S*****P
发帖数: 323 | 1 http://news.sciencemag.org/scienceinsider/2011/06/sequence-yiel
DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli outbreak
by Martin Enserink on 2 June 2011, 5:50 PM |
Just from the high number of deaths and severe cases, scientists and public
health experts battling Germany's massive E. coli outbreak knew they were up
against something unusual. Now, early results from sequencing projects of
the enterohemorrhagic Escherichia coli (EHEC) strain appear to confirm that
a never-before-seen hybrid, combining the worst of several bacterial strains
, is causing the havoc.
The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
announced that it has sequenced the microbe's entire 5.2-million-base-pair
genome—says that its acquisition of several virulence genes make this EHEC
strain "supertoxic."
The outbreak, which has caused mayhem in European trade relations, is still
growing; so far, more than 16 patients have died. The origin of the microbe
remains a riddle; cucumbers from Spain, originally fingered as the potential
source, were acquitted on Tuesday and have not been replaced by other
suspects. All researchers know is that raw vegetables are the most likely
carrier.
Scientific results announced in two press releases today—both also intended
to tout the extraordinary speed of today's sequencing technology—suggest
that within the microbe's DNA lie clues to its aggressive nature.
The second came from Life Technologies Corporation, which manufactures so-
called third-generation sequencing machines. Today, the company announced
that sequencing at its lab in Darmstadt, Germany, in collaboration with the
nearby University of Münster, "strongly suggests that the bacterium … is a
new hybrid type of pathogenic E. coli strains." Spokespeople for the
company in the United States and Germany could not provide details today. "
Further analyses on Ion PGMT"—the company's flagship sequencing machine—"
will confirm [the] data," the press release promised.
BGI, meanwhile, says that the microbe's genome—which it says took just 3
days to sequence, also using Life Technologies equipment—reveals that it
shares 93% of its sequence with EAEC 55989 E. coli, a strain isolated in the
Central African Republic and known to cause serious diarrhea. It appears to
have acquired several genes that make it more pathogenic, however, probably
in a process called horizontal gene transfer, by which microbes exchange
bits of genetic information.
In an e-mail to ScienceInsider, Yang Bicheng, director of BGI's marketing
department, wrote that one gene fragment appears to have come from another
food-borne pathogen, Salmonella enterica, while other genes are highly
homologous to those found in other, phylogenetically distinct E. coli
strains, including a strain called O25:H4-ST131.
BGI, which has made the sequence available for researchers to download, says
the analysis also confirmed that the microbe is resistant to many
antibiotics. These include aminoglycoside, the macrolides, and the beta-
lactams—"all of which makes antibiotic treatment extremely difficult,"
according to the press release. However, German EHEC patients aren't treated
with antibiotics; most scientists believe they make matters worse, because
killing EHEC results in the release of more toxin.
Yang acknowledged that finding the resistance genes may not be clinically
relevant, but says they may help understand how the strain arose. "The
evolutionary process … of this very strange hybrid strain may be a very
interesting scientific story," Yang wrote in his e-mail.
Microbial genomicist Frederick Blattner of the University of Wisconsin,
Madison—who worked for almost 15 years to sequence the first E. coli strain
and finished in 1997—says the results have to be considered preliminary;
it's not clear whether BGI assembled the entire genome from its sequenced
pieces, he notes, and usually in such efforts, a number of stretches need to
be resequenced. Still, "they did this at an amazing speed, and it looks
like they found some very intriguing information," Blattner says. |
K******S
发帖数: 10109 | 2 indeed,
public
up
that
strains
【在 S*****P 的大作中提到】
: http://news.sciencemag.org/scienceinsider/2011/06/sequence-yiel
: DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli outbreak
: by Martin Enserink on 2 June 2011, 5:50 PM |
: Just from the high number of deaths and severe cases, scientists and public
: health experts battling Germany's massive E. coli outbreak knew they were up
: against something unusual. Now, early results from sequencing projects of
: the enterohemorrhagic Escherichia coli (EHEC) strain appear to confirm that
: a never-before-seen hybrid, combining the worst of several bacterial strains
: , is causing the havoc.
: The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
|
I*****y
发帖数: 6402 | 3 牛，中国有钱了
public
up
that
strains
【在 S*****P 的大作中提到】
: http://news.sciencemag.org/scienceinsider/2011/06/sequence-yiel
: DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli outbreak
: by Martin Enserink on 2 June 2011, 5:50 PM |
: Just from the high number of deaths and severe cases, scientists and public
: health experts battling Germany's massive E. coli outbreak knew they were up
: against something unusual. Now, early results from sequencing projects of
: the enterohemorrhagic Escherichia coli (EHEC) strain appear to confirm that
: a never-before-seen hybrid, combining the worst of several bacterial strains
: , is causing the havoc.
: The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
|
K******S
发帖数: 10109 | 4 And this case can usually generate a pretty high impact paper.
【在 I*****y 的大作中提到】
: 牛，中国有钱了
:
: public
: up
: that
: strains
|
W*****o
发帖数: 1780 | 5 真的很牛。而且口碑不错。我觉得BGI很可能会成为中国生物领域、甚至整个科研领域
赶超世界一流的一个突破口。 |
m***T
发帖数: 11058 | 6 军功章也有我的一半。
我一个月前刚培训的他们，一个月后居然有成果了，不错。不得不说，这些孩子挺拼的
。当然人家老大也挺会做市场、吸引眼球的。 |
z*t
发帖数: 863 | 7 当年写文章批评杨焕明只会忽悠，远远不如蒲慕明的人今天作何感想？
public
up
that
strains
【在 S*****P 的大作中提到】
: http://news.sciencemag.org/scienceinsider/2011/06/sequence-yiel
: DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli outbreak
: by Martin Enserink on 2 June 2011, 5:50 PM |
: Just from the high number of deaths and severe cases, scientists and public
: health experts battling Germany's massive E. coli outbreak knew they were up
: against something unusual. Now, early results from sequencing projects of
: the enterohemorrhagic Escherichia coli (EHEC) strain appear to confirm that
: a never-before-seen hybrid, combining the worst of several bacterial strains
: , is causing the havoc.
: The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
|
z*t
发帖数: 863 | 8 niu!他们需要神马培训啊？
【在 m***T 的大作中提到】
: 军功章也有我的一半。
: 我一个月前刚培训的他们，一个月后居然有成果了，不错。不得不说，这些孩子挺拼的
: 。当然人家老大也挺会做市场、吸引眼球的。
|
m***T
发帖数: 11058 | 9 Ion Torrent呀
【在 z*t 的大作中提到】
: niu!他们需要神马培训啊？
|
m***T
发帖数: 11058 | 10 杨早已经跟华大没关系了吧
【在 z*t 的大作中提到】
: 当年写文章批评杨焕明只会忽悠，远远不如蒲慕明的人今天作何感想？
:
: public
: up
: that
: strains
|
|
|
z*t
发帖数: 863 | 11 前几天还看到不靠谱的pacbio也在招深圳实习生。。。现在华大手段好丰富
【在 m***T 的大作中提到】
: Ion Torrent呀
|
w******y
发帖数: 8040 | 12 和杨有个P关系， 杨学术上狗屁都不懂
BGI牛在wang老板上层有关系有资源，加上IT组确实有个把技术牛人
【在 z*t 的大作中提到】
: 当年写文章批评杨焕明只会忽悠，远远不如蒲慕明的人今天作何感想？
:
: public
: up
: that
: strains
|
m*********r
发帖数: 2456 | 13 medIT, are you in ABI?? |
c*********r
发帖数: 1312 | 14 赞一个！
【在 m***T 的大作中提到】
: Ion Torrent呀
|
h****i
发帖数: 94 | 15 wang jun 什么背景？IT有什么绝招？
//bow
【在 w******y 的大作中提到】
: 和杨有个P关系， 杨学术上狗屁都不懂
: BGI牛在wang老板上层有关系有资源，加上IT组确实有个把技术牛人
|
m***T
发帖数: 11058 | 16 yes
【在 m*********r 的大作中提到】
: medIT, are you in ABI??
|
L*******a
发帖数: 293 | 17 I think he was talking about Wang Jian.
【在 h****i 的大作中提到】
: wang jun 什么背景？IT有什么绝招？
: //bow
|
l****n
发帖数: 844 | 18 用Ion torrent测的？
【在 m***T 的大作中提到】
: 军功章也有我的一半。
: 我一个月前刚培训的他们，一个月后居然有成果了，不错。不得不说，这些孩子挺拼的
: 。当然人家老大也挺会做市场、吸引眼球的。
|
z*t
发帖数: 863 | 19 兄弟俺少见多怪了。。。
【在 w******y 的大作中提到】
: 和杨有个P关系， 杨学术上狗屁都不懂
: BGI牛在wang老板上层有关系有资源，加上IT组确实有个把技术牛人
|
i****e
发帖数: 157 | 20 how do you think of ion torrent?
will it completely change the sequencing market in the near future?
【在 m***T 的大作中提到】
: yes
|
|
|
m***T
发帖数: 11058 | 21 对，ＬＺ的贴子里有提到。
【在 l****n 的大作中提到】
: 用Ion torrent测的？
|
m***T
发帖数: 11058 | 22 对于discovery的领域应该说冲击不大，毕竟throughput有限制。不过对于Target Req
尤其是临床诊断方面，可能会有所做为。不光是Ion，包括454的GS junior和ILMN即将
出来的MiSEQ都是想要进军这个方向。
【在 i****e 的大作中提到】
: how do you think of ion torrent?
: will it completely change the sequencing market in the near future?
|
M*****n
发帖数: 16729 | |
j****x
发帖数: 1704 | 24 这个领域的竞争主要看试剂了
Req
【在 m***T 的大作中提到】
: 对于discovery的领域应该说冲击不大，毕竟throughput有限制。不过对于Target Req
: 尤其是临床诊断方面，可能会有所做为。不光是Ion，包括454的GS junior和ILMN即将
: 出来的MiSEQ都是想要进军这个方向。
|
S*****s
发帖数: 242 | 25 basically an useless research except a good paper, even he said:
"Yang acknowledged that finding the resistance genes may not be clinically
relevant, .....
It is clinically irrelevant for a clinical research! How ironically this
statement is! It sounds awkward and even stupid! These days, researchers in
the field of life science forget what they are doing research for, like many
people in this forum. This purpose become publishing CNS paper, get the job
et al. but not advance of human health. What a waste!
public
up
that
strains
【在 S*****P 的大作中提到】
: http://news.sciencemag.org/scienceinsider/2011/06/sequence-yiel
: DNA Sequence Yields Clues to Germany's 'Super Toxic' E. coli outbreak
: by Martin Enserink on 2 June 2011, 5:50 PM |
: Just from the high number of deaths and severe cases, scientists and public
: health experts battling Germany's massive E. coli outbreak knew they were up
: against something unusual. Now, early results from sequencing projects of
: the enterohemorrhagic Escherichia coli (EHEC) strain appear to confirm that
: a never-before-seen hybrid, combining the worst of several bacterial strains
: , is causing the havoc.
: The Beijing Genomics Institute (BGI), in Shenzhen, China—which today
|
i****e
发帖数: 157 | 26 麦地，你觉得ion和next gen的荧光方法相比，究竟有哪些明显的优势和劣势呀？
我感觉用电信号似乎是趋势，但是不知道具体现在ion的limitation还有哪些
还有你觉得现在还有哪些其它的promising的sequencing技术呀？
Req
【在 m***T 的大作中提到】
: 对于discovery的领域应该说冲击不大，毕竟throughput有限制。不过对于Target Req
: 尤其是临床诊断方面，可能会有所做为。不光是Ion，包括454的GS junior和ILMN即将
: 出来的MiSEQ都是想要进军这个方向。
|
s******s
发帖数: 13035 | 27 强多了。荧光的东西你要有一个照相机不是？相机分辨率不够
你是不是每一步要拍N张然后合起来？如果以后芯片升级了是不是
要买一个新机器？ion同一个机器用不同的芯片耗材就可以了。
更加重要的是，荧光的东西一般要加一个带荧光基团的dNTP,
这个东西polymerase不喜欢，ion就是最普通的dNTP，廉价又自然
【在 i****e 的大作中提到】
: 麦地，你觉得ion和next gen的荧光方法相比，究竟有哪些明显的优势和劣势呀？
: 我感觉用电信号似乎是趋势，但是不知道具体现在ion的limitation还有哪些
: 还有你觉得现在还有哪些其它的promising的sequencing技术呀？
:
: Req
|
i****e
发帖数: 157 | 28 那ion现在的缺点呢？我知道原理上讲，ion很牛，但是现在illumina还是sequencing的
大佬，他们
现在的优势除了marketing做的很好外，还有别的技术上，或者数据上的优势吗？
或者说，ion可以完全取代现在所有的sequencing的机器吗？
【在 s******s 的大作中提到】
: 强多了。荧光的东西你要有一个照相机不是？相机分辨率不够
: 你是不是每一步要拍N张然后合起来？如果以后芯片升级了是不是
: 要买一个新机器？ion同一个机器用不同的芯片耗材就可以了。
: 更加重要的是，荧光的东西一般要加一个带荧光基团的dNTP,
: 这个东西polymerase不喜欢，ion就是最普通的dNTP，廉价又自然
|
i****e
发帖数: 157 | 29 麦地，ion现在的318 chip 两个小时1Gb的读量还不够high throughput吗？
现在最好的荧光的机器能到多少的throughput呀？
Req
【在 m***T 的大作中提到】
: 对于discovery的领域应该说冲击不大，毕竟throughput有限制。不过对于Target Req
: 尤其是临床诊断方面，可能会有所做为。不光是Ion，包括454的GS junior和ILMN即将
: 出来的MiSEQ都是想要进军这个方向。
|
s******s
发帖数: 13035 | 30 缺点就是产品还没有经过考验。如果能够做到吹牛的那种chip升级
水平，好像是半年一代，每代四倍，两年之后其他人都没得混了，毕竟
illumina的潜力已经挖掘的差不多了。问题是能不能实现。就好像
pacbio，也是理论超牛，但是产品不行
【在 i****e 的大作中提到】
: 那ion现在的缺点呢？我知道原理上讲，ion很牛，但是现在illumina还是sequencing的
: 大佬，他们
: 现在的优势除了marketing做的很好外，还有别的技术上，或者数据上的优势吗？
: 或者说，ion可以完全取代现在所有的sequencing的机器吗？
|
|
|
s******s
发帖数: 13035 | 31 solid或者hiseq基本每次百G以上。ion的计算其实比较鬼，因为
illumina什么的cluster generation什么的都算在里面了
【在 i****e 的大作中提到】
: 麦地，ion现在的318 chip 两个小时1Gb的读量还不够high throughput吗？
: 现在最好的荧光的机器能到多少的throughput呀？
:
: Req
|
m***T
发帖数: 11058 | 32 楼上shakuras的几个贴子已经解释得挺清楚了。每个平台都有它的优缺点。Ion的优势是
simplicity, speed and scalability。说得通俗些，它的机器本身就是一台敏感度很
高的pH meter，核心技术其实都在chip里，所以它的运营成本会比较低。这些优点在
IVD方向都是比较重要的几个因素。
但它目前也有自己的缺点，比如throughput相对低，再有就是还需要emulsion PCR，都
是不利因素。好在目前整个公司对Ion项目的支持力度很大，有了invitrogen和ambion
的reagents，再加上AB这么多年在仪器方面的经验，所以Ion的前景应该还是不错的。
比如，Ion能在这么短的时间内发布OneTouch（自动化地emPCR），和整个公司对它的大
力支持是分不开的。 |
m***T
发帖数: 11058 | 33 目前318还没出来，按计划应该是年底或明年年初的事情了。如果按单位时间来算，它
也许不算低，但它每一个chip的能力就在那里，没有太大的余地去提高。提高通量的主
要办法就是新设计的chip。如果按$/base来计算，用Ion的平台来run比较大而复杂的
genome的成本应该比其它平台要高一些。所以它主要针对的是target reseq，而非whole genome sequencing。316 chip因为有100M的通量，所以做whole transcriptome应该也是能胜任的。
【在 i****e 的大作中提到】
: 麦地，ion现在的318 chip 两个小时1Gb的读量还不够high throughput吗？
: 现在最好的荧光的机器能到多少的throughput呀？
:
: Req
|
y***i
发帖数: 11639 | 34 "finding the resistance genes may not be clinically relevant"
=\= the whole research is clinically irrelevant.
in
many
job
were
of
【在 S*****s 的大作中提到】
: basically an useless research except a good paper, even he said:
: "Yang acknowledged that finding the resistance genes may not be clinically
: relevant, .....
: It is clinically irrelevant for a clinical research! How ironically this
: statement is! It sounds awkward and even stupid! These days, researchers in
: the field of life science forget what they are doing research for, like many
: people in this forum. This purpose become publishing CNS paper, get the job
: et al. but not advance of human health. What a waste!
:
: public
|
i****e
发帖数: 157 | 35 多谢麦地。
对了，你觉得squencing下一代可能会出什么技术？或者现在除了ion和pacific bio外
，还有啥比
较promising的牛东西？
whole
genome sequencing。316 chip因为有100M的通量，所以做whole transcriptome应该也
是能
胜任的。
【在 m***T 的大作中提到】
: 目前318还没出来，按计划应该是年底或明年年初的事情了。如果按单位时间来算，它
: 也许不算低，但它每一个chip的能力就在那里，没有太大的余地去提高。提高通量的主
: 要办法就是新设计的chip。如果按$/base来计算，用Ion的平台来run比较大而复杂的
: genome的成本应该比其它平台要高一些。所以它主要针对的是target reseq，而非whole genome sequencing。316 chip因为有100M的通量，所以做whole transcriptome应该也是能胜任的。
|
s******s
发帖数: 13035 | 36 不是可能。出了生化pyroseq, 最牛的就是物理方法，直接拉过小孔测电场啥的变化
【在 i****e 的大作中提到】
: 多谢麦地。
: 对了，你觉得squencing下一代可能会出什么技术？或者现在除了ion和pacific bio外
: ，还有啥比
: 较promising的牛东西？
:
: whole
: genome sequencing。316 chip因为有100M的通量，所以做whole transcriptome应该也
: 是能
: 胜任的。
|
i****e
发帖数: 157 | 37 NABsys?
这个还是很悬吧
【在 s******s 的大作中提到】
: 不是可能。出了生化pyroseq, 最牛的就是物理方法，直接拉过小孔测电场啥的变化
|
