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A New Rhesus Macaque Assembly And Annotation For Next-Generation Sequencing Analyses, Aleksey V. Zimin, Adam S. Cornish, Mnirnal D. Maudhoo, Robert M. Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T. Meehan, Kristin Wipfler, Steven E. Bosinger, Zachary P. Johnson, Gregory K. Tharp, Guillaume Marçais, Michael Roberts, Betsy Ferguson, Howard S. Fox, Todd Treangen, Steven L. Salzberg, James A. Yorke, Robert B. Norgren Jr.

Journal Articles: Genetics, Cell Biology & Anatomy

BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.

RESULTS: We report a new de novo assembly of the …

Molecular Genetic Evidence For Overlap Between General Cognitive Ability And Risk For Schizophrenia: A Report From The Cognitive Genomics Consortium (Cogent), T. Lencz, E. Knowles, G. Davies, S. Guha, D. C. Liewald, J. M. Starr, S. Djurovic, I. Melle, K. Sundet, A. Christoforou, I. Reinvang, S. Mukherjee, P. Derosse, A. Lundervold, V. M. Steen, M. John, T. Espeseth, K. Raikkonen, E. Widen, A. Palotie, J. G. Eriksson, I. Giegling, B. Konte, M. Ikeda, P. Roussos, S. Giakoumaki, K. E. Burdick, A. Payton, W. Ollier, M. Horan, G. Donohoe, D. Morris, A. Corvin, M. Gill, N. Pendleton, N. Iwata, A. Darvasi, P. Bitsios, D. Rujescu, J. Lahti, S. L. Hellard, M. C. Keller, O. A. Andreassen, I. J. Deary, D. C. Glahn, Anil Malhotra

Journal Articles

It has long been recognized that generalized deficits in cognitive ability represent a core component of schizophrenia (SCZ), evident before full illness onset and independent of medication. The possibility of genetic overlap between risk for SCZ and cognitive phenotypes has been suggested by the presence of cognitive deficits in first-degree relatives of patients with SCZ; however, until recently, molecular genetic approaches to test this overlap have been lacking. Within the last few years, large-scale genome-wide association studies (GWAS) of SCZ have demonstrated that a substantial proportion of the heritability of the disorder is explained by a polygenic component consisting of …

The Relationship Between Fasting Serum Glucose And Cerebral Glucose Metabolism In Late-Life Depression And Normal Aging, C. M. Marano, C. I. Workman, C. H. Lyman, E. Kramer, C. R. Hermann, Y. L. Ma, V. Dhawan, T. Chaly, D. Eidelberg, G. S. Smith

Journal Articles

Evidence exists for late-life depression (LLD) as both a prodrome of and risk factor for Alzheimer's disease (AD). The underlying neurobiological mechanisms are poorly understood. Impaired peripheral glucose metabolism may explain the association between depression and AD given the connection between type 2 diabetes mellitus with both depression and AD. Positron emission tomography (PET) measures of cerebral glucose metabolism are sensitive to detecting changes in neural circuitry in LLD and AD. Fasting serum glucose (FSG) in non-diabetic young (YC; n=20) and elderly controls (EC; n=12) and LLD patients (n = 16) was correlated with PET scans of cerebral glucose metabolism …

Biological Insights From 108 Schizophrenia-Associated Genetic Loci, S. Ripke, B. M. Neale, A. Corvin, J. T. R. Walters, K. H. Farh, T. Lencz, A. K. Malhotra, Consortium Psychiat Genomics, Conso Psychosis Endophenotypes Int, Consor Wellcome Trust Case-Control, +292 Additional Authors

Journal Articles

Schizophrenia is a highly heritable disorder. Genetic risk is conferred by a large number of alleles, including common alleles of small effect that might be detected by genome-wide association studies. Here we report a multi-stage schizophrenia genome-wide association study of up to 36,989 cases and 113,075 controls. We identify 128 independent associations spanning 108 conservatively defined loci that meet genome-wide significance, 83 of which have not been previously reported. Associations were enriched among genes expressed in brain, providing biological plausibility for the findings. Many findings have the potential to provide entirely new insights into aetiology, but associations at DRD2 and …

Aggression In Schizophrenia And Its Relationship To Neural Circuitry Of Urgency, P. Szeszko

Journal Articles

No abstract provided.

Functional Development In Clinical High Risk Youth: Prediction Of Schizophrenia Versus Other Psychotic Disorders, S. I. Tarbox, J. Addington, K. S. Cadenhead, T. D. Cannon, B. Cornblatt, D. O. Perkins, L. J. Seidman, M. T. Tsuang, E. F. Walker, S. W. Woods, +2 Additional Authors

Journal Articles

This study evaluates premorbid social and academic functioning in clinical high-risk individuals as predictors of transition to schizophrenia versus another psychotic disorder. Participants were 54 individuals enrolled in phase one of the North American Prodrome Longitudinal Study who over two and a half years of follow-up met criteria for schizophrenia/schizophreniform disorder (n=28) or another psychotic disorder (n=26). Social and academic functioning in childhood, early adolescence, and late adolescence was assessed at baseline using the Cannon-Spoor Premorbid Adjustment Scale. Social maladjustment in late adolescence predicted significantly higher odds of transition to schizophrenia versus another psychotic disorder independent of childhood and early …

Stress Exposure And Sensitivity In The Clinical High-Risk Syndrome: Initial Findings From The North American Prodrome Longitudinal Study (Napls), H. D. Trotman, C. W. Holtzman, E. F. Walker, J. M. Addington, C. E. Bearden, K. S. Cadenhead, T. D. Cannon, B. Cornblatt, R. K. Heinssen, T. H. Mcglashan, +5 Additional Authors

Journal Articles

There is inconsistent evidence for increased stress exposure among individuals at clinical high risk (CHR) for psychosis. Yet similar to patients with a diagnosed psychotic illness, the preponderance of evidence suggests that CHR individuals tend to experience stressful life events (LE) and daily hassles (DH) as more subjectively stressful than healthy individuals. The present study utilizes data from the North American Prodrome Longitudinal Study Phase 2 (NAPLS-2) to test the hypotheses that (1) CHR individuals manifest higher self-reported stress in response to both LE and DH when compared to healthy controls (HC), (2) group differences in self-reported stress increase with …

Moderator Effects Of Working Memory On The Stability Of Adhd Symptoms By Dopamine Receptor Gene Polymorphisms During Development, J. Trampush, M. M. Jacobs, Y. L. Hurd, J. H. Newcorn, J. M. Halperin

Journal Articles

We tested the hypothesis that dopamine D1 and D2 receptor gene (DRD1 and DRD2, respectively) polymorphisms and the development of working memory skills can interact to influence symptom change over 10 years in children with attention-deficit/hyperactivity disorder (ADHD). Specifically, we examined whether improvements in working memory maintenance and manipulation from childhood to early adulthood predicted the reduction of ADHD symptoms as a function of allelic variation in DRD1 and DRD2. Participants were 76 7-11-year-old children with ADHD who were genotyped and prospectively followed for almost 10 years. ADHD symptoms were rated using the Attention Problems scale on the Child Behavior …

Rdocs Redux, D. R. Weinberger, T. Goldberg

Journal Articles

No abstract provided.

Bone Morphogenetic Protein-Focused Strategies To Induce Cytotoxicity In Lung Cancer Cells, A. Fotinos, N. Nagarajan, A. S. Martins, D. T. Fritz, D. Garsetti, A. T. Lee, C. C. Hong, M. B. Rogers

Journal Articles

Background: High bone morphogenetic protein (BMP)-2 expression in lung carcinoma correlates with poor patient prognosis. The present study explored strategies to repress BMP signaling. Materials and Methods: The cytotoxicity of BMP2-knockdown, dorsomorphin derivatives, and microRNAs was tested in transformed and non-transformed lung cells. Microarray analyses of 1,145 microRNAs in A549 lung adenocarcinoma cells and two other transformed lung cell types relative to BEAS-2B bronchial epithelial cells were performed. Results: Reduced BMP2 synthesis inhibited A549 cell growth. The dorsomorphin derivative LDN-193189, but not DMH1 or DMH4, was strongly cytotoxic towards A549 cells, but not towards BEAS-2B cells. Microarray analysis revealed that …

Farewell Statement From Dr. Cerami And Dr. Tracey As Outgoing Co-Editors In Chief Of Molecular Medicine, A. Cerami, K. J. Tracey

Journal Articles

No abstract provided.

Reply: Evidence Against Volume Conduction To Explain Normal Meps In Muscles With Low Motor Power In Sci, D. J. Edwards, M. Cortes, G. W. Thickbroom, A. Rykman, A. Pascual-Leone, B. T. Volpe

Journal Articles

No abstract provided.

Chmp1 Negatively Regulates Epidermal Growth Factor Signaling In The Drosophila Wing, Meagan Elisabeth Valentine

Theses, Dissertations and Capstones

A critical step in cellular signaling through transmembrane receptors is the down-regulation of activated receptors through the multivesicular body (MVB) pathway to the lysosome. MVB generation is mediated by the highly conserved ESCRT (0, I, II, and III) protein complexes. Though the ESCRT-III complex provides the core function of the ESCRT machinery, it is the least characterized of the ESCRT complexes. The Chmp1 protein is an ESCRT-III component and a putative tumor suppressor that has been linked to pancreatic and renal cancers in humans. However, published data on Chmp1 activity are conflicting and its role during tissue development is not …

Identification And Characterization Of Downstream Effector Protein(S) Regulated By P53 And Prb, Miranda B. Carper

Theses, Dissertations and Capstones

A commonality among cancer types is the high frequency of mutations that inhibit or alter signaling of the p53 and pRb (Retinoblastoma) tumor suppressors. These genes regulate processes vital for cancer suppression such as apoptosis, senescence, and cell cycle arrest among others. Loss of both p53 and pRb promotes processes that support cancer progression and is associated with decreased patient survival and increased rates of tumor reoccurrence. Although data points to the ability of p53 and pRb to collaborate and to inhibit tumorigenesis, it remains unclear how p53 and pRb cooperate toward this task. Using RNA expression profiling, 179 p53 …

Concordant Integrative Gene Set Enrichment Analysis Of Multiple Large-Scale Two-Sample Expression Data Sets, Yinglei Lai, Fanni Zhang, Tapan K. Nayak, Reza Modarres, Norman H. Lee, Timothy A. Mccaffrey

Pharmacology and Physiology Faculty Publications

Background

Gene set enrichment analysis (GSEA) is an important approach to the analysis of coordinate expression changes at a pathway level. Although many statistical and computational methods have been proposed for GSEA, the issue of a concordant integrative GSEA of multiple expression data sets has not been well addressed. Among different related data sets collected for the same or similar study purposes, it is important to identify pathways or gene sets with concordant enrichment.

Methods

We categorize the underlying true states of differential expression into three representative categories: no change, positive change and negative change. Due to data noise, what …

Novel Neuroprotective Gsk-3Β Inhibitor Restricts Tat-Mediated Hiv-1 Replication, Irene Guendel, Sergey N. Iordanskiy, Rachel Van Duyne, Kylene Kehn-Hall, Mohammed Saifuddin, Ravi Das, Elizabeth Jaworski, Gavin C. Sampey, Svetlana Senina, Leonard Shultz, Aarthi Narayanan, Chen Hao, Benjamin Lepene, Chen Zeng, Fatah Kashanchi

Microbiology, Immunology, and Tropical Medicine Faculty Publications

The implementation of new antiretroviral therapies targeting transcription of early viral proteins in postintegrated HIV-1 can aid in overcoming current therapy limitations. Using high-throughput screening assays, we have previously described a novel Tat-dependent HIV-1 transcriptional inhibitor named 6-bromoindirubin-3′-oxime (6BIO). The screening of 6BIO derivatives yielded unique compounds that show potent inhibition of HIV-1 transcription. We have identified a second-generation derivative called 18BIOder as an inhibitor of HIV-1 Tat-dependent transcription in TZM-bl cells and a potent inhibitor of GSK-3β kinase in vitro. Structurally, 18BIOder is half the molecular weight and structure of its parental compound, 6BIO. More importantly, we also …

Trans-Activation, Post-Transcriptional Maturation, And Induction Of Antibodies To Herv-K (Hml-2) Envelope Transmembrane Protein In Hiv-1 Infection, Henri-Alexandre Michaud, Miguel De Mulder, Devi Sengupta, Steven G. Deeks, Jeffrey N. Martin, Christopher D. Pilcher, Frederick M. Hecht, Jonah B. Sacha, Douglas F. Nixon

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Background

Human Endogenous Retroviruses (HERVs) comprise about 8% of the human genome and have lost their ability to replicate or to produce infectious particles after having accumulated mutations over time. We assessed the kinetics of expression of HERV-K (HML-2) Envelope mRNA transcript and surface unit (SU) and transmembrane (TM) subunit proteins during HIV-1 infection. We also mapped the specificity of the humoral response to HERV-K (HML-2) Envelope protein in HIV-1 infected subjects at different stages of disease, and correlated the response with plasma viral load.

Results

We found that HIV-1 modified HERV-K (HML-2) Env mRNA expression, resulting in the expression …

Suppression Of Aquaporin, A Mediator Of Water Channel Control In The Carcinogenic Liver Fluke, Opisthorchis Viverrini, Sirikanda Thanasuwan, Supawadee Piratae, Paul J. Brindley, Alex Loukas, Sasithorn Kaewkes, Thewarach Laha

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Background

Opisthorchiasis and Opisthorchis viverrini-associated bile duct cancer represent major public health threats in Thailand and Laos. The tegument of this food borne fluke plays pivotal roles in parasite metabolism, homeostasis and osmoregulation. Excretory/secretory products also pass from the fluke to the biliary environment, products that likely underlie pathogenesis of liver fluke infection. Aquaporins (AQPs), belong to the major intrinsic protein superfamily of integral plasma membrane channel proteins that selectively transport water across cell membranes. AQPs play key roles as water and ion transport channels through the tegument of helminth parasites.

Methods

Here, two forms of AQP mRNAs from the …

Bioclojure: A Functional Library For The Manipulation Of Biological Sequences, Jordan L. Plieskatt, Gabriel Rinaldi, Paul J. Brindley, Xinying Jia, Jeremy Potriquet, Jeffrey M. Bethony, Jason Mulvenna

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large data sets.

Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, fasta and fastq. In addition it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure's functional style and emphasize laziness and composability, so that BioClojure, …

Schistosomes And Snails: A Molecular Encounter, Matty Knight, Halime D. Arican-Goktas, Wannaporn Ittiprasert, Edwin C. Odoemelam, Andre N. Miller, Joanna M. Bridger

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Biomphalaria glabrata snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis in the Western hemisphere. For the past two decades, tremendous advances have been made in research aimed at elucidating the molecular basis of the snail/parasite interaction. The growing concern that there is no vaccine to prevent schistosomiasis and only one effective drug in existence provides the impetus to develop new control strategies based on eliminating schistosomes at the snail-stage of the life cycle. To elucidate why a given snail is not always compatible to each and every schistosome it encounters, B. …

Microrna-21 Down-Regulates Rb1 Expression By Targeting Pdcd4 In Retinoblastoma, Fengmei Shen, Meng-Hsuan Mo, Shejuan An, Xiaohui Tan, Yebo Fu, M. Katayoon Rezaei, Zuoren Wang, Lin Zhang, Sidney W. Fu

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Retinoblastoma (RB) is a children’s ocular cancer caused by mutated retinoblastoma 1 (Rb1) gene on both alleles. Rb1 and other related genes could be regulated by microRNAs (miRNA) via complementarily pairing with their target sites. MicroRNA-21 (miR-21) possesses the oncogenic potential to target several tumor suppressor genes, including PDCD4, and regulates tumor progression and metastasis. However, the mechanism of how miR-21 regulates PDCD4 is poorly understood in RB. We investigated the expression of miRNAs in RB cell lines and identified that miR-21 is one of the most deregulated miRNAs in RB. Using qRT-PCR, we verified the expression level of several …

Schistosome And Liver Fluke Derived Catechol-Estrogens And Helminth Associated Cancers., José M. Correia Da Costa, Nuno Vale, Maria J. Gouveia, Mónica C. Botelho, Banchob Sripa, Lúcio L. Santos, Júlio H. Santos, Gabriel Rinaldi, Paul J. Brindley

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Infection with helminth parasites remains a persistent public health problem in developing countries. Three of these pathogens, the liver flukes Clonorchis sinensis, Opisthorchis viverrini and the blood fluke Schistosoma haematobium, are of particular concern due to their classification as Group 1 carcinogens: infection with these worms is carcinogenic. Using liquid chromatography-mass spectrometry (LC-MS/MS) approaches, we identified steroid hormone like (e.g., oxysterol-like, catechol estrogen quinone-like, etc.) metabolites and related DNA-adducts, apparently of parasite origin, in developmental stages including eggs of S. haematobium, in urine of people with urogenital schistosomiasis, and in the adult stage of O. viverrini. Since these kinds of …

Fusion, 2014, George Washington University, William H. Beaumont Medical Research Honor Society

Fusion

No abstract provided.

Phenoxybenzamine Is Neuroprotective In A Rat Model Of Severe Traumatic Brain Injury, Thomas Rau, Aakriti Kothiwal, Annela Rova, Joseph F. Rhoderick, David J. Poulsen

Biomedical and Pharmaceutical Sciences Faculty Publications

Phenoxybenzamine (PBZ) is an FDA approved α-1 adrenergic receptor antagonist that is currently used to treat symptoms of pheochromocytoma. However, it has not been studied as a neuroprotective agent for traumatic brain injury (TBI). While screening neuroprotective candidates, we found that phenoxybenzamine reduced neuronal death in rat hippocampal slice cultures following exposure to oxygen glucose deprivation (OGD). Using this system, we found that phenoxybenzamine reduced neuronal death over a broad dose range (0.1 μM–1 mM) and provided efficacy when delivered up to 16 h post-OGD. We further tested phenoxybenzamine in the rat lateral fluid percussion model of TBI. When administered …

Sequestering Hmgb1 Via Dna-Conjugated Beads Ameliorates Murine Colitis, Z. Ju, S. S. Chavan, M. Dancho, T. Tsaava, J. Li, B. Lu, Y. Al-Abed, J. Roth, K. J. Tracey, H. Yang, +4 Additional Authors

Journal Articles

Inflammatory bowel disease (IBD) is chronic inflammation of the gastrointestinal tract that affects millions of people worldwide. Although the etiology of IBD is not clear, it is known that products from stressed cells and enteric microbes promote intestinal inflammation. High mobility group box 1 (HMGB1), originally identified as a nuclear DNA binding protein, is a cytokine-like protein mediator implicated in infection, sterile injury, autoimmune disease, and IBD. Elevated levels of HMGB1 have been detected in inflamed human intestinal tissues and in feces of IBD patients and mouse models of colitis. Neutralizing HMGB1 activity by administration of anti-HMGB1 antibodies or HMGB1-specific …

Inhibition Of Amp-Activated Protein Kinase Signaling Alleviates Impairments In Hippocampal Synaptic Plasticity Induced By Amyloid Beta, T. Ma, Y. R. Chen, V. Vingtdeux, H. T. Zhao, B. Viollet, P. Marambaud, E. Klann

Journal Articles

The AMP-activated protein kinase (AMPK) is a Ser/Thr kinase that is activated in response to low-energy states to coordinate multiple signaling pathways to maintain cellular energy homeostasis. Dysregulation of AMPK signaling has been observed in Alzheimer's disease (AD), which is associated with abnormal neuronal energy metabolism. In the current study we tested the hypothesis that aberrant AMPK signaling underlies AD-associated synaptic plasticity impairments by using pharmacological and genetic approaches. We found that amyloid beta (A beta)-induced inhibition of long-term potentiation (LTP) and enhancement of long-term depression were corrected by the AMPK inhibitor compound C (CC). Similarly, LTP impairments in APP/PS1 …

Candidate Chromosome 1 Disease Susceptibility Genes For Sjogren's Syndrome Xerostomia Are Narrowed By Novel Nod.B10 Congenic Mice, P. K. A. Mongini, J. M. Kramer, T. Ishikawa, H. Herschman, D. Esposito

Journal Articles

Sjogren's syndrome (SS) is characterized by salivary gland leukocytic infiltrates and impaired salivation (xerostomia). Cox-2 (Ptgs2) is located on chromosome 1 within the span of the Aec2 region. In an attempt to demonstrate that COX-2 drives antibody-dependent hyposalivation, NOD.B10 congenic mice bearing a Cox-2flox gene were generated. A congenic line with non-NOD alleles in Cox-2-flanking genes failed manifest xerostomia. Further backcrossing yielded disease-susceptible NOD.B10 Cox-2flox lines; fine genetic mapping determined that critical Aec2 genes lie within a 1.56 to 2.17 Mb span of DNA downstream of Cox-2. Bioinformatics analysis revealed that susceptible and non-susceptible lines exhibit non-synonymous coding SNPs in …

Sucrose-Conditioned Flavor Preferences In Sweet Ageusic T1r3 And Calhm1 Knockout Mice, A. Sclafani, P. Marambaud, K. Ackroff

Journal Articles

The present study compared the ability of sweet ageusic T1r3 knockout (KO) and Calhm1 KO mice to acquire preferences for a sucrose-paired flavor as well as for unflavored sucrose. The KO and wildtype (WT) mice were given 24-h one-bottle access to 8% sucrose containing one flavor CS+, e.g., grape) and to water containing a different flavor (CS-, e.g., cherry) over 4 training days. In subsequent two-bottle tests with the flavors in water only, the T1r3 KO and Calhm1 KO mice, like WT mice, preferred the CS+ to the CS-. After training with flavored solutions, both KO groups also preferred unflavored …

Evaluation Of Amniotic-Derived Membrane Biomaterial As An Adjunct For Repair Of Critical Sized Bone Defects, M. Starecki, J. A. Schwartz, D. A. Grande

Journal Articles

No abstract provided.

Salty Taste Deficits In Calhm1 Knockout Mice, M. G. Tordoff, H. T. Ellis, T. R. Aleman, A. Downing, P. Marambaud, J. K. Foskett, R. M. Dana, S. A. Mccaughey

Journal Articles

Genetic ablation of calcium homeostasis modulator 1 (CALHM1), which releases adenosine triphosphate from Type 2 taste cells, severely compromises the behavioral and electrophysiological responses to tastes detected by G protein-coupled receptors, such as sweet and bitter. However, the contribution of CALHM1 to salty taste perception is less clear. Here, we evaluated several salty taste-related phenotypes of CALHM1 knockout (KO) mice and their wild-type (WT) controls: 1) In a conditioned aversion test, CALHM1 WT and KO mice had similar NaCl avoidance thresholds. 2) In two-bottle choice tests, CALHM1 WT mice showed the classic inverted U-shaped NaCl concentration-preference function but CALHM1 KO …