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关于BAC文库和陈晓宁的工作

原作：UC
翻译：方舟子

1.细菌人工染色体（BAC）是DNA插入片段可达200到300千碱基对(kb)的人工克隆。
BAC系统比酵母菌人工染色体（YAC）开发得晚，后者有两个严重的缺点，即容易
嵌合（chimeric）和不稳定（内源缺失）。这些文库用于物理作图（physical mapping）。
大约在几年前，建造包含染色体或某段染色体区域的YAC，BAC和噬菌体人工染色
体（PAC）的叠连群（contig）是一个热点。自几年前以来，BAC和PAC叠连群被
用于基因组测序（即所谓预备测序叠连群）。现在人类基因组计划已经完成了整
个基因组的测序，这些叠连群就变得不那么重要。

2.但是BAC文库用于荧光素原位杂交（FISH）工作还是有用的，也就是说，如果
一个BAC克隆含有已知基因，就能用于FISH实验检测是否有该基因参与其中。然
而，由于BAC很大而且可能含有其他未知DNA片段，即使用FISH检测到了断裂信号，
也并不意味着该基因发生了变化。最后的结果还必须用分子遗传学的办法确定，
即用Southern印迹和测序。在FISH实验中用如此大的探针必须十分小心。而且，
用BAC检测小缺失也是很困难的。

3.BAC能够用于帮助基因归属（assignment），也就是说，如果一个新的cDNA由于
太短而难以用FISH定位，但是该cDNA与某个BAC中的序列标定位点（STS）有相同的
标记，那么这个BAC是有助于基因归属的。但是，因为整个基因组序列已测定，新
的cDNA可以通过简单的序列检索排列而将之归属到某段染色体区域。因此，BAC在
现在来说对基因作图的作用是很有限的。

4.如上所说，BAC对检测某个基因是有用处的。但是在美国和德国，BAC迄今还没有
被用于产前诊断。在美国，FISH技术使用食品药物管理署批准的中心粒探针（大
部分由Vysis公司提供），被用于产前诊断，但必须与常规的染色体分析相结合。
在德国，FISH技术甚至还未被批准用于常规的和正式的产前诊断。BAC由于已解释的
原因，不被用于谨严的产前诊断。

5.BAC较多地被用于在癌症研究中检测某种基因病变。但是在大多数情况下，它只
用于研究，而不是临床报告。BAC是细胞遗传学和分子遗传学的中介，用于首批筛
选。在少数情况下，BAC对基因鉴定有用。

6. 象其他克隆，BAC能够保存在-70摄氏度下，并很容易取出用于以后的分离实验。

7. 陈教授带回国的BAC克隆可能很大，包含了整个基因组序列，也可能很小，只
含有某些染色体片段。最有用的BAC文库是其他实验室建造的，而不是陈或她的老板
建造的（她们用这些BAC制作叠连群）。在美国，这些文库已被转让给几家商业公
司。但是在欧洲，在研究中可免费使用它们。

8. 建造叠连群的目的是为了鉴定该区域中的疾病基因。Korenberg博士（陈的老板）
未能够发现任何与先天愚型有关的基因，虽然许多年来这是她的实验室最重要的
项目，而且她也未能发现其他疾病基因。陈的工作很显然只是限于建造已不那么有
用的叠连群以及基因制图。在大多数她做为共同作者的论文中，她帮助他人做基因
定位。她可能是那个实验室中第一位掌握了FISH技术的（在一篇中文采访中，她
说她在1993年到耶鲁大学的David Ward实验室学技术），并主管技术支持。她可能
是个研究人员，但是做的是高级技术员的工作。

9. 她是四篇论文中的第一作者。其中一篇发表在《美国人类遗传学杂志》（AM J 
Hum Genetics，影响因子较高。方按：该论文被引用了九次），这是一篇原创论
文，提供了一些新信息（没有基因被鉴定）。其他三篇论文只是只有一到三页的关
于基因作图的小论文。它们真的很简单（影响因素在2和3之间）（许多使用FISH技
术的人如果乐意，能够定位几个基因并发表论文）。她只是如此简单的论文的第一
作者（而在7年内仅有四篇），结果并不好。很难相信她竟会认为她是一位顶级科
学家。

10. Korenberg是《细胞遗传学杂志》（Journal of CYTOGENETICS AND CELL
GENETICS）的分子细胞遗传学和基因制图方面的编审（该杂志有两个主编，两个
副主编和至少8个不同方面的编辑。在陈的四篇第一作者论文中，有两篇发表在该
杂志）。有可能陈正式或非正式地被她的老板要求审阅送到该杂志的论文。对那些
在编辑或著名科学家手下工作的人来说，这是很正常的。但是审阅和编审是很不同
的。

1. BAC is an artificial clone with an insert of up to 200-300kb. BAC system was
developed later than YAC which has two serious disadvantages, i.e. chimeric and
unstable (internal deletion). These libraries were used for physical mapping.
About several years ago, it was hot to make a contig of YAC, BAC, PAC contig of
certain chromosome or chromosome regions. Since few years ago, BAC and PAC
contig were used for genomic sequencing (i.e. so called sequencing-ready contig)
. Now Human Genome Project finished sequencing of whole genome, these contigs
become less important. 
2. But BAC library is still useful now for FISH work. I.e. if a BAC clone
contains a known gene, it can be used in FISH experiment to screen whether the
gene is involved. However, since BAC is big and may contain other unknown DNA
fragment, it is not neccesarily mean the gene is changed even if a split signal
is detected in FISH. Final confirmation is done only by molecular genetics, i.e.
southern, and sequencing. It should be very careful in FISH with such big
probes. It is also difficult for BAC to detect small deletions.
3. BAC can be used to help gene assignment, i.e. a new cDNA (too short) is very
difficult to be localized with FISH, but if the cDNA has same STS marker which
is in a BAC, this BAC is helpful for gene assignment. However, because the
whole genome sequence is ready, new cDNA is easily assigned to certain
chromosome region by simple sequence alignment. Therefore, BAC role is very
limited now for gene mapping.
4. As indicated above, BAC is also useful for detection of certain genes. But
BAC is not used so far in prenatal diagnosis, also in USA and Germany. In
America, FISH is used in prenatal diagnosis with FDA approved centromeric
probes (most of them are from Vysis) and must be in combination with
conventional chromosome analysis. In Germany, FISH is even not approved as
routine and official examination for prenatal diagnosis. BAC is not used for
such serious cases in prenatal disgnosis becuse of problem of results explanation.
5. BAC is more used in cancer research to detect certain gene abnormalities.
But it is in most cases only for research and not for clinical report. BAc is a
bridge between cytogenetics and molecular geneitcs and is used for first screen.
In few cases, BAC is helpful for gene identification.
6. Like other clones, BAC can be kept at -70C and easily recovered for DNA
isolation later.
7. The BAC clones Professor Chen brought back can be very big and contains
whole genomic sequences or small containing only certain chromosome fragments.
The most useful BAC library was oconstructed by others, but not by Chen or her
boss (they used these BAC for contig-make up). These libraries have been
transfered to several companies in USA. But in europe it is free for researhc purpose.
8. The aim of construction of contig is to identify disease gene involved in
the region. Dr.Korenberg was unable to find any genes for Down's syndrome which
was her most important project for many many years and for other diseases. Chen'
s work is obviouly limited to construction of contig which is less useful now
and to gene mapping. She helped others to make gene localization in most papers
which she served as a coauthor.She may be the first in that group/lab to master
the FISH technique (in a Chinese interview report she said she went to David
Ward's lab at Yale in 1993) and in charge of technique support. She may be an
researcher but works as a senior technician.
9. She is the first author in four papers. One published in AM J Hum Genetics (i
mpact factor in high) was an original paper and gave some new information (no
gene identified). Other three papers are just gene mapping paper of 1-3 pages.
They are really simple one (impact factor is between 2-3). (many people who use
FISH technique can localize several genes and publish it if they want). However,
these papers also fairly reflect her research level. It is not a good result
she served as first author only in such simple papers (and only four after 7
years). It is unbelievable she think herself is a top scientist. 
10. Korenberg is an editor of the section of molecular cytogenetics and gene
mapping of the Journal of CYTOGENETICS AND CELL GENETICS (The journal has two
editor-in-Chief, two associate editor and atleast eight editors for several
aspects; Chen published two of her four papers wich she served as the first
author). It is possible Chen was officially or unofficially asked by her boss
to review some papers submitted ot that journal. It is much normal to do that
for some persons who work with an editor or with an famous scientist. But it is
really different between reviewer and editor.

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