Biochemistry, Biophysics, and Structural Biology Commons^™

Nack Is An Integral Component Of The Notch Transcriptional Activation Complex And Is Critical For Development And Tumorigenesis, Kelly L Weaver, Marie-Clotilde Alves-Guerra, Ke Jin, Zhiqiang Wang, Xiaoqing Han, Prathibha Ranganathan, Xiaoxia Zhu, Thiago Dasilva, Wei Liu, Francesca Ratti, Renee M Demarest, Cristos Tzimas, Meghan Rice, Rodrigo Vasquez-Del Carpio, Nadia Dahmane, David J Robbins, Anthony J Capobianco

Rowan-Virtua School of Osteopathic Medicine Departmental Research

The Notch signaling pathway governs many distinct cellular processes by regulating transcriptional programs. The transcriptional response initiated by Notch is highly cell context dependent, indicating that multiple factors influence Notch target gene selection and activity. However, the mechanism by which Notch drives target gene transcription is not well understood. Herein, we identify and characterize a novel Notch-interacting protein, Notch activation complex kinase (NACK), which acts as a Notch transcriptional coactivator. We show that NACK associates with the Notch transcriptional activation complex on DNA, mediates Notch transcriptional activity, and is required for Notch-mediated tumorigenesis. We demonstrate that Notch1 and NACK are …

Ion Structure And Energetics In The Gas Phase Characterized Using Fourier Transfom Ion Cyclotron Resonance Mass Spectrometry, Chad A. Jones

Theses and Dissertations

In this dissertation, I use Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to study the structure and energetics of gas phase ions. Infrared multiphoton dissociation spectroscopy (IRMPD) is a technique for measuring the IR spectrum of gas phase ions in a Penning trap. I use this technique to investigate the conformation of cucurbituril complexes, terminal diamines, and protonated amino acids. Cross sectional areas by Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) is a technique developed by the Dearden lab to measure the cross section of gas phase ions. In this work, I further develop a fundamental understanding of …

Sensitivity Analysis Of Biological Boolean Networks Using Information Fusion Based On Nonadditive Set Functions, Naomi Kochi, Tomáš Helikar, Laura Allen, Jim A. Rogers, Zhenyuan Wang, Mihaela T. Matache

Department of Biochemistry: Faculty Publications

Background: An algebraic method for information fusion based on nonadditive set functions is used to assess the joint contribution of Boolean network attributes to the sensitivity of the network to individual node mutations. The node attributes or characteristics under consideration are: in-degree, out-degree, minimum and average path lengths, bias, average sensitivity of Boolean functions, and canalizing degrees. The impact of node mutations is assessed using as target measure the average Hamming distance between a non-mutated/wild-type network and a mutated network.

Results: We find that for a biochemical signal transduction network consisting of several main signaling pathways whose nodes …

Use Of Cysteine-Reactive Crosslinkers To Probe Conformational Flexibility Of Human Dj-1 Demonstrates That Glu18 Mutations Are Dimers, Janani Prahlad, David N. Hauser, Nicole M. Milkovic, Mark R. Cookson, Mark A. Wilson

Department of Biochemistry: Faculty Publications

The oxidation of a key cysteine residue (Cys106) in the parkinsonism-associated protein DJ-1 regulates its ability to protect against oxidative stress and mitochondrial damage. Cys106 interacts with a neighboring protonated Glu18 residue, stabilizing the Cys106-SO₂ ⁻ (sulfinic acid) form of DJ-1. To study this important post-translational modification, we previously designed several Glu18 mutations (E18N, E18D, E18Q) that alter the oxidative propensity of Cys106. However, recent results suggest these Glu18 mutations cause loss of DJ-1 dimerization, which would severely compromise the protein’s function. The purpose of this study was to conclusively determine the oligomerization state of these mutants using X-ray …

Investigating Propargyl-Linked Antifolates In Inhibiting Bacterial And Fungal Dihydrofolate Reductase, Joshua Andrade

Honors Scholar Theses

Antimicrobial agents have been invaluable in reducing illness and death associated with bacterial infection. However, over time, bacteria have evolved resistance to all major drug classes as a result of selective pressure. The advancement of new drug compounds is therefore vital. The Anderson-Wright Lab has focused on developing potent and selective inhibitors of dihydrofolate reductase (DHFR), an enzyme key in cell proliferation and survival, in several pathogenic species. The lab has found that a set of compounds, known as propargyl-linked antifolates, are DHFR inhibitors that are both biologically effective and have strong pharmacokinetic properties.

The efficacy of novel propargyl-linked antifolates …

Transcriptional Regulation Of Sinorhizobium Meliloti Cell Cycle-Related Genes In The Δcbra Mutant And Root Nodules Of Medicago Sativa, Corey S. Hazekamp

Graduate Masters Theses

Sinorhizobium meliloti is a Gram-negative alphaproteobacterium and nitrogen-fixing symbiont, which undergoes a novel cell cycle modification during its' host-microbe interaction. I intend to monitor the transcriptional regulation of cell cycle-related genes during free-loving growth, in addition to monitoring their expression during symbiosis. Using genes known to be regulated by CtrA in C. crescentus or predicted to be regulated by CtrA in S. meliloti, I aim to show how certain cell cycle genes are regulated in S. meliloti. In C. crescentus, CtrA acts as a transcription factor that is active when phosphorylated and inactive when not phosphorylated. In …

Targeting Grp78 In Cancer With Nucleic Acid Bioconjugates, Pradeepkumar L. Patel

Seton Hall University Dissertations and Theses (ETDs)

Nucleic acid bioconjugates have gained widespread use in medicinal chemistry research programs aimed at fighting human malignancies such as cancer, diabetes, genetic and infectious diseases. Their popularity stems from their ability to accelerate the drug development process by conjugating chemical functionality that may improve the pharmacology of a bioactive nucleoside. Moreover, this strategy has been proven to be effective with small molecule nucleoside analogs and those derived from lengthy oligonucleotide sequences. Considering these fruitful applications, my research and this thesis aims to explore the synthesis, characterization and therapeutic potential of novel classes of nucleic acid bioconjugates.

These are based on, …

Acute Effects Of Tio2 Nanomaterials On The Viability And Taxonomic Composition Of Aquatic Bacterial Communities Assessed Via High-Throughput Screening And Next Generation Sequencing, Binh Chu, Tiezheng Tong, Jean-François Gaillard, Kimberley A. Gray, John J. Kelly

Biology: Faculty Publications and Other Works

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of …

Identification Of Soybean Lipoxygenase Products By Gas Chromatography-Mass Spectrometry (Ge-Ms), Rehan Ahmad Malik

Journal of Undergraduate Research at Minnesota State University, Mankato

Lipoxygenases (LOXs) are enzymes which catalyze peroxidation of polyunsaturated fatty acids containing at least one cis, cis 1, 4-pentadiene moiety to form conjugated diene-hydroperoxides. Soybean seeds contain three LOX isoenzymes while at least five different isoenzymes are in the vegetative tissue. Lipoxygenases have been related to several functions i.e. plant growth, defense mechanisms against pathogens and pests, and lipid metabolism. Given the proposed roles of LOX isoenzymes and the presence of multiple LOX isoenzymes in soybean vegetative tissue, it is likely that individual isoenzymes play specific functions. Do the isoenzymes show differences in which products they form? The basic goal …

Translation Initiation Rate Determines The Impact Of Ribosome Stalling On Bacterial Protein Synthesis, Steven J. Hersch, Sara Elgamal, Assaf Katz, Michael Ibba, William Wiley Navarre

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ribosome stalling during translation can be caused by a number of characterized mechanisms. However, the impact of elongation stalls on protein levels is variable, and the reasons for this are often unclear. To investigate this relationship, we examined the bacterial translation elongation factor P (EF-P), which plays a critical role in rescuing ribosomes stalled at specific amino acid sequences including polyproline motifs. In previous proteomic analyses of both Salmonella and Escherichia coli efp mutants, it was evident that not all proteins containing a polyproline motif were dependent on EF-P for efficient expression in vivo . The α- and β-subunits of …

Thiosulfoxide (Sulfane) Sulfur: New Chemistry And New Regulatory Roles In Biology, John Toohey, Arthur J L Cooper

NYMC Faculty Publications

The understanding of sulfur bonding is undergoing change. Old theories on hypervalency of sulfur and the nature of the chalcogen-chalcogen bond are now questioned. At the same time, there is a rapidly expanding literature on the effects of sulfur in regulating biological systems. The two fields are inter-related because the new understanding of the thiosulfoxide bond helps to explain the newfound roles of sulfur in biology. This review examines the nature of thiosulfoxide (sulfane, S0) sulfur, the history of its regulatory role, its generation in biological systems, and its functions in cells. The functions include synthesis of cofactors (molybdenum cofactor, …

Ef-P Dependent Pauses Integrate Proximal And Distal Signals During Translation, Sara Elgamal, Assaf Katz, Steven J. Hersch, David Newsom, Peter White, William Wiley Navarre, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at …

Submonomer Synthesis And Structure-Activity Relationship Studies Of Azapeptide Inhibitors Of The Insulin Receptor Tyrosine Kinase, Lathamol A. Kurian

Seton Hall University Dissertations and Theses (ETDs)

Azapeptides are a class of peptide mimics (peptidomimetics), which have served as valuable tools for the development of peptide based therapeutic agents. The therapeutic promise of azapeptides has been correlated to its primary sequence modification which translates into bio-active secondary structures that improves the pharmacological properties of the native peptide sequence. More specifically, azapeptides contain a semicarbazide within the peptide backbone which restricts the peptide bond torsion angles (φ, ψ) into pre-organized b-turn secondary structures. Thus, azapeptides have been shown to stabilize bio-active b-turn secondary structures responsible for high affinity and selective binding to a target …

Simple, Label-Free And Non-Instrumented Analyte Quantitation By Flow Distance Measurement In Microfluidic Devices, Debolina Chatterjee

Theses and Dissertations

Rapid determination of the concentrations of molecules related to diseases can provide timely information for treatment options. However, most biomarker quantitation methods require costly and complex equipment. On the other hand, point-of-care systems have less complex instrumentation needs than laboratory-based equipment, but often provide less information; for example, biomarker presence or absence instead of concentration. A complete analysis setup addressing key limitations of both laboratory-based and portable systems is highly desirable. I developed microfluidic devices with visual inspection readout of a target’s concentration from microliter volumes of solution flowed into a microchannel. Microchannels are formed within polydimethylsiloxane (PDMS), and the …

The Microtubule-Associated Protein, Eb1, Links Aim2 Inflammasomes With Autophagy-Dependent Secretion, Li-Jie Wang, Hsin-Yi Huang, Meng-Pin Huang, Willisa Liou, Ya-Ting Chang, Chih-Ching Wu, David M. Ojcius, Yu-Sun Chang

All Dugoni School of Dentistry Faculty Articles

Inflammasomes are multi-protein complexes that regulate chronic inflammation-associated diseases by inducing interleukin-1 β (IL-1β) secretion. Numerous components involved in inflammasome activation have been identified, but the mechanisms of inflammasome-mediated IL-1β secretion have not yet been fully explored. Here, we demonstrate that end-binding protein 1 (EB1), which is required for activation of AIM2 inflammasome complex, links the AIM2 inflammasome to autophagy-dependent secretion. Imaging studies revealed that AIM2 inflammasomes colocalize with microtubule organizing centers and autophagosomes. Biochemical analyses showed that poly(dA-dT)-activated AIM2 inflammasomes induce autophagy and IL-1β secretion in an LC3-dependent fashion. Furthermore, depletion of EB1 decreases autophagic shedding and intracellular trafficking. …

Poly(Arginine) Derived Cancer-Targeting Peptides For The Development Of A Cancer-Targeted Gene Therapy Approach In Hepg2 Liver Cancer Cells, Stesha C. Joseph

Seton Hall University Dissertations and Theses (ETDs)

Cancer is a disease that has eluded medicinal approaches for many years and as a result new and improved therapeutic approaches are in constant demand. Although chemotherapy and radiation treatments have assisted in suppressing the growth of tumors, their poor selectivity and efficacy are major limitations for effective therapy en route towards the development of a cure for the cancer epidemic. With the mission of conquering cancer at heart, researchers have pursued a new form of cancer therapy, aptly named, a cancer targeting approach. This method revolves around the selection of a suitable biomarker, typically a cell surface receptor …

The Effect Of Maternal Aldosterone Levels On The Expression Of 11b-Hsd Isoenzymes In Normal And Hypertensive Rat Placentae, Nicole Jorissen

Journal of Undergraduate Research at Minnesota State University, Mankato

In this project, we developed a Western blotting procedure to semi-quantitate levels of 11β-HSD1 and 11β-HSD2 in whole cell extracts. Then, we applied this technique to analyze the effect of reduced maternal aldosterone levels on the expression of 11β-HSD1 and 11β-HSD2 isoenzymes in the placental tissue in both normal and hypertensive rats. These enzymes control levels of glucocorticoids which compete for aldosterone’s mineralocorticoid receptor. Overstimulation of this receptor results in hypertension. If aldosterone levels decrease, levels of the enzymes controlling active glucocorticoid concentrations might change to compensate for the lowered aldosterone levels. Decreased placental 11β-HSD2 expression could affect hypertension in …

Evaluation Of Pretreatment Methods In The Production Of Ethanol From Cattail Leaves, Kristen Krahmer, Elijah Wreh

Journal of Undergraduate Research at Minnesota State University, Mankato

Previous research in this lab indicated that cattails are a potential source of biomass for the production of cellulosic ethanol since their carbohydrate composition is comparable to that of other plants being considered for biofuel production. To further test their viability, we tested various pretreatment methods on dried cattail leaves. Before polysaccharides in plants can be enzymatically hydrolyzed to fermentable sugars, the plant material must be pretreated to render the polysaccharides accessible to the enzymes. The purpose of this project has been to compare the efficiency of sulfuric acid and ammonia pretreatment methods in preparing cattail biomass for ethanol production. …

Effects Of Individual Phenotypic Variation On Predator-Prey Relationships Of Xanthid Crabs In North Inlet Estuary, South Carolina, Benjamin J. Toscano

Theses and Dissertations

Ecological communities and the biological interactions that regulate community structure are notoriously complex. To make these systems more tractable, ecologists traditionally measure and model communities at the population level, treating individuals as functionally equivalent. While this approach has yielded tremendous insight into the factors governing communities, it remains unclear whether accounting for individual-level variation could improve our capacity to predict the responses of communities to perturbation, a major goal in the midst of unprecedented rates of environmental change.

The objective of this study was to examine the magnitude of individual-level phenotypic variation in predatory crabs (family Xanthidae), and the effects …

The Effect Of Transient Hmg-Coa Reductase And 1-Deoxy-D-Xylulose-5-Phosphate Synthase Overexpression On Terpene Production In Transgenic Tomato Fruits, Scott A. Gentry, Michael Gutensohn, Laura Henry, Natalia Dudareva

The Summer Undergraduate Research Fellowship (SURF) Symposium

Isoprenoids are secondary metabolites that control numerous plant functions including signaling, growth, photosynthesis, and membrane structure. The bioengineering of isoprenoid synthesis could produce plants with a variety of beneficial traits. Plants form isoprenoids using two different pathways, the mevalonate (MVA) pathway and the methylerithritol phosphate (MEP) pathway, which cooperate via metabolic cross-talk. Transgenic tomato lines expressing both the plastidic and cytosolic forms of the snapdragon nerolidol/linalool terpene synthase under a fruit ripening specific promoter were transiently transformed to overexpress key enzymes in the two isoprenoid pathways. Hydroxymethylglutaryl-coenzyme A reductase (HMGR) is the rate limiting enzyme in the MVA pathway that …

Electrophoresis Staining: A New Method Of Whole Mount Staining, Mitchell G. Ayers, Sarah Calve, Zhiyu Li

The Summer Undergraduate Research Fellowship (SURF) Symposium

Advances in tissue clearing techniques have allowed almost a ten-fold increase in the viewing depth of confocal microscopy. This allows for intact cellular structures to be rendered in 3D. However, viewing tissues to this depth is often limited to endogenous fluorescence as passive diffusion of antibodies via whole mount staining can take weeks. Our lab is developing a new method involving electrophoresis as a driving force that will promote active antibody binding deep into tissue, reducing the amount of time needed to stain for cellular structures. Due to the inherent charge within antibodies, they are able to be directionally forced …

Determining The Binding Between Saga Subunits And Spliceosomal Components, Peyton J. Spreacker, Rachel L. Stegeman, Vikki M. Weake

The Summer Undergraduate Research Fellowship (SURF) Symposium

Proper gene regulation is vital to the health and development of an organism. Determining the relationship between splicing, transcription, and chromatin structure is vital for understanding gene regulation as a whole. There have been previous studies linking these elements pairwise; however, no evidence exists for a direct link between all three. Recent data shows that splicing components of the U2 small nuclear ribonucleic protein (snRNP) co-purify with Spt-Ada-Gcn5-acetyltransferase (SAGA), a highly conserved transcriptional co-activator and chromatin modifier. We hypothesize that SAGA binds with splicing components through a multi-protein binding surface with certain core components based on preliminary yeast two-hybrid data. …

Development Of Electron Microscopy Analysis And Simulation Tools For Nanohub, Mingxuan Lu, Chang Wan Han, Benjamin P. Haley, Volkan Ortalan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Electron microscopy has a crucial role in the field of materials science and structural biology. Although electron microscopy gives lots of important results and findings, some additional simulations and image processing/reconstruction is required to get more information from the data that are collected from the experiments. For this purpose, researchers are using IMOD¹ and QSTEM² for electron microscopy analysis and simulation. IMOD is a set of programs used for tomographic reconstruction and 3D visualization and QSTEM is used for quantitative simulations of TEM and STEM images. However, IMOD and QSTEM are hard to install or use for beginners …

The Effect Of Docosahexaenoic Acid (Dha)-Containing Phosphatidylcholine (Pc) On Liquid-Ordered And Liquid-Disordered Coexistence, Yongwen Gu

Dissertations and Theses

Plasma membranes are essential to both the structure and function of mammalian cells. The first unifying paradigm of membrane structure, the Fluid Mosaic Model, is no longer considered adequate to describe the many non-homogeneous lipid structures that have been observed in both natural and model membranes over the past approximately thirty years. The field of membrane biophysics now appreciates that the complex mixture of different lipid species found in natural membranes produces a range of dynamic, laterally segregated, non-homogeneous structures which exist on time scales ranging from microseconds to minutes.

When sphingomyelin (SM), POPC and cholesterol are all present in …

High Level Protein Expression Slows Down Rate Of Growth Of Bacterial Broth Cultures, Saad Chaudhry, Kenechukwu Ekwemalor, Shobhit Keswani, Odutayo Odunuge

Undergraduate Research Conference

No abstract provided.

Determination Of Anions In Lanana Creek By Ion Chromatography, Tania Benavides

Undergraduate Research Conference

Abstract

Lanana Creek is one of two springs that surround Nacogdoches, TX. Lanana Creek starts southwest of Lake Naconiche, conjoining with several other bodies of water along its path, and becomes part of the Angelina River. This body of water eventually ends in the Gulf of Mexico which may contribute to the dead zone. Contaminants in water may be of small concentration; however, prolonged exposure could produce many negative effects. To prevent further contamination, the source of the contamination must be identified through testing the water for contaminants. Some possible sources of contamination may be from fertilizers and pesticides used …

Elcs In Ice: Cryo-Electron Microscopy Of Nuclear Envelope Limited Chromatin Sheets, Mikhail Eltsov, Sergey Sosnovksi, Ada L. Olins, Donald E. Olins

Pharmaceutical Sciences Faculty Posters

Nuclear Envelope-Limited Chromatin Sheets (ELCS) form during excessive interphase nuclear envelope growth in a variety of cells. ELCS appear as extended sheets within the cytoplasm connecting distant nuclear lobes. Cross-section stained images of ELCS, viewed by transmission electron microscopy, resemble a sandwich of apposed nuclear envelopes separated by ~30 nm, containing a layer of ordered chromatin fibers. EM Procedures: The ultrastructure of ELCS was compared by three different methods: 1) aldehyde fixation/dehydration/plastic embedding/sectioning and staining; 2) high-pressure freezing/freeze substitution into plastic/sectioning and staining; 3) high-pressure freezing/cryo-sectioning/cryo-electron microscopy. Human leukemic (HL-60/S4) cells were treated with retinoic acid (4 days) to induce …

Xrf Analyses Of Prehanford Orchards, Komal Rana

STAR Program Research Presentations

Subsequent to 1943, the use of Lead Arsenic was banned from the Orchards standing on the Hanford site. This use of Lead Arsenate pesticide was popular among the orchard owners and was dispersed over the site in a myriad of ways. The presence of the traces of lead and arsenic are found today, more than half a century later. Using a portable X-ray florescence analyzer (XRF), the values of lead and arsenic are evaluated while determining the efficiency of the equipment itself. Samples from different decision sites were collected, with lead arsenic values in the low, high and medium range …

Assessing A Reconciliation Ecology Approach To Suburban Landscaping: Biodiversity On A College Campus, Christopher Bouma, Emily Huizenga, David P. Warners

Student Papers and Reports

No abstract provided.

Antiviral Responses In Mouse Embryonic Stem Cells: Differential Development Of Cellular Mechanisms In Type I Interferon Production And Response, Ruoxing Wang

Dissertations

Embryonic stem cells (ESCs) have been recognized as a promising cell source for regenerative medicine. Intensive research over the past decade has led to the possibility that ESC-derived cells will be used for the treatment of human diseases. However, increasing evidence indicates that ESC-derived cells generated by the current differentiation methods are not fully functional. It is recently recognized that ESC-derived cells lack innate immunity to a wide range of infectious agents and inflammatory cytokines. When used in patients, ESC-derived cells would be placed in wounded sites that are exposed to various pathogens and inflammatory cytokines; therefore, their viability and …