Kif17 Phosphorylation Regulates Photoreceptor Outer Segment Turnover Tylor R
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Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
XP725 Antibody List Lot 129K4830
Panorama® Antibody Microarray-XPRESS Profiler725, XP725 List of Antibodies Lot: 129K4830 Reactivity Number Antibody Sigma No. Gene Ids Gene Symbols P/M Accessions Human Mouse Rat 3 Actin A5060 58 ACTA1 P NP_001091.1 n/d n/d n/d 5 Actin, αβ-Smooth Muscle A5228 59 ACTA2 M NP_001135417.1, NP_001604.1, yyy 6 β-Actin A1978 60 ACTB M NP_001092.1 yyy 7 β-Actin A2228 60 ACTB M NP_001092.1 yyy 8 a-Actinin A5044 87 ACTN1 M NP_001093.1 y y n/d 555 PARP P7605 142 PARP1 P NP_001609.2 y n/d n/d 11 β1 and β2-Adaptins A4450 162 AP1B1 M NP_001118.3 y n/d y 167 Chondroitin Sulfate C8035 176 ACAN M NP_001126.3, NP_037359.3 yyy 574 Protein Kinase Ba /Akt1 P2482 207 AKT1 M NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 575 Protein Kinase Ba /Akt1 P1601 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 577 phospho-PKB (pSer473) P4112 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 578 phospho-PKB (pThr308) P3862 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 22 Annexin V A8604 308 ANXA5 M NP_001145.1 y n/d n/d 23 Annexin VII A4475 310 ANXA7 M NP_001147.1 yyy 29 Apaf1, N-Terminal A8469 317 APAF1 P NP_001151.1 y y n/d 457 Mint2 M3319 321 APBA2 P NP_001123886.1 n/d n/d y 28 AP Endonuclease A2105 328 APEX1 M NP_001632.2,NP_542379.1,NP_542380.1 yyy 692 Survivin S8191 332 BIRC5 P NP_001012270.1 yyy 17 β-Amyloid A8354 351 APP M NP_000475.1,NP_001129488.1 ,NP_001129601.1 ,NP_001129602.1 ,NP_001129603.1 ,NP_001191230.1 ,NP_001191231.1 ,NP_001191232.1,NP_958816.1,NP_9 y n/d n/d 18 Amyloid Precursor Protein, C-Terminal A8717 -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Supplemental Information For
Supplemental Information for: Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Ribeiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Cherng Liang, Lee-Yung Shih, Ching-Hon Pui & James R. Downing Table of Contents Section I. Patient Datasets Table S1. Diagnostic AML characteristics Table S2. Cytogenetics Summary Table S3. Adult diagnostic AML characteristics Table S4. Additional T-ALL characteristics Section II. Methods Table S5. Summary of filtered probe sets Table S6. MLL-PTD primers Additional Statistical Methods Section III. Genetic Subtype Discriminating Genes Figure S1. Unsupervised Heirarchical clustering Figure S2. Heirarchical clustering with class discriminating genes Table S7. Top 100 probe sets selected by SAM for t(8;21)[AML1-ETO] Table S8. Top 100 probe sets selected by SAM for t(15;17) [PML-RARα] Table S9. Top 63 probe sets selected by SAM for inv(16) [CBFβ-MYH11] Table S10. Top 100 probe sets selected by SAM for MLL chimeric fusion genes Table S11. Top 100 probe sets selected by SAM for FAB-M7 Table S12. Top 100 probe sets selected by SAM for CBF leukemias (whole dataset) Section IV. MLL in combined ALL and AML dataset Table S13. Top 100 probe sets selected by SAM for MLL chimeric fusions irrespective of blast lineage (whole dataset) Table S14. Class discriminating genes for cases with an MLL chimeric fusion gene that show uniform high expression, irrespective of blast lineage Section V. -
Cilium Structure, Assembly, and Disassembly Regulated by the Cytoskeleton
Biochemical Journal (2018) 475 2329–2353 https://doi.org/10.1042/BCJ20170453 Review Article Cilium structure, assembly, and disassembly regulated by the cytoskeleton Mary Mirvis1,*, Tim Stearns2,3 and W. James Nelson1,2 1Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, U.S.A.; 2Department of Biology, Stanford University, Stanford, CA 94305, U.S.A.; 3Department of Genetics, Stanford University, Stanford, CA 94305, U.S.A. Correspondence: W. James Nelson ([email protected]) The cilium, once considered a vestigial structure, is a conserved, microtubule-based organelle critical for transducing extracellular chemical and mechanical signals that control cell polarity, differentiation, and proliferation. The cilium undergoes cycles of assembly and disassembly that are controlled by complex inter-relationships with the cytoskeleton. Microtubules form the core of the cilium, the axoneme, and are regulated by post-translational modifications, associated proteins, and microtubule dynamics. Although actin and septin cytoskeletons are not major components of the axoneme, they also regulate cilium organization and assembly state. Here, we discuss recent advances on how these different cytoskeletal systems affect cilium function, structure, and organization. Introduction Cilia are specialized, conserved organelles that are evolutionarily optimized for interaction with the world outside of the cell. They protrude into the extracellular space, are structurally resilient but also flexible and dynamic, and have unique mechanisms to tightly control their internal and membrane composition. These features ensure that the cilium is primed to perform highly regulated signaling, mechanosensory, and motile functions. In this review, we consider cilia mostly from the perspective of vertebrate animal cells, with additional information from the wide range of ciliated eukaryotes where appropriate. -
Structure of Cone Photoreceptors
Progress in Retinal and Eye Research 28 (2009) 289–302 Contents lists available at ScienceDirect Progress in Retinal and Eye Research journal homepage: www.elsevier.com/locate/prer Structure of cone photoreceptors Debarshi Mustafi a, Andreas H. Engel a,b, Krzysztof Palczewski a,* a Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106-4965, USA b Center for Cellular Imaging and Nanoanalytics, M.E. Mu¨ller Institute, Biozentrum, WRO-1058, Mattenstrasse 26, CH 4058 Basel, Switzerland abstract Keywords: Although outnumbered more than 20:1 by rod photoreceptors, cone cells in the human retina mediate Cone photoreceptors daylight vision and are critical for visual acuity and color discrimination. A variety of human diseases are Rod photoreceptors characterized by a progressive loss of cone photoreceptors but the low abundance of cones and the Retinoids absence of a macula in non-primate mammalian retinas have made it difficult to investigate cones Retinoid cycle directly. Conventional rodents (laboratory mice and rats) are nocturnal rod-dominated species with few Chromophore Opsins cones in the retina, and studying other animals with cone-rich retinas presents various logistic and Retina technical difficulties. Originating in the early 1900s, past research has begun to provide insights into cone Vision ultrastructure but has yet to afford an overall perspective of cone cell organization. This review Rhodopsin summarizes our past progress and focuses on the recent introduction of special mammalian models Cone pigments (transgenic mice and diurnal rats rich in cones) that together with new investigative techniques such as Enhanced S-cone syndrome atomic force microscopy and cryo-electron tomography promise to reveal a more unified concept of cone Retinitis pigmentosa photoreceptor organization and its role in retinal diseases. -
Overexpression of Motor Protein KIF17 Enhances Spatial and Working Memory in Transgenic Mice
Overexpression of motor protein KIF17 enhances spatial and working memory in transgenic mice Richard Wing-Chuen Wong, Mitsutoshi Setou, Junlin Teng, Yosuke Takei, and Nobutaka Hirokawa* Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan Edited by Tomas Hokfelt, Karolinska Institute, Stockholm, Sweden, and approved September 11, 2002 (received for review June 28, 2002) The kinesin superfamily proteins (KIFs) play essential roles in where noted. Control WT mice were chosen from the same receptor transportation along the microtubules. KIF17 transports littermates. For the behavioral experiments, the same groups of the N-methyl-D-aspartate receptor NR2B subunit in vitro, but its male mice were used (10–12 wk). role in vivo is unknown. To clarify this role, we generated trans- genic mice overexpressing KIF17 tagged with GFP. The KIF17 Histological Analysis and Electron Microscopy. Mice (10–12 wk) were transgenic mice exhibited enhanced learning and memory in a anesthetized and fixed in FEA solution (5% formalin͞70% etha- series of behavioral tasks, up-regulated NR2B expression with the nol͞5% acetic acid). The brain tissues were then removed, washed, potential involvement of a transcriptional factor, the cAMP-depen- dehydrated in a graded series of ethanol, and embedded in Para- dent response element-binding protein, and increased phosphor- plast (Oxford Labware, St. Louis). The blocks were cut by using a ylation of the cAMP-dependent response element-binding protein. rotatory microtome (HM355; Rotary Microtome Zeiss) and sec- Our results suggest that the motor protein KIF17 contributes to tioned serially at 12-m thickness by using the same microtome. -
THE ROLE of ROM-1 in MAPNTAINING PHOTORECEPTOR STRUCTURE AM) VUBILITY, and a MATHEMATICAL MODEL EXPLOIUNG the Icinetics of NEURONAL DEGENERATION
THE ROLE OF ROM-1 IN MAPNTAINING PHOTORECEPTOR STRUCTURE AM) VUBILITY, AND A MATHEMATICAL MODEL EXPLOIUNG THE ICINETiCS OF NEURONAL DEGENERATION Geoffrey Alïan Clarke A thesis submittd in cdormity with the requirements foi the degree of Worof Philosophy, Graduate Department of Mobdar and Medical Genetics, in the University of Toronto O Copyri@ by Geofffey AUan Clarke 2ûûû The author has gnmted a non- L'auteur a accordé une licence non exclusive licence ailowing the exclusive pennettaat à la National Library of Canada to Bibliothèque nationale du Canada de reprduce, 10- distnïute or sel reproduire, prêter, distribuer ou copies of this thesis in microfonn, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantiaî extracts firom it Ni la thèse ni des extraits substantiels may be printed or otherwise de ceiîe-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. Cana The Rok Of Rom-1 In MainWning Photoreceptor Structure and ViabUity, and a Matbernatical Mode1 Explorlng the ainetics of Neuronal Degeneration Geoffrey Ailan Clarke Department of Molecular and Medical Genetics University of Toronto Doctor of Philosophy,2000 Abstract Rom-1 and peripherinhds are homoIogous membrane proteins localized to the disk rims of photoreceptor outer segments (OSs), where they are postulated to be critical for disk -1- morphogenesis, OS renewal, and the maintenance of OS structure. -
The Influence of Light on Cone Disk Shedding in the Lizard, Sceloporus Occidentalis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central REGULAR ARTICLES The Influence of Light on Cone Disk Shedding in the Lizard, Sceloporus occidentalis STEVEN A. BERNSTEIN, DAVID J . BREDING, and STEVEN K . FISHER Department of Biological Sciences, University of California, Santa Barbara, Santa Barbara 93106 ABSTRACT The lizard, Sceloporus occidentalis has an all-cone retina. In lizards maintained on a 12-h light:12-h dark (12L:12D) cycle, a burst of cone outer segment (COS) shedding occurs 2 h after light offset (1400 h circadian time) (Young, R . W ., 1977, /. Ultrastruct. Res . 61 :172- 72). In this investigation, we studied the effect of different lighting regimes on the pattern of cone disk shedding in this species. When lizards entrained to a 121-:12D cycle are kept in constant darkness (DD), the shedding peak is advanced -2 h and the magnitude of shedding is reduced to 30% of control. COS increased in mean length from 12 Am in controls to 14 Am after one cycle in DD and maintained this length during a second cycle in DD. In constant light (LL), disk shedding was damped to -10% of control values. Shedding synchrony in LL was also perturbed and therefore cyclic shedding bursts could not be distinguished . During LL there was a much larger increase in COS mean length than in DD . After one cycle of LL, COS length was 15 Am and after two cycles COS length exceeded 17 Am . When lizards entrained to 121-:1 2D are shifted to a 6L:18D regimen, the first shedding cycle is biphasic . -
RPE Cell Biology David William 2020 Review
NOTICE WARNING CONCERNING COPYRIGHT RESTRICTIONS The copyright law of the United States [Title 17, United States Code] governs the making of photocopies or other reproductions of copyrighted material. Under certain conditions specified in the law, libraries and archives are authorized to furnish a photocopy or other reproduction. One of these specified conditions is that the reproduction is not to be used for any purpose other than private study, scholarship, or research. If a user makes a request for, or later uses, a photocopy or reproduction for purposes in excess of "fair use," that use may be liable for copyright infringement. This institution reserves the right to refuse to accept a copying order if, in its judgement, fullfillment of the order would involve violation of copyright law. No further reproduction and distribution of this copy is permitted by transmission or any other means. Progress in Retinal and Eye Research xxx (xxxx) xxxx Contents lists available at ScienceDirect Progress in Retinal and Eye Research journal homepage: www.elsevier.com/locate/preteyeres ☆ The cell biology of the retinal pigment epithelium Aparna Lakkarajua,1, Ankita Umapathyb,c,1, Li Xuan Tana, Lauren Danieled, Nancy J. Philpe, ∗ Kathleen Boesze-Battagliad, David S. Williamsb,c, a Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA b Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA,USA c Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA,USA d Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA e Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA ARTICLE INFO ABSTRACT Keywords: The retinal pigment epithelium (RPE), a monolayer of post-mitotic polarized epithelial cells, strategically si- Phagocytosis tuated between the photoreceptors and the choroid, is the primary caretaker of photoreceptor health and Phagosome maturation function. -
Cytoskeletal Remodeling in Cancer
biology Review Cytoskeletal Remodeling in Cancer Jaya Aseervatham Department of Ophthalmology, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; [email protected]; Tel.: +146-9767-0166 Received: 15 October 2020; Accepted: 4 November 2020; Published: 7 November 2020 Simple Summary: Cell migration is an essential process from embryogenesis to cell death. This is tightly regulated by numerous proteins that help in proper functioning of the cell. In diseases like cancer, this process is deregulated and helps in the dissemination of tumor cells from the primary site to secondary sites initiating the process of metastasis. For metastasis to be efficient, cytoskeletal components like actin, myosin, and intermediate filaments and their associated proteins should co-ordinate in an orderly fashion leading to the formation of many cellular protrusions-like lamellipodia and filopodia and invadopodia. Knowledge of this process is the key to control metastasis of cancer cells that leads to death in 90% of the patients. The focus of this review is giving an overall understanding of these process, concentrating on the changes in protein association and regulation and how the tumor cells use it to their advantage. Since the expression of cytoskeletal proteins can be directly related to the degree of malignancy, knowledge about these proteins will provide powerful tools to improve both cancer prognosis and treatment. Abstract: Successful metastasis depends on cell invasion, migration, host immune escape, extravasation, and angiogenesis. The process of cell invasion and migration relies on the dynamic changes taking place in the cytoskeletal components; actin, tubulin and intermediate filaments. This is possible due to the plasticity of the cytoskeleton and coordinated action of all the three, is crucial for the process of metastasis from the primary site. -
Photoreceptor Autophagy: Effects of Light History on Number and Opsin Content of Degradative Vacuoles
Photoreceptor Autophagy: Effects of Light History on Number and Opsin Content of Degradative Vacuoles Charlotte E. Reme´,1 Uwe Wolfrum,2 Cornelia Imsand,1 Farhad Hafezi,1 and Theodore P. Williams3 PURPOSE. To investigate whether regulation of rhodopsin levels as a response to changed lighting environment is performed by autophagic degradation of opsin in rod inner segments (RISs). METHODS. Groups of albino rats were kept in 3 lux or 200 lux. At 10 weeks of age, one group was transferred from 3 lux to 200 lux, another group was switched from 200 lux to 3 lux, and two groups remained in their native lighting (baselines). Rats were killed at days 1, 2, and 3 after switching. Another group was switched from 3 lux to 200 lux, and rats were killed at short intervals after the switch. Numbers of autophagic vacuoles (AVs) in RISs were counted, and immunogold labeling was performed for opsin and ubiquitin in electron microscopic sections. RESULTS. The number of AVs increased significantly after switching from 3 lux to 200 lux at days 1 and 2 and declined at day 3, whereas the reverse intensity change did not cause any increase. Early time points after change from 3 lux to 200 lux showed a significant increase of AVs 2 and 3 hours after switching. Distinct opsin label was observed in AVs of rats switched to 200 lux. Ubiquitin label was present in all investigated specimens and was also seen in AVs especially in 200-lux immigrants. CONCLUSIONS. Earlier studies had shown that an adjustment to new lighting environment is per- formed by changes in rhodopsin levels in ROSs.