Life Sciences Commons^™

Cryo-Em Structures Of Eastern Equine Encephalitis Virus Reveal Mechanisms Of Virus Disassembly And Antibody Neutralization, Saif Hasan, Chengqun Sun, Arthur S. Kim, Yasunori Watanabe, Chun-Liang Chen, Thomas Klose, Geeta Buda, Max Crispin, Michael S. Diamond, William B. Klimstra, Michael G. Rossmann

Department of Biological Sciences Faculty Publications

Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid …

Community-Scale Water Treatment Systems In The Dominican Republic, Jonathan Racey, Annabelle Papai, Elise Fischer, Becca Johnson

Engagement & Service-Learning Summit

Engagement and Service-Learning Summit: Reciprocal and Sustainable Partnerships

The Uniform Soybean Tests: Northern Region 2017, Gary L. Nowling, Guohong Cai

Uniform Soybean Tests Northern Region

United States Department of Agriculture Agricultural Research Service, West Lafayette, Indiana, Cooperating with State Agricultural Experiment Stations, Northern States.

Impacts Of Urbanization On Costs Of Production And Land Use In The Central Southern Seaboard: A Farm-Level Analysis, Richard F. Nehring, Kenneth Erickson, James M. Harris, Charlie Hallahan, Ani Katchova, Flavius Badau

Journal of Applied Farm Economics

This study uses stochastic production frontier (SPF) and DEA frontier methods to estimate the impact of urban influence on the cost of production for traditional corn/soybeans farms in the Southern Seaboard (excepting Virginia and Alabama). We hypothesize that urban influence decreases the technical efficiency of these farms. Although states in this region are not entirely subject to urban influence, some parts of states in this region are highly urbanized. We find that farmers in urban-influenced locations are less technically efficient than farmers in rural locations in the region examined. During 2002-2014, stochastic production frontier and DEA frontier procedures indicate that …

Profitability Of Developing Beef Heifers On Stockpiled Winter Forages, Zachary David Mcfarlane, Chris Boyer, J. Travis Mulliniks

Journal of Applied Farm Economics

We estimate the profitability of developing heifers on one stockpiled cool-season grass and two stockpiled warm-season grasses during the winter months by comparing distributions of net present value (NPV) over an 11-year useful life. Furthermore, distributions of payback period and the break-even price for each calf over the heifer’s production life were generated for each forage species. These results are compared across forages as well as to a simulated drylot system for heifer development. Data comes from a grazing experiment in Tennessee, where heifers grazed big bluestem and Indian grass combination (BBIG), switchgrass (SW), or endophyte-infected tall fescue (TF) pastures. …

Profile Interview With Norman E. Fenn, Shannon L. Castek

Purdue Journal of Service-Learning and International Engagement

Shannon L. Castek is a fourth-generation Boilermaker and fourth-professional-year student in the Purdue University College of Pharmacy. Throughout her time in pharmacy school, Shannon has enjoyed supplementing her curricular work with service-learning activities, participating in health screenings and immunization events with the Purdue chapter of the American Pharmacists Association–Academy of Student Pharmacists. She plans to pursue a pharmacy residency following graduation to achieve her dream of becoming an ambulatory care pharmacist. In this article, Shannon highlights the service-learning endeavors of Dr. Norman Fenn in the College of Pharmacy.

Hands Of The Future, Inc.: Connecting Children To Nature, Rebecca Busse

Purdue Journal of Service-Learning and International Engagement

Rebecca Busse is the project coordinator for the Nature of Teaching Extension Program. This provides K–5 teachers with standards-based lesson plans related to wildlife, food waste, and health and wellness. She has been volunteering with Hands of the Future, Inc., for three years. In this article, she describes the organization and her experiences with it.

My Experience In Swaziland With Give Hope, Fight Poverty, Megan Kaser

Purdue Journal of Service-Learning and International Engagement

Megan Kaser, a recent 2017 alum in the College of Health and Human Sciences at Purdue University, describes her experience with Give Hope, Fight Poverty (GHFP)—a nonprofit organization in Indianapolis, Indiana. She is currently pursuing a master’s degree in physician assistant studies. GHFP’s mission is “to foster philanthropy domestically by designing service-learning programs that engage U.S. college students with rural communities in Swaziland, Africa, and work together to educate, empower, and lift orphaned and vulnerable children—particularly those living in child-headed households— out of poverty” (Give Hope, Fight Poverty, n.d.). By incorporating college students in the implementation of GHFP orphan education …

The Pharmaceutical Industry: A Pharmacy Student's Guide, Christian Egly, Yaman Kaakeh

Purdue Journal of Service-Learning and International Engagement

Christian Egly is a fourth-year (P4) pharmacy student in the Purdue University College of Pharmacy. During his years at Purdue, he worked in labs performing bench research in clinical pharmacology and biochemistry. He plans to work in the pharmaceutical industry after graduation. During his fourth year, he completed rotations in business development at Kashiv Pharma, LLC, and was hired there for an internship in 2017. In the article, Christian describes his personal experiences at Kashiv Pharma, LLC, and how industry can positively affect patient communities.

De Novo Sequence And Copy Number Variants Are Strongly Associated With Tourette Disorder And Implicate Cell Polarity In Pathogenesis, Sheng Wang, Jeffrey D. Mandell, Yogesh Kumar, Nawei Sun, Montana T. Morris, Juan Arbelaez, Cara Nasello, Shan Dong, Clif Duhn, Xin Zhao, Zhiyu Yang, Shanmukha S. Padmanabhuni, Dongmei Yu, Robert A. King, Andrea Dietrich, Najah Khalifa, Niklas Dahl, Alden Y. Huang, Benjamin M. Neale, Giovanni Coppola, Carol A. Mathews, Jeremiah M. Scharf, Tourette International Collaborative Genetics Study (Tic Genetics), Tourette Syndrome Genetics Southern And Eastern Europe Initiative (Tsgenesee), Tourette Association Of America International Consortium For Genetics (Taaicg), Thomas V. Fernandez, Joseph D. Buxbaum, Silvia De Rubeus, Dorothy E. Grice, Jinchuan Xing, Gary A. Heiman, Jay A. Tischfield, Peristera Paschou, A Jeremy Wilsey, Matthew W. State

Department of Biological Sciences Faculty Publications

We previously established the contribution of de novo damaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novo damaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3 (cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novo …

High-Throughput Nanoliter Dispensing Device For Biological Applications, Cole Reynolds, Euiwon Bae Dr., J Paul Robinson Dr.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Pathogen identification is a field that can contribute largely to the prevention of the spreading of illness and disease. In the past, pathogen identification has been a long and arduous process due to the time-consuming processes and steps that requires technician’s time and effort. With new technologies emerging however, screening of bacteria colonies can be done in a quick and high-throughput way. The problem is that using the current methods, bacteria cannot be transferred to petri dishes fast enough to keep up with the new screening methods. The current study focuses on exploring different methods to create an ergonomic device …

Structural Analysis Of The Bama-B Complex In Acinetobacter Baumannii, Abigael Gichaba, Nicholas Noinaj, Robert E. Stephenson

The Summer Undergraduate Research Fellowship (SURF) Symposium

There are 2 types of bacteria, gram-negative and gram-positive bacteria. Gram-negative bacteria have both a plasma membrane and an outer membrane, while gram-positive only have a plasma membrane. The outer membranes of gram-negative bacteria have outer membrane proteins which are essential for the bacteria’s survival. Also located within the outer membrane is a multicomponent protein complex named the beta-barrel assembly machinery (BAM) complex. BAM is responsible for folding and inserting outer membrane proteins into the outer membrane. This protein complex serves an essential role but not much is understood about its function. In this study, two subunits of the BAM …

Water Temperature And Harmful Algal Bloom Rate, Geoff Bright, Greg Michalski, Benjamin P. Wilkins

The Summer Undergraduate Research Fellowship (SURF) Symposium

Harmful algal blooms, made up of cyanobacteria, is an increasing problem in Midwestern lakes. Nitrogen and phosphorus fertilizers used in crops such as corn and soybeans run off into streams and eventually lakes. Nitrogen and phosphorus in the form of nitrate and phosphate respectively is then used by cyanobacteria as a food source, allowing them to bloom at an alarming rate. Massive bloom events can be hazardous to both human health and the natural environment because of the release of neurotoxins, hepatotoxins and others into the air and drinking water. We set out to find if different water temperature can …

Structural And Functional Characterization Of Hyper-Phosphorylated Grk5 Protein Expressed From E. Coli, Joseph M. Krampen, John Tesmer, Qiuyan Chen

The Summer Undergraduate Research Fellowship (SURF) Symposium

G protein-coupled receptor (GPCR) kinases (GRKs) are proteins in the cell responsible for regulating GPCRs located on the cell membrane. GRKs regulate active GPCRs by phosphorylating them at certain sites which causes them to stop normal signaling on the membrane. This ultimately affects how the cell responds to its environment. GRK5 is a kinase of particular interest due to its involvement in the pathology of diseases such as cardiac failure, cancers, and diabetes. Understanding the structure and function of GRK5 is essential for discovering ways to manipulate its behavior with these diseases, but not much is known about how GRK5 …

Does Stat5a Have An Effect On Bmal1 Levels In Mammary Epithelial Cells?, Clare E. Aduwari, Aridany Suarez-Trujillo, Karen I. Plaut, Theresa M. Casey

The Summer Undergraduate Research Fellowship (SURF) Symposium

The mammary gland is a very important organ for reproduction in mammals because it produces milk which serves as the primary source of nutrients for newly-born offspring. Previous studies suggest that its development is regulated by circadian clocks, biochemical oscillators that generate circadian rhythms (the body’s internal clock). The circadian system plays a major role in homeostasis, coordinating the body’s internal physiology and synchronizing it with the external environment. Our lab showed that levels of the BMAL1 protein, a core clock component, increased in the mammary gland at the onset of lactation. Treatment of mammary epithelial cells (HC11) with the …

Engineering Bioluminescent Sensors Of Cyclic Amp To Study Opioid Signaling, Alexander L. Tesmer, Alexander R. French, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Opioids are small signaling molecules which bind to opioid receptors on the surface of cells. The kappa opioid receptor (KOR) is one of three major types of opioid receptors found in human neurons. When an opioid binds to a KOR, a variety of biochemical signaling pathways are activated inside the cell. Each of these pathways are associated with different physiological effects of KOR activation. The production of a small signaling molecule, cyclic adenosine monophosphate (cAMP), is known to be inhibited during KOR activation of the analgesic (pain-killing) signaling pathway. The ability to interrogate the individual responses of KOR signaling pathways …

Improving Biomanufacturing Production With Novel Elp-Based Transcriptional Regulators, Juya Jeon, Logan R. Readnour, Kevin V. Solomon

The Summer Undergraduate Research Fellowship (SURF) Symposium

Microbes can be used to produce valuable drugs, chemicals, and biofuels, but their potential has not been fully realized due to low production yields. To improve biomanufacturing processes and yield, we are developing novel, transcriptional regulators using biosynthesis technology in order to improve cellular health and overall production. Our regulator contains elastin-like polypeptides (ELPs), which make ideal sensors since they exhibit a sharp, inverse phase transition to indicators of cell health such as intracellular pH and ionic strength, and external stimuli such as temperature. We hypothesize that ELP can be fused to transcription factors to control expression of target genes. …

Cost-Effective Paper-Based Diagnostic Using Split Proteins To Detect Yeast Infections, Zachary R. Berglund, Kevin V. Solomon, Mohit S. Verma, Moiz Rasheed, Zachary Hartley, Kevin Fitzgerald, Kok Zhi Lee, Janice Chan, Julianne Dejoie, Makayla Schacht, Alex Zavala

The Summer Undergraduate Research Fellowship (SURF) Symposium

The common yeast infection, vulvovaginal candidiasis, affects three out of four women throughout their lifetime and can be spread to their child in the form of oral candidiasis (thrush). This disease is caused by the fungal pathogen Candida albicans, which is also a major cause of systemic candidiasis, a rarer but deadly disease with up to a 49% lethality rate. Current widely-used diagnostic methods include cell cultures, pH tests, and antibody detection, to assist effective treatment. Despite availability of various diagnostic methods, there is no inexpensive, rapid, and accurate way to detect C. albicans infection. This project aims to …

Engineering Dub-Deficient Viral Proteases From Fipv And Pedv Coronaviruses, Daniel T. Wesenberg, Jozlyn R. Clasman, Andrew D. Mesecar

The Summer Undergraduate Research Fellowship (SURF) Symposium

Coronaviruses form a class of viral pathogens lethal to humans and livestock. This issue is compounded by a lack of commercially available treatments or vaccines. In 2014, porcine epidemic diarrhea virus (PEDV) emerged in the United States and accounted for an estimated 7 million porcine deaths. Deaths of humans, companion animals, and livestock caused by coronaviruses highlight the need for therapeutic strategies to combat this devastating disease. One strategy involves engineering papain-like protease 2 (PLP2), an enzyme conserved among coronavirus species that is critical for virus replication and pathogenesis. PLP2’s de-ubiquitinating (DUB) activity aids in the suppression of the host’s …

Expression Of Carbohydrates Biosynthetic Genes In Developing Soybean Seeds, Jayden Rosen, Karen A. Hudson

The Summer Undergraduate Research Fellowship (SURF) Symposium

An essential part of livestock diets is soybean meal, which is a major source of protein, but which also consists of antinutritional carbohydrates. Antinutritional carbohydrates such as raffinose and stachyose lead to irritation to the gut for monogastric livestock as well as unhealthy weight gain. A major objective of soybean genetics is to reduce these antinutritional carbohydrates within the seed and increase the levels of good carbohydrates. This will lead to healthier livestock and better meat quality. To select genes potentially responsible for variation in carbohydrate levels in seeds, the expression of genes encoding several biosynthetic enzymes was measured during …

Structural Characterization Of The Dep Domains Of P-Rex1, Samantha R. Allgood, John J.G. Tesmer, Sandeep K. Ravala

The Summer Undergraduate Research Fellowship (SURF) Symposium

P-Rex1 is a guanine nucleotide exchange factor for Rho-GTPases, which is indirectly involved in the regulation of cell migration and proliferation. It contains a tandem DH/PH domain archetypal of the Dbl family of GEFs, two DEP and two PDZ domains, and a C-terminal end with weak homology to inositol polyphosphate 4-phosphatase. P-Rex1 is regulated by both intra-domain interactions and interactions with other proteins such as G-protein beta gamma, PKA and phosphatidylinositol (3,4,5)-trisphosphate. Upregulation of P-Rex1 has been found in multiple human cancers, making it a potential target for anti-cancer drug therapies. Therefore, structural characterization of P-Rex1 is critical. Currently, only …

Targeting Pro-Inflammatory Function Of Microglia Using Small Molecules To Combat Neurodegeneration, Gabrielle C. Williams, Priya Prakash, Gaurav Chopra

The Summer Undergraduate Research Fellowship (SURF) Symposium

Microglia are the brain’s resident immune cells that are responsible for maintaining homeostasis in healthy conditions. During injury or infection, resting microglia get activated and produce pro-inflammatory cytokines such as IL-1b, IL-1a, IL-6, etc. along with reactive oxygen species like nitric oxide (NO) to combat neuroinflammatory diseases such as Alzheimer’s disease (AD). Inflammation is characterized by the activation of resident-immune cells in the brain called microglia that respond to the eat-me signals released by the toxic amyloid beta peptides as well as the dying neurons in the microenvironment. Recent studies have shown that activated microglia induce neuronal death by secreting …

Effect Of Carbohydrates On The Gut Microbiome, Maciej Filar, Mohit S. Verma

The Summer Undergraduate Research Fellowship (SURF) Symposium

The microbiome within the gut is directly linked to biological processes within a person, influencing factors such as metabolism, signaling pathways, and available nutrients. Long term dieting is known to alter ecological conditions within the gut, allowing certain types of microbes to flourish. Therefore, the overall health of an individual is ultimately influenced by shifts in the microbial community state caused by persistent dieting. This study investigates the connection between diet and the microbiome and draws an understanding of how common carbohydrates in food can affect bacterial composition. Using KBase software, anaerobic bacterial growth was investigated for bacteria subject to …

Targeted Epigenetic Editing Using Optogenetic Tools, Joshua Hahn, Chongli Yuan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Epigenetics markers, such as DNA methylation and histone post-translational modifications, are modifications to the structure of DNA that impact gene expression without altering the genetic code. Among them, DNA methylation plays a critical role in various biological processes including the differentiation of stem cells, regulation of gene expression, and adaptation to environmental signals. The ability to modify DNA methylation at particular genes in various cell types is thus desirable for engineering specific cell phenotypes. Although technologies exist that can alter DNA methylation at target genes, these techniques lack spatial and temporal resolution and are not able to selectively edit individual …

Neural Coding Of An Auditory Pitch Illusion, Maria Alejandra Barrera, Mark Sayles, Ravinderjit Singh

The Summer Undergraduate Research Fellowship (SURF) Symposium

Pitch is an important perceptual dimension in audition, supporting auditory object segregation, melody recognition and lexical distinction. Huggins’ pitch, for example, is a phenomenon evoked by two sources of broadband noise presented binaurally with an inter-aural phase shift over a narrow frequency band. Huggins’ pitch and other dichotic pitches have been studied extensively using perceptual experiments. Several models have been proposed to explain and predict the perception of pitch; however, no studies have tried to record in vivo neuron responses to Huggins’ pitch (HP) nor have tried to explain how the HP is coded by neurons. The existence of pitches …

Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bacteriophage are viruses that infect and kill bacteria. They can be used as treatments for antibiotic resistant bacterial infections, but more knowledge is needed about phage and how they interact with bacteria in order to develop safe and effective phage therapy treatments. This study examines the genomes of eighteen mycobacteriophage that were isolated from the environment on and surrounding Purdue University. Phage genomes were annotated using several bioinformatics software, including DNA Master, GeneMark, and PECAAN. Evidence was examined to determine the correct location within the genome and the potential function. Approximately two thousand genes were annotated in this study. A …

Targeting Neuropeptides To Bone Fractures For Accelerated Healing, Nicholas A. Young, Jeffery J. Nielsen, Philip S. Low

The Summer Undergraduate Research Fellowship (SURF) Symposium

In patients over the age of 65 especially, bone fractures represent a significant disease burden. Non-invasive drug therapies are not available for bone fractures which represents a problem for this population. Vasoactive intestinal peptide (VIP) and Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP), two neuromodulator peptides in the glucagon superfamily, have demonstrated positive regulation of osteoblast proliferation and activity. Using acidic oligopeptides, we have developed ligands that target to and accumulate at fracture sites. These targeting ligands can be synthesized in sequence with bone anabolic peptides to minimize off target effects and increase potency at the fracture site to create safer and …

Blue Light Induces A Neuroprotective Open Access Gene Expression Program In Drosophila Photoreceptors, Hana Hall, Jingqun Ma, Sudhanshu Shekhar, Walter D. Leon-Salas, Vikki M. Weake

Department of Biochemistry Faculty Publications

Background: Light exposure induces oxidative stress, which contributes to ocular diseases of aging. Blue light provides a model for light‑induced oxidative stress, lipid peroxidation and retinal degeneration in Drosophila melanogaster. In contrast to mature adults, which undergo retinal degeneration when exposed to prolonged blue light, newly‑eclosed fies are resistant to blue light‑induced retinal degeneration. Here, we sought to characterize the gene expression programs induced by blue light in fies of diferent ages to identify neuroprotective pathways utilized by photoreceptors to cope with light‑induced oxidative stress.

Results: To identify gene expression changes induced by blue light exposure, we profled the nuclear …

Proper Splicing Contributes To Visual Function In The Aging Drosophila Eye, Rachel Stegeman, Hana Hall, Spencer E. Escobedo, Henry C. Chang, Vikki M. Weake

Department of Biochemistry Faculty Publications

Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age‐related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age‐regulated splicing‐associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function …

Xp-Antarctik Expedition: The Effect Of A Month-Long Expedition In Antarctica On Physiological Performance, Andrée-Anne Parent, Daniel Martin, Sandra Morales, Jean Boucher, Alain-Steve Comtois

Journal of Human Performance in Extreme Environments

Antarctica is a challenging habitat for humans. A group of 6 explorers (3 women and 3 men) participated in an expedition in Antarctica. The objective was to observe the physiological acclimatization of the explorers using the following strategies: physical preparation, highcaloric nutritional intake, and the latest physiological monitoring and outdoor equipment. Anthropometric measures (dual x-ray absorptiometry), specific maximal aerobic test, maximal aerobic running speed test, submaximal aerobic cold testing, strength tests (grip strength, leg press and chin up), and endurance tests (bar suspension and chair position) were conducted pre- and post-expedition. Due to the sample size, a paired t-test was …