重点就是倒数第二页的一小段,颜院报道了数据收集和结构确定的过程 (DATA COLLECTION AND STRUCTURE DETERMINATION)。 我来给大家总结浓缩一下:
第一步,收集了数据,这没什么可说的(The initial phases of D-xylose-bound XylE were obtainedfrom the Hg-derivative crystals by single anomalous diffraction (SAD) using the program ShelxC/D/E)。
第二步,用一个软件从晶体数据中算出了一个粗结构(The electron density shows that there is one molecule in each asymmetry unit. Then a crude helical model was built manually using the program COOT)。
我们都知道水银这种物质特别重,X射线轰击这样的物质,会在感光底片上留下格外特别的印记,这个水银原子就像如天书一般的结构衍射图中的一参照物。最后,纯体蛋白的衍射云图,和被水银标记的蛋白图一比较叠加,相位问题大为改善,整个蛋白分子结构就浮出海面了(With this partial model as input, the identified Hg atom positions were refined and phases were recalculated using the PHASER SAD experimental phasing module)。
4. 剩下的步骤,就如同钓鱼收杆一样,整个蛋白分子的结构如鱼咬钩被拉出海面,这个鱼钩就是这个水银标记分子。文章用的术语就是:原始的粗结构用XXXX软件得以重建和细化(With the improved map, the crude model was rebuilt using COOT and refined with PHENIX)。
我看了颜院确定结构的步骤和参考文献,她阐述了他们课题组独立地根据晶体衍射云图推导出葡萄糖转运子的结构,引经据典,无懈可击,用个英语词讲就叫“BY THE BOOK”。
另外,你如果仔细读颜院文章摘要里的文字,有这么一句话:尽管有大量(前人)的工作,葡萄糖受体的结构信息,依然在很大程度上是未知的(Despite rigorous efforts, the structural information for GLUT1–4 or their homologues remains largely unknown)。 什么叫做“很大程度上未知”(largely),这个词的解读,恐怕有很大的伸缩空间。否则为什么不叫“完全未知”呢?
可是骂归骂,你还不能真正去指控巴尔违反了什么规条,因为这个人所作的一切,完全是在规章制度之内,“by the book”!
这个规章制度是什么呢?根据司法部的“特别检察官法”,穆勒报告是提交给司法部长的一份“保密”材料,原文如下:At the conclusion of the Special Counsel's work, he or she shall provide the Attorney General with a confidential report explaining the prosecution or declination decisions reached by the Special Counsel。
如果不是漏看,而是有意忽略的话,那动机就好解释了。颜院文章的取胜之处在于机理和结构一把抓,一举突破了半个世纪的自然之谜,于是得到了NATURE的青睐。然而,如果说成是靠结构研究证实了某某人20年前老文章里的分子机理,就成了拾人牙慧了,NATURE主编可能要建议她们转投《结构生物学杂志》(Journal of Structual Biology)这样的二流期刊。
Your description of William Barr is neither relevant nor correct. He published the full (redacted as stipulated by law) Mueller report immediately after his summary for everyone to see. What conclusion can a group of experienced attorneys draw that would be different from that of Barr?
nightrider 发表评论于
回复 'cng' 的评论 :
Informative article.
However, your explanation of the phase problem in response to gx123 is incorrect. The detector of diffracted x-ray captures the temporal average of the electromagnetic power (Poynting vector) of the incoming light. The averaging process erases the phase information. The phase information is erased even when there is only one atom. The interference is irrelevant to the phase loss. If the phase information of the incoming light is not lost but determined, it is precisely the interference (in phase) or the superposition that submits the diffraction to the power of the Fourier analysis.
The Uptake of Hexose Phosphates (Uhp) is a protein system found in bacteria. It is a type of two-component sensory transduction pathway which helps bacteria react to their environment.
The uhp system is composed of UhpA, UhpB, UhpC, and UhpT. UhpB and UhpC are both transmembrane proteins which form a complex with each other. UhpA is a signal protein found in the cytoplasm.[2] UhpT is a transporter protein which facilitates the uptake of phosphorylated hexose molecules into the cell.
JessAB 发表评论于 2019-05-14 14:47:43
2. In 2012 Nieng’s Nature paper, she actually referenced Pao's 1998 review paper where Pao cited Yan’s 1993 and 1995 papers, which means Nieng indeed cited R. Yan's papers indirectly.
I believe that similar incidents happened more than once in academia. To safeguard one's results and credit, the only way is to build up on them, keeping publishing papers on that topic till people can't ignore them. If this is just one paper and the author moves on to something else, well who knows what's gonna happen.
但是,IT IS EASIER SAID THAN DONE. 从晶格电子密度图到衍射斑点,丢失了很多信息。举一个例子,你在感光片上看到一个比较弱的感光点,它有可能是一个较弱(振幅小)的X波击中了底片;而另一种可能是有两束很强的X波,由于他们的相位可能差了180度,一个X波的波峰,刚好碰到了另一个X波的峰底,结果,两个相反的强振幅反而互相抵消了,所以在底片上留下的也是一个弱感光点。
After reading previous blogs about this topic, I am wondering what is the point of arguing why Nieng did not mention Yan’s work on her papers.
1. Nieng’s two papers were about crystal structures determined by X-ray which no one ever reported before although R. Yan had studied in the similar field before.
2. In 2012 Nieng’s Nature paper, she actually referenced Pao's 1998 review paper where Pao cited Yan’s 1993 and 1995 papers, which means Nieng indeed cited R. Yan's papers indirectly.
3. I think there is no requirement to reference directly every related paper especially when it was 20 years old.
Don’t get me wrong I have tremendous respect for the work R. Yan did 20 years ago.
(I can only type English on my computer)
北佛风光 发表评论于
“如果不是漏看,而是有意忽略的话,那动机就好解释了。颜院文章的取胜之处在于机理和结构一把抓,一举突破了半个世纪的自然之谜,于是得到了NATURE的青睐。然而,如果说成是靠结构研究证实了某某人20年前老文章里的分子机理,就成了拾人牙慧了,NATURE主编可能要建议她们转投《结构生物学杂志》(Journal of Structual Biology)这样的二流期刊。”