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Development and Validation of a New Tumor-Based Gene Signature
Zhu et al. J Transl Med (2019) 17:203 https://doi.org/10.1186/s12967-019-1946-8 Journal of Translational Medicine RESEARCH Open Access Development and validation of a new tumor-based gene signature predicting prognosis of HBV/HCV-included resected hepatocellular carcinoma patients Gui‑Qi Zhu1,2†, Yi Yang1,2†, Er‑Bao Chen3†, Biao Wang1,2, Kun Xiao1,2, Shi‑Ming Shi4, Zheng‑Jun Zhou1,2, Shao‑Lai Zhou1,2, Zheng Wang1,2, Ying‑Hong Shi1,2, Jia Fan1,2, Jian Zhou1,2, Tian‑Shu Liu3 and Zhi Dai1,2* Abstract Background: Due to the phenotypic and molecular diversity of hepatocellular carcinomas (HCC), it is still a challenge to determine patients’ prognosis. We aim to identify new prognostic markers for resected HCC patients. Methods: 274 patients were retrospectively identifed and samples collected from Zhongshan hospital, Fudan Uni‑ versity. We analyzed the gene expression patterns of tumors and compared expression patterns with patient survival times. We identifed a “9‑gene signature” associated with survival by using the coefcient and regression formula of multivariate Cox model. This molecular signature was then validated in three patients cohorts from internal cohort (n 69), TCGA (n 369) and GEO dataset (n 80). = = = Results: We identifed 9‑gene signature consisting of ZC2HC1A, MARCKSL1, PTGS1, CDKN2B, CLEC10A, PRDX3, PRKCH, MPEG1 and LMO2. The 9‑gene signature was used, combined with clinical parameters, to ft a multivariable Cox model to the training cohort (concordance index, ci 0.85), which was successfully validated (ci 0.86 for internal cohort; ci 0.78 for in silico cohort). The signature showed= improved performance compared with= clinical parameters alone (ci= 0.70). -
The Hypothalamus in Schizophrenia Research: No Longer a Wallflower Existence
The Open Neuroendocrinology Journal, 2010, 3, 59-67 59 Open Access The Hypothalamus in Schizophrenia Research: No Longer a Wallflower Existence Hans-Gert Bernstein*,1, Gerburg Keilhoff 2, Johann Steiner1, Henrik Dobrowolny1 and Bernhard Bogerts1 1Department of Psychiatry and 2Institute of Biochemistry and Cell Biology, Otto v. Guericke University Magdeburg, Leipziger Str. 44, D-39120 Magdeburg, Germany Abstract: The hypothalamus is commonly believed to play only a subordinated role in schizophrenia. The present review attempts at condensing findings of the last two decades showing that hypothalamus is involved in many pathways found disturbed in schizophrenia (hypothalamus-pituitary- axis, hypothalamus-pituitary-thyroid axis, hypothalamus-pituitary- gonadal axis, metabolic syndrome, sleep-wakefulness cycle, and neuroimmune dysfunction). On the basis of this knowl- edge it is suggested to reconsider the place of the hypothalamus in the puzzle of schizophrenia. Keywords: Hypothalamus, schizophrenia, hippocampus, depression, stress, neuroendocrinology, neuroimmunology. 1. INTRODUCTION to be less, or even only marginally, affected in schizophre- nia. Until recently, the hypothalamus is thought to belong to Schizophrenia is a severe, chronic brain disorder afflict- the latter group. With this review we try to show that this ing about 1% percent of the population. The disease mainly important brain region is in many ways involved in the impairs multiple cognitive domains including memory, at- pathophysiology of schizophrenia, and that we therefore tention and executive function, and typically produces a life- should reconsider the place of the hypothalamus in the puz- time of disability and severe emotional distress for affected zle of schizophrenia. individuals [1]. The clinical features of the disorder appear in the second to third decade of life. -
Endogenous Peptide Discovery of the Rat Circadian Clock a FOCUSED STUDY of the SUPRACHIASMATIC NUCLEUS by ULTRAHIGH PERFORMANCE TANDEM MASS □ SPECTROMETRY* S
Research Endogenous Peptide Discovery of the Rat Circadian Clock A FOCUSED STUDY OF THE SUPRACHIASMATIC NUCLEUS BY ULTRAHIGH PERFORMANCE TANDEM MASS □ SPECTROMETRY* S Ji Eun Lee‡§, Norman Atkins, Jr.¶, Nathan G. Hatcherʈ, Leonid Zamdborg‡§, Martha U. Gillette§¶**, Jonathan V. Sweedler‡§¶ʈ, and Neil L. Kelleher‡§‡‡ Understanding how a small brain region, the suprachias- pyroglutamylation, or acetylation. These aspects of peptide matic nucleus (SCN), can synchronize the body’s circa- synthesis impact the properties of neuropeptides, further ex- dian rhythms is an ongoing research area. This important panding their diverse physiological implications. Therefore, time-keeping system requires a complex suite of peptide unveiling new peptides and unreported peptide properties is hormones and transmitters that remain incompletely critical to advancing our understanding of nervous system characterized. Here, capillary liquid chromatography and function. FTMS have been coupled with tailored software for the Historically, the analysis of neuropeptides was performed analysis of endogenous peptides present in the SCN of the rat brain. After ex vivo processing of brain slices, by Edman degradation in which the N-terminal amino acid is peptide extraction, identification, and characterization sequentially removed. However, analysis by this method is from tandem FTMS data with <5-ppm mass accuracy slow and does not allow for sequencing of the peptides con- produced a hyperconfident list of 102 endogenous pep- taining N-terminal PTMs (5). Immunological techniques, such tides, including 33 previously unidentified peptides, and as radioimmunoassay and immunohistochemistry, are used 12 peptides that were post-translationally modified with for measuring relative peptide levels and spatial localization, amidation, phosphorylation, pyroglutamylation, or acety- but these methods only detect peptide sequences with known lation. -
Changes of Tlqp-21 in Response to Glucose Load
bioRxiv preprint doi: https://doi.org/10.1101/626283; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. CHANGES OF TLQP-21 IN RESPONSE TO GLUCOSE LOAD Giulia Corda1, Barbara Noli1, Barbara Manconi2, Carla Brancia1, Manuela Pellegrini3, Fabio Naro3, Gian-Luca Ferri1 and Cristina Cocco1 1NEF-Laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato (CA), Italy2 Department of Life and Enviromental Sciences, University of Cagliari, Monserrato (CA), Italy 3Department of Anatomical, Istological and Legal medicine Sciences of the locomotor apparatus, University of “La Sapienza’, Roma, Italy Abstract 5 The TLQP-21 peptide peripherally potentiates glucose-stimulated insulin secretion. The aim of this study was to investigate a possible endocrine mechanism through which TLQP- 21 increases the insulin secretion. Using an antibody specific for the common N-terminal portion of the TLQP peptides, we studied pancreas and plasma of mice subjected to intraperitoneal glucose load, by immunohistochemistry and immunosorbent assay (ELISA), 10 alone or coupled to High Performance Liquid Chromatography (HLPC). Mice underwent a period of starvation hence have received a glucose load, or saline, and were sacrificed 30 or 120 minutes later. In normal endocrine pancreas, the TLQP-antiserum stained either peripheral or central cells. Interestingly, 30 min after a glucose load, TLQP immunostaining was disappeared in pancreas and, when analysed by ELISA, the TLQP-levels started to 15 increase in plasma reaching peak concentration at 120 min. -
C-Jun N-Terminal Kinase Signaling Guides the Migration of Interneurons During Cortical Development
Graduate Theses, Dissertations, and Problem Reports 2017 C-Jun N-Terminal Kinase Signaling Guides the Migration of Interneurons During Cortical Development Abigail K. Myers Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Myers, Abigail K., "C-Jun N-Terminal Kinase Signaling Guides the Migration of Interneurons During Cortical Development" (2017). Graduate Theses, Dissertations, and Problem Reports. 6285. https://researchrepository.wvu.edu/etd/6285 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. c-Jun N-terminal kinase signaling guides the migration of interneurons during cortical development Abigail K Myers Dissertation submitted to the School of Medicine at West Virginia University In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Neuroscience Eric S Tucker, -
Ncomms8838.Pdf
ARTICLE Received 2 Feb 2015 | Accepted 17 Jun 2015 | Published 21 Jul 2015 DOI: 10.1038/ncomms8838 OPEN Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst Daniel B. Graham1,2, Christine E. Becker3, Aivi Doan1, Gautam Goel3, Eduardo J. Villablanca1,2,3, Dan Knights4, Amanda Mok1, Aylwin C.Y. Ng1,5, John G. Doench1, David E. Root1, Clary B. Clish1 & Ramnik J. Xavier1,2,3,5,6 The phagocyte oxidative burst, mediated by Nox2 NADPH oxidase-derived reactive oxygen species, confers host defense against a broad spectrum of bacterial and fungal pathogens. Loss-of-function mutations that impair function of the Nox2 complex result in a life-threatening immunodeficiency, and genetic variants of Nox2 subunits have been implicated in pathogenesis of inflammatory bowel disease (IBD). Thus, alterations in the oxidative burst can profoundly impact host defense, yet little is known about regulatory mechanisms that fine-tune this response. Here we report the discovery of regulatory nodes controlling oxidative burst by functional screening of genes within loci linked to human inflammatory disease. Implementing a multi-omics approach, we define transcriptional, metabolic and ubiquitin-cycling nodes controlled by Rbpj, Pfkl and Rnf145, respectively. Furthermore, we implicate Rnf145 in proteostasis of the Nox2 complex by endoplasmic reticulum-associated degradation. Consequently, ablation of Rnf145 in murine macrophages enhances bacterial clearance, and rescues the oxidative burst defects associated with Ncf4 haploinsufficiency. 1 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. 2 Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA. 3 Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA. -
RNA Sequencing Analysis Reveals the Gnrh Induced Citrullinome
Authors Michelle A. Londe, Kenneth G. Gerow, Amy M. Navratil, Shaihla A. Khan, Brian S. Edwards, Paul R. Thompson, John Diller, Kenneth L. Jones, and Brian D. Cherrington This dissertation/thesis is available at Wyoming Scholars Repository: http://repository.uwyo.edu/honors_theses_15-16/48 Londe 1 RNA sequencing analysis reveals the GnRH induced citrullinome Michelle A. Londe1, Shaihla A. Khan2, Brian S. Edwards2, Paul R. Thompson3, John Diller4, Kenneth L. Jones4, Kenneth G. Gerow1, Brian D. Cherrington2, Amy M. Navratil2 1Department of Statistics, University of Wyoming, Laramie, Wyoming, 82071 2Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, 82071 3University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA, United States of America 4 Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz campus, Aurora, 80045. Key words: histone modification, peptidylarginine deiminase, gene regulation, RNA-sequencing Londe 2 Secretion of gonadotropin releasing hormone (GnRH) from the hypothalamus is critical for the secretion of the gonadotropins luteinizing hormone (LH) and follicle stimulating hormone (FSH). GnRH binds to its receptors on the plasma membrane of anterior pituitary gonadotropes and stimulates the release of these hormones. LH is crucial for regulating the function of the testes in men and the ovaries in women. In women, LH is important in carrying out functions in women’s menstrual cycles and stimulates the release of progesterone if pregnancy occurs.1 FSH is also important for reproduction, with its main roles also responsible for the maintenance of the menstrual cycle, release of estrogen and progesterone, as well as the growth of ovarian follicles.2 Given the essential role of gonadotropin production to fertility, major effort has gone into defining the mechanisms initiated by GnRH to regulate gonadotropin gene expression at the promoter/transcription factor level. -
Selective Expression of TLQP-21 and Other VGF Peptides in Gastric Neuroendocrine Cells and Modulation by Feeding
329 Selective expression of TLQP-21 and other VGF peptides in gastric neuroendocrine cells and modulation by feeding Carla Brancia1, Cristina Cocco1, Filomena D’Amato1, Barbara Noli1, Fabrizio Sanna2, Roberta Possenti3, Antonio Argiolas2 and Gian-Luca Ferri1 1NEF-Laboratory, Department of Cytomorphology and 2Department of Neuroscience, University of Cagliari, 09042 Monserrato (Cagliari), Italy 3Institute of Neurobiology and Molecular Medicine, CNR, and Department of Neuroscience, Tor Vergata University, 00133 Rome, Italy (Correspondence should be addressed to G-L Ferri; Email: [email protected]) Abstract Although vgf gene knockout mice are hypermetabolic, confined to neurons. VGF mRNA was present in the above administration of the VGF peptide TLQP-21 itself increased gastric endocrine cell types, and was prominent in chief cells, energy consumption. Agonist–antagonist roles are thus in parallel with low-intensity staining for further cleaved suggested for different VGF peptides, and the definition of products from the C-terminal region of VGF (HVLL their tissue heterogeneity is mandatory. We studied the rat peptides: VGF605–614). In swine stomach, a comparable stomach using antisera to C- or N-terminal sequences of profile of VGF peptides was revealed by immunohistochem- known or predicted VGF peptides in immunohistochemistry istry. When fed and fasted rats were studied, a clear-cut, and ELISA. TLQP (rat VGF556–565) peptide/s were most selective decrease on fasting was observed for TLQP peptides abundant (162G11 pmol/g, meanGS.E.M.) and were brightly only (162G11 vs 74G5.3 pmol/g, fed versus fasted rats, immunostained in enterochromaffin-like (ECL) cells and meanGS.E.M., P!0.00001). In conclusion, specific VGF somatostatin cells. -
Reduced Serum VGF Levels Are Linked with Suicide Risk in Chinese Han
Li et al. BMC Psychiatry (2020) 20:225 https://doi.org/10.1186/s12888-020-02634-9 RESEARCH ARTICLE Open Access Reduced serum VGF levels are linked with suicide risk in Chinese Han patients with major depressive disorder Xingxing Li1†, Huifei Ge2†, Dongsheng Zhou1†, Xiangping Wu1†, Gangqiao Qi2, Zan Chen1, Chang Yu1, Yuanyuan Zhang1, Haihang Yu1 and Chuang Wang3* Abstract Background: VGF (nonacronymic) is a neuropeptide that plays an important role in the pathogenesis of major depressive disorder (MDD). However, no studies have yet investigated VGF levels in patients with MDD who are at risk of suicide. The purpose of the present study was to determine whether serum VGF levels are related to suicide risk in patients with MMD. Methods: A total of 107 patients with MDD and 40 normal control participated in the present study. The risk of suicide was assessed using the Nurses Global Assessment of Suicide Risk (NGASR). On this basis, 60 patients were assigned to a high-risk group (NGASR≥9) and 47 were assigned to a low-risk group (NGASR< 9). The severity of depression was measured using the 17-item Hamilton Depression Rating Scale (HDRS). Levels of serum VGF were determined using a double antibody sandwich enzyme-linked immunosorbent assay. Results: Serum VGF levels in the high-risk group (883.34 ± 139.67 pg/mL) were significantly lower than in the low- risk group (1020.56 ± 131.76 pg/mL) and in the control group (1107.00 ± 155.38 pg/mL) (F = 31.90, p < 0.001). In patients with MDD, suicide risk was significantly negatively correlated with VGF levels (r = − 0.55, p = 0.001). -
Neuroendocrine Role for VGF
REVIEW ARTICLE published: 02 February 2015 doi: 10.3389/fendo.2015.00003 Neuroendocrine role for VGF 1 2 2 Jo E. Lewis , John M. Brameld and Preeti H. Jethwa * 1 Queen’s Medical Centre, School of Life Sciences, University of Nottingham Medical School, Nottingham, UK 2 Division of Nutritional Sciences, School of Biosciences, University of Nottingham, Loughborough, UK Edited by: The vgf gene (non-acronymic) is highly conserved and was identified on the basis of its Hubert Vaudry, University of Rouen, rapid induction in vitro by nerve growth factor, although can also be induced by brain- France derived neurotrophic factor, and glial-derived growth factor. The VGF gene gives rise to a Reviewed by: Alena Sumova, Academy of Sciences 68 kDa precursor polypeptide, which is induced robustly, relatively selectively and is syn- of the Czech Republic, Czech Republic thesized exclusively in neuronal and neuroendocrine cells. Post-translational processing by Ruud Buijs, Universidad Autónoma de neuroendocrine specific prohormone convertases in these cells results in the production of México, Mexico a number of smaller peptides.TheVGF gene and peptides are widely expressed throughout *Correspondence: the brain, particularly in the hypothalamus and hippocampus, in peripheral tissues including Preeti H. Jethwa, Division of Nutritional Sciences, School of the pituitary gland, the adrenal glands, and the pancreas, and in the gastrointestinal tract in Biosciences, University of both the myenteric plexus and in endocrine cells. VGF peptides have been associated with Nottingham, Sutton Bonington a number of neuroendocrine roles, and in this review, we aim to describe these roles to Campus, Loughborough, LE12 5RD, highlight the importance of VGF as therapeutic target for a number of disorders, particularly UK e-mail: preeti.jethwa@nottingham. -
Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity
New Research Development Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience- Dependent Cortical Plasticity Milo R. Smith1,2,3,4,5,6,7,8, Poromendro Burman1,3,4,5,8, Masato Sadahiro1,3,4,5,6,8, Brian A. Kidd,2,7 Joel T. Dudley,2,7 and Hirofumi Morishita1,3,4,5,8 DOI:http://dx.doi.org/10.1523/ENEURO.0240-16.2016 1Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 3Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 4Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 5Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 6Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 7Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, and 8Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 Visual Abstract Throughout childhood and adolescence, periods of heightened neuroplasticity are critical for the development of healthy brain function and behavior. Given the high prevalence of neurodevelopmental disorders, such as autism, identifying disruptors of developmental plasticity represents an essential step for developing strategies for prevention and intervention. Applying a novel computational approach that systematically assessed connections between 436 transcriptional signatures of disease and multiple signatures of neuroplasticity, we identified inflammation as a common pathological process central to a diverse set of diseases predicted to dysregulate Significance Statement During childhood and adolescence, heightened neuroplasticity allows the brain to reorganize and adapt to its environment. -
Transdifferentiation of Human Mesenchymal Stem Cells
Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone