Molecular Biology Commons^™

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Parameterizing Ion–Lipid Interactions From Local Clusters To Reproduce Experimental Bulk Properties Of Lipid Bilayers, W. Matthew Saunders

USF Tampa Graduate Theses and Dissertations

Phospholipids are the main component of cell membranes, providing a delimiting boundary for cells from their environments or from their organelles from the cytosol. Thiscompartmentalization allows cells to maintain quite different solutions within their cells and organelles, including different mixtures dissolved ions. Consequently, these membranes are constantly flanked by complex mixtures of salts at varied concentrations. To study membrane structure, one cannot neglect the contribution of the salts in the local solution. Ions perturb bilayer structure via specific interaction with the phospholipids, primarily with the headgroups. Experimental studies of these systems are somewhat at odds — scattering experiments with different …

Improving Coral Restoration Outcomes Through Novel Molecular Applications, Matthew H. Gamache

USF Tampa Graduate Theses and Dissertations

Coral reef ecosystems are declining globally from numerous stressors, including localized pollution, disease, and marine heatwaves induced by climate change. To preserve these ecosystems, it is critical to identify corals that can withstand stressors—primarily future marine heatwaves—and prioritize them for coral restoration efforts until these stressors are mitigated. Coral responses to thermal stress can be influenced by several partners, including mutualistic microalgae and a vast prokaryotic community. Here, I use advanced molecular techniques to examine which partners (coral host, algal symbiont, and microbial communities) are associated with coral health, how they contribute to holobiont physiology, and their potential to increase …

Screening For Potential Plant Growth‐Promoting Rhizobacteria (Pgpr)-Assisted Phytoremediation To Mitigate Lead Toxicity In Uae Soils, Zeinab Mohamed Abdalla

Theses

This study investigates the potential of lead (Pb)-tolerant actinobacteria that possess 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity and plant growth-promoting (PGP) traits to serve as a biological tool for enhancing the growth of corn (Zea mays L.) under Pb stress. The primary objective of this research was to isolate and characterize novel, Pb-tolerant, rhizosphere-competent actinobacteria and to evaluate their efficacy in mitigating Pb toxicity, reducing its uptake, and promoting biomass accumulation in corn grown in contaminated soil. A total of 43 actinobacterial isolates were obtained from Pb-contaminated rhizosphere soil and screened for Pb tolerance, rhizosphere competence, ACCD activity, and PGP traits. …

Targeting The Bcl2 Family: Advances And Challenges In Bh3 Mimetic-Based Therapies, Nabanita Mukherjee, James Sheetz, Yiqun Shellman

Student Papers, Posters & Projects

The BCL2 family of proteins plays a pivotal role in regulating apoptosis and cellular homeostasis, making them critical therapeutic targets in cancer and other diseases characterized by pathological cell survival. BH3 mimetics, small molecules that selectively inhibit anti-apoptotic BCL2 family members, have achieved significant clinical success, particularly in hematologic malignancies. However, several challenges remain, including resistance mechanisms, toxicity (such as MCL1 inhibitor-associated cardiotoxicity), and the intricate balance between apoptotic and non-apoptotic functions. This review provides a comprehensive overview of BCL2 family biology, the development and clinical application and outcomes of BH3 mimetics, and the emerging resistance mechanism known as double-bolt …

Insights Into Cardiac O-Glcnacylation As A Link Between The Diabetic State And Increased Cardiovascular Disease Susceptibility And Pathology, Samuel Formosa Chang

All ETDs from UAB

With diabetes prevalence around the world nearing 10%, and half of the US population having either diabetes or pre-diabetes, many epidemiological studies show diabetic patients have both increased risk for developing major cardiovascular disease (CVD), and increased mortality rates due to CVD. Additionally, within this field, studies have shown that indi-viduals with previously higher HbA1C levels have higher long-lasting risk for major ad-verse cardiac events compared to those with previously lower HbA1C levels—establishing the concept of “metabolic memory”. Within the diabetic milieu, cardiac protein O-GlcNAcylation (O-linked B-N-acetyl-glucosamine) is important for cardiac pathology de-velopment. Specifically, our lab generated a cardiomyocyte specific, …

Proteomic Approaches To Investigate Pp2a-B55 Substrates And Cellular Function, Brennan C. Mcewan

Dartmouth College Ph.D Dissertations

Cell division is controlled in large part by reversible protein phosphorylation. The phosphorylation state of proteins during mitosis and other phases of the cell cycle represents a careful balance of activity between kinases and opposing phosphatases. The phosphoprotein phosphatase (PPP) family is responsible for the majority of serine and threonine dephosphorylation. Members of the PPP family are composed of a catalytic subunit paired with a regulatory subunit that targets them towards specific substrates.

The most abundant PPP, PPP2A, paired with its regulatory B55 subunit, is thought to be the phosphatase responsible for the dephosphorylation of substrates during mitotic exit. Despite …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

From Venom To Medicine: Harnessing Animal Toxins For Drug Discovery, Christine Vega, Ying Jia

Research Colloquium

Background: Drug development research has long focused on synthesizing novel therapeutics while overlooking isolation from naturally available sources such as animal venoms. Recently, the discovery of the therapeutic effects of highly bioavailable animal venom caused the field of venom research to soar in popularity. Animal venom serves as a natural, sophisticated tool optimized over millions of years by evolution with the ability to bind to ion channels such as nAChRs, non-specific ligand-gated ion channels distributed throughout the human nervous system. However, purifying individual venom toxins from crude venom is challenging due to its availability. Therefore, synthesizing large quantities of venom …

Binding Of A [2fe-2s] Cluster Drives Dimerization Of Ferric Uptake Regulator (Fur) In Escherichia Coli, Fatemeh Najafi, Aidan G. Purcell, Finbar H. Homes, Huangen Ding

Faculty Publications

The ferric uptake regulator (Fur) is a global transcription factor that reversibly binds an iron-sulfur [2Fe-2S] cluster via the cysteine residues (site 3) in response to elevation of intracellular free Fe content in Escherichia coli. Here, we report that when E. coli Fur is expressed in E. coli cells grown in M9 medium supplemented with Fe or zinc (Zn), purified Fur binds a [2Fe-2S] cluster or Zn(II), respectively. While apo-form Fur is a monomer and has no DNA-binding activity, both the [2Fe-2S] cluster-bound Fur and the Zn(II)-bound Fur are homodimers and have a similar binding activity for the DNA sequence …

The Effects Of Tfeα And Promoter Sequence On Early Events In Archaeal Transcription Initiation, Madolyn Toli

Dissertations and Theses

Expression of genes is dependent on promoter sequences in DNA, which direct transcription by RNA polymerase. Transcription factors interact with promoters and RNAP and are often conserved and are essential for proper gene expression. In this thesis, a functional region of archaeal TFEα, homologous to eukaryotic TFIIEα, has been identified, and specific amino acids in these regions have been determined to have significant importance in TFEα's ability to promote transcription in early initiation. All three Domains of life encode a 16S rRNA promoter, which is responsible for production of the 16S portion of ribosome. Transcription with this promoter is not …

Stayin' Alive (Even Without Oxygen): Retinal Development In Austrofundulus Limnaeus, Carmen Zecilia Rodriguez

Dissertations and Theses

The vertebrate eye is one of the most metabolically active organs in the body and is particularly sensitive to environmental stressors such as oxygen deprivation. Understanding how eye development proceeds under such conditions can provide critical insights into mechanisms of cellular resilience, tissue organization, and developmental plasticity. The annual killifish Austrofundulus limnaeus represents a unique model for investigating these processes due to its remarkable tolerance to anoxia during embryogenesis. However, the wild-type form is heavily pigmented, limiting the effectiveness of traditional imaging techniques for studying eye development. This thesis characterizes eye development and anoxia resilience in both wild-type and melanin-deficient …

From Sequence To Allostery: How Amino Acid Differences Rewire Coupled Conformational Heterogeneity In The Ptp Enzyme Family, Shivani Sharma

Dissertations, Theses, and Capstone Projects

Protein Tyrosine Phosphatases (PTPs) are critical regulators of cellular signaling, and their activity is often modulated through allosteric mechanisms. Allostery is defined as a chemical or conformational change in one site of the protein due to a binding event at another site. Although several studies have investigated aspects of allostery in PTPs, the mechanistic foundations underlying allosteric regulation remain poorly understood. Despite a highly conserved catalytic domain across PTPs, regions with low or no conservation suggest potential "rewiring" of allosteric networks. This raises key questions about the universality versus individuality of allosteric mechanisms across the PTP family.

In this work, …

The Sonic Hedgehog Effector Smoothened Modulates Cholinergic Interneuron Activity, Physiology, And Striatum-Dependent Behaviors, Santiago Uribe-Cano

Dissertations, Theses, and Capstone Projects

The striatum is a central node in action selection and associative learning, integrating cortical, thalamic, and neuromodulatory input. Among its principal modulators, dopamine (DA) and acetylcholine (ACh) are known for their temporally coordinated yet mechanistically distinct influences on striatal output. However, the upstream signals that regulate their dynamic interplay, particularly within cholinergic interneurons (CINs)—the primary source of striatal ACh—remain incompletely characterized. This dissertation investigates the role of Smoothened (Smo), a G protein-coupled receptor (GPCR) effector of Sonic Hedgehog (Shh) signaling, in modulating ACh signaling dynamics in the striatum.

Building on evidence that midbrain DA neurons co-release Shh and that CINs …

Investigating The Role Of Early Growth Response 1 (Egr1) Gene In Riluzole-Induced Apoptosis In Osteosarcoma, Syeda Maryam Azeem

Dissertations, Theses, and Capstone Projects

Osteosarcoma is a rare but aggressive bone malignancy most commonly affecting adolescents and young adults (AYA). With 5-year survival rate stagnating over the last four decades despite the advancements in multi-modal therapy, drug repurposing offers a rapid path to new osteosarcoma treatments. Recent studies suggest that Riluzole, a drug approved for amyotrophic lateral sclerosis (ALS), may be repurposed for osteosarcoma treatment due to its ability to slow tumor progression and induce apoptosis. Previously, we have shown that Riluzole increases reactive oxygen species (ROS), activating c-Abl, which phosphorylates YAP in the nucleus. YAP then forms a complex with p73 to enhance …

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Role Of Nucleic Acids As Chaperones In Protein Folding, Zijue Huang

Electronic Theses and Dissertations

Many proteins have slow folding times in vitro that are physiologically untenable. To combat this challenge, ATP-dependent chaperonins are thought to possess the unique ability to catalyze protein folding. Performing quantitative model selection using protein folding and unfolding data, we here show that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding. Performing the experiments as a function of temperature demonstrates that the G4 reshapes the underlying driving forces of protein folding. To understand the structural basis of this catalytic activity, we introduce NMR method to solve the structures, at base-level resolution, of a multiconformer G4 with …

Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation., Nicholas Marano, Liza Elif Guner, Rachel S Riley, James M Holaska

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Emery-Dreifuss muscular dystrophy 1 (EDMD1) arises from mutations in EMD. Most EDMD1 patients lack detectable emerin expression. They experience symptoms such as skeletal muscle wasting, joint contractures, and cardiac conduction defects. Currently, physicians rely on treating patient symptoms without addressing the underlying cause-lack of functional emerin protein. Thus, there is a need for therapeutic approaches that restore emerin protein expression to improve patient outcomes. One way would be to deliver emerin mRNA or protein directly to affected tissues to restore tissue homeostasis. Here, we evaluated the utility of lipid nanoparticles (LNPs) to deliver emerin mRNA to diseased cells. LNPs …

Long Intergenic Non-Coding Rna 00511 (Linc00511) Genetic Variations And Haplotype Implication For Colorectal Cancer Susceptibility And Prognosis, Eman Fouad Sanad, Ahmad Abd El Hady, Mohamed Ali, Shorouk Eldash, Nermeen H. Elmorshedy, Farah Ayman, Hams M. Khattab, Amr Maher, Hadeel Ashree, Mahitab Abdelhady, Mazen Mohamed, Ahmed Adel, Sajed Khalil, Omar Alyan, Ahmed Samir, Alhassan A. Bakr, Nadia Hamdy

Pharmacy

Long intergenic non-coding RNA 00,511 (LINC00511) is considered an oncogene for various cancers. However, the association between LINC00511 single nucleotide polymorphisms (SNPs) and colorectal cancer (CRC) remains unclear. Our study aims to study whether LINC00511 SNPs could predict CRC susceptibility or prognosis, an important step-toward precision-health, based on an Egyptian CRC patient cohort. A total of 200 CRC patients and 200 cancer-free controls were genotyped for three LINC00511 SNPs − rs9906859, rs1558535, and rs17780195 using qRT-PCR. Studied SNPs were in strong linkage disequilibrium and moderately correlated in all groups. Genotype association concerning tumor stage, revealed rs1558535 AT and rs17780195 AG …

An Rna Modification Prevents Extended Codon-Anticodon Interactions From Facilitating +1 Frameshifting, Evelyn M. Kimbrough, Ha An Nguyen, Haixing Li, Jacob M. Mattingly, Nevette A. Bailey, Wei Ning, Howard Gamper, Ya-Ming Hou, Ruben L. Gonzalez, Christine M. Dunham

Department of Biochemistry and Molecular Biology Faculty Papers

RNA post-transcriptional modifications act by stabilizing the functional conformations of RNA. While their role in messenger RNA (mRNA) decoding is well established, it is less clear how transfer RNA (tRNA) modifications outside the anticodon contribute to tRNA stability and accurate protein synthesis. Absence of such modifications causes translation errors, including mRNA frameshifting. By integrating single-molecule fluorescence resonance energy transfer and cryogenic electron microscopy, we demonstrate that the N1-methylguanosine (m1G) modification at position 37 of Escherichia coli tRNAProL is necessary and sufficient for modulating the conformational energy of this tRNA on the ribosome so as to suppress +1 frameshifting otherwise induced …