Life Sciences Commons^™

Proteomic Investigation Of Aging And Omega-3 Supplementation In Rat Skeletal Muscle, Francesco Maria Del Re, David W. Russ, Kalina P. Dimova, Stylianos P. Scordilis

Biological Sciences: Faculty Publications

Aging is a pan-organ process with an intricate and multimodal nature. Deciphering the aging phenomenon is complex, yet recent attention is analyzing the potential benefits of non-invasive life adjustments to achieve healthy aging. Omega-3 polyunsaturated fatty acids (FA) have emerged as promising nutraceuticals for a plethora of different medical conditions. In the current study we conducted an in-depth, bottom-up, global, shotgun proteomic study (LC-MS/MS) investigating both the effects of aging on skel- etal muscle and the potential alterations due to ω-3 FA. Sprague Dawley rats were fed different diets and divided into four groups (n = 5 per group): adult …

The Aquatic Symbiosis Genomics Project: Probing The Evolution Of Symbiosis Across The Tree Of Life, Matthew Berriman, Victoria Mckenna, Roxanne Beinart, John M. Archibald, Ute Hentschel, Michael N. Dawson, Jose V. Lopez, Patrick J. Keeling, Jillian M. Petersen, Anne W. Thompson, Multiple Addiional Authors

Biology Faculty Publications and Presentations

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbioses. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial …

Aging-Induced Increase In Top-Down Connectivity From Dlpfc To Sma/M1 And Decrease In Inter-Limb Motor Coordination During Standing Tasks, Jiahao Pan, Shuqi Zhang

International Journal of Physical Activity and Health

This study aimed to investigate the effects of aging on inhibitory control from the prefrontal cortex (PFC) to the motor cortices and inter-limb coordination during dual task standing. Participants performed single-task and dual-task standing. Ground reaction force, center-of-pressure, muscle activity, and cortical activation were measured. The older group showed a greater effective connectivity index from the intra-hemispheric dorsolateral PFC (DLPFC) to supplementary motor area (SMA) (right, p = 0.009; left, p = 0.003) and left DLPFC to right M1 (p = 0.020)than the young group across task conditions. Also, the older group had greater inter-tibialis anterior coherence at 15–35 …

The Impact Of Breast Radiotherapy On The Tumor Genome And Immune Ecosystem, Aislyn Schalck, Tuan Tran, Jianzhuo Li, Emi Sei, Shanshan Bai, Min Hu, Jerome Lin, Scott J Bright, Samuel Reddick, Fei Yang, Harsh Batra, Alejandro Contreras, Maria Gabriela Raso, Michael C Stauder, Karen E Hoffman, Jay P Reddy, Kevin T Nead, Benjamin D Smith, Gabriel O Sawakuchi, Wendy A Woodward, Stephanie S Watowich, Jennifer K Litton, Isabelle Bedrosian, Elizabeth A Mittendorf, Huong Le-Petross, Nicholas E Navin, Simona F Shaitelman

Faculty, Staff and Student Publications

Radiotherapy is a pillar of breast cancer treatment; however, it remains unclear how radiotherapy modulates the tumor microenvironment. We investigated this question in a cohort of 20 patients with estrogen-receptor positive (ER+) breast tumors who received neoadjuvant radiotherapy. Tumor biopsies were collected before and 7 days postradiation. Single-cell DNA sequencing (scDNA-seq) and scRNA-seq were conducted on 8 and 11 patients, respectively, at these two time points. The scRNA data showed increased infiltration of naive-like CD4 T cells and an early, activated CD8 T cell population following radiotherapy. Radiotherapy also eliminated existing cytotoxic T cells and resulted in myeloid cell increases. …

Cytogenetic Annotation Automation In Myelodysplastic Syndrome Research Databases, Samuel Urrutia, Kelly S Chien, Ziyi Li, Alexandre Bazinet, Guilin Tang, Guillermo Garcia-Manero

Faculty, Staff and Student Publications

No abstract provided.

Overcoming Nk-Mediated Rejection By Anti-3rd-Party Central Memory Veto Cd8 T Cells Through Downregulation Of Dnam-1 On Alloreactive Nk Cells, Wei-Hsin Liu, Aloukick Kumar Singh, Christa Blagdon, Sandeep Kumar Yadav, Einav Shoshan, Esther Bachar-Lustig, Yair Reisner

Faculty, Staff and Student Publications

Anti-3rd-party central memory veto CD8 T (veto Tcm) cells can overcome T cell-mediated graft rejection under mild conditioning without causing significant graft versus host disease (GVHD). We previously demonstrated that these veto Tcm cells can effectively delete anti-donor T cell clones through a Fas-FasL mechanism, whereas their ability to neutralize alloreactive natural killer (NK) cells and the mechanism of such potential activity remained unknown. Using “nude” mice as recipients of allogeneic T cell-depleted hematopoietic stem cell transplantation (HSCT), we demonstrate effective inhibition of NK-mediated rejection by Tcm cells. Ex vivo studies revealed that Tcm cells express high levels of CD155, …

Heterozygous Kmt2d Loss Diminishes Enhancers To Render Medulloblastoma Cells Vulnerable To Combinatory Inhibition Of Lsd1 And Oxphos, Shilpa S Dhar, Calena Brown, Ali Rizvi, Lauren Reed, Sivareddy Kotla, Constantin Zod, Janak Abraham, Jun-Ichi Abe, Veena Rajaram, Kaifu Chen, Min Gyu Lee

Faculty, Staff and Student Publications

The histone H3 lysine 4 (H3K4) methyltransferase KMT2D (also called MLL4) is one of the most frequently mutated epigenetic modifiers in many cancers, including medulloblastoma (MB). Notably, heterozygous KMT2D loss frequently occurs in MB and other cancers. However, its oncogenic role remains largely uncharacterized. Here, we show that heterozygous Kmt2d loss in murine cerebellar regions promotes MB genesis driven by heterozygous loss of the MB-suppressor gene Ptch via the upregulation of tumor-promoting programs (e.g., oxidative phosphorylation [OXPHOS]). Downregulation of the transcription-repressive tumor suppressor NCOR2 by heterozygous Kmt2d loss, along with Ptch

Tickborne Colpodella Species Infections: Time For A New Integrated Approach To Understand Transmission And Pathogenicity, T. Y. Sam-Yellowe, Trinity Nims, Sona Qaderi, Mary M. Asraf

Biological, Geological, and Environmental Faculty Publications

Colpodella species are free-living predatory protists that prey on algae, ciliates and bodonids using myzocytosis. Colpodella species have been reported in human and animal infections. Polymerase chain reaction (PCR) using primers targeting 18S rRNA genes of Cryptosporidium and piroplasms have identified Colpodella species in arthropods, host blood and feces, demonstrating the phylogenetic closeness of Colpodella species to the apicomplexa. However, in human, animal and arthropod hosts, the life cycle stages of Colpodella are unknown. In this literature review, we provide an overview of the widespread occurrence of Colpodella species in ticks, and pathogenicity in humans and animals. We discuss methods …

The Impact Of Narratives And Active Video Games Among Black And Hispanic Children With Overweight And Obesity: A Randomized Controlled Trial, Amy S Lu, Tom Baranowski, Tiago V Barreira, Amy Fleischman, Melanie C Green, Shirley Y Huang, I-Min Lee, Lynne L Levitsky, Farzad Noubary, Debbe Thompson

Children’s Nutrition Research Center Staff Publications

Background: Overweight and obesity disproportionately affect Black and Hispanic children who also play more video games. Narratives, coupled with home-based active video games (AVGs), may enhance PA and mitigate these disparities. This study tested the effect of narrative-enhanced home-based AVGs among predominantly Black and Hispanic children with overweight and obesity.

Methods: This 6-month three-group RCT recruited 135 children aged 7-14 from pediatric clinics in Boston, MA (January 2020 - May 2022) during the COVID-19 pandemic. Participants were randomized into: [Narrative + AVG], receiving an Xbox/Kinect with six AVGs interspersed with a narrative animation Ataraxia (72 episodes over six months), which …

Correction: Complement Activity And Autophagy Are Dysregulated In The Lungs Of Patients With Nonresolvable Covid-19 Requiring Lung Transplantation, Pooja Shivshankar, Stacey L Mueller-Ortiz, Aleksey Y Domozhirov, Weizhen Bi, Scott D Collum, Marie-Francoise Doursout, Manish Patel, Isabella N Lefebvre, Bindu Akkanti, Simon Yau, Howard J Huang, Rahat Hussain, Harry Karmouty-Quintana

Faculty, Staff and Student Publications

No abstract provided.

Sustainable Management Of Copper-Contaminated Soils Using Vetiver Root Biochar, Sameer Neve, Dibyendu Sarkar, Zhiming Zhang, Rupali Datta

Michigan Tech Publications

Throughout the 19th and early 20th centuries, copper mining was a predominant industry in Michigan's Upper Peninsula, resulting in substantial environmental issues due to the generation of mining waste. This waste, referred to as stamp sands, was disposed of in Lake Superior, causing severe harm to aquatic ecosystems. Later, the stamp sands were dredged and deposited along the lake shores, causing large-scale contamination with copper. This rendered the land incapable of supporting vegetation. This study investigates the efficacy of vetiver (Chrysopogon zizanioides) root biochar as a soil amendment to enhance the quality of copper-contaminated stamp sands. The biochar was produced …

Wildlife Road Mortalities During Covid-19 Pandemic-Related Lockdown In South Texas: A Comparative Survey, Bradley Evan Beer, Kevin W. Ryer, Md Saydur Rahman, John H. Young Jr., Richard J. Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

Mortalities of wildlife caused by collisions with vehicles along roads are increasing in prevalence, threatening the existence of various species and populations. The COVID-19 pandemic-related lockdown provided an opportunity to gain a better understanding of how wildlife vehicle mortality occurrences change in response to anthropogenic variables and how varying survey methods influence obtaining mortality data. In this study, data were collected in three observation periods: pre-lockdown (PreL), during lockdown (DL), and post-lockdown (PostL) in south Texas. There were 194 wildlife mortalities recorded during weeks 4–27 of 2020. Results of this study showed that road mortality survey counts did not change …

Developing A Murine Model To Investigate The Mechanisms Of Peanut, Cashew, Shrimp Multifood Allergy, Aaron Wilson

NYMC Student Theses and Dissertations

Approximately 32 million people in the United States have food allergies, which is approximately 10 percent of the population. Food allergies can be mild, moderate, or even severe, resulting in anaphylaxis. The most predominant food groups that trigger food allergies include peanuts, tree nuts, fish, and shellfish. Peanuts and tree nuts have some similarities in protein structure. Shellfish is not associated with the protein properties of peanuts or tree nuts, it is the leading cause of adult anaphylaxis and often co-exist with peanut and tree nut allergies Currently, there are few studies that have established a murine model for allergy …

Ammonia Regulation In Aedes Taeniorhynchus, A Salt-Water Mosquito, Joseph Edmonds

Undergraduate Honors Theses

The salt tolerant mosquito species Aedes taeniorhynchus has been observed in high salinity and ammonia conditions. Previous studies indicate Na+/K+ ATPase (NKA), the proton pump vacuolar-type H+ ATPase (VHA) and sodium-dependent cation-chloride cotransporters (NKCC’s) in sodium secretion in larval Aedes taeniorhynchus. However ammonia transporter such as Rh-protein, Amt1, and Amt2 have only been characterized in Aedes taeniorhynchus’s fresh water relative Aedes aegypti. Our research exhibits the expression of these transporters in A.taeniorhynchus using immunohistochemistry techniques. Evidence of VHA and NKA function in ammonia transport was characterized in vivo using drug antagonists in varying saline and ammonia concentrations. Ammonia flux rates …

Color Tests For The Presumptive Identification Of A Range Of Benzodiazepines, Regan Mulvin

Honors Projects

Color tests are presumptive chemical tests that determine the class of drug in both laboratory and field settings. Despite the rising popularity of benzodiazepines and the usefulness of color tests, there is no widely accepted color test for identifying them. This study tested six different color tests against five benzodiazepines, including diazepam, clonazepam, lorazepam, alprazolam, and flualprazolam, to identify which of the tests would work most generally across all benzodiazepines. Of the six tests, the McKibben test, the Janovsky test, and the Zimmerman test all showed potential usefulness as a presumptive color test. More studies should be done on a …

Low Cd25 In Alk+ Anaplastic Large Cell Lymphoma Is Associated With Older Age, Thrombocytopenia, And Increased Expression Of Surface Cd3 And Cd8, Shuyu E, L Jeffrey Medeiros, Hong Fang, Shaoying Li, Guilin Tang, Sa A Wang, Wei Wang, C Cameron Yin, M James You, Swaminathan P Iyer, Luis Malpica, Lianqun Qiu, Zhenya Tang, Qing Wei, Pei Lin, Jie Xu

Faculty, Staff and Student Publications

Background/objectives: Anaplastic lymphoma kinase (ALK)-positive (+) anaplastic large cell lymphoma (ALCL) is known to express CD25, but its significance has not been well studied.

Methods: In the present study, we identified 54 ALK+ ALCL patients with CD25 results available and investigated the significance of CD25 expression levels.

Results: Forty-two (78%) cases had high CD25 expressions, whereas low CD25 expressions were found in 12 (22%) cases. Compared with ALK+ ALCL patients with CD25-high neoplasms, patients with CD25-low neoplasms were older (median: 40 years vs. 29 years, p = 0.01) and more often had thrombocytopenia (40% vs. 0%, p = 0.02). Between …

The Impact Of Growth Hormone-Releasing Hormone Antagonist On Human Adipose-Derived Stem Cells, Jeanne Michelle Dugas

Master's Theses

Obesity is a condition that affects over 40% of American adults and contributes to numerous preventable health issues. This condition is caused by increased adipose tissue, which forms when stem cells transform into adipocytes. Mesenchymal stem cells, including human adipose-derived stem cells (hASC), are multipotent with the ability to differentiate into adipocytes, osteocytes, or chondrocytes. Many factors affect this transformation, including the peptide growth hormone-releasing hormone (GHRH). The main role of GHRH is to trigger the release of growth hormone, but it has also been found to play an important role in adipocyte metabolism. We expect that if the differentiation …

The Antioxidant Potential Of Rosemary Leaf-Derived Nanovesicles, Shani Akila Griffin

Master's Theses

Human dermal fibroblasts are essential for maintaining skin homeostasis. However, exposure to exogenous and endogenous stressors can lead to fibroblast instability, extracellular matrix degradation, and excessive reactive oxygen species (ROS) production. These factors contribute to skin aging and ROS-induced skin disorders leading to hair loss. Adverse effects from synthetic treatments have driven interest in natural alternatives like plant extracts for skin therapy. However, the polyphenols in these treatments require an effective delivery system to ensure their stability and targeted application. Plant derived nanovesicles (PDNVs) are emerging as a promising natural alternative for therapeutic applications. Their biocompatibility, stability, and encapsulated compounds …

Targeting Neuronal Nitric Oxide Synthase (Nnos) As A Novel Approach To Enhancing The Anti-Melanoma Activity Of Immune Checkpoint Inhibitors, Anika R. Patel, Shirley Tong, Kate Alison Lozada, Amardeep Awasthi, Richard B. Silverman, Jennifer Totonchy, Sun Yang

Pharmacy Faculty Articles and Research

Background and Objectives: Neuronal nitric oxide synthase (nNOS) overexpressed in melanoma plays a critical role in disease progression. Our previous studies demonstrated that nNOS inhibitors exhibited potent anti-melanoma activity and regulated PD-L1 expressions in the presence of interferon-gamma (IFN-γ). However, the role of nNOS in the melanoma immune response has not been well defined. Methods: Changes in gene expression profiles after nNOS inhibitor treatment were determined by transcriptomic analysis. A melanoma mouse model was used to determine the effects of nNOS inhibition on peripheral T cells and the in vivo anti-tumor activity of combining nNOS inhibitors with immune …

“Non-Markovian” And “Directional” Errors Inhibit Scientific Self-Correction And Can Lead Fields Of Study Astray: An Illustration Using Gardening And Obesity-Related Outcomes, Jon Agley, Sarah E Deemer, David B Allison

Children’s Nutrition Research Center Staff Publications

Herein we coin the terms non-Markovian error and biased Markovian error to describe categories of scientific errors for which general progress within a field of study may be unlikely to result in scientific self-correction. We provide examples of such errors and show their impact on studies about gardening and obesity.

Thsd1 Is A Multifaceted Regulator In Health And Disease, Mengjun Dai, Kuizhi Qu, Sophie Liu, Zhen Xu, Yan-Ning Rui

Faculty, Staff and Student Publications

Thrombospondin Type 1 Domain-Containing Protein 1 (THSD1) is a transmembrane protein increasingly recognized for its critical roles in vascular biology and disease pathogenesis. Initially identified as a marker of hematopoietic stem and endothelial cells during embryogenesis, THSD1 has since been implicated in a wide spectrum of physiological and pathological processes. This paper consolidates current knowledge on THSD1, with a focus on its roles in vascular integrity, perinatal disorders, and tumorigenesis. In vascular systems, THSD1 promotes focal adhesion assembly and suppresses autophagy-mediated adhesion turnover, thereby stabilizing endothelial attachment and maintaining barrier function. Genetic and functional studies support its protective role against …

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

Intergenerational Toxic Stress In Preschool Children, Cynthia R. Rovnaghi

Doctoral Dissertations and Projects

Worldwide there is an outcry for understanding, integrating, preventing, coordinating, and collaboratively treating the neuropsychosocial components of intergenerational transmission of trauma-induced toxic stress (ITTS). The purpose of this quasi-experimental, cross-sectional, secondary analysis of the Hair Biomarkers Study Phase I (HBS-I) was to obtain empirical evidence supporting the introduction of the Theory of Neurogenesis Abruption (ToNA) and to standardize the use of hair biomarkers and child developmental scales for early detection of central nervous system (CNS) dysregulation. Birth and developmental outcomes of children born to parents with a diagnosed serious mental health condition (DSMHC) and/or substance (ab)use (SA/SU) disorder (children, n …

Factors Influencing Student Motivations And Experiences In Stem Course Office Hours, Gabriella R. Dauber, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Office hours are a part of nearly all science, technology, engineering, and mathematics (STEM) courses, with many academic and affective benefits for students who attend. However, despite their ubiquity, there has only been limited past work examining the sources of knowledge students draw from to shape their perceptions of office hours, as well as the factors that influence students' experiences in STEM course office hours. Here, we conducted semistructured interviews with 20 students enrolled in an introductory STEM course to investigate what motivates students to attend STEM course office hours, the factors that shape their experiences in office hours, and …

Global Maintenance Of Histone Post-Translational Modifications During The Transition Into Anoxia In Embryos Of The Annual Killifish, Chelsea Hughes, Elizabeth A. Mojica, Dietmar Kültz, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Many organisms have adapted to survive anoxic or hypoxic environments, but the epigenetic responses involved in this successful stress response are not well described in most species. Embryos of the annual killifish have the greatest tolerance to anoxia of all vertebrates, making them a powerful model to study the cellular mechanisms necessary for anoxia tolerance. However, the global histone landscape of this species has never been quantified or explored in relation to stress tolerance. Liquid chromatography-mass spectrometry and a Python bioinformatics workflow were used to identify histones and their post-translational modifications. This pipeline resulted in the detection of 252 unique …

More Than 9 Lives: Improving Shelter Cat Intake And Adoption Rates, Arthur S. Loomis

Masters Theses

Municipal animal shelters across the United States struggle to properly care for the cats housed in their facilities due to overpopulation. The sheer volume of cats entering shelters greatly outpaces the rate in which they are adopted out, resulting in an immense resource strain that too often results in the euthanasia of millions of shelter cats across the country each year. The enormous influx of cats is largely due to abandonment or considerable populations of feral, stray, or community cats living on the streets. In addition, shelter cat adoptions occur at a much slower pace, with many cats spending months, …

Role Of Minimalist Footwear On Stability, Change Of Direction, And Power Production: A Randomized Crossover Trial, Logan Allen

Masters Theses

The purpose of the present study was to examine the acute effects of minimalist footwear (MFW) on participants’ ability to stabilize, change direction, and produce power. A randomized crossover design was used. Eighteen subjects participated. Participants tested in MFW and traditional running shoes (RS) and were randomly assigned an order. The protocol included a warm-up, limits of stability (LS) assessment, pro-agility test (PA), modified t-test (MT), countermovement jump (CMJ), and an isometric mid-thigh pull (IMTP). No significant differences were found (p £ 0.05), and the effect sizes were trivial to small. For the LS assessment, time (ES = 0.350) and …

Personalizing Neoadjuvant Chemotherapy Regimens For Triple-Negative Breast Cancer Using A Biology-Based Digital Twin, Chase Christenson, Chengyue Wu, David A Hormuth, Jingfei Ma, Clinton Yam, Gaiane M Rauch, Thomas E Yankeelov

Faculty, Staff and Student Publications

Despite advances triple negative breast cancer treatment, ~50% of patients will not achieve a pathological complete response prior to surgery with standard of care neoadjuvant therapy (NAT). We hypothesize that personalized regimens for NAT could significantly improve patient outcomes, which we address with a patient-specific digital twin framework. This framework is established by calibrating a biology-based model to longitudinal magnetic resonance images with approximate Bayesian computation. We then apply optimal control theory to either (1) reduce the final tumor cell number with equivalent dose, or (2) reduce the total dose of NAT with equivalent response. For (1), the personalized regimens …

Comparative Efficacy Of Combined Versus Singular Auditory Alpha-Theta Brainwave Entrainment And Hypnotherapy Modalities In Chronic Pain Management, Jennifer Nicole Leavitt

Doctoral Dissertations and Projects

This experimental quantitative research, a randomized controlled trial, evaluated combined efficacy of auditory alpha-theta brainwave entrainment (BWE) and hypnotherapy in chronic pain management versus each modality alone. Chronic pain is a serious clinical challenge that may benefit from novel, nonpharmacological interventions. Previous studies have demonstrated benefits of both BWE and hypnotherapy for pain; but research on combined effects was not identified. This study hypothesized that a synergistic approach would offer superior pain relief compared to singular modalities. The study utilized a randomized controlled trial design with a sample size of 38 participants, initially, aged 25 to 65 years old, recruited …

Effectiveness Of Exercise-Based Rehabilitation In Chronic Fatigue Syndrome: A Systematic Review And Meta-Analysis, Antonio De Vera Martín, Alberto Díaz Salazar, Isidro Miguel Martín Pérez, Sebastián Eustaquio Martín Pérez

International Journal of Exercise Science

International Journal of Exercise Science 18(5): 495-530, 2025. Chronic Fatigue Syndrome is a complex and debilitating disorder characterized by persistent fatigue, musculoskeletal pain, sleep disturbances, and cognitive impairments. The global prevalence is estimated between 0.2% and 0.4%, affecting over 17 million individuals worldwide, with an estimated burden exceeding 40,000 cases in Spain. Despite the exploration of exercise-based rehabilitation as a therapeutic strategy, its clinical efficacy remains a subject of ongoing debate. This study aims to evaluate the effectiveness of exercise-based rehabilitation relative to conventional treatments in improving functional capacity and alleviating fatigue among adults with CFS A systematic review and …