A New CURE in Molecular Biology: Testing a Novel Pyrrolidine Compound to Determine Mechanism of Action in an Upper-Division Molecular Biology Course

The COVID-19 pandemic shut down forced introductory biology and chemistry laboratory courses online at DePauw University from March 2020-June 2021, leaving multiple classes of students without the opportunity to learn basic laboratory skills that are essential for the molecular biology laboratory. In an effort to provide students with both basic laboratory skills and advanced molecular biology skills, a new course-based undergraduate research experience (CURE) was developed for the 2022-23 academic year. In collaboration with Dr. Jeff Hansen in the Chemistry and Biochemistry department, novel compounds with potential anti-tumor properties were identified. The CURE in Molecular Biology was designed to have students use Saccharomyces cerevisiae as a model system to evaluate possible cellular pathways affected by the compound, including: cytoskeleton and cell migration, nucleotide biosynthesis, glucose metabolism, apoptosis, and cell cycle regulation. Students learned techniques DNA isolation and PCR, transformation, RNA isolation, cDNA synthesis, qPCR, and Western Blotting, while contributing to an active research project. At the conclusion of the project, students were surveyed about their comfort with molecular techniques and data analysis.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Post-translational modifications: Host defence mechanism, pathogenic weapon, and emerged target of anti-infective drugs

Post-translational modifications are changes introduced to proteins after their translation. They are the means to generate molecular diversity, expand protein function, control catalytic activity and trigger quick responses to a wide range of stimuli. Moreover, they regulate numerous biological processes, including pathogen invasion and host defence mechanisms. It is well established that bacteria and viruses utilize post-translational modifications on their own or their host's proteins to advance their pathogenicity. Doing so, they evade immune responses, target signaling pathways and manipulate host cytoskeleton to achieve survival, replication and propagation. Many bacterial species secrete virulence factors into the host and mediate hostpathogen interactions by inducing post-translational modifications that subvert fundamental cellular processes. Viral pathogens also utilize post translational modifications in order to overcome the host defence mechanisms and hijack its cellular machinery for their replication and propagation. For example, many coronavirus proteins are modified to achieve host invasion, evasion of immune responses and utilization of the host translational machinery. PTMs are also considered potential targets for the development of novel therapeutics from natural products with antibiotic properties, like lasso peptides and lantibiotics. The last decade, significant progress was made in understanding the mechanisms that govern PTMs and mediate regulation of protein structure and function. This urges the identification of relevant molecular targets, the design of specific drugs and the discovery of PTM-based medicine. Therefore, PTMs emerge as a highly promising field for the investigation and discovery of new therapeutics for many infectious diseases.Copyright © 2021 Bentham Science Publishers.

The regulation of host cytoskeleton during SARS-CoV-2 infection in the nervous system

The global economy and public health are currently under enormous pressure since the outbreak of COVID-19. Apart from respiratory discomfort, a subpopulation of COVID-19 patients exhibits neurological symptoms such as headache, myalgia, and loss of smell. Some have even shown encephalitis and necrotizing hemorrhagic encephalopathy. The cytoskeleton of nerve cells changes drastically in these pathologies, indicating that the cytoskeleton and its related proteins are closely related to the pathogenesis of nervous system diseases. In this review, we present the up-to-date association between host cytoskeleton and coronavirus infection in the context of the nervous system. We systematically summarize cytoskeleton-related pathogen-host interactions in both the peripheral and central nervous systems, hoping to contribute to the development of clinical treatment in COVID-19 patients.

Administration of Exogenous Surfactant and Cytosolic Phospholipase A2alpha Inhibitors may Help COVID-19 Infected Patients with Chronic Diseases

Background: Coronavirus-19 (COVID-19) pandemic is a worldwide public health problem causing 347,070 deaths from December 25, 2019, till May 25, 2020. Phospholipids are structural components of mammalian cytoskeleton and cell membranes. Phosphatidylglycerol is an anionic lipid found in mammalian membranes in low amounts (1-2%) of the total phospholipids. Also, phosphatidylglycerol suppresses viral attachment to the plasma membrane and subsequent replication in lung cells. Phosphatidylglycerol depletion caused by over expression of cytosolic phos-pholipase A2alpha induces lipid accumulation in lung alveoli and promotes acute respiratory distress syndrome (ARDS). An exogenous-surfactant replacement has been successfully achieved in ARDS and improved oxygenation and lung mechanics. Inhibition of cytosolic phospholipase A2alpha impairs an early step of COVID-19 replication. Aim(s): The present study was carried out to explain the correlation between the administration of exogenous artificial surfactant as well as cytosolic phospholipase A2alpha inhibitors to improve oxygenation and lung mechanics and inhibit COVID-19 replication. Method(s): Database research was carried out on Medline, Embase, Cochrane Library, country-spe-cific journals, and following-up WHO reports published between December 25, 2019-May 25, 2020. Result(s): Till 25 May 2020, coronavirus cases were 5,307,298, with 347,070 deathsand 2,314,849 recovered cases. According to the WHO reports, most COVID-19 deaths seen are in people who suffered from other chronic diseases characterized by phospholipidosis and phosphatidylglycerol deficiency, including hypertension, liver, heart, and lung diseases and diabetes. Phospholipases A2 (PLA2) catalyze the cleavage of fatty acids esterified at the sn-2 position of glycerophospholipids leading to enhanced inflammation and lung damage. Also, cytosolic phospholipase A2alpha inhibitors may reduce the accumulation of viral proteins and RNA. In addition, administration of exogenous phospholipid surfactant may help COVID-19 infected patients with ARDS to remove inflammatory mediators. Conclusion(s): The present study showed a relation between phosphatidylglycerol deficiency in COVID-19 infected patients with ARDS and/or chronic diseases and their mortality. These findings also showed an important approach for the prevention and treatment of COVID-19 infections by using cytosolic phospholipase A2alpha inhibitors and exogenous administration of a specific phos-pholipid surfactant.Copyright © 2021 Bentham Science Publishers.

Ultrastructural analysis and three-dimensional reconstruction of cellular structures involved in SARS-CoV-2 spread.

The cytoskeleton not only deals with numerous interaction and communication mechanisms at the cellular level but also has a crucial role in the viral infection cycle. Although numerous aspects of SARS-CoV-2 virus interaction at the cellular level have been widely studied, little has been reported about the structural and functional response of the cytoskeleton. This work aims to characterize, at the ultrastructural level, the modifications in the cytoskeleton of infected cells, namely, its participation in filopodia formation, the junction of these nanostructures forming bridges, the viral surfing, and the generation of tunnel effect nanotubes (TNT) as probable structures of intracellular viral dissemination. The three-dimensional reconstruction from the obtained micrographs allowed observing viral propagation events between cells in detail for the first time. More profound knowledge about these cell-cell interaction models in the viral spread mechanisms could lead to a better understanding of the clinical manifestations of COVID-19 disease and to find new therapeutic strategies.

Small-Molecule RAF265 as an Antiviral Therapy Acts against PEDV Infection.

Porcine epidemic diarrhea virus (PEDV), a member of the family Coronaviridae, causes acute diarrhea, vomiting, dehydration, and high mortality in newborn piglets, and has caused significant economic losses in the pig industry. There are currently no specific drugs available to treat PEDV. Viruses depend exclusively on the cellular machinery to ensure an efficient replication cycle. In the present study, we found that small-molecule RAF265, an anticancer drug that has been shown to be a potent inhibitor of RAF, reduced viral loads of PEDV by 4 orders of magnitude in Vero cells, and protected piglets from virus challenge. RAF265 reduced PEDV production by mediating cytoskeleton arrangement and targeting the host cell's translation machinery. Treatment with RAF265 inhibited viral entry of PEDV S-glycoprotein pseudotyped viral vector particle (PEDV-pp), at half maximal effective concentrations (EC50) of 79.1 nM. RAF265 also presented potent inhibitory activity against viral infection by SARS-CoV-2-pp and SARS-CoV-pp. The present work may provide a starting point for further progress toward the development of antiviral strategies effective against coronavirus PEDV.

The REEP family of proteins: Molecular targets and role in pathophysiology.

Receptor expression-enhancing proteins (REEPs) are an evolutionarily conserved protein family that is pivotal to the structure and function of the endoplasmic reticulum (ER). The REEP family can be classified into two major subfamilies in higher species, the REEP1-4 and REEP5-6 subfamilies. Within the REEP1-4 subfamily, REEP1 and REEP2 are closely related, and REEP3 and REEP4 are similarly related. The REEP family is widely distributed in various tissues. Recent studies indicate that the REEP family is involved in many pathological and physiological processes, such as ER morphogenesis and remodeling, microtubule cytoskeleton regulation, and the trafficking and expression of G protein-coupled receptors (GPCRs). Moreover, the REEP family plays crucial roles in the occurrence and development of many diseases, including neurological diseases, diabetes, retinal diseases, cardiac diseases, infertility, obesity, oligoarticular juvenile idiopathic arthritis (OJIA), COVID-19, and cancer. In the present review, we describe the distribution and structure of the REEP family. Furthermore, we summarize the functions and the associated diseases of this family. Based on the pleiotropic actions of the REEP family, the study of its family members is crucial to understanding the relevant pathophysiological processes and developing strategies to modulate and control these related diseases.

Actin cytoskeleton remodeling primes RIG-I-like receptor activation.

The current dogma of RNA-mediated innate immunity is that sensing of immunostimulatory RNA ligands is sufficient for the activation of intracellular sensors and induction of interferon (IFN) responses. Here, we report that actin cytoskeleton disturbance primes RIG-I-like receptor (RLR) activation. Actin cytoskeleton rearrangement induced by virus infection or commonly used reagents to intracellularly deliver RNA triggers the relocalization of PPP1R12C, a regulatory subunit of the protein phosphatase-1 (PP1), from filamentous actin to cytoplasmic RLRs. This allows dephosphorylation-mediated RLR priming and, together with the RNA agonist, induces effective RLR downstream signaling. Genetic ablation of PPP1R12C impairs antiviral responses and enhances susceptibility to infection with several RNA viruses including SARS-CoV-2, influenza virus, picornavirus, and vesicular stomatitis virus. Our work identifies actin cytoskeleton disturbance as a priming signal for RLR-mediated innate immunity, which may open avenues for antiviral or adjuvant design.

GLOMERULAR HYPERFILTRATION MAY CONTRIBUTE TO RENAL TROPISM AND KIDNEY INJURY IN COVID-19 BY UPREGULATING ACE2 IN HUMAN PODOCYTES

Objective: Apart from the respiratory system, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can potentially infect multiple other organs including podocytes in the kidney. The latter play a crucial role in glomerular filtration. Podocytes can be damaged by increased fluid flow shear stress (FFSS) of the ultrafiltrate in Bowman's space in the setting of glomerular hyperfiltration that occurs in disease states such as hypertension, diabetes or in several forms of chronic kidney disease. These conditions are associated with an increased risk of a more severe course of coronavirus disease 2019 (COVID-19) and mortality. Design and method: To assess the susceptibility of human podocytes (hPC) for SARS-CoV-2 infection in the context of hyperfiltration in vitro, we used a recently established model system (Streamer Shear Stress Device)) to mimic hyperfiltration by exposing hPC to increased FFSS of 1 dyne/cm2 for 2 h. In this setting we nalysed the effects of FFSS on mRNA expression of angiotensin I-converting enzyme 2 (ACE2) as the pivotal entry receptor for SARS-CoV-2 infection in hPC. Moreover, other potential critical host cell factors including transmembrane serine protease 2 (TMPRSS2), furin (FURIN), and neuropilin 1 (NRP1) were also assessed in parallel with changes of the F-actin fiber structure, i.e. an important cytoskeletal marker in hPC. Results: Under control conditions, hPC displayed long, parallel F-actin fibers crossing the entire cell body. After FFSS, an enrichment of cells that express F-actin in a cortically condensed pattern near the cell membrane was observed. FFSS induced a significant upregulation of ACE2 expression (about twofold) and of all other nalysed SARS-CoV-2 entry factors in hPC (p < 0.05, respectively compared to control conditions, Figure 1 with data plotted as log2fold change [FC]). Conclusions: Our data support a potential link between glomerular hyperfiltration, podocyte damage and renal tropism of SARS-CoV-2 that may contribute to kidney damage including albuminuria development in COVID-19 patients.

A rare case of cardiomyopaty: a case report

A 46-years old Egyptian man was admitted to our department because of the onset of worsening dyspnea. In his clinical history were present: hypothyroidism, obesity, hyperuricemia, hypertension and recent Sars-Cov2 infection. Bilateral pleuric effusion was suspected during physical examination and confirmed by chest CT. Blood data showed mild macrocytic anemia, increased levels of creatinine, transaminases, pro-BNP (3574 pg/ml cut-off 0-125) and D-dimer. Multiple molecular swabs for research of Sars-Cov2 were negative. ECG showed sinus rhythm and non specific atypia of repolarization. An eco-fast was performed at bedside and revelead left ventricular dilatation and severe systolic disfunction due to diffuse hypokinesia (EF 30%). Diuretic therapy was set up with improvement of the clinical status. In order to exclude ischaemic genesis of the cardiopathy a coronary angiography was performed without evidence of obstructive lesions. An echocardiogram was repeated and it showed a parietal ipertrabeculation of the left ventricle. This aspect was suggestive of non-compact myocardium, a rare disease due to the arrest of the myocardial maturation process during fetal development, leading to the persistence of embryonic structures in the heart muscle. Genetic inheritance arises in 30-50% of patients and are involved genes that generally seem to encode sarcomeric or cytoskeletal proteins.Cardiac MRI is planned in order to have further confirmation of our diagnostic hypothesis. In the meantime wearable defibrillator was prescribed for the prevention of sudden death.

The mammalian endocytic cytoskeleton.

Clathrin-mediated endocytosis (CME) is the major route through which cells internalise various substances and recycle membrane components. Via the coordinated action of many proteins, the membrane bends and invaginates to form a vesicle that buds off-along with its contents-into the cell. The contribution of the actin cytoskeleton to this highly dynamic process in mammalian cells is not well understood. Unlike in yeast, where there is a strict requirement for actin in CME, the significance of the actin cytoskeleton to mammalian CME is variable. However, a growing number of studies have established the actin cytoskeleton as a core component of mammalian CME, and our understanding of its contribution has been increasing at a rapid pace. In this review, we summarise the state-of-the-art regarding our understanding of the endocytic cytoskeleton, its physiological significance, and the questions that remain to be answered.

Comparative miRNA transcriptomics of macaques and mice reveals MYOC is an inhibitor for Cryptococcus neoformans invasion into the brain.

Cryptococcal meningoencephalitis (CM) is emerging as an infection in HIV/AIDS patients shifted from primarily ART-naive to ART-experienced individuals, as well as patients with COVID-19 and immunocompetent hosts. This fungal infection is mainly caused by the opportunistic human pathogen Cryptococcus neoformans. Brain or central nervous system (CNS) dissemination is the deadliest process for this disease; however, mechanisms underlying this process have yet to be elucidated. Moreover, illustrations of clinically relevant responses in cryptococcosis are currently limited due to the low availability of clinical samples. In this study, to explore the clinically relevant responses during C. neoformans infection, macaque and mouse infection models were employed and miRNA-mRNA transcriptomes were performed and combined, which revealed cytoskeleton, a major feature of HIV/AIDS patients, was a centric pathway regulated in both infection models. Notably, assays of clinical immune cells confirmed an enhanced macrophage "Trojan Horse" in patients with HIV/AIDS, which could be shut down by cytoskeleton inhibitors. Furthermore, myocilin, encoded by MYOC, was found to be a novel enhancer for the macrophage "Trojan Horse," and an enhanced fungal burden was achieved in the brains of MYOC-transgenic mice. Taken together, the findings from this study reveal fundamental roles of the cytoskeleton and MYOC in fungal CNS dissemination, which not only helps to understand the high prevalence of CM in HIV/AIDS but also facilitates the development of novel therapeutics for meningoencephalitis caused by C. neoformans and other pathogenic microorganisms.

RAGE/Diaph1, Diabetes, and Kidney Disease: Mechanisms and Novel Therapeutic Strategies

In Year Three of the funded grant, we have substantial progress in the following critical areas: 1). As noted in the project narrative, we generated four different lines of mice to directly test the hypothesis that RAGE and DIAPH1 contribute to the pathogenesis of diabetes-associated nephropathy in the podocytes and/or in myeloid cells/macrophages. All of the mouse lines are now generated and largely completed (mice sacrificed) and samples being evaluation by Dr DAgati. There are no new pending mice to generate all are generated and on time course. 2). We have determined that the small molecule RAGE/DIAPH1 antagonist is best administered orally and that the RAGE antagonist survives the medicated chow pelleting, heating and irradiation. Our first data on treated vs. untreated male and female diabetic mice illustrates reduction in mesangial sclerosis, reduced thickening of the glomerular basement membrane and reduction in podocyte effacement in diabetic mice receiving RAGE229 medicated chow (vs vehicle). Additional mice are on study and time course at this time to complete the indicated enrollment.3). For transcriptomics and metabolomics/lipidomics assay, Dr. Ramasamy will be testing the macrophages from the mice through the time course and he has verified all of his experimental systems for the performance of the outlined studies. Dr. Ramasamy identifies substantial progress in the development and validation of metabolomics and lipidomics assays here at NYU and in transcriptomic data (all on macrophages) in order to understand detailed mechanisms of the role of these molecules in the diabetic kidney. Taken together, despite the >3 month shutdown due to COVID19 our work in Year 3 has been productive and we await tissue and other analyses, as above, to render final conclusions.

Vaccine Design from the Microtubules Role in Coronavirus Entry and Exit: A Molecular Dynamic and Docking Simulation

The accurate assembling of microtubules identifies microtubular filaments for a coronavirus that directs the site of viral. By this work, we are able to design a peptide-based multi-epitope vaccine from the surface glycoprotein inside the microtubules via molecular dynamic and docking simulation.Therefore, cell-mediated immunity can be killing the viral particles of the coronavirus. Predicted epitopes were merged using appropriate linkers to increase the immunogenicity of the vaccine. A wide range of bioinformatics analyses was accomplished based on published biological protein sequences in this study. Using molecular docking technology of Discovery-Studio 201673, the receptor-ligand docking of viral proteins with human heme (or porphyrins) was simulated.

Topological Relationships Cytoskeleton-Membrane Nanosurface-Morphology as a Basic Mechanism of Total Disorders of RBC Structures.

The state of red blood cells (RBCs) and their functional possibilities depend on the structural organization of the membranes. Cell morphology and membrane nanostructure are compositionally and functionally related to the cytoskeleton network. In this work, the influence of agents (hemin, endogenous oxidation during storage of packed RBCs, ultraviolet (UV) radiation, temperature, and potential of hydrogen (pH) changes) on the relationships between cytoskeleton destruction, membrane nanostructure, and RBC morphology was observed by atomic force microscope. It was shown that the influence of factors of a physical and biochemical nature causes structural rearrangements in RBCs at all levels of organization, forming a unified mechanism of disturbances in relationships "cytoskeleton-membrane nanosurface-cell morphology". Filament ruptures and, consequently, large cytoskeleton pores appeared. The pores caused membrane topological defects in the form of separate grain domains. Increasing loading doses led to an increase in the number of large cytoskeleton pores and defects and their fusion at the membrane nanosurfaces. This caused the changes in RBC morphology. Our results can be used in molecular cell biology, membrane biophysics, and in fundamental and practical medicine.

Vimentin and its role as a biomarker in health and disease

Vimentin is an intermediate filament protein responsible for maintaining cellular integrity and resistance to stress. It has a widespread distribution in many cells throughout the body where it forms a cytoskeletal framework. Vimentin plays an important role in the regulation of many cellular and tissue functions. It is overexpressed in malignancies, potentially malignant oral disorders and autoimmune conditions like rheumatoid arthritis and Crohn’s disease. It is associated with cell surface binding and replication of viruses such as human immunodeficiency virus (HIV), severe acute respiratory syndrome-related Coronavirus, dengue and encephalitis. In HIV, it is associated with the viral infectivity factor which is associated with HIV replication. It can be used as a biomarker for diagnosis and prognosis and has potential as a therapeutic target in many conditions. The present review focuses on the structure, functions, clinical implications and future scope of vimentin in the management of various diseases.

Bioinformatics analyses reveal cell-barrier junction modulations in lung epithelial cells on SARS-CoV-2 infection.

Cell junctions maintain the blood-tissue barriers to preserve vascular and tissue integrity. Viral infections reportedly modulate cell-cell junctions to facilitate their invasion. However, information on the effect of COVID-19 infection on the gene expression of cell junction and cytoskeletal proteins is limited. Using the Gene Expression Omnibus and Reactome databases, we analyzed the data on human lung A549, NHBE, and Calu-3 cells for the expression changes in cell junction and cytoskeletal proteins by SARS-CoV-2 (CoV-2) infection. The analysis revealed changes in 3,660 genes in A549, 100 genes in NHBE, and 592 genes in Calu-3 cells with CoV-2 infection. Interestingly, EGOT (9.8-, 3- and 8.3-fold; p < .05) and CSF3 (4.3-, 33- and 56.3-fold; p < .05) were the only two genes significantly elevated in all three cell lines (A549, NHBE and Calu-3, respectively). On the other hand, 39 genes related to cell junctions and cytoskeleton were modulated in lung cells, with DLL1 demonstrating alterations in all cells. Alterations were also seen in several miRNAs associated with the cell junction and cytoskeleton genes modulated in the analysis. Further, matrix metalloproteinases involved in disease pathologies, including MMP-3, -9, and -12 demonstrated elevated expression on CoV-2 infection (p < .05). The study findings emphasize the integral role of cell junction and cytoskeletal genes in COVID-19, suggesting their therapeutic potential. Our analysis also identified a distinct EGOT gene that has not been previously implicated in COVID-19. Further studies on these newly identified genes and miRNAs could lead to advances in the pathogenesis and therapeutics of COVID-19.

Rap1 Small GTPase Regulates Vascular Endothelial-Cadherin-Mediated Endothelial Cell-Cell Junctions and Vascular Permeability.

The vascular permeability of the endothelium is finely controlled by vascular endothelial (VE)-cadherin-mediated endothelial cell-cell junctions. In the majority of normal adult tissues, endothelial cells in blood vessels maintain vascular permeability at a relatively low level, while in response to inflammation, they limit vascular barrier function to induce plasma leakage and extravasation of immune cells as a defense mechanism. Thus, the dynamic but also simultaneously tight regulation of vascular permeability by endothelial cells is responsible for maintaining homeostasis and, as such, impairments of its underlying mechanisms result in hyperpermeability, leading to the development and progression of various diseases including coronavirus disease 2019 (COVID-19), a newly emerging infectious disease. Recently, increasing numbers of studies have been unveiling the important role of Rap1, a small guanosine 5'-triphosphatase (GTPase) belonging to the Ras superfamily, in the regulation of vascular permeability. Rap1 enhances VE-cadherin-mediated endothelial cell-cell junctions to potentiate vascular barrier functions via dynamic reorganization of the actin cytoskeleton. Importantly, Rap1 signaling activation reportedly improves vascular barrier function in animal models of various diseases associated with vascular hyperpermeability, suggesting that Rap1 might be an ideal target for drugs intended to prevent vascular barrier dysfunction. Here, we describe recent progress in understanding the mechanisms by which Rap1 potentiates VE-cadherin-mediated endothelial cell-cell adhesions and vascular barrier function. We also discuss how alterations in Rap1 signaling are related to vascular barrier dysfunction in diseases such as acute pulmonary injury and malignancies. In addition, we examine the possibility of Rap1 signaling as a target of drugs for treating diseases associated with vascular hyperpermeability.