Category Archives: Genome

2. UCSC Genome Browser Tutorial: tracks
UCSC Genome Browser Tutorial Video 2 A discussion of tracks in the genome browser, the building blocks of the graphical user interface. Here I discuss: --how...

By: Sam Allon

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2. UCSC Genome Browser Tutorial: tracks - Video

CHARACTERIZATION OF UTERINE LEIOMYOMAS BY WHOLE GENOME SEQUENCING

By: karen perez

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CHARACTERIZATION OF UTERINE LEIOMYOMAS BY WHOLE GENOME SEQUENCING - Video

PUBLIC RELEASE DATE:

10-Sep-2014

Contact: Glenna Picton picton@bcm.edu 713-798-4710 Baylor College of Medicine @bcmhouston

HOUSTON (Sep. 10. 2014) With the completion of the sequencing and analysis of the gibbon genome, scientists now know more about why this small ape has a rapid rate of chromosomal rearrangements, providing information that broadens understanding of chromosomal biology.

Chromosomes, essentially the packaging that encases the genetic information stored in the DNA sequence, are fundamental to cellular function and the transmission of genetic information from one generation to the next. Chromosome structure and function is also intimately related to human genetic diseases, especially cancer.

The sequence and analysis of the gibbon genome (all the chromosomes) was published today in the journal Nature and led by scientists at Oregon Health & Science University, the Baylor College of Medicine Human Genome Sequencing Center and the Washington University School of Medicine's Genome Institute.

"Everything we learn about the genome sequence of this particular primate and others analyzed in the recent past helps us to understand human biology in a more detailed and complete way," said Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center at Baylor and a lead author on the report. "The gibbon sequence represents a branch of the primate evolutionary tree that spans the gap between the Old World Monkeys and great apes and has not yet been studied in this way. The new genome sequence provides important insight into their unique and rapid chromosomal rearrangements."

For years, experts have known that gibbon chromosomes evolve quickly and have many breaks and rearrangements, but up until now there has been no explanation why, Rogers said. The genome sequence helps to explain the genetic mechanism unique to gibbons that results in these large scale rearrangements.

The sequencing was led by Dr. Kim Worley, professor in the Human Genome Sequencing Center, and Rogers, both of Baylor and Drs. Wesley Warren and Richard Wilson of Washington University.

The analysis was led by Dr. Lucia Carbone, an assistant professor of behavioral neuroscience in the OHSU School of Medicine and an assistant scientist in the Division of Neuroscience at OHSU's Oregon National Primate Research Center. Carbone is an expert in the study of gibbons and the lead and corresponding author on the report.

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Gibbon genome sequence deepens understanding of primates rapid chromosomal rearrangements

Gibbons have such strange, scrambled DNA, it looks like someone has taken a hammer to it. Their genome has been massively reshuffled, and some biologists say that could be how new gibbon species evolved.

Gibbons are apes, and were the first to break away from the line that led to humans. There are around 16 living gibbon species, in four genera. They all have small bodies, long arms and no tails. But it's what gibbons don't share that is most unusual. Each species carries a distinct number of chromosomes in its genome: some species have just 38 pairs, some as many as 52 pairs.

"This 'genome plasticity' has always been a mystery," says Wesley Warren of Washington University in St Louis, Missouri. It is almost as if the genome exploded and was then pieced back together in the wrong order.

To understand why, Warren and his colleagues have now produced the first draft of a gibbon genome. It comes from a female northern white-cheeked gibbon (Nomascus leucogenys) called Asia.

Inside the genome, Warren and his colleagues may have identified one of the players responsible for the reshuffling. It is called LAVA, and it is a piece of DNA called a retrotransposon that inserts itself into the genetic code. Seemingly unique to gibbons, LAVA tends to slip into genes that help control the way chromosomes pair up during cell division. By altering how those genes work, LAVA has made the gibbon genome unstable.

"We believe this is the driving force that causes, for want of a better word, the 'scrambling' of the genome," says Warren.

However, solving this mystery has created another. Such dramatic genome changes are normally associated with diseases such as cancer, and should be harmful. "It's a complete mystery still how these genomes are able to pass from one generation to the next and not cause any major issues in terms of survival of the species," says Warren.

It may be that genomes are much more resilient than anyone expected, says James Shapiro at the University of Chicago. "The genome can endure lots of changes and still function."

Shapiro is one of a growing number of researchers convinced that such major reshuffling has been crucial throughout evolutionary history. He says it is how new species form. This challenges the standard idea that mutations in one or a few genes are enough to establish a new species.

Shapiro's controversial idea has a long history. One of its most famous to some, notorious proponents was German geneticist Richard Goldschmidt. In 1940, he called the animals produced by genome reshuffling "hopeful monsters" (Nature Reviews Genetics, DOI: 10.1038/nrg979). They were "monstrous" because they differed hugely from their parents, but they carried the "hope" of founding a new species because of those differences.

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Shattering DNA may have let gibbons evolve new species

PUBLIC RELEASE DATE:

10-Sep-2014

Contact: Billy Gomila bgomila@lsu.edu 225-578-3867 Louisiana State University @LSUResearchNews

BATON ROUGE LSU's Mark Batzer, LSU Boyd Professor and Dr. Mary Lou Applewhite Distinguished Professor, along with Research Assistant Professor Miriam Konkel and Research Associate Jerilyn Walker in Department of Biological Sciences in the College of Science, contributed to an article featured on the cover of the scientific journal Nature, titled "Gibbon Genome and the Fast Karyotype Evolution of Small Apes."

An abstract of the article can be found at http://www.nature.com/nature/journal/v513/n7517/full/nature13679.html?WT.ec_id=NATURE-20140911. The issue of Nature will be published on Sept. 11.

Batzer, Konkel and Walker contributed to the analysis of the mobile elements in the gibbon genome. This included the characterization of the mobile genetic element called LAVA.

LAVA is made up of pieces of known jumping genes and named after its main components: L1, Alu, and the VA section of SVA mobile elements. The gibbon-specific LAVA element represents only the second type of composite mobile element discovered in primates, since the discovery of the mobile element SVA in humans.

The sequencing, assembly and analysis of the gibbon genome provide new insights into the biology and evolutionary history of this family of apes. Factors that might have contributed to gibbon diversity and that might have helped gibbons to adapt to their jungle habitat are reported.

As part of the gibbon genome project, Batzer analyzed the evolution of gibbon-specific mobile elements, including their subfamily structure and distribution among the various gibbon species. The discovery of LAVA further highlights the dynamic evolution of mobile elements and their dynamic impact on primate genomes.

Gibbons are small, tree-living apes from Southeast Asia, many species of which are endangered. They are part of the same superfamily as humans and great apes, but sit on the divide between Old-World monkeys and the great apes. These creatures have several distinctive traits, such as an unusually large number of chromosomal rearrangements, and different numbers of chromosomes are seen in individual species.

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Gibbon genome and the fast karyotype evolution of small apes

1. UCSC Genome Browser Tutorial: the basics
UCSC Genome Browser Tutorial Video 1 An introduction to the UCSC Genome Browser, a tool used by researchers around the world. Here I discuss: --genomes and assemblies --chromosome coordinates...

By: Sam Allon

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1. UCSC Genome Browser Tutorial: the basics - Video

Jesus or Genome - Kafeneio Coffee House - March 14, 2013
Jesus or Genome - Kafeneio Coffee House - March 14, 2013.

By: Pariah Music Club

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Jesus or Genome - Kafeneio Coffee House - March 14, 2013 - Video

September 6, 2014

Chuck Bednar for redOrbit.com Your Universe Online

By sequencing the genome of the coffee plant, an international team of researchers has discovered genetic secrets that could enable them to create new varieties of coffee that taste better, have varied levels or caffeine, or are better able to survive drought conditions and diseases.

In addition, Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD), and his colleagues discovered that the coffee plant developed caffeine-linked genes independently and did not inherit them from a common ancestor. Their findings are detailed in Thursdays online edition of the journal Science.

According to the researchers, they decided to sequence the coffee genome because it is one of the most important crops on Earth, with 8.7 million tons of coffee produced last year and over 2.25 billion cups of the beverage consumed on a daily basis. They selected the species Coffea canephora as it displayed a conserved chromosomal gene order among asterid angiosperms, and because they were able to generate a high-quality draft genome of the plant.

Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee, Lashermes, one of the principal authors of the study, said in a statement. By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special.

After sequencing the Coffea canephora genome, the study authors examined how its genetic composition differed from other types of plants. In comparison to several other species, including grapes and tomatoes, they discovered larger families of genes associated with the production of alkaloid and flavonoid compounds in coffee plants compounds with contribute to traits such as the aroma of the coffee and the bitterness of the beans.

Furthermore, they discovered that coffee has an expanded group of enzymes known as N-methyltransferases, which are involved in caffeine production. After examining these enzymes more closely, the researchers learned that they were more closely related to other genes in the coffee plant than to caffeine enzymes found in tea and chocolate a discovery which suggests caffeine production developed independently in coffee plants, since the enzymes would have been more similar between species if they had been inherited from a common ancestor.

The coffee genome helps us understand whats exciting about coffee other than that it wakes me up in the morning, said Victor Albert, professor of biological sciences at the University at Buffalo and co-principle author. By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffees independent pathway in evolution.

Albert told Reuters reporter Will Dunham that the coffee genome was about as large as the average plant genome, and had approximately 25,500 genes responsible for various proteins. He also suggested that coffee plants might have started producing caffeine in order to entice pollinators to return, or to prevent herbivorous insects from eating their leaves.

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Sequencing Of Coffee Genome Reveals Secrets Of Caffeine Development

A crack team of international researchers have revealed the freshly sequenced genome of the coffee plant and, as a result, unearthed interesting findings about the kick ass chemical caffeine.

Scientists found that coffee developed caffeine-linked genes independently of any common ancestor, such as chocolate and tea.

The boffins pored over "a high-quality draft" of the genome of Coffee canephora, which - we're told - accounts for roughly 30 per cent of the globe's coffee production.

They were able to find special qualities in the plant that were distinct from the genetic make-up of other species such as the grape and tomato.

The researchers said that coffee "harbours larger families of genes that relate to the production of alkaloid and flavonoid compounds," which in turn accounts for the strong, heady aroma of a cup of joe. It also explains the bitterness of the beans.

Lots more caffeine-making enzymes are packed into coffee compared with other plants, the boffins said. It carries an "expanded collection of N-methyltransferases" apparently.

But coffee's caffeine enzymes have bigger links with other genes found in the coffee plant compared with those caffeine enzymes commonly found in tea and chocolate.

Researchers were able to conclude that coffee appeared to have independently produced caffeine due to the marked difference in enzymes uncovered in the genome sequence.

Victor Albert, professor of biological sciences at the University at Buffalo, said:

The coffee genome helps us understand what's exciting about coffee other than that it wakes me up in the morning.

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Boffins hunch over steaming cups of coffee to find HIDDEN SECRETS of caffeine

Next-Generation Genome Engineering for Improving the Production of Recombinant Proteins in Cells
New genome engineering technologies can be utilized engineer cellular systems to improve and otherwise specifically alter their capacity to properly produce ...

By: Transposagen

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Next-Generation Genome Engineering for Improving the Production of Recombinant Proteins in Cells - Video