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Wednesday, 31 October 2007
Cat Genome Sequenced
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Human tests of embryonic stem cell therapies to start?
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Stem cells can improve memory after brain injury

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Thursday, 25 October 2007
New group of tiny RNAs - the piRNAs
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Wednesday, 24 October 2007
Differentiation in human embryonic stem cells
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Signal that switches on eye development
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Friday, 19 October 2007
Interspecies Chimeric Mice Using ESCs Created

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Xenotransplanting embryonic pig pancreatic cells
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Thursday, 18 October 2007
Zerhouni again urges more stem cell research
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microRNA scan uncovers reasons behind muscle dystrophies
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Friday, 12 October 2007
First Complete Asian Genome
American scientists earlier this year created the first two genome sequence maps, that of James Watson and Craig Venter respectively.
"We can never change our genes, but we can understand our genetic structure better by creating a fine map of our genome sequence. This is very helpful in preventing or controlling diseases, such as cancers," Wang Jun, the leader of the project and vice-director of BGI's Shenzhen branch, said.
The next step of the project will be to sequence the genomes of more individuals to identify genetic variations in Asian populations and explore the essential mechanisms behind many diseases.
Wang said the researchers would soon select 99 Chinese people for the project. The number of research subjects will be expanded to 10,000 in the following couple of years.
"Everyone will have his genome sequenced in the near future for better healthcare," he said.
At the same time, the project is trying to lower the cost to popularize the technology, Yang Huanming, director of the Beijing Institute of Genomics of the Chinese Academy of Sciences, said.
The project in Shenzhen has lowered the cost to US$5 million. It is expected that the cost will drop to 200,000 yuan (US$26,300) by 2010.
"Our final goal is to reduce the cost to less than 10,000 yuan, so that the technology will benefit more people," Yang said.
He said he hoped that in the near future genome sequencing for patients would become as common as a physical examination.
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See also: First Asian genome sequenced Nature 12 October 2007 doi:10.1038/news.2007.161
Reference to the published result (added 5 November, 2008): The diploid genome sequence of an Asian individual Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A. san, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane Ka-Shu Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang & Jian Wang Nature 456, 60-65, 6 November 2008, doi:10.1038/nature07484
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Thursday, 11 October 2007
Stem cell nuclei are soft and plastic
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Adult stem cells not equal to ESCs
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Wednesday, 10 October 2007
Endogenous retrovirus in humans and monkeys
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Tuesday, 9 October 2007
Back to the question: How much is a human egg worth?
Back to the question: How much is a human egg worth? Tuesday, 09 October 2007 Massachusetts regulations prohibit researchers from paying women for their eggs when donated for research. Similar regulations exist in California, and guidelines from both the National Academy of Sciences and the International Society for Stem Cell Research permit only limited compensation for egg donors. The law is meant to prevent coercion of poor women who might undergo the procedure out of financial need. But women who undergo the same procedure to donate eggs for assisted reproductive technology (ART), in which infertile women use another woman's eggs to get pregnant, are paid anywhere from $3,000 to $10,000. The United Kingdom has taken a different approach. Last year, the regulatory board that oversees embryonic stem-cell research in the United Kingdom (HFEA) approved an "egg sharing" program, something that some scientists and ethicists want to see adopted in the United States too. Women who plan to undergo in vitro fertilization (IVF) agree to donate to research any excess eggs gathered during the procedure in exchange for subsidized medical costs. See also: Human Ovulation Caught on Camera What is a human egg worth - £15 or US$10,000? How much is a human egg worth? Back to the question: How much is a human egg worth? Human Therapeutic Cloning at a Standstill ......... ZenMaster
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Therapeutic Cloning at a Standstill
............................. Human Therapeutic Cloning at a Standstill A lack of human eggs has created a major roadblock in one of the most promising areas of stem-cell research. Technology Review - Tuesday, October 09, 2007 .........
ZenMasterFor more on stem cells and cloning, go to CellNEWS at http://www.geocities.com/giantfideli/index.html
Venter makes synthetic life... or not yet?
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Read more: Creating life in the laboratory BBC - 2007/10/19 RELATED INTERNET LINKS: J Craig Venter Institute Massachusetts Institute of Technology Vanderbilt University Medical Center Harvard Medical School University of Rome Three Princeton University Los Alamos National Laboratory Southampton University Biobricks
Which came first, the chicken genome or the egg genome?
Which came first, the chicken genome or the egg genome? Researchers from UC San Diego, U. of Washington School of Medicine and elsewhere have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates? This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations. The chicken shape in the image is actual segmental duplication data from figure 2 of the Nature Genetics paper. The egg was created with graphics editing software. Image Credit: Daniel Kane/ UC San Diego.
Genomes have a remarkable ability to copy a long stretch of DNA from one chromosome and insert it into another region of the genome. The resulting chunks of repeated DNA – called “segmental duplications” – hold many evolutionary secrets and uncovering them is a difficult biological and computational challenge with implications for both medicine and our understanding of evolution.
The new evolutionary history, published in Nature Genetics, is from an interdisciplinary team led by biologist Evan Eichler from the University of Washington School of Medicine and computer scientists Pavel Pevzner from University of California, San Diego.
In the past, the highly complex patterns of DNA duplication – including duplications within duplications – have prevented the construction of an evolutionary history of these long DNA duplications.
Non-random distribution of sequence divergence. The distribution of sequence divergence between ancestral and derivative loci is shown as a function of the location of duplication blocks in the human genome. The authors found 20 of 437 duplication blocks that significantly depart from a continuous genomic duplication model. Eighteen blocks suggest a preponderance of evolutionary younger events (red) and two duplication blocks suggest that duplication activity occurred and then ceased; (green) The effect predominates for particular chromosomes (for example, chr2, chr4, chr5, chr9, chr16 and chrY). The researchers, including UC San Diego’s Pavel Pevzner, tracked down the ancestral origin of more than two thirds of the long DNA duplications in the human genome known as “segmental duplications” and published their results in Nature Genetics.
To crack the duplication code and determine which of the DNA segments are originals (ancestral duplications) and which are copies (derivative duplications), the researchers looked to both algorithmic biology and comparative genomics.
“Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable,” said Pavel Pevzner a UCSD computer science professor who modified an algorithmic genome assembly technique in order to deconstruct the mosaics of repeated stretches of DNA and identify the original sequences.
“Maybe there is something special about the originals, some clue or insight into what causes this colonization of the human genome,” said Pevzner.
“This is the first time that we have a global view of the evolutionary origin of some of the most complicated regions of the human genome,” said paper author Evan Eichler, a professor from the University of Washington School of Medicine and the Howard Hughes Medical Institute.
The researchers tracked down the ancestral origin of more than two thirds of these long DNA duplications. In the Nature Genetics paper they highlight two big picture findings.
First, the researchers suggest that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications.
Second, the researchers show that a large fraction of the recent duplication architecture centres around a rather small subset of “core duplicons” – short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations.
“We found that not all of the duplications in the human genome are created equal. Some of them – the core duplicons – appear to be responsible for recent genetic innovations the in human genome,” explained Pevzner, who is the director of the UCSD Center for Algorithmic and Systems Biology, located at the UCSD division of Calit2.
The researchers, including UC San Diego’s Pavel Pevzner, tracked down the ancestral origin of more than two thirds of the long DNA duplications in the human genome known as “segmental duplications” and published their results in Nature Genetics. This colourful image (figure 2 in the paper) illustrates the process of ancestral-state determination for one 750-kb duplication block on human chromosome 2p11. In this example, 15 of 16 ancestral loci were accurately predicted by the computational method.
The authors uncovered 14 such core duplicons.
“We note that in 4 of the 14 cases, there is compelling evidence that genes embedded within the cores are associated with novel human gene innovations. In two cases the core duplicons has been part of novel fusion genes whose functions appear to be radically different from their antecedents,” the authors write in their Nature Genetics paper.
“The results suggest that the high rate of disease caused by these duplications in the normal population – estimated at 1/500 and 1/1000 events per birth – may be offset by the emergence of newly minted human/great-ape specific genes embedded within the duplications. The next challenge will be determining the function of these novel genes," said Eichler.
To reach these insights, the researchers worked to systematically pinpoint the ancestral origin of each human segmental duplication and organized duplication blocks based on their shared evolutionary history.
Pevzner and his associate Haixu Tang (now professor at University of Indiana) applied their expertise in assembling genomes from millions of small fragments – a problem that is not unlike the “mosaic decomposition” problem in analyzing duplications that the team faced.
Over the years, Pevzner has applied the 250-year old algorithmic idea first proposed by 18th century mathematician Leonhard Euler (of the fame of pi) to a variety of problems and demonstrated that it works equally well for a set of seemingly unrelated biological problems including DNA fragment assembly, reconstructing snake venoms, and now dissecting the mosaic structure of segmental duplications.
In the future, the researchers plan to continue their exploration of evolution.
“We want to figure out how the human genome evolved. In the future, we will combine what we know about the evolution within genomes with comparative genomics in order to extend our view of evolution,” said Pevzner.
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ZenMaster
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Thursday, 4 October 2007
Clinton Would Fund Stem Cell Research
NEW YORK — If elected president, Democrat Hillary Rodham Clinton says she would sign an executive order rescinding President Bush's restrictions on federal funding for embryonic stem cell research.
She says she also would bar political appointees from altering or removing scientific conclusions from government research without a legitimate reason for doing so.
The New York senator was to announce these and other proposals of her science agenda in a speech in Washington on Thursday. ......... ZenMaster
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