Takaho A. Endo. Quality control method for RNA-seq using single nucleotide polymorphism allele frequency. Genes to Cells Published online: 21 SEP 2014. DOI: 10.1111/gtc.12178
RNA sequencing (RNA-seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole-genome single nucleotide polymorphism (SNP) variant information, the allele frequency can show the genetic composition of the cell population and/or chromosomal aberrations. Here, I show how SNPs in mRNAs can be used to evaluate RNA-seq experiments by focusing on RNA-seq data based on a recently retracted paper on stimulus-triggered acquisition of pluripotency (STAP) cells. The analysis indicated that different types of cells and chromosomal abnormalities might have been erroneously included in the dataset. This re-evaluation showed that observing allele frequencies could help in assessing the quality of samples during a study and with retrospective evaluation of experimental quality.
(http://onlinelibrary.wiley.com/doi/10.1111/gtc.12178/abstract)
科研費に採択されるための最良の方法は，「書き上げた申請書を誰かに見せて添削してもらうこと」だと思う．見てもらう人が採択経験豊富な人ならなおよい．そういった人に申請書を見てもらって何度も何度も直すのが一番よい方法だ．（小噺その10：科研費に採択されるための最良の方法 Smart Lab Life 羊土社）
サイエンスへ投稿されたときの査読内容（全文へのリンク retractionwatch.comウェブサイト内）
論文タイトル：Stress altered somatic cells capable of forming an embryo
時期：2012年8月21日
Reviewer 1: ” … This is such an extraordinary claim that a very high level of proof is required to sustain it and I do not think this level has been reached. I suspect that the results are artifacts derived from the following processes: (1) the tendency of cells with GFP reporters to go green as they are dying. (2) the ease of cross contamination of cell lines kept in the same lab. …”
Reviewer 2: ” … Unfortunately, the paper presents only a superficial description of many critical aspects of the work. …”
Reviewer 3: “… If these results are repeatable, a paradigm of developmental biology would be changed. …”
”The DNA analysis of the chimeric mice is the only piece of data that does not fit with the contamination theory. But the DNA fragments in the chimeras don’t look the same as those in the lymphocytes. This assay is not properly explained. If it is just an agarose gel then the small bands could be anything. Moreover this figure has been reconstructed. It is normal practice to insert thin white lines between lanes taken from different gels (lanes 3 and 6 are spliced in). Also I find the leading edge of the GL band suspiciously sharp in #2-#5.”
Referee #1: ” … This is a very interesting manuscript and potentially groundbraking. However, the presentation and data supporting the conclusions are somewhat speculative and, in some cases, preliminary. …”
Refree #2: ” … Most convincing, however, would be to demonstrate visually by time lapse tracking of single cells conversion of CD45 immunofluorescent cells into CD45 negative/Oct4 GFP positive cells that can also be stained with Ecadherin and/or Nanog. …”
Refree #3: “… the claim that these cells are pluripotent is not fully validated. The possibility remains that the tissues formed in vitro or in teratomas or chimeras are derived from multiple (perhaps partially ) reprogrammed cells, each with limited differetiation capacity. The authors might take advantage of the fact that some of the reprogrammed cells have T-cell receptor rearrangements to elucidate whether the differentiated cells in teratomas or mice are clonally derived. …”
NATUREに同時に投稿されたレター論文「Developmental potential for embryonic and placental lineages in reprogrammed cells with acquired pluripotency」に対する査読者のコメント（2013年4月4日）
Referee #1: ” .. it is important to realize not single experimetn in any of the two manuscript evaluates the “quality” of the cells, performs comparative genome-wide analysis or precise quantifiable assays side-by-side with ESCs/iPSCs. ..”
Referee #2: “. .. they do not decisively illuminate the identity of STAP cells. …”
Referee #3: ” … It is important to report the properties of clonally derived STAP ES like stem cells, otherwise, it is not clear whter one cell population gives rise to all the lineages in teratomas or in chimeras. …”
“While they find your work of great potential interest, as do we, they have raised important concerns that in our view need to be addressed before we can consider publication in Nautre. Should further experimental data allow you to address these criticisms, we would be happy to look at a revised manuscript (unless something similar has been accepted at Nature or appeared elsewhere in the meantime). …””
この後、2回の改訂を経て最終的にネイチャーに受理されたようです。
Obokata et al., Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505, 641–647 (30 January 2014)
Obokata et al., Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature 505, 676–680 (30 January 2014)
Received 10 March 2013
Accepted 20 December 2013
Published online 29 January 2014
Retraction (July, 2014)
“.. Yoshiki struck me as a happy scientist. He spoke softly and with a unique smile as he described Japanese traditions or revealed his astonishing findings. .. Sasai was a master at deciphering the code by which cells learn their place in a developing embryo. ..Yoshiki Sasai (1962–2014):Stem-cell biologist who decoded signals in embryos. Arturo Alvarez-Buylla. Nature 513,34 (04 September 2014) doi:10.1038/513034a
“.. Yoshiki had an unmatched ability to decipher the embryo—specifically, to uncover how this developmental marvel generates the extraordinary diversity of cell types that become organized into unique structures, like the pituitary gland, the brain, or the eye. .. “Obituary Yoshiki Sasai (1962–2014). Arnold R. Kriegsteinemail DOI: http://dx.doi.org/10.1016/j.stem.2014.08.007 Cell Stem Cell Volume 15, Issue 3, p265–266, 4 September 2014
“.. Yoshiki had a unique ability to see things clearly while others were left wandering in the dark. .. “OBITUARY Yoshiki Sasai: stem cell Sensei
Stefano Piccolo Development (2014) 141, 1-2 doi:10.1242/dev.116509
サイエンス 2006年6月2日第312巻5778号 (目次）
Fujiwara et al., The Rubble-Pile Asteroid Itokawa as Observed by Hayabusa.Science 2 June 2006: 1330-1334.
Abe et al., Near-Infrared Spectral Results of Asteroid Itokawa from the Hayabusa Spacecraft.Science 2 June 2006: 1334-1338.
Okada et al., X-ray Fluorescence Spectrometry of Asteroid Itokawa by Hayabusa.Science 2 June 2006: 1338-1341.
Saito et al., Detailed Images of Asteroid 25143 Itokawa from Hayabusa.Science 2 June 2006: 1341-1344.
Abe et al., Mass and Local Topography Measurements of Itokawa by Hayabusa.Science 2 June 2006: 1344-1347.
Demura et al., Pole and Global Shape of 25143 Itokawa.Science 2 June 2006: 1347-1349.
Yano et al., Touchdown of the Hayabusa Spacecraft at the Muses Sea on Itokawa.Science 2 June 2006: 1350-1353.
ところが、はやぶさが取得した蛍光X線データに基づいて小惑星「イトカワ」の元素組成を解析した論文(Okada et al., 2006)に誤りがあったとして、宇宙航空研究開発機構（JAXA）は、掲載誌サイエンスに論文撤回を申し入れました。
2006年にこの著者らが蛍光X線分光データ分析により検証しようとした仮説は、後に探査機「はやぶさ」が持ち帰ったサンプルを実際に分析することにより検証され、その結果は2011年にサイエンス誌に発表された6本の論文の一つ(Nakamura et al., 2011)で報告されました。
サイエンス 2011年8月26日 第333巻6046号 (目次）(成果を解説するポッドキャスト）
Nakamura et al., Itokawa Dust Particles: A Direct Link Between S-Type Asteroids and Ordinary Chondrites. Science 26 August 2011: 1113-1116.
Yurimoto et al., Oxygen Isotopic Compositions of Asteroidal Materials Returned from Itokawa by the Hayabusa Mission. Science 26 August 2011: 1116-1119.
Ebihara et al., Neutron Activation Analysis of a Particle Returned from Asteroid Itokawa. Science 26 August 2011: 1119-1121.
Noguchi et al., Incipient Space Weathering Observed on the Surface of Itokawa Dust Particles.Science26 August 2011: 1121-1125.
Tsuchiyama et al., Three-Dimensional Structure of Hayabusa Samples: Origin and Evolution of Itokawa Regolith.Science 26 August 2011: 1125-1128.
Nagao et al., Irradiation History of Itokawa Regolith Material Deduced from Noble Gases in the Hayabusa Samples.Science 26 August 2011: 1128-1131.
はやぶさXRSに係る論文撤回の申し入れについて：” 当機構 宇宙科学研究所に所属する研究者が主著者となって投稿し、平成18年6月2日のサイエンス誌に掲載された論文「X-ray Fluorescence Spectrometry of Asteroid Itokawa by Hayabusa」について、本日、主著者らがサイエンス誌編集部に論文の撤回を申し入れましたのでお知らせいたします。なお、当該論文は、「はやぶさ」 に関連して発表された査読付き論文129件（うちサイエンス誌には14件掲載）の内の１件です。..” （JAXA 宇宙高校研究開発機構 平成26年8 月29日）
“Hello Kitty, the white cat with a pink bow on her ear, is the ultimate embodiment of Japan’s cute culture: She has no background and no mouth.” (From Anne Frank to Hello Kitty.(Norihiro Kato, The New York Times March 12, 2014. )
“The celebrity cat adorns everything from diamond-studded jewellery, Fender guitars and digital cameras to lunch boxes, T-shirts and stationery.” (AL Jazeera 08 Aug 2007)
ハローキティーの公式プロフィール：“Hello Kitty is a cheerful and happy little girl with a heart of gold. She lives in London with her mama (Mary White), papa (George White), and her twin sister Mimmy. Hello Kitty loves to bake and she can make really delicious cookies. She learned her baking talents from her mama, who makes scrumptious apple pies that are enjoyed by the whole family.”
Pink Globalization: Hello Kitty’s Trek across the Pacific: “In Pink Globalization, Christine R. Yano examines the creation and rise of Hello Kitty as a part of Japanese Cute-Cool culture. Yano argues that the international popularity of Hello Kitty is one aspect of what she calls pink globalization—the spread of goods and images labeled cute (kawaii) from Japan to other parts of the industrial world.” (アマゾン)
Christine Yano, PhD. Professor Department of Anthropology, University of Hawaii at Manoa
Ebola kills Liberia doctor despite ZMapp treatment (BBC 25 August 2014):”..It is not clear whether T-705 (or Avigan) will actually work against Ebola, and no monkey or human trials of the drug have been done, the BBC’s Rupert Wingfield-Hayes in Tokyo reports. ..”
Family of British Ebola sufferer says he is in ‘best possible place’(RTE News Monday 25 August 2014):”Tokyo stands ready to offer an experimental drug developed by a Japanese company to help stem the global tide of the deadly Ebola virus, the top government spokesman has said…”
Ethical considerations for use of unregistered interventions for Ebola virus disease Report of an advisory panel to WHO ：世界保健機関（ＷＨＯ）が実験段階の未承認治療薬の使用を認める見解を発表した報告書”Conclusion In the particular context of the current Ebola outbreak in West Africa, it is ethically acceptable to offer unproven interventions that have shown promising results in the laboratory and in animal models but have not yet been evaluated for safety and efficacy in humans as potential treatment or prevention. … “
Ebola therapy hopes shift to small California biotech (Reuters Tue Aug 5, 2014 GMT):”Hopes of finding a treatment for the deadly Ebola virus shifted on Monday to a small California-based biotech company whose experimental drug has been used to treat two American missionary workers. …”
Five things to know about the ZMapp Ebola drug (Fortune.com August 5, 2014, 10:45 AM EDT): “In the wake of an Ebola outbreak in West Africa that has resulted in nearly 900 deaths, a tiny pharmaceutical maker has allowed an experimental treatment to be used for two Americans infected with the deadly virus. ..”
Ebola drug ZMapp tested in Europe, on Spanish priest infected in Liberia (The Washington Times – Sunday, August 10, 2014): “The 75-year-old Spanish priest who became the first patient evacuated to Europe with the deadly Ebola virus now will become the first European to be treated with the experimental drug ZMapp. ..”
Beluga Whale Named Noc Mimics Human Noises With Spot-On Imitation (AUDIO) Huffpost 10/23/2012):”..In 1984, scientists at the National Marine Mammal Foundation in San Diego began noticing unusual noises emanating from where they kept the whales and dolphins. These resembled two people conversing in the distance, just beyond the range of the understanding of listeners…”
サイエンス論文の筆頭著者の二人が、新しいコンピュータチップ開発の動機を解説している動画。
SyNAPSE: IBM Cognitive Computing Project – Hardware
A Cognitive Information Superhighway
”IBM’s brain-inspired architecture consists of a network of neurosynaptic cores. Cores are distributed and operate in parallel. Cores operate—without a clock—in an event-driven fashion. Cores integrate memory, computation, and communication. Individual cores can fail and yet, like the brain, the architecture can still function. Cores on the same chip communicate with one another via an on-chip event-driven network. Chips communicate via an inter-chip interface leading to seamless scalability like the cortex, enabling creation of scalable neuromorphic systems.”（http://www.research.ibm.com/cognitive-computing/neurosynaptic-chips.shtml#fbid=15Zz4zjXf0H）
Bringing Computing to the Data
”A video camera on Hoover Tower at Stanford University is looking down at the plaza, below. A simulated network of IBM TrueNorth chips takes in the video data and locates interesting objects. Objects might look interesting to the system because they are moving or have a different color or texture than the background. The system then further processes those portions of the interesting video to determine what the objects are. It is trained in several specific categories, such as buses, cars, people, and cyclists. In a monitoring application, the camera would only need to communicate when it found an interesting object, rather than continually streaming video to a central location.”（http://www.research.ibm.com/cognitive-computing/neurosynaptic-chips.shtml#fbid=15Zz4zjXf0H）
DARPA SyNAPSE Program (artificialbrains.com Jan 11, 2013):” SyNAPSE is a DARPA-funded program to develop electronic neuromorphic machine technology that scales to biological levels. More simply stated, it is an attempt to build a new kind of computer with similar form and function to the mammalian brain. Such artificial brains would be used to build robots whose intelligence matches that of mice and cats. SyNAPSE is a backronym standing for Systems of Neuromorphic Adaptive Plastic Scalable Electronics. It started in 2008 and as of January 2013 has received $102.6 million in funding. It is scheduled to run until around 2016. The project is primarily contracted to IBM and HRL who in turn subcontract parts of the research to various US universities. ..”
