Biochemistry Commons^™

From Synthesis To Utilization: The Ins And Outs Of Mitochondrial Heme, Samantha A. Swenson, Courtney M. Moore, Jason R. Marcero, Amy E. Medlock, Amit R. Reddi, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.

Connecting Theory To Practice: Using Self-Determination Theory To Better Understand Inclusion In Stem, Michael E. Moore, Dulce M. Vega, Katie M. Wiens, Natalia Caporale

Department of Biochemistry: Faculty Publications

In the United States, persistence for women and ethnic minorities in science, technology, engineering, and math (STEM) careers is strongly impacted by affective factors such as science identity, agency, and sense of belonging. Policies aimed at increasing the diversity of the national STEM student population and workforce have recently focused on fostering inclusive learning environments that can positively impact the experi-ences of underrepresented minorities (URMs) in STEM, thus increasing their retention. While research on inclusion in STEM in higher education is relatively new, inclusion research has a rich history in several other disciplines. These fields have developed theoretical frameworks and …

Systematic Age-, Organ-, And Diet-Associated Ionome Remodeling And The Development Of Ionomic Aging Clocks, Bohan Zhang, Dmitriy I. Podolskiy, Marco Mariotti, Javier Seravalli, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (ionome) and how these changes lead to dysfunction and dis-ease remain unclear. Here, we quantified changes in the ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire ionome stead-ily transitions along the young-to-old trajectory, individual organs are characterized by …

Training Population Optimization For Genomic Selection In Miscanthus, Marcus O. Olatoye, Lindsay V. Clark, Nicholas R. Labonte, Hongxu Dong, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal K. Ghimire, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Katarzyna Głowacka, Kweon Heo, Xiaoli Jin, Hironori Nagano, Junhua Peng, Chang Y. Yu, Ji H. Yoo, Hua Zhao, Stephen P. Long, Toshihiko Yamada, Erik J. Sacks, Alexander E. Lipka

Department of Biochemistry: Faculty Publications

Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus x giganteus (M·g) beyond the single clone used in many programs. Germplasm from the corresponding parental speciesM. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M·g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel …

Differences In Blood-Derived Francisella Tularensis Type B Strains From Clinical Cases Of Tularemia, Marilyn A. Larson, Baha Abdalhamid, Bhanwar Lal Puniya, Tomáš Helikar, David W. Kelley, Peter C. Iwen

Department of Biochemistry: Faculty Publications

Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with …

Metabolic Feedback Inhibition Influences Metabolite Secretion By The Human Gut Symbiont Bacteroides Thetaiotaomicron, Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron (B. theta) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic …

Amphiphiliccyclobutenes And Cylobutanes, Wantanee Sittiwong, Patrick H. Dussault, Raul Barletta, Robert Power

Department of Biochemistry: Faculty Publications

This disclosure relates to amphiphilic compounds containing a cyclobutene or cyclobutane moiety. In some embodiments, the compounds are useful for treating infection by Mycobacterium such as Mycobacterium tuberculosis. Cyclobutene containing compounds are also useful as monomers in the preparation of amphiphilic polymers.

Reactive Oxygen Species (Ros) Mediated Degradation Of Organophosphate T Pesticides By The Green Microalgae Coccomyxa Subellipsoidea☆, Timothy J Nicodemus, Concetta C. Dirusso, Mark A. Wilson, Paul N. Black

Department of Biochemistry: Faculty Publications

The aim of this study was to define the mechanism allowing the green alga Coccomyxa subellipsoidea to break down organophosphates from agricultural run-off. This study found that metabolically active cultures of the microalga C. subellipsoidea breakdown organophosphates (paraoxon, malathion and diazinon) with differing structural conformations in freshwater through a mechanism that requires the formation of reactive oxygen species (ROS) with little to no toxic effects on the algae. Under these conditions, organophosphate levels were reduced to 0.1 mg/mL or less over the 8–10 day experimental period. These findings demonstrate a biological- based system can be tailored for the remediation of …

Sestrins Are Evolutionarily Conserved Mediators Of Exercise Benefits, Myungjin Kim, Alyson Sujkowski, Sim Namkoong, Bondong Gu, Tyler Cobb, Boyoung Kim, Allison H. Kowalsky, Chun-Seok Cho, Ian Semple, Seung-Hyun Ro, Carol Davis, Susan V. Brooks, Michael Karin, Robert J. Wessells, Jun Hee Lee

Department of Biochemistry: Faculty Publications

Exercise is among the most effective interventions for age-associated mobility decline and metabolic dysregulation. Although long-term endurance exercise promotes insulin sensitivity and expands respiratory capacity, genetic components and pathways mediating the meta- bolic benefits of exercise have remained elusive. Here, we show that Sestrins, a family of evolutionarily conserved exercise-inducible proteins, are critical mediators of exercise ben- efits. In both fly and mouse models, genetic ablation of Sestrins prevents organisms from acquiring metabolic benefits of exercise and improving their endurance through training. Conversely, Sestrin upregulation mimics both molecular and physiological effects of exercise, suggesting that it could be a major …

Automated Inference Of Boolean Models From Molecular Interaction Maps Using Casq, Sara Sadat Aghamiri, Vidisha Singh, Aurelien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

Department of Biochemistry: Faculty Publications

Motivation: Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap be- tween static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner.

Results: We developed CaSQ by defining conversion rules and …

Sbml Level 3: An Extensible Format For The Exchange And Reuse Of Biological Models, Sarah M. Keating, Dagmar Waltemath, Tomáš Helikar, Michael Hucka, 50 Additional Co-Authors

Department of Biochemistry: Faculty Publications

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraintbased models, reaction-diffusion models, logical network models, and rule-based models. The format leverages …

Photosynthetic Efficiency And Mesophyll Conductance Are Unaffected In Arabidopsis Thaliana Aquaporin Knock-Out Lines, Johannes Kromdijk, Katarzyna Głowacka, Stephen P. Long

Department of Biochemistry: Faculty Publications

Improving photosynthetic efficiency is widely regarded as a major route to achieving much-needed yield gains in crop plants. In plants with C₃ photosynthesis, increasing the diffusion conductance for CO₂ transfer from substomatal cavity to chloroplast stroma (g_m) could help to improve the efficiencies of CO₂ assimilation and photosynthetic water use in parallel. The diffusion pathway from substomatal cavity to chloroplast traverses cell wall, plasma membrane, cytosol, chloroplast envelope membranes, and chloroplast stroma. Specific membrane intrinsic proteins of the aquaporin family can facilitate CO₂ diffusion across membranes. Some of these aquaporins, such as PIP1;2 …

Serotonin 5-Ht2a And 5-Ht2c Receptors Regulate Rat Maternal Behavior Through Distinct Behavioral And Neural Mechanisms, Jun Gao, Lina Nie, Yu Li, Ming Li

Department of Psychology: Faculty Publications

Serotonin 5-HT_2A and 5-HT_2C receptors play important yet distinctive roles in the regulation of rat maternal behavior. The present study investigated their neural substrates and explored the possible behavioral mechanisms (i.e., behavioral organization or maternal motivation). Sprague-Dawley postpartum females were microinjected with either a selective 5-HT_2A agonist (TCB-2, 0.4 or 4.0 μg/side) or a 5-HT_2C agonist (MK212, 2.5 or 5.0 μg/side) into the medial prefrontal cortex (mPFC) or ventral tegmental area (VTA). Ten and 60 min later, their maternal activities were observed in the home cage; and their motivational responses towards pups were examined in a …

Structural Basis Of Non-Canonical Transcriptional Regulation By The A-Bound Iron-Sulfur Protein Whib1 In M. Tuberculosis, Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang, Donald F. Becker, Limei Zhang

Department of Biochemistry: Faculty Publications

WhiB1 is amonomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress inM. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 A° -resolution crystal structure of the [4Fe–4S] cluster-bound (holo- )WhiB1 in complex with the C-terminal domain of the 70-family primary sigma factor A of M. tuberculosis containing the conserved region 4 (A 4). Region 4 of the 70-family primary sigma factors is commonly used by transcription factors …

High-Throughput Nano-Scale Characterization Of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography, Alex J. Vecchio, Robert M. Stroud

Department of Biochemistry: Faculty Publications

Structural biology has revealed predicting heterologous expression levels, homogeneity, and stability of a protein from its primary structure are exceedingly difficult. Membrane proteins, in particular, present numerous challenges that make obtaining milligram quantities of quality samples problematic. For structural and functional investigation of these molecules, however, this is what is required. Fluorescence size-exclusion chromatography (F-SEC), a technique where a protein of biological interest is fused to green fluorescent protein (GFP) and monitored, circumvents many bottlenecks inherent to membrane protein structural biology. In vivo expression yields, as well as in vitro homogeneity and stability, can be rapidly evaluated utilizing nanogram quantities …

Xenobiotic Exposure Requires Mitochondrial Metabolism For Redox Homeostasis And Survival In Astrocytes, Jordan Rose

Department of Biochemistry: Dissertations, Theses, and Student Research

Astrocytes are integral components of glutamatergic neurotransmission, providing essential metabolic processes for neuronal homeostasis and acting as the first line of defense against xenobiotics crossing the blood brain barrier. Arsenic is a xenobiotic with widespread natural and industrial prevalence, and has been linked to impaired neurodevelopment and neuronal death. Given the integrated metabolic nature of astrocytes and neurons, we sought to explore how arsenic impacts astrocyte metabolism in order to better understand the mechanisms of xenobiotic toxicity in the mammalian brain.

We demonstrate that astrocyte viability depends upon de novoglutathione (GSH) synthesis during arsenic exposure, and sub-lethal arsenic exposure …

Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah

Department of Biochemistry: Faculty Publications

Background: The ETDRS stereoscopic seven-field (7F) has been a standard imaging and grading protocol for assessment of diabetic retinopathy (DR) severity score in many clinical trials. To the best of our knowledge, the comparison between montage and stereoscopic 7F has not been reported in the literature. Therefore, the main purpose of this study is to compare agreement between montage and stereoscopic seven-field (7F) photographs in the assessment of DR severity.

Methods: Stereoscopic 7F photographs were captured from subjects with DR. Montages of monoscopic 7F images were created using Adobe Photoshop CS6 Extended©. The best quality image of each stereo pair …

Transcriptomic Analyses And Computational Modeling Reveal That Fatty Acid Transport Protein 2 (Fatp2) Impacts The Transcriptional Activity Of Pparα Thus Altering The Lipid Metabolic Landscape, Vincent M. Perez

Department of Biochemistry: Dissertations, Theses, and Student Research

Fatty acid transport protein 2 (FATP2) is highly expressed in liver, small intestine, and kidney where it functions in both the uptake of exogenous long chain fatty acids (LCFAs) and in the activation of very long chain fatty acids (VLCFAs). Here we address the phenotypic impacts of deleting FATP2 with the following three separate approaches: [1] Utilizing an unbiased next-generation sequencing analysis of FATP2-null (fatp2-/-) mice fed a standard chow diet; [2] Utilizing an unbiased next-generation sequencing analysis of fatp2-null (fatp2-/-) mice fed a high-fat ketogenic diet (KD) and fasted for 24-hours [3] Building dynamic computer models built with data …

Remodeling Of Chlamydomonas Metabolism Using Synthetic Inducers Results In Lipid Storage During Growth, Nishikant Wase, Boqiang Tu, Girish Kumar Rasineni, Ronald Cerny, Ryan Grove, Jiri Adamec, Paul N. Black, Concetta Dirusso

Department of Biochemistry: Faculty Publications

Microalgae accumulate lipids during stress such as that of nutrient deprivation, concomitant with cessation of growth and depletion of chloroplasts. By contrast, certain small chemical compounds selected by high-throughput screening in Chlamydomonas reinhardtii can induce lipid accumulation during growth, maintaining biomass. Comprehensive pathway analyses using proteomics, transcriptomics, and metabolomics data were acquired from Chlamydomonas cells grown in the presence of one of two structurally distinct lipid activators. WD10784 stimulates both starch and lipid accumulation, whereas WD30030-treated cells accumulate only lipids. The differences in starch accumulation are largely due to differential effects of the two compounds on substrate levels that feed …

Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic, Abigale Miller

Honors Program: Senior Projects (Public)

Naloxone is a life-saving drug with the ability to reverse an opioid overdose. As the opioid epidemic’s death toll rises, we can turn to Naloxone as a tool to combat the crisis. The epidemic, born of corruption, has a wide reach among the people of the United States, with especially firm grasps on middle-aged people, sufferers of chronic pain, white Americans and those living in the eastern portion of the country. Naloxone’s elegant design saves lives by effectively competing for a position on an opioid biding receptor in the brain to almost instantly end an overdose and restore normal breathing. …

Advanced Selection Methodologies For Dnazymes In Sensing And Healthcare Applications, Sandeep Kumar, Shikha Jain, Neeraj Dilbaghi, Amrik Singh Ahluwalia, Ashraf Aly Hassan, Ki-Hyun Kim

Department of Civil and Environmental Engineering: Faculty Publications

DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes …

Reintegrating Biology Through The Nexus Of Information And Energy, Kim L. Hoke, Sara L. Zimmer, Mary Jo Ondrechen, Amedee Des Georges, Adam B. Roddy, Nicole R. Buan, Craig E. Williamson

Department of Biochemistry: Faculty Publications

Recent rapid advances in biology have led to diversification and sub-specialization of many fields, as well as a corresponding explosion of new findings. Advances in tools ranging from genomic techniques and high-resolution imaging to automated ecosystem- and biosphere-level sensors, along with correspondingly advanced analytics, have led to critical new insights that are transforming our understanding of biological systems. One of the consequences of these rapid advances has been accelerated splintering of biology into sub-disciplines with highly focused questions, vocabulary, and techniques. This splintering creates barriers to synergy across fields of biology and hinders the insights that could be gained at …

Ligand Binding And Signaling Of Hare/Stabilin-2, Edward N. Harris, Fatima Cabral

Department of Biochemistry: Faculty Publications

The Stabilin receptors are a two-member family in the type H class of scavenger receptors. These dynamic receptors bind and internalize multiple ligands from the cell surface for the purpose of clearing extracellular material including some synthetic drugs and for sensing the external environment of the cell. Stabilin-1 was the first receptor to be cloned, though the biological activity of Hyaluronic Acid Receptor for Endocytosis (HARE)/Stabilin-2 was observed about 10 years prior to the cloning of Stabilin-1. Stabilin-1 has a more diverse expression profile among the tissues than HARE/Stabilin-2. This review will focus on HARE/Stabilin-2 and its interactions with hyaluronan, …

Genome‐Wide Association And Genomic Prediction For Biomass Yield In A Genetically Diverse Miscanthus Sinensis Germplasm Panel Phenotyped At Five Locations In Asia And North America, Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Glowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander E. Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

To improve the efficiency of breeding of Miscanthus for biomass yield, there is a need to develop genomics‐assisted selection for this long‐lived perennial crop by relating genotype to phenotype and breeding value across a broad range of environments. We present the first genome‐wide association (GWA) and genomic prediction study of Miscanthus that utilizes multilocation phenotypic data. A panel of 568 Miscanthus sinensis accessions was genotyped with 46,177 single nucleotide polymorphisms (SNPs) and evaluated at one subtropical and five temperate locations over 3 years for biomass yield and 14 yield‐component traits. GWA and genomic prediction were performed separately for different years …

Downregulation Of A Cyp74 Rubber Particle Protein Increases Natural Rubber Production In Parthenium Argentatum, Dante F. Placido, Niu Dong, Chen Dong, Von Mark V. Cruz, David A. Dierig, Rebecca E. Cahoon, Byung-Guk Kang, Trinh Huynh, Maureen Whalen, Grisel Ponciano, Colleen Mcmahan

Department of Biochemistry: Faculty Publications

We report functional genomics studies of a CYP74 rubber particle protein from Parthenium argentatum, commonly called guayule. Previously identified as an allene oxide synthase (AOS), this CYP74 constitutes the most abundant protein found in guayule rubber particles. Transgenic guayule lines with AOS gene expression down-regulated by RNAi (AOSi) exhibited strong phenotypes that included agricultural traits conducive to enhancing rubber yield. AOSi lines had higher leaf and stem biomass, thicker stembark tissues, increased stem branching and improved net photosynthetic rate. Importantly, the rubber content was significantly increased in AOSi lines compared to the wild-type (WT), vector control and …

Biomass Yield In A Genetically Diverse Miscanthus Sinensis Germplasm Panel Evaluated At Five Locations Revealed Individuals With Exceptional Potential, Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Glowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander E. Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the highest‐yielding and best‐adapted genotypes of its parental species, Miscanthus sinensis and Miscanthus sacchariflorus. We phenotyped a diverse clonally propagated panel of 569 M. sinensis and nine natural diploid M. ×giganteus at one subtropical (Zhuji, China) and five temperate locations (Sapporo, Japan; Leamington, Ontario, Canada; Fort Collins, CO; Urbana, IL; and Chuncheon, Korea) for dry biomass yield and 14 yield‐component traits, in trials grown for 3 years. Notably, dry biomass yield of four Miscanthus accessions exceeded 80 Mg/ha in Zhuji, China, approaching …

An Arabidopsis Protoplast Isolation Method Reduces Cytosolic Acidification And Activation Of The Chloroplast Stress Sensor Sensitive To Freezing 2, Allison C. Barnes, Christian G. Elowsky, Rebecca Roston

Department of Biochemistry: Faculty Publications

Chloroplasts adapt to freezing and other abiotic stresses in part by modifying their membranes. One key-remodeling enzyme is SENSITIVE TO FREEZING2 (SFR2). SFR2 is unusual because it does not respond to initial cold stress or cold acclimation, instead it responds during freezing conditions in Arabidopsis. This response has been shown to be sensitive to cytosolic acidification. The unique lipid products of SFR2 have also been detected in response to non-freezing stresses, but what causes SFR2 to respond in these stresses is unknown. Here, we investigate protoplast isolation as a representative of wounding stress. We show that SFR2 oligogalactolipid products accumulate …

Treatment Of Plastic Wastes Using Plasma Gasification Technology, Zachary Homolka

Honors Program: Senior Projects (Public)

Plasma gasification (PG) complements traditional recycling when applied to contaminated or mixed plastics. Without PG these plastics cost recyclers more to process than they are worth on the market, and sometimes they are landfilled or incinerated instead of being recycled. Plasma gasification can take plastic not suitable for traditional recycling and break it down into high-quality syngas for use in electricity generation, chemical manufacturing, or hydrogen production. The technology can be implemented without changing the behavior of consumers, which is a major advantage over attempting to decrease contamination or reduce use of low-value plastic. Due to high capital requirements and …

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle Howell, Karin Van Dijk, Christine S. Booth, Tomáš Helikar, Brain A. Couch, Rebecca Roston

Department of Biochemistry: Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7). Building on recent technological advances, 3D printing (3DP) potentiates an era in which …

Autophagy In Adipocyte Browning: Emerging Drug Target For Intervention In Obesity, Seung-Hyun Ro, Yura Jang, Jiyoung Bae, Isaac M. Kim, Cameron Schaecher, Zachery D. Shomo

Department of Biochemistry: Faculty Publications

Autophagy, lipophagy, and mitophagy are considered to be the major recycling processes for protein aggregates, excess fat, and damaged mitochondria in adipose tissues in response to nutrient status-associated stress, oxidative stress, and genotoxic stress in the human body. Obesity with increased body weight is often associated with white adipose tissue (WAT) hypertrophy and hyperplasia and/or beige/brown adipose tissue atrophy and aplasia, which significantly contribute to the imbalance in lipid metabolism, adipocytokine secretion, free fatty acid release, and mitochondria function. In recent studies, hyperactive autophagy in WAT was observed in obese and diabetic patients, and inhibition of adipose autophagy through targeted …