Daily Archives: January 9, 2014

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]

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Elephant shark genome decoded

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."

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Slow-evolving elephant shark genome is first to be sequenced from cartilaginous fish

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.

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First 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."

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

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.

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Cuomo envisions $100 million genome research facility

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.

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Cuomo sees $100 million genome center in Buffalo

Norbert Wu/Minden Pictures/Getty Images

The elephant shark has changed little in the last 420 million years, making its DNA sequence valuable for comparison with other vertebrate species.

A funky-looking fish with an outsized snout has become the most primitive jawed vertebrate to have its genome sequenced. The DNA sequence of the elephant shark helps to explain why sharks have a cartilaginous skeleton and how humans and other vertebrates evolved acquired immunity.

Elephant sharks (Callorhinchus milii) are part of an early evolutionary branch of cartilaginous fishes known as chimaeras, which are related to sharks and rays. They patrol the deep waters off southern Australia and New Zealand, and use their distinctive snouts to hunt for shellfish buried in the sand. Although elephant sharks are not known to attack humans, they sport a seven-centimetre-long spike on their dorsal fin, which is used to defend against predators.

Six years ago, scientists singled out C. milii as the first cartilaginous fish to be sequenced because of its relatively small genome about one-third the size of the human genome. We have had many genomes for amphibians, for birds and for mammals, but no sharks, says study author Byrappa Venkatesh, a comparative-genomics expert at the Agency for Science, Technology and Research in Singapore.

Because the elephant shark is an early jawed vertebrate and has changed little since bony fishes appeared around 420 million years ago making it the slowest-evolving of all known vertebrates it serves as an important baseline for comparative genomics. We are going to use this as a reference for years to come, Venkatesh says. The genome was published today in Nature1.

So far, scientists have sequenced the genomes of eight bony fish and two jawless vertebrates known as lampreys. Sharks, skates, rays and chimaeras stand apart from other jawed vertebrates in having a skeleton that is made primarily of cartilage rather than bone. Although scientists knew what genes were involved in bone formation, it wasnt clear whether sharks had lost their bone-forming ability or just never had it in the first place. After all, sharks do make bone in their teeth and fin spines.

The sequence reveals that members of this group are missing a single gene family that regulates the process of turning cartilage into bone, and that a gene duplication event gave rise to the transformation in bony vertebrates. In fact, when the researchers knocked out one of these same genes in a zebrafish, it significantly reduced its ability to form bone.

John Postlethwait, a developmental biologist at the University of Oregon in Eugene, calls the findings illuminating. He studies Antarctic icefish (Notothenioidei), which lost the ability to form bone over the course of evolution, and will look to see whether they lack the same genes that are missing from the elephant shark genome.

The C. milii genome also helps to answer important questions about the evolution of acquired immunity, which is the basis for vaccination and allows humans and other vertebrates to fight off new pathogens. Elephant sharks have killer T cells, which directly destroy body cells that have been infected by viruses, but they lack helper T cells, which help to regulate the overall immune response to an infection. The new sequence data suggest that acquired immunity evolved in a two-step process rather than in one step as previously thought.

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Why sharks have no bones