Category Archives: Genome

The Nightlife Genome Project
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Humanoid Opera - Paralyzed Genome (Live in The Cinema House Moscow)
Humanoid Opera - Paralyzed Genome (Live in The Cinema House Moscow) " " 2014.

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Humanoid Opera - Paralyzed Genome (Live in The Cinema House Moscow) - Video

November 26, 2014

Image Caption: This is Strigamia maritima, the centipede species genetically sequenced in the study. Credit: Dr. Carlo Brena

Eric Hopton for redOrbit.com Your Universe Online

An international group of scientists has completed the first ever genome sequence of a blind myriapod, Strigamia maritima. The species is one of a group of venomous centipedes that are unusual in the way in which they care for their eggs. The research also provides new insights into the biological evolution of Strigamia maritima and its unique absence of vision and circadian rhythm.

The work was partly carried out and the sequencing completed at Baylor College of Medicine in Houston, Texas, and the findings have been published online in the journal PLOS Biology.

This is the first myriapod and the last of the four classes of arthropods to have its genome sequenced, said Dr. Stephen Richards, assistant professor in the Human Genome Sequencing Center at Baylor. Arthropods are particularly interesting for scientific study because they diverged into more species than any other animal group as they adapted in many ways to conquer the planet. The genome of the myriapod in comparison with previously completed genomes of the other arthropod classes gives us an important view of the evolutionary changes of these exciting species.

Other scientists involved in the study were Dr. Ariel Chipman, of the Hebrew University of Jerusalem in Israel, Dr. David Ferrier, of The University of St. Andrews in the United Kingdom, and Dr. Michael Akam of the University of Cambridge in the UK.

Chipman, associate professor at the Hebrew University, said that The arthropods have been around for over 500 million years and the relationship between the different groups and early evolution of the species is not really well understood. We have good sampling of insects but this is the first time a centipede, one of the more simple arthropods simple in terms of body plan, no wings, simple repetitive segments, etc. has been sequenced. This is a more conservative genome, not necessarily ancient or primitive, but one that has retained ancient features more than other groups.

Fossil evidence shows that the myriapods, along with insects and spiders, were one of three independent arthropod invasions of the land from the sea. To adapt to life on land they had to learn to smell chemicals in the air, rather than taste them in the water. The research did indeed discover evidence of large gene expansions of the gustatory receptors which are believed to perform the same olfactory role that olfactory receptors play in insects, Richards said. This is a nice example of parallel evolution where different group of genes expanded, providing a different solution to the same problem, he added.

The findings indicate that this centipede group lost its eyes at least 200 million years ago. No vision-specific genes or genes related to the circadian (or internal) clock were found in the genome.

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Blind Scottish Centipede Genome Unlocks Evolutionary Secrets

As one of the most diverse plant family, orchid now has its first genome sequenced and the result is published at Nature Genetics as a cover article.

This study is an accomplishment of the Orchid Genome Project, an international collaboration led by Lai-Qiang Huang and Zhong-Jian Liu at Tsinghua University and National Orchid Conservation Center in Shenzhen China, with colleagues from different institutions, including Chengkong University in Taiwan, Ghent University in Belgium, and Institute of Botany of CAS in Beijing.

The team carried out whole genome sequencing on phalaenopsis equestris, which is an important parental species for breeding of commercial phalaenopsis strains. P. equestris is also the first plant with Crassulacean Acid Metabolism (CAM) for which the genome has been sequenced. The assembled genome contains 29,431 predicted protein-coding genes. The average intron length is 2,922 base pairs, which is much longer than in any sequenced plant genomes. Further analysis indicate that transposable elements in introns are the major reason why orchid genes have so big introns.

As heterozygosity post great challenge for whole genome sequencing and assembly, the orchid genome is by no means an exception. In the orchid genome, they found that contigs likely to be under-assembled owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. Those genes could be candidates for further research on the mechanism of self-incompatibility in orchid.

As in many plant genomes, they also found evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades. This is possibly an important clue to why orchid developed into one of the largest plant families on earth.

By comparing with homolog genes in other plant genomes, they found gene duplication and loss in CAM genes along the lineage to orchid. This result suggests that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris.

Finally, they found expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

All around the world, orchids are highly endangered species because of illegal collection and habitat loss. The complete genome sequence of P. equestris will provide an important resource to explore orchid diversity and evolution at the genome level. The genome sequence will also be a key resource for the development of new concepts and techniques in genetic engineering, such as molecular marker-assisted breeding and the production of transgenic plants, which are necessary to increase the efficiency of orchid breeding and aid orchid horticulture research.

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The above story is based on materials provided by ResearchSEA. Note: Materials may be edited for content and length.

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Scientists completed the first orchid whole genome sequencing

Researchers in human genetics have known that long nucleotide repeats in DNA lead to instability of the genome and ultimately to human hereditary diseases such Freidreich's ataxia and Huntington's disease.

Scientists have believed that the lengthening of those repeats occur during DNA replication when cells divide or when the cellular DNA repair machinery gets activated. Recently, however, it became apparent that yet another process called transcription, which is copying the information from DNA into RNA, could also been involved.

A Tufts University study published online on November 20 in the journal Cell Reports by a research team lead by Sergei Mirkin, the White Family Professor of Biology at Tufts' School of Arts and Sciences, along with former graduate student Kartick Shah and graduate students Ryan McGuity and Vera Egorova, explores the relationship between transcription and the expansions of DNA repeats. It concludes that the active transcriptional state of a DNA segment containing a DNA repeat predisposes it for expansions. The print version of the study will be published on December 11.

"There are a great many simple repetitive motifs in our DNA, such as GAAGAAGAA or CGGCGGCGG," says Mirkin. "They are stable and cause no harm if they stay short. Occasionally, however, they start lengthening compulsively, and these uncontrollable expansions lead to dramatic changes in genome stability, gene expression, which can lead to human disease."

In their study, the researchers used baker's yeast to monitor the progress and the fundamental genetic machineries for transcription, replication and repair in genome functioning.

"The beauty of the yeast system is that it provides one with a practically unlimited arsenal of tools to study the mechanisms of genome functioning," says Mirkin. "We created genetic systems to track down expansions of the repeats that were positioned in either transcribed or non-transcribed parts of reporter genes."

After measuring the rate of repeat expansions in all these cases, the authors found that a repeat can expand under the condition when there is practically no transcription, but the likelihood of the expansion process is drastically (10-fold) higher when the reporter is transcriptionally active.

Surprisingly, however, transcription machinery does not need to physically pass through the repeat to stimulate its expansion. Thus, it is the active transcription state of the repeat-containing DNA segment, rather than RNA synthesis through the repeat that promotes expansions.

In the transcriptionally active state, DNA is packaged in chromatin more loosely than when it is transcriptionally inactive. More specifically, the density of nucleosomes along the transcribed DNA segment is significantly lower than that in the non-transcribed segment. This packaging of repetitive DNA within the transcribed areas gives much more room for DNA strand gymnastics, ultimately leading to repeat expansions.

Whatever the exact model, says Mirkin, the fact that expandable DNA repeats were always found in transcribed areas of our genome may not be that surprising after all.

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Link between DNA transcription, disease-causing expansions

PUBLIC RELEASE DATE:

25-Nov-2014

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

HOUSTON - (Nov. 25, 2014) - An international collaboration of scientists including Baylor College of Medicine has completed the first genome sequence of a myriapod, Strigamia maritima - a member of a group venomous centipedes that care for their eggs - and uncovered new clues about their biological evolution and unique absence of vision and circadian rhythm.

Over 100 researchers from 12 countries completed the project. They published their work online today in the journal PLOS Biology.

"This is the first myriapod and the last of the four classes of arthropods to have its genome sequenced," said Dr. Stephen Richards, assistant professor in the Human Genome Sequencing Center at Baylor, where the sequencing of the project was completed, and the corresponding author on the report. "Arthropods are particularly interesting for scientific study because they diverged into more species than any other animal group as they adapted in many ways to conquer the planet. The genome of the myriapod in comparison with previously completed genomes of the other arthropod classes gives us an important view of the evolutionary changes of these exciting species."

Dr. Ariel Chipman, of the Hebrew University of Jerusalem in Israel, Dr. David Ferrier, of The University of St. Andrews in the United Kingdom, and Dr. Michael Akam of the University of Cambridge in the UK, together with Richards served as key players in the collaboration.

"The arthropods have been around for over 500 million years and the relationship between the different groups and early evolution of the species is not really well understood," said Chipman, associate professor at the Hebrew University. "We have good sampling of insects but this is the first time a centipede, one of the more simple arthropods - simple in terms of body plan, no wings, simple repetitive segments, etc. -- has been sequenced. This is a more conservative genome, not necessarily ancient or primitive, but one that has retained ancient features more than other groups."

"From fossil evidence, we know the myriapods are one of three independent arthropod invasions of the land (from the sea), in addition to the insects and spiders. So they had to find a way to smell chemicals in air, rather then taste them in water. The team identified large gene expansions of the gustatory (taste) receptors suspected to fill the olfactory role that olfactory (smell) receptors play in insects," Richards said. "This is a nice example of parallel evolution where different group of genes expanded, providing a different solution to the same problem."

One interesting finding revolved around this particular centipede group losing its eyes at least 200 million years ago.

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International collaboration completes genome sequence of centipede

PUBLIC RELEASE DATE:

25-Nov-2014

Contact: PLOS Biology biologypress@plos.org 415-590-3486 PLOS

The arthropods are one of Earth's real success stories, with more species of arthropod than in any other animal phylum, but our knowledge of arthropod genomes has been heavily skewed towards the insects. Recent work has furnished us with the genome sequences of an arachnid and a crustacean, but the myriapods (centipedes and millipedes) have remained the one class of arthropods whose genomes are still in the dark.

An international team of scientists (over 100 from 15 countries) with Stephen Richards (Baylor College of Medicine) as senior author has now sequenced the genome of the centipede Strigamia maritima, enabling them to reconstruct many features of the genetic make-up of the ancestral arthropod that lived more than half a billion years ago. In a report publishing November 25 in the open access journal PLOS Biology, the team reveals our first glimpse of a myriapod genome and uses it to explore the genetic basis of centipede biology and of the incredible diversification of arthropods.

Myriapods probably arose from marine ancestors that invaded the land more than 400 million years ago. They have a large number of near-identical segments, each bearing one or two pairs of legs. Despite their name, centipedes never have a hundred legs (the number of pairs is always odd), though Strigamia itself gets close with 45 to 51 pairs. Although most of us are familiar with centipedes in gardens and woodland, Strigamia lives in coastal habitats, and like most centipedes is a venomous carnivore.

Over a decade ago a team from Cambridge University, headed by Professor Michael Akam, started making the long trip up to Brora on the coast of the Moray Firth in Scotland to lie on their bellies on the beach, digging under the pebbles to hunt out their favorite centipede. Strigamia is favored by scientists for the accessibility of its nests, from which embryos can be gathered for study - making the species an ideal candidate for obtaining the first genome sequence from a myriapod, and opening the door to new understandings of the developmental biology and ecology of these secretive animals.

Ariel Chipman (Hebrew University of Jerusalem) and David Ferrier (University of St. Andrews) are lead co-authors of the report. "This genome of Strigamia has proved to be particularly valuable in deducing the content of important gene families in the ancestral arthropod, this ancestor then being the starting point for the evolution of the huge diversity of arthropods that we currently see today", said David Ferrier.

"There has been a high turn-over in arthropod gene and genome organization, with lots of rearrangements and plenty of gene losses during the evolution of animals like the insects. The sorts of reconstructions that have been made possible by this new myriapod genome provide a foundation for delving more deeply into the biology of these genetic changes to see how they were linked to the diversification of the incredible range of body forms and modes of life that we now find in the arthropods."

One of the most surprising findings is that these centipedes appear to have lost the genes encoding all of the known light receptors used by animals, as well as the genes controlling circadian rhythm - the body's internal clock.

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Blind scottish centipede unlocks clues to the origins of creepy crawlies

25.11.2014 - (idw) CECAD - Cluster of Excellence at the University of Cologne

The team of scientists led by Prof. Dr. Bjrn Schumacher at CECAD Cluster of Excellence at the University of Cologne has shown that a longevity assurance program in nematodes increases tolerance to genome damage. DNA damage accumulates with age and results in an aging-associated decrease in tissue function. Defects in DNA repair mechanisms can therefore lead to premature aging and early death of affected patients. The Cologne scientists findings open up new perspectives for the treatment of aging-associated diseases. Cologne, 24 November 2014. The genome in every cell is constantly under physical and chemical attack. These attacks can come from outside, such as UV radiation from sunlight, or from inside, like the toxic byproducts of our own metabolism. DNA damage can interfere already with developmental growth and the invariant gradual accumulation of DNA damage drives the aging process. People born with defects in the DNA repair systems suffer from retarded body growth and succumb to premature aging already during childhood. How does the body respond when DNA damage cannot be repaired or accumulates with age? Prof. Dr. Bjrn Schumacher at the CECAD Research Center: We investigated nematodes with exactly the same genetic defects in DNA repair as patients who suffer from growth retardation and premature aging. When the nematodes are unable to repair the damaged DNA, they activate a longevity assurance response. The Cologne-based research team has published their influential results in the current issue of Nature Cell Biology on 2014, November 24.

Contact: Prof. Dr. Bjrn Schumacher CECAD Excellence Cluster at the University of Cologne Telephone +49 221 478-84202 bjoern.schumacher@uni-koeln.de

Astrid Bergmeister MBA Head CECAD PR & Marketing Telephone + 49 (0) 221-478 84043 astrid.bergmeister@uk-koeln.de Weitere Informationen:http://www.cecad.uni-koeln.de

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Genome Damage Tolerance Extends Lifespan

1 hour ago Strigamia maritima. Credit: ArthropodBase wiki

An international collaboration of scientists including Baylor College of Medicine has completed the first genome sequence of a myriapod, Strigamia maritima - a member of a group venomous centipedes that care for their eggs - and uncovered new clues about their biological evolution and unique absence of vision and circadian rhythm.

Over 100 researchers from 12 countries completed the project. They published their work online today in the journal PLOS Biology.

"This is the first myriapod and the last of the four classes of arthropods to have its genome sequenced," said Dr. Stephen Richards, assistant professor in the Human Genome Sequencing Center at Baylor, where the sequencing of the project was completed, and the corresponding author on the report. "Arthropods are particularly interesting for scientific study because they diverged into more species than any other animal group as they adapted in many ways to conquer the planet. The genome of the myriapod in comparison with previously completed genomes of the other arthropod classes gives us an important view of the evolutionary changes of these exciting species."

Dr. Ariel Chipman, of the Hebrew University of Jerusalem in Israel, Dr. David Ferrier, of The University of St. Andrews in the United Kingdom, and Dr. Michael Akam of the University of Cambridge in the UK, together with Richards served as key players in the collaboration.

"The arthropods have been around for over 500 million years and the relationship between the different groups and early evolution of the species is not really well understood," said Chipman, associate professor at the Hebrew University. "We have good sampling of insects but this is the first time a centipede, one of the more simple arthropods - simple in terms of body plan, no wings, simple repetitive segments, etc.has been sequenced. This is a more conservative genome, not necessarily ancient or primitive, but one that has retained ancient features more than other groups."

"From fossil evidence, we know the myriapods are one of three independent arthropod invasions of the land (from the sea), in addition to the insects and spiders. So they had to find a way to smell chemicals in air, rather then taste them in water. The team identified large gene expansions of the gustatory (taste) receptors suspected to fill the olfactory role that olfactory (smell) receptors play in insects," Richards said. "This is a nice example of parallel evolution where different group of genes expanded, providing a different solution to the same problem."

One interesting finding revolved around this particular centipede group losing its eyes at least 200 million years ago.

No genes related solely to vision were found in the genome, and interestingly, genes related to the circadian clock were also missing. The circadian clock regulates sleep and causes jetlag and also relies on light input to synchronize with day and night.

"This teaches us about how evolution works and how things change, how things can be conserved and others lost," said Chipman. "In general, this just gives us a better understanding of biology and how it works over long periods of time."

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International team completes genome sequence of centipede

PUBLIC RELEASE DATE:

21-Nov-2014

Contact: Dan Krotz dakrotz@lbl.gov 510-486-4019 DOE/Lawrence Berkeley National Laboratory @BerkeleyLab

Scientists from the US Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have learned new details about how an important tumor-suppressing protein, called p53, binds to the human genome. As with many things in life, they found that context makes a big difference.

The researchers mapped the places where p53 binds to the genome in a human cancer cell line. They compared this map to a previously obtained map of p53 binding sites in a normal human cell line. These binding patterns indicate how the protein mobilizes a network of genes that quell tumor growth.

They found that p53 occupies various types of DNA sequences, among them are sequences that occur in many copies and at multiple places in the genome. These sequences, called repeats, make up about half of our genome, but their function is much less understood than the non-repeated parts of the genome that code for genes.

It's been known for some time that p53 binds to repeats, but the Berkeley Lab scientists discovered something new: The protein is much more enriched at repeats in cancer cells than in normal cells. The binding patterns in these cell lines are very different, despite the same experimental conditions. This is evidence, they conclude, that in response to the same stress signal, p53 binds to the human genome in a way that is selective and dependent on cell context--an idea that has been an open question for years.

The research is published online Nov. 21 in the journal PLOS ONE.

"It is well established that p53 regulates specific sets of genes, depending on the cell type and the DNA damage type. But how that specificity is achieved, and whether p53 binds to the genome in a selective manner, has been a matter of debate. We show that p53 binding is indeed selective and dependent on cell context," says Krassimira Botcheva of Berkeley Lab's Life Sciences Division. She conducted the research with Sean McCorkle of Brookhaven National Laboratory.

What exactly does cell context mean in this case? The DNA that makes up the genome is organized into chromatin, which is further packed into chromosomes. Different cell types differ by their chromatin state. Cancer can change chromatin in a way that doesn't affect DNA sequences, a type of change that is called epigenetic. The new research indicates that epigenetic changes to chromatin may have a big impact on how p53 does its job.

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For important tumor-suppressing protein, context is key