augix.com | 里昂印象

Posted by 西瓜 at 10:49 AM | Comments (0)

xigua
10:56 AM

有一些朋友似乎比较关心我是哪里人。临平？

我81年（国庆节）出生在海宁许巷许村一个很普通的农民家庭，大概在我三四岁的时候，爷爷因为肺炎去世，而奶奶只能靠在邻近的镇上（临平镇）卖花生获得一些收入。为了维持这个家，还有帮老爸的两个弟弟成家，老爸老妈带着我来临平做生意。

开始很苦，老妈在镇上摆个水果摊，因为没有执照，经常会有工商所的人来抓。记得老妈说过，有一次在”西洋桥“那里卖水果，突然看到工商所的人过来，旁边的小摊贩都跑了，老妈也跑，可是她跑不动，只好一屁股坐在地上，因为当时我弟弟在老妈肚子里已经好几个月了……

老爸从来没有说过那段时间的辛苦……

老妈摆水果摊的同时，老爸卖香烟，老爸的香烟生意越做越大，成了改革开发后的第一批“万元户”，后来老爸又被请去供销社，业务越来越多，他也跑遍了全国各地。

这样一晃十几年，我就已经在临平读了小学，读了中学。

到高中毕业为止，我一直呆在临平。考大学的时候，老妈希望我考得近一点，可以经常回家。我确实考得很近，浙大，而且还是华家池校区，回家也就40来分钟的公交车时间，但是我回家的次数很少，也许是男孩子都这样吧，我喜欢在外面。

（最近忙的事情很多，没有机会写更多东西，我也不善于表达自己的情感，这是西瓜的感恩第一篇，里面还有很多故事，以后再说。）

Posted by 西瓜 at 10:56 AM | Comments (0)

今天我的朋友Leylop踏上了去西藏的旅途。

昨晚，她在她的blog上这样写道：
I am reading a Tibet guidebook tonight, the landscapes there are so fascinating, and the temples are just awesome. I always envy people who have been there, but not anymore-- I'll be there in a few days!

Bought the air ticket to Chengdu today (2.5 hours by plane, 43hours by train), I'll leave Hangzhou tomorrow, and I'll do it alone. Since I've got some unpleasant experience of traveling with groups, I'll leave them this time. And still couldn't find any travel partner, some say they're busy, some say these areas are too remote and dangerous, and some say the trip costs too much... I don't have much money either; I'll take all I have, probably still not enough, but I think I could save some money by staying in cheap hotels, eating street food as main meals or something... And I'm fine with traveling alone too. At least I'm totally free, which might be the best way to experience the real feeling of travel.

As for travel plan, I'lll go to Sichuan province first, visiting Chengdu, JiuZhaiGou, Huanglong Scenic Area , Emei Mountain and Giant Buddha of Leshan . And then move to Tibet area. Not sure how long the trip takes, more than two weeks I guess. If I still have some money left after finishing Sichuan and Tibet trip, I’ll go to more places. If not, I’ll go home by train. Never been on a train for more than 3 hours, it'd be interesting to be sitting in one seat for two days and two nights.

I probably couldn't update my blog for a while, I'm sure I’ll miss it a lot. But I think I can bring lots of pictures when getting back, and write about my travel stories.

See you in two weeks

从刚认识她那会儿开始，我一直很佩服这个女孩子。我常常对别人说做人应该率性而为，自己却经常做不到，倒是这个女孩子让我真正感受到什么叫率性而为。西藏，我也特别想去，但怎么也下不了决心，而她不同，想去就去，而且还是单枪匹马。我祝她一路顺风。

下面是她在网上的两张照片。
高中时的她

她特别喜欢西瓜

Posted by 西瓜 at 08:47 PM | Comments (0)

xigua
21:01 PM

What Are ESTs and How Are They Made?

ESTs are small pieces of DNA sequence (usually 200 to 500 nucleotides long) that are generated by sequencing either one or both ends of an expressed gene. The idea is to sequence bits of DNA that represent genes expressed in certain cells, tissues, or organs from different organisms and use these "tags" to fish a gene out of a portion of chromosomal DNA by matching base pairs. The challenge associated with identifying genes from genomic sequences varies among organisms and is dependent upon genome size as well as the presence or absence of introns, the intervening DNA sequences interrupting the protein coding sequence of a gene.


Separating the Wheat from the Chaff: Using mRNA to Generate cDNA

Gene identification is very difficult in humans, because most of our genome is composed of introns interspersed with a relative few DNA coding sequences, or genes. These genes are expressed as proteins, a complex process comprised of two main two steps. Each gene (DNA) must be converted, or transcribed, into messenger RNA (mRNA), RNA that serves as a template for protein synthesis. The resulting mRNA then guides the synthesis of a protein through a process called translation. Interestingly, mRNAs in a cell do not contain sequences from the regions between genes, nor from the non-coding introns that are present within many genes. Therefore, isolating mRNA is key to finding expressed genes in the vast expanse of the human genome.

Figure 1. An overview of the process of protein synthesis.
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Protein synthesis is the process whereby DNA codes for the production of amino acids and proteins. The process is divided into two parts: transcription and translation. During transcription, one strand of a DNA double helix is used as a template by mRNA polymerase to synthesize a mRNA. During this step, mRNA passes through various phases, including one called splicing, where the non-coding sequences are eliminated. In the next step, translation, the mRNA guides the synthesis of the protein by adding amino acids,one by one, as dictated by the DNA and represented by the mRNA.
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The problem, however, is that mRNA is very unstable outside of a cell; therefore, scientists use special enzymes to convert it to complementary DNA (cDNA). cDNA is a much more stable compound and, importantly, because it was generated from a mRNA in which the introns had been removed, cDNA represents only expressed DNA sequence.

From cDNAs to ESTs

Once cDNA representing an expressed gene has been isolated, scientists can then sequence a few hundred nucleotides from either end of the molecule to create two different kinds of ESTs. Sequencing only the beginning portion of the cDNA produces what is called a 5' EST. A 5' EST is obtained from the portion of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. Sequencing the ending portion of the cDNA molecule produces what is called a 3' EST. Because these ESTs are generated from the 3' end of a transcript, they are likely to fall within non-coding, or untranslated regions (UTRs), and therefore tend to exhibit less cross-species conservation than do coding sequences.

Figure 2. An overview of how ESTs are generated.
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ESTs are generated by sequencing cDNA, which itself is synthesized from the mRNA molecules in a cell. The mRNA in a cell are copies of the genes that are being expressed. mRNA does not contain sequences from the regions between genes, nor from the non-coding introns that are present within many interesting parts of the genome.
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REFERENCES

http://www.ncbi.nlm.nih.gov/About/primer/est.html

Posted by 西瓜 at 09:01 PM | Comments (0)

Nucleotide base codes (IUPAC)

Authority Nomenclature Committee of the International Union of Biochemistry
Reference Cornish-Bowden, A. Nucl Acid Res 13, 3021-3030 (1985)
Contact EMBL
Scope Location descriptors, /codon

Listing

Symbol Meaning
------ -------

a a; adenine
c c; cytosine
g g; guanine
t t; thymine in DNA; uracil in RNA
m a or c
r a or g
w a or t
s c or g
y c or t
k g or t
v a or c or g; not t
h a or c or t; not g
d a or g or t; not c
b c or g or t; not a
n a or c or g or t

Amino acid abbreviations

Authority IUPAC-IUB Joint Commission on Biochemical Nomenclature.
Reference IUPAC-IUB JOint Commission on Biochemical Nomenclature.
Nomenclature and Symbolism for Amino Acids and Peptides.
Eur. J. Biochem. 138:9-37(1984).
Scope /anticodon, /codon, /transl_except
Contact EMBL
Listing (note that the abbreviations are legal values for amino acids, not the full names)

Abbreviation Amino acid name
------------ ---------------

Ala A Alanine
Arg R Arginine
Asn N Asparagine
Asp D Aspartic acid (Aspartate)
Cys C Cysteine
Gln Q Glutamine
Glu E Glutamic acid (Glutamate)
Gly G Glycine
His H Histidine
Ile I Isoleucine
Leu L Leucine
Lys K Lysine
Met M Methionine
Phe F Phenylalanine
Pro P Proline
Ser S Serine
Thr T Threonine
Trp W Tryptophan
Tyr Y Tyrosine
Val V Valine
Asx B Aspartic acid or Asparagine
Glx Z Glutamine or Glutamic acid.
Xaa X Any amino acid.
TERM termination codon

Biosino数据库(核酸)简单使用手册

Posted by 西瓜 at 04:06 PM | Comments (0)

黄龙体育中心外

场内

Posted by 西瓜 at 08:29 PM | Comments (0)

xigua
20:17 PM

::::人类基因组计划的完成::::

基因组(genome), 由英文 “基因(gene)”和“全部”得来, 已成为21世纪每个人的日常熟语. 2002年2月12日, 历时10载耗资20亿美元的人类基因组计划最终完成, 并报道了99% 的人类基因组序列. 世纪初基本完成的这项工作堪与阿姆斯特朗和奥尔德林乘坐阿波罗11号宇宙飞船登月相媲美. 从这时起, 生物学被重新划分为前基因组和后基因组两部分, 我们正生活在后基因组时代.

DNA 由包含遗传信息的基因组构成. 四种碱基 A,T, G 和 C 组装成线性高分子, A-T, C-G 配对结合形成螺旋, 从而构成 DNA 链. 正如计算机系统采用二进制那样, DNA采用4进制储存信息. 遗传信息指导蛋白质的合成, 于是子代遗传了蛋白质的组成并产生了生理活性. 因此, 一旦我们已知了一个物种的DNA序列, 我们就可以推断它可以产生的所有蛋白质, 从而理论推测这个物种的所有生物特征. 有关蛋白质的遗传信息的单位称作基因, 一个生物的所有基因称作基因组. 由此创立了一个新兴的学科来研究基因组, 即基因组学(Genomics).

DNA 及 染色体结构

U.S. Department of Energy Human Genome Program

来自法国，德国，日本，中国等六国的科学家自1990年组成了一个多国合作小组 开展人类DNA测序工作以揭开人类基因组之谜. 最初他们希望2005年前能够获得人类DNA序列的图谱, 但是到1997年, 在耗费了巨额资金和一半预定时间之后，多国合作小组仅完成了3%的测序工作. 与此同时, 遗传生物学家Craig Venter博士, 创立了一个名为“Celera Genomics”的风险投资公司并宣称他将在无政府投资条件下早于多国合作小组完成人类基因组计划. 尽管很多科学家表示怀疑, Celera采用了如“散弹枪”等一系列新的方法并很快真的追上了多国合作小组. 看到自己即将失利, 多国合作小组在Clinton总统的撮合下开始与Celera合作, 在2000年6月完成了90%, 2001年初完成了99%的人类基因组草图. 有意思的是多国合作小组在英国的自然（Nature)上而Celera在美国的科学（Science)上各自独立的在同一周发表论文, 在2001年2月12日的记者招待会上联合宣布人类基因组测序工作的完成. 也许是出于政治原因,两大权威科学杂志均在没有100%检验并证实结论的情况下刊登了他们的论文, 而且两个小组由于竞争关于统一课题的成果都没有做足够的方差检验. 事实上他们的成果中大概有0.14%(大约400万碱基对)序列差异, 还需更完整的检验.

转载自: http://www.nyu.edu/classes/ytchang/book/c001.html
参考文献: http://www.chemmate.com/news/n2.htm
基因组学在线辞典: http://www.genomicglossaries.com/

Posted by 西瓜 at 08:17 PM | Comments (0)

xigua
11:10 AM

昨天开同学会，一句话：happy 啊！

Posted by 西瓜 at 11:10 AM | Comments (0)

xigua
18:36 PM

中心大楼4楼有个小机房，是浙江大学生物信息研究所（IBI-ZJU）存放工作站的地方，这里有8台DELL Workstation，都是超爽的电脑，双CPU,1.7GHz，1G的内存，运行程序狂快。特别是他的键盘，敲上去超舒服，打字狂轻松狂快，我都不想用别的键盘了。最近机房里一个人都没有，几个师兄都有了去处，上任管理员zhongxian去了医学院读博，现在就我在这里玩，吹了一天的空调，感冒了。

Posted by 西瓜 at 06:36 PM | Comments (0)

Posted by 西瓜 at 03:16 PM | Comments (0)

xigua
13:29 PM

被召回实验室,今天下午有一个程序要写,还有一堆数据要做GC content.好,马上开工,早点完成早点回临平.

Posted by 西瓜 at 01:29 PM | Comments (0)

xigua
21:02 PM

这几天充当通讯员组织开同学会，在网上张贴集体照，在上面一个一个“通缉”过来，感觉不错哦

Posted by 西瓜 at 09:02 PM | Comments (0)

xigua
02:02 AM

我要祝福每一个看我的blog的朋友幸福快乐。而且来的次数越多越快乐。嘿嘿
想说点什么就留言吧，什么话题都可以。

Posted by 西瓜 at 02:02 AM | Comments (0)

xigua
00:29 AM

今天在中心大楼碰到了Dotti(一直没有问他是不是这样拼写的),他是一个有趣的印度人,在这里读博士后.

第一次遇到他是上学期的一个晚上,我一个人在实验室写程序到很晚,就想回寝室去睡觉.我没有像往常那样直接去坐电梯,而是先走到四楼,然后去电梯,Dotti这个时候也从实验室出来,跟我进了电梯.他说:"Hello, what's your name?"这句话我听懂了,我说:"Michael".之后我们的对话就保持在一个他说两三遍我回一句的状态下,因为他的英语饶舌得很厉害,还有主要原因是我口语烂啦.

但是我们还都能理解对方的意思.我们走出中心大楼,去了他在留学生楼的房间聊了一会儿,谈些很平常的东西.他说早上起来的时候会绕华家池跑一圈,但是我觉得早锻炼是不科学的,因为人早上起床后的血压偏高,激素水平也高,其实是不适宜锻炼,而且如果是在天刚亮的时候的话,空气也不好,因为植物才刚刚开始光合作用.但是他说,他这样可以free mind.那我就没有再反对了.

我问他平时在哪里吃饭,喜欢吃些什么.他告诉我他从来都只吃蔬菜,我很吃惊,我还是第一次遇到一个素食主义者,之前我也遇到过一个印度人,他说他晚上9点吃饭(也许是时差的缘故),他会给自己煮一点鸡蛋.但是Dotti不吃egg,他并不承认自己是素食主义者,他只是不吃肉,而且也不喝牛奶,只吃水果,也许只是习惯.不过,有一点可以肯定,这样的饮食习惯是很健康的,他的好气色就是一个证明,当然他也根本没有肥胖的问题.

Posted by 西瓜 at 12:29 AM | Comments (0)

xigua
21:35 PM

今天最高温度37度,到目前为止是今年最热的一天了.上午在种子楼做实验,内容是感受态细胞的制备,另外也把昨天PCR扩增来的DNA片段接种到了E.coli里面.

下午去了延安路上的中国银行省总行,幸好我作出了明智的选择——坐K21路去,如果我是骑自行车去的话,回来肯定和小黑(班长)一个肤色了,因为今天在杭州大马路上骑车无异于铁板烧.我去中国银行是为了兑现那张支票,刚进了大厅,问了大厅经理,她让我做在她的办公桌前,沙发挺舒服的,她单独给我处理,让我有种大户的感觉.结果让我在好几张单子上面签了4,5个名,另外还收了我30块钱的手续费,可就是不给我钱,说还要25天以后来取.这什么效率嘛!

晚上把席子拖到了实验室,今天就在这里过夜了,寝室里实在热得呆不下去.实验室有空调,我现在好爽啊,爽得要感冒了,嘿嘿

Posted by 西瓜 at 09:35 PM | Comments (0)

xigua
20:09 PM

今天去实验室，一进门，师兄说明天去池畔苑搓一顿。我还以为他要请客。原来我的挑战杯项目批下来了，这回又有一笔科研经费可以拿，虽然只有1200元。不过嘛，搓个四五顿是没有问题。我的项目名是利用基因组序列分析植物基因启动信号。

Posted by 西瓜 at 08:09 PM | Comments (0)

xigua
18:29 PM

刚刚收到ETS还我的60美元，它是以支票的形式从Princeton,NJ寄来的，我现在还不知道去哪儿兑现。明天去找个银行问问。

Posted by 西瓜 at 06:29 PM | Comments (0)