December genes. causative eye, degeneration, Words: Key forms. orphan RP of etiopathogenesisthe in eventualroletheirand genes a importantclarifytothe possible involvement ofother is genes. causative RP known Since already the in mutations forms” of absence the in patients, RP of “orphan condition phenotipic called so geographical the their are there if even Pigmentosa, Retinitis of causative as to according localization.Mo people 1/750 to 1/9000 from affecting blindness, and impairment visual of causes main the of one considered is disease The photoreceptors. cones and rods of degeneration ret the Pigmentosa Retinitis is Abstract Phone number: e C Italy 2 and Pre 1 Antonina Sidoti Donato Luigi FORMS INVOLVED GENES NOVEL O

Department of Vanguard Medicine and Therapies, Biomolecular Strategies and Neuroscience, I.E.ME.S.T., Neuroscience, and Strategies Biomolecular Therapies, and Medicine Vanguard of Department Biomed of Department - ORRESPONDANCE RIGINAL mail: mail:

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2019 | Volume 7 | ISSUE 3 7 Volume 2019 ISSUE || ) [3].

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2019 | Volume 7 | ISSUE 3 7 Volume 2019 ISSUE ||

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| ©LIFE SAFETY AND SECURITY ISSN: 2283 ISSN: SECURITY AND SAFETY ©LIFE |

References

- 7604| DOI:7604|10.1 8. 7. 6. 5. 4. 3. 2. 1.

Marshall ForscherP, JohnsonKA, KozminskiKG, Mc J Orphanet pigmentosa. Retinitis C, Hamel Bravo Miller LS, Hancox B, N Gallo M, A Newman 2. H KH, Kim KimHJ, NaKH, Pigmentosa. Retinitis EE. Luther TB, O'Neal outer doublet microtubules: implications for for of implications microtubules: turnover doublet outer continuous balances transport Natl Acad Proc beating. eukaryotic flagellar to the unrelated flagellum in motility A RosenbaumJL. in Cell Biology 2016;132:35 protein G ciliary Rare Dis2006;1:40 cases. PigmentosaRetinitis simplex of basis genetic the Unravelling G. Antiñolo S, Borrego E, Rúa Méndez M, Sánchez networks. phenotype and biomarkers global reveals degeneration macular related LV, Systems Johnson MJ. DH, Radeke Anderson GS, Hageman NJ, Korea 2017;176:157 Ophthalmology in Population Retinitis Diagnosis, in Death at Pigmentosa of Cause Age and Prevalence, Mortality, HS. Ahn StatPearls2019. lgla lnt cnrl J el Biol Cell J control. 2001;155:405 length flagellar IntyreHege JC, M, Berbary N. Trafficking of

aee M Mlny A Coe JB, Cooper A, M Maloney CM, Radeke

- i N G N, Gil Sci Rep Sci 2017;7:41937Rep 2882/2283

Sci USA 1993;90:5519 Sci USA F Rosenbaum WF, Genome Genome Medicine 2012;4:16. - ae Study. based

onzález

- - coupled receptors. Methods Methods receptors. coupled 7604.2019.7.3

- ia C Rodríguez C, Vidal - ee aayi o age of analysis level - e Pz M Martín M, Pozo del

American Journal of of Journal American anS, KimS, HannHJ, HannHJ, KimS, anS, - — - 54 specific functional specific

L Intraflagellar JL.

Nationwide A -

165 – 5523

-

de la la de 178 - -

Available online at https://www.iemest.eu/life-safety-and-secrity/ December

15. 14. 13. 12. 11. 10. 9.

Mukhopadhyay S, Wen X, , Chih B, Nelson CD, CD, Nelson B, Chih , X, Wen S, Mukhopadhyay N. Kajimura H, Hirata T, Chaya M, Boubakri M Gorovsky CC, Tsao DR, Diener ES, Seeley DG, Cole JA, Deane Photoreceptor H. Khanna M, Anand Yildiz, L, Li Intraflagellar The E. Lorentzen M, Taschner Intraflagellar GB. Witman JL, Rosenbaum cilia. protein G of trafficking promote to IFT phosphoinositides the bridges PK.TULP3 Jackson SJ, Scales WS, Lane Slow, Progressive Photoreceptor Photoreceptor Opsin Inefficient 24474 to Progressive Transport. Two Degeneration Intraflagellar Slow, Retrograde to Leads Component, Complex IFT122, (IFT) Transport of Loss 436 2008;121:428 Sci Cell J. body. cell the to tip ciliary the from proteins IFT returning in role a plays butassembly cilia foressential not is IFT Bio2001;11:1586Curr. for particles. site docking the as fibers transitional body basal identifies IFT52 protein intraflagellar transport of Localization JL. Rosenbaum Disorders. Associated Ocul and Cilium Sensory 2016;3:8 of Medicine Library National US Machinery. Transport 2002;3:813Biology transpor

2019 | Volume 7 | ISSUE 3 7 Volume 2019 ISSUE ||

ar Diseases ar 2012Diseases

Genes Genes & development

- coupled receptors into primary primary into receptors coupled t. -

cmlx n membrane and complex A aue eiw Mlclr Cell Molecular Reviews Nature Bo Ce 2016;291:24465 Chem Biol J

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2010;24:2180 – 1590

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0.4960721 0.48670177005309756 0.42310083188408387 0.3783101081638127 0.35553249725991987 0.3502737364863011 0.305643837243711 0.2 0.21090905863967624 0.2091196431982565 0.20448896649165416 0.19205121544732173 0.17794282978111609 0.1764408992291817 0.14685313352987983 0.14577160987480242 0.1451076056568107 0.14413279826038028 0.13979926067522508 0.12831632310169372 0.10529546498853315 0.09237710243688901 0.07868772687984649 0.06431811643559371 0.056775087709612704 0.04850301326100315 0.034780757920341854 0.034607476105210755 0.030051923515502565 0.0014377614980 1,76E+10 pValue Overall 2885949333019662

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