Digital Commons Network^™

Testing Multiple Hypotheses Through Imp Weighted Fdr Based On A Genetic Functional Network With Application To A New Zebrafish Transcriptome Study, Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim

Dartmouth Scholarship

In genome-wide studies, hundreds of thousands of hypothesis tests are performed simultaneously. Bonferroni correction and False Discovery Rate (FDR) can effectively control type I error but often yield a high false negative rate. We aim to develop a more powerful method to detect differentially expressed genes. We present a Weighted False Discovery Rate (WFDR) method that incorporate biological knowledge from genetic networks. We first identify weights using Integrative Multi-species Prediction (IMP) and then apply the weights in WFDR to identify differentially expressed genes through an IMP-WFDR algorithm. We performed a gene expression experiment to identify zebrafish genes that change expression …

Strategic Distribution Of The Mitochondrial Ca2+ Uniporter In Cardiac Mitochondria, Sergio De La Fuente, Caitlin Vail, Elorm J. Agra, Kira Holmstrom, Junhui Sun, Jyotsna Mishra, Toren Finkel, Elizabeth Murphy, Shey-Shing Sheu, György Csordás

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Background:

1) Control of the mitochondrial ATP production by SR-derived Ca²⁺ signals includes local, nanodomain Ca²⁺ transfer from ryanodine receptors (RyR2) to the mitochondrial matrix (excitation-bioenergetics coupling).

2) Ca²⁺ crosses the inner mitochondrial membrane (IMM) via the mtCU, a low-affinity Ca²⁺-activated Ca²⁺ channel complex.

3) The surface area of cardiac IMM is extensively enhanced by cristae folding; however, mitoplast patch clamp studies showed mtCU current density the lowest amongst a range of tissues (Fieni 2012. Nat Commun).

Low Level Lead Exposure Impairs Attentional Set Shifting Task Performance Depending Upon Sex And Developmental Periods Of Exposure, L.S. Neuwirth, D.W. Anderson, J. S. Schneider

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Introduction

Exposure to low levels of lead (Pb) impairs a variety of cognitive processes. Although children exposed to Pb developmentally present with a variety of cognitive impairments that include deficits in learning, memory, language, and executive functioning, experimental work on Pb toxicity in rats has focused mostly on learning and memory deficits and less on executive functions. However, detrimental effects on executive functioning could lead to or even underlie a variety of other cognitive problems attributed to Pb exposure. In this study, we examined the ability of Long Evans rats (control and Pb-exposed: 150ppm Pb-acetate in food given perinatally (gestation …

Links Between Anr And Quorum Sensing In Pseudomonas Aeruginosa Biofilms, John H. Hammond, Emily F. Dolben, T. Jarrod Smith, Sabin Bhuju, Deborah Hogan

Dartmouth Scholarship

In Pseudomonas aeruginosa, the transcription factor Anr controls the cellular response to low oxygen or anoxia. Anr activity is high in oxygen-limited environments, including biofilms and populations associated with chronic infections, and Anr is necessary for persistence in a model of pulmonary infection. In this study, we characterized the Anr regulon in biofilm-grown cells at 1% oxygen in the laboratory strain PAO1 and in a quorum sensing (QS)-deficient clinical isolate, J215. As expected, transcripts related to denitrification, arginine fermentation, high-affinity cytochrome oxidases, and CupA fimbriae were lower in the Δanr derivatives. In addition, we observed that transcripts associated with quorum …

Connectivity Measures Are Robust Biomarkers Of Cortical Function And Plasticity After Stroke, Jennifer Wu, Erin Burke Quinlan, Lucy Dodakian, Alison Mckenzie, Nikhita Kathuria, Robert J. Zhou, Renee Augsburger, Jill See, Vu H. Lee, Ramesh Srinivasan, Steven C. Cramer

Physical Therapy Faculty Articles and Research

Valid biomarkers of motor system function after stroke could improve clinical decision-making. Electroencephalography-based measures are safe, inexpensive, and accessible in complex medical settings and so are attractive candidates. This study examined specific electroencephalography cortical connectivity measures as biomarkers by assessing their relationship with motor deficits across 28 days of intensive therapy. Resting-state connectivity measures were acquired four times using dense array (256 leads) electroencephalography in 12 hemiparetic patients (7.3 ± 4.0 months post-stroke, age 26–75 years, six male/six female) across 28 days of intensive therapy targeting arm motor deficits. Structural magnetic resonance imaging measured corticospinal tract injury and infarct volume. …

Arsenic Inhibits Dna Mismatch Repair By Promoting Egfr Expression And Pcna Phosphorylation, Dan Tong, Janice Ortega, Christine Kim, Jian Huang, Liya Gu, Guo-Min Li

Toxicology and Cancer Biology Faculty Publications

Both genotoxic and non-genotoxic chemicals can act as carcinogens. However, while genotoxic compounds lead directly to mutations that promote unregulated cell growth, the mechanism by which non-genotoxic carcinogens lead to cellular transformation is poorly understood. Using a model non-genotoxic carcinogen, arsenic, we show here that exposure to arsenic inhibits mismatch repair (MMR) in human cells, possibly through its ability to stimulate epidermal growth factor receptor (EGFR)-dependent tyrosine phosphorylation of proliferating cellular nuclear antigen (PCNA). HeLa cells exposed to exogenous arsenic demonstrate a dose- and time-dependent increase in the levels of EGFR and tyrosine 211-phosphorylated PCNA. Cell extracts derived from arsenic-treated …

Membrane Proximal Ectodomain Cleavage Of Muc16 Occurs In The Acidifying Golgi/Post-Golgi Compartments., Srustidhar Das, Prabin D. Majhi, Mona H. Al-Mugotir, Satyanarayana Rachagani, Paul Sorgen, Surinder K. Batra

Journal Articles: Biochemistry & Molecular Biology

MUC16, precursor of the most widely used ovarian cancer biomarker CA125, is up regulated in multiple malignancies and is associated with poor prognosis. While the pro-tumorigenic and metastatic roles of MUC16 are ascribed to the cell-associated carboxyl-terminal MUC16 (MUC16-Cter), the exact biochemical nature of MUC16 cleavage generating MUC16-Cter has remained unknown. Using different lengths of dual-epitope (N-terminal FLAG- and C-terminal HA-Tag) tagged C-terminal MUC16 fragments, we demonstrate that MUC16 cleavage takes place in the juxta-membrane ectodomain stretch of twelve amino acids that generates a ~17 kDa cleaved product and is distinct from the predicted sites. This was further corroborated by …

Amyloid Peptide Inactivating Enzyme To Treat Alzheimer's Disease Peripherally, Louis B. Hersh, Hanjun Guan

Molecular and Cellular Biochemistry Faculty Patents

Methods for treatment and/or prevention of Alzheimer's disease comprising inactivating peripheral AP in serum to a reduce A(3 in the brain. Methods comprise expression of amyloid peptide inactivating enzyme on bone marrow cells; and coupling of amyloid peptide inactivating enzyme to hematopoietic cells.

Fructose Mediated Non-Alcoholic Fatty Liver Is Attenuated By Ho-1-Sirt1 Module In Murine Hepatocytes And Mice Fed A High Fructose Diet, Komal Sodhi, Nitin Puri, Gaia Favero, Sarah Stevens, Charles Meadows, Nader G. Abraham, Rita Rezzani, Hayden A. Ansinelli, Edward Lebovics, Joseph I. Shapiro

Biochemistry and Microbiology

Background

Oxidative stress underlies the etiopathogenesis of nonalcoholic fatty liver disease (NAFLD), obesity and cardiovascular disease (CVD). Heme Oxygenase-1 (HO-1) is a potent endogenous antioxidant gene that plays a key role in decreasing oxidative stress. Sirtuin1 (SIRT1) belongs to the family of NAD-dependent de-acyetylases and is modulated by cellular redox.

Hypothesis

We hypothesize that fructose-induced obesity creates an inflammatory and oxidative environment conducive to the development of NAFLD and metabolic syndrome. The aim of this study is to determine whether HO-1 acts through SIRT1 to form a functional module within hepatocytes to attenuate steatohepatitis, hepatic fibrosis and cardiovascular dysfunction.

Methods …

Week Of June 1, 2015, New York Medical College

InTouch

• NYMC Bids Farewell to the Class of 2015
• AOA Iota Chapter Hosts Annual Lecture and Induction Ceremony
• School of Medicine Class of 2018 Hosts 27th Annual Convocation of Thanks
• SHSP Hosts Third Annual Research and Scholarship Day
• Department of Family and Community Medicine Presents Third Annual Research Day
• Department of Pediatrics Hosts Fifth Annual Paul K. Woolf, M.D., Pediatric Trainee Research Day
• NYMC Inducts Inaugural Members of Delta Omega Honorary Society in Public Health
• LEND Graduates 19 From Interdisciplinary Leadership Program
• NYMC Hosts AHA Research Reception
• Students Host Annual Health Fair
• NYMC Shows Support for the National Alliance on Mental …

Curcumin: A Multi-Dimensional Approach To Pancreatic Cancer Targeting Cell Death And Exosomes, Carlos J. Diaz Osterman

Loma Linda University Electronic Theses, Dissertations & Projects

Pancreatic cancer is currently one of the most difficult diseases to treat due to difficulty of detection and the aggressive nature of the disease. In addition, pancreatic cancer has the highest mortality rates compared to other cancer types. These mortality rates are attributable in part to increasing resistance to cancer therapy. Cancer therapy resistance is caused by adaptations that favor survival within cancer cells and their environment, termed the tumor microenvironment. Intracellular adaptations include the overexpression of resistance-linked genes, such as the inhibitor of apoptosis (IAP) family of proteins and overall resistance to cell death. Adaptations in the tumor microenvironment …

Long-Term Hypoxia Alters Ovine Fetal Adrenal Enos And Cortisol Biosynthesis, Elizabeth Anne Newby

Loma Linda University Electronic Theses, Dissertations & Projects

Maintaining normal levels of cortisol in response to chronic stress, while retaining the ability to respond to acute stress, is important for ensuring normal fetal growth and development. Long-term hypoxia (LTH) causes adaptations in the fetal hypothalamopituitary- adrenal (HPA) axis that maintain basal cortisol levels but enhance production in response to a secondary stress. Nitric oxide (NO), produced by endothelial nitric oxide synthase (eNOS) in the adrenal cortex, plays a significant role in regulating cortisol production in the LTH fetus. The production of NO is regulated by eNOS activity which can be altered via phosphorylation through key signaling pathways. In …

Crotalus Snake Venom Preconditioning To Prevent Surgical Brain Injury, Cherine Hee-Sun Kim

Loma Linda University Electronic Theses, Dissertations & Projects

Preventive measures are increasingly relevant to medical practice. Preconditioning, a preemptive therapy that administers mildly harmful stimuli to induce endogenous protective mechanisms before major injury, has been shown to minimize injury in many animal models. Given the elective nature of most neurosurgical procedures, the surgical brain injury (SBI) rodent model provides an ideal platform for preconditioning. Our work shows that preconditioning with Crotalus rattlesnake venom, known for its hemorrhagic and inflammatory effects, mitigates some harmful effects of SBI. We have identified two proteins of interest in Crotalus venom: snake venom metalloproteinase (SVMP), an enzyme with hemorrhagic effects, and phospholipase A2 …

Lipid Regulation As A Critical Factor In The Development Of Alzheimer's Disease, Michael A. Castello

Loma Linda University Electronic Theses, Dissertations & Projects

Alzheimer’s disease (AD) is the most common form of dementia in the United States, representing around eighty percent of all cases. For more than two decades, researchers have been led by the amyloid cascade hypothesis, which assumes that accumulation of the amyloid peptide Aβ, derived by proteolytic processing from the amyloid precursor protein (APP), is the key pathogenic trigger in AD. To date, therapies have largely focused on removing Aβ from the brain, an approach that has produced disappointing clinical outcomes. I present an alternative hypothesis in which Aβ production and aggregation is a symptom of a larger, systemic disease …

Acclimatization To High-Altitude, Long-Term Hypoxia Alters Bk Channel Structure And Function, Xiaoxiao Tao

Loma Linda University Electronic Theses, Dissertations & Projects

We examined the major possible mechanisms for the left shift of the BK channel I-V relationship in native basilar artery myocytes from the two LTH groups. These mechanisms included: differential expression of the accessary BK -1 subunit; differential phosphorylation of the BK subunit; and splice variation of the BK subunit. Using molecular cloning, heterologous expression, and patch-clamp electrophysiology techniques, we elucidated a mechanism that, at least in part, contributes to the differences we observed between channels from native normoxic and LTH myocytes.

Molecular Characterization And Inhibition Of Antibodies Elicited Against Galactosyltransferase Knockout Pig Xenografts, John M. Stewart

Loma Linda University Electronic Theses, Dissertations & Projects

On average, 21 people in the United States die every day while waiting for a transplantable organ. Moreover, at the end of 2014, nearly 130,000 additional individuals were still on the transplant waiting list. Xenotransplantation, the transplantation of cells and/or organs from a member of another species, is both a viable supplement for, and bridge to, allotransplantation. Pigs are the favored organ donor because they: 1) breed and grow rapidly, 2) can be genetically modified, and 3) present few ethical concerns. However, due in part to their phylogenetic distance, several barriers must be successfully overcome before clinical xenotransplantation can be …

Tslp-Induced Mechanisms And Potential Therapies For Crlf2 B-Cell Acute Lymphoblastic Leukemia, Olivia L. Francis

Loma Linda University Electronic Theses, Dissertations & Projects

Childhood CRLF2 B-cell Acute Lymphoblastic Leukemia (CRLF2 B-ALL) is a high-risk form of leukemia that is associated with poor patient survival outcomes. CRLF2 B-ALL is five times more prevalent in Hispanic children than others and is associated with a higher rate of relapse, thus contributing significantly to childhood cancer health disparities. This disease occurs due to alterations of the CRLF2 gene, leading to overexpression of the CRLF2 protein- a component of the receptor signaling complex for the cytokine Thymic Stromal LymphoPoietin (TSLP) on the surface of B-ALL cells. TSLP has been shown to induce proliferation of human and mouse B-cell …

Nonparametric Inference In Hidden Markov Models Using P-Splines, Roland Langrock, Thomas Kneib, Alexander Sohn, Stacy L. Deruiter

University Faculty Publications and Creative Works

Hidden Markov models (HMMs) are flexible time series models in which the distribution of the observations depends on unobserved serially correlated states. The state-dependent distributions in HMMs are usually taken from some class of parametrically specified distributions. The choice of this class can be difficult, and an unfortunate choice can have serious consequences for example on state estimates, and more generally on the resulting model complexity and interpretation. We demonstrate these practical issues in a real data application concerned with vertical speeds of a diving beaked whale, where we demonstrate that parametric approaches can easily lead to overly complex state …

Vitamin D As An Adjunctive Therapy In Asthma. Part 1: A Review Of Potential Mechanisms, Conor Kerley, Basil Elnazir, John Faul, Liam Cormican

Articles

Vitamin D deficiency (VDD) is highly prevalent worldwide. The classical role for vitamin D is to regulate calcium absorption form the gastrointestinal tract and influence bone health. Recently vitamin D receptors and vitamin D metabolic enzymes have been discovered in numerous sites systemically supporting diverse extra-skeletal roles of vitamin D, for example in asthmatic disease. Further, VDD and asthma share several common risk factors including high latitude, winter season, industrialization, poor diet, obesity, and dark skin pigmentation. Vitamin D has been demonstrated to possess potent immunomodulatory effects, including effects on T cells and B cells as well as increasing production …

Molecular Mechanisms That Govern Human Cardiac Stem Cell Age Disparity, Tania Fuentes

Loma Linda University Electronic Theses, Dissertations & Projects

Transplantation of adult endogenous cardiovascular progenitor cells for heart repair results in some clinical benefit, however these stem cells lack the regenerative capacity unique to neonatal cardiovascular stem cells. The goal of this work was to identify mechanisms that contribute to the decline of cardiac stem cell regenerative ability with age and investigate novel therapeutic strategies to improve cardiac stem cell function. When comparing neonatal and adult cardiovascular stem cell clones, both cell types were capable of cardiomyogenic differentiation. However, the expression levels of forty-one microRNAs were significantly altered with age. Expression differences were correlated with reduced proliferation and a …

Chlorinated Tyrosine Species As Markers Of Inflammation: A Kinetic Study, Matthew Peter Curtis

Loma Linda University Electronic Theses, Dissertations & Projects

Chronic inflammation is associated with numerous human diseases. During inflammation, leukocytes release the enzyme myeloperoxidase (MPO) which generates reactive oxygen species such as hypochlorous acid (HOCl). Additionally, MPO generates reactive nitrogen species. These reactive species can damage host fats, proteins, and DNA, contributing to disease pathology. Because of the reactivity and short half-lives of reactive species, measurement of surrogate markers is necessary to determine their extent and source. Chlorination of the tyrosine phenol ring by HOCl to produce 3-chlorotyrosine (3ClTyr) or nitration of the phenol ring by reactive nitrogen species to produce 3-nitrotyrosine (NO2Tyr) are two such markers. Both are …

Pseudomonas Aeruginosa Reduces Vx-809 Stimulated F508del-Cftr Chloride Secretion By Airway Epithelial Cells, Bruce A. Stanton, Bonita Coutermarsh, Roxanna Barnaby, Deborah Hogan

Dartmouth Scholarship

Background:

P. aeruginosa is an opportunistic pathogen that chronically infects the lungs of 85% of adult patients with Cystic Fibrosis (CF). Previously, we demonstrated that P. aeruginosa reduced wt-CFTR Cl secretion by airway epithelial cells. Recently, a new investigational drug VX-809 has been shown to increase F508del-CFTR Cl secretion in human bronchial epithelial (HBE) cells, and, in combination with VX-770, to increase FEV1 (forced expiratory volume in 1 second) by an average of 3-5% in CF patients homozygous for the F508del-CFTR mutation. We propose that P. aeruginosa infection of CF lungs reduces VX-809 + VX-770- stimulated F508del-CFTR Cl secretion, and …

Astrocyte Morphology, Heterogeneity, And Density In The Developing African Giant Rat (Cricetomys Gambianus), Matthew A. Olude, Oluwaseun A. Mustapha, Oluwatunde A. Aderounmu, James O. Olopade, Amadi O. Ihunwo

Brain and Mind Institute

Astrocyte morphologies and heterogeneity were described in male African giant rats (AGR; Cricetomys gambianus, Waterhouse) across three age groups (five neonates, five juveniles, and five adults) using Silver impregnation method and immunohistochemistry against glial fibrillary acidic protein. Immunopositive cell signaling, cell size and population were least in neonates, followed by adults and juveniles, respectively. In neonates, astrocyte processes were mostly detected within the glia limitans of the mid and hind brain; their cell bodies measuring 32 ± 4.8 μm in diameter against 91 ± 5.4 μm and 75 ± 1.9 μm in juveniles and adults, respectively. Astrocyte heterogeneity in …

Human Dna Exonuclease Trex1 Is Also An Exoribonuclease That Acts On Single-Stranded Rna, Fenghua Yuan, Tanmay Dutta, Ling Wang, Lei Song, Liya Gu, Liangyue Qian, Anaid Benitez, Shunbin Ning, Arun Malhotra, Murray P. Deutscher, Yanbin Zhang

Toxicology and Cancer Biology Faculty Publications

3' repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent K_m of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native …

Novel Advances In Alzheimer's Disease, Jacob P. Naumann

The Downtown Review: An Interdisciplinary Journal Written and Peer-Reviewed by Mandel Honors College Students at Cleveland State University

Alzheimer’s disease, the most common form of dementia in adults, is a progressive degenerative neurological disease that affects memory, cognition, and behavior. Dr. Alois Alzheimer discovered and diagnosed the irreversible disease in 1906 after documenting the famous case of Auguste Deter.¹ Since the discovery of the disease, numerous advances have made it possible to not only better understand the causal factors, but also to improve the medical diagnosis and preventative measures that healthcare providers can implement. For the first time since 1984, the National Institute on Aging (NIAA) and the Alzheimer’s Association (AA) proposed and published new diagnostic guideline …

Transport Of Bovine Milk Exosomes In Human Endothelial Cell, Rio Jati Kusuma

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

MicroRNAs (miRNAs) can be synthesized endogenously and cause gene repression. Encapsulation of miRNAs in exosomes confers protection against degradation and a vehicle for shuttling between cells and tissues, and cellular uptake by endocytosis. Exosomes can be found in biological fluids and foods including milk. Evidence suggests that humans absorb cow’s milk exosomes and deliver the microRNA cargo to peripheral tissues, consistent with gene regulation by nucleic acids across species boundaries. There is strong evidence that milk exosomes may cross the mucosa without re-packaging in mice. Here, we tested the hypothesis that human vascular endothelial cells transport milk exosomes by endocytosis, …

Week Of May 18, 2015, New York Medical College

InTouch

• Dr. Jan K. Richardson Will Address the Class of 2015
• NYMC Celebrates 27th Annual Employee Recognition Program
• View the NYMC Corporate Citizenship Award Video
• NYMC Ranks in Top Ten Med Schools with the Most Applicants

Functional Analysis Of The Molluscum Contagiosum Virus Mc160 Death Effector Domain-Containing Protein Rxdl Motif, Sarah Weber

Seton Hall University Dissertations and Theses (ETDs)

The Molluscum contagiosum virus (MCV) is a member of the Poxviridae family that causes benign skin lesions. MCV lesions persist on average for 8-12 months in otherwise healthy individuals. MCV lesions are characterized by reduced inflammation. The persistence and reduction of inflammation at the site of MCV lesions have been attributed to MCV immune evasion genes. MCV encodes two death effector domain (DED) containing proteins, MC159 and MC160. DEDs are found in cellular proteins such as FADD and procaspase-8. These cellular proteins are involved in several innate immune responses such as apoptosis and activation of interferon (IFN). Presumably, MC159 and …

Antibacterial Evaluation Of Polygonum Multiflorum, Andy S. Demianicz

Seton Hall University Dissertations and Theses (ETDs)

Polygonum multiflorum, commonly known as Chinese Knotweed, is a tonic herb primarily used to enhance bodily functions. Recently, it has been shown to contain strong antioxidant, antibacterial and antiviral activity. The extract from the roots of Chinese Knotweed was used to assess its antibacterial properties against a broad spectrum of bacterial species, including 5 Gram-positive (B. cereus, B. megaterium, S. epidermidis, S. mutans and S. pyogenes) and 4 Gram-negative (E. aerogenes, E. coli, P. vulgaris and P. aeruginosa). Microtiter assays were carried out to evaluate the antibacterial activity of Chinese Knotweed at 0.5%, 1%, 1.5% and 2.5% concentrations in order …

Effect Of Chinese Knotweed Extract On Hsv-1 Infection Of Vero Cells, Derek J. Prince

Seton Hall University Dissertations and Theses (ETDs)

HSV-1 is an opportunistic virus responsible for infecting the majority of the global population. The ability of this virus to strategically alternate between lytic and latent states has made the development of effective treatments challenging. Polygonum multiflorum (Chinese Knotweed, CK) is a perennial plant local to the south central regions of China. The thunb (root) constituents of this compound have been used in traditional Chinese medicines to treat a broad range of illnesses for centuries. In the present study, CK root extracts were evaluated for potential anti-HSV-1 activity. Cytopathic effect (CPE) monitoring studies indicate that Vero cells infected with HSV-1 …