Category Archives: Genome

Prof. Eric Lander Secrets of the Human Genome II Medicine - Technion Lecture
"Secrets of the Human Genome II - Medicine" by Prof. Eric S. Lander at Technion-Israel Institute of Technology, Rappaport Faculty of Medicine. April 30, 2013...

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The Incomplete Map of the Cosmic Genome Teaser
In the words of Richard Feynman, "We are matter with curiosity." TIMOFCG is an app for the interested. Available from the iTunes App Store June 2013. There i...

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The Incomplete Map of the Cosmic Genome Teaser - Video

A team of 70 scientists from the United States, China, Australia and Japan reports having sequenced and annotated the genome of the "sacred lotus," which is believed to have a powerful genetic system that repairs genetic defects, and may hold secrets about aging successfully.

The scientists sequenced more than 86 percent of the nearly 27,000 genes of the plant, Nelumbo nucifera, which is revered in China and elsewhere as a symbol of spiritual purity and longevity.

"The lotus genome is an ancient one, and we now know its ABCs," said Jane Shen-Miller, one of three corresponding authors of the research and a senior scientist with UCLA's Center for the Study of Evolution and the Origin of Life. "Molecular biologists can now more easily study how its genes are turned on and off during times of stress and why this plant's seeds can live for 1,300 years. This is a step toward learning what anti-aging secrets the sacred lotus plant may offer."

The research was published today in the journal Genome Biology.

Shen-Miller said the lotus' genetic repair mechanisms could be very useful if they could be transferred to humans or to crops such as rice, corn and wheat whose seeds have life spans of only a few years. "If our genes could repair disease as well as the lotus' genes, we would have healthier aging. We need to learn about its repair mechanisms, and about its biochemical, physiological and molecular properties, but the lotus genome is now open to everybody."

In the early 1990s, Shen-Miller led a UCLA research team that recovered a viable lotus seed that was almost 1,300 years old from a lake bed in northeastern China. It was a remarkable discovery, given that many other plant seeds are known to remain viable for just 20 years or less.

In 1996, Shen-Miller led another visit to China. Working in Liaoning province, her team collected about 100 lotus seeds - most were approximately 450 to 500 years old - with help from local farmers. To the researchers' surprise, more than 80 percent of the lotus seeds that were tested for viability germinated. That indicated that the plant must have a powerful genetic system capable of repairing germination defects arising from hundreds of years of aging, Shen-Miller said.

Understanding how the lotus repair mechanism works and its possible implications for human health is essentially a three-step process, said Crysten Blaby-Haas, a UCLA postdoctoral scholar in chemistry and biochemistry and co-author of the research. "Knowing the genome sequence was step one. Step two would be identifying which of these genes contributes to longevity and repairing genetic damage. Step three would be potential applications for human health, if we find and characterize those genes. The genome sequence will aid in future analysis.

"The next question is what are these genes doing, and the biggest question is how they contribute to the longevity of the lotus plant and its other interesting attributes," Blaby-Haas said. "Before this, when scientists studied the lotus, it's almost as if they were blind; now they can see. Once you know the repertoire of genes, you have a foundation to study their functions."

The genome sequence reveals that, when compared with known gene sequences of dozens of other plants, the lotus bears the closest resemblance to the ancestor of all eudicots, a broad category of flowering plants that includes the apple, peanut, tomato, cotton, cactus and tobacco plants.

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Genome of lotus may hold anti-aging secrets

May 10, 2013 The sacred lotus (Nelumbo nucifera) is a symbol of spiritual purity and longevity. Its seeds can survive up to 1,300 years, its petals and leaves repel grime and water, and its flowers generate heat to attract pollinators.

Now researchers report in the journal Genome Biology that they have sequenced the lotus genome, and the results offer insight into the heart of some of its mysteries. The sequence reveals that of all the plants sequenced so far -- and there are dozens -- sacred lotus bears the closest resemblance to the ancestor of all eudicots, a broad category of flowering plants that includes apple, cabbage, cactus, coffee, cotton, grape, melon, peanut, poplar, soybean, sunflower, tobacco and tomato.

The plant lineage that includes the sacred lotus forms a separate branch of the eudicot family tree, and so lacks a signature triplication of the genome seen in most other members of this family, said University of Illinois plant biology and Institute for Genomic Biology professor Ray Ming, who led the analysis with Jane Shen-Miller, a plant and biology professor at the University of California at Los Angeles (who germinated a 1,300-year-old sacred lotus seed); and Shaohua Li, the director of the Wuhan Botanical Garden at the Chinese Academy of Sciences.

"Whole-genome duplications -- the doubling, tripling (or more) of an organism's entire genetic endowment -- are important events in plant evolution," Ming said. Some of the duplicated genes retain their original structure and function, and so produce more of a given gene product -- a protein, for example, he said. Some gradually adapt new forms to take on new functions. If those changes are beneficial, the genes persist; if they're harmful, they disappear from the genome.

Many agricultural crops benefit from genome duplications, including banana, papaya, strawberry, sugarcane, watermelon and wheat, said Robert VanBuren, a graduate student in Ming's lab and collaborator on the study.

Although it lacks the 100 million-year-old triplication of its genome seen in most other eudicots, sacred lotus experienced a separate, whole-genome duplication about 65 million years ago, the researchers found. A large proportion of the duplicated genes (about 40 percent) have been retained, they report.

"A neat thing about the duplication is that we can look at the genes that were retained and see if they are in specific pathways," VanBuren said. The researchers found evidence that duplicated genes related to wax formation (which allows the plant to repel water and remain clean) and survival in a mineral-starved watery habitat were retained, for example.

By looking at changes in the duplicated genes, the researchers found that lotus has a slow mutation rate relative to other plants, Ming said.

These traits make lotus an ideal reference plant for the study of other eudicots, the researchers said.

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Sacred lotus genome sequence enlightens scientists

The results of an avian genome project conducted by a team of Texas A&M researchers were published this month in a scientific journal.

Spearheaded by Christopher Seabury and Ian Tizard at the Schubot Exotic Bird Health Center, which is part of the Texas A&M College of Veterinary Medicine and Biomedical Sciences, the team studied the DNA of a Scarlet Macaw named "Neblina" in producing the first genome sequence of the breed.

The macaw is a rare type of parrot known for its intelligence, ability to fly long distances and their long lives, with some living up to 75 years, according to Tizard.

Because of their unique characteristics, affectionate demeanor and colorful feathers, the Scarlet Macaw is coveted by illegal pet traders. Neblina, who lives in a Iowa zoo, is believed to be from Brazil and was recovered during a raid on illegally imported exotic birds.

Seabury said the project is significant for several reasons. It's one of just a handful of avian genomes that's been assembled and published in a peer-reviewed scientific journal.

Additionally, the techniques used by the team have the potential to lead the way in future avian genome research.

"We demonstrated that genome projects like this are absolutely feasible for small scientific groups," Seabury said.

He added that by studying the Scarlet Macaw genome in comparison to other known bird genomes, scientists can gain a better understanding of avian biology.

"The Scarlet Macaw Genome Project opens a variety of doors ranging from modern forensics to determining how the macaws utilize their natural habitat and landscape, as inferred from variable genetic markers," Seabury said.

The research also helps define genetic components that influence traits commonly found in parrots such as longevity and intelligence.

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Texas A&M researchers uncover genome sequence of Scarlet Macaw

Newswise COLLEGE STATION, May 8, 2013 In a groundbreaking move that provides new insight into avian evolution, biology and conservation, researchers at Texas A&M University have successfully sequenced the complete genome of a Scarlet macaw for the first time.

The team was led by Drs. Christopher Seabury and Ian Tizard at the Schubot Exotic Bird Health Center in the College of Veterinary Medicine & Biomedical Sciences at Texas A&M. Their work is published in the current issue of the open access and peer-reviewed scientific journal PLOS ONE (http://dx.plos.org/10.1371/journal.pone.0062415).

The bird selected for the sequencing was a female named Neblina who lives in the Blank Park Zoo in Des Moines, Iowa. Neblina is believed to be from Brazil. She was confiscated during a raid on illegally imported exotic birds by the U.S. Fish and Wildlife Service in 1995.

Tizard says that a blood sample was taken from Neblina, DNA was extracted for sequencing, and after a series of steps, the sequence of the genome was assembled by Seabury and his team.

The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals, Tizard explains. Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA.

The final completed genome demonstrates some similarities to that of the chicken. But there are significant differences at both the genome and biological level, he adds. For example, Macaws can fly great distances, while chickens cant. In addition, brain development and volume are very different in macaws, which is unsurprising since they are very intelligent birds compared to chickens. Likewise, macaws can live many years, while chickens usually do not, and therefore, our macaw genome sequence may help shed light on the genetic factors that influence longevity and intelligence.

Tizard notes that a Scarlet macaw was selected for the first such sequencing of its type because Texas A&M researchers have been studying the bird for many years. Working primarily at the Tambopata Research Center in Peru, Texas A&M bird experts have been investigating macaw diseases, behavior and genetics.

We now have the ability to initiate large-scale, genome-wide approaches for population and phylogeography studies, explains Seabury, who is a collaborator of Donald Brightsmith, director of the Tambopata Macaw Research Project in Peru (http://www.macawproject.org/).

Seabury and Brightsmith add that the array of research possibilities regarding the Scarlet Macaw has now been significantly broadened by this research initiative.

Macaws are found in tropical Central and South America, from southern Mexico to northern Argentina. Trapping of the birds for the pet trade, plus loss of habitat due to deforestation in their native lands, has severely decreased their numbers since the 1960s.

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Save the Parrots: Texas A&M Team Sequences Macaw Genome

Public release date: 9-May-2013 [ | E-mail | Share ]

Contact: Linda Aagard 801-587-7639 University of Utah Health Sciences

SALT LAKE CITYResearchers from Huntsman Cancer Institute (HCI) at the University of Utah have discovered that while the genes provided by the father arrive at fertilization pre-programmed to the state needed by the embryo, the genes provided by the mother are in a different state and must be reprogrammed to match. The findings have important implications for both developmental biology and cancer biology.

In the earliest stages, embryo cells have the potential to develop into any type of cell, a state called totipotency. Later, this potency becomes restricted through a process called differentiation. As a result, as cells continue to differentiate, they give rise to only a subset of the possible cell types.

"In cancer, normal processes of cell differentiation and growth go wrong, and cells either become arrested at an early state of differentiation, or instead go backwards and are 'reprogrammed' to become more like early embryo cells," said Bradley R. Cairns, co-author of the article and Senior Director of Basic Science at HCI. "By understanding how cells are normally programmed to the totipotent state, and how they develop from that totipotent state into specific cell types, we hope to better understand how cancer cells misregulate this process, and to use that knowledge to help us devise strategies to reverse this process." The research results will be published online as the cover story in the journal Cell on May 9.

Earlier work in the Cairns Lab showed that most genes important for guiding the early development of the embryo are already present in human sperm cells of the father in a "poised" stateturned off, but with attached markers that make gene activation easy. "The logic is that all the important decision-making genes for early development are ready to go," said Cairns. "This poised state is never seen in fully differentiated cells such as skin cells."

In the current study, researchers in the Cairns Lab used high-throughput gene sequencing to comprehensively and precisely analyze DNA methylation patterns in the genomes of zebrafish, which is a common laboratory model both for developmental and cancer biology. Here, they examined egg cells, sperm cells, and four phases of embryonic development: three phases between fertilization and when the embryo's genome becomes active, and one phase after that point. Methylationin which molecules called methyl groups are selectively attached to certain areas of the DNA and turn off gene activity in those areasis one of the main markers of gene poising; poised genes lack DNA methylation, enabling gene activity later in embryo development.

Cairns' group found that the methylation pattern of the soon-to-differentiate embryo is identical to that of the sperm cell. In contrast, the pattern of the egg cell was initially quite different, but undergoes a striking set of changes to become exactly matched to that of the sperm DNA. Cairns' work suggests that egg DNA goes through this extensive reprogramming to prepare for the process of differentiation.

"The maternal genes that underwent DNA methylation reprogramming are among the most important loci for determining embryo development," said Cairns. "For example, many hox genes, which determine the body plan and also differentiation during hematopoiesis [the formation of blood cells], are methylated in the mother's genetic contribution and demethylated in the father's, and therefore, also in the embryo."

He said the work added another interesting finding. "We found that the mother's genome takes care of that remodeling on its own, without using the father's genome as a template." Cairns' experiments showed that when the father's genetic contribution was removed, the mother's genome still remodeled itself to the correct state.

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Dad's genome more ready at fertilization than mom's is -- but hers catches up

May 8, 2013 In a groundbreaking move that provides new insight into avian evolution, biology and conservation, researchers at Texas A&M University have successfully sequenced the complete genome of a Scarlet macaw for the first time.

The team was led by Drs. Christopher Seabury and Ian Tizard at the Schubot Exotic Bird Health Center in the College of Veterinary Medicine & Biomedical Sciences at Texas A&M. Their work is published in the current issue of the open access and peer-reviewed scientific journal PLOS ONE.

The bird selected for the sequencing was a female named "Neblina" who lives in the Blank Park Zoo in Des Moines, Iowa. Neblina is believed to be from Brazil. She was confiscated during a raid on illegally imported exotic birds by the U.S. Fish and Wildlife Service in 1995.

Tizard says that a blood sample was taken from Neblina, DNA was extracted for sequencing, and after a series of steps, the sequence of the genome was assembled by Seabury and his team.

"The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals," Tizard explains. "Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA."

The final completed genome demonstrates some similarities to that of the chicken. "But there are significant differences at both the genome and biological level," he adds. For example, "Macaws can fly great distances, while chickens can't. In addition, brain development and volume are very different in macaws, which is unsurprising since they are very intelligent birds compared to chickens. Likewise, macaws can live many years, while chickens usually do not, and therefore, our macaw genome sequence may help shed light on the genetic factors that influence longevity and intelligence."

Tizard notes that a Scarlet macaw was selected for the first such sequencing of its type because Texas A&M researchers have been studying the bird for many years. Working primarily at the Tambopata Research Center in Peru, Texas A&M bird experts have been investigating macaw diseases, behavior and genetics.

"We now have the ability to initiate large-scale, genome-wide approaches for population and phylogeography studies," explains Seabury, who is a collaborator of Donald Brightsmith, director of the Tambopata Macaw Research Project in Peru.

Seabury and Brightsmith add that the array of research possibilities regarding the Scarlet Macaw has now been significantly broadened by this research initiative.

Macaws are found in tropical Central and South America, from southern Mexico to northern Argentina. Trapping of the birds for the pet trade, plus loss of habitat due to deforestation in their native lands, has severely decreased their numbers since the 1960s.

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Save the parrots: Macaw genome sequenced

Miracle of the genome!

By: Sweetitly

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Miracle of the genome! - Video

Salutations, Genome
5/1/13 Tonic Room, Chicago.

By: Carmel O #39;Farrell

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Salutations, Genome - Video