The Kinesin-2 Family Member KIF3C Regulates Microtubule Dynamics and Is Required for Axon Growth and Regeneration
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Analysis of the Human Serum Proteome
Cedarville University DigitalCommons@Cedarville Pharmaceutical Sciences Faculty Publications Department of Pharmaceutical Sciences 6-2004 Analysis of the Human Serum Proteome King C. Chan David A. Lucas Denise Hise Carl F. Schaefer Zhen Xiao See next page for additional authors Follow this and additional works at: https://digitalcommons.cedarville.edu/ pharmaceutical_sciences_publications Part of the Pharmacy and Pharmaceutical Sciences Commons This Article is brought to you for free and open access by DigitalCommons@Cedarville, a service of the Centennial Library. It has been accepted for inclusion in Pharmaceutical Sciences Faculty Publications by an authorized administrator of DigitalCommons@Cedarville. For more information, please contact [email protected]. Authors King C. Chan, David A. Lucas, Denise Hise, Carl F. Schaefer, Zhen Xiao, George M. Janini, Kenneth H. Buetow, Haleem J. Issaq, Timothy D. Veenstra, and Thomas P. Conrads Clinical Proteomics Journal Copyright ©Humana Press Inc. All rights of any nature whatsoever are reserved. ISSN 1542-6416/04/01:101–225/$25.00 Serum/Plasma Proteome Analysis of the Human Serum Proteome King C. Chan,1,† David A. Lucas,1,† Denise Hise,2 Carl F. Schaefer,2 Zhen Xiao,1 George M. Janini,1 Kenneth H. Buetow,2 Haleem J. Issaq,1 Timothy D.Veenstra,1 and Thomas P. Conrads1,* 1Laboratory of Proteomics and Analytical Technologies, National Cancer Institute at Frederick, SAIC-Frederick, Inc, PO Box B, Frederick, MD 21702 2Center for Bioinformatics, National Cancer Institute, Bethesda, MD 20892 †These authors contributed equally to this work. each of which was analyzed by microcapillary Abstract reversed-phase liquid chromatography coupled Changes in serum proteins that signal online with MS/MS analysis. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Comprehensive Analysis of Expression, Prognosis and Immune Infltrates for Kinesin Superfamily Members in Human Pancreatic Adenocarcinoma
Comprehensive Analysis of Expression, Prognosis and Immune Inltrates for Kinesin Superfamily Members in Human Pancreatic Adenocarcinoma Zehao Chen ( [email protected] ) Wuhan University https://orcid.org/0000-0001-9440-0782 Jie Wang Wuhan University Jian Xu Wuhan University Wenjie Zhu Wuhan University Jianxin Jiang Wuhan University Research Keywords: Kinesin superfamily, Pancreatic Adenocarcinoma, Expression, Prognostic value, Immune Inltrates Posted Date: June 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-550619/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/26 Abstract Background Kinesin superfamily (KIFs) has a long-reported signicant inuence on the initiation, development, and progress of pancreatic adenocarcinoma (PAAD). However, the expression level of different KIFs in PAAD and its relationship with the prognosis and immune inltration in patients with PAAD have not been fully elucidated. Methods Comprehensive bioinformatics analyses were done using data from UCSC XENA data hubs, TCGA databaseOncomine databases, GEO datasets, GEPIA, GTEx, The human protein atlas, Kaplan Meier plotter, cBioPortal, STRING and KEGG database. Then, the relationship between KIFs expression and tumor immune inltrates was studied by using the TIMER database. Results A total of 24 differentially expressed KIFs at transcriptional levels were identied between tumor tissues and normal tissues with 1 (KIF1A) downregulated and 23 (KIF2A, KIF2C, KIF3A, KIF3B, KIF3C, KIF4A, KIF5B, KIF7, KIF9, KIF10, KIF11, KIF13A, KIF13B, KIF15, KIF16B, KIF18B, KIF20A, KIF20B, KIF21B, KIF22, KIF23, KIF26B, KIFC1) overexpressed by GEPIA. The protein expression level of KIF3A, KIF3B, KIF4A, KIF5B, KIF7, KIF9, CENPE, KIF11, KIF13A, KIF13B, KIF15, KIF16B, KIF18B, KIF20A, KIF20B, KIF21B, KIF22, KIF23, KIF26B, KIFC1 are higher in PAAD tissues than in the adjacent tissues, which is almost the same as the results of KIFs at transcriptional levels in PAAD. -
Gene Networks Activated by Specific Patterns of Action Potentials in Dorsal Root Ganglia Neurons Received: 10 August 2016 Philip R
www.nature.com/scientificreports OPEN Gene networks activated by specific patterns of action potentials in dorsal root ganglia neurons Received: 10 August 2016 Philip R. Lee1,*, Jonathan E. Cohen1,*, Dumitru A. Iacobas2,3, Sanda Iacobas2 & Accepted: 23 January 2017 R. Douglas Fields1 Published: 03 March 2017 Gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and adaptation that occur throughout neonatal and postnatal life. Here we show that the transcriptional response in neurons is exquisitely sensitive to the temporal nature of action potential firing patterns. Neurons were electrically stimulated with the same number of action potentials, but with different inter-burst intervals. We found that these subtle alterations in the timing of action potential firing differentially regulates hundreds of genes, across many functional categories, through the activation or repression of distinct transcriptional networks. Our results demonstrate that the transcriptional response in neurons to environmental stimuli, coded in the pattern of action potential firing, can be very sensitive to the temporal nature of action potential delivery rather than the intensity of stimulation or the total number of action potentials delivered. These data identify temporal kinetics of action potential firing as critical components regulating intracellular signalling pathways and gene expression in neurons to extracellular cues during early development and throughout life. Adaptation in the nervous system in response to external stimuli requires synthesis of new gene products in order to elicit long lasting changes in processes such as development, response to injury, learning, and memory1. Information in the environment is coded in the pattern of action-potential firing, therefore gene transcription must be regulated by the pattern of neuronal firing. -
Strong Correlation Between Air-Liquid Interface Cultures and in Vivo Transcriptomics of Nasal Brush Biopsy
Am J Physiol Lung Cell Mol Physiol 318: L1056–L1062, 2020. First published April 1, 2020; doi:10.1152/ajplung.00050.2020. RAPID REPORT Translational Physiology Strong correlation between air-liquid interface cultures and in vivo transcriptomics of nasal brush biopsy X Baishakhi Ghosh,1 Bongsoo Park,1 Debarshi Bhowmik,2 Kristine Nishida,3 Molly Lauver,3 Nirupama Putcha,3 Peisong Gao,4 Murugappan Ramanathan, Jr.,5 Nadia Hansel,3 Shyam Biswal,1 and Venkataramana K. Sidhaye1,3 1Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; 2Department of Biology, Johns Hopkins University, Baltimore, Maryland; 3Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland; 4Division of Allergy and Clinical Immunology, Johns Hopkins School of Medicine, Baltimore, Maryland; and 5Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland Submitted 18 February 2020; accepted in final form 24 March 2020 Ghosh B, Park B, Bhowmik D, Nishida K, Lauver M, Putcha N, RNA sequencing to determine the correlation between ALI- Gao P, Ramanathan M Jr, Hansel N, Biswal S, Sidhaye VK. cultured epithelial cells and epithelial cells obtained from nasal Strong correlation between air-liquid interface cultures and in vivo brushing and identify differences that may arise as a result of transcriptomics of nasal brush biopsy. Am J Physiol Lung Cell Mol redifferentiation. Physiol 318: L1056–L1062, 2020. First published April 1, 2020; doi:10.1152/ajplung.00050.2020.—Air-liquid interface (ALI) cultures METHODS are ex vivo models that are used extensively to study the epithelium of patients with chronic respiratory diseases. -
The Role of Kinesin-2 in Navigating Microtubule Obstacles: Implications for the Regulation of Axonal Transport Gregory Hoeprich University of Vermont
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2016 The Role Of Kinesin-2 In Navigating Microtubule Obstacles: Implications For The Regulation Of Axonal Transport Gregory Hoeprich University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Biophysics Commons Recommended Citation Hoeprich, Gregory, "The Role Of Kinesin-2 In Navigating Microtubule Obstacles: Implications For The Regulation Of Axonal Transport" (2016). Graduate College Dissertations and Theses. 558. https://scholarworks.uvm.edu/graddis/558 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. THE ROLE OF KINESIN-2 IN NAVIGATING MICROTUBULE OBSTACLES: IMPLICATIONS FOR THE REGULATION OF AXONAL TRANSPORT A Dissertation Presented by Gregory Joseph Hoeprich to The Faculty of the Graduate College of The University of Vermont In Partial Fulfilment of the Requirements For the Degree of Doctor of Philosophy Specializing in Molecular Physiology and Biophysics May, 2016 Defense Date: March 8, 2016 Dissertation Examination Committee: Christopher Berger, Ph.D., Advisor Victor May, Ph.D., Chairperson David Warshaw, Ph.D. Teresa Ruiz, Ph.D. Jason Stumpff, Ph.D. Cynthia J. Forehand, Ph.D., Dean of the Graduate College ABSTRACT Neurons are specialized cells that transmit information through electrical and chemical signals using structural processes known as dendrites and axons. Dendrites receive information for the cell to interpret while the exceedingly long axon transmits the processed information to its target destination. -
Specific Depletion of the Motor Protein KIF5B Leads to Deficits in Dendritic
RESEARCH ARTICLE Specific depletion of the motor protein KIF5B leads to deficits in dendritic transport, synaptic plasticity and memory Junjun Zhao1†, Albert Hiu Ka Fok1†, Ruolin Fan1, Pui-Yi Kwan1, Hei-Lok Chan1, Louisa Hoi-Ying Lo1, Ying-Shing Chan2, Wing-Ho Yung3, Jiandong Huang1,2,4, Cora Sau Wan Lai1,2*, Kwok-On Lai1,2* 1School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China; 2State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China; 3School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China; 4Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China Abstract The kinesin I family of motor proteins are crucial for axonal transport, but their roles in dendritic transport and postsynaptic function are not well-defined. Gene duplication and subsequent diversification give rise to three homologous kinesin I proteins (KIF5A, KIF5B and KIF5C) in vertebrates, but it is not clear whether and how they exhibit functional specificity. Here we show that knockdown of KIF5A or KIF5B differentially affects excitatory synapses and dendritic transport in hippocampal neurons. The functional specificities of the two kinesins are determined by their diverse carboxyl-termini, where arginine methylation occurs in KIF5B and regulates its *For correspondence: function. KIF5B conditional knockout mice exhibit deficits in dendritic spine morphogenesis, [email protected] (CSWL); synaptic plasticity and memory formation. Our findings provide insights into how expansion of the [email protected] (K-OL) kinesin I family during evolution leads to diversification and specialization of motor proteins in †These authors contributed regulating postsynaptic function. -
The Role of Nuclear Positioning in Muscle Function
UNIVERSIDADE DE LISBOA Faculdade de Medicina The role of nuclear positioning in muscle function Mafalda Ramos de Melo Pimentel Orientador: Prof. Doutor Edgar Rodrigues Almeida Gomes Tese especialmente elaborada para obtenção do grau de Doutor em Ciências Biomédicas especialidade em Biologia Celular e Molecular 2019 UNIVERSIDADE DE LISBOA Faculdade de Medicina The role of nuclear positioning in muscle function Mafalda Ramos de Melo Pimentel Orientador: Prof. Doutor Edgar Rodrigues Almeida Gomes Tese especialmente elaborada para obtenção do grau de Doutor em Ciências Biomédicas especialidade em Biologia Celular e Molecular Júri: Presidente: Doutor João Eurico Cortez Cabral da Fonseca, Professor Catedrático e Vice-Presidente do Conselho Cientifico da Faculdade de Medicina da Universidade de Lisboa Vogais: Doctor Antoine Guichet, Group Leader and Principal Investigator, Institut Jacques Monod, Université Paris Diderot; Doutor Reto Gassmann, Group Leader and Investigador do Instituto de Biologia Molecular e Celular da Universidade do Porto; Doutor Ramiro Daniel Carvalho de Almeida, Professor Auxiliar do Departamento de Ciências Médicas da Universidade de Aveiro; Doutora Solveig Thorsteinsdottir, Professora Associada com Agregação da Faculdade de Ciências da Universidade de Lisboa; Doutora Maria do Carmo Salazar Velez Roque da Fonseca, Professora Catedrática da Faculdade de Medicina da Universidade de Lisboa; Doutor Edgar Rodrigues Almeida Gomes, Professor Associado Convidado da Faculdade de Medicina da Universidade de Lisboa; Instituição Financiadora: Fundação para a Ciência e Tecnologia SFRH/BD/52227/2013 2019 A impressão desta tese foi aprovada pelo Conselho Científico da Faculdade de Medicina de Lisboa em reunião de 16 de Outubro de 2018. As opiniões expressas nesta publicação são da exclusiva respondabilidade do seu autor. -
Identification and Classification of 16 New Kinesin Superfamily (KIF) Proteins in Mouse Genome
4214 Corrections Proc. Natl. Acad. Sci. USA 96 (1999) Cell Biology. In the article “Identification and classification of Medical Sciences. In the article “CM101-mediated recovery of 16 new kinesin superfamily (KIF) proteins in mouse genome” walking ability in adult mice paralyzed by spinal cord injury” by Terunaga Nakagawa, Yosuke Tanaka, Eiji Matsuoka, Sa- by Artur W. Wamil, Barbara D. Wamil, and Carl G. Heller- toru Kondo, Yasushi Okada, Yasuko Noda, Yoshimitsu Kanai, qvist, which appeared in number 22, October 27, 1998, of Proc. and Nobutaka Hirokawa, which appeared in number 18, Natl. Acad. Sci. USA (95, 13188–13193), the authors request September 2, 1997 of Proc. Natl. Acad. Sci. USA (94, 9654– that the following two corrections be noted. First, the following 9659), the authors request that the following correction be sentence on page 13188, “CM101 is an antipathoangiogenic noted. In Fig. 5, due to a technical error in the genetic mapping polysaccaride (20) derived from group B streptococcus (GBS) program, the cytogenetic map of the mouse kif5B gene was (21) that inhibits angiogenesis and subsequent infiltration of misidentified. The corrected Fig. 5 and legend are reproduced inflammatory cells and thereby formation of granulation below. tissue, which produces scarring (M. Neeman, R. Abramowitch, B.D.W., and C.G.H., unpublished data),” should read “CM101 is an antipathoangiogenic polysaccharide (20) derived from group B streptococcus (GBS) that inhibits angiogenesis (21) and scarring (B.D.W. and C.G.H., unpublished data). Gran- ulation tissue, which produces scarring, contains new capillar- ies and inflammatory cells [Rubin, E. & Farber, J. L., eds. -
Departamento De Biología Cel·Lular I Anatomia Patològica Facultat De Medicina
DEPARTAMENTO DE BIOLOGÍA CEL·LULAR I ANATOMIA PATOLÒGICA FACULTAT DE MEDICINA DINÁMICA DE LA ACTINA Y TRÁFICO DE MEMBRANAS ASOCIADO AL COMPLEJO DE GOLGI: PAPEL REGULADOR DE RHOA, RAC1 Y CDC42 Tesis presentada por Olga B. Matas Guadix y dirigida por el Dr. Gustavo Egea Guri para optar al grado de Doctora en Bioquímica Barcelona, Mayo del 2005 VIII. BIBLIOGRAFÍA Bibliografía Abo, A., Qu, J., Cammarano, M. S., Dan, C., Fritsch, A., Baud, V., Belisle, B., and Minden, A., 1998, PAK4, a novel effector for Cdc42Hs, is implicated in the reorganization of the actin cytoskeleton and in the formation of filopodia: Embo Journal, 17, 6527-6540. Adamson, P., Paterson, H. F., and Hall, A., 1992, Intracellular-Localization of the P21(Rho) Proteins: Journal of Cell Biology, 119, 617-627. Aderem, A. and Underhill, D. M., 1999, Mechanisms of phagocytosis in macrophages: Annual Review of Immunology, 17, 593-623. Alberts, A. S., 2001, Identification of a carboxyl-terminal diaphanous-related formin homology protein autoregulatory domain: Journal of Biological Chemistry, 276, 2824- 2830. Allan, V. J. and Schroer, T. A., 1999, Membrane motors: Current Opinion in Cell Biology, 11, 476-482. Amann, K. J. and Pollard, T. D., 2001, The Arp2/3 complex nucleates actin filament branches from the sides of pre-existing filaments: Nature Cell Biology, 3, 306-310. Apodaca, G., 2001, Endocytic traffic in polarized epithelial cells: role of the actin and microtubule cytoskeleton: Traffic, 2, 149-159. Aridor, M., Bannykh, S. I., Rowe, T., and Balch, W. E., 1995, Sequential coupling between COPII and COPI vesicle coats in endoplasmic reticulum to Golgi transport: Journal of Cell Biology, 131, 875-893. -
Emerging Role of the Kinesin Family Member Genes in Birth Defects Silvia Kalantari ,1 Isabel Filges 1,2
Developmental defects J Med Genet: first published as 10.1136/jmedgenet-2019-106769 on 19 May 2020. Downloaded from REVIEW ‘Kinesinopathies’: emerging role of the kinesin family member genes in birth defects Silvia Kalantari ,1 Isabel Filges 1,2 ► Additional material is ABSTRact The first kinesins were observed in the context published online only. To view, Motor kinesins are a family of evolutionary conserved of axonal transport in neurons, and a novel disease please visit the journal online proteins involved in intracellular trafficking of various entity of ‘motor–proteinopathy’ was proposed for (http:// dx. doi. org/ 10. 1136/ 4 jmedgenet- 2019- 106769). cargoes, first described in the context of axonal transport. the pathogenesis of axonal neuropathies in 2001. They were discovered to have a key importance in cell- Due to their role in cellular membrane trafficking, 1 Medical Genetics, Institute cycle dynamics and progression, including chromosomal however, kinesins are essential for the functioning of Medical Genetics and condensation and alignment, spindle formation and of many polar cell types, such as neurons, epithelial Pathology, University Hospital Basel and University of Basel, cytokinesis, as well as ciliogenesis and cilia function. cells, sperm cells or stem cells during organogen- Basel, Switzerland Recent evidence suggests that impairment of kinesins is esis. Kinesins also play a fundamental role in cell- 2Department of Clinical associated with a variety of human diseases consistent cycle dynamics, both during mitotic