z*******0
发帖数: 35 | 1 求助： 如何用image J 或其它软件计算 3D 图像的 surface area 啊？
用confocal 扫了一个scaffold 的sample， 想看看细胞和scafflod 面积的比例，请问
如何计算？？ |
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b*****e
发帖数: 288 | 2 随便去pubmed搜了下：
A large intergenic noncoding RNA induced by p53 mediates global gene
repression in the p53 response.
Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D,
Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T,
Rinn JL.
Cell. 2010 Aug 6;142(3):409-19.
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer
metastasis.
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T,
Argani P, Rinn JL, Wang Y, Brzoska P, ... 阅读全帖 |
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l**********n
发帖数: 240 | 3 Josef Martin Penninger
Most significant scientific contributions:
Our basic approach is to genetically manipulate and change genes in mice and
to
determine the effects of these mutations in development of the whole
organism and in
diseases. From these mutations we are trying to establish basic principles
of
development and basic mechanisms of disease pathogenesis. My laboratory
focuses on
heart diseases, autoimmune diseases and cancers, and bone diseases. On all
the listed
contributions below I ... 阅读全帖 |
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f********n
发帖数: 6465 | 4 Aptamers are oligonucleic acid or peptide molecules that bind to a specific
target molecule. Aptamers are usually created by selecting them from a large
random sequence pool, but natural aptamers also exist in riboswitches.
Aptamers can be used for both basic research and clinical purposes as
macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave
in the presence of their target molecule. These compound molecules have
additional research, industrial and clinical applications... 阅读全帖 |
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f*******h
发帖数: 38 | 5 吴号Michael Karin强强联手
搞结构灌水灌的真快
Crystal structure of inhibitor of κB kinase β
Guozhou Xu, Yu-Chih Lo, Qiubai Li, Gennaro Napolitano, Xuefeng Wu, Xuliang Jiang, Michel Dreano,
Michael Karin & Hao Wu
Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, USA
Guozhou Xu, Yu-Chih Lo, Qiubai Li & Hao Wu
Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, USA
Gennaro Napolitano, Xuefeng Wu & Michael Karin
Nature (2011) doi:1... 阅读全帖 |
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h**********r
发帖数: 671 | 6 Keasling主要是在yeast中玩的，再说了K先生组在e. coli中偏好arabionose
inducible的Pbad,早期Keasling在这个promoter上花了不少功夫包括模型和实验。
最近WHO已经发现青蒿素的耐药性出现了。这个比较搞，synthetic biology还没有搞好
，人家那边耐药性已经出现了。其实这工作也就这种大组有稳定的funding能玩玩儿。
不过说不定有些enzyme能对前体物修饰，一定程度上对抗这种耐药机制。
以前有篇报道，说这种pathway组装，需要大量的人力来完成（千老的作用显现出来了
），说Keasling的工作（从基因到产量）需要多少个postdoc 50年完成（数字不记得了
）。现在也有人在想发明更高效的pathway assembling的过程。keasling的工作有点像
是“炮轰”式，遇到问题了一堆人来做mutant克服inhibition啊尝试不同的表达量啊。
不喜欢思考形而上学的东东。这么些年来，其实让人印象深刻的东西不太多(scaffold
上蛋白的表达synthetic operon等)。去年发的那篇nature关于... 阅读全帖 |
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X******n
发帖数: 914 | 7 150个postdoc一年的工作量。
scaffold |
|
s******9
发帖数: 283 | 8 呵呵，老板私底下对他研究有相似的评价。想当初联系他postdoc的时候email，mail都
石沉大海。现在一看见人说用bacteria合成pharmaceutical，biofuel就觉得boring。
scaffold |
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s******y
发帖数: 28562 | 9 合成Taxol 其实更重要，不过这个难度挺高。
scaffold |
|
h**********r
发帖数: 671 | 10 Keasling主要是在yeast中玩的，再说了K先生组在e. coli中偏好arabionose
inducible的Pbad,早期Keasling在这个promoter上花了不少功夫包括模型和实验。
最近WHO已经发现青蒿素的耐药性出现了。这个比较搞，synthetic biology还没有搞好
，人家那边耐药性已经出现了。其实这工作也就这种大组有稳定的funding能玩玩儿。
不过说不定有些enzyme能对前体物修饰，一定程度上对抗这种耐药机制。
以前有篇报道，说这种pathway组装，需要大量的人力来完成（千老的作用显现出来了
），说Keasling的工作（从基因到产量）需要多少个postdoc 50年完成（数字不记得了
）。现在也有人在想发明更高效的pathway assembling的过程。keasling的工作有点像
是“炮轰”式，遇到问题了一堆人来做mutant克服inhibition啊尝试不同的表达量啊。
不喜欢思考形而上学的东东。这么些年来，其实让人印象深刻的东西不太多(scaffold
上蛋白的表达synthetic operon等)。去年发的那篇nature关于... 阅读全帖 |
|
X******n
发帖数: 914 | 11 150个postdoc一年的工作量。
scaffold |
|
s******9
发帖数: 283 | 12 呵呵，老板私底下对他研究有相似的评价。想当初联系他postdoc的时候email，mail都
石沉大海。现在一看见人说用bacteria合成pharmaceutical，biofuel就觉得boring。
scaffold |
|
s******y
发帖数: 28562 | 13 合成Taxol 其实更重要，不过这个难度挺高。
scaffold |
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m*******e
发帖数: 1280 | 14 Two other points, after finally took a look at her research description as
pasted below:
1) She AIN't doing GWAS (Genome Wide Association Study). The array-based
GWAS has been concluded and announced as a big failure,she would have been
dumb for focusing on that.Sequencing is the way and it IS her approach.
2) Neurologic/psychatric disease is a great direction. Latest data on US
School Age Children says the Autism rate is 10 times higher over 10 years
ago to a stunning 1%. Sure, there are arguem... 阅读全帖 |
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s******y
发帖数: 28562 | 15 这么听起来很奇怪啊，好像和那个新闻里讲的不相符，
新闻里说的是 They removed all the muscle cells in a rat heart, leaving just
a “scaffold” of other tissues such as blood vessels and valves.
不知道是不是那个记者写错了。
不过，假如他们能够特异性在体外的用化学/物理方法除去心肌细胞而不影响其他
细胞的话也够令人惊讶的了。我倾向认为是那个记者写错了。
leaving ECM behind. They argue ECM in the
cell to differentiate to endothelial cell
they demonstrate the "heart"
initiate the heart beating.
toxic gene in cardiomyocyte and kill
is a quite different story. |
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s******y
发帖数: 28562 | 16 谢谢！
另外，麻烦你一下，关于那个心脏里面的细胞构成（70%是fibroblast) 那个，
我对这个很感兴趣，能不能大概告诉我一下出处？
cells
scaffold |
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z*t
发帖数: 863 | 17 他现在怎么不追epigenetics?
要我说现在structral biology其实对epigenetics更有指导意义哈，比如emory的
Xiaodong Cheng，从结构里推测DNMT3L可能得结合H3K9me3，并形成DNMT scaffold，相
当有指导性，还有不能不提的Dinsaw Partel对RNAi相关蛋白的结构和一系列Histone相
关的结构，对目前epigenetics很有帮助哈 |
|
|
s******y
发帖数: 28562 | 19 呵呵，我就不去趟这种浑水了。
我就是查文献的时候看到有的实验室已经在做PTEN在autism里面的功能，
觉得挺纳闷的。
就像你说的那样，大部分功能特别重要的基因（那些很多都是oncogene)，
在neuron 里面都肯定有功能的。
比方说我要是发个神经在纹状区把tubulin KO了，几乎也肯定能够产生
autism 症状吧？可是这么做有意义么？
SHANK3, 和Neuroligin 的意义在于他们是非常组织特异性的蛋白，
在基因上搞乱这两个蛋白后产生的形状主要集中在神经和行为上，
这个和autism 病人的特点一致。因为autism 病人主要是行为异常，
其他发育大致都还正常。
而PTEN这种蛋白，在自然情况下不管是以什么方式被搞乱（比方说基因
突变，或者mis-regulation)，其表型不太可能集中在脑部，所以不太可能是
autism 的致病原因。
在这个意义上来说，我觉得对SHANK3, Neurologin等几个post-synaptic
scaffold protein 的调控，才是最有可能的autism 的致病原因。 |
|
a*******u
发帖数: 19 | 20 GST-fused protein A 拉下了B,C,D.且ABCD在胞浆和核内都有分布。文献报道BC、BD在
胞浆和核内都有直接的相互作用，但BCD是否在一个复合物未知或未报道。现在猜想
ABCD很有可能在一个复合物，A作为一个scaffold protein的角色。有什么方法说明4个
蛋白或者至少3个蛋白形成一个complex？有没有比较简单点的方法，国内实验室的设备
条件比较限制。 |
|
L********g
发帖数: 4204 | 21 agree, gel-filtratioin has its limit, thats why I list it on option 2 only
to add some more evidence to the GST, co-IP results.
But if A/B is the hub/scaffold, mutated A/B or KO AB may cause the
disassoation of B C D, then you will see differnt gel-filtration profilings.
through this comparison, you can say A/others are important for forming a
complex.
Also for linyijvn1, have you done some genetic analysis to add evidence that
A, B, C, D are depending on each other for functions? Personally I t... 阅读全帖 |
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w******e
发帖数: 1187 | 22 mRNA/ribosome/phage/bateria/yeast/microbeads/micro droplet display的铜锈们
都去什么会啊？
只知道有抗体相关的会，那做peptide/alternative scaffold/enzyme evolution
的有啥类似的会否？gordon系列有这个topic否？
多谢！ |
|
w******e
发帖数: 1187 | 23 是有很多工作可以做，但如何入手就是另一回事了呵呵。
比如说，我觉得ultimate goal for affinity reagent development是thermostable,
self-integrated with detection & amplification mechanism, adaptable into
multi-target platform, tunable affinity under enviromental cue，tunable
density to achieve multivalent interaction.
那么怎么去实现这个目标？我脚的on paper aptamer其实是最好的candidate，但
过去二十年都被技术瓶颈限制着呐。最近的breakthrough能把boundary push到
多远？我没本事判断。类似的，protein engineering在thermostability上，
在integrating detection module/scaffolding module上，在molecular
switchin... 阅读全帖 |
|
t****t
发帖数: 45 | 24 Job Title: Postdoctoral Position in Biomaterials, Stem Cells, and Tissue
Regeneration
Application Deadline: Open Until Filled
Job Description
Description:
The Department of Biomedical Engineering at the University of Minnesota
currently has an opening for a post-doctoral fellow to conduct studies in
the area of biomaterials and tissue regeneration. The project involves
materials engineering on the molecular level, scaffold fabrication, and stem
cells.
Qualifications:
Candidates must have a Ph.D.... 阅读全帖 |
|
s********n
发帖数: 2939 | 25 Baker现在的主要方向是protein ab initio design，利用现有的scaffolds design
novel catalysts or pharmaceuticals.
check |
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l**********1
发帖数: 5204 | 26 It is CS PhD and Biostatistic MD/PhD schlors both their duties, not wet bio/
medi MD/PhD's works.
pls check,
http://www.cs.helsinki.fi/u/vmakinen/
or
DAlign Computes the unit cost edit distance between a haploid and a
reference guided recombination of two diploids.
Maximal Unique Matches computed with a bidirectional BWT-index.
Traph. A software for RNA transcript expression prediction from RNA-
sequencing data. See RECOMB-seq and WABI 2013 papers below.
Normalized N50 calculator. A tool to extr... 阅读全帖 |
|
l**********1
发帖数: 5204 | 27 It is CS PhD and Biostatistic MD/PhD schlors both their duties, not wet bio/
medi MD/PhD's works.
pls check,
http://www.cs.helsinki.fi/u/vmakinen/
or
DAlign Computes the unit cost edit distance between a haploid and a
reference guided recombination of two diploids.
Maximal Unique Matches computed with a bidirectional BWT-index.
Traph. A software for RNA transcript expression prediction from RNA-
sequencing data. See RECOMB-seq and WABI 2013 papers below.
Normalized N50 calculator. A tool to extr... 阅读全帖 |
|
|
z*h
发帖数: 773 | 29 Most biofuels seemingly "big" papers just cheated laymen.
Example 1. E.J. Steen, Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure,
S.B. del Cardayre, J.D. Keasling, Microbial production of fatty-acid-
derived fuels and chemicals from plant biomass, Nature, 463 (2010) 559-562.
This is a combination of X. Lu, H. Vora, C. Khosla, Overproduction of free
fatty acids in E. coli: Implications for biodiesel production, Metab. Eng.,
10 (2008) 333-339. and a lot of old papers about xylan-utilization.
... 阅读全帖 |
|
i****g
发帖数: 3896 | 30 http://loyalyang.blog.163.com/blog/static/164764085201110240388
系统生物学大牛们
2011-11-24 12:38:08| 分类： 默认分类 |字号 订阅
这个推荐给以后想做系统生物学的同学，大概是我这两年半的时间里，看过的一些文章
的通讯作者。因为系统生物学本身暂时没有一个特别固定的研究套路，但是会有几个比
较有前途的方向，list里面的这些人大都是系统生物学领域里提出过很多新方法和新想
法的人，当然系统生物学并不是一个新的学科，只是系统生物学这个名词出现于1999年
左右，因为目前深入到分子水平以后，生物系统的复杂性超出人们的想象。所以目前我
们所说的系统生物学只是处于起始阶段，有很多人提出了很多种观点和研究方法，也有
很多人风光一时，但是后来又被时代的马车抛弃了。
鉴于我水平有限，这个只是介绍一下我知道的一些实验室，大部分是通过读文章了解的
，所以应该也比较有限，也许会涉及到一些Synthetic Biology的，不会太多。
Leroy Hood@ISB
此人就是第一个系统生物学研究所的所长，现在貌似做董事去了... 阅读全帖 |
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b******y
发帖数: 627 | 31 "他做过一系列的scaffold protein的研究，发表的那些
文章perfect"
The quoted statement about Wendell Lim is not quite accurate. Some of his
data are not solid enough to draw the conclusions he drew, although the
conclusions themselves are interesting and important. |
|
h****r
发帖数: 152 | 32 找到一篇，第三作者
Biomaterials. 2008 Jan;29(1):75-84.
Growth, differentiation, transplantation and survival of human skeletal
myofibers on biodegradable scaffolds.
Thorrez L, Shansky J, Wang L, Fast L, VandenDriessche T, Chuah M, Mooney D,
Vandenburgh H.
Source
Department of Pathology, Brown Medical School/The Miriam Hospital, 14 Third
Street, Providence, RI 02906, USA. l************[email protected] |
|
h****r
发帖数: 152 | 33 找到一篇，第三作者
Biomaterials. 2008 Jan;29(1):75-84.
Growth, differentiation, transplantation and survival of human skeletal
myofibers on biodegradable scaffolds.
Thorrez L, Shansky J, Wang L, Fast L, VandenDriessche T, Chuah M, Mooney D,
Vandenburgh H.
Source
Department of Pathology, Brown Medical School/The Miriam Hospital, 14 Third
Street, Providence, RI 02906, USA. l************[email protected] |
|
l**********1
发帖数: 5204 | 34 她拿哪一份专利的排名作为千青的申请材料的
World Patents in Skin Care Actives Published in 2011
她排名第五 她的Brown 导师VANDENBURGH 排名第三
Publication No.: WO2011109834A2 Published: 09/Sep/2011
Title: ENHANCEMENT OF SKELETAL MUSCLE STEM CELL ENGRAFMENT BY DUAL DELIVERY
OF VEGF AND IGF-1
Applicant/Assignee: PRESIDENT AND FELLOWS OF HARVARD COLLEGE, BROWN
UNIVERSITY
Application No.: US2011/027446
Filing Date: 07/Mar/2011
Abstract:An improved device and method for extended repair and regeneration
of muscle tissue. An exempl... 阅读全帖 |
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l**********1
发帖数: 5204 | 35 人家各做一个residue 3D
Molecular Modeling 的话 还是可能的
//www.ncbi.nlm.nih.gov/pubmed/22448988
Crystal structures of Bcl-xL with 118 (PDB entry 2YXJ) and 4 were used to
model the binding poses of our designed compounds with Bcl-xL. In the
binding models, the structure of Bcl-xL in complex with 4 was superimposed
on that of Bcl-xL in complex with 1. The core scaffold of 4 then replaced
the 4′-chloro-2-methyl-1,1′-biphenyl group of 1 to generate the initial
binding model, which was then refined by a 1 ns mo... 阅读全帖 |
|
s******y
发帖数: 28562 | 36 PSD-95 is a member of the membrane-associated guanylate kinase (MAGUK)
family. With PSD-93 it is recruited into the same NMDA receptor and
potassium channel clusters. These two MAGUK proteins may interact at
postsynaptic sites to form a multimeric scaffold for the clustering of
receptors, ion channels, and associated signaling proteins.[1]
针对于PSD-95设计的抑制多肽药品NA-1(Tat-NR289c)日前在加拿大和美国并行进行的双
盲测试中取得良好成果.
研究人员对脑部手术的病人术后出现的轻微中风使用该药品。在没有采用该药物的对照
组中，有３２％的病人会出现不同程度的脑部损伤，采用了该药物的病人则有非常明显
的保护作用。 |
|
v*********d
发帖数: 382 | 37 10 nm scaffolding filaments of the nuclear endoskeleton 很早就在电镜下观察到
了，molecular composition 却一直还是个谜
大哥，下个诺奖就是你的了！ |
|
c***y
发帖数: 615 | 38 最近在看mass spec 结果, 用的是scaffold viewer 3
说明书说是"protein window, green amino acid indicates PTM ". 我发现所有蛋白
的green amino acid都是M
google 了一下, 没有发现methionine有特别的转录后修饰啊.除了首位被切除以外.
我这里的green M 全是中间的
是我的理解错了吗? |
|
W*********n
发帖数: 775 | 39 2个样品：对照样品和处理样品；然后作三次生物重复。就有3个对照样品，3个处理样
品。每个样品做了LCMS/MS后，数据输入Scaffold 软件。然后用“quantitative
analysis” 中选择“Fisher's exact T-test”.得到大约100个蛋白p<0.05.
然后我的问题是：怎么把这100个蛋白分类输出“表达上升的蛋白”和“表达下降的蛋
白”两组？
觉得有的蛋白，在两组重视上升趋势，在第三组中是下降趋势，结果也是p<0/05.不知
道这个蛋白应该是上升还是下降？怎么区分？
谢谢！ |
|
s******s
发帖数: 13035 | 40 我的印象中，这玩意儿现在认为就像一个scaffold protein，loop出来无数
binding domain, 识别以及recruit各种分子在一起。我觉得，如果能figure
out识别序列，进而设计新的ncRNA，尤其如果做epigenetic editing，肯定很火 |
|
l*********1
发帖数: 351 | 41 The half-life of nanobody can be tuned by a HSA binding module (tandem
repeats of nanobodies). Lack of cytotoxicity is definitely a major problem
of such alternative scaffolds in case of tumor treatment. Therefore,
conjugation of cytotoxic small molecules may come into play (kind of ADC
mimetics). |
|
j****x
发帖数: 1704 | 42 这里我倒是还知道一个“唯二”的特例：
如果在哺乳动物表达质粒的转录单位后面接上一段nuclear scaffold matrix
attached region（SMAR序列），那么该质粒就可以在不需要真核复制起始位点的情况
下以episome的形式存在并跟随基因组染色体在细胞分裂的过程中自我复制无需任何其
他条件。这种情况下的组蛋白的结合和修饰都是存在的，但有其特殊性。 |
|
M***7
发帖数: 2420 | 43 发几行数据上来看看，我写个简单的脚本帮你提出来。
我。 |
|
t*****z
发帖数: 1598 | 44 楼主，顺便说下你用的什么操作系统，有没有装什么语言环境（如果你知道的话）。 |
|
s****l
发帖数: 10462 | 45 NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
The new grants are awarded (pending available funds) to:
University of California Santa Cruz, $2.29 million over three years
Principal Investigator: Mark Akeson, Ph.D.
Investigators plan to sequence single DNA molecules by using a nanopore
device comprised of a sensor that touches, examines and identifies each
nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
it through the pore. The scientists will focus on DNA “resequencing” —
examining th... 阅读全帖 |
|
s****l
发帖数: 10462 | 46 NIH最近又房顶了八个小组，大家看看哪一个最有可能成功？
The new grants are awarded (pending available funds) to:
University of California Santa Cruz, $2.29 million over three years
Principal Investigator: Mark Akeson, Ph.D.
Investigators plan to sequence single DNA molecules by using a nanopore
device comprised of a sensor that touches, examines and identifies each
nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves
it through the pore. The scientists will focus on DNA “resequencing” —
examining th... 阅读全帖 |
|
n******7
发帖数: 12463 | 47 1k要看得到啥
1k做个30x的WGS那是不错
这个是MinION啊
最近一个文章就测了3个gene，coverage倒是有1000左右
最长reads我上面贴的那个是146,992bp
这个技术现阶段的亮点也就是读长，用来做scaffold 还凑合 |
|
n******7
发帖数: 12463 | 48 好处是可以做scaffold
我感觉对isoform 或者SV 分析会很有用，这对准确率要求不高
但是目前的通量也太低了
还在玩票阶段
high |
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s****l
发帖数: 10462 | 49 有人愿意讨论这里面提及的测序技术吗？优缺点，可行性，第一手经验等等
这里面谁现在是赢家很清楚，但是可见的将来和更远的将来谁会赢？
http://cen.acs.org/articles/92/i33/Next-Gen-Sequencing-Numbers-
全文拷贝如下
试试看图能不能贴上
/1407973177171.jpg
/1408028636124.jpg
OVER STORY
Next-Gen Sequencing Is A Numbers Game
As technical and cost barriers fall, instrument firms move their systems
into research and clinical markets
By Ann M. Thayer
Department: Business
Keywords: instrumentation, gene sequencing, diagnostics, genomics, cancer
[+]Enlarge
09233-cover-Openercxd_17647969-690
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z*****g
发帖数: 2 | 50 如果是靶向一个酶的话，可以设计它底物的类似物，从而开发成底物竞争性的
inhibitor，像一些kinase的inhibitor都是ATP的类似物；即Mechanism-based
inhibition，共价和非共价结合的都有，academic groups 开发比较多。但这类
compounds选择性可能不好，对同类型的酶都或多或少有抑制作用。
另外，从已经报道的ligand去设计similar analogs，可能很难跳出别人compound的骨
架(scaffold)，发文章的novelty或专利申请受影响。
如果是靶向protein-protein interaction 的话，尤其是你知道它们的complex
structure，以其中一个为receptor，另一个的peptide为ligand，不断优化（突变和/
或改变长度）这个peptide，使其达到活性达到最优；并且可以再对这个peptide进行化
学modification，提高其透膜性或水溶性。
zjianyun (Four) 提到的假阳性结果，是指Pan Assay Interference Compounds
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