Our Thoughts (桀靜精微雷風相薄)

Jun 9, 2015

IRB 問與答 2014年題庫

由 sufang 在二, 06/09/2015 - 09:09 發表

Oral Cancer

Su-Fang Lin <sflin1@gmail.com> Jun 5 Reply to 張書銘, 陳雅雯, 江士昇, 夏興國
Dear All,

我PP計畫的IRB審查回來了, 兩個reviewer都有一點問題. 總評皆為「修正後推薦」。想請問大家先前有沒有碰到類似的問題, 其正解為何? 先謝謝大家的幫忙! 之後如果大家不介意的話, 我們是不是把各自的問題集合在一起、弄成一本題庫? 具IRB同仁說送出去的審委不一樣、同樣的申請件, 碰到的問題都不一樣。 Thanks again! Su-Fang (ext 35107) (餘刪, 見下6/8回覆)

Ya-Wen Chen Jun 5 Reply to me, 張書銘, 江士昇, 夏興國

以下是我遇到的問題及回答, 素芳的問題與我的問題有相似, 重點是(簡易審查核對表)提及使用合法生物資料庫..
簡易審查核對表我更改成接續前階段研究之後續資料分析(湘如建議).

EBV and NGS

由 sufang 在四, 06/04/2015 - 13:38 發表

3552_2012_12_Whole genome sequencing of the Akata and Mutu Epstein-Barr virus (EBV) strains.pdf

3577_2011_11_Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology

3964_2014_02_Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems

Jun 3, 2015

2015/05 Methylation Marker Paper from JAMA Oncology

Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer JAMA Oncol. Published online May 14, 2015. doi:10.1001/jamaoncol.2015.1053

Andrew E. Teschendorff, PhD^1,2; Zhen Yang, PhD²; Andrew Wong, PhD^3; Christodoulos P. Pipinikas, PhD⁴; Yinming Jiao, MSc²; Allison Jones, BSc⁵; Shahzia Anjum, PhD⁵; Rebecca Hardy, PhD³; Helga B. Salvesen, MD⁶; Christina Thirlwell, PhD⁴; Samuel M. Janes, PhD⁷; Diana Kuh, PhD³; Martin Widschwendter, MD⁵

At a Glance

¶ The purpose of the research was to assess the suitability of buccal cells as an epithelial source of tissue to examine the effects of smoking on the epigenome, and to test whether these effects are also seen in smoke-related epithelial cancers.

¶ Smoking is associated with widespread changes in the DNA methylation landscape of buccal cells.

¶ Some smoking-associated DNA methylation changes are common to buccal and blood tissue, but buccal cells exhibit significantly more changes than blood cells.

¶ Smoking-associated DNA methylation changes in buccal cells correlate with DNA methylation changes in epithelial cancers and do so most strongly in smoke-related epithelial cancer.

2016/105年待辦事項

由 sufang 在三, 05/27/2015 - 08:45 發表 Pre-published Gene Fusion HOK Lin Lab Oral Cancer

Paper Submission

宛樺: DDR1 overexpression in OSCC

嬿如: EBV Rta mediated DNA methylation in the host genome

FGFR Gene Fusion related (玉蓮、奕宏)

1. FGFR2 gene fusion in cholangiocarcinoma (Post 連結)

2. FGFR3 gene fusion in oral cancer (Post 連結)

Carcinogen induced epigenetic transformation in human oral keratinocytes (嬿如、英潔)

1. Molas analysis of RNA-Seq data (Post 連結)

2. MTHFR SNPs and epigenetic transformation

3. Develop methylation markers for head and neck patients

Mutational landscape of cholangiocarcinoma (Post 連結)

Mutational landscape of OSPCC and Oral Cancer (Post 連結)

Grant Proposal and Report

1. 104-CAPP05

月報 x 12 (in progress)

期中報告 (done by 佩瑩)

期末報告

2. 105-CAPP 執行與考核點設定

3. 106-CAPP 計畫書撰寫

4. MOHW 衛福部OPMD計畫

實驗進行 (記得送OSCC DNA給Jeffrey Lab. 一併測試MTHFR)

5. 105-MOST 科技部計畫 (11月中 call for proposal)

6. 105-MOST PPG (LOI submitted)

Reading Notes

Wiki Biological action (2015/05/17)

In many Asian cultures, the areca nut is chewed along with betel leaf to obtain a stimulating effect. Arecoline is the primary active ingredient responsible for the central nervous system effects of the areca nut. Arecoline has been compared to nicotine; however, nicotine acts primarily on the nicotinic acetylcholine receptor. Arecoline is known to be a partial agonist of muscarinic acetylcholine M1, M2, M3 receptors and M4 which is believed to be the primary cause of its parasympathetic effects (such as pupillary constriction, bronchial constriction, etc.).

LD50: 100 mg/kg, administered subcutaneously in mouse.

2015/05/25

pdf 4377 2014-Feb New nucleophilic mechanisms of ROS-dependent epigenetic modifications: comparison of aging and cancer

Igor Afanas'ev Vitamine Research Institute, Moscow, Russia, Poetom Portugal

ROS-induced DNA Methylation in Cancer 共舉12例

2015-05-05 Journal Club

各位老師學長學姊大家好:

我是下周二要在journal club報告的學生-Yi-Hong

題目:

Massive parallel sequencing uncovers actionable FGFR2–PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

本文文章

supplementary information

Apr 1, 2015

RBBS

RBBS
由 sufang 在三, 04/01/2015 - 09:00 發表 Pre-published RBBS

須細讀, 台大擬用此法screen HNSCC patients.

Start: 04/01/2015

2015-04-21 Journal Club Paper

大家好: 這篇是我下周要報的paper

感謝!

Mar 30, 2015

OSCC Cell Line STR information 20150312 更新版

OSCC Cell Line STR information 20150312 更新版
由 sufang 在一, 03/30/2015 - 08:45 發表 Oral Cancer OSCC Cell Line STR analysis

Dear all,

更新oral cancer相關細胞株之STR資訊
共有16個細胞株, 其中DOK, FaDu, HOK, HSC-3, KB, OEC-M1, SCC-15, SCC-9, Tu-183(共9株)有送件STR的資訊(詳如附件)
須請大家注意的資訊如下:
1. HSC-3, 於Dr.郭靜娟's lab的新HSC-3為真, 請非此來源者把舊的細胞扔了吧! (p.s Dr. 李岳倫於2014年7月及9月分別定的STR結果同新HSC-3, 推測亦為可用細胞株)
2. KB, 於Dr.郭靜娟's lab定STR結果為HeLa細胞, ATCC/JCRB資料庫也證明KB為HeLa. 請勿使用此細胞株!
3. SCC-15, Dr.李岳倫's lab 於2014年9月及10月分別定的STR結果皆與SAS細胞株相符(90.9% match), 使用此細胞株請小心!
4. Tu-183, 於Dr.江士昇's lab於2014年12月所定STR結果未比對到現今資料庫中任何細胞株, 推測可能為可用細胞株. 但Dr. 江提供資訊:expression pattern與預期不同, 大家使用此細胞株請小心!

以上,
如有問題或錯誤的地方, 敬請不吝指正! 謝謝!

敬祝研究順利

嬿如敬上

原檔按我下載 (2015_0320_cell_lines_str_information20150312ding_gao.xlsx)