications

The oxidation of L-proline to glutamate in Gram-negative bacteria is catalyzed by the proline utilization A (PutA) flavoenzyme, which contains proline dehydrogenase (PRODH) and _1-pyrroline-5-carboxylate (P5C) dehydrogenase domains in a single polypeptide. Previous studies have suggested that aside from providing energy, proline metabolism influences oxidative stress resistance in different organisms. To explore this potential role and the mechanism, we characterized the oxidative stress resistance of wild-type and putA mutant strains of Escherichia coli. Initial stress assays revealed that the putA mutant strain was significantly more sensitive to oxidative stress than the parental wild-type strain. Expression of PutA in the …

Tissue-Specific Splice Variants Of Hare/Stabilin-2 Are Expressed In Bone Marrow, Lymph Node, And Spleen, Amanda K. Hare, Edward N. Harris

Department of Biochemistry: Faculty Publications

The hyaluronan receptor for endocytosis (HARE), or Stabilin-2, is the mammalian endocytic clearance receptor for HA, heparin, advanced glycation end-products, acetylated and oxidized low-density lipoproteins and collagen N-terminal propeptides. This large 2551 amino acid receptor is encoded by a gene that covers over 180 kbp on human chromosome 12 and is predicted to be composed of 69 exons. Due to the expression profile of this gene and the number of exons it contains, we hypothesized that splice variants of stab2 are encoded in these tissues. In addition, a correlation between alternative splice variants and cancer progression has been shown in …

Hyaluronidase Hyal1 Increases Tumor Cell Proliferation And Motility Through Accelerated Vesicle Trafficking, Caitlin O Mcatee, Abigail R. Berkebile, Christian Elowsky, Teresa Fangman, Joseph J. Barycki, James K. Wahl Iii, Oleh Khalimonchuk, Naava Naslavsky, Steve Caplan, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

Background: Hyal1 is a turnover enzyme for hyaluronan that accelerates metastatic cancer by increasing cell motility.

Results: Hyal1-overexpressing cells have a higher rate of endocytosis that impacts cargo internalization and recycling.

Conclusion: The higher rate of vesicle trafficking increases motility receptor function and nutrient uptake.

Significance: This novel mechanism implicates Hyal1 trafficking in multiple signaling events during tumor progression.

Overaccumulation Of Γ-Glutamylcysteine In A Jasmonate-Hypersensitive Arabidopsis Mutant Causes Jasmonate-Dependent Growth Inhibition, Hsin-Ho Wei, Martha Rowe, Jean-Jack M. Riethoven, Ryan Grove, Jiri Adamec, Yusuke Jikumaru, Paul E. Staswick

Department of Biochemistry: Faculty Publications

Glutathione (GSH) is essential for many aspects of plant biology and is associated with jasmonate signaling in stress responses. We characterized an Arabidopsis (Arabidopsis thaliana) jasmonate-hypersensitive mutant (jah2) with seedling root growth 100-fold more sensitive to inhibition by the hormone jasmonyl-isoleucine than the wild type. Genetic mapping and genome sequencing determined that the mutation is in intron 6 of GLUTATHIONE SYNTHETASE2, encoding the enzyme that converts γ-glutamylcysteine (γ-EC) to GSH. The level of GSH in jah2 was 71% of the wild type, while the phytoalexin-deficient2-1 (pad2-1) mutant, defective in GSH1 and …

Cytosolic Fe-S Cluster Protein Maturation And Iron Regulation Are Independent Of The Mitochondrial Erv1/Mia40 Import System, Hatice K. Ozer, Adrienne C. Dlouhy, Jeremy D. Thornton, Jingjing Hu, Yilin Liu, Joseph J. Barycki, Janneke Balk, Caryn E. Outten

Department of Biochemistry: Faculty Publications

Background: The mitochondrial sulfhydryl oxidase Erv1 is implicated in cytosolic iron-sulfur protein maturation and iron regulation.

Results: An erv1 yeast strain used in previous iron metabolism studies is glutathione-deficient, and erv1/mia40 mutants with sufficient glutathione do not exhibit iron-related defects.

Conclusion: Iron homeostasis is independent of Erv1/Mia40 function. Significance: The unexplained role of Erv1 in yeast iron metabolism is resolved.

Drosophila Muller F Elements Maintain A Distinct Set Of Genomic Properties Over 40 Million Years Of Evolution, Wilson Leung, Cheryl Bailey, Participating Students And Faculty Of The Genomics Education Partnership

Department of Biochemistry: Faculty Publications

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F …

Overexpression Of Alpha-Synuclein At Non-Toxic Levels Increases Dopaminergic Cell Death Induced By Copper Exposure Via Modulation Of Protein Degradation Pathways, Annadurai Anandhan, Humberto Rodriguez-Rocha, Iryna Bohovych, Amy M. Griggs, Laura Zavala-Flores, Elsa M. Reyes-Reyes, Javier Seravalli, Lia A. Stanciu, Jaekwon Lee, Jean-Christophe Rochet, Oleh Khalimonchuk, Rodrigo Franco

Department of Biochemistry: Faculty Publications

Gene multiplications or point mutations in alpha (α)-synuclein are associated with familial and sporadic Parkinson’s disease (PD). An increase in copper (Cu) levels has been reported in the cerebrospinal fluid and blood of PD patients, while occupational exposure to Cu has been suggested to augment the risk to develop PD. We aimed to elucidate the mechanisms by which α-synuclein and Cu regulate dopaminergic cell death. Short-term overexpression of WT or A53T α-synuclein had no toxic effect in human dopaminergic cells and primary midbrain cultures, but it exerted a synergistic effect on Cu-induced cell death. Cell death induced by Cu was …

Metalloprotease Oma1 Fine-Tunes Mitochondrial Bioenergetic Function And Respiratory Supercomplex Stability, Iryna Bohovych, Mario R. Fernandez, Jennifer J. Rahn, Krista D. Stackley, Jennifer E. Bestman, Annadurai Anandhan, Rodrigo Franco, Steven M. Claypool, Robert E. Lewis, Sherine S.L. Chan, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Mitochondria are involved in key cellular functions including energy production, metabolic homeostasis, and apoptosis. Normal mitochondrial function is preserved by several interrelated mechanisms. One mechanism – intramitochondrial quality control (IMQC) – is represented by conserved proteases distributed across mitochondrial compartments. Many aspects and physiological roles of IMQC components remain unclear. Here, we show that the IMQC protease Oma₁ is required for the stability of the respiratory supercomplexes and thus balanced and tunable bioenergetic function. Loss of Oma1 activity leads to a specific destabilization of respiratory supercomplexes and consequently to unbalanced respiration and progressive respiratory decline in yeast. Similarly, experiments …

Rerouting Cellular Electron Flux To Increase The Rate Of Biological Methane Production, Jennie L. Catlett, Alicia M. Ortiz, Nicole R. Baun

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme HdrABC increased the rate of methane production from methanol by 30% without affecting the growth rate relative to the parent strain. Hdr enzymes are essential in all known methane-producing archaea. They function as the terminal oxidases in the methanogen electron transport system by reducing the coenzymeM(2-mercaptoethane sulfonate) and coenzyme B (7-mercaptoheptanoylthreonine sulfonate) heterodisulfide, CoM-S-S-CoB, to regenerate the thiol-coenzymes for reuse. In Methanosarcina acetivorans, HdrABC expression caused …

Organization Of The Mammalian Ionome According To Organ Origin, Lineage Specialization, And Longevity, Siming Ma, Sang-Goo Lee, Eun Bae Kim, Thomas J. Park, Andrei Seluanov, Vera Gorbunova, Rochelle Buffenstein, Javier Seravalli, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Trace elements are essential to all mammals, but their distribution and utilization across species and organs remains unclear. Here, we examined 18 elements in the brain, heart, kidney, and liver of 26 mammalian species and report the elemental composition of these organs, the patterns of utilization across the species, and their correlation with body mass and longevity. Across the organs, we observed distinct distribution patterns for abundant elements, transition metals, and toxic elements. Some elements showed lineage-specific patterns, including reduced selenium utilization in African mole rats, and positive correlation between the number of selenocysteine residues in selenoprotein P and the …

Hare-Mediated Endocytosis Of Hyaluronan And Heparin Is Targeted By Different Subsets Of Three Endocytic Motifs, Madhu S. Pandey, Edward N. Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

The hyaluronan (HA) receptor for endocytosis (HARE) is a multifunctional recycling clearance receptor for 14 different ligands, including HA and heparin (Hep), which bind to discrete nonoverlapping sites. Four different functional endocytic motifs (M) in the cytoplasmic domain (CD) target coated pit mediated uptake: (YSYFRI²⁴⁸⁵ (M1), FQHF²⁴⁹⁵ (M2), NPLY²⁵¹⁹ (M3), and DPF²⁵³⁴ (M4)). We previously found (Pandey et al. J. Biol. Chem. 283, 21453, 2008) that M1, M2, and M3 mediate endocytosis of HA. Here we assessed the ability of HARE variants with a single-motif deletion …

Advances In Hyaluronan Biology: Signaling, Regulation, And Disease Mechanisms, Melanie A. Simpson, Carol De La Motte, Larry S. Sherman, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Hyaluronan is an extracellular glycosaminoglycan polymer consisting of linear disaccharide units containing alternating glucuronate and N-acetylglucosamine.Many cell types make hyaluronan, which unlike most other macromolecules is assembled at the plasmamembrane and concurrently translocated through the hyaluronan synthase enzyme. The normal function of large hyaluronan polymers (>1MDa) in tissue cushioning, hydration, and lubrication is well established. The aberrant accumulation and degradation of hyaluronan and the receptor-mediated signaling of smaller hyaluronan fragments have also been extensively implicated in a variety of pathological states including inflammation and cancer. More recently, the discovery that hyaluronan can either be a structural matrix component or …

Janus-Faced Sestrin2 Controls Ros And Mtor Signalling Through Two Separate Functional Domains, Hanseong Kim, Sojin An, Seung-Hyun Ro, Filipa Teixeira, Gyeong Jin Park, Cheal Kim, Chun-Seok Cho, Jeong-Sig Kim, Ursula Jakob, Jun Hee Lee, Uhn-Soo Cho

Department of Biochemistry: Faculty Publications

Sestrins are stress-inducible metabolic regulators with two seemingly unrelated but physiologically important functions: reduction of reactive oxygen species (ROS) and inhibition of the mechanistic target of rapamycin complex 1 (mTORC1). How Sestrins fulfil this dual role has remained elusive so far. Here we report the crystal structure of human Sestrin2 (hSesn2), and show that hSesn2 is twofold pseudo-symmetric with two globular subdomains, which are structurally similar but functionally distinct from each other. While the N-terminal domain (Sesn-A) reduces alkylhydroperoxide radicals through its helix–turn–helix oxidoreductase motif, the C-terminal domain (Sesn-C) modified this motif to accommodate physical interaction with GATOR2 and subsequent …

Sestrin2, A Regulator Of Thermogenesis And Mitohormesis In Brown Adipose Tissue, Seung-Hyun Ro, Ian Semple, Allison Ho, Hwan-Woo Park, Jun Hee Lee

Department of Biochemistry: Faculty Publications

Sestrin2 is a stress-inducible protein that functions as an antioxidant and inhibitor of mTOR complex 1. In a recent study, we found that Sestrin2 overexpression in brown adipocytes interfered with normal metabolism by reducing mitochondrial respiration through the suppression of uncoupling protein 1 (UCP1) expression. The metabolic effects of Sestrin2 in brown adipocytes were dependent on its antioxidant activity, and chemical antioxidants produced similar effects in inhibiting UCP1-dependent thermogenesis. These observations suggest that low levels of reactive oxygen species (ROS) in brown adipocytes can actually be beneficial and necessary for proper metabolic homeostasis. In addition, considering that Sestrins are ROS …

Genetic Variation In Miscanthus X Giganteus And The Importance Of Estimating Genetic Distance Thresholds For Differentiating Clones, Katarzyna Glowacka, Lindsay V. Clark, Shivani Adhikari, Junhua Peng, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Uffe Jorgensen, Trevor R. Hodkinson, Justin Gifford, John A. Juvik, Erik J. Sacks

Department of Biochemistry: Faculty Publications

Miscanthus x giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type-specimen. A subset of …

Use Of Designer Nucleases For Targeted Gene And Genome Editing In Plants, Donald P. Weeks, Martin H. Spalding, Bing Yang

Department of Biochemistry: Faculty Publications

The ability to efficiently inactivate or replace genes in model organisms allowed a rapid expansion of our understanding of many of the genetic, biochemical, molecular and cellular mechanisms that support life. With the advent of new techniques for manipulating genes and genomes that are applicable not only to single-celled organisms, but also to more complex organisms such as animals and plants, the speed with which scientists and biotechnologists can expand fundamental knowledge and apply that knowledge to improvements in medicine, industry and agriculture is set to expand in an exponential fashion. At the heart of these advancements will be the …

Connecting Proline Metabolism And Signaling Pathways In Plant Senescence, Lu Zhang, Donald F. Becker

Department of Biochemistry: Faculty Publications

The amino acid proline has a unique biological role in stress adaptation. Proline metabolism is manipulated under stress by multiple and complex regulatory pathways and can profoundly influence cell death and survival in microorganisms, plants, and animals. Though the effects of proline are mediated by diverse signaling pathways, a common theme appears to be the generation of reactive oxygen species (ROS) due to proline oxidation being coupled to the respiratory electron transport chain. Considerable research has been devoted to understand how plants exploit proline metabolism in response to abiotic and biotic stress. Here, we review potential mechanisms by which proline …

Conservation Of Lipid Storage Droplet Proteins In Evolution Of Animalia, Jacob D. Bowman

Undergraduate Honors Thesis Projects

Lipolysis is a conserved pathway used by organisms for the mobilization of fatty acid (FA) out of triacylglycerol (TAG). Neutral lipids are stored in lipid-storage droplets (LSD) which are in nearly every cell of an organism. LSDs are the location of lipolysis. Perilipin proteins are lipid-droplet associated proteins. Perilipins interact with other proteins such as ATGL that breaks down TAG into FA and DAG. Because of its conservation as a whole system, this suggests that proteins of the same pathway are evolving together. This present study traces the evolutionary history of lipolysis-related proteins amongst individual organisms and classes of organisms …