Diverse Origins Of Near-Identical Antifreeze Proteins In Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms Of New Gene Birth And Protein Sequence Convergence,
2024
University of Arkansas, Fayetteville
Diverse Origins Of Near-Identical Antifreeze Proteins In Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms Of New Gene Birth And Protein Sequence Convergence, Nathan Rives, Vinita Lamba, C.H. Christina Cheng, Xuan Zhuang
Biological Sciences Faculty Publications and Presentations
Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical …
Understanding The Mystery Of R-Loops And Their Relationship To Nucleolar Stress,
2024
Loyola University of Chicago Graduate School
Understanding The Mystery Of R-Loops And Their Relationship To Nucleolar Stress, Kevin Shane
Master's Theses
Genomic instability is an increase in the likelihood of DNA mutations and genetic changes during cell division, a common feature in cancer cells. One cause of genomic instability comes from the aberrant formation of three-stranded nucleic acid structures called R-loops. R-loop form when an RNA strand hybridizes to its complementary strand of DNA, forming a stable RNA:DNA hybrid and displacing one free strand of DNA 1. Accumulation of unscheduled R-loops can lead to replication stress, fork collision, gene expression changes, and double-strand breaks that are underlying causes of genome instability and the development of many diseases, including cancer 2. Many …
Noise Leads To The Perceived Increase In Evolutionary Rates Over Short Time Scales,
2024
University of Tennessee, Knoxville
Noise Leads To The Perceived Increase In Evolutionary Rates Over Short Time Scales, Brian C. O'Meara, Jeremy M. Beaulieu
Biological Sciences Faculty Publications and Presentations
Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show …
Pm2.5 In The Respirable Air A Threat To Heart Health Investigating The Influence On Cardiovascular Performance And Unmasking The Potential Strategies For Cardio Protection,
2024
SASTRA Deemed to be University
Pm2.5 In The Respirable Air A Threat To Heart Health Investigating The Influence On Cardiovascular Performance And Unmasking The Potential Strategies For Cardio Protection, Bhavana Sivakumar
Theses and Dissertations
Air pollution, characterized by the presence of harmful substances in the atmosphere, represents a significant environmental and public health challenge impacting millions worldwide. The World Health Organization (WHO) reports that approximately 90% of the global population resides in regions where air pollution surpasses the recommended thresholds for healthy air quality. Within the realm of air pollution, the composition of particulate matter emerges as a pivotal consideration, particularly regarding PM2.5, comprising minute particles originating from diverse sources such as combustion processes, industrial operations, and natural phenomena like wildfires and dust storms. PM2.5 exhibit a range of chemical and physical attributes contingent …
Emerin Deficiency Drives Mcf7 Cells To An Invasive Phenotype,
2024
Rowan University
Emerin Deficiency Drives Mcf7 Cells To An Invasive Phenotype, Emily Hansen, Christal Rolling, Matthew Wang, James M Holaska
Rowan-Virtua School of Osteopathic Medicine Departmental Research
During metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer …
Antimicrobial Studies Of Novel Pyrazole And Thiazole-Based Antibacterial Agents,
2024
Arkansas State University - Jonesboro
Antimicrobial Studies Of Novel Pyrazole And Thiazole-Based Antibacterial Agents, Hansa Raj Kc
Student Theses and Dissertations
In recent years, the rise of antibiotic-resistant bacteria has become a global concern, resulting in fewer effective antibiotics. Several conventional antibacterial agents are ineffective against these, necessitating novel molecules with enhanced efficacy and diverse actions. We developed pyrazole and thiazole-based antibacterial agents and demonstrated that they have significant potency (minimum inhibitory concentration as low as 0.39 µg/mL) against antibiotic-resistant and susceptible bacteria, as well as promising anti-biofilm and anti-persister activity. In vivo toxicity tests on Caenorhabditis elegans showed no significant harm to this model host organism at low compound concentrations. These compounds rescued C. elegans from methicillin-resistant Staphylococcus aureus (MRSA) …
Unraveling The Role Of Hid-1: Insights Into Sgii Regulation,
2024
University of Denver
Unraveling The Role Of Hid-1: Insights Into Sgii Regulation, Breanna L. Sellers
Electronic Theses and Dissertations
The regulated secretory pathway is important for the secretion of hormones and neuropeptides from large dense core vesicles (LDCVs). Dysregulation of the biogenesis of LDCVs can result in metabolic and neurological diseases. Recent studies have suggested that the peripheral membrane protein HID-1 plays a role in the sorting and storage of granins which contribute to LDCV biogenesis. To further understand how HID-1 influences the regulation of granins, we investigated potential HID-1 interactors. We determined that while HID-1 is likely functioning in the same pathway as USP25, a deubiquitinating enzyme (DUB), the cause of reduced cellular SgII levels is likely not …
Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2,
2024
University of Denver
Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire
Electronic Theses and Dissertations
The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …
Structural Basis For Substrate Binding And Selection By Human Mitochondrial Rna Polymerase,
2024
Thomas Jefferson University
Structural Basis For Substrate Binding And Selection By Human Mitochondrial Rna Polymerase, Karl Herbine, Ashok Nayak, Dmitry Temiakov
Department of Biochemistry and Molecular Biology Faculty Papers
The mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM structures of human mitochondrial transcription elongation complexes that reveal substrate ATP bound in Entry and Insertion Sites. In the Entry Site, the substrate binds along the O helix of the fingers domain of mtRNAP but does not interact with the templating DNA base. Interactions between RNAP and the triphosphate moiety of the NTP in the Entry Site ensure discrimination against nucleosides and their diphosphate and monophosphate derivatives but not against non-cognate rNTPs and …
Absolute Quantification Of Human Myosin And Titin Isoforms In Disease By A Mass Spectrometry Approach,
2024
Loyola University of Chicago Graduate School
Absolute Quantification Of Human Myosin And Titin Isoforms In Disease By A Mass Spectrometry Approach, Nitha Aima Muntu
Master's Theses
Heart failure (HF) is the leading cause of death worldwide and produces an immense economic burden. Dilated cardiomyopathy (DCM), characterized by contractile weakness and chamber dilation, is a significant cause of HF. The sarcomeric proteins play a crucial role in regulating the contractile properties of the heart. As the primary motor protein, the expression of cardiac myosin isoforms (α-MHC and β-MHC) dictates the performance and cardiac energy utilization of the sarcomere. Titin is the giant spring protein in the sarcomere, and titin isoform expression impacts the passive stiffness of the myocardium. Small changes in the α-MHC/β-MHC and titin isoform ratios …
Role Of Pycr2 In Colorectal Cancer,
2024
University of Nebraska Medical Center
Role Of Pycr2 In Colorectal Cancer, Raju Lama Tamang
Theses & Dissertations
Despite significant progress in clinical management, colorectal cancer (CRC) remains the 3rd most common cause of cancer-related deaths. A positive association of PYCR2 (Pyrroline-5-carboxylate reductase-2), a terminal enzyme of proline metabolism, with CRC aggressiveness was recently reported including by us. However, how PYCR2 promotes colon carcinogenesis remains ill understood. In our studies, comprehensive in-silico and biochemical evaluations were performed along with genetic manipulations and in-vivo tumor growth assays to gain mechanistic understanding. Results showed that PYCR2 expression was significantly upregulated in CRC and associated with poor patient survival specifically among PYCR isoforms (PYCR-1, -2 and -3). Genetic inhibition of PYCR2 …
Determining If Cx45 Acts As An Arrythmogenic Substrate In The Diseased Myocardium,
2024
University of Nebraska Medical Center
Determining If Cx45 Acts As An Arrythmogenic Substrate In The Diseased Myocardium, Stephen R. Sobota
Theses & Dissertations
Proper contraction of the heart relies on gap junction channels (GJCs) composed of Cx40 and Cx43 in the atrial and ventricular tissues which mediate electrical conductance in the working myocardium. Also expressed is Cx45, which is limited to the pacemaker system. Studies in diseased human hypertrophic cardiac tissue have shown expression of Cx45 and decrease of Cx43 in the myocardium. Cx43 and Cx45 in vitro form heterometric GJCs, where the channel characteristics (metabolite transfer, electrical conductance, etc.) resemble those of Cx45. There is little-to-no data showing whether GJCs composed of Cx43 and Cx45 in cardiac hypertrophy result in altered conductance. …
Enpp1 Enzyme Replacement Therapy Improves Ectopic Calcification But Does Not Rescue Skeletal Phenotype In A Mouse Model For Craniometaphyseal Dysplasia,
2024
Thomas Jefferson University
Enpp1 Enzyme Replacement Therapy Improves Ectopic Calcification But Does Not Rescue Skeletal Phenotype In A Mouse Model For Craniometaphyseal Dysplasia, Ernst Reichenberger, Kevin O'Brien, Ayano Hatori, Thomas Carpenter, Koen Van De Wetering, Lisa Flaman, Jennifer Howe, Daniel Ortiz, Yves Sabbagh, I-Ping Chen
Jefferson Institute of Molecular Medicine Papers and Presentations
Craniometaphyseal dysplasia (CMD) is a rare genetic bone disorder, characterized by progressive thickening of craniofacial bones and flared metaphyses of long bones. Craniofacial hyperostosis leads to the obstruction of neural foramina and neurological symptoms such as facial palsy, blindness, deafness, or severe headache. Mutations in ANKH (mouse ortholog ANK), a transporter of small molecules such as citrate and ATP, are responsible for autosomal dominant CMD. Knock-in (KI) mice carrying an ANKF377del mutation (AnkKI/KI) replicate many features of human CMD. Pyrophosphate (PPi) levels in plasma are significantly reduced in AnkKI/KI mice. PPi is a potent inhibitor of …
Stem-Loop And Circle-Loop Tads Generated By Directional Pairing Of Boundary Elements Have Distinct Physical And Regulatory Properties,
2024
Thomas Jefferson University
Stem-Loop And Circle-Loop Tads Generated By Directional Pairing Of Boundary Elements Have Distinct Physical And Regulatory Properties, Wenfan Ke, Miki Fujioka, Paul Schedl, James Jaynes
Department of Biochemistry and Molecular Biology Faculty Papers
The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary …
Assessment Of Tripeptides Self-Assembly & Er Stress On Cell Viability And Exosome Secretion In Mda-Mb231,
2024
CUNY Hunter College
Assessment Of Tripeptides Self-Assembly & Er Stress On Cell Viability And Exosome Secretion In Mda-Mb231, Azmat Parveen
Theses and Dissertations
This study delves into the effects of tripeptides KYpF and WYpK(NBD) on MDA-MB-231 cells, uncovering KYpF's ability to reduce cell proliferation and exosome secretion in peptide treated cells. Conversely, WYpK(NBD) demonstrated significant toxicity at 10 μM. These insights pave the way for optimizing peptide-based cellular treatments for exosome secretion purposes.
G12/13 Signaling In Asthma,
2024
Thomas Jefferson University
G12/13 Signaling In Asthma, Elizabeth L. Mcduffie, Reynold A Panettieri, Charles P. Scott
Department of Biochemistry and Molecular Biology Faculty Papers
Shortening of airway smooth muscle and bronchoconstriction are pathognomonic for asthma. Airway shortening occurs through calcium-dependent activation of myosin light chain kinase, and RhoA-dependent calcium sensitization, which inhibits myosin light chain phosphatase. The mechanism through which pro-contractile stimuli activate calcium sensitization is poorly understood. Our review of the literature suggests that pro-contractile G protein coupled receptors likely signal through G12/13 to activate RhoA and mediate calcium sensitization. This hypothesis is consistent with the effects of pro-contractile agonists on RhoA and Rho kinase activation, actin polymerization and myosin light chain phosphorylation. Recognizing the likely role of G12/13 signaling in the pathophysiology …
Detection Of Cryptosporidium Spp. In Surface Water And Tissues Of Bivalves In Waterways Of Coney Island, New York (Usa),
2024
Pace University
Detection Of Cryptosporidium Spp. In Surface Water And Tissues Of Bivalves In Waterways Of Coney Island, New York (Usa), Manasvi Patel
Biochemistry and Molecular Biology
Combined sewer overflows (CSOs) are major sources of pollutants such as microbial pathogens, total suspended solids (TSS), oxygen depleting substances, toxicants, and nutrients. Untreated wastewater contains parasites like Giardia, Cryptosporidium and Entamoeba which impact human health. Cryptosporidium is the leading cause of diarrheal diseases which spreads through contaminated water supplies. Our research on Coney Island in Brooklyn investigated the amount of Cryptosporidium oocysts found in the water and bivalves/shellfish tissue and to supports a parallel study examining both people's use of waterways around Coney Island (for religious ceremonies, fishing, foraging, swimming, etc.) and their perceptions of how polluted the …
Furthering Ascidian Taxonomy Using Molecular Biology,
2024
Coastal Carolina University
Furthering Ascidian Taxonomy Using Molecular Biology, Nicholas Gulnick
Electronic Theses and Dissertations
Ascidians are our closest invertebrate relatives and comprise nearly 3,000 species separated into three orders: Aplousobranchia (most speciose), Stolidobranchia, and Phlebobranchia (least speciose). Ascidians can be classified as either solitary or colonial organisms. Species delimitation using morphological characters alone has had varied results. Well known, widely distributed, morphological species have turned out to be catch all species comprised of several cryptic species. Molecular markers can help mitigate some of the issues presented by strictly using morphological observations, including resolving the status of cryptic species, and accessing the expert knowledge required to identify a species. By incorporating molecular markers and pairing …
Deciphering The Wheat Seed Core Mycobiome Of Two Egyptian Cultivars (Giza 171 And Sids 14) By Using High Throughput Amplicon Sequencing Of The Its2 Region,
2024
Faculty of Agriculture
Deciphering The Wheat Seed Core Mycobiome Of Two Egyptian Cultivars (Giza 171 And Sids 14) By Using High Throughput Amplicon Sequencing Of The Its2 Region, Sobhy S.H. Abdelsalam, Muziri Mugwanya, Ahmed G. Gad, Ayman B.A. Basyony
Faculty Journal Articles
Wheat (Triticum aestivum L.) is an important food crop throughout the world. The seed mycobiome is the primary inoculum affecting the overall health and productivity of wheat plants. Seed-borne fungi can have an impact on the production of wheat and cause health complications upon consumption. Therefore, for durable and sustainable wheat production, it is imperative to characterise the wheat mycobiome. The rationale of this study was to investigate the wheat seed mycobiome of two Egyptian wheat cultivars (Sids 14 and Giza 171) using a culture-independent technique. The fungal community in 6 wheat seed samples was identified by high-throughput amplicon sequencing …
Elucidating The Roles Of Septin Proteins In Thermotolerance And Cell Wall Integrity In Cryptococcus Neoformans,
2024
Clemson University
Elucidating The Roles Of Septin Proteins In Thermotolerance And Cell Wall Integrity In Cryptococcus Neoformans, Stephani S. Martinez Barrera
All Dissertations
Cryptococcus neoformans is a globally distributed fungal pathogen responsible for causing cryptococcal meningitis in immunocompromised individuals. This pathogenic yeast must adapt to changes in temperature upon entering the human host. Septin proteins are conserved filament-forming GTPases that assemble as higher-order complexes at the cell cortex to support cytokinesis and morphogenesis in fungal and animal cells. In C. neoformans, four septin homologs (Cdc3, Cdc10, Cdc11, and Cdc12) assemble at the mother-bud neck, contributing to cytokinesis through poorly understood mechanisms. C. neoformans strains lacking the septins Cdc3 or Cdc12 are viable at 25°C, but fail to proliferate at 37°C, and are …
