Top 10 stories of 2006 News@nature.com's hit lists of hot news.
Nicola Jones
Here news@nature.com collects our top stories from 2006 — enjoy!
http://www.nature.com/news/specials/2006/topten/readerschoice.htmlThe most clicked stories of 2006..
http://www.nature.com/news/specials/2006/topten/editorschoice.htmlOur favourites, from the silly to the serious..
NEWS FEATURES Longer tales worth another read.
MOST TALKED ABOUT The stories that got the most comments from you, our readers.
READERS' CHOICE
The most clicked stories of 2006.
Record-breaking laser is hot stuff The record for the fastest rise in temperature has just been topped.12 May 2006
Geometric whirlpools revealed Recipe for making symmetrical holes in water is easy.19 May 2006
Web users judge sites in the blink of an eye Potential readers can make snap decisions in just 50 milliseconds.13 January 2006
The fish that hunts on land Catfish show how the first tetrapods might have caught dinner.12 April 2006
Supercomputer builds a virus Vast simulation captures molecules in motion.14 March 2006
The fish that crawled out of the water A newly found fossil links fish to land-lubbers.5 April 2006
Desktop fusion is back on the table Physicist claims to have definitive data, but can they be replicated?10 January 2006
Lingerie makes hagglers happy-go-lucky Sexy pictures and lacy underwear take men's minds off getting a good deal.19 April 2006
Sharpest cut from nanotube sword Carbon nanotech may have given swords of Damascus their edge.15 November 2006
Polar core is hot stuff There was once little difference between equatorial and arctic climates.31 May 2006
EDITOR'S CHOICE
Our favourites, from the silly to the serious.
'Vegetative' patient shows signs of conscious thought Evidence of brain activity raises issues for neurologists.13 September 2006
A comet's tale Scientists are just beginning to examine the pieces of a comet brought back to Earth by NASA's Stardust mission. Mark Peplow tagged along to one lab to watch researchers examine their prize catch.13 February 2006
Sociologist fools physics judges But do social scientists understand science?5 July 2006
My fish is smaller than yours Contenders line up to net credit for smallest vertebrate.31 January 2006
Popular physics myth is all at sea Does the ghostly Casimir effect really cause ships to attract each other?4 May 2006
Hawking rewrites history... backwards To understand the Universe we must start from the here and now.21 June 2006
Puzzle of leaping liquid solved Physicists explain how shampoo streams can bounce.6 April 2006
Blindfolded humans steered by remote control Artificial electric currents guide walkers round obstacles.7 August 2006
World's most infamous iceberg dies Swell from Alaskan storm breaks up megaberg at opposite end of the globe.3 October 2006
Bubble fusion: silencing the hype Nature reveals serious doubts over claims for fusion in collapsing bubbles.8 March 2006
NEWS FEATURES
Longer tales worth another read.
Science on the solstice In this special feature news@nature.com brings you a composite picture of the summer solstice. 28 June 2006
The trouble with replication The idea that readers should be able to replicate published scientific results is seen as the bedrock of modern science. But what if replication proves difficult or impossible? Jim Giles tracks the fate of one group of papers.26 July 2006
Environmental activism: In the name of nature What drives environmental activists to fire-bomb laboratories? Emma Marris investigates a radical fringe of the US green movement.4 October 2006
Climate change: A sea change A collapse in ocean currents triggered by global warming could be catastrophic, but only now is the Atlantic circulation being properly monitored. Quirin Schiermeier investigates.18 January 2006
Climate change: The tipping point of the iceberg Could climate change run away with itself? Gabrielle Walker looks at the balance of evidence.14 June 2006
Nuclear weapons: The next nuke US nuclear weapons scientists are designing a warhead that is meant to be 'reliable' without ever having been tested. Geoff Brumfiel asks whether it could renew the United States' ageing stockpile.5 July 2006
Ornithology: Digging for dodo No one has seen a dodo in three and a half centuries, but that hasn't stopped the bizarre speculation about this extinct bird. Henry Nicholls investigates whether recent excavations in Mauritius could reveal the real creature.13 September 2006
Fractals and art: In the hands of a master Fractal analysis has been used to assess the authenticity of paintings purporting to be the work of Jackson Pollock. Alison Abbott reports.8 February 2006
Bioethics: An easy way out? Scientists say they gas mice and rats with carbon dioxide because it is humane. It's also simple, cheap and keeps their hands clean. Emma Marris analyses the final seconds of the lab rodents' life.31 May 2006
Depression: Comfortably numb It started life as an anaesthetic, then became a psychedelic club drug. Now researchers think ketamine could hold the key to understanding and treating depression, says Erika Check.11 October 2006
TOP OF THE NEWSBLOG
The stories that got the most comments from you, our readers.
The fish that crawled out of the water
Does gender matter?
Islam and science
Found: one Earth-like planet
Delusions of faith as a science
Top 5 science blogs
'Tenth Planet' found to be a whopper
Study challenges prayers for the sick
Tragic drug trial spotlights potent molecule
The space elevator: going down?
from News Published online: 28 December 2006; doi:10.1038/news061225-1
2006-12-29
Haircut and Hairdress
I have no time to go to the Barber's these days. At noon, my two friends together with me decided to have a hair cut , so we three went to a new opened one nearby. Once we entered the Barber's, a young man came up to serve us.
"Welcome, i will try to satisfy you. Sir, which hairstyle of movie star do you like? what about a new hairstyle? According to the character your hair and head I strongly advise you to…… " "But，I don't care it too much and I just want to have a hair cut." I listened to him carefully.
"It doesn't matter. Nobody refuse to beautify himself, if i can make your hair look cool and energetic, why not try another new style? Additionally, we can give a discount for you students……"
"Thank you for your advice, but, I don't intend to have a hairdress and i have no more time to look after it." several minutes later, he failed to persuade me while I was a bit impatient.
" Sir, what about this simple and easy hairstyle? ……" Faint! I'm afraid he would not start to mend my hair if I didn't enjoy one of his advice, so I acquiesced in his polite chatter.
When went out we found one of my friends got default setting of haircut even without asking for advice.
"Welcome, i will try to satisfy you. Sir, which hairstyle of movie star do you like? what about a new hairstyle? According to the character your hair and head I strongly advise you to…… " "But，I don't care it too much and I just want to have a hair cut." I listened to him carefully.
"It doesn't matter. Nobody refuse to beautify himself, if i can make your hair look cool and energetic, why not try another new style? Additionally, we can give a discount for you students……"
"Thank you for your advice, but, I don't intend to have a hairdress and i have no more time to look after it." several minutes later, he failed to persuade me while I was a bit impatient.
" Sir, what about this simple and easy hairstyle? ……" Faint! I'm afraid he would not start to mend my hair if I didn't enjoy one of his advice, so I acquiesced in his polite chatter.
When went out we found one of my friends got default setting of haircut even without asking for advice.
2006-12-28
rethink Edge of Existence
Baiji dolphin is listed as first of the top 100 speices on EDGE. see the following link:
http://www.edgeofexistence.org/conservation/yangtze_river_dolphin.asp
http://www.edgeofexistence.org/conservation/yangtze_river_dolphin.asp
2006-12-27
《Science》: Breakthrough of the Year
1.The Poincaré Conjecture--Proved
庞加莱猜想属于被称为拓扑的数学分支，通常被描述成“橡皮上的几何”，因为它涉及能够经历任意拉伸的表面。这个1904年由庞加莱提出的猜想描述一个空间是否与“超球面”(四维球体的三维表面)等价的检验。 基本上与外界隔绝地工作了7年的俄罗斯数学家Grigori Perelman 2002年在互联网上提交了三篇文章的第一篇，这些文章把庞加莱猜想作为一个更雄心勃勃的结果的一部分，给其证明提供了一个轮廓。但是在2003年访问美国之后，这位俄罗斯数学隐士回国后停止了与外界的电话和电子信往来。到了2006年，其他人终于赶了上来。三个独立的小组写出报告填补了佩雷尔曼的证明中缺失的关键细节，现在佩雷尔曼的同行几乎都没有疑问地认为他证明了这个著名的难题。
2.DIGGING OUT FOSSIL DNA.
从化石中取出DNA: 研究人员用一种解码和分析DNA的新技术，从尼安德特人和猛犸化石中捕获到遗传信息。
3.SHRINKING ICE.
冰架在缩小: 研究人员今年记录了这一令人不安的趋势。南极洲和格陵兰岛的冰架都在以更快的速度消失到海洋中。
4.NEITHER FISH NOR FOWL.
鱼迈出的第一步: 一个具有结实的连接着的鳍的鱼化石的发现曾是2006年的头版新闻。这种鱼是有肢脊椎动物已知的最近亲，它为生命如何离开海洋登上陆地提供了一个视窗。
5.THE ULTIMATE CAMOUFLAGE.
隐身术的科学: 虽然它看上去一点也不像哈里波特的魔术披风，科学家今年制造的隐身“斗篷”是第一个将物体在视觉上屏蔽起来的初步装置。这个装置引导入射的微波使其既不反射、也没有影子。
6.A RAY OF HOPE FOR MACULAR DEGENERATION PATIENTS.
黄斑病变患者的希望: 研究一种被称为老年黄斑病变失明的研究人员揭示，药物ranibimuzab能改善某些患者的视觉，他们还找到了几个影响人们该症易患性的基因。
7.DOWN THE BIODIVERSITY ROAD
生物多样性是如何发生的: 从沙滩小鼠、到果蝇、到蝴蝶，这些不同的动物帮助科学家发现导致新物种进化的遗传变化。
8.PEERING BEYOND THE LIGHT BARRIER.
显微学的新前沿: 今年，生物学家用新的显微技术来帮助他们观察小于200纳米的细节，为了解细胞和蛋白质的精细结构提供了更清晰的视野。
9.THE PERSISTENCE OF MEMORY.
制造记忆: 2006年的几个发现使神经科学家对了解大脑如何记录新记忆更接近了一步。增强神经元之间连接的被称为“长时程增强”的过程看来很可能是记忆的基础。
10.MINUTE MANIPULATIONS.---piRNA
新一类的小RNA: 科学家发现了一类关闭基因表达的新小RNA分子，把它们命名为 "Piwi-干扰 RNA"。
本年度的崩溃-科学骗局: 干细胞研究者黄禹锡以及其合作者曾在《科学》发表两篇重要论文，他们制造的骗局在2006年被彻底调查了，本年度也发生了几起其它的科学不端行为。
值得注意的领域: 《科学》预测来年的热门领域和主题包括整基因组相关性研究、光晶格、寻找宇宙的原始氢、以及比较灵长类的基因组。
Science 22 December 2006:Vol. 314. no. 5807, p. 1841DOI: 10.1126/science.1138510
Editorial
Breakthrough of the Year
Donald Kennedy
Last year, evolution was the breakthrough of the year; We found it full of new developments in understanding how new species originate. But we did get a complaint or two that perhaps we were just paying extra attention to the lively political/religious debate that was taking place over the issue, particularly in the United States.
Perish the thought! Our readers can relax this year: Religion and politics are off the table, and n-dimensional geometry is on instead. This year's Breakthrough salutes the work of a lone, publicity-shy Russian mathematician named Grigori Perelman, who was at the Steklov Institute of Mathematics of the Russian Academy of Sciences until 2005. The work is very technical but has received unusual public attention because Perelman appears to have proven the Poincaré Conjecture, a problem in topology whose solution will earn a $1 million prize from the Clay Mathematics Institute. That's only if Perelman survives what's left of a 2-year gauntlet of critical attack required by the Clay rules, but most mathematicians think he will.
The analysis supplied by Dana Mackenzie on p. 1848 struck me as a fascinating exploration, full of metaphors suggesting a multidisciplinary dimension in Perelman's analysis. He first got interested in Ricci flow, a process by which topological regions of high curvature flow into regions of lower curvature. He also identified a quantity, which he called "entropy," that increased during the flow, providing a gradient. Tight spots in spatial connections block the application of these rules to dimensions higher than two, so Perelman dealt with these through "surgical intervention." This story is rich with borrowings: from fluid mechanics, thermodynamics, and even surgery! It's hard to deal with a three-dimensional object in four-dimensional space. Perelman's solution is a stunning triumph of intellect. Alas, it has led to bitter controversy, involving others but not Perelman.
Of course, in any Breakthrough year we are obliged to have a Breakdown. This time around, we had to blow the whistle on ourselves. In recognizing this as a year in which scientific fraud took center stage, it was clear that we had to lead with the story involving the retraction of two of our own papers, an event that drew worldwide press attention and required us to ask for an outside evaluation of how we had handled the papers. That brought us some tough news about how competitive the scientific enterprise has become, and the consequential incentive to push (or shred) the ethical envelope.
On the positive side, it was a rich year for important experimental studies. My favorites include some new explanations for how species originate, one of the daunting post-Darwinian puzzles. Among other examples, there is a clear case for speciation through hybridization, an exception to the more general rule that hybrids either don't make it or are reproductively incompetent. Because I like coastlines, when I see new evidence about sea-level rise, I pay attention. This year we got new measures of rates of glacial melting at both ends of the globe: in Greenland, where rates are in hundreds of gigatons a year, and in Antarctica, where drainage by ice streams is accelerating. I also follow the Neanderthal story, because it's interesting to ponder how different human species--now thought from archaeological evidence to have overlapped for perhaps 10,000 years--might have interacted. New sequencing of the Neanderthal genome indicates that the point of divergence is nearly half a million years old and opens up a wealth of comparisons with the human genome sequence. The question everyone asks--"Did they have sex?"--is still open, though barely.
All in all, it's not been a bad year. The predictions we made in 2005 of "Areas to Watch" turned out pretty well. We said RNA interference would be an active sector--good call. Cosmic-ray capture didn't work out, but there was the predicted level of activity on the "small worlds" of microbial communities. We predicted lots of activity on high-temperature superconductivity, and there were more applications, although less new theory. The worst miss was the prediction that the ivory-billed woodpecker would be re-found. Come on, birders, give us some help out there; a good photo, please, not the skin.
10.1126/science.1138510
Donald Kennedy is the Editor-in-Chief of Science.
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS BREAKTHROUGH OF THE YEAR: The Poincaré Conjecture--Proved
Dana Mackenzie (22 December 2006)Science 314 (5807), 1848. [DOI: 10.1126/science.314.5807.1848] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: The Runners-Up
(22 December 2006)Science 314 (5807), 1850a. [DOI: 10.1126/science.314.5807.1850a] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: Scorecard 2006
(22 December 2006)Science 314 (5807), 1850b. [DOI: 10.1126/science.314.5807.1850b] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: BREAKDOWN OF THE YEAR: Scientific Fraud
Jennifer Couzin (22 December 2006)Science 314 (5807), 1853. [DOI:10.1126/science.314.5807.1853] Summary » Full Text » PDF »
NEWSBREAKTHROUGH OF THE YEAR: Areas to Watch in 2007
(22 December 2006)Science 314 (5807), 1854. [DOI: 10.1126/science.314.5807.1854] Summary » Full Text » PDF »
Papers and Articles on piRNA
A. Girard et al., "A Germline-Specific Class of Small RNAs Binds Mammalian Piwi Proteins," Nature 442, 199 (2006)
A. Aravin et al., "A Novel Class of Small RNAs Bind to MILI Protein in Mouse Testes," Nature 442, 203 (2006)
S.T. Grivna et al., "A Novel Class of Small RNAs in Mouse Spermatogenic Cells," Genes Dev. 20, 1709 (2006)
N.C. Lau et al., "Characterization of the piRNA Complex from Rat Testes; Science 313, 363 (2006)
R.W. Carthew, "A New RNA Dimension to Genome Control," Science 313, 305 (2006)Perspective article highlighting the Lau et al. study.
V.N. Kim, "Small RNAs Just Got Bigger: Piwi-Interacting RNAs (piRNAs) in Mammalian Testes," Genes Dev. 20, 1993 (2006)
S.T. Grivna et al., "MIWI Associates with Translational Machinery and PIWI-Interacting RNAs (piRNAs) in Regulating Spermatogenesis," Proc. Natl. Acad. Sci. U.S.A. 103, 13415 (2006)
Selected Labs
Gregory Hannon (Cold Spring Harbor Laboratory)
Thomas Tuschl (Rockefeller University)
David Bartel (MIT)
Robert Kingston (Massachusetts General Hospital/Harvard Medical School)
Haifan Lin (Yale Stem Cell Center)
庞加莱猜想属于被称为拓扑的数学分支，通常被描述成“橡皮上的几何”，因为它涉及能够经历任意拉伸的表面。这个1904年由庞加莱提出的猜想描述一个空间是否与“超球面”(四维球体的三维表面)等价的检验。 基本上与外界隔绝地工作了7年的俄罗斯数学家Grigori Perelman 2002年在互联网上提交了三篇文章的第一篇，这些文章把庞加莱猜想作为一个更雄心勃勃的结果的一部分，给其证明提供了一个轮廓。但是在2003年访问美国之后，这位俄罗斯数学隐士回国后停止了与外界的电话和电子信往来。到了2006年，其他人终于赶了上来。三个独立的小组写出报告填补了佩雷尔曼的证明中缺失的关键细节，现在佩雷尔曼的同行几乎都没有疑问地认为他证明了这个著名的难题。
2.DIGGING OUT FOSSIL DNA.
从化石中取出DNA: 研究人员用一种解码和分析DNA的新技术，从尼安德特人和猛犸化石中捕获到遗传信息。
3.SHRINKING ICE.
冰架在缩小: 研究人员今年记录了这一令人不安的趋势。南极洲和格陵兰岛的冰架都在以更快的速度消失到海洋中。
4.NEITHER FISH NOR FOWL.
鱼迈出的第一步: 一个具有结实的连接着的鳍的鱼化石的发现曾是2006年的头版新闻。这种鱼是有肢脊椎动物已知的最近亲，它为生命如何离开海洋登上陆地提供了一个视窗。
5.THE ULTIMATE CAMOUFLAGE.
隐身术的科学: 虽然它看上去一点也不像哈里波特的魔术披风，科学家今年制造的隐身“斗篷”是第一个将物体在视觉上屏蔽起来的初步装置。这个装置引导入射的微波使其既不反射、也没有影子。
6.A RAY OF HOPE FOR MACULAR DEGENERATION PATIENTS.
黄斑病变患者的希望: 研究一种被称为老年黄斑病变失明的研究人员揭示，药物ranibimuzab能改善某些患者的视觉，他们还找到了几个影响人们该症易患性的基因。
7.DOWN THE BIODIVERSITY ROAD
生物多样性是如何发生的: 从沙滩小鼠、到果蝇、到蝴蝶，这些不同的动物帮助科学家发现导致新物种进化的遗传变化。
8.PEERING BEYOND THE LIGHT BARRIER.
显微学的新前沿: 今年，生物学家用新的显微技术来帮助他们观察小于200纳米的细节，为了解细胞和蛋白质的精细结构提供了更清晰的视野。
9.THE PERSISTENCE OF MEMORY.
制造记忆: 2006年的几个发现使神经科学家对了解大脑如何记录新记忆更接近了一步。增强神经元之间连接的被称为“长时程增强”的过程看来很可能是记忆的基础。
10.MINUTE MANIPULATIONS.---piRNA
新一类的小RNA: 科学家发现了一类关闭基因表达的新小RNA分子，把它们命名为 "Piwi-干扰 RNA"。
本年度的崩溃-科学骗局: 干细胞研究者黄禹锡以及其合作者曾在《科学》发表两篇重要论文，他们制造的骗局在2006年被彻底调查了，本年度也发生了几起其它的科学不端行为。
值得注意的领域: 《科学》预测来年的热门领域和主题包括整基因组相关性研究、光晶格、寻找宇宙的原始氢、以及比较灵长类的基因组。
Science 22 December 2006:Vol. 314. no. 5807, p. 1841DOI: 10.1126/science.1138510
Editorial
Breakthrough of the Year
Donald Kennedy
Last year, evolution was the breakthrough of the year; We found it full of new developments in understanding how new species originate. But we did get a complaint or two that perhaps we were just paying extra attention to the lively political/religious debate that was taking place over the issue, particularly in the United States.
Perish the thought! Our readers can relax this year: Religion and politics are off the table, and n-dimensional geometry is on instead. This year's Breakthrough salutes the work of a lone, publicity-shy Russian mathematician named Grigori Perelman, who was at the Steklov Institute of Mathematics of the Russian Academy of Sciences until 2005. The work is very technical but has received unusual public attention because Perelman appears to have proven the Poincaré Conjecture, a problem in topology whose solution will earn a $1 million prize from the Clay Mathematics Institute. That's only if Perelman survives what's left of a 2-year gauntlet of critical attack required by the Clay rules, but most mathematicians think he will.
The analysis supplied by Dana Mackenzie on p. 1848 struck me as a fascinating exploration, full of metaphors suggesting a multidisciplinary dimension in Perelman's analysis. He first got interested in Ricci flow, a process by which topological regions of high curvature flow into regions of lower curvature. He also identified a quantity, which he called "entropy," that increased during the flow, providing a gradient. Tight spots in spatial connections block the application of these rules to dimensions higher than two, so Perelman dealt with these through "surgical intervention." This story is rich with borrowings: from fluid mechanics, thermodynamics, and even surgery! It's hard to deal with a three-dimensional object in four-dimensional space. Perelman's solution is a stunning triumph of intellect. Alas, it has led to bitter controversy, involving others but not Perelman.
Of course, in any Breakthrough year we are obliged to have a Breakdown. This time around, we had to blow the whistle on ourselves. In recognizing this as a year in which scientific fraud took center stage, it was clear that we had to lead with the story involving the retraction of two of our own papers, an event that drew worldwide press attention and required us to ask for an outside evaluation of how we had handled the papers. That brought us some tough news about how competitive the scientific enterprise has become, and the consequential incentive to push (or shred) the ethical envelope.
On the positive side, it was a rich year for important experimental studies. My favorites include some new explanations for how species originate, one of the daunting post-Darwinian puzzles. Among other examples, there is a clear case for speciation through hybridization, an exception to the more general rule that hybrids either don't make it or are reproductively incompetent. Because I like coastlines, when I see new evidence about sea-level rise, I pay attention. This year we got new measures of rates of glacial melting at both ends of the globe: in Greenland, where rates are in hundreds of gigatons a year, and in Antarctica, where drainage by ice streams is accelerating. I also follow the Neanderthal story, because it's interesting to ponder how different human species--now thought from archaeological evidence to have overlapped for perhaps 10,000 years--might have interacted. New sequencing of the Neanderthal genome indicates that the point of divergence is nearly half a million years old and opens up a wealth of comparisons with the human genome sequence. The question everyone asks--"Did they have sex?"--is still open, though barely.
All in all, it's not been a bad year. The predictions we made in 2005 of "Areas to Watch" turned out pretty well. We said RNA interference would be an active sector--good call. Cosmic-ray capture didn't work out, but there was the predicted level of activity on the "small worlds" of microbial communities. We predicted lots of activity on high-temperature superconductivity, and there were more applications, although less new theory. The worst miss was the prediction that the ivory-billed woodpecker would be re-found. Come on, birders, give us some help out there; a good photo, please, not the skin.
10.1126/science.1138510
Donald Kennedy is the Editor-in-Chief of Science.
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS BREAKTHROUGH OF THE YEAR: The Poincaré Conjecture--Proved
Dana Mackenzie (22 December 2006)Science 314 (5807), 1848. [DOI: 10.1126/science.314.5807.1848] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: The Runners-Up
(22 December 2006)Science 314 (5807), 1850a. [DOI: 10.1126/science.314.5807.1850a] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: Scorecard 2006
(22 December 2006)Science 314 (5807), 1850b. [DOI: 10.1126/science.314.5807.1850b] Summary » Full Text » PDF »
NEWS BREAKTHROUGH OF THE YEAR: BREAKDOWN OF THE YEAR: Scientific Fraud
Jennifer Couzin (22 December 2006)Science 314 (5807), 1853. [DOI:10.1126/science.314.5807.1853] Summary » Full Text » PDF »
NEWSBREAKTHROUGH OF THE YEAR: Areas to Watch in 2007
(22 December 2006)Science 314 (5807), 1854. [DOI: 10.1126/science.314.5807.1854] Summary » Full Text » PDF »
Papers and Articles on piRNA
A. Girard et al., "A Germline-Specific Class of Small RNAs Binds Mammalian Piwi Proteins," Nature 442, 199 (2006)
A. Aravin et al., "A Novel Class of Small RNAs Bind to MILI Protein in Mouse Testes," Nature 442, 203 (2006)
S.T. Grivna et al., "A Novel Class of Small RNAs in Mouse Spermatogenic Cells," Genes Dev. 20, 1709 (2006)
N.C. Lau et al., "Characterization of the piRNA Complex from Rat Testes; Science 313, 363 (2006)
R.W. Carthew, "A New RNA Dimension to Genome Control," Science 313, 305 (2006)Perspective article highlighting the Lau et al. study.
V.N. Kim, "Small RNAs Just Got Bigger: Piwi-Interacting RNAs (piRNAs) in Mammalian Testes," Genes Dev. 20, 1993 (2006)
S.T. Grivna et al., "MIWI Associates with Translational Machinery and PIWI-Interacting RNAs (piRNAs) in Regulating Spermatogenesis," Proc. Natl. Acad. Sci. U.S.A. 103, 13415 (2006)
Selected Labs
Gregory Hannon (Cold Spring Harbor Laboratory)
Thomas Tuschl (Rockefeller University)
David Bartel (MIT)
Robert Kingston (Massachusetts General Hospital/Harvard Medical School)
Haifan Lin (Yale Stem Cell Center)
2006-12-26
怎样做PhD
NaturejobsPublished online: 14 December 2006; doi:10.1038/nj0137
How to get a PhD
Evaluating PhD progress both highlights accomplishments and suggests daunting challenges ahead.
Mhairi Dupré
There's a book handed down in my lab from previous graduate students called "How to get a PhD". It can be boiled down to five steps: 1. Become a postgraduate. 2. Choose project question. 3. Get data. 4. Write thesis. 5. Pass thesis defence. But a PhD is more than getting your mates to call you 'doctor'. (Although that does have a ring about it...) PhD students need to make themselves known to the scientific community, they need to learn many different skills that make them employable as a postdoc, and most of all, they need to publish.A publication record is the scientific yardstick by which potential employers and funding bodies will measure your ability. Sometimes I feel disheartened by this. What if my experiments are valid and interesting but the laborious nature of the research requires five years to produce a paper rather than one? What if I'm great at designing experiments, thinking laterally and interpreting results but can't extract DNA to save my life? Good experimental design and interpretation are important for a principal investigator, but before you become one you need to generate data and publish. Then, finally, you will reach that level where you don't need to work in the lab anymore.
To get a PhD one must also have a lot of determination and commitment. This means not just putting up with a lab mate's obsession with David Bowie, but getting out of bed every morning (ok, afternoon). Scientists certainly won't be doing it for the money. There are ups and downs to graduate life, and an awful lot of the time I feel really rubbish. When my experiments repeatedly fail, I feel incompetent. When I know I'm not putting in enough work, I feel inadequate. And when I compare myself with the other students who seem to have a new paper every time I talk to them, I feel like eating my own lab book. This is where one's colleagues and lab environment come into play.
The people I work with have a great influence on whether I enjoy my PhD. When colleagues are kind, open, helpful and happy, it can really ease the pain of 'I-should-have-known-better' experiments and 'did-I-forget-to-add-reagent-X?' results. I feel that I'm not alone and this makes a whole lot of difference. I spend lengthy amounts of time telling myself not to be scared to admit when I don't know or understand something — with helpful colleagues you can ask straight away if what you are doing is OK. Otherwise it's easy to get discouraged and end up going a long way down the wrong path.
My PhD is also time to discover who I am, what I like, and what I want to do with my life. At the moment running, learning Japanese and organizing the departmental Christmas party are taking most of my time, so if some things are going badly I have other areas of my life that are going well. You can't completely separate work and non-work during your PhD, or at least I can't. I find myself thinking of experiments to do in the middle of the night, and during the day, I wonder about what to cook for dinner and if I remembered to lock the door.
What has this year taught me? After doing my PhD for 12 months I feel better about quitting the previous one. I know where my experiments are going and I can talk to my supervisor whenever I want; people are helpful and it's exciting coming to work most days — things are very different from my previous lab. I'm still not particularly confident, though. At the end of my first year I am more aware of how much work a PhD requires. One thing they don't tell you before starting graduate school is how deceptive time can be— four years, I thought. That's ages. Now I realize that I have only three years left in which to stop pipetting around and get something done!So, as I look back over this year, I'm grateful for a second chance at a graduate degree and I'm glad I've survived so far. As I look to the near future, I'm worried but also excited about where my project is going, not to mention my life in general. Will I get an academic position one day? Will I be in Europe or elsewhere?
To mark my progress against the checklist: 1. I'm a postgraduate, check. 2. I have a question, check: what am I doing here? Scientifically, I hope to understand more about the evolution of leaf development — although there are many research questions I'd like to answer! 3. Data collection— I just hope I can manage it in time. The next steps, writing a thesis and defending it? That's the easy bit!
Mhairi Dupré is a first-year PhD student in evolutionary developmental biology at the University of Oxford, UK.
Article brought to you by: Nature Jobs
How to get a PhD
Evaluating PhD progress both highlights accomplishments and suggests daunting challenges ahead.
Mhairi Dupré
There's a book handed down in my lab from previous graduate students called "How to get a PhD". It can be boiled down to five steps: 1. Become a postgraduate. 2. Choose project question. 3. Get data. 4. Write thesis. 5. Pass thesis defence. But a PhD is more than getting your mates to call you 'doctor'. (Although that does have a ring about it...) PhD students need to make themselves known to the scientific community, they need to learn many different skills that make them employable as a postdoc, and most of all, they need to publish.A publication record is the scientific yardstick by which potential employers and funding bodies will measure your ability. Sometimes I feel disheartened by this. What if my experiments are valid and interesting but the laborious nature of the research requires five years to produce a paper rather than one? What if I'm great at designing experiments, thinking laterally and interpreting results but can't extract DNA to save my life? Good experimental design and interpretation are important for a principal investigator, but before you become one you need to generate data and publish. Then, finally, you will reach that level where you don't need to work in the lab anymore.
To get a PhD one must also have a lot of determination and commitment. This means not just putting up with a lab mate's obsession with David Bowie, but getting out of bed every morning (ok, afternoon). Scientists certainly won't be doing it for the money. There are ups and downs to graduate life, and an awful lot of the time I feel really rubbish. When my experiments repeatedly fail, I feel incompetent. When I know I'm not putting in enough work, I feel inadequate. And when I compare myself with the other students who seem to have a new paper every time I talk to them, I feel like eating my own lab book. This is where one's colleagues and lab environment come into play.
The people I work with have a great influence on whether I enjoy my PhD. When colleagues are kind, open, helpful and happy, it can really ease the pain of 'I-should-have-known-better' experiments and 'did-I-forget-to-add-reagent-X?' results. I feel that I'm not alone and this makes a whole lot of difference. I spend lengthy amounts of time telling myself not to be scared to admit when I don't know or understand something — with helpful colleagues you can ask straight away if what you are doing is OK. Otherwise it's easy to get discouraged and end up going a long way down the wrong path.
My PhD is also time to discover who I am, what I like, and what I want to do with my life. At the moment running, learning Japanese and organizing the departmental Christmas party are taking most of my time, so if some things are going badly I have other areas of my life that are going well. You can't completely separate work and non-work during your PhD, or at least I can't. I find myself thinking of experiments to do in the middle of the night, and during the day, I wonder about what to cook for dinner and if I remembered to lock the door.
What has this year taught me? After doing my PhD for 12 months I feel better about quitting the previous one. I know where my experiments are going and I can talk to my supervisor whenever I want; people are helpful and it's exciting coming to work most days — things are very different from my previous lab. I'm still not particularly confident, though. At the end of my first year I am more aware of how much work a PhD requires. One thing they don't tell you before starting graduate school is how deceptive time can be— four years, I thought. That's ages. Now I realize that I have only three years left in which to stop pipetting around and get something done!So, as I look back over this year, I'm grateful for a second chance at a graduate degree and I'm glad I've survived so far. As I look to the near future, I'm worried but also excited about where my project is going, not to mention my life in general. Will I get an academic position one day? Will I be in Europe or elsewhere?
To mark my progress against the checklist: 1. I'm a postgraduate, check. 2. I have a question, check: what am I doing here? Scientifically, I hope to understand more about the evolution of leaf development — although there are many research questions I'd like to answer! 3. Data collection— I just hope I can manage it in time. The next steps, writing a thesis and defending it? That's the easy bit!
Mhairi Dupré is a first-year PhD student in evolutionary developmental biology at the University of Oxford, UK.
Article brought to you by: Nature Jobs
2006-12-16
白鳍豚灭绝了？!The Baiji Yangtze Dolphin is with all probability extinct!
痛心疾首啊，长江白鳍豚从地球上消失了!！我真不愿意相信这是真的!!我们只能从历史文献中寻找她的踪迹了——
两千多年前，《尔雅》便有记载：“鱀，体似鲟，尾如鱼。喙小，锐而长，齿罗生，上下相衔，鼻在额上，能作声，少肉多膏，胎生，健啖细鱼，大者长丈余。江中多有之。”
蒲松龄《聊斋志异•白秋练》原文被收录在新版高中语文书中，作为阅读材料[另：现代白话文介绍]。不知大家读过没有？别只当爱情故事读，人与白鳍豚确是处在共同生存的生物链上啊！白鳍豚的绝灭，将是人类绝灭之始[观点来自一个钟爱白鳍豚的人]！
白鳍豚
Lipotes vexillifer Miller白鳍豚又名白鱀豚，俗称白鳍、白夹、江马，英文名：Yangtze river dolphin，属于鲸目(Cetacea)，喙豚科。
识别特点为：吻突狭长，长约300毫米。额部圆而隆起。背鳍三角形，位于身体的3/5处，有低皮肤脊与尾鳍相连。头顶的偏左侧有一个能启闭自如的呼吸孔。尾鳍水平向，向缘凹入呈新月形。白暨豚种群数量很小，为我国特有的珍稀水生兽类，亟待加强保护。白鳍豚属的哺乳动物，是中国特有的淡水豚类，也是世界上淡水豚类中数量最少的一种，由于数量稀少且为中国特有，被人们称为“水中大熊猫”。它是国家一级保护动物，目前仅分布在长江中、下游干流的湖北枝城至长江口约1600余公里的江段内。以鱼为食，结群活动，小群2～3头，大群10～16头。近年来种群数量下降极快。据报道，80年代初有400多头，80年代中期减至300来头，1990年调查时有200来头，至1993年为130余头，而到1995年已不足100头，被列为世界级的濒危动物。 三峡工程建在长江上游的出口处，不在白鳍豚的栖息范围内，不会直接危及它们的生存。但是三峡工程对长江水文情势的调节，则有可能对其栖息地产生影响。白鳍豚主要栖息在弯曲河段和弯曲分汉河段的大回水区中，当河势改变，大回水区发生移动时，白鳍豚也相应迁移，迁移距离的长短，与大回水区移动距离长短有关。三峡水库下泄清水对河床的冲刷，有可能使大回水区变动，使白鳍豚的栖息地迁移，按最严重的估计，白鳍豚的栖息地有可能下移150余公里，不到现在分布范围的1／10。另外，航运条件改善后，航行船舶增多，有可能使白鳍豚发生意外死亡的几率增加。为保护这一濒临绝灭的珍贵水生动物，国家已在长江中游的螺山至新滩口江段和石首天鹅洲长江故道以及长江下游的铜陵江段分别建立了白鳍豚自然保护区。
分类地位：哺乳纲、鲸目、淡水豚科，白鳍豚属。
外部形态：体长2米，体重100～200千克。吻部狭长，约有30厘米，上下颔两边密排着130多棵圆锥形的牙齿，前额呈园形隆起。皮肤细腻光滑，背面是浅灰蓝色，腹面是洁白色，体表呈流线形，前肢为鳍肢，背鳍呈三角形。后肢退化，尾部未端左右平展，分成两叶，呈新月形。有一个长园形凹穴状的鼻子或呼吸孔长在头顶的左上方。眼睛只有绿豆粒一般大小，已经退化，位于嘴角的后上方。耳朵只有一个针眼大小的洞，位于眼的后方，外耳道已经消失。
分布地点：分布于我国长江自三峡的黄陵庙以下，一直到长江口，以及沿江的大型湖泊和较大的支流中。生活习性：视觉、听觉、嗅觉均己退化。在水中联系同类，趋避敌害，识别物体和探测食物等，完全依靠发出的声纳信号。性情温顺。以鲤鱼、鲢鱼、草鱼、青鱼、三角鲂、赤眼鳟、鲶鱼等淡水鱼类为食。每年有两次发情期，分别在3～5月和8～10月。怀孕期10～ll个月。每胎仅产1仔。生存状况：50年代时长江中尚可见到较大群体，但此后白鳍豚的数量却急剧下降，在沿江湖泊和支流中消失，长江中的个体己不足100只，仅残存在长江中游的枝城到南京一段。在我国《国家重点保护野生动物名录》中被列为1级保护动物；在《中国濒危动物红皮书·兽类》中被列为濒危种，列《华盛顿公约》附录：一类保护动物。 以上转自百度百科
白鳍豚似鱼非鱼，胎生、哺乳。为适应水中的生活环境，它逐渐变化成像鱼的样子，但却没有腮，而用肺呼吸。长有130颗牙齿，却不用它咀嚼，而是咬住食物以后，囫囵吞下。白鳍豚两个后肢蜕化消失，前肢演化为鳍，但内部结构却有和人手相似的桡骨、尺骨、腕骨、指骨。白鳍豚心脏分四腔，体温恒定。所有这一切都说明它是哺乳动物而并非鱼类。
背呈浅灰色或蓝色，腹面为纯白色，背鳍形如一个小三角，胸鳍宛如两只手掌，尾鳍扁平，中间分叉，善于游水，时速可达80千米左右。尾鳍不像鱼一样上下垂直，而是从水平方向分成两叶，可以上下摆动，从而推动躯体前进。加之它是标准的流线体型，皮肤构造特殊，所以游动速度特别快。它还能发出叫声，不同的声音反映其不同的感情。它可长到2～3米长，200～300公斤重，可额头上的一对眼睛却小如绿豆。它对气候变化特别敏感，风雨之前常频频露出水面，所以被鱼民看作可以呼风唤雨的“神鱼” 。
由于长期生活在浑浊的江水中，白鳍豚的视听器官已经退化。它眼小如瞎子，耳孔似针眼，位于双眼后下方。但大脑特别发达，声纳系统极为灵敏，头部还有一种超声波功能，能将江面上几万米范围内的声响迅速传入脑中。一旦遇上紧急情况，便立刻潜水躲避。白鳍豚耐寒，体温通常在36℃左右，喜欢生活在江河的深水区，很少靠近岸边和船只，但它时常游弋至浅水区，追逐鱼虾充饥。它的吻宽细长，上下颌长有130多枚圆锥形的同型齿，可它却懒得咀嚼,只管张口吞下鱼食，消化能力很强。白鳍豚往往成对或三五成群一起活动，但人们很少有机会看到它，只有在它露出水面呼吸时才能瞥见一眼。
今年曾进行过初测，当时就认为是最后的希望，现在大规模的探测之后，一头也没发现！难道我们连最后的希望也没了么？我们是历史的罪人……
News
Last hope for river dolphins [Nature 440, 1096-1097 (27 April 2006) doi:10.1038/4401096b]
Rex Dalton
Abstract
But preliminary survey fails to find any surviving 'baiji'.
The world's most critically endangered cetacean, the Chinese 'baiji' river dolphin, may finally have a chance of being saved from extinction. But it could be too late; researchers who carried out a nine-day pilot search for the dolphins last month didn't find a single one.
The freshwater baiji (Lipotes vexillifer) once thrived in their only habitat, the Yangtze River, which runs though central China. But fewer than 100 dolphins are thought to be left in the river, which has become a busy, polluted highway. "If the giant panda is China's symbol of the destruction of forests, the baiji stands for polluted waters," says Wang Ding, from the Wuhan Institute of Hydrobiology.
An international team of scientists, led by Ding, is hoping to catch the animals and release them in a safer place, possibly the Shishou reserve, which is a 20-kilometre arm off the Yangtze.
But first the researchers —from China, the United States, Britain and Switzerland — need to find out exactly how many of the dolphins remain and where they are. They are preparing to conduct a search of 1,700 kilometres of the river in November, but carried out a pilot survey in March to refine their techniques.
The baiji are so few and far between that the best way to spot them is with acoustic devices. But that's a challenge. "The river is so noisy you can't use traditional acoustic equipment," explains Jay Barlow, a marine mammalogist from the US National Marine Fisheries Service in La Jolla, California, who was on last month's cruise. He and his colleagues are working on a method to clean up recordings from hydrophones, to isolate the baiji's distinctive whistles.
The researchers were disappointed not to see a single baiji on their recent search, but their hopes are now focused on the full-scale survey in November. "If none are found then, the burden of proof will change," says Barlow. "The species will be considered extinct unless proven otherwise."
两千多年前，《尔雅》便有记载：“鱀，体似鲟，尾如鱼。喙小，锐而长，齿罗生，上下相衔，鼻在额上，能作声，少肉多膏，胎生，健啖细鱼，大者长丈余。江中多有之。”
蒲松龄《聊斋志异•白秋练》原文被收录在新版高中语文书中，作为阅读材料[另：现代白话文介绍]。不知大家读过没有？别只当爱情故事读，人与白鳍豚确是处在共同生存的生物链上啊！白鳍豚的绝灭，将是人类绝灭之始[观点来自一个钟爱白鳍豚的人]！
白鳍豚
Lipotes vexillifer Miller白鳍豚又名白鱀豚，俗称白鳍、白夹、江马，英文名：Yangtze river dolphin，属于鲸目(Cetacea)，喙豚科。
识别特点为：吻突狭长，长约300毫米。额部圆而隆起。背鳍三角形，位于身体的3/5处，有低皮肤脊与尾鳍相连。头顶的偏左侧有一个能启闭自如的呼吸孔。尾鳍水平向，向缘凹入呈新月形。白暨豚种群数量很小，为我国特有的珍稀水生兽类，亟待加强保护。白鳍豚属的哺乳动物，是中国特有的淡水豚类，也是世界上淡水豚类中数量最少的一种，由于数量稀少且为中国特有，被人们称为“水中大熊猫”。它是国家一级保护动物，目前仅分布在长江中、下游干流的湖北枝城至长江口约1600余公里的江段内。以鱼为食，结群活动，小群2～3头，大群10～16头。近年来种群数量下降极快。据报道，80年代初有400多头，80年代中期减至300来头，1990年调查时有200来头，至1993年为130余头，而到1995年已不足100头，被列为世界级的濒危动物。 三峡工程建在长江上游的出口处，不在白鳍豚的栖息范围内，不会直接危及它们的生存。但是三峡工程对长江水文情势的调节，则有可能对其栖息地产生影响。白鳍豚主要栖息在弯曲河段和弯曲分汉河段的大回水区中，当河势改变，大回水区发生移动时，白鳍豚也相应迁移，迁移距离的长短，与大回水区移动距离长短有关。三峡水库下泄清水对河床的冲刷，有可能使大回水区变动，使白鳍豚的栖息地迁移，按最严重的估计，白鳍豚的栖息地有可能下移150余公里，不到现在分布范围的1／10。另外，航运条件改善后，航行船舶增多，有可能使白鳍豚发生意外死亡的几率增加。为保护这一濒临绝灭的珍贵水生动物，国家已在长江中游的螺山至新滩口江段和石首天鹅洲长江故道以及长江下游的铜陵江段分别建立了白鳍豚自然保护区。
分类地位：哺乳纲、鲸目、淡水豚科，白鳍豚属。
外部形态：体长2米，体重100～200千克。吻部狭长，约有30厘米，上下颔两边密排着130多棵圆锥形的牙齿，前额呈园形隆起。皮肤细腻光滑，背面是浅灰蓝色，腹面是洁白色，体表呈流线形，前肢为鳍肢，背鳍呈三角形。后肢退化，尾部未端左右平展，分成两叶，呈新月形。有一个长园形凹穴状的鼻子或呼吸孔长在头顶的左上方。眼睛只有绿豆粒一般大小，已经退化，位于嘴角的后上方。耳朵只有一个针眼大小的洞，位于眼的后方，外耳道已经消失。
分布地点：分布于我国长江自三峡的黄陵庙以下，一直到长江口，以及沿江的大型湖泊和较大的支流中。生活习性：视觉、听觉、嗅觉均己退化。在水中联系同类，趋避敌害，识别物体和探测食物等，完全依靠发出的声纳信号。性情温顺。以鲤鱼、鲢鱼、草鱼、青鱼、三角鲂、赤眼鳟、鲶鱼等淡水鱼类为食。每年有两次发情期，分别在3～5月和8～10月。怀孕期10～ll个月。每胎仅产1仔。生存状况：50年代时长江中尚可见到较大群体，但此后白鳍豚的数量却急剧下降，在沿江湖泊和支流中消失，长江中的个体己不足100只，仅残存在长江中游的枝城到南京一段。在我国《国家重点保护野生动物名录》中被列为1级保护动物；在《中国濒危动物红皮书·兽类》中被列为濒危种，列《华盛顿公约》附录：一类保护动物。 以上转自百度百科
白鳍豚似鱼非鱼，胎生、哺乳。为适应水中的生活环境，它逐渐变化成像鱼的样子，但却没有腮，而用肺呼吸。长有130颗牙齿，却不用它咀嚼，而是咬住食物以后，囫囵吞下。白鳍豚两个后肢蜕化消失，前肢演化为鳍，但内部结构却有和人手相似的桡骨、尺骨、腕骨、指骨。白鳍豚心脏分四腔，体温恒定。所有这一切都说明它是哺乳动物而并非鱼类。
背呈浅灰色或蓝色，腹面为纯白色，背鳍形如一个小三角，胸鳍宛如两只手掌，尾鳍扁平，中间分叉，善于游水，时速可达80千米左右。尾鳍不像鱼一样上下垂直，而是从水平方向分成两叶，可以上下摆动，从而推动躯体前进。加之它是标准的流线体型，皮肤构造特殊，所以游动速度特别快。它还能发出叫声，不同的声音反映其不同的感情。它可长到2～3米长，200～300公斤重，可额头上的一对眼睛却小如绿豆。它对气候变化特别敏感，风雨之前常频频露出水面，所以被鱼民看作可以呼风唤雨的“神鱼” 。
由于长期生活在浑浊的江水中，白鳍豚的视听器官已经退化。它眼小如瞎子，耳孔似针眼，位于双眼后下方。但大脑特别发达，声纳系统极为灵敏，头部还有一种超声波功能，能将江面上几万米范围内的声响迅速传入脑中。一旦遇上紧急情况，便立刻潜水躲避。白鳍豚耐寒，体温通常在36℃左右，喜欢生活在江河的深水区，很少靠近岸边和船只，但它时常游弋至浅水区，追逐鱼虾充饥。它的吻宽细长，上下颌长有130多枚圆锥形的同型齿，可它却懒得咀嚼,只管张口吞下鱼食，消化能力很强。白鳍豚往往成对或三五成群一起活动，但人们很少有机会看到它，只有在它露出水面呼吸时才能瞥见一眼。
今年曾进行过初测，当时就认为是最后的希望，现在大规模的探测之后，一头也没发现！难道我们连最后的希望也没了么？我们是历史的罪人……
News
Last hope for river dolphins [Nature 440, 1096-1097 (27 April 2006) doi:10.1038/4401096b]
Rex Dalton
Abstract
But preliminary survey fails to find any surviving 'baiji'.
The world's most critically endangered cetacean, the Chinese 'baiji' river dolphin, may finally have a chance of being saved from extinction. But it could be too late; researchers who carried out a nine-day pilot search for the dolphins last month didn't find a single one.
The freshwater baiji (Lipotes vexillifer) once thrived in their only habitat, the Yangtze River, which runs though central China. But fewer than 100 dolphins are thought to be left in the river, which has become a busy, polluted highway. "If the giant panda is China's symbol of the destruction of forests, the baiji stands for polluted waters," says Wang Ding, from the Wuhan Institute of Hydrobiology.
An international team of scientists, led by Ding, is hoping to catch the animals and release them in a safer place, possibly the Shishou reserve, which is a 20-kilometre arm off the Yangtze.
But first the researchers —from China, the United States, Britain and Switzerland — need to find out exactly how many of the dolphins remain and where they are. They are preparing to conduct a search of 1,700 kilometres of the river in November, but carried out a pilot survey in March to refine their techniques.
The baiji are so few and far between that the best way to spot them is with acoustic devices. But that's a challenge. "The river is so noisy you can't use traditional acoustic equipment," explains Jay Barlow, a marine mammalogist from the US National Marine Fisheries Service in La Jolla, California, who was on last month's cruise. He and his colleagues are working on a method to clean up recordings from hydrophones, to isolate the baiji's distinctive whistles.
The researchers were disappointed not to see a single baiji on their recent search, but their hopes are now focused on the full-scale survey in November. "If none are found then, the burden of proof will change," says Barlow. "The species will be considered extinct unless proven otherwise."
Dolphin feared extinct in polluted Yangtze
Overfishing and boat noise are killing aquatic mammals in Chinese river.
by Michael Hopkin news@nature.com
Human activity in China's Yangtze river is causing the region's dolphins to go extinct and more species will follow if fishing is not regulated, conservationists have warned.
Scientists on an expedition in China claimed this week that the freshwater baiji (Lipotes vexillifer), also called the river dolphin, should be declared 'functionally extinct' in the river. This means that even if a tiny handful of individuals still remains, their numbers will not be enough for them to bounce back. The creature does not live anywhere else making it the first cetacean to be driven to extinction by humans.
"There's no hope to save them," says August Pfluger, chief executive of the Baiji.org foundation, which has just completed a six-week survey of the Yangtze during which they found no baijis. The news is a blow to the team although a shorter survey in March also found no evidence of the dolphins, they had still hoped that around 100 dolphins might remain in the river (see ' Last hope for river dolphins').
Only the International Conservation Union can officially declare a species extinct, and only after it has not been sighted after several years of searching. "There's not enough data," says Rob Shore, freshwater programmes officer for the WWF in Godalming, UK. "But what we do know is that there are very, very few individuals left."
Thousands no more
What's more, another Yangtze mammal, the finless porpoise (Neophocaena phocaenoides), is also heading the same way, Pfluger says. "In the 1980s there were thousands and thousands," he says. "In the 1990s there were around 6,000, according to surveys. Now there are a
Overfishing and boat noise are killing aquatic mammals in Chinese river.
by Michael Hopkin news@nature.com
Human activity in China's Yangtze river is causing the region's dolphins to go extinct and more species will follow if fishing is not regulated, conservationists have warned.
Scientists on an expedition in China claimed this week that the freshwater baiji (Lipotes vexillifer), also called the river dolphin, should be declared 'functionally extinct' in the river. This means that even if a tiny handful of individuals still remains, their numbers will not be enough for them to bounce back. The creature does not live anywhere else making it the first cetacean to be driven to extinction by humans.
"There's no hope to save them," says August Pfluger, chief executive of the Baiji.org foundation, which has just completed a six-week survey of the Yangtze during which they found no baijis. The news is a blow to the team although a shorter survey in March also found no evidence of the dolphins, they had still hoped that around 100 dolphins might remain in the river (see ' Last hope for river dolphins').
Only the International Conservation Union can officially declare a species extinct, and only after it has not been sighted after several years of searching. "There's not enough data," says Rob Shore, freshwater programmes officer for the WWF in Godalming, UK. "But what we do know is that there are very, very few individuals left."
Thousands no more
What's more, another Yangtze mammal, the finless porpoise (Neophocaena phocaenoides), is also heading the same way, Pfluger says. "In the 1980s there were thousands and thousands," he says. "In the 1990s there were around 6,000, according to surveys. Now there are a
RELATED LINKS
Baiji.org
Dolphin Ring: river dolphins
Dolphin Research Centre
Understanding the baiji dolphin
Vaquita Marina
Baiji.org
Dolphin Ring: river dolphins
Dolphin Research Centre
Understanding the baiji dolphin
Vaquita Marina
Wuhan, 13 December 2006 – The Baiji Yangtze Dolphin is with all probability extinct! On Wednesday, in the city of Wuhan in central China, a search expedition, under the direction of the Institute for Hydrobiology Wuhan and the Swiss-based baiji.org Foundation, drew to a finish without any results. During the six-week expedition scientists from six nations desperately searched the Yangtze in vain.
2006-12-12
10 Promising Treatments for World's Biggest Health Threats
Cutting-edge pharmaceuticals now being tested could revolutionize the fight against cancer, Alzheimer's, HIV, diabetes, nicotine addiction and other devastating diseases
By Charles Q. Choi
Alzheimer's Disease--AlzhemedA new drug targeting the root of this debilitating degenerative disease could be the vanguard of a novel class of treatments
Dengue--Live attenuated 17D yellow fever and dengue chimera
A disease afflicting half a million people annually requires a special kind of vaccine
Diabetes--Technosphere Insulin SystemInhalable insulin could help diabetics regulate blood sugar to an unprecedented degree
Hepatitis C--E1E2/MF59The world's first preventative vaccine against Hepatitis C could curb the spread of the disease that killed Allen Ginsberg and thousands of others
Arthritis--NaproxcinodPotential replacement for Vioxx combines the powers of nitroglycerin with those of nonsteroidal anti-inflammatory drugs
Lung Cancer--StimuvaxNew vaccine against the deadliest of all cancers teaches the body to defend itself while avoiding the side effects of more traditional therapies
Malaria--RTS,S/AS02AKilling more than two million people, mostly children, every year, this disease will finally face the first ever commercially available vaccine designed to fight it
Smoking--NicVAXImmunizing the body against nicotine might be just what smokers need to quit for good
Vision Loss--BevasiranibFirst a Nobel Prize, and now a potentially viable treatment: the world's first interfering RNA drug could be the first of many
HIV--HPTN 046 and NevirapinePreventing the half-million cases of mother to child transmission of HIV every year would go a long way to turning the tide of an epidemic
from ScienceAmerican.com
By Charles Q. Choi
Alzheimer's Disease--AlzhemedA new drug targeting the root of this debilitating degenerative disease could be the vanguard of a novel class of treatments
Dengue--Live attenuated 17D yellow fever and dengue chimera
A disease afflicting half a million people annually requires a special kind of vaccine
Diabetes--Technosphere Insulin SystemInhalable insulin could help diabetics regulate blood sugar to an unprecedented degree
Hepatitis C--E1E2/MF59The world's first preventative vaccine against Hepatitis C could curb the spread of the disease that killed Allen Ginsberg and thousands of others
Arthritis--NaproxcinodPotential replacement for Vioxx combines the powers of nitroglycerin with those of nonsteroidal anti-inflammatory drugs
Lung Cancer--StimuvaxNew vaccine against the deadliest of all cancers teaches the body to defend itself while avoiding the side effects of more traditional therapies
Malaria--RTS,S/AS02AKilling more than two million people, mostly children, every year, this disease will finally face the first ever commercially available vaccine designed to fight it
Smoking--NicVAXImmunizing the body against nicotine might be just what smokers need to quit for good
Vision Loss--BevasiranibFirst a Nobel Prize, and now a potentially viable treatment: the world's first interfering RNA drug could be the first of many
HIV--HPTN 046 and NevirapinePreventing the half-million cases of mother to child transmission of HIV every year would go a long way to turning the tide of an epidemic
from ScienceAmerican.com
2006-12-11
Secondary siRNAs Result from Unprimed RNA Synthesis and Form a Distinct Class
In C. elegans, an effective RNA interference (RNAi) response requires the production of secondary siRNAs by RNA-directed RNA polymerases (RdRPs). We cloned secondary siRNAs from transgenic C. elegans lines expressing a single 22 nucleotide primary siRNA. Several secondary siRNAs start a few nucleotides downstream of the primary siRNA, indicating that non-RISC (RNA-induced silencing complex) cleaved mRNAs are substrates for secondary siRNA production. In lines expressing primary siRNAs with single-nucleotide mismatches, secondary siRNAs do not carry the mismatch, but contain the nucleotide complementary to the mRNA. We infer that RdRPs perform unprimed RNA synthesis. Secondary siRNAs are only of antisense polarity, carry 5' di- or triphosphates and are only in minority associated with RDE-1, the RNAi-specific argonaute protein. Therefore, secondary siRNAs represent a distinct class of small RNAs. Their biogenesis depends on RdRPs, and we propose that each secondary siRNA is an individual RdRP product.
http://www.sciencemag.org/cgi/content/abstract/1136699v1
http://www.sciencemag.org/cgi/content/abstract/1136699v1
2006-12-07
Everyday life is new!
"Thanks for your mail. This should be fixed now."This morning I receive a mail at sanger.ac.uk, remind me of a email sended to miRBase a week ago. During data collection for a research project on microRNAs, my colleague ZX and I found an error in a famous microRNA database that was one of fruit fly microRNAs －－dme-bantam was omitted from the list of 78 known fruit fly miRNAs which should have been displayed on the fly miRNAs list validated to date. Now the administrator lists the dme-bantam first! :-) Wow, instant gratification swelled my heart despite that it's not enough to be proud of this few contribution to the public database! Happy a new day! Take pride in your work! Enjoy your life!
2006-12-05
balancer chromosome
What's a balancer chromosome?
Any lethal recessive gene is likely to be lost from a population, because it confers a disadvantage on the progeny of heterozygotes. Imagine that we discover a lethal allele of our gene, vha55-. How can we keep it alive, perhaps for years? Here's what happens when we try to breed two heterozygotes:
The population does not breed true, because in the next generation the wild-type (+/+) appears. In subsequent generations, this will come to dominate the population, because 100% of the progeny of a wild-type fly survives, whereas only 75% of the progeny of a vha55-/+ fly survives. So our only option for keeping this line alive is to select for mutant heterozygotes (assuming we can recognise them!) and perform virgin crosses in each generation. This is so labour intensive as to be impracticable for a large lab with a lot of mutant lines.
But what if we immediately cross our mutant fly to another recessive lethal on the same chromosome? We're not interested in the second lethal, it's just a "balancer" for reasons that will become clear below:
Now, the line DOES breed true, because the only class of progeny which survives is identical to the parents. So once we've gone to the initial effort of crossing-in our balancer chromosome (in this case, TM3), there is no need to select particular flies in subsequent generations, and the mutation can be kept for many years with minimal effort.
Crossing-over and recombinationIn fact, there are a couple of other wrinkles associated with a balancer chromosome. The first is that the order of genes in the balancer chromosome has been jumbled up by a series of previous mutagenic events. The effect of this is to prevent recombination between the two chromosomes: otherwise, the two lethal alleles would eventually recombine onto the same chromosome, and a wild-type chromosome would then occur, leading to the problems discussed earlier.
MarkersThe second desirable property of the balancer is that it should carry a clearly visible dominant marker, that allows us to follow the fate of the balancer chromosome in any cross we should subsequently choose to do. In the case of TM3, this is Sb (Stubble), which conspicously makes the hairs on the back of the fly short and stubbly. Beleive it or not, this is a relatively easy marker to score!
This may sound complex, but you're about to see it in action, when it should become more obvious.
The population does not breed true, because in the next generation the wild-type (+/+) appears. In subsequent generations, this will come to dominate the population, because 100% of the progeny of a wild-type fly survives, whereas only 75% of the progeny of a vha55-/+ fly survives. So our only option for keeping this line alive is to select for mutant heterozygotes (assuming we can recognise them!) and perform virgin crosses in each generation. This is so labour intensive as to be impracticable for a large lab with a lot of mutant lines.
But what if we immediately cross our mutant fly to another recessive lethal on the same chromosome? We're not interested in the second lethal, it's just a "balancer" for reasons that will become clear below:
Now, the line DOES breed true, because the only class of progeny which survives is identical to the parents. So once we've gone to the initial effort of crossing-in our balancer chromosome (in this case, TM3), there is no need to select particular flies in subsequent generations, and the mutation can be kept for many years with minimal effort.
Crossing-over and recombinationIn fact, there are a couple of other wrinkles associated with a balancer chromosome. The first is that the order of genes in the balancer chromosome has been jumbled up by a series of previous mutagenic events. The effect of this is to prevent recombination between the two chromosomes: otherwise, the two lethal alleles would eventually recombine onto the same chromosome, and a wild-type chromosome would then occur, leading to the problems discussed earlier.
MarkersThe second desirable property of the balancer is that it should carry a clearly visible dominant marker, that allows us to follow the fate of the balancer chromosome in any cross we should subsequently choose to do. In the case of TM3, this is Sb (Stubble), which conspicously makes the hairs on the back of the fly short and stubbly. Beleive it or not, this is a relatively easy marker to score!
This may sound complex, but you're about to see it in action, when it should become more obvious.
2006-12-04
Relax us
Had a good time yesterday! Our boss after his visiting CSHL treat us lab staff to dinner. At noon we had an active seminar, "how about firstly going bowling?" he asked smilely, triggering our excitability. Then, in a Bowling alley, all of us were in good shape despite that it's first time for some of us :) . We, together with our young boss and his wife had two complete Bowling games and a complete one consists 0f 10 frames——to be exhausted. Approaching evening, we had a Korea Food in a Korea Food restaurant immersed in a warm atmosphere. Drunk much, talked too much ……In closing, a happy time! :)
2006-12-03
P(acman)——new method to Unlock Virtually All Areas of the Fruit Fly Genome
P(acman) takes bite out of deciphering Drosophila DNA– a new method of introducing DNA into the genome of fruit flies or Drosophila – promises to transform the ability of scientists to study the structure and function of virtually all the fly's genes, and the method may be applicable to other frequently studied organisms such as mice, said its Baylor College of Medicine developers in an article in the current issue of the journal Science.
P/phiC31 artificial chromosome for manipulation, or P(acman), combines three recently developed technologies: BAC+recombineering +phiC31-mediated transgenesis:
http://www.bcm.edu/news/item.cfm?newsID=765
http://www.sciencedaily.com/releases/2006/11/061130191541.htm
P/phiC31 artificial chromosome for manipulation, or P(acman), combines three recently developed technologies: BAC+recombineering +phiC31-mediated transgenesis:
- The bacterial artificial chromosome(BAC), allows the scientist to maintain large chunks of DNA in the bacteria, but it is present in only one or few copies. However, the bacteria can be induced to produce many copies of the DNA when needed.
- Recombineering facilitates the scientist to clone large chunks of DNA and subsequently allows them to make specific mutations anywhere he or she wants in the gene.
- The third technique allows the researcher to pinpoint where he or she wants to the mutant gene to go in the genetic blueprint of the fly, eliminating the apples-and-oranges problem. This third technique – phiC31 – works also in mouse and human cells, implying that this new technique could be used in those cells as well.
http://www.bcm.edu/news/item.cfm?newsID=765
http://www.sciencedaily.com/releases/2006/11/061130191541.htm
2006-11-23
Scientists Explore Function Of 'Junk DNA'
http://www.sciencedaily.com/releases/2006/11/061113180029.htm
Source: University of Iowa Date: November 21, 2006
University of Iowa scientists have made a discovery that broadens understanding of a rapidly developing area of biology known as functional genomics and sheds more light on the mysterious, so-called "junk DNA" that makes up the majority of the human genome.
The team, led by Beverly Davidson, Ph.D., a Roy J. Carver Biomedical Research Chair in Internal Medicine and UI professor of internal medicine, physiology and biophysics, and neurology, have discovered a new mechanism for the expression of microRNAs -- short segments of RNA that do not give rise to a protein, but do play a role in regulating protein production. In their study, Davidson and colleagues not only discovered that microRNAs could be expressed in a different way than previously known, they also found that some of the junk DNA is not junk at all, but instead consists of sequences that can generate microRNAs.
Davidson and her colleagues, including Glen Borchert, a graduate student in her lab, investigated how a set of microRNAs in the human genome is turned on, or expressed. In contrast to original assertions, they discovered that the molecular machinery used to express these microRNAs is different than that used to express RNA that encodes proteins. Expression of the microRNAs required an enzyme called RNA Polymerase III (Pol III) rather than the RNA Polymerase II (Pol II), which mediates expression of RNA that encode proteins. The study is published in Nature Structural and Molecular Biology Advance Online Publication (AOP) on Nov. 12.
"MicroRNAs are being shown to play roles in cancer and in normal development, so learning how these microRNAs are expressed may give us insight into these critical biological processes," said Borchert, who is lead author of the study. "Up to now it's been understood that one enzyme controls their expression, and we now show that in some cases it's a completely different one."
Genes that code for proteins make up only a tiny fraction of the human genome. The function of the remaining non-coding sequence is just beginning to be unraveled. In fact, until very recently, much of the non-coding sequence was dismissed as junk DNA. In 1998, scientists discovered that some DNA produced small pieces of non-coding RNA that could turn off, or silence, genes. This discovery won Andrew Fire and Craig Mello the 2006 Nobel Prize for medicine or physiology. Since their discovery, the field has exploded and small, non-coding RNAs have been shown to play an important role in development and disease in ways that scientists are only just beginning to understand.
"Not so many years ago our understanding was that DNA was transcribed to RNA, which was then translated to protein. Now we know that the levels of control are much more varied and that many RNAs don't make protein, but instead regulate the expression of proteins," Davidson explained. "Non-coding RNA like microRNAs represent a set of refined control switches, and understanding how microRNAs work and how they are themselves controlled is likely to be very important in many areas of biology and medicine."
Over 450 microRNAs have been identified in the human genome. Learning how they are turned on and in what cells and what they do, may allow scientists to turn that knowledge to their advantage as a medical tool.
In addition to Davidson and Borchert, William Lanier, a graduate student in the UI Department of Biological Sciences, was also part of the research team. The study was funded in part by the National Institutes of Health.
Source: University of Iowa Date: November 21, 2006
University of Iowa scientists have made a discovery that broadens understanding of a rapidly developing area of biology known as functional genomics and sheds more light on the mysterious, so-called "junk DNA" that makes up the majority of the human genome.
The team, led by Beverly Davidson, Ph.D., a Roy J. Carver Biomedical Research Chair in Internal Medicine and UI professor of internal medicine, physiology and biophysics, and neurology, have discovered a new mechanism for the expression of microRNAs -- short segments of RNA that do not give rise to a protein, but do play a role in regulating protein production. In their study, Davidson and colleagues not only discovered that microRNAs could be expressed in a different way than previously known, they also found that some of the junk DNA is not junk at all, but instead consists of sequences that can generate microRNAs.
Davidson and her colleagues, including Glen Borchert, a graduate student in her lab, investigated how a set of microRNAs in the human genome is turned on, or expressed. In contrast to original assertions, they discovered that the molecular machinery used to express these microRNAs is different than that used to express RNA that encodes proteins. Expression of the microRNAs required an enzyme called RNA Polymerase III (Pol III) rather than the RNA Polymerase II (Pol II), which mediates expression of RNA that encode proteins. The study is published in Nature Structural and Molecular Biology Advance Online Publication (AOP) on Nov. 12.
"MicroRNAs are being shown to play roles in cancer and in normal development, so learning how these microRNAs are expressed may give us insight into these critical biological processes," said Borchert, who is lead author of the study. "Up to now it's been understood that one enzyme controls their expression, and we now show that in some cases it's a completely different one."
Genes that code for proteins make up only a tiny fraction of the human genome. The function of the remaining non-coding sequence is just beginning to be unraveled. In fact, until very recently, much of the non-coding sequence was dismissed as junk DNA. In 1998, scientists discovered that some DNA produced small pieces of non-coding RNA that could turn off, or silence, genes. This discovery won Andrew Fire and Craig Mello the 2006 Nobel Prize for medicine or physiology. Since their discovery, the field has exploded and small, non-coding RNAs have been shown to play an important role in development and disease in ways that scientists are only just beginning to understand.
"Not so many years ago our understanding was that DNA was transcribed to RNA, which was then translated to protein. Now we know that the levels of control are much more varied and that many RNAs don't make protein, but instead regulate the expression of proteins," Davidson explained. "Non-coding RNA like microRNAs represent a set of refined control switches, and understanding how microRNAs work and how they are themselves controlled is likely to be very important in many areas of biology and medicine."
Over 450 microRNAs have been identified in the human genome. Learning how they are turned on and in what cells and what they do, may allow scientists to turn that knowledge to their advantage as a medical tool.
In addition to Davidson and Borchert, William Lanier, a graduate student in the UI Department of Biological Sciences, was also part of the research team. The study was funded in part by the National Institutes of Health.
returned to my blogger
wow, after three weeks I can access my blogger again! During the passed days, I asked for help from the google help group and The Blogger Team but without good result. I even lost hope to my disappoint, but today I try to back to my homepage——success! Maybe it was given as a Thanksgiving Day gift from the God! I must also extend my heartfelt thanks to all that love me, though I don't believe in the God, as the saying goes,"To love and to be loved is the greatest happiness of existence" :) Hooray!
2006-11-01
On the art of identifying effective and specific siRNAs
Nature Methods - 3, 670 - 676 (2006) Published online: 23 August 2006; doi:10.1038/nmeth911
Yi Pei & Thomas Tuschl
Table 1 Representative siRNA sequence selection web tools
Tools
URLs
Comments
siDESIGN
http://www.dharmacon.com/
Scores and ranks candidate siRNAs based on thermodynamic and sequence-related criteria. BLAST search is conducted by default.
RNAi Designer
https://rnaidesigner.invitrogen.com/rnaiexpress/
Ranks candidate siRNAs using a primitive scoring system. BLAST search is automatic and the results are shown.
BIOPREDsi
http://www.biopredsi.org
An artificial neural network–based tool, which was trained with 2,500 experimentally assessed siRNAs. Analysis of genome-wide specificity is included.
Whitehead siRNA Selection server
http://jura.wi.mit.edu/bioc/siRNA
Offers flexibility in defining siRNA sequence patterns and selection of filter functions. Different properties of selected siRNAs are calculated, including thermodynamic values, polymorphisms are identified and the results of configurable BLAST search and filtering are shown. The user can sort the output in various ways and balance decisions.
siDE
http://side.bioinfo.ochoa.fib.es/
Developed for high-throughput applications of siRNAs using several published algorithms for efficacy prediction and a nonredundant database for specificity analysis.
siSearch
http://sisearch.cgb.ki.se/
The kernel algorithm focuses primarily on energy features of effective siRNAs. Alternative algorithms are also implemented and integrated in the tool. siSearch is expandable to include newly discovered rules.
Sirna
http://sfold.wadsworth.org/sirna.pl
Sequence selection tool, which incorporates the target accessibility in the evaluation. No specificity analysis.
siRNA design software
http://www.cs.hku.hk/sirna
Candidate siRNAs proposed by various previously developed sequence selection tools are classified based on target accessibility.
Yi Pei & Thomas Tuschl
Table 1 Representative siRNA sequence selection web tools
Tools
URLs
Comments
siDESIGN
http://www.dharmacon.com/
Scores and ranks candidate siRNAs based on thermodynamic and sequence-related criteria. BLAST search is conducted by default.
RNAi Designer
https://rnaidesigner.invitrogen.com/rnaiexpress/
Ranks candidate siRNAs using a primitive scoring system. BLAST search is automatic and the results are shown.
BIOPREDsi
http://www.biopredsi.org
An artificial neural network–based tool, which was trained with 2,500 experimentally assessed siRNAs. Analysis of genome-wide specificity is included.
Whitehead siRNA Selection server
http://jura.wi.mit.edu/bioc/siRNA
Offers flexibility in defining siRNA sequence patterns and selection of filter functions. Different properties of selected siRNAs are calculated, including thermodynamic values, polymorphisms are identified and the results of configurable BLAST search and filtering are shown. The user can sort the output in various ways and balance decisions.
siDE
http://side.bioinfo.ochoa.fib.es/
Developed for high-throughput applications of siRNAs using several published algorithms for efficacy prediction and a nonredundant database for specificity analysis.
siSearch
http://sisearch.cgb.ki.se/
The kernel algorithm focuses primarily on energy features of effective siRNAs. Alternative algorithms are also implemented and integrated in the tool. siSearch is expandable to include newly discovered rules.
Sirna
http://sfold.wadsworth.org/sirna.pl
Sequence selection tool, which incorporates the target accessibility in the evaluation. No specificity analysis.
siRNA design software
http://www.cs.hku.hk/sirna
Candidate siRNAs proposed by various previously developed sequence selection tools are classified based on target accessibility.
2006-10-30
2006-10-29
Love code
1. Chemistry 爱情化学秘方
请听题：我和他不来电怎么说？答案：We have no chemistry.
现代生理学 physiology 研究发现，当你遇到心爱的人，会心跳加速、血压上升，一旦触及她的身体，仿如触电般，而这感觉就是 chemical reaction 哦，所以爱情也就和化学和化学工程师 Chemical Engineer 有瓜葛了。你可以认为浪漫 romance 就是 Roman 的 Chemical Engineer （罗马的化学工程师）来的。
romance 浪漫 =Roman罗马人+ CE 化学工程师
例句：
--“I love you madly!我爱你爱疯了Say you＇re going to marry me, say yes!说你要嫁给我” David pop the question (求婚) to Mary.--“You are not my type!你不是我爱的类型We have no chemistry! 我对你不来电Not if you were the last man on earth!即便你是世界上唯一的男子，我也不会嫁给你”
2. platonic love 精神恋爱
Plato 柏拉图； Platonic 纯精神的，理想的
“爱情教母”琼瑶曾写过一篇杂感《白骆驼之爱》，她认为 one-night stand（一夜情）并不能带来true love（真爱），只有“白骆驼之爱”才能引向（lead to）真正的幸福（true happiness）。所谓“白骆驼”原来就是 platonic love，原是她的 Mr. Right (如意郎君)严重的吴侬软语，把“柏拉图”误读成“白骆驼”。
3. puppy love 初恋
每个人对自己的初恋都难以忘怀，那种纯真的感情恐怕在以后的恋爱中很难再能找到。而英语中表示初恋却很有意思，叫做 puppy love，puppy 本意是未满一岁的小狗，用它们的爱情来表示青涩年代少男少女短暂的爱情再恰当不过了。
4. date 爱情如蜜枣
date 约会，日期，枣；
约会怎么和日期，枣子联系在一起呢？中国婚俗很讲究，一定要选个吉利的日子（date）, 还要将枣(date)和栗子塞到新人的被子里，隐喻“早立子”。这么说大概就能记住了吧。
5. Prince Charming 白马王子
“What a stud! 太帅了He was really my type! 他正是我心中的偶像My Prince Charming 我的白马王子啊!” Mary 回忆着，“I walked directly to Putin，Mr. Big(黑帮老大) and say ‘I love you, I will marry you!”他接受了她，并改邪归正，如今已是她的Mr. Right了。记得张爱玲的《爱》中∶“于千万人之中遇见你所要遇见的人，于千万年之中，时间的无涯的荒野里，没有早一步，也没有晚一步，刚巧赶上了。” Mr. Right 也许就是在恰当的时间（right time），恰当的地点（right place）遇上适合的人（right person）吧！
Mr. Right 如意郎君Miss Right 窈窕淑女，君子好逑啊！Beauty is in the eyes of beholder! 情人眼里出西施。
6. court: 求婚
“That does it!够了 You shacked up （同居）with my daughter and make her in a family way（怀孕）。You must sue for her hand （求婚）or I will sue you and bring you into the jail!”。
真是 shotgun marriage（强迫的婚姻）! 现在，未婚同居（cohabitant；free love）甚至试婚（trial marriage）的越来越多，如果双方情投意合（suit each other）才正式 suit 求婚，否则分道扬镳。但是未婚同居，缺乏法律保护，suitor（求婚者）当不成倒常常成了suitor（起诉者）了。更荒唐的是，有些爱情直到失去，才知道她的可贵，居然到了 court（法庭），才想起 court（求爱）了，只可惜 too late!
suitor 求婚者，起诉者，请愿者；sue 求婚，起诉
pursue 献殷勤； suit套装，适合，求婚
7. taken 名花有主
I love her with all my heart. 我真心真意地爱着她!I will date her this Valentine＇s Day. 情人节我要约她。But she＇s taken and always play the field. 但她名花有主而且脚踩多条船。
请听题：我和他不来电怎么说？答案：We have no chemistry.
现代生理学 physiology 研究发现，当你遇到心爱的人，会心跳加速、血压上升，一旦触及她的身体，仿如触电般，而这感觉就是 chemical reaction 哦，所以爱情也就和化学和化学工程师 Chemical Engineer 有瓜葛了。你可以认为浪漫 romance 就是 Roman 的 Chemical Engineer （罗马的化学工程师）来的。
romance 浪漫 =Roman罗马人+ CE 化学工程师
例句：
--“I love you madly!我爱你爱疯了Say you＇re going to marry me, say yes!说你要嫁给我” David pop the question (求婚) to Mary.--“You are not my type!你不是我爱的类型We have no chemistry! 我对你不来电Not if you were the last man on earth!即便你是世界上唯一的男子，我也不会嫁给你”
2. platonic love 精神恋爱
Plato 柏拉图； Platonic 纯精神的，理想的
“爱情教母”琼瑶曾写过一篇杂感《白骆驼之爱》，她认为 one-night stand（一夜情）并不能带来true love（真爱），只有“白骆驼之爱”才能引向（lead to）真正的幸福（true happiness）。所谓“白骆驼”原来就是 platonic love，原是她的 Mr. Right (如意郎君)严重的吴侬软语，把“柏拉图”误读成“白骆驼”。
3. puppy love 初恋
每个人对自己的初恋都难以忘怀，那种纯真的感情恐怕在以后的恋爱中很难再能找到。而英语中表示初恋却很有意思，叫做 puppy love，puppy 本意是未满一岁的小狗，用它们的爱情来表示青涩年代少男少女短暂的爱情再恰当不过了。
4. date 爱情如蜜枣
date 约会，日期，枣；
约会怎么和日期，枣子联系在一起呢？中国婚俗很讲究，一定要选个吉利的日子（date）, 还要将枣(date)和栗子塞到新人的被子里，隐喻“早立子”。这么说大概就能记住了吧。
5. Prince Charming 白马王子
“What a stud! 太帅了He was really my type! 他正是我心中的偶像My Prince Charming 我的白马王子啊!” Mary 回忆着，“I walked directly to Putin，Mr. Big(黑帮老大) and say ‘I love you, I will marry you!”他接受了她，并改邪归正，如今已是她的Mr. Right了。记得张爱玲的《爱》中∶“于千万人之中遇见你所要遇见的人，于千万年之中，时间的无涯的荒野里，没有早一步，也没有晚一步，刚巧赶上了。” Mr. Right 也许就是在恰当的时间（right time），恰当的地点（right place）遇上适合的人（right person）吧！
Mr. Right 如意郎君Miss Right 窈窕淑女，君子好逑啊！Beauty is in the eyes of beholder! 情人眼里出西施。
6. court: 求婚
“That does it!够了 You shacked up （同居）with my daughter and make her in a family way（怀孕）。You must sue for her hand （求婚）or I will sue you and bring you into the jail!”。
真是 shotgun marriage（强迫的婚姻）! 现在，未婚同居（cohabitant；free love）甚至试婚（trial marriage）的越来越多，如果双方情投意合（suit each other）才正式 suit 求婚，否则分道扬镳。但是未婚同居，缺乏法律保护，suitor（求婚者）当不成倒常常成了suitor（起诉者）了。更荒唐的是，有些爱情直到失去，才知道她的可贵，居然到了 court（法庭），才想起 court（求爱）了，只可惜 too late!
suitor 求婚者，起诉者，请愿者；sue 求婚，起诉
pursue 献殷勤； suit套装，适合，求婚
7. taken 名花有主
I love her with all my heart. 我真心真意地爱着她!I will date her this Valentine＇s Day. 情人节我要约她。But she＇s taken and always play the field. 但她名花有主而且脚踩多条船。
2006-10-28
454Sequncing LifeScinecesTM——update our new technology to research microRNA
Sequencing Medicago truncatulaexpressed sequenced tags using 454 Life Sciences technology
Foo Cheung , Brian J Haas , Susanne M D Goldberg , Gregory D May , Yongli Xiao and Christopher D Town BMC Genomics 2006, 7:272 doi:10.1186/1471-2164-7-272
Published
24 October 2006Abstract (provisional)
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.
Background
In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced via this technology are of value in gene structure annotation.
Results
A single 454 GS20 sequencing run on adapter-ligated cDNA, from a normalized cDNA library, generated 292,465 reads that were reduced to 252,384 reads with an average read length of 92 nucleotides after cleaning. After clustering and assembly, a total of 184,599 unique sequences were generated containing over 400 SSRs. The 454 sequences generated hits to more genes than a comparable amount of sequence from MtGI. Although short, the 454 reads are of sufficient length to map to a unique genome location as effectively as longer ESTs produced by conventional sequencing. Functional interpretation of the sequences was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of GO categories. 53,796 assemblies and singletons (29%) had no match in the existing MtGI. Within the previously unobserved Medicago transcripts, thousands had matches in a comprehensive protein database and one or more of the TIGR Plant Gene Indices. Approximately 20% of these novel sequences could be found in the Medicago genome sequence. A total of 70,026 reads generated by the 454 technology were mapped to 785 Medicago finished BACs using PASA and over 1,000 gene models required modification. In parallel to 454 sequencing, 4,445 5-prime reads were generated by conventional sequencing using the same library and from the assembled sequences it was shown to contain about 52% full length cDNAs encoding proteins from 50 to over 500 amino acids in length.
Conclusions
Due to the large number of reads afforded by the 454 DNA sequencing technology, it is effective in revealing the expression of transcripts from a broad range of GO categories and contains many rare transcripts in normalized cDNA libraries, although only a limited portion of their sequence is uncovered. As with longer ESTs, 454 reads can be mapped uniquely onto genomic sequence to provide support for, and modifications of, gene predictions.
中文链接 生物通
Foo Cheung , Brian J Haas , Susanne M D Goldberg , Gregory D May , Yongli Xiao and Christopher D Town BMC Genomics 2006, 7:272 doi:10.1186/1471-2164-7-272
Published
24 October 2006Abstract (provisional)
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.
Background
In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced via this technology are of value in gene structure annotation.
Results
A single 454 GS20 sequencing run on adapter-ligated cDNA, from a normalized cDNA library, generated 292,465 reads that were reduced to 252,384 reads with an average read length of 92 nucleotides after cleaning. After clustering and assembly, a total of 184,599 unique sequences were generated containing over 400 SSRs. The 454 sequences generated hits to more genes than a comparable amount of sequence from MtGI. Although short, the 454 reads are of sufficient length to map to a unique genome location as effectively as longer ESTs produced by conventional sequencing. Functional interpretation of the sequences was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of GO categories. 53,796 assemblies and singletons (29%) had no match in the existing MtGI. Within the previously unobserved Medicago transcripts, thousands had matches in a comprehensive protein database and one or more of the TIGR Plant Gene Indices. Approximately 20% of these novel sequences could be found in the Medicago genome sequence. A total of 70,026 reads generated by the 454 technology were mapped to 785 Medicago finished BACs using PASA and over 1,000 gene models required modification. In parallel to 454 sequencing, 4,445 5-prime reads were generated by conventional sequencing using the same library and from the assembled sequences it was shown to contain about 52% full length cDNAs encoding proteins from 50 to over 500 amino acids in length.
Conclusions
Due to the large number of reads afforded by the 454 DNA sequencing technology, it is effective in revealing the expression of transcripts from a broad range of GO categories and contains many rare transcripts in normalized cDNA libraries, although only a limited portion of their sequence is uncovered. As with longer ESTs, 454 reads can be mapped uniquely onto genomic sequence to provide support for, and modifications of, gene predictions.
中文链接 生物通
2006-10-26
An RNA map predicting Nova-dependent splicing regulation
Article
Nature advance online publication 25 October 2006 doi:10.1038/nature05304; Received 5 May 2006; Accepted 3 October 2006; Published online 25 October 2006
An RNA map predicting Nova-dependent splicing regulation
Jernej Ule1,2,6,7, Giovanni Stefani1,2,6,7, Aldo Mele1,2, Matteo Ruggiu1,2, Xuning Wang3, Bahar Taneri4,7, Terry Gaasterland4,7, Benjamin J. Blencowe5 and Robert B. Darnell1,2
Abstract
Nova proteins are a neuron-specific alternative splicing factors. We have combined bioinformatics, biochemistry and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-messenger RNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led us to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harbouring (or closest to) YCAY clusters. These results define a genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein, namely that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.
Nature advance online publication 25 October 2006 doi:10.1038/nature05304; Received 5 May 2006; Accepted 3 October 2006; Published online 25 October 2006
An RNA map predicting Nova-dependent splicing regulation
Jernej Ule1,2,6,7, Giovanni Stefani1,2,6,7, Aldo Mele1,2, Matteo Ruggiu1,2, Xuning Wang3, Bahar Taneri4,7, Terry Gaasterland4,7, Benjamin J. Blencowe5 and Robert B. Darnell1,2
Abstract
Nova proteins are a neuron-specific alternative splicing factors. We have combined bioinformatics, biochemistry and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-messenger RNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led us to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harbouring (or closest to) YCAY clusters. These results define a genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein, namely that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.
Nature教你十步掌握写综述
http://www.nature.com/news/2006/061016/full/nj7113-880b.html
Career View
NaturejobsPublished online: 18 October 2006; doi:10.1038/nj7113-880b
Training peer reviewersTen steps to master the art of peer review.
David A. Mackey
The peer-review process provides an opportunity for clinicians and scientists to train their fellows and postgraduate students as part of a one-on-one journal-club exercise. Supervisors can assess students' critical thinking and writing skills early in their careers. Consider these ten steps to teach the art of reviewing.
1) Explain how to proceed with a peer review, stressing the importance of respecting confidentiality and the rules of the journal or grant body.
2) Establish a submission deadline. The review process should take up to three hours. Set a time for final discussion before the deadline, allowing both student and supervisor time to read and review the work.
3) Adopt the right mindset. Don't accept the manuscript 'as is', and don't be hypercritical. The student might imagine that it's their own manuscript about to be rejected, and that they have the opportunity to improve it.
4) Read the manuscript once, taking rudimentary notes.
5) Follow the journal-specific author and reviewer instructions. Note those pertaining to the category of the manuscript, the word length, abstract structure and the format for references, figures and tables.
6) Verify each citation with PubMed or similar — which also gives you a chance to read generally on the topic. Highlighting minor citation errors shows that the paper has been read thoroughly. Ask the following: does the submitted work complement or duplicate the authors' and others' previous work?
7) Re-read the manuscript armed with the specific author instructions and good background knowledge.
8) Write the review envisaging that the editor is too busy to read the manuscript in-depth. Summarize the key features in a paragraph, stating the topic of the paper, what was performed, the key conclusions drawn, why this is important, and why this is a novel contribution. Strengths or problems with the manuscript or methodology should then be detailed.9) Write all comments as if they will be seen by the authors. Although most reviewers are anonymous, caution students that a disgruntled author could recognize one's spelling variances, grammar or clichés.
10) Submit the review, telling the editor the review was written with a student and that you agree with their assessment. Show the student the submitted review as well as the editor's and other reviewers' comments.
David A. Mackey is an associate professor of ophthalmology at the University of Melbourne, Australia.
Article brought to you by: Nature Jobs
Career View
NaturejobsPublished online: 18 October 2006; doi:10.1038/nj7113-880b
Training peer reviewersTen steps to master the art of peer review.
David A. Mackey
The peer-review process provides an opportunity for clinicians and scientists to train their fellows and postgraduate students as part of a one-on-one journal-club exercise. Supervisors can assess students' critical thinking and writing skills early in their careers. Consider these ten steps to teach the art of reviewing.
1) Explain how to proceed with a peer review, stressing the importance of respecting confidentiality and the rules of the journal or grant body.
2) Establish a submission deadline. The review process should take up to three hours. Set a time for final discussion before the deadline, allowing both student and supervisor time to read and review the work.
3) Adopt the right mindset. Don't accept the manuscript 'as is', and don't be hypercritical. The student might imagine that it's their own manuscript about to be rejected, and that they have the opportunity to improve it.
4) Read the manuscript once, taking rudimentary notes.
5) Follow the journal-specific author and reviewer instructions. Note those pertaining to the category of the manuscript, the word length, abstract structure and the format for references, figures and tables.
6) Verify each citation with PubMed or similar — which also gives you a chance to read generally on the topic. Highlighting minor citation errors shows that the paper has been read thoroughly. Ask the following: does the submitted work complement or duplicate the authors' and others' previous work?
7) Re-read the manuscript armed with the specific author instructions and good background knowledge.
8) Write the review envisaging that the editor is too busy to read the manuscript in-depth. Summarize the key features in a paragraph, stating the topic of the paper, what was performed, the key conclusions drawn, why this is important, and why this is a novel contribution. Strengths or problems with the manuscript or methodology should then be detailed.9) Write all comments as if they will be seen by the authors. Although most reviewers are anonymous, caution students that a disgruntled author could recognize one's spelling variances, grammar or clichés.
10) Submit the review, telling the editor the review was written with a student and that you agree with their assessment. Show the student the submitted review as well as the editor's and other reviewers' comments.
David A. Mackey is an associate professor of ophthalmology at the University of Melbourne, Australia.
Article brought to you by: Nature Jobs
Nature Genetics_MicroRNA专题
http://www.nature.com/ng/journal/v38/n6s/index.html
Nature Genetics_MicroRNA Special
June 2006, Volume 38 No 6s
Web-Only Materials
Editorial
Perspectives
Review
About the cover
Web-Only Materials
Library
Sponsors
Animation: "Lifecycle of an miRNA"
Editorial
The microRevolution pS1doi:10.1038/ng0606s-S1Full text PDF (50K)
Perspectives
Approaches to microRNA discovery ppS2 - S7Eugene Berezikov, Edwin Cuppen & Ronald H A PlasterkPublished online: 30 May 2006 doi:10.1038/ng1794Abstract Full text PDF (279K)
microRNA target predictions in animals ppS8 - S13Nikolaus RajewskyPublished online: 30 May 2006 doi:10.1038/ng1798Abstract Full text PDF (250K)
Strategies to determine the biological function of microRNAs ppS14 - S19Jan Krützfeldt, Matthew N Poy & Markus StoffelPublished online: 30 May 2006 doi:10.1038/ng1799Abstract Full text PDF (292K)
Canalization of development by microRNAs ppS20 - S24Eran Hornstein & Noam ShomronPublished online: 30 May 2006 doi:10.1038/ng1803Abstract Full text PDF (306K)
Viruses and microRNAs ppS25 - S30Bryan R CullenPublished online: 30 May 2006 doi:10.1038/ng1793Abstract Full text PDF (320K)
Review
Functions of microRNAs and related small RNAs in plants ppS31 - S36Allison C Mallory & Hervé VaucheretPublished online: 30 May 2006 doi:10.1038/ng1791Abstract Full text PDF (328K)
Nature Genetics_MicroRNA Special
June 2006, Volume 38 No 6s
Web-Only Materials
Editorial
Perspectives
Review
About the cover
Web-Only Materials
Library
Sponsors
Animation: "Lifecycle of an miRNA"
Editorial
The microRevolution pS1doi:10.1038/ng0606s-S1Full text PDF (50K)
Perspectives
Approaches to microRNA discovery ppS2 - S7Eugene Berezikov, Edwin Cuppen & Ronald H A PlasterkPublished online: 30 May 2006 doi:10.1038/ng1794Abstract Full text PDF (279K)
microRNA target predictions in animals ppS8 - S13Nikolaus RajewskyPublished online: 30 May 2006 doi:10.1038/ng1798Abstract Full text PDF (250K)
Strategies to determine the biological function of microRNAs ppS14 - S19Jan Krützfeldt, Matthew N Poy & Markus StoffelPublished online: 30 May 2006 doi:10.1038/ng1799Abstract Full text PDF (292K)
Canalization of development by microRNAs ppS20 - S24Eran Hornstein & Noam ShomronPublished online: 30 May 2006 doi:10.1038/ng1803Abstract Full text PDF (306K)
Viruses and microRNAs ppS25 - S30Bryan R CullenPublished online: 30 May 2006 doi:10.1038/ng1793Abstract Full text PDF (320K)
Review
Functions of microRNAs and related small RNAs in plants ppS31 - S36Allison C Mallory & Hervé VaucheretPublished online: 30 May 2006 doi:10.1038/ng1791Abstract Full text PDF (328K)
2006-10-25
ncRNA database
Non-coding RNA database
In conjunction with the RIKEN and Karolinska Institutes, the IMB has developed a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied noncoding RNAs, including many associated with diseases and/or developmental processes. The database includes microRNAs and snoRNAs, but not infrastructural RNAs such as rRNAs and tRNAs which are catalogued elsewhere. The database also includes over 1200 putative antisense ncRNAs and almost 20,000 putative noncoding RNAs identified in high quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. For ncRNAs listed in RNAdb, sequence data as well as other information including Genbank accessions, references, chromosomal location, transcript length, splicing status, conservation notes, function, disease associations, antisense relationships, imprinting status, and tissue expression patterns are provided wherever possible. The database is searchable by many criteria, and will we hope be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.
NONCODE
is a brand-new database of all kinds of noncoding RNAs (except tRNAs and rRNAs). It is distinguished from other ncRNA databases by:
1.The data amount of NONCODE is big, and almost all traditional ncRNA classes are included.
2.All the sequences are confirmed by consulting the references manually, more than 80% data are from experiments.
3.We introduced a new classification system--process function classification system, which based on the cellular process it takes part in.
4.NONCODE also provides an efficient search option, allowing recovery of sequence, related publications and other information.
In conjunction with the RIKEN and Karolinska Institutes, the IMB has developed a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied noncoding RNAs, including many associated with diseases and/or developmental processes. The database includes microRNAs and snoRNAs, but not infrastructural RNAs such as rRNAs and tRNAs which are catalogued elsewhere. The database also includes over 1200 putative antisense ncRNAs and almost 20,000 putative noncoding RNAs identified in high quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. For ncRNAs listed in RNAdb, sequence data as well as other information including Genbank accessions, references, chromosomal location, transcript length, splicing status, conservation notes, function, disease associations, antisense relationships, imprinting status, and tissue expression patterns are provided wherever possible. The database is searchable by many criteria, and will we hope be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.
NONCODE
is a brand-new database of all kinds of noncoding RNAs (except tRNAs and rRNAs). It is distinguished from other ncRNA databases by:
1.The data amount of NONCODE is big, and almost all traditional ncRNA classes are included.
2.All the sequences are confirmed by consulting the references manually, more than 80% data are from experiments.
3.We introduced a new classification system--process function classification system, which based on the cellular process it takes part in.
4.NONCODE also provides an efficient search option, allowing recovery of sequence, related publications and other information.
2006-10-22
14 things you can learn from the Google story
- Connections - human, computer, biology - are everything. Life = networks.
- Never compromise your ideals because someone said it's impossible, stupid, or a waste of time.
- Do focus on changing the world, don't focus on the money. If you provide value, the money will come.
- Have a healthy disregard for the impossible. If someone hasn't done it yet, that doesn't mean it's impossible.
- Money is a problem, not a solution. Money cannot solve your problems, but your solutions can solve the money problem.
- Value creativity, not money. View creativity as your company's true bottom-line, or your company will stop growing and die.
- Go against the grain. Don't believe in other people's visions for you, believe in your own.
- Speed is more important than looking good. A shiny, beautiful car isn't impressive when it gets overtaken by an old jalopy; the same applies to software.
- Organic growth is best. Only grow as fast as you need to, don't waste money on advertising a product you won't want your mom to use.
- Focus on users above all else, e.g. don't do something that might annoy your users just to make more money, they won't forget.
- Never betray users' trust, or anyone else's.
- Spend 20% of your time on blue-sky ideas without worrying about how they will make a profit. If it might change the world for the better, it needs to be done, even if it can't make money.
- Don't make enemies of your competitors to stay driven. Be driven by your own values and mission.
- Beat your own path through the wilderness.
Copy from Digital Samurai 's blog, and I can't agree with 2,3,4,6,11,13[ in bold] any more. While studying&working, I can't help taking google products as my role model, e.g. gmail, personal search, talk etc.
2006-10-21
one piece of Song poetry
水调歌头
明月几时有，把酒问青天。不知天上宫阙，今夕是何年。我欲乘风归去, 又恐琼楼玉宇，高处不胜寒，起舞弄清影，何似在人间。
转朱阁，低绮户，照无眠。不应有恨，何事长向别时圆。人有悲欢离合，月有阴晴圆缺，此事古难全。但愿人长久，千里共婵娟。
When will the moon be clear and bright? With a cup of wine in my hand, I ask the blue sky. I don't know what season it would be in the heavens on this night. I'd like to ride the wind to fly home. Yet I fear the crystal and jade mansions are much too high and cold for me. Dancing with my moon-lit shadow, It does not seem like the human world.
The moon rounds the red mansion Stoops to silk-pad doors, Shines upon the sleepless. Bearing no grudge, Why does the moon tend to be full when people are apart? People may have sorrow or joy, be near or far apart,The moon may be dim or bright, wax or wane, This has been going on since the beginning of time. May we all be blessed with longevity Though far apart, we are still able to share the beauty of the moon together.
明月几时有，把酒问青天。不知天上宫阙，今夕是何年。我欲乘风归去, 又恐琼楼玉宇，高处不胜寒，起舞弄清影，何似在人间。
转朱阁，低绮户，照无眠。不应有恨，何事长向别时圆。人有悲欢离合，月有阴晴圆缺，此事古难全。但愿人长久，千里共婵娟。
When will the moon be clear and bright? With a cup of wine in my hand, I ask the blue sky. I don't know what season it would be in the heavens on this night. I'd like to ride the wind to fly home. Yet I fear the crystal and jade mansions are much too high and cold for me. Dancing with my moon-lit shadow, It does not seem like the human world.
The moon rounds the red mansion Stoops to silk-pad doors, Shines upon the sleepless. Bearing no grudge, Why does the moon tend to be full when people are apart? People may have sorrow or joy, be near or far apart,The moon may be dim or bright, wax or wane, This has been going on since the beginning of time. May we all be blessed with longevity Though far apart, we are still able to share the beauty of the moon together.
Structural basis for messenger RNA movement on the ribosome
Gulnara Yusupova1,2, Lasse Jenner1,2, Bernard Rees1, Dino Moras1 and Marat Yusupov1
Translation initiation is a major determinant of the overall expression level of a gene1, 2, 3. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits4, 5, 6, 7, 8, the empty 70S ribosome9 and the 70S ribosome containing functional ligands10, 11, 12, 13 have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine–Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.
resource
Translation initiation is a major determinant of the overall expression level of a gene1, 2, 3. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits4, 5, 6, 7, 8, the empty 70S ribosome9 and the 70S ribosome containing functional ligands10, 11, 12, 13 have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine–Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.
resource
2006-10-15
The Nobel Prize in Chemistry 2006
This year's Nobel Prize in Chemistry is awarded to Roger D. Kornberg for "for his studies of the molecular basis of eukaryotic transcription". His fundamental studies uncovered how the information stored in the genes is copied, and then transferred to those parts ofthe cells that produce proteins. Kornberg was the first to create an actual picture of this process at themolecular level, in the important group of organisms called eukaryotes (which, as opposed to bacteria,have well-defined cell nuclei). Mammals like ourselves, as well as ordinary yeast, belong to this groupof organisms.
Advanced information: http://nobelprize.org/nobel_prizes/chemistry/laureates/2006/chemadv06.pdf
Original scientific articles:
Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8ångstrom resolution. Science 292, 1863-1876.
Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: An RNApolymerase II elongation complex at 3.3 Å resolution. Science 292, 1876-1882.
Bushnell, D.A., Westover, K.D., Davis, R.E. and Kornberg, R.D. (2004) Structural basis of transcription: An RNApolymerase II – TFIIB cocrystal at 4.5 angstroms. Science 303, 983-988.
Review article:Boeger, H., Bushnell, D.A., Davis, R., Griesenbeck, J., Lorch, Y., Strattan, J.S., Westover, K.D. and Kornberg, R.D.(2005). Structural basis of eukaryotic gene transcription. FEBS Lett. 579, 899-903.
Link:Film of transcription: The Dolan DNA learning center – genes in education. http://www.dnalc.org/home.html.Media showcase; Transcription: DNA codes for mRNA, 3D animation.
Advanced information: http://nobelprize.org/nobel_prizes/chemistry/laureates/2006/chemadv06.pdf
Original scientific articles:
Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8ångstrom resolution. Science 292, 1863-1876.
Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: An RNApolymerase II elongation complex at 3.3 Å resolution. Science 292, 1876-1882.
Bushnell, D.A., Westover, K.D., Davis, R.E. and Kornberg, R.D. (2004) Structural basis of transcription: An RNApolymerase II – TFIIB cocrystal at 4.5 angstroms. Science 303, 983-988.
Review article:Boeger, H., Bushnell, D.A., Davis, R., Griesenbeck, J., Lorch, Y., Strattan, J.S., Westover, K.D. and Kornberg, R.D.(2005). Structural basis of eukaryotic gene transcription. FEBS Lett. 579, 899-903.
Link:Film of transcription: The Dolan DNA learning center – genes in education. http://www.dnalc.org/home.html.Media showcase; Transcription: DNA codes for mRNA, 3D animation.
2006-10-13
竟然从一篇发表在PNAS上的文章中挑出错误
I can't belive myself that I have found a mistake in a paper published in PNAS[ Proceedings of the National Academy of Sciences ] ! The following is the correspondent author's reply after I send a email to him:
Dear Qian,
Many thanks for your email - you are correct, we have mentioned the wrong diet in the text. We should have said the 19:33 diet not the 30:22 diet. Focus on the diamond symbols (both open and closed) and see how they shift to the left along the x-axis from generation 4-8. The square symbols (30:22) move down from generations 1-4 but not from 4 to 8. However, the general point is the same (the statistical test mentioned was based on all diets) - there is a decline in consumption which is unrelated to selection regime.Well spotted!Yours ever,Steve This indicates a decline in consumption of the 30:22 diet, but since the decline was similar for both selection regimes (high-carb and high-protein), it is unrelated to At 21:56 11/10/2006, you wrote:
Dear Prof. **,
I'm a graduate student majored in Plant protection from Nanjing Agricultural University, Nanjing, Jiangsu Province, PR of China. I apologize for my disturbing you, because when I read your paper "***" published in PNAS ,September 19, 2006 ** I find myself can't follow with you about the result of Shift in Lipid Deposition on Artificial Diet Regimes in the last two sentences--" In particular, there was a pronounced reduction from generation four to eight in the amount eaten of the P/C of 30:22 diet (Fig. 1 B vs.C). However, this pattern occurred in both selection regimes:hence, it apparently was unrelated to changes in lipid accumulation in response to dietary regime (interaction term regime by test diet: F4,60 = 2.16, P = 0.085; regime by generation by test diet: F8,60= 1.30, P= 0.261)."
I'm confused about the pronounced reduction: if it refers to the amount eaten of the P/C of 30:22 diet (Fig. 1 B vs.C), but there seems to be a slight increase of the high-protein selected regime (open square) inconsistent with the description; however, if it can be regarded as the pupal lipid content (intuitively from the figure 1C, dashed lines) there is also conflict with high-protein regime(solid line). Would you explain it to me in your convenient time? I will appreciate your reply and assistant!
Yours,
Qian,**
Dear Qian,
Many thanks for your email - you are correct, we have mentioned the wrong diet in the text. We should have said the 19:33 diet not the 30:22 diet. Focus on the diamond symbols (both open and closed) and see how they shift to the left along the x-axis from generation 4-8. The square symbols (30:22) move down from generations 1-4 but not from 4 to 8. However, the general point is the same (the statistical test mentioned was based on all diets) - there is a decline in consumption which is unrelated to selection regime.Well spotted!Yours ever,Steve This indicates a decline in consumption of the 30:22 diet, but since the decline was similar for both selection regimes (high-carb and high-protein), it is unrelated to At 21:56 11/10/2006, you wrote:
Dear Prof. **,
I'm a graduate student majored in Plant protection from Nanjing Agricultural University, Nanjing, Jiangsu Province, PR of China. I apologize for my disturbing you, because when I read your paper "***" published in PNAS ,September 19, 2006 ** I find myself can't follow with you about the result of Shift in Lipid Deposition on Artificial Diet Regimes in the last two sentences--" In particular, there was a pronounced reduction from generation four to eight in the amount eaten of the P/C of 30:22 diet (Fig. 1 B vs.C). However, this pattern occurred in both selection regimes:hence, it apparently was unrelated to changes in lipid accumulation in response to dietary regime (interaction term regime by test diet: F4,60 = 2.16, P = 0.085; regime by generation by test diet: F8,60= 1.30, P= 0.261)."
I'm confused about the pronounced reduction: if it refers to the amount eaten of the P/C of 30:22 diet (Fig. 1 B vs.C), but there seems to be a slight increase of the high-protein selected regime (open square) inconsistent with the description; however, if it can be regarded as the pupal lipid content (intuitively from the figure 1C, dashed lines) there is also conflict with high-protein regime(solid line). Would you explain it to me in your convenient time? I will appreciate your reply and assistant!
Yours,
Qian,**
2006-10-08
RNAi and microRNA/siRNA
RNAi wins the Nobel Prize!
We would like to extend our congratulations to Dr. Andrew Fire and Dr. Craig Mello for winning the Nobel Prize in Physiology for the discovery of RNA interference - gene silencing by couble-stranded RNA on Tuesday, October 03, 2006. Their work laid the ground work for what is now an exciting and vibrant area of RNA research.
To read their paper, please see: Fire A., Xu S.Q., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-811.
Advanced information:http://nobelprize.org/nobel_prizes/medicine/laureates/2006/adv.html
Further more, there are some resource online about RNA to share with you if you like!
The RNA World Website
Substantial collection of Web links to an array of RNA-related resources, from databases to tutorials; maintained by the Institute of Molecular Biotechnology, Jena.
RNA Interference and Gene Silencing: History and Overview
Brief survey of historical development of RNAi science, from Ambion Inc.
RNAi Information on the Web
A comprehensive list of papers, labs, and other resources focused on RNAi, provided by Orbigen, Inc.
RNA Webring
Collection of Web sites of molecular biology groups interested in various aspects of RNA.
Developmental Biology: RNAi
Interesting discussion of RNAi, on Web site developed to accompany textbook by S. F. Gilbert.
RNAi Database
Catalog of results from RNAi phenotypic analysis of C. elegans genes.
The siRNA User Guide
Protocols for siRNA preparation for Drosophila knockout experiments, and links to commercial sources for siRNAs.
The RNA Society
The RNA Society was formed in 1993 to facilitate sharing and dissemination of experimental results and emerging concepts in ribonucleic acid research. The Society encompasses RNA research in the broadest sense: from the ribosome to the spliceosome, from RNA viruses to catalytic RNAs. It is a multidisciplinary society, representing molecular, evolutionary and structural biology, biochemistry, biomedical sciences, chemistry, genetics, and virology as they relate to questions of the structure and function of RNA and of ribonucleoprotein assemblies.
some Labs link:
Robin Allshire (Wellcome Trust Center for Cell Biology)
Victor Ambros (Dartmouth Medical School)
David Bartel (MIT)
Martin A. Gorovsky (University of Rochester)
Ronald H. A. Plasterk (Hubrecht Laboratory)
Phil Sharp (MIT)
Thomas Tuschl (Max Planck Institute for Biophysical Chemistry)
Phillip D. Zamore (University of Massachusetts Medical School)
We would like to extend our congratulations to Dr. Andrew Fire and Dr. Craig Mello for winning the Nobel Prize in Physiology for the discovery of RNA interference - gene silencing by couble-stranded RNA on Tuesday, October 03, 2006. Their work laid the ground work for what is now an exciting and vibrant area of RNA research.
To read their paper, please see: Fire A., Xu S.Q., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-811.
Advanced information:http://nobelprize.org/nobel_prizes/medicine/laureates/2006/adv.html
Further more, there are some resource online about RNA to share with you if you like!
The RNA World Website
Substantial collection of Web links to an array of RNA-related resources, from databases to tutorials; maintained by the Institute of Molecular Biotechnology, Jena.
RNA Interference and Gene Silencing: History and Overview
Brief survey of historical development of RNAi science, from Ambion Inc.
RNAi Information on the Web
A comprehensive list of papers, labs, and other resources focused on RNAi, provided by Orbigen, Inc.
RNA Webring
Collection of Web sites of molecular biology groups interested in various aspects of RNA.
Developmental Biology: RNAi
Interesting discussion of RNAi, on Web site developed to accompany textbook by S. F. Gilbert.
RNAi Database
Catalog of results from RNAi phenotypic analysis of C. elegans genes.
The siRNA User Guide
Protocols for siRNA preparation for Drosophila knockout experiments, and links to commercial sources for siRNAs.
The RNA Society
The RNA Society was formed in 1993 to facilitate sharing and dissemination of experimental results and emerging concepts in ribonucleic acid research. The Society encompasses RNA research in the broadest sense: from the ribosome to the spliceosome, from RNA viruses to catalytic RNAs. It is a multidisciplinary society, representing molecular, evolutionary and structural biology, biochemistry, biomedical sciences, chemistry, genetics, and virology as they relate to questions of the structure and function of RNA and of ribonucleoprotein assemblies.
some Labs link:
Robin Allshire (Wellcome Trust Center for Cell Biology)
Victor Ambros (Dartmouth Medical School)
David Bartel (MIT)
Martin A. Gorovsky (University of Rochester)
Ronald H. A. Plasterk (Hubrecht Laboratory)
Phil Sharp (MIT)
Thomas Tuschl (Max Planck Institute for Biophysical Chemistry)
Phillip D. Zamore (University of Massachusetts Medical School)
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