Digital Commons Network^™

Doxorubicin-Induced Transcriptome Meets Interactome: Identification Of New Drug Targets, Hi̇lal Taymaz-Ni̇kerel

Turkish Journal of Biology

The working mechanism of the chemotherapeutic drug doxorubicin, which is frequently used in cancer treatment, its effects on cell metabolism, and pathways activated solely by doxorubicin are not fully known. Understanding these principles is important both in improving existing therapies and in finding new drug targets. Here, I describe a systems-biology approach to find a generalizable working principle for doxorubicin by superimposition of human interactome over gene datasets commonly expressed among various cancer types. The common ?in at least two different diseases?transcriptional response of distinctive cancer cell lines to doxorubicin was reflected via 199 significantly and differentially expressed genes, mostly …

Screening Ocean Samples From Georgia For The Presence Of Msx And Dermo Using Pcr And Qpcr Methods, Olivia Michelle Williams

Honors Theses and Capstones

This Senior Thesis project aimed to be able to screen samples that came in from a PhD student in Georgia for the presence of two oyster diseases, MSX and Dermo. This study was done using PCR followed by visualizing on E-gels for initial presence of disease. These were then followed by qPCR and visualization on Criterion gels. These Criterion gels were able to be analyzed in order to calculate the pg/uL of MSX and Dermo in the original ocean samples. Since the samples were sent in over the course of February-August ‘21 the presence over time was also able to …

Mortality In Interspecific Hybrids Of Nasonia Vitripennis And Nasonia Giraulti, Bonnie Cobb

College of Graduate Studies: Theses & Dissertations

Nasonia is a parasitoid wasp genus that serves as an emerging model for studying speciation due to an incompatibility between nuclear and mitochondrial genomes between sister taxa. Short generation times, easy rearing in a lab setting, producing large amounts of progeny, and whole genome sequencing make Nasonia is an excellent candidate for studying incomplete reproductive isolation. Nasonia have five chromosomes and exhibit haplo-diploid sex determination in which fertilized eggs develop into diploid females and unfertilized eggs develop into haploid males. Recessive phenotypes are hidden in diploid females but are laid bare in haploid males as there is no interaction between …

Validation Of Edna Metabarcoding : A Comparison To Traditional Survey Methods In Ozark Streams, Veronica Marian Lee

Masters Theses

Environmental DNA (eDNA) sampling provides a method for assessing fish communities that has potential as a supplement to traditional sampling methods due to its ability to save time as well as its non-invasive nature. This is a method in which from just one sample, eDNA from multiple individual species are able to be sequenced in tandem and the resulting reads identified to describe a community. In order to evaluate this technique and its efficacy for monitoring fish community diversity, we collected water samples alongside surveys performed by the Missouri Department of Conservation sampling program in summers 2020-21. DNA were extracted …

Analyzing The Viability Of Direct Pcr For Use In Conjunction With Cyanoacrylate Enhanced Fingerprints, Coral M. Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Efficient methods for DNA analysis are desperately needed in laboratories due to the influx in DNA analysis requests. The current DNA processing methods are costly, time consuming, and involve multiple tube changes, increasing the risk of contamination. However, the use of direct PCR can simplify the DNA analysis process by eliminating the extraction, purification and quantitation steps. Presently, the FBI Quality Assurance Standard 9.4 requires all evidence samples to be quantitated. As a result, the direct PCR method of DNA processing cannot be implemented on evidence samples at this time. Direct PCR presents the opportunity to provide efficient DNA analysis, …

Cancer Testis Antigen Pasd1 Expression And Immunogenicity In Human Colorectal Cancer And Polyps, Nur Fazilah Sukor, Azyani Yahaya, Ismail Sagap, Rahman Jamal, Nor Adzimah Johdi

Turkish Journal of Biology

Colorectal cancer (CRC) is a malignant tumor arising from a human inner colon lining that may spread to other organs such as the liver and lungs. Per ARNT Sim domain containing 1 (PASD1) is a cancer-testis antigen expressed in cancers including CRC but not in normal tissues except for normal testes. This study aims to study PASD1 protein as a potential target for CRC immunotherapy. A total of 90 CRC and polyps tissue samples were investigated for PASD1 RNA and protein expression using a real-time polymerase chain reaction and immunohistochemical staining, respectively. Matched patients? peripheral blood mononuclear cells were pulsed …

Xpo1 As A Therapeutic Target In Gastric Cancer, Rachel Sexton

Wayne State University Dissertations

Gastric cancer is a leading cause of cancer related deaths worldwide. Throughout the world, there is around one million new diagnosed cases per year and only an approximate 25% survival rate. This disease is highly heterogeneous, chemotherapy resistant and deadly. Currently there is no gold standard for care but rather it is physician’s choice. Various chemotherapeutic agents can be used including microtubule inhibitors, DNA damaging agents and anti-metabolite compounds. We have found that nuclear export protein 1 (XPO1) is overexpressed in gastric cancer patients and cell lines compared to normal gastric tissues leading to an aggressive cancerous phenotype that is …

A Serological Analysis Of Sars-Cov-2 Infection In The Obstetric Population, Sophia Rose

CMC Senior Theses

In December 2019, the surfacing and spread of a novel coronavirus, SARS-CoV-2, resulted in the global COVID-19 pandemic. As a viral antigen, SARS-CoV-2 poses a particular threat to the obstetric population due to physiological and immunological changes that women face during pregnancy. While recent studies have found that SARS-CoV-2 may have better clinical outcomes as compared to other betacoronaviruses, adverse pregnancy events such as ICU admission, preeclampsia, and/or preterm birth have been associated with COVID-19. Progress has been made in better understanding the pathophysiology of SARS-CoV-2 in pregnancy, but there is still much to be known about the interaction …

Physician Assisted Dying (Pad): An Investigation Into The Mechanistic Action Of Opioid, Benzodiazepine, And Barbiturate Administration As An Alternative Measure To Forgoing Life Sustaining Treatment And Aggressive Palliation., Jordana Chanel Deighton

CMC Senior Theses

Whilst modern medicine has increased longevity, the rise in life expectancy has brought about new struggles, namely that of aging and age related disease. Thus, humanity has been presented with a new problem: at what point is death preferable to aggressive life-prolonging treatment in the face of inevitable death? And if so, what right do individuals have to control the circumstances of their death? In the West, traditionally, individuals who seek to end their own lives in the face of terminal illness opt for forgoing artificial hydration and nutrition. Driven by an increase in desire for autonomous dignified death, a …

Effects Of Drought On Habitat Quality For Native Bees In Residential Gardens Of Claremont, Ca, Max Proctor

CMC Senior Theses

Over 1,500 of the 4000 bee species found in North America inhabit California. Native bees are declining however, largely due to climate change and agricultural intensification. Previous research shows that cities can sustain diverse bee communities, due to the diversity of ornamental flowers. Urban green space represents an opportunity for native bee conservation. Residential gardens provide lots of green space and are urban pollinator hotspots. Managing yards for increased floral resources and nesting habitat can benefit native bee communities. Turfgrass provides few floral or nesting resources and negatively correlates with bee diversity. The 2011-2017 California drought caused many homeowners to …

College Of Natural Sciences Newsletter, January 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 1

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Outreach in Harrisburg, SD
Page 4 Geography Alumni Named Among 'Highly Cited Researchers', 53rd Annual Geography Convention
Page 5 Geography Convention Speakers, Brookings/SDSU Day
Page 6 Media Coverage of Natural Sciences
Page 7 Open PRAIRIE Data
Page 8 Fall 2021 Dean's List
Page 9 Fall 2021 Dean's List, cont.

A Review Of Virus-Vectored Vaccines: Current Production Methods, Uses, Issues, And Future Perspectives, Jaden Marks

Biology and Microbiology Graduate Students Plan B Research Projects

Viral vector vaccines have recently risen to the forefront of vaccinology, but there are multiple factors that must be addressed before they achieve widespread approval and use. The concept of using viruses as vectors is not new, and numerous attempts to create vaccines that utilize virus vectors have been made in the past 25 years. Despite this, only one viral vector vaccine has gained full approval by the FDA. The goal of this review is to provide a comprehensive overview of the types of viral vector vaccines, production and purification methods, current and future viral vector vaccines, the issues and …

Review Of A Chimeric Hemagglutinin-Based Influenza Vaccine Approach, Whitney Muck

Biology and Microbiology Graduate Students Plan B Research Projects

Influenza virus has affected human populations for centuries, causing an acute respiratory effect on the body. Even with scientific advancements in vaccine research, there are still serious limitations to the influenza vaccine. Varying strains and the constant recombination of the influenza virus has caused annual influenza circulation to be difficult to predict. The ongoing 40 race to develop a more efficient vaccine to broadly protect against the variety of influenza strains remains a public health priority. Many strategies have been studied to improve the current vaccine. The use of a chimeric hemagglutinin-based vaccine is in the first stages of human …

Chimeric Antigen Receptor T-Cell Therapy In Cancer, Brian Stahl

Biology and Microbiology Graduate Students Plan B Research Projects

The development of immune-checkpoint-inhibitors (ICIs) has led to promising advancements in the treatment of patients with cancers, leading with the use of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) as a negative regulator of T cell activation in the mid-1990s. With the discovery of two ligands for program cell death protein-1 (PD-1) and promising checkpoint blockades in 2010, this sparked a cascade of hallmark immunotherapy drug patents, focusing on the mechanism of anti PD-1 and anti PD-L1 antibody inhibitors. Since then, chimeric antigen receptor (CAR)-engineered T (CAR-T) cells have emerged into the immuno-oncologic scene for treatment of hematological malignancies. These genetically …

A Review Of T1d: Prevalence, Current Therapies, And Cellular Therapies For The Future, Fahd Nazir

Biology and Microbiology Graduate Students Plan B Research Projects

Type 1 diabetes (T1D) is a chronic autoimmune disease that is characterized by the destruction of pancreatic β-cells and therefore, creating an insulin deficiency within the body. A deficiency of insulin within the body disrupts homeostatic glucose control leading to hyperglycemia and therefore, the need for exogenous insulin. Global incidence of T1D has been increasing for several decades and if current trajectory trends continue, incidence could double in the next year. In addition, diabetes is the seventh leading cause of death in the United States. Current therapies for the treatment of T1D include insulin injections, insulin-pump therapy, pancreatic transplant, and …

Alzheimer’S Disease: An Overview And Current Phase 3 Disease-Modifying Biologic Treatments, Haley Jahnke

Biology and Microbiology Graduate Students Plan B Research Projects

Alzheimer’s Disease (AD) is a degenerative brain disease caused by cell damage leading to brain changes such as amyloid plaques and neurofibrillary tangles. Alois Alzheimer was a clinical psychiatrist and neuroanatomist in Germany who first discovered Alzheimer’s Disease through microscopic viewing of Auguste D’s brain. Through more research following Dr. Alzheimer’s death, they began to stage AD. The six stages are: pre-clinical, mild, moderate, moderately severe, severe, and very severe. The current treatments approved by the FDA work to slow the progression of AD, rather than modify the disease. There are currently three Disease-Modifying Biologic clinical-trial drugs on the market …

Oral Microbiome And Its Effect On Respiratory Disease, Cole Pudwill

Biology and Microbiology Graduate Students Plan B Research Projects

The oral microbiome is composed of several different types of bacteria that can affect how our body operates. There are over 700 different bacteria living in our mouths. These bacteria can be helpful and harmful to our bodies, but they are synergistic in a way. There are several factors such as age, diet, smoking, and oral care that affect bacterial makeup. When there 10 is a significant difference, our immune system becomes weakened and respiratory disease set in. The immune system then works to return the microbiome back to homeostasis. When this fails, the diseases become chronic. Thus, the oral …

Myrmecochorous Plants And Their Ant Seed Dispersers Through Successional Stages In Temperate Cove Forests, Robert Warren, Mary Schultz, James Costa, Beverly Collins, Mark Bradford

Biology Faculty Datasets

Anthropogenic disturbance can decrease woodland diversity in the species-rich herbaceous layer of eastern deciduous forests, and ant-dispersed (myrmecochorous) plants may be particularly affected due to their limited ability to re-colonize secondary forests. Consequently, we predicted that myrmecochorous plants and their keystone seed-dispersing ants would increase with time since last disturbance, as reflected by young, middle or mature forest successional stage. Specifically, we hypothesized that myrmecochore abundance and richness would be relatively lowest in the youngest forests, moderate in middle-aged forests and highest in mature forests. We also hypothesized that experimentally introducing ant bait in a regular pattern, as might be …

Laurentian Great Lakes Warming Threatens Northern Fruit Belt Refugia, Robert Warren

Biology Faculty Datasets

Climate refugia are anomalous ‘pockets’ of spatially or temporally disjunct environmental conditions that buffer distinct flora and fauna against prevailing climatic conditions. Physiographic landscape features, such as large water bodies, can create these micro-to-macro-scale terrestrial habitats, such as the prevailing westerly winds across the Laurentian Great Lakes that create relatively cooler leeward conditions in spring and relatively warmer leeward conditions in autumn. The leeward Great Lakes climate effects create a refugia (popularly known as a ‘fruit belt’) favorable for fruit-bearing trees and shrubs. This fruit belt refugia owes its existence to seasonal inversions whereby spring cooling prevents early flower budding …

The Relevance Of Pedigrees In The Conservation Genomics Era, Stephanie J. Galla, Julie A. Heath

Biology Faculty Publications and Presentations

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic …

Chemosensitivity Of Locus Coeruleus Neurons Decreases With Postnatal Development, Yasmeen Samar

Browse all Theses and Dissertations

The locus coeruleus (LC) is a chemosensory area partially responsible for ventilation. Control over ventilation relies on inter-network communication via chemical and electrical synapses and chemosensitivity to CO2/pH. As the LC develops, it’s neural control over ventilation changes. This study investigates the chemosensitivity of the locus coeruleus over the course of development in postnatal rats. We hypothesize that 1) the CO2 sensitivity of LC neurons is highest at birth and declines with development 2) LC neurons are intrinsically chemosensitive and this chemosensitivity does not decrease with development and 3) the presence of gap junctions is highest at the beginning of …

An Analysis On Various Treatment Options For Triple-Negative Breast Cancer, Elisheva Dusowitz

The Science Journal of the Lander College of Arts and Sciences

Triple-Negative Breast Cancer (TNBC) is a highly invasive, under-researched subtype of Breast Cancer. Patients lack receptors for the protein Human Epidermal Growth Factor, and both estrogen and progesterone. This negatively impacts treatment by making all hormone-sensitive treatments unavailable to TNBC patients. Since the effectiveness of various options has remained understudied, the prognosis remains poor. This paper attempts to analyze and compare the effectiveness of various treatment options. Because TNBC is very aggressive, the standard approach is to jump in with harsh surgical procedures, including mastectomies and lumpectomies. This analysis finds that more aggressive treatment may not be necessary to treat …

Full Issue: Volume 15, Number 2, Spring 2022

The Science Journal of the Lander College of Arts and Sciences

Complete .pdf file of Volume 15, Number 2 of The Science Journal of the Lander College of Arts and Sciences. Published Spring 2022.

Cardiovascular Disease - Is A Whole Food Plant-Based Diet The Answer?, Shalom Katz

The Science Journal of the Lander College of Arts and Sciences

Objective: To determine if a whole food plant-based diet can prevent and cure cardiovascular disease. Results: People on whole food plant-based diets exhibit extremely low levels of plasma LDL. Another risk factor for developing atherosclerosis, is inhibited production of nitric oxide, which is vital for healthy blood flow. One of the main inhibitors of nitric oxide production is asymmetric dimethyl-l-arginine (ADMA). An inverse relationship was found between dietary fat and ADMA levels. The diets with the best results were the diets where oil intake was reduced to a minimum. Clinically, people who went on whole food plant-based diets had their …

Osteoporosis: A Comprehensive Review, Eliyahu Greenberg

The Science Journal of the Lander College of Arts and Sciences

Osteoporosis is a disease of the skeleton that becomes more common with advanced age, especially in postmenopausal women. Osteoporosis increases the risk of fractures, thereby reducing the quality of life for those who suffer from it. Due to the aging population, direct costs resulting from osteoporosis are projected to reach upward of $25 billion per year by 2025. The main pharmaceuticals primarily target osteoclasts. Exercise may be an effective method of preventing osteoporosis, although more research needs to be done. More research should be conducted to explore potential ways to enhance osteoblastic activity as a method to treat and/or reverse …

Does Exercise Make You Smarter?, Avi Derkhidam

The Science Journal of the Lander College of Arts and Sciences

Physical exercise has been applauded for its beneficial cardiovascular and mental effects for decades. Recently, researchers have begun to study exercise from a different perspective, focusing on the positive relationship between exercise and cognition. One area of cognition highlighted in association with exercise is its positive impact on executive function. Executive function refers to the collection of neurocognitive processes involved in goal-directed problem-solving. Improved levels of cognitive function have been found to impact significant achievements throughout life. Because of this, the development, improvement, and preservation of these functions are essential. While research has proven a correlation between exercise and improved …

Effective Treatments For Ductal Carcinoma In Situ, Moshe Picciotto

The Science Journal of the Lander College of Arts and Sciences

Ductal Carcinoma In Situ (DCIS) is the most common form of breast cancer wherein its progression interrupts the hormonal receptors and genetic variation of one’s DNA. DCIS can be caused by hereditary means, or through mutations. Fortunately, due to the many different modes of contraction, there is a plethora of treatments available in the forms of mastectomy, radiation, chemotherapeutic drugs, and PARP inhibitors, each with their own mechanism of action to combat the tumor and any metastatic effects the cancer may have on the body. This paper analyzes the cancer’s mechanism of action upon the body and the positive effects …

It's A Small World After All: Insights, Interferences, And Implications Of In Situ Chlorophyll Fluorescence Monitoring In Estuaries, James Silas Tanner

UNF Graduate Theses and Dissertations

Concentrations of the photosynthetic pigment chlorophyll a are used as a proxy for phytoplankton biomass by estuarine scientists to study eutrophication, food web dynamics, and harmful algal blooms. Coastal managers use chlorophyll as an indicator of nutrient pollution and for assessments to meet Clean Water Act standards. Chlorophyll a, as measured in the laboratory by extraction from monthly discrete water samples, is a core component of the National Estuarine Research Reserve (NERR) System-Wide Monitoring Program (SWMP). Field-deployable sensors based on the excitation and emission spectra of in situ chlorophyll have not been incorporated into SWMP to date because past …

Inferring Phylogenetic Relationships Using The Smith-Waterman Algorithm And Hierarchical Clustering, Rafael Hidalgo, Anthony Devito, Nesreen Salah, Aparna S. Varde, Robert W. Meredith

Department of Biology Faculty Scholarship and Creative Works

All biological species undergo change over time due to the evolutionary process. These changes can occur rapidly and unpredictably. Due to their high potential to spread quickly, it is critical to be able to monitor changes and detect viral variants. Phylogenetic trees serve as good methods to study evolutionary relationships. Complex big data in biomedicine is plentiful in regards to viral data. In this paper, we analyze phylogenetic trees with reference to viruses and conduct dynamic programming using the Smith-Waterman algorithm, followed by hierarchical clustering. This methodology constitutes an intelligent approach for data mining, paving the way for examining variations …

Influences Of Grazing On Habitat Characteristics, Avian Community Composition And Nesting Bird Abundance Within Cheyenne Bottoms, Ks, Kirsten Granstrom-Arndt

Master's Theses or Doctor of Nursing Practice

Cheyenne Bottoms is a 41,000-acre prairie-marsh ecosystem in central Kansas. Approximately 8,000 acres of mixed grassland are dedicated for the conservation of bird populations, but little is known about the status of bird communities within these areas. This study took place within grassland areas of Cheyenne Bottoms from May – July 2021. I investigated bird community composition, relative abundance of frequently observed bird species, vegetative characteristics, and similarity of sites across different grazing intensities (continuous, rotational, and non-grazed). The four most common bird species observed were dickcissel (Spiza americana), grasshopper sparrow (Ammodramus savannarum), meadowlark species ( …