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Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu

Philips Institute for Oral Health Research Publications

Streptococcus sanguinis is a commensal and early colonizer of oral cavity as well as an opportunistic pathogen of infectious endocarditis. Extracting the soluble proteome of this bacterium provides deep insights about the physiological dynamic changes under different growth and stress conditions, thus defining “proteomic signatures” as targets for therapeutic intervention. In this protocol, we describe an experimentally verified approach to extract maximal cytoplasmic proteins from Streptococcus sanguinis SK36 strain. A combination of procedures was adopted that broke the thick cell wall barrier and minimized denaturation of the intracellular proteome, using optimized buffers and a sonication step. Extracted proteome was quantitated …

Slowly Cycling Rho Kinase-Dependent Actomyosin Cross-Bridge "Slippage" Explains Intrinsic High Compliance Of Detrusor Smooth Muscle, Christopher J. Neal, Jia B. Lin, Tanner Hurley, Amy S. Miner, John E. Speich, Adam P. Klausner, Paul H. Ratz

Biochemistry and Molecular Biology Publications

Biological soft tissues are viscoelastic because they display timeindependent pseudoelasticity and time-dependent viscosity. However, there is evidence that the bladder may also display plasticity, defined as an increase in strain that is unrecoverable unless work is done by the muscle. In the present study, an electronic lever was used to induce controlled changes in stress and strain to determine whether rabbit detrusor smooth muscle (rDSM) is best described as viscoelastic or viscoelastic plastic. Using sequential ramp loading and unloading cycles, stress-strain and stiffness-stress analyses revealed that rDSM displayed reversible viscoelasticity, and that the viscous component was responsible for establishing a …

Epigenetic Silencing Of Socs3 Expression Contributes To Fibrosis In Crohn’S Disease, Emily T. Marshall, Chao Li, John K. Kuemmerle

MD Student Summer Research Fellowship Program Posters

Identified risk polymorphisms affecting the Jak-STAT3 pathway in patients with Crohn’s disease could affect TGF-β1 and collagen I expression and in the pathway’s negative regulator, SOCS3. Genetic factors, however, account for only ~25% of disease. Epigenetic events also shape gene expression. Recent experiments showed that autocrine IL-6 production in mesenchymal cells, subepithelial myofibroblasts (SEMF) and muscle cells, of patients with fibrostenotic Crohn’s disease causes sustained Jak-STAT3 activity, excess TGF-β1 and Collagen I production and fibrosis. SOCS3 paradoxically decreased in these cells. We now identify epigenetic mechanisms that silence SOCS3 expression in SEMF of patients with fibrostenotic Crohn’s disease. In a …

Rare Mutations And Potentially Damaging Missense Variants In Genes Encoding Fibrillar Collagens And Proteins Involved In Their Production Are Candidates For Risk For Preterm Premature Rupture Of Membranes, Bhavi P. Modi, Maria E. Teves, Laurel N. Pearson, Hardik I. Parikh, Piya Chaemsaithong, Nihar U. Sheth, Timothy P. York, Roberto Romero, Jerome F. Strauss

Human and Molecular Genetics Publications

Preterm premature rupture of membranes (PPROM) is the leading identifiable cause of preterm birth with ~ 40% of preterm births being associated with PPROM and occurs in 1% - 2% of all pregnancies. We hypothesized that multiple rare variants in fetal genes involved in extracellular matrix synthesis would associate with PPROM, based on the assumption that impaired elaboration of matrix proteins would reduce fetal membrane tensile strength, predisposing to unscheduled rupture. We performed whole exome sequencing (WES) on neonatal DNA derived from pregnancies complicated by PPROM (49 cases) and healthy term deliveries (20 controls) to identify candidate mutations/variants. Genotyping for …

Substrate Stiffness Controls Osteoblastic And Chondrocytic Differentiation Of Mesenchymal Stem Cells Without Exogenous Stimuli, Rene Olivares-Navarrete, Erin M. Lee, Kathryn Smith, Sharon L. Hyzy, Maryam Doroudi, Joseph K. Williams, Ken Gall, Barbara D. Boyan, Zvi Schwartz

Biomedical Engineering Publications

Stem cell fate has been linked to the mechanical properties of their underlying substrate, affecting mechanoreceptors and ultimately leading to downstream biological response. Studies have used polymers to mimic the stiffness of extracellular matrix as well as of individual tissues and shown mesenchymal stem cells (MSCs) could be directed along specific lineages. In this study, we examined the role of stiffness in MSC differentiation to two closely related cell phenotypes: osteoblast and chondrocyte. We prepared four methyl acrylate/methyl methacrylate (MA/MMA) polymer surfaces with elastic moduli ranging from 0.1 MPa to 310 MPa by altering monomer concentration. MSCs were cultured in …

Predictive Behavior Of A Computational Foot/Ankle Model Through Artificial Neural Networks, Ruchi D. Chande, Rosalyn Hobson Hargraves, Norma Ortiz-Robinson, Jennifer S. Wayne

Biomedical Engineering Publications

Computational models are useful tools to study the biomechanics of human joints. Their predictive performance is heavily dependent on bony anatomy and soft tissue properties. Imaging data provides anatomical requirements while approximate tissue properties are implemented from literature data, when available. We sought to improve the predictive capability of a computational foot/ankle model by optimizing its ligament stiffness inputs using feedforward and radial basis function neural networks. While the former demonstrated better performance than the latter per mean square error, both networks provided reasonable stiffness predictions for implementation into the computational model.

Breastfeeding After Gestational Diabetes: Does Perceived Benefits Mediate The Relationship?, Jordyn T. Wallenborn, Robert A. Perera, Saba W. Masho

Family Medicine and Population Health Publications

Introduction. Breastfeeding is recognized as one of the best ways to decrease infant mortality and morbidity. However, women with gestational diabetes mellitus (GDM) may have breastfeeding barriers due to the increased risk of neonatal and pregnancy complications. While the prevalence of GDM is increasing worldwide, it is important to understand the full implications of GDM on breastfeeding outcomes.The current study aims to investigate the (1) direct effect of GDM on breastfeeding duration and (2) indirect effect of GDM on breastfeeding duration through perceived benefits of breastfeeding. Methods. Prospective cohort data from the Infant Feeding and Practices Study II was analyzed …

Structural Modeling And Functional Analysis Of The Essential Ribosomal Processing Protease Prp From Staphylococcus Aureus, Erin A. Wall, Adam L. Johnson, Darrell L. Peterson, Gail E. Christie

Microbiology and Immunology Publications

In Firmicutes and related bacteria, ribosomal large subunit protein L27 is encoded with a conserved N-terminal extension that is removed to expose residues critical for ribosome function. Bacteria encoding L27 with this N-terminal extension also encode a sequence-specific cysteine protease, Prp, which carries out this cleavage. In this work, we demonstrate that L27 variants with an un-cleavable N-terminal extension, or lacking the extension (pre-cleaved), are unable to complement an L27 deletion in Staphylococcus aureus. This indicates that N-terminal processing of L27 is not only essential but possibly has a regulatory role. Prp represents a new clade of previously uncharacterized cysteine …

Tetr Family Regulator Brpt Modulates Biofilm Formation In Streptococcus Sanguinis, Jinlin Liu, Victoria N. Stone, Xiuchun Ge, Madison Tang, Fadi Elrami, Ping Xu

Microbiology and Immunology Publications

Biofilms are a key component in bacterial communities providing protection and contributing to infectious diseases. However, mechanisms involved in S. sanguinis biofilm formation have not been clearly elucidated. Here, we report the identification of a novel S. sanguinis TetR repressor, brpT (Biofilm Regulatory Protein TetR), involved in biofilm formation. Deletion of brpT resulted in a significant increase in biofilm formation. Interestingly, the mutant accumulated more water soluble and water insoluble glucans in its biofilm compared to the wild-type and the complemented mutant. The brpT mutation led to an altered biofilm morphology and structure exhibiting a rougher appearance, uneven …

Identification Of Naegleria Fowleri Proteins Linked To Primary Amoebic Meningoencephalitis, Melissa Jamerson, Jacqueline A. Schmoyer, Jay Park, Francine Marciano-Cabral, Guy A. Cabral

Microbiology and Immunology Publications

Naegleria fowleri (N. fowleri) causes primary amoebic meningoencephalitis, a rapidly fatal disease of the central nervous system. N. fowleri can exist in cyst, flagellate or amoebic forms, depending on environmental conditions. The amoebic form can invade the brain following introduction into the nasal passages. When applied intranasally to a mouse model, cultured N. fowleri amoebae exhibit low virulence. However, upon serial passage in mouse brain, the amoebae acquire a highly virulent state. In the present study, a proteomics approach was applied to the identification of N. fowleri amoeba proteins whose expression was associated with the highly virulent state …

Saikosaponins Induced Hepatotoxicity In Mice Via Lipid Metabolism Dysregulation And Oxidative Stress: A Proteomic Study, Xiaoyu Li, Xiaojiaoyang Li, Junxian Lu, Youyi Huang, Lili Lv, Yongfu Luan, Runping Liu, Rong Sun

Microbiology and Immunology Publications

Background

Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury.

Methods

Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice. Serum and liver total triglyceride and cholesterol were used to indicate lipid metabolism homeostasis. Liver ROS, GSH, MDA and iNOS were used to examine …

Virginia Commonwealth University Commencement Program [2017], Virginia Commonwealth University

VCU Commencement Programs

No abstract provided.

Virginia Commonwealth University Fall Commencement Program [2017], Virginia Commonwealth University

VCU Commencement Programs

No abstract provided.

Virginia Commonwealth University Undergraduate Bulletin [2017], Virginia Commonwealth University

VCU Bulletins

Undergraduate bulletin for Virginia Commonwealth University for the academic year 2017-2018. It includes information on academic regulations, degree requirements, course offerings, faculty, academic calendar, and tuition and expenses for undergraduate programs.

The Anti-Sepsis Activity Of The Components Of Huanglian Jiedu Decoction With High Lipid A-Binding Affinity, Guirong Chen, Yubin Xu, Jing Jing, Brianna Mackie, Xinchuan Zheng, Xu Zhang, Jing Wang, Xuetao Li

Medicinal Chemistry Publications

Huanglian Jiedu Decoction (HJD), one of the classic recipes for relieving toxicity and fever, is a common method for treating sepsis in China. However, the effective components of HJD have not yet been identified. This experiment was carried out to elucidate the effective components of HJD against sepsis. Thus, seven fractions from HJD were tested using a biosensor to test their affinity for lipid A. The components obtained that had high lipid A-binding fractions were further separated, and their affinities to lipid A were assessed with the aid of a biosensor. The levels of LPS in the blood were measured, …

Virginia Commonwealth University Graduate Bulletin [2017], Virginia Commonwealth University

VCU Bulletins

Graduate bulletin for Virginia Commonwealth University for the academic year 2017-2018. It includes information on academic regulations, degree requirements, course offerings, faculty, academic calendar, and tuition and expenses for graduate programs.

Sharing Extended Summary Data From Contemporary Genetics Studies Is Unlikely To Threaten Subject Privacy, Silviu-Alin Bacanu

Psychiatry Publications

Background

Starting from a forensic problem, Homer et al. showed that it was possible to detect if an individual contributes only 0.5% of the DNA in a pool. The finding was extended to prove the possibility of detecting whether a subject participated in a small homogeneous GWAS. We denote this as the detection of a subject belonging to a certain cohort (SBCC). Subsequently, Visscher and Hill showed that the power to detect SBCC signal for an ethnically homogeneous cohort depends roughly on the ratio of the number of independent markers and total sample size. However, it …

Medical Literary Messenger (Vol. 5, No. 1, Fall/Winter 2017)

Medical Literary Messenger

Home Visit / Melissa Fournier -- Stiffness / Hannah Shea -- Exile / Lane Falcon -- Good Intentions / Laura Foley -- Resurrection / Les Cohen -- Visits / Craig W. Steele -- That Last Night / Laura Foley -- Taste / Dan Campion -- Bumblebees Don’t Always Sting / Diane M. Parker -- Mental Status Exam / Melissa Fournier -- Dystrophia I / Ashley Purdy -- Muck Out / Mitchell Krockmalnik Grabois -- Endoscope / Lane Falcon -- Leftovers / Erynn Porter -- Another Autumn / Deborah Fleming -- Autism / Laura Foley -- Nearly Sunset / Craig W. …

In Defense Of Science—What Would John Do?, Mohamed Gad-El-Hak

Mechanical and Nuclear Engineering Publications

Recent onslaughts on the importance of pure research to our collective well-being are trending. In this essay, I discuss the issues involved and offer a rebuttal. The thoughts are inspired by my mentor, academic sibling, and idol John Leask Lumley.

Predictive Behavior Of A Computational Foot/Ankle Model Through Artificial Neural Networks, Ruchi D. Chande, Rosalyn Hobson Hargraves, Norma Ortiz-Robinson, Jennifer S. Wayne

Biomedical Engineering Publications

Computational models are useful tools to study the biomechanics of human joints. Their predictive performance is heavily dependent on bony anatomy and soft tissue properties. Imaging data provides anatomical requirements while approximate tissue properties are implemented from literature data, when available. We sought to improve the predictive capability of a computational foot/ankle model by optimizing its ligament stiffness inputs using feedforward and radial basis function neural networks. While the former demonstrated better performance than the latter per mean square error, both networks provided reasonable stiffness predictions for implementation into the computational model.

Study Of In Vitro Transcriptional Binding Effects And Noise Using Constitutive Promoters Combined With Up Element Sequences In Escherichia Coli, Qiang Yan, Stephen S. Fong

Chemical and Life Science Engineering Publications

Background

UP elements (upstream element) are DNA sequences upstream of a promoter that interact with the α-subunit of RNA polymerase (RNAP) and can affect transcription by altering the binding RNAP to DNA. However, details of UP element and binding affinity effects on transcriptional strength are unclear.

Results

Here, we investigated the effects of UP element sequences on gene transcription, binding affinity, and gene expression noise. Addition of UP elements resulted in increased gene expression (maximum 95.7-fold increase) and reduced gene expression noise (8.51-fold reduction). Half UP element sequences at the proximal subsite has little effect on transcriptional strength despite increasing …

The Role Of Kinase Fusion Dnajb1-Prkaca In Fibrolamellar Hepatocellular Carcinoma, Yi Guo

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Regulation Of Biliary Progenitor Cell Proliferation By Hedgehog Signaling In In Vivo And Ex Vivo Organoid Models, Nataliya Razumilava M.D., Junya Shiota M.D., Ramon Ocadiz-Ruiz Ph.D., Nureen Hanisah Mohamad Zaki, Kais Zakharia M.D., Michael Mathew Hayes, Juanita Lynn Merchant M.D., Ph.D.

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Hepatocyte-Specific Deletion Of Tristetraprolin Family Of Rna Binding Proteins Result In The Development Of Hepatocellular Carcinomas, Sonika Patial

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Virginia Commonwealth University Courses [2017], Virginia Commonwealth University

VCU Bulletins

Listing of courses for the 2017-2018 year.

Locomotor Adaptability In Persons With Unilateral Transtibial Amputation, Benjamin J. Darter, Amy J. Bastian, Erik J. Wolf, Elizabeth M. Husson, Bethany A. Labrecque, Brad D. Hendershot

Physical Medicine and Rehabilitation Publications

Background

Locomotor adaptation enables walkers to modify strategies when faced with challenging walking conditions. While a variety of neurological injuries can impair locomotor adaptability, the effect of a lower extremity amputation on adaptability is poorly understood.

Objective

Determine if locomotor adaptability is impaired in persons with unilateral transtibial amputation (TTA).

Methods

The locomotor adaptability of 10 persons with a TTA and 8 persons without an amputation was tested while walking on a split-belt treadmill with the parallel belts running at the same (tied) or different (split) speeds. In the split condition, participants walked for 15 minutes with the respective belts …

A Mathematical System For Human Implantable Wound Model Studies, Salomonsky Paul-Michael, Rebecca Segal

Mathematics and Applied Mathematics Publications

In this work, we present a mathematical model, which accounts for two fundamental processes involved in the repair of an acute dermal wound. These processes include the inflammatory response and fibroplasia. Our system describes each of these events through the time evolution of four primary species or variables. These include the density of initial damage, inflammatory cells, fibroblasts and deposition of new collagen matrix. Since it is difficult to populate the equations of our model with coefficients that have been empirically derived, we fit these constants by carrying out a large number of simulations until there is reasonable agreement between …

Chronic Health Conditions As A Risk Factor For Falls Among The Community-Dwelling Us Older Adults: A Zero-Inflated Regression Modeling Approach, Yoshita Paliwal, Patricia W. Slattum, Scott M. Ratliff

Pharmacotherapy and Outcomes Science Publications

Falls are an important health concern among older adults due to age-related changes in the body. Having a medical history of chronic health condition may pose even higher risk of falling. Only few studies have assessed a number of chronic health conditions as risk factor for falls over a large nationally representative sample of US older adults. In this study, Behavioral Risk Factor Surveillance System (BRFSS) 2014 participants aged 65 years and older (n = 159,336) were evaluated. It was found that 29.7% (n = 44,550) of the sample experienced at least one fall and 16.3% (n = 20,444) …

Functional Responses Can’T Unify Invasion Ecology, James Vonesh, Mike Mccoy, Res Altwegg, Pietro Landi, John Measey

Biology Publications

Dick et al. (Biol Invasions, 2017) propose that the comparative functional response framework provides a unifying approach for the study of invasive species. We agree that functional responses are an important and powerful quantitative description of consumer effects on resources, and co-opting classical ecological theory to better predict invasive species impacts is a laudable move for invasion biology. However, we fear that the early successes of select examples of the comparative functional response (CFR) approach has led Dick et al. to exaggerate the generality of its utility, and about its ability to unify the field. Further, they fail to provide …

Nerve Conduction Through Dendrites Via Proton Hopping, Lemont B. Kier

Biology Publications

Background: In our previous studies of nerve conduction conducted by proton hopping, we have considered the axon, soma, synapse and the nodes of Ranvier. The role of proton hopping described the passage of information through each of these units of a typical nerve system. The synapse projects information from the axon to the dendrite and their associated spines.

Methods: We have invoked the passage of protons via a hopping mechanism to illustrate the continuum of the impulse through the system, via the soma following the dendrites. This is proposed to be a continuum invoked by the proton hopping method.

Results: …