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
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