Molecular Biology Commons^™

Antiestrogens As Bone Protective Therapeutics For Estrogen Receptor-Positive Breast Cancer In The Presence Of Osteoporosis, Faith E. Parker, Emily K. Zboril, David C. Boyd, Rachel Myrick, J. Chuck Harrell

Undergraduate Research Posters

Breast cancer (BC) is one of the most significant causes of mortality among women and the second leading cause of cancer death in women. The estrogen receptor (ER) is a key oncogenic driver in the majority of breast cancer. ER+ BC is the most common molecular subtype of BC. Management of ER+ breast cancer varies depending on menopausal status. For premenopausal women, the goal is to suppress estradiol production from the ovaries with surgical oophorectomy and/or aromatase inhibitors. In postmenopausal women, endocrine therapy (ET) serves to suppress estradiol production from sources other than the ovaries. During the menopausal transition, estradiol …

Development Of A Cure In Principles Of Cell And Molecular Biology, Heather Seitz

Sabbatical Projects

This project presentation highlights the work done during sabbatical to develop an authentic research experience into BIOL135 Principles of Cell and Molecular Biology. The sabbatical allowed for development time but further work was done to measure impact and outcomes for future implementation.

The Impact Of Mutations In The Arabidopsis Apetela (Ap3) Gene, Hazel R. Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

The purpose of this research is to understand the molecular functioning of the Arabidopsis thaliana Apetela (Ap3) gene. We created mutations in two sites of the gene, AP3-3 and AP3-5. These are predicted to change AP3 protein structure, which may result in a mutated flower. Analyzing the effects of new mutations allows an understanding of protein formation both in plants and humans.

Nsp3 Protein-Portion Interaction Of Sars-Cov-2 Using Two Yeast-Hybrid System, Ghadeer Jassem Zakareya

Selected Full-Text Master Theses 2021-

The NSP3 protein of SARS-CoV-2 plays a crucial role in the virus-host interaction during infection. This thesis explores the protein-protein interactions between NSP3 and host factors, shedding light on their significance in viral replication and pathogenesis. NSP3 is known to interact with various host proteins involved in key cellular processes, including innate immune response modulation, RNA processing and protein degradation pathways. Understanding these interactions is essential for developing targeted therapeutic strategies against COVID-19. Application of The Matchmaker GAL4Two-Hybrid Systems, to isolate the NSP3 protein and study the interactions, elucidating the NSP3 host protein interactions and attempting to identify potential key …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Effects Of Doxorubicin On Extracellular Matrix Regulation In Primary Cardiac Fibroblasts From Mice, Cameron Skaggs, Steve Nick, Conner Patricelli, Laura Bond, Kali Woods, Luke Woodbury, Julia Thom Oxford, Xinzhu Pu

Biomedical Research Institute Publications and Presentations

Objective Doxorubicin (DOX) is a highly effective chemotherapeutic used to treat many adult and pediatric cancers. However, its use is limited due to a dose-dependent cardiotoxicity, which can lead to lethal cardiomyopathy. In contrast to the extensive research efforts on toxic effects of DOX in cardiomyocytes, its effects and mechanisms on cardiac extracellular matrix (ECM) homeostasis and remodeling are poorly understood. In this study, we examined the potential effects of DOX on cardiac ECM to further our mechanistic understanding of DOX-induced cardiotoxicity.

Results DOX-induced significant down-regulation of several ECM related genes in primary cardiac fibroblasts, including Adamts1, Adamts5, Col4a1, Col4a2, …

In Vitro Characterization Of Fluorogenic Chemical Tools To Study Human Carboxylesterases (Cess), Taylor Parish Spidle

Undergraduate Honors Theses

Human carboxylesterases (CESs) are enzymes that are responsible for the metabolism of many important pharmaceuticals. Although CESs are key players in the hydrolysis of many ester-containing drugs, they remain understudied. Our group hypothesizes that this is primarily because there are few methods capable of reporting activity in live cells. Here, I report a new series of fluorogenic chemical tools to study the CES activity of one of the two major CESs in humans, CES1, in live cells. MCP-Me, MCP-Et, and MCP-iPr utilize the same carbonate group of a previously developed chemical tool in our group, FCP-1, and work to mimic …

A Novel Role Of Lipin1 In The Regulation Of Expression And Function Of Nnos, Ayat Azzam

Browse all Theses and Dissertations

Duchenne muscular dystrophy (DMD) is a severe and progressive muscular dystrophy that develops in the skeletal muscles because of mutations in the dystrophin gene. Dystrophin stabilizes sarcolemma and assembles neuronal nitric oxide synthase (nNOS) into the dystrophin-associated protein complex on the sarcolemma. The absence of dystrophin triggers the delocalization of nNOS and contributes to the misregulation of muscle development, blood flow, muscle fatigue, and inflammation. Lipin1 was reduced in the skeletal muscles of patients with DMD and the mdx mouse model of DMD. In this study, we explored the role of lipin1 in the regulation of nNOS expression and function. …

Development And Analysis Of Next-Generation Polymeric And Bio-Ceramic Based Orthopedic Scaffolds By Advanced Manufacturing Techniques, Sudeep K. Gummadi

ETD Archive

Gliomas express mutant isocitrate dehydrogenases producing excessive amounts of D 2-hydroxyglutarate (D2HG) and releasing some of it into the environment. The immune surveillance is reduced as a result, however, the mechanisms behind lymphocyte suppression by the D2HG stereoisomer remain unknown. I incubated Jurkat T cells with D2HG at concentrations present within and surrounding gliomas, or its obverse L2HG stereoisomer, and quantified 2HG isomers within washed cells by TSPC derivatization with stable isotope-labeled D2HG and L2HG internal standards, HPLC separation, and mass spectrometry. D2HG was found in quiescent cells in double the amount of L2HG. External D2HG or L2HG increased the …

Bci Validation: Yfiler Plus Kit Validation, Chloe Koon

Honors Projects

In order to have access and use the Combined DNA Index System (CODIS), it is required by the Federal Bureau of Investigation's Quality Assurance Standards (FBI-QAS) for Forensic DNA Units to complete comprehensive validation studies on all equipment, materials, and methods used in the process of DNA analysis. This study continues validation previous done within the Ohio Bureau of Criminal Investigation (BCI). YFiler Plus is a DNA amplification kit that is used in cases where it is most useful to examine only male DNA profile(s) within a sample by amplifying loci only on the Y-Chromosome. Components of this study include …

Genomic Instability At A Polypurine/Polypyrimidine Repeat Sequence, Nathen S. Zavada

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Microsatellite repeat sequences have been shown to induce replication stalling, fork collapse, double-strand breaks (DSBs), and possibly stimulate break-induced replication. In this study we use a dual-fluorescent HeLa model that is designed to monitor recombination at an ectopic site through use of flow cytometry and inverse PCR with a microsatellite in the lagging strand for DNA synthesis. To test the stability of the 78 bp polypurine/pyrimidine repeat from the PDK1 locus, we subjected cells to replication stress drugs designed to induce DSBs and measure break-induced replication (BIR). The study revealed that polypurine repeat cells undergo endogenous stress contributing to instability …

Bioactive Recombinant Human Oncostatin M For Nmr-Based Screening In Drug Discovery, Olga A. Mass, Joseph Tuccinardi, Luke Woodbury, Cody L. Wolf, Bri Grantham, Kelsey Holdaway, Xinzhu Pu, Matthew D. King, Don L. Warner, Cheryl L. Jorcyk, Lisa R. Warner

Biomedical Research Institute Publications and Presentations

Oncostatin M (OSM) is a pleiotropic, interleukin-6 family inflammatory cytokine that plays an important role in inflammatory diseases, including inflammatory bowel disease, rheumatoid arthritis, and cancer progression and metastasis. Recently, elevated OSM levels have been found in the serum of COVID-19 patients in intensive care units. Multiple anti-OSM therapeutics have been investigated, but to date no OSM small molecule inhibitors are clinically available. To pursue a high-throughput screening and structure-based drug discovery strategy to design a small molecule inhibitor of OSM, milligram quantities of highly pure, bioactive OSM are required. Here, we developed a reliable protocol to produce highly pure …

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Microsatellites And Their Association With Break Induced Replication, French J. Damewood Iv

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To study microsatellites instability and their repair pathways a dual fluorescent (DF2) and selectable (ganciclovir sensitive/ thymidine kinase (TK) expressing) cell system was assayed using replication fork stalling agents hydroxyurea and telomestatin. These cell lines carried ectopically integrated microsatellites derived from the Dystrophia Myotonica Protein Kinase (DMPK) gene ((CTG)102 microsatellite), or an 88 bp polypurine/ polypyrimidine (Pu/Py) repeat from the PKD-1 locus, inserted into a FLP recombinase target site. These microsatellites form non-B DNA structures in -vivo and in-vitro causing replication fork stalling and double strand breaks. DF2 myc (CTG)102 -TK cells treated with hydroxyurea were assayed for mutagenesis of …

Microsatellites And Their Association With Break Induced Replication, French J. Damewood Iv

Browse all Theses and Dissertations

To study microsatellites instability and their repair pathways a dual fluorescent (DF2) and selectable (ganciclovir sensitive/ thymidine kinase (TK) expressing) cell system was assayed using replication fork stalling agents hydroxyurea and telomestatin. These cell lines carried ectopically integrated microsatellites derived from the Dystrophia Myotonica Protein Kinase (DMPK) gene ((CTG)102 microsatellite), or an 88 bp polypurine/ polypyrimidine (Pu/Py) repeat from the PKD-1 locus, inserted into a FLP recombinase target site. These microsatellites form non-B DNA structures in -vivo and in-vitro causing replication fork stalling and double strand breaks. DF2 myc (CTG)102 -TK cells treated with hydroxyurea were assayed for mutagenesis of …

Investigation Of Multiphasic 3d-Bioplotted Scaffolds For Site-Specific Chondrogenic And Osteogenic Differentiation Of Human Adipose-Derived Stem Cells For Osteochondral Tissue Engineering Applications, Julia T. Oxford

Biomedical Research Institute Publications and Presentations

Osteoarthritis is a degenerative joint disease that limits mobility of the affected joint due to the degradation of articular cartilage and subchondral bone. The limited regenerative capacity of cartilage presents significant challenges when attempting to repair or reverse the effects of cartilage degradation. Tissue engineered medical products are a promising alternative to treat osteochondral degeneration due to their potential to integrate into the patient's existing tissue. The goal of this study was to create a scaffold that would induce site-specific osteogenic and chondrogenic differentiation of human adipose-derived stem cells (hASC) to generate a full osteochondral implant. Scaffolds were fabricated using …

High Expression Of Osm And Il-6 Are Associated With Decreased Breast Cancer Survival: Synergistic Induction Of Il-6 Secretion By Osm And Il-1Β, Ken Tawara, Hannah Scott, Jacqueline Emathinger, Cody Wolf, Dollie Lajoie, Danielle Hedeen, Laura Bond, Cheryl Jorcyk

Biomedical Research Institute Publications and Presentations

Chronic inflammation has been recognized as a risk factor for the development and maintenance of malignant disease. Cytokines such as interleukin-6 (IL-6), oncostatin M (OSM), and interleukin-1 beta (IL-1β) promote the development of both acute and chronic inflammation while promoting in vitro metrics of breast cancer metastasis. However, anti-IL-6 and anti-IL-1β therapeutics have not yielded significant results against solid tumors in clinical trials. Here we show that these three cytokines are interrelated in expression. Using the Curtis TCGA™ dataset, we have determined that there is a correlation between expression levels of OSM, IL-6, and IL-1β and reduced breast cancer patient …

Erk3 Negatively Regulates The Il-6/Stat3 Signaling Via Socs3, Astha Shakya

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Mitogen activated protein kinases (MAPKs) are Ser/Thr kinases that relay the extracellular signal into intracellular responses and regulate several biological responses. They are classified into conventional MAPKs and atypical MAPKs. Extracellular signal regulated kinase 3 (ERK3) is an atypical MAPK that has a single phospho-acceptor site (Ser 189) in its activation motif instead of the canonical Thr-Xaa-Tyr (TXY) motif of conventional MAPK like ERK1/2. ERK3 comprises of a unique C terminal tail and a central C34 domain that further distinguishes it from ERK1/2. Moreover, compared to ERK1/2, much less is known about the upstream activators and the downstream targets of …

Extracellular Matrix In Development And Disease, Julia Thom Oxford, Jonathon C. Reeck, Makenna J. Hardy

Biomedical Research Institute Publications and Presentations

The evolution of multicellular metazoan organisms was marked by the inclusion of an extracellular matrix (ECM), a multicomponent, proteinaceous network between cells that contributes to the spatial arrangement of cells and the resulting tissue organization. The development of an ECM that provides support in larger organisms may have represented an advantage in the face of selection pressure for the evolution of the ECM.

Development Of A Biomarker Panel For Identifying Stressed Marine Mammals, Laura Pujade

University of the Pacific Theses and Dissertations

Increasing anthropogenic disturbance in marine ecosystems such as fishing, oil-drilling, and noise pollution can have detrimental effects on the reproduction and survival of apex predators such as marine mammals. Stress activates the hypothalamic-pituitary-adrenal (HPA) axis, resulting in increased circulating glucocorticoid (GCs) hormones, which alter expression of target genes encoding metabolic enzymes and other mediators of stress. Prolonged HPA axis stimulation may increase catabolism of nutrient stores and suppress immune and reproductive functions, impacting the fitness of marine mammals. GCs measurements are used to identify wild animals experiencing stress. However, these measurements may not be sensitive enough to distinguish between an …

Lipin1 Regulates Skeletal Muscle Differentiation Through The Pkc/Hdac5/Mef2c:Myod -Mediated Pathway, Abdulrahman M. Jama

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Our previous characterization of global lipin1-deficient (fld) mice demonstrated that lipin1 played a novel role in skeletal muscle (SM) regeneration. The clinical relevance of lipin1 has been observed in patients with lipin1 null mutations where they exhibited severe rhabdomyolysis with aggregated and dysfunctional mitochondria. Lipin1 is a key gene that plays an important role in lipid biosynthesis and metabolism. It has dual functions as it contains a phosphatase activity that converts phosphatidic acid (PA) to diacylglycerol (DAG), the penultimate step in triglycerides (TAG) biosynthesis as well as transcriptional co-activator function. In the cytosol and ER, lipin1 carries out its lipid …

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.

Serum Proteins Enhance Dispersion Stability And Influence The Cytotoxicity And Dosimetry Of Zno Nanoparticles In Suspension And Adherent Cancer Cell Models, Catherine B. Anders, Jordan J. Chess, Denise G. Wingett, Alex Punnoose

Biomedical Research Institute Publications and Presentations

Agglomeration and sedimentation of nanoparticles (NPs) within biological solutions is a major limitation in their use in many downstream applications. It has been proposed that serum proteins associate with the NP surface to form a protein corona that limits agglomeration and sedimentation. Here, we investigate the effect of fetal bovine serum (FBS) proteins on the dispersion stability, dosimetry, and NP-induced cytotoxicity of cationic zinc oxide nanoparticles (nZnO) synthesized via forced hydrolysis with a core size of 10 nm. Two different in vitro cell culture models, suspension and adherent, were evaluated by comparing a phosphate buffered saline (PBS) nZnO dispersion (nZnO/PBS) …

Wintering Bald Eagle Count Trends In The Conterminous United States, 1986-2010, Wade L. Eakle, Laura Bond, Mark R. Fuller, Richard A. Fischer, Karen Steenhof

Biomedical Research Institute Publications and Presentations

We analyzed counts from the annual Midwinter Bald Eagle Survey to examine state, regional, and national trends in counts of wintering Bald Eagles (Haliaeetus leucocephalus) within the conterminous 48 United States from 1986 to 2010. Using hierarchical mixed model methods, we report trends in counts from 11 729 surveys along 844 routes in 44 states. Nationwide Bald Eagle counts increased 0.6% per yr over the 25-yr period, compared to an estimate of 1.9% per yr from 1986 to 2000. Trend estimates for Bald Eagles were significant (P ≤ 0.05) and positive in the northeastern and northwestern U.S. …

The Effect Of Osm On Mc3t3-E1 Osteoblastic Cells In Simulated Microgravity With Radiation, Jake Goyden, Ken Tawara, Danielle Hedeen, Jeffrey S. Willey, Julia Thom Oxford, Cheryl L. Jorcyk

Biomedical Research Institute Publications and Presentations

Bone deterioration is a challenge in long-term spaceflight with significant connections to patients experiencing disuse bone loss. Prolonged unloading and radiation exposure, defining characteristics of space travel, have both been associated with changes in inflammatory signaling via IL-6 class cytokines in bone. While there is also evidence for perturbed IL-6 class signaling in spaceflight, there has been scant examination of the connections between microgravity, radiation, and inflammatory stimuli in bone. Our lab and others have shown that the IL-6 class cytokine oncostatin M (OSM) is an important regulator of bone remodeling. We hypothesize that simulated microgravity alters osteoblast OSM signaling, …

A Model Of How Different Biology Experts Explain Molecular And Cellular Mechanisms, Caleb M. Trujillo, Trevor R. Anderson, Nancy J. Pelaez

PIBERG Publications

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular …

Modeling Atp-Binding Cassette G2 (Abcg2) Substrate Specificity, Raghav D. Acharya, Aurijit Sarkar, Glen E. Kellogg

Undergraduate Research Posters

How well can we predict efflux by ATP-binding cassette G2?

It is estimated that there will be about 1.6 million new cases of cancer and half a million cancer deaths in the US during 2015.ATP-binding cassette (ABC) efflux transporters such as ABCG2 are overexpressed in chemotherapy-resistant cancer cells. Anticancer drugs are prone to efflux by these transporters. Being able to identify drugs that are effluxed is of great interest in drug discovery.The current arsenal of methods used to detect efflux are not easily adaptable to high throughput formats and are limited in scope, making experimental analysis an expensive prospect. Hence, …

Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton

Honors Scholar Theses

The flu virus was investigated to find a common recognition domain to which an antibody against human-infected viruses can bind. If such a target site is structurally and electrostaticly conserved or invariant, only a single antibody would be required to attack the virus in all cases. The sequence of one of the viral surface proteins contains 24 amino acids that do not vary through mutation. However, these amino acids are neither contiguous in sequence or in space, and the ones that are associated with each other are not readily accessible to an antibody. They do provide a first impression of …

Biology And Ecology Of Glyphosate-Resistant Giant Ragweed, Kabelo Segobye

Open Access Theses

Giant ragweed (Ambrosia trifida L.) is a competitive annual plant found in disturbed landscapes and is the most troublesome weed in Indiana and the US Corn Belt. It is one of the most common and problematic weeds in corn and soybean production. The introduction of herbicide glyphosate, N-(phosphonomethyl) glycine in early 1970's provided farmers with a better and low-cost tool to control weeds. The use of glyphosate drastically increased after the development of glyphosate resistant agronomic crops in 1996 and was use as a post-emergence selective herbicide. This led to overreliance and repeated use of glyphosate for weed control especially …

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …