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2021

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Articles 331 - 360 of 862

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Effect Of Clinical Isolate Or Cleavage Site Mutations In The Sars-Cov-2 Spike Protein On Protein Stability, Cleavage, And Cell-Cell Fusion, Chelsea T. Barrett, Hadley E. Neal, Kearstin Edmonds, Carole L. Moncman, Rachel Thompson, Jean M. Branttie, Kerri Beth Boggs, Cheng-Yu Wu, Daisy W. Leung, Rebecca E. Dutch Jun 2021

Effect Of Clinical Isolate Or Cleavage Site Mutations In The Sars-Cov-2 Spike Protein On Protein Stability, Cleavage, And Cell-Cell Fusion, Chelsea T. Barrett, Hadley E. Neal, Kearstin Edmonds, Carole L. Moncman, Rachel Thompson, Jean M. Branttie, Kerri Beth Boggs, Cheng-Yu Wu, Daisy W. Leung, Rebecca E. Dutch

Molecular and Cellular Biochemistry Faculty Publications

The trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2-infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. A furin cleavage site at the border between the S1 and S2 subunits (S1/S2) has …


Left Ventricular Recovery With Explantation Of Continuous-Flow Left Ventricular Assist Device After 5 Years Of Support, Andre Critsinelis, Chitaru Kurihara, Masashi Kawabori, Tadahisa Sugiura, Andrew B Civitello, Jeffrey A Morgan Jun 2021

Left Ventricular Recovery With Explantation Of Continuous-Flow Left Ventricular Assist Device After 5 Years Of Support, Andre Critsinelis, Chitaru Kurihara, Masashi Kawabori, Tadahisa Sugiura, Andrew B Civitello, Jeffrey A Morgan

Faculty, Staff and Students Publications

Mechanical circulatory support may result in sufficient myocardial recovery to allow for explantation of the left ventricular assist device (LVAD). The duration of support associated with left ventricular recovery has generally been 6-12 months. In this report, we present a patient in whom the left ventricle recovered after 5 years of support with a LVAD. Our report demonstrates that long-term monitoring for left ventricular recovery is prudent and may allow for late device explantation.


A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra Jun 2021

A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …


Annotated Genome Sequence Of The High-Biomass-Producing Yellow-Green Alga Tribonema Minus, Kristina M. Mahan, Jüergen E.W. Polle, Zaid Mckie-Krisberg, Anna Lipzen, Alan Kuo, Igor V. Grigoriev, Todd W. Lane, Aubrey K. Davis Jun 2021

Annotated Genome Sequence Of The High-Biomass-Producing Yellow-Green Alga Tribonema Minus, Kristina M. Mahan, Jüergen E.W. Polle, Zaid Mckie-Krisberg, Anna Lipzen, Alan Kuo, Igor V. Grigoriev, Todd W. Lane, Aubrey K. Davis

Publications and Research

Here, we report the annotated genome sequence for a heterokont alga from the class Xanthophyceae. This high-biomass-producing strain, Tribonema minus UTEX B 3156, was isolated from a wastewater treatment plant in California. It is stable in outdoor raceway ponds and is a promising industrial feedstock for biofuels and bioproducts.


Impacts Of Detritivore Diversity Loss On Instream Decomposition Are Greatest In The Tropics, Luz Boyero, Naiara López-Rojo, Alan M. Tonin, Javier Pérez, Francisco Correa-Araneda, Richard G. Pearson, Jaime Bosch, Ricardo J. Albariño, Sankarappan Anbalagan, Leon A. Barmuta, Ana Basaguren, Francis J. Burdon, Adriano Caliman, Marcos Callisto, Ian C. Campbell, Bradley J. Cardinale, J. Jesús Casas, Ana M. Chará-Serna, Eric Chauvet, Szymon Ciapała, Jose Checo Colón-Gaud, Aydeé Cornejo, Aaron M. Davis, Monika Degebrodt, Emerson S. Dias, María E. Díaz, Michael M. Douglas, Andrea C. Encalada, Ricardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, Erica A. García, Gabriela García, Pavel E. García, Mark O. Gessner, Jesús E. Gómez, Sergio Gómez, Jose F. Gonçalves Jr, Manuel A. S. Graça, Daniel C. Gwinn, Robert O. Hall Jr., Neusa Hamada, Cang Hui, Daichi Imazawa, Tomoya Iwata, Samuel K. Kariuki, Andrea Landeira-Dabarca, Kelsey A. Laymon, María Leal, Richard Marchant, Renato T. Martins, Frank O. Masese, Megan Maul, Brendan G. Mckie, Adriana O. Medeiros, Charles M. M’ Erimba, Jen A. Middleton, Silvia Monroy, Timo Muotka, Junjiro N. Negishi, Alonso Ramírez, John S. Richardson, José Rincón, Juan Rubio-Ríos, Gisele M. Dos Santos, Romain Sarremejane, Fran Sheldon, Augustine Sitati, Nathalie S. D. Tenkiano, Scott D. Tiegs, Janine R. Tolod, Michael Venarsky, Anne Watson, Catherine M. Yule Jun 2021

Impacts Of Detritivore Diversity Loss On Instream Decomposition Are Greatest In The Tropics, Luz Boyero, Naiara López-Rojo, Alan M. Tonin, Javier Pérez, Francisco Correa-Araneda, Richard G. Pearson, Jaime Bosch, Ricardo J. Albariño, Sankarappan Anbalagan, Leon A. Barmuta, Ana Basaguren, Francis J. Burdon, Adriano Caliman, Marcos Callisto, Ian C. Campbell, Bradley J. Cardinale, J. Jesús Casas, Ana M. Chará-Serna, Eric Chauvet, Szymon Ciapała, Jose Checo Colón-Gaud, Aydeé Cornejo, Aaron M. Davis, Monika Degebrodt, Emerson S. Dias, María E. Díaz, Michael M. Douglas, Andrea C. Encalada, Ricardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, Erica A. García, Gabriela García, Pavel E. García, Mark O. Gessner, Jesús E. Gómez, Sergio Gómez, Jose F. Gonçalves Jr, Manuel A. S. Graça, Daniel C. Gwinn, Robert O. Hall Jr., Neusa Hamada, Cang Hui, Daichi Imazawa, Tomoya Iwata, Samuel K. Kariuki, Andrea Landeira-Dabarca, Kelsey A. Laymon, María Leal, Richard Marchant, Renato T. Martins, Frank O. Masese, Megan Maul, Brendan G. Mckie, Adriana O. Medeiros, Charles M. M’ Erimba, Jen A. Middleton, Silvia Monroy, Timo Muotka, Junjiro N. Negishi, Alonso Ramírez, John S. Richardson, José Rincón, Juan Rubio-Ríos, Gisele M. Dos Santos, Romain Sarremejane, Fran Sheldon, Augustine Sitati, Nathalie S. D. Tenkiano, Scott D. Tiegs, Janine R. Tolod, Michael Venarsky, Anne Watson, Catherine M. Yule

Biology: Faculty Publications

The relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods to test the hypothesis that detritivore diversity enhances litter decomposition in streams, to establish the role of other characteristics of detritivore assemblages (abundance, biomass and body size), and to determine how patterns vary across realms, biomes and climates. We observed a positive relationship between diversity and decomposition, strongest in tropical …


Fructose Causes Liver Damage, Polyploidy, And Dysplasia In The Setting Of Short Telomeres And P53 Loss, Christopher Chronowski, Viktor Akhanov, Doug Chan, Andre Catic, Milton Finegold, Ergün Sahin Jun 2021

Fructose Causes Liver Damage, Polyploidy, And Dysplasia In The Setting Of Short Telomeres And P53 Loss, Christopher Chronowski, Viktor Akhanov, Doug Chan, Andre Catic, Milton Finegold, Ergün Sahin

Faculty, Staff and Students Publications

Studies in humans and model systems have established an important role of short telomeres in predisposing to liver fibrosis through pathways that are incompletely understood. Recent studies have shown that telomere dysfunction impairs cellular metabolism, but whether and how these metabolic alterations contribute to liver fibrosis is not well understood. Here, we investigated whether short telomeres change the hepatic response to metabolic stress induced by fructose, a sugar that is highly implicated in non-alcoholic fatty liver disease. We find that telomere shortening in telomerase knockout mice (TKO) imparts a pronounced susceptibility to fructose as reflected in the activation of p53, …


Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur Jun 2021

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.


Vascular Endothelial Senescence: Pathobiological Insights, Emerging Long Noncoding Rna Targets, Challenges And Therapeutic Opportunities, Xinghui Sun, Mark W. Feinberg Jun 2021

Vascular Endothelial Senescence: Pathobiological Insights, Emerging Long Noncoding Rna Targets, Challenges And Therapeutic Opportunities, Xinghui Sun, Mark W. Feinberg

Department of Biochemistry: Faculty Publications

Cellular senescence is a stable form of cell cycle arrest in response to various stressors. While it serves as an endogenous pro-resolving mechanism, detrimental effects ensue when it is dysregulated. In this review, we introduce recent advances for cellular senescence and inflammaging, the underlying mechanisms for the reduction of nicotinamide adenine dinucleotide in tissues during aging, new knowledge learned from p16 reporter mice, and the development of machine learning algorithms in cellular senescence. We focus on pathobiological insights underlying cellular senescence of the vascular endothelium, a critical interface between blood and all tissues. Common causes and hallmarks of endothelial senescence …


Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan Jun 2021

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …


The Role Of Native Lens Α-Crystallin In Amyloid Suppression Using Β-Amyloid As A Model Amyloid Client, Leilani Lopes Jun 2021

The Role Of Native Lens Α-Crystallin In Amyloid Suppression Using Β-Amyloid As A Model Amyloid Client, Leilani Lopes

University Honors Theses

Cataracts are a result of age-related protein aggregate formation in the eye lens, and the leading cause of blindness worldwide. α-crystallin, a small heat shock protein, acts a molecular chaperone that serves as the primary defense mechanism against protein aggregate formation in the lens. Recent evidence suggest amyloid formation in the lens may contribute to cataract formation, and that β-amyloid is present in lens epithelia of age-related cataracts. Previous studies have shown that αB-crystallin in other parts of the body, such as the brain, is protective against neurodegenerative diseases such as Alzheimer’s disease that are associated with plaque deposits containing …


Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner Jun 2021

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …


Molecular Dynamics Simulations Provide Insight Into Stability Of Hyperthermophilic Endoglucanases, Logan E. Sheffield Jun 2021

Molecular Dynamics Simulations Provide Insight Into Stability Of Hyperthermophilic Endoglucanases, Logan E. Sheffield

Electronic Theses and Dissertations

Endoglucanases play a key role in the industrial production of bioethanol, but the most efficient method requires the utilization of high temperatures and is currently limited by the thermostability of endoglucanases. For this reason, it would be beneficial to discover more high-efficiency, thermostable enzymes to utilize in the hydrolytic process. In this study molecular dynamics simulations were performed on structurally similar endoglucanases with varying levels of thermostability to gain insight on what factors contribute to thermostability in endoglucanases. RMSD, RMSF, PCA, hydrogen bonding and salt bridges were analyzed. Finally, protein energy networks were constructed from nonbonded interaction potentials and analysis …


Development And Validation Of Machine Learning-Based Race-Specific Models To Predict 10-Year Risk Of Heart Failure: A Multicohort Analysis, Matthew W Segar, Byron C Jaeger, Kershaw V Patel, Vijay Nambi, Chiadi E Ndumele, Adolfo Correa, Javed Butler, Alvin Chandra, Colby Ayers, Shreya Rao, Alana A Lewis, Laura M Raffield, Carlos J Rodriguez, Erin D Michos, Christie M Ballantyne, Michael E Hall, Robert J Mentz, James A De Lemos, Ambarish Pandey Jun 2021

Development And Validation Of Machine Learning-Based Race-Specific Models To Predict 10-Year Risk Of Heart Failure: A Multicohort Analysis, Matthew W Segar, Byron C Jaeger, Kershaw V Patel, Vijay Nambi, Chiadi E Ndumele, Adolfo Correa, Javed Butler, Alvin Chandra, Colby Ayers, Shreya Rao, Alana A Lewis, Laura M Raffield, Carlos J Rodriguez, Erin D Michos, Christie M Ballantyne, Michael E Hall, Robert J Mentz, James A De Lemos, Ambarish Pandey

Faculty, Staff and Students Publications

BACKGROUND: Heart failure (HF) risk and the underlying risk factors vary by race. Traditional models for HF risk prediction treat race as a covariate in risk prediction and do not account for significant parameters such as cardiac biomarkers. Machine learning (ML) may offer advantages over traditional modeling techniques to develop race-specific HF risk prediction models and to elucidate important contributors of HF development across races.

METHODS: We performed a retrospective analysis of 4 large, community cohort studies (ARIC [Atherosclerosis Risk in Communities], DHS [Dallas Heart Study], JHS [Jackson Heart Study], and MESA [Multi-Ethnic Study of Atherosclerosis]) with adjudicated HF events. …


Attenuated Strain Of Cvb3 With A Mutation In The Car‑Interacting Region Protects Against Both Myocarditis And Pancreatitis, Ninaad Lasrado, Arunakumar Gangaplara, Chandirasegaran Massilamany, Rajkumar Arumugam, Allison Shelbourn, Mahima T. Rasquinha, Rakesh H. Basavalingappa, Gustavo Delhon, Shi-Hua Xiang, Asit K. Pattnaik, David Steffen, Jay Reddy Jun 2021

Attenuated Strain Of Cvb3 With A Mutation In The Car‑Interacting Region Protects Against Both Myocarditis And Pancreatitis, Ninaad Lasrado, Arunakumar Gangaplara, Chandirasegaran Massilamany, Rajkumar Arumugam, Allison Shelbourn, Mahima T. Rasquinha, Rakesh H. Basavalingappa, Gustavo Delhon, Shi-Hua Xiang, Asit K. Pattnaik, David Steffen, Jay Reddy

School of Veterinary and Biomedical Sciences: Faculty Publications

Coxsackievirus B3 (CVB3), is commonly implicated in myocarditis, which can lead to dilated cardiomyopathy, in addition to causing acute pancreatitis and meningitis. Yet, no vaccines are currently available to prevent this infection. Here, we describe the derivation of a live attenuated vaccine virus, termed mutant (Mt) 10, encoding a single amino acid substitution H790A within the viral protein 1, that prevents CVB3 infection in mice and protects from both myocarditis and pancreatitis in challenge studies. We noted that animals vaccinated with Mt 10 developed virus neutralizing antibodies, predominantly containing IgG2a and IgG2b, and to a lesser extent IgG3 and IgG1. …


Targeting The Apoa1 Locus For Liver-Directed Gene Therapy, Marco De Giorgi, Ang Li, Ayrea Hurley, Mercedes Barzi, Alexandria M Doerfler, Nikitha A Cherayil, Harrison E Smith, Jonathan D Brown, Charles Y Lin, Karl-Dimiter Bissig, Gang Bao, William R Lagor Jun 2021

Targeting The Apoa1 Locus For Liver-Directed Gene Therapy, Marco De Giorgi, Ang Li, Ayrea Hurley, Mercedes Barzi, Alexandria M Doerfler, Nikitha A Cherayil, Harrison E Smith, Jonathan D Brown, Charles Y Lin, Karl-Dimiter Bissig, Gang Bao, William R Lagor

Faculty, Staff and Students Publications

Clinical application of somatic genome editing requires therapeutics that are generalizable to a broad range of patients. Targeted insertion of promoterless transgenes can ensure that edits are permanent and broadly applicable while minimizing risks of off-target integration. In the liver, the Albumin (Alb) locus is currently the only well-characterized site for promoterless transgene insertion. Here, we target the Apoa1 locus with adeno-associated viral (AAV) delivery of CRISPR-Cas9 and achieve rates of 6% to 16% of targeted hepatocytes, with no evidence of toxicity. We further show that the endogenous Apoa1 promoter can drive robust and sustained expression of therapeutic …


Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan Jun 2021

Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan

Mathematics Faculty Publications

The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as …


Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed Jun 2021

Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed

Honors Scholar Theses

Parkinson's Disease (PD) is a progressive neurodegenerative and movement disorder primarily caused by the degradation of dopaminergic neurons. Known markers of neurodegeneration in PD are Lewy Bodies, which are fibrillar aggregates that are found in the brains of PD patients. Lewy Bodies can accumulate from specific mutations in the SNCA gene that codes for alpha-synuclein, a protein enriched in presynaptic neurons. A mutated SNCA gene can cause conformational aggregates of alpha-synuclein to form toxic species mediating neuronal death. Research into alpha-synuclein has led to the discovery of a binding partner known as synphilin-1 that is also found in protein aggregates …


Circrev1 Expression In Triple-Negative Breast Cancer, Meagan P. Horton Jun 2021

Circrev1 Expression In Triple-Negative Breast Cancer, Meagan P. Horton

USF Tampa Graduate Theses and Dissertations

Triple-negative breast cancer (TNBC) comprises only 24% of breast cancer cases, yet is the second leading cause of cancer mortality in women due to its aggressive nature (1). This increase in mortality is due to the lack of receptors for three targetable growth factors (HER2, progesterone, and estrogen receptors). Our previous studies have indicated that these cancers are highly dysregulated in respect to alternative splicing. Hence, we undertook a study aimed at identifying circular RNAs (circRNAs) generated from back-splicing events which were dysregulated in TNBC. We have identified a novel circRNA transcript, circular REV1 (circREV1), which is upregulated in our …


Evidence-Based Approach To Early Outpatient Treatment Of Sars-Cov-2 (Covid-19) Infection, J Drew Payne, Kimberly Sims, Cynthia Peacock, Tanis Welch, Ruth E Berggren Jun 2021

Evidence-Based Approach To Early Outpatient Treatment Of Sars-Cov-2 (Covid-19) Infection, J Drew Payne, Kimberly Sims, Cynthia Peacock, Tanis Welch, Ruth E Berggren

Faculty, Staff and Students Publications

Misinformation and promotion of well-intended but disproved therapies for COVID-19 have plagued evidence-based shared decision-making throughout the COVID-19 pandemic. In times of crisis, clinicians may feel that their strong inclination to prescribe potentially harmful, unproven therapies on behalf of their patients is supported by beneficence. Clinicians should mindfully identify and avoid commission bias during this pandemic, especially as more data have accumulated to assist with clinically sound decision-making. We describe a more evidence-based approach to treatment of early outpatient COVID-19, stressing the availability of Food and Drug Administration emergency use authorization therapies and considering plausibly beneficial, nonprescription supplements that are …


Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina Jun 2021

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …


Rapid Warming Events In A Small Coastal Upwelling Embayment, Tatjana E. Ellis Jun 2021

Rapid Warming Events In A Small Coastal Upwelling Embayment, Tatjana E. Ellis

Physics

Temperature variability in the nearshore coastal ocean influences various biological processes and can drive changes in biodiversity and habitat range. Despite recent progress, there are still significant gaps in the understanding of drivers of temperature variability in upwelling bays, particularly at higher frequencies. In this study, we analyzed a decade of nearshore temperature measurements both inside and outside a small coastal embayment located in central California [San Luis Obispo (SLO) bay], as well as temperature data from satellites, to characterize rapid warming events. We found that rapid warming events, defined using rates of temperature change across different thresholds, occurred more …


Computational Prediction Of Mutagenesis In Glycine Max Rubisco Activase Monomer For Increased Thermal Stability, Catherine B. Emanuel, Hamza Haq '21, Vasanth Ramesh '21, Jaden Wang '21, Angela Ahrendt, Sarah Stainbrook Jun 2021

Computational Prediction Of Mutagenesis In Glycine Max Rubisco Activase Monomer For Increased Thermal Stability, Catherine B. Emanuel, Hamza Haq '21, Vasanth Ramesh '21, Jaden Wang '21, Angela Ahrendt, Sarah Stainbrook

Student Publications & Research

No abstract provided.


Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea Jun 2021

Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea

Physics Faculty Publications and Presentations

Liposomes are spherical-shaped vesicles that enclose an aqueous milieu surrounded by bilayer or multilayer membranes formed by self-assembly of lipid molecules. They are intensively exploited as either model membranes for fundamental studies or as vehicles for delivery of active substances in vivo and in vitro. Irrespective of the method adopted for production of loaded liposomes, obtaining the final purified product is often achieved by employing multiple, time consuming steps. To alleviate this problem, we propose a simplified approach for concomitant production and purification of loaded liposomes by exploiting the Electrodialysis-Driven Depletion of charged molecules from solutions. Our investigations show that …


Molecular Mechanisims Underlying The Anti-Cancer Activity Of Gum Arabic From Acacia Sp. In Triple-Negative Breast Cancer Cells, Sawsan Yaslam Hussein Alyafii Jun 2021

Molecular Mechanisims Underlying The Anti-Cancer Activity Of Gum Arabic From Acacia Sp. In Triple-Negative Breast Cancer Cells, Sawsan Yaslam Hussein Alyafii

Theses

Metastatic breast cancer is the leading cause of cancer-related deaths among women worldwide. Triple-negative breast cancer (TNBC) is the most aggressive, accounting for 15-20% of all breast cancer cases. As TNBC cells lack the expression of hormone receptors estrogen receptors (ER) and progesterone receptors (PR) and human epidermal growth factor receptor 2 (HER2), TNBCs are unresponsive to hormonal therapy and often become highly resistant when exposed to standard chemotherapy, which has been identified as a major obstacle in TNBC treatment. Gum Arabic, a natural exudate produced from plants, is widely used traditionally for religious, cosmetics as well as medicinal purposes …


The Role Of Nutrient Sensitive Protein O-Glcnacylation In Developmental Cortical Neurogenesis, Shama Parween Jun 2021

The Role Of Nutrient Sensitive Protein O-Glcnacylation In Developmental Cortical Neurogenesis, Shama Parween

Dissertations

The nutrient responsive O-GlcNAcylation is a dynamic, posttranslational protein modification present on many nucleocytoplasmic and mitochondrial proteins. Previous research has indicated that hyperglycaemia increases the levels of total O-GlcNAcylation within cells. Transcription factors and histones are among hundreds of proteins that have been reported to be O-GlcNAcylated and have importance in cell fate determination during cell growth, proliferation, and differentiation. However, the role of protein O-GlcNAcylation in epigenome control in response to nutritional perturbations is poorly understood. Hyperglycaemia induced protein O-GlcNAcylation have been linked to several pathologies, including obesity, diabetes, cancer, cardiovascular and neurodegenerative diseases. …


Tailored Porous Carbons Enabled By Persistent Micelles With Glassy Cores, Eric R. Williams, Paige L. Mcmahon, Joseph E. Reynolds Iii, Jonathan L. Snider, Vitalie Stavila, Mark Allendorf, Morgan Stefik Jun 2021

Tailored Porous Carbons Enabled By Persistent Micelles With Glassy Cores, Eric R. Williams, Paige L. Mcmahon, Joseph E. Reynolds Iii, Jonathan L. Snider, Vitalie Stavila, Mark Allendorf, Morgan Stefik

Faculty Publications

Porous nanoscale carbonaceous materials are widely employed for catalysis, separations, and electrochemical devices where device performance often relies upon specific and well-defined regular feature sizes. The use of block polymers as templates has enabled affordable and scalable production of diverse porous carbons. However, popular carbon preparations use equilibrating micelles which can change dimensions in response to the processing environment. Thus, polymer methods have not yet demonstrated carbon nanomaterials with constant average template diameter and tailored wall thickness. In contrast, persistent micelle templates (PMTs) use kinetic control to preserve constant micelle template diameters, and thus PMT has enabled constant pore diameter …


College Of Natural Sciences Newsletter, June 2021, College Of Natural Sciences Jun 2021

College Of Natural Sciences Newsletter, June 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 6.

Page 1 Dean's Message
Page 2-6 Remembering the Life of Dr. Pengra and Celebrating His legacy for Entire Generations to Come.


Novel Facet Of An Old Dietary Molecule? Direct Influence Of Caffeine On Glucose And Biogenic Amine Handling By Human Adipocytes, Wiem Haj Ahmed, Nathalie Boulet, Anaïs Briot, Barry J. Ryan, Gemma K. Kinsella, Jeffrey O’Sullivan, Francisco Les, Josep Mercader-Barceló, Gary T. Henehan, Christian Carpéné Jun 2021

Novel Facet Of An Old Dietary Molecule? Direct Influence Of Caffeine On Glucose And Biogenic Amine Handling By Human Adipocytes, Wiem Haj Ahmed, Nathalie Boulet, Anaïs Briot, Barry J. Ryan, Gemma K. Kinsella, Jeffrey O’Sullivan, Francisco Les, Josep Mercader-Barceló, Gary T. Henehan, Christian Carpéné

Articles

Caffeine is a plant alkaloid present in food and beverages consumed worldwide. It has high lipid solubility with recognized actions in the central nervous system and in peripheral tissues, notably the adipose depots. However, the literature is scant regarding caffeine’s influence on adipocyte functions other than lipolysis, such as glucose incorporation into lipids (lipogenesis) and amine oxidation. The objective of this study was to explore the direct effects of caffeine and of isobutylmethylxanthine (IBMX) on these adipocyte functions. Glucose transport into fat cells freshly isolated from mice, rats, or humans was monitored by determining [3H]-2-deoxyglucose (2-DG) uptake, while the incorporation …


Diffusive Search And Trajectories On Tubular Networks A Propagator Approach, Zubenelgenubi C. Scott, Aidan I. Brown, Saurabh S. Mogre, Laura M. Westrate Jun 2021

Diffusive Search And Trajectories On Tubular Networks A Propagator Approach, Zubenelgenubi C. Scott, Aidan I. Brown, Saurabh S. Mogre, Laura M. Westrate

University Faculty Publications and Creative Works

Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins diffusively searching through the network to encounter binding partners or localized target regions. Predicting the behavior of such pathways requires a quantitative understanding of how confinement to a reticulated structure modulates reaction kinetics. In this work, we develop both exact analytical methods to compute mean first passage times and efficient kinetic Monte Carlo algorithms to simulate trajectories of particles diffusing in a tubular network. Our approach leverages exact propagator functions …


Design, Synthesis And Evaluation Of Molecules With Selective And Poly-Pharmacological Actions At D1r, D3r And Sigma Receptors, Pierpaolo Cordone Jun 2021

Design, Synthesis And Evaluation Of Molecules With Selective And Poly-Pharmacological Actions At D1r, D3r And Sigma Receptors, Pierpaolo Cordone

Dissertations, Theses, and Capstone Projects

The dopamine D3 receptor (D3R) is one of the most studied receptors involved in drug addiction. One of the most common strategies to treat substance use disorders is via D3R antagonism. The majority of the D3R antagonists synthesized so far have poor pharmacokinetic properties and/or lack selectivity toward D3R. In this thesis, the design, synthesis and biological evaluation of novel molecules that target the dopamine D1 receptor (D1R), D3R and the serendipitous discovery of molecules that target s receptors will be described.

Chapter 1 presents a survey of the fundamental pharmacology of D1R, D3R and s receptors and the therapeutic …