Category Archives: Transhuman News

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27 November 2013 - 100 Species Conservation Track now available on hg19

After 15.4 years of CPU run-time in 9,905,594 individual 'jobs' and 99 cluster runs for lastz pair-wise alignment...we are excited to announce the release of a 100 species alignment on the hg19/GRCh37 human Genome Browser.

This new Conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. This adds 40 more species to the existing 60-way on the mm10 mouse browser. For more information about the 100 species Conservation track, see its description page.

We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the information for this track: Hiram Clawson and Pauline Fujita.

24 October 2013 - Job Opening: UCSC Genome Browser Trainer

The Center for Biomolecular Science and Engineering (CBSE) at University of California Santa Cruz seeks an articulate, self-motivated educator for the two-year position of UCSC Genome Browser trainer. The trainer develops curriculum and provides in-person training on the UCSC Genome Browser at universities, hospitals, institutes, and professional meetings in the United States and internationally. Typical audiences include graduate and post-graduate biologists and doctors, with Genome Browser experience ranging from novice users to bioinformatics specialists. Presentations include formal talks, problem-solving sessions, and two-day workshops.

This position requires a Master's degree in a biological science, depth in molecular biology, experience in a research environment, working knowledge of the UCSC Genome Browser, understanding of its role in research methodology, and experience teaching or training in a scientific environment. Preferred qualifications include a PhD in a relevant field, experience with video production, and experience with HTML or web content management systems.

For more information and to apply for this position, see Job #1304619 on the UCSC Staff Employment website.

23 October 2013 - dbSNP 138 Available for hg19: We are pleased to announce the release of four tracks derived from NCBI dbSNP Build 138 data, available on the human assembly (GRCh37/hg19). Read more.

See original here:
UCSC Genome Browser - Official Site

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.

Excerpt from:
Neanderthal genome suggests new, mysterious human lineage

Image Caption: The newly sequenced genome of the Amborella plant will be published in the journal Science on 20 December 2013. The genome sequence sheds new light on a major event in the history of life on Earth: the origin of flowering plants, including all major food crop species. Credit: Sangtae Kim

redOrbit Staff & Wire Reports Your Universe Online

The newly-sequenced genome of the Amborella plant is shedding new light on the origin of the more than 300,000 flowering plants on the Earth today, including all major food crop species.

Amborella trichopoda, a small understory tree found only on the main island of New Caledonia in the South Pacific, is unique as the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants. This heritage gives the plant a special role in the study of flowering plants, the researchers said.

In the same way that the genome sequence of the platypus a survivor of an ancient lineage can help us study the evolution of all mammals, the genome sequence of Amborella can help us learn about the evolution of all flowers, said study researcher Victor Albert of the University at Buffalo.

The researchers who sequenced the Amborella genome say that it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a genome doubling event that occurred about 200 million years ago. Some duplicated genes were lost over time but others took on new functions, including contributions to the development of floral organs, the researchers said.

Genome doubling may, therefore, offer an explanation to Darwins abominable mystery the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period, said Claude dePamphilis of Penn State University, one of the studys researchers.

Generations of scientists have worked to solve this puzzle.

Comparative analyses of the Amborella genome are already providing scientists with a new perspective on the genetic origins of important traits in all flowering plants, including all major food crop species.

Because of Amborellas pivotal phylogenetic position, it is an evolutionary reference genome that allows us to better understand genome changes in those flowering plants that evolved later, including genome evolution of our many crop plants hence, it will be essential for crop improvement, said Doug Soltis of the University of Florida.

Original post:
Genome Sequence Gives Insight Into Evolution Of Flowering Plants

Affecting the Shelf Life of Chromosomes

12/19/2013

Just like the chicken or milk you buy at a store, chromosomes have a shelf life too. Of course, chromosomes dont spoil because of growing bacteria. Instead, they go bad because they lose a little of the telomeres at their ends each time they are copied. Once these telomeres get too short, the chromosome stops working and the cell dies. Turns out food and chromosomes have another thing in commonthe rates of spoilage of both can...read more >

12/17/2013

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Winter 2013 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know. ...read more >

12/12/2013

The most interesting board games cant be played right out of the box. You can admire the board and the game pieces, but before the fun can begin you need to spend some time reading the instructions and understanding the strategy. Gene Ontology (GO) annotations are a little bit like that. You can get interesting information very quickly by just reading the GO terms on the Locus Summary page of your favorite yeast protein in SGD....read more >

12/03/2013

Our friend Saccharomyces cerevisiae has it pretty easy when it comes to sex. There is no club scene or online dating. Pretty much if an a and an are close enough together, odds are that they will shmoo towards each other and fuse to create a diploid cell. No fuss, no muss. Of course there arent any visual cues that indicate whether a yeast is aor . Instead yeast relies on detecting gender-specific pheromones each cell...read more >

Continue reading here:
Saccharomyces Genome Database - Official Site

Neanderthals

Nidhi Subbaraman NBC News

Dec. 18, 2013 at 1:01 PM ET

Bence Viola

Researchers extracted DNA from this toe bone of a Siberian Neanderthal female who lived about 50,000 years ago.

The first high-quality genome sequence of a Siberian Neanderthal female is throwing up racy details about our ancient relatives sex lives: Siberian Neanderthals mated within their families, the new research shows, while another group, the Denisovans, interbred with Neanderthals, humans and a third, as yet undiscovered mystery hominin living in Asia.

The first anthropologists relied on skull shapes and bone lengths of fossils to identify ancestors in the hominin family tree. Recently though, geneticists have bulked up their toolset, and have identified new species from material taken from mere milligrams of bone. This time, they didn't even need that.

"There is not even a bone splinter here," Svante Pbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology, said of the unknown species. "Its an inference from those other genomes."

By comparing genetic evidence of the Neanderthal female who lived some 50,000 years ago, with the sequence of a Denisovan girl published in August last year, Pbo and team discovered a small but discrete signature of a much older species, which the paleoanthropologists suspect might be Homo erectus. The full analysis of the Siberian Neanderthal genome is published in the Thursday issue of Nature.

Bence Viola

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Sex and the Siberian Neanderthal: Incest and inter-species action

Dec. 19 (UPI) -- The most complete sequence of the Neanderthal genome shows inbreeding as well as interbreeding among at least four different types of early humans.

DNA extracted from the fossilized toe of a 50,000 year-old Siberian Neanderthal woman revealed that she was the child of two closely related parents, who were either half-siblings or double first cousins, the offspring of two siblings who married siblings.

Researchers found that Neanderthals and Denisovans, another type of early human, were closely related and that their common ancestor split off from the ancestor of modern humans around 400,000 years ago.

Further analysis suggests that the population sizes of Denisovans and Neanderthals were small, leading to interbreeding. Researchers also found evidence of interbreeding with a mysterious fourth type of early human.

The international team of anthropologists and geneticists published their findings in the journal Nature.

These two types of early humans eventually died out but left some of their genetic history because they occasionally interbred with modern humans. Researchers said that close to 1.5 to 2.1 percent of modern non-African genomes can be traced back to Neanderthals.

The paper really shows that the history of humans and hominins during this period was very complicated, said Montgomery Slatkin, a professor at UC Berkeley. There was lot of interbreeding that we know about and probably other interbreeding we havent yet discovered.

Graduate student Fernando Racimo found 87 specific genes that were significantly different from those found in Neanderthals and Denisovans, and could be the distinguishing factor between modern humans and their ancestors.

There is no gene we can point to and say, This accounts for language or some other unique feature of modern humans, Slatkin said. But from this list of genes, we will learn something about the changes that occurred on the human lineage, though those changes will probably be very subtle.

[UC Berkeley] [Nature]

Read more here:
Neanderthal genome reveals inbreeding and interbreeding

Dec. 18, 2013 The most complete sequence to date of the Neanderthal genome, using DNA extracted from a woman's toe bone that dates back 50,000 years, reveals a long history of interbreeding among at least four different types of early humans living in Europe and Asia at that time, according to University of California, Berkeley, scientists.

Population geneticist Montgomery Slatkin, graduate student Fernando Racimo and post-doctoral student Flora Jay were part of an international team of anthropologists and geneticists who generated a high-quality sequence of the Neanderthal genome and compared it with the genomes of modern humans and a recently recognized group of early humans called Denisovans.

The comparison shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago. Neanderthals and Denisovans split about 300,000 years ago.

Though Denisovans and Neanderthals eventually died out, they left behind bits of their genetic heritage because they occasionally interbred with modern humans. The research team estimates that between 1.5 and 2.1 percent of the genomes of modern non-Africans can be traced to Neanthertals.

Denisovans also left genetic traces in modern humans, though only in some Oceanic and Asian populations. The genomes of Australian aborigines, New Guineans and some Pacific Islanders are about 6 percent Denisovan genes, according to earlier studies. The new analysis finds that the genomes of Han Chinese and other mainland Asian populations, as well as of native Americans, contain about 0.2 percent Denisovan genes.

The genome comparisons also show that Denisovans interbred with a mysterious fourth group of early humans also living in Eurasia at the time. That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia a million or more years ago.

"The paper really shows that the history of humans and hominins during this period was very complicated," said Slatkin, a UC Berkeley professor of integrative biology. "There was lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered."

The genome analysis will be published in the Dec. 19 issue of the journal Nature. Slatkin, Racimo and Jay are members of a large team led by former UC Berkeley post-doc Svante Pbo, who is now at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In another analysis, Jay discovered that the Neanderthal woman whose toe bone provided the DNA was highly inbred. The woman's genome indicates that she was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins (the offspring of two siblings who married siblings).

Further analyses suggest that the population sizes of Neanderthals and Denisovans were small and that inbreeding may have been more common in Neanderthal groups than in modern populations.

Read more here:
Neanderthal genome shows early human interbreeding, inbreeding

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.

Read the original post:
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.

Subscribe Today to the Monitor

Click Here for your FREE 30 DAYS of The Christian Science Monitor Weekly Digital Edition

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.

See original here:
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?

Excerpt from:
Human Genome