Category Archives: Genome

Sangtee Kim

The plant Amborella is found natively only in New Caledonia.

A shrub with cream-coloured flowers that is the closest living descendant of Earths first flowering plants has had its genome decoded. The sequence of Amborella trichopoda hints at the genetic adaptations that helped flowers to emerge and conquer the world some 160 million years ago an evolutionary explosion described by Charles Darwin as an abominable mystery.

Nearly everything about Amborella is fodder for a botanists pub quiz. It grows natively in 18 known spots on the New Caledonian island of Grande Terre in the South Pacific, and nowhere else on Earth. The plants reproductive structures are encased in tepals a hybrid between petals and leaf-like support structures called sepals.

Amborella is the only species in its genus, family and order. Phylogenetically, its really the equivalent of the duck-billed platypus and monotremes, says Claude dePamphilis, a plant evolutionary biologist at Pennsylvania State University in University Park, who co-led researchers on the Amborella Genome Project. The fruits of their labour are published in three papers in Science today13.

Just as the platypus genome yielded insights into the emergence of mammals, Amborellas gives a glimpse at changes that helped flowering plants, or angiosperms, to diversify from a common ancestor with gymnosperms another major plant lineage, which includes conifer trees such as spruces.

Comparisons of the genomes of Amborella and those of other plants suggest that an early ancestor of flowering plants gained a duplicate copy of its genome, a feature known as polyploidy. Many angiosperms are known to be polyploid potatoes, for instance, have between two and six copies of each chromosome. But the duplication in Amborella predates all the other polyploids, says dePamphilis, who led a team in 2011 that inferred this ancient duplication from more limited genetic data4.

The duplication may have spurred the diversification and expansion of flowering plants by providing an extra copy of each gene for evolution to play around with to yield new functions, dePamphilis suggests.

The origin of flowers the defining features of angiosperms might be explained by a collection of genes that appeared when angiosperms split from gymnosperms, analysis of the Amborella genome reveals. About one-quarter of the genes involved in flowering lack obvious counterparts in the genomes of gymnosperms, whereas the other three-quarters existed in the common ancestor of both plant lineages. His teams analysis also provides insight into the evolution of complex seeds, floral scents and other features of flowering plants.

Keith Adams, a plant molecular geneticist at the University of British Columbia in Vancouver, Canada, thinks the idea that a genome duplication helped flowering plants to diversify is an intriguing hypothesis although its impossible to prove. Botanists studying other plants should find the Amborella genome useful as a reference point to identify and study families of genes in other plants, including crops, he says.

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Shrub genome reveals secrets of flower power

A genome sequenced from the toe bone of a Neanderthal woman has yielded several new insights into the evolution of early humans and their contemporaries.

The existence of a mysterious ancient human lineage and the genetic changes that separate modern humans from their closest extinct relatives are among the many secrets now revealed in the first high-quality genome sequence from a Neanderthal woman, researchers say.

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TheNeanderthal womanwhose toe bone was sequenced also reveals inbreeding may have been common among her recent ancestors, as her parents were closely related, possibly half-siblings or another near relation.

Although modern humans are the world's only surviving human lineage, others also once lived on Earth. These includedNeanderthals, the closest extinct relatives of modern humans, and the relatively newfoundDenisovans, whosegenetic footprintapparently extended from Siberia to the Pacific islands of Oceania. Both Neanderthals and Denisovans descended from a group that diverged from the ancestors of all modern humans. [See Photos of Neanderthal Bone & Denisovan Fossils]

The first signs of Denisovans came from a finger bone and a molar tooth discovered in Denisova Cave in southern Siberia in 2008. To learn more about Denisovans, scientists examined a woman's toe bone, which was unearthed in the cave in 2010 and showed physical features resembling those of both Neanderthals and modern humans. The fossil is thought to be about 50,000 years old, and slightly older than previously analyzed Denisovan fossils.

Human interbreeding

The scientists focused mostly on the fossil'snuclear DNA, the genetic material from the chromosomes in the nucleus of the cell that a person receives from both their mother and father. They also examined the genome of this fossil's mitochondria the powerhouses of the cell, which possess their own DNA and get passed down solely from the mother.

The investigators completely sequenced the fossil's nuclear DNA, with each position (or nucleotide) sequenced an average of 50 times. This makes the sequence's quality at least as high as that of genomes sequenced from present-day people.

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Neanderthal genome suggests new, mysterious human lineage (+video)

The Human Genome Project is one of the largest collaborative biological projects ever initiated. It was officially funded by the US Department of Energy's Office of Health and Environmental Research during the Reagan Administration, it was planned originally for 15 years. A rough draft of the human genome was available in June 2000, and within 3 more years final sequencing mapping of the genome was published. Work hasn't stopped here, further analysis and discoveries continue to this day. Through the sequencing of our DNA scientists are able to understand diseases in a way that was never possible before. They can now manage the genotyping of specific viruses to more accurately direct treatment. Cancer detection and treatment has also changed radically since the project.

Advances like this may all change if news from the states on the level of funding remains unchecked and continues to decline.

Recent analysis has shown that the United States may be losing ground as one of the leaders in biomedical research and design.

High ranking officials associated with the funding programs and scientists alike are hoping House of Senate budget negotiators will succeed in finding some common ground and resolve these funding issues.

At a recent conference key advisors identified projects that could not have happened if government spend had not been available, one of those projects was the human genome project. One of the leaders of the projected said it may have produced more than 400,000 jobs directly and at least 7 million indirectly and generated in total $965 billion in economic growth.

Surely this is compelling evidence to review budget strategy?

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Human Genome

Incredible Microprocessor Protein Acts as Genome Guardian
http://www.icr.org/article/7844/

By: Dave Flang

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Incredible Microprocessor Protein Acts as Genome Guardian - Video

Genome Laser at London Decompression 2013
Following the inaugural public genome laser broadcast at Black Rock City, Alex and Vincent decided the project must continue. London Decompression was the id...

By: Genome Laser

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Genome Laser at London Decompression 2013 - Video

Non-coding regions in the genome - Robert Tjian (Berkeley/HHMI)
The significance of non-coding versus coding regions in the human genome.

By: iBioEducation

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Non-coding regions in the genome - Robert Tjian (Berkeley/HHMI) - Video

28c3 4730 en crowdsourcing genome wide association studies h264

By: rabatakeu

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28c3 4730 en crowdsourcing genome wide association studies h264 - Video

Nov. 13, 2013 Johns Hopkins researchers report that the deletion of any single gene in yeast cells puts pressure on the organism's genome to compensate, leading to a mutation in another gene. Their discovery, which is likely applicable to human genetics because of the way DNA is conserved across species, could have significant consequences for the way genetic analysis is done in cancer and other areas of research, they say.

Summarized in a report to be published on Nov. 21 in the journal Molecular Cell, the team's results add new evidence that genomes, the sum total of species' genes, are like supremely intricate machines, in that the removal of a single, tiny part stresses the whole mechanism and might cause another part to warp elsewhere to fill in for the missing part.

"The deletion of any given gene usually results in one, or sometimes two, specific genes being 'warped' in response," says J. Marie Hardwick, Ph.D., the David Bodian Professor of Molecular Microbiology and Immunology at the Johns Hopkins Bloomberg School of Public Health and a professor of pharmacology and molecular sciences at the school of medicine. "Pairing the originally deleted gene with the gene that was secondarily mutated gave us a list of gene interactions that were largely unknown before."

Hardwick says the findings call researchers to greater scrutiny in their genetic analyses because they could unwittingly attribute a phenomenon to a gene they mutated, when it is actually due to a secondary mutation.

"This work has the potential to transform the field of cancer genetics," Hardwick says. "We had been thinking of cancer as progressing from an initial mutation in a tumor-suppressor gene, followed by additional mutations that help the cancer thrive. Our work provides hard evidence that a single one of those 'additional mutations' might come first and actively provoke the mutations seen in tumor-suppressor genes. We hope that our findings in yeast will help to identify these 'first' mutations in tumors."

The beauty of working with yeast, Hardwick says, is that it is easy to delete, or "knock out," any given gene. Her team started with a readily available collection of thousands of different yeast strains, each with a different gene knockout.

At their preferred temperature, each of these strains of yeast grows robustly even though they each have a different gene missing. Hardwick's team first asked a fundamental question: Within a given strain of yeast, does each cell have the same genetic sequence as the other cells, as had generally been presumed?

"We know, for example, that within a given tumor, different cells have different mutations or versions of a gene," explains Hardwick. "So it seemed plausible that other cell populations would exhibit a similar genetic diversity."

To test this idea, her team randomly chose 250 single-knockout strains from the thousands of strains in the collection. For each strain, they generated six sub-strains, each derived from a single yeast cell from the "parental batch."

They then put each sub-strain through a "stress test" designed to detect sub-strains with behaviors that varied from the behavior of the parental batch. All of the sub-strains grew indistinguishably without stress, but when the temperature was gradually raised for only a few minutes, some sub-strains died because they could not handle the stress. When the Hardwick team examined their genes, they found that, in addition to the originally knocked-out gene, each of the sub-strains that faltered also had a mutation in another gene, leading the team to conclude that the cells in each strain of the single-gene knockouts do not all share the same genetic sequence.

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Deletion of any single gene provokes mutations elsewhere in the genome

A cartoon in the current issue of the New Yorker magazine shows a couple at the altar exchanging wedding vows. The cutline says: "Do you, Ashley, take Nesbitt and his genome to be your husband?"

Very funny -- and possibly of sign of what's soon to come.

The cost of sequencing a person's entire genome is expected to fall to about $1,000 over the next year or so. You can already get part of your DNA analyzed by 23andMe for $99. Routine genetic screening is just ahead, and we'll take a look at the possible consequences in an upcoming story.

We're nearing the point where genetic analysis will more clearly tell a young couple whether they can produce a healthy child. People who get married in mid-life could learn whether their partner is predisposed to such neurological diseases as Alzheimer's and Parkinsons.

How is this going to change how we think about love and marriage? We'd like to hear you thoughts. Some comments will be included in the upcoming article. We want to hear from everyone: wedding planners to couples who are engaged to people who simply find the question to be provocative.

Specifically, do you think:

Email your thoughts to gary.robbins@utsandiego.com. Please include your full name, hometown and occupation.

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Will you marry me - and my genome?

Big Data in the Post-genome Era: What can the human genome sequence do for you?
Big Data in the Post-genome Era: What can the human genome sequence do for you?

By: SITN Boston

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Big Data in the Post-genome Era: What can the human genome sequence do for you? - Video