Systems Biology Commons^™

Regeneration In Planarians Modifies Behavioral Switching, N. S. Tellakula, Eva-Maria S. Collins, W. B. Kristan Jr.

Biology Faculty Works

The planarian Dugesia japonica responds differently to localized stimuli: anterior regions turn, middle regions elongate, and posterior regions contract. If cut into several pieces, each piece immediately produces the same three responses. Over several days, each piece regenerates all transected body parts. This study tested how the pieces coordinate behavioral responses during regeneration. We first determined the locations of the turning/elongation and elongation/contraction behavioral switches. Immediately, all transections moved both switching sites away from the cut sites so that the worm pieces produced the same three responses as intact worms. During regeneration, the sites of behavioral switching moved progressively closer …

Trpv1 And Its Co‑Expressed Genes Are Associated With The Progression Of Hepatocellular Carcinoma, Bhuvnesh P. Sharma, Himanshu N. Singh, Sanjay Kumar, Deepak Verma, Deepak Parashar, Murali M. Yallapu, Everardo Cobos, Subhash C. Chauhan, Vivek K. Kashyap

Research Symposium

Background: Hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transient receptor potential vanilloid 1 (TRPV1) is a nonselective Ca²⁺ channel protein widely expressed and plays a significant role in cancer initiation and progression. However, the biological significance of TRPV1 in HCC has not been systematically and comprehensively investigated. This study used deep data mining and transcriptomics analyses to describe the significance of TRPV1 expression and its association with HCC prognosis.

Methods: Download the RNA expression of TRPV1 from the Cancer Genome Atlas (TCGA), Genotype Tissue Expression Atlas (GTEx), Tumor Immune Estimation Resource (TIMER), and the UALCAN …

The Correlation Between Temporomandibular Disorder (Tmd) And Vitamin D Deficiency, Iris Kim, Claudia Freitas

Annual Research Symposium

No abstract provided.

Identification Of Novel Genetic Biomarkers Linked To The Prodromal Stage Of Parkinson’S Disease (Pd) Patients, Marwa Tawfik Badawy

Theses and Dissertations

Background and Objective: The early diagnosis of neurodegenerative diseases, such as Parkinson's disease (PD), is particularly challenging because symptoms appear only after significant neuronal damage has already occurred. This study is utilizing variant call format (VCF) analysis to identify genetic variants and novel genes that could serve as early prognostic markers for prodromal PD. Materials and Methods: Data were sourced from the Parkinson's Progression Markers Initiative (PPMI), focusing on prodromal patients with gVCF data from the 2021 cohort. The study included 304 participants, comprising 100 healthy controls, 146 individuals with prodromal genetic indicators, 21 individuals with prodromal hyposmia, and 37 …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Genome-Wide Profiling Of Trna Modifications By Induro-Trnaseq Reveals Coordinated Changes, Yuko Nakano, Howard Gamper, Henri Mcguigan, Sunita Maharjan, Jiatong Li, Zhiyi Sun, Erbay Yigit, Sebastian Grünberg, Keerthana Krishnan, Nan-Sheng Li, Joseph Piccirilli, Ralph Kleiner, Nicole Nichols, Brian Gregory, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and …

An Agent-Based Model Of Microglia And Neuron Interaction: Implications In Neurodegenerative Disease, Cheyenne Ty, Amanda Case, Emmanuel Mezzulo, Abigail Penland, Kamila Larripa

Spora: A Journal of Biomathematics

Whether immune cells protect or harm the brain is an open question depending on context, and their role is implicated in multiple diseases such as Alzheimer's disease, dementia, and other neurological disorders. Microglia, a specific type of immune cell in the central nervous system, play a key role in homeostasis, and genes associated with an elevated risk of Alzheimer's disease correspond with deficiencies in their behavior. We created an agent-based model that incorporates inflammatory signaling, chemotaxis, and phagocytosis of damaged neurons and allows the exploration of crucial pathways in the maintenance of brain health. We specifically investigated pathways related to …