Life Sciences Commons^™

Biology Department Publications: 2013, Sam Lindgren

Biology Department Bibliographies

This document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2013. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions.

Biology Department Publications: 2023, Sam Lindgren

Biology Department Bibliographies

This document is a non-comprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2023. It indexes those publications available through PubMed and Scopus, and serves as an archival record of the Department’s robust scholarly contributions.

Biology Department Publications: 2008, Sam Lindgren

Biology Department Bibliographies

This document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2008. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions.

Understanding And Addressing Statistics Anxiety, Hairui Liu

AI Assignment Library

This assignment is a critical first step in understanding the psychological barriers that students may face when learning statistics. It acknowledges the prevalence of statistics anxiety and its potential impact on academic success. The reflection is intended to be a safe space for students to express their concerns, with the ultimate goal of creating a more supportive and effective learning environment. By sharing their experiences, students contribute to the development of strategies that can help them and their peers navigate the challenges of statistics with greater confidence.

Assessing Prevalence Of Blood Parasites And Ranaviruses In Hong Kong Freshwater Turtles, Julia Leung

Lingnan Theses (MPhil & PhD)

Blood parasites and ranaviruses are pathogens that impact freshwater turtles worldwide. Given that native turtle species in Hong Kong are already at a high risk of extinction, their survival becomes even more threatened in the event of a disease outbreak. However, prevalence of these pathogens among the native population in Hong Kong remains unstudied.

In this study, I aim to (1) obtain baseline prevalence data of blood parasites and ranaviruses in Hong Kong freshwater turtles, (2) compare different methods for detecting blood parasites and ranaviruses, (3) evaluate the applicability of using blood parasites as a wildlife forensic tool, assess and …

Multi-Omics Analysis Of Nf1 Deficiency In Various Cell Types Implicates Roles Outside Of Ras For Cells And Their Microenvironment, Christian Xavier Fay

All ETDs from UAB

Neurofibromatosis type 1 is an autosomal dominant disease in which many patients develop the hallmark feature, neurofibromas, benign tumors that develop along the peripheral nerves. Currently there is no known cure for NF1, and more than 3000 germline pathogenic variants (PVs) in NF1 have been observed. The neurofibromin gene encodes the 320kDa NF1 protein which has multiple predicted functions. Its most under-stood molecular role is in binding GTP-Ras and stimulating Ras-GTPase to cleave GTP to GDP and inactivate Ras signaling. In fact, the only FDA-approved therapeutic is the MEK inhibitor selumetinib which acts downstream of Ras. NF1 also has Ras …

Biomedical Informatic Analysis Of Critical Care Outcomes & Chronic Sequelae Of Sars-Cov-2 Infection, Michael John Patton

All ETDs from UAB

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of coronavirus disease 2019 (COVID-19), resulted in an unprecedented loss of life over the past 4 years and has left an indelible mark on nearly every facet of medical care. Unlike pandemics of the 20th century or earlier, global adoption of electronic medical records (EMR) in the decade prior to the COVID-19 pandemic provided the bedrock for real-time healthcare innovation guided by biomedical informatics research. Mirroring the needs of healthcare providers, early informatics studies focused on identifying biomarkers and risk factors for severe presentations of COVID-19 and their …

Elucidating The Role Of Glut3 In Glioblastoma Invasion And The Tumor Microenvironment, Sarah Elizabeth Williford

All ETDs from UAB

GBM is characterized by aggressive growth and therapy resistance, with a median survival of 14 months despite treatment. Brain tumor initiating cells (BTICs), as a subset of stem-like GBM cells known for their invasiveness, therapy resistance, and immune evasion. BTICs have increased GLUT3 expression, which is correlated with poor patient prognosis. This study identifies a novel role of GLUT3 in GBM invasion, distinct from its canonical function in glucose uptake and glycolysis, as well as a mechanism by which GLUT3 contained in exosomes promotes monocyte migration. Our data show that blocking phosphorylation of GLUT3 at T492, abolishes its pro-invasive phenotype, …

Computational Approaches To Identify Circular Rnas In Parkinson's Disease, Lisa Shrestha

All ETDs from UAB

Parkinson’s Disease (PD) is the second most common neurodegenerative disease, affecting approximately a million individuals in the United States. Despite its high prevalence, PD is generally diagnosed at a progressed stage after the manifestation of characteristic motor symptoms (bradykinesia, tremor, rigidity, etc.). Hence, it is imperative to understand the underlying molecular mechanisms involved in the progression of PD at an early stage. Several non-coding RNAs have emerged as important regulators in several key cellular processes, among which circular RNAs' role has not been studied well enough. Here, we explore the changes in the expression of circRNAs with respect to the …

Uncovering The Contribution Of Desmoplakin Isoforms To Desmosome Structure And Function, Krishna Patel

All ETDs from UAB

UNCOVERING THE CONTRIBUTION OF DESMOPLAKIN ISOFORMS TO DESMOSOME STRUCTURE AND FUNCTION KRISHNA PATEL MULTIDISCIPLINARY BIOMEDICAL SCIENCE ABSTRACT Desmosomes are cell-cell junctions that maintain the integrity of tissues that experience significant mechanical stress, such as the skin and heart. Desmosomal plaque proteins are connected to the intermediate filaments by desmoplakin (DP), and genetic variants in DP are associated with several skin and heart pathologies, including erythrokeratodermia and arrhythmogenic cardiomyopathy. DP contains three domains: an N-terminal plakin head, a central rod, and an intermediate filament-binding C-terminal tail. Furthermore, DP has three splice isoforms (DPI, DPIa, and DPII) that differ only in the …

Biochemical Characterization Of Rna Polymerases Across The Domains Of Life, Stephanie Lois Cooper

All ETDs from UAB

RNA polymerases perform the essential function of RNA synthesis from a DNA template. This process, known as transcription, is critical for all living species and a key point for regulation of gene expression. The function of RNA polymerases allow species from all domains of life to not only survive, but also respond to environmental changes such as heat and nutrient deprivation. In biological taxonomy, the highest classification is domain. The three domains are Eukarya, Bacteria, and Archaea. The domain Eukarya contains all eukaryotic organisms, ranging from yeast, to plants, to metazoans. Bacteria and Archaea are both prokaryotic domains, the species …

Investigating Theoretical Constructs Of Social Cognitive Theory As Working Mechanisms Of Web-Based Diet And Physical Activity Interventions Among Cancer Survivors, Harleen Kaur

All ETDs from UAB

Cancer survivors are a high-risk population with poor lifestyle behaviors and a higher prevalence of obesity, necessitating effective lifestyle interventions to promote weight management, consumption of a healthy diet, and increased physical activity. Recently, lifestyle interventions have evolved to web-based platforms that are easily accessible. However, there is a need to understand how web-based lifestyle interventions work, and who they work best for to maximize impact. Thus, the objective of this dissertation was to evaluate social cognitive theory (SCT) mechanisms (i.e., self-efficacy, social support, and perceived barriers) through which two web-based lifestyle interventions, DUET and AMPLIFY, mediate changes in diet, …

Drug Resistance Mechanisms Of Trichomonas Vaginalis, Keonte Graves

All ETDs from UAB

Trichomonas vaginalis is a facultative anaerobic parasitic protozoan and the main causative agent of the most common non-viral sexually transmitted infection, trichomoniasis. Trichomoniasis affects both men and women but is more commonly observed in women. The majority of infections are asymptomatic, but those with symptomatic infections often experience malodorous and discolored vaginal discharge, pruritis, dysuria, and/or dyspareunia. T. vaginalis infections have been associated with multiple adverse health outcomes including an increased risk of acquiring HIV and other STIs, infertility, adverse birth outcomes, and cervical cancer. The only current FDA-approved treatments come from the 5-nitroimidazole class of drugs (metronidazole, tinidazole, and …

Identifying Links Between Cardiovascular Disease And Insomnia Using Human Genetics And Drosophila Models, Farah Abou Daya

All ETDs from UAB

Cardiovascular disease (CVD) is the leading cause of death worldwide and its in- cidence remains on the rise globally. In addition to other factors, CVD is associated with insomnia, which is the most common sleep disorder. It is defined as the persistent diffi- culty in initiating and/or maintaining sleep. Insomnia symptoms were found to double the risk of incident CVD. However, the specific shared causal pathways remain poorly un- derstood, making it difficult to identify new therapeutic targets that ameliorate insomnia- related CVD risks. Recently, genome-wide association studies (GWAS) identified genet- ic loci significantly associated with insomnia symptoms. Here, we …

The Effects Of Acute Beetroot Juice Intake On Glycemic And Blood Pressure Responses When Controlling For Medication In Individuals With Type 2 Diabetes, Andrew Tyler

All ETDs from UAB

The prevalence of cardiometabolic diseases has continued to rise within the United. Physical activity and poor dietary choices are two factors that are known to contribute to the rise in cardiometabolic diseases. Thus, it is critical to identify strategies that may mitigate the negative impact from these behaviors. Several recent studies have shown that consumption of dietary inorganic nitrate (diNO3) may improve vascular health and glucose regulation in animal models and some human studies. However, the improvements in glucose regulation have yet to be corroborated in humans with type 2 diabetes (T2D). Thus, the purpose of this study was to …

Elucidating The Nanoscale Architecture Of The Desmosome, William F. Dean

All ETDs from UAB

Desmosomes are intercellular anchoring junctions that are crucial for maintaining the mechanical integrity of tissues routinely subjected to large forces, such as epithelia and cardiac muscle. Adhesion in desmosomes is mediated by a specialized class of transmembrane glycoproteins known as the desmosomal cadherins (DCs). Defects in desmosomal adhesion are associated with severe disease of the heart and skin and are frequently linked to mutations in the DCs. It is therefore important to understand the relationship between DC architecture and desmosome function. Accordingly, several groups have attempted to elucidate DC architecture—primarily using electron tomography (ET). However, ET studies of the desmosome …

Use Of Molecular Dynamics Simulations To Characterize Structural Interactions Of Protein And Drug In Antiviral Drug Discovery, Caitlin Joan Smith

All ETDs from UAB

Since 2019, the novel coronavirus SARS-CoV-2 the etiological cause of the COVID-19 pandemic has led researchers and physicians to look for effective antiviral treatments as interventions in mitigating COVID-19 disease. The severity of the disease and the limitations of current treatments have led to antiviral drug research beyond currently approved antiviral drugs. Many antivirals exist and are currently approved by the Food and Drug Administration (FDA) for other viral illnesses, yet currently only remdesivir and nirmatrelvir/ritonivir are approved for COVID-19 (October 2020, May 2023, respectively), while molnupiravir is still under emergency FDA use authorization [1, 2, 3]. Here, we have …

A Histone Methyltransferase Contributes To Treatment Resistance In Npm1c Aml, Neha Srinivas

All ETDs from UAB

Acute myeloid leukemia (AML) is a blood cancer marked by the rapid growth of abnormal myeloid cells, driven by various genetic mutations. AML accounts for approximately 1% of all cancers and presents complicated prognosis and treatment. Menin inhibitors have shown potential in targeting AML. However, resistance to these inhibitors presents a significant clinical obstacle, as patients treated with menin inhibitors are increasingly developing resistance to the treatment. Using CRISPR-Cas9 mediated screening, we identified an epigenetic regulator contributing to resistance against menin inhibitors in AML. Utilizing knockout (KO) models of the epigenetic regulator in-vitro, ex-vivo, and in-vivo, we observed a growth …

Investigating The Impacts Of Staphylococcus Aureus Small Colony Variant Infection In The Cystic Fibrosis Rat Lung, Gretchen E. Bollar

All ETDs from UAB

Cystic fibrosis (CF) is an autosomal-recessive genetic disease characterized by recurrent and chronic airway infections. Staphylococcus aureus is currently the most common organism isolated from the CF lung, but its role as a pathogen has been historically difficult to characterize due to a broad range of genetic diversity and subtypes seen across infectious strains. Small colony variants (SCVs) are a subpopulation of S. aureus marked by slow growth rate and impaired metabolism that have been associated with worse respiratory outcomes in people with CF (pwCF). SCVs also exhibit altered colony morphology and can confound the results of traditional diagnostic assays, …

Investigating The Role Of The Static And Hyperviscous Mucus Defect On The Development Of Bacterial Infection In The Cystic Fibrosis Rat, Mikayla Murphree-Terry

All ETDs from UAB

INVESTIGATING THE ROLE OF THE STATIC AND HYPERVISCOUS MUCUS DEFECT ON THE DEVELOPMENT OF BACTERIAL INFECTION IN THE CYSTIC FIBROSIS RAT MIKAYLA MURPHREE-TERRY GRADUATE BIOMEDICAL SCIENCES - MICROBIOLOGY ABSTRACT Cystic fibrosis (CF) is a genetic disease caused by mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in dysfunctional CFTR. In the lungs, CFTR dysfunction results in dehydrated mucus that is adherent to epithelia. In the gut, thick mucus can mix with feces to form an obstruction, known as distal intestinal obstruction syndrome (DIOS). Additionally, CF mucus has a higher percentage of solids. The main solid component of …

Impact Of Exercise Modalities On Quality Of Life And Performance Metrics In Breast Cancer Survivors, Shannon Anderson

All ETDs from UAB

Background: Advancements in research have caused the survival rate for breast cancer to increase making the population of breast cancer survivors (BCS) much larger than in previous decades. Breast cancer can have a lasting impression on a person’s quality of life (QoL) even after completing treatment. Breast cancer is also associated with various side effects as a result of treatment as well as comorbidities. Different types of exercise and physical activity have been shown to improve QoL as well as other health outcomes. Purpose: This study aimed to compare the effects of aerobic exercise versus flexibility and toning exercise on …

Combination Of 64/67cu Theranostics And Immunotherapy Targeting Fibroblast Activation Protein In Triple Negative Breast Cancer, Fnu Sharmila Sridhar

All ETDs from UAB

Triple negative breast cancer (TNBC) makes up 10-20% of breast cancer cases. Even with advancements in science, TNBC is treatment resistant due to the lack of any type of hormonal receptors on the cell surface making it difficult for targeted hormonal therapy. New research avenues have led to studies of the Tumor-microenvironment (TME) in detail. TME is a complex network of stromal cells, extracellular matrix (ECM) and cancer associated fibroblasts (CAFs) with pro-tumorigenic properties and plays a major role in tumor growth. Fibroblast activation protein (FAP) is a marker of CAF and promotes ECM remodeling through several pathways and has …

Biologic Evaluation Of 64cu & 67cu As Potential Theranostic Agents For Cancer Radiotherapy, Lakshmi Madhusoodanan

All ETDs from UAB

Immunotherapy has become a mainstay in the treatment of several types of cancer, with the potential to induce durable remission, albeit in a limited percentage of patients. More recently, radiopharmaceuticals have gained recognition in cancer treatment due to their ability to localize within cancer cells and deliver radiation, reducing adverse effects precisely. Cancer radiotherapy has the potential to synergize with immunotherapy due to its induction of immunogenic cell death (ICD), which results in distinct cellular injuries such as the formation of single-strand breaks (SSBs) and double-stranded breaks (DSBs), disruption of mitochondrial integrity, and the excessive generation of reactive oxygen species …

Determination Of Readthrough Susceptibility Among Different Schwann Cell Lines Carrying Nonsense Mutations, Trushali Vansadia

All ETDs from UAB

Neurofibromatosis Type 1 (NF1) is a genetic disorder that affects the nervous system through the formation of tumors or neurofibromas. Encoded by the NF1 gene, neurofibromin functions as a tumor suppressor by converting active GTP-Ras to inactive GDP-Ras. 20% of NF1 patients carry a genomic nonsense mutation, which generates a premature termination codon (PTC) in the NF1 mRNA, leading to the formation of a truncated neurofibromin protein. Termination at PTCs can be suppressed by the incorporation of an amino acid at the site of the PTC, also known as readthrough. Readthrough results in continued translation elongation downstream of the PTC …

Disruption Of Cochlear Development By Murine Cytomegalovirus Infection And Therapeutic Approaches That Prevent Hearing Loss, Matthew Smith

All ETDs from UAB

Human cytomegalovirus (HCMV) is a ubiquitous virus, infecting greater than 50% of most populations worldwide. Although rarely causing symptomatic infection in immunocompetent individuals, HCMV can cause life-threatening and severe end-organ disease in immunocompromised hosts including the developing fetus. HCMV can cross the placenta and is the most common viral infection of the developing fetus. Most newborn infants with congenital HCMV infection (cCMV) exhibit no clinical evidence of infection; however, up to 15% will develop long term neurodevelopmental sequelae including sensorineural hearing loss (SNHL). No prophylactic vaccines or effective antiviral treatments exist for cCMV infection, which may in part be secondary …

Biology Department Publications: 2021, Sam Lindgren

Biology Department Bibliographies

This document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2021. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions.

A Case Demonstration Of The Open Health Natural Language Processing Toolkit From The National Covid-19 Cohort Collaborative And The Researching Covid To Enhance Recovery Programs For A Natural Language Processing System For Covid-19 Or Postacute Sequelae Of Sars Cov-2 Infection: Algorithm Development And Validation, Sijia Liu, David A Hanauer, Daniel R Harris, Ramakanth Kavuluru, Rui Zhang, Karthik Natarajan, Nishanth P Pavinkurve, Janos Hajagos, Sritha Rajupet, Veena Lingam, Mary Saltz, Corey Elowsky, Richard A Moffitt, Farrukh M Koraishy, Matvey B Palchuk, Jordan Donovan, Lora Lingrey, Garo Stone-Derhagopian, Robert T Miller, Andrew E Williams, Peter J Leese, Paul I Kovach, Emily R Pfaff, Mikhail Zemmel, Robert D Pates, Nick Guthe, Melissa A Haendel, Christopher G Chute, Hongfang Liu, National Covid Cohort Collaborative, Recover Initiative

Faculty, Staff and Student Publications

BACKGROUND: A wealth of clinically relevant information is only obtainable within unstructured clinical narratives, leading to great interest in clinical natural language processing (NLP). While a multitude of approaches to NLP exist, current algorithm development approaches have limitations that can slow the development process. These limitations are exacerbated when the task is emergent, as is the case currently for NLP extraction of signs and symptoms of COVID-19 and postacute sequelae of SARS-CoV-2 infection (PASC).

OBJECTIVE: This study aims to highlight the current limitations of existing NLP algorithm development approaches that are exacerbated by NLP tasks surrounding emergent clinical concepts and …

Aars Online: A Collaborative Database On The Structure, Function, And Evolution Of The Aminoacyl-Trna Synthetases, Jordan Douglas, Haissi Cui, John J. Perona, Oscar Vargas-Rodriguez, Henna Tyynismaa, Claudia Alvarez Carreño, Jiqiang Ling, Lluís Ribas De Pouplana, Xiang-Lei Yang, Michael Ibba, Hubert Becker, Frédéric Fischer, Marie Sissler, Charles W. Carter Jr., Peter Wills

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like …

A Citizen Science Approach To Assess Management Of An Invasive Species, William Lester, Emily Kraus

Journal of Extension

Citizen science allows for broadening the scope of research by increasing data points and geographical scale. Here, Institute A and Institute B show that citizens utilized various outreach platforms to increase their knowledge of an invasive species the air potato vine, Dioscorea bulbifera, and its biological control agent the air potato beetle, Lilioceris cheni. Citizen scientists also contributed data on the distribution and establishment of the beetle, and reported on behavior change, and attitude toward the project. Valuable lessons were learned in designing surveys and training the citizens in order to increase the quality of their contributions.

The Kras Mutational Spectrum And Its Clinical Implications In Pancreatic Cancer, Luigi Perelli, Giannicola Genovese, Giulio F Draetta

Faculty, Staff and Student Publications

In this issue of Cancer Cell, McIntyre et al. show that specific mutations in the KRAS proto-oncogene shape clinical progression of pancreatic ductal adenocarcinoma (PDAC). Importantly, they find that the KRASG12R mutation is enriched in early-stage PDAC, and it is characterized by distinctly activated molecular programs.