Category Archives: 学习工作 Work & Learn

试图记录学习和工作。

Nature: 最流行的科学博客

Nature 442, 9(6 July 2006) | doi:10.1038/442009a; Published online 5 July 2006

Nature援引Technorati,于正刊报道了排名所有Blog前3500的科学家Blog。

179th

http://scienceblogs.com/pharyngula

1,647th

http://www.pandasthumb.org

1,884th

http://www.realclimate.org

2,174th

http://cosmicvariance.com

3,429th

http://scienceblogs.com/scientificactivist

这些Blog的具体介绍,请访问Nature

科研需要钱来堆

最新一期Science上发表了文章《Metagenomic Analysis of the Human Distal Gut Microbiome》,文章采样两个健康人体排泄物内的细菌,进行了相当于environmental环境测序的研究。如下面引用,他们一共获取了接近140,000(十四万)高质量测序读取结果,获取了接近80,000,000bp(八千万碱基对)的序列,平均每个read有570bp。相当于仅仅是高质量的测序反应,就有至少十四万个。如果一次测序成本为3美元,单就测序反应成本就有四十多万美元以上,如果有一半的反应是低质量的测序结果,成本随即提高一倍。

A total of 65,059 and 74,462 high-quality sequence reads were generated from random DNA libraries created with fecal specimens of two healthy humans (subjects 7 and 8). These two subjects, ages 28 and 37, female and male, respectively, had not used antibiotics or any other medications during the year before specimen collection (11). The combined sequenced distal gut “microbiome” of subjects 7 and 8 consisted of 17,668 contigs that assembled into 14,572 scaffolds, totaling 33,753,108 bp. The scaffolds ranged in size from 1000 to 57,894 bp and the contigs from 92 to 44,747 bp. The average depth of sequence coverage in contigs was 2.13-fold. Forty percent of the reads (56,292 total) could not be assembled into contigs, most likely because of a combination of low depth of coverage and low abundance of some organisms within the specimens. Together, these singletons accounted for an additional 45,078,063 bp of DNA.

文章最后说,需要进行更多的研究,采样更多的微生物种类,不同年龄、饮食、疾病状态、不同环境,以及间隔不同的时间。这片文章基本上也就采了两个样,花掉了很多钱。如果采样要如此丰富,需要多少钱呢?不过文章表示,这项研究很有意义,基本上对于人类健康有方方面面的好处,这也是为什么只要和人有关的研究,经费总是比较容易拿的:

The results should provide a broader view of human biology, including new biomarkers for defining our health; new ways for optimizing our personal nutrition; new ways for predicting the bioavailability of orally administered drugs; and new ways to forecast our individual and societal predispositions to disorders such as infections with pathogens, obesity, and misdirected or maladapted host immune responses of the gut.

金山词霸可以用来学英语?

刚才上了一下金山词霸在线辞典的网站,看到有一个每日一句,说的是“I am broke.”后面接着的翻译是“我身无分文。”

这样的翻译不仅不地道,更是不准确的。I am broke虽然不是说我已经破产,但是并非等同于我身无分文。美国人常常在别人邀请你出去玩,但是你没有足够的钱来afford这个开支的时候说I am broke。总之,是没有足够的钱来afford一样东西、一件事情的时候,说I am broke。但是此时身上并非绝对没有钱,只是消费不起而已。中文“我身无分文”则是直接的没有一分钱。我身上常常也不带钱,那么我是不是随时都可以说,I am broke呢?

金山词霸,可以用来学英语吗?

New Building in VaTech to be Named Latham Hall

William and Elizabeth Latham decided to give $5 million to Virginia Tech to support research in agricultural and life sciences. The Board of Visitors at Virginia Tech decided to name the new building which our lab is moving to as the William C. and Elizabeth H. Latham Agriculture and Natural Resources Building.

Although this building is smaller and narrower than previously planned, it is said that this building is going to be the hub of plant science research that will enhance research productivity, aid in recruitment of and retention of world-class faculty, and provide a beneficial environment to train a future workforce in agriculture and other life sciences.

Virginia Tech is ranked 11th in agricultural research expenditures by the National Science Foundation.

However, funding for agricultural research is much less than other life sciences such as human disease related field.

看到牛人才会感觉到差距才会奋斗

昨天去听了一个UC Berkeley来的Associate Prof.的Seminar,内容相当精彩和有启发性。

他们的思路其实不复杂却很少有人这样去想,而且需要有人手和有很专业的技能的人来实现。这也是为什么国内生物水平那么低的原因啊。国内不仅没有思路,也没有人才。

这位教授口齿伶俐,思路清晰,说话速度非常之快,确实可以感觉到他对自己的领域了如指掌,并且大脑运行速度非常之块,确实让我倍感压力和差距。

但是话说回来,看到牛人才会感觉到差距才会奋斗。

对生命,宇宙和一切的答案是42

Google计算器是这样认为的

银河系漫游指南是这样说的。

现在连一个不知道是谁的科学家也是这样说的。

为什么是42?没有看懂。随便理解一下,似乎是质数是数学里面最神秘的数字。有两个科学家作出了一个公式来预测质数;按理说质数看起来是完全随机没有规律的;这个公式似乎又可以给出一个怎么样的数字序列。这个序列的前三个数字是:1, 2, 42。

Research competition

We have competition everywhere. Research is not an exception.

So we know who are doing similar researches as we do. And we are curious what they are doing. They will sure be interested what we are doing as well. In this case, it would be very interesting when we meet at a conference in May. Lots of cool people will be there, we will be able to see many posters, and of course, Arizona!

And yes. If it is a huge project, who made it first get to publish in the very best journal.

Unix power of Mac OS X: Backup

Our lab has three Macs. One 20-inch iMac G5, one 17-inch iMac G5 and a Mac mini. There was a PowerMac G4 but it is not serving for many people downstairs. Because our lab work rely heavily on computer: we create Excel worksheet to help us calculate reaction formula easily and then keep record of our every PCR reaction(in silicon and print out as hard copy), we store digital pictures of the plants, bacteria and such, we need to use computer to calculate phylogenetic tree, use Lasergene to do DNA operation etc., so we really need to make sure our data is safe.

Before I came to this lab, they were copying files manually through Apple Personal File Share from 17-inch and Mac mini to 20-inch. And then manually copy files to an Firewire external hard drive from the 20-inch iMac. I set up the 20-inch to copy the files automaticly to external hard drive soon after I came to my current lab by using Automator. However, it is not very good doing it that way, because 1). People forget to copy files from 17-inch and Mac mini. 2). 10Mb ethernet is not fast enough for copying files of over 3 GB. 3).Every time it takes a long time to copy everything through Firewire to external hard drive. 4). Copying folder and override in Mac OS X will override everything, so if you accidently delete something here, and you automatically back up files everyday by copying and overriding folders, you end up actually losing files.

So later I think I should try something else. Because Mac OS X is a Unix system, we can run rsync. One good thing is Mac OS X has SSH and rsync built in. So I think the best way to back up all the files on the three computers is to use rsync over SSH to have one copy on 20-inch and on the external hard drive. Good thing about this method: 1). The back up will be incremental, so every time it will take very short time to back up because the computer will only copy new and changed files. 2). Everything about back up can be done automactically, people in my lab are freed. 3). This way of back up will never delete file by overriding folders.

It is not that difficult to set this up. I just met some problem making SSH connection between these computers password free. By using public signature, it is possible you can SSH connect two computers without entering password, and this is neccessary for automatic connection and rsync.

Now everything is running almost perfectly. These computers will sync files every work day at a given time. And that’s actually easy to set up as long as you know a little bit things about Automator, rsync, and CLI. Also, Lingo is a very useful software that helps you take advantage of Launchd.

一身猪的味道过22岁生日

一个下午都在教本科生解剖猪。那些都是用防腐剂保存的接近出生的猪。恩……现在我觉得我一身都是猪的味道了!不过为了庆祝22岁生日,在学校里面一家店子买了一块pizza,一碗spaghetti,花掉接近9美元,奢侈一把。哪个spaghetti里面的cheeze哪个丝拉的才是小资。可惜味道淡了点,桌子上居然没有盐,吃多了颇有要吐的感觉。反正是吃不玩的,够两个人吃了。吃完之后呢,去研究生生活中心一家店里面喝杯咖啡吧。说来我还没有在美国单独喝过咖啡呢。本来说去星巴克,可惜哪个地方前不着村后不着店的,一直都没有去。想想花了9块钱吃晚饭,咖啡就来杯简单的normal的吧……说拿中杯也是好大一杯……

喝着咖啡,就来写blog。写完blog,还要去实验室跑我10小时的PCR。就等着回家去洗掉我的猪味了!

Virginia Tech: Invent the Future

VT, invent the futureVirginia Tech is now launching a new brand campain called Invent the Future. With the updated logo, Virginia Tech is now trying to advertise itself to the public with a slightly new look’n’feel, especially a new trademarked tagline “Invent the Future.”

Besides that, Virginia Tech is now going to start its own Podcast. One is Distinguished Professors. And starting Feb. 6th, we will also have HokieCast, VT Pod News and A Touch of Tech.

Nematode 线虫的电镜照片

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Nematode, again this week. I have to look at them in lectures, still pictures and animations, dealing with them alive in the lab. These two pictures are nematodes’ head and mouth. The color is artificial. I might even post some animations later 🙂 I personally quite like the predator type of the nematodes. They way they feed on other namatodes are just… gross, cruel and amazing. One thing you should know is that human only have twice the number of genes than these worms, which don’t even have brain and eyes.

The worms in many scary and gross Sci-fi movies are not completed fictioned.

第一次真的当老师了。

说实话,我觉得自己也不比这些本科生强。我不也就是本科才毕业吗?出来真的对人是一种锻炼。从开始申请到现在,以及在未来,都是锻炼,都是在国内无法接受到的锻炼。所以从这方面看来,国内现在流行看不起海龟。但是一个真的海龟,确实是经受了呆在国内的人无法理解的锻炼的。海龟的水平,不管怎么说,也应该是有一个基础在那里(锻炼出来的)。

第一节课是很失败的。课堂的秩序没有很好的维持。不是纪律,是秩序。同时个人也没有能够把实验怎么做说得很清楚,导致不少学生犯了错误。第二节课就好多了。第一节课将一些文字知识也是把我折腾得。

教学还是一个很有趣的事情,明天去看看Native speaker的课的状况,然后总结自己的缺陷,以及学生方面的问题。

今天做线虫!从土壤里面提取大量线虫!

Nematode.

我们学植物病理的,当然就是多学科交叉的。虽然我做的研究和线虫倒是没有什么关系,但是长远来看,细菌、真菌、病毒、线虫这些都是要学的。好处还是有的。这样知识面可能还是比较全。

我们使用一种机器在土壤里面把线虫洗出来,沉淀出来,再用蔗糖溶液离心让它们浮出来。土壤里面是有很多线虫的,线虫带来的植物病害所造成的损失是很可怕的。美国70年代以前,完全没有意识到线虫的危害。之后对线虫的研究才被重视起来。而且研究动物发育当然也是有用线虫作为模式生物。我们本周要做5片标本。汗……

Every time I handle EtBr I feel headache

I think I am having some kind of psycological problems with EtBr. Every time I handle them, like the gel, I kind of worry too much, or I am just being really careful. And this might have some intense effects on my nerves. Usually after the work I feel headache. Kind of like when I was too nervous or under a lot of pressure. I don’t know what to do. Maybe I just need to get used to it. But I have being working with it for a long time by now.

EtBr does not cause headache and I am sure I am not contaiminated. EtBr causes cancer and tumor instead of headache.