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For the first time ever, researchers have captured on film how a gene goes about the business of directing a cell to make a protein. Researchers at Cold Spring Harbor Laboratory in Cold Spring Harbor, New York, tagged different molecules different colors so they could see the process by which a living cell makes protein from DNA within its nucleus. The process is much more dynamic than they had imagined.


Most studies of gene expression are conducted on isolated genes in the test tube and focus on only one step of the whole process. The Cold Spring Harbor team put it all together.

?oWe wanted to develop a system where we could study all aspects of the system,? says David L. Spector, who led the research. ?oWe wanted to see gene expression played out in real time and space.?

The process of gene expression?"making a protein from the DNA codê?"occurs in several steps. The gene sequence is first copied from the DNA strand into a similar but smaller molecule known as RNA. The RNA then travels out of the nucleus and its sequence is ?oread? by cell machinery that translates it into a specific protein.

Spector and his colleagues designed a gene sequence that could be inserted into the human genome. Once there, it could be turned on, or activated, at will and the ensuing sequence of events could be directly visualized by labeling DNA, RNA, and protein different colors in living cells.

The movie first shows a tightly compacted region of DNA opening up as the gene is activated. RNA?"tagged yellow with a fluorescent protein?"appears first in the nucleus and then moves out to the cytoplasm, the region of the cell surrounding the nucleus. Ultimately, blue-colored protein appears in the cytoplasm in structures called peroxisomes.

The researchers also labeled some of the proteins that package the DNA and were able to see that one of those proteins is replaced by a variant form that specifically zeroes in on the region of DNA that is being read.

Not all genes are active in a cell at a given time. Some genes in specialized cells are only turned on when needed and others are shut down permanently. Researchers studying stem cells and embryonic development are keenly interested in how the genome is programmed so that cells become the kind of cells needed by the body. And many diseases are thought to result from genes or combinations of genes being activated or silenced inappropriately.

Spector says his system can provide a direct view of gene expression and may help researchers understand what happens when things go wrong. He envisions inserting the easily visualized gene that he constructed into specific spots in the genome to get a clearer view of how genes are regulated in the context of a living cell.

?oWe might also use this system to see how small molecules such as anticancer drugs work in a living cell,? says Spector. ?oWe could get a direct view into whether a drug is shutting down gene activation or affecting the way RNA is processed. Ultimately this could help us do a better job at identifying and designing new drugs.?

"Janicki, S.M. et al. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683-698 (March 5, 2004)."

Gene Expression Movie(AVI Format - 11.2 MB)http://www.cell.com/cgi/content/full/116/5/683/DC1/Movie%201.avi"

Concay

Bác ConCay kiếm ra đâu được cái bài thiệt là hấp dẫn đăng mấy bữa nay mà chưa có thì giờ dơ tay xin đặt mấy câu hỏi.
Dần dần các nhà sinh học ngày nay đã tìm cách để nhìn vào những quá trình sinh lý tế bào một cách rỏ ràng hơn và tế bào giờ đây không còn là một cái hộp đen nữa. Tuy đoạn movie ngắn ngủi trong bài báo này có thể được xem thường bởi các thế hệ ở tương lai rằng nó chỉ là một đoạn phim hoạt hình của con nít nhưng nó đã chứng minh một cách hùng hồn sức mạnh của quá trình làm khoa học thực nghiệm, tức là quan sát, lập giả thuyết, kiểm chứng giả thuyết, và lập mô hình để giải thích thế giới tự nhiên. Cuốn phim ngắn này đã kiểm chứng lại những gì mà người ta đã biết từ rất lâu.
Bây giờ đến phần câu hỏi. Không biết có bạn nào rảnh chịu khó đọc những bài này để giải thích thêm cho mọi người những chi tiết mà đoạn phim này muốn nói lên (vì kỷ thuật còn thô sơ quá nên người ta chưa có thể thu âm được những phân tử đóng vai trong phim này đang nói gì).
1. Kỷ thuật đánh dấu các phân tử để chúng có thể được ghi nhận bởi máy camera?
2. Thế nào là sự khác biệt giữa euchromatin và heterochromatin? Việc diển tả được đoạn gien mà tác giả dùng trong vùng heterochromatin có ý nghĩa gì?
3. Thời gian của từng bước (transcription, translation,...) trong quá trình sản xuất ra protein?

WhiteHead Institute News-April 7,2004-Tools of the Trade
In the film ?oIt?Ts a Wonderful Life,? an angel shows a suicidal George Bailey how his small town would have fared had he never been born. For years, scientists have conducted countless George Bailey experiments on genes, identifying their function by knocking them out with specially designed complex molecules, then observing what happens to the cell.
In the past, such complex molecules took months to engineer. But since 2001, more scientists are adopting a new method that shuts down a single gene within days using small segments of RNA called short interfering RNA, or siRNA. Now, Whitehead Institutê?Ts Bioinformatics and Research Computing group has developed a Web-based tool that increases the accuracy and speed of this widely used technique.
When placed in a cell, these short strands of RNA interfere with a genê?Ts ability to produce protein. Several academic labs and drug companies have pursued siRNA?Ts ability to immobilize key genes involved in viral and immunological diseases, cancers and other illnesses. But sorting out which siRNA sequences block which genes is cumbersome; scientists must randomly select siRNA segments from thousands of possibilities in the hopes of hitting the bull?Ts-eye.
The siRNA Selection Program, completed in February 2003 by Whitehead?Ts Bioinformatics group, could make the process less cumbersome ?" and faster. Last September, the group received a grant from the National Science Foundation to improve its accuracy. Developed by Bingbing Yuan, the siRNA Selection Program enables scientists to quickly pinpoint a small number of specific siRNAs that likely will knock out a specific gene. Users enter the DNA sequence for the human or mouse genes they?Tre studying, and the program returns potential siRNA sequences that can be used to target the gene.
A recent survey in Genome Technology magazine ranked Whitehead?Ts program as one of the top three most used siRNA design tools. ?oThe advantage of our tool over other available software is that we identify sequences that exclusively target the gene of interest, and provide information as to why the resulting siRNA candidates got selected,? says Fran Lewitter, director of the Bioinformatics group.
In collaboration with Thomas Tuschl, former Whitehead postdoc and a pioneer in siRNA research, and other leading siRNA researchers, the Bioinformatics group is now developing a public database that will help the team further refine its program. Lewitter?Ts team also has launched a new project to produce ad***ional experimental data that could yield an even more sophisticated program.
http://www.wi.mit.edu/nap/features/nap_feature_tools_trade.html
http://jura.wi.mit.edu/pubint/http://iona.wi.mit.edu/siRNAext/
Concay

Chlamydial evolution probed
The last common ancestor of the Chlamydiales group of bacteria lived about 700 million years ago inside a eukaryotic host cell, according to a new study. This primeval chlamydia encoded many virulence factors now found in modern pathogenic chlamydiae as well as in Salmonella and Escherichia coli, according to the authors of the paper in Science published on April 8, 2004.
Matthias Horn and colleagues at the University of Vienna used the genome sequence of the group''s recently discovered closest living relativê?"an endosymbiotic chlamydia living in amoebaê?"to reconstruct the genetic makeup of the last common ancestor. Among the species'' virulence factors, now found in a wide range of bacterial pathogens, was a type III secretion system?"a mechanism by which bacteria can inject their proteins into host cells in order to force the host cells do something to the bacteria''s advantage.
Horn showed that the sequence of the symbiotic chlamydia had to be close to the ancient sequence. "We could see that the genome was stable for many [millions of years because] we didn''t see any evidence for horizontal gene transfer," he told The Scientist.
The team discovered that, compared with the pathogenic chlamydiae, certain metabolic pathways, such as those required for the production of certain amino acids or vitamins, are still missing in the symbiont. "They need to get them from the host, so we can argue that this organism has had to live within an eukaryotic host cell for many years," Horn said.
Calculating the divergence of these symbionts from pathogenic chlamydiae by mathematical modeling allowed the team to determine that the last common ancestor of these two organisms lived during the Precambrian age, when the first eukaryotes were starting to evolve. "We could show that they have been living within eukaryotic cells for hundreds of millions of years, and the basic mechanisms *****rvive within eukaryotic cells obviously were developed in ancient times long before animals or plants occurred on planet Earth," Horn said.
Amoebae have been considered a kind of "biological gymnasium" in which originally free-living bacteria acquire the necessary fitness to become intracellular bacterial pathogens, according to Michael E. Ward, professor at Southampton University School of Medicine. "The sequence gives an insight into how intracellular pathogens may have evolved and how future emerging bacterial pathogens from amoebae might arise."
The authors of the paper suggest that their observations of symbiosis of chlamydia in amoebae could bolster the theory that eukaryotic cells acquired mitochondria or chloroplasts early on in evolution by capturing cyanobacteria. However, Radhey S. Gupta, professor of biochemistry at McMasters University, who was not involved in the study, said that "chlamydiae are very different from cyanobacteria, and the little similarity that is seen in a small number of genes probably can be explained by other means than common ancestry of these two groups."
Symbiotic chlamydiae could be a potential source of new pathogenic organisms, according to Gupta. However, since the organisms have been in the environment for a long time, he said, it is not likely that they would pose any kind of a new threat that was not there previously.
http://www.biomedcentral.com/news/20040413/01/
http://www.sciencemag.org/cgi/content/abstract/1096330v1