Biochemistry, Biophysics, and Structural Biology Commons^™

A Study Of Defensive Mechanisms Employed By Two Species Of Nudibranchs Using Toxicity And Unpalatability Analyses, Sean Youn

Independent Study Project (ISP) Collection

Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays were used …

Design Of Drug Nano-Carriers For Study Of Multidrug Resistance In Single Live Cells, Pavan Kumar Cherukuri

Chemistry & Biochemistry Theses & Dissertations

Multidrug resistance (MDR) exists in both prokaryotic and eukaryotic cells. MDR is responsible for ineffective treatment of a wide range of diseases, such as infections and cancer. The ATP-binding cassette (ABC) membrane transporters (efflux pumps) are one of the largest and most diverse super-families of membrane proteins found in all living organisms, ranging from bacteria to humans. All ABC transporters share a common structure of four core domains; two transmembrane domains (TMD) with variable sequence and topology and two nucleotide-binding domains (NBD) with conserved sequences. Conventional methods for the study of the efflux functions are radioactively labeled substrates and fluorescent …

Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger

Biological Sciences Faculty Research

Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses …

Characterization Of The Rcf1 Q-X3-R-X-R-X3-Q Motif And Its Role In Supporting Oxidative Phosphorylation Enzyme Complexes, Joshua Garlich

Dissertations (1934 -)

Mitochondrial respiratory complexes are critical components of cellular energy production that require tight regulation to ensure optimal function. Rcf1 and Rcf2 are mitochondrial proteins that can physically associate with the yeast respiratory complexes III and IV, and the higher-ordered III-IV respiratory supercomplex that also contains the ADP/ATP translocase, AAC. Rcf1 can physically associate with both complex III and IV independently, and can be chemically crosslinked to AAC, indicating a close physical proximity to a predominant regulator of energy flux within the cell. It was therefore hypothesized that Rcf1, through its physical association with complexes III and IV, and its close …

Sweating The Small Stuff: Linking Plankton To Climate Change, Brian Kim '18 Makes Conncetions, Stephen Collins

Colby Magazine

It takes an expansive mind to connect microscopic marine copepods (certain crustacean plankton) unwittingly chomping on floating microplastics with a bigger picture: the planet’s carbon pump and global climate change. But that’s what Brian Kim ’18 decided to investigate during Jan Plan, working with Bigelow Lab Senior Research Scientist David Fields.

Dissection Of Molecular Assembly Dynamics By Tracking Orientation And Position Of Single Molecules In Live Cells, Shalin B. Mehta, Molly Mcquilken, Patrick J. La Riviere, Patricia Occhipinti, Amitabh Verma, Rudolf Oldenbourg, Amy Gladfelter, Tomomi Tani

Dartmouth Scholarship

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system …

Fhf-Independent Conduction Of Action Potentials Along The Leak-Resistant Cerebellar Granule Cell Axon, Katarzyna Dover, Christopher Marra, Sergio Solinas, Marko Popovic, Sathyaa Subramaniyam, Dejan Zecevic, Egidio D'Angelo, Mitchell Goldfarb

Publications and Research

Neurons in vertebrate central nervous systems initiate and conduct sodium action potentials in distinct subcellular compartments that differ architecturally and electrically. Here, we report several unanticipated passive and active properties of the cerebellar granule cell’s unmyelinated axon. Whereas spike initiation at the axon initial segment relies on sodium channel (Nav)-associated fibroblast growth factor homologous factor (FHF) proteins to delay Nav inactivation, distal axonal Navs show little FHF association or FHF requirement for high-frequency transmission, velocity and waveforms of conducting action potentials. In addition, leak conductance density along the distal axon is estimated as o1% that of somatodendritic membrane. The faster …

Insights Into The Molecular Roles Of Heparan Sulfate Proteoglycans (Hspgs-Syndecans) In Autocrine And Paracrine Growth Factor Signaling In The Pathogenesis Of Hodgkin's Lymphoma, Rajendra Ghardbaran

Publications and Research

Syndecans (SDC, SYND) comprise a group of four structurally related type 1 transmembrane heparan sulfate proteoglycans (HSPGs) that play important roles in tumorigenic processes. SDCs exert signaling via their protein cores and their conserved transmembrane and cytoplasmic domains or by forming complexes with growth factors (GFs). In classical Hodgkin's lymphoma (cHL), a lymphoid neoplasm of predominantly B cell origin, SDC1 and SDC4 are the active SDCs, and a number of GF (vascular endothelial growth factor, fibroblast growth factor, etc.) signaling pathways have been studied. However, despite extensive pre-clinical and clinical research on SDC-mediated GF signaling in many cancer types, there …

App Regulates Microglial Phenotype In A Mouse Model Of Alzheimer's Disease, Gunjan Manocha, Angela Floden, Keiko Rausch, Joshua Kulas, Brett Mcgregor, Lalida Rojanathammanee, Kelley Puig, Kendra Puig, Sanjib Karki, Michael Nichols, Diane Darland, James Porter, Colin Combs

Chemistry & Biochemistry Faculty Works

Prior work suggests that amyloid precursor protein (APP) can function as a proinflammatory receptor on immune cells, such as monocytes and microglia. Therefore, we hypothesized that APP serves this function in microglia during Alzheimer's disease. Although fibrillar amyloid β (Aβ)-stimulated cytokine secretion from both wild-type and APP knock-out (mAPP−/−) microglial cultures, oligomeric Aβ was unable to stimulate increased secretion from mAPP−/− cells. This was consistent with an ability of oligomeric Aβ to bind APP. Similarly, intracerebroventricular infusions of oligomeric Aβ produced less microgliosis in mAPP−/− mice compared with wild-type mice. The mAPP−/− mice crossed to an APP/PS1 transgenic mouse line …

Autophagic Turnover Of Inactive 26s Proteasomes In Yeast Is Directed By The Ubiquitin Receptor Cue5 And The Hsp42 Chaperone, Richard S. Marshall, Fionn Mcloughlin, Richard D. Vierstra

Biology Faculty Research

Highlights

• The yeast 26S proteasome is degraded by Atg8-mediated autophagy
• Nitrogen starvation and inactivation stimulate proteaphagy via distinct pathways
• Proteasome inhibition is accompanied by extensive ubiquitylation of the complex
• Proteaphagy engages the Cue5 autophagy receptor and the Hsp42 chaperone

Summary

The autophagic clearance of 26S proteasomes (proteaphagy) is an important homeostatic mechanism within the ubiquitin system that modulates proteolytic capacity and eliminates damaged particles. Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation. Whereas the core autophagic machineries required for Atg8 lipidation and vesiculation are essential for both routes, the upstream Atg1 …

Mapping Mayapple Growth In Restored Forest, Jonathan Walt, Stephanie Praamsma, Tanner Vincent, David P. Warners

Student Papers and Reports

No abstract provided.

Runoff Volume Reduction From Subbasins In Plaster Creek Watershed, Kent County, Mi, Julie Wildschut, Dena De Kryger

Student Papers and Reports

No abstract provided.

The Green Team And The Restoration Of Plaster Creek, Leira Lew, Micah Warners, Gail Heffner, David P. Warners

Student Papers and Reports

No abstract provided.

Curb-Cut Rain Garden Research, Patrick Jonker, David P. Warners

Student Papers and Reports

No abstract provided.

Characterization Of Sip470, A Family 1 Lipid Transfer Protein And Its Role In Plant Stress Signaling, Timothy Ndagi Audam

Electronic Theses and Dissertations

SIP470, a putative tobacco lipid transfer protein, was identified in a yeast two-hybrid screen to interact with SABP2. SABP2 is a critical role in SA-mediated signaling in tobacco and other plants. In vitro studies using purified recombinant SIP470 confirmed that it is a lipid binding protein. In an attempt to determine its role in mediating stress responses, Arabidopsis T-DNA insertion knockout lines lacking SIP470 homolog were used for the analysis. These mutant plants were defective in basal resistance against microbial pathogens. Expression of defense gene PR-1 was also delayed in these mutant plants. Interestingly, these mutant plants were not defective …

Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta

USF Tampa Graduate Theses and Dissertations

Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. Understanding molecular details of this stimulation process have been challenging mainly because, …

Distinct And Shared Functions Of Als-Associated Proteins Tdp-43, Fus And Taf15 Revealed By Multisystem Analyses, Katannya Kapeli, Gabriel A. Pratt, Anthony Q. Vu, Kasey R. Hutt, Fernando J. Martinez, Balaji Sundararaman, Ranjan Batra, Peter Freese, Nicole J. Lambert, Stephanie C. Huelga, Seung J. Chun, Tiffany Y. Liang, Jeremy Chang, John P. Donohue, Lily Shiue, Jiayu Zhang, Haining Zhu, Franca Cambi, Edward J. Kasarskis, Shawn Hoon, Manuel Ares Jr., Christopher B. Burge, John Ravits, Frank Rigo, Gene W. Yeo

Molecular and Cellular Biochemistry Faculty Publications

The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3′ untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor …

Arsenite Resistance Of Euglena Mutabilis, Nicole Loumarinett Rosendo Mercado, Doug G. Cole (Mentor)

Idaho Conference on Undergraduate Research

Euglena are photosynthetic unicellular protozoa. Commonly found in rivers, lakes and ponds, some Euglena are found in toxic environments, like areas of acid mine drainage where they can grow at low pH and in the presence of heavy metals and metalloids such as arsenite (e.g. Euglena mutabilis). The goal of this research is to determine if an Idaho Euglena isolate (SG6) belongs to the E. mutabilis species and to compare it’s level of arsenite resistance with other E. mutabilis strains. As part of the methodology, we have developed microtiter plate assays in which the cells are …

Tunable Nano-Delivery System For Cancer Treatment: A New Approach For Targeted Localized Drug Delivery, Rana Falahat

USF Tampa Graduate Theses and Dissertations

Localized drug delivery systems have been widely studied as potential replacements for conventional chemotherapy with the capability of providing sustained and controlled drug release in specific targeted sites. They offer numerous benefits over conventional chemotherapy such as enhancing the stability of embedded drugs and preserving their anticancer activity, providing sustained and controlled drug release in the tumor site, reducing toxicity and diminishing subsequent side effects, minimizing the drug loss, averting the need for frequent administrations, and minimizing the cost of therapy.

The aim of this study is to develop a localized drug delivery system with niosomes embedded in a chitosan …

Cmg Helicase Assembly And Activation: Regulation By C-Myc Through Chromatin Decondensation And Novel Therapeutic Avenues For Cancer Treatment, Victoria Bryant

USF Tampa Graduate Theses and Dissertations

The CMG (Cdc45, MCM, GINS) helicase is required for cellular proliferation and functions to unwind double-stranded DNA to allow the replication machinery to duplicate the genome. Cancer cells mismanage helicase activation through a variety of mechanisms, leading to the potential for the development of novel anti-cancer treatments. Mammalian cells load an excess of MCM complexes that act as reserves for new replication origins to be created when replication forks stall due to stress conditions, such as drug treatment. Targeting the helicase through inhibition of the MCM complex has sensitized cancer cells to drugs that inhibit DNA replication, such as aphidicolin …

Population Viability Analysis For Endangered Roanoke Logperch, James Henry Roberts, Paul L. Angermeier, Gregory B. Anderson

Biology: Faculty Publications

A common strategy for recovering endangered species is ensuring that populations exceed the minimum viable population size (MVP), a demographic benchmark that theoretically ensures low long-term extinction risk. One method of establishing MVP is population viability analysis, a modeling technique that simulates population trajectories and forecasts extinction risk based on a series of biological, environmental, and management assumptions. Such models also help identify key uncertainties that have a large influence on extinction risk. We used stochastic count-based simulation models to explore extinction risk, MVP, and the possible benefits of alternative management strategies in populations of Roanoke logperch Percina rex, an …

A Long-Term Study Of Ecological Impacts Of River Channelization On The Population Of An Endangered Fish: Lessons Learned For Assessment And Restoration, James Henry Roberts, Gregory B. Anderson, Paul L. Angermeier

Biology: Faculty Publications

Projects to assess environmental impact or restoration success in rivers focus on project-specific questions but can also provide valuable insights for future projects. Both restoration actions and impact assessments can become “adaptive” by using the knowledge gained from long-term monitoring and analysis to revise the actions, monitoring, conceptual model, or interpretation of findings so that subsequent actions or assessments are better informed. Assessments of impact or restoration success are especially challenging when the indicators of interest are imperiled species and/or the impacts being addressed are complex. From 1997 to 2015, we worked closely with two federal agencies to monitor habitat …

The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez

Lawrence University Honors Projects

A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation …

Influencing Pathways That Cause Metastasis And Stemness In Epithelial Ovarian Cancer, Alyse Lynn Huisken-Hill

Electronic Theses, Projects, and Dissertations

Ovarian cancer is the fifth leading cause of cancer death in women between the ages of 35 and 74. With 22 thousand new cases and 15 thousand deaths annually ovarian cancer is among the most deadly cancers with a death to incidence ratio of 68%. With 70% of cases High Grade Serous Ovarian Carcinoma (HGSOC) is the most common type of ovarian cancer and causes 90% of ovarian cancer deaths. 80% of patients have reoccurrence within five years and only 15-30% of patients with recurrent metastatic ovarian cancer respond to current therapies, chemotherapy and surgery. One reason for the high …

Purification, Optimization, And Growth Of New Delhi Metallo-Β-Lactamase-1 Protein Crystals Mixed With Nz218 Inhibitor, Brandon M. Wills

Celebration of Learning

New Delhi metallo-β-lactamase-1 is a problematic gene found in certain strains of bacteria that cause them to become antibiotic resistant to nearly all known antibiotics. While some antibiotics are available to treat patients with a bacterial infection, most are toxic or do not have 100% success rates. With that being said, it is imperative that we search for a molecule that is successfully able to inhibit the effects of this gene every time. Such a discovery would help tremendously with new antibiotic drug development and also prevent further damage by these dangerous bacteria. In this presentation, I will describe the …

Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine, Omar A. Garcia Martinez

Biology: Student Scholarship & Creative Works

ABSTRACT: The HIV-1 pandemic continues to thrive due to ineffective HIV-1 vaccines. Historically, the world’s most infectious diseases, such as polio and smallpox, have been eradicated or have come close to eradication due to the advent of effective vaccines. Highly active antiretroviral therapy is able to delay the onset of AIDS but can neither rid the body of HIV-1 proviral DNA nor prevent further transmission. A prophylactic vaccine that prevents the various mechanisms HIV-1 has to evade and attack our immune system is needed to end the HIV-1 pandemic. Recent advances in engineered nuclease systems, like the CRISPR/Cas9 system, have …

The Function Of Shoc2: A Scaffold And Beyond, Eun Ryoung Jang, Emilia Galperin

Molecular and Cellular Biochemistry Faculty Publications

The extracellular signal-regulated kinase (ERK1/2) cascade regulates a myriad of functions in multicellular organisms. Scaffold proteins provide critical spatial and temporal control over the specificity of signaling. Shoc2 is a scaffold that accelerates activity of the ERK1/2 pathway. Loss of Shoc2 expression in mice results in embryonic lethality, thus highlighting the essential role of Shoc2 in embryogenesis. In agreement, patients carrying mutated Shoc2 suffer from a wide spectrum of developmental deficiencies. Efforts to understand the mechanisms by which Shoc2 controls ERK1/2 activity revealed the intricate machinery that governs the ability of Shoc2 to transduce signals of the ERK1/2 pathway. Understanding …

Non-Specific Phospholipase C1 Affects Silicon Distribution And Mechanical Strength In Stem Nodes Of Rice, Huasheng Cao, Lin Zhuo, Yuan Su, Linxiao Sun, Xuemin Wang

Biology Department Faculty Works

Silicon, the second abundant element in the crust, is beneficial for plant growth, mechanical strength, and stress responses. Here we show that manipulation of the non‐specific phospholipase C1, NPC1, alters silicon content in nodes and husks of rice (Oryza sativa). Silicon content in NPC1‐overexpressing (OE) plants was decreased in nodes but increased in husks compared to wild‐type, whereas RNAi suppression of NPC1 resulted in the opposite changes to those of NPC1‐OE plants. NPC1 from rice hydrolyzed phospholipids and galactolipids to generate diacylglycerol that can be phosphorylated to phosphatidic acid. Phosphatidic acid interacts with Lsi6, a silicon transporter that is expressed …

The Effects Of The Environmental Estrogens Cadmium And Arsenite On Phosphorylation Of Erk1/2 Via Gpr30 In Human Lung Adenocarcinoma Cells, Katarzyna Krauss

Undergraduate Theses

Nanomolar concentrations of both cadmium and arsenite, two environmental estrogens present in cigarette smoke, have been documented in rapidly phosphorylating ERK1/2, a type of MAPK, in the human non-small cell lung cancer (NSCLC) line NHI-1793 in a manner similar to that of estrogen. Pretreatment of cells with a general, nonspecific estrogen receptor antagonist reduced the levels of phosphorylated MAPK, indicating that this phosphorylation event is achieved through use of an estrogen signaling pathway. The specific estrogen receptor involved in this process, however, is currently unknown. To determine whether GPR30, one of the three types of estrogen receptors, is necessary for …

A Novel Variant In Cmah Is Associated With Blood Type Ab In Ragdoll Cats, Barbara Gandolfi, Robert Grahn, Nicholas Gustafson, Daniela Proverbio, Eva Spada, Badri Adhikari, Janling Cheng, Gordon Andrews, Leslie Lyons, Chris Helps

Computer Science Faculty Works

The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood …