Category Archives: Genome

Cuomo to bring genome center to Buffalo
In his State of the State address Wednesday, Governor Andrew Cuomo announced plans to establish a genome center in Buffalo.

By: WIVBTV

Read more here:
Cuomo to bring genome center to Buffalo - Video

Yacatisma - Genome [HQ]
Suscribe: http://bit.ly/SBlasphemyYouTube == Band Information == Band: Yacatisma Album: Supraliminal Invasion Year: 2014 Genre: Technical Deathcore Facebook: https://www.facebook.com/pages/Yacati...

By: SniperMetal

Read more from the original source:
Yacatisma - Genome [HQ] - Video

The collaboration with 12 international institutions(1) was headed by IMCB's Prof Byrappa Venkatesh, who is also a chairperson of the "Genome10K" Project. The project was largely funded by the National Institutes of Health (NIH), USA, the world's foremost centre for the support of biomedical research.

Analysis of the elephant shark genome

Elephant shark is a member of cartilaginous fishes, which are the oldest living group of jawed vertebrates that diverged from bony vertebrates about 450 million years ago. Cartilaginous fishes include sharks, rays, skates and chimaeras. Unlike humans and other bony vertebrates, cartilaginous fishes are unable to replace cartilage with bone. Among over 1,200 species of cartilaginous fishes, the elephant shark was sequenced due to its compact genome size. Analysis of the elephant shark genome identified a family of genes absent in elephant shark but present in all bony vertebrates. A significant reduction in bone formation was observed when a member of this gene family was knocked out in zebrafish, thereby indicating the importance of this gene family in bone formation. The finding has important implications towards our understanding of bone-related diseases such as osteoporosis and hence the development of effective therapeutic strategies for them.

An unexpected finding was that elephant shark appears to lack special types of immune cells previously considered essential for defence against viral/bacterial infections and preventing autoimmune reactions such as diabetes and rheumatoid arthritis(2). Despite this seemingly primitive organization of the immune system, sharks exhibit robust immune defences and are long-lived. By challenging long-held notions, this discovery has opened up a new avenue towards the development of nonintuitive strategies to shape the immune functions of humans.

The study also found that the elephant shark genome is the slowest evolving among all vertebrates, including the coelacanth, popularly known as a "living fossil", whose genes were recently shown to be evolving slower than those of other bony vertebrates(3). Furthermore, large blocks of elephant shark and human chromosomes were found to be highly similar. The markedly slow evolution of the elephant shark genome and its similarity to the human genome, further underscores its importance as a reference genome for comparative genomic studies aimed at better understanding of the human genome.

Prof Byrappa Venkatesh, Research Director at IMCB, and lead author of the Nature paper added, "The slow evolving genome of the elephant shark is probably the best proxy for the ancestor of all jawed-vertebrates that became extinct a long time ago. It is a cornerstone for improving our understanding of the development and physiology of human and other vertebrates as illustrated by our analysis of the skeletal system and immune system genes."

Dr Wes Warren, senior author of the Nature paper commented, "Although cartilaginous vertebrates and bony vertebrates diverged about 450 million years ago, with the elephant shark genome in hand, we can now begin to identify key genetic adaptations in the evolutionary tree."

Prof Hong Wanjin, Executive Director of IMCB, said, "Over the years, IMCB has carried out several remarkable genomic projects and we are excited to showcase yet another milestone. Not only has our research team sequenced the first shark-family member genome, they have also uncovered many insights significant to the field of genomic and medical research through the genome analysis."

Prof Sir David Lane, Chief Scientist at A*STAR, said, "We are delighted that a Singapore laboratory conceived and led a major international genome project. The international research grant from NIH, USA is a testimony of Singapore's world-class standard in genomics research."

(1) 1) Institute of Molecular and Cell Biology, A*STAR, Singapore; 2) Yong Loo Lin School of Medicine, National University of Singapore, Singapore; 3) Max-Planck-Institute of Immunobiology and Epigenetics, Germany; 4) University of Maryland, Baltimore, USA; 5) Hokkaido University Graduate School of Medicine, Japan; 6) Molecular Engineering Laboratory, A*STAR, Singapore; 7) San Francisco State University, San Francisco, USA; 8) Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Canada; 9) Institut de Biologia Evolutiva, Barcelona, Spain; 10) Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Spain; 11) Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, USA; 12) The Genome Institute at Washington University, St. Louis, USA. (2) Rheumatoid arthritis is an autoimmune disease which results in a chronic, systemic inflammatory disorder that may affect many tissues and organs. (3) Amemiya, CT. et al. 2013 The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311-316.

Read the original post:
Analysis of the elephant shark genome

Researchers have mapped the genome of the elephant shark, and they say it helps explain the genetic basis of how bones form.

It turns out that studying a boneless animal can help explain the genetic basis of bones.

Subscribe Today to the Monitor

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

An international group of researchers has sequenced the genome of the elephant shark, "a curious-looking fish with a snout that resembles the end of an elephant's trunk." The species, which despite its name is not actually a shark, is a member ofthe family of the world's oldest-living jawed vertebrates.

But why elephant sharks?

The elephant shark was selected for sequencing because of its compact genome, which is one-third the size of the human genome, according to a press release by The Genome Institute at Washington University School of Medicine.

Like actual sharks, the elephant shark, which belongs to the order chimaera, has a "skeleton" made of cartilage rather than bone, making it an oddity on the evolutionary tree.

After comparing the shark genome with those of other vertebrates with bones, researchers noticed that the elephant shark lacked a family of genes that are crucial for bone formation. They confirmed this by removing a member of this gene family in zebrafish, a tropical freshwater fish. It was observed that a gene's absence correlated with a reduction in bone formation in zebrafish, highlighting the importance of this gene family in making bones.

"So now we know what genes are missing in elephant sharks and from that we learned about this new gene family, which is important in bone formation," Patrick Minx from The Genome Institute at Washington University School of Medicine, told the Monitor. Therefore, the findings have important implications for understanding bone diseases, he says.

Read more:
Where do your bones come from? Shark genome study offers insights.

You might not think of the Buffalo Niagara region as a hotbed of genetic medical research, but Marnie LaVigne thinks the pieces already are in place here.

Its just a question of putting them all together.

Thats why LaVigne, the University at Buffalos associate vice president of economic development, is so excited about Gov. Andrew M. Cuomos plans to invest $50 million in genomic medical research here, building on UBs supercomputing capacity, the modest-but-growing life sciences industry here and the regions large database of electronic medical records.

Weve got phenomenal genomics capability, LaVigne said.

The high-performance computing isnt in other places, as it is here, she said. The access to patient data is excellent here, with medical data from more than 1 million medical records available for researchers to analyze as they seek out new cures and treatments.

Its not just data storage. Its analytics, she said.

And thats the big selling point of UBs involvement in the $105 million project that will upgrade the computing facilities and forge a partnership with the New York Genome Center, a consortium of 16 institutions in New York that are using genetic information to try to develop new medical tests and treatments.

Its all part of a quest for a holy grail thats sometimes called personalized medicine. By studying a patients genes, researchers look for genetic clues that show how susceptible that person is to certain diseases or conditions. Essentially, the makeup of a patients DNA and other genetic coding can help determine what diseases they are more likely to contract and how they can be treated most effectively.

You can test it here. You can expand it here. You can co-locate here, LaVigne said. Groups outside of Buffalo are going to want to access what we have, even international firms.

If that sounds familiar, it should. Its the same type of mantra that the Cuomo administration has been following for most of its high-profile economic development initiatives here.

Here is the original post:
Genome research here is perfect fit

PUBLIC RELEASE DATE:

8-Jan-2014

Contact: Nan Broadbent nbroadbe@sfsu.edu 415-338-7108 San Francisco State University

SAN FRANCISCO -- A team of researchers including SF State Assistant Professor of Biology Scott Roy has sequenced the entire genome of the elephant shark, uncovering several features that may shed light on the evolution of bony vertebrates.

The study is the first whole-genome analysis of a cartilaginous fish. Cartilaginous fishes include sharks, rays and skates. Together with bony fish, birds, reptiles, amphibians and mammals, they make up the branch of jawed vertebrates on life's family tree.

The elephant shark genome is relatively small, consisting of slightly fewer than a billion DNA base pairs compared with 3 billion base pairs in humans. But this spare sequence has yielded some intriguing details, the researchers write. For instance, the elephant shark lacks the genes for secreted phosphoproteins, which may explain why their cartilage is not converted into bone as in the other jawed vertebrates.

They also lack the genes for several key immune system cells and protein receptors in the adaptive immune system, which provides carefully targeted defenses against specific disease threats. This finding, say the researchers, may suggest that the adaptive immune system in jawed vertebrates gradually became more elaborate over time.

One of the most notable features of the elephant shark's genome is its incredibly slow rate of evolution, said Roy. Even slower than in "living fossils" such as the coelacanth, the elephant shark's genome has not changed substantially in hundreds of millions of years.

This slow rate of evolution was uncovered in part by Roy's analysis of the genome's introns. Introns are the part of the genetic sequence that "interrupts" genes, and must be spliced out before the gene can be expressed. In vertebrates, these introns can be thousands of DNA letters long and must include their own splicing instructions.

There have been very few intron changes in the elephant shark genome, but this isn't entirely surprising, noted Roy, who has studied intron organization across a variety of organisms, including humans. "It's pretty well established in vertebrates that very little of this intron loss and creation occurs."

Read the original here:
Slow-evolving elephant shark genome is first to be sequenced from cartilaginous fish

Jan. 8 (UPI) -- The first shark genome decoded belongs to the slow-evolving elephant shark, providing researchers new insight into cartilaginous fish, and the differences between sharks and other bony vertebrates.

A team of international researchers, including researchers from the Max Planck Institute of Immunobiology and Epigenetics and San Francisco State University, have decoded the one billion DNA pairs found in the elephant shark genome and compared them to the 3 billion DNA pairs found in humans.

The findings, published in Nature, have given them a better understanding of why a shark's skeleton is largely composed of cartilage rather than bone, and why their immune system is simpler than that of humans.

The researchers found a family of genes missing that are critical for bone formation and found in most bony vertebrates. This family of genes enables other vertebrates to replace cartilage with bone and researchers believe they could use this data to better understand bone diseases like osteoporosis.

Analysis of genes linked to the immune system showed that sharks lacked T-helper lymphocytes, which until now were considered essential for fighting off viral and bacterial infections. But despite the absence of these lymphocytes the shark has a robust immune defense system.

It is obvious that sharks can efficiently deal with all kinds of infections without this particular cell type. This indicates that nature can come up with different solutions to the same problem, said Thomas Boehm, co-author and director at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg.

The study also provided evidence that elephant shark genome is the slowest evolving among all vertebrates. The study of a shark's genome is considered essential because they are the oldest living group of jawed-vertebrates that diverged from bony vertebrates about 450 million years ago.

[Max Planck Institute of Immunobiology and Epigenetics] [Nature]

Follow this link:
Elephant shark genome decoded

Jan. 8, 2014 An international team of researchers has sequenced the genome of the elephant shark, a curious-looking fish with a snout that resembles the end of an elephant's trunk.

The elephant shark and its cousins the sharks, rays, skates and chimaeras are the world's oldest-living jawed vertebrates. But their skeletons are made of cartilage rather than bone, making this group of vertebrates an oddity on the evolutionary tree.

Now, by comparing the genome of the elephant shark with human and other vertebrate genomes, researchers at Washington University School of Medicine in St. Louis and elsewhere have discovered why the skeleton of sharks is cartilaginous. An analysis of the creature's genome, published Jan. 9 in the journal Nature, offers new insights into the genetic basis of bone formation and the molecular origins of adaptive immunity, which provides organisms with a more sophisticated immune response to pathogens.

Collectively, the findings have important implications for understanding bone diseases such as osteoporosis and for developing more effective therapies to treat these conditions. Findings related to the elephant shark's immune system provide new opportunities for studying adaptive immunity in humans and for formulating new strategies to fine-tune the immune response.

"We now have the genetic blueprint of a species that is considered a critical outlier for understanding the evolution and diversity of bony vertebrates, including humans," said senior author Wesley Warren, PhD, research associate professor of genetics at The Genome Institute at Washington University School of Medicine. "Although cartilaginous vertebrates and bony vertebrates diverged about 450 million years ago, with the elephant shark genome in hand, we can begin to identify key genetic adaptations in the evolutionary tree."

Among the cartilaginous fishes, the elephant shark was selected for sequencing because of its compact genome, which is one-third the size of the human genome. The fish lives in the waters off the southern coast of Australia and New Zealand, at depths of 200 to 500 meters, and uses its snout to dig for crustaceans at the bottom of the ocean floor.

By analyzing the elephant shark genome and comparing it with other genomes, the scientists discovered a family of genes that is absent in the elephant shark but present in all bony vertebrates, including the chicken, cow, mouse and human. When the researchers deleted a member of this gene family in zebrafish, they observed a reduction in bone formation, highlighting the gene family's significance in making bone.

In a surprise finding, the team found that the elephant shark appears to lack special types of immune cells that are essential to mounting a defense against viral and bacterial infections and for preventing autoimmune diseases such as diabetes and rheumatoid arthritis.

However, despite possessing a relatively rudimentary immune system, sharks exhibit robust immune responses and live long lives. The new discovery opens up the possibility of developing new strategies to shape the immune response in humans.

The researchers also determined that the elephant shark genome is the slowest-evolving among all vertebrates, including the coelacanth, a prehistoric fish popularly known as a "living fossil."

More:
Elephant shark genome decoded: New insights gained into bone formation and immunity

Jan. 8, 2014 An international team of researchers, including scientists of the Max Planck Institute of Immunobiology and Epigenetics, has sequenced and analyzed the genome of the elephant shark. Comparison of the elephant shark genome with human and other vertebrate genomes has revealed why the skeleton of sharks is made up largely of cartilage and not bone like the human skeleton and that the immune system of the shark is much simpler than that of humans. The findings of Byrappa Venkatesh and his coworkers are published in the latest issue of the scientific journal, Nature.

An unexpected finding of the immune system analysis was that sharks appear to lack special types of so-called T-helper lymphocytes, that -- until now -- were considered to be essential for defence against viral/bacterial infections and preventing autoimmune reactions such as diabetes and rheumatoid arthritis in vertebrates.

Despite this seemingly primitive organization of the immune system, sharks exhibit robust immune defences and are long-lived. "The structure of the immune system of the elephant shark is very different from mammals," said Thomas Boehm, co-author and director at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany. "It is obvious that sharks can efficiently deal with all kinds of infections without this particular cell type. This indicates that nature can come up with different solutions to the same problem," stated Boehm.

What happens when T-helper cells are being destroyed can be observed in AIDS patients, who succumb to viral and bacterial infections. Up to now, it was assumed that cells are essential for an immune system. The new results are challenging this long-held notion and open up an unprecedented avenue towards the development of non-intuitive strategies to modulate the immune functions of humans.

The researchers also investigated why cartilaginous fishes, including the elephant shark, are unable to replace cartilage with bone like humans and other bony vertebrates. Genome analysis was able to highlight a family of genes that are absent in sharks but present in all bony vertebrates and are critical for bone formation. When the researchers inactivated these genes in bony fishes such as the zebrafish, calcification did not occur. This finding is a strong indication that the investigated gene family could be a starting point for a better understanding of bone diseases such as osteoporosis.

In addition, the study revealed that the elephant shark genome is the slowest evolving among all vertebrates. The elephant shark even beats the coelacanth, also called "the living fossil," that has recently been shown to evolve extremely slowly. Therefore, the elephant shark is probably the best proxy for the ancestor of all jawed-vertebrates that became extinct a long time ago.

Cartilaginous fishes (comprising sharks, rays, skates and chimaeras) are the oldest living group of jawed-vertebrates that diverged from bony vertebrates about 450 million years ago. The elephant shark (Callorhinchus milii) is a chimaera that inhabits temperate waters of the continental shelves off southern Australia and New Zealand, at depths of 200 to 500 meters. From approximately 1,000 species of cartilaginous fishes, elephant shark was chosen as a model because of its relatively compact genome which is one third the size of the human genome.

Here is the original post:
First shark genome decoded

ALBANY Gov. Andrew M. Cuomo unveiled an election-year grab bag of policy proposals Wednesday in his fourth State of the State, including funding for a genome research consortium between Buffalo and Manhattan, bonuses for top-performing public school teachers, modest tax breaks for property owners and tougher penalties for repeat drunk drivers and teens who text and drive.

Cuomo said he will dip again into his pledge made several years ago to spend $1 billion on Buffalo job creation efforts by authorizing a $100 million genome research program with $50 million going to the University at Buffalo and potentially other groups in the Buffalo area to connect scientists in Western New York with genome researchers at a new center in Manhattan.

Cuomo and researchers involved in the project said jobs and scientific breakthroughs to treat cancer and other diseases will result from the state investment. He said five companies already have committed to locate or expand on the Buffalo Niagara Medical Campus to be a part of a consortium with a not-for-profit genome center in Manhattan that opened last fall. Cuomo said the research work will create an entirely new industry for Western New York.

The 69-minute address also included a call for a major, $2 billion borrowing to fund new technological expansions and space for prekindergarten classrooms a bond program political analysts say is likely to bolster turnout in key geographic areas for an initiative that will appear on the same ballot as Cuomo in his first re-election bid this November.

A number of ideas, including expansion of abortion rights and taxpayer-financed campaigns, were rejected less than a year ago by Republicans who control the State Senate, and Cuomo made no mention, despite claims last fall to The Buffalo News that he would, about penalties or dramatic action for failing public schools.

Cuomo spent a third of his speech talking about what he called his accomplishments in his first three years, from a property tax cap to legalizing gay marriage to a sweeping gun-control measure.

In three years, my friends, you have reversed decades of decline, Cuomo told lawmakers in a state convention center near the Capitol.

Republican and Conservative Party leaders dismissed the Cuomo speech as election-year rhetoric with major new spending plans from a governor who should have embraced deeper tax cuts when he first took office.

In a hall with teeth-chattering temperatures, a favorite thermostat setting by this governor for his major, longer speeches, Cuomo offered the political spectrum of ideas in his address. For liberals, he said he will issue regulations to permit people with certain medical conditions to obtain marijuana to treat pain and other ailments at 20 hospitals around the state, seek to expand abortion rights, and raise the automatic, mandatory age from 16 to 18 at which teens arrested for crimes can be tried as an adult.

For right-of-center New Yorkers, he offered up a tax cut package for upstate manufacturers and beleaguered property taxpayers, a new state college focusing on counter-terrorism and homeland security and several criminal-justice measures, including crackdowns on repeat drunk drivers who he said should permanently lose their license if convicted of three DWI offenses.

Read the rest here:
Cuomo envisions $100 million genome research facility