Cell and Developmental Biology Commons^™

The Slit-Binding Ig1 Domain Is Required For Multiple Axon Guidance Activities Of Drosophila Robo2, Lafreda J. Howard, Marie C. Reichert, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. Robo receptors signal midline repulsion in response to Slit ligands, which bind to the N-terminal Ig1 domain in most family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 signal Slit-dependent midline repulsion, while Robo2 also regulates the medial-lateral position of longitudinal axon pathways and acts non-autonomously to promote midline crossing of commissural axons. While Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2's other activities are also Slit-dependent. To determine which of Robo2's axon guidance roles …

Identification Of Phenotypic Defects In The Zinc Finger Transcription Factor Ztf-29, Trae Dunn

Symposium of Student Scholars

Aging and many aging-associated diseases such as Alzheimer’s disease and cancer are characterized by a progressive decline in physiological functions and a decline in the ability to respond to stress. The underlying causes for many aging-associated diseases are unknown. Identifying genes that control normal aging will advance our understanding of the molecular changes that underlie the aging process and might help treat age-associated diseases. In order to get a better understanding of the molecular mechanisms behind these diseases, we utilize the nematode Caenorhabditis elegans as a model organism to examine defects in physiology and aging.

The human PRDM genes code …

Temperature Changes Seen In Lower Extremities After Cpn Local Anesthetic Block, Lora Asberry

Symposium of Student Scholars

Many older patients often suffer from walking issues such as Drop Foot. Drop Foot is caused by the malfunction of nerves in the foot, resulting in the loss of control of the front foot muscle. Within all of our patients, there has been a common fibular palsy, caused by the entrapment of the peroneal nerve. Due to this, they cannot lift up their foot. Some cases are permanent, while others are temporary. In the temporary cases, we have indicated a Phoenix Sign. The Phoenix Sign indicates that a nerve, presumed to be dead, has the capability to be recessed back …

Complimenting A Chlamydomonas Reinhardtii Mutation Using Cell Penetrating Peptides, Matthew Mckenzie

Symposium of Student Scholars

Complimenting a Chlamydomonas reinhardtii Mutation Using Cell Penetrating Peptides

Matthew McKenzie and Jennifer L. Cooper

Chlamydomonas reinhardtii is a photosynthetic model organism most notable for its easily manipulatable genetics. C. reinhardtii uses flagella to swim and optimize its growth conditions in the light. We plan to use cell penetrating peptides (CPPs) to compliment C. reinhardtii that is affected with the IFT46 mutation. Cell penetrating peptides are short peptides that can move across a cell membrane. The novel CPP that we are using is called TaT-CaM. It consists of the trans-activator of transcription (TaT) and the calmodulin domain (CaM) that binds …

The Role Of Proneural Transcription Factor Ngn-1/Neurogenin During Caenorhabditis Elegans Embryonic Development, Michaela Diane Crego

Symposium of Student Scholars

Accurate control of neuronal cell identification and movement is crucial to embryonic development. Defects in this process can lead to neurodevelopmental disorders, creating an imperative for further study. The transcription factor neurogenin is required for multiple neurodevelopmental processes during vertebrate embryonic development and mutations in this gene underpin multiple human neurological disorders. Despite this, little is known about how this gene controls nervous system development and function. Neurogenin is deeply conserved across phyla. As such, we can investigate neurogenin function in simple systems such as the nematode Caenorhabditis elegans, which has a close ortholog of neurogenin, ngn-1. Previous work in …

Understanding Molecular Mechanisms Controlling Muscle Type Specificity, Geoffrey Andrews

Symposium of Student Scholars

Skeletal muscle is a compound tissue made of individual muscle fibers. To accommodate everyday activities, such as walking, running, jumping, etc., our muscles are composed of several types of fibers, each expressing a unique set of muscle genes. Interestingly, early in development all muscles in the body are made of the same fiber type, but later they acquire different properties. The mechanism of muscle fiber diversity is not clear, although it may be critical in treating muscle-related diseases or enhancing physical performance. The goal of my project is to identify critical genes and possible mechanisms that control the fate of …

Determining Malignancy: Can Mammogram Results Help Predict The Diagnosis Of Breast Tumors?, Taylor Behrens

Symposium of Student Scholars

Even with advancements in treatment and preventative care, breast cancer remains an epidemic claiming more than 40,000 American male and female lives each year. The mammogram dataset that I am analyzing was initially complied in the early 1990s by a team from the University of Wisconsin - Madison. Past research diagnoses breast cancer from fine-needle aspirates. My research focuses on predicting whether we can determine breast cancer diagnoses without the use of invasive procedures and, in particular, whether we can predict breast cancer based on mammogram data. Do measures of gray-scale texture, radius, concavity, perimeter, compactness, area, and smoothness of …

Growth, Maturation, And Weight Status: Insights From A Longitudinal Cohort Of Nebraska Youth, John William Masker

Kinesiology and Sport Sciences Theses, Dissertations, and Student Creative Activity

Pediatric obesity continues to be a major public health concern in the United States, with well-known short-term and long-term consequences. In efforts to combat pediatric obesity and identify children at high-risk for potential health problems, physicians and health professionals widely practice screening and classifying weight status using age-and-sex-specific body mass index (BMI) percentiles. However, some studies suggest the use of BMI for establishing weight status in relation to health risk in youth is problematic, especially during the period of the adolescent growth spurt. More importantly, maturation-related misclassification may result in overestimations of overweight prevalence among early-maturing youth, and underestimations of …

Vitamin D Modulates Rett Syndrome Phenotypes And Underlying Cellular Pathways In An Mecp2-Mutant Mouse Model, Mayara De Cassia Ribeiro

Dissertations - ALL

Rett syndrome (RTT) is a progressive and severe X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MECP2. There is currently no effective treatment for RTT. Female RTT patients develop relatively normally during the first 6-18 months of life, after which they undergo a period of rapid regression, losing the ability to talk, walk and purposefully use their hands, in addition to suffering from deceleration of head growth, and onset of repetitive, autistic behaviors. RTT symptoms can be partially reversed by the re-expression of Mecp2 in adult mice, suggesting the potential for post-symptomatic therapeutic intervention. Among the many dysfunctions …

Association Of Oral Microbiota With Lung Cancer Risk In A Low-Income Population In The Southeastern Usa, Jiajun Shi, Yaohua Yang, Hua Xie, Xiaofei Wang, Jie Wu, Jirong Long, Regina Courtney, Xiao-Ou Shu, Wei Zheng, William J. Blot, Qiuyin Cai

Biology Faculty Research

Purpose

Oral microbiome plays an important role in oral health and systemic diseases, including cancer. We aimed to prospectively investigate the association of oral microbiome with lung cancer risk.

Methods

We analyzed 156 incident lung cancer cases (73 European Americans and 83 African Americans) and 156 individually matched controls nested within the Southern Community Cohort Study. Oral microbiota were assessed using 16S rRNA gene sequencing in pre-diagnostic mouth rinse samples. Paired t test and the permutational multivariate analysis of variance test were used to evaluate lung cancer risk association with alpha diversity or beta diversity, respectively. Conditional logistic regression models …

Tail-Anchored Protein Insertion Under Er Stress Conditions: Calcium Is Key, Matthew Jordan, Malaiyalam Mariappan

The Yale Undergraduate Research Journal

Tail-anchored (TA) membrane proteins are critical for protein translocation, intracellular trafficking, and programmed cell death. TA proteins contain hydrophobic transmembrane domains and traverse through the cytosol to post-translationally insert into cellular membranes. It is unclear how this post-translational insertion is affected by Endoplasmic Reticulum (ER) stress. Here, we find that TA protein insertion is significantly reduced with ER stress inducer thapsigargin (Tg), a calcium pump inhibitor that blocks the import of calcium into the ER causing ER stress, but not when treated with other ER stress inducers. Interestingly, out data suggests that increased calcium in the cytosol may decrease TA …

Investigating Factors That Affect Hiv-1 Capsid Stability, Max Mao, Joshua Temple

The Yale Undergraduate Research Journal

TKH HIV caSVLd, a SURWHLQ VKHOO cRPSRVHd RI PRQRPHULc XQLWV RI CA, IRUPV a IXOOHUHQH cRQH WKaW SURWHcWV HIV¶V YLUaO JHQRPH aQd enzymes during infection. I am interested in elucidating the factors that influence stability of the capsid shell and capturing the structural interactions between HIV capsid, host restriction factors, and small molecules using biochemical and structural biology techniques. HIV capsid shell was broken down and purified into hexamer and pentamer units for in vitro study. Structural assays were performed using X-ray crystallography and biochemical analysis was performed using pelleting assays. By understanding capsid structure with factors that confer stability, …

Altering Sensory Learning By Chronic Inactivation Of Vip Interneurons, Christopher Alba, Hannah Selwyn, Katie Ferguson, Jessica Cardin

The Yale Undergraduate Research Journal

Vasoactive intestinal polypeptide-expressing interneurons (VIP-INs) play a key role in the regulation of cortical circuits and are implicated in perceptual function and psychiatric disease. However, their role in perceptual augmentation and learning remains understudied. We performed chronic, localized ablation of VIP-INs in the primary visual cortex of adult mice using caspase-induced apoptosis to better understand how VIP-INs contribute to visual perception and the ability to learn a visual detection task. We find that chronic VIP-IN ablation does not affect naïve performance on a full-screen visual contrast detection task. However, mice with suppressed levels of VIP-INs achieved their final expert state …

A Comparison Of The Evolution, Structure, And Function Of Sars-Cov And Sars-Cov-2 Spike Proteins, Tai Michaels

The Yale Undergraduate Research Journal

As the COVID-19 pandemic has developed into the largest pandemic of the twenty-first century, it has become apparent that this disease, caused by the SARS-CoV-2 virus, is unlike anything the modern world has faced before. Not only has the disease infected more than 16 million people worldwide, but its rapid spread has drawn global attention to the gaps in our understanding of its pathogenesis and the development of vaccines and treatments. One of the most important topics of research in the disease is the viral spike (S) protein which facilitates binding and entering host cells and plays a key role …

High-Spatial-Resolution Transcriptomic Map Of The Mouse Lymph Node Microenvironment Using Deterministic Barcoding, Archibald Enninful, Yang Liu, Rong Fan

The Yale Undergraduate Research Journal

Spatial transcriptomics is an emerging approach which characterizes gene expression profiles for a more nuanced understanding of biological processes at a tissue level. This offers significant advantages over traditional omics which require the digestion of tissues and subsequent isolation of cells, during which the spatial information is completely lost. Lymph nodes are an integral part of the immune system and an in-depth analysis of its spatial organization will provide useful insights which can be applicable in the development of novel immunotherapies. In this study, the mouse lymph node is characterized using the newly developed microfluidic-based approach, Deterministic Barcoding in Tissue …

A Systematic Review Of Datasets That Can Help Elucidate Relationships Among Gene Expression, Race, And Immunohistochemistry-Defined Subtypes In Breast Cancer., Ifeanyichukwu O. Nwosu, Stephen Piccolo

Faculty Publications

Scholarly requirements have led to a massive increase of transcriptomic data in the public domain, with millions of samples available for secondary research. We identified gene-expression datasets representing 10,214 breast-cancer patients in public databases. We focused on datasets that included patient metadata on race and/or immunohistochemistry (IHC) profiling of the ER, PR, and HER-2 proteins. This review provides a summary of these datasets and describes findings from 32 research articles associated with the datasets. These studies have helped to elucidate relationships between IHC, race, and/or treatment options, as well as relationships between IHC status and the breast-cancer intrinsic subtypes. We …

Innate Immune Activation By Checkpoint Inhibition In Human Patient-Derived Lung Cancer Tissues, Teresa W. M. Fan, Richard M. Higashi, Huan Song, Saeed Daneshmandi, Angela L. Mahan, Matthew S. Purdom, Therese J. Bocklage, Thomas A. Pittman, Daheng He, Chi Wang, Andrew N. Lane

Center for Environmental and Systems Biochemistry Faculty Publications

Although Pembrolizumab-based immunotherapy has significantly improved lung cancer patient survival, many patients show variable efficacy and resistance development. A better understanding of the drug’s action is needed to improve patient outcomes. Functional heterogeneity of the tumor microenvironment (TME) is crucial to modulating drug resistance; understanding of individual patients’ TME that impacts drug response is hampered by lack of appropriate models. Lung organotypic tissue slice cultures (OTC) with patients’ native TME procured from primary and brain-metastasized (BM) non-small cell lung cancer (NSCLC) patients were treated with Pembrolizumab and/or beta-glucan (WGP, an innate immune activator). Metabolic tracing with ¹³C₆-Glc/ …

Indicators Of Senescence And Their Relationship With The Antioxidant Response Element In Ovarian Cancer Cells—Toward A More Encompassing View Of Enzyme Activity Levels In Cells, Shaniqua Analycia Hayes

LSU Doctoral Dissertations

Enzymes and other related proteins are promising targets as biomarkers for cancer diagnostics, and it is therefore important to be able to quantify intracellular enzyme activity levels, not just presence of enzyme. Thus, there is a great need for the development of methods that offer spatiotemporal quantification of intracellular enzyme activity levels in respiring 2- and 3-dimensional cultures or their sample-processed variants. Previous studies have demonstrated that ß-gal is upregulated in senescence and in select ovarian cancers, and its expression/activity is upregulated when cells are under oxidative stress conditions. To that end, the primary goal of this work was to …

Threshold Concentration And Random Collision Determine The Growth Of The Huntingtin Inclusion From A Stable Core, Sen Pei, Theresa C. Swayne, Jeffrey F. Morris, Lesley Emtage

Publications and Research

The processes underlying formation and growth of unfolded protein inclusions are relevant to neurodegenerative diseases but poorly characterized in living cells. In S. cerevisiae, inclusions formed by mutant huntingtin (mHtt) have some characteristics of biomolecular condensates but the physical nature and growth mechanisms of inclusion bodies remain unclear. We have probed the relationship between concentration and inclusion growth in vivo and find that growth of mHtt inclusions in living cells is triggered at a cytoplasmic threshold concentration, while reduction in cytoplasmic mHtt causes inclusions to shrink. The growth rate is consistent with incorporation of new material through collision and coalescence. …

Human Ipsc Tissue-Engineered Cartilage For Disease Modeling Of Skeletal Dysplasia-Causing Trpv4 Mutations, Amanda R. Dicks

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cartilage is essential to joint development and function. However, there is a variety of cartilage diseases, ranging from developmental (e.g., skeletal dysplasias) to degenerative (e.g., arthritis), in which treatments and therapeutics are lacking. For example, specific point mutations in the ion channel transient receptor potential vanilloid 4 (TRPV4) prevent proper joint development, leading to mild brachyolmia and severe, neonatally lethal metatropic dysplasia. Tissue-engineered cartilage offers an opportunity to elucidate the underlying mechanisms of these cartilage diseases for the development of treatments. Human induced pluripotent stem cells (hiPSCs) are an improved cell source option for cartilage tissue engineering given their minimal …

Utilizing Proteolysis-Targeting Chimeras To Target The Transcriptional Cyclin-Dependent Kinases 9 And 12, Hannah King

Theses & Dissertations

Cyclin-dependent kinases (CDKs) are a family of serine-threonine kinases involved in various cellular functions, such as regulating the cell cycle and gene transcription. CDK9, a transcriptional CDK, regulates highly expressed enhancer-associated oncogenic transcription factors, including the oncogene Myc. CDK9 is responsible for the transcription and stabilization of Myc; consequently, it was a validated target for pancreatic cancer treatment.

As such, we developed a panel of aminopyrazole based proteolysis targeting chimera where we identified PROTAC 2 as a selective degrader of CDK9 (DC₅₀ = 158 ± 6 nM). PROTAC 2 was capable of cereblon mediated proteasomal degradation of CDK9 while …

Gene Expression Profiling Of Mapk Pathway Inhibitor Resistance In Cutaneous Melanoma: Can Bioinformatics Be Used To Select Better Melanoma Cell Lines?, Stephen Luebker

Theses & Dissertations

Melanoma is the deadliest form of skin cancer, and incidence has continued to increase. Half of all melanomas have a BRAF V600E mutation and respond to MAPK pathway inhibitors, including BRAF inhibitor therapy or BRAF/MEK inhibitor combination therapy, but nearly all patients develop treatment resistance. Melanoma cell lines produce variable results as models of MAPK pathway inhibitor resistance. To better understand how the genomic similarity of a melanoma cell line to patient-derived tumors affects resistance mechanisms, differences in DNA mutations and copy-number alterations were compared between melanoma cell lines profiled by the Cancer Cell Line Encyclopedia and cutaneous melanoma tumors …

Fgfr4 Glycosylation And Processing In Cholangiocarcinoma Promote Cancer Signaling, Andrew J. Phillips

Theses & Dissertations

Cholangiocarcinoma is a cancer of cholangiocytes, or epithelial cells lining the biliary tract. It is associated with a poor prognosis and additional therapeutic treatments are needed to help patients affected by this disease. Fibroblast growth factor receptor 4 (FGFR4) is receptor tyrosine kinase that is involved in various physiologic and pathologic processes. TCGA analysis of thirty different tumor types showed the highest FGFR4 mRNA levels in cholangiocarcinoma. At the protein level, FGFR4 was observed in the majority of cholangiocarcinomas screened and, higher levels were associated with a poorer prognosis. FGFR4 is an N-linked glycosylated receptor tyrosine kinase that we show …

Characterization Of Metabolic Gene Expression In The Raw 264.7 Monocyte Cell Line, Lauren Macaisa

PANDION: The Osprey Journal of Research and Ideas

Immune cells undergo changes in gene expression and metabolism when activated by a foreign molecule. Although the changes are short-lived in response to an acute infection, they persist in disorders with underlying chronic inflammation. To understand how changes in gene expression relate to changes in metabolism, the expression of metabolic transporter proteins, was analyzed in response to chronic inflammation in a mouse monocyte cell line. Specifically, Glucose Transporter-1 (GLUT1), Monocarboxylate Transporter-1 (MCT1), Monocarboxylate Transporter-4 (MCT4), and Glutamate Aspartate Transporter (GLAST) were analyzed, and it was hypothesized that all the transporters would increase in expression in response to a prolonged inflammatory …

Associations Of Hair Dye And Relaxer Use With Breast Tumor Clinicopathologic Features: Findings From The Women’S Circle Of Health Study, Rohan Rao, Jasmine A. Mcdonald, Emily Barrett, Patricia Greenberg, Dede K. Teteh, Susanne B. Montgomery, Bo Qin, Yong Lin, Chi-Chen Hong, Christine B. Ambrosone, Kitaw Demissie, Elisa V. Bandera, Adana A.M. Llanos

Health Sciences and Kinesiology Faculty Articles

Background

Building upon our earlier findings of significant associations between hair dye and relaxer use with increased breast cancer risk, we evaluated associations of select characteristics of use with breast tumor clinicopathology.

Methods

Using multivariable-adjusted models we examined the associations of interest in a case-only study of 2998 women with breast cancer, overall and stratified by race and estrogen receptor (ER) status, addressing multiple comparisons using Bonferroni correction.

Results

Compared to salon application of permanent hair dye, home kit and combination application (both salon and home kit application) were associated with increased odds of poorly differentiated tumors in the overall …

Decoding The Roles Of Astrocytes And Hedgehog Signaling In Medulloblastoma, Terence Teixeira Duarte, Silvia Aparecida Teixeira, Luis Gonzalez-Reyes, Rui Manuel Reis

Publications and Research

The molecular evolution of medulloblastoma is more complex than previously imagined, as emerging evidence suggests that multiple interactions between the tumor cells and components of the tumor microenvironment (TME) are important for tumor promotion and progression. The identification of several molecular networks within the TME, which interact with tumoral cells, has provided new clues to understand the tumorigenic roles of many TME components as well as potential therapeutic targets. In this review, we discuss the most recent studies regarding the roles of astrocytes in supporting sonic hedgehog (SHH) subgroup medulloblastoma (MB) and provide an overview of MB progression through SHH …

Trem2 Is Thyroid Hormone Regulated Making The Trem2 Pathway Druggable With Ligands For Thyroid Hormone Receptor., Skylar J. Ferrara, Priya Chaudhary, Margaret J. Debell, Gail Marracci, Hannah Miller, Evan Calkins, Edvinas Pocius, Brooke A. Napier, Ben Emery, Dennis Bourdette, Thomas S. Scanlan

Biology Faculty Publications and Presentations

Triggering receptor expressed on myeloid cells-2 (TREM2) is a cell surface receptor on macrophages and microglia that senses and responds to disease-associated signals to regulate the phenotype of these innate immune cells. The TREM2 signaling pathway has been implicated in a variety of diseases ranging from neurodegeneration in the central nervous system to metabolic disease in the periphery. Here, we report that TREM2 is a thyroid hormone-regulated gene and its expression in macrophages and microglia is stimulated by thyroid hormone and synthetic thyroid hormone agonists (thyromimetics). Our findings report the endocrine regulation of TREM2 by thyroid hormone, and provide a …

Identifying The Molecular Pathways That Drive Retinal Degeneration In The Childhood Neurodegenerative Disease: Mucolipidosis Type Iv, Michael Pamonag

Masters Theses, 2020-current

Humans, like many other vertebrates, possess five Aristotelian senses (vision, olfaction, hearing, taste, and touch) which we use to experience and navigate our environment. Our visual system is the only source of light detection and light signaling in our bodies. This makes our visual system essential for detecting movement, distance, time of day, and seasonal changes in the length of days within our environment. The visual systems of most animals are designed to capture photons of visible light and convert that energy into a neurological signal (visual signal) to be transmitted to brain regions responsible for visual perception1 . This …

Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh

Biology Faculty Publications

Numerous imaging modules are utilized to study changes that occur during cellular processes. Besides qualitative (immunohistochemical) or semiquantitative (Western blot) approaches, direct quantitation method(s) for detecting and analyzing signal intensities for disease(s) biomarkers are lacking. Thus, there is a need to develop method(s) to quantitate specific signals and eliminate noise during live tissue imaging. An increase in reactive oxygen species (ROS) such as superoxide (O2•-) radicals results in oxidative damage of biomolecules, which leads to oxidative stress. This can be detected by dihydroethidium staining in live tissue(s), which does not rely on fixation and helps prevent stress on tissues. However, …

Effect Of Borrelia Burgdorferi On The Amyloid-Beta And Phospho-Tau Markers And Oxidative Stress Response Of Neuroblastoma Cells, Dina Elzohiry

Master's Theses

In Alzheimer's disease (AD), the neurons are injured and mostly subjected to death throughout the brain, interconnections between neural networks may detach, and several regions of the brain begin to shrink in size. Amyloid-Beta (Aβ) and phospho-tau (p-Tau) are considered as main hallmarks of AD. Lyme-causing bacteria Borrelia burgdorferi can invade central nervous system resulting in neurological disorders. To evaluate how B. burgdorferi bacteria can contribute to the development and/or progress of AD, protein expression of Amyloid-Beta aggregates and p-Tau protein tangles were assessed before and after infection with B. burgdorferi in BE2C and Kelly neuroblastoma cell lines. To assess …